Citrus Sinensis ID: 042716

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------
Protein Sequence
IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWEDDITNIATKIIEEQSPKQ
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHHHHHcccccEEEEEEcccccccccccccccEEcccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHccccHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEccccccccccccEEEEEcccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
IILCEADKLSTDALLYMRWLLERYKGLNKvffccsdvsklqpikSLCTViqllppskQEIVEVLEFIAeqegiqlpHQLAEKIADNSKNNLRQAIRSFEAsrqmnypfvegqviLTGWEDDITNIATKIIEEQSPKQ
Flexible Loop (DISEMBL)
iilceadklstDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFeasrqmnypFVEGQVILTGWEDDITNIATKiieeqspkq
Low Complexity Region (SEG)
IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWEDDITNIATKIIEEQSPKQ
Disordered region (IsUnstruct)
**LCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLA**************IRSFEASRQMNYPFVEGQVILTGWEDDITNIATKII*******
Disordered Region (DISOPRED)
IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWEDDITNIATKI*EEQ****
Disordered Region (DISEMBL)
IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWEDDITNIATKIIEEQSPKQ
Disordered Region (DISPRO)
IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWEDDITNIATKIIEEQ****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWEDDITNIATKIIEEQSPKQ
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	137	2.2.26 [Sep-21-2011]
P40938	356	Replication factor C subu	no	no	1.0	0.384	0.366	1e-20
Q2TBV1	356	Replication factor C subu	yes	no	1.0	0.384	0.366	2e-20
Q8R323	356	Replication factor C subu	yes	no	1.0	0.384	0.366	3e-20
Q54BN3	347	Probable replication fact	yes	no	1.0	0.394	0.384	6e-20
Q8X082	352	Replication factor C subu	N/A	no	1.0	0.389	0.316	6e-13
O94697	358	Replication factor C subu	yes	no	1.0	0.382	0.272	1e-10
Q9YBS7	325	Replication factor C smal	yes	no	0.854	0.36	0.296	2e-10
A3DNV9	329	Replication factor C smal	yes	no	0.854	0.355	0.296	2e-10
Q975D3	327	Replication factor C smal	yes	no	0.737	0.308	0.294	2e-08
A1RWU7	325	Replication factor C smal	yes	no	0.802	0.338	0.306	3e-08

>sp|P40938|RFC3_HUMAN Replication factor C subunit 3 OS=Homo sapiens GN=RFC3 PE=1 SV=2

 Score = 98.2 bits (243), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 51/139 (36%), Positives = 82/139 (58%), Gaps = 2/139 (1%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQE 59
           ++L E DKL+ DA   +R  +E+Y    ++  CC+  SK + PI+S C  +++  PS ++
Sbjct: 132 VLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIED 191

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVIL-TGW 118
           I  VL  + ++EG+ LP QLA ++A+ S  NLR+A+   EA R   YPF   Q I  T W
Sbjct: 192 ICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCEACRVQQYPFTADQEIPETDW 251

Query: 119 EDDITNIATKIIEEQSPKQ 137
           E  +   A  I+ +Q+P++
Sbjct: 252 EVYLRETANAIVSQQTPQR 270

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1.
Homo sapiens (taxid: 9606)

>sp|Q2TBV1|RFC3_BOVIN Replication factor C subunit 3 OS=Bos taurus GN=RFC3 PE=2 SV=1

 Score = 97.4 bits (241), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 51/139 (36%), Positives = 82/139 (58%), Gaps = 2/139 (1%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQE 59
           ++L E DKL+ DA   +R  +E+Y    ++  CC+  SK + PI+S C  +++  PS ++
Sbjct: 132 VLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIED 191

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVIL-TGW 118
           I  VL  + ++EG+ LP QLA ++A+ S  NLR+A+   EA R   YPF   Q I  T W
Sbjct: 192 ICHVLSTVCKKEGLNLPPQLAHRLAEKSCRNLRKALLMCEACRVQQYPFTADQEIPETDW 251

Query: 119 EDDITNIATKIIEEQSPKQ 137
           E  +   A  I+ +Q+P++
Sbjct: 252 EVYLRETANAIVSQQTPQR 270

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1.

Bos taurus (taxid: 9913)

>sp|Q8R323|RFC3_MOUSE Replication factor C subunit 3 OS=Mus musculus GN=Rfc3 PE=2 SV=1

 Score = 97.1 bits (240), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 51/139 (36%), Positives = 81/139 (58%), Gaps = 2/139 (1%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQE 59
           ++L E DKL+ DA   +R  +E+Y    ++  CC+  SK + PI+S C  +++  PS ++
Sbjct: 132 VLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIED 191

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVIL-TGW 118
           I  VL  +  +EG+ LP  LA ++A+ S  NLR+A+   EA R   YPF E Q I  T W
Sbjct: 192 ICSVLSTVCRKEGLALPSTLARRLAEKSCRNLRKALLMCEACRVQQYPFTEDQEIPETDW 251

Query: 119 EDDITNIATKIIEEQSPKQ 137
           E  +   A  I+ +Q+P++
Sbjct: 252 EVYLRETANAIVSQQTPQR 270

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1.

Mus musculus (taxid: 10090)

>sp|Q54BN3|RFC3_DICDI Probable replication factor C subunit 3 OS=Dictyostelium discoideum GN=rfc3 PE=3 SV=1

 Score = 95.9 bits (237), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 53/138 (38%), Positives = 77/138 (55%), Gaps = 1/138 (0%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQE 59
           +IL E DKLS DA   +R  +E+Y    ++  CC   +K + PIKS C  I++  PS++E
Sbjct: 132 VILNEVDKLSKDAQHALRRTMEKYATFCRLILCCDSTAKVIDPIKSRCLGIRVPAPSQEE 191

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWE 119
           I +VL  +A  E   LP +LA  +A  S  NLR A+   E+ +   YPF   ++ L  WE
Sbjct: 192 IEKVLAKVATAEKFDLPSKLAVNVAKQSGGNLRYALMLLESQKAKQYPFQSTELPLLDWE 251

Query: 120 DDITNIATKIIEEQSPKQ 137
           + I+ I     EEQSP +
Sbjct: 252 NYISQIVKDCFEEQSPAR 269

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins PCNA and activator 1.

Dictyostelium discoideum (taxid: 44689)

>sp|Q8X082|RFC5_NEUCR Replication factor C subunit 5 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=B14D6.460 PE=3 SV=1

 Score = 72.8 bits (177), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 44/139 (31%), Positives = 76/139 (54%), Gaps = 2/139 (1%)

Query: 1   IILCEADKLSTDALLYMRWLLERYK-GLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQE 59
           +++ EAD L+ DA   +R  +E+Y   L  +    S  + + PI+S C ++++  P+ +E
Sbjct: 132 VVINEADHLTRDAQAALRRTMEKYSPNLRLILLANSTANIIAPIRSRCLLVRVAAPTHKE 191

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVI-LTGW 118
           I +VL   A++EG  +   L ++IA+ S  NLR+A+  +EA    N    +   I    W
Sbjct: 192 ICDVLASSAKKEGWPIVKGLHQRIAEESGRNLRRALLMYEAVYAQNEKVTDSTPIPPPDW 251

Query: 119 EDDITNIATKIIEEQSPKQ 137
           E  I  IA +I+EE +P +
Sbjct: 252 EALIGQIAKEIMEEHTPAR 270

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

>sp|O94697|RFC5_SCHPO Replication factor C subunit 5 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rfc5 PE=1 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 39/143 (27%), Positives = 76/143 (53%), Gaps = 6/143 (4%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           +++  AD+L+ DA   +R  +E+Y    ++    +  SK+ +PI+S   ++++  P+ +E
Sbjct: 131 VVINVADELTRDAQAALRRTMEKYSNNIRLILIANSTSKIIEPIRSRTLMVRVAAPTPEE 190

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAI---RSFEASRQMNYPFVE--GQVI 114
           I+ V+  I   +G++ P  L   IA+N   NLR+AI    +  A    N   ++   Q+ 
Sbjct: 191 IILVMSKILTAQGLEAPDSLLNNIANNCDRNLRKAILLLETVHAKSPGNKQLIDTGAQLP 250

Query: 115 LTGWEDDITNIATKIIEEQSPKQ 137
           L  W+  I  +   +++EQSP +
Sbjct: 251 LPDWQTFIQQVGDSMLQEQSPAR 273

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins PCNA and activator 1.

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

>sp|Q9YBS7|RFCS_AERPE Replication factor C small subunit OS=Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) GN=rfcS PE=3 SV=3

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 65/118 (55%), Gaps = 1/118 (0%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           ++L EAD +++DA   +R L+E Y  + +     +  SK+  PI+S C   +  P SKQ+
Sbjct: 108 VLLDEADNMTSDAQQALRRLMELYSSVTRFILIANYPSKIIDPIQSRCAFFRFQPLSKQD 167

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTG 117
           ++E L +IAE EG+    +  + I + S+ ++R+AI   +A+  +    V+    + G
Sbjct: 168 VIERLRYIAENEGVDYEEEALDAIYEISEGDMRKAINVLQAASYLGKVTVDAVYRVVG 225

Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA.

Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) (taxid: 272557)

>sp|A3DNV9|RFCS_STAMF Replication factor C small subunit OS=Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / F1) GN=rfcS PE=3 SV=1

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 66/118 (55%), Gaps = 1/118 (0%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           ++L EAD ++ DA   +R L+E Y    +     +  SK+ +PI+S C V +  P  K++
Sbjct: 112 VLLDEADNMTADAQQALRRLMEMYTATTRFILIANYPSKIIEPIQSRCAVFRFAPLKKED 171

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTG 117
           ++  L++IAEQE +++  +  E I D S+ ++R+AI   +A+  +    V+    + G
Sbjct: 172 VISRLKWIAEQEKVEIDEEALEAIHDLSEGDMRRAINILQAAAALGKVTVDSVYKVVG 229

Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA.

Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / F1) (taxid: 399550)

>sp|Q975D3|RFCS_SULTO Replication factor C small subunit OS=Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) GN=rfcS PE=3 SV=1

 Score = 58.2 bits (139), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/102 (29%), Positives = 58/102 (56%), Gaps = 1/102 (0%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           ++L EAD ++ DA   +R  +E Y    +    C+ +SK+ +PI+S   + +  P  K++
Sbjct: 108 VLLDEADNMTADAQQALRRTMELYTETTRFILACNYLSKIIEPIQSRTALFRFYPLKKED 167

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS 101
           +V  L +IA+ E ++   +  E I D ++ ++R+AI   +AS
Sbjct: 168 VVARLAYIAKNEKVEYDQKALETIYDITQGDMRKAINILQAS 209

Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA.

Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (taxid: 273063)

>sp|A1RWU7|RFCS_THEPD Replication factor C small subunit OS=Thermofilum pendens (strain Hrk 5) GN=rfcS PE=3 SV=1

 Score = 57.4 bits (137), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 60/111 (54%), Gaps = 1/111 (0%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           +IL EAD ++ DA   +R  +E +    +     +  SK+ +PI+S C V +  P  K +
Sbjct: 105 VILDEADNMTGDAQQALRRTMELFSRNTRFILIANYASKIIEPIQSRCAVFRFQPLPKGD 164

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVE 110
             + L +IA+QEGI +     E I + S+ +LR+AI + +A+  ++    E
Sbjct: 165 AFQRLRWIAQQEGITVDDGALEAIWEESQGDLRKAINTLQAASAISRNVTE 215

Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA.

Thermofilum pendens (strain Hrk 5) (taxid: 368408)

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	137
224129392	725	predicted protein [Populus trichocarpa]	1.0	0.188	0.766	9e-57
359489140	659	PREDICTED: uncharacterized protein LOC10	1.0	0.207	0.715	9e-51
297744802	530	unnamed protein product [Vitis vinifera]	1.0	0.258	0.715	3e-50
255586016	661	Replication factor C subunit, putative [	1.0	0.207	0.693	5e-49
414867860	638	TPA: hypothetical protein ZEAMMB73_19015	1.0	0.214	0.583	1e-41
357147528	565	PREDICTED: probable replication factor C	1.0	0.242	0.569	5e-40
357467569	800	Replication factor C subunit [Medicago t	1.0	0.171	0.569	1e-39
326491965	591	predicted protein [Hordeum vulgare subsp	1.0	0.231	0.562	7e-37
224071367	432	predicted protein [Populus trichocarpa]	1.0	0.317	0.569	2e-36
147811404	494	hypothetical protein VITISV_006668 [Viti	1.0	0.277	0.576	7e-36

>gi|224129392|ref|XP_002320575.1| predicted protein [Populus trichocarpa] gi|222861348|gb|EEE98890.1| predicted protein [Populus trichocarpa]

 Score =  224 bits (571), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 105/137 (76%), Positives = 121/137 (88%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEI 60
           IIL EAD LSTDALLY++W+LERYKG +K FFCC+DVS+LQPI+SLCTV+QLLPPSK+E+
Sbjct: 455 IILYEADMLSTDALLYIKWVLERYKGFSKFFFCCNDVSRLQPIRSLCTVVQLLPPSKREV 514

Query: 61  VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWED 120
           V+VLEFIAEQE I+LP+ LAEKIAD SKNNLRQAIRSFEAS   +YPF E Q ILTGWED
Sbjct: 515 VQVLEFIAEQEAIELPYPLAEKIADKSKNNLRQAIRSFEASWHGSYPFTEDQEILTGWED 574

Query: 121 DITNIATKIIEEQSPKQ 137
           DI NIA  ++EEQSPKQ
Sbjct: 575 DIANIAKDMVEEQSPKQ 591

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489140|ref|XP_002265263.2| PREDICTED: uncharacterized protein LOC100265748 [Vitis vinifera]

 Score =  204 bits (519), Expect = 9e-51,   Method: Compositional matrix adjust.
 Identities = 98/137 (71%), Positives = 113/137 (82%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEI 60
           I+L EA+KLST+ALLY +WLL++Y+G N VFF CSD SKLQPIKSLCT++QLLPPS +EI
Sbjct: 425 IVLYEAEKLSTEALLYFKWLLDKYEGHNMVFFSCSDTSKLQPIKSLCTMVQLLPPSDEEI 484

Query: 61  VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWED 120
           VEVLE IA+QE I LP +LAEKI  NSKNNLRQAIRSFEA+ +  YPF E Q I TGWED
Sbjct: 485 VEVLELIAKQESINLPRELAEKIVGNSKNNLRQAIRSFEATWKFKYPFEEDQEIRTGWED 544

Query: 121 DITNIATKIIEEQSPKQ 137
           DI  IA  IIEEQ+PKQ
Sbjct: 545 DIARIAKNIIEEQTPKQ 561

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297744802|emb|CBI38070.3| unnamed protein product [Vitis vinifera]

 Score =  202 bits (515), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 98/137 (71%), Positives = 113/137 (82%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEI 60
           I+L EA+KLST+ALLY +WLL++Y+G N VFF CSD SKLQPIKSLCT++QLLPPS +EI
Sbjct: 339 IVLYEAEKLSTEALLYFKWLLDKYEGHNMVFFSCSDTSKLQPIKSLCTMVQLLPPSDEEI 398

Query: 61  VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWED 120
           VEVLE IA+QE I LP +LAEKI  NSKNNLRQAIRSFEA+ +  YPF E Q I TGWED
Sbjct: 399 VEVLELIAKQESINLPRELAEKIVGNSKNNLRQAIRSFEATWKFKYPFEEDQEIRTGWED 458

Query: 121 DITNIATKIIEEQSPKQ 137
           DI  IA  IIEEQ+PKQ
Sbjct: 459 DIARIAKNIIEEQTPKQ 475

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255586016|ref|XP_002533677.1| Replication factor C subunit, putative [Ricinus communis] gi|223526428|gb|EEF28707.1| Replication factor C subunit, putative [Ricinus communis]

 Score =  198 bits (504), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 95/137 (69%), Positives = 112/137 (81%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEI 60
           IIL  AD+LS DA+LY++WLLERY+G +K FFCCSDVSKLQ IK LC ++QL  PS  EI
Sbjct: 429 IILYNADRLSADAVLYIKWLLERYQGSSKFFFCCSDVSKLQAIKELCNLVQLFMPSNDEI 488

Query: 61  VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWED 120
           V+VL+FIA+QEGI+LP Q AE+IA  SKNNLRQAIRS EAS + +YPF E Q ILTGWED
Sbjct: 489 VKVLKFIAKQEGIELPFQFAERIALESKNNLRQAIRSLEASWRRSYPFAEDQEILTGWED 548

Query: 121 DITNIATKIIEEQSPKQ 137
           DI NIA  +I+EQSPKQ
Sbjct: 549 DIANIAKNMIQEQSPKQ 565

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414867860|tpg|DAA46417.1| TPA: hypothetical protein ZEAMMB73_190155 [Zea mays]

 Score =  174 bits (441), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 80/137 (58%), Positives = 101/137 (73%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEI 60
           I++ +ADKLS D   Y+ W L RY G NK+ FCCSD S L+ IK LC V+ L PPS  EI
Sbjct: 382 IVIHDADKLSFDLQHYIGWFLGRYAGCNKIIFCCSDASNLEAIKHLCKVVTLQPPSFDEI 441

Query: 61  VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWED 120
           + VLE+IA QE I LP  LA +I   + NNLRQ IRSFEA+ + NYPF++GQVILTGWE+
Sbjct: 442 INVLEYIATQESIDLPRDLARRITVGANNNLRQTIRSFEATWKANYPFIDGQVILTGWEE 501

Query: 121 DITNIATKIIEEQSPKQ 137
           +I+N+A+ I+EE SPKQ
Sbjct: 502 EISNVASNIMEEPSPKQ 518

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357147528|ref|XP_003574379.1| PREDICTED: probable replication factor C subunit 3-like [Brachypodium distachyon]

 Score =  169 bits (427), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 78/137 (56%), Positives = 105/137 (76%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEI 60
           I++ +AD++S+D   Y+ W L RY G +K+ FCCS+ S L+ +K LC VI LLPPS  EI
Sbjct: 313 IVVHDADRISSDLQHYIGWFLGRYVGCSKIIFCCSNSSNLEAVKHLCKVITLLPPSFDEI 372

Query: 61  VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWED 120
           ++VLEFIA +EGI LP ++A +IA ++  NLRQAIRSFEA+ + NYPFVE Q ILTGWE+
Sbjct: 373 IKVLEFIATKEGIYLPREIASRIATSASTNLRQAIRSFEATWKANYPFVEDQPILTGWEE 432

Query: 121 DITNIATKIIEEQSPKQ 137
           +I ++A KI+EE SPKQ
Sbjct: 433 EIFDVAKKIMEEPSPKQ 449

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357467569|ref|XP_003604069.1| Replication factor C subunit [Medicago truncatula] gi|355493117|gb|AES74320.1| Replication factor C subunit [Medicago truncatula]

 Score =  167 bits (423), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 78/137 (56%), Positives = 106/137 (77%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEI 60
           IIL EA+KLS +++LY++WL+E+YKG NK+FFCCSD S+LQPI+S CT ++L  PS Q+I
Sbjct: 555 IILYEAEKLSLESVLYIKWLVEKYKGCNKLFFCCSDESRLQPIQSYCTTVRLSSPSTQQI 614

Query: 61  VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWED 120
           V++LE+I ++EGI+L H+  + I   SKNNLRQAIRS EA+ +      +  ++LTGWED
Sbjct: 615 VKILEYIVQEEGIKLSHESIKSIVLRSKNNLRQAIRSLEATYRNKNALNDDDLVLTGWED 674

Query: 121 DITNIATKIIEEQSPKQ 137
           DI NIA  II EQSP+Q
Sbjct: 675 DILNIARNIITEQSPRQ 691

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326491965|dbj|BAJ98207.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  158 bits (400), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 77/137 (56%), Positives = 103/137 (75%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEI 60
           I++ +AD+LS+D   Y+ W L RY G NK+ F CS  S L+ ++ LC V++L PPS  EI
Sbjct: 339 IVVHDADRLSSDLQHYIGWFLGRYAGCNKIIFSCSSSSNLESVEHLCKVVRLKPPSFDEI 398

Query: 61  VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWED 120
           ++VLEFIA QEGI LPH LA +IA ++ NNLRQAIRSFEA+ + +YPF + Q ILTGWE+
Sbjct: 399 IKVLEFIATQEGIDLPHGLASRIAASASNNLRQAIRSFEATWKASYPFTKDQPILTGWEE 458

Query: 121 DITNIATKIIEEQSPKQ 137
           +I ++A KI+EE SPKQ
Sbjct: 459 EIYDVAKKIMEEPSPKQ 475

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224071367|ref|XP_002303425.1| predicted protein [Populus trichocarpa] gi|222840857|gb|EEE78404.1| predicted protein [Populus trichocarpa]

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 78/137 (56%), Positives = 102/137 (74%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEI 60
           II+ EA++LS DA L ++  L+ Y+G  KV FCC D+S+L  +  LC VI LLPPS ++I
Sbjct: 194 IIVNEAERLSKDAQLRIKSFLQTYRGHCKVIFCCYDISRLHDLSPLCMVIPLLPPSDEQI 253

Query: 61  VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWED 120
           VEVL FIA+++ I+LP QLA  IA+ SK  L+QAIRSFEA+   NYPF E Q++LTGWE 
Sbjct: 254 VEVLHFIAKKQDIELPDQLANNIAEKSKRCLQQAIRSFEATWHSNYPFKEEQLVLTGWEK 313

Query: 121 DITNIATKIIEEQSPKQ 137
           +I +IAT IIEEQS K+
Sbjct: 314 EIADIATSIIEEQSSKR 330

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147811404|emb|CAN63339.1| hypothetical protein VITISV_006668 [Vitis vinifera]

 Score =  155 bits (391), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 79/137 (57%), Positives = 103/137 (75%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEI 60
           IILC A+KLS    L +R  L+ Y+G  KV+FC S  S LQ +KSLCTVIQ+  PSK+EI
Sbjct: 254 IILCGAEKLSEGDQLLIRDHLQTYRGHFKVYFCYSGTSMLQHLKSLCTVIQIPTPSKEEI 313

Query: 61  VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWED 120
           VEVLEFIA+ E I+LP +LAE +A+ +K+++RQAIRSFEA+ ++NYPF E Q  +TGWE+
Sbjct: 314 VEVLEFIAKHEAIELPPRLAENMAEKAKHSVRQAIRSFEATWKLNYPFKEDQEPITGWEE 373

Query: 121 DITNIATKIIEEQSPKQ 137
           +   IA K+I EQS KQ
Sbjct: 374 EFAEIAKKVIAEQSAKQ 390

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	137
TAIR|locus:2180315	354	EMB2775 "EMBRYO DEFECTIVE 2775	1.0	0.387	0.431	1.4e-25
UNIPROTKB|F1RSR4	356	RFC3 "Uncharacterized protein"	1.0	0.384	0.366	1.9e-21
UNIPROTKB|E2R7L0	356	RFC3 "Uncharacterized protein"	1.0	0.384	0.374	2.4e-21
RGD|1306832	356	Rfc3 "replication factor C (ac	1.0	0.384	0.374	3e-21
UNIPROTKB|P40938	356	RFC3 "Replication factor C sub	1.0	0.384	0.366	4.9e-21
UNIPROTKB|Q2TBV1	356	RFC3 "Replication factor C sub	1.0	0.384	0.366	6.3e-21
MGI|MGI:1916513	356	Rfc3 "replication factor C (ac	1.0	0.384	0.366	8e-21
ZFIN|ZDB-GENE-020809-3	356	rfc3 "replication factor C (ac	1.0	0.384	0.366	2.7e-20
DICTYBASE|DDB_G0293702	347	rfc3 "replication factor C sub	0.985	0.389	0.389	4.4e-20
UNIPROTKB|F1P3C0	356	RFC3 "Uncharacterized protein"	1.0	0.384	0.352	7.8e-20

TAIR|locus:2180315 EMB2775 "EMBRYO DEFECTIVE 2775" [Arabidopsis thaliana (taxid:3702)]

 Score = 290 (107.1 bits), Expect = 1.4e-25, P = 1.4e-25
 Identities = 60/139 (43%), Positives = 91/139 (65%)

Query:     1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
             ++L E DKLS +A   +R  +E+Y    ++  CC+  SK+ + IKS C  +++  PS++E
Sbjct:   134 LVLNEVDKLSREAQHSLRRTMEKYSSSCRLILCCNSSSKVTEAIKSRCLNVRINAPSQEE 193

Query:    60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILT-GW 118
             IV+VLEF+A++E +QLP   A +IA+ S  +LR+AI S E  R  NYPF   QVI    W
Sbjct:   194 IVKVLEFVAKKESLQLPQGFAARIAEKSNRSLRRAILSLETCRVQNYPFTGNQVISPMDW 253

Query:   119 EDDITNIATKIIEEQSPKQ 137
             E+ +  IAT +++EQSPK+
Sbjct:   254 EEYVAEIATDMMKEQSPKK 272

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006260 "DNA replication" evidence=IEA

GO:0009793 "embryo development ending in seed dormancy" evidence=IMP

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

GO:0006261 "DNA-dependent DNA replication" evidence=RCA

UNIPROTKB|F1RSR4 RFC3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 251 (93.4 bits), Expect = 1.9e-21, P = 1.9e-21
 Identities = 51/139 (36%), Positives = 84/139 (60%)

Query:     1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQE 59
             ++L E DKL+ DA   +R  +E+Y    ++  CC+  SK + PI+S C  +++  PS ++
Sbjct:   132 VLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIED 191

Query:    60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPF-VEGQVILTGW 118
             I  VL  + ++EG+ LP QLA K+A+ S  NLR+A+   EA R   YPF V+ ++  T W
Sbjct:   192 ICHVLSTVCKKEGLSLPSQLARKLAEKSCRNLRKALLMCEACRVQQYPFTVDQEIPETDW 251

Query:   119 EDDITNIATKIIEEQSPKQ 137
             E  +   A  I+ +Q+P++
Sbjct:   252 EVYLRETANAIVSQQTPQR 270

GO:0046683 "response to organophosphorus" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|E2R7L0 RFC3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 250 (93.1 bits), Expect = 2.4e-21, P = 2.4e-21
 Identities = 52/139 (37%), Positives = 82/139 (58%)

Query:     1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQE 59
             ++L E DKL+ DA   +R  +E+Y    ++  CC+  SK + PI+S C  +++  PS ++
Sbjct:   132 VLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIED 191

Query:    60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVIL-TGW 118
             I  VL  + ++EG+ LP QLA ++A+ S  NLR+A+   EA R   YPF   Q I  T W
Sbjct:   192 ICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCEACRVQQYPFTADQEIPETDW 251

Query:   119 EDDITNIATKIIEEQSPKQ 137
             E  +   A  I+ EQ+P++
Sbjct:   252 EVYLRETANAIVSEQTPQR 270

GO:0046683 "response to organophosphorus" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

RGD|1306832 Rfc3 "replication factor C (activator 1) 3" [Rattus norvegicus (taxid:10116)]

 Score = 249 (92.7 bits), Expect = 3.0e-21, P = 3.0e-21
 Identities = 52/139 (37%), Positives = 83/139 (59%)

Query:     1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQE 59
             ++L E DKL+ DA   +R  +E+Y    ++  CC+  SK + PI+S C  I++  PS ++
Sbjct:   132 VLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAIRVPAPSIED 191

Query:    60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVIL-TGW 118
             I  VL  + ++EG+ LP +LA ++A+ S  NLR+A+   EA R   YPF E Q I  T W
Sbjct:   192 ICSVLSTVCKKEGLALPSKLARRLAEKSCRNLRKALLMCEACRVQQYPFTEDQEIPETDW 251

Query:   119 EDDITNIATKIIEEQSPKQ 137
             E  +   A  I+ +Q+P++
Sbjct:   252 EVYLRETANAIVSQQTPQR 270

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA;ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005663 "DNA replication factor C complex" evidence=ISO

GO:0006200 "ATP catabolic process" evidence=ISO

GO:0006260 "DNA replication" evidence=IEA;ISO

GO:0008150 "biological_process" evidence=ND

GO:0016887 "ATPase activity" evidence=IEA;ISO

GO:0046683 "response to organophosphorus" evidence=IEA;ISO

UNIPROTKB|P40938 RFC3 "Replication factor C subunit 3" [Homo sapiens (taxid:9606)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 51/139 (36%), Positives = 82/139 (58%)

Query:     1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQE 59
             ++L E DKL+ DA   +R  +E+Y    ++  CC+  SK + PI+S C  +++  PS ++
Sbjct:   132 VLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIED 191

Query:    60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVIL-TGW 118
             I  VL  + ++EG+ LP QLA ++A+ S  NLR+A+   EA R   YPF   Q I  T W
Sbjct:   192 ICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCEACRVQQYPFTADQEIPETDW 251

Query:   119 EDDITNIATKIIEEQSPKQ 137
             E  +   A  I+ +Q+P++
Sbjct:   252 EVYLRETANAIVSQQTPQR 270

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005663 "DNA replication factor C complex" evidence=IDA;TAS

GO:0000731 "DNA synthesis involved in DNA repair" evidence=TAS

GO:0003677 "DNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0006260 "DNA replication" evidence=IDA;TAS

GO:0003689 "DNA clamp loader activity" evidence=TAS

GO:0016887 "ATPase activity" evidence=IDA

GO:0046683 "response to organophosphorus" evidence=IEP

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0000722 "telomere maintenance via recombination" evidence=TAS

GO:0000723 "telomere maintenance" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006271 "DNA strand elongation involved in DNA replication" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0006297 "nucleotide-excision repair, DNA gap filling" evidence=TAS

GO:0032201 "telomere maintenance via semi-conservative replication" evidence=TAS

GO:0006200 "ATP catabolic process" evidence=IDA

UNIPROTKB|Q2TBV1 RFC3 "Replication factor C subunit 3" [Bos taurus (taxid:9913)]

 Score = 246 (91.7 bits), Expect = 6.3e-21, P = 6.3e-21
 Identities = 51/139 (36%), Positives = 82/139 (58%)

Query:     1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQE 59
             ++L E DKL+ DA   +R  +E+Y    ++  CC+  SK + PI+S C  +++  PS ++
Sbjct:   132 VLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIED 191

Query:    60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVIL-TGW 118
             I  VL  + ++EG+ LP QLA ++A+ S  NLR+A+   EA R   YPF   Q I  T W
Sbjct:   192 ICHVLSTVCKKEGLNLPPQLAHRLAEKSCRNLRKALLMCEACRVQQYPFTADQEIPETDW 251

Query:   119 EDDITNIATKIIEEQSPKQ 137
             E  +   A  I+ +Q+P++
Sbjct:   252 EVYLRETANAIVSQQTPQR 270

GO:0005634 "nucleus" evidence=IEA

GO:0046683 "response to organophosphorus" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1916513 Rfc3 "replication factor C (activator 1) 3" [Mus musculus (taxid:10090)]

 Score = 245 (91.3 bits), Expect = 8.0e-21, P = 8.0e-21
 Identities = 51/139 (36%), Positives = 81/139 (58%)

Query:     1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQE 59
             ++L E DKL+ DA   +R  +E+Y    ++  CC+  SK + PI+S C  +++  PS ++
Sbjct:   132 VLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIED 191

Query:    60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVIL-TGW 118
             I  VL  +  +EG+ LP  LA ++A+ S  NLR+A+   EA R   YPF E Q I  T W
Sbjct:   192 ICSVLSTVCRKEGLALPSTLARRLAEKSCRNLRKALLMCEACRVQQYPFTEDQEIPETDW 251

Query:   119 EDDITNIATKIIEEQSPKQ 137
             E  +   A  I+ +Q+P++
Sbjct:   252 EVYLRETANAIVSQQTPQR 270

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005663 "DNA replication factor C complex" evidence=ISO

GO:0006200 "ATP catabolic process" evidence=ISO

GO:0006260 "DNA replication" evidence=ISO

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

ZFIN|ZDB-GENE-020809-3 rfc3 "replication factor C (activator 1) 3" [Danio rerio (taxid:7955)]

 Score = 240 (89.5 bits), Expect = 2.7e-20, P = 2.7e-20
 Identities = 51/139 (36%), Positives = 82/139 (58%)

Query:     1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQE 59
             ++L E D+L+ DA   +R  +E+Y    ++  CC+  SK + PI+S C  +++  PS +E
Sbjct:   132 VLLTEVDRLTKDAQHALRRTMEKYMATCRLILCCNSTSKVIAPIRSRCLAVRVPLPSVEE 191

Query:    60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVIL-TGW 118
             +  VL  +  +EG+ LP +LA++IA+ S  NLR+A+   EA R   YPF   Q I  T W
Sbjct:   192 VCSVLSGVCRKEGLLLPPELAKQIAEKSGRNLRKALLMCEACRVQQYPFSPDQDIPETDW 251

Query:   119 EDDITNIATKIIEEQSPKQ 137
             E  +   A  I+ +QSP++
Sbjct:   252 EVYLRETANAIVSQQSPQR 270

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0006260 "DNA replication" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

DICTYBASE|DDB_G0293702 rfc3 "replication factor C subunit 3" [Dictyostelium discoideum (taxid:44689)]

 Score = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 53/136 (38%), Positives = 76/136 (55%)

Query:     1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQE 59
             +IL E DKLS DA   +R  +E+Y    ++  CC   +K + PIKS C  I++  PS++E
Sbjct:   132 VILNEVDKLSKDAQHALRRTMEKYATFCRLILCCDSTAKVIDPIKSRCLGIRVPAPSQEE 191

Query:    60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWE 119
             I +VL  +A  E   LP +LA  +A  S  NLR A+   E+ +   YPF   ++ L  WE
Sbjct:   192 IEKVLAKVATAEKFDLPSKLAVNVAKQSGGNLRYALMLLESQKAKQYPFQSTELPLLDWE 251

Query:   120 DDITNIATKIIEEQSP 135
             + I+ I     EEQSP
Sbjct:   252 NYISQIVKDCFEEQSP 267

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

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003689 "DNA clamp loader activity" evidence=ISS

GO:0031391 "Elg1 RFC-like complex" evidence=ISS

GO:0031389 "Rad17 RFC-like complex" evidence=ISS

GO:0006298 "mismatch repair" evidence=ISS

GO:0006272 "leading strand elongation" evidence=ISS

GO:0005663 "DNA replication factor C complex" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|F1P3C0 RFC3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 236 (88.1 bits), Expect = 7.8e-20, P = 7.8e-20
 Identities = 49/139 (35%), Positives = 83/139 (59%)

Query:     1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
             ++L E DKL+ DA   +R  +E+Y    ++  CC+ +SK+  PI+S C  +++  PS ++
Sbjct:   132 VLLTEVDKLTKDAQHALRRTMEKYMATCRLILCCNSISKIIGPIQSRCLSVRVPAPSIED 191

Query:    60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILT-GW 118
             I  VL  + ++EG+ LP +LA+++A+ S  NLR+A+   E+ R   YPF   Q I    W
Sbjct:   192 ICHVLSSVCKKEGLNLPPELAQRLAEKSGRNLRKALLMCESCRVQQYPFSADQDIPEMDW 251

Query:   119 EDDITNIATKIIEEQSPKQ 137
             E  +   A  I+ +QSP++
Sbjct:   252 EIYLRETANAIVSQQSPQR 270

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

GO:0046683 "response to organophosphorus" 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: fgenesh4_pg.C_LG_XIV001182 hypothetical protein (725 aa) (Populus trichocarpa)

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	137
PRK12402	337	PRK12402, PRK12402, replication factor C small sub	2e-11
PRK00440	319	PRK00440, rfc, replication factor C small subunit;	6e-11
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	7e-11
PRK04132	846	PRK04132, PRK04132, replication factor C small sub	5e-10
PLN03025	319	PLN03025, PLN03025, replication factor C subunit;	1e-06
PHA02544	316	PHA02544, 44, clamp loader, small subunit; Provisi	1e-04
PRK14953	486	PRK14953, PRK14953, DNA polymerase III subunits ga	2e-04
PRK14962	472	PRK14962, PRK14962, DNA polymerase III subunits ga	6e-04
COG0593	408	COG0593, DnaA, ATPase involved in DNA replication	9e-04

>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed

 Score = 59.2 bits (144), Expect = 2e-11
 Identities = 34/98 (34%), Positives = 51/98 (52%), Gaps = 1/98 (1%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           I+L  A+ L  DA   +R ++E+Y    +        SKL  PI+S C  +    P+  E
Sbjct: 129 ILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDE 188

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRS 97
           +V+VLE IAE EG+       E IA  +  +LR+AI +
Sbjct: 189 LVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILT 226

Length = 337

>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed

 Score = 58.0 bits (141), Expect = 6e-11
 Identities = 36/102 (35%), Positives = 57/102 (55%), Gaps = 1/102 (0%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           I L EAD L++DA   +R  +E Y    +    C+  SK+  PI+S C V +  P  K+ 
Sbjct: 106 IFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEA 165

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS 101
           + E L +IAE EGI++     E I   S+ ++R+AI + +A+
Sbjct: 166 VAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAA 207

Length = 319

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 58.0 bits (141), Expect = 7e-11
 Identities = 25/90 (27%), Positives = 45/90 (50%), Gaps = 9/90 (10%)

Query: 39  KLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSF 98
            L+ +++ C +I+    S + IV VL+ I  +EGI+   +  ++IA+ S  +LR AI   
Sbjct: 144 SLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDL 203

Query: 99  EASRQMNYPFVEGQVILTGWEDDITNIATK 128
           +A         EG   LT   +D+  +  +
Sbjct: 204 QAI-------AEGYGKLT--LEDVKTLGRR 224

Length = 482

>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit; Provisional

 Score = 55.6 bits (134), Expect = 5e-10
 Identities = 31/102 (30%), Positives = 57/102 (55%), Gaps = 1/102 (0%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           I L EAD L+ DA   +R  +E +    +    C+  SK+ +PI+S C + +  P   ++
Sbjct: 634 IFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDED 693

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS 101
           I + L +IAE EG++L  +  + I   ++ ++R+AI   +A+
Sbjct: 694 IAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAA 735

Length = 846

>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional

 Score = 45.9 bits (109), Expect = 1e-06
 Identities = 29/102 (28%), Positives = 54/102 (52%), Gaps = 1/102 (0%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQE 59
           +IL EAD +++ A   +R  +E Y    +    C+  SK ++PI+S C +++    S QE
Sbjct: 103 VILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQE 162

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS 101
           I+  L  + E E +    +  E I   +  ++RQA+ + +A+
Sbjct: 163 ILGRLMKVVEAEKVPYVPEGLEAIIFTADGDMRQALNNLQAT 204

Length = 319

>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 26/96 (27%), Positives = 47/96 (48%), Gaps = 10/96 (10%)

Query: 1   IILCEADKLST-DALLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSLCTVIQLLPPSKQ 58
           II+ E D+L   DA  ++R  +E Y          ++ +  ++P++S C VI    P+K+
Sbjct: 104 IIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKE 163

Query: 59  EIVEV-------LEFIAEQEGIQL-PHQLAEKIADN 86
           E +E+        + I E EG+++    LA  +  N
Sbjct: 164 EQIEMMKQMIVRCKGILEAEGVEVDMKVLAALVKKN 199

Length = 316

>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau; Provisional

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 1/94 (1%)

Query: 2   ILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQP-IKSLCTVIQLLPPSKQEI 60
           I+ EA  L+ +A   +   LE          C ++  K+ P I S C       P+K++I
Sbjct: 124 IIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQI 183

Query: 61  VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQA 94
            E L+ I  +E I+   +  + +A  S+  +R A
Sbjct: 184 KEYLKRICNEEKIEYEEKALDLLAQASEGGMRDA 217

Length = 486

>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau; Provisional

 Score = 37.8 bits (88), Expect = 6e-04
 Identities = 19/59 (32%), Positives = 30/59 (50%)

Query: 41  QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFE 99
             I S C VI+    S + I++ L+ +AE EGI++  +    IA  +   LR A+   E
Sbjct: 162 PTIISRCQVIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLE 220

Length = 472

>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

 Score = 37.6 bits (88), Expect = 9e-04
 Identities = 13/49 (26%), Positives = 26/49 (53%)

Query: 47  CTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAI 95
             V+++ PP  +  + +L   AE  GI++P ++ E +A     N+R+  
Sbjct: 236 GLVVEIEPPDDETRLAILRKKAEDRGIEIPDEVLEFLAKRLDRNVRELE 284

Length = 408

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	137
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	99.97
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	99.97
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	99.96
PRK04132	846	replication factor C small subunit; Provisional	99.94
PLN03025	319	replication factor C subunit; Provisional	99.94
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.93
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.93
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.92
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.92
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.91
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	99.91
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.91
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.91
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.9
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.89
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.89
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.89
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.89
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.89
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.89
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.88
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.88
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.88
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.88
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	99.88
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.88
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.88
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.88
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.86
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	99.86
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.86
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.86
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.86
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.85
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.85
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.85
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.84
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	99.84
PRK12402	337	replication factor C small subunit 2; Reviewed	99.84
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.84
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.82
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.82
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.82
PRK04195	482	replication factor C large subunit; Provisional	99.81
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.81
PRK07993	334	DNA polymerase III subunit delta'; Validated	99.81
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.8
PRK08485	206	DNA polymerase III subunit delta'; Validated	99.8
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.8
PRK08769	319	DNA polymerase III subunit delta'; Validated	99.78
PRK06871	325	DNA polymerase III subunit delta'; Validated	99.78
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.77
PRK05707	328	DNA polymerase III subunit delta'; Validated	99.77
PRK06090	319	DNA polymerase III subunit delta'; Validated	99.77
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.76
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.74
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.73
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.73
PHA02544	316	44 clamp loader, small subunit; Provisional	99.73
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.72
PRK06964	342	DNA polymerase III subunit delta'; Validated	99.72
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.7
PRK07276	290	DNA polymerase III subunit delta'; Validated	99.69
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	99.69
PRK05818	261	DNA polymerase III subunit delta'; Validated	99.68
PRK07132	299	DNA polymerase III subunit delta'; Validated	99.67
PRK05917	290	DNA polymerase III subunit delta'; Validated	99.66
KOG1969	877	consensus DNA replication checkpoint protein CHL12	99.6
PRK13342	413	recombination factor protein RarA; Reviewed	99.59
PRK06581	263	DNA polymerase III subunit delta'; Validated	99.59
PRK08084	235	DNA replication initiation factor; Provisional	99.57
PRK13341	725	recombination factor protein RarA/unknown domain f	99.56
PRK08727	233	hypothetical protein; Validated	99.56
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.55
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.52
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.5
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.49
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	99.47
PRK06893	229	DNA replication initiation factor; Validated	99.43
PRK05642	234	DNA replication initiation factor; Validated	99.42
PRK06620	214	hypothetical protein; Validated	99.42
PRK09087	226	hypothetical protein; Validated	99.41
KOG2028	554	consensus ATPase related to the helicase subunit o	99.4
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.38
PRK14700	300	recombination factor protein RarA; Provisional	99.38
TIGR01128	302	holA DNA polymerase III, delta subunit. subunit ar	99.36
PRK08699	325	DNA polymerase III subunit delta'; Validated	99.35
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.34
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	99.34
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.33
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	99.32
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.29
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.24
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.23
PRK12422	445	chromosomal replication initiation protein; Provis	99.22
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.2
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.2
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.19
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.19
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.19
KOG2680	454	consensus DNA helicase TIP49, TBP-interacting prot	99.16
CHL00181	287	cbbX CbbX; Provisional	99.16
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	99.12
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.1
PRK07452	326	DNA polymerase III subunit delta; Validated	99.08
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	99.06
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.04
COG0593	408	DnaA ATPase involved in DNA replication initiation	98.99
PRK07914	320	hypothetical protein; Reviewed	98.95
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.93
PRK05629	318	hypothetical protein; Validated	98.91
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.89
PF06144	172	DNA_pol3_delta: DNA polymerase III, delta subunit;	98.82
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	98.79
PRK08487	328	DNA polymerase III subunit delta; Validated	98.76
PRK05574	340	holA DNA polymerase III subunit delta; Reviewed	98.7
PRK06585	343	holA DNA polymerase III subunit delta; Reviewed	98.64
PRK05907	311	hypothetical protein; Provisional	98.64
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.63
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	98.6
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	98.59
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.59
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	98.56
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.56
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.43
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	98.37
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.3
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	98.24
CHL00095	821	clpC Clp protease ATP binding subunit	98.22
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	98.22
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	98.21
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.21
PRK10865	857	protein disaggregation chaperone; Provisional	98.2
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.18
COG1221	403	PspF Transcriptional regulators containing an AAA-	98.11
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	98.1
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.08
PRK15115	444	response regulator GlrR; Provisional	98.07
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	98.07
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.07
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	98.04
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	98.03
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	98.02
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.01
CHL00176	638	ftsH cell division protein; Validated	98.0
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	97.98
PRK10365	441	transcriptional regulatory protein ZraR; Provision	97.98
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	97.97
COG1466	334	HolA DNA polymerase III, delta subunit [DNA replic	97.95
PRK05022	509	anaerobic nitric oxide reductase transcription reg	97.9
PRK11608	326	pspF phage shock protein operon transcriptional ac	97.88
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.87
CHL00095	821	clpC Clp protease ATP binding subunit	97.87
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.87
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	97.84
PRK10865	857	protein disaggregation chaperone; Provisional	97.81
PF00004	132	AAA: ATPase family associated with various cellula	97.77
COG2204	464	AtoC Response regulator containing CheY-like recei	97.77
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	97.75
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	97.73
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	97.73
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.72
PRK15424	538	propionate catabolism operon regulatory protein Pr	97.69
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	97.69
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.67
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	97.58
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.58
CHL00195	489	ycf46 Ycf46; Provisional	97.56
PHA02244	383	ATPase-like protein	97.56
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.54
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	97.52
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	97.5
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	97.5
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	97.36
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	97.34
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	97.24
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	97.23
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.21
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	97.21
KOG1514	767	consensus Origin recognition complex, subunit 1, a	97.19
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	97.18
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	97.15
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	96.99
smart00350	509	MCM minichromosome maintenance proteins.	96.94
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	96.94
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	96.92
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	96.89
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	96.85
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.76
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	96.75
PF13173	128	AAA_14: AAA domain	96.73
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	96.7
PRK04841	903	transcriptional regulator MalT; Provisional	96.63
PRK13765	637	ATP-dependent protease Lon; Provisional	96.62
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	96.6
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	96.54
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	96.4
CHL00206	2281	ycf2 Ycf2; Provisional	96.4
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	96.35
PRK13531	498	regulatory ATPase RavA; Provisional	96.34
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	96.29
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	96.28
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	96.27
COG0714	329	MoxR-like ATPases [General function prediction onl	96.21
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	96.17
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	96.0
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	95.96
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	95.96
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	95.91
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	95.9
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	95.86
CHL00195	489	ycf46 Ycf46; Provisional	95.85
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	95.84
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	95.83
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	95.8
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	95.79
PRK09862	506	putative ATP-dependent protease; Provisional	95.76
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	95.71
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	95.61
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	95.38
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.24
PRK08116	268	hypothetical protein; Validated	95.22
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	95.12
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	94.9
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	94.85
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	94.72
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	94.63
PF05729	166	NACHT: NACHT domain	94.56
PF10923	416	DUF2791: P-loop Domain of unknown function (DUF279	94.45
PRK06526	254	transposase; Provisional	94.26
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	94.26
PF14516	331	AAA_35: AAA-like domain	94.05
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	93.97
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	93.65
PRK08181	269	transposase; Validated	93.36
PRK12377	248	putative replication protein; Provisional	93.25
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	92.84
PF07726	131	AAA_3: ATPase family associated with various cellu	92.53
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	92.03
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	91.91
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	91.77
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	91.6
PRK09183	259	transposase/IS protein; Provisional	91.34
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	90.97
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	90.53
COG1241	682	MCM2 Predicted ATPase involved in replication cont	90.3
KOG0736	953	consensus Peroxisome assembly factor 2 containing	90.08
KOG0480	764	consensus DNA replication licensing factor, MCM6 c	89.7
smart00382	148	AAA ATPases associated with a variety of cellular	89.6
PRK06835	329	DNA replication protein DnaC; Validated	89.49
smart00487	201	DEXDc DEAD-like helicases superfamily.	89.26
PF05872	502	DUF853: Bacterial protein of unknown function (DUF	88.96
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	88.63
PRK06921	266	hypothetical protein; Provisional	88.58
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	88.54
PF07034	330	ORC3_N: Origin recognition complex (ORC) subunit 3	88.31
PRK13695	174	putative NTPase; Provisional	88.17
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	87.8
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	87.11
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	86.73
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	85.43
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	85.27
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	84.08
PLN03210	1153	Resistant to P. syringae 6; Provisional	84.01
COG1067	647	LonB Predicted ATP-dependent protease [Posttransla	83.98
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	83.98
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	83.77
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	83.37
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	83.3
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	82.79
COG1485	367	Predicted ATPase [General function prediction only	82.61
PRK07952	244	DNA replication protein DnaC; Validated	82.32
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	81.88
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	80.1

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.97  E-value=2.1e-31  Score=201.90  Aligned_cols=137  Identities=39%  Similarity=0.668  Sum_probs=132.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ++|.|+|.|+.+||++|+++||+++.++++|++||+.+++ +||||||..++.+.|+++++...|..++++||+.++.+.
T Consensus       131 vvi~ead~LT~dAQ~aLRRTMEkYs~~~RlIl~cns~SriIepIrSRCl~iRvpaps~eeI~~vl~~v~~kE~l~lp~~~  210 (351)
T KOG2035|consen  131 VVINEADELTRDAQHALRRTMEKYSSNCRLILVCNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQLPKEL  210 (351)
T ss_pred             EEEechHhhhHHHHHHHHHHHHHHhcCceEEEEecCcccchhHHhhheeEEeCCCCCHHHHHHHHHHHHHHhcccCcHHH
Confidence            5789999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcccC-ccc-cCCcHHHHHHHHHHHHhcCCCCC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFVEG-QVI-LTGWEDDITNIATKIIEEQSPKQ  137 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~-~~~-~~~~~~~~~~i~~~i~~~~~~~~  137 (137)
                      +..|++.|+||+|.|+-+|+.+...+.+++.+ +++ .+||+.++.+++..|+++|||.+
T Consensus       211 l~rIa~kS~~nLRrAllmlE~~~~~n~~~~a~~~~i~~~dWe~~i~e~a~~i~~eQs~~~  270 (351)
T KOG2035|consen  211 LKRIAEKSNRNLRRALLMLEAVRVNNEPFTANSQVIPKPDWEIYIQEIARVILKEQSPAK  270 (351)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHhccccccccCCCCCCccHHHHHHHHHHHHHhccCHHH
Confidence            99999999999999999999999999999888 666 69999999999999999999963

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=99.97  E-value=2.3e-30  Score=198.35  Aligned_cols=135  Identities=24%  Similarity=0.443  Sum_probs=123.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      |||||+|.|+.++|++|+++||.++.+++|||+||+..+| ++|.|||+-|+|+++.++++..+|+.||.+||+++++++
T Consensus       133 iIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~KfrFk~L~d~~iv~rL~~Ia~~E~v~~d~~a  212 (346)
T KOG0989|consen  133 IILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKKLKDEDIVDRLEKIASKEGVDIDDDA  212 (346)
T ss_pred             EEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHhcCCCcchHHHHHHHHHHHHHhCCCCCHHH
Confidence            6899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCccc--cCC--cHHHHHHHHHHHHhcCCC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVI--LTG--WEDDITNIATKIIEEQSP  135 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~~--~~~--~~~~~~~i~~~i~~~~~~  135 (137)
                      +..|++.|+||+|+|+.+||+++..+.+|+.+.+.  .-|  -.+.+.++.+..++.+.|
T Consensus       213 l~~I~~~S~GdLR~Ait~Lqsls~~gk~It~~~~~e~~~GvVp~~~l~~lle~a~S~d~~  272 (346)
T KOG0989|consen  213 LKLIAKISDGDLRRAITTLQSLSLLGKRITTSLVNEELAGVVPDEKLLDLLELALSADTP  272 (346)
T ss_pred             HHHHHHHcCCcHHHHHHHHHHhhccCcccchHHHHHHHhccCCHHHHHHHHHHHHccChH
Confidence            99999999999999999999999988888866654  222  355667777877777655

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=99.96  E-value=1.9e-29  Score=187.93  Aligned_cols=131  Identities=21%  Similarity=0.365  Sum_probs=120.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ||+||+|+|+.++|++|+++||-++..|+|.|+||...|| .||.|||.+++|.+++++++.++|.++++.|++.++++.
T Consensus       117 iILDEADSMT~gAQQAlRRtMEiyS~ttRFalaCN~s~KIiEPIQSRCAiLRysklsd~qiL~Rl~~v~k~Ekv~yt~dg  196 (333)
T KOG0991|consen  117 IILDEADSMTAGAQQALRRTMEIYSNTTRFALACNQSEKIIEPIQSRCAILRYSKLSDQQILKRLLEVAKAEKVNYTDDG  196 (333)
T ss_pred             EEeeccchhhhHHHHHHHHHHHHHcccchhhhhhcchhhhhhhHHhhhHhhhhcccCHHHHHHHHHHHHHHhCCCCCcch
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCc-ccCccc-cCC--cHHHHHHHHHHHHhc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPF-VEGQVI-LTG--WEDDITNIATKIIEE  132 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~-~~~~~~-~~~--~~~~~~~i~~~i~~~  132 (137)
                      ++.++..+.||||+++|.||+.. .+.++ +.+.|+ ..|  ++..++.+++.++..
T Consensus       197 Leaiifta~GDMRQalNnLQst~-~g~g~Vn~enVfKv~d~PhP~~v~~ml~~~~~~  252 (333)
T KOG0991|consen  197 LEAIIFTAQGDMRQALNNLQSTV-NGFGLVNQENVFKVCDEPHPLLVKKMLQACLKR  252 (333)
T ss_pred             HHHhhhhccchHHHHHHHHHHHh-ccccccchhhhhhccCCCChHHHHHHHHHHHhc
Confidence            99999999999999999999998 56664 445555 444  899999998888764

>PRK04132 replication factor C small subunit; Provisional

Probab=99.94  E-value=9.3e-27  Score=199.34  Aligned_cols=132  Identities=27%  Similarity=0.469  Sum_probs=119.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|+|+.++|++|+++||+|+++++|||+||++.++ +||+|||+.++|++++.+++..+|.++|++||+++++++
T Consensus       634 vIIDEaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi~i~~e~  713 (846)
T PRK04132        634 IFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEG  713 (846)
T ss_pred             EEEECcccCCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCcccc---CCcHHHHHHHHHHHHhc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVIL---TGWEDDITNIATKIIEE  132 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~~~---~~~~~~~~~i~~~i~~~  132 (137)
                      +..++..++||+|.|+|+||.+...+..++.+.+..   ...+..+.++++.++.+
T Consensus       714 L~~Ia~~s~GDlR~AIn~Lq~~~~~~~~It~~~V~~~~~~~~~~~I~~il~~~l~~  769 (846)
T PRK04132        714 LQAILYIAEGDMRRAINILQAAAALDDKITDENVFLVASRARPEDIREMMLLALKG  769 (846)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCCHHHHHHHHHHHhcC
Confidence            999999999999999999999886666777777652   23456777777766644

>PLN03025 replication factor C subunit; Provisional

Probab=99.94  E-value=5.6e-26  Score=177.50  Aligned_cols=133  Identities=24%  Similarity=0.336  Sum_probs=118.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+..+|++|++++|+++.+++||++||..+++ ++|+|||..++|++++++++..+|..++++||+.+++++
T Consensus       103 iiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~f~~l~~~~l~~~L~~i~~~egi~i~~~~  182 (319)
T PLN03025        103 VILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVPYVPEG  182 (319)
T ss_pred             EEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhcccCCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCccc---cCCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVI---LTGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~~i~~~~  133 (137)
                      +.++++.++||+|.++|.||........++.+.+.   ....+..+..+++.+..++
T Consensus       183 l~~i~~~~~gDlR~aln~Lq~~~~~~~~i~~~~v~~~~~~~~~~~i~~~i~~~~~~~  239 (319)
T PLN03025        183 LEAIIFTADGDMRQALNNLQATHSGFGFVNQENVFKVCDQPHPLHVKNIVRNCLKGK  239 (319)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCCHHHHHHHHHHHHcCC
Confidence            99999999999999999999876544456655554   2336778888888776543

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.93  E-value=2e-25  Score=188.25  Aligned_cols=133  Identities=20%  Similarity=0.192  Sum_probs=116.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+..++|+|+|+||+++.+++|||+||+.++| ++|+|||+.|+|++++.+++.++|++++++||+.+++++
T Consensus       123 IIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KIp~TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI~id~eA  202 (830)
T PRK07003        123 YMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERILGEERIAFEPQA  202 (830)
T ss_pred             EEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhccchhhhheEEEecCCcCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHH-hcCCCcccCccc-cCC--cHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASR-QMNYPFVEGQVI-LTG--WEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~-~~~~~~~~~~~~-~~~--~~~~~~~i~~~i~~~~  133 (137)
                      +..|++.++||+|.++++|+... ..+..++.+.+. ..+  -...+.++.+.++.++
T Consensus       203 L~lIA~~A~GsmRdALsLLdQAia~~~~~It~~~V~~~LG~~d~~~i~~ll~aL~~~d  260 (830)
T PRK07003        203 LRLLARAAQGSMRDALSLTDQAIAYSANEVTETAVSGMLGALDQTYMVRLLDALAAGD  260 (830)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhccCCcCHHHHHHHhCCCCHHHHHHHHHHHHcCC
Confidence            99999999999999999976544 333456666554 222  3556788888877755

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.93  E-value=1.8e-25  Score=181.73  Aligned_cols=133  Identities=14%  Similarity=0.135  Sum_probs=119.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||||+|+.+++++|++++|+|+.++.||++|+++++| ++|+|||+.|.|++++.+++..+|++++++||+.+++++
T Consensus       125 ~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~TI~SRCq~~~f~~ls~~~i~~~L~~i~~~Egi~~e~eA  204 (484)
T PRK14956        125 YIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRCQDFIFKKVPLSVLQDYSEKLCKIENVQYDQEG  204 (484)
T ss_pred             EEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHHHHhhhheeeecCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc-CCCcccCccc-c--CCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM-NYPFVEGQVI-L--TGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~-~~~~~~~~~~-~--~~~~~~~~~i~~~i~~~~  133 (137)
                      +..|++.++||+|.|+++|+.+... +..++...+. .  ..+...+.++++.|...+
T Consensus       205 L~~Ia~~S~Gd~RdAL~lLeq~i~~~~~~it~~~V~~~lg~~~~~~~~~l~~si~~~d  262 (484)
T PRK14956        205 LFWIAKKGDGSVRDMLSFMEQAIVFTDSKLTGVKIRKMIGYHGIEFLTSFIKSLIDPD  262 (484)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHHhCCCCcCHHHHHHHhCCCCHHHHHHHHHHHHcCC
Confidence            9999999999999999999875433 3346666664 2  336777888888888754

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

Probab=99.92  E-value=5.1e-25  Score=180.23  Aligned_cols=133  Identities=20%  Similarity=0.256  Sum_probs=116.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++|+|+|++||||.++.|||+|+++.|+ .|++|||+.|.|++++.+++...|..++.+||+.+++++
T Consensus       123 yiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip~TIlSRcq~f~fkri~~~~I~~~L~~i~~~E~I~~e~~a  202 (515)
T COG2812         123 YIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAAILDKEGINIEEDA  202 (515)
T ss_pred             EEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCchhhhhccccccccCCCHHHHHHHHHHHHHhcCCccCHHH
Confidence            4899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCC-CcccCccc-cCC--cHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNY-PFVEGQVI-LTG--WEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~-~~~~~~~~-~~~--~~~~~~~i~~~i~~~~  133 (137)
                      +..+++.++|++|+++++|+.+...+. .++.+.+. ..|  -...+...+..|+.++
T Consensus       203 L~~ia~~a~Gs~RDalslLDq~i~~~~~~It~~~v~~~lG~~~~~~~~~~~~~i~~~d  260 (515)
T COG2812         203 LSLIARAAEGSLRDALSLLDQAIAFGEGEITLESVRDMLGLTDIEKLLSLLEAILKGD  260 (515)
T ss_pred             HHHHHHHcCCChhhHHHHHHHHHHccCCcccHHHHHHHhCCCCHHHHHHHHHHHHccC
Confidence            999999999999999999998886654 35555554 233  3555566666666554

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.92  E-value=1.1e-24  Score=181.72  Aligned_cols=132  Identities=20%  Similarity=0.203  Sum_probs=113.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++|+|+|+||+|++++.|||+||++++| ++|+|||+.|+|++++.+++.++|++++.+||+.+++++
T Consensus       128 iIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~Egi~~d~eA  207 (700)
T PRK12323        128 YMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEGIAHEVNA  207 (700)
T ss_pred             EEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhhhhHHHHHHHhcccCCCChHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHh-cCCCcccCccc-cCC--cHHHHHHHHHHHHhc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQ-MNYPFVEGQVI-LTG--WEDDITNIATKIIEE  132 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~-~~~~~~~~~~~-~~~--~~~~~~~i~~~i~~~  132 (137)
                      +..|++.++|++|.++++++.... .+..++.+.+. ..+  -...+.++++.+..+
T Consensus       208 L~~IA~~A~Gs~RdALsLLdQaia~~~~~It~~~V~~~LG~~d~~~i~~Ll~aL~~~  264 (700)
T PRK12323        208 LRLLAQAAQGSMRDALSLTDQAIAYSAGNVSEEAVRGMLGAIDQSYLVRLLDALAAE  264 (700)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhccCCcCHHHHHHHhCCCCHHHHHHHHHHHHcC
Confidence            999999999999999999876443 33345555443 233  244566666666644

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.91  E-value=3.4e-24  Score=176.45  Aligned_cols=133  Identities=17%  Similarity=0.172  Sum_probs=119.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|+.++.|||+|+++.++ ++|+|||..|+|++++.+++.+++.+++++||+.+++++
T Consensus       123 ~iIDE~~~ls~~a~naLLk~LEepp~~~~fIlattd~~kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi~~~~~a  202 (509)
T PRK14958        123 YLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEENVEFENAA  202 (509)
T ss_pred             EEEEChHhcCHHHHHHHHHHHhccCCCeEEEEEECChHhchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc-CCCcccCccc-c--CCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM-NYPFVEGQVI-L--TGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~-~~~~~~~~~~-~--~~~~~~~~~i~~~i~~~~  133 (137)
                      +..+++.++||+|.++|.|+.+... +..++.+.|. .  ..-+..++++++.|..++
T Consensus       203 l~~ia~~s~GslR~al~lLdq~ia~~~~~It~~~V~~~lg~~~~~~i~~ll~al~~~d  260 (509)
T PRK14958        203 LDLLARAANGSVRDALSLLDQSIAYGNGKVLIADVKTMLGTIEPLLLFDILEALAAKA  260 (509)
T ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCCcCHHHHHHHHCCCCHHHHHHHHHHHHcCC
Confidence            9999999999999999999765543 3446666664 2  346888888888888754

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=99.91  E-value=8.8e-24  Score=174.22  Aligned_cols=133  Identities=20%  Similarity=0.259  Sum_probs=117.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|++++.|||+|+++.++ ++|+|||+.|+|.+++.+++..++.+++++||+.+++++
T Consensus       121 vIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~ttd~~kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi~i~~~A  200 (535)
T PRK08451        121 FIIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGVSYEPEA  200 (535)
T ss_pred             EEEECcccCCHHHHHHHHHHHhhcCCceEEEEEECChhhCchHHHhhceeEEcCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcC-CCcccCccc-cCC--cHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMN-YPFVEGQVI-LTG--WEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~-~~~~~~~~~-~~~--~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+++.|+.+...+ ..++.+.+. ..+  -+..+.++++.++.++
T Consensus       201 l~~Ia~~s~GdlR~alnlLdqai~~~~~~It~~~V~~~lg~~~~~~I~~li~ai~~~d  258 (535)
T PRK08451        201 LEILARSGNGSLRDTLTLLDQAIIYCKNAITESKVADMLGLLDPSKLEDFFQAILNQD  258 (535)
T ss_pred             HHHHHHHcCCcHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCCHHHHHHHHHHHHhcC
Confidence            99999999999999999998765433 356666654 223  4667888888777654

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.91  E-value=1.1e-23  Score=176.69  Aligned_cols=113  Identities=20%  Similarity=0.217  Sum_probs=103.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|+|+.+++|+|+|++|+|+++++|||+|+++++| ++|+|||+.|+|++++.+++..+|.+++++||+.+++++
T Consensus       123 ~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~TI~SRC~~~~f~~Ls~~ei~~~L~~il~~e~i~~e~~a  202 (647)
T PRK07994        123 YLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRQQLEHILQAEQIPFEPRA  202 (647)
T ss_pred             EEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccchHHHhhheEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcC-CCcccCcc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMN-YPFVEGQV  113 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~-~~~~~~~~  113 (137)
                      +..|+..++||+|.++++++.+...+ ..++.+.+
T Consensus       203 L~~Ia~~s~Gs~R~Al~lldqaia~~~~~it~~~v  237 (647)
T PRK07994        203 LQLLARAADGSMRDALSLTDQAIASGNGQVTTDDV  237 (647)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhcCCCcCHHHH
Confidence            99999999999999999997655433 33544443

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.91  E-value=1.3e-23  Score=175.04  Aligned_cols=133  Identities=14%  Similarity=0.137  Sum_probs=116.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|+++||+|+.++.|||+|++++++ ++|+|||+.|+|++++.+++.++|.++++++|+.+++++
T Consensus       122 vIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll~TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi~i~~~a  201 (584)
T PRK14952        122 FIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRSRTHHYPFRLLPPRTMRALIARICEQEGVVVDDAV  201 (584)
T ss_pred             EEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhHHHHHHhceEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcC--CCcccCccc-cCC--cHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMN--YPFVEGQVI-LTG--WEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~--~~~~~~~~~-~~~--~~~~~~~i~~~i~~~~  133 (137)
                      +..+++.++||+|.++|.|+.+....  ..++...+. ..+  -+..++++++.+..++
T Consensus       202 l~~Ia~~s~GdlR~aln~Ldql~~~~~~~~It~~~v~~llg~~~~~~i~~lv~al~~~d  260 (584)
T PRK14952        202 YPLVIRAGGGSPRDTLSVLDQLLAGAADTHVTYQRALGLLGATDVALIDDAVDALAADD  260 (584)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhccCCCCcCHHHHHHHHCCCCHHHHHHHHHHHHcCC
Confidence            99999999999999999999887542  346655554 222  4666777777766544

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.90  E-value=2.7e-23  Score=177.95  Aligned_cols=132  Identities=19%  Similarity=0.223  Sum_probs=111.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|+|+.+++++|+|+||+|+++++|||+|+++++| ++|+|||+.|+|++++.+++..+|.+++.++|+.+++++
T Consensus       123 iIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~~kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il~~EgI~~edeA  202 (944)
T PRK14949        123 YLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPVTVLSRCLQFNLKSLTQDEIGTQLNHILTQEQLPFEAEA  202 (944)
T ss_pred             EEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCchhchHHHHHhheEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcC-CCcccCccc-cCC--cHHHHHHHHHHHHhc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMN-YPFVEGQVI-LTG--WEDDITNIATKIIEE  132 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~-~~~~~~~~~-~~~--~~~~~~~i~~~i~~~  132 (137)
                      +..|+..++||+|.++++|+.+...+ ..++.+.+. ..+  -..++..+++.|..+
T Consensus       203 L~lIA~~S~Gd~R~ALnLLdQala~~~~~It~~~V~~llG~iD~~~V~~llksI~~~  259 (944)
T PRK14949        203 LTLLAKAANGSMRDALSLTDQAIAFGGGQVMLTQVQTMLGSIDEQHVIALLKALTDA  259 (944)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhcCCcccHHHHHHHhCCCCHHHHHHHHHHHHcC
Confidence            99999999999999999997544322 223333332 111  244455666665543

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.89  E-value=5.2e-23  Score=172.01  Aligned_cols=133  Identities=23%  Similarity=0.235  Sum_probs=117.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|+|+..++++|++++|+++.+++|||+|+++.++ ++++|||..|+|++++.+++.++|.+++++||+.+++++
T Consensus       122 ~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~~kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~kEgI~id~eA  201 (702)
T PRK14960        122 YLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQIAADQDA  201 (702)
T ss_pred             EEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECChHhhhHHHHHhhheeeccCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHh-cCCCcccCccc-cCC--cHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQ-MNYPFVEGQVI-LTG--WEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~-~~~~~~~~~~~-~~~--~~~~~~~i~~~i~~~~  133 (137)
                      +..|++.++||+|.++|.|+.+.. .+..++.+.+. ..+  -+..++++++.++.++
T Consensus       202 L~~IA~~S~GdLRdALnLLDQaIayg~g~IT~edV~~lLG~~d~e~IfdLldAI~k~d  259 (702)
T PRK14960        202 IWQIAESAQGSLRDALSLTDQAIAYGQGAVHHQDVKEMLGLIDRTIIYDLILAVHQNQ  259 (702)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhcCCCcCHHHHHHHhccCCHHHHHHHHHHHHhcC
Confidence            999999999999999999865443 33446666654 233  3556888888887765

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.89  E-value=5.5e-23  Score=171.99  Aligned_cols=133  Identities=17%  Similarity=0.207  Sum_probs=117.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|+|+.+++|+|++++|+|+.++.|||+|+++.++ ++++|||..|+|++++.+++..+|.+++.+||+.+++++
T Consensus       128 ~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~kil~TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi~ie~~A  207 (618)
T PRK14951        128 FMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPVTVLSRCLQFNLRPMAPETVLEHLTQVLAAENVPAEPQA  207 (618)
T ss_pred             EEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhhhHHHHHhceeeecCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcC-CCcccCccc-c--CCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMN-YPFVEGQVI-L--TGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~-~~~~~~~~~-~--~~~~~~~~~i~~~i~~~~  133 (137)
                      +..|++.++||+|.++++++.+...+ ..++...+. .  ..-+..++++++.+..++
T Consensus       208 L~~La~~s~GslR~al~lLdq~ia~~~~~It~~~V~~~Lg~~~~~~i~~LldaL~~~d  265 (618)
T PRK14951        208 LRLLARAARGSMRDALSLTDQAIAFGSGQLQEAAVRQMLGSVDRSHVFRLIDALAQGD  265 (618)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhcCCCcCHHHHHHHHcCCCHHHHHHHHHHHHcCC
Confidence            99999999999999999997554333 346655553 2  224777888888887765

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.89  E-value=5e-23  Score=168.43  Aligned_cols=134  Identities=25%  Similarity=0.271  Sum_probs=119.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|++++.|||+|++..++ ++|+|||+.+.|++++.+++.+++..++++||+.+++++
T Consensus       120 vIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlatte~~Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~Egi~i~~eA  199 (491)
T PRK14964        120 YIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENIEHDEES  199 (491)
T ss_pred             EEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEeCChHHHHHHHHHhheeeecccccHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc-CCCcccCccc-cCC--cHHHHHHHHHHHHhcCC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM-NYPFVEGQVI-LTG--WEDDITNIATKIIEEQS  134 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~-~~~~~~~~~~-~~~--~~~~~~~i~~~i~~~~~  134 (137)
                      +..|++.++||+|.+++.|+.+... +..++.+.|. ..+  -+..++++++.|+.++.
T Consensus       200 L~lIa~~s~GslR~alslLdqli~y~~~~It~e~V~~llg~~~~~~If~L~~aI~~~d~  258 (491)
T PRK14964        200 LKLIAENSSGSMRNALFLLEQAAIYSNNKISEKSVRDLLGCVDKHILEDLVEAILLGDA  258 (491)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHccCCHHHHHHHHHHHHCCCH
Confidence            9999999999999999999877643 3456666654 222  36668899999888763

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.89  E-value=5e-23  Score=171.80  Aligned_cols=133  Identities=23%  Similarity=0.308  Sum_probs=115.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|+++||+|+.++.|||+|+++.+| ++|+|||+.|.|++++.+++..+|..+++++|+.+++++
T Consensus       123 vIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~tI~SRc~~~~f~~l~~~~i~~~L~~i~~~egi~i~~~a  202 (576)
T PRK14965        123 FIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITILSRCQRFDFRRIPLQKIVDRLRYIADQEGISISDAA  202 (576)
T ss_pred             EEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHHHHHhhhhhhcCCCCHHHHHHHHHHHHHHhCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc-CCCcccCccc-cCC--cHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM-NYPFVEGQVI-LTG--WEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~-~~~~~~~~~~-~~~--~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+++.|+.+... +..++...+. .++  -+..+.++++.++.++
T Consensus       203 l~~la~~a~G~lr~al~~Ldqliay~g~~It~edV~~llG~~~~~~l~~ll~al~~~d  260 (576)
T PRK14965        203 LALVARKGDGSMRDSLSTLDQVLAFCGDAVGDDDVAELLGVVDRRLLLDISAAVFGRD  260 (576)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhccCCCCHHHHHHHhCCCCHHHHHHHHHHHHcCC
Confidence            9999999999999999999876533 3345555443 222  3555777777776654

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.89  E-value=7.3e-23  Score=175.86  Aligned_cols=133  Identities=14%  Similarity=0.125  Sum_probs=117.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|+|+.+++|+|+|+||+++.++.|||+|++.++| ++|+|||++|+|++++.+++.++|.+++++||+.+++++
T Consensus       124 ~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~EGv~id~ea  203 (824)
T PRK07764        124 FIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPDKVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQEGVPVEPGV  203 (824)
T ss_pred             EEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc--CCCcccCccc-c--CCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM--NYPFVEGQVI-L--TGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~--~~~~~~~~~~-~--~~~~~~~~~i~~~i~~~~  133 (137)
                      +..+++.++||+|.+++.|+.+...  ...++...+. .  ...+..++++++.+..++
T Consensus       204 l~lLa~~sgGdlR~Al~eLEKLia~~~~~~IT~e~V~allg~~~~~~I~~lidAL~~~D  262 (824)
T PRK07764        204 LPLVIRAGGGSVRDSLSVLDQLLAGAGPEGVTYERAVALLGVTDSALIDEAVDALAAGD  262 (824)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHcCC
Confidence            9999999999999999999987743  2346666554 2  335667777877776543

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.89  E-value=1.5e-22  Score=160.72  Aligned_cols=133  Identities=20%  Similarity=0.200  Sum_probs=117.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+..++++|++++|+|+.++.||++|++.+++ ++|+|||+.++|++++.+++.++|..+++++|+.+++++
T Consensus       123 iIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l~~tI~SRc~~~~~~~l~~~el~~~L~~~~~~~g~~i~~~a  202 (363)
T PRK14961        123 YLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKESIDTDEYA  202 (363)
T ss_pred             EEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhhhHHHHhhceEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcC-CCcccCccc---cCCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMN-YPFVEGQVI---LTGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~-~~~~~~~~~---~~~~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+++.|+.+...+ ..++...+.   ....+..++++++.+..++
T Consensus       203 l~~ia~~s~G~~R~al~~l~~~~~~~~~~It~~~v~~~l~~~~~~~i~~l~~ai~~~~  260 (363)
T PRK14961        203 LKLIAYHAHGSMRDALNLLEHAINLGKGNINIKNVTDMLGLLNEKQSFLLTDALLKKD  260 (363)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCCHHHHHHHHHHHHcCC
Confidence            99999999999999999998775443 335555443   2346778888888887654

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.88  E-value=3e-22  Score=165.67  Aligned_cols=132  Identities=23%  Similarity=0.275  Sum_probs=112.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|+|+.+++++|++++|+|++++.|||+|++..++ ++|+|||++++|++++.+++..+|..++++||+.+++++
T Consensus       123 iIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~Ttd~~kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~egi~~e~~A  202 (546)
T PRK14957        123 YLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENINSDEQS  202 (546)
T ss_pred             EEEechhhccHHHHHHHHHHHhcCCCCceEEEEECChhhhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 899999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc-CCCcccCccc-c--CCcHHHHHHHHHHHHhc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM-NYPFVEGQVI-L--TGWEDDITNIATKIIEE  132 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~-~~~~~~~~~~-~--~~~~~~~~~i~~~i~~~  132 (137)
                      +..++..++||+|.++|+|+.+... +..++.+.+. .  ..-+..++++++.+..+
T Consensus       203 l~~Ia~~s~GdlR~alnlLek~i~~~~~~It~~~V~~~l~~~~~~~v~~ll~Al~~~  259 (546)
T PRK14957        203 LEYIAYHAKGSLRDALSLLDQAISFCGGELKQAQIKQMLGIIDSEEVYSIINAIIDN  259 (546)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhccCCCCHHHHHHHHccCCHHHHHHHHHHHHcC
Confidence            9999999999999999999976543 3334443332 1  12345566766666553

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.88  E-value=1.8e-22  Score=169.68  Aligned_cols=133  Identities=20%  Similarity=0.234  Sum_probs=118.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+..++++|+++||++++++.|||+|+++.++ .+|+|||..|+|++++.+++..+|.+++++||+.+++++
T Consensus       123 IIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi~id~eA  202 (709)
T PRK08691        123 YIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIAYEPPA  202 (709)
T ss_pred             EEEECccccCHHHHHHHHHHHHhCCCCcEEEEEeCCccccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHcCCCcCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcC-CCcccCccc-cCC--cHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMN-YPFVEGQVI-LTG--WEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~-~~~~~~~~~-~~~--~~~~~~~i~~~i~~~~  133 (137)
                      +..|++.++||+|.++++|+.+...+ ..++.+.|. ..+  -+..++++++.|+.++
T Consensus       203 L~~Ia~~A~GslRdAlnLLDqaia~g~g~It~e~V~~lLG~~d~~~If~LldAL~~~d  260 (709)
T PRK08691        203 LQLLGRAAAGSMRDALSLLDQAIALGSGKVAENDVRQMIGAVDKQYLYELLTGIINQD  260 (709)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHhcCCCcCHHHHHHHHcccCHHHHHHHHHHHHcCC
Confidence            99999999999999999997765433 346655544 223  3667888888888765

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.88  E-value=5e-22  Score=163.46  Aligned_cols=134  Identities=19%  Similarity=0.168  Sum_probs=123.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+..++++|++.+|+++.++.||++|+++.++ ++++|||..|+|.+++.+++..+|.++++++|+.+++++
T Consensus       120 VIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SRc~~~~f~~ls~~el~~~L~~i~~~egi~i~~~A  199 (504)
T PRK14963        120 YILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQHFRFRRLTEEEIAGKLRRLLEAEGREAEPEA  199 (504)
T ss_pred             EEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcceEEEEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCccc---cCCcHHHHHHHHHHHHhcCC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVI---LTGWEDDITNIATKIIEEQS  134 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~~i~~~~~  134 (137)
                      +..+++.++||+|.++|.|+.+...+..++.+.+.   ...|+..++++++.+..++.
T Consensus       200 l~~ia~~s~GdlR~aln~Lekl~~~~~~It~~~V~~~l~~~~~~~if~Li~al~~~d~  257 (504)
T PRK14963        200 LQLVARLADGAMRDAESLLERLLALGTPVTRKQVEEALGLPPQERLRGIAAALAQGDA  257 (504)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCcHHHHHHHHHHHHcCCH
Confidence            99999999999999999999987665567777765   35589999999999987653

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.88  E-value=2.6e-22  Score=166.03  Aligned_cols=133  Identities=22%  Similarity=0.240  Sum_probs=113.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++|+|++++|+|+.++.|||+|++++++ ++|+|||+.++|++++.+++.++|.+++++||+.+++++
T Consensus       123 vIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t~d~~kil~tI~SRc~~~~f~~l~~~~i~~~L~~il~~egi~~~~~a  202 (527)
T PRK14969        123 YIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQENIPFDATA  202 (527)
T ss_pred             EEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEeCChhhCchhHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 899999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCC-CcccCccc-cCC--cHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNY-PFVEGQVI-LTG--WEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~-~~~~~~~~-~~~--~~~~~~~i~~~i~~~~  133 (137)
                      +..+++.++||+|.++++++.+...+. .++...+. ..+  -+..++++++.+..++
T Consensus       203 l~~la~~s~Gslr~al~lldqai~~~~~~I~~~~v~~~~~~~~~~~i~~ll~al~~~~  260 (527)
T PRK14969        203 LQLLARAAAGSMRDALSLLDQAIAYGGGTVNESEVRAMLGAIDQDYLFALLEALLAQD  260 (527)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCCCHHHHHHHHHHHHcCC
Confidence            999999999999999999986654433 34444432 122  2455667777766543

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=99.88  E-value=1.7e-22  Score=155.82  Aligned_cols=133  Identities=22%  Similarity=0.244  Sum_probs=122.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ||+||+|.|+.+||++|++++|++..+++|.++||++.++ ++++|||..|+|.+++.++...++.++++.|..+++++.
T Consensus       135 vILDEADaMT~~AQnALRRviek~t~n~rF~ii~n~~~ki~pa~qsRctrfrf~pl~~~~~~~r~shi~e~e~~~~~~~~  214 (360)
T KOG0990|consen  135 VILDEADAMTRDAQNALRRVIEKYTANTRFATISNPPQKIHPAQQSRCTRFRFAPLTMAQQTERQSHIRESEQKETNPEG  214 (360)
T ss_pred             EEecchhHhhHHHHHHHHHHHHHhccceEEEEeccChhhcCchhhcccccCCCCCCChhhhhhHHHHHHhcchhhcCHHH
Confidence            6899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCc-----cc-cCC--cHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQ-----VI-LTG--WEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~-----~~-~~~--~~~~~~~i~~~i~~~~  133 (137)
                      ...++..+.||||.++|.||.........++..     ++ +.+  .+.++..|.++++...
T Consensus       215 ~~a~~r~s~gDmr~a~n~Lqs~~~~~~~~~e~~~~~~~vy~c~g~p~~~dI~~I~~~il~~~  276 (360)
T KOG0990|consen  215 YSALGRLSVGDMRVALNYLQSILKKVMERKELNNPNDLVYQCKGAPQPSDIRQIIEKRMNGE  276 (360)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHhCCCCCCCCchhhHHHhcCCCChhHHHHHHHHHhcCc
Confidence            999999999999999999999987766666666     55 555  4668899999988764

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.88  E-value=5.1e-22  Score=165.28  Aligned_cols=133  Identities=22%  Similarity=0.320  Sum_probs=115.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|+.++.|||+|+.++++ ++|+|||+.+.|++++.+++..+|..+++++|+.+++++
T Consensus       123 iIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~tI~SRc~~~~f~~~~~~ei~~~L~~i~~~egi~i~~~a  202 (559)
T PRK05563        123 YIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPATILSRCQRFDFKRISVEDIVERLKYILDKEGIEYEDEA  202 (559)
T ss_pred             EEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcHHHHhHheEEecCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc-CCCcccCccc-cCC--cHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM-NYPFVEGQVI-LTG--WEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~-~~~~~~~~~~-~~~--~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+++.|+.+... +..++.+.+. .++  -+..++++++.+..++
T Consensus       203 l~~ia~~s~G~~R~al~~Ldq~~~~~~~~It~~~V~~vlg~~~~~~i~~l~~al~~~d  260 (559)
T PRK05563        203 LRLIARAAEGGMRDALSILDQAISFGDGKVTYEDALEVTGSVSQEALDDLVDAIVEGD  260 (559)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhccCCCCHHHHHHHhCCCCHHHHHHHHHHHHccC
Confidence            9999999999999999999877543 3345555544 223  3555677777776554

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.88  E-value=6.1e-22  Score=162.81  Aligned_cols=134  Identities=23%  Similarity=0.224  Sum_probs=120.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|+.++.||++|++..++ ++|+|||+.+.|++++.+++.+++..++++||+.+++++
T Consensus       132 vIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~egi~ie~eA  211 (507)
T PRK06645        132 FIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIISRCQRYDLRRLSFEEIFKLLEYITKQENLKTDIEA  211 (507)
T ss_pred             EEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHhhHHHHhcceEEEccCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCC----CcccCccc---cCCcHHHHHHHHHHHHhcCC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNY----PFVEGQVI---LTGWEDDITNIATKIIEEQS  134 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~----~~~~~~~~---~~~~~~~~~~i~~~i~~~~~  134 (137)
                      +..|+..++||+|.+++.|+.+...+.    .++.+.|.   ...-+..++++++.|+.++.
T Consensus       212 L~~Ia~~s~GslR~al~~Ldkai~~~~~~~~~It~~~V~~llg~~~~~~if~L~~ai~~~d~  273 (507)
T PRK06645        212 LRIIAYKSEGSARDAVSILDQAASMSAKSDNIISPQVINQMLGLVDSSVIIEFVEYIIHRET  273 (507)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhhccCCCCcCHHHHHHHHCCCCHHHHHHHHHHHHcCCH
Confidence            999999999999999999998754332    47666664   23368889999999987763

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.88  E-value=4.7e-22  Score=166.86  Aligned_cols=133  Identities=20%  Similarity=0.225  Sum_probs=116.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|+.++.|||+|++..++ ++|+|||.+++|.+++.+++..+|..+++++|+.+++++
T Consensus       125 vIIdea~~Ls~~a~naLLK~LEepp~~tifIL~tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi~i~~~a  204 (614)
T PRK14971        125 YIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGITAEPEA  204 (614)
T ss_pred             EEEECcccCCHHHHHHHHHHHhCCCCCeEEEEEeCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHh-cCCCcccCccc---cCCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQ-MNYPFVEGQVI---LTGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~-~~~~~~~~~~~---~~~~~~~~~~i~~~i~~~~  133 (137)
                      +..|+..++||+|.+++.|+.+.. .+..++...+.   ...-+..++++++.+++++
T Consensus       205 l~~La~~s~gdlr~al~~Lekl~~y~~~~It~~~V~~~l~~~~~~~iF~L~dai~~~~  262 (614)
T PRK14971        205 LNVIAQKADGGMRDALSIFDQVVSFTGGNITYKSVIENLNILDYDYYFRLTDALLAGK  262 (614)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhccCCccHHHHHHHhCCCCHHHHHHHHHHHHcCC
Confidence            999999999999999999987643 34446655443   2223445688888888765

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.86  E-value=3e-21  Score=161.40  Aligned_cols=133  Identities=17%  Similarity=0.220  Sum_probs=116.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      |||||+|.|+.+++++|++++|+|+.++.|||+|++..++ ++|+|||+.|.|++++.+++..||.++++++|+.+++++
T Consensus       136 vIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kll~tI~SRcq~~~f~~l~~~el~~~L~~i~~kegi~i~~eA  215 (598)
T PRK09111        136 YIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKVPVTVLSRCQRFDLRRIEADVLAAHLSRIAAKEGVEVEDEA  215 (598)
T ss_pred             EEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCC-CcccCccc-c--CCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNY-PFVEGQVI-L--TGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~-~~~~~~~~-~--~~~~~~~~~i~~~i~~~~  133 (137)
                      +..|+..++||+|.+++.|+.+...+. .++.+.|- .  ...+..++++.+.++.++
T Consensus       216 l~lIa~~a~Gdlr~al~~Ldkli~~g~g~It~e~V~~llg~~~~~~if~L~~ai~~gd  273 (598)
T PRK09111        216 LALIARAAEGSVRDGLSLLDQAIAHGAGEVTAEAVRDMLGLADRARVIDLFEALMRGD  273 (598)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhhcCCCcCHHHHHHHhCCCCHHHHHHHHHHHHcCC
Confidence            999999999999999999987654332 35555554 2  335667778887777654

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=99.86  E-value=2.3e-21  Score=163.92  Aligned_cols=132  Identities=25%  Similarity=0.245  Sum_probs=112.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|+++||+|+.++.|||+|+++.+| ++|+|||+.++|.+++.+++..+|..+++++|+.+++++
T Consensus       122 ~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl~TI~SRcq~ieF~~L~~eeI~~~L~~il~kegI~id~eA  201 (725)
T PRK07133        122 YIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPLTILSRVQRFNFRRISEDEIVSRLEFILEKENISYEKNA  201 (725)
T ss_pred             EEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhhHHHHhhceeEEccCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCC-CcccCccc-cCC--cHHHHHHHHHHHHhc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNY-PFVEGQVI-LTG--WEDDITNIATKIIEE  132 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~-~~~~~~~~-~~~--~~~~~~~i~~~i~~~  132 (137)
                      +..++..++||+|.|+++|+.+...+. .++...+. ..+  .+..+..+++.|...
T Consensus       202 l~~LA~lS~GslR~AlslLekl~~y~~~~It~e~V~ellg~~~~e~If~Ll~aI~~k  258 (725)
T PRK07133        202 LKLIAKLSSGSLRDALSIAEQVSIFGNNKITLKNVEELFGLVSNENLINLLNLLYSK  258 (725)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhccCCCCHHHHHHHHcCCCHHHHHHHHHHHHcC
Confidence            999999999999999999997754332 24444332 122  344466666666554

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.86  E-value=1.9e-21  Score=161.84  Aligned_cols=133  Identities=22%  Similarity=0.224  Sum_probs=113.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|++++.|||+|+.+.++ ++|+|||+.++|.+++.+++..+|..++.++|+.+++++
T Consensus       123 IIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~TI~SRcq~ieF~~Ls~~eL~~~L~~il~kegi~Is~ea  202 (605)
T PRK05896        123 YIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTIISRCQRYNFKKLNNSELQELLKSIAKKEKIKIEDNA  202 (605)
T ss_pred             EEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhHHHHhhhhhcccCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCC-CcccCcccc-C--CcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNY-PFVEGQVIL-T--GWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~-~~~~~~~~~-~--~~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.|++.|+.+..... +++...+.. .  .-+..+..+++.+...+
T Consensus       203 l~~La~lS~GdlR~AlnlLekL~~y~~~~It~e~V~ellg~~~~~~Vf~Ll~AI~~kd  260 (605)
T PRK05896        203 IDKIADLADGSLRDGLSILDQLSTFKNSEIDIEDINKTFGLVDNNKKINLIELIQKND  260 (605)
T ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhhcCCCCCHHHHHHHhccCCHHHHHHHHHHHHCCC
Confidence            999999999999999999998765332 255544331 1  12344566666665543

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.86  E-value=4e-21  Score=161.37  Aligned_cols=132  Identities=22%  Similarity=0.234  Sum_probs=115.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|+.++.|||+|+++.++ ++|+|||+.+.|++++.+++..+|.++++++|+.+++++
T Consensus       125 iIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~llpTIrSRc~~~~f~~l~~~ei~~~L~~ia~kegi~is~~a  204 (620)
T PRK14948        125 YVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTIISRCQRFDFRRIPLEAMVQHLSEIAEKESIEIEPEA  204 (620)
T ss_pred             EEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHhCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCccc-c--CCcHHHHHHHHHHHHhc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVI-L--TGWEDDITNIATKIIEE  132 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~~-~--~~~~~~~~~i~~~i~~~  132 (137)
                      +..+++.++||+|.|+++|+.+......++.+.+. .  ...+..+.++++.+..+
T Consensus       205 l~~La~~s~G~lr~A~~lLeklsL~~~~It~e~V~~lvg~~~e~~i~~Ll~ai~~~  260 (620)
T PRK14948        205 LTLVAQRSQGGLRDAESLLDQLSLLPGPITPEAVWDLLGAVPEQDLLNLLKALASN  260 (620)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhccCCCCHHHHHHHhcCCCHHHHHHHHHHHHCC
Confidence            99999999999999999999887655555554443 1  12355566777776643

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.86  E-value=3.4e-21  Score=160.86  Aligned_cols=131  Identities=14%  Similarity=0.147  Sum_probs=111.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      |||||+|.|+.+++++|++++|+++.++.|||+|+++.++ ++|+|||++|+|++++.+++..+|..+++++|+.+++++
T Consensus       123 IIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll~TI~SRcq~i~F~pLs~~eL~~~L~~il~~egi~id~ea  202 (624)
T PRK14959        123 FIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIVSRCQHFTFTRLSEAGLEAHLTKVLGREGVDYDPAA  202 (624)
T ss_pred             EEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhhHHHHhhhhccccCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCC-CcccCccc-c--CCcHHHHHHHHHHHHh
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNY-PFVEGQVI-L--TGWEDDITNIATKIIE  131 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~-~~~~~~~~-~--~~~~~~~~~i~~~i~~  131 (137)
                      +..+++.++||+|.++++|+.+...+. .++.+.+. .  ......++++++.+..
T Consensus       203 l~lIA~~s~GdlR~Al~lLeqll~~g~~~It~d~V~~~lg~~~~e~vfeLl~AL~~  258 (624)
T PRK14959        203 VRLIARRAAGSVRDSMSLLGQVLALGESRLTIDGARGVLGLAGQELFLRLMEALAA  258 (624)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCCCHHHHHHHHHHHhc
Confidence            999999999999999999986553332 35544443 1  2234456666666544

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.85  E-value=1.1e-20  Score=153.98  Aligned_cols=132  Identities=22%  Similarity=0.274  Sum_probs=113.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      |||||+|.|+.+++++|++++|+|++++.||++|++..++ ++|+|||..++|++++.+++.++|..+++++|+.+++++
T Consensus       125 vIIdead~lt~~~~n~LLk~lEep~~~~~~Il~t~~~~kl~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~~i~~~a  204 (451)
T PRK06305        125 YIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPGTILSRCQKMHLKRIPEETIIDKLALIAKQEGIETSREA  204 (451)
T ss_pred             EEEecHHhhCHHHHHHHHHHhhcCCCCceEEEEeCChHhcchHHHHhceEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc-CCCcccCccc---cCCcHHHHHHHHHHHHhc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM-NYPFVEGQVI---LTGWEDDITNIATKIIEE  132 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~-~~~~~~~~~~---~~~~~~~~~~i~~~i~~~  132 (137)
                      +..++..++||+|.+++.|+.+... +..++...+.   ...-+..++++++.+..+
T Consensus       205 l~~L~~~s~gdlr~a~~~Lekl~~~~~~~It~~~V~~l~~~~~~~~vf~L~~ai~~~  261 (451)
T PRK06305        205 LLPIARAAQGSLRDAESLYDYVVGLFPKSLDPDSVAKALGLLSQDSLYTLDEAITTQ  261 (451)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhccCCcCHHHHHHHHCCCCHHHHHHHHHHHHcC
Confidence            9999999999999999999987632 2234444332   122456666666666543

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.85  E-value=9.2e-21  Score=157.71  Aligned_cols=133  Identities=21%  Similarity=0.243  Sum_probs=114.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|+.++.|||+|+++.++ ++|+|||+.++|++++.+++..+|.++++++|+.+++++
T Consensus       123 vIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~~tI~SRc~~~~f~~l~~~el~~~L~~i~~~egi~id~eA  202 (563)
T PRK06647        123 YIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIKSRCQHFNFRLLSLEKIYNMLKKVCLEDQIKYEDEA  202 (563)
T ss_pred             EEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhHHHHHHhceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc-CCCcccCccc-c--CCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM-NYPFVEGQVI-L--TGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~-~~~~~~~~~~-~--~~~~~~~~~i~~~i~~~~  133 (137)
                      +..|+..++||+|.+++.|+.+... +..++...+. .  ...+..+.++++.|..++
T Consensus       203 l~lLa~~s~GdlR~alslLdklis~~~~~It~e~V~~llg~~~~~~if~LidaI~~~D  260 (563)
T PRK06647        203 LKWIAYKSTGSVRDAYTLFDQVVSFSDSDITLEQIRSKMGLTGDEFLEKLASSILNED  260 (563)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHhCCCCHHHHHHHHHHHHcCC
Confidence            9999999999999999999876543 2335544443 1  224556777777776654

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.85  E-value=1.2e-20  Score=154.19  Aligned_cols=133  Identities=21%  Similarity=0.221  Sum_probs=117.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++.+|++++++.||++|+++.++ ++|+|||.++.|.+++.+++..+++.+++++|+.+++++
T Consensus       121 vIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Ilattn~~kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi~i~~ea  200 (472)
T PRK14962        121 YIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGIEIDREA  200 (472)
T ss_pred             EEEEChHHhHHHHHHHHHHHHHhCCCcEEEEEEeCChHhhhHHHhcCcEEEEECCccHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999998899 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc-CCCcccCccc---cCCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM-NYPFVEGQVI---LTGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~-~~~~~~~~~~---~~~~~~~~~~i~~~i~~~~  133 (137)
                      +..|++.++||+|.++|.|+.+... +..++.+.+.   ....+..+.++++.|..++
T Consensus       201 l~~Ia~~s~GdlR~aln~Le~l~~~~~~~It~e~V~~~l~~~~~~~i~~li~si~~~d  258 (472)
T PRK14962        201 LSFIAKRASGGLRDALTMLEQVWKFSEGKITLETVHEALGLIPIEVVRDYINAIFNGD  258 (472)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHcCC
Confidence            9999999999999999999987643 2346655553   2235667788888887654

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.84  E-value=2.4e-20  Score=156.41  Aligned_cols=133  Identities=21%  Similarity=0.228  Sum_probs=114.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|++++.|||+|++..++ ++|+|||++++|++++.+++..+|..+++++|+.+++++
T Consensus       131 vIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~kLl~TI~SRc~~vef~~l~~~ei~~~L~~i~~~egi~I~~ea  210 (620)
T PRK14954        131 YIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLDEIQSQLQMICRAEGIQIDADA  210 (620)
T ss_pred             EEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhhceEEecCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcC------CCcccCccc---cCCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMN------YPFVEGQVI---LTGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~------~~~~~~~~~---~~~~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+++.|+.+....      ..++...+.   ...-+..++++++.|..++
T Consensus       211 l~~La~~s~Gdlr~al~eLeKL~~y~~~~~~~~~It~~~V~~lv~~~~e~~iF~L~dai~~~d  273 (620)
T PRK14954        211 LQLIARKAQGSMRDAQSILDQVIAFSVGSEAEKVIAYQGVAELLNYIDDEQFFDVTDAIAEND  273 (620)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHhccccccCCccCHHHHHHHHcCCCHHHHHHHHHHHHcCC
Confidence            99999999999999999999766432      235544332   1224666777777766554

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.84  E-value=2.4e-20  Score=153.01  Aligned_cols=133  Identities=20%  Similarity=0.281  Sum_probs=115.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|+.++.||++|++..++ ++|+|||+.+.|++++.+++..+|..+++++|+.+++++
T Consensus       123 vIIDEad~Lt~~a~naLLk~LEepp~~~v~Il~tt~~~kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi~id~~a  202 (486)
T PRK14953        123 YIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIEYEEKA  202 (486)
T ss_pred             EEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEECCHHHHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcC-CCcccCcccc-CC--cHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMN-YPFVEGQVIL-TG--WEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~-~~~~~~~~~~-~~--~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+++.|+.+...+ ..++...+.. .+  -+..++++++.|+.++
T Consensus       203 l~~La~~s~G~lr~al~~Ldkl~~~~~~~It~~~V~~~lg~~~~~~vf~Li~ai~~~d  260 (486)
T PRK14953        203 LDLLAQASEGGMRDAASLLDQASTYGEGKVTIKVVEEFLGIVSQESVRKFLNLLLESD  260 (486)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCCCHHHHHHHHHHHHCCC
Confidence            99999999999999999999875433 2355555442 22  3555778888777654

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.84  E-value=7.1e-20  Score=142.78  Aligned_cols=133  Identities=27%  Similarity=0.368  Sum_probs=120.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      |||||+|.|+.++++.|++++|+++.+++||++|+.+.++ ++|+|||..+.|.+++.+++..++..++.++|+.+++++
T Consensus       129 lilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~~~~~~~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~~~~~a  208 (337)
T PRK12402        129 ILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDYDDDG  208 (337)
T ss_pred             EEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCChhhCchhhcCCceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999998899999999988888 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCccc---c-CCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVI---L-TGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~~---~-~~~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+++.|+.+...+..++...+-   . ..++..++++++.+..++
T Consensus       209 l~~l~~~~~gdlr~l~~~l~~~~~~~~~It~~~v~~~~~~~~~~~~i~~l~~ai~~~~  266 (337)
T PRK12402        209 LELIAYYAGGDLRKAILTLQTAALAAGEITMEAAYEALGDVGTDEVIESLLDAAEAGD  266 (337)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHcCC
Confidence            99999999999999999999887555567766654   2 357889999999887764

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.84  E-value=7.8e-20  Score=141.48  Aligned_cols=133  Identities=30%  Similarity=0.473  Sum_probs=120.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ++|||+|.++...++.|+++++.++.++.||++||...++ ++++|||..+.|++++.+++..++..++.++|+.+++++
T Consensus       106 viiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~l~~~ei~~~l~~~~~~~~~~i~~~a  185 (319)
T PRK00440        106 IFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIEITDDA  185 (319)
T ss_pred             EEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhheeeeCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5799999999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCccc---cCCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVI---LTGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+++.|+.+...+..++.+.+.   ....+..++++++.++.++
T Consensus       186 l~~l~~~~~gd~r~~~~~l~~~~~~~~~it~~~v~~~~~~~~~~~i~~l~~~~~~~~  242 (319)
T PRK00440        186 LEAIYYVSEGDMRKAINALQAAAATGKEVTEEAVYKITGTARPEEIREMIELALNGD  242 (319)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCCHHHHHHHHHHHHcCC
Confidence            99999999999999999999988766667777665   2346778888888887543

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.82  E-value=1.2e-19  Score=142.65  Aligned_cols=133  Identities=20%  Similarity=0.231  Sum_probs=115.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      |+|||+|.|+.+++++|++.+|+++.++.||++|+++.++ ++|+|||..+.|++|+.+++..++..+++++|+.+++++
T Consensus       121 viidea~~l~~~~~~~Ll~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~~i~~~a  200 (355)
T TIGR02397       121 YIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGIKIEDEA  200 (355)
T ss_pred             EEEeChhhcCHHHHHHHHHHHhCCccceeEEEEeCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCC-CcccCccc---cCCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNY-PFVEGQVI---LTGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~-~~~~~~~~---~~~~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+++.|+.+...+. .++...+-   ....+..++++++.+++++
T Consensus       201 ~~~l~~~~~g~~~~a~~~lekl~~~~~~~it~~~v~~~~~~~~~~~i~~l~~ai~~~~  258 (355)
T TIGR02397       201 LELIARAADGSLRDALSLLDQLISFGNGNITYEDVNELLGLVDDEKLIELLEAILNKD  258 (355)
T ss_pred             HHHHHHHcCCChHHHHHHHHHHHhhcCCCCCHHHHHHHhCCCCHHHHHHHHHHHHcCC
Confidence            999999999999999999998765433 25544443   2235667788888877644

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.82  E-value=9e-20  Score=146.44  Aligned_cols=133  Identities=18%  Similarity=0.192  Sum_probs=114.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++.+|+|++.+.||++|++..++ ++|+|||.+++|++++.+++..++..+++++|+.+++++
T Consensus       131 vIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~kl~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~~i~~~a  210 (397)
T PRK14955        131 YIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLEEIQQQLQGICEAEGISVDADA  210 (397)
T ss_pred             EEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999998999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc------CCCcccCccc---cCCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM------NYPFVEGQVI---LTGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~------~~~~~~~~~~---~~~~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+++.|+.+...      +..++.+.+.   ...-+..++++++.+.+++
T Consensus       211 l~~l~~~s~g~lr~a~~~L~kl~~~~~~~~~~~~It~~~v~~~v~~~~~~~vf~l~~ai~~~~  273 (397)
T PRK14955        211 LQLIGRKAQGSMRDAQSILDQVIAFSVESEGEGSIRYDKVAELLNYIDDEHFFAVTDAVADGD  273 (397)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhccccCCCCccCHHHHHHHHCCCCHHHHHHHHHHHHcCC
Confidence            9999999999999999999976532      2235554442   2224656777777766544

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.82  E-value=1.6e-19  Score=143.33  Aligned_cols=134  Identities=22%  Similarity=0.237  Sum_probs=115.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      |+|||+|.|+..++++|++.+|+++.++.||++|+...++ ++++|||.+++|++++.+++..++..+++++|+.+++++
T Consensus       112 viIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~sr~~~v~~~~~~~~~l~~~l~~~~~~~g~~i~~~a  191 (367)
T PRK14970        112 YIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEGIKFEDDA  191 (367)
T ss_pred             EEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHHhcceeEecCCccHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc-CCCcccCccc---cCCcHHHHHHHHHHHHhcCC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM-NYPFVEGQVI---LTGWEDDITNIATKIIEEQS  134 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~-~~~~~~~~~~---~~~~~~~~~~i~~~i~~~~~  134 (137)
                      +..++..++||+|.+++.|+.+... +.+++...+.   ...-+..++++++.+..++.
T Consensus       192 l~~l~~~~~gdlr~~~~~lekl~~y~~~~it~~~v~~~~~~~~~~~if~l~~ai~~~~~  250 (367)
T PRK14970        192 LHIIAQKADGALRDALSIFDRVVTFCGKNITRQAVTENLNILDYDTYINVTDLILENKI  250 (367)
T ss_pred             HHHHHHhCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCCHHHHHHHHHHHHcCCH
Confidence            9999999999999999999987743 3335444332   22234567788888877654

>PRK04195 replication factor C large subunit; Provisional

Probab=99.81  E-value=1.7e-19  Score=147.91  Aligned_cols=133  Identities=22%  Similarity=0.308  Sum_probs=117.0

Q ss_pred             CcccccCcCCH----HHHHHHHHHHHhccCCceEEEEeCCCCCc-h-hhhhcceeeEecCCCHHHHHHHHHHHHHHcCCC
Q 042716            1 IILCEADKLST----DALLYMRWLLERYKGLNKVFFCCSDVSKL-Q-PIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQ   74 (137)
Q Consensus         1 iiiDEid~l~~----~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~-~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~   74 (137)
                      |||||+|.|+.    +++++|+++++  ..++++||+||++..+ . +|+|||..+.|++|+..++..+|..++.++|+.
T Consensus       102 IiIDEaD~L~~~~d~~~~~aL~~~l~--~~~~~iIli~n~~~~~~~k~Lrsr~~~I~f~~~~~~~i~~~L~~i~~~egi~  179 (482)
T PRK04195        102 ILLDEVDGIHGNEDRGGARAILELIK--KAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIE  179 (482)
T ss_pred             EEEecCcccccccchhHHHHHHHHHH--cCCCCEEEeccCccccchhhHhccceEEEecCCCHHHHHHHHHHHHHHcCCC
Confidence            68999999987    67899999999  5678899999999887 5 999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCcc--c-cCCcHHHHHHHHHHHHhcCCC
Q 042716           75 LPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQV--I-LTGWEDDITNIATKIIEEQSP  135 (137)
Q Consensus        75 i~~~~l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~--~-~~~~~~~~~~i~~~i~~~~~~  135 (137)
                      ++++++..|++.++||+|.++|.||.+......++.+.+  + ..+|+..++++++.++..+.+
T Consensus       180 i~~eaL~~Ia~~s~GDlR~ain~Lq~~a~~~~~it~~~v~~~~~~d~~~~if~~l~~i~~~k~~  243 (482)
T PRK04195        180 CDDEALKEIAERSGGDLRSAINDLQAIAEGYGKLTLEDVKTLGRRDREESIFDALDAVFKARNA  243 (482)
T ss_pred             CCHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCcHHHHHHhhcCCCCCCHHHHHHHHHCCCCH
Confidence            999999999999999999999999997654445665555  2 377888999999999986543

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.81  E-value=3.4e-19  Score=149.15  Aligned_cols=133  Identities=22%  Similarity=0.226  Sum_probs=116.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      |||||+|.|+.+++++|++++|+++.++.|||+|++..++ ++|+|||..+.|++++.+++..++.+++.++|+.+++++
T Consensus       124 vIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll~tI~SR~~~i~f~~l~~~el~~~L~~~a~~egl~i~~ea  203 (585)
T PRK14950        124 YIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILSRCQRFDFHRHSVADMAAHLRKIAAAEGINLEPGA  203 (585)
T ss_pred             EEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhhHHHHhccceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc-CCCcccCccc---cCCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM-NYPFVEGQVI---LTGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~-~~~~~~~~~~---~~~~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+++.|+.+... +..++.+.+.   ...-+..++++++.++.++
T Consensus       204 l~~La~~s~Gdlr~al~~LekL~~y~~~~It~e~V~~ll~~s~~~~vf~Lidal~~~d  261 (585)
T PRK14950        204 LEAIARAATGSMRDAENLLQQLATTYGGEISLSQVQSLLGISGDEEVKALAEALLAKD  261 (585)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHcCC
Confidence            9999999999999999999987642 2345554442   2224667788888887655

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=99.81  E-value=9.8e-20  Score=143.38  Aligned_cols=94  Identities=19%  Similarity=0.228  Sum_probs=86.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +|||++|.|+.+++|+|+|++|||++++.|||+|++++++ +||+|||+.+.|++|+.+++..+|.+     ...++++.
T Consensus       112 ~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRCq~~~~~~~~~~~~~~~L~~-----~~~~~~~~  186 (334)
T PRK07993        112 VWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRCRLHYLAPPPEQYALTWLSR-----EVTMSQDA  186 (334)
T ss_pred             EEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhccccccCCCCCHHHHHHHHHH-----ccCCCHHH
Confidence            5899999999999999999999999999999999999999 99999999999999999999999964     23467777


Q ss_pred             HHHHHHHcCCcHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFE   99 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~   99 (137)
                      +..++..++|++..|+.+++
T Consensus       187 a~~~~~la~G~~~~Al~l~~  206 (334)
T PRK07993        187 LLAALRLSAGAPGAALALLQ  206 (334)
T ss_pred             HHHHHHHcCCCHHHHHHHhc
Confidence            88899999999999998865

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.80  E-value=2e-19  Score=142.46  Aligned_cols=98  Identities=21%  Similarity=0.323  Sum_probs=91.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|+.++.|||+|+.+.++ ++|+|||+.++|++++.+++..+|.+.+..++  +++++
T Consensus       145 viIDeAd~l~~~aanaLLk~LEEpp~~~~fiLit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~~~--~~~~~  222 (351)
T PRK09112        145 VIIDPADDMNRNAANAILKTLEEPPARALFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSSQG--SDGEI  222 (351)
T ss_pred             EEEEchhhcCHHHHHHHHHHHhcCCCCceEEEEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcccC--CCHHH
Confidence            5899999999999999999999999999999999999999 99999999999999999999999998655444  77999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFEA  100 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~  100 (137)
                      +..++..++|++|.|+++++.
T Consensus       223 ~~~i~~~s~G~pr~Al~ll~~  243 (351)
T PRK09112        223 TEALLQRSKGSVRKALLLLNY  243 (351)
T ss_pred             HHHHHHHcCCCHHHHHHHHhc
Confidence            999999999999999999953

>PRK08485 DNA polymerase III subunit delta'; Validated

Probab=99.80  E-value=8.2e-20  Score=133.48  Aligned_cols=101  Identities=21%  Similarity=0.136  Sum_probs=93.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhccee-------------eEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTV-------------IQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~-------------i~~~~~~~~~i~~~l~~   66 (137)
                      ++|+++|.|+.+++|+|+|++||||.++.|||+|++++++ +|++|||+.             +.|++++.+++...|.+
T Consensus        58 ~iI~~a~~l~~~A~NaLLK~LEEPp~~~~fiL~t~~~~~llpTI~SRc~~~~~~~~~~~~~l~l~l~~l~~~~i~~~L~~  137 (206)
T PRK08485         58 IIVIAAPSYGIEAQNALLKILEEPPKNICFIIVAKSKNLLLPTIRSRLIIEKRKQKKPVKPLDLDLKKLDLKDIYEFLKE  137 (206)
T ss_pred             EEEEchHhhCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCchHHHhhheeccccccccccccccccCCCCHHHHHHHHHH
Confidence            4789999999999999999999999999999999999999 999999986             77999999999999999


Q ss_pred             HHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           67 IAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        67 i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                       .++|++...++++..|+..+.|.+|+++.+.+..-
T Consensus       138 -~~ke~~~~~~ea~~lIa~la~~s~r~~l~l~~q~l  172 (206)
T PRK08485        138 -LEKENKLSKEELKELIESLLKECVKYKIPLNEEEL  172 (206)
T ss_pred             -HHHcccccHHHHHHHHHHHHHHHHHHHcCccHHHH
Confidence             78899988899999999999999999987776543

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=99.80  E-value=2.8e-19  Score=139.73  Aligned_cols=98  Identities=16%  Similarity=0.221  Sum_probs=87.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +|||++|.|+.+++|+|+|++|+|+ ++.|||+|+++.++ +||+|||+.++|++++.+++..+|......++.+   ..
T Consensus       128 vII~~ae~m~~~aaNaLLK~LEEPp-~~~fILi~~~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~~~~---~~  203 (314)
T PRK07399        128 VVIEDAETMNEAAANALLKTLEEPG-NGTLILIAPSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEILN---IN  203 (314)
T ss_pred             EEEEchhhcCHHHHHHHHHHHhCCC-CCeEEEEECChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhccccch---hH
Confidence            5899999999999999999999999 88999999999999 9999999999999999999999999876555433   23


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ...++..++||++.|++.++...
T Consensus       204 ~~~l~~~a~Gs~~~al~~l~~~~  226 (314)
T PRK07399        204 FPELLALAQGSPGAAIANIEQLQ  226 (314)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHH
Confidence            57889999999999999997543

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=99.78  E-value=1e-18  Score=136.76  Aligned_cols=93  Identities=18%  Similarity=0.244  Sum_probs=84.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +|||++|.|+.+++|+|+|++|||++++.|||+|++++++ +||+|||+.++|.+|+.+++..+|..    .|  +++..
T Consensus       117 ~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIrSRCq~i~~~~~~~~~~~~~L~~----~~--~~~~~  190 (319)
T PRK08769        117 VIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRCQRLEFKLPPAHEALAWLLA----QG--VSERA  190 (319)
T ss_pred             EEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHHhhheEeeCCCcCHHHHHHHHHH----cC--CChHH
Confidence            5899999999999999999999999999999999999999 99999999999999999999999974    34  45666


Q ss_pred             HHHHHHHcCCcHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFE   99 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~   99 (137)
                      ...++..++|.+..|+..++
T Consensus       191 a~~~~~l~~G~p~~A~~~~~  210 (319)
T PRK08769        191 AQEALDAARGHPGLAAQWLR  210 (319)
T ss_pred             HHHHHHHcCCCHHHHHHHhc
Confidence            67789999999998887764

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=99.78  E-value=1.2e-18  Score=136.58  Aligned_cols=94  Identities=16%  Similarity=0.117  Sum_probs=83.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +|||++|.|+.+++|+|+|++|||++++.|||+|++++++ +||+|||+.++|.+|+.+++..+|....     ..++..
T Consensus       111 ~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~~~~~~~~~~~~~L~~~~-----~~~~~~  185 (325)
T PRK06871        111 VYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQQALDWLQAQS-----SAEISE  185 (325)
T ss_pred             EEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceEEeCCCCCHHHHHHHHHHHh-----ccChHH
Confidence            5799999999999999999999999999999999999999 9999999999999999999999998643     223445


Q ss_pred             HHHHHHHcCCcHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFE   99 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~   99 (137)
                      +...+..++|.+..|+.+++
T Consensus       186 ~~~~~~l~~g~p~~A~~~~~  205 (325)
T PRK06871        186 ILTALRINYGRPLLALTFLE  205 (325)
T ss_pred             HHHHHHHcCCCHHHHHHHhh
Confidence            66778889999988887764

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

Probab=99.77  E-value=2.2e-18  Score=136.49  Aligned_cols=104  Identities=17%  Similarity=0.194  Sum_probs=89.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCC--c-hhhhhcceeeEecCCCHHHHHHHHHHHHH--HcCCC-
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK--L-QPIKSLCTVIQLLPPSKQEIVEVLEFIAE--QEGIQ-   74 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~--i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~--~egi~-   74 (137)
                      +||||||++++..|.+|+..+|  .+...||-+|++.+.  + ++|+|||++|.|++++.+++.+.|.+.+.  .+|+. 
T Consensus       108 LflDEIHRfnK~QQD~lLp~vE--~G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra~~~~~rgl~~  185 (436)
T COG2256         108 LFLDEIHRFNKAQQDALLPHVE--NGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRALLDEERGLGG  185 (436)
T ss_pred             EEEehhhhcChhhhhhhhhhhc--CCeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHHHHHHHHHHhhhhcCCCc
Confidence            5899999999999999999999  555556666655543  7 99999999999999999999999999554  55666 


Q ss_pred             ----CCHHHHHHHHHHcCCcHHHHHHHHHHHHhcCC
Q 042716           75 ----LPHQLAEKIADNSKNNLRQAIRSFEASRQMNY  106 (137)
Q Consensus        75 ----i~~~~l~~i~~~~~gd~R~aln~L~~~~~~~~  106 (137)
                          +++++...++..++||.|.++|+|+.+.....
T Consensus       186 ~~~~i~~~a~~~l~~~s~GD~R~aLN~LE~~~~~~~  221 (436)
T COG2256         186 QIIVLDEEALDYLVRLSNGDARRALNLLELAALSAE  221 (436)
T ss_pred             ccccCCHHHHHHHHHhcCchHHHHHHHHHHHHHhcC
Confidence                78999999999999999999999999986554

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=99.77  E-value=1.8e-18  Score=135.90  Aligned_cols=95  Identities=18%  Similarity=0.174  Sum_probs=84.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +|||++|.|+.+++|+|+|++|+|++++.|||+|++++++ +||+|||+.++|.+|+.+++..+|....    -..+++.
T Consensus       110 ~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~L~~~~----~~~~~~~  185 (328)
T PRK05707        110 VLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQWLQQAL----PESDERE  185 (328)
T ss_pred             EEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHHHHHHHHhc----ccCChHH
Confidence            5799999999999999999999999999999999999999 9999999999999999999999997532    1345667


Q ss_pred             HHHHHHHcCCcHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFE   99 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~   99 (137)
                      ...++..++|++..|+.+++
T Consensus       186 ~~~~l~la~Gsp~~A~~l~~  205 (328)
T PRK05707        186 RIELLTLAGGSPLRALQLHE  205 (328)
T ss_pred             HHHHHHHcCCCHHHHHHHHC
Confidence            77889999999999887754

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=99.77  E-value=1.5e-18  Score=135.78  Aligned_cols=91  Identities=16%  Similarity=0.185  Sum_probs=82.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +|||++|.|+.+++|+|+|++|||++++.|||+|++++++ +||+|||+.++|.+|+.+++..+|..    +|++    .
T Consensus       112 ~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~L~~----~~~~----~  183 (319)
T PRK06090        112 FVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWVVTPPSTAQAMQWLKG----QGIT----V  183 (319)
T ss_pred             EEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcceeEeCCCCCHHHHHHHHHH----cCCc----h
Confidence            5899999999999999999999999999999999999999 99999999999999999999999864    5654    2


Q ss_pred             HHHHHHHcCCcHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFE   99 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~   99 (137)
                      ...++..++|++..|+.+++
T Consensus       184 ~~~~l~l~~G~p~~A~~~~~  203 (319)
T PRK06090        184 PAYALKLNMGSPLKTLAMMK  203 (319)
T ss_pred             HHHHHHHcCCCHHHHHHHhC
Confidence            35678889999999988775

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

Probab=99.76  E-value=2.6e-19  Score=138.61  Aligned_cols=93  Identities=35%  Similarity=0.430  Sum_probs=83.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      |||||+|.|+.+++++|++++|+|+.+++|||+||++.++ +||+|||+.++|++++.      +..++..+     +++
T Consensus       113 iiidead~mt~~A~nallk~lEep~~~~~~il~~n~~~~il~tI~SRc~~i~f~~~~~------~~~i~~~e-----~~~  181 (325)
T COG0470         113 VIIDEADKLTEDAANALLKTLEEPPKNTRFILITNDPSKILPTIRSRCQRIRFKPPSR------LEAIAWLE-----DQG  181 (325)
T ss_pred             EEeCcHHHHhHHHHHHHHHHhccCCCCeEEEEEcCChhhccchhhhcceeeecCCchH------HHHHHHhh-----ccc
Confidence            5899999999999999999999999999999999999999 99999999999998544      44444445     567


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM  104 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~  104 (137)
                      +..++..+.||+|.++|.||.....
T Consensus       182 l~~i~~~~~gd~r~~i~~lq~~~~~  206 (325)
T COG0470         182 LEEIAAVAEGDARKAINPLQALAAL  206 (325)
T ss_pred             hhHHHHHHHHHHHcCCCHHHHHHHh
Confidence            8999999999999999999999865

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.74  E-value=4.3e-18  Score=123.60  Aligned_cols=88  Identities=20%  Similarity=0.251  Sum_probs=82.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      |||||+|.|++.++++|++.+|++++++.|||+|++..++ ++++|||.++.|.+++.+++.++|...    |  +++++
T Consensus       100 iiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~~~~~~~~~~~~~~~~~l~~~----g--i~~~~  173 (188)
T TIGR00678       100 VIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQWLIRQ----G--ISEEA  173 (188)
T ss_pred             EEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhcEEeeCCCCCHHHHHHHHHHc----C--CCHHH
Confidence            5899999999999999999999999999999999998889 999999999999999999999999774    5  68999


Q ss_pred             HHHHHHHcCCcHHHH
Q 042716           80 AEKIADNSKNNLRQA   94 (137)
Q Consensus        80 l~~i~~~~~gd~R~a   94 (137)
                      +..++..++||+|.|
T Consensus       174 ~~~i~~~~~g~~r~~  188 (188)
T TIGR00678       174 AELLLALAGGSPGAA  188 (188)
T ss_pred             HHHHHHHcCCCcccC
Confidence            999999999999975

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.

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.73  E-value=1.7e-17  Score=129.35  Aligned_cols=94  Identities=17%  Similarity=0.235  Sum_probs=84.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +|||++|.|+.+++|+|++++|+|++++.|||+|++++++ +||+|||++++|.+++.+++..+|.....    .++++.
T Consensus        97 ~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~l~~~~~----~~~~~~  172 (313)
T PRK05564         97 IIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEIEKFISYKYN----DIKEEE  172 (313)
T ss_pred             EEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhceeeeCCCcCHHHHHHHHHHHhc----CCCHHH
Confidence            5899999999999999999999999999999999999999 99999999999999999999999976332    467888


Q ss_pred             HHHHHHHcCCcHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSF   98 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L   98 (137)
                      +..++..++|++..|...+
T Consensus       173 ~~~l~~~~~g~~~~a~~~~  191 (313)
T PRK05564        173 KKSAIAFSDGIPGKVEKFI  191 (313)
T ss_pred             HHHHHHHcCCCHHHHHHHh
Confidence            8999999999998887554

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.73  E-value=1.2e-17  Score=134.04  Aligned_cols=94  Identities=22%  Similarity=0.334  Sum_probs=85.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+++++++|++++|+|+.++.||++|+++..+ +||+|||+.++|++|+.+++..+|..   ++|  ++++.
T Consensus       121 iiIDead~m~~~aanaLLk~LEep~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~---~~~--~~~~~  195 (394)
T PRK07940        121 VVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVR---RDG--VDPET  195 (394)
T ss_pred             EEEechhhcCHHHHHHHHHHhhcCCCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHH---hcC--CCHHH
Confidence            5899999999999999999999999999999999999999 99999999999999999999999873   334  57888


Q ss_pred             HHHHHHHcCCcHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFE   99 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~   99 (137)
                      +..++..++|+++.|+.++.
T Consensus       196 a~~la~~s~G~~~~A~~l~~  215 (394)
T PRK07940        196 ARRAARASQGHIGRARRLAT  215 (394)
T ss_pred             HHHHHHHcCCCHHHHHHHhc
Confidence            89999999999999987753

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.73  E-value=6.1e-17  Score=125.76  Aligned_cols=128  Identities=22%  Similarity=0.358  Sum_probs=103.1

Q ss_pred             CcccccCcC-CHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHH-------HHHHHHHc
Q 042716            1 IILCEADKL-STDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEV-------LEFIAEQE   71 (137)
Q Consensus         1 iiiDEid~l-~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~-------l~~i~~~e   71 (137)
                      ++|||+|.+ +.++++.|+.++|+++.+++||++||...++ ++|+|||..+.|+.|+.++...+       +..++.++
T Consensus       104 liiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~~~l~sR~~~i~~~~p~~~~~~~il~~~~~~~~~~~~~~  183 (316)
T PHA02544        104 IIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQMIVRCKGILEAE  183 (316)
T ss_pred             EEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhchHHHHhhceEEEeCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            589999999 7778899999999999999999999999999 99999999999999999876644       45567789


Q ss_pred             CCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCccccCCcHHHHHHHHHHHH
Q 042716           72 GIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWEDDITNIATKII  130 (137)
Q Consensus        72 gi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~  130 (137)
                      |+.++++++..+++.+.||+|.+++.|+.... +..++... +..-+...++++++.+.
T Consensus       184 ~~~i~~~al~~l~~~~~~d~r~~l~~l~~~~~-~~~i~~~~-l~~~~~~~~~~l~~~l~  240 (316)
T PHA02544        184 GVEVDMKVLAALVKKNFPDFRRTINELQRYAS-TGKIDAGI-LSEVTNSDIDDVVEALK  240 (316)
T ss_pred             CCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHc-cCCCCHHH-HHHhhHHHHHHHHHHHH
Confidence            99999999999999999999999999998763 33333222 11113445555655543

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.72  E-value=1.8e-17  Score=130.31  Aligned_cols=93  Identities=24%  Similarity=0.346  Sum_probs=81.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++|+|+|++|+||+++.|||+|+++.++ +||+|||++++|.+++.+++..+|..    +|  ++++.
T Consensus       114 viI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TIrSRc~~i~~~~~~~~~~~~~L~~----~g--i~~~~  187 (329)
T PRK08058        114 YIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQE----EG--ISESL  187 (329)
T ss_pred             EEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHHHhhceeeeCCCCCHHHHHHHHHH----cC--CChHH
Confidence            5899999999999999999999999999999999999999 99999999999999999999888853    56  45666


Q ss_pred             HHHHHHHcCCcHHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFEA  100 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~  100 (137)
                      ...++.. .|+++.|+.+++.
T Consensus       188 ~~~l~~~-~g~~~~A~~l~~~  207 (329)
T PRK08058        188 ATLLAGL-TNSVEEALALSED  207 (329)
T ss_pred             HHHHHHH-cCCHHHHHHHhcC
Confidence            6566655 4789999887653

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=99.72  E-value=2.5e-17  Score=129.97  Aligned_cols=90  Identities=17%  Similarity=0.215  Sum_probs=79.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +|||++|.|+.+++|+|+|++|||++++.|||+|++++++ +||+|||+.++|++|+.+++..+|..    .|+  ++  
T Consensus       136 ~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~----~~~--~~--  207 (342)
T PRK06964        136 VVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAA----QGV--AD--  207 (342)
T ss_pred             EEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHH----cCC--Ch--
Confidence            5899999999999999999999999999999999999999 99999999999999999999999975    243  33  


Q ss_pred             HHHHHHHcCCcHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSF   98 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L   98 (137)
                      ...++..++|++..|+.++
T Consensus       208 ~~~~l~~~~Gsp~~Al~~~  226 (342)
T PRK06964        208 ADALLAEAGGAPLAALALA  226 (342)
T ss_pred             HHHHHHHcCCCHHHHHHHH
Confidence            2345777899999888765

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.70  E-value=9e-17  Score=127.93  Aligned_cols=96  Identities=20%  Similarity=0.339  Sum_probs=86.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ++|||+|.|+..++++|++++|+|+.++.||++|++++.+ ++++|||+.++|.+++.+++..+|..    .+...+++.
T Consensus       145 viIDead~m~~~aanaLLK~LEepp~~~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~----~~~~~~~~~  220 (365)
T PRK07471        145 VIVDTADEMNANAANALLKVLEEPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAA----AGPDLPDDP  220 (365)
T ss_pred             EEEechHhcCHHHHHHHHHHHhcCCCCeEEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHH----hcccCCHHH
Confidence            5899999999999999999999999999999999999999 99999999999999999999999976    334456666


Q ss_pred             HHHHHHHcCCcHHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFEA  100 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~  100 (137)
                      +..++..++|+++.++++++.
T Consensus       221 ~~~l~~~s~Gsp~~Al~ll~~  241 (365)
T PRK07471        221 RAALAALAEGSVGRALRLAGG  241 (365)
T ss_pred             HHHHHHHcCCCHHHHHHHhcc
Confidence            678999999999999999863

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=99.69  E-value=8.2e-17  Score=124.46  Aligned_cols=91  Identities=22%  Similarity=0.304  Sum_probs=75.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +|||++|.|+.+++|+|+|++|||++++.|||+|++++++ |||+|||+.++|++ +.+++..+|.    ++|+.  .+.
T Consensus       108 ~II~~ad~m~~~AaNaLLKtLEEPp~~t~~iL~t~~~~~lLpTI~SRcq~i~f~~-~~~~~~~~L~----~~g~~--~~~  180 (290)
T PRK07276        108 FIIKDADKMHVNAANSLLKVIEEPQSEIYIFLLTNDENKVLPTIKSRTQIFHFPK-NEAYLIQLLE----QKGLL--KTQ  180 (290)
T ss_pred             EEeehhhhcCHHHHHHHHHHhcCCCCCeEEEEEECChhhCchHHHHcceeeeCCC-cHHHHHHHHH----HcCCC--hHH
Confidence            5899999999999999999999999999999999999999 99999999999966 6777666664    46754  444


Q ss_pred             HHHHHHHcCCcHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFE   99 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~   99 (137)
                      ...++..+ |++..|+.+++
T Consensus       181 a~~la~~~-~s~~~A~~l~~  199 (290)
T PRK07276        181 AELLAKLA-QSTSEAEKLAQ  199 (290)
T ss_pred             HHHHHHHC-CCHHHHHHHhC
Confidence            44455444 57988888773

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

Probab=99.69  E-value=1.9e-17  Score=118.30  Aligned_cols=56  Identities=34%  Similarity=0.389  Sum_probs=49.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCC
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPS   56 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~   56 (137)
                      +||||+|.|+.++||+|+|+||+|+.+++|||+|+++.+| +||+|||+.++|+++|
T Consensus       106 iiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~~il~TI~SRc~~i~~~~ls  162 (162)
T PF13177_consen  106 IIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPSKILPTIRSRCQVIRFRPLS  162 (162)
T ss_dssp             EEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GGGS-HHHHTTSEEEEE----
T ss_pred             EEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChHHChHHHHhhceEEecCCCC
Confidence            5899999999999999999999999999999999999999 9999999999999875

...

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=99.68  E-value=1.6e-16  Score=120.71  Aligned_cols=92  Identities=13%  Similarity=0.132  Sum_probs=79.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCC----------CHHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPP----------SKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~----------~~~~i~~~l~~i~~   69 (137)
                      +||+++|+|+.+++|+|+|++|||++++.|||+|++++++ +||+|||+.+.|+++          +++++...+..   
T Consensus        92 ~II~~ae~m~~~AaNaLLK~LEEPp~~t~fiLit~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~~~~~~~i~~~L~~---  168 (261)
T PRK05818         92 YIIYGIEKLNKQSANSLLKLIEEPPKNTYGIFTTRNENNILNTILSRCVQYVVLSKEKKVPFKVESNDRYFQYILLS---  168 (261)
T ss_pred             EEeccHhhhCHHHHHHHHHhhcCCCCCeEEEEEECChHhCchHhhhheeeeecCChhhhcccccccChHHHHHHHHH---
Confidence            5899999999999999999999999999999999999999 999999999999888          55565555543   


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHH
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS  101 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~  101 (137)
                      +.+  +++    .++..++|++.+++..++.+
T Consensus       169 ~~~--~d~----~i~~~a~g~~~~a~~l~~~l  194 (261)
T PRK05818        169 FYS--VDE----QLQAYNNGSFSKLKNIIETL  194 (261)
T ss_pred             ccC--ccH----HHHHHcCCCHHHHHHHHHHH
Confidence            222  343    77788999999999999965

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=99.67  E-value=4.1e-16  Score=121.17  Aligned_cols=91  Identities=20%  Similarity=0.185  Sum_probs=80.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +|||++|.|+.+++++|++++|+||+++.|||+|+++.++ +||+|||++++|.+++.+++..+|..    .|  ++++.
T Consensus        94 vII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~f~~l~~~~l~~~l~~----~~--~~~~~  167 (299)
T PRK07132         94 LIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPDQQKILAKLLS----KN--KEKEY  167 (299)
T ss_pred             EEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEEECCCCCHHHHHHHHHH----cC--CChhH
Confidence            5899999999999999999999999999999999999999 99999999999999999999999875    24  56777


Q ss_pred             HHHHHHHcCCcHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSF   98 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L   98 (137)
                      ...++..++ ++.+|+.++
T Consensus       168 a~~~a~~~~-~~~~a~~~~  185 (299)
T PRK07132        168 NWFYAYIFS-NFEQAEKYI  185 (299)
T ss_pred             HHHHHHHcC-CHHHHHHHH
Confidence            677777776 488888765

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=99.66  E-value=2.6e-16  Score=121.58  Aligned_cols=77  Identities=16%  Similarity=0.173  Sum_probs=67.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +|||++|.|+.+++|+|+|++|||++++.|||+|++++++ +||+|||+.++|+++.               ...++++.
T Consensus        99 ~ii~~ad~mt~~AaNaLLK~LEEPp~~~~fiL~~~~~~~ll~TI~SRcq~~~~~~~~---------------~~~i~~~~  163 (290)
T PRK05917         99 YIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTIRSRSLSIHIPMEE---------------KTLVSKED  163 (290)
T ss_pred             EEEechhhcCHHHHHHHHHHhhcCCCCeEEEEEeCChhhCcHHHHhcceEEEccchh---------------ccCCCHHH
Confidence            4899999999999999999999999999999999999999 9999999999998862               12357777


Q ss_pred             HHHHHHHcCCcHH
Q 042716           80 AEKIADNSKNNLR   92 (137)
Q Consensus        80 l~~i~~~~~gd~R   92 (137)
                      +..++..++|+++
T Consensus       164 ~~~l~~~~~g~~~  176 (290)
T PRK05917        164 IAYLIGYAQGKES  176 (290)
T ss_pred             HHHHHHHhCCChh
Confidence            7777777888774

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.60  E-value=1.8e-14  Score=121.09  Aligned_cols=131  Identities=18%  Similarity=0.301  Sum_probs=108.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHh--c----cC---------------CceEEEEeCCCCC--chhhhhcceeeEecCCCH
Q 042716            1 IILCEADKLSTDALLYMRWLLER--Y----KG---------------LNKVFFCCSDVSK--LQPIKSLCTVIQLLPPSK   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~--~----~~---------------~~~~Il~~n~~~~--i~~l~SRc~~i~~~~~~~   57 (137)
                      +||||||+=...+.+.++++++.  .    ++               .-|+|++||+.+.  +++||--|.++.|.+|++
T Consensus       391 LViDEIDGa~~~~Vdvilslv~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNdLYaPaLR~Lr~~A~ii~f~~p~~  470 (877)
T KOG1969|consen  391 LVIDEIDGAPRAAVDVILSLVKATNKQATGKQAKKDKKRKKKRSKLLTRPIICICNDLYAPALRPLRPFAEIIAFVPPSQ  470 (877)
T ss_pred             EEEecccCCcHHHHHHHHHHHHhhcchhhcCcccchhhhhhhccccccCCEEEEecCccchhhhhcccceEEEEecCCCh
Confidence            58999999999999999999982  1    11               2469999999865  699999999999999999


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhcCCCc----ccCccc-----cCCcHHHHHHHHHH
Q 042716           58 QEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPF----VEGQVI-----LTGWEDDITNIATK  128 (137)
Q Consensus        58 ~~i~~~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~~~~~~----~~~~~~-----~~~~~~~~~~i~~~  128 (137)
                      ..++++|+.||.+||+..+..++..+++.+++|+|.++|+||.+...+...    +...+-     .++..+.++.+++.
T Consensus       471 s~Lv~RL~~IC~rE~mr~d~~aL~~L~el~~~DIRsCINtLQfLa~~~~r~ds~i~~~~i~a~~~~~k~~~~slf~~w~e  550 (877)
T KOG1969|consen  471 SRLVERLNEICHRENMRADSKALNALCELTQNDIRSCINTLQFLASNVDRRDSSISVKLICAKNVGAKSNSDSLFSWWKE  550 (877)
T ss_pred             hHHHHHHHHHHhhhcCCCCHHHHHHHHHHhcchHHHHHHHHHHHHHhcccccccchhhhhhhhhhcccccccchHHHHHH
Confidence            999999999999999999999999999999999999999999999877653    222211     23345556777777


Q ss_pred             HHh
Q 042716          129 IIE  131 (137)
Q Consensus       129 i~~  131 (137)
                      |++
T Consensus       551 i~q  553 (877)
T KOG1969|consen  551 IFQ  553 (877)
T ss_pred             HHH
Confidence            765

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.59  E-value=1e-14  Score=117.76  Aligned_cols=108  Identities=16%  Similarity=0.198  Sum_probs=89.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCC--CCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHc--CC-C
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDV--SKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQE--GI-Q   74 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~--~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~e--gi-~   74 (137)
                      +||||+|.++...|++|++.+|+  +...+|.+++..  ..+ ++|+|||.++.|.+++.+++..++..++...  |+ .
T Consensus        96 L~IDEi~~l~~~~q~~LL~~le~--~~iilI~att~n~~~~l~~aL~SR~~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~  173 (413)
T PRK13342         96 LFIDEIHRFNKAQQDALLPHVED--GTITLIGATTENPSFEVNPALLSRAQVFELKPLSEEDIEQLLKRALEDKERGLVE  173 (413)
T ss_pred             EEEechhhhCHHHHHHHHHHhhc--CcEEEEEeCCCChhhhccHHHhccceeeEeCCCCHHHHHHHHHHHHHHhhcCCCC
Confidence            58999999999999999999994  444455554433  357 9999999999999999999999999987653  55 8


Q ss_pred             CCHHHHHHHHHHcCCcHHHHHHHHHHHHhcCCCccc
Q 042716           75 LPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVE  110 (137)
Q Consensus        75 i~~~~l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~  110 (137)
                      ++++++..+++.++||+|.++|.|+.+...+..++.
T Consensus       174 i~~~al~~l~~~s~Gd~R~aln~Le~~~~~~~~It~  209 (413)
T PRK13342        174 LDDEALDALARLANGDARRALNLLELAALGVDSITL  209 (413)
T ss_pred             CCHHHHHHHHHhCCCCHHHHHHHHHHHHHccCCCCH
Confidence            999999999999999999999999988654333433

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=99.59  E-value=5.1e-15  Score=111.36  Aligned_cols=99  Identities=13%  Similarity=0.110  Sum_probs=79.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ++|+++|.|+.+|+|+|+|++|||++++.|||+|+++..+ +||+|||+.++|+.|.......+....+.-.   .+...
T Consensus        93 iII~~ae~mt~~AANALLKtLEEPP~~t~fILit~~~~~LLpTIrSRCq~i~~~~p~~~~~~e~~~~~~~p~---~~~~~  169 (263)
T PRK06581         93 AIIYSAELMNLNAANSCLKILEDAPKNSYIFLITSRAASIISTIRSRCFKINVRSSILHAYNELYSQFIQPI---ADNKT  169 (263)
T ss_pred             EEEechHHhCHHHHHHHHHhhcCCCCCeEEEEEeCChhhCchhHhhceEEEeCCCCCHHHHHHHHHHhcccc---cccHH
Confidence            5899999999999999999999999999999999999999 9999999999999999977766654432222   23445


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ++.|.+....|-..++...+.+.
T Consensus       170 l~~i~~~~~~d~~~w~~~~~~~~  192 (263)
T PRK06581        170 LDFINRFTTKDRELWLDFIDNLL  192 (263)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHH
Confidence            77777777767666666655443

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.57  E-value=1.7e-14  Score=108.51  Aligned_cols=102  Identities=14%  Similarity=0.216  Sum_probs=87.2

Q ss_pred             CcccccCcCCH--HHHHHHHHHHHhc--cCCceEEEEeCCCCC----c-hhhhhcc---eeeEecCCCHHHHHHHHHHHH
Q 042716            1 IILCEADKLST--DALLYMRWLLERY--KGLNKVFFCCSDVSK----L-QPIKSLC---TVIQLLPPSKQEIVEVLEFIA   68 (137)
Q Consensus         1 iiiDEid~l~~--~~~~~L~~~le~~--~~~~~~Il~~n~~~~----i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~   68 (137)
                      ++|||+|.+..  ..+..|+.+++..  .+++.+|++++.++.    + ++|+|||   .++.+.+|++++...+|++.+
T Consensus       101 liiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~~~~~~~~~~~l~~~a  180 (235)
T PRK08084        101 VCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEKLQALQLRA  180 (235)
T ss_pred             EEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHHHhCCceeeecCCCHHHHHHHHHHHH
Confidence            48999999964  4466666666654  334579999987743    5 9999999   899999999999999999989


Q ss_pred             HHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           69 EQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        69 ~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ..+|+.++++++.+|+++++||+|.+++.|+.+.
T Consensus       181 ~~~~~~l~~~v~~~L~~~~~~d~r~l~~~l~~l~  214 (235)
T PRK08084        181 RLRGFELPEDVGRFLLKRLDREMRTLFMTLDQLD  214 (235)
T ss_pred             HHcCCCCCHHHHHHHHHhhcCCHHHHHHHHHHHH
Confidence            9999999999999999999999999999999875

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

Probab=99.56  E-value=1.5e-14  Score=123.53  Aligned_cols=101  Identities=11%  Similarity=0.196  Sum_probs=87.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCC--CCc-hhhhhcceeeEecCCCHHHHHHHHHHHHH-------H
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDV--SKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAE-------Q   70 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~--~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~-------~   70 (137)
                      +||||+|.|+...|++|++.+|+  +...+|.+++..  ..+ ++|+|||.+|.|++++.+++..++.+++.       +
T Consensus       113 L~IDEIh~Ln~~qQdaLL~~lE~--g~IiLI~aTTenp~~~l~~aL~SR~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~  190 (725)
T PRK13341        113 LFIDEVHRFNKAQQDALLPWVEN--GTITLIGATTENPYFEVNKALVSRSRLFRLKSLSDEDLHQLLKRALQDKERGYGD  190 (725)
T ss_pred             EEEeChhhCCHHHHHHHHHHhcC--ceEEEEEecCCChHhhhhhHhhccccceecCCCCHHHHHHHHHHHHHHHHhhcCC
Confidence            58999999999999999999983  333344444333  357 99999999999999999999999999887       5


Q ss_pred             cCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           71 EGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        71 egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      +++.++++++..|++.++||+|.++|.|+.+..
T Consensus       191 ~~v~I~deaL~~La~~s~GD~R~lln~Le~a~~  223 (725)
T PRK13341        191 RKVDLEPEAEKHLVDVANGDARSLLNALELAVE  223 (725)
T ss_pred             cccCCCHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            789999999999999999999999999998764

>PRK08727 hypothetical protein; Validated

Probab=99.56  E-value=4.3e-14  Score=106.24  Aligned_cols=102  Identities=12%  Similarity=0.173  Sum_probs=89.9

Q ss_pred             CcccccCcCC--HHHHHHHHHHHHhccC-CceEEEEeCCCCC----c-hhhhhc---ceeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLS--TDALLYMRWLLERYKG-LNKVFFCCSDVSK----L-QPIKSL---CTVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~--~~~~~~L~~~le~~~~-~~~~Il~~n~~~~----i-~~l~SR---c~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.+.  .+.+..|+.+++.... +.++|+++|.++.    + ++|+||   |.++.|++|++++...+|+..|.
T Consensus        97 LiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~SRl~~~~~~~l~~~~~e~~~~iL~~~a~  176 (233)
T PRK08727         97 VALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSRLAQCIRIGLPVLDDVARAAVLRERAQ  176 (233)
T ss_pred             EEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHHHHhcCceEEecCCCHHHHHHHHHHHHH
Confidence            5899999995  4557788888886433 4569999997754    5 999999   89999999999999999999999


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      .+|+.++++++.+|+++++||+|.++++|+.+.
T Consensus       177 ~~~l~l~~e~~~~La~~~~rd~r~~l~~L~~l~  209 (233)
T PRK08727        177 RRGLALDEAAIDWLLTHGERELAGLVALLDRLD  209 (233)
T ss_pred             HcCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            999999999999999999999999999999775

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

Probab=99.55  E-value=1.5e-14  Score=107.84  Aligned_cols=102  Identities=20%  Similarity=0.195  Sum_probs=82.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccC------------------CceEEEEeCCCCCc-hhhhhccee-eEecCCCHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKG------------------LNKVFFCCSDVSKL-QPIKSLCTV-IQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~------------------~~~~Il~~n~~~~i-~~l~SRc~~-i~~~~~~~~~i   60 (137)
                      +||||+|+|++..|+.|+..||.+.-                  ...+|-+|+....+ +||++|+.+ .++..++.+++
T Consensus       105 LFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FTligATTr~g~ls~pLrdRFgi~~~l~~Y~~~el  184 (233)
T PF05496_consen  105 LFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFTLIGATTRAGLLSSPLRDRFGIVLRLEFYSEEEL  184 (233)
T ss_dssp             EEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----EEEEEESSGCCTSHCCCTTSSEEEE----THHHH
T ss_pred             EEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCCCceEeeeeccccccchhHHhhcceecchhcCCHHHH
Confidence            58999999999999999999997631                  23366667777889 999999966 58999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      .+++++.+...|+++++++...|+.+|.|++|-|.++|+.+.
T Consensus       185 ~~Iv~r~a~~l~i~i~~~~~~~Ia~rsrGtPRiAnrll~rvr  226 (233)
T PF05496_consen  185 AKIVKRSARILNIEIDEDAAEEIARRSRGTPRIANRLLRRVR  226 (233)
T ss_dssp             HHHHHHCCHCTT-EE-HHHHHHHHHCTTTSHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhCCCcCHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence            999999999999999999999999999999999999998875

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

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.52  E-value=1.1e-13  Score=108.48  Aligned_cols=102  Identities=19%  Similarity=0.184  Sum_probs=91.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc------------------CCceEEEEeCCCCCc-hhhhhcc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK------------------GLNKVFFCCSDVSKL-QPIKSLC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~------------------~~~~~Il~~n~~~~i-~~l~SRc-~~i~~~~~~~~~i   60 (137)
                      +||||+|.++...++.|+..+|.+.                  +...+|.+||....+ ++|+||| ..+.|.+++.+++
T Consensus       106 l~IDEi~~l~~~~~e~l~~~~e~~~~~~~l~~~~~~~~~~~~l~~~~li~at~~~~~l~~~L~sRf~~~~~l~~~~~~e~  185 (328)
T PRK00080        106 LFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRAGLLTSPLRDRFGIVQRLEFYTVEEL  185 (328)
T ss_pred             EEEecHhhcchHHHHHHHHHHHhcceeeeeccCccccceeecCCCceEEeecCCcccCCHHHHHhcCeeeecCCCCHHHH
Confidence            5899999999999999999999753                  124578888888889 9999998 6799999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ..++...+.+.++.++++++..|+++++|++|.+.+.|+...
T Consensus       186 ~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~  227 (328)
T PRK00080        186 EKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVR  227 (328)
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHH
Confidence            999999999999999999999999999999999999998754

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.50  E-value=1.7e-13  Score=106.06  Aligned_cols=102  Identities=18%  Similarity=0.203  Sum_probs=91.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc------------------CCceEEEEeCCCCCc-hhhhhcc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK------------------GLNKVFFCCSDVSKL-QPIKSLC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~------------------~~~~~Il~~n~~~~i-~~l~SRc-~~i~~~~~~~~~i   60 (137)
                      ++|||+|.+.+..++.|+..+++..                  ....+|.++|.+.++ ++++||| ..+.|.+++.+++
T Consensus        85 l~iDEi~~l~~~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li~~t~~~~~l~~~l~sR~~~~~~l~~l~~~e~  164 (305)
T TIGR00635        85 LFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPLRDRFGIILRLEFYTVEEL  164 (305)
T ss_pred             EEEehHhhhCHHHHHHhhHHHhhhheeeeeccCccccceeecCCCeEEEEecCCccccCHHHHhhcceEEEeCCCCHHHH
Confidence            5899999999999999999988544                  124577788888889 9999999 5689999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      .++++..+..+++.++++++..+++.+.|++|.+.++++.+.
T Consensus       165 ~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~  206 (305)
T TIGR00635       165 AEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVR  206 (305)
T ss_pred             HHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHH
Confidence            999999999999999999999999999999999999998764

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.

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.49  E-value=2.6e-13  Score=112.80  Aligned_cols=102  Identities=21%  Similarity=0.246  Sum_probs=89.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc----------------------------cCCceEEEEeC-CCCCc-hhhhhcceee
Q 042716            1 IILCEADKLSTDALLYMRWLLERY----------------------------KGLNKVFFCCS-DVSKL-QPIKSLCTVI   50 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~----------------------------~~~~~~Il~~n-~~~~i-~~l~SRc~~i   50 (137)
                      ++|||+|.|+...|+.|++++|+.                            +.++++|++|+ ++..+ ++++|||..+
T Consensus       179 L~IdEI~~L~~~~q~~LL~~Le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~rlI~ATt~~p~~L~paLrsR~~~I  258 (531)
T TIGR02902       179 LFIDEIGELHPVQMNKLLKVLEDRKVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRNPEEIPPALRSRCVEI  258 (531)
T ss_pred             EEEechhhCCHHHHHHHHHHHHhCeeeeccccccccCcccccchhhhcccCcccceEEEEEecCCcccCChHHhhhhhee
Confidence            589999999999999999999862                            12346666655 56678 9999999999


Q ss_pred             EecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           51 QLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        51 ~~~~~~~~~i~~~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      .|++++.+++..++++.++++|+.+++++++.+..++. |.|.+.|+++.+..
T Consensus       259 ~f~pL~~eei~~Il~~~a~k~~i~is~~al~~I~~y~~-n~Rel~nll~~Aa~  310 (531)
T TIGR02902       259 FFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYAS-NGREAVNIVQLAAG  310 (531)
T ss_pred             eCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhh-hHHHHHHHHHHHHH
Confidence            99999999999999999999999999999998887764 99999999998764

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.

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

Probab=99.47  E-value=2.2e-13  Score=107.86  Aligned_cols=100  Identities=17%  Similarity=0.315  Sum_probs=80.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCce-EEEEeC------------CCCCc-hhhhhcceeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNK-VFFCCS------------DVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~-~Il~~n------------~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~   66 (137)
                      +||||+|.|+-++...|.+.+|  +.-.| +||+||            .++.+ .+|++||.+++..|++.+++.++|.-
T Consensus       282 LFIDEvHmLDiEcFsfLnralE--s~~sPiiIlATNRg~~~irGt~~~sphGiP~DlLDRllII~t~py~~~ei~~Il~i  359 (398)
T PF06068_consen  282 LFIDEVHMLDIECFSFLNRALE--SELSPIIILATNRGITKIRGTDIISPHGIPLDLLDRLLIIRTKPYSEEEIKQILKI  359 (398)
T ss_dssp             EEEESGGGSBHHHHHHHHHHHT--STT--EEEEEES-SEEE-BTTS-EEETT--HHHHTTEEEEEE----HHHHHHHHHH
T ss_pred             EEecchhhccHHHHHHHHHHhc--CCCCcEEEEecCceeeeccCccCcCCCCCCcchHhhcEEEECCCCCHHHHHHHHHh
Confidence            5899999999999999999999  66777 777777            33568 89999999999999999999999999


Q ss_pred             HHHHcCCCCCHHHHHHHHHH-cCCcHHHHHHHHHHHH
Q 042716           67 IAEQEGIQLPHQLAEKIADN-SKNNLRQAIRSFEASR  102 (137)
Q Consensus        67 i~~~egi~i~~~~l~~i~~~-~~gd~R~aln~L~~~~  102 (137)
                      .|+.|+++++++++..+.+. .+.++|+|+++|..++
T Consensus       360 R~~~E~v~i~~~al~~L~~ig~~~SLRYAiqLi~~a~  396 (398)
T PF06068_consen  360 RAKEEDVEISEDALDLLTKIGVETSLRYAIQLITPAS  396 (398)
T ss_dssp             HHHHCT--B-HHHHHHHHHHHHHS-HHHHHHCHHHHH
T ss_pred             hhhhhcCcCCHHHHHHHHHHhhhccHHHHHHhhhhhh
Confidence            99999999999999999986 6789999999997654

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

>PRK06893 DNA replication initiation factor; Validated

Probab=99.43  E-value=1.1e-12  Score=98.25  Aligned_cols=102  Identities=17%  Similarity=0.170  Sum_probs=86.0

Q ss_pred             CcccccCcCC--HHHHHHHHHHHHhccC-Cce-EEEEeCCCCC----c-hhhhhcce---eeEecCCCHHHHHHHHHHHH
Q 042716            1 IILCEADKLS--TDALLYMRWLLERYKG-LNK-VFFCCSDVSK----L-QPIKSLCT---VIQLLPPSKQEIVEVLEFIA   68 (137)
Q Consensus         1 iiiDEid~l~--~~~~~~L~~~le~~~~-~~~-~Il~~n~~~~----i-~~l~SRc~---~i~~~~~~~~~i~~~l~~i~   68 (137)
                      ++|||+|.+.  ...+..|+.+++.... +.+ ++++++..+.    . ++|+||+.   ++++++|++++...++++.+
T Consensus        95 LilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a  174 (229)
T PRK06893         95 VCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRNA  174 (229)
T ss_pred             EEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHHH
Confidence            5899999985  3346678888876543 333 4666776543    4 89999986   99999999999999999999


Q ss_pred             HHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           69 EQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        69 ~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ..+|+.++++++.+|+++++||+|.+++.|+.+.
T Consensus       175 ~~~~l~l~~~v~~~L~~~~~~d~r~l~~~l~~l~  208 (229)
T PRK06893        175 YQRGIELSDEVANFLLKRLDRDMHTLFDALDLLD  208 (229)
T ss_pred             HHcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHH
Confidence            9999999999999999999999999999999875

>PRK05642 DNA replication initiation factor; Validated

Probab=99.42  E-value=1.6e-12  Score=97.77  Aligned_cols=102  Identities=17%  Similarity=0.240  Sum_probs=88.4

Q ss_pred             CcccccCcCC--HHHHHHHHHHHHhccC-CceEEEEeCCCCC----c-hhhhhcc---eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLS--TDALLYMRWLLERYKG-LNKVFFCCSDVSK----L-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~--~~~~~~L~~~le~~~~-~~~~Il~~n~~~~----i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.+.  +..+..|+.+++.... +.+++++|+..+.    . ++|+||+   .++.+++|++++...+++..+.
T Consensus       101 LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~ka~  180 (234)
T PRK05642        101 VCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQLRAS  180 (234)
T ss_pred             EEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHHHHH
Confidence            4799999885  3457889999987554 5678888886542    4 9999999   8999999999999999998888


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ..|+.++++++.+++++++||+|.+.+.|+.+.
T Consensus       181 ~~~~~l~~ev~~~L~~~~~~d~r~l~~~l~~l~  213 (234)
T PRK05642        181 RRGLHLTDEVGHFILTRGTRSMSALFDLLERLD  213 (234)
T ss_pred             HcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence            899999999999999999999999999999875

>PRK06620 hypothetical protein; Validated

Probab=99.42  E-value=2.9e-12  Score=95.31  Aligned_cols=99  Identities=14%  Similarity=0.156  Sum_probs=80.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccC-CceEEEEeCCCCC---chhhhhcce---eeEecCCCHHHHHHHHHHHHHHcCC
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKG-LNKVFFCCSDVSK---LQPIKSLCT---VIQLLPPSKQEIVEVLEFIAEQEGI   73 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~-~~~~Il~~n~~~~---i~~l~SRc~---~i~~~~~~~~~i~~~l~~i~~~egi   73 (137)
                      ++|||+|.+..   ..|..+++.... +..++++++.++.   +++|+||+.   ++.+++|+++++..++++.+...|+
T Consensus        89 lliDdi~~~~~---~~lf~l~N~~~e~g~~ilits~~~p~~l~l~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~~~l  165 (214)
T PRK06620         89 FIIEDIENWQE---PALLHIFNIINEKQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLNSPDDELIKILIFKHFSISSV  165 (214)
T ss_pred             EEEeccccchH---HHHHHHHHHHHhcCCEEEEEcCCCccccchHHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcCC
Confidence            57999997743   345555443322 3457777765543   399999987   9999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           74 QLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        74 ~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      .++++++.+|+++++||+|.+++.|+.+.
T Consensus       166 ~l~~ev~~~L~~~~~~d~r~l~~~l~~l~  194 (214)
T PRK06620        166 TISRQIIDFLLVNLPREYSKIIEILENIN  194 (214)
T ss_pred             CCCHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence            99999999999999999999999999875

>PRK09087 hypothetical protein; Validated

Probab=99.41  E-value=1.3e-12  Score=97.94  Aligned_cols=101  Identities=10%  Similarity=0.064  Sum_probs=87.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccC-CceEEEEeCCCCC----c-hhhhhcc---eeeEecCCCHHHHHHHHHHHHHHc
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKG-LNKVFFCCSDVSK----L-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAEQE   71 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~-~~~~Il~~n~~~~----i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~~e   71 (137)
                      ++|||+|.+. ..+.+|+.+++.... ++.++++|+..+.    . ++|+||+   .++.+++|+.++...+|++.++.+
T Consensus        91 l~iDDi~~~~-~~~~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~~~~~~~  169 (226)
T PRK09087         91 VLIEDIDAGG-FDETGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKLFADR  169 (226)
T ss_pred             EEEECCCCCC-CCHHHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHHHHHHHc
Confidence            5789999884 357788888887655 5678888886643    4 8999999   899999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           72 GIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        72 gi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      |+.++++++++|++++.||+|.++..|..+.
T Consensus       170 ~~~l~~ev~~~La~~~~r~~~~l~~~l~~L~  200 (226)
T PRK09087        170 QLYVDPHVVYYLVSRMERSLFAAQTIVDRLD  200 (226)
T ss_pred             CCCCCHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence            9999999999999999999999998666554

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=99.40  E-value=8e-13  Score=104.64  Aligned_cols=100  Identities=17%  Similarity=0.191  Sum_probs=84.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCC--Cc-hhhhhcceeeEecCCCHHHHHHHHHHHHH----Hc--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVS--KL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAE----QE--   71 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~--~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~----~e--   71 (137)
                      +||||+|++.+..|..++..+|  .+...+|-+|++.+  .+ .+|.|||.+|-+.+++.+.+..+|.+...    .|  
T Consensus       226 lFiDEiHRFNksQQD~fLP~VE--~G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~v~~iL~raia~l~dser~  303 (554)
T KOG2028|consen  226 LFIDEIHRFNKSQQDTFLPHVE--NGDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRAIASLGDSERP  303 (554)
T ss_pred             EEeHHhhhhhhhhhhcccceec--cCceEEEecccCCCccchhHHHHhccceeEeccCCHHHHHHHHHHHHHhhcccccc
Confidence            5899999999999999999999  55666777666554  47 99999999999999999999999987432    11  


Q ss_pred             -------CCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           72 -------GIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        72 -------gi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                             .+.+++..+++++..+.||.|.++|.||+..
T Consensus       304 ~~~l~n~s~~ve~siidyla~lsdGDaR~aLN~Lems~  341 (554)
T KOG2028|consen  304 TDPLPNSSMFVEDSIIDYLAYLSDGDARAALNALEMSL  341 (554)
T ss_pred             CCCCCCcchhhhHHHHHHHHHhcCchHHHHHHHHHHHH
Confidence                   1246788999999999999999999999873

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.38  E-value=4.4e-12  Score=94.43  Aligned_cols=102  Identities=14%  Similarity=0.275  Sum_probs=88.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCce--EEEEeCCCC---Cc-hhhhhcc---eeeEecCCCHHHHHHHHHHHHHHc
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNK--VFFCCSDVS---KL-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAEQE   71 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~--~Il~~n~~~---~i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~~e   71 (137)
                      ++|||+|.++...+..|+.+++....+..  ++++++..+   .+ ++|+||+   ..+.+++|+.++....+...+.++
T Consensus        94 liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~~~~~~~~l~~~~~~~  173 (227)
T PRK08903         94 YAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLSDADKIAALKAAAAER  173 (227)
T ss_pred             EEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCCHHHHHHHHHHHHHHc
Confidence            58999999999999999999987554433  555555443   36 8999996   799999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           72 GIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        72 gi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      |+.++++++.++++++.||+|.+.+.|+.+.
T Consensus       174 ~v~l~~~al~~L~~~~~gn~~~l~~~l~~l~  204 (227)
T PRK08903        174 GLQLADEVPDYLLTHFRRDMPSLMALLDALD  204 (227)
T ss_pred             CCCCCHHHHHHHHHhccCCHHHHHHHHHHHH
Confidence            9999999999999999999999999999875

>PRK14700 recombination factor protein RarA; Provisional

Probab=99.38  E-value=1.4e-12  Score=100.78  Aligned_cols=79  Identities=13%  Similarity=0.123  Sum_probs=68.0

Q ss_pred             cCCceEEEEeCCCC--Cc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHc------CCCCCHHHHHHHHHHcCCcHHHHH
Q 042716           25 KGLNKVFFCCSDVS--KL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQE------GIQLPHQLAEKIADNSKNNLRQAI   95 (137)
Q Consensus        25 ~~~~~~Il~~n~~~--~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~e------gi~i~~~~l~~i~~~~~gd~R~al   95 (137)
                      .+...+|-+|++.+  .+ ++|+|||++|.|++++.+++...|++....+      .+.++++++..|+..++||.|.++
T Consensus         6 ~G~i~LIGATTENP~f~vn~ALlSR~~v~~l~~L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~~a~GDaR~aL   85 (300)
T PRK14700          6 SGKIILIGATTENPTYYLNDALVSRLFILRLKRLSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHNYNEGDCRKIL   85 (300)
T ss_pred             CCcEEEEeecCCCccceecHhhhhhhheeeecCCCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHHhcCCHHHHHH
Confidence            45566777776554  47 9999999999999999999999999988752      368999999999999999999999


Q ss_pred             HHHHHHHh
Q 042716           96 RSFEASRQ  103 (137)
Q Consensus        96 n~L~~~~~  103 (137)
                      |+|+.+..
T Consensus        86 N~LE~a~~   93 (300)
T PRK14700         86 NLLERMFL   93 (300)
T ss_pred             HHHHHHHh
Confidence            99999653

>TIGR01128 holA DNA polymerase III, delta subunit

Probab=99.36  E-value=9.8e-12  Score=95.70  Aligned_cols=133  Identities=12%  Similarity=0.142  Sum_probs=105.9

Q ss_pred             CcccccCcCC-HHHHHHHHHHHHhccCCceEEEEeCCCCC---c-hhhh--hcceeeEecCCCHHHHHHHHHHHHHHcCC
Q 042716            1 IILCEADKLS-TDALLYMRWLLERYKGLNKVFFCCSDVSK---L-QPIK--SLCTVIQLLPPSKQEIVEVLEFIAEQEGI   73 (137)
Q Consensus         1 iiiDEid~l~-~~~~~~L~~~le~~~~~~~~Il~~n~~~~---i-~~l~--SRc~~i~~~~~~~~~i~~~l~~i~~~egi   73 (137)
                      |+|++++.+. ....++|.+.+++++.++.+|++++...+   + +.+.  ++|.++.|.+++..++..++...++++|+
T Consensus        50 iii~~~~~~~~~~~~~~L~~~l~~~~~~~~~i~~~~~~~~~~~~~k~~~~~~~~~~i~~~~~~~~~~~~~i~~~~~~~g~  129 (302)
T TIGR01128        50 VELRNPEGKPGAKGLKALEEYLANPPPDTLLLIEAPKLDKRKKLTKWLKALKNAQIVECKTPKEQELPRWIQARLKKLGL  129 (302)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHhcCCCCEEEEEecCCCCHhHHHHHHHHHhcCeeEEEecCCCHHHHHHHHHHHHHHcCC
Confidence            5789999986 45689999999999999999998886543   2 3333  59999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHcCCcHHHHHHHHHHHHhc--CCCcccCccc-c--CCcHHHHHHHHHHHHhcC
Q 042716           74 QLPHQLAEKIADNSKNNLRQAIRSFEASRQM--NYPFVEGQVI-L--TGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        74 ~i~~~~l~~i~~~~~gd~R~aln~L~~~~~~--~~~~~~~~~~-~--~~~~~~~~~i~~~i~~~~  133 (137)
                      .+++++++.+++.++||++.+.|.++.+...  +.+++...+. .  ...+..++++++.++.++
T Consensus       130 ~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~~~~~~if~l~dal~~~~  194 (302)
T TIGR01128       130 RIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSDSARFNVFDLTDALLEGK  194 (302)
T ss_pred             CCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhhhhcCCHHHHHHHHHCCC
Confidence            9999999999999999999999999988764  2345544443 1  123344666777666554

subunit around DNA forming a DNA sliding clamp.

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=99.35  E-value=2.4e-12  Score=101.24  Aligned_cols=66  Identities=23%  Similarity=0.273  Sum_probs=62.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~   66 (137)
                      ++||++|+|+.+++++|++++|+|+.++.||++|.++..+ ++++|||+.++|.+|+.+++..+|..
T Consensus       117 ~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~~~L~~  183 (325)
T PRK08699        117 ILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLRE  183 (325)
T ss_pred             EEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHHHHHHh
Confidence            4789999999999999999999999889999999999999 99999999999999999999999964

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.34  E-value=1.2e-11  Score=94.14  Aligned_cols=103  Identities=16%  Similarity=0.155  Sum_probs=86.3

Q ss_pred             CcccccCcCC--------HHHHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcc-eeeEecCCCHHHHHHHHH
Q 042716            1 IILCEADKLS--------TDALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLC-TVIQLLPPSKQEIVEVLE   65 (137)
Q Consensus         1 iiiDEid~l~--------~~~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc-~~i~~~~~~~~~i~~~l~   65 (137)
                      +||||+|.|.        .++++.|++.||+.+.+..+|++++...     .+ ++|+||| ..+.|++++.+++..+++
T Consensus       109 L~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~vila~~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el~~Il~  188 (261)
T TIGR02881       109 LFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVLILAGYSDEMDYFLSLNPGLRSRFPISIDFPDYTVEELMEIAE  188 (261)
T ss_pred             EEEechhhhccCCccchHHHHHHHHHHHHhccCCCEEEEecCCcchhHHHHhcChHHHhccceEEEECCCCHHHHHHHHH
Confidence            5899999986        4578899999998766666777664332     36 8999999 679999999999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHH----------cCCcHHHHHHHHHHHHh
Q 042716           66 FIAEQEGIQLPHQLAEKIADN----------SKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        66 ~i~~~egi~i~~~~l~~i~~~----------~~gd~R~aln~L~~~~~  103 (137)
                      +.+...++.++++++..+.+.          +.||.|.+.|+++.+..
T Consensus       189 ~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~~~~gn~R~~~n~~e~a~~  236 (261)
T TIGR02881       189 RMVKEREYKLTEEAKWKLREHLYKVDQLSSREFSNARYVRNIIEKAIR  236 (261)
T ss_pred             HHHHHcCCccCHHHHHHHHHHHHHHHhccCCCCchHHHHHHHHHHHHH
Confidence            999999999999999888653          36999999999998664

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.

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

Probab=99.34  E-value=6.7e-12  Score=98.92  Aligned_cols=99  Identities=20%  Similarity=0.343  Sum_probs=89.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCce-EEEEeC------------CCCCc-hhhhhcceeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNK-VFFCCS------------DVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~-~Il~~n------------~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~   66 (137)
                      +||||+|.|.-++...|.+.||  +.-+| +||+||            .|+.| .+|..|..+++-.|++.+++..+++.
T Consensus       295 LFIDEvHmLDIE~FsFlnrAlE--se~aPIii~AtNRG~~kiRGTd~~sPhGIP~DlLDRllII~t~py~~~EireIi~i  372 (450)
T COG1224         295 LFIDEVHMLDIECFSFLNRALE--SELAPIIILATNRGMTKIRGTDIESPHGIPLDLLDRLLIISTRPYSREEIREIIRI  372 (450)
T ss_pred             EEEechhhhhHHHHHHHHHHhh--cccCcEEEEEcCCceeeecccCCcCCCCCCHhhhhheeEEecCCCCHHHHHHHHHH
Confidence            5899999999999999999999  66677 666676            34568 89999999999999999999999999


Q ss_pred             HHHHcCCCCCHHHHHHHHHH-cCCcHHHHHHHHHHH
Q 042716           67 IAEQEGIQLPHQLAEKIADN-SKNNLRQAIRSFEAS  101 (137)
Q Consensus        67 i~~~egi~i~~~~l~~i~~~-~~gd~R~aln~L~~~  101 (137)
                      .|+.|++.++++++++++.. ...++|+++++|.-+
T Consensus       373 Ra~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa  408 (450)
T COG1224         373 RAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPA  408 (450)
T ss_pred             hhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHH
Confidence            99999999999999999997 568999999999833

>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=99.33  E-value=2.2e-11  Score=90.89  Aligned_cols=103  Identities=18%  Similarity=0.310  Sum_probs=83.3

Q ss_pred             CcccccCcCCHHH--HHHHHHHHHhcc-CCceEEEEeCCCCC----c-hhhhhcc---eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDA--LLYMRWLLERYK-GLNKVFFCCSDVSK----L-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~~~--~~~L~~~le~~~-~~~~~Il~~n~~~~----i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++||++|.+....  |..|..+++... .+.++|++++.++.    + +.|+||+   .++.+.+|++++...+|++.+.
T Consensus       101 L~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~~a~  180 (219)
T PF00308_consen  101 LIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDEDRRRILQKKAK  180 (219)
T ss_dssp             EEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHHHHHHHHHHHH
T ss_pred             EEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHHHHHHHHHHHH
Confidence            5899999997665  899999999864 34579999976643    6 8999995   6899999999999999999999


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      ..|+.++++++.+++++..+|+|.+...|..+..
T Consensus       181 ~~~~~l~~~v~~~l~~~~~~~~r~L~~~l~~l~~  214 (219)
T PF00308_consen  181 ERGIELPEEVIEYLARRFRRDVRELEGALNRLDA  214 (219)
T ss_dssp             HTT--S-HHHHHHHHHHTTSSHHHHHHHHHHHHH
T ss_pred             HhCCCCcHHHHHHHHHhhcCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999999987764

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.

>TIGR00602 rad24 checkpoint protein rad24

Probab=99.32  E-value=1.4e-11  Score=104.03  Aligned_cols=105  Identities=16%  Similarity=0.211  Sum_probs=79.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHH-hc--cCCceEEEEeCCCC--------------C-c-hhhhh--cceeeEecCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLE-RY--KGLNKVFFCCSDVS--------------K-L-QPIKS--LCTVIQLLPPSKQE   59 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le-~~--~~~~~~Il~~n~~~--------------~-i-~~l~S--Rc~~i~~~~~~~~~   59 (137)
                      |+|||++.+......++..++. .+  .+.+++|+++++.+              . + +.|+|  ||.+|.|+|++..+
T Consensus       199 ILIDEiPn~~~r~~~~lq~lLr~~~~e~~~~pLI~I~TE~~~~~~~~~~~~f~~~~lL~~eLls~~rv~~I~FnPia~t~  278 (637)
T TIGR00602       199 ILVEDLPNQFYRDTRALHEILRWKYVSIGRCPLVFIITESLEGDNNQRRLLFPAETIMNKEILEEPRVSNISFNPIAPTI  278 (637)
T ss_pred             EEeecchhhchhhHHHHHHHHHHHhhcCCCceEEEEecCCccccccccccccchhcccCHhHhcccceeEEEeCCCCHHH
Confidence            5899997765433333333333 11  45678888887431              1 4 68998  56779999999999


Q ss_pred             HHHHHHHHHHHcCCC------C-CHHHHHHHHHHcCCcHHHHHHHHHHHHhcC
Q 042716           60 IVEVLEFIAEQEGIQ------L-PHQLAEKIADNSKNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        60 i~~~l~~i~~~egi~------i-~~~~l~~i~~~~~gd~R~aln~L~~~~~~~  105 (137)
                      +.++|..|+++|+..      + +++++..|+..+.||+|.|||+||.+...+
T Consensus       279 l~K~L~rIl~~E~~~~~~~~~~p~~~~l~~I~~~s~GDiRsAIn~LQf~~~~~  331 (637)
T TIGR00602       279 MKKFLNRIVTIEAKKNGEKIKVPKKTSVELLCQGCSGDIRSAINSLQFSSSKS  331 (637)
T ss_pred             HHHHHHHHHHhhhhccccccccCCHHHHHHHHHhCCChHHHHHHHHHHHHhcC
Confidence            999999999988643      2 467899999999999999999999986544

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

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

Probab=99.29  E-value=2.6e-11  Score=93.14  Aligned_cols=102  Identities=20%  Similarity=0.218  Sum_probs=91.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc------------------CCceEEEEeCCCCCc-hhhhhcc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK------------------GLNKVFFCCSDVSKL-QPIKSLC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~------------------~~~~~Il~~n~~~~i-~~l~SRc-~~i~~~~~~~~~i   60 (137)
                      +||||+|+|++...+.|+..||.+.                  +...+|-+|+....+ .|||+|+ .+.++..++.+++
T Consensus       107 LFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTLIGATTr~G~lt~PLrdRFGi~~rlefY~~~eL  186 (332)
T COG2255         107 LFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTLIGATTRAGMLTNPLRDRFGIIQRLEFYTVEEL  186 (332)
T ss_pred             EEEehhhhcChhHHHHhhhhhhheeEEEEEccCCccceEeccCCCeeEeeeccccccccchhHHhcCCeeeeecCCHHHH
Confidence            5899999999999999999999884                  122355566777788 9999998 6789999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ..++.+-+..-++++++++...|+++|.|.+|-|.++|....
T Consensus       187 ~~Iv~r~a~~l~i~i~~~~a~eIA~rSRGTPRIAnRLLrRVR  228 (332)
T COG2255         187 EEIVKRSAKILGIEIDEEAALEIARRSRGTPRIANRLLRRVR  228 (332)
T ss_pred             HHHHHHHHHHhCCCCChHHHHHHHHhccCCcHHHHHHHHHHH
Confidence            999999999999999999999999999999999999998765

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.24  E-value=1.4e-10  Score=94.67  Aligned_cols=102  Identities=19%  Similarity=0.284  Sum_probs=85.4

Q ss_pred             CcccccCcCCH--HHHHHHHHHHHhcc-CCceEEEEeCCCC----Cc-hhhhhcc---eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLST--DALLYMRWLLERYK-GLNKVFFCCSDVS----KL-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~--~~~~~L~~~le~~~-~~~~~Il~~n~~~----~i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.+..  ..|..|+.+++... .+..+|++|+.++    .+ +.|+||+   .++.|.+|+.++...+|+..++
T Consensus       215 LiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~il~~~~~  294 (450)
T PRK00149        215 LLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIAILKKKAE  294 (450)
T ss_pred             EEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHHHHHHHHH
Confidence            58999999854  34777888776643 3456888888764    37 8999998   5899999999999999999999


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ..|+.++++++.+|+.++.||+|.+...|..+.
T Consensus       295 ~~~~~l~~e~l~~ia~~~~~~~R~l~~~l~~l~  327 (450)
T PRK00149        295 EEGIDLPDEVLEFIAKNITSNVRELEGALNRLI  327 (450)
T ss_pred             HcCCCCCHHHHHHHHcCcCCCHHHHHHHHHHHH
Confidence            999999999999999999999999777776654

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.23  E-value=8.8e-11  Score=86.90  Aligned_cols=103  Identities=17%  Similarity=0.278  Sum_probs=87.1

Q ss_pred             CcccccCcCCHHH--HHHHHHHHHhcc-CCceEEEEeCCCC----Cc-hhhhhcc---eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDA--LLYMRWLLERYK-GLNKVFFCCSDVS----KL-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~~~--~~~L~~~le~~~-~~~~~Il~~n~~~----~i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.+....  ++.|+.+++... .+.++|++|+...    .. +.|+||+   ..+++++++.++....+...+.
T Consensus        94 LvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~~~i~l~~l~~~e~~~~l~~~~~  173 (226)
T TIGR03420        94 VCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWGLVFQLPPLSDEEKIAALQSRAA  173 (226)
T ss_pred             EEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcCeeEecCCCCHHHHHHHHHHHHH
Confidence            5799999998744  888988887643 3457888888653    23 7889996   5899999999999999999999


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      +.|+.++++++..++..+.||+|.+.+.++.+..
T Consensus       174 ~~~~~~~~~~l~~L~~~~~gn~r~L~~~l~~~~~  207 (226)
T TIGR03420       174 RRGLQLPDEVADYLLRHGSRDMGSLMALLDALDR  207 (226)
T ss_pred             HcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999999887653

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.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.22  E-value=9.2e-11  Score=95.77  Aligned_cols=102  Identities=12%  Similarity=0.143  Sum_probs=89.2

Q ss_pred             CcccccCcCCH--HHHHHHHHHHHhc-cCCceEEEEeCCCC----Cc-hhhhhcc---eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLST--DALLYMRWLLERY-KGLNKVFFCCSDVS----KL-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~--~~~~~L~~~le~~-~~~~~~Il~~n~~~----~i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.+..  ..|+.|+.+++.. ..+.++|++|+.++    .+ ++|+|||   .++.+.+|+.++...+|++.++
T Consensus       206 LiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k~~  285 (445)
T PRK12422        206 LFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERKAE  285 (445)
T ss_pred             EEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHHHH
Confidence            58999999964  4578888887753 34567999998763    47 8999999   7999999999999999999999


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ..|+.++++++.+++.+..+|+|.+.+.|..+.
T Consensus       286 ~~~~~l~~evl~~la~~~~~dir~L~g~l~~l~  318 (445)
T PRK12422        286 ALSIRIEETALDFLIEALSSNVKSLLHALTLLA  318 (445)
T ss_pred             HcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence            999999999999999999999999999999884

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.20  E-value=3.2e-10  Score=91.32  Aligned_cols=102  Identities=19%  Similarity=0.302  Sum_probs=85.1

Q ss_pred             CcccccCcCCH--HHHHHHHHHHHhc-cCCceEEEEeCCCC----Cc-hhhhhcc---eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLST--DALLYMRWLLERY-KGLNKVFFCCSDVS----KL-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~--~~~~~L~~~le~~-~~~~~~Il~~n~~~----~i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.+..  ..|..|+.+++.. ..+.++|++++.++    .+ +.|+||+   .++.|++|+.++...+|+..++
T Consensus       203 LiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~~~~  282 (405)
T TIGR00362       203 LLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQKKAE  282 (405)
T ss_pred             EEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHHHHHH
Confidence            58999999854  3577788888764 34567899988764    36 8899998   5799999999999999999999


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ..|+.++++++.+|+.+..||+|.+...|..+.
T Consensus       283 ~~~~~l~~e~l~~ia~~~~~~~r~l~~~l~~l~  315 (405)
T TIGR00362       283 EEGLELPDEVLEFIAKNIRSNVRELEGALNRLL  315 (405)
T ss_pred             HcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence            999999999999999999999998666655443

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).

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.20  E-value=1.9e-10  Score=97.19  Aligned_cols=101  Identities=17%  Similarity=0.206  Sum_probs=84.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc--------------------------CCceEEEEe---CCCCCc-hhhhhcceee
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK--------------------------GLNKVFFCC---SDVSKL-QPIKSLCTVI   50 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~--------------------------~~~~~Il~~---n~~~~i-~~l~SRc~~i   50 (137)
                      +||||+|.|+...|+.|++++++..                          ..+.|++++   +++..+ ++|+|||..+
T Consensus       269 L~LDEi~~Ld~~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i  348 (615)
T TIGR02903       269 LFIDEIGELDPLLQNKLLKVLEDKRVEFSSSYYDPDDPNVPKYIKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEV  348 (615)
T ss_pred             EEEeccccCCHHHHHHHHHHHhhCeEEeecceeccCCcccchhhhhhcccCccceEEEEEeccccccccCHHHHhceeEE
Confidence            5899999999999999999998632                          122355553   345568 9999999999


Q ss_pred             EecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           51 QLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        51 ~~~~~~~~~i~~~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      .|.+++.+++..++.+.+.+.++.++++++..|..++. +.|+++|.|+.+.
T Consensus       349 ~~~pls~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~-~gRraln~L~~~~  399 (615)
T TIGR02903       349 FFEPLTPEDIALIVLNAAEKINVHLAAGVEELIARYTI-EGRKAVNILADVY  399 (615)
T ss_pred             EeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCC-cHHHHHHHHHHHH
Confidence            99999999999999999999999999998888888764 7899999998664

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.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.19  E-value=7.8e-11  Score=101.85  Aligned_cols=104  Identities=16%  Similarity=0.142  Sum_probs=85.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc---CCceEEEEeCCC---CCc-hhhhhcce--eeEecCCCHHHHHHHHHHHHHHc
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK---GLNKVFFCCSDV---SKL-QPIKSLCT--VIQLLPPSKQEIVEVLEFIAEQE   71 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~---~~~~~Il~~n~~---~~i-~~l~SRc~--~i~~~~~~~~~i~~~l~~i~~~e   71 (137)
                      |+|||+|.|....|..|+.+++-+.   ....+|.++|+.   ..+ +.++|||.  .+.|+|++.+++..+|...++..
T Consensus       873 IILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLIGISNdlDLperLdPRLRSRLg~eeIvF~PYTaEQL~dILk~RAe~A  952 (1164)
T PTZ00112        873 LIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLIAISNTMDLPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENC  952 (1164)
T ss_pred             EEeehHhhhCccHHHHHHHHHHHhhccCCeEEEEEecCchhcchhhhhhhhhccccccccCCCCCHHHHHHHHHHHHHhC
Confidence            5899999998878888888877543   223466777764   457 99999985  49999999999999999988865


Q ss_pred             CCCCCHHHHHHHHH---HcCCcHHHHHHHHHHHHhc
Q 042716           72 GIQLPHQLAEKIAD---NSKNNLRQAIRSFEASRQM  104 (137)
Q Consensus        72 gi~i~~~~l~~i~~---~~~gd~R~aln~L~~~~~~  104 (137)
                      .-.+++++++.++.   ...||+|.|+++|+.+...
T Consensus       953 ~gVLdDdAIELIArkVAq~SGDARKALDILRrAgEi  988 (1164)
T PTZ00112        953 KEIIDHTAIQLCARKVANVSGDIRKALQICRKAFEN  988 (1164)
T ss_pred             CCCCCHHHHHHHHHhhhhcCCHHHHHHHHHHHHHhh
Confidence            45689999999998   6789999999999988753

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.19  E-value=4.1e-10  Score=91.85  Aligned_cols=102  Identities=16%  Similarity=0.233  Sum_probs=85.3

Q ss_pred             CcccccCcCCH--HHHHHHHHHHHhccC-CceEEEEeCCCC----Cc-hhhhhcce---eeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLST--DALLYMRWLLERYKG-LNKVFFCCSDVS----KL-QPIKSLCT---VIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~--~~~~~L~~~le~~~~-~~~~Il~~n~~~----~i-~~l~SRc~---~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.+..  ..|..|+.+++.... +..+|++|+..+    .+ +.++||+.   ++.|.+|+.+....+|++.++
T Consensus       198 LlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~~~  277 (440)
T PRK14088        198 LLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIARKMLE  277 (440)
T ss_pred             EEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHHHHHH
Confidence            58999998843  346778777776433 456888886553    36 89999986   999999999999999999999


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      .+|+.++++++.+|++++.||+|.+...|..+.
T Consensus       278 ~~~~~l~~ev~~~Ia~~~~~~~R~L~g~l~~l~  310 (440)
T PRK14088        278 IEHGELPEEVLNFVAENVDDNLRRLRGAIIKLL  310 (440)
T ss_pred             hcCCCCCHHHHHHHHhccccCHHHHHHHHHHHH
Confidence            999999999999999999999999988887664

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.19  E-value=1.8e-10  Score=94.16  Aligned_cols=102  Identities=10%  Similarity=0.163  Sum_probs=88.7

Q ss_pred             CcccccCcCC--HHHHHHHHHHHHhccC-CceEEEEeCCCC----Cc-hhhhhcc---eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLS--TDALLYMRWLLERYKG-LNKVFFCCSDVS----KL-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~--~~~~~~L~~~le~~~~-~~~~Il~~n~~~----~i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.+.  ...++.|+.+++.... +..+|++++.++    .+ +.|+||+   .++.+++|+.++...+|++.++
T Consensus       210 LiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~~~~  289 (450)
T PRK14087        210 LIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKKEIK  289 (450)
T ss_pred             EEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHHHHHH
Confidence            5899999997  5678889998887543 346899988775    36 8999997   5999999999999999999999


Q ss_pred             HcCC--CCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           70 QEGI--QLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        70 ~egi--~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ..|+  .++++++.+|+++++||+|.+.+.|..+.
T Consensus       290 ~~gl~~~l~~evl~~Ia~~~~gd~R~L~gaL~~l~  324 (450)
T PRK14087        290 NQNIKQEVTEEAINFISNYYSDDVRKIKGSVSRLN  324 (450)
T ss_pred             hcCCCCCCCHHHHHHHHHccCCCHHHHHHHHHHHH
Confidence            9886  69999999999999999999999998775

>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=99.16  E-value=2.8e-10  Score=88.45  Aligned_cols=101  Identities=14%  Similarity=0.281  Sum_probs=88.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEE-EEeC------------CCCCc-hhhhhcceeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVF-FCCS------------DVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~I-l~~n------------~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~   66 (137)
                      +||||+|.|.-++...|.+.+|  ...+|++ +++|            +++.+ .++..|..++.-.|++.+++.++|+-
T Consensus       292 LFIDEvHMLDIEcFsFlNrAlE--~d~~PiiimaTNrgit~iRGTn~~SphGiP~D~lDR~lII~t~py~~~d~~~IL~i  369 (454)
T KOG2680|consen  292 LFIDEVHMLDIECFSFLNRALE--NDMAPIIIMATNRGITRIRGTNYRSPHGIPIDLLDRMLIISTQPYTEEDIKKILRI  369 (454)
T ss_pred             EEEeeehhhhhHHHHHHHHHhh--hccCcEEEEEcCCceEEeecCCCCCCCCCcHHHhhhhheeecccCcHHHHHHHHHh
Confidence            5899999999999999999999  6677754 4454            33568 89999999999999999999999999


Q ss_pred             HHHHcCCCCCHHHHHHHHHH-cCCcHHHHHHHHHHHHh
Q 042716           67 IAEQEGIQLPHQLAEKIADN-SKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        67 i~~~egi~i~~~~l~~i~~~-~~gd~R~aln~L~~~~~  103 (137)
                      .|..|++.++++++..+... .+-++|++++++-...+
T Consensus       370 Rc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~  407 (454)
T KOG2680|consen  370 RCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASL  407 (454)
T ss_pred             hhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHH
Confidence            99999999999999999886 56789999999976654

>CHL00181 cbbX CbbX; Provisional

Probab=99.16  E-value=2.9e-10  Score=88.03  Aligned_cols=103  Identities=16%  Similarity=0.201  Sum_probs=86.6

Q ss_pred             CcccccCcC---------CHHHHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcce-eeEecCCCHHHHHHHH
Q 042716            1 IILCEADKL---------STDALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLCT-VIQLLPPSKQEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l---------~~~~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc~-~i~~~~~~~~~i~~~l   64 (137)
                      +||||+|.|         +.++++.|+..||....++.+|++++...     .+ |+|+|||. .+.|++++.+++..++
T Consensus       126 LfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~~~~~~vI~ag~~~~~~~~~~~np~L~sR~~~~i~F~~~t~~el~~I~  205 (287)
T CHL00181        126 LFIDEAYYLYKPDNERDYGSEAIEILLQVMENQRDDLVVIFAGYKDRMDKFYESNPGLSSRIANHVDFPDYTPEELLQIA  205 (287)
T ss_pred             EEEEccchhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhcCHHHHHhCCceEEcCCcCHHHHHHHH
Confidence            589999987         56679999999998777777777765331     35 89999985 7999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHH--------cCCcHHHHHHHHHHHHh
Q 042716           65 EFIAEQEGIQLPHQLAEKIADN--------SKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        65 ~~i~~~egi~i~~~~l~~i~~~--------~~gd~R~aln~L~~~~~  103 (137)
                      ...+++++..+++++...+..+        ..|+.|.+.|+++.+..
T Consensus       206 ~~~l~~~~~~l~~~~~~~L~~~i~~~~~~~~~GNaR~vrn~ve~~~~  252 (287)
T CHL00181        206 KIMLEEQQYQLTPEAEKALLDYIKKRMEQPLFANARSVRNALDRARM  252 (287)
T ss_pred             HHHHHHhcCCCChhHHHHHHHHHHHhCCCCCCccHHHHHHHHHHHHH
Confidence            9999999999999988777764        34889999999997765

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=99.12  E-value=4.1e-10  Score=87.35  Aligned_cols=99  Identities=20%  Similarity=0.379  Sum_probs=87.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCce-EEEEeC-------------CCCCc-hhhhhcceeeEecCCCHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNK-VFFCCS-------------DVSKL-QPIKSLCTVIQLLPPSKQEIVEVLE   65 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~-~Il~~n-------------~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~   65 (137)
                      +||||+|.|.-++...|.+.+|  ++-.| +||++|             .++.+ ++|..|..+++-.+++++++..+++
T Consensus       300 LFIDEVhMLDiEcFTyL~kalE--S~iaPivifAsNrG~~~irGt~d~~sPhGip~dllDRl~Iirt~~y~~~e~r~Ii~  377 (456)
T KOG1942|consen  300 LFIDEVHMLDIECFTYLHKALE--SPIAPIVIFASNRGMCTIRGTEDILSPHGIPPDLLDRLLIIRTLPYDEEEIRQIIK  377 (456)
T ss_pred             eEeeehhhhhhHHHHHHHHHhc--CCCCceEEEecCCcceeecCCcCCCCCCCCCHHHhhheeEEeeccCCHHHHHHHHH
Confidence            5899999999999999999999  44445 677776             33568 8999999999999999999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHH-cCCcHHHHHHHHHHH
Q 042716           66 FIAEQEGIQLPHQLAEKIADN-SKNNLRQAIRSFEAS  101 (137)
Q Consensus        66 ~i~~~egi~i~~~~l~~i~~~-~~gd~R~aln~L~~~  101 (137)
                      ..++.||+.++++++..+... ...++|+++.+|--+
T Consensus       378 ~Ra~~E~l~~~e~a~~~l~~~gt~tsLRy~vqLl~p~  414 (456)
T KOG1942|consen  378 IRAQVEGLQVEEEALDLLAEIGTSTSLRYAVQLLTPA  414 (456)
T ss_pred             HHHhhhcceecHHHHHHHHhhccchhHHHHHHhcCHH
Confidence            999999999999999999985 678999999998733

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.10  E-value=8.3e-10  Score=85.36  Aligned_cols=103  Identities=15%  Similarity=0.149  Sum_probs=87.4

Q ss_pred             CcccccCcC---------CHHHHHHHHHHHHhccCCceEEEEeCCC-----CCc-hhhhhcc-eeeEecCCCHHHHHHHH
Q 042716            1 IILCEADKL---------STDALLYMRWLLERYKGLNKVFFCCSDV-----SKL-QPIKSLC-TVIQLLPPSKQEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l---------~~~~~~~L~~~le~~~~~~~~Il~~n~~-----~~i-~~l~SRc-~~i~~~~~~~~~i~~~l   64 (137)
                      +||||+|.|         +.+.++.|+..||....+..+|++++..     ..+ ++++||| ..+.|++++.+++...+
T Consensus       125 L~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~l~~edl~~I~  204 (284)
T TIGR02880       125 LFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMDSFFESNPGFSSRVAHHVDFPDYSEAELLVIA  204 (284)
T ss_pred             EEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHHHHHHH
Confidence            589999988         3556899999999877777777776543     236 8999999 57999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHH--------cCCcHHHHHHHHHHHHh
Q 042716           65 EFIAEQEGIQLPHQLAEKIADN--------SKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        65 ~~i~~~egi~i~~~~l~~i~~~--------~~gd~R~aln~L~~~~~  103 (137)
                      ...+++.+..+++++...+..+        ..||.|.+.|+++.+..
T Consensus       205 ~~~l~~~~~~l~~~a~~~L~~~l~~~~~~~~~GN~R~lrn~ve~~~~  251 (284)
T TIGR02880       205 GLMLKEQQYRFSAEAEEAFADYIALRRTQPHFANARSIRNAIDRARL  251 (284)
T ss_pred             HHHHHHhccccCHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHH
Confidence            9999999999999999888775        45999999999998775

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.

>PRK07452 DNA polymerase III subunit delta; Validated

Probab=99.08  E-value=2e-09  Score=84.21  Aligned_cols=133  Identities=14%  Similarity=0.184  Sum_probs=104.9

Q ss_pred             CcccccCc---CCHHHHHHHHHHHHhccCCceEEEEeCC-CC---Cc-hhhhhcceeeEecCC---CHHHHHHHHHHHHH
Q 042716            1 IILCEADK---LSTDALLYMRWLLERYKGLNKVFFCCSD-VS---KL-QPIKSLCTVIQLLPP---SKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~---l~~~~~~~L~~~le~~~~~~~~Il~~n~-~~---~i-~~l~SRc~~i~~~~~---~~~~i~~~l~~i~~   69 (137)
                      |++++++.   .+++..++|...++.+++++.+|+++.. ..   +. +.+...+.+..|.++   +.+++.+|+...++
T Consensus        65 Vvv~~~~~~~~~~~~~~~~L~~~l~~~~~~~~li~~~~~~~d~r~k~~k~l~k~~~~~~~~~~~~~~~~~l~~~i~~~~~  144 (326)
T PRK07452         65 VWLKNSPLCQGCSEELLAELERTLPLIPENTHLLLTNTKKPDGRLKSTKLLQKLAEEKEFSLIPPWDTEGLKQLVERTAQ  144 (326)
T ss_pred             EEEeCchhhccCCHHHHHHHHHHHcCCCCCcEEEEEeCCCcchHHHHHHHHHHceeEEEecCCCcccHHHHHHHHHHHHH
Confidence            35666654   3567788999999999889988887543 32   36 778888888888766   45779999999999


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhc----CCCcccCccc--cCCcHHHHHHHHHHHHhcC
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQM----NYPFVEGQVI--LTGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~~----~~~~~~~~~~--~~~~~~~~~~i~~~i~~~~  133 (137)
                      ++|+.+++++++.++...++|++.+.|-|+.+..-    +.+++.+.+-  +.+.+..++++++.++.++
T Consensus       145 ~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~if~l~dai~~~~  214 (326)
T PRK07452        145 ELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQNSLQLADALLQGN  214 (326)
T ss_pred             HcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCcHHHHHHHHHCCC
Confidence            99999999999999999999999999999998764    2247766664  2344556778888888765

>KOG1968 consensus Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair]

Probab=99.06  E-value=5.8e-10  Score=96.85  Aligned_cols=101  Identities=21%  Similarity=0.322  Sum_probs=92.0

Q ss_pred             CcccccCcCCH---HHHHHHHHHHHhccCCceEEEEeCCCCCc--hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCC
Q 042716            1 IILCEADKLST---DALLYMRWLLERYKGLNKVFFCCSDVSKL--QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQL   75 (137)
Q Consensus         1 iiiDEid~l~~---~~~~~L~~~le~~~~~~~~Il~~n~~~~i--~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i   75 (137)
                      |++||+|.|..   +.+..|-.+++  ....++|++||+....  +++.+-|..++|+.|+...+..++..+|..|++.+
T Consensus       432 il~devD~~~~~dRg~v~~l~~l~~--ks~~Piv~~cndr~~p~sr~~~~~~~~l~f~kP~~~~i~~ri~si~~se~~ki  509 (871)
T KOG1968|consen  432 ILMDEVDGMFGEDRGGVSKLSSLCK--KSSRPLVCTCNDRNLPKSRALSRACSDLRFSKPSSELIRSRIMSICKSEGIKI  509 (871)
T ss_pred             EEEeccccccchhhhhHHHHHHHHH--hccCCeEEEecCCCCccccchhhhcceeeecCCcHHHHHhhhhhhhcccceec
Confidence            58999999987   45777888888  5678999999999764  78888899999999999999999999999999999


Q ss_pred             CHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           76 PHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        76 ~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      +++.++.+++.++||+|++++.|+++..
T Consensus       510 ~~~~l~~~s~~~~~DiR~~i~~lq~~~~  537 (871)
T KOG1968|consen  510 SDDVLEEISKLSGGDIRQIIMQLQFWSL  537 (871)
T ss_pred             CcHHHHHHHHhcccCHHHHHHHHhhhhc
Confidence            9999999999999999999999999953

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.04  E-value=2e-09  Score=90.48  Aligned_cols=102  Identities=14%  Similarity=0.206  Sum_probs=88.6

Q ss_pred             CcccccCcCCH--HHHHHHHHHHHhccC-CceEEEEeCCCC----Cc-hhhhhcc---eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLST--DALLYMRWLLERYKG-LNKVFFCCSDVS----KL-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~--~~~~~L~~~le~~~~-~~~~Il~~n~~~----~i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.+..  ..+..|+.+++.... +..+|++|+..+    .+ +.|+||+   .++.+.+|+.+....+|+..++
T Consensus       381 LlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~kka~  460 (617)
T PRK14086        381 LLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAILRKKAV  460 (617)
T ss_pred             EEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHHHHHH
Confidence            58999999944  347888899887654 456888888774    36 8999997   6899999999999999999999


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      .+|+.++++++++|+.+..+|+|.+...|..+.
T Consensus       461 ~r~l~l~~eVi~yLa~r~~rnvR~LegaL~rL~  493 (617)
T PRK14086        461 QEQLNAPPEVLEFIASRISRNIRELEGALIRVT  493 (617)
T ss_pred             hcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHH
Confidence            999999999999999999999999998888765

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

Probab=98.99  E-value=8.7e-09  Score=83.06  Aligned_cols=103  Identities=17%  Similarity=0.273  Sum_probs=89.5

Q ss_pred             CcccccCcCCHH--HHHHHHHHHHhccCCc-eEEEEeCCCCC----c-hhhhhcc---eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTD--ALLYMRWLLERYKGLN-KVFFCCSDVSK----L-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~~--~~~~L~~~le~~~~~~-~~Il~~n~~~~----i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++||+++.+...  .|..++.+.+....+. .++++|..+++    + +.|+||+   .++.+.+|+.+....+|+..++
T Consensus       179 llIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r~aiL~kka~  258 (408)
T COG0593         179 LLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAILRKKAE  258 (408)
T ss_pred             eeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHHHHHHHHHHHH
Confidence            479999999665  3888888888765544 68888877764    6 8999996   7999999999999999999999


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      ..|+.++++++.+++.+..+|+|.+...|..+..
T Consensus       259 ~~~~~i~~ev~~~la~~~~~nvReLegaL~~l~~  292 (408)
T COG0593         259 DRGIEIPDEVLEFLAKRLDRNVRELEGALNRLDA  292 (408)
T ss_pred             hcCCCCCHHHHHHHHHHhhccHHHHHHHHHHHHH
Confidence            9999999999999999999999999988876654

>PRK07914 hypothetical protein; Reviewed

Probab=98.95  E-value=1.2e-08  Score=79.86  Aligned_cols=134  Identities=13%  Similarity=0.067  Sum_probs=107.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCC---Cc-hhhhhc-ceeeEecCC-CHHHHHHHHHHHHHHcCCC
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVS---KL-QPIKSL-CTVIQLLPP-SKQEIVEVLEFIAEQEGIQ   74 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~---~i-~~l~SR-c~~i~~~~~-~~~~i~~~l~~i~~~egi~   74 (137)
                      |+++++..+.+.....|...++.+++.+.+||+++...   ++ ++|+.. +.++.+.++ +..++.+|+.+.+++.|+.
T Consensus        68 V~v~~~~~~~~~~~~~l~~~l~~~~~~t~lil~~~~~~~~kk~~K~L~k~g~~~v~~~~~~~~~~l~~wi~~~a~~~g~~  147 (320)
T PRK07914         68 VVLEAAAEAGKDAAALILSAAADLPPGTVLVVVHSGGGRAKALANQLRKLGAEVHPCARITKAAERADFVRKEFRSLRVK  147 (320)
T ss_pred             EEEeChHhccHHHHHHHHHHHhCCCCCeEEEEEecCCcchhHHHHHHHHCCCEEEecCCCCCHHHHHHHHHHHHHHcCCC
Confidence            35566666666677889999999988888888765432   25 678776 468999999 9999999999999999999


Q ss_pred             CCHHHHHHHHHHcCCcHHHHHHHHHHHHh-cCCCcccCccc--cCCc-HHHHHHHHHHHHhcCC
Q 042716           75 LPHQLAEKIADNSKNNLRQAIRSFEASRQ-MNYPFVEGQVI--LTGW-EDDITNIATKIIEEQS  134 (137)
Q Consensus        75 i~~~~l~~i~~~~~gd~R~aln~L~~~~~-~~~~~~~~~~~--~~~~-~~~~~~i~~~i~~~~~  134 (137)
                      +++++++.++...++|+..+-+-|+.+.. .+..++...|-  +.+. +..++++++.+++++.
T Consensus       148 i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~~~It~e~V~~~v~~~~~~~vf~L~dAi~~g~~  211 (320)
T PRK07914        148 VDDDTVTALLDAVGSDLRELASACSQLVADTGGAVDAAAVRRYHSGKAEVKGFDIADKAVAGDV  211 (320)
T ss_pred             CCHHHHHHHHHHHCccHHHHHHHHHHHhcCCCCCcCHHHHHHHcCCCeechHHHHHHHHHCCCH
Confidence            99999999999999999999999998764 34457766664  3343 5578899999887764

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.93  E-value=5.6e-09  Score=82.49  Aligned_cols=103  Identities=22%  Similarity=0.171  Sum_probs=76.1

Q ss_pred             CcccccCcCCHHHHH---HHHHH--HHhcc-CCceEEEEeCCCC---Cc-hhhhhcc--eeeEecCCCHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALL---YMRWL--LERYK-GLNKVFFCCSDVS---KL-QPIKSLC--TVIQLLPPSKQEIVEVLEFIA   68 (137)
Q Consensus         1 iiiDEid~l~~~~~~---~L~~~--le~~~-~~~~~Il~~n~~~---~i-~~l~SRc--~~i~~~~~~~~~i~~~l~~i~   68 (137)
                      ++|||+|.|....+.   .|+++  ..+.+ .+..+|+++|.+.   .+ +.+.||+  ..+.|++++.+++..++...+
T Consensus       133 lvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~  212 (365)
T TIGR02928       133 IVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGISNDLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRA  212 (365)
T ss_pred             EEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEECCcchHhhcCHHHhccCCcceeeeCCCCHHHHHHHHHHHH
Confidence            589999999643333   34444  22222 4567899999875   47 8899998  479999999999999999887


Q ss_pred             HH--cCCCCCHHHHHHHHH---HcCCcHHHHHHHHHHHHh
Q 042716           69 EQ--EGIQLPHQLAEKIAD---NSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        69 ~~--egi~i~~~~l~~i~~---~~~gd~R~aln~L~~~~~  103 (137)
                      +.  .+-.++++++..++.   .+.||+|.++++|+.+..
T Consensus       213 ~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~  252 (365)
T TIGR02928       213 EKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGE  252 (365)
T ss_pred             HhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            63  233478888777554   457999999999987654

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.

>PRK05629 hypothetical protein; Validated

Probab=98.91  E-value=2.8e-08  Score=77.77  Aligned_cols=134  Identities=10%  Similarity=0.031  Sum_probs=108.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCC---c-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCC
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK---L-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLP   76 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~---i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~   76 (137)
                      |++++.+...+.....+...++.+++.+.+|+++....+   + +.++..+.++.+.++...++..|+.+.+++.|+.++
T Consensus        68 V~v~~~~~~~~~~~~~l~~~l~~~~~~~~Lil~~~~~~~~kk~~K~l~k~~~~ve~~~~~~~~l~~wi~~~~~~~g~~i~  147 (318)
T PRK05629         68 IVLTNMEQAGKEPTDLALSAAVDPSPGIYLIIMHSGGGRTKSMVPKLEKIAVVHEAAKLKPRERPGWVTQEFKNHGVRPT  147 (318)
T ss_pred             EEEeChHhcChhHHHHHHHHHhCCCCCeEEEEEcCCcchhhHHHHHHHhcceEeeCCCCCHHHHHHHHHHHHHHcCCCCC
Confidence            355666666555677889999998888888888864432   5 688889999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHHHhc-CCCcccCccc--cCC-cHHHHHHHHHHHHhcCC
Q 042716           77 HQLAEKIADNSKNNLRQAIRSFEASRQM-NYPFVEGQVI--LTG-WEDDITNIATKIIEEQS  134 (137)
Q Consensus        77 ~~~l~~i~~~~~gd~R~aln~L~~~~~~-~~~~~~~~~~--~~~-~~~~~~~i~~~i~~~~~  134 (137)
                      +++++.++..+++|+..+-+-++.+... +.++|...|-  +.+ -+..++++++.++.++.
T Consensus       148 ~~A~~~L~~~~g~dl~~l~~EleKL~~~~~~~It~e~V~~~v~~~~~~~iF~l~dAv~~g~~  209 (318)
T PRK05629        148 PDVVHALLEGVGSDLRELASAISQLVEDTQGNVTVEKVRAYYVGVAEVSGFDIADLACAGQV  209 (318)
T ss_pred             HHHHHHHHHHHCccHHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCccchHHHHHHHHHcCCH
Confidence            9999999999999999999999987643 3457766664  233 36678899998887764

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.89  E-value=1.6e-08  Score=80.80  Aligned_cols=102  Identities=25%  Similarity=0.264  Sum_probs=79.6

Q ss_pred             CcccccCcCC----HHHHHHHHHHHHhccC-CceEEEEeCCCC---Cc-hhhhhcc--eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLS----TDALLYMRWLLERYKG-LNKVFFCCSDVS---KL-QPIKSLC--TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~----~~~~~~L~~~le~~~~-~~~~Il~~n~~~---~i-~~l~SRc--~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      |+|||+|.+.    .+....|++.++..+. +..+|+++|...   .+ +.++||+  ..+.|++++.+++..++...++
T Consensus       142 iviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~v~vI~i~~~~~~~~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~  221 (394)
T PRK00411        142 VALDDINYLFEKEGNDVLYSLLRAHEEYPGARIGVIGISSDLTFLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVE  221 (394)
T ss_pred             EEECCHhHhhccCCchHHHHHHHhhhccCCCeEEEEEEECCcchhhhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHHH
Confidence            5799999996    3345556666655443 455899998774   36 7888987  5789999999999999998876


Q ss_pred             Hc--CCCCCHHHHHHHHHHc---CCcHHHHHHHHHHHH
Q 042716           70 QE--GIQLPHQLAEKIADNS---KNNLRQAIRSFEASR  102 (137)
Q Consensus        70 ~e--gi~i~~~~l~~i~~~~---~gd~R~aln~L~~~~  102 (137)
                      ..  +-.+++++++.+++.+   .||+|.++++|..+.
T Consensus       222 ~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~  259 (394)
T PRK00411        222 EGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAG  259 (394)
T ss_pred             hhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            43  2358999999998877   899999999998654

>PF06144 DNA_pol3_delta: DNA polymerase III, delta subunit; InterPro: IPR010372 DNA polymerase III, delta subunit (2

Probab=98.82  E-value=1.3e-08  Score=72.30  Aligned_cols=101  Identities=20%  Similarity=0.242  Sum_probs=77.4

Q ss_pred             ccccc----CcCCHHHHHHHHHHHHhccCCceEEEEeC-CCC---Cc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcC
Q 042716            2 ILCEA----DKLSTDALLYMRWLLERYKGLNKVFFCCS-DVS---KL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEG   72 (137)
Q Consensus         2 iiDEi----d~l~~~~~~~L~~~le~~~~~~~~Il~~n-~~~---~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~eg   72 (137)
                      ++.++    +.........|...++.+++++.+|+.++ ...   ++ +.+...+.++.+.+|+..++..|++..+++.|
T Consensus        62 ii~~~~~l~~~~~~~~~~~l~~~l~~~~~~~~lii~~~~~~~~~~k~~k~l~~~~~~~~~~~~~~~~~~~~i~~~~~~~g  141 (172)
T PF06144_consen   62 IIKNAPFLKDKLKKKEIKALIEYLSNPPPDCILIIFSEEKLDKRKKLYKALKKQAIVIECKKPKEQELPRWIKERAKKNG  141 (172)
T ss_dssp             EEE-----TT-S-TTHHHHHHHHTTT--SSEEEEEEES-S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHHHHTT
T ss_pred             EEecCccccccccHHHHHHHHHHHhCCCCCEEEEEEeCCchhhhhhHHHHHhcccceEEecCCCHHHHHHHHHHHHHHcC
Confidence            45565    55666778999999999999999999988 443   36 88888999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           73 IQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        73 i~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      +.+++++++.+++..++|++.+.+-|+.+.
T Consensus       142 ~~i~~~a~~~L~~~~~~d~~~l~~EleKL~  171 (172)
T PF06144_consen  142 LKIDPDAAQYLIERVGNDLSLLQNELEKLS  171 (172)
T ss_dssp             -EE-HHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHhChHHHHHHHHHHHhc
Confidence            999999999999999999999999998765

7.7.7 from EC) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction []. The delta subunit is also known as HolA.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 3GLG_F 1XXH_A 1JQL_B 3GLF_F 1JQJ_C 3GLI_F.

>TIGR00763 lon ATP-dependent protease La

Probab=98.79  E-value=8.4e-09  Score=89.34  Aligned_cols=99  Identities=15%  Similarity=0.189  Sum_probs=74.6

Q ss_pred             CcccccCcCCHHH----HHHHHHHHHhc---------------cCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHH
Q 042716            1 IILCEADKLSTDA----LLYMRWLLERY---------------KGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~----~~~L~~~le~~---------------~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i   60 (137)
                      |+|||+|.+++..    .++|+.+++..               .+++.||+|||....+ ++|++||.++.|++++.++.
T Consensus       418 illDEidk~~~~~~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I~TtN~~~~i~~~L~~R~~vi~~~~~~~~e~  497 (775)
T TIGR00763       418 FLLDEIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSIDTIPRPLLDRMEVIELSGYTEEEK  497 (775)
T ss_pred             EEEechhhcCCccCCCHHHHHHHhcCHHhcCccccccCCceeccCCEEEEEecCCchhCCHHHhCCeeEEecCCCCHHHH
Confidence            5899999997643    47899988731               0356789999999999 99999999999999999988


Q ss_pred             HHHHHHHH-----HH-----cCCCCCHHHHHHHHHHcC--CcHHHHHHHHH
Q 042716           61 VEVLEFIA-----EQ-----EGIQLPHQLAEKIADNSK--NNLRQAIRSFE   99 (137)
Q Consensus        61 ~~~l~~i~-----~~-----egi~i~~~~l~~i~~~~~--gd~R~aln~L~   99 (137)
                      ..+++...     ++     +++.++++++..+++...  ...|.+-..++
T Consensus       498 ~~I~~~~l~~~~~~~~~l~~~~~~~~~~~l~~i~~~~~~e~g~R~l~r~i~  548 (775)
T TIGR00763       498 LEIAKKYLIPKALEDHGLKPDELKITDEALLLLIKYYTREAGVRNLERQIE  548 (775)
T ss_pred             HHHHHHHHHHHHHHHcCCCcceEEECHHHHHHHHHhcChhcCChHHHHHHH
Confidence            88776543     22     346799999999998543  23444444333

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.

>PRK08487 DNA polymerase III subunit delta; Validated

Probab=98.76  E-value=1.4e-07  Score=74.13  Aligned_cols=132  Identities=15%  Similarity=0.202  Sum_probs=101.0

Q ss_pred             cccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCC---c-hhhhhc--ceeeEecCCCHHHHHHHHHHHHHHcCCCC
Q 042716            2 ILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK---L-QPIKSL--CTVIQLLPPSKQEIVEVLEFIAEQEGIQL   75 (137)
Q Consensus         2 iiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~---i-~~l~SR--c~~i~~~~~~~~~i~~~l~~i~~~egi~i   75 (137)
                      ++.+...........|...++.++..+.+|++.+...+   + +-+...  ...+.|.+++..++..|+...+++.|+.+
T Consensus        76 iv~~~~~~~~~~~~~L~~~l~~~~~~~~lv~~~~~~~k~kkl~k~~~~~k~~~~v~~~~~~~~~l~~~i~~~~~~~g~~i  155 (328)
T PRK08487         76 IIKLDKKIPKKELKLLIELCEKNSDNYFIIELYGADSKTKDIEKLFQKKDEAVFVRFFKPNAREALELLQERAKELGLDI  155 (328)
T ss_pred             EEecccccCHHHHHHHHHHHhcCCCCEEEEEecCCcchhHHHHHHhccCCCceEEEeeCCCHHHHHHHHHHHHHHhCCCC
Confidence            44555555566677888889888766655554444432   3 322222  56899999999999999999999999999


Q ss_pred             CHHHHHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCccc--cCC-cHHHHHHHHHHHHhcC
Q 042716           76 PHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVI--LTG-WEDDITNIATKIIEEQ  133 (137)
Q Consensus        76 ~~~~l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~~--~~~-~~~~~~~i~~~i~~~~  133 (137)
                      +++++..++..+++|+..+.+-|+.+......+|...+-  +.+ -+..++++++.+++++
T Consensus       156 ~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~~It~edV~~~v~~~~e~~vF~l~dai~~g~  216 (328)
T PRK08487        156 DQNALNHLYFIHNEDLALAANELEKLAILNEPITLKDIQELVFGLGSVSFEDFFEKLLNKK  216 (328)
T ss_pred             CHHHHHHHHHHhCcHHHHHHHHHHHHHHhcCCCCHHHHHHHhcccccccHHHHHHHHHCCC
Confidence            999999999999999999999999988765567777664  233 4666888888888765

>PRK05574 holA DNA polymerase III subunit delta; Reviewed

Probab=98.70  E-value=2.5e-07  Score=72.42  Aligned_cols=133  Identities=14%  Similarity=0.139  Sum_probs=93.1

Q ss_pred             CcccccCcCCHHH-HHHHHHHHH--hccCC--ceEEEEeCCCC------Cc-hhhhhcceeeEecCCCHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDA-LLYMRWLLE--RYKGL--NKVFFCCSDVS------KL-QPIKSLCTVIQLLPPSKQEIVEVLEFIA   68 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~L~~~le--~~~~~--~~~Il~~n~~~------~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~   68 (137)
                      |++++++.+.... ...+..+.+  +++++  ..+++.++..+      +. +++.++|.++.+.+++..++..++...+
T Consensus        80 vii~~~~~l~~~~~~~~l~~l~~~l~~~~~~~~~li~~~~~~~~~~k~~k~~k~~~~~~~~~~~~~~~~~~~~~~i~~~~  159 (340)
T PRK05574         80 VELRLPEFLTGAKGEKALKRLEAYLNPLPHPDLLLIVRLPKLDKAKKKSAWFKALKKKAVVVEAQPPKEAELPQWIQQRL  159 (340)
T ss_pred             EEEECCCCCCchhHHHHHHHHHHhccCCCCCcEEEEEECCcCCHHHHhhHHHHHHHhCceEEEcCCCCHHHHHHHHHHHH
Confidence            4788999886653 233333332  23333  33444444432      22 6788899999999999999999999999


Q ss_pred             HHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhcC--CCcccCccc-c--CCcHHHHHHHHHHHHhcC
Q 042716           69 EQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMN--YPFVEGQVI-L--TGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        69 ~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~~~--~~~~~~~~~-~--~~~~~~~~~i~~~i~~~~  133 (137)
                      ++.|+.+++++++.+++.++||++.+.+-++.+....  .+++.+.+- .  ..-+..++++++.+++.+
T Consensus       160 ~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~~~~~~~f~l~dai~~~~  229 (340)
T PRK05574        160 KQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPDSARFDVFDLVDAILAGK  229 (340)
T ss_pred             HHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhhhhcCCHHHHHHHHHCCC
Confidence            9999999999999999999999999999999887532  235555443 1  112344556666665543

>PRK06585 holA DNA polymerase III subunit delta; Reviewed

Probab=98.64  E-value=5.5e-07  Score=70.93  Aligned_cols=124  Identities=10%  Similarity=0.096  Sum_probs=97.5

Q ss_pred             HHHHHHHHHHHHhccCCceEEEEeCCCCC---c-hhhh--hcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 042716           11 TDALLYMRWLLERYKGLNKVFFCCSDVSK---L-QPIK--SLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIA   84 (137)
Q Consensus        11 ~~~~~~L~~~le~~~~~~~~Il~~n~~~~---i-~~l~--SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~l~~i~   84 (137)
                      +.....|...++.++..+.+|+.+....+   + +.+.  .....+.+.+++..++..|+.+.+++.|+.+++++++.++
T Consensus        92 ~~~~~~L~~~l~~~~~~~~lil~~~~~~~~~kl~k~~~~~~~~~~v~~~~~~~~~l~~~i~~~~~~~g~~i~~~a~~~L~  171 (343)
T PRK06585         92 KNLAAALKALLESPPGDAFIVIEAGDLKKGSSLRKLFETAAYAAAIPCYADDERDLARLIDDELAEAGLRITPDARALLV  171 (343)
T ss_pred             hhHHHHHHHHHcCCCCCcEEEEEcCCCCcccHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHH
Confidence            34566788899988888888887755432   4 3331  2346789999999999999999999999999999999999


Q ss_pred             HHcCCcHHHHHHHHHHHHhcC---CCcccCccc--cCC-cHHHHHHHHHHHHhcCC
Q 042716           85 DNSKNNLRQAIRSFEASRQMN---YPFVEGQVI--LTG-WEDDITNIATKIIEEQS  134 (137)
Q Consensus        85 ~~~~gd~R~aln~L~~~~~~~---~~~~~~~~~--~~~-~~~~~~~i~~~i~~~~~  134 (137)
                      +.++||++.+.|-|+.+....   ..+|.+.+.  +.+ -+..++++++.+++++.
T Consensus       172 ~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~~~e~~if~l~dai~~~~~  227 (343)
T PRK06585        172 ALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGDASALSLDDAADAALAGDL  227 (343)
T ss_pred             HHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCcccccHHHHHHHHHCCCH
Confidence            999999999999999988642   247777765  222 36668888888887764

>PRK05907 hypothetical protein; Provisional

Probab=98.64  E-value=4e-07  Score=71.37  Aligned_cols=129  Identities=12%  Similarity=0.164  Sum_probs=98.5

Q ss_pred             cccCcCCHHHHHHHHHHHHhccCCceEE-EEeCCCCC---c-hhhhhcceee----EecCCCHHHHHHHHHHHHHHcCCC
Q 042716            4 CEADKLSTDALLYMRWLLERYKGLNKVF-FCCSDVSK---L-QPIKSLCTVI----QLLPPSKQEIVEVLEFIAEQEGIQ   74 (137)
Q Consensus         4 DEid~l~~~~~~~L~~~le~~~~~~~~I-l~~n~~~~---i-~~l~SRc~~i----~~~~~~~~~i~~~l~~i~~~egi~   74 (137)
                      .+.+.++......|.+.+++|++.+.+| +++ ...+   + +.+. .+..+    .|.++...++..|+.+.++++|..
T Consensus        76 ~~~~~~~~~~~~~L~~Yl~np~~~~~liv~~~-~~d~~kkl~K~i~-k~~~v~~~~e~~~l~e~~L~~Wi~~~~~~~g~~  153 (311)
T PRK05907         76 YQAEKMSSSTQEFLIRYARNPNPHLTLFLFTT-KQECFSSLSKKLS-SALCLSLFGEWFADRDKRIAQLLIQRAKELGIS  153 (311)
T ss_pred             ecccccccccHHHHHHHHhCCCCCeEEEEEEe-cccHHHHHHHHHh-hcceeccccccCCCCHHHHHHHHHHHHHHcCCC
Confidence            3445566666788999999999876666 555 3322   3 4444 35555    899999999999999999999999


Q ss_pred             CCHHHHHHHHHHc-CCcHHHHHHHHHHHHhc---CCCcccCccc--cCC-cHHHHHHHHHHHHhcCC
Q 042716           75 LPHQLAEKIADNS-KNNLRQAIRSFEASRQM---NYPFVEGQVI--LTG-WEDDITNIATKIIEEQS  134 (137)
Q Consensus        75 i~~~~l~~i~~~~-~gd~R~aln~L~~~~~~---~~~~~~~~~~--~~~-~~~~~~~i~~~i~~~~~  134 (137)
                      ++++++..++..+ ++|+..+.+-|+.+...   +..|+.+.+-  +.+ -+..++++++.|+.++.
T Consensus       154 i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~~s~e~nIF~L~dai~~~~~  220 (311)
T PRK05907        154 CSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVVKKEAASLWKLRDALLRRDR  220 (311)
T ss_pred             cCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhcCcccccHHHHHHHHHccCH
Confidence            9999999999999 69999999999988654   2347666664  233 46668888888887653

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

Probab=98.63  E-value=7.2e-07  Score=67.54  Aligned_cols=103  Identities=19%  Similarity=0.189  Sum_probs=78.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccC---CceEEEEeCCC-------CCchhhhhcc-eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKG---LNKVFFCCSDV-------SKLQPIKSLC-TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~---~~~~Il~~n~~-------~~i~~l~SRc-~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.++..+.+.|+.+.+....   ...+++++...       +...++++|. ..+.+++++.+++..++...+.
T Consensus       127 liiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~r~~~~~~l~~l~~~e~~~~l~~~l~  206 (269)
T TIGR03015       127 LVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPEFRETLQSPQLQQLRQRIIASCHLGPLDREETREYIEHRLE  206 (269)
T ss_pred             EEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHHHHHHHcCchhHHHHhheeeeeeCCCCCHHHHHHHHHHHHH
Confidence            58999999999888888766553221   23456665432       1125688884 6799999999999999998887


Q ss_pred             HcC----CCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           70 QEG----IQLPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        70 ~eg----i~i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      ..|    ..++++++..|.+.+.|++|.+..++..+..
T Consensus       207 ~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~  244 (269)
T TIGR03015       207 RAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLL  244 (269)
T ss_pred             HcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHH
Confidence            665    4799999999999999999998777776643

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

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=98.60  E-value=1.6e-06  Score=66.25  Aligned_cols=120  Identities=14%  Similarity=0.166  Sum_probs=87.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc----------------cCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCCHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERY----------------KGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPSKQ   58 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~----------------~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~~~   58 (137)
                      ++|||+|++.++.|+.|+.++|+.                ++++++|+|+|...     .+ ++|++||..+.+..|+.+
T Consensus       109 lllDEi~r~~~~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~~~g~~~l~~aL~~R~~~i~i~~P~~~  188 (262)
T TIGR02640       109 LVYDEFTRSKPETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVEYAGVHETQDALLDRLITIFMDYPDID  188 (262)
T ss_pred             EEEcchhhCCHHHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCccccceecccHHHHhhcEEEECCCCCHH
Confidence            589999999999999999999863                13567888888652     36 899999999999999998


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHc----------CCcHHHHHHHHHHHHhcCCCcccCccccCCcHHHHHHHHHH
Q 042716           59 EIVEVLEFIAEQEGIQLPHQLAEKIADNS----------KNNLRQAIRSFEASRQMNYPFVEGQVILTGWEDDITNIATK  128 (137)
Q Consensus        59 ~i~~~l~~i~~~egi~i~~~~l~~i~~~~----------~gd~R~aln~L~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~  128 (137)
                      +-..++...     ..++++.++++++..          .-.+|.++...+.+...+.+       ....++++.++...
T Consensus       189 ~e~~Il~~~-----~~~~~~~~~~iv~~~~~~R~~~~~~~~~~r~~i~~~~~~~~~~~~-------~~~~~~~~~~~~~~  256 (262)
T TIGR02640       189 TETAILRAK-----TDVAEDSAATIVRLVREFRASGDEITSGLRASLMIAEVATQQDIP-------VDVDDEDFVDLCID  256 (262)
T ss_pred             HHHHHHHHh-----hCCCHHHHHHHHHHHHHHHhhCCccCCcHHHHHHHHHHHHHcCCC-------CCCCcHHHHHHHHH
Confidence            888887753     346777777766543          12378888887777654321       00136667777777


Q ss_pred             HHhc
Q 042716          129 IIEE  132 (137)
Q Consensus       129 i~~~  132 (137)
                      ++.+
T Consensus       257 ~~~~  260 (262)
T TIGR02640       257 ILAS  260 (262)
T ss_pred             Hhcc
Confidence            7754

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).

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=98.59  E-value=7.4e-07  Score=74.20  Aligned_cols=103  Identities=21%  Similarity=0.308  Sum_probs=73.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc--cCCc-eEEEEeCCC---------C-------Cc--hhhhhc--ceeeEecCCCH
Q 042716            1 IILCEADKLSTDALLYMRWLLERY--KGLN-KVFFCCSDV---------S-------KL--QPIKSL--CTVIQLLPPSK   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~--~~~~-~~Il~~n~~---------~-------~i--~~l~SR--c~~i~~~~~~~   57 (137)
                      |+|+|.=.+.......++..+.++  ...+ |+|++.++.         .       .+  +.+++.  +..+.|.|+..
T Consensus       136 ILVEDlPN~~~~~~~~f~~~L~~~l~~~~~~PlV~iiSe~~~~~~~~~~~~~~~t~~~L~~~~il~~~~i~~I~FNpIa~  215 (519)
T PF03215_consen  136 ILVEDLPNVFHRDTSRFREALRQYLRSSRCLPLVFIISETESLSGDNSYRSNSFTAERLFPKEILNHPGITRIKFNPIAP  215 (519)
T ss_pred             EEeeccccccchhHHHHHHHHHHHHHcCCCCCEEEEEecccccCCCCcccccchhhhhccCHHHHhCCCceEEEecCCCH
Confidence            356666665433334555554443  3455 866665521         1       13  566654  57899999999


Q ss_pred             HHHHHHHHHHHHHc-----CC-CCC--HHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           58 QEIVEVLEFIAEQE-----GI-QLP--HQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        58 ~~i~~~l~~i~~~e-----gi-~i~--~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      .-+.+.|.+|+.+|     |. ..+  ..+++.|+..+.||+|.|+|.||++..
T Consensus       216 T~mkKaL~rI~~~E~~~~~~~~~~p~~~~~l~~I~~~s~GDIRsAIn~LQf~~~  269 (519)
T PF03215_consen  216 TFMKKALKRILKKEARSSSGKNKVPDKQSVLDSIAESSNGDIRSAINNLQFWCL  269 (519)
T ss_pred             HHHHHHHHHHHHHHhhhhcCCccCCChHHHHHHHHHhcCchHHHHHHHHHHHhc
Confidence            99999999999999     33 333  346899999999999999999999987

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.59  E-value=3.1e-07  Score=80.44  Aligned_cols=103  Identities=15%  Similarity=0.218  Sum_probs=85.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-----------------------------CCc
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-----------------------------SKL   40 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-----------------------------~~i   40 (137)
                      |+|||+|.++++.++.|+.++++..           .++.||||+|-.                             ...
T Consensus       672 vllDEieka~~~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSNlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f  751 (852)
T TIGR03345       672 VLLDEVEKAHPDVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNAGSDLIMALCADPETAPDPEALLEALRPELLKVF  751 (852)
T ss_pred             EEEechhhcCHHHHHHHHHHhhcceeecCCCcEEeccccEEEEeCCCchHHHHHhccCcccCcchHHHHHHHHHHHHHhc
Confidence            5899999999999999999999765           678899998831                             015


Q ss_pred             -hhhhhcceeeEecCCCHHHHHHHHHHHHH--------HcC--CCCCHHHHHHHHHHcCC---cHHHHHHHHHHHHh
Q 042716           41 -QPIKSLCTVIQLLPPSKQEIVEVLEFIAE--------QEG--IQLPHQLAEKIADNSKN---NLRQAIRSFEASRQ  103 (137)
Q Consensus        41 -~~l~SRc~~i~~~~~~~~~i~~~l~~i~~--------~eg--i~i~~~~l~~i~~~~~g---d~R~aln~L~~~~~  103 (137)
                       |.++|||.++.|.+++.+++.+++.....        +.|  +.++++++.+|++.+.+   +.|.+.+.++....
T Consensus       752 ~PEflnRi~iI~F~pLs~e~l~~Iv~~~L~~l~~rl~~~~gi~l~i~d~a~~~La~~g~~~~~GAR~L~r~Ie~~i~  828 (852)
T TIGR03345       752 KPAFLGRMTVIPYLPLDDDVLAAIVRLKLDRIARRLKENHGAELVYSEALVEHIVARCTEVESGARNIDAILNQTLL  828 (852)
T ss_pred             cHHHhcceeEEEeCCCCHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHHHHHHcCCCCCChHHHHHHHHHHHH
Confidence             78999999999999999998888754332        225  47899999999999887   89999999987653

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.

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

Probab=98.56  E-value=1.1e-07  Score=82.57  Aligned_cols=86  Identities=15%  Similarity=0.109  Sum_probs=68.6

Q ss_pred             CcccccCcCCHHH----HHHHHHHHHhc---------------cCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHH
Q 042716            1 IILCEADKLSTDA----LLYMRWLLERY---------------KGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~----~~~L~~~le~~---------------~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i   60 (137)
                      ++|||+|.+++..    +.+|+.+++.-               -+++.||+|+|+. .| ++|++||.+++|.+++.++.
T Consensus       420 illDEidk~~~~~~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~-~i~~aLl~R~~ii~~~~~t~eek  498 (784)
T PRK10787        420 FLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSM-NIPAPLLDRMEVIRLSGYTEDEK  498 (784)
T ss_pred             EEEEChhhcccccCCCHHHHHHHHhccccEEEEecccccccccCCceEEEEcCCCC-CCCHHHhcceeeeecCCCCHHHH
Confidence            5899999998765    58999999831               1466688888776 59 99999999999999999999


Q ss_pred             HHHHHHHHH-----H-----cCCCCCHHHHHHHHHHc
Q 042716           61 VEVLEFIAE-----Q-----EGIQLPHQLAEKIADNS   87 (137)
Q Consensus        61 ~~~l~~i~~-----~-----egi~i~~~~l~~i~~~~   87 (137)
                      ..+++....     +     ..+.++++++..+++.+
T Consensus       499 ~~Ia~~~L~~k~~~~~~l~~~~l~i~~~ai~~ii~~y  535 (784)
T PRK10787        499 LNIAKRHLLPKQIERNALKKGELTVDDSAIIGIIRYY  535 (784)
T ss_pred             HHHHHHhhhHHHHHHhCCCCCeEEECHHHHHHHHHhC
Confidence            888765542     2     13578999999999754

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

Probab=98.56  E-value=2.6e-07  Score=79.68  Aligned_cols=100  Identities=16%  Similarity=0.180  Sum_probs=81.2

Q ss_pred             CcccccCcCC---------HHHHHHHHHHHHhccCCceEEEEeCCC-----CCc-hhhhhcceeeEecCCCHHHHHHHHH
Q 042716            1 IILCEADKLS---------TDALLYMRWLLERYKGLNKVFFCCSDV-----SKL-QPIKSLCTVIQLLPPSKQEIVEVLE   65 (137)
Q Consensus         1 iiiDEid~l~---------~~~~~~L~~~le~~~~~~~~Il~~n~~-----~~i-~~l~SRc~~i~~~~~~~~~i~~~l~   65 (137)
                      +||||+|.+.         ..+++.|+..++  .+...+|.+||..     ... ++|.+||..+.+.+|+.++...+|+
T Consensus       278 LfiDEih~l~~~g~~~~~~~~~~~~L~~~l~--~g~i~~IgaTt~~e~~~~~~~d~al~rRf~~i~v~~p~~~~~~~il~  355 (731)
T TIGR02639       278 LFIDEIHTIVGAGATSGGSMDASNLLKPALS--SGKLRCIGSTTYEEYKNHFEKDRALSRRFQKIDVGEPSIEETVKILK  355 (731)
T ss_pred             EEEecHHHHhccCCCCCccHHHHHHHHHHHh--CCCeEEEEecCHHHHHHHhhhhHHHHHhCceEEeCCCCHHHHHHHHH
Confidence            5899999995         235788888888  5677788888863     236 8999999999999999999999998


Q ss_pred             HHHHH----cCCCCCHHHHHHHHHHcCC---c---HHHHHHHHHHHH
Q 042716           66 FIAEQ----EGIQLPHQLAEKIADNSKN---N---LRQAIRSFEASR  102 (137)
Q Consensus        66 ~i~~~----egi~i~~~~l~~i~~~~~g---d---~R~aln~L~~~~  102 (137)
                      ....+    .++.++++++..++..+.+   |   +++|+.+|+.+.
T Consensus       356 ~~~~~~e~~~~v~i~~~al~~~~~ls~ryi~~r~~P~kai~lld~a~  402 (731)
T TIGR02639       356 GLKEKYEEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAG  402 (731)
T ss_pred             HHHHHHHhccCcccCHHHHHHHHHhhhcccccccCCHHHHHHHHHhh
Confidence            76654    4678999999999988754   3   888999997654

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.43  E-value=4.5e-07  Score=79.41  Aligned_cols=99  Identities=13%  Similarity=0.178  Sum_probs=78.4

Q ss_pred             CcccccCcCCH-----H---HHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKLST-----D---ALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l~~-----~---~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~~~~i~~~l~~   66 (137)
                      +||||+|.|.+     +   +.+.|...++  .+...+|.+|+...     .+ ++|++||+.+.+++|+.++...+|+.
T Consensus       284 LfIDEih~l~~~g~~~~~~d~~n~Lkp~l~--~G~l~~IgaTT~~e~~~~~~~d~AL~rRf~~i~v~eps~~~~~~iL~~  361 (852)
T TIGR03345       284 LFIDEAHTLIGAGGQAGQGDAANLLKPALA--RGELRTIAATTWAEYKKYFEKDPALTRRFQVVKVEEPDEETAIRMLRG  361 (852)
T ss_pred             EEEeChHHhccCCCccccccHHHHhhHHhh--CCCeEEEEecCHHHHhhhhhccHHHHHhCeEEEeCCCCHHHHHHHHHH
Confidence            58999999964     2   2346888887  66777888888641     26 99999999999999999999999766


Q ss_pred             HHHH----cCCCCCHHHHHHHHHHcCC------cHHHHHHHHHHH
Q 042716           67 IAEQ----EGIQLPHQLAEKIADNSKN------NLRQAIRSFEAS  101 (137)
Q Consensus        67 i~~~----egi~i~~~~l~~i~~~~~g------d~R~aln~L~~~  101 (137)
                      +...    .++.++++++..++..+.+      =+.+|+.+|+.+
T Consensus       362 ~~~~~e~~~~v~i~d~al~~~~~ls~ryi~~r~LPDKAIdlldea  406 (852)
T TIGR03345       362 LAPVLEKHHGVLILDEAVVAAVELSHRYIPGRQLPDKAVSLLDTA  406 (852)
T ss_pred             HHHhhhhcCCCeeCHHHHHHHHHHcccccccccCccHHHHHHHHH
Confidence            5543    4788999999999998853      367888888754

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.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=98.37  E-value=2.6e-06  Score=67.20  Aligned_cols=105  Identities=17%  Similarity=0.146  Sum_probs=81.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcc--eeeEecCCC--H
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLC--TVIQLLPPS--K   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc--~~i~~~~~~--~   57 (137)
                      ++|||+|.|+...|..|+.++++..           .++++|++++..       ..+ ++|..|+  ..+.++|+.  .
T Consensus        97 L~Ldei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~at~~~l~~~~~~g~fr~dL~~rl~~~~i~lPpLReR~  176 (329)
T TIGR02974        97 LFLDELATASLLVQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNADLPALAAEGRFRADLLDRLAFDVITLPPLRERQ  176 (329)
T ss_pred             EEeCChHhCCHHHHHHHHHHHHcCcEEecCCCceeccceEEEEechhhHHHHhhcCchHHHHHHHhcchhcCCCchhhhh
Confidence            5899999999999999999998642           346888888754       246 8899998  467887777  3


Q ss_pred             HHHHHHHHH----HHHHcC----CCCCHHHHHHHHHHc-CCcHHHHHHHHHHHHhcC
Q 042716           58 QEIVEVLEF----IAEQEG----IQLPHQLAEKIADNS-KNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        58 ~~i~~~l~~----i~~~eg----i~i~~~~l~~i~~~~-~gd~R~aln~L~~~~~~~  105 (137)
                      +|+...+..    .+.+.|    ..++++++..+..+. .||+|.+-|.++.+....
T Consensus       177 eDI~~L~~~fl~~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvrEL~n~i~~~~~~~  233 (329)
T TIGR02974       177 EDIMLLAEHFAIRMARELGLPLFPGFTPQAREQLLEYHWPGNVRELKNVVERSVYRH  233 (329)
T ss_pred             hhHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHhCCCCchHHHHHHHHHHHHHhC
Confidence            566555443    444444    358999999999985 999999999999887644

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

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

Probab=98.30  E-value=2.8e-06  Score=68.01  Aligned_cols=106  Identities=20%  Similarity=0.166  Sum_probs=79.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc---CCceEEEEeCCCC---Cc-hhhhhcce--eeEecCCCHHHHHHHHHHHHHH-
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK---GLNKVFFCCSDVS---KL-QPIKSLCT--VIQLLPPSKQEIVEVLEFIAEQ-   70 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~---~~~~~Il~~n~~~---~i-~~l~SRc~--~i~~~~~~~~~i~~~l~~i~~~-   70 (137)
                      |++||+|.|....+..|+.+..-+.   .++-+|.++|+..   .+ +.++|+..  .+.|+|++.+|+.++|...++. 
T Consensus       127 vvLDEid~L~~~~~~~LY~L~r~~~~~~~~v~vi~i~n~~~~~~~ld~rv~s~l~~~~I~F~pY~a~el~~Il~~R~~~~  206 (366)
T COG1474         127 VILDEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPRVKSSLGPSEIVFPPYTAEELYDILRERVEEG  206 (366)
T ss_pred             EEEcchhhhccccchHHHHHHhhccccceeEEEEEEeccHHHHHHhhhhhhhccCcceeeeCCCCHHHHHHHHHHHHHhh
Confidence            5899999997776555555554333   2334777777774   36 89999973  5789999999999999987763 


Q ss_pred             -cCCCCCHHHHHHHHHH---cCCcHHHHHHHHHHHHhcCC
Q 042716           71 -EGIQLPHQLAEKIADN---SKNNLRQAIRSFEASRQMNY  106 (137)
Q Consensus        71 -egi~i~~~~l~~i~~~---~~gd~R~aln~L~~~~~~~~  106 (137)
                       ..-.+++++++.++..   ..||.|.|+..|..+...+.
T Consensus       207 ~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe  246 (366)
T COG1474         207 FSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAE  246 (366)
T ss_pred             ccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHH
Confidence             3346888888887743   56799999999998776443

>TIGR01817 nifA Nif-specific regulatory protein

Probab=98.24  E-value=9.2e-06  Score=67.79  Aligned_cols=105  Identities=12%  Similarity=0.134  Sum_probs=79.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcce--eeEecCCC--H
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLCT--VIQLLPPS--K   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc~--~i~~~~~~--~   57 (137)
                      ++|||+|.|+...|..|+.++++..           .++++|++|+..       ..+ ++|..|+.  .+.++|+.  .
T Consensus       294 L~ldei~~L~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~s~~~l~~~~~~~~f~~~L~~rl~~~~i~lPpLreR~  373 (534)
T TIGR01817       294 LFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLYYRINVVPIFLPPLRERR  373 (534)
T ss_pred             EEEechhhCCHHHHHHHHHHHhcCcEEECCCCceEeecEEEEEeCCCCHHHHHHcCCCCHHHHHHhcCCeeeCCCccccc
Confidence            5899999999999999999998632           136888888765       235 78888874  56677776  4


Q ss_pred             HHHHHHHHHH----HHHcC--CCCCHHHHHHHHHH-cCCcHHHHHHHHHHHHhcC
Q 042716           58 QEIVEVLEFI----AEQEG--IQLPHQLAEKIADN-SKNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        58 ~~i~~~l~~i----~~~eg--i~i~~~~l~~i~~~-~~gd~R~aln~L~~~~~~~  105 (137)
                      +++...+...    +.+.|  +.++++++..+..+ -+||+|.+.|.++.+....
T Consensus       374 eDi~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~~~WPGNvrEL~~v~~~a~~~~  428 (534)
T TIGR01817       374 EDIPLLAEAFLEKFNRENGRPLTITPSAIRVLMSCKWPGNVRELENCLERTATLS  428 (534)
T ss_pred             ccHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhCCCCChHHHHHHHHHHHHHhC
Confidence            5665554443    33333  57899999999998 5999999999999887543

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

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.22  E-value=8e-06  Score=71.46  Aligned_cols=101  Identities=13%  Similarity=0.193  Sum_probs=75.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc-----------cCCceEEEEeCCCCC------------------------------
Q 042716            1 IILCEADKLSTDALLYMRWLLERY-----------KGLNKVFFCCSDVSK------------------------------   39 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~-----------~~~~~~Il~~n~~~~------------------------------   39 (137)
                      |++||+|.++++.+++|+.++|+.           -.++.||+|||....                              
T Consensus       615 vllDeieka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~  694 (821)
T CHL00095        615 VLFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLV  694 (821)
T ss_pred             EEECChhhCCHHHHHHHHHHhccCceecCCCcEEecCceEEEEeCCcchHHHHhhccccCCcccccccccccHHHHHHHH
Confidence            579999999999999999999974           257789999884210                              


Q ss_pred             -------c-hhhhhcc-eeeEecCCCHHHHHHHHHHHHH-------HcC--CCCCHHHHHHHHHHcC---CcHHHHHHHH
Q 042716           40 -------L-QPIKSLC-TVIQLLPPSKQEIVEVLEFIAE-------QEG--IQLPHQLAEKIADNSK---NNLRQAIRSF   98 (137)
Q Consensus        40 -------i-~~l~SRc-~~i~~~~~~~~~i~~~l~~i~~-------~eg--i~i~~~~l~~i~~~~~---gd~R~aln~L   98 (137)
                             . |.+.+|+ .++.|++++.+++..++.....       ..|  +.+++++..++++.+.   .-.|.+-..+
T Consensus       695 ~~~~~~~f~peflnRid~ii~F~pL~~~~l~~Iv~~~l~~l~~rl~~~~i~l~~~~~~~~~La~~~~~~~~GAR~l~r~i  774 (821)
T CHL00095        695 NEELKQFFRPEFLNRLDEIIVFRQLTKNDVWEIAEIMLKNLFKRLNEQGIQLEVTERIKTLLIEEGYNPLYGARPLRRAI  774 (821)
T ss_pred             HHHHHHhcCHHHhccCCeEEEeCCCCHHHHHHHHHHHHHHHHHHHHHCCcEEEECHHHHHHHHHhcCCCCCChhhHHHHH
Confidence                   3 5689999 8999999999999888765443       233  5788999999998742   1245444444


Q ss_pred             HHH
Q 042716           99 EAS  101 (137)
Q Consensus        99 ~~~  101 (137)
                      +..
T Consensus       775 ~~~  777 (821)
T CHL00095        775 MRL  777 (821)
T ss_pred             HHH
Confidence            433

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

Probab=98.22  E-value=1.4e-06  Score=74.10  Aligned_cols=99  Identities=15%  Similarity=0.207  Sum_probs=75.4

Q ss_pred             CcccccCcCCHHH----HHHHHHHHHhcc---------------CCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHH
Q 042716            1 IILCEADKLSTDA----LLYMRWLLERYK---------------GLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~----~~~L~~~le~~~---------------~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i   60 (137)
                      ++|||+|.|+...    ..||+.+++--.               +++-||+|+|+...| .||+.|..++++..++.++-
T Consensus       421 ~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTANsl~tIP~PLlDRMEiI~lsgYt~~EK  500 (782)
T COG0466         421 FLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATANSLDTIPAPLLDRMEVIRLSGYTEDEK  500 (782)
T ss_pred             EEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccchhheEEEeecCccccCChHHhcceeeeeecCCChHHH
Confidence            5799999997653    889999986211               255699999999999 99999999999999999998


Q ss_pred             HHHHHHH-----HHHcC-----CCCCHHHHHHHHHHcCC--cHHHHHHHHH
Q 042716           61 VEVLEFI-----AEQEG-----IQLPHQLAEKIADNSKN--NLRQAIRSFE   99 (137)
Q Consensus        61 ~~~l~~i-----~~~eg-----i~i~~~~l~~i~~~~~g--d~R~aln~L~   99 (137)
                      ..+.++.     .+..|     +.++++++..|+++..+  -.|.+-.-+.
T Consensus       501 l~IAk~~LiPk~~~~~gL~~~el~i~d~ai~~iI~~YTREAGVR~LeR~i~  551 (782)
T COG0466         501 LEIAKRHLIPKQLKEHGLKKGELTITDEAIKDIIRYYTREAGVRNLEREIA  551 (782)
T ss_pred             HHHHHHhcchHHHHHcCCCccceeecHHHHHHHHHHHhHhhhhhHHHHHHH
Confidence            8877653     34444     46899999999987532  2444444443

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.21  E-value=1.4e-05  Score=66.59  Aligned_cols=59  Identities=22%  Similarity=0.232  Sum_probs=53.3

Q ss_pred             hhcceeeEecCCCHHHHHHHHHHHHHHcCCCCC------HHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           44 KSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLP------HQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        44 ~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~------~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      .-|...+.|.|+.+.-+.+.|..||..|+...+      ...++.++..+.||+|.|+|+||..+
T Consensus       256 ~~ri~~IsFNPIa~T~MKK~L~ric~~e~~~~s~~k~~~~~~v~~i~~~s~GDIRsAInsLQlss  320 (634)
T KOG1970|consen  256 EPRISNISFNPIAPTIMKKFLKRICRIEANKKSGIKVPDTAEVELICQGSGGDIRSAINSLQLSS  320 (634)
T ss_pred             ccCcceEeecCCcHHHHHHHHHHHHHHhcccccCCcCchhHHHHHHHHhcCccHHHHHhHhhhhc
Confidence            344578999999999999999999999998888      67789999999999999999999985

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=98.21  E-value=1.6e-06  Score=70.77  Aligned_cols=100  Identities=20%  Similarity=0.244  Sum_probs=77.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-CCce--EEEEeCCCC---Cc-hhhhhcc----eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-GLNK--VFFCCSDVS---KL-QPIKSLC----TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-~~~~--~Il~~n~~~---~i-~~l~SRc----~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      +++||.|.|....+..|+.+.|-+. .+.+  +|-++|...   .. +.|..||    .++.|+|++.+|+..+|++...
T Consensus       260 lVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~  339 (529)
T KOG2227|consen  260 LVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLS  339 (529)
T ss_pred             EEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHHh
Confidence            5789999999888999888887653 2344  445567664   35 8999976    5899999999999999998877


Q ss_pred             HcCCCCC-HHHHHHHHHH---cCCcHHHHHHHHHH
Q 042716           70 QEGIQLP-HQLAEKIADN---SKNNLRQAIRSFEA  100 (137)
Q Consensus        70 ~egi~i~-~~~l~~i~~~---~~gd~R~aln~L~~  100 (137)
                      .+-...- +.+++..+.-   ..||+|+|+..++.
T Consensus       340 ~~~t~~~~~~Aie~~ArKvaa~SGDlRkaLdv~R~  374 (529)
T KOG2227|consen  340 EESTSIFLNAAIELCARKVAAPSGDLRKALDVCRR  374 (529)
T ss_pred             cccccccchHHHHHHHHHhccCchhHHHHHHHHHH
Confidence            7655433 4477777653   57999999999983

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.20  E-value=1.8e-05  Score=69.55  Aligned_cols=102  Identities=16%  Similarity=0.236  Sum_probs=77.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------------------------CCc-hhh
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------------------------SKL-QPI   43 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------------------------~~i-~~l   43 (137)
                      ++|||+|.+++..++.|+.++++..           .++.||+|||..                         ... |.|
T Consensus       674 LllDEieka~~~v~~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TSN~g~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEL  753 (857)
T PRK10865        674 ILLDEVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEF  753 (857)
T ss_pred             EEEeehhhCCHHHHHHHHHHHhhCceecCCceEEeecccEEEEeCCcchHHHHHhccccchHHHHHHHHHHHcccccHHH
Confidence            5899999999999999999998642           345589999862                         125 789


Q ss_pred             hhcc-eeeEecCCCHHHHHHHHHHHHHH-------cC--CCCCHHHHHHHHHHcCC---cHHHHHHHHHHHH
Q 042716           44 KSLC-TVIQLLPPSKQEIVEVLEFIAEQ-------EG--IQLPHQLAEKIADNSKN---NLRQAIRSFEASR  102 (137)
Q Consensus        44 ~SRc-~~i~~~~~~~~~i~~~l~~i~~~-------eg--i~i~~~~l~~i~~~~~g---d~R~aln~L~~~~  102 (137)
                      ++|+ .++.|.|++.+++..++.....+       .|  +.++++++.+|++....   ..|.+-+.++...
T Consensus       754 lnRld~iivF~PL~~edl~~Iv~~~L~~l~~rl~~~gi~l~is~~al~~L~~~gy~~~~GARpL~r~I~~~i  825 (857)
T PRK10865        754 INRIDEVVVFHPLGEQHIASIAQIQLQRLYKRLEERGYEIHISDEALKLLSENGYDPVYGARPLKRAIQQQI  825 (857)
T ss_pred             HHhCCeeEecCCCCHHHHHHHHHHHHHHHHHHHHhCCCcCcCCHHHHHHHHHcCCCccCChHHHHHHHHHHH
Confidence            9999 89999999999988876654432       24  46799999999986532   3666666666554

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.18  E-value=1.7e-05  Score=69.71  Aligned_cols=103  Identities=12%  Similarity=0.203  Sum_probs=81.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCCC-------------------------Cc-hhh
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDVS-------------------------KL-QPI   43 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~~-------------------------~i-~~l   43 (137)
                      +++||+|.+++..++.|+.++++..           .++.||+|||-..                         .. |.|
T Consensus       671 lllDeieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~g~~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel  750 (852)
T TIGR03346       671 VLFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELAGGDDYEEMREAVMEVLRAHFRPEF  750 (852)
T ss_pred             EEEeccccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCcchHhHhhhcccccHHHHHHHHHHHHHhhcCHHH
Confidence            5899999999999999999998752           4566999998621                         14 678


Q ss_pred             hhcc-eeeEecCCCHHHHHHHHHHHH-------HHcC--CCCCHHHHHHHHHHc---CCcHHHHHHHHHHHHh
Q 042716           44 KSLC-TVIQLLPPSKQEIVEVLEFIA-------EQEG--IQLPHQLAEKIADNS---KNNLRQAIRSFEASRQ  103 (137)
Q Consensus        44 ~SRc-~~i~~~~~~~~~i~~~l~~i~-------~~eg--i~i~~~~l~~i~~~~---~gd~R~aln~L~~~~~  103 (137)
                      .+|+ .++.|.|++.+++.+++....       ...|  +.++++++.+|++..   .+..|.+-+.++....
T Consensus       751 ~~Rid~IivF~PL~~e~l~~I~~l~L~~l~~~l~~~~~~l~i~~~a~~~L~~~~~~~~~gaR~L~~~i~~~i~  823 (852)
T TIGR03346       751 LNRIDEIVVFHPLGREQIARIVEIQLGRLRKRLAERKITLELSDAALDFLAEAGYDPVYGARPLKRAIQREIE  823 (852)
T ss_pred             hcCcCeEEecCCcCHHHHHHHHHHHHHHHHHHHHHCCCeecCCHHHHHHHHHhCCCCCCCchhHHHHHHHHHH
Confidence            8888 799999999998887765433       2233  578999999999974   4889999999887763

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.

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.11  E-value=2.1e-05  Score=63.55  Aligned_cols=106  Identities=15%  Similarity=0.163  Sum_probs=79.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHh-----------ccCCceEEEEeCCCC--Cc-h--hhhhcce--eeEecCCCHH--HH
Q 042716            1 IILCEADKLSTDALLYMRWLLER-----------YKGLNKVFFCCSDVS--KL-Q--PIKSLCT--VIQLLPPSKQ--EI   60 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~-----------~~~~~~~Il~~n~~~--~i-~--~l~SRc~--~i~~~~~~~~--~i   60 (137)
                      +|+||+|.|.++.|..|++++|+           .+.++++|++|+...  .+ .  ++..|+.  .++++++..-  |+
T Consensus       177 LfLDEI~~LP~~~Q~kLl~~le~g~~~rvG~~~~~~~dVRli~AT~~~l~~~~~~g~dl~~rl~~~~I~LPpLrER~~Di  256 (403)
T COG1221         177 LFLDEIHRLPPEGQEKLLRVLEEGEYRRVGGSQPRPVDVRLICATTEDLEEAVLAGADLTRRLNILTITLPPLRERKEDI  256 (403)
T ss_pred             EehhhhhhCCHhHHHHHHHHHHcCceEecCCCCCcCCCceeeeccccCHHHHHHhhcchhhhhcCceecCCChhhchhhH
Confidence            58999999999999999999998           456788999988773  46 7  9999885  4555555442  33


Q ss_pred             H----HHHHHHHHHcCCCCC---HHHHHHHHHH-cCCcHHHHHHHHHHHHhcCC
Q 042716           61 V----EVLEFIAEQEGIQLP---HQLAEKIADN-SKNNLRQAIRSFEASRQMNY  106 (137)
Q Consensus        61 ~----~~l~~i~~~egi~i~---~~~l~~i~~~-~~gd~R~aln~L~~~~~~~~  106 (137)
                      .    -.++..|++-|..++   ++++..+..+ ..|++|...|.++.......
T Consensus       257 ~~L~e~Fl~~~~~~l~~~~~~~~~~a~~~L~~y~~pGNirELkN~Ve~~~~~~~  310 (403)
T COG1221         257 LLLAEHFLKSEARRLGLPLSVDSPEALRALLAYDWPGNIRELKNLVERAVAQAS  310 (403)
T ss_pred             HHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCCCcHHHHHHHHHHHHHHhc
Confidence            3    334566777777544   4667776665 79999999999998877654

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=98.10  E-value=3.9e-06  Score=71.62  Aligned_cols=87  Identities=17%  Similarity=0.202  Sum_probs=69.3

Q ss_pred             CcccccCcCCHH----HHHHHHHHHHhcc---------------CCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHH
Q 042716            1 IILCEADKLSTD----ALLYMRWLLERYK---------------GLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~----~~~~L~~~le~~~---------------~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i   60 (137)
                      |+|||+|.+..+    ...||+.+++--.               +.+-||+|+|....| +||+.|..++.+..+..++-
T Consensus       509 iLiDEvDKlG~g~qGDPasALLElLDPEQNanFlDHYLdVp~DLSkVLFicTAN~idtIP~pLlDRMEvIelsGYv~eEK  588 (906)
T KOG2004|consen  509 ILIDEVDKLGSGHQGDPASALLELLDPEQNANFLDHYLDVPVDLSKVLFICTANVIDTIPPPLLDRMEVIELSGYVAEEK  588 (906)
T ss_pred             EEeehhhhhCCCCCCChHHHHHHhcChhhccchhhhccccccchhheEEEEeccccccCChhhhhhhheeeccCccHHHH
Confidence            579999999743    3778888886211               245699999999999 99999999999999999998


Q ss_pred             HHHHHHHH-----HH-----cCCCCCHHHHHHHHHHc
Q 042716           61 VEVLEFIA-----EQ-----EGIQLPHQLAEKIADNS   87 (137)
Q Consensus        61 ~~~l~~i~-----~~-----egi~i~~~~l~~i~~~~   87 (137)
                      .++.++..     +.     +.++++++++..++++.
T Consensus       589 v~IA~~yLip~a~~~~gl~~e~v~is~~al~~lI~~Y  625 (906)
T KOG2004|consen  589 VKIAERYLIPQALKDCGLKPEQVKISDDALLALIERY  625 (906)
T ss_pred             HHHHHHhhhhHHHHHcCCCHHhcCccHHHHHHHHHHH
Confidence            88876543     33     34689999999988764

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

Probab=98.08  E-value=2.1e-05  Score=68.01  Aligned_cols=102  Identities=11%  Similarity=0.184  Sum_probs=77.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCCC-------------------------Cc-hhh
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDVS-------------------------KL-QPI   43 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~~-------------------------~i-~~l   43 (137)
                      |+|||+|.++++.++.|+.++++..           .++.||+|+|-..                         .+ |.+
T Consensus       557 vllDEieka~~~~~~~Ll~~ld~g~~~d~~g~~vd~~~~iii~Tsn~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef  636 (731)
T TIGR02639       557 LLLDEIEKAHPDIYNILLQVMDYATLTDNNGRKADFRNVILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEF  636 (731)
T ss_pred             EEEechhhcCHHHHHHHHHhhccCeeecCCCcccCCCCCEEEECCCcchhhhhhccCCcchhhhHHHHHHHHHhhcChHH
Confidence            5899999999999999999999641           3566888887531                         25 788


Q ss_pred             hhcc-eeeEecCCCHHHHHHHHHHHHH-------HcC--CCCCHHHHHHHHHHcC---CcHHHHHHHHHHHH
Q 042716           44 KSLC-TVIQLLPPSKQEIVEVLEFIAE-------QEG--IQLPHQLAEKIADNSK---NNLRQAIRSFEASR  102 (137)
Q Consensus        44 ~SRc-~~i~~~~~~~~~i~~~l~~i~~-------~eg--i~i~~~~l~~i~~~~~---gd~R~aln~L~~~~  102 (137)
                      ++|+ .++.|++++.+++.+++....+       ..|  +.++++++.+|++.+.   ...|.+-..++...
T Consensus       637 ~~Rid~Vi~F~pLs~e~l~~Iv~~~L~~l~~~l~~~~~~l~i~~~a~~~La~~~~~~~~GaR~l~r~i~~~~  708 (731)
T TIGR02639       637 RNRLDAIIHFNPLSEEVLEKIVQKFVDELSKQLNEKNIKLELTDDAKKYLAEKGYDEEFGARPLARVIQEEI  708 (731)
T ss_pred             HhcCCeEEEcCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEeCHHHHHHHHHhCCCcccCchHHHHHHHHHh
Confidence            9998 6999999999999988876553       222  6789999999998642   33566655555444

>PRK15115 response regulator GlrR; Provisional

Probab=98.07  E-value=6.1e-05  Score=61.12  Aligned_cols=105  Identities=12%  Similarity=0.160  Sum_probs=73.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcce--eeEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLCT--VIQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc~--~i~~~~~~~--   57 (137)
                      ++|||+|.|+...|..|++.+++..           .++++|++|+..       ..+ +.|..|..  .+.++|+.+  
T Consensus       232 l~l~~i~~l~~~~q~~L~~~l~~~~~~~~g~~~~~~~~~rii~~~~~~l~~~~~~~~f~~~l~~~l~~~~i~lPpLr~R~  311 (444)
T PRK15115        232 LFLDEIGDMPAPLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHRDLPKAMARGEFREDLYYRLNVVSLKIPALAERT  311 (444)
T ss_pred             EEEEccccCCHHHHHHHHHHHhhCCEEeCCCCceeeeeEEEEEeCCCCHHHHHHcCCccHHHHHhhceeeecCCChHhcc
Confidence            5899999999999999999998642           145788888754       123 45555543  344444433  


Q ss_pred             HHHHHH----HHHHHHHcC---CCCCHHHHHHHHHHc-CCcHHHHHHHHHHHHhcC
Q 042716           58 QEIVEV----LEFIAEQEG---IQLPHQLAEKIADNS-KNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        58 ~~i~~~----l~~i~~~eg---i~i~~~~l~~i~~~~-~gd~R~aln~L~~~~~~~  105 (137)
                      +++...    +...+.+.|   ..++++++..+..+. +||+|++.|.++.+....
T Consensus       312 eDi~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~WpgNvreL~~~i~~~~~~~  367 (444)
T PRK15115        312 EDIPLLANHLLRQAAERHKPFVRAFSTDAMKRLMTASWPGNVRQLVNVIEQCVALT  367 (444)
T ss_pred             ccHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCCCChHHHHHHHHHHHHHhC
Confidence            344333    333344334   248999999999987 999999999999877543

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

Probab=98.07  E-value=1.3e-05  Score=69.65  Aligned_cols=100  Identities=14%  Similarity=0.187  Sum_probs=76.5

Q ss_pred             CcccccCcCC---------HHHHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCCHHHHHHHHH
Q 042716            1 IILCEADKLS---------TDALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPSKQEIVEVLE   65 (137)
Q Consensus         1 iiiDEid~l~---------~~~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~~~~i~~~l~   65 (137)
                      +||||+|.|.         .+..+.|...++  .+...+|.+||...     .. ++|.+|+..+.+++|+.++...+|+
T Consensus       282 LfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~--~g~i~vIgATt~~E~~~~~~~D~AL~rRFq~I~v~ePs~~~~~~IL~  359 (758)
T PRK11034        282 LFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIIN  359 (758)
T ss_pred             EEeccHHHHhccCCCCCcHHHHHHHHHHHHh--CCCeEEEecCChHHHHHHhhccHHHHhhCcEEEeCCCCHHHHHHHHH
Confidence            5899999982         123455667776  55667777777653     35 8999999999999999999999998


Q ss_pred             HHH----HHcCCCCCHHHHHHHHHHcCC------cHHHHHHHHHHHH
Q 042716           66 FIA----EQEGIQLPHQLAEKIADNSKN------NLRQAIRSFEASR  102 (137)
Q Consensus        66 ~i~----~~egi~i~~~~l~~i~~~~~g------d~R~aln~L~~~~  102 (137)
                      .+.    ...++.++++++..+++.+.+      =+.+|+.+|+.+.
T Consensus       360 ~~~~~ye~~h~v~i~~~al~~a~~ls~ryi~~r~lPdKaidlldea~  406 (758)
T PRK11034        360 GLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAG  406 (758)
T ss_pred             HHHHHhhhccCCCcCHHHHHHHHHHhhccccCccChHHHHHHHHHHH
Confidence            654    345789999999988876554      2458999998765

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.07  E-value=1.8e-05  Score=69.58  Aligned_cols=101  Identities=14%  Similarity=0.158  Sum_probs=78.9

Q ss_pred             CcccccCcCCH--------HHHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKLST--------DALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l~~--------~~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~~~~i~~~l~~   66 (137)
                      +||||+|.|.+        ++++.|...++  .+..++|.+|+...     .. +++.+|++.+.+..|+.++...+|+.
T Consensus       270 LfIDEih~l~~~g~~~~~~d~~~~Lk~~l~--~g~i~~IgaTt~~e~r~~~~~d~al~rRf~~i~v~~p~~~~~~~iL~~  347 (852)
T TIGR03346       270 LFIDELHTLVGAGKAEGAMDAGNMLKPALA--RGELHCIGATTLDEYRKYIEKDAALERRFQPVFVDEPTVEDTISILRG  347 (852)
T ss_pred             EEeccHHHhhcCCCCcchhHHHHHhchhhh--cCceEEEEeCcHHHHHHHhhcCHHHHhcCCEEEeCCCCHHHHHHHHHH
Confidence            58999999963        24667777776  56677888887662     36 89999999999999999999998876


Q ss_pred             HHHH----cCCCCCHHHHHHHHHHcC---Cc---HHHHHHHHHHHHh
Q 042716           67 IAEQ----EGIQLPHQLAEKIADNSK---NN---LRQAIRSFEASRQ  103 (137)
Q Consensus        67 i~~~----egi~i~~~~l~~i~~~~~---gd---~R~aln~L~~~~~  103 (137)
                      ...+    .++.++++++...+..+.   +|   +.+|+.+|+.+..
T Consensus       348 ~~~~~e~~~~v~~~d~~i~~~~~ls~~yi~~r~lPdkAidlld~a~a  394 (852)
T TIGR03346       348 LKERYEVHHGVRITDPAIVAAATLSHRYITDRFLPDKAIDLIDEAAA  394 (852)
T ss_pred             HHHHhccccCCCCCHHHHHHHHHhccccccccCCchHHHHHHHHHHH
Confidence            6543    467889999988887664   44   7899999987653

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.

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=98.04  E-value=4.5e-05  Score=61.91  Aligned_cols=106  Identities=12%  Similarity=0.097  Sum_probs=76.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcce--eeEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLCT--VIQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc~--~i~~~~~~~--   57 (137)
                      ++|||+|.|+...|..|++++++..           .++++|++++..       ..+ +.|..|+.  .+.++|+.+  
T Consensus       237 l~l~~i~~l~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~~~~~L~~~l~~~~i~lPpLr~R~  316 (445)
T TIGR02915       237 LFLDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIAEGTFREDLFYRIAEISITIPPLRSRD  316 (445)
T ss_pred             EEEechhhCCHHHHHHHHHHHhhCeEEeCCCCceeeeceEEEEecCCCHHHHHHcCCccHHHHHHhccceecCCCchhch
Confidence            5899999999999999999998632           256889988765       235 67878875  455555544  


Q ss_pred             HHHHH----HHHHHHHHcC---CCCCHHHHHHHHHHc-CCcHHHHHHHHHHHHhcCC
Q 042716           58 QEIVE----VLEFIAEQEG---IQLPHQLAEKIADNS-KNNLRQAIRSFEASRQMNY  106 (137)
Q Consensus        58 ~~i~~----~l~~i~~~eg---i~i~~~~l~~i~~~~-~gd~R~aln~L~~~~~~~~  106 (137)
                      +++..    .+.+.+.+.|   ..++++++..+..+. +||+|.+-|.++.+.....
T Consensus       317 ~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNvreL~~~i~~a~~~~~  373 (445)
T TIGR02915       317 GDAVLLANAFLERFARELKRKTKGFTDDALRALEAHAWPGNVRELENKVKRAVIMAE  373 (445)
T ss_pred             hhHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHhCCCCChHHHHHHHHHHHHHhCC
Confidence            23332    3344444444   468999999998874 8999999999998876443

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=98.03  E-value=5.6e-05  Score=61.61  Aligned_cols=106  Identities=16%  Similarity=0.106  Sum_probs=80.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCCC-------Cc-hhhhhcce--eeEecCCC--H
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDVS-------KL-QPIKSLCT--VIQLLPPS--K   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~~-------~i-~~l~SRc~--~i~~~~~~--~   57 (137)
                      ++|||+|.|+...|..|+.++++..           .++++|++++...       .. +.|..|..  .+.++|+.  .
T Consensus       232 l~l~ei~~l~~~~q~~ll~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~f~~~L~~rl~~~~i~lPpLr~R~  311 (463)
T TIGR01818       232 LFLDEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFREDLFHRLNVIRIHLPPLRERR  311 (463)
T ss_pred             EEEEchhhCCHHHHHHHHHHHhcCcEEECCCCceeeeeeEEEEeCCCCHHHHHHcCCcHHHHHHHhCcceecCCCcccch
Confidence            5899999999999999999998632           2457888887552       35 68888864  67777777  5


Q ss_pred             HHHHHHHH----HHHHHcC---CCCCHHHHHHHHHH-cCCcHHHHHHHHHHHHhcCC
Q 042716           58 QEIVEVLE----FIAEQEG---IQLPHQLAEKIADN-SKNNLRQAIRSFEASRQMNY  106 (137)
Q Consensus        58 ~~i~~~l~----~i~~~eg---i~i~~~~l~~i~~~-~~gd~R~aln~L~~~~~~~~  106 (137)
                      +++...+.    +.+.+.|   ..++++++..+..+ -.||+|.+-|.++.+...+.
T Consensus       312 ~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNvreL~~~~~~~~~~~~  368 (463)
T TIGR01818       312 EDIPRLARHFLALAARELDVEPKLLDPEALERLKQLRWPGNVRQLENLCRWLTVMAS  368 (463)
T ss_pred             hhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCCCChHHHHHHHHHHHHHhCC
Confidence            66665554    3444444   46899999999887 58999999999998876543

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

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

Probab=98.02  E-value=1.4e-05  Score=61.56  Aligned_cols=86  Identities=17%  Similarity=0.203  Sum_probs=66.9

Q ss_pred             CcccccCcCCH------------HHHHHHHHHHHhccC--CceEEEEeCCCCCc-hhhhhcc-eeeEecCCCHHHHHHHH
Q 042716            1 IILCEADKLST------------DALLYMRWLLERYKG--LNKVFFCCSDVSKL-QPIKSLC-TVIQLLPPSKQEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l~~------------~~~~~L~~~le~~~~--~~~~Il~~n~~~~i-~~l~SRc-~~i~~~~~~~~~i~~~l   64 (137)
                      +||||.|.+.-            +..|||+.-|+-...  ++.+|.+||.+.-+ +++|||+ ..+.|.-|++++....|
T Consensus       214 vFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGVvtIaaTN~p~~LD~aiRsRFEeEIEF~LP~~eEr~~il  293 (368)
T COG1223         214 VFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAATNRPELLDPAIRSRFEEEIEFKLPNDEERLEIL  293 (368)
T ss_pred             EEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCceEEEeecCChhhcCHHHHhhhhheeeeeCCChHHHHHHH
Confidence            58999998732            236788877765443  34577888888889 9999999 47999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHc
Q 042716           65 EFIAEQEGIQLPHQLAEKIADNS   87 (137)
Q Consensus        65 ~~i~~~egi~i~~~~l~~i~~~~   87 (137)
                      ...+++--+.++-. +.+++..+
T Consensus       294 e~y~k~~Plpv~~~-~~~~~~~t  315 (368)
T COG1223         294 EYYAKKFPLPVDAD-LRYLAAKT  315 (368)
T ss_pred             HHHHHhCCCccccC-HHHHHHHh
Confidence            99998887776655 56666553

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

Probab=98.01  E-value=2.8e-05  Score=56.80  Aligned_cols=94  Identities=27%  Similarity=0.239  Sum_probs=62.8

Q ss_pred             CcccccCcCC------HHHHHHHHHHHHh--ccCCceEEEEeCCCC------Cc-hhhhhcceeeEecCCCHHHHHHHHH
Q 042716            1 IILCEADKLS------TDALLYMRWLLER--YKGLNKVFFCCSDVS------KL-QPIKSLCTVIQLLPPSKQEIVEVLE   65 (137)
Q Consensus         1 iiiDEid~l~------~~~~~~L~~~le~--~~~~~~~Il~~n~~~------~i-~~l~SRc~~i~~~~~~~~~i~~~l~   65 (137)
                      |+|||+|.+.      +.....|...++.  ...+..+|+++....      .- .++..|+..+.+++++.++..+.+.
T Consensus       122 iviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v~~~S~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~e~~~~~~  201 (234)
T PF01637_consen  122 IVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNVSIVITGSSDSLMEEFLDDKSPLFGRFSHIELKPLSKEEAREFLK  201 (234)
T ss_dssp             EEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTEEEEEEESSHHHHHHTT-TTSTTTT---EEEE----HHHHHHHHH
T ss_pred             EEEecHHHHhhcccchHHHHHHHHHHHhhccccCCceEEEECCchHHHHHhhcccCccccccceEEEeeCCHHHHHHHHH
Confidence            5899999998      4557778888886  234455666665431      22 5788999889999999999999999


Q ss_pred             HHHHHcCCCC--CHHHHHHHHHHcCCcHHHHH
Q 042716           66 FIAEQEGIQL--PHQLAEKIADNSKNNLRQAI   95 (137)
Q Consensus        66 ~i~~~egi~i--~~~~l~~i~~~~~gd~R~al   95 (137)
                      ...... .++  +++.+..+...++|.++.+.
T Consensus       202 ~~~~~~-~~~~~~~~~~~~i~~~~gG~P~~l~  232 (234)
T PF01637_consen  202 ELFKEL-IKLPFSDEDIEEIYSLTGGNPRYLQ  232 (234)
T ss_dssp             HHHHCC-------HHHHHHHHHHHTT-HHHHH
T ss_pred             HHHHHh-hcccCCHHHHHHHHHHhCCCHHHHh
Confidence            876665 655  99999999999999998764

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

>CHL00176 ftsH cell division protein; Validated

Probab=98.00  E-value=6.5e-05  Score=64.19  Aligned_cols=95  Identities=18%  Similarity=0.231  Sum_probs=68.3

Q ss_pred             CcccccCcCC-----------HHHHHHHHHHHHh---cc--CCceEEEEeCCCCCc-hhhhhcc---eeeEecCCCHHHH
Q 042716            1 IILCEADKLS-----------TDALLYMRWLLER---YK--GLNKVFFCCSDVSKL-QPIKSLC---TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~-----------~~~~~~L~~~le~---~~--~~~~~Il~~n~~~~i-~~l~SRc---~~i~~~~~~~~~i   60 (137)
                      +||||+|.+.           .+.++.|..++++   +.  .+..+|.+||.+..+ +++++++   ..+.|..|+.++.
T Consensus       279 LfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R  358 (638)
T CHL00176        279 VFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGR  358 (638)
T ss_pred             EEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHH
Confidence            5899999984           2334455555543   22  345688888888888 8888743   6899999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCC----cHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKN----NLRQAIR   96 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~g----d~R~aln   96 (137)
                      ..+++..+++..+ .++..+..++..+.|    |++.++|
T Consensus       359 ~~IL~~~l~~~~~-~~d~~l~~lA~~t~G~sgaDL~~lvn  397 (638)
T CHL00176        359 LDILKVHARNKKL-SPDVSLELIARRTPGFSGADLANLLN  397 (638)
T ss_pred             HHHHHHHHhhccc-chhHHHHHHHhcCCCCCHHHHHHHHH
Confidence            9999998877543 245567889988777    5555555

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=97.98  E-value=5.8e-05  Score=63.01  Aligned_cols=105  Identities=15%  Similarity=0.172  Sum_probs=80.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCCC-------Cc-hhhhhcc--eeeEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDVS-------KL-QPIKSLC--TVIQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~~-------~i-~~l~SRc--~~i~~~~~~~--   57 (137)
                      ++|||+|.|+...|..|+.++++..           .++++|++|+...       .. ++|..|.  ..+.++|+.+  
T Consensus       302 L~LdeI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~vRiI~st~~~l~~l~~~g~f~~dL~~rL~~~~i~lPpLreR~  381 (520)
T PRK10820        302 VLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGEFREDLYYRLNVLTLNLPPLRDRP  381 (520)
T ss_pred             EEEeChhhCCHHHHHHHHHHHhcCCcccCCCCcceeeeeEEEEecCCCHHHHHHcCCccHHHHhhcCeeEEeCCCcccCh
Confidence            5899999999999999999998631           2457888887652       35 7899995  5677777766  


Q ss_pred             HHHHHH----HHHHHHHcCC---CCCHHHHHHHHHH-cCCcHHHHHHHHHHHHhcC
Q 042716           58 QEIVEV----LEFIAEQEGI---QLPHQLAEKIADN-SKNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        58 ~~i~~~----l~~i~~~egi---~i~~~~l~~i~~~-~~gd~R~aln~L~~~~~~~  105 (137)
                      +++...    +.+.+.+.|.   .++++++..+..+ -.||+|++-|.++.+....
T Consensus       382 ~Di~~L~~~fl~~~~~~~g~~~~~ls~~a~~~L~~y~WPGNvreL~nvl~~a~~~~  437 (520)
T PRK10820        382 QDIMPLTELFVARFADEQGVPRPKLAADLNTVLTRYGWPGNVRQLKNAIYRALTQL  437 (520)
T ss_pred             hHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHhcCCCCCHHHHHHHHHHHHHHhC
Confidence            344433    4555666654   6899999999888 8999999999999887543

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=97.98  E-value=9.2e-05  Score=59.86  Aligned_cols=104  Identities=12%  Similarity=0.109  Sum_probs=73.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCCC-------Cc-hhhhhcceee--EecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDVS-------KL-QPIKSLCTVI--QLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~~-------~i-~~l~SRc~~i--~~~~~~~--   57 (137)
                      ++|||+|.|+...|..|+..+++..           .++++|++++...       .+ +.|..|+..+  .++|+..  
T Consensus       237 l~ldei~~l~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~~~~~~~~~~~~~~l~~~l~~~~i~~ppLreR~  316 (441)
T PRK10365        237 LFLDEIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVAIEVPSLRQRR  316 (441)
T ss_pred             EEEeccccCCHHHHHHHHHHHccCcEEeCCCCceeeeceEEEEeCCCCHHHHHHcCCchHHHHHHhccceecCCChhhcc
Confidence            5899999999999999999998632           1456888876652       24 6677776544  4444443  


Q ss_pred             HHHHHHH----HHHHHHcC---CCCCHHHHHHHHHHc-CCcHHHHHHHHHHHHhc
Q 042716           58 QEIVEVL----EFIAEQEG---IQLPHQLAEKIADNS-KNNLRQAIRSFEASRQM  104 (137)
Q Consensus        58 ~~i~~~l----~~i~~~eg---i~i~~~~l~~i~~~~-~gd~R~aln~L~~~~~~  104 (137)
                      +++...+    .+.+.+.|   ..++++++..+..+. +||+|.+.|.++.+...
T Consensus       317 ~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgN~reL~~~~~~~~~~  371 (441)
T PRK10365        317 EDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAVERAVVL  371 (441)
T ss_pred             hhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCCCCHHHHHHHHHHHHHHh
Confidence            2343333    33344333   358999999999986 99999999999987654

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=97.97  E-value=9.5e-05  Score=62.96  Aligned_cols=105  Identities=10%  Similarity=0.049  Sum_probs=77.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcc--eeeEecCCCHH-
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLC--TVIQLLPPSKQ-   58 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc--~~i~~~~~~~~-   58 (137)
                      ++|||+|.|....|..|++++++..           -++++|++|+..       ..+ +.|..|.  ..+.++|+.+- 
T Consensus       420 L~ldei~~l~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~t~~~l~~~~~~~~f~~dL~~~l~~~~i~lPpLreR~  499 (638)
T PRK11388        420 LFLEKVEYLSPELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNRFSRQLYYALHAFEITIPPLRMRR  499 (638)
T ss_pred             EEEcChhhCCHHHHHHHHHHHhcCcEEeCCCCceEEeeEEEEEeccCCHHHHHhcCCChHHHhhhhceeEEeCCChhhhh
Confidence            5899999999999999999998542           145788888754       235 6777775  45666666653 


Q ss_pred             -HHHHHHHHH----HHHcC--CCCCHHHHHHHHHHc-CCcHHHHHHHHHHHHhcC
Q 042716           59 -EIVEVLEFI----AEQEG--IQLPHQLAEKIADNS-KNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        59 -~i~~~l~~i----~~~eg--i~i~~~~l~~i~~~~-~gd~R~aln~L~~~~~~~  105 (137)
                       |+...+...    +.+.|  +.++++++..+..+. +||+|.+.|.++.+....
T Consensus       500 ~Di~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvreL~~~l~~~~~~~  554 (638)
T PRK11388        500 EDIPALVNNKLRSLEKRFSTRLKIDDDALARLVSYRWPGNDFELRSVIENLALSS  554 (638)
T ss_pred             hHHHHHHHHHHHHHHHHhCCCCCcCHHHHHHHHcCCCCChHHHHHHHHHHHHHhC
Confidence             454444433    33322  568999999999986 999999999999877543

>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]

Probab=97.95  E-value=0.0001  Score=58.27  Aligned_cols=124  Identities=15%  Similarity=0.147  Sum_probs=89.3

Q ss_pred             HHHHHHHHHHHHhcc-CCceEEEEeCCCCC---c-hhhhhc--ceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 042716           11 TDALLYMRWLLERYK-GLNKVFFCCSDVSK---L-QPIKSL--CTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKI   83 (137)
Q Consensus        11 ~~~~~~L~~~le~~~-~~~~~Il~~n~~~~---i-~~l~SR--c~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~l~~i   83 (137)
                      ......+......++ ..+.+++.++...+   . +.+.+-  +.++...+++.+++..|+...+++.|+.+++++++.+
T Consensus        89 ~~~~~~l~~~~~~~p~~~~~l~~~~~kl~~~~~~~k~~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~l~i~~~a~~~L  168 (334)
T COG1466          89 KDKNLALLELAALLPSTDLLLLVESNKLDKAKKLTKWLKKLAKAVVVECKPLDEAELPQWIKKRAKELGLKIDQEAIQLL  168 (334)
T ss_pred             chhHHHHHHHHcCCCCCCEEEEEecCCcchHHHHHHHHHHhccCceEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            344455556665555 44445555555443   3 444443  6689999999999999999999999999999999999


Q ss_pred             HHHcCCcHHHHHHHHHHHHhcCCC--cccCccc--cCC-cHHHHHHHHHHHHhcCC
Q 042716           84 ADNSKNNLRQAIRSFEASRQMNYP--FVEGQVI--LTG-WEDDITNIATKIIEEQS  134 (137)
Q Consensus        84 ~~~~~gd~R~aln~L~~~~~~~~~--~~~~~~~--~~~-~~~~~~~i~~~i~~~~~  134 (137)
                      +...+||++.+.+-++.+.....+  ++.+.+.  ..+ -+...++.++.++.++.
T Consensus       169 ~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~~~~~~~f~l~dail~g~~  224 (334)
T COG1466         169 LEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSDVAEFNIFDLADALLKGDV  224 (334)
T ss_pred             HHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhccccCCHHHHHHHHHCCCH
Confidence            999999999999999988875443  6655554  122 23345677777777664

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=97.90  E-value=0.00016  Score=60.14  Aligned_cols=105  Identities=10%  Similarity=0.100  Sum_probs=78.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcce--eeEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLCT--VIQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc~--~i~~~~~~~--   57 (137)
                      ++|||+|.|....|..|++++++..           .++++|++|+..       ..+ .+|..|..  .+.++|+.+  
T Consensus       285 L~ldeI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~l~~~~~~~~f~~dL~~rl~~~~i~lPpLreR~  364 (509)
T PRK05022        285 LFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRDLREEVRAGRFRADLYHRLSVFPLSVPPLRERG  364 (509)
T ss_pred             EEecChhhCCHHHHHHHHHHHhcCCEeeCCCCcceecceEEEEecCCCHHHHHHcCCccHHHHhcccccEeeCCCchhch
Confidence            5899999999999999999998532           256899999865       235 77888864  456666554  


Q ss_pred             HHHHHHH----HHHHHHcC---CCCCHHHHHHHHHH-cCCcHHHHHHHHHHHHhcC
Q 042716           58 QEIVEVL----EFIAEQEG---IQLPHQLAEKIADN-SKNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        58 ~~i~~~l----~~i~~~eg---i~i~~~~l~~i~~~-~~gd~R~aln~L~~~~~~~  105 (137)
                      +++-..+    .+.+.+.|   +.++++++..+..+ -.||+|.+-|.++.+....
T Consensus       365 eDI~~L~~~fl~~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvrEL~~~i~ra~~~~  420 (509)
T PRK05022        365 DDVLLLAGYFLEQNRARLGLRSLRLSPAAQAALLAYDWPGNVRELEHVISRAALLA  420 (509)
T ss_pred             hhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCCCcHHHHHHHHHHHHHhc
Confidence            3444433    34444433   57999999998887 6899999999999887644

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=97.88  E-value=0.00018  Score=56.75  Aligned_cols=104  Identities=15%  Similarity=0.135  Sum_probs=78.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcc--eeeEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLC--TVIQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc--~~i~~~~~~~--   57 (137)
                      ++|||+|.|+...|..|+.+++...           .++++|++++..       ..+ ++|..|+  ..+.++|+.+  
T Consensus       104 L~l~~i~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~s~~~l~~l~~~g~f~~dL~~~l~~~~i~lPpLReR~  183 (326)
T PRK11608        104 LFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGKFRADLLDRLAFDVVQLPPLRERQ  183 (326)
T ss_pred             EEeCChhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCchhHHHHHHcCCchHHHHHhcCCCEEECCChhhhh
Confidence            5899999999999999999998532           146788888764       236 8888887  4577777765  


Q ss_pred             HHHHHHHH----HHHHHcCC----CCCHHHHHHHHHH-cCCcHHHHHHHHHHHHhc
Q 042716           58 QEIVEVLE----FIAEQEGI----QLPHQLAEKIADN-SKNNLRQAIRSFEASRQM  104 (137)
Q Consensus        58 ~~i~~~l~----~i~~~egi----~i~~~~l~~i~~~-~~gd~R~aln~L~~~~~~  104 (137)
                      +|+...+.    +.+.+.|.    .++++++..+..+ -.||+|.+-|.++.+...
T Consensus       184 eDI~~L~~~fl~~~~~~~~~~~~~~~s~~al~~L~~y~WPGNvrEL~~vl~~a~~~  239 (326)
T PRK11608        184 SDIMLMAEHFAIQMCRELGLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYR  239 (326)
T ss_pred             hhHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHHh
Confidence            35544443    34555443    4799999998886 789999999999987754

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

Probab=97.87  E-value=8e-05  Score=64.75  Aligned_cols=100  Identities=13%  Similarity=0.183  Sum_probs=73.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------------------------CCc-hhh
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------------------------SKL-QPI   43 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------------------------~~i-~~l   43 (137)
                      +++||+|.++++.++.|+.++++..           .++.||+|||.-                         ..+ |.+
T Consensus       561 lllDEieka~~~v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~g~~~~~~~~~g~~~~~~~~~~~~~~~~~f~pef  640 (758)
T PRK11034        561 LLLDEIEKAHPDVFNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEF  640 (758)
T ss_pred             EEeccHhhhhHHHHHHHHHHHhcCeeecCCCceecCCCcEEEEeCCcCHHHHhhcccCcccchhhHHHHHHHHHhcCHHH
Confidence            5899999999999999999999642           356699999822                         125 889


Q ss_pred             hhcc-eeeEecCCCHHHHHHHHHHHH-------HHcCC--CCCHHHHHHHHHHcC---CcHHHHHHHHHH
Q 042716           44 KSLC-TVIQLLPPSKQEIVEVLEFIA-------EQEGI--QLPHQLAEKIADNSK---NNLRQAIRSFEA  100 (137)
Q Consensus        44 ~SRc-~~i~~~~~~~~~i~~~l~~i~-------~~egi--~i~~~~l~~i~~~~~---gd~R~aln~L~~  100 (137)
                      .+|+ .++.|++++.+++..++....       +..|+  .++++++.+|++.+.   ...|.+-+.++.
T Consensus       641 l~Rid~ii~f~~L~~~~l~~I~~~~l~~~~~~l~~~~i~l~~~~~~~~~l~~~~~~~~~GAR~l~r~i~~  710 (758)
T PRK11034        641 RNRLDNIIWFDHLSTDVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPMARVIQD  710 (758)
T ss_pred             HccCCEEEEcCCCCHHHHHHHHHHHHHHHHHHHHHCCCCceECHHHHHHHHHhCCCCCCCCchHHHHHHH
Confidence            9999 589999999999887765432       33354  578999999997642   124444444443

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.87  E-value=5.4e-05  Score=66.34  Aligned_cols=101  Identities=15%  Similarity=0.156  Sum_probs=79.1

Q ss_pred             CcccccCcCCHH--------HHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKLSTD--------ALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l~~~--------~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~~~~i~~~l~~   66 (137)
                      +||||+|.+...        +++.|...+.  .+..++|.+|+...     .. +.+.+|+..+.+..|+.++...+++.
T Consensus       275 LfiDEih~l~~~g~~~g~~~~a~lLkp~l~--rg~l~~IgaTt~~ey~~~ie~D~aL~rRf~~I~v~ep~~~e~~aILr~  352 (821)
T CHL00095        275 LVIDEVHTLIGAGAAEGAIDAANILKPALA--RGELQCIGATTLDEYRKHIEKDPALERRFQPVYVGEPSVEETIEILFG  352 (821)
T ss_pred             EEEecHHHHhcCCCCCCcccHHHHhHHHHh--CCCcEEEEeCCHHHHHHHHhcCHHHHhcceEEecCCCCHHHHHHHHHH
Confidence            589999988542        4677777777  56677888888653     25 89999999999999999998877765


Q ss_pred             HHH----HcCCCCCHHHHHHHHHHcCC---c---HHHHHHHHHHHHh
Q 042716           67 IAE----QEGIQLPHQLAEKIADNSKN---N---LRQAIRSFEASRQ  103 (137)
Q Consensus        67 i~~----~egi~i~~~~l~~i~~~~~g---d---~R~aln~L~~~~~  103 (137)
                      +..    ..++.++++++..++..+.|   |   +++|+.+|+.+..
T Consensus       353 l~~~~e~~~~v~i~deal~~i~~ls~~yi~~r~lPdkaidlld~a~a  399 (821)
T CHL00095        353 LRSRYEKHHNLSISDKALEAAAKLSDQYIADRFLPDKAIDLLDEAGS  399 (821)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHhhccCccccCchHHHHHHHHHHH
Confidence            443    35677999999998887764   3   7889999997653

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.87  E-value=6.9e-05  Score=59.71  Aligned_cols=95  Identities=18%  Similarity=0.221  Sum_probs=64.6

Q ss_pred             CcccccCcCC-----------HHHHHHHHHHHHhc-----cCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLS-----------TDALLYMRWLLERY-----KGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~-----------~~~~~~L~~~le~~-----~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      |+|||+|.+.           ...+..+...+.+.     ..++.+|++||.+..+ ++++.  |+ ..+.|+.|+.++.
T Consensus       219 l~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r  298 (364)
T TIGR01242       219 IFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGR  298 (364)
T ss_pred             EEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHH
Confidence            5899999983           23355566665442     2467799999999888 88874  65 5799999999999


Q ss_pred             HHHHHHHHHHcCCCCCH-HHHHHHHHHcC----CcHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPH-QLAEKIADNSK----NNLRQAIRS   97 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~-~~l~~i~~~~~----gd~R~aln~   97 (137)
                      ..++...+.+.++  ++ -....++..+.    +|++.+.+.
T Consensus       299 ~~Il~~~~~~~~l--~~~~~~~~la~~t~g~sg~dl~~l~~~  338 (364)
T TIGR01242       299 LEILKIHTRKMKL--AEDVDLEAIAKMTEGASGADLKAICTE  338 (364)
T ss_pred             HHHHHHHHhcCCC--CccCCHHHHHHHcCCCCHHHHHHHHHH
Confidence            9999877655443  22 13455665554    366655443

Many proteins may score above the trusted cutoff because an internal

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=97.84  E-value=0.00013  Score=60.45  Aligned_cols=95  Identities=14%  Similarity=0.145  Sum_probs=65.5

Q ss_pred             CcccccCcCCHH--------------HHHHHHHHHHhccC--CceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLSTD--------------ALLYMRWLLERYKG--LNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~--------------~~~~L~~~le~~~~--~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      |||||+|.+...              ..+.|+..|+.+..  +..+|.+||.+..+ +++++  |+ ..+.|+.|+.++.
T Consensus       151 l~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R  230 (495)
T TIGR01241       151 IFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGR  230 (495)
T ss_pred             EEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHH
Confidence            589999998532              23345555554433  34577778888889 99987  54 5799999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcC----CcHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSK----NNLRQAIR   96 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~----gd~R~aln   96 (137)
                      ..+++..+.+.++. ++..+..++..+.    +|++.+++
T Consensus       231 ~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgadl~~l~~  269 (495)
T TIGR01241       231 EEILKVHAKNKKLA-PDVDLKAVARRTPGFSGADLANLLN  269 (495)
T ss_pred             HHHHHHHHhcCCCC-cchhHHHHHHhCCCCCHHHHHHHHH
Confidence            99998877665543 3344667777654    45565555

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.81  E-value=3.4e-05  Score=67.88  Aligned_cols=100  Identities=13%  Similarity=0.109  Sum_probs=76.1

Q ss_pred             CcccccCcCCHH--------HHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKLSTD--------ALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l~~~--------~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~~~~i~~~l~~   66 (137)
                      +||||+|.|.+.        +++.|...++  .+...+|.+|+..+     .. +++++||+.+.+..|+.++....|+.
T Consensus       275 LfIDEih~l~~~~~~~~~~d~~~~lkp~l~--~g~l~~IgaTt~~e~r~~~~~d~al~rRf~~i~v~eP~~~~~~~iL~~  352 (857)
T PRK10865        275 LFIDELHTMVGAGKADGAMDAGNMLKPALA--RGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAILRG  352 (857)
T ss_pred             EEEecHHHhccCCCCccchhHHHHhcchhh--cCCCeEEEcCCCHHHHHHhhhcHHHHhhCCEEEeCCCCHHHHHHHHHH
Confidence            589999999643        5888888887  66777888887764     26 89999999999999999999998877


Q ss_pred             HHHH----cCCCCCHHHHHHHHHHcC------CcHHHHHHHHHHHH
Q 042716           67 IAEQ----EGIQLPHQLAEKIADNSK------NNLRQAIRSFEASR  102 (137)
Q Consensus        67 i~~~----egi~i~~~~l~~i~~~~~------gd~R~aln~L~~~~  102 (137)
                      +..+    .++.++++++...+..+.      .=+.+|+.++....
T Consensus       353 l~~~~e~~~~v~~~d~a~~~a~~ls~ry~~~~~~pdkAi~LiD~aa  398 (857)
T PRK10865        353 LKERYELHHHVQITDPAIVAAATLSHRYIADRQLPDKAIDLIDEAA  398 (857)
T ss_pred             HhhhhccCCCCCcCHHHHHHHHHHhhccccCCCCChHHHHHHHHHh
Confidence            6543    367888888887655542      33456777776655

>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=97.77  E-value=3.1e-05  Score=51.96  Aligned_cols=52  Identities=21%  Similarity=0.184  Sum_probs=43.9

Q ss_pred             CcccccCcCCHHH-----------HHHHHHHHHhccC---CceEEEEeCCCCCc-hhhh-hcce-eeEe
Q 042716            1 IILCEADKLSTDA-----------LLYMRWLLERYKG---LNKVFFCCSDVSKL-QPIK-SLCT-VIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~~-----------~~~L~~~le~~~~---~~~~Il~~n~~~~i-~~l~-SRc~-~i~~   52 (137)
                      ++|||+|.+....           .+.|+..++....   ++.+|++||...++ ++++ +||. .++|
T Consensus        62 l~iDe~d~l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~~i~~~l~~~rf~~~i~~  130 (132)
T PF00004_consen   62 LFIDEIDKLFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPDKIDPALLRSRFDRRIEF  130 (132)
T ss_dssp             EEEETGGGTSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGGGSCHHHHSTTSEEEEEE
T ss_pred             eeeccchhcccccccccccccccccceeeecccccccccccceeEEeeCChhhCCHhHHhCCCcEEEEc
Confidence            5899999998876           8889999998776   36799999999999 9999 9985 4555

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 ....

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

Probab=97.77  E-value=0.0003  Score=57.90  Aligned_cols=106  Identities=12%  Similarity=0.135  Sum_probs=82.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcceeeEecCCCHH---
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLCTVIQLLPPSKQ---   58 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc~~i~~~~~~~~---   58 (137)
                      +|||||..|.-+.|..|++++++-.           -++++|.+||..       .+. .+|..|.-++++.-|+-.   
T Consensus       239 LfLDEI~~mpl~~Q~kLLRvLqe~~~~rvG~~~~i~vdvRiIaaT~~dL~~~v~~G~FReDLyyRLnV~~i~iPpLRER~  318 (464)
T COG2204         239 LFLDEIGEMPLELQVKLLRVLQEREFERVGGNKPIKVDVRIIAATNRDLEEEVAAGRFREDLYYRLNVVPLRLPPLRERK  318 (464)
T ss_pred             EEeeccccCCHHHHHHHHHHHHcCeeEecCCCcccceeeEEEeecCcCHHHHHHcCCcHHHHHhhhccceecCCcccccc
Confidence            5899999999999999999999642           246788888866       346 899999877666655543   


Q ss_pred             -HHH----HHHHHHHHHcCC---CCCHHHHHHHHHH-cCCcHHHHHHHHHHHHhcCC
Q 042716           59 -EIV----EVLEFIAEQEGI---QLPHQLAEKIADN-SKNNLRQAIRSFEASRQMNY  106 (137)
Q Consensus        59 -~i~----~~l~~i~~~egi---~i~~~~l~~i~~~-~~gd~R~aln~L~~~~~~~~  106 (137)
                       ||-    ..+++.|++.|.   .++++++..+..+ -.|++|.+-|.++.+.....
T Consensus       319 EDIp~L~~hfl~~~~~~~~~~~~~~s~~a~~~L~~y~WPGNVREL~N~ver~~il~~  375 (464)
T COG2204         319 EDIPLLAEHFLKRFAAELGRPPKGFSPEALAALLAYDWPGNVRELENVVERAVILSE  375 (464)
T ss_pred             hhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCChHHHHHHHHHHHHHhcCC
Confidence             333    345566666655   6889999998887 79999999999998887654

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=97.75  E-value=0.00069  Score=53.83  Aligned_cols=103  Identities=13%  Similarity=0.072  Sum_probs=70.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC--C-Cc-hhhhhcce-eeEecCCCH-HHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV--S-KL-QPIKSLCT-VIQLLPPSK-QEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~--~-~i-~~l~SRc~-~i~~~~~~~-~~i~~~   63 (137)
                      +++||++.|+...|..|+..|++..           ..++|++++...  . .+ +++.+|+. .+.+..+++ ++-...
T Consensus       135 L~lDEi~~L~~~~Q~~Ll~~l~~g~~~v~r~G~~~~~~~r~iviat~np~eg~l~~~LldRf~l~i~l~~p~~~eer~eI  214 (337)
T TIGR02030       135 LYIDEVNLLEDHLVDVLLDVAASGWNVVEREGISIRHPARFVLVGSGNPEEGELRPQLLDRFGLHAEIRTVRDVELRVEI  214 (337)
T ss_pred             EEecChHhCCHHHHHHHHHHHHhCCeEEEECCEEEEcCCCEEEEeccccccCCCCHHHHhhcceEEECCCCCCHHHHHHH
Confidence            4799999999999999999998632           134567666543  2 47 89999984 578887876 443444


Q ss_pred             HHHHH-----------------------------HHcCCCCCHHHHHHHHHH---cCC-cHHHHHHHHHHHHh
Q 042716           64 LEFIA-----------------------------EQEGIQLPHQLAEKIADN---SKN-NLRQAIRSFEASRQ  103 (137)
Q Consensus        64 l~~i~-----------------------------~~egi~i~~~~l~~i~~~---~~g-d~R~aln~L~~~~~  103 (137)
                      +....                             .-.++.++++.+.+++..   .+. ++|..+.++..+..
T Consensus       215 L~~~~~~~~~~~~~~~~~~~e~~~~~~~I~~a~~~~~~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA  287 (337)
T TIGR02030       215 VERRTEYDADPHAFCEKWQTEQEALQAKIVNAQNLLPQVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKA  287 (337)
T ss_pred             HHhhhhcccCchhhhhhhhhhhhcCHHHHHHHHHHhccCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHH
Confidence            43311                             113567888888887764   222 57888888876554

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.

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=97.73  E-value=0.00045  Score=56.15  Aligned_cols=105  Identities=12%  Similarity=0.115  Sum_probs=75.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcce--eeEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLCT--VIQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc~--~i~~~~~~~--   57 (137)
                      ++|||+|.|....|..|+.++++..           .++++|++++..       ..+ +.+..|+.  .+.++|+..  
T Consensus       241 l~ld~i~~l~~~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~l~~~~~~g~~~~~l~~~l~~~~i~~ppLreR~  320 (457)
T PRK11361        241 LLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFREDLFYRLNVIHLILPPLRDRR  320 (457)
T ss_pred             EEEechhhCCHHHHHHHHHHHhcCcEEeCCCCceeeeceEEEEeCCCCHHHHHHcCCchHHHHHHhccceecCCChhhch
Confidence            5899999999999999999998532           246888888755       235 66777764  345555542  


Q ss_pred             HHHHHH----HHHHHHHcC---CCCCHHHHHHHHHH-cCCcHHHHHHHHHHHHhcC
Q 042716           58 QEIVEV----LEFIAEQEG---IQLPHQLAEKIADN-SKNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        58 ~~i~~~----l~~i~~~eg---i~i~~~~l~~i~~~-~~gd~R~aln~L~~~~~~~  105 (137)
                      +++...    +.+.+.+.|   ..++++++..+..+ ..||+|.+-|.++.+....
T Consensus       321 ~di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNv~eL~~~~~~~~~~~  376 (457)
T PRK11361        321 EDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIERAVVMN  376 (457)
T ss_pred             hhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHcCCCCCcHHHHHHHHHHHHHhC
Confidence            344332    344444333   35899999999887 5999999999999877544

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=97.73  E-value=0.00034  Score=57.17  Aligned_cols=105  Identities=14%  Similarity=0.137  Sum_probs=77.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcce--eeEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLCT--VIQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc~--~i~~~~~~~--   57 (137)
                      ++|||+|.|+...|..|++++++..           .++++|++++..       ..+ ++|..|+.  .+.++|+.+  
T Consensus       236 l~l~~i~~l~~~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~~~~~L~~~l~~~~i~~PpLreR~  315 (469)
T PRK10923        236 LFLDEIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEGKFREDLFHRLNVIRVHLPPLRERR  315 (469)
T ss_pred             EEEeccccCCHHHHHHHHHHHhcCcEEeCCCCCeEEeeEEEEEeCCCCHHHHHHcCCchHHHHHHhcceeecCCCcccch
Confidence            4899999999999999999998642           235899998765       246 88999974  566666554  


Q ss_pred             HHHHHHH----HHHHHHcCC---CCCHHHHHHHHHH-cCCcHHHHHHHHHHHHhcC
Q 042716           58 QEIVEVL----EFIAEQEGI---QLPHQLAEKIADN-SKNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        58 ~~i~~~l----~~i~~~egi---~i~~~~l~~i~~~-~~gd~R~aln~L~~~~~~~  105 (137)
                      +++...+    .+.+.+.|.   .++++++..+..+ -.||+|.+-|.++.+....
T Consensus       316 ~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNv~eL~~~i~~~~~~~  371 (469)
T PRK10923        316 EDIPRLARHFLQVAARELGVEAKLLHPETEAALTRLAWPGNVRQLENTCRWLTVMA  371 (469)
T ss_pred             hhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhCCCCChHHHHHHHHHHHHHhC
Confidence            3444443    333444443   4789999998887 7899999999999887643

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

Probab=97.72  E-value=0.00029  Score=57.10  Aligned_cols=101  Identities=13%  Similarity=0.140  Sum_probs=66.3

Q ss_pred             CcccccCcCCH-----------HHHHHHHHHHHhc-----cCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLST-----------DALLYMRWLLERY-----KGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~-----------~~~~~L~~~le~~-----~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      |+|||+|.+..           ..+..+..++...     ..++.+|++||.+..+ ++++.  |+ ..+.|+.|+.++.
T Consensus       242 LfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R  321 (398)
T PTZ00454        242 IFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQK  321 (398)
T ss_pred             EEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCCCCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHH
Confidence            58999998732           2344555554432     2356699999999999 88764  65 5699999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcC-CcHHHHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSK-NNLRQAIRSFEASR  102 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~-gd~R~aln~L~~~~  102 (137)
                      ..+++..+.+.++.-+ -.+..++..+. -+.+.+.++++.+.
T Consensus       322 ~~Il~~~~~~~~l~~d-vd~~~la~~t~g~sgaDI~~l~~eA~  363 (398)
T PTZ00454        322 RLIFQTITSKMNLSEE-VDLEDFVSRPEKISAADIAAICQEAG  363 (398)
T ss_pred             HHHHHHHHhcCCCCcc-cCHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            9999888777665422 23555665543 23444444444444

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=97.69  E-value=0.00037  Score=58.52  Aligned_cols=104  Identities=13%  Similarity=0.071  Sum_probs=74.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCCC-------Cc-hhhhhcc--eeeEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDVS-------KL-QPIKSLC--TVIQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~~-------~i-~~l~SRc--~~i~~~~~~~--   57 (137)
                      +||||++.|....|..|++++++..           .++++|++|+..-       .. ++|..|+  ..+.++|+.+  
T Consensus       326 LfLdeI~~Lp~~~Q~kLl~~L~e~~~~r~G~~~~~~~dvRiIaat~~~L~~~v~~g~Fr~dL~yrL~~~~I~lPPLReR~  405 (538)
T PRK15424        326 LFLDEIGEMPLPLQTRLLRVLEEKEVTRVGGHQPVPVDVRVISATHCDLEEDVRQGRFRRDLFYRLSILRLQLPPLRERV  405 (538)
T ss_pred             EEEcChHhCCHHHHHHHHhhhhcCeEEecCCCceeccceEEEEecCCCHHHHHhcccchHHHHHHhcCCeecCCChhhch
Confidence            5899999999999999999998632           2457888887652       24 5777786  4566666655  


Q ss_pred             HHHHHHHHHH----HHHcCCCCCHHHH-------HHHHHH-cCCcHHHHHHHHHHHHhc
Q 042716           58 QEIVEVLEFI----AEQEGIQLPHQLA-------EKIADN-SKNNLRQAIRSFEASRQM  104 (137)
Q Consensus        58 ~~i~~~l~~i----~~~egi~i~~~~l-------~~i~~~-~~gd~R~aln~L~~~~~~  104 (137)
                      +|+...+...    +.+.+..++++++       ..+..+ -+||+|.+-|.++.+...
T Consensus       406 eDI~~L~~~fl~~~~~~~~~~~~~~a~~~~~~a~~~L~~y~WPGNvREL~nvier~~i~  464 (538)
T PRK15424        406 ADILPLAESFLKQSLAALSAPFSAALRQGLQQCETLLLHYDWPGNVRELRNLMERLALF  464 (538)
T ss_pred             hHHHHHHHHHHHHHHHHcCCCCCHHHHHhhHHHHHHHHhCCCCchHHHHHHHHHHHHHh
Confidence            4555444443    3446777888776       344443 689999999999987753

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=97.69  E-value=0.00031  Score=58.87  Aligned_cols=104  Identities=14%  Similarity=0.054  Sum_probs=77.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCCC-------Cc-hhhhhcc--eeeEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDVS-------KL-QPIKSLC--TVIQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~~-------~i-~~l~SRc--~~i~~~~~~~--   57 (137)
                      +||||+|.|....|..|++++++..           .++++|++|+..-       .+ ++|..|.  ..+.++|+.+  
T Consensus       311 LfLdeI~~Lp~~~Q~~Ll~~L~~~~~~r~g~~~~~~~dvRiIaat~~~l~~~v~~g~fr~dL~~rL~~~~I~lPPLReR~  390 (526)
T TIGR02329       311 LFLDEIGEMPLPLQTRLLRVLEEREVVRVGGTEPVPVDVRVVAATHCALTTAVQQGRFRRDLFYRLSILRIALPPLRERP  390 (526)
T ss_pred             EEecChHhCCHHHHHHHHHHHhcCcEEecCCCceeeecceEEeccCCCHHHHhhhcchhHHHHHhcCCcEEeCCCchhch
Confidence            5899999999999999999998642           2347888887652       24 5777775  5677777766  


Q ss_pred             HHHHHH----HHHHHHHcCCCCCHHHHHH-------HHHH-cCCcHHHHHHHHHHHHhc
Q 042716           58 QEIVEV----LEFIAEQEGIQLPHQLAEK-------IADN-SKNNLRQAIRSFEASRQM  104 (137)
Q Consensus        58 ~~i~~~----l~~i~~~egi~i~~~~l~~-------i~~~-~~gd~R~aln~L~~~~~~  104 (137)
                      +|+...    |.+.+...++.++++++..       +..+ -+||+|.+-|.++.+...
T Consensus       391 eDI~~L~~~fl~~~~~~~~~~~~~~a~~~~~~~~~~L~~y~WPGNvrEL~nvier~~i~  449 (526)
T TIGR02329       391 GDILPLAAEYLVQAAAALRLPDSEAAAQVLAGVADPLQRYPWPGNVRELRNLVERLALE  449 (526)
T ss_pred             hHHHHHHHHHHHHHHHHcCCCCCHHHHHHhHHHHHHHHhCCCCchHHHHHHHHHHHHHh
Confidence            455444    3444445577899999887       6665 789999999999988753

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

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.67  E-value=0.0004  Score=56.02  Aligned_cols=97  Identities=16%  Similarity=0.223  Sum_probs=66.4

Q ss_pred             CcccccCcCC-----------HHHHHHHHHHHHhcc-----CCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLS-----------TDALLYMRWLLERYK-----GLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~-----------~~~~~~L~~~le~~~-----~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      |||||+|.+.           .+.+..+..++.+..     .+..+|++||.+..+ ++++.  |+ ..+.|++|+.++.
T Consensus       228 lfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R  307 (389)
T PRK03992        228 IFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGR  307 (389)
T ss_pred             EEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCCCCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHH
Confidence            5899999983           344566666664432     356799999999889 88874  66 5799999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHc----CCcHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNS----KNNLRQAIRSF   98 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~----~gd~R~aln~L   98 (137)
                      ..+++..+.+.++.- +-.+..++..+    .+|++.+.+..
T Consensus       308 ~~Il~~~~~~~~~~~-~~~~~~la~~t~g~sgadl~~l~~eA  348 (389)
T PRK03992        308 LEILKIHTRKMNLAD-DVDLEELAELTEGASGADLKAICTEA  348 (389)
T ss_pred             HHHHHHHhccCCCCC-cCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            999988776544421 12345566554    35666554443

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=97.58  E-value=0.0011  Score=56.98  Aligned_cols=106  Identities=13%  Similarity=0.135  Sum_probs=77.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCCC-------Cc-hhhhhcc--eeeEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDVS-------KL-QPIKSLC--TVIQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~~-------~i-~~l~SRc--~~i~~~~~~~--   57 (137)
                      ++|||+|.|....|..|+.++++..           .++++|++++..-       .+ +.|..|.  ..+.++|+.+  
T Consensus       474 L~Ldei~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~l~~~~~~~~f~~~L~~~l~~~~i~lPpLreR~  553 (686)
T PRK15429        474 LFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLKKMVADREFRSDLYYRLNVFPIHLPPLRERP  553 (686)
T ss_pred             EEEechhhCCHHHHHHHHHHHHhCCEEeCCCCCcccceEEEEEeCCCCHHHHHHcCcccHHHHhccCeeEEeCCChhhhH
Confidence            5899999999999999999998632           3568888887652       24 5677775  4566666655  


Q ss_pred             HHHHHHH----HHHHHHcCC---CCCHHHHHHHHHH-cCCcHHHHHHHHHHHHhcCC
Q 042716           58 QEIVEVL----EFIAEQEGI---QLPHQLAEKIADN-SKNNLRQAIRSFEASRQMNY  106 (137)
Q Consensus        58 ~~i~~~l----~~i~~~egi---~i~~~~l~~i~~~-~~gd~R~aln~L~~~~~~~~  106 (137)
                      +++-..+    .+.+.+.|.   .++++++..+..+ -+||+|.+-|.++.+.....
T Consensus       554 ~Di~~L~~~~l~~~~~~~~~~~~~~s~~al~~L~~y~WPGNvrEL~~~i~~a~~~~~  610 (686)
T PRK15429        554 EDIPLLVKAFTFKIARRMGRNIDSIPAETLRTLSNMEWPGNVRELENVIERAVLLTR  610 (686)
T ss_pred             hHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhCCCCCcHHHHHHHHHHHHHhCC
Confidence            3444333    344554453   4789999998876 78999999999998876443

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.58  E-value=0.00018  Score=62.30  Aligned_cols=86  Identities=14%  Similarity=0.172  Sum_probs=60.4

Q ss_pred             CcccccCcCCH------------HHHHHHHHHHHh--ccCCceEEEEeCCCCCc-hhhh--hcc-eeeEecCCCHHHHHH
Q 042716            1 IILCEADKLST------------DALLYMRWLLER--YKGLNKVFFCCSDVSKL-QPIK--SLC-TVIQLLPPSKQEIVE   62 (137)
Q Consensus         1 iiiDEid~l~~------------~~~~~L~~~le~--~~~~~~~Il~~n~~~~i-~~l~--SRc-~~i~~~~~~~~~i~~   62 (137)
                      |||||+|.|.+            ...+.|+..|+.  ...+..+|.+||.+..+ ++++  +|| ..+.|+.|+.++...
T Consensus       550 ifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~  629 (733)
T TIGR01243       550 IFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKE  629 (733)
T ss_pred             EEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHH
Confidence            58999998842            124556666763  23456688888999999 8887  588 679999999999888


Q ss_pred             HHHHHHHHcCCCCCHH-HHHHHHHHcC
Q 042716           63 VLEFIAEQEGIQLPHQ-LAEKIADNSK   88 (137)
Q Consensus        63 ~l~~i~~~egi~i~~~-~l~~i~~~~~   88 (137)
                      +++....  +..++++ .+..+++.+.
T Consensus       630 i~~~~~~--~~~~~~~~~l~~la~~t~  654 (733)
T TIGR01243       630 IFKIHTR--SMPLAEDVDLEELAEMTE  654 (733)
T ss_pred             HHHHHhc--CCCCCccCCHHHHHHHcC
Confidence            8876544  3444433 3667777654

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

>CHL00195 ycf46 Ycf46; Provisional

Probab=97.56  E-value=0.00021  Score=59.36  Aligned_cols=97  Identities=18%  Similarity=0.108  Sum_probs=67.3

Q ss_pred             CcccccCcCCHH------------HHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHHHHHH
Q 042716            1 IILCEADKLSTD------------ALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l~~~------------~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i~~~l   64 (137)
                      ++|||+|.+...            ..+.++..|.+......+|.+||++..+ ++++-  |+ ..+.++.|+.++...++
T Consensus       322 L~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il  401 (489)
T CHL00195        322 LWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIF  401 (489)
T ss_pred             EEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceEEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHH
Confidence            579999987431            1344566666555556688888999999 88864  77 67999999999999999


Q ss_pred             HHHHHHcCCC-CCHHHHHHHHHH----cCCcHHHHHHH
Q 042716           65 EFIAEQEGIQ-LPHQLAEKIADN----SKNNLRQAIRS   97 (137)
Q Consensus        65 ~~i~~~egi~-i~~~~l~~i~~~----~~gd~R~aln~   97 (137)
                      +....+.+.. .++..+..++..    +++|++.++..
T Consensus       402 ~~~l~~~~~~~~~~~dl~~La~~T~GfSGAdI~~lv~e  439 (489)
T CHL00195        402 KIHLQKFRPKSWKKYDIKKLSKLSNKFSGAEIEQSIIE  439 (489)
T ss_pred             HHHHhhcCCCcccccCHHHHHhhcCCCCHHHHHHHHHH
Confidence            8888775432 234446666665    44566655543

>PHA02244 ATPase-like protein

Probab=97.56  E-value=0.00063  Score=54.69  Aligned_cols=58  Identities=14%  Similarity=0.087  Sum_probs=49.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHh-----------ccCCceEEEEeCCC-----------CCc-hhhhhcceeeEecCCCH
Q 042716            1 IILCEADKLSTDALLYMRWLLER-----------YKGLNKVFFCCSDV-----------SKL-QPIKSLCTVIQLLPPSK   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~-----------~~~~~~~Il~~n~~-----------~~i-~~l~SRc~~i~~~~~~~   57 (137)
                      ++|||++.+.+..+..|...++.           .+.++++|+++|..           ..+ +++++|+..+.|..|+.
T Consensus       184 LiLDEId~a~p~vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~~~~G~~~~y~G~k~L~~AllDRFv~I~~dyp~~  263 (383)
T PHA02244        184 FFIDEIDASIPEALIIINSAIANKFFDFADERVTAHEDFRVISAGNTLGKGADHIYVARNKIDGATLDRFAPIEFDYDEK  263 (383)
T ss_pred             EEEeCcCcCCHHHHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCCCccCcccccCCCcccCHHHHhhcEEeeCCCCcH
Confidence            58999999999999999999962           24678899999973           347 99999999999999874


Q ss_pred             H
Q 042716           58 Q   58 (137)
Q Consensus        58 ~   58 (137)
                      .
T Consensus       264 ~  264 (383)
T PHA02244        264 I  264 (383)
T ss_pred             H
Confidence            3

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

Probab=97.54  E-value=0.00014  Score=48.69  Aligned_cols=53  Identities=19%  Similarity=0.118  Sum_probs=44.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc------CCceEEEEeCCCC--Cc-hhhhhcc-eeeEec
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK------GLNKVFFCCSDVS--KL-QPIKSLC-TVIQLL   53 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~------~~~~~Il~~n~~~--~i-~~l~SRc-~~i~~~   53 (137)
                      +++||+|.+....+..+...++...      .++++|++++...  .+ +.+++|| ..+.|.
T Consensus        88 lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~r~~~~i~~~  150 (151)
T cd00009          88 LFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIP  150 (151)
T ss_pred             EEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHhhhccEeecC
Confidence            5899999998888889999888863      5778999999887  67 9999999 666664

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.

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

Probab=97.52  E-value=0.00029  Score=56.71  Aligned_cols=87  Identities=13%  Similarity=0.169  Sum_probs=65.2

Q ss_pred             CcccccCcCCHH---------HH---HHHHHHHHh--------------ccCCceEEEEeCCCCCc-hhhhh--cceeeE
Q 042716            1 IILCEADKLSTD---------AL---LYMRWLLER--------------YKGLNKVFFCCSDVSKL-QPIKS--LCTVIQ   51 (137)
Q Consensus         1 iiiDEid~l~~~---------~~---~~L~~~le~--------------~~~~~~~Il~~n~~~~i-~~l~S--Rc~~i~   51 (137)
                      |||||+|.+.+.         .|   ..|+..++.              ....+++|.+||.++.| ++|+-  |+-.+ 
T Consensus       216 LFIDEIDA~~g~r~~~~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd~LDpALlRpGRfDk~-  294 (413)
T PLN00020        216 LFINDLDAGAGRFGTTQYTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFSTLYAPLIRDGRMEKF-  294 (413)
T ss_pred             EEEehhhhcCCCCCCCCcchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCCCcccCCHhHcCCCCCCce-
Confidence            589999988542         11   345555543              23457789999999999 99988  77543 


Q ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCc
Q 042716           52 LLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNN   90 (137)
Q Consensus        52 ~~~~~~~~i~~~l~~i~~~egi~i~~~~l~~i~~~~~gd   90 (137)
                      |..|+.++...+|+.+.++.++  +...+..++...+|-
T Consensus       295 i~lPd~e~R~eIL~~~~r~~~l--~~~dv~~Lv~~f~gq  331 (413)
T PLN00020        295 YWAPTREDRIGVVHGIFRDDGV--SREDVVKLVDTFPGQ  331 (413)
T ss_pred             eCCCCHHHHHHHHHHHhccCCC--CHHHHHHHHHcCCCC
Confidence            3479999999999988887765  578889999998875

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

Probab=97.50  E-value=0.00061  Score=55.92  Aligned_cols=94  Identities=16%  Similarity=0.222  Sum_probs=62.8

Q ss_pred             CcccccCcCCH-----------HHHHHHHHHHHhc-----cCCceEEEEeCCCCCc-hhhh--hcc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLST-----------DALLYMRWLLERY-----KGLNKVFFCCSDVSKL-QPIK--SLC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~-----------~~~~~L~~~le~~-----~~~~~~Il~~n~~~~i-~~l~--SRc-~~i~~~~~~~~~i   60 (137)
                      +||||+|.+..           +.+..++.++.+.     ..+..+|++||.+..+ +.+.  +|+ ..+.|+.|+.++.
T Consensus       280 LfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R  359 (438)
T PTZ00361        280 VFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTK  359 (438)
T ss_pred             EeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhcccCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHH
Confidence            58999998732           2345555555432     3467799999999999 8776  466 5799999999999


Q ss_pred             HHHHHHHHHHcCCCCCHH-HHHHHHHH----cCCcHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQ-LAEKIADN----SKNNLRQAIR   96 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~-~l~~i~~~----~~gd~R~aln   96 (137)
                      ..+++..+.+.++.  ++ .+..++..    +..|++.++.
T Consensus       360 ~~Il~~~~~k~~l~--~dvdl~~la~~t~g~sgAdI~~i~~  398 (438)
T PTZ00361        360 RRIFEIHTSKMTLA--EDVDLEEFIMAKDELSGADIKAICT  398 (438)
T ss_pred             HHHHHHHHhcCCCC--cCcCHHHHHHhcCCCCHHHHHHHHH
Confidence            99998877665543  22 24445533    4445555443

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

Probab=97.50  E-value=0.00062  Score=55.45  Aligned_cols=47  Identities=19%  Similarity=0.289  Sum_probs=36.5

Q ss_pred             hhhhhcc-eeeEecCCCHHHHHHHHH-----------HHHHHcCC--CCCHHHHHHHHHHc
Q 042716           41 QPIKSLC-TVIQLLPPSKQEIVEVLE-----------FIAEQEGI--QLPHQLAEKIADNS   87 (137)
Q Consensus        41 ~~l~SRc-~~i~~~~~~~~~i~~~l~-----------~i~~~egi--~i~~~~l~~i~~~~   87 (137)
                      |.+..|+ .++.|++++.+++..++.           .....+|+  .++++++.+|++.+
T Consensus       297 PEflgRld~iv~f~~L~~~~L~~Il~~~~~~l~~q~~~~l~~~~i~L~~t~~al~~Ia~~~  357 (412)
T PRK05342        297 PEFIGRLPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKA  357 (412)
T ss_pred             HHHhCCCCeeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHhC
Confidence            6777787 678999999999888886           22234454  58899999999874

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=97.36  E-value=0.00082  Score=57.59  Aligned_cols=101  Identities=14%  Similarity=0.102  Sum_probs=70.6

Q ss_pred             CcccccCcCCHH--------------HHHHHHHHHHhccCC--ceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLSTD--------------ALLYMRWLLERYKGL--NKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~--------------~~~~L~~~le~~~~~--~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      |||||+|.+...              ..+.|+..|+.+..+  +.+|.+||.+..+ ++++.  |+ ..+.|+.|+.++.
T Consensus       248 ifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R  327 (644)
T PRK10733        248 IFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGR  327 (644)
T ss_pred             EEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCHHHH
Confidence            589999998431              234555556654443  4577788888889 88773  77 6899999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCC----cHHHHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKN----NLRQAIRSFEASR  102 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~g----d~R~aln~L~~~~  102 (137)
                      ..+++....+..+.- +-.+..+++.+.|    |+..+++......
T Consensus       328 ~~Il~~~~~~~~l~~-~~d~~~la~~t~G~sgadl~~l~~eAa~~a  372 (644)
T PRK10733        328 EQILKVHMRRVPLAP-DIDAAIIARGTPGFSGADLANLVNEAALFA  372 (644)
T ss_pred             HHHHHHHhhcCCCCC-cCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Confidence            999888776554321 1235668888887    8888887766544

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=97.34  E-value=0.0034  Score=49.88  Aligned_cols=103  Identities=14%  Similarity=0.169  Sum_probs=70.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCCC---Cc-hhhhhcce-eeEecCCCH-HHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDVS---KL-QPIKSLCT-VIQLLPPSK-QEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~~---~i-~~l~SRc~-~i~~~~~~~-~~i~~~   63 (137)
                      +++||++.+++..|++|+..|++..           ...+|++++...+   .+ +++..|+. .+.+.++++ ++-...
T Consensus       132 L~lDEInrl~~~~q~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP~e~~l~~aLldRF~~~v~v~~~~~~~e~~~i  211 (334)
T PRK13407        132 LYIDEVNLLEDHIVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEGELRPQLLDRFGLSVEVRSPRDVETRVEV  211 (334)
T ss_pred             EEecChHhCCHHHHHHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCcccCCCCHHHHhhcceEEEcCCCCcHHHHHHH
Confidence            5799999999999999999998642           2345777765442   47 89999984 577777766 443333


Q ss_pred             HHHHH-----------------------------HHcCCCCCHHHHHHHHHHc----CCcHHHHHHHHHHHHh
Q 042716           64 LEFIA-----------------------------EQEGIQLPHQLAEKIADNS----KNNLRQAIRSFEASRQ  103 (137)
Q Consensus        64 l~~i~-----------------------------~~egi~i~~~~l~~i~~~~----~gd~R~aln~L~~~~~  103 (137)
                      +....                             .-.++.++++.+.++++.+    ...+|..+.++..+..
T Consensus       212 l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~a~~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a  284 (334)
T PRK13407        212 IRRRDAYDADHDAFMAKWGAEDMQLRGRILGARARLPQLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARA  284 (334)
T ss_pred             HHHhhcccccchhhhccccccccCCHHHHHHHHHhcCCcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHH
Confidence            33211                             1134678999888877652    2468888887765543

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=97.24  E-value=0.00052  Score=56.06  Aligned_cols=102  Identities=16%  Similarity=0.254  Sum_probs=72.5

Q ss_pred             CcccccCcCCHH------------HHHHHHHHHHhcc--------CCceEEEEeC------CCCCc-hhhhhcc-eeeEe
Q 042716            1 IILCEADKLSTD------------ALLYMRWLLERYK--------GLNKVFFCCS------DVSKL-QPIKSLC-TVIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~------------~~~~L~~~le~~~--------~~~~~Il~~n------~~~~i-~~l~SRc-~~i~~   52 (137)
                      |||||+|.+...            .|++|++++|-..        .+..+.|+|.      .++.+ |-|.-|. .++.+
T Consensus       251 VfiDEiDKIa~~~~~~~~DvS~eGVQ~~LLkilEGt~v~~k~~~v~T~~ILFI~~GAF~~~kp~DlIPEl~GR~Pi~v~L  330 (441)
T TIGR00390       251 IFIDEIDKIAKKGESSGADVSREGVQRDLLPIVEGSTVNTKYGMVKTDHILFIAAGAFQLAKPSDLIPELQGRFPIRVEL  330 (441)
T ss_pred             EEEEchhhhcccCCCCCCCCCccchhccccccccCceeeecceeEECCceeEEecCCcCCCChhhccHHHhCccceEEEC
Confidence            689999999532            4999999999421        1233455543      23447 9999999 57999


Q ss_pred             cCCCHHHHHHHHH-----------HHHHHcCC--CCCHHHHHHHHHHc--------CCcHHHHHHHHHHHH
Q 042716           53 LPPSKQEIVEVLE-----------FIAEQEGI--QLPHQLAEKIADNS--------KNNLRQAIRSFEASR  102 (137)
Q Consensus        53 ~~~~~~~i~~~l~-----------~i~~~egi--~i~~~~l~~i~~~~--------~gd~R~aln~L~~~~  102 (137)
                      .+++.+++..+|.           ...+.+|+  .++++++..|++.+        +--.|.+-..++.+-
T Consensus       331 ~~L~~edL~rILteP~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A~~~N~~~~~iGAR~LrtilE~~l  401 (441)
T TIGR00390       331 QALTTDDFERILTEPKNSLIKQYKALMKTEGVNIEFSDEAIKRIAELAYNVNEKTENIGARRLHTVLERLL  401 (441)
T ss_pred             CCCCHHHHHHHhcCChhHHHHHHHHHHhhcCcEEEEeHHHHHHHHHHHHHhcccccccchhhHHHHHHHHH
Confidence            9999999998872           23356676  46899999999875        444666666666544

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

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

Probab=97.23  E-value=0.00073  Score=55.21  Aligned_cols=102  Identities=18%  Similarity=0.261  Sum_probs=72.8

Q ss_pred             CcccccCcCCH------------HHHHHHHHHHHhcc--------CCceEEEEeCC------CCCc-hhhhhcc-eeeEe
Q 042716            1 IILCEADKLST------------DALLYMRWLLERYK--------GLNKVFFCCSD------VSKL-QPIKSLC-TVIQL   52 (137)
Q Consensus         1 iiiDEid~l~~------------~~~~~L~~~le~~~--------~~~~~Il~~n~------~~~i-~~l~SRc-~~i~~   52 (137)
                      |||||+|.+..            +.|++|++++|-..        .+..++|+|.-      ++.+ |.|.-|. .++.+
T Consensus       253 VfiDEiDKIa~~~~~~~~DvS~eGVQ~~LLki~EG~~v~~k~~~i~T~~ILFI~~GAF~~~kp~DlIPEl~GR~Pi~v~L  332 (443)
T PRK05201        253 VFIDEIDKIAARGGSSGPDVSREGVQRDLLPLVEGSTVSTKYGMVKTDHILFIASGAFHVSKPSDLIPELQGRFPIRVEL  332 (443)
T ss_pred             EEEEcchhhcccCCCCCCCCCccchhcccccccccceeeecceeEECCceeEEecCCcCCCChhhccHHHhCccceEEEC
Confidence            68999999942            35999999999522        12335555532      3347 9999999 57999


Q ss_pred             cCCCHHHHHHHHH-----------HHHHHcCC--CCCHHHHHHHHHHc--------CCcHHHHHHHHHHHH
Q 042716           53 LPPSKQEIVEVLE-----------FIAEQEGI--QLPHQLAEKIADNS--------KNNLRQAIRSFEASR  102 (137)
Q Consensus        53 ~~~~~~~i~~~l~-----------~i~~~egi--~i~~~~l~~i~~~~--------~gd~R~aln~L~~~~  102 (137)
                      .+++.+++..+|.           ...+.+|+  .++++++..|++.+        +--.|.+-..++.+-
T Consensus       333 ~~L~~~dL~~ILteP~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A~~~N~~~~~iGAR~LrtI~E~~L  403 (443)
T PRK05201        333 DALTEEDFVRILTEPKASLIKQYQALLATEGVTLEFTDDAIRRIAEIAYQVNEKTENIGARRLHTVMEKLL  403 (443)
T ss_pred             CCCCHHHHHHHhcCChhHHHHHHHHHHhhcCcEEEEcHHHHHHHHHHHHHhcccccccchhhHHHHHHHHH
Confidence            9999999998883           23455676  57799999999875        334666666666554

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.21  E-value=0.00079  Score=56.22  Aligned_cols=76  Identities=11%  Similarity=0.092  Sum_probs=55.3

Q ss_pred             CcccccCcCCHH------------HHHHHHHHHHhcc--CCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHHHH
Q 042716            1 IILCEADKLSTD------------ALLYMRWLLERYK--GLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEIVE   62 (137)
Q Consensus         1 iiiDEid~l~~~------------~~~~L~~~le~~~--~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i~~   62 (137)
                      |||||+|.+...            ..+.|+..|+...  .+..+|.+||.+..| ++|+.  |+ ..+.|++|+.++...
T Consensus       293 IfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~  372 (512)
T TIGR03689       293 VFFDEMDSIFRTRGSGVSSDVETTVVPQLLSELDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAAD  372 (512)
T ss_pred             EEEehhhhhhcccCCCccchHHHHHHHHHHHHhcccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHH
Confidence            589999998432            1245666665433  356688888999999 99986  76 469999999999999


Q ss_pred             HHHHHHHHcCCCCCH
Q 042716           63 VLEFIAEQEGIQLPH   77 (137)
Q Consensus        63 ~l~~i~~~egi~i~~   77 (137)
                      +++..... .+.+++
T Consensus       373 Il~~~l~~-~l~l~~  386 (512)
T TIGR03689       373 IFSKYLTD-SLPLDA  386 (512)
T ss_pred             HHHHHhhc-cCCchH
Confidence            99887654 455543

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.

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=97.21  E-value=0.0026  Score=50.85  Aligned_cols=103  Identities=13%  Similarity=0.067  Sum_probs=72.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCCC---Cc-hhhhhcc-eeeEecCCCH-HHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDVS---KL-QPIKSLC-TVIQLLPPSK-QEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~~---~i-~~l~SRc-~~i~~~~~~~-~~i~~~   63 (137)
                      +++||++.|++..|..|+..|++..           ...+|+++++..+   .+ +.+..|+ ..+.+..|+. ++-...
T Consensus       148 L~lDEInrL~~~~Q~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np~eg~l~~~LldRf~l~i~l~~~~~~~~e~~i  227 (350)
T CHL00081        148 LYVDEVNLLDDHLVDILLDSAASGWNTVEREGISIRHPARFVLVGSGNPEEGELRPQLLDRFGMHAEIRTVKDPELRVKI  227 (350)
T ss_pred             EEecChHhCCHHHHHHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCcccCCCCHHHHHHhCceeecCCCCChHHHHHH
Confidence            5799999999999999999998621           2356777776552   47 9999998 4688888874 444344


Q ss_pred             HHHHH-----------------------------HHcCCCCCHHHHHHHHHHc---C-CcHHHHHHHHHHHHh
Q 042716           64 LEFIA-----------------------------EQEGIQLPHQLAEKIADNS---K-NNLRQAIRSFEASRQ  103 (137)
Q Consensus        64 l~~i~-----------------------------~~egi~i~~~~l~~i~~~~---~-gd~R~aln~L~~~~~  103 (137)
                      +++..                             .-.++.++++.+.++++.+   + .++|..+.+++.+..
T Consensus       228 l~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~ar~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA  300 (350)
T CHL00081        228 VEQRTSFDKNPQEFREKYEESQEELRSKIVAAQNLLPKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKA  300 (350)
T ss_pred             HHhhhccccChhhhhhhhccccccCHHHHHHHHHhcCCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHH
Confidence            33211                             1135778999988877653   2 368998888876654

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=97.19  E-value=0.0016  Score=55.92  Aligned_cols=105  Identities=15%  Similarity=0.174  Sum_probs=78.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-CCce--EEEEeCCCC---C-c-hhhhhcc--eeeEecCCCHHHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-GLNK--VFFCCSDVS---K-L-QPIKSLC--TVIQLLPPSKQEIVEVLEFIAEQ   70 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-~~~~--~Il~~n~~~---~-i-~~l~SRc--~~i~~~~~~~~~i~~~l~~i~~~   70 (137)
                      |+|||.|.|-...|..|+-+.+=|. ++.+  +|.++|...   + + ..+-||.  ..+.|.|++.+|+..++.....-
T Consensus       512 vLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~IaNTmdlPEr~l~nrvsSRlg~tRi~F~pYth~qLq~Ii~~RL~~  591 (767)
T KOG1514|consen  512 VLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIAIANTMDLPERLLMNRVSSRLGLTRICFQPYTHEQLQEIISARLKG  591 (767)
T ss_pred             EEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEEecccccCHHHHhccchhhhccceeeecCCCCHHHHHHHHHHhhcc
Confidence            5799999999999999999888654 2333  555566654   3 3 6777885  78999999999988887654432


Q ss_pred             cCCCCCHHHHHHHHHH---cCCcHHHHHHHHHHHHhcCC
Q 042716           71 EGIQLPHQLAEKIADN---SKNNLRQAIRSFEASRQMNY  106 (137)
Q Consensus        71 egi~i~~~~l~~i~~~---~~gd~R~aln~L~~~~~~~~  106 (137)
                      - -.++.++++.+++.   -.||.|+|+..+..+..-..
T Consensus       592 ~-~~f~~~aielvarkVAavSGDaRraldic~RA~Eia~  629 (767)
T KOG1514|consen  592 L-DAFENKAIELVARKVAAVSGDARRALDICRRAAEIAE  629 (767)
T ss_pred             h-hhcchhHHHHHHHHHHhccccHHHHHHHHHHHHHHhh
Confidence            2 24567777777664   46999999999998876443

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

Probab=97.18  E-value=0.0016  Score=53.14  Aligned_cols=48  Identities=10%  Similarity=0.234  Sum_probs=36.6

Q ss_pred             c-hhhhhcc-eeeEecCCCHHHHHHHHHH----HHH-------HcCC--CCCHHHHHHHHHHc
Q 042716           40 L-QPIKSLC-TVIQLLPPSKQEIVEVLEF----IAE-------QEGI--QLPHQLAEKIADNS   87 (137)
Q Consensus        40 i-~~l~SRc-~~i~~~~~~~~~i~~~l~~----i~~-------~egi--~i~~~~l~~i~~~~   87 (137)
                      + |.+..|+ .++.|.+++.+++..++..    +.+       .+|+  .++++++.+|++.+
T Consensus       301 ~~PEflgRld~Iv~f~pL~~~~L~~Il~~~~n~l~kq~~~~l~~~gi~L~~t~~a~~~Ia~~~  363 (413)
T TIGR00382       301 LIPEFIGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKA  363 (413)
T ss_pred             hHHHHhCCCCeEeecCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCeEEEECHHHHHHHHHhC
Confidence            5 7888888 6789999999998888754    121       2244  57899999999874

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

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

Probab=97.15  E-value=0.0022  Score=51.38  Aligned_cols=85  Identities=19%  Similarity=0.243  Sum_probs=63.8

Q ss_pred             CcccccCcCC-----------HHHHHHHHHHHHhc-----cCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLS-----------TDALLYMRWLLERY-----KGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~-----------~~~~~~L~~~le~~-----~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      |||||+|.+.           .+-|.-++.++.+.     .+++.+|++||-+.-+ |+|.-  |. ..+.|+.|+.+.-
T Consensus       248 IFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR  327 (406)
T COG1222         248 IFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGR  327 (406)
T ss_pred             EEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHH
Confidence            6899999983           23488888888775     3578899999999999 88765  44 6799999999988


Q ss_pred             HHHHHHHHHHcCCC--CCHHHHHHHHHHcC
Q 042716           61 VEVLEFIAEQEGIQ--LPHQLAEKIADNSK   88 (137)
Q Consensus        61 ~~~l~~i~~~egi~--i~~~~l~~i~~~~~   88 (137)
                      ..+++-.+.+.++.  ++   ++.++..++
T Consensus       328 ~~Il~IHtrkM~l~~dvd---~e~la~~~~  354 (406)
T COG1222         328 AEILKIHTRKMNLADDVD---LELLARLTE  354 (406)
T ss_pred             HHHHHHHhhhccCccCcC---HHHHHHhcC
Confidence            88888877776653  33   444555433

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=96.99  E-value=0.0083  Score=51.41  Aligned_cols=102  Identities=14%  Similarity=0.075  Sum_probs=65.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-------------CCceEEEEeCCC-CCc-hhhhhcce-eeEecCCCH-HHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-------------GLNKVFFCCSDV-SKL-QPIKSLCT-VIQLLPPSK-QEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-------------~~~~~Il~~n~~-~~i-~~l~SRc~-~i~~~~~~~-~~i~~~   63 (137)
                      ++|||++.|+...|+.|+..|++..             ..+.+|.++|-. ..+ ++|.+|+. .+.+..+.. ++....
T Consensus       130 L~lDEi~~l~~~~q~~Ll~~le~g~~~v~r~g~~~~~~~~~~lIat~np~eg~l~~~L~dR~~l~i~v~~~~~~~~~~~i  209 (633)
T TIGR02442       130 LYIDEVNLLDDHLVDVLLDAAAMGVNRVEREGLSVSHPARFVLIGTMNPEEGDLRPQLLDRFGLCVDVAAPRDPEERVEI  209 (633)
T ss_pred             EEeChhhhCCHHHHHHHHHHHhcCCEEEEECCceeeecCCeEEEEecCCCCCCCCHHHHhhcceEEEccCCCchHHHHHH
Confidence            5899999999999999999998541             123344444422 247 89999983 466666653 332222


Q ss_pred             HHHH-------------------------H----HHcCCCCCHHHHHHHHHHc---CC-cHHHHHHHHHHHH
Q 042716           64 LEFI-------------------------A----EQEGIQLPHQLAEKIADNS---KN-NLRQAIRSFEASR  102 (137)
Q Consensus        64 l~~i-------------------------~----~~egi~i~~~~l~~i~~~~---~g-d~R~aln~L~~~~  102 (137)
                      +...                         +    ....+.++++++.+++..+   +- .+|..+.+++.+.
T Consensus       210 l~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~ar~~~~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ar  281 (633)
T TIGR02442       210 IRRRLAFDADPEAFAARWAAEQEELRNRIARARSLLPSVRISDSLIRFISELCIEFGVDGHRADIVMARAAR  281 (633)
T ss_pred             HHHHHhhccCcHHHHHHhhhhHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHH
Confidence            2211                         0    1125788988888887764   22 4788887777654

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

>smart00350 MCM minichromosome maintenance proteins

Probab=96.94  E-value=0.0064  Score=50.76  Aligned_cols=67  Identities=15%  Similarity=0.139  Sum_probs=48.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-------------CCceEEEEeCCCC-------------Cc-hhhhhcc-eeeEe
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-------------GLNKVFFCCSDVS-------------KL-QPIKSLC-TVIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-------------~~~~~Il~~n~~~-------------~i-~~l~SRc-~~i~~   52 (137)
                      ++|||+|.|....|.+|+..||+..             ..+++|.++|...             .+ +++.||+ .++.+
T Consensus       304 l~iDEi~~l~~~~q~~L~e~me~~~i~i~k~G~~~~l~~~~~viAa~NP~~g~y~~~~~~~~n~~l~~~lLsRFdLi~~~  383 (509)
T smart00350      304 CCIDEFDKMDDSDRTAIHEAMEQQTISIAKAGITTTLNARCSVLAAANPIGGRYDPKLTPEENIDLPAPILSRFDLLFVV  383 (509)
T ss_pred             EEEechhhCCHHHHHHHHHHHhcCEEEEEeCCEEEEecCCcEEEEEeCCCCcccCCCcChhhccCCChHHhCceeeEEEe
Confidence            4799999999999999999998643             3466777777542             47 9999999 55444


Q ss_pred             -cCCCHHHHHHHHHHH
Q 042716           53 -LPPSKQEIVEVLEFI   67 (137)
Q Consensus        53 -~~~~~~~i~~~l~~i   67 (137)
                       ..++.+.-...+.++
T Consensus       384 ~d~~~~~~d~~i~~~i  399 (509)
T smart00350      384 LDEVDEERDRELAKHV  399 (509)
T ss_pred             cCCCChHHHHHHHHHH
Confidence             455555444444443

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=96.94  E-value=0.011  Score=50.25  Aligned_cols=127  Identities=10%  Similarity=0.035  Sum_probs=76.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-------------CCceEEEEeCCCC---Cc-hhhhhccee-eEecCC-CHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-------------GLNKVFFCCSDVS---KL-QPIKSLCTV-IQLLPP-SKQEIV   61 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-------------~~~~~Il~~n~~~---~i-~~l~SRc~~-i~~~~~-~~~~i~   61 (137)
                      +++||++.+++..|+.|+..|++..             ..+++|.++|...   .+ ++|..|+.+ +.+..+ +.++-.
T Consensus        88 L~lDEi~rl~~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~LldRf~l~v~~~~~~~~~er~  167 (589)
T TIGR02031        88 LYVDMANLLDDGLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLDRLALHVSLEDVASQDLRV  167 (589)
T ss_pred             EeccchhhCCHHHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHHhccCeeecCCCCCHHHHH
Confidence            5899999999999999999998643             2345665555443   57 999999843 444443 333323


Q ss_pred             HHHHHH---------------------H--HHcCCCCCHHHHHHHHHHc---C-CcHHHHHHHHHHHHhcCCCcccCccc
Q 042716           62 EVLEFI---------------------A--EQEGIQLPHQLAEKIADNS---K-NNLRQAIRSFEASRQMNYPFVEGQVI  114 (137)
Q Consensus        62 ~~l~~i---------------------~--~~egi~i~~~~l~~i~~~~---~-gd~R~aln~L~~~~~~~~~~~~~~~~  114 (137)
                      .++...                     +  ....+.++++.+.+++..+   + ..+|..+.+++.+..... +..... 
T Consensus       168 eil~~~~~~~~~~~~~~~~~~~~~i~~ar~~~~~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aa-l~gr~~-  245 (589)
T TIGR02031       168 EIVRRERCNEVFRMNDELELLRGQIEAARELLPQVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAA-LHGRTE-  245 (589)
T ss_pred             HHHHHHHHhhhhhcchhhHHHHHHHHHHHHhcCCccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHH-HhCCCC-
Confidence            333221                     1  1235788999888877652   2 247888877775543210 000000 


Q ss_pred             cCCcHHHHHHHHHHHHh
Q 042716          115 LTGWEDDITNIATKIIE  131 (137)
Q Consensus       115 ~~~~~~~~~~i~~~i~~  131 (137)
                        --++++...+..++.
T Consensus       246 --V~~~Dv~~a~~lvl~  260 (589)
T TIGR02031       246 --VTEEDLKLAVELVLL  260 (589)
T ss_pred             --CCHHHHHHHHHHHhh
Confidence              125666666666663

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.

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=96.92  E-value=0.0089  Score=49.74  Aligned_cols=105  Identities=16%  Similarity=0.115  Sum_probs=80.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcceeeEecCCCHH---
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLCTVIQLLPPSKQ---   58 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc~~i~~~~~~~~---   58 (137)
                      +|+|||-.|....|-.|++++-+..           -.+++|.+||-.       .+. .+|.-|.-+|++.-|+--   
T Consensus       321 LFLDEIGelPL~lQaKLLRvLQegEieRvG~~r~ikVDVRiIAATNRDL~~~V~~G~FRaDLYyRLsV~Pl~lPPLRER~  400 (550)
T COG3604         321 LFLDEIGELPLALQAKLLRVLQEGEIERVGGDRTIKVDVRVIAATNRDLEEMVRDGEFRADLYYRLSVFPLELPPLRERP  400 (550)
T ss_pred             EechhhccCCHHHHHHHHHHHhhcceeecCCCceeEEEEEEEeccchhHHHHHHcCcchhhhhhcccccccCCCCcccCC
Confidence            5899999999999999999997642           246789999854       356 788888887777666543   


Q ss_pred             -HH----HHHHHHHHHHcCC---CCCHHHHHHHHHH-cCCcHHHHHHHHHHHHhcC
Q 042716           59 -EI----VEVLEFIAEQEGI---QLPHQLAEKIADN-SKNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        59 -~i----~~~l~~i~~~egi---~i~~~~l~~i~~~-~~gd~R~aln~L~~~~~~~  105 (137)
                       ++    ...+++...+.|.   .+++++++.+.++ ..|+.|..-|.++..+...
T Consensus       401 ~DIplLA~~Fle~~~~~~gr~~l~ls~~Al~~L~~y~wPGNVRELen~veRavlla  456 (550)
T COG3604         401 EDIPLLAGYFLEKFRRRLGRAILSLSAEALELLSSYEWPGNVRELENVVERAVLLA  456 (550)
T ss_pred             ccHHHHHHHHHHHHHHhcCCcccccCHHHHHHHHcCCCCCcHHHHHHHHHHHHHHh
Confidence             22    2334555555555   7899999999987 8999999999999888744

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=96.89  E-value=0.007  Score=51.66  Aligned_cols=101  Identities=14%  Similarity=0.178  Sum_probs=70.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc---------------------CCceEEEEeCCC--CCc-hhhhhcce----eeEe
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK---------------------GLNKVFFCCSDV--SKL-QPIKSLCT----VIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~---------------------~~~~~Il~~n~~--~~i-~~l~SRc~----~i~~   52 (137)
                      ++|||++.|....|..|++.+++..                     .++++|+++|..  ..+ +++++|+.    .+.|
T Consensus       221 L~Ldei~~L~~~~q~~Ll~~L~~~~i~~~g~~e~~~~~~~~~~~ip~dvrvIa~~~~~~l~~l~~~l~~rf~~y~v~v~~  300 (608)
T TIGR00764       221 LYIDEIKTMPLEVQQYLLTALQDKKFPITGQSENSSGAMVRTEPVPCDFILVASGNLDDLEGMHPALRSRIRGYGYEVYM  300 (608)
T ss_pred             EEEEChHhCCHHHHHHHHHHHHhCcEEecCccccccccccCCCCCccceEEEEECCHHHHhhcCHHHHHHhcCCeEEEEe
Confidence            5799999999999999999997531                     234577777754  568 99999986    2344


Q ss_pred             c---CCCHHH---HHHHHHHHHHHcC-C-CCCHHHHHHHHHHcC----------CcHHHHHHHHHHH
Q 042716           53 L---PPSKQE---IVEVLEFIAEQEG-I-QLPHQLAEKIADNSK----------NNLRQAIRSFEAS  101 (137)
Q Consensus        53 ~---~~~~~~---i~~~l~~i~~~eg-i-~i~~~~l~~i~~~~~----------gd~R~aln~L~~~  101 (137)
                      +   +.+.+.   +..++.+.+++.| + .++++++..+++.+.          .+.|.+-++++.+
T Consensus       301 ~~~~~~~~e~~~~~~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A  367 (608)
T TIGR00764       301 KDTMPDTPENRDKLVQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAA  367 (608)
T ss_pred             eccCCCCHHHHHHHHHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHH
Confidence            3   223333   3455555566664 3 589999999986432          3578888888766

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

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

Probab=96.85  E-value=0.00061  Score=46.62  Aligned_cols=47  Identities=15%  Similarity=0.183  Sum_probs=36.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-------------C------CceEEEEeCCCC----Cc-hhhhhcc
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-------------G------LNKVFFCCSDVS----KL-QPIKSLC   47 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-------------~------~~~~Il~~n~~~----~i-~~l~SRc   47 (137)
                      ++|||++...++.+++|+.++++-.             .      +.++|.++|...    .+ ++++|||
T Consensus        69 l~lDEin~a~~~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~l~~al~~Rf  139 (139)
T PF07728_consen   69 LVLDEINRAPPEVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKELSPALLDRF  139 (139)
T ss_dssp             EEESSCGG--HHHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTTTCHHHHTT-
T ss_pred             EEECCcccCCHHHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCcCCHHHHhhC
Confidence            5899999999999999999998642             1      268899999887    68 9999997

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

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.76  E-value=0.0063  Score=52.87  Aligned_cols=89  Identities=18%  Similarity=0.236  Sum_probs=62.2

Q ss_pred             CcccccCcCCH-----------HHHHHHHHHHHhccCCc--eEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHHHHH
Q 042716            1 IILCEADKLST-----------DALLYMRWLLERYKGLN--KVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~-----------~~~~~L~~~le~~~~~~--~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i~~~   63 (137)
                      ++|||+|.+.+           ..++.|+..++......  .+|.+||.+..+ ++++.  |+ ..+.|..|+.++...+
T Consensus       275 l~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~I  354 (733)
T TIGR01243       275 IFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEI  354 (733)
T ss_pred             EEeehhhhhcccccCCcchHHHHHHHHHHHHhhccccCCCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHH
Confidence            58999998843           34677888887654433  355577888889 88876  55 5789999999998888


Q ss_pred             HHHHHHHcCCCCC-HHHHHHHHHHcCCcH
Q 042716           64 LEFIAEQEGIQLP-HQLAEKIADNSKNNL   91 (137)
Q Consensus        64 l~~i~~~egi~i~-~~~l~~i~~~~~gd~   91 (137)
                      ++...  .++.+. +..+..++..+.|-.
T Consensus       355 l~~~~--~~~~l~~d~~l~~la~~t~G~~  381 (733)
T TIGR01243       355 LKVHT--RNMPLAEDVDLDKLAEVTHGFV  381 (733)
T ss_pred             HHHHh--cCCCCccccCHHHHHHhCCCCC
Confidence            87544  344443 334677777776643

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.

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=96.75  E-value=0.0061  Score=48.29  Aligned_cols=134  Identities=13%  Similarity=0.149  Sum_probs=81.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHh--------------ccCCceEEEEeCCCC------------Cc-hhhhhcce-eeEe
Q 042716            1 IILCEADKLSTDALLYMRWLLER--------------YKGLNKVFFCCSDVS------------KL-QPIKSLCT-VIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~--------------~~~~~~~Il~~n~~~------------~i-~~l~SRc~-~i~~   52 (137)
                      +++||+|...++.+.+|..++|.              +++..++|.|+|...            .+ .+.++|+. ++.+
T Consensus       138 lllDEin~a~p~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~Gd~~G~y~Gt~~l~~A~lDRF~i~~~~  217 (327)
T TIGR01650       138 LCFDEYDAGRPDVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLGDTTGLYHGTQQINQAQMDRWSIVTTL  217 (327)
T ss_pred             EEechhhccCHHHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcCCCCcceeeeecCCHHHHhheeeEeeC
Confidence            47999999999999999999983              123455677777632            36 89999996 4689


Q ss_pred             cCCCHHHHHHHHHHHHHHcCCC--CCHHHHHHHHHH---cCC-----------cHHHHHHHHHHHHhcCCCcccCcccc-
Q 042716           53 LPPSKQEIVEVLEFIAEQEGIQ--LPHQLAEKIADN---SKN-----------NLRQAIRSFEASRQMNYPFVEGQVIL-  115 (137)
Q Consensus        53 ~~~~~~~i~~~l~~i~~~egi~--i~~~~l~~i~~~---~~g-----------d~R~aln~L~~~~~~~~~~~~~~~~~-  115 (137)
                      ..|+.++=.++|...+  .++.  .++..++++++.   ...           ++|..+...+.....+.++...-..+ 
T Consensus       218 ~Yp~~e~E~~Il~~~~--~~~~~~~~~~i~~~mV~la~~tR~~~~~~~i~~~~SpR~li~w~~~~~~f~~~~~~a~~~~~  295 (327)
T TIGR01650       218 NYLEHDNEAAIVLAKA--KGFDDTEGKDIINAMVRVADMTRNAFINGDISTVMSPRTVITWAENAEIFDHDIALAFRLTF  295 (327)
T ss_pred             CCCCHHHHHHHHHhhc--cCCCccchHHHHHHHHHHHHHHHhhhccCCccccccHHHHHHHHHHHHhhCccHHHHHHHHH
Confidence            9999988777776533  2222  123455554433   222           56666666655443221111111111 


Q ss_pred             ---CC--cHHHHHHHHHHHHhcCCCC
Q 042716          116 ---TG--WEDDITNIATKIIEEQSPK  136 (137)
Q Consensus       116 ---~~--~~~~~~~i~~~i~~~~~~~  136 (137)
                         .+  -+.-+.++.+.++..+-|+
T Consensus       296 ~n~~~~~er~~~~e~~q~~f~~~~~~  321 (327)
T TIGR01650       296 LNKCDELERPTVAEFFQRAFGEDLPE  321 (327)
T ss_pred             HhcCCHHHHHHHHHHHHHHcCCCCcc
Confidence               11  2344668888888776553

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.

>PF13173 AAA_14: AAA domain

Probab=96.73  E-value=0.0022  Score=43.55  Aligned_cols=58  Identities=22%  Similarity=0.236  Sum_probs=47.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCC----c-hhhhhcceeeEecCCCHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSK----L-QPIKSLCTVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~----i-~~l~SRc~~i~~~~~~~~~i   60 (137)
                      +||||+|.+. +....+..+.+.. .+..|++++.....    . ..+..|...+++.|++-.|.
T Consensus        65 i~iDEiq~~~-~~~~~lk~l~d~~-~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   65 IFIDEIQYLP-DWEDALKFLVDNG-PNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             EEEehhhhhc-cHHHHHHHHHHhc-cCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            5899999996 6888888888855 57889999887743    4 67888999999999998764

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=96.70  E-value=0.017  Score=48.41  Aligned_cols=103  Identities=13%  Similarity=0.124  Sum_probs=76.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcceeeEecCCCH----
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLCTVIQLLPPSK----   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc~~i~~~~~~~----   57 (137)
                      +|+||+-.|...-|..|++++.+-.           -..|+|-+||..       ... .+|.-|.-++++.=|+-    
T Consensus       344 LFLDEIgempl~LQaKLLRVLQEkei~rvG~t~~~~vDVRIIAATN~nL~~~i~~G~FReDLYYRLNV~~i~iPPLReR~  423 (560)
T COG3829         344 LFLDEIGEMPLPLQAKLLRVLQEKEIERVGGTKPIPVDVRIIAATNRNLEKMIAEGTFREDLYYRLNVIPITIPPLRERK  423 (560)
T ss_pred             EEehhhccCCHHHHHHHHHHHhhceEEecCCCCceeeEEEEEeccCcCHHHHHhcCcchhhheeeeceeeecCCCcccCc
Confidence            6899999999999999999998742           256789999876       236 78888886655544442    


Q ss_pred             HHHHHH----HHHHHHHcCC--C-CCHHHHHHHHHH-cCCcHHHHHHHHHHHHh
Q 042716           58 QEIVEV----LEFIAEQEGI--Q-LPHQLAEKIADN-SKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        58 ~~i~~~----l~~i~~~egi--~-i~~~~l~~i~~~-~~gd~R~aln~L~~~~~  103 (137)
                      +|+...    |.+..++.|-  . ++++++..+.++ -+|++|.+-|+++.+..
T Consensus       424 eDI~~L~~~Fl~k~s~~~~~~v~~ls~~a~~~L~~y~WPGNVRELeNviER~v~  477 (560)
T COG3829         424 EDIPLLAEYFLDKFSRRYGRNVKGLSPDALALLLRYDWPGNVRELENVIERAVN  477 (560)
T ss_pred             chHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHhCCCCchHHHHHHHHHHHHh
Confidence            344333    3444455554  3 789999998886 78999999999998874

>PRK04841 transcriptional regulator MalT; Provisional

Probab=96.63  E-value=0.025  Score=49.65  Aligned_cols=98  Identities=7%  Similarity=0.083  Sum_probs=73.6

Q ss_pred             CcccccCcCCHHH-HHHHHHHHHhccCCceEEEEeCCCCCc--hhhhhcceeeEec----CCCHHHHHHHHHHHHHHcCC
Q 042716            1 IILCEADKLSTDA-LLYMRWLLERYKGLNKVFFCCSDVSKL--QPIKSLCTVIQLL----PPSKQEIVEVLEFIAEQEGI   73 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~L~~~le~~~~~~~~Il~~n~~~~i--~~l~SRc~~i~~~----~~~~~~i~~~l~~i~~~egi   73 (137)
                      ++|||+|.+.... ...|..++...+.+..+|+++...+.+  ..++-+-..+.+.    +.+.++....+..   ..|.
T Consensus       125 lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~---~~~~  201 (903)
T PRK04841        125 LVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQ---RLSS  201 (903)
T ss_pred             EEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCCCCchHhHHhcCcceecCHHhCCCCHHHHHHHHHh---ccCC
Confidence            5899999997555 557888888878888998988876554  4555444445555    8899999888754   3577


Q ss_pred             CCCHHHHHHHHHHcCCcHHHHHHHHHHH
Q 042716           74 QLPHQLAEKIADNSKNNLRQAIRSFEAS  101 (137)
Q Consensus        74 ~i~~~~l~~i~~~~~gd~R~aln~L~~~  101 (137)
                      .++++.+..+.+.++|.+-.+--.....
T Consensus       202 ~~~~~~~~~l~~~t~Gwp~~l~l~~~~~  229 (903)
T PRK04841        202 PIEAAESSRLCDDVEGWATALQLIALSA  229 (903)
T ss_pred             CCCHHHHHHHHHHhCChHHHHHHHHHHH
Confidence            8999999999999999997665444333

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=96.62  E-value=0.012  Score=50.63  Aligned_cols=102  Identities=11%  Similarity=0.116  Sum_probs=70.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc---------------------CCceEEEEeCCC--CCc-hhhhhcce----eeEe
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK---------------------GLNKVFFCCSDV--SKL-QPIKSLCT----VIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~---------------------~~~~~Il~~n~~--~~i-~~l~SRc~----~i~~   52 (137)
                      ++|||++.|.+..|..|++.+++..                     -++++|+++|..  +.+ ++|++|+.    .+.|
T Consensus       230 L~LDei~~L~~~~q~~Llr~L~~~~i~i~g~~e~~~~~~~~~~~ip~dvrvI~a~~~~ll~~~dpdL~~rfk~~~v~v~f  309 (637)
T PRK13765        230 LFIDEINTLDLESQQSLLTAMQEKKFPITGQSERSSGAMVRTEPVPCDFIMVAAGNLDALENMHPALRSRIKGYGYEVYM  309 (637)
T ss_pred             EEEeChHhCCHHHHHHHHHHHHhCCEEecccccccccccCCCcceeeeeEEEEecCcCHHHhhhHHHHHHhccCeEEEEc
Confidence            5899999999999999999996432                     134688888765  347 99999984    3556


Q ss_pred             cCC---CHHHHHHHHHHHHHH---c--CCCCCHHHHHHHHHHcC---Cc-------HHHHHHHHHHHH
Q 042716           53 LPP---SKQEIVEVLEFIAEQ---E--GIQLPHQLAEKIADNSK---NN-------LRQAIRSFEASR  102 (137)
Q Consensus        53 ~~~---~~~~i~~~l~~i~~~---e--gi~i~~~~l~~i~~~~~---gd-------~R~aln~L~~~~  102 (137)
                      +.-   +.+....++..+++.   +  -..++++++..+++++.   |+       .|.+-++++.+.
T Consensus       310 ~~~~~d~~e~~~~~~~~iaqe~~~~G~l~~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~  377 (637)
T PRK13765        310 RDTMEDTPENRRKLVRFVAQEVKRDGKIPHFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAG  377 (637)
T ss_pred             ccccCCCHHHHHHHHHHHHHHhhhccCCCCCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHH
Confidence            532   345566666655543   2  23689999999987532   33       667777766543

>TIGR00368 Mg chelatase-related protein

Probab=96.60  E-value=0.005  Score=51.39  Aligned_cols=59  Identities=14%  Similarity=0.103  Sum_probs=46.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-------------CCceEEEEeCCC-----------------------CCc-hhh
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-------------GLNKVFFCCSDV-----------------------SKL-QPI   43 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-------------~~~~~Il~~n~~-----------------------~~i-~~l   43 (137)
                      +||||++.+.+..|+.|+..||...             .++++|.++|.-                       .++ .+|
T Consensus       299 LfLDEi~e~~~~~~~~L~~~LE~~~v~i~r~g~~~~~pa~frlIaa~Npcpcg~~~~~~~~c~c~~~~~~~y~~~is~pl  378 (499)
T TIGR00368       299 LFLDELPEFKRSVLDALREPIEDGSISISRASAKIFYPARFQLVAAMNPCPCGHYGGKNTHCRCSPQQISRYWNKLSGPF  378 (499)
T ss_pred             EecCChhhCCHHHHHHHHHHHHcCcEEEEecCcceeccCCeEEEEecCCcccCcCCCCcccccCCHHHHHHHhhhccHhH
Confidence            5899999999999999999998642             356788888742                       158 999


Q ss_pred             hhcc-eeeEecCCCHHH
Q 042716           44 KSLC-TVIQLLPPSKQE   59 (137)
Q Consensus        44 ~SRc-~~i~~~~~~~~~   59 (137)
                      ++|+ ..+.+++++.++
T Consensus       379 lDR~dl~~~~~~~~~~~  395 (499)
T TIGR00368       379 LDRIDLSVEVPLLPPEK  395 (499)
T ss_pred             HhhCCEEEEEcCCCHHH
Confidence            9998 567887775543

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

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=96.54  E-value=0.018  Score=48.84  Aligned_cols=106  Identities=16%  Similarity=0.170  Sum_probs=77.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc----C------CceEEEEeCCC-------CCc-hhhhhcc--eeeEecCCCHH-H
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK----G------LNKVFFCCSDV-------SKL-QPIKSLC--TVIQLLPPSKQ-E   59 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~----~------~~~~Il~~n~~-------~~i-~~l~SRc--~~i~~~~~~~~-~   59 (137)
                      +|+||+-.|.-+.|..|++++++-.    +      ..++|-+|+..       .+. .+|.-|.  .++.++|+.+- +
T Consensus       411 lFldeIgd~p~~~Qs~LLrVl~e~~v~p~g~~~~~vdirvi~ath~dl~~lv~~g~fredLyyrL~~~~i~lP~lr~R~d  490 (606)
T COG3284         411 LFLDEIGDMPLALQSRLLRVLQEGVVTPLGGTRIKVDIRVIAATHRDLAQLVEQGRFREDLYYRLNAFVITLPPLRERSD  490 (606)
T ss_pred             cHHHHhhhchHHHHHHHHHHHhhCceeccCCcceeEEEEEEeccCcCHHHHHHcCCchHHHHHHhcCeeeccCchhcccc
Confidence            5899999999999999999999742    1      23466666543       346 7888887  45666555442 3


Q ss_pred             HHHHHHHHHHHc---CCCCCHHHHHHHHHH-cCCcHHHHHHHHHHHHhcCC
Q 042716           60 IVEVLEFIAEQE---GIQLPHQLAEKIADN-SKNNLRQAIRSFEASRQMNY  106 (137)
Q Consensus        60 i~~~l~~i~~~e---gi~i~~~~l~~i~~~-~~gd~R~aln~L~~~~~~~~  106 (137)
                      -...|.++..++   .+.++++++..+..+ -.|++|.+.|.++.++...+
T Consensus       491 ~~~~l~~~~~~~~~~~~~l~~~~~~~l~~~~WPGNirel~~v~~~~~~l~~  541 (606)
T COG3284         491 RIPLLDRILKRENDWRLQLDDDALARLLAYRWPGNIRELDNVIERLAALSD  541 (606)
T ss_pred             cHHHHHHHHHHccCCCccCCHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCC
Confidence            344455555544   478999999997664 89999999999999987654

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

Probab=96.40  E-value=0.003  Score=50.59  Aligned_cols=87  Identities=14%  Similarity=0.186  Sum_probs=56.5

Q ss_pred             CcccccCcCCHHH----HHHHHHHHHhc---------cCCce-EEE-EeCCCCCc-hhhhhcc-eeeEecCCCHHHHHHH
Q 042716            1 IILCEADKLSTDA----LLYMRWLLERY---------KGLNK-VFF-CCSDVSKL-QPIKSLC-TVIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~~~----~~~L~~~le~~---------~~~~~-~Il-~~n~~~~i-~~l~SRc-~~i~~~~~~~~~i~~~   63 (137)
                      |||||+|.+...-    -++-..+-.++         ..+.+ +|+ +||.+..+ .++.+|. ..|.+.-|+..+-.++
T Consensus       190 IFIDEvds~L~~R~s~dHEa~a~mK~eFM~~WDGl~s~~~~rVlVlgATNRP~DlDeAiiRR~p~rf~V~lP~~~qR~kI  269 (386)
T KOG0737|consen  190 IFIDEVDSFLGQRRSTDHEATAMMKNEFMALWDGLSSKDSERVLVLGATNRPFDLDEAIIRRLPRRFHVGLPDAEQRRKI  269 (386)
T ss_pred             eehhhHHHHHhhcccchHHHHHHHHHHHHHHhccccCCCCceEEEEeCCCCCccHHHHHHHhCcceeeeCCCchhhHHHH
Confidence            6899999986321    11111111112         12323 444 45666779 9999994 7899999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHcC
Q 042716           64 LEFIAEQEGIQLPHQLAEKIADNSK   88 (137)
Q Consensus        64 l~~i~~~egi~i~~~~l~~i~~~~~   88 (137)
                      |+-+.++|.++ ++=.+..+++.++
T Consensus       270 LkviLk~e~~e-~~vD~~~iA~~t~  293 (386)
T KOG0737|consen  270 LKVILKKEKLE-DDVDLDEIAQMTE  293 (386)
T ss_pred             HHHHhcccccC-cccCHHHHHHhcC
Confidence            99999999885 2223555555544

>CHL00206 ycf2 Ycf2; Provisional

Probab=96.40  E-value=0.01  Score=56.19  Aligned_cols=88  Identities=13%  Similarity=0.037  Sum_probs=58.1

Q ss_pred             CcccccCcCCHHH-----HHHHHHHHHhc-----cCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKLSTDA-----LLYMRWLLERY-----KGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l~~~~-----~~~L~~~le~~-----~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i~~~l~~   66 (137)
                      |+|||+|.+....     .+.|+..|...     ..++.+|.+||.+..| |+|+.  |. ..+.++.|+..+-.+.+..
T Consensus      1736 IFIDEIDaL~~~ds~~ltL~qLLneLDg~~~~~s~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R~kiL~I 1815 (2281)
T CHL00206       1736 IWIPNIHDLNVNESNYLSLGLLVNSLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKHFFT 1815 (2281)
T ss_pred             EEEEchhhcCCCccceehHHHHHHHhccccccCCCCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhHHHHHHH
Confidence            5899999997653     34555666422     1234466667777888 99997  76 6788888887766666654


Q ss_pred             HHHHcCCCCCHH--HHHHHHHHcC
Q 042716           67 IAEQEGIQLPHQ--LAEKIADNSK   88 (137)
Q Consensus        67 i~~~egi~i~~~--~l~~i~~~~~   88 (137)
                      .....|+.+.++  .+..+++.+.
T Consensus      1816 Ll~tkg~~L~~~~vdl~~LA~~T~ 1839 (2281)
T CHL00206       1816 LSYTRGFHLEKKMFHTNGFGSITM 1839 (2281)
T ss_pred             HHhhcCCCCCcccccHHHHHHhCC
Confidence            445556666543  2566777653

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

Probab=96.35  E-value=0.0045  Score=44.49  Aligned_cols=39  Identities=18%  Similarity=0.042  Sum_probs=32.1

Q ss_pred             CcccccCcCCH-----------HHHHHHHHHHHhcc-----------CCceEEEEeCCCCC
Q 042716            1 IILCEADKLST-----------DALLYMRWLLERYK-----------GLNKVFFCCSDVSK   39 (137)
Q Consensus         1 iiiDEid~l~~-----------~~~~~L~~~le~~~-----------~~~~~Il~~n~~~~   39 (137)
                      |++||+|+.++           +.|++|++++|+-.           .++.||+|+|-...
T Consensus        72 VllDEidKa~~~~~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~~~  132 (171)
T PF07724_consen   72 VLLDEIDKAHPSNSGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFGAE  132 (171)
T ss_dssp             EEEETGGGCSHTTTTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSSTH
T ss_pred             hhhHHHhhccccccccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEecccccc
Confidence            58999999999           99999999999642           35668888886654

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.34  E-value=0.035  Score=46.26  Aligned_cols=102  Identities=14%  Similarity=0.065  Sum_probs=67.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc---------CCceEEEEeCC-CC---Cc-hhhhhcce-eeEecCCCH-HHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK---------GLNKVFFCCSD-VS---KL-QPIKSLCT-VIQLLPPSK-QEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~---------~~~~~Il~~n~-~~---~i-~~l~SRc~-~i~~~~~~~-~~i~~~l   64 (137)
                      +|+||++.+++..|++|+..|++-.         -..+|+++|++ .+   .. +++..|+. .+.+++|++ ++....|
T Consensus       111 LfLDEI~rasp~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN~LPE~g~~leAL~DRFliri~vp~l~~~~~e~~lL  190 (498)
T PRK13531        111 VFLDEIWKAGPAILNTLLTAINERRFRNGAHEEKIPMRLLVTASNELPEADSSLEALYDRMLIRLWLDKVQDKANFRSML  190 (498)
T ss_pred             EeecccccCCHHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECCCCcccCCchHHhHhhEEEEEECCCCCchHHHHHHH
Confidence            5899999999999999999996533         23456665553 33   13 68999985 488888874 4434444


Q ss_pred             HHH-----------------------HHHcCCCCCHHHHHHHHHHcC----------CcHHHHHHHHHHHH
Q 042716           65 EFI-----------------------AEQEGIQLPHQLAEKIADNSK----------NNLRQAIRSFEASR  102 (137)
Q Consensus        65 ~~i-----------------------~~~egi~i~~~~l~~i~~~~~----------gd~R~aln~L~~~~  102 (137)
                      ...                       ..-..+.+++.+.++|.+...          -+.|..+.++..+.
T Consensus       191 ~~~~~~~~~~~~~~~vis~eel~~lq~~v~~V~v~d~v~eyI~~L~~~lr~~r~~~~~SpR~~~~l~~~ak  261 (498)
T PRK13531        191 TSQQDENDNPVPASLQITDEEYQQWQKEIGKITLPDHVFELIFQLRQQLDALPNAPYVSDRRWKKAIRLLQ  261 (498)
T ss_pred             HcccccccCCCcccCCCCHHHHHHHHHHhcceeCCHHHHHHHHHHHHHHhcCCCCCCcCcHHHHHHHHHHH
Confidence            321                       112456788888888766531          35677776665443

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

Probab=96.29  E-value=0.0054  Score=43.96  Aligned_cols=52  Identities=13%  Similarity=0.125  Sum_probs=38.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc-----------cCCceEEEEeCCC-------CCc-hhhhhcceeeEe
Q 042716            1 IILCEADKLSTDALLYMRWLLERY-----------KGLNKVFFCCSDV-------SKL-QPIKSLCTVIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~-----------~~~~~~Il~~n~~-------~~i-~~l~SRc~~i~~   52 (137)
                      ++|||++.|+...|..|++++++.           +.++++|++|+..       ..+ ++|.-|..++++
T Consensus        97 L~Ld~I~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~st~~~l~~~v~~g~fr~dLy~rL~~~~i  167 (168)
T PF00158_consen   97 LFLDEIEDLPPELQAKLLRVLEEGKFTRLGSDKPVPVDVRIIASTSKDLEELVEQGRFREDLYYRLNVFTI  167 (168)
T ss_dssp             EEEETGGGS-HHHHHHHHHHHHHSEEECCTSSSEEE--EEEEEEESS-HHHHHHTTSS-HHHHHHHTTEEE
T ss_pred             EeecchhhhHHHHHHHHHHHHhhchhccccccccccccceEEeecCcCHHHHHHcCCChHHHHHHhceEec
Confidence            589999999999999999999964           2367899999866       245 778777765554

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

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=96.28  E-value=0.16  Score=43.35  Aligned_cols=127  Identities=12%  Similarity=0.128  Sum_probs=82.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCC-----------ceEEEEeCCCC-----Cc-hhhhhcc-eeeEecCCCHHHHH-
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGL-----------NKVFFCCSDVS-----KL-QPIKSLC-TVIQLLPPSKQEIV-   61 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~-----------~~~Il~~n~~~-----~i-~~l~SRc-~~i~~~~~~~~~i~-   61 (137)
                      +++||+..+.+..+.+|+..||+-.-.           .+|++++.+..     ++ +++..|+ ..+.+..++..+.. 
T Consensus        97 L~lDe~n~~~~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~~~L~~~lLDRf~l~v~v~~~~~~~~~~  176 (584)
T PRK13406         97 LVLAMAERLEPGTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEEDERAPAALADRLAFHLDLDGLALRDARE  176 (584)
T ss_pred             EEecCcccCCHHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcccCCCHHhHhheEEEEEcCCCChHHhcc
Confidence            589999999999999999999964211           35888875433     48 8999998 56888888766532 


Q ss_pred             ------HHHHHHHHHcCCCCCHHHHHHHHHH---cCC-cHHHHHHHHHHHHhcCCCcccCccccCCcHHHHHHHHHHHHh
Q 042716           62 ------EVLEFIAEQEGIQLPHQLAEKIADN---SKN-NLRQAIRSFEASRQMNYPFVEGQVILTGWEDDITNIATKIIE  131 (137)
Q Consensus        62 ------~~l~~i~~~egi~i~~~~l~~i~~~---~~g-d~R~aln~L~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~  131 (137)
                            .++.....-.++.++++.+.+++..   .+- ++|..+.++..+..... +.....+   -++++.+.+..+|.
T Consensus       177 ~~~~~~~I~~AR~rl~~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~Aa-L~Gr~~V---~~~dv~~Aa~lvL~  252 (584)
T PRK13406        177 IPIDADDIAAARARLPAVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAA-LAGRTAV---EEEDLALAARLVLA  252 (584)
T ss_pred             cCCCHHHHHHHHHHHccCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHH-HcCCCCC---CHHHHHHHHHHHHH
Confidence                  1111111224789999999987764   222 67888888876654221 1111111   25566666666654

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

Probab=96.27  E-value=0.015  Score=44.98  Aligned_cols=73  Identities=18%  Similarity=0.289  Sum_probs=56.0

Q ss_pred             CcccccCcCC-----------HHHHHHHHHHHHhc-----cCCceEEEEeCCCCCc-hhhhhcc---eeeEecCCCHHHH
Q 042716            1 IILCEADKLS-----------TDALLYMRWLLERY-----KGLNKVFFCCSDVSKL-QPIKSLC---TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~-----------~~~~~~L~~~le~~-----~~~~~~Il~~n~~~~i-~~l~SRc---~~i~~~~~~~~~i   60 (137)
                      ||+||+|++.           .+.|..++.++++.     +.|..+|++||...-+ ++|.--.   ..+.|++|+.+..
T Consensus       244 ifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfeatknikvimatnridild~allrpgridrkiefp~p~e~ar  323 (404)
T KOG0728|consen  244 IFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEAR  323 (404)
T ss_pred             EeeecccccccccccCCCCccHHHHHHHHHHHHhccccccccceEEEEeccccccccHhhcCCCcccccccCCCCCHHHH
Confidence            6899999983           23477788888764     3578899999999888 7776533   4699999999988


Q ss_pred             HHHHHHHHHHcCC
Q 042716           61 VEVLEFIAEQEGI   73 (137)
Q Consensus        61 ~~~l~~i~~~egi   73 (137)
                      .++|+-..++.++
T Consensus       324 ~~ilkihsrkmnl  336 (404)
T KOG0728|consen  324 LDILKIHSRKMNL  336 (404)
T ss_pred             HHHHHHhhhhhch
Confidence            8888766665543

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

Probab=96.21  E-value=0.017  Score=45.45  Aligned_cols=58  Identities=12%  Similarity=0.075  Sum_probs=42.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc----------cCCceEEE-Ee-C-----CCCCc-hhhhhcc-eeeEecCCCHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERY----------KGLNKVFF-CC-S-----DVSKL-QPIKSLC-TVIQLLPPSKQ   58 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~----------~~~~~~Il-~~-n-----~~~~i-~~l~SRc-~~i~~~~~~~~   58 (137)
                      +++||+++-.+..|++|+..|++.          .-..+|++ +| |     ..+.+ .+++.|| ..+.+..|..+
T Consensus       116 ll~DEInra~p~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~g~~~l~eA~ldRf~~~~~v~yp~~~  192 (329)
T COG0714         116 LLLDEINRAPPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEGTYPLPEALLDRFLLRIYVDYPDSE  192 (329)
T ss_pred             EEEeccccCCHHHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccCCCcCCCHHHHhhEEEEEecCCCCch
Confidence            479999999999999999999983          12233333 34 4     22448 9999999 77888888444

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=96.17  E-value=0.014  Score=44.26  Aligned_cols=99  Identities=18%  Similarity=0.114  Sum_probs=58.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCchhhhhcceeeEecCCCHHHHHHHHHHHHHHcC---CCCCH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEG---IQLPH   77 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~eg---i~i~~   77 (137)
                      +|+|+++...  ....+...+-....++++|+||.+..-.......+..+++.+++.++....+...+....   -.-.+
T Consensus       105 lVlDdv~~~~--~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~  182 (287)
T PF00931_consen  105 LVLDDVWDEE--DLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLSEEEALELFKKRAGRKESESPEDLE  182 (287)
T ss_dssp             EEEEEE-SHH--HH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--HHHHHHHHHHHHTSHS----TTSC
T ss_pred             eeeeeecccc--cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            4788887655  444455555444567899999987542255544488999999999999999998876544   11224


Q ss_pred             HHHHHHHHHcCCcHHHHHHHHHHH
Q 042716           78 QLAEKIADNSKNNLRQAIRSFEAS  101 (137)
Q Consensus        78 ~~l~~i~~~~~gd~R~aln~L~~~  101 (137)
                      +....|++.|+|-+-.+.-+-..+
T Consensus       183 ~~~~~i~~~c~glPLal~~~a~~l  206 (287)
T PF00931_consen  183 DLAKEIVEKCGGLPLALKLIASYL  206 (287)
T ss_dssp             THHHHHHHHTTT-HHHHHHHHHHH
T ss_pred             cccccccccccccccccccccccc
Confidence            567899999988665544443333

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

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

Probab=96.00  E-value=0.015  Score=49.80  Aligned_cols=100  Identities=13%  Similarity=0.135  Sum_probs=64.4

Q ss_pred             CcccccCcCCHHH-----------HHHHHHHHHhc--cCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHHHHH
Q 042716            1 IILCEADKLSTDA-----------LLYMRWLLERY--KGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~~~-----------~~~L~~~le~~--~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i~~~   63 (137)
                      +|+||+|.+..+-           -+.|+.-|+=.  .+++.+|-+||-+..| ++|..  |. .++.++.|+.+....+
T Consensus       531 iFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~I  610 (693)
T KOG0730|consen  531 IFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEI  610 (693)
T ss_pred             EehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCcEEEEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHH
Confidence            5899999985432           33344444321  2345566667777889 99999  77 7899999999888888


Q ss_pred             HHHHHHHcCCCCCHH-HHHHHHHHcCC-cHHHHHHHHHHHH
Q 042716           64 LEFIAEQEGIQLPHQ-LAEKIADNSKN-NLRQAIRSFEASR  102 (137)
Q Consensus        64 l~~i~~~egi~i~~~-~l~~i~~~~~g-d~R~aln~L~~~~  102 (137)
                      ++..+++  ++++++ .+..|+...+| +=+.+.++.|.+.
T Consensus       611 lk~~~kk--mp~~~~vdl~~La~~T~g~SGAel~~lCq~A~  649 (693)
T KOG0730|consen  611 LKQCAKK--MPFSEDVDLEELAQATEGYSGAEIVAVCQEAA  649 (693)
T ss_pred             HHHHHhc--CCCCccccHHHHHHHhccCChHHHHHHHHHHH
Confidence            8876654  556666 57777774322 2333444444433

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

Probab=95.96  E-value=0.026  Score=46.72  Aligned_cols=102  Identities=13%  Similarity=0.079  Sum_probs=67.5

Q ss_pred             CcccccCcCCH-----------HHHHHHHHHHH--hccCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHHHHH
Q 042716            1 IILCEADKLST-----------DALLYMRWLLE--RYKGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~-----------~~~~~L~~~le--~~~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i~~~   63 (137)
                      |||||+|.+..           ...+.|+..++  +...++.+|.+||.+..+ ++++-  |+ ..+.|++|+.++..+.
T Consensus       339 iFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i  418 (494)
T COG0464         339 IFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEI  418 (494)
T ss_pred             EEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCCCHHHHHHH
Confidence            68999999822           34666777774  233445567778888888 77666  77 5899999999999999


Q ss_pred             HHHHHHHcCCC-CCHHHHHHHHHHcCC-cHHHHHHHHHHHH
Q 042716           64 LEFIAEQEGIQ-LPHQLAEKIADNSKN-NLRQAIRSFEASR  102 (137)
Q Consensus        64 l~~i~~~egi~-i~~~~l~~i~~~~~g-d~R~aln~L~~~~  102 (137)
                      ++......+.. ..+-.+..+++...| .-..+.+.++.+.
T Consensus       419 ~~~~~~~~~~~~~~~~~~~~l~~~t~~~sgadi~~i~~ea~  459 (494)
T COG0464         419 FKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAA  459 (494)
T ss_pred             HHHHhcccCCcchhhhhHHHHHHHhcCCCHHHHHHHHHHHH
Confidence            98887766554 233445556664332 3334444444443

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

Probab=95.96  E-value=0.039  Score=47.29  Aligned_cols=90  Identities=16%  Similarity=0.201  Sum_probs=69.4

Q ss_pred             CcccccCcCCH----------HHHHHHHHHHHhcc--CCceEEEEeCCCCCc-hhhhh-cc-eeeEecCCCHHHHHHHHH
Q 042716            1 IILCEADKLST----------DALLYMRWLLERYK--GLNKVFFCCSDVSKL-QPIKS-LC-TVIQLLPPSKQEIVEVLE   65 (137)
Q Consensus         1 iiiDEid~l~~----------~~~~~L~~~le~~~--~~~~~Il~~n~~~~i-~~l~S-Rc-~~i~~~~~~~~~i~~~l~   65 (137)
                      ++|||+|.+.+          .....|+..++-..  .+..++-++|.+..| +.+|- |+ ..+.+.-|+..+-.++++
T Consensus       282 i~IdEld~l~p~r~~~~~~e~Rv~sqlltL~dg~~~~~~vivl~atnrp~sld~alRRgRfd~ev~IgiP~~~~RldIl~  361 (693)
T KOG0730|consen  282 IFIDELDALCPKREGADDVESRVVSQLLTLLDGLKPDAKVIVLAATNRPDSLDPALRRGRFDREVEIGIPGSDGRLDILR  361 (693)
T ss_pred             EeHHhHhhhCCcccccchHHHHHHHHHHHHHhhCcCcCcEEEEEecCCccccChhhhcCCCcceeeecCCCchhHHHHHH
Confidence            58999999975          23566888888665  444466667888889 99994 77 568888899999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHcCCcH
Q 042716           66 FIAEQEGIQLPHQLAEKIADNSKNNL   91 (137)
Q Consensus        66 ~i~~~egi~i~~~~l~~i~~~~~gd~   91 (137)
                      ...++.+.. ++..+..++..+.|-.
T Consensus       362 ~l~k~~~~~-~~~~l~~iA~~thGyv  386 (693)
T KOG0730|consen  362 VLTKKMNLL-SDVDLEDIAVSTHGYV  386 (693)
T ss_pred             HHHHhcCCc-chhhHHHHHHHccchh
Confidence            998888876 6677888887766543

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

Probab=95.91  E-value=0.013  Score=40.24  Aligned_cols=54  Identities=22%  Similarity=0.210  Sum_probs=39.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc-cCCceEEEEeCCCC-------Cc-hhhhhcc--eeeEecC
Q 042716            1 IILCEADKLSTDALLYMRWLLERY-KGLNKVFFCCSDVS-------KL-QPIKSLC--TVIQLLP   54 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~-~~~~~~Il~~n~~~-------~i-~~l~SRc--~~i~~~~   54 (137)
                      ++|+|+|.|+.+.|..|...+++. ..++++|++|....       .+ +.|..|.  ..+.+++
T Consensus        73 L~l~~i~~L~~~~Q~~L~~~l~~~~~~~~RlI~ss~~~l~~l~~~~~~~~~L~~~l~~~~i~lPp  137 (138)
T PF14532_consen   73 LYLKNIDRLSPEAQRRLLDLLKRQERSNVRLIASSSQDLEELVEEGRFSPDLYYRLSQLEIHLPP  137 (138)
T ss_dssp             EEEECGCCS-HHHHHHHHHHHHHCTTTTSEEEEEECC-CCCHHHHSTHHHHHHHHCSTCEEEE--
T ss_pred             EEECChHHCCHHHHHHHHHHHHhcCCCCeEEEEEeCCCHHHHhhccchhHHHHHHhCCCEEeCCC
Confidence            579999999999999999999964 56789999998663       25 6777775  3455543

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

Probab=95.90  E-value=0.073  Score=46.69  Aligned_cols=102  Identities=18%  Similarity=0.257  Sum_probs=75.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCCC---------------------------C-c-
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDVS---------------------------K-L-   40 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~~---------------------------~-i-   40 (137)
                      |++||+++=++.-.+.|+-+++.-.           .||.+|||+|--.                           + . 
T Consensus       597 iLlDEIEKAHpdV~nilLQVlDdGrLTD~~Gr~VdFrNtiIImTSN~Gs~~i~~~~~~~~~~~~~~~~~~v~~~l~~~F~  676 (786)
T COG0542         597 ILLDEIEKAHPDVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNAGSEEILRDADGDDFADKEALKEAVMEELKKHFR  676 (786)
T ss_pred             EEechhhhcCHHHHHHHHHHhcCCeeecCCCCEEecceeEEEEecccchHHHHhhccccccchhhhHHHHHHHHHHhhCC
Confidence            5799999999999999999999643           4778999998210                           1 3 


Q ss_pred             hhhhhcce-eeEecCCCHHHHHHHHHH-------HHHHcCC--CCCHHHHHHHHHHcC---CcHHHHHHHHHHHH
Q 042716           41 QPIKSLCT-VIQLLPPSKQEIVEVLEF-------IAEQEGI--QLPHQLAEKIADNSK---NNLRQAIRSFEASR  102 (137)
Q Consensus        41 ~~l~SRc~-~i~~~~~~~~~i~~~l~~-------i~~~egi--~i~~~~l~~i~~~~~---gd~R~aln~L~~~~  102 (137)
                      |.+++|.- ++.|.+++.+++..++..       ...+.|+  .+++++..++++.+.   .-.|-+-+.+|...
T Consensus       677 PEFLNRid~II~F~~L~~~~l~~Iv~~~L~~l~~~L~~~~i~l~~s~~a~~~l~~~gyd~~~GARpL~R~Iq~~i  751 (786)
T COG0542         677 PEFLNRIDEIIPFNPLSKEVLERIVDLQLNRLAKRLAERGITLELSDEAKDFLAEKGYDPEYGARPLRRAIQQEI  751 (786)
T ss_pred             HHHHhhcccEEeccCCCHHHHHHHHHHHHHHHHHHHHhCCceEEECHHHHHHHHHhccCCCcCchHHHHHHHHHH
Confidence            66777875 999999999987766532       3334454  678999999998754   33566666666554

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=95.86  E-value=0.094  Score=42.52  Aligned_cols=103  Identities=17%  Similarity=0.167  Sum_probs=75.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhccee--eEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLCTV--IQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc~~--i~~~~~~~--   57 (137)
                      +++||+-.|++.-|..|++++..-+           -++++|++|..+       .+. .+|--|.-+  ++++|+-+  
T Consensus       297 VlLDeIgEmSp~lQaKLLRFL~DGtFRRVGee~Ev~vdVRVIcatq~nL~~lv~~g~fReDLfyRLNVLtl~~PpLRer~  376 (511)
T COG3283         297 VLLDEIGEMSPRLQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQVNLVELVQKGKFREDLFYRLNVLTLNLPPLRERP  376 (511)
T ss_pred             EEeehhhhcCHHHHHHHHHHhcCCceeecCCcceEEEEEEEEecccccHHHHHhcCchHHHHHHHhheeeecCCccccCc
Confidence            5899999999999999999997432           246788887654       346 788888754  44444433  


Q ss_pred             HHH----HHHHHHHHHHcCC---CCCHHHHHHHHHH-cCCcHHHHHHHHHHHHh
Q 042716           58 QEI----VEVLEFIAEQEGI---QLPHQLAEKIADN-SKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        58 ~~i----~~~l~~i~~~egi---~i~~~~l~~i~~~-~~gd~R~aln~L~~~~~  103 (137)
                      +++    .-.+.+++.+-|+   +++++.+.++.++ -.|++|+.-|.+-.+..
T Consensus       377 ~di~pL~e~Fv~q~s~elg~p~pkl~~~~~~~L~~y~WpGNVRqL~N~iyRA~s  430 (511)
T COG3283         377 QDIMPLAELFVQQFSDELGVPRPKLAADLLTVLTRYAWPGNVRQLKNAIYRALT  430 (511)
T ss_pred             ccchHHHHHHHHHHHHHhCCCCCccCHHHHHHHHHcCCCccHHHHHHHHHHHHH
Confidence            222    2346778888887   4678888888876 78999999999876543

>CHL00195 ycf46 Ycf46; Provisional

Probab=95.85  E-value=0.21  Score=41.68  Aligned_cols=97  Identities=18%  Similarity=0.259  Sum_probs=66.9

Q ss_pred             cccccCcC--CHHHHHHHHHHHHhccCCc-eEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCH
Q 042716            2 ILCEADKL--STDALLYMRWLLERYKGLN-KVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPH   77 (137)
Q Consensus         2 iiDEid~l--~~~~~~~L~~~le~~~~~~-~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~   77 (137)
                      ++.|.|.+  .+.....|+.+........ .+|+.+ ..-.+ +.|..-+.++.|+-|+.+++...+..++...++.+++
T Consensus        86 vl~d~h~~~~~~~~~r~l~~l~~~~~~~~~~~i~~~-~~~~~p~el~~~~~~~~~~lP~~~ei~~~l~~~~~~~~~~~~~  164 (489)
T CHL00195         86 LLKDFNRFLNDISISRKLRNLSRILKTQPKTIIIIA-SELNIPKELKDLITVLEFPLPTESEIKKELTRLIKSLNIKIDS  164 (489)
T ss_pred             EEecchhhhcchHHHHHHHHHHHHHHhCCCEEEEEc-CCCCCCHHHHhceeEEeecCcCHHHHHHHHHHHHHhcCCCCCH
Confidence            56667776  3334555655554443333 344444 34557 6777778899999999999999999998888999999


Q ss_pred             HHHHHHHHHcCCc-HHHHHHHHH
Q 042716           78 QLAEKIADNSKNN-LRQAIRSFE   99 (137)
Q Consensus        78 ~~l~~i~~~~~gd-~R~aln~L~   99 (137)
                      +.++.+++.+.|= .-.+-+.+.
T Consensus       165 ~~~~~l~~~~~gls~~~~~~~~~  187 (489)
T CHL00195        165 ELLENLTRACQGLSLERIRRVLS  187 (489)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHH
Confidence            9999999986553 333333333

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=95.84  E-value=0.028  Score=49.97  Aligned_cols=58  Identities=14%  Similarity=0.205  Sum_probs=43.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-------------CCceEEEEeCCC-------------CCc-hhhhhcc-eeeEe
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-------------GLNKVFFCCSDV-------------SKL-QPIKSLC-TVIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-------------~~~~~Il~~n~~-------------~~i-~~l~SRc-~~i~~   52 (137)
                      ++|||+|.|+...|.+|+..||+..             ..+++|.+||..             -.+ ++|.||+ .+|-+
T Consensus       561 L~IDEidkms~~~Q~aLlEaMEqqtIsI~KaGi~~tL~ar~rVIAAaNP~~gryd~~~s~~eni~Lp~~LLSRFDLIf~l  640 (915)
T PTZ00111        561 CCIDELDKCHNESRLSLYEVMEQQTVTIAKAGIVATLKAETAILASCNPINSRYNKNKAVIENINISPSLFTRFDLIYLV  640 (915)
T ss_pred             EEecchhhCCHHHHHHHHHHHhCCEEEEecCCcceecCCCeEEEEEcCCcccccCcccCcccccCCChHHhhhhcEEEEe
Confidence            4799999999999999999999753             356788888753             137 8999999 55444


Q ss_pred             cCCCHH
Q 042716           53 LPPSKQ   58 (137)
Q Consensus        53 ~~~~~~   58 (137)
                      ....+.
T Consensus       641 ~D~~d~  646 (915)
T PTZ00111        641 LDHIDQ  646 (915)
T ss_pred             cCCCCh
Confidence            444443

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=95.83  E-value=0.14  Score=39.45  Aligned_cols=98  Identities=18%  Similarity=0.186  Sum_probs=74.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc---CCceEEEEeCCC--C--C--c-hhhhhccee-eEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK---GLNKVFFCCSDV--S--K--L-QPIKSLCTV-IQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~---~~~~~Il~~n~~--~--~--i-~~l~SRc~~-i~~~~~~~~~i~~~l~~i~~   69 (137)
                      +++||+|.++.++-.+|+.+.|--.   +.-.+++++-..  +  +  . ..+.-||.+ |.++|++.++...+|++..+
T Consensus       135 l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~~~~~t~~yl~~~Le  214 (269)
T COG3267         135 LMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLTEAETGLYLRHRLE  214 (269)
T ss_pred             EeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecCCcChHHHHHHHHHHHh
Confidence            3689999999999999988877533   223366666432  1  1  2 677789988 99999999999999999888


Q ss_pred             HcCCC---CCHHHHHHHHHHcCCcHHHHHHHH
Q 042716           70 QEGIQ---LPHQLAEKIADNSKNNLRQAIRSF   98 (137)
Q Consensus        70 ~egi~---i~~~~l~~i~~~~~gd~R~aln~L   98 (137)
                      ..|..   ++++++..+...+.|-+|..-+..
T Consensus       215 ~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~  246 (269)
T COG3267         215 GAGLPEPLFSDDALLLIHEASQGIPRLINNLA  246 (269)
T ss_pred             ccCCCcccCChhHHHHHHHHhccchHHHHHHH
Confidence            77664   568889999999999666554443

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

Probab=95.80  E-value=0.016  Score=50.62  Aligned_cols=101  Identities=14%  Similarity=0.182  Sum_probs=77.9

Q ss_pred             CcccccCcCC---------HHHHHHHHHHHHhccCCceEEEEeCCC-C-C-c---hhhhhcceeeEecCCCHHHHHHHHH
Q 042716            1 IILCEADKLS---------TDALLYMRWLLERYKGLNKVFFCCSDV-S-K-L---QPIKSLCTVIQLLPPSKQEIVEVLE   65 (137)
Q Consensus         1 iiiDEid~l~---------~~~~~~L~~~le~~~~~~~~Il~~n~~-~-~-i---~~l~SRc~~i~~~~~~~~~i~~~l~   65 (137)
                      +||||+|.+.         ..+.|.|...+.  .+..++|-+|+.. + + +   ++|--|++.+.+..|+.++...+|+
T Consensus       266 LFIDEiHtiVGAG~~~G~a~DAaNiLKPaLA--RGeL~~IGATT~~EYRk~iEKD~AL~RRFQ~V~V~EPs~e~ti~ILr  343 (786)
T COG0542         266 LFIDEIHTIVGAGATEGGAMDAANLLKPALA--RGELRCIGATTLDEYRKYIEKDAALERRFQKVLVDEPSVEDTIAILR  343 (786)
T ss_pred             EEEechhhhcCCCcccccccchhhhhHHHHh--cCCeEEEEeccHHHHHHHhhhchHHHhcCceeeCCCCCHHHHHHHHH
Confidence            5899999982         225677777887  6667788888644 2 2 3   7888899999999999999999997


Q ss_pred             HHHH----HcCCCCCHHHHHHHHHHcCCc------HHHHHHHHHHHHh
Q 042716           66 FIAE----QEGIQLPHQLAEKIADNSKNN------LRQAIRSFEASRQ  103 (137)
Q Consensus        66 ~i~~----~egi~i~~~~l~~i~~~~~gd------~R~aln~L~~~~~  103 (137)
                      -+..    ..|+.++++++.+.+..|.+-      +.+|+.+++.+..
T Consensus       344 Glk~~yE~hH~V~i~D~Al~aAv~LS~RYI~dR~LPDKAIDLiDeA~a  391 (786)
T COG0542         344 GLKERYEAHHGVRITDEALVAAVTLSDRYIPDRFLPDKAIDLLDEAGA  391 (786)
T ss_pred             HHHHHHHHccCceecHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHH
Confidence            6654    458899999999988877543      4578888876653

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

Probab=95.79  E-value=0.011  Score=47.29  Aligned_cols=87  Identities=18%  Similarity=0.294  Sum_probs=63.6

Q ss_pred             CcccccCcCCHH------------HHHHHHHHHHhccC--------CceEEEEeCC------CCCc-hhhhhcce-eeEe
Q 042716            1 IILCEADKLSTD------------ALLYMRWLLERYKG--------LNKVFFCCSD------VSKL-QPIKSLCT-VIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~------------~~~~L~~~le~~~~--------~~~~Il~~n~------~~~i-~~l~SRc~-~i~~   52 (137)
                      |||||+|.+...            .|..|+.++|-..-        +-+++|++.-      |+.+ |.|+-|+- .+.+
T Consensus       254 vFIDEIDKIa~~~~~g~~dvSREGVQRDlLPlvEGstV~TKyG~VkTdHILFIasGAFh~sKPSDLiPELQGRfPIRVEL  333 (444)
T COG1220         254 VFIDEIDKIAKRGGSGGPDVSREGVQRDLLPLVEGSTVSTKYGPVKTDHILFIASGAFHVAKPSDLIPELQGRFPIRVEL  333 (444)
T ss_pred             EEEehhhHHHhcCCCCCCCcchhhhcccccccccCceeeccccccccceEEEEecCceecCChhhcChhhcCCCceEEEc
Confidence            689999998322            38889999984321        2246666653      3457 99999995 5999


Q ss_pred             cCCCHHHHHHHHH-----------HHHHHcCC--CCCHHHHHHHHHHc
Q 042716           53 LPPSKQEIVEVLE-----------FIAEQEGI--QLPHQLAEKIADNS   87 (137)
Q Consensus        53 ~~~~~~~i~~~l~-----------~i~~~egi--~i~~~~l~~i~~~~   87 (137)
                      .+++.++...+|.           ...+-||+  .++++++..|++.+
T Consensus       334 ~~Lt~~Df~rILtep~~sLikQY~aLlkTE~v~l~FtddaI~~iAeiA  381 (444)
T COG1220         334 DALTKEDFERILTEPKASLIKQYKALLKTEGVELEFTDDAIKRIAEIA  381 (444)
T ss_pred             ccCCHHHHHHHHcCcchHHHHHHHHHHhhcCeeEEecHHHHHHHHHHH
Confidence            9999999988873           23456776  46799999988764

>PRK09862 putative ATP-dependent protease; Provisional

Probab=95.76  E-value=0.026  Score=47.21  Aligned_cols=58  Identities=14%  Similarity=0.149  Sum_probs=44.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-------------CCceEEEEeCCCC---------------------Cc-hhhhh
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-------------GLNKVFFCCSDVS---------------------KL-QPIKS   45 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-------------~~~~~Il~~n~~~---------------------~i-~~l~S   45 (137)
                      +|+||++.+....+++|+..||+..             .++++|.++|..+                     ++ .++++
T Consensus       298 LfLDEi~e~~~~~~~~L~~~LE~g~v~I~r~g~~~~~pa~f~lIAa~NP~pcG~~~~~~c~c~~~~~~~Y~~~ls~plLD  377 (506)
T PRK09862        298 LFLDELPEFERRTLDALREPIESGQIHLSRTRAKITYPARFQLVAAMNPSPTGHYQGNHNRCTPEQTLRYLNRLSGPFLD  377 (506)
T ss_pred             EecCCchhCCHHHHHHHHHHHHcCcEEEecCCcceeccCCEEEEEeecCccceecCCCCCCcCHHHHHHHHhhCCHhHHh
Confidence            5899999999999999999998642             2456777777542                     47 79999


Q ss_pred             cce-eeEecCCCHH
Q 042716           46 LCT-VIQLLPPSKQ   58 (137)
Q Consensus        46 Rc~-~i~~~~~~~~   58 (137)
                      |+- .+.+.+++.+
T Consensus       378 RfdL~v~v~~~~~~  391 (506)
T PRK09862        378 RFDLSLEIPLPPPG  391 (506)
T ss_pred             hccEEEEeCCCCHH
Confidence            994 5788877533

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=95.71  E-value=0.073  Score=46.00  Aligned_cols=57  Identities=18%  Similarity=0.216  Sum_probs=40.8

Q ss_pred             cccccCcCCHHHHHHHHHHHHhcc-------------CCceEEEEeCCC------C-------Cc-hhhhhcce--eeEe
Q 042716            2 ILCEADKLSTDALLYMRWLLERYK-------------GLNKVFFCCSDV------S-------KL-QPIKSLCT--VIQL   52 (137)
Q Consensus         2 iiDEid~l~~~~~~~L~~~le~~~-------------~~~~~Il~~n~~------~-------~i-~~l~SRc~--~i~~   52 (137)
                      +|||+|+|+...+..|..+||+-.             ..+-++-+||..      .       .+ ++|+||+-  .+-|
T Consensus       531 CIDEFDKM~dStrSvLhEvMEQQTvSIAKAGII~sLNAR~SVLAaANP~~skynp~k~i~eNI~LpptLLSRFDLIylll  610 (804)
T KOG0478|consen  531 CIDEFDKMSDSTRSVLHEVMEQQTLSIAKAGIIASLNARCSVLAAANPIRSKYNPNKSIIENINLPPTLLSRFDLIFLLL  610 (804)
T ss_pred             EchhhhhhhHHHHHHHHHHHHHhhhhHhhcceeeeccccceeeeeeccccccCCCCCchhhccCCChhhhhhhcEEEEEe
Confidence            699999999999999999999653             133466666622      1       26 89999983  3455


Q ss_pred             cCCCHH
Q 042716           53 LPPSKQ   58 (137)
Q Consensus        53 ~~~~~~   58 (137)
                      .+++..
T Consensus       611 D~~DE~  616 (804)
T KOG0478|consen  611 DKPDER  616 (804)
T ss_pred             cCcchh
Confidence            565554

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

Probab=95.61  E-value=0.04  Score=42.76  Aligned_cols=74  Identities=16%  Similarity=0.202  Sum_probs=54.1

Q ss_pred             CcccccCcCC-----------HHHHHHHHHHHHhcc-----CCceEEEEeCCCCCc-hhhhhcc---eeeEecCCCHHHH
Q 042716            1 IILCEADKLS-----------TDALLYMRWLLERYK-----GLNKVFFCCSDVSKL-QPIKSLC---TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~-----------~~~~~~L~~~le~~~-----~~~~~Il~~n~~~~i-~~l~SRc---~~i~~~~~~~~~i   60 (137)
                      |||||+|.+.           .+.|.-|+.++++..     .|+.+|++||....+ |+|.--.   ..+.|+-|+..+-
T Consensus       252 ifideidaiatkrfdaqtgadrevqril~ellnqmdgfdq~~nvkvimatnradtldpallrpgrldrkiefplpdrrqk  331 (408)
T KOG0727|consen  252 IFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQK  331 (408)
T ss_pred             EEeehhhhHhhhhccccccccHHHHHHHHHHHHhccCcCcccceEEEEecCcccccCHhhcCCccccccccCCCCchhhh
Confidence            6899999983           334788888887653     367799999999988 7776533   4688877777776


Q ss_pred             HHHHHHHHHHcCCC
Q 042716           61 VEVLEFIAEQEGIQ   74 (137)
Q Consensus        61 ~~~l~~i~~~egi~   74 (137)
                      .-....++.+.++.
T Consensus       332 rlvf~titskm~ls  345 (408)
T KOG0727|consen  332 RLVFSTITSKMNLS  345 (408)
T ss_pred             hhhHHhhhhcccCC
Confidence            66667777766553

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

Probab=95.38  E-value=0.026  Score=46.18  Aligned_cols=70  Identities=9%  Similarity=0.004  Sum_probs=51.9

Q ss_pred             CceEEEEeCCCCCc-hhhhhcce-eeEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH----cCCcHHHHHH
Q 042716           27 LNKVFFCCSDVSKL-QPIKSLCT-VIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADN----SKNNLRQAIR   96 (137)
Q Consensus        27 ~~~~Il~~n~~~~i-~~l~SRc~-~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~l~~i~~~----~~gd~R~aln   96 (137)
                      +..+|-+||-+..+ .+++-|+. .+.++.|+.+.....+.+...+.+..+.+..+..+++.    +.+|+.....
T Consensus       290 rvlvigaTN~P~e~Dea~~Rrf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~~~Tegysgsdi~~l~k  365 (428)
T KOG0740|consen  290 RVLVIGATNRPWELDEAARRRFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLAKVTEGYSGSDITALCK  365 (428)
T ss_pred             eEEEEecCCCchHHHHHHHHHhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCcccccHHHHHH
Confidence            34466666777778 76666984 56688888888888888888888888888888888876    4456655443

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

Probab=95.24  E-value=0.076  Score=45.56  Aligned_cols=91  Identities=13%  Similarity=0.086  Sum_probs=64.3

Q ss_pred             CcccccCcCCHHH-----------HHHHHHHHHhccCC------ceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHH
Q 042716            1 IILCEADKLSTDA-----------LLYMRWLLERYKGL------NKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQE   59 (137)
Q Consensus         1 iiiDEid~l~~~~-----------~~~L~~~le~~~~~------~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~   59 (137)
                      +||||+|.+++.-           ...|+..|++....      +.+|-+||-+..+ ++||-  |+ ..+.+.-|+..+
T Consensus       286 vFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~a  365 (802)
T KOG0733|consen  286 VFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTKGDPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETA  365 (802)
T ss_pred             EEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccccCCCCeEEEecCCCCcccCHHHhccccccceeeecCCchHH
Confidence            5899999997653           23456666655422      3366677888889 99986  44 478999999999


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHH
Q 042716           60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLR   92 (137)
Q Consensus        60 i~~~l~~i~~~egi~i~~~~l~~i~~~~~gd~R   92 (137)
                      ..++|+.+|+.-.++-+ -....|++...|=..
T Consensus       366 R~~IL~~~~~~lrl~g~-~d~~qlA~lTPGfVG  397 (802)
T KOG0733|consen  366 REEILRIICRGLRLSGD-FDFKQLAKLTPGFVG  397 (802)
T ss_pred             HHHHHHHHHhhCCCCCC-cCHHHHHhcCCCccc
Confidence            99999999986655432 235667777766443

>PRK08116 hypothetical protein; Validated

Probab=95.22  E-value=0.028  Score=43.18  Aligned_cols=57  Identities=12%  Similarity=0.021  Sum_probs=45.1

Q ss_pred             Cccccc--CcCCHHHHHHHHHHHHhc-cCCceEEEEeCCCCC-----c-hhhhhc----ceeeEecCCCH
Q 042716            1 IILCEA--DKLSTDALLYMRWLLERY-KGLNKVFFCCSDVSK-----L-QPIKSL----CTVIQLLPPSK   57 (137)
Q Consensus         1 iiiDEi--d~l~~~~~~~L~~~le~~-~~~~~~Il~~n~~~~-----i-~~l~SR----c~~i~~~~~~~   57 (137)
                      ++|||+  +..+...+..|+.+++.- ..+.++|++||.++.     + ..+.||    |..+.|..++.
T Consensus       182 LviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~~~eL~~~~~~ri~sRl~e~~~~v~~~g~d~  251 (268)
T PRK08116        182 LILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLSLEELKNQYGKRIYDRILEMCTPVENEGKSY  251 (268)
T ss_pred             EEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHhHHHHHHHHHcCEEEEeeCcCh
Confidence            579999  667888899999999963 455779999998753     4 578888    78899987764

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

Probab=95.12  E-value=0.23  Score=37.91  Aligned_cols=89  Identities=12%  Similarity=0.184  Sum_probs=66.6

Q ss_pred             HHHHHHHHH----hccCCceEEEEeCCCCCc-h-----------------------hhhhcc-eeeEecCCCHHHHHHHH
Q 042716           14 LLYMRWLLE----RYKGLNKVFFCCSDVSKL-Q-----------------------PIKSLC-TVIQLLPPSKQEIVEVL   64 (137)
Q Consensus        14 ~~~L~~~le----~~~~~~~~Il~~n~~~~i-~-----------------------~l~SRc-~~i~~~~~~~~~i~~~l   64 (137)
                      -..|..++|    ..|.|+.+..|+|--+-+ .                       .|-.|+ ..+.|.+|+.++-.+++
T Consensus       124 yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E~~~d~~~~~~~eih~~d~~eEklSLsDRFGL~l~F~~~~q~~YL~IV  203 (249)
T PF05673_consen  124 YKALKSVLEGGLEARPDNVLIYATSNRRHLVPESFSDREDIQDDEIHPSDTIEEKLSLSDRFGLWLSFYPPDQEEYLAIV  203 (249)
T ss_pred             HHHHHHHhcCccccCCCcEEEEEecchhhccchhhhhccCCCccccCcchHHHHHHhHHHhCCcEEEecCCCHHHHHHHH
Confidence            445555554    456677777777733211 1                       455666 68999999999999999


Q ss_pred             HHHHHHcCCCCC-----HHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           65 EFIAEQEGIQLP-----HQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        65 ~~i~~~egi~i~-----~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ...+++.|+.++     .+++++-..+..++-|.|-.....+.
T Consensus       204 ~~~~~~~g~~~~~e~l~~~Al~wa~~rg~RSGRtA~QF~~~l~  246 (249)
T PF05673_consen  204 RHYAERYGLELDEEELRQEALQWALRRGGRSGRTARQFIDDLA  246 (249)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHh
Confidence            999999999999     45667777788889999998887664

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=94.90  E-value=0.14  Score=40.40  Aligned_cols=38  Identities=24%  Similarity=0.275  Sum_probs=31.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccC-------CceEEEEeCCCC
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKG-------LNKVFFCCSDVS   38 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~-------~~~~Il~~n~~~   38 (137)
                      +|+||+|.|.++-.++|...++.++.       ++.|||.+|.-.
T Consensus       182 FIFDE~DKmp~gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg  226 (344)
T KOG2170|consen  182 FIFDEVDKLPPGLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGG  226 (344)
T ss_pred             EEechhhhcCHhHHHHHhhhhccccccccccccceEEEEEcCCcc
Confidence            47999999999999999999996653       456999998543

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=94.85  E-value=0.045  Score=43.31  Aligned_cols=56  Identities=20%  Similarity=0.173  Sum_probs=35.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc-------------cCCceEEEEeCCCC-------------Cc-hhhhhcce-eeEe
Q 042716            1 IILCEADKLSTDALLYMRWLLERY-------------KGLNKVFFCCSDVS-------------KL-QPIKSLCT-VIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~-------------~~~~~~Il~~n~~~-------------~i-~~l~SRc~-~i~~   52 (137)
                      ++|||.|.|..+...+|...||.-             +..|.++.+||...             .+ ++|.||+= +|.+
T Consensus       125 ccIDe~dk~~~~~~~~l~eaMEqq~isi~kagi~~~l~ar~svlaa~NP~~g~~~~~~~~~~ni~l~~~LLSRFDLif~l  204 (331)
T PF00493_consen  125 CCIDEFDKMKEDDRDALHEAMEQQTISIAKAGIVTTLNARCSVLAAANPKFGRYDPNKSLSENINLPPPLLSRFDLIFLL  204 (331)
T ss_dssp             EEECTTTT--CHHHHHHHHHHHCSCEEECTSSSEEEEE---EEEEEE--TT--S-TTS-CGCCT-S-CCCHCC-SEEECC
T ss_pred             eeecccccccchHHHHHHHHHHcCeeccchhhhcccccchhhhHHHHhhhhhhcchhhhhHHhcccchhhHhhcCEEEEe
Confidence            379999999999999999999963             23456888887553             36 79999984 4444


Q ss_pred             -cCCC
Q 042716           53 -LPPS   56 (137)
Q Consensus        53 -~~~~   56 (137)
                       .+++
T Consensus       205 ~D~~d  209 (331)
T PF00493_consen  205 RDKPD  209 (331)
T ss_dssp             --TTT
T ss_pred             ccccc
Confidence             4444

; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.

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

Probab=94.72  E-value=0.12  Score=40.57  Aligned_cols=102  Identities=15%  Similarity=0.077  Sum_probs=65.8

Q ss_pred             CcccccCcC---CHHHHHHHHHHHHhc--cCCceEEEEeCCCC----Cc-hhhhhcceeeEecCCCHHH-HHHHHHHHHH
Q 042716            1 IILCEADKL---STDALLYMRWLLERY--KGLNKVFFCCSDVS----KL-QPIKSLCTVIQLLPPSKQE-IVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l---~~~~~~~L~~~le~~--~~~~~~Il~~n~~~----~i-~~l~SRc~~i~~~~~~~~~-i~~~l~~i~~   69 (137)
                      +||||+|.+   +...|..++..+...  .-..++|++++...    .- +.+.||+..+.+++-..++ ....|...-.
T Consensus       149 LIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~A~~al~~D~QLa~RF~~~~Lp~W~~d~ef~~LL~s~e~  228 (302)
T PF05621_consen  149 LIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTREAYRALRTDPQLASRFEPFELPRWELDEEFRRLLASFER  228 (302)
T ss_pred             EEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccHHHHHHhccCHHHHhccCCccCCCCCCCcHHHHHHHHHHH
Confidence            589999997   233355554444433  23566787765442    23 7899999998888776653 3333332211


Q ss_pred             ------HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           70 ------QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        70 ------~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                            ..++ -+++...+|...|+|.+....++|..+..
T Consensus       229 ~LPLr~~S~l-~~~~la~~i~~~s~G~iG~l~~ll~~aA~  267 (302)
T PF05621_consen  229 ALPLRKPSNL-ASPELARRIHERSEGLIGELSRLLNAAAI  267 (302)
T ss_pred             hCCCCCCCCC-CCHHHHHHHHHHcCCchHHHHHHHHHHHH
Confidence                  1122 24566688999999999999999887664

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

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

Probab=94.63  E-value=0.062  Score=44.25  Aligned_cols=70  Identities=17%  Similarity=0.217  Sum_probs=52.1

Q ss_pred             CcccccCcC---------CHHHHHHHHHHHHh---ccCCceEEEEeCCCCCc-hhhhhcc-eeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKL---------STDALLYMRWLLER---YKGLNKVFFCCSDVSKL-QPIKSLC-TVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l---------~~~~~~~L~~~le~---~~~~~~~Il~~n~~~~i-~~l~SRc-~~i~~~~~~~~~i~~~l~~   66 (137)
                      +||||+|.+         +.....+|..++=+   .+....++|++|.+..+ .++-.|. .++.|+-|-.++..+.|..
T Consensus       447 lFIDEADAFLceRnktymSEaqRsaLNAlLfRTGdqSrdivLvlAtNrpgdlDsAV~DRide~veFpLPGeEERfkll~l  526 (630)
T KOG0742|consen  447 LFIDEADAFLCERNKTYMSEAQRSALNALLFRTGDQSRDIVLVLATNRPGDLDSAVNDRIDEVVEFPLPGEEERFKLLNL  526 (630)
T ss_pred             EEehhhHHHHHHhchhhhcHHHHHHHHHHHHHhcccccceEEEeccCCccchhHHHHhhhhheeecCCCChHHHHHHHHH
Confidence            589999974         54444445444432   34455688899999999 9999998 7899999999998888876


Q ss_pred             HHHH
Q 042716           67 IAEQ   70 (137)
Q Consensus        67 i~~~   70 (137)
                      +..+
T Consensus       527 Ylnk  530 (630)
T KOG0742|consen  527 YLNK  530 (630)
T ss_pred             HHHH
Confidence            5543

>PF05729 NACHT: NACHT domain

Probab=94.56  E-value=0.1  Score=35.80  Aligned_cols=68  Identities=19%  Similarity=0.172  Sum_probs=47.0

Q ss_pred             CcccccCcCCHHHHH--------HHHHHHHh-ccCCceEEEEeCCCCC--chhhhhcceeeEecCCCHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALL--------YMRWLLER-YKGLNKVFFCCSDVSK--LQPIKSLCTVIQLLPPSKQEIVEVLEFIA   68 (137)
Q Consensus         1 iiiDEid~l~~~~~~--------~L~~~le~-~~~~~~~Il~~n~~~~--i~~l~SRc~~i~~~~~~~~~i~~~l~~i~   68 (137)
                      ++||-+|.+......        .|...+.. ...+++++++|+....  +.........+.+.+.+.+++..++++..
T Consensus        85 lilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~f  163 (166)
T PF05729_consen   85 LILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEEDIKQYLRKYF  163 (166)
T ss_pred             EEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHHHHHHHHHHh
Confidence            478888888764432        45556665 3567889999986654  43333333789999999999999887643

>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria

Probab=94.45  E-value=0.51  Score=38.73  Aligned_cols=102  Identities=16%  Similarity=0.240  Sum_probs=69.8

Q ss_pred             CcccccCcC----C----HHHHHHHHHHHHhccC----CceEEEEeCCC-----C-Cc---hhhhhcc------------
Q 042716            1 IILCEADKL----S----TDALLYMRWLLERYKG----LNKVFFCCSDV-----S-KL---QPIKSLC------------   47 (137)
Q Consensus         1 iiiDEid~l----~----~~~~~~L~~~le~~~~----~~~~Il~~n~~-----~-~i---~~l~SRc------------   47 (137)
                      |+|||++.+    +    ...-+.|+.++++..+    +..|+++++..     . .+   ++|.+|.            
T Consensus       243 I~lDE~e~l~kl~~~~~R~~~ye~lr~lidd~~~G~~~gL~~~~~gTPef~eD~rrGv~sY~AL~~RL~~~~~~~~~~~n  322 (416)
T PF10923_consen  243 ILLDELENLYKLRNDQAREKNYEALRQLIDDIDQGRAPGLYFVFAGTPEFFEDGRRGVYSYEALAQRLAEEFFADDGFDN  322 (416)
T ss_pred             EEEechHHHHhcCChHHHHHHHHHHHHHHHHHhcCCCCceEEEEeeCHHHhhCccccccccHHHHHHHhccccccccccC
Confidence            579999987    1    1236788899887543    56677887632     1 23   7888884            


Q ss_pred             ---eeeEecCCCHHHHHHHHHHHHH------HcCCCCCHHHHHHHHHHcCCc------------HHHHHHHHHHHH
Q 042716           48 ---TVIQLLPPSKQEIVEVLEFIAE------QEGIQLPHQLAEKIADNSKNN------------LRQAIRSFEASR  102 (137)
Q Consensus        48 ---~~i~~~~~~~~~i~~~l~~i~~------~egi~i~~~~l~~i~~~~~gd------------~R~aln~L~~~~  102 (137)
                         .++++++++.+++...+.++..      .....++++.+..+++.+.+.            +|..++.|..+.
T Consensus       323 ~~~pvIrL~~l~~eel~~l~~klr~i~a~~~~~~~~v~d~~l~~~~~~~~~r~G~~~~~tPR~~ik~fv~~Ld~~~  398 (416)
T PF10923_consen  323 LRAPVIRLQPLTPEELLELLEKLRDIYAEAYGYESRVDDEELKAFAQHVAGRLGGDVFVTPREFIKDFVDVLDILE  398 (416)
T ss_pred             ccCceecCCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHhccCcccccCHHHHHHHHHHHHHHHH
Confidence               3788999999999888776653      122478899998888665433            455666666665

Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.

>PRK06526 transposase; Provisional

Probab=94.26  E-value=0.067  Score=40.86  Aligned_cols=58  Identities=14%  Similarity=0.080  Sum_probs=42.2

Q ss_pred             CcccccCcC--CHHHHHHHHHHHHhccCCceEEEEeCCCCC----------c-hhhhhc----ceeeEecCCCHH
Q 042716            1 IILCEADKL--STDALLYMRWLLERYKGLNKVFFCCSDVSK----------L-QPIKSL----CTVIQLLPPSKQ   58 (137)
Q Consensus         1 iiiDEid~l--~~~~~~~L~~~le~~~~~~~~Il~~n~~~~----------i-~~l~SR----c~~i~~~~~~~~   58 (137)
                      +||||++.+  +...++.|+.+++.-..+..+|++||.+..          + .++.||    |.++.|...|.-
T Consensus       163 LIIDD~g~~~~~~~~~~~L~~li~~r~~~~s~IitSn~~~~~w~~~~~d~~~a~ai~dRl~~~~~~i~~~g~s~R  237 (254)
T PRK06526        163 LIVDEVGYIPFEPEAANLFFQLVSSRYERASLIVTSNKPFGRWGEVFGDDVVAAAMIDRLVHHAEVISLKGDSYR  237 (254)
T ss_pred             EEEcccccCCCCHHHHHHHHHHHHHHHhcCCEEEEcCCCHHHHHHHcCChHHHHHHHHHHhcCceEEeecCCCcc
Confidence            589999987  577788899998865555679999998742          2 345565    677888776644

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

Probab=94.26  E-value=0.43  Score=36.90  Aligned_cols=68  Identities=13%  Similarity=0.094  Sum_probs=47.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc--CCceEEEEeCCCC---------------Cc-hhhhhcc--eeeEecCCCHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK--GLNKVFFCCSDVS---------------KL-QPIKSLC--TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~--~~~~~Il~~n~~~---------------~i-~~l~SRc--~~i~~~~~~~~~i   60 (137)
                      |+|||.|++.++....++..+...-  +++.||++++...               .. .....+.  ..|.+++++..++
T Consensus       176 iiIDdLDR~~~~~i~~~l~~ik~~~~~~~i~~Il~~D~~~l~~ai~~~~~~~~~~~~~~~yLeKiiq~~~~lP~~~~~~~  255 (325)
T PF07693_consen  176 IIIDDLDRCSPEEIVELLEAIKLLLDFPNIIFILAFDPEILEKAIEKNYGEGFDEIDGREYLEKIIQVPFSLPPPSPSDL  255 (325)
T ss_pred             EEEcchhcCCcHHHHHHHHHHHHhcCCCCeEEEEEecHHHHHHHHHhhcCcccccccHHHHHHhhcCeEEEeCCCCHHHH
Confidence            5899999999997766666665432  5777888886431               12 3334444  3588999999888


Q ss_pred             HHHHHHHH
Q 042716           61 VEVLEFIA   68 (137)
Q Consensus        61 ~~~l~~i~   68 (137)
                      ...+....
T Consensus       256 ~~~~~~~~  263 (325)
T PF07693_consen  256 ERYLNELL  263 (325)
T ss_pred             HHHHHHHH
Confidence            88887663

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

>PF14516 AAA_35: AAA-like domain

Probab=94.05  E-value=0.81  Score=36.15  Aligned_cols=98  Identities=16%  Similarity=0.201  Sum_probs=67.5

Q ss_pred             CcccccCcCCH------HHHHHHHHHHHhcc-----CCceEEEEeCCCCC----c--hhhhhcceeeEecCCCHHHHHHH
Q 042716            1 IILCEADKLST------DALLYMRWLLERYK-----GLNKVFFCCSDVSK----L--QPIKSLCTVIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~------~~~~~L~~~le~~~-----~~~~~Il~~n~~~~----i--~~l~SRc~~i~~~~~~~~~i~~~   63 (137)
                      ++|||+|.+..      +-...|+...++-.     .+.+|+++......    .  .|+ +.+..+.++..+.+++...
T Consensus       131 L~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~~~~~~~~~~SPF-NIg~~i~L~~Ft~~ev~~L  209 (331)
T PF14516_consen  131 LFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPIWQKLRLILAGSTEDYIILDINQSPF-NIGQPIELPDFTPEEVQEL  209 (331)
T ss_pred             EEEechhhhccCcchHHHHHHHHHHHHHhcccCcccceEEEEEecCcccccccCCCCCCc-ccccceeCCCCCHHHHHHH
Confidence            57999999865      22555667776533     22346665543322    2  344 5678899999999998776


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           64 LEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        64 l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      +..    .|.+.+++.++.+....+|-+=-.-.++..++.
T Consensus       210 ~~~----~~~~~~~~~~~~l~~~tgGhP~Lv~~~~~~l~~  245 (331)
T PF14516_consen  210 AQR----YGLEFSQEQLEQLMDWTGGHPYLVQKACYLLVE  245 (331)
T ss_pred             HHh----hhccCCHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            544    578889999999999999998655555555553

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

Probab=93.97  E-value=0.13  Score=44.10  Aligned_cols=85  Identities=18%  Similarity=0.162  Sum_probs=59.2

Q ss_pred             CcccccCcCCHH-----------HHHHHHHHHHhc--cCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHHHHH
Q 042716            1 IILCEADKLSTD-----------ALLYMRWLLERY--KGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~~-----------~~~~L~~~le~~--~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i~~~   63 (137)
                      ||+||+|.|.+.           -.|.|+--|+-.  ..++++|-+||-+..| ++++-  |. ..+.+..|+.++...+
T Consensus       608 IFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~I  687 (802)
T KOG0733|consen  608 IFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEERVAI  687 (802)
T ss_pred             EEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHHHHH
Confidence            689999999432           255666655432  2356677777888888 77765  44 5678888999999999


Q ss_pred             HHHHHHHcCCCCCHHH-HHHHHH
Q 042716           64 LEFIAEQEGIQLPHQL-AEKIAD   85 (137)
Q Consensus        64 l~~i~~~egi~i~~~~-l~~i~~   85 (137)
                      |+.+.+..+..+++++ +..|+.
T Consensus       688 LK~~tkn~k~pl~~dVdl~eia~  710 (802)
T KOG0733|consen  688 LKTITKNTKPPLSSDVDLDEIAR  710 (802)
T ss_pred             HHHHhccCCCCCCcccCHHHHhh
Confidence            9999887666666554 444554

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

Probab=93.65  E-value=0.042  Score=44.73  Aligned_cols=100  Identities=12%  Similarity=0.082  Sum_probs=55.0

Q ss_pred             CcccccCcCCHH------------HHHHHHHHHHhcc-----CCceEEEEeCCC-CCc-hhhhhcceeeEecCCCHHHHH
Q 042716            1 IILCEADKLSTD------------ALLYMRWLLERYK-----GLNKVFFCCSDV-SKL-QPIKSLCTVIQLLPPSKQEIV   61 (137)
Q Consensus         1 iiiDEid~l~~~------------~~~~L~~~le~~~-----~~~~~Il~~n~~-~~i-~~l~SRc~~i~~~~~~~~~i~   61 (137)
                      |||||||.|...            -..-|+--|+-..     ....|+|++++. -.| .++|-|+..=-|-|+++.+-.
T Consensus       308 IFiDEIDslcs~RG~s~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN~PWdiDEAlrRRlEKRIyIPLP~~~~R  387 (491)
T KOG0738|consen  308 IFIDEIDSLCSQRGGSSEHEASRRVKSELLVQMDGVQGTLENSKVVMVLAATNFPWDIDEALRRRLEKRIYIPLPDAEAR  387 (491)
T ss_pred             eehhhHHHHHhcCCCccchhHHHHHHHHHHHHhhccccccccceeEEEEeccCCCcchHHHHHHHHhhheeeeCCCHHHH
Confidence            799999999322            1333444443211     133577776554 579 999999964333355555566


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHH----cCCcHHHHHHHHHH
Q 042716           62 EVLEFIAEQEGIQLPHQLAEKIADN----SKNNLRQAIRSFEA  100 (137)
Q Consensus        62 ~~l~~i~~~egi~i~~~~l~~i~~~----~~gd~R~aln~L~~  100 (137)
                      +.|.+++-.+-..-++-.+..|++.    ++-|++.+.....+
T Consensus       388 ~~Li~~~l~~~~~~~~~~~~~lae~~eGySGaDI~nvCreAsm  430 (491)
T KOG0738|consen  388 SALIKILLRSVELDDPVNLEDLAERSEGYSGADITNVCREASM  430 (491)
T ss_pred             HHHHHHhhccccCCCCccHHHHHHHhcCCChHHHHHHHHHHHH
Confidence            6666665544332233234445544    44466655444333

>PRK08181 transposase; Validated

Probab=93.36  E-value=0.17  Score=39.06  Aligned_cols=57  Identities=9%  Similarity=0.033  Sum_probs=41.4

Q ss_pred             CcccccCcC--CHHHHHHHHHHHHhccCCceEEEEeCCCCC----------c-hhhhhc----ceeeEecCCCH
Q 042716            1 IILCEADKL--STDALLYMRWLLERYKGLNKVFFCCSDVSK----------L-QPIKSL----CTVIQLLPPSK   57 (137)
Q Consensus         1 iiiDEid~l--~~~~~~~L~~~le~~~~~~~~Il~~n~~~~----------i-~~l~SR----c~~i~~~~~~~   57 (137)
                      +||||++.+  +...++.|+.+++.-..+.++|+++|.+..          + .++.||    |.++.|...|.
T Consensus       171 LIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~~~~w~~~~~D~~~a~aildRL~h~~~~i~~~g~s~  244 (269)
T PRK08181        171 LILDDLAYVTKDQAETSVLFELISARYERRSILITANQPFGEWNRVFPDPAMTLAAVDRLVHHATIFEMNVESY  244 (269)
T ss_pred             EEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCCHHHHHHhcCCccchhhHHHhhhcCceEEecCCccc
Confidence            589999887  445577899999976556789999997732          2 345555    67788877553

>PRK12377 putative replication protein; Provisional

Probab=93.25  E-value=0.13  Score=39.27  Aligned_cols=56  Identities=11%  Similarity=0.137  Sum_probs=42.2

Q ss_pred             Cccccc--CcCCHHHHHHHHHHHHhccC-CceEEEEeCCCCC-----c-hhhhhcc-----eeeEecCCC
Q 042716            1 IILCEA--DKLSTDALLYMRWLLERYKG-LNKVFFCCSDVSK-----L-QPIKSLC-----TVIQLLPPS   56 (137)
Q Consensus         1 iiiDEi--d~l~~~~~~~L~~~le~~~~-~~~~Il~~n~~~~-----i-~~l~SRc-----~~i~~~~~~   56 (137)
                      ++|||+  +.+++..+..|+.+++.-.. ..+.|+++|....     + ..+.||.     ..+.|...|
T Consensus       167 LiIDDlg~~~~s~~~~~~l~~ii~~R~~~~~ptiitSNl~~~~l~~~~~~ri~dRl~~~~~~~v~~~g~s  236 (248)
T PRK12377        167 LVLDEIGIQRETKNEQVVLNQIIDRRTASMRSVGMLTNLNHEAMSTLLGERVMDRMTMNGGRWVNFNWES  236 (248)
T ss_pred             EEEcCCCCCCCCHHHHHHHHHHHHHHHhcCCCEEEEcCCCHHHHHHHhhHHHHHHHhhCCCeEEEeCCcC
Confidence            589999  66788899999999998544 5789999997632     4 5666763     457777665

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

Probab=92.84  E-value=0.56  Score=36.74  Aligned_cols=73  Identities=21%  Similarity=0.263  Sum_probs=49.4

Q ss_pred             CcccccCcCC-----------HHHHHHHHHHHHhccC-----CceEEEEeCCCCCc-hhhh-h-cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLS-----------TDALLYMRWLLERYKG-----LNKVFFCCSDVSKL-QPIK-S-LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~-----------~~~~~~L~~~le~~~~-----~~~~Il~~n~~~~i-~~l~-S-Rc-~~i~~~~~~~~~i   60 (137)
                      |||||+|.+.           .+.|..++.++++..+     ...+|-+||...-+ |+|. | |. ..+.|+.|+.+..
T Consensus       268 IFIDElDAIGtKRfDSek~GDREVQRTMLELLNQLDGFss~~~vKviAATNRvDiLDPALlRSGRLDRKIEfP~Pne~aR  347 (424)
T KOG0652|consen  268 IFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSDDRVKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEAR  347 (424)
T ss_pred             EEEechhhhccccccccccccHHHHHHHHHHHHhhcCCCCccceEEEeecccccccCHHHhhcccccccccCCCCChHHH
Confidence            6899999983           3447788888876432     34477778877778 6654 3 33 5799988888766


Q ss_pred             HHHHHHHHHHcCC
Q 042716           61 VEVLEFIAEQEGI   73 (137)
Q Consensus        61 ~~~l~~i~~~egi   73 (137)
                      ..+++-.+++.++
T Consensus       348 arIlQIHsRKMnv  360 (424)
T KOG0652|consen  348 ARILQIHSRKMNV  360 (424)
T ss_pred             HHHHHHhhhhcCC
Confidence            6666655555544

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=92.53  E-value=0.21  Score=34.56  Aligned_cols=48  Identities=6%  Similarity=-0.012  Sum_probs=32.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCC----c------eEEEEeCCC-C-----Cc-hhhhhcce
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGL----N------KVFFCCSDV-S-----KL-QPIKSLCT   48 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~----~------~~Il~~n~~-~-----~i-~~l~SRc~   48 (137)
                      +++||+.+-.+..|.+|+..|++..-.    +      -+|++|-++ .     .+ .+++.|+.
T Consensus        66 ll~DEiNrappktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~DRF~  130 (131)
T PF07726_consen   66 LLADEINRAPPKTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLDRFM  130 (131)
T ss_dssp             EEEETGGGS-HHHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT--S------HHHHTTSS
T ss_pred             eeecccccCCHHHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhcccc
Confidence            478999999999999999999986422    1      255555444 2     47 78888864

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

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

Probab=92.03  E-value=0.35  Score=40.13  Aligned_cols=65  Identities=11%  Similarity=0.108  Sum_probs=46.8

Q ss_pred             CcccccCcCCHHH-HHHHHHHHHh----------------------ccCCceEEEEeCCCC----Cc-hhhhhcceeeEe
Q 042716            1 IILCEADKLSTDA-LLYMRWLLER----------------------YKGLNKVFFCCSDVS----KL-QPIKSLCTVIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~L~~~le~----------------------~~~~~~~Il~~n~~~----~i-~~l~SRc~~i~~   52 (137)
                      +||||+++-.... ...++..+|.                      .|.|.++|.|.|...    .+ .+++-|+..+++
T Consensus       276 liIDEINRani~kiFGel~~lLE~~~rg~~~~v~l~y~e~d~e~f~iP~Nl~IIgTMNt~Drs~~~lD~AlrRRF~fi~i  355 (459)
T PRK11331        276 FIIDEINRANLSKVFGEVMMLMEHDKRGENWSVPLTYSENDEERFYVPENVYIIGLMNTADRSLAVVDYALRRRFSFIDI  355 (459)
T ss_pred             EEEehhhccCHHHhhhhhhhhccccccccccceeeeccccccccccCCCCeEEEEecCccccchhhccHHHHhhhheEEe
Confidence            5899999998664 6666666662                      235667888888876    37 899999999999


Q ss_pred             cCC-CHHHHHHHHH
Q 042716           53 LPP-SKQEIVEVLE   65 (137)
Q Consensus        53 ~~~-~~~~i~~~l~   65 (137)
                      .+- +...+.+++.
T Consensus       356 ~p~~~~~~~~~~l~  369 (459)
T PRK11331        356 EPGFDTPQFRNFLL  369 (459)
T ss_pred             cCCCChHHHHHHHH
Confidence            873 4445555543

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

Probab=91.91  E-value=0.94  Score=41.18  Aligned_cols=98  Identities=10%  Similarity=0.124  Sum_probs=70.2

Q ss_pred             CcccccCcCCHH-----------HHHHHHHHHHhccCCceE--EEEeCCCCCc-hhhhhcc---eeeEecCCCHHHHHHH
Q 042716            1 IILCEADKLSTD-----------ALLYMRWLLERYKGLNKV--FFCCSDVSKL-QPIKSLC---TVIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~~-----------~~~~L~~~le~~~~~~~~--Il~~n~~~~i-~~l~SRc---~~i~~~~~~~~~i~~~   63 (137)
                      |++||+|+|.+-           -..-|+.+|.-.+...++  |-+||.+..+ ++||-+.   ..|.|.-|+.+.-.++
T Consensus       367 IffdeIdGlapvrSskqEqih~SIvSTLLaLmdGldsRgqVvvigATnRpda~dpaLRRPgrfdref~f~lp~~~ar~~I  446 (1080)
T KOG0732|consen  367 IFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDSRGQVVVIGATNRPDAIDPALRRPGRFDREFYFPLPDVDARAKI  446 (1080)
T ss_pred             EeccccccccccccchHHHhhhhHHHHHHHhccCCCCCCceEEEcccCCccccchhhcCCcccceeEeeeCCchHHHHHH
Confidence            588999988432           134567777765555554  4446778899 9997664   5799999988888888


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHH
Q 042716           64 LEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSF   98 (137)
Q Consensus        64 l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L   98 (137)
                      +.-.-.+..-.++...+..+++.+.|-...-+..|
T Consensus       447 l~Ihtrkw~~~i~~~l~~~la~~t~gy~gaDlkaL  481 (1080)
T KOG0732|consen  447 LDIHTRKWEPPISRELLLWLAEETSGYGGADLKAL  481 (1080)
T ss_pred             HHHhccCCCCCCCHHHHHHHHHhccccchHHHHHH
Confidence            87666677778888889999987666554444333

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=91.77  E-value=0.95  Score=37.14  Aligned_cols=89  Identities=17%  Similarity=0.145  Sum_probs=56.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC---CCc-hhhhhcc-eeeEecCCCH-HHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV---SKL-QPIKSLC-TVIQLLPPSK-QEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~---~~i-~~l~SRc-~~i~~~~~~~-~~i~~~   63 (137)
                      +.+||+-.|...-|++|+.++++-.           --..|+|+++..   ..| +.|+.|+ ..+....+++ ++-..+
T Consensus       148 lYvDEvnlL~d~lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNPEeGeLrpqLlDRfg~~v~~~~~~~~~~rv~I  227 (423)
T COG1239         148 LYVDEVNLLDDHLVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPEEGELRPQLLDRFGLEVDTHYPLDLEERVEI  227 (423)
T ss_pred             EEEeccccccHHHHHHHHHHHHhCCceeeeCceeeccCccEEEEeecCccccccchhhHhhhcceeeccCCCCHHHHHHH
Confidence            4689999999999999999999731           123477765544   248 9999996 5677777665 344455


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHcCCcHH
Q 042716           64 LEFIAEQEGIQLPHQLAEKIADNSKNNLR   92 (137)
Q Consensus        64 l~~i~~~egi~i~~~~l~~i~~~~~gd~R   92 (137)
                      +.+.+..+  ..++..++.+... ...+|
T Consensus       228 i~r~~~f~--~~Pe~f~~~~~~~-~~~lR  253 (423)
T COG1239         228 IRRRLAFE--AVPEAFLEKYADA-QRALR  253 (423)
T ss_pred             HHHHHHhh--cCcHHHHHHHHHH-HHHHH
Confidence            55544443  3344444444333 23455

>smart00763 AAA_PrkA PrkA AAA domain

Probab=91.60  E-value=0.4  Score=38.62  Aligned_cols=85  Identities=8%  Similarity=-0.069  Sum_probs=55.5

Q ss_pred             cccccCcCCHHHHHHHHHHHHhccC----C-------ceEEEEeCCC-------CCc-hhhhhcceeeEecCCCHHH-HH
Q 042716            2 ILCEADKLSTDALLYMRWLLERYKG----L-------NKVFFCCSDV-------SKL-QPIKSLCTVIQLLPPSKQE-IV   61 (137)
Q Consensus         2 iiDEid~l~~~~~~~L~~~le~~~~----~-------~~~Il~~n~~-------~~i-~~l~SRc~~i~~~~~~~~~-i~   61 (137)
                      -++|+.......++.|+.++++..-    .       ..||.++|..       .+. .+|+.||..+.++.+..=. =.
T Consensus       241 ~f~Ei~K~~~~~l~~LL~~~qE~~v~~~~~~~~~~~d~liia~sNe~e~~~~~~~k~~eaf~dR~~~i~vpY~l~~~~E~  320 (361)
T smart00763      241 EFVEMFKADIKFLHPLLTATQEGNIKGTGGFAMIPIDGLIIAHSNESEWQRFKSNKKNEALLDRIIKVKVPYCLRVSEEA  320 (361)
T ss_pred             EEeehhcCCHHHHHHHhhhhhcceEecCCcccccccceEEEEeCCHHHHhhhhccccchhhhhceEEEeCCCcCCHHHHH
Confidence            4679999999999999999997421    1       1145555655       256 9999999998887766522 22


Q ss_pred             HHHHHHHHH---cCCCCCHHHHHHHHHH
Q 042716           62 EVLEFIAEQ---EGIQLPHQLAEKIADN   86 (137)
Q Consensus        62 ~~l~~i~~~---egi~i~~~~l~~i~~~   86 (137)
                      ++.++.+..   .+..+.|.+++.++..
T Consensus       321 ~Iy~k~~~~s~~~~~~~aP~~le~aa~~  348 (361)
T smart00763      321 QIYEKLLRNSDLTEAHIAPHTLEMAALF  348 (361)
T ss_pred             HHHHHHhccCcCcccccCchHHHHHHHH
Confidence            333333332   2556777766665543

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

>PRK09183 transposase/IS protein; Provisional

Probab=91.34  E-value=0.36  Score=36.90  Aligned_cols=57  Identities=14%  Similarity=0.089  Sum_probs=40.3

Q ss_pred             CcccccCcC--CHHHHHHHHHHHHhccCCceEEEEeCCCCC-----------c-hhhhhc----ceeeEecCCCH
Q 042716            1 IILCEADKL--STDALLYMRWLLERYKGLNKVFFCCSDVSK-----------L-QPIKSL----CTVIQLLPPSK   57 (137)
Q Consensus         1 iiiDEid~l--~~~~~~~L~~~le~~~~~~~~Il~~n~~~~-----------i-~~l~SR----c~~i~~~~~~~   57 (137)
                      ++|||++.+  +...++.|+.+++.-..+..+|+|+|.+..           + .++.||    |.++.|...|.
T Consensus       168 LiiDdlg~~~~~~~~~~~lf~li~~r~~~~s~iiTsn~~~~~w~~~~~~d~~~~~ai~dRl~~~~~~i~~~g~s~  242 (259)
T PRK09183        168 LIIDEIGYLPFSQEEANLFFQVIAKRYEKGSMILTSNLPFGQWDQTFAGDAALTSAMLDRLLHHSHVVQIKGESY  242 (259)
T ss_pred             EEEcccccCCCChHHHHHHHHHHHHHHhcCcEEEecCCCHHHHHHHhcCchhHHHHHHHHHhcceEEEeecCCCC
Confidence            489999974  666677899999765555678999987632           2 356665    56788877553

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=90.97  E-value=0.73  Score=40.88  Aligned_cols=94  Identities=13%  Similarity=0.142  Sum_probs=70.5

Q ss_pred             CcccccCcCCHHH-HHHHHHHHHhccCCceEEEEeCCCCCc--hhhhhcceeeEec----CCCHHHHHHHHHHHHHHcCC
Q 042716            1 IILCEADKLSTDA-LLYMRWLLERYKGLNKVFFCCSDVSKL--QPIKSLCTVIQLL----PPSKQEIVEVLEFIAEQEGI   73 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~L~~~le~~~~~~~~Il~~n~~~~i--~~l~SRc~~i~~~----~~~~~~i~~~l~~i~~~egi   73 (137)
                      ++|||-|.++..+ ..+|...++..|.+..+|++|...+.+  ..+|=|-..+.+.    ..+.++....+..   .-|.
T Consensus       133 LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~l~la~lRlr~~llEi~~~~Lrf~~eE~~~fl~~---~~~l  209 (894)
T COG2909         133 LVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQLGLARLRLRDELLEIGSEELRFDTEEAAAFLND---RGSL  209 (894)
T ss_pred             EEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCCCcccceeehhhHHhcChHhhcCChHHHHHHHHH---cCCC
Confidence            4799999997776 777999999989999999999988875  6666664433332    3466777766654   2348


Q ss_pred             CCCHHHHHHHHHHcCCcHHHHHHHH
Q 042716           74 QLPHQLAEKIADNSKNNLRQAIRSF   98 (137)
Q Consensus        74 ~i~~~~l~~i~~~~~gd~R~aln~L   98 (137)
                      .++...++.+.+.++| --.++.+.
T Consensus       210 ~Ld~~~~~~L~~~teG-W~~al~L~  233 (894)
T COG2909         210 PLDAADLKALYDRTEG-WAAALQLI  233 (894)
T ss_pred             CCChHHHHHHHhhccc-HHHHHHHH
Confidence            9999999999999998 44555444

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

Probab=90.53  E-value=1  Score=39.61  Aligned_cols=99  Identities=16%  Similarity=0.162  Sum_probs=66.2

Q ss_pred             CcccccCcCCHH----------H----HHHHHHHHHhccC---CceEEEEeCCCCCc-hhhhhc--c-eeeEecCCCHHH
Q 042716            1 IILCEADKLSTD----------A----LLYMRWLLERYKG---LNKVFFCCSDVSKL-QPIKSL--C-TVIQLLPPSKQE   59 (137)
Q Consensus         1 iiiDEid~l~~~----------~----~~~L~~~le~~~~---~~~~Il~~n~~~~i-~~l~SR--c-~~i~~~~~~~~~   59 (137)
                      |++|++|.|...          .    ..+|..++..+.+   ...||.+.++...+ +.|.|-  + .++.+++|...+
T Consensus       498 IvLDdld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~  577 (952)
T KOG0735|consen  498 IVLDDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAVTR  577 (952)
T ss_pred             EEEcchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCCcchhH
Confidence            578999988441          1    2233333343332   23467777777778 766664  3 478999999999


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-cHHHHHHHHH
Q 042716           60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKN-NLRQAIRSFE   99 (137)
Q Consensus        60 i~~~l~~i~~~egi~i~~~~l~~i~~~~~g-d~R~aln~L~   99 (137)
                      ..++|..++.+....+..+.+..++..++| +++...-+.+
T Consensus       578 R~~IL~~~~s~~~~~~~~~dLd~ls~~TEGy~~~DL~ifVe  618 (952)
T KOG0735|consen  578 RKEILTTIFSKNLSDITMDDLDFLSVKTEGYLATDLVIFVE  618 (952)
T ss_pred             HHHHHHHHHHhhhhhhhhHHHHHHHHhcCCccchhHHHHHH
Confidence            999999999988877778888888777665 3343333333

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=90.30  E-value=0.38  Score=41.75  Aligned_cols=46  Identities=17%  Similarity=0.172  Sum_probs=36.3

Q ss_pred             cccccCcCCHHHHHHHHHHHHhcc-------------CCceEEEEeCCCC-------------Cc-hhhhhcc
Q 042716            2 ILCEADKLSTDALLYMRWLLERYK-------------GLNKVFFCCSDVS-------------KL-QPIKSLC   47 (137)
Q Consensus         2 iiDEid~l~~~~~~~L~~~le~~~-------------~~~~~Il~~n~~~-------------~i-~~l~SRc   47 (137)
                      +|||.|.|......++...||+..             ..|-++.+||...             .+ ++|.||+
T Consensus       388 cIDEfdKm~~~dr~aihEaMEQQtIsIaKAGI~atLnARcsvLAAaNP~~Gryd~~~~~~enI~l~~~lLSRF  460 (682)
T COG1241         388 CIDEFDKMNEEDRVAIHEAMEQQTISIAKAGITATLNARCSVLAAANPKFGRYDPKKTVAENINLPAPLLSRF  460 (682)
T ss_pred             EEEeccCCChHHHHHHHHHHHhcEeeecccceeeecchhhhhhhhhCCCCCcCCCCCCHHHhcCCChhHHhhC
Confidence            699999999999999999999763             1334666677542             26 8999998

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

Probab=90.08  E-value=0.78  Score=40.55  Aligned_cols=90  Identities=16%  Similarity=0.168  Sum_probs=54.6

Q ss_pred             CcccccCcCCHHH-------------HHHHHHHHHhccC--Cc-eEEEEe-CCCCCc-hhhhh--cc-eeeEecCCCHHH
Q 042716            1 IILCEADKLSTDA-------------LLYMRWLLERYKG--LN-KVFFCC-SDVSKL-QPIKS--LC-TVIQLLPPSKQE   59 (137)
Q Consensus         1 iiiDEid~l~~~~-------------~~~L~~~le~~~~--~~-~~Il~~-n~~~~i-~~l~S--Rc-~~i~~~~~~~~~   59 (137)
                      ||+||+|.+.++-             ...|+.-|+-.+.  +. .||+.+ |-|+-+ ++|.-  |+ ..+.+.+..+++
T Consensus       768 IFFDELDSlAP~RG~sGDSGGVMDRVVSQLLAELDgls~~~s~~VFViGATNRPDLLDpALLRPGRFDKLvyvG~~~d~e  847 (953)
T KOG0736|consen  768 IFFDELDSLAPNRGRSGDSGGVMDRVVSQLLAELDGLSDSSSQDVFVIGATNRPDLLDPALLRPGRFDKLVYVGPNEDAE  847 (953)
T ss_pred             EEeccccccCccCCCCCCccccHHHHHHHHHHHhhcccCCCCCceEEEecCCCccccChhhcCCCccceeEEecCCccHH
Confidence            6899999996542             5567777776553  22 255554 555556 77765  55 467777777665


Q ss_pred             HHHH-HHHHHHHcCCCCCHHH-HHHHHHHcCCcHH
Q 042716           60 IVEV-LEFIAEQEGIQLPHQL-AEKIADNSKNNLR   92 (137)
Q Consensus        60 i~~~-l~~i~~~egi~i~~~~-l~~i~~~~~gd~R   92 (137)
                      -..+ |+...++  +.+++++ +..|++.|..++-
T Consensus       848 sk~~vL~AlTrk--FkLdedVdL~eiAk~cp~~~T  880 (953)
T KOG0736|consen  848 SKLRVLEALTRK--FKLDEDVDLVEIAKKCPPNMT  880 (953)
T ss_pred             HHHHHHHHHHHH--ccCCCCcCHHHHHhhCCcCCc
Confidence            4443 4433333  4444443 6778887765554

>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]

Probab=89.70  E-value=0.8  Score=39.60  Aligned_cols=57  Identities=18%  Similarity=0.159  Sum_probs=39.7

Q ss_pred             cccccCcCCHHHHHHHHHHHHhccC-------------CceEEEEeCCCC-------------Cc-hhhhhcce--eeEe
Q 042716            2 ILCEADKLSTDALLYMRWLLERYKG-------------LNKVFFCCSDVS-------------KL-QPIKSLCT--VIQL   52 (137)
Q Consensus         2 iiDEid~l~~~~~~~L~~~le~~~~-------------~~~~Il~~n~~~-------------~i-~~l~SRc~--~i~~   52 (137)
                      +|||.|.|+...|.|+...||+-.-             .+.++-++|...             ++ +||.||+-  .+-+
T Consensus       447 CIDEFDKMd~~dqvAihEAMEQQtISIaKAGv~aTLnARtSIlAAANPv~GhYdR~ktl~eNi~msApimSRFDL~FiLl  526 (764)
T KOG0480|consen  447 CIDEFDKMDVKDQVAIHEAMEQQTISIAKAGVVATLNARTSILAAANPVGGHYDRKKTLRENINMSAPIMSRFDLFFILL  526 (764)
T ss_pred             EechhcccChHhHHHHHHHHHhheehheecceEEeecchhhhhhhcCCcCCccccccchhhhcCCCchhhhhhcEEEEEe
Confidence            6999999999999999999997531             223555555331             36 89999983  3444


Q ss_pred             cCCCHH
Q 042716           53 LPPSKQ   58 (137)
Q Consensus        53 ~~~~~~   58 (137)
                      ..++..
T Consensus       527 D~~nE~  532 (764)
T KOG0480|consen  527 DDCNEV  532 (764)
T ss_pred             cCCchH
Confidence            555443

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=89.60  E-value=1.2  Score=28.81  Aligned_cols=36  Identities=22%  Similarity=0.156  Sum_probs=26.2

Q ss_pred             CcccccCcCCHHHHHHHHH--------HHHhccCCceEEEEeCC
Q 042716            1 IILCEADKLSTDALLYMRW--------LLERYKGLNKVFFCCSD   36 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~--------~le~~~~~~~~Il~~n~   36 (137)
                      +++||++.+..........        .......+..+|+++|.
T Consensus        82 iiiDei~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  125 (148)
T smart00382       82 LILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTND  125 (148)
T ss_pred             EEEECCcccCCHHHHHHHHhhhhhHHHHHHHhcCCCEEEEEeCC
Confidence            5899999998887666543        33344567778888885

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

>PRK06835 DNA replication protein DnaC; Validated

Probab=89.49  E-value=0.57  Score=37.18  Aligned_cols=56  Identities=11%  Similarity=0.084  Sum_probs=40.8

Q ss_pred             CcccccCc--CCHHHHHHHHHHHHhccC-CceEEEEeCCCCC-----c-hhhhhc----ceeeEecCCC
Q 042716            1 IILCEADK--LSTDALLYMRWLLERYKG-LNKVFFCCSDVSK-----L-QPIKSL----CTVIQLLPPS   56 (137)
Q Consensus         1 iiiDEid~--l~~~~~~~L~~~le~~~~-~~~~Il~~n~~~~-----i-~~l~SR----c~~i~~~~~~   56 (137)
                      +||||+..  .+...+..|+.+++.-.. +.+.|++||.+..     + +.+.||    |.++.|...+
T Consensus       250 LIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~tIiTSNl~~~el~~~~~eri~SRL~~~~~~i~~~G~d  318 (329)
T PRK06835        250 LIIDDLGTEKITEFSKSELFNLINKRLLRQKKMIISTNLSLEELLKTYSERISSRLLGNFTLLKFYGED  318 (329)
T ss_pred             EEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHhHHHHHHHHcCCEEEEecCcC
Confidence            58999954  577778999999997543 5679999997743     4 577777    4577776543

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=89.26  E-value=0.22  Score=34.56  Aligned_cols=39  Identities=18%  Similarity=0.115  Sum_probs=26.3

Q ss_pred             CcccccCcCCH-HHHHHHHHHHHhccCCceEEEEeCCCCC
Q 042716            1 IILCEADKLST-DALLYMRWLLERYKGLNKVFFCCSDVSK   39 (137)
Q Consensus         1 iiiDEid~l~~-~~~~~L~~~le~~~~~~~~Il~~n~~~~   39 (137)
                      +|+||+|.+.. .....+..++.......++++.+..+.+
T Consensus       133 iIiDE~h~~~~~~~~~~~~~~~~~~~~~~~~v~~saT~~~  172 (201)
T smart00487      133 VILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPE  172 (201)
T ss_pred             EEEECHHHHhcCCcHHHHHHHHHhCCccceEEEEecCCch
Confidence            58999999987 4555555666554456666666666654

>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold

Probab=88.96  E-value=0.55  Score=39.04  Aligned_cols=47  Identities=17%  Similarity=0.127  Sum_probs=37.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc-----cCCceEEEEeCCCCCc-hhhhhcc
Q 042716            1 IILCEADKLSTDALLYMRWLLERY-----KGLNKVFFCCSDVSKL-QPIKSLC   47 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~-----~~~~~~Il~~n~~~~i-~~l~SRc   47 (137)
                      +|+||+|.|-.++-.+|+.-+|..     ++.+-+.|+|-+|..| .++.|-+
T Consensus       259 fFfDEAHLLF~da~kall~~ieqvvrLIRSKGVGv~fvTQ~P~DiP~~VL~QL  311 (502)
T PF05872_consen  259 FFFDEAHLLFNDAPKALLDKIEQVVRLIRSKGVGVYFVTQNPTDIPDDVLGQL  311 (502)
T ss_pred             EEEechhhhhcCCCHHHHHHHHHHHHHhhccCceEEEEeCCCCCCCHHHHHhh
Confidence            479999999888877877777764     4566788999888888 7777765

This family is restricted to bacterial proteins, none of which have currently been characterised.

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

Probab=88.63  E-value=0.81  Score=36.74  Aligned_cols=66  Identities=18%  Similarity=0.312  Sum_probs=47.1

Q ss_pred             CcccccCcCCHH---------------HHHHHHHHHHhccCCc-eEEEEeCCC-CCc-hhhhhcc-eeeEecCCCHHHHH
Q 042716            1 IILCEADKLSTD---------------ALLYMRWLLERYKGLN-KVFFCCSDV-SKL-QPIKSLC-TVIQLLPPSKQEIV   61 (137)
Q Consensus         1 iiiDEid~l~~~---------------~~~~L~~~le~~~~~~-~~Il~~n~~-~~i-~~l~SRc-~~i~~~~~~~~~i~   61 (137)
                      ++|||++.|+..               ..|+|+.-+++.+..- .+||+|.+. ..+ .++..|. .++.+.+|+.+.+.
T Consensus       254 vLIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDrlK~~~NvliL~TSNl~~siD~AfVDRADi~~yVG~Pt~~ai~  333 (423)
T KOG0744|consen  254 VLIDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDRLKRYPNVLILATSNLTDSIDVAFVDRADIVFYVGPPTAEAIY  333 (423)
T ss_pred             EEeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHhccCCCEEEEeccchHHHHHHHhhhHhhheeecCCccHHHHH
Confidence            479999998432               2678887777654322 255555554 679 9999999 56888888888888


Q ss_pred             HHHHH
Q 042716           62 EVLEF   66 (137)
Q Consensus        62 ~~l~~   66 (137)
                      .+++.
T Consensus       334 ~Ilks  338 (423)
T KOG0744|consen  334 EILKS  338 (423)
T ss_pred             HHHHH
Confidence            87754

>PRK06921 hypothetical protein; Provisional

Probab=88.58  E-value=0.73  Score=35.38  Aligned_cols=56  Identities=11%  Similarity=0.084  Sum_probs=38.3

Q ss_pred             CcccccCc-------CCHHHHHHHHHHHHhccC-CceEEEEeCCCCC----c-hhhhhc----ce--eeEecCCC
Q 042716            1 IILCEADK-------LSTDALLYMRWLLERYKG-LNKVFFCCSDVSK----L-QPIKSL----CT--VIQLLPPS   56 (137)
Q Consensus         1 iiiDEid~-------l~~~~~~~L~~~le~~~~-~~~~Il~~n~~~~----i-~~l~SR----c~--~i~~~~~~   56 (137)
                      +||||++.       ++...+..|+.+++.... +.++|+++|.++.    + +.+.||    |.  ++.|...|
T Consensus       181 LiIDDl~~~~~g~e~~t~~~~~~lf~iin~R~~~~k~tIitsn~~~~el~~~~~~l~sRi~~r~~~~~i~~~g~s  255 (266)
T PRK06921        181 LFIDDLFKPVNGKPRATEWQIEQMYSVLNYRYLNHKPILISSELTIDELLDIDEALGSRIVEMCKDYLVIIKGDS  255 (266)
T ss_pred             EEEeccccccCCCccCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHhhhhhHHHHHHHHhccCeEEEecCcc
Confidence            58999954       555567789999987543 4678999997643    3 455665    43  67776654

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

Probab=88.54  E-value=0.59  Score=34.78  Aligned_cols=24  Identities=25%  Similarity=0.236  Sum_probs=21.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc
Q 042716            1 IILCEADKLSTDALLYMRWLLERY   24 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~   24 (137)
                      +|+||+-.+.+...++|+..+|+.
T Consensus       110 LflDE~~ef~~~vld~Lr~ple~g  133 (206)
T PF01078_consen  110 LFLDELNEFDRSVLDALRQPLEDG  133 (206)
T ss_dssp             EEECETTTS-HHHHHHHHHHHHHS
T ss_pred             EEechhhhcCHHHHHHHHHHHHCC
Confidence            489999999999999999999964

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

>PF07034 ORC3_N: Origin recognition complex (ORC) subunit 3 N-terminus; InterPro: IPR020795 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []

Probab=88.31  E-value=8.8  Score=30.35  Aligned_cols=103  Identities=17%  Similarity=0.178  Sum_probs=76.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeC---CC----CCc-hhhhhcceeeEecCCCHHHHHHHHH-HHHH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCS---DV----SKL-QPIKSLCTVIQLLPPSKQEIVEVLE-FIAE--   69 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n---~~----~~i-~~l~SRc~~i~~~~~~~~~i~~~l~-~i~~--   69 (137)
                      |+|.|.+.++.+.-+.|..++-.+....||+|+-.   ..    ..+ ....|+...-.|.-++..+....+- .+.-  
T Consensus       203 Ii~eD~EsF~~~VL~dlI~ils~~~~~lP~vli~GiaTs~~~~~~~Lp~~~~~~L~~~~F~~~~~~~~l~~v~~~~l~~~  282 (330)
T PF07034_consen  203 IIFEDFESFDSQVLQDLILILSSYLDRLPFVLIFGIATSVEAFHSRLPRSTLSLLRIKKFQLQSSSEILERVLEKVLLSP  282 (330)
T ss_pred             EEEcccccCCHHHHHHHHHHHHhccCCcCEEEEEecCCChHHHHhhCCHHHHhhcCceEEEeCChHHHHHHHHHHHhcCC
Confidence            57899999999999999999988888888766643   22    235 7788888777788888777666654 3322  


Q ss_pred             HcCCCCCHHHHHHHHHH---cCCcHHHHHHHHHHHHh
Q 042716           70 QEGIQLPHQLAEKIADN---SKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~---~~gd~R~aln~L~~~~~  103 (137)
                      ...+.+++.++..+..+   .+.++...+..|+.+.+
T Consensus       283 ~~~~~l~~~~~~~L~~~f~~~~~Sv~~fi~~lk~~~m  319 (330)
T PF07034_consen  283 DFPFKLGPRVLQFLLDRFLDHDFSVDSFISGLKYAYM  319 (330)
T ss_pred             CCCceECHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            23567888888887764   67888888888886654

ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex

>PRK13695 putative NTPase; Provisional

Probab=88.17  E-value=2  Score=30.34  Aligned_cols=63  Identities=24%  Similarity=0.202  Sum_probs=44.8

Q ss_pred             CcccccCcC---CHHHHHHHHHHHHhccCCceEEEEeCCCC--Cc-hhhhhc--ceeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKL---STDALLYMRWLLERYKGLNKVFFCCSDVS--KL-QPIKSL--CTVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l---~~~~~~~L~~~le~~~~~~~~Il~~n~~~--~i-~~l~SR--c~~i~~~~~~~~~i~~~l~~   66 (137)
                      +++||+-.+   +....+.+...++   .+.++|++++...  .. +.|.+|  +.++.+.+-+.+++...+.+
T Consensus       100 lllDE~~~~e~~~~~~~~~l~~~~~---~~~~~i~v~h~~~~~~~~~~i~~~~~~~i~~~~~~~r~~~~~~~~~  170 (174)
T PRK13695        100 IIIDEIGKMELKSPKFVKAVEEVLD---SEKPVIATLHRRSVHPFVQEIKSRPGGRVYELTPENRDSLPFEILN  170 (174)
T ss_pred             EEEECCCcchhhhHHHHHHHHHHHh---CCCeEEEEECchhhHHHHHHHhccCCcEEEEEcchhhhhHHHHHHH
Confidence            578986443   4445667777774   3567899988753  35 778887  68899988888887776655

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=87.80  E-value=1.7  Score=34.08  Aligned_cols=96  Identities=17%  Similarity=0.180  Sum_probs=62.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCC--------CCc-hhhhhcce---eeEecCCCHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDV--------SKL-QPIKSLCT---VIQLLPPSKQEIVEVLEFIA   68 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~--------~~i-~~l~SRc~---~i~~~~~~~~~i~~~l~~i~   68 (137)
                      |++||+|.|...+.+.|+++.++  ..+-+++..+.-        ... .-+.||..   .+...-+..++.......  
T Consensus       169 iivDEA~~L~~~ale~lr~i~d~--~Gi~~vLvG~prL~~~l~~~~~~~~rl~srv~v~~~~~~~~~d~d~~~~~~~~--  244 (297)
T COG2842         169 IIVDEADRLPYRALEELRRIHDK--TGIGVVLVGMPRLFKVLRRPEDELSRLYSRVRVGKLLGEKFPDADELAEIAAL--  244 (297)
T ss_pred             eeeehhhccChHHHHHHHHHHHh--hCceEEEecChHHHhccccchHHHHHHHHHhhhHhhhhhhhhhhHHHHHHHHh--
Confidence            57999999999999999999994  456688887644        112 34555532   122111221333333222  


Q ss_pred             HHcCCC-CCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           69 EQEGIQ-LPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        69 ~~egi~-i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                         +++ ..+.++..+.....|.+|.+-..|.....
T Consensus       245 ---~l~~~~~~~v~~~~~~~~g~~~~L~~~l~~~~~  277 (297)
T COG2842         245 ---VLPTEDELVLMQVIKETEGNIRRLDKILAGAVG  277 (297)
T ss_pred             ---hCccchHHHHHHHHHhcchhHhHHHHHHhhhhh
Confidence               222 46778888999999999998888776654

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=87.11  E-value=0.91  Score=36.53  Aligned_cols=57  Identities=14%  Similarity=0.162  Sum_probs=42.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc-cCCceEEEEeCCCCC---------------chhhhhcceeeEecCCCH
Q 042716            1 IILCEADKLSTDALLYMRWLLERY-KGLNKVFFCCSDVSK---------------LQPIKSLCTVIQLLPPSK   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~-~~~~~~Il~~n~~~~---------------i~~l~SRc~~i~~~~~~~   57 (137)
                      +++||.|--.....-.|.++++.. ..++.+|.|+|.++.               |..|.++|.++++....+
T Consensus       131 LcfDEF~V~DiaDAmil~rLf~~l~~~gvvlVaTSN~~P~~Ly~~gl~r~~Flp~I~~l~~~~~vv~ld~~~D  203 (362)
T PF03969_consen  131 LCFDEFQVTDIADAMILKRLFEALFKRGVVLVATSNRPPEDLYKNGLQRERFLPFIDLLKRRCDVVELDGGVD  203 (362)
T ss_pred             EEEeeeeccchhHHHHHHHHHHHHHHCCCEEEecCCCChHHHcCCcccHHHHHHHHHHHHhceEEEEecCCCc
Confidence            478999988877776666666653 456778888887641               357889999999988744

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

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

Probab=86.73  E-value=0.84  Score=36.37  Aligned_cols=88  Identities=14%  Similarity=0.112  Sum_probs=47.4

Q ss_pred             CcccccCcCCHH----HHHHHHHHHHhc---------cCCceEEEEeCC-CCCc-hhhhhccee-eEecCCCHHHHHHHH
Q 042716            1 IILCEADKLSTD----ALLYMRWLLERY---------KGLNKVFFCCSD-VSKL-QPIKSLCTV-IQLLPPSKQEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l~~~----~~~~L~~~le~~---------~~~~~~Il~~n~-~~~i-~~l~SRc~~-i~~~~~~~~~i~~~l   64 (137)
                      |||||+|.|...    --.+-+++--++         .....++|.+++ +-.+ .+||-|+.. +.+ |+++......+
T Consensus       229 IFiDEiDslcg~r~enEseasRRIKTEfLVQMqGVG~d~~gvLVLgATNiPw~LDsAIRRRFekRIYI-PLPe~~AR~~M  307 (439)
T KOG0739|consen  229 IFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGVGNDNDGVLVLGATNIPWVLDSAIRRRFEKRIYI-PLPEAHARARM  307 (439)
T ss_pred             EEeehhhhhccCCCCCchHHHHHHHHHHHHhhhccccCCCceEEEecCCCchhHHHHHHHHhhcceec-cCCcHHHhhhh
Confidence            689999999332    244444443332         112335555544 4567 999999954 444 45554444333


Q ss_pred             HHH-HHHcCCCCCHHHHHHHHHHcCC
Q 042716           65 EFI-AEQEGIQLPHQLAEKIADNSKN   89 (137)
Q Consensus        65 ~~i-~~~egi~i~~~~l~~i~~~~~g   89 (137)
                      -.+ .-.--..+++.....++...+|
T Consensus       308 F~lhlG~tp~~LT~~d~~eL~~kTeG  333 (439)
T KOG0739|consen  308 FKLHLGDTPHVLTEQDFKELARKTEG  333 (439)
T ss_pred             heeccCCCccccchhhHHHHHhhcCC
Confidence            221 1111235666677777765443

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

Probab=85.43  E-value=1.5  Score=34.97  Aligned_cols=63  Identities=19%  Similarity=0.254  Sum_probs=44.5

Q ss_pred             CcccccCcCCH-----------HHHHHHHHHHHhcc-----CCceEEEEeCCCCCc-hhhhhcc---eeeEecCCCHHHH
Q 042716            1 IILCEADKLST-----------DALLYMRWLLERYK-----GLNKVFFCCSDVSKL-QPIKSLC---TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~-----------~~~~~L~~~le~~~-----~~~~~Il~~n~~~~i-~~l~SRc---~~i~~~~~~~~~i   60 (137)
                      +||||+|.+..           +.|..++.++++..     +.+.+|++||....+ |+|.--.   ..+.|+.|+...-
T Consensus       282 vFiDEIdAiGtKRyds~SggerEiQrtmLELLNQldGFdsrgDvKvimATnrie~LDPaLiRPGrIDrKIef~~pDe~Tk  361 (440)
T KOG0726|consen  282 VFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTK  361 (440)
T ss_pred             EEeehhhhhccccccCCCccHHHHHHHHHHHHHhccCccccCCeEEEEecccccccCHhhcCCCccccccccCCCchhhh
Confidence            58999999832           23788888888653     356799999999998 7765432   4588877766544


Q ss_pred             HHH
Q 042716           61 VEV   63 (137)
Q Consensus        61 ~~~   63 (137)
                      .++
T Consensus       362 kkI  364 (440)
T KOG0726|consen  362 KKI  364 (440)
T ss_pred             cee
Confidence            433

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=85.27  E-value=1  Score=35.44  Aligned_cols=39  Identities=18%  Similarity=0.182  Sum_probs=25.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-CCceEEEEeCCCCC
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-GLNKVFFCCSDVSK   39 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-~~~~~Il~~n~~~~   39 (137)
                      +||||+|.+.......+..+++... .++++++.|...++
T Consensus       128 iViDE~h~~~~~~~~~l~~~l~~l~~~~~~~i~~SATlp~  167 (358)
T TIGR01587       128 LIFDEVHFYDEYTLALILAVLEVLKDNDVPILLMSATLPK  167 (358)
T ss_pred             EEEeCCCCCCHHHHHHHHHHHHHHHHcCCCEEEEecCchH
Confidence            5899999998765555666555433 45666665544433

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.

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

Probab=84.08  E-value=12  Score=29.05  Aligned_cols=59  Identities=10%  Similarity=0.152  Sum_probs=49.0

Q ss_pred             hhcc-eeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH-----HHHHHHHcCCcHHHHHHHHHHHH
Q 042716           44 KSLC-TVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL-----AEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        44 ~SRc-~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~-----l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      -.|+ .-+.|.+.+.++..+.+...+++.|++++++.     ++.-..+.+++=|.|....+.+.
T Consensus       214 SDRFGLwL~F~~~~Q~~YL~~V~~~a~~~~l~~~~e~l~~eAl~WAt~rg~RSGR~A~QF~~~~~  278 (287)
T COG2607         214 SDRFGLWLSFYPCDQDEYLKIVDHYAKHFGLDISDEELHAEALQWATTRGGRSGRVAWQFIRDLA  278 (287)
T ss_pred             hhhcceeecccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhcCCCccHhHHHHHHHHH
Confidence            3454 56899999999999999999999999998744     45556678889999999888776

>PLN03210 Resistant to P

Probab=84.01  E-value=5.4  Score=36.75  Aligned_cols=89  Identities=16%  Similarity=0.120  Sum_probs=55.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCchhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCC--HH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLP--HQ   78 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~--~~   78 (137)
                      |++|+++.  ....++|....+-...+.++|+||.+..-+.... -..++.+..++.++....+.+.|.+....-+  .+
T Consensus       300 LVLDdv~~--~~~l~~L~~~~~~~~~GsrIIiTTrd~~vl~~~~-~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~  376 (1153)
T PLN03210        300 IFIDDLDD--QDVLDALAGQTQWFGSGSRIIVITKDKHFLRAHG-IDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFME  376 (1153)
T ss_pred             EEEeCCCC--HHHHHHHHhhCccCCCCcEEEEEeCcHHHHHhcC-CCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHH
Confidence            47898875  3445555554443345678899888765442110 1257888999999988888877765432211  13


Q ss_pred             HHHHHHHHcCCcHH
Q 042716           79 LAEKIADNSKNNLR   92 (137)
Q Consensus        79 ~l~~i~~~~~gd~R   92 (137)
                      ....+++.++|-+-
T Consensus       377 l~~~iv~~c~GLPL  390 (1153)
T PLN03210        377 LASEVALRAGNLPL  390 (1153)
T ss_pred             HHHHHHHHhCCCcH
Confidence            45667888887553

syringae 6; Provisional

>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]

Probab=83.98  E-value=6.4  Score=34.25  Aligned_cols=103  Identities=14%  Similarity=0.086  Sum_probs=66.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc---------------------cCCceEEEEeCCC--CCc-hhhhhccee----eEe
Q 042716            1 IILCEADKLSTDALLYMRWLLERY---------------------KGLNKVFFCCSDV--SKL-QPIKSLCTV----IQL   52 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~---------------------~~~~~~Il~~n~~--~~i-~~l~SRc~~----i~~   52 (137)
                      +||||+..|....|+.+++.+.+-                     |-...+|+++|..  ..+ ++.+||-.-    ..|
T Consensus       229 LiIdei~lL~~~~~w~~LKa~~~k~~~~~~~~~~s~~~~v~~e~vP~d~klI~~Gn~~~l~~l~~~~~~r~~g~~y~ae~  308 (647)
T COG1067         229 LIIDEIGLLAQPLQWKLLKALLDKEQPIWGSSEPSSGAPVRPESVPLDLKLILAGNREDLEDLHEPDRSRIEGFGYEAEF  308 (647)
T ss_pred             EEEEhhhhhCcHHHHHHHHHHHhccccccCcCccccCcccCCCCcccceEEEeeCCHHHHHhhcccCHHHHhhcceEEEE
Confidence            589999999988887777777653                     1233466666644  457 888888533    344


Q ss_pred             cC--C-CHHHHHHH----HHHHHHH-cCCCCCHHHHHHHHHHc----------CCcHHHHHHHHHHHHh
Q 042716           53 LP--P-SKQEIVEV----LEFIAEQ-EGIQLPHQLAEKIADNS----------KNNLRQAIRSFEASRQ  103 (137)
Q Consensus        53 ~~--~-~~~~i~~~----l~~i~~~-egi~i~~~~l~~i~~~~----------~gd~R~aln~L~~~~~  103 (137)
                      +.  + +++...+.    .+.+++. .-..++.+++..|+..+          .-.+|.+.++++.+..
T Consensus       309 ~~~m~~~~~nr~k~~~~~~q~v~~d~~ip~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~  377 (647)
T COG1067         309 EDTMPITDANRSKLVQFYVQELARDGNIPHLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGD  377 (647)
T ss_pred             cCCCCCChHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhH
Confidence            33  3 34443333    3444555 34468889988887654          2468888888885543

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

Probab=83.98  E-value=1.7  Score=37.17  Aligned_cols=94  Identities=14%  Similarity=0.183  Sum_probs=57.0

Q ss_pred             CcccccCcCCH-----------HHHHHHHHHHHhccCCceEE--EEeCCCCCc-hhhhh--cc-eeeEecCCCHHHHHHH
Q 042716            1 IILCEADKLST-----------DALLYMRWLLERYKGLNKVF--FCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~-----------~~~~~L~~~le~~~~~~~~I--l~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i~~~   63 (137)
                      |||||+|.+..           ...|.|+.-|+-+++|-.+|  -+||-+..+ ++|.-  |+ ..+.++.|+..=..++
T Consensus       400 IFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe~LD~AL~RPGRFD~~v~Vp~PDv~GR~eI  479 (752)
T KOG0734|consen  400 IFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPEALDKALTRPGRFDRHVTVPLPDVRGRTEI  479 (752)
T ss_pred             EEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChhhhhHHhcCCCccceeEecCCCCcccHHHH
Confidence            68999999832           22566677777677765544  445666778 66654  44 5788888887767777


Q ss_pred             HHHHHHHcCCCCCHHH-HHHHHHHcC----CcHHHHHH
Q 042716           64 LEFIAEQEGIQLPHQL-AEKIADNSK----NNLRQAIR   96 (137)
Q Consensus        64 l~~i~~~egi~i~~~~-l~~i~~~~~----gd~R~aln   96 (137)
                      |+....+-  .+++++ ...|++.+.    -|+-.++|
T Consensus       480 L~~yl~ki--~~~~~VD~~iiARGT~GFsGAdLaNlVN  515 (752)
T KOG0734|consen  480 LKLYLSKI--PLDEDVDPKIIARGTPGFSGADLANLVN  515 (752)
T ss_pred             HHHHHhcC--CcccCCCHhHhccCCCCCchHHHHHHHH
Confidence            77665443  233222 344555433    34544444

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

Probab=83.77  E-value=4.4  Score=32.95  Aligned_cols=59  Identities=22%  Similarity=0.294  Sum_probs=46.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCC----Cc-hhhhhcceeeEecCCCHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVS----KL-QPIKSLCTVIQLLPPSKQEIVE   62 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~----~i-~~l~SRc~~i~~~~~~~~~i~~   62 (137)
                      +|+||||.+- +=+.++..+.+....  .+++++++..    ++ ..|.-|...+.+.|+|-.+...
T Consensus        98 ifLDEIq~v~-~W~~~lk~l~d~~~~--~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Efl~  161 (398)
T COG1373          98 IFLDEIQNVP-DWERALKYLYDRGNL--DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREFLK  161 (398)
T ss_pred             EEEecccCch-hHHHHHHHHHccccc--eEEEECCchhhhccchhhhcCCCceeEEECCCCHHHHHh
Confidence            5899999985 477788888884332  5677766553    35 7888899999999999999875

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=83.37  E-value=3.5  Score=40.46  Aligned_cols=91  Identities=21%  Similarity=0.274  Sum_probs=63.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccC------------Cce-EEEEeCCCC------C-c-hhhhhcceeeEecCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKG------------LNK-VFFCCSDVS------K-L-QPIKSLCTVIQLLPPSKQE   59 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~------------~~~-~Il~~n~~~------~-i-~~l~SRc~~i~~~~~~~~~   59 (137)
                      |++||...-....-++|.+++.....            +-- .+|+|-+|+      | + +++|.|+..++|...+.++
T Consensus       959 IVLDELNLApTDVLEaLNRLLDDNRelfIPETqevV~PHp~F~lFATQNppg~YgGRK~LSrAFRNRFlE~hFddipedE 1038 (4600)
T COG5271         959 IVLDELNLAPTDVLEALNRLLDDNRELFIPETQEVVVPHPNFRLFATQNPPGGYGGRKGLSRAFRNRFLEMHFDDIPEDE 1038 (4600)
T ss_pred             EEeeccccCcHHHHHHHHHhhccccceecCCcceeeccCCCeeEEeecCCCccccchHHHHHHHHhhhHhhhcccCcHHH
Confidence            57888877777778999999875421            111 344554443      2 6 8999999999999999999


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHcC-CcHHHHHH
Q 042716           60 IVEVLEFIAEQEGIQLPHQLAEKIADNSK-NNLRQAIR   96 (137)
Q Consensus        60 i~~~l~~i~~~egi~i~~~~l~~i~~~~~-gd~R~aln   96 (137)
                      +..+|..     +.++.+.-...|++... -+.|+-.+
T Consensus      1039 le~ILh~-----rc~iapSyakKiVeVyr~Ls~rRs~~ 1071 (4600)
T COG5271        1039 LEEILHG-----RCEIAPSYAKKIVEVYRGLSSRRSIN 1071 (4600)
T ss_pred             HHHHHhc-----cCccCHHHHHHHHHHHHHhhhhhhHH
Confidence            9988864     56777777777776532 23444333

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

Probab=83.30  E-value=0.65  Score=33.65  Aligned_cols=55  Identities=13%  Similarity=0.075  Sum_probs=33.3

Q ss_pred             CcccccCcCCHHHH------HHHHHHHHhccC-CceEEEEeCCCCCc-hhhhhcce-eeEecCC
Q 042716            1 IILCEADKLSTDAL------LYMRWLLERYKG-LNKVFFCCSDVSKL-QPIKSLCT-VIQLLPP   55 (137)
Q Consensus         1 iiiDEid~l~~~~~------~~L~~~le~~~~-~~~~Il~~n~~~~i-~~l~SRc~-~i~~~~~   55 (137)
                      ++||||+..-+...      ......+..+.. +.-++|+|-++..+ +.+|..+. .+.+..+
T Consensus        83 iviDEa~~~~~~r~~~~~~~~~~~~~l~~hRh~g~diiliTQ~~~~id~~ir~lve~~~~~~k~  146 (193)
T PF05707_consen   83 IVIDEAQNFFPSRSWKGKKVPEIIEFLAQHRHYGWDIILITQSPSQIDKFIRDLVEYHYHCRKL  146 (193)
T ss_dssp             EEETTGGGTSB---T-T----HHHHGGGGCCCTT-EEEEEES-GGGB-HHHHCCEEEEEEEEE-
T ss_pred             EEEECChhhcCCCccccccchHHHHHHHHhCcCCcEEEEEeCCHHHHhHHHHHHHheEEEEEee
Confidence            58999998733322      223355554433 34499999999999 99998763 4555444

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

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

Probab=82.79  E-value=6.6  Score=34.80  Aligned_cols=90  Identities=13%  Similarity=0.102  Sum_probs=62.0

Q ss_pred             CcccccCcCCHHH---------------HHHHHHHHHhccCCc--eEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHH
Q 042716            1 IILCEADKLSTDA---------------LLYMRWLLERYKGLN--KVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQE   59 (137)
Q Consensus         1 iiiDEid~l~~~~---------------~~~L~~~le~~~~~~--~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~   59 (137)
                      |+|||+|.++..-               .|.|+--|+-+..+.  .|+.+||.+.-+ ++|+-  |+ ..+.+..|+...
T Consensus       407 ifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~  486 (774)
T KOG0731|consen  407 IFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKG  486 (774)
T ss_pred             EEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCCccccCHHhcCCCccccceeccCCchhh
Confidence            5899999874321               456666666554443  355556666667 77765  44 578999999999


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHcCCc
Q 042716           60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNN   90 (137)
Q Consensus        60 i~~~l~~i~~~egi~i~~~~l~~i~~~~~gd   90 (137)
                      -..+++..+.+-.+..++..+..++.+..|-
T Consensus       487 r~~i~~~h~~~~~~~~e~~dl~~~a~~t~gf  517 (774)
T KOG0731|consen  487 RASILKVHLRKKKLDDEDVDLSKLASLTPGF  517 (774)
T ss_pred             hHHHHHHHhhccCCCcchhhHHHHHhcCCCC
Confidence            9999988777776665666677788776653

>COG1485 Predicted ATPase [General function prediction only]

Probab=82.61  E-value=2.1  Score=34.46  Aligned_cols=57  Identities=16%  Similarity=0.165  Sum_probs=41.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHh-ccCCceEEEEeCCCCC---------------chhhhhcceeeEecCCCH
Q 042716            1 IILCEADKLSTDALLYMRWLLER-YKGLNKVFFCCSDVSK---------------LQPIKSLCTVIQLLPPSK   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~-~~~~~~~Il~~n~~~~---------------i~~l~SRc~~i~~~~~~~   57 (137)
                      +++||.+-=.....--|.++++. +..++.++.|+|..+.               |..|.++|.++++..+.+
T Consensus       134 LCfDEF~VtDI~DAMiL~rL~~~Lf~~GV~lvaTSN~~P~~LY~dGlqR~~FLP~I~li~~~~~v~~vD~~~D  206 (367)
T COG1485         134 LCFDEFEVTDIADAMILGRLLEALFARGVVLVATSNTAPDNLYKDGLQRERFLPAIDLIKSHFEVVNVDGPVD  206 (367)
T ss_pred             EEeeeeeecChHHHHHHHHHHHHHHHCCcEEEEeCCCChHHhcccchhHHhhHHHHHHHHHheEEEEecCCcc
Confidence            47899888777777777777777 3556667777776531               367899999988887743

>PRK07952 DNA replication protein DnaC; Validated

Probab=82.32  E-value=1.8  Score=32.97  Aligned_cols=56  Identities=7%  Similarity=0.008  Sum_probs=39.0

Q ss_pred             CcccccCcCC--HHHHHHHHHHHHh-ccCCceEEEEeCCCCC-----c-hhhhhcc-----eeeEecCCC
Q 042716            1 IILCEADKLS--TDALLYMRWLLER-YKGLNKVFFCCSDVSK-----L-QPIKSLC-----TVIQLLPPS   56 (137)
Q Consensus         1 iiiDEid~l~--~~~~~~L~~~le~-~~~~~~~Il~~n~~~~-----i-~~l~SRc-----~~i~~~~~~   56 (137)
                      ++|||++...  ...+..|..+++. +..+.+.|++||....     + ..+.||+     ..+.|...|
T Consensus       166 LvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl~~~~l~~~~g~ri~sRl~~~~~~~i~f~~~s  235 (244)
T PRK07952        166 LVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNSNMEEMTKLLGERVMDRMRLGNSLWVIFNWDS  235 (244)
T ss_pred             EEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCCCHHHHHHHhChHHHHHHHHCCceEEEeeCCc
Confidence            5899998864  3346678889986 3346789999997743     4 5666665     367777654

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=81.88  E-value=1.8  Score=30.55  Aligned_cols=38  Identities=21%  Similarity=0.167  Sum_probs=21.3

Q ss_pred             CcccccCcCCHHHH--HHHHHHHHhccCCceEEEEeCCCCC
Q 042716            1 IILCEADKLSTDAL--LYMRWLLERYKGLNKVFFCCSDVSK   39 (137)
Q Consensus         1 iiiDEid~l~~~~~--~~L~~~le~~~~~~~~Il~~n~~~~   39 (137)
                      ||+||+|-.++.+.  ..+++..++ .+.+.+|+.+-.++.
T Consensus        99 II~DEcH~~Dp~sIA~rg~l~~~~~-~g~~~~i~mTATPPG  138 (148)
T PF07652_consen   99 IIMDECHFTDPTSIAARGYLRELAE-SGEAKVIFMTATPPG  138 (148)
T ss_dssp             EEECTTT--SHHHHHHHHHHHHHHH-TTS-EEEEEESS-TT
T ss_pred             EEEeccccCCHHHHhhheeHHHhhh-ccCeeEEEEeCCCCC
Confidence            68999999998863  333444432 344577777766654

The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....

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

Probab=80.10  E-value=3  Score=32.88  Aligned_cols=44  Identities=20%  Similarity=0.279  Sum_probs=32.8

Q ss_pred             CcccccCcCC-----------HHHHHHHHHHHHhc-----cCCceEEEEeCCCCCc-hhhh
Q 042716            1 IILCEADKLS-----------TDALLYMRWLLERY-----KGLNKVFFCCSDVSKL-QPIK   44 (137)
Q Consensus         1 iiiDEid~l~-----------~~~~~~L~~~le~~-----~~~~~~Il~~n~~~~i-~~l~   44 (137)
                      ||+||+|.+.           .+.|..++.++.+.     .+|..++++||.+.-+ |+|.
T Consensus       274 iffdeidaiggarfddg~ggdnevqrtmleli~qldgfdprgnikvlmatnrpdtldpall  334 (435)
T KOG0729|consen  274 IFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIKVLMATNRPDTLDPALL  334 (435)
T ss_pred             EEeeccccccCccccCCCCCcHHHHHHHHHHHHhccCCCCCCCeEEEeecCCCCCcCHhhc
Confidence            5889999883           33477788888764     4678899999988766 5554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	137
1sxj_D	353	Crystal Structure Of The Eukaryotic Clamp Loader (R		4e-09
1iqp_A	327	Crystal Structure Of The Clamp Loader Small Subunit		8e-09
1sxj_E	354	Crystal Structure Of The Eukaryotic Clamp Loader (R		3e-08
2chg_A	226	Replication Factor C Domains 1 And 2 Length = 226		8e-08
2chq_A	319	Replication Factor C Adpnp Complex Length = 319		1e-07
1sxj_B	323	Crystal Structure Of The Eukaryotic Clamp Loader (R		2e-05

>pdb|1SXJ|D Chain D, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 353

Iteration: 1
 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 32/117 (27%), Positives = 61/117 (52%), Gaps = 1/117 (0%)
Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           IIL EAD ++ DA   +R  +E Y G+ +    C+ V+++  P+ S C+  +        
Sbjct: 137 IILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASN 196
Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILT 116
            ++ L FI+EQE ++    + E+I D S  +LR+ I   +++ +      +G+ I +
Sbjct: 197 AIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITS 253

>pdb|1IQP|A Chain A, Crystal Structure Of The Clamp Loader Small Subunit From Pyrococcus Furiosus Length = 327

Iteration: 1
 Score = 55.8 bits (133), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 32/118 (27%), Positives = 62/118 (52%), Gaps = 1/118 (0%)
Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           I L EAD L+ DA   +R  +E +    +    C+  SK+ +PI+S C + +  P   ++
Sbjct: 114 IFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDED 173
Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTG 117
           I + L +IAE EG++L  +  + I   ++ ++R+AI   +A+  ++    +  V +  
Sbjct: 174 IAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALDKKITDENVFMVA 231

>pdb|1SXJ|E Chain E, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 354

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 41/138 (29%), Positives = 69/138 (50%), Gaps = 4/138 (2%)
Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           +I+ EA+ L+ DA   +R  +E+Y    ++   C  +S +  PIKS C +I+   PS  E
Sbjct: 138 VIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSE 197
Query: 60  IVEVLEFIAEQEGIQL-PHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQ--VILT 116
           I  +L  +   E IQL    + ++IA  S  NLR ++   E+    N   ++    +I  
Sbjct: 198 ISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMALNNELALKSSSPIIKP 257
Query: 117 GWEDDITNIATKIIEEQS 134
            W   I  +  KI++E+S
Sbjct: 258 DWIIVIHKLTRKIVKERS 275

>pdb|2CHG|A Chain A, Replication Factor C Domains 1 And 2 Length = 226

Iteration: 1
 Score = 52.4 bits (124), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 31/102 (30%), Positives = 54/102 (52%), Gaps = 1/102 (0%)
Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           I L EAD L+ DA   +R  +E Y    +    C+ VS++ +PI+S C V +  P  K+ 
Sbjct: 106 IFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEA 165
Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS 101
           + + L  I E+EG+++     E +   S  + R+AI + + +
Sbjct: 166 MKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQGA 207

>pdb|2CHQ|A Chain A, Replication Factor C Adpnp Complex Length = 319

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/102 (30%), Positives = 54/102 (52%), Gaps = 1/102 (0%)
Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           I L EAD L+ DA   +R  +E Y    +    C+ VS++ +PI+S C V +  P  K+ 
Sbjct: 106 IFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEA 165
Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS 101
           + + L  I E+EG+++     E +   S  + R+AI + + +
Sbjct: 166 MKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQGA 207

>pdb|1SXJ|B Chain B, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 323

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/102 (24%), Positives = 57/102 (55%), Gaps = 1/102 (0%)
Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           +IL EAD ++  A   +R  +E Y    +  F C+  +K+ +P++S C +++    S ++
Sbjct: 111 VILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDED 170
Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS 101
           +++ L  I + E ++  +   E I   ++ ++RQAI + +++
Sbjct: 171 VLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQST 212

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	137
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	3e-33
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	5e-22
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	4e-18
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	9e-18
2chq_A	319	Replication factor C small subunit; DNA-binding pr	5e-14
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	6e-14
2chg_A	226	Replication factor C small subunit; DNA-binding pr	2e-13
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	2e-13
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	2e-07

>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 Length = 354

 Score =  118 bits (297), Expect = 3e-33
 Identities = 41/141 (29%), Positives = 69/141 (48%), Gaps = 4/141 (2%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           +I+ EA+ L+ DA   +R  +E+Y    ++   C  +S +  PIKS C +I+   PS  E
Sbjct: 138 VIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSE 197

Query: 60  IVEVLEFIAEQEGIQL-PHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEG--QVILT 116
           I  +L  +   E IQL    + ++IA  S  NLR ++   E+    N   ++    +I  
Sbjct: 198 ISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMALNNELALKSSSPIIKP 257

Query: 117 GWEDDITNIATKIIEEQSPKQ 137
            W   I  +  KI++E+S   
Sbjct: 258 DWIIVIHKLTRKIVKERSVNS 278

>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 Length = 353

 Score = 88.3 bits (219), Expect = 5e-22
 Identities = 35/134 (26%), Positives = 67/134 (50%), Gaps = 2/134 (1%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           IIL EAD ++ DA   +R  +E Y G+ +    C+ V+++  P+ S C+  +        
Sbjct: 137 IILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASN 196

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTG-W 118
            ++ L FI+EQE ++    + E+I D S  +LR+ I   +++ +      +G+ I +   
Sbjct: 197 AIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQV 256

Query: 119 EDDITNIATKIIEE 132
           E+    +   I+ E
Sbjct: 257 EELAGVVPHDILIE 270

>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 Length = 327

 Score = 77.4 bits (191), Expect = 4e-18
 Identities = 32/137 (23%), Positives = 65/137 (47%), Gaps = 2/137 (1%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           I L EAD L+ DA   +R  +E +    +    C+  SK+ +PI+S C + +  P   ++
Sbjct: 114 IFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDED 173

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGWE 119
           I + L +IAE EG++L  +  + I   ++ ++R+AI   +A+  ++    +  V +    
Sbjct: 174 IAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALDKKITDENVFMV-AS 232

Query: 120 DDITNIATKIIEEQSPK 136
                   +++      
Sbjct: 233 RARPEDIREMMLLALKG 249

>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 Length = 516

 Score = 77.2 bits (190), Expect = 9e-18
 Identities = 22/98 (22%), Positives = 44/98 (44%), Gaps = 3/98 (3%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFC-CSDVS--KLQPIKSLCTVIQLLPPSK 57
           II+ E D +S      +  L +  +  +      C++ +  K++P   +C  IQ   P  
Sbjct: 152 IIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDA 211

Query: 58  QEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAI 95
             I   L  IA +E  +L   + +++   ++ ++RQ I
Sbjct: 212 NSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVI 249

>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 Length = 319

 Score = 66.2 bits (162), Expect = 5e-14
 Identities = 31/96 (32%), Positives = 51/96 (53%), Gaps = 1/96 (1%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           I L EAD L+ DA   +R  +E Y    +    C+ VS++ +PI+S C V +  P  K+ 
Sbjct: 106 IFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEA 165

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAI 95
           + + L  I E+EG+++     E +   S  + R+AI
Sbjct: 166 MKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAI 201

>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 Length = 323

 Score = 65.9 bits (161), Expect = 6e-14
 Identities = 25/96 (26%), Positives = 53/96 (55%), Gaps = 1/96 (1%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           +IL EAD ++  A   +R  +E Y    +  F C+  +K+ +P++S C +++    S ++
Sbjct: 111 VILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDED 170

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAI 95
           +++ L  I + E ++  +   E I   ++ ++RQAI
Sbjct: 171 VLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAI 206

>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} Length = 226

 Score = 63.8 bits (156), Expect = 2e-13
 Identities = 32/98 (32%), Positives = 51/98 (52%), Gaps = 5/98 (5%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFC--CSDVSKL-QPIKSLCTVIQLLPPSK 57
           I L EAD L+ DA   +R  +E Y       F   C+ VS++ +PI+S C V +  P  K
Sbjct: 106 IFLDEADALTADAQAALRRTMEMYS--KSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPK 163

Query: 58  QEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAI 95
           + + + L  I E+EG+++     E +   S  + R+AI
Sbjct: 164 EAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAI 201

>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 Length = 340

 Score = 64.8 bits (158), Expect = 2e-13
 Identities = 22/96 (22%), Positives = 44/96 (45%), Gaps = 1/96 (1%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           IIL EAD ++  A   +R ++ERY    +     +   KL   + S CT  +  P  ++ 
Sbjct: 114 IILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEA 173

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAI 95
           I   +  +   E ++L     + + + S  ++R+ +
Sbjct: 174 IERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVL 209

>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* Length = 324

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 20/105 (19%), Positives = 47/105 (44%), Gaps = 10/105 (9%)

Query: 1   IILCEADKLST-DALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQ 58
           I++ E D+    ++  ++R  +E Y     +    +++  + +P++S C VI    P+ +
Sbjct: 109 IVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDE 168

Query: 59  EIVEV-------LEFIAEQEGIQLPHQLA-EKIADNSKNNLRQAI 95
           + +E+       L  I + EGI +        +   +  + R+ I
Sbjct: 169 DKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRKTI 213

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	137
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.9
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.86
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.83
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.83
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.83
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.81
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	99.8
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.8
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.78
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.78
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.77
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.76
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.72
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.68
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.66
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.59
3pvs_A	447	Replication-associated recombination protein A; ma	99.57
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.5
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.48
3bos_A	242	Putative DNA replication factor; P-loop containing	99.47
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.44
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.39
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.35
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.32
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.3
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.3
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.29
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.29
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.23
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.21
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.16
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.09
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.08
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.04
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.04
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.03
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.02
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.02
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.01
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.01
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	98.99
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	98.98
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.93
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	98.93
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.92
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	98.89
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.85
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.84
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.79
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	98.76
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.74
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	98.66
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.55
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.49
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	98.46
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	98.43
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	98.38
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.35
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	98.35
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	98.31
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	98.3
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	98.29
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.29
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	98.25
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.22
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	98.16
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.16
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	98.14
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	98.12
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	97.98
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	97.89
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	97.87
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.86
2fna_A	357	Conserved hypothetical protein; structural genomic	97.77
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	97.73
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	97.72
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.66
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	97.64
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	97.61
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	97.56
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	97.55
3co5_A	143	Putative two-component system transcriptional RES	97.54
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	97.48
3f8t_A	506	Predicted ATPase involved in replication control,	97.37
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	97.3
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.8
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.8
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.31
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.07
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	95.93
1tue_A	212	Replication protein E1; helicase, replication, E1E	95.79
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	95.79
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	95.65
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	94.31
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	94.17
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	93.76
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	92.82
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	92.64
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	91.33
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	89.22
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	88.69
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	88.61
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	87.46
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	85.83
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	85.73
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	85.59
2qgz_A	308	Helicase loader, putative primosome component; str	84.95
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	84.8
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	84.46
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	84.24
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	84.07
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	83.41
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	82.8
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	82.63
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	81.31
3bor_A	237	Human initiation factor 4A-II; translation initiat	80.62
3h1t_A	590	Type I site-specific restriction-modification syst	80.28

>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=99.90  E-value=1.1e-23  Score=163.23  Aligned_cols=135  Identities=30%  Similarity=0.475  Sum_probs=124.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCC-HH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLP-HQ   78 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~-~~   78 (137)
                      ++|||+|.|+..++++|++++|+++.++.||++|+++.++ ++++|||..++|++|+.+++..+|..+++++|+.++ ++
T Consensus       138 lilDE~~~L~~~~~~~L~~~le~~~~~~~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  217 (354)
T 1sxj_E          138 VIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKD  217 (354)
T ss_dssp             EEEECTTSSCHHHHHHHHHHHHHSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSH
T ss_pred             EEEeCccccCHHHHHHHHHHHHhhcCCCEEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCCCCcHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999 99


Q ss_pred             HHHHHHHHcCCcHHHHHHHHHHHHhcCC-CcccCccc-cCCcHHHHHHHHHHHHhcCCC
Q 042716           79 LAEKIADNSKNNLRQAIRSFEASRQMNY-PFVEGQVI-LTGWEDDITNIATKIIEEQSP  135 (137)
Q Consensus        79 ~l~~i~~~~~gd~R~aln~L~~~~~~~~-~~~~~~~~-~~~~~~~~~~i~~~i~~~~~~  135 (137)
                      ++..+++.++||+|.+++.|+.+...+. .++...++ ..+|+..++++++.++..+.+
T Consensus       218 ~l~~i~~~~~G~~r~a~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~i~~~~~~  276 (354)
T 1sxj_E          218 ILKRIAQASNGNLRVSLLMLESMALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSV  276 (354)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHTHHHHTTTTEECSSCCCCCCHHHHHHHHHHHHHHHCCSH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHhCCCCcCcCcCCCCccHHHHHHHHHHHHHHhcch
Confidence            9999999999999999999999987665 57777666 366899999999999887543

>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=99.86  E-value=2.2e-21  Score=150.59  Aligned_cols=132  Identities=19%  Similarity=0.321  Sum_probs=116.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ++|||+|.|+.+++++|++++|+++.+++||++||.+.++ ++|+|||..+.|.+++.+++..++..+++++|+.+++++
T Consensus       114 iiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~~~~~~~~l~~~~~~~~l~~~~~~~~~~i~~~~  193 (340)
T 1sxj_C          114 IILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNA  193 (340)
T ss_dssp             EEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTCCBCHHH
T ss_pred             EEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhceeEeccCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            4799999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCC-----CcccCccc-c--CCcHHHHHHHHHHHHhc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNY-----PFVEGQVI-L--TGWEDDITNIATKIIEE  132 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~-----~~~~~~~~-~--~~~~~~~~~i~~~i~~~  132 (137)
                      +..+++.++||+|.+++.|+.+.....     .++.+.+. .  ..++..+.++++.+..+
T Consensus       194 ~~~i~~~s~G~~r~~~~~l~~~~~~~~~~~~~~it~~~v~~~~~~~~~~~i~~l~~~i~~~  254 (340)
T 1sxj_C          194 EKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRPSDLKAVLKSILED  254 (340)
T ss_dssp             HHHHHHHHTTCHHHHHHHTTTTTTTTCSSSCCCBCHHHHHHHTTCCCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhcCCcccccccHHHHHHHhCCCCHHHHHHHHHHHHcC
Confidence            999999999999999999998875433     35555553 2  23577788888887764

>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=99.83  E-value=1.8e-20  Score=144.08  Aligned_cols=130  Identities=17%  Similarity=0.365  Sum_probs=105.6

Q ss_pred             CcccccCcCC-HHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHH-------HHHHHHHHHHHc
Q 042716            1 IILCEADKLS-TDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE-------IVEVLEFIAEQE   71 (137)
Q Consensus         1 iiiDEid~l~-~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~-------i~~~l~~i~~~e   71 (137)
                      ++|||+|.|+ ++++++|++++|+++.+++||++||.+.++ ++|+|||.++.|++|+.++       +..++..++.++
T Consensus       109 liiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~  188 (324)
T 3u61_B          109 IVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHE  188 (324)
T ss_dssp             EEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHHSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhhCcEEEeCCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence            5899999999 999999999999999999999999999999 9999999999999999876       567788889999


Q ss_pred             CCCCCH-HHHHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCccc-cCCcHHHHHHHHHHHHh
Q 042716           72 GIQLPH-QLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVI-LTGWEDDITNIATKIIE  131 (137)
Q Consensus        72 gi~i~~-~~l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~~-~~~~~~~~~~i~~~i~~  131 (137)
                      |+.+++ +++..+++.++||+|.++|.|+.+. .+..++.+.+. ..+.+..+.++++.+..
T Consensus       189 ~~~~~~~~~~~~l~~~~~gd~R~a~~~L~~~~-~~~~i~~~~v~~~~~~~~~i~~~~~~~~~  249 (324)
T 3u61_B          189 GIAIADMKVVAALVKKNFPDFRKTIGELDSYS-SKGVLDAGILSLVTNDRGAIDDVLESLKN  249 (324)
T ss_dssp             TCCBSCHHHHHHHHHHTCSCTTHHHHHHHHHG-GGTCBCC------------CHHHHHHHHT
T ss_pred             CCCCCcHHHHHHHHHhCCCCHHHHHHHHHHHh-ccCCCCHHHHHHHhCCHHHHHHHHHHHHc
Confidence            999998 9999999999999999999999998 45556666554 22223344555555443

>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=99.83  E-value=2e-20  Score=142.29  Aligned_cols=133  Identities=25%  Similarity=0.425  Sum_probs=118.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ++|||+|.|+.+++++|++++|+++.+++||++||...++ ++++|||..++|.+|+.+++..++..+++++|+.+++++
T Consensus       106 liiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~  185 (319)
T 2chq_A          106 IFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDG  185 (319)
T ss_dssp             EEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCEEEECCCCCHHHHHHHHHHHHHTTCCCBCHHH
T ss_pred             EEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCccc-c--CCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVI-L--TGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~~-~--~~~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+++.|+.+...+..++.+.+. .  ...+..+.++++.++.++
T Consensus       186 l~~l~~~~~G~~r~~~~~l~~~~~~~~~i~~~~v~~~~~~~~~~~~~~l~~~~~~~~  242 (319)
T 2chq_A          186 LEALIYISGGDFRKAINALQGAAAIGEVVDADTIYQITATARPEEMTELIQTALKGN  242 (319)
T ss_dssp             HHHHHHTTTTCHHHHHHHHHHHHHSSSCBCHHHHHHHTTCCCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCCHHHHHHHHHHHHhCC
Confidence            99999999999999999999988765556666554 2  235667788888877653

>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=99.83  E-value=5e-20  Score=140.47  Aligned_cols=133  Identities=26%  Similarity=0.463  Sum_probs=118.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ++|||+|.++.+++++|++++|+++.+++||++||.+.++ ++++|||..+.|++++.+++..++..++.++|+.+++++
T Consensus       114 liiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~  193 (327)
T 1iqp_A          114 IFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEG  193 (327)
T ss_dssp             EEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTTCEECHHH
T ss_pred             EEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhCcEEEecCCCHHHHHHHHHHHHHhcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCccc-c--CCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVI-L--TGWEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~~-~--~~~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+++.++.+......++.+.+. .  ...+..+.++++.++.++
T Consensus       194 ~~~l~~~~~g~~r~~~~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~  250 (327)
T 1iqp_A          194 LQAILYIAEGDMRRAINILQAAAALDKKITDENVFMVASRARPEDIREMMLLALKGN  250 (327)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTCSEECHHHHHHHTTCCCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCCHHHHHHHHHHHHcCC
Confidence            99999999999999999999888655556655554 2  236777888888877643

>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=99.81  E-value=5.4e-20  Score=142.94  Aligned_cols=97  Identities=19%  Similarity=0.198  Sum_probs=90.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|+.++.||++|+++.++ ++|+|||+.++|++|+.+++..+|.+.+     .+++++
T Consensus       112 viIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~~~l~~ti~SRc~~~~~~~~~~~~~~~~L~~~~-----~~~~~~  186 (334)
T 1a5t_A          112 VWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREV-----TMSQDA  186 (334)
T ss_dssp             EEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHC-----CCCHHH
T ss_pred             EEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHhhcceeeeCCCCCHHHHHHHHHHhc-----CCCHHH
Confidence            5899999999999999999999999999999999999999 9999999999999999999999998754     678999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      +..++..++||+|.+++.++...
T Consensus       187 ~~~l~~~s~G~~r~a~~~l~~~~  209 (334)
T 1a5t_A          187 LLAALRLSAGSPGAALALFQGDN  209 (334)
T ss_dssp             HHHHHHHTTTCHHHHHHTTSSHH
T ss_pred             HHHHHHHcCCCHHHHHHHhccch
Confidence            99999999999999999987654

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=99.80  E-value=5.1e-20  Score=142.93  Aligned_cols=133  Identities=8%  Similarity=0.010  Sum_probs=111.4

Q ss_pred             CcccccCc-CCHHHHHHHHHHHHhccCCceEEEEeCCC------CCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcC
Q 042716            1 IILCEADK-LSTDALLYMRWLLERYKGLNKVFFCCSDV------SKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEG   72 (137)
Q Consensus         1 iiiDEid~-l~~~~~~~L~~~le~~~~~~~~Il~~n~~------~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~eg   72 (137)
                      |+|||+|. |+.+++++|++++|+|++++.||++|++.      .++ ++|+|||.++.|.+++.+++..|+.++++++|
T Consensus        80 vii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~~~~l~~~l~~~~~~~g  159 (343)
T 1jr3_D           80 LLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLN  159 (343)
T ss_dssp             EEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTTHHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCCHHHHHHHHHHHHHHcC
Confidence            58999999 99999999999999999999999999874      357 99999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhc--CCCcccCccc-cCC--cHHHHHHHHHHHHhcC
Q 042716           73 IQLPHQLAEKIADNSKNNLRQAIRSFEASRQM--NYPFVEGQVI-LTG--WEDDITNIATKIIEEQ  133 (137)
Q Consensus        73 i~i~~~~l~~i~~~~~gd~R~aln~L~~~~~~--~~~~~~~~~~-~~~--~~~~~~~i~~~i~~~~  133 (137)
                      +.++++++..+++.++||+|.+.+.|+.+...  +..++.+.+. ..+  -+..++++++.++.++
T Consensus       160 ~~i~~~a~~~l~~~~~gdl~~~~~elekl~l~~~~~~It~e~V~~~~~~~~~~~if~l~~ai~~~d  225 (343)
T 1jr3_D          160 LELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGK  225 (343)
T ss_dssp             CEECHHHHHHHHHSSTTCHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHCCCCHHHHHHHHTTSC
T ss_pred             CCCCHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHhhhhcCCHHHHHHHHHCCC
Confidence            99999999999999999999999999988763  2335544432 111  1234556666666554

>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=99.80  E-value=3.1e-19  Score=135.86  Aligned_cols=113  Identities=23%  Similarity=0.391  Sum_probs=104.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ++|||+|.|+.+++++|++++|+++.++.||++||...++ ++++|||..++|++|+.+++..++..+++++|+.+++++
T Consensus       111 iiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  190 (323)
T 1sxj_B          111 VILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDG  190 (323)
T ss_dssp             EEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHH
T ss_pred             EEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhceEEeecCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCcc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQV  113 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~  113 (137)
                      +..++..++||+|.+++.|+........++.+.+
T Consensus       191 ~~~l~~~~~G~~r~a~~~l~~~~~~~~~i~~~~v  224 (323)
T 1sxj_B          191 LEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNV  224 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHSSBCHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcCCCcCHHHH
Confidence            9999999999999999999988754444554444

>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=99.78  E-value=3.2e-18  Score=132.89  Aligned_cols=133  Identities=20%  Similarity=0.221  Sum_probs=113.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ++|||+|.|+.+++++|++++|+++.++.||++|++..++ ++++|||..+.|.+++.+++..++..+++++|+.+++++
T Consensus       123 liiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~~~l~sr~~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~a  202 (373)
T 1jr3_A          123 YLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRA  202 (373)
T ss_dssp             EEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHH
T ss_pred             EEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCcHHHHhheeEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcC-CCcccCccc-cCC--cHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMN-YPFVEGQVI-LTG--WEDDITNIATKIIEEQ  133 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~-~~~~~~~~~-~~~--~~~~~~~i~~~i~~~~  133 (137)
                      +..++..++||+|.+.+.++.+...+ ..++.+.+. ..+  .+..+.++++.+..++
T Consensus       203 ~~~l~~~~~G~~r~~~~~l~~~~~~~~~~i~~~~v~~~~~~~~~~~~~~l~~~~~~~~  260 (373)
T 1jr3_A          203 LQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDDQALSLVEAMVEAN  260 (373)
T ss_dssp             HHHHHHHSSSCHHHHHHHHHHHHHHTTTCBCHHHHHHHTTCCCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHhCCCCHHHHHHHHHHHHcCC
Confidence            99999999999999999998776433 345544443 122  2555667777666543

>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=99.78  E-value=1.5e-18  Score=133.86  Aligned_cols=103  Identities=29%  Similarity=0.544  Sum_probs=99.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ++|||+|.++...+++|++++|+++.+++||++||++.++ ++++|||..+.|.+++.+++..++..++.++|+.+++++
T Consensus       137 liiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~  216 (353)
T 1sxj_D          137 IILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENVKCDDGV  216 (353)
T ss_dssp             EEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHH
T ss_pred             EEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCceEEeCCCCHHHHHHHHHHHHHHhCCCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      +..+++.+.||+|.+++.|+.+..
T Consensus       217 l~~l~~~~~G~~r~~~~~l~~~~~  240 (353)
T 1sxj_D          217 LERILDISAGDLRRGITLLQSASK  240 (353)
T ss_dssp             HHHHHHHTSSCHHHHHHHHHHTHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHH
Confidence            999999999999999999997764

>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=99.77  E-value=4.6e-19  Score=136.81  Aligned_cols=122  Identities=12%  Similarity=0.143  Sum_probs=97.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.+++++|++++|+|++++.|||+|+++.++ ++|+||  +++|++++.+++..+|.+++   |  +++++
T Consensus        86 viIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR--~~~f~~l~~~~i~~~L~~~~---~--i~~~~  158 (305)
T 2gno_A           86 VIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR--VFRVVVNVPKEFRDLVKEKI---G--DLWEE  158 (305)
T ss_dssp             EEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT--SEEEECCCCHHHHHHHHHHH---T--THHHH
T ss_pred             EEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce--eEeCCCCCHHHHHHHHHHHh---C--CCHHH
Confidence            5899999999999999999999999999999999999999 999999  99999999999999999877   3  56666


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHh---------cCCCcccCccc-cCC--cHH--HHHHHHHHHHhcCC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQ---------MNYPFVEGQVI-LTG--WED--DITNIATKIIEEQS  134 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~---------~~~~~~~~~~~-~~~--~~~--~~~~i~~~i~~~~~  134 (137)
                      +    ..+.||+|.++|+++....         ..++ +.+.+. .++  .+.  .++++++.+++++.
T Consensus       159 ~----~~~~g~~~~al~~l~~~~~~~~~l~~~~~~~~-~~~~v~~~~~~~~~~~~~v~~l~~ai~~~~~  222 (305)
T 2gno_A          159 L----PLLERDFKTALEAYKLGAEKLSGLMESLKVLE-TEKLLKKVLSKGLEGYLACRELLERFSKVES  222 (305)
T ss_dssp             C----GGGGTCHHHHHHHHHHHHHHHHHHHHHHHHSC-HHHHTTTTTCSHHHHHHHHHHHHHHHHHSCG
T ss_pred             H----HHHCCCHHHHHHHHHHHHHHHHHHHHHHHhcc-cHHHHHHHHccCCcchHHHHHHHHHHHCCCH
Confidence            5    5579999999999974321         1111 122222 233  333  78899999988764

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

Probab=99.76  E-value=1.6e-18  Score=139.82  Aligned_cols=101  Identities=17%  Similarity=0.326  Sum_probs=94.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEe---------CC----CCCc-hhhhhcceeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCC---------SD----VSKL-QPIKSLCTVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~---------n~----~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~   66 (137)
                      +||||+|.|+.+++++|++++|+|+.+ .|||+|         ++    +.++ ++|+|||+.++|++++.+++..+|+.
T Consensus       299 liIDEa~~l~~~a~~aLlk~lEe~~~~-~~il~tn~~~~~i~~~~~~~~~~~l~~~i~sR~~~~~~~~~~~~e~~~iL~~  377 (456)
T 2c9o_A          299 LFVDEVHMLDIECFTYLHRALESSIAP-IVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKI  377 (456)
T ss_dssp             EEEESGGGCBHHHHHHHHHHTTSTTCC-EEEEEECCSEEECBTTSSCEEETTCCHHHHTTEEEEECCCCCHHHHHHHHHH
T ss_pred             EEEechhhcCHHHHHHHHHHhhccCCC-EEEEecCCccccccccccccccccCChhHHhhcceeeCCCCCHHHHHHHHHH
Confidence            589999999999999999999999888 688888         44    5678 99999999999999999999999999


Q ss_pred             HHHHcCCCCCHHHHHHHHHHc-CCcHHHHHHHHHHHH
Q 042716           67 IAEQEGIQLPHQLAEKIADNS-KNNLRQAIRSFEASR  102 (137)
Q Consensus        67 i~~~egi~i~~~~l~~i~~~~-~gd~R~aln~L~~~~  102 (137)
                      +++.+|+.++++++..++..+ +|++|.++++|+.+.
T Consensus       378 ~~~~~~~~~~~~~~~~i~~~a~~g~~r~a~~ll~~a~  414 (456)
T 2c9o_A          378 RAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPAN  414 (456)
T ss_dssp             HHHHHTCCBCHHHHHHHHHHHHHSCHHHHHHTHHHHH
T ss_pred             HHHHhCCCCCHHHHHHHHHHccCCCHHHHHHHHHHHH
Confidence            999999999999999999999 999999999999763

>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=99.72  E-value=5e-17  Score=116.45  Aligned_cols=108  Identities=29%  Similarity=0.462  Sum_probs=101.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ++|||+|.+....++.|++.+++++.++++|++||.+..+ +++++||..+.|.+++.+++..++...+.++|+.+++++
T Consensus       106 liiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  185 (226)
T 2chg_A          106 IFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDG  185 (226)
T ss_dssp             EEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHH
T ss_pred             EEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCceeecCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            5899999999999999999999988899999999999888 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPF  108 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~  108 (137)
                      +..+++.++||+|.+++.++.+...+..+
T Consensus       186 ~~~l~~~~~g~~r~l~~~l~~~~~~~~~I  214 (226)
T 2chg_A          186 LEALIYISGGDFRKAINALQGAAAIGEVV  214 (226)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTCSCB
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcCcee
Confidence            99999999999999999999988665333

>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=99.68  E-value=5.7e-16  Score=111.92  Aligned_cols=105  Identities=22%  Similarity=0.224  Sum_probs=99.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ++|||+|.++...++.|++.+++++.++.+|++|+....+ +++++||..+.|++++.+++..++...+.++|+.+++++
T Consensus       130 lviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~~~l~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~  209 (250)
T 1njg_A          130 YLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRA  209 (250)
T ss_dssp             EEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHH
T ss_pred             EEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCCHHHHHHhhhccCCCCCHHHHHHHHHHHHHhcCCCCCHHH
Confidence            5899999999999999999999988889999999999888 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~  105 (137)
                      +..+++.++|++|.+.++++.+...+
T Consensus       210 ~~~l~~~~~G~~~~~~~~~~~~~~~~  235 (250)
T 1njg_A          210 LQLLARAAEGSLRDALSLTDQAIASG  235 (250)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcc
Confidence            99999999999999999999887543

>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=99.66  E-value=2e-16  Score=129.34  Aligned_cols=131  Identities=21%  Similarity=0.363  Sum_probs=111.6

Q ss_pred             CcccccCcCCHHHH---HHHHHHHHhccCCceEEEEeCCCC--CchhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCC
Q 042716            1 IILCEADKLSTDAL---LYMRWLLERYKGLNKVFFCCSDVS--KLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQL   75 (137)
Q Consensus         1 iiiDEid~l~~~~~---~~L~~~le~~~~~~~~Il~~n~~~--~i~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i   75 (137)
                      +||||+|.|+...+   ++|+.++++  .+.++|++||+..  .++++++||..+.|++|+.+++..+|..++.++|+.+
T Consensus       152 liIDEid~l~~~~~~~l~~L~~~l~~--~~~~iIli~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i  229 (516)
T 1sxj_A          152 IIMDEVDGMSGGDRGGVGQLAQFCRK--TSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKL  229 (516)
T ss_dssp             EEECSGGGCCTTSTTHHHHHHHHHHH--CSSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCC
T ss_pred             EEEECCCccchhhHHHHHHHHHHHHh--cCCCEEEEEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCCC
Confidence            58999999987655   889999984  5778999999875  3488999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCccc--cCCcHH----HHHHHHHHHHhcC
Q 042716           76 PHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVI--LTGWED----DITNIATKIIEEQ  133 (137)
Q Consensus        76 ~~~~l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~~--~~~~~~----~~~~i~~~i~~~~  133 (137)
                      +++++..|++.++||+|.+++.|+.+...+..++.+.+.  ...|++    ..+++++.++.++
T Consensus       230 ~~~~l~~la~~s~GdiR~~i~~L~~~~~~~~~It~~~v~~~~~~~~~~~~~~~f~~~~~il~~~  293 (516)
T 1sxj_A          230 DPNVIDRLIQTTRGDIRQVINLLSTISTTTKTINHENINEISKAWEKNIALKPFDIAHKMLDGQ  293 (516)
T ss_dssp             CTTHHHHHHHHTTTCHHHHHHHHTHHHHHSSCCCTTHHHHHHHHHHTTTTSHHHHHHHHHTBGG
T ss_pred             CHHHHHHHHHHcCCcHHHHHHHHHHHHhcCCCCchHHHHHHHHhhccCCCCCHHHHHHHHhcCC
Confidence            999999999999999999999999988777777777654  222433    4678899888754

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

Probab=99.59  E-value=4.7e-15  Score=115.20  Aligned_cols=102  Identities=14%  Similarity=0.225  Sum_probs=90.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeC------------CCCCc-hhhhhcceeeEecCCCHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCS------------DVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFI   67 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n------------~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i   67 (137)
                      +||||+|.|+.+++++|++.+|++... .++++++            .+..+ ++|+|||..+.|++|+.+++..++...
T Consensus       193 l~IDEi~~l~~~~~~~L~~~le~~~~~-~~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~~  271 (368)
T 3uk6_A          193 LFIDEVHMLDIESFSFLNRALESDMAP-VLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIR  271 (368)
T ss_dssp             EEEESGGGSBHHHHHHHHHHTTCTTCC-EEEEEESCSEEECBTSSCEEETTCCHHHHTTEEEEEECCCCHHHHHHHHHHH
T ss_pred             EEEhhccccChHHHHHHHHHhhCcCCC-eeeeecccceeeeeccCCCCcccCCHHHHhhccEEEecCCCHHHHHHHHHHH
Confidence            589999999999999999999986654 3455554            24568 999999999999999999999999999


Q ss_pred             HHHcCCCCCHHHHHHHHHHcC-CcHHHHHHHHHHHHh
Q 042716           68 AEQEGIQLPHQLAEKIADNSK-NNLRQAIRSFEASRQ  103 (137)
Q Consensus        68 ~~~egi~i~~~~l~~i~~~~~-gd~R~aln~L~~~~~  103 (137)
                      +.++|+.++++++..+++.+. ||+|.++++|+.+..
T Consensus       272 ~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll~~a~~  308 (368)
T 3uk6_A          272 CEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASL  308 (368)
T ss_dssp             HHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence            999999999999999999998 999999999998654

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

Probab=99.57  E-value=4.8e-15  Score=119.60  Aligned_cols=103  Identities=20%  Similarity=0.233  Sum_probs=87.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCC--CCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHH-------
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDV--SKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQ-------   70 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~--~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~-------   70 (137)
                      +||||+|.|+...|++|++.+|+  +.+.||++|+..  ..+ ++|+|||.++.|++|+.+++..++.+.+.+       
T Consensus       110 LfIDEI~~l~~~~q~~LL~~le~--~~v~lI~att~n~~~~l~~aL~sR~~v~~l~~l~~edi~~il~~~l~~~~~~~~~  187 (447)
T 3pvs_A          110 LFVDEVHRFNKSQQDAFLPHIED--GTITFIGATTENPSFELNSALLSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGG  187 (447)
T ss_dssp             EEEETTTCC------CCHHHHHT--TSCEEEEEESSCGGGSSCHHHHTTEEEEECCCCCHHHHHHHHHHHHHCTTTSSTT
T ss_pred             EEEeChhhhCHHHHHHHHHHHhc--CceEEEecCCCCcccccCHHHhCceeEEeeCCcCHHHHHHHHHHHHHHHhhhhcc
Confidence            58999999999999999999994  677888888655  368 999999999999999999999999999987       


Q ss_pred             cCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhcC
Q 042716           71 EGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        71 egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~~~  105 (137)
                      +++.++++++..++..++||+|.++|.|+.+....
T Consensus       188 ~~~~i~~~al~~L~~~~~Gd~R~lln~Le~a~~~a  222 (447)
T 3pvs_A          188 QDIVLPDETRRAIAELVNGDARRALNTLEMMADMA  222 (447)
T ss_dssp             SSEECCHHHHHHHHHHHCSCHHHHHHHHHHHHHHS
T ss_pred             ccCcCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhc
Confidence            67889999999999999999999999999887654

>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=99.50  E-value=3.5e-13  Score=102.82  Aligned_cols=103  Identities=19%  Similarity=0.180  Sum_probs=94.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc------------------CCceEEEEeCCCCCc-hhhhhcc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK------------------GLNKVFFCCSDVSKL-QPIKSLC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~------------------~~~~~Il~~n~~~~i-~~l~SRc-~~i~~~~~~~~~i   60 (137)
                      +||||+|.+....++.|++.+++..                  .++.+|++||....+ ++|++|| .++.|.+|+.+++
T Consensus        94 l~lDEi~~l~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~  173 (324)
T 1hqc_A           94 LFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEEL  173 (324)
T ss_dssp             EEETTTTSCCHHHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEEEEEESCCSSCSCSTTTTCSCEEECCCCCHHHH
T ss_pred             EEEECCcccccchHHHHHHHHHhhhhHHhccccccccccccCCCCEEEEEeCCCcccCCHHHHhcccEEEecCCCCHHHH
Confidence            5899999999999999999999753                  346799999999999 9999999 6999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      ..++...+.+.|+.++++++..++.+++|++|.+.++++.+..
T Consensus       174 ~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l~~~~~  216 (324)
T 1hqc_A          174 AQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRD  216 (324)
T ss_dssp             HHHHHHHHHTTTCCCCHHHHHHHHHHSCSCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999998764

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

Probab=99.48  E-value=2.7e-13  Score=104.38  Aligned_cols=102  Identities=19%  Similarity=0.169  Sum_probs=93.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccC------------------CceEEEEeCCCCCc-hhhhhcc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKG------------------LNKVFFCCSDVSKL-QPIKSLC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~------------------~~~~Il~~n~~~~i-~~l~SRc-~~i~~~~~~~~~i   60 (137)
                      +||||+|.|....++.|++.+++...                  .+.+|.+||....+ ++|++|| ..+.|++|+.+++
T Consensus       110 l~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~  189 (338)
T 3pfi_A          110 LFIDEIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRAGMLSNPLRDRFGMQFRLEFYKDSEL  189 (338)
T ss_dssp             EEEETGGGCCHHHHHHHHHHHHTSCC---------CCCCCCCCCCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHH
T ss_pred             EEEechhhcCHHHHHHHHHHHHhccchhhcccCccccceecCCCCeEEEEeCCCccccCHHHHhhcCEEeeCCCcCHHHH
Confidence            58999999999999999999997531                  25788999998889 9999999 8999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ..++...+.+.++.++++++..++..+.|++|.+.+.++.+.
T Consensus       190 ~~il~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l~~~~  231 (338)
T 3pfi_A          190 ALILQKAALKLNKTCEEKAALEIAKRSRSTPRIALRLLKRVR  231 (338)
T ss_dssp             HHHHHHHHHHTTCEECHHHHHHHHHTTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999753

>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=99.47  E-value=2.5e-13  Score=98.75  Aligned_cols=103  Identities=17%  Similarity=0.197  Sum_probs=90.7

Q ss_pred             CcccccCcCCHHH--HHHHHHHHHhccCC-c-eEEEEeCCCC----Cc-hhhhhcc---eeeEecCCCHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDA--LLYMRWLLERYKGL-N-KVFFCCSDVS----KL-QPIKSLC---TVIQLLPPSKQEIVEVLEFIA   68 (137)
Q Consensus         1 iiiDEid~l~~~~--~~~L~~~le~~~~~-~-~~Il~~n~~~----~i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~   68 (137)
                      ++|||+|.+....  ++.|+.+++..... . ++|++|+...    .+ ++++|||   ..+.|++|+.++...++...+
T Consensus       108 liiDe~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~  187 (242)
T 3bos_A          108 ICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVSRMHWGLTYQLQPMMDDEKLAALQRRA  187 (242)
T ss_dssp             EEEETGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCCHHHHHHHHHSEEEECCCCCGGGHHHHHHHHH
T ss_pred             EEEeccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhhhhhhHhhcCceEEeCCCCHHHHHHHHHHHH
Confidence            5899999997766  88899998875433 2 5899988665    46 9999999   899999999999999999999


Q ss_pred             HHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           69 EQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        69 ~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      ++.|+.++++++..+++.++||+|.+.+.++.+..
T Consensus       188 ~~~~~~~~~~~~~~l~~~~~g~~r~l~~~l~~~~~  222 (242)
T 3bos_A          188 AMRGLQLPEDVGRFLLNRMARDLRTLFDVLDRLDK  222 (242)
T ss_dssp             HHTTCCCCHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHcCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999997764

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

Probab=99.44  E-value=2.3e-13  Score=103.33  Aligned_cols=103  Identities=15%  Similarity=0.159  Sum_probs=93.1

Q ss_pred             CcccccCcC---------CHHHHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcc-eeeEecCCCHHHHHHHH
Q 042716            1 IILCEADKL---------STDALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLC-TVIQLLPPSKQEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l---------~~~~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc-~~i~~~~~~~~~i~~~l   64 (137)
                      ++|||+|.|         +...++.|+..+++++.++.+|+++|...     .+ ++|+||| ..+.|++|+.+++..++
T Consensus       134 l~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~~~~~~~~~il  213 (309)
T 3syl_A          134 LFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLVVILAGYADRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIA  213 (309)
T ss_dssp             EEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTTCEEEEEECHHHHHHHHHHSTTHHHHEEEEEEECCCCHHHHHHHH
T ss_pred             EEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCCEEEEEeCChHHHHHHHhhCHHHHHhCCeEEEcCCcCHHHHHHHH
Confidence            589999988         88899999999999888899999997653     36 8999999 89999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHH--------cCCcHHHHHHHHHHHHh
Q 042716           65 EFIAEQEGIQLPHQLAEKIADN--------SKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        65 ~~i~~~egi~i~~~~l~~i~~~--------~~gd~R~aln~L~~~~~  103 (137)
                      ...+.+.++.++++++..++.+        ..||+|.+.+.++.+..
T Consensus       214 ~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~gn~r~l~~~l~~a~~  260 (309)
T 3syl_A          214 GHMLDDQNYQMTPEAETALRAYIGLRRNQPHFANARSIRNALDRARL  260 (309)
T ss_dssp             HHHHHHTTCEECHHHHHHHHHHHHHHTTSSSCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHHH
Confidence            9999999999999999999986        45999999999998774

>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=99.39  E-value=1.2e-12  Score=105.14  Aligned_cols=103  Identities=16%  Similarity=0.220  Sum_probs=91.2

Q ss_pred             CcccccCcCCH--HHHHHHHHHHHhcc-CCceEEEEeCCCCC----c-hhhhhcc---eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLST--DALLYMRWLLERYK-GLNKVFFCCSDVSK----L-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~--~~~~~L~~~le~~~-~~~~~Il~~n~~~~----i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.+..  ..|+.|+.+++... .+..+|++|+.++.    + ++|+|||   .++.|.+|+.++...+|...+.
T Consensus       198 L~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~sR~~~g~~i~l~~p~~e~r~~iL~~~~~  277 (440)
T 2z4s_A          198 LLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLE  277 (440)
T ss_dssp             EEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHHHHHSSBCCBCCCCCHHHHHHHHHHHHH
T ss_pred             EEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHhhccCCeEEEeCCCCHHHHHHHHHHHHH
Confidence            58999999986  78999999998743 45678888887543    7 9999999   6999999999999999999999


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      .+|+.++++++.+|+..++||+|.+.+.|+.+..
T Consensus       278 ~~~~~i~~e~l~~la~~~~gn~R~l~~~L~~~~~  311 (440)
T 2z4s_A          278 IEHGELPEEVLNFVAENVDDNLRRLRGAIIKLLV  311 (440)
T ss_dssp             HHTCCCCTTHHHHHHHHCCSCHHHHHHHHHHHHH
T ss_pred             HcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999999997664

>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=99.35  E-value=6.7e-12  Score=96.27  Aligned_cols=102  Identities=8%  Similarity=0.153  Sum_probs=89.3

Q ss_pred             CcccccCcCCH--HHHHHHHHHHHhc-cCCceEEEEeCCCC----Cc-hhhhhcc---eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLST--DALLYMRWLLERY-KGLNKVFFCCSDVS----KL-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~~--~~~~~L~~~le~~-~~~~~~Il~~n~~~----~i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.+..  ..|+.++.+++.. ..+.++|++|+.++    .+ ++|+|||   .++.|++ +.++...++...+.
T Consensus       102 L~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~sR~~~~~~i~l~~-~~~e~~~il~~~~~  180 (324)
T 1l8q_A          102 LLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIEL-DNKTRFKIIKEKLK  180 (324)
T ss_dssp             EEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECCC-CHHHHHHHHHHHHH
T ss_pred             EEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhhcccCceEEEeCC-CHHHHHHHHHHHHH
Confidence            58999999986  6788888888764 34567888887664    47 9999999   7899999 99999999999999


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhc
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQM  104 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~~  104 (137)
                      +.|+.++++++.+++..+ ||+|.+.+.|+.+...
T Consensus       181 ~~~~~l~~~~l~~l~~~~-g~~r~l~~~l~~~~~~  214 (324)
T 1l8q_A          181 EFNLELRKEVIDYLLENT-KNVREIEGKIKLIKLK  214 (324)
T ss_dssp             HTTCCCCHHHHHHHHHHC-SSHHHHHHHHHHHHHH
T ss_pred             hcCCCCCHHHHHHHHHhC-CCHHHHHHHHHHHHHc
Confidence            999999999999999999 9999999999987754

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.32  E-value=8.4e-12  Score=96.78  Aligned_cols=103  Identities=13%  Similarity=0.145  Sum_probs=83.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc---cCCceEEEEeCCCCC----c-hhhhhcc--eeeEecCCCHHHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERY---KGLNKVFFCCSDVSK----L-QPIKSLC--TVIQLLPPSKQEIVEVLEFIAEQ   70 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~---~~~~~~Il~~n~~~~----i-~~l~SRc--~~i~~~~~~~~~i~~~l~~i~~~   70 (137)
                      |+|||+|.|.  .|+.|+.+++-+   ..+..+|+++|....    + +.++|||  ..+.|++++.+++..+|++.++.
T Consensus       136 i~lDE~d~l~--~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~~~~L~~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl~~  213 (318)
T 3te6_A          136 ILIQNPENLL--SEKILQYFEKWISSKNSKLSIICVGGHNVTIREQINIMPSLKAHFTEIKLNKVDKNELQQMIITRLKS  213 (318)
T ss_dssp             EEEECCSSSC--CTHHHHHHHHHHHCSSCCEEEEEECCSSCCCHHHHHTCHHHHTTEEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             EEEecHHHhh--cchHHHHHHhcccccCCcEEEEEEecCcccchhhcchhhhccCCceEEEeCCCCHHHHHHHHHHHHHh
Confidence            5899999999  788888887632   234557788888743    5 7889998  67999999999999999988875


Q ss_pred             c--C---------------------------------CCCCHHHHHHHHH---HcCCcHHHHHHHHHHHHhcC
Q 042716           71 E--G---------------------------------IQLPHQLAEKIAD---NSKNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        71 e--g---------------------------------i~i~~~~l~~i~~---~~~gd~R~aln~L~~~~~~~  105 (137)
                      .  |                                 +.+++++++.+++   ...||+|.|+++|+.+....
T Consensus       214 ~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ai~~~A~~vA~~~GD~R~Al~ilr~A~~~a  286 (318)
T 3te6_A          214 LLKPFHVKVNDKKEMTIYNNIREGQNQKIPDNVIVINHKINNKITQLIAKNVANVSGSTEKAFKICEAAVEIS  286 (318)
T ss_dssp             HCCCEEEEECTTCCEEECCCC--------CTTEEEECEECCHHHHHHHHHHHHHHHCSHHHHHHHHHHHHHHH
T ss_pred             hhccccccccccccccccccccccccccccccccccccccCHHHHHHHHHHHHhhCChHHHHHHHHHHHHHHH
Confidence            3  1                                 1479999999999   57899999999999877543

>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=99.30  E-value=2.6e-11  Score=93.89  Aligned_cols=102  Identities=20%  Similarity=0.218  Sum_probs=89.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccC------------------CceEEEEeCCCCCc-hhhhhcce-eeEecCCCHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKG------------------LNKVFFCCSDVSKL-QPIKSLCT-VIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~------------------~~~~Il~~n~~~~i-~~l~SRc~-~i~~~~~~~~~i   60 (137)
                      ++|||+|.+.+..++.|+..++.+..                  ...++.+++.+..+ ++++|||. .+.|++++.+++
T Consensus       106 ~~iDE~~~l~~~~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l~~~~li~at~~~~~Ls~~l~sR~~l~~~Ld~~~~~~l  185 (334)
T 1in4_A          106 LFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKEL  185 (334)
T ss_dssp             EEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHH
T ss_pred             EEEcchhhcCHHHHHHHHHHHHhcccceeeccCcccccccccCCCeEEEEecCCcccCCHHHHHhcCceeeCCCCCHHHH
Confidence            47999999999889999988876421                  23466677888889 99999995 689999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ..+|++.++..|+.++++++..|+..+.||+|.++++|+.+.
T Consensus       186 ~~iL~~~~~~~~~~~~~~~~~~ia~~~~G~~R~a~~ll~~~~  227 (334)
T 1in4_A          186 KEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVR  227 (334)
T ss_dssp             HHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence            999999999999999999999999999999999999998653

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

Probab=99.30  E-value=5.1e-12  Score=97.75  Aligned_cols=103  Identities=17%  Similarity=0.148  Sum_probs=88.3

Q ss_pred             CcccccCcCCHH--HHHHHHHHHHhc-----cCCceEEEEeCCC---CCc-hhhhhcc--eeeEecCCCHHHHHHHHHHH
Q 042716            1 IILCEADKLSTD--ALLYMRWLLERY-----KGLNKVFFCCSDV---SKL-QPIKSLC--TVIQLLPPSKQEIVEVLEFI   67 (137)
Q Consensus         1 iiiDEid~l~~~--~~~~L~~~le~~-----~~~~~~Il~~n~~---~~i-~~l~SRc--~~i~~~~~~~~~i~~~l~~i   67 (137)
                      ++|||+|.+...  .++.|..+++..     ..+..+|+++|..   ..+ ++++|||  ..+.|++++.+++..++...
T Consensus       134 lilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~  213 (387)
T 2v1u_A          134 IVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETR  213 (387)
T ss_dssp             EEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEECSCSTTSSSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHH
T ss_pred             EEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEECCCchHhhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHH
Confidence            589999999877  788888888755     4567799999988   567 9999999  78999999999999999998


Q ss_pred             HHH--cCCCCCHHHHHHHHHHcC---CcHHHHHHHHHHHHh
Q 042716           68 AEQ--EGIQLPHQLAEKIADNSK---NNLRQAIRSFEASRQ  103 (137)
Q Consensus        68 ~~~--egi~i~~~~l~~i~~~~~---gd~R~aln~L~~~~~  103 (137)
                      +..  .+..++++++..++..+.   ||+|.++++++.+..
T Consensus       214 ~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~~l~~a~~  254 (387)
T 2v1u_A          214 AEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLLRVAGE  254 (387)
T ss_dssp             HHHHBCTTTBCSSHHHHHHHHHHSSSCCHHHHHHHHHHHHH
T ss_pred             HHhhccCCCCCHHHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            876  567889999999999998   999999999998764

>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=99.29  E-value=1.1e-11  Score=96.17  Aligned_cols=103  Identities=20%  Similarity=0.193  Sum_probs=90.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc----CCceEEEEeCCC---CCc-hhhhhcce--eeEecCCCHHHHHHHHHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK----GLNKVFFCCSDV---SKL-QPIKSLCT--VIQLLPPSKQEIVEVLEFIAEQ   70 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~----~~~~~Il~~n~~---~~i-~~l~SRc~--~i~~~~~~~~~i~~~l~~i~~~   70 (137)
                      ++|||+|.++...++.|++++++++    .++.+|++||.+   ..+ ++++|||.  .+.|++++.+++..++...+..
T Consensus       129 lilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~  208 (389)
T 1fnn_A          129 LVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKA  208 (389)
T ss_dssp             EEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHH
T ss_pred             EEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHh
Confidence            5899999999999999999998755    478899999988   568 99999986  6999999999999999998876


Q ss_pred             c--CCCCCHHHHHHHHHHc---------CCcHHHHHHHHHHHHh
Q 042716           71 E--GIQLPHQLAEKIADNS---------KNNLRQAIRSFEASRQ  103 (137)
Q Consensus        71 e--gi~i~~~~l~~i~~~~---------~gd~R~aln~L~~~~~  103 (137)
                      .  ...++++++..++..+         .||+|.++++++.+..
T Consensus       209 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~a~~  252 (389)
T 1fnn_A          209 GLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAY  252 (389)
T ss_dssp             HBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHH
T ss_pred             hcCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHHHHHH
Confidence            2  2478999999999999         8999999999997764

>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=99.29  E-value=7.1e-12  Score=94.61  Aligned_cols=102  Identities=17%  Similarity=0.173  Sum_probs=83.0

Q ss_pred             CcccccCcCCHHH------------HHHHHHHHHhc----------cCCceEEEEeC----CCCCc-hhhhhcc-eeeEe
Q 042716            1 IILCEADKLSTDA------------LLYMRWLLERY----------KGLNKVFFCCS----DVSKL-QPIKSLC-TVIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~~------------~~~L~~~le~~----------~~~~~~Il~~n----~~~~i-~~l~SRc-~~i~~   52 (137)
                      ++|||+|.+....            ++.|+.++|..          ..++.||++++    .+..+ ++|+||| ..+.|
T Consensus       120 l~iDEi~~l~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~R~~~~i~~  199 (310)
T 1ofh_A          120 VFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLPIRVEL  199 (310)
T ss_dssp             EEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHHTCCEEEEC
T ss_pred             EEEEChhhcCccccccccchhHHHHHHHHHHHhcCCeEecccccccCCcEEEEEcCCcccCCcccCCHHHHhhCCceEEc
Confidence            5899999998665            89999999963          23566777753    44567 9999999 46999


Q ss_pred             cCCCHHHHHHHHH-----------HHHHHcCC--CCCHHHHHHHHHHc--------CCcHHHHHHHHHHHH
Q 042716           53 LPPSKQEIVEVLE-----------FIAEQEGI--QLPHQLAEKIADNS--------KNNLRQAIRSFEASR  102 (137)
Q Consensus        53 ~~~~~~~i~~~l~-----------~i~~~egi--~i~~~~l~~i~~~~--------~gd~R~aln~L~~~~  102 (137)
                      ++|+.+++..++.           ..+..+|.  .+++++++.++..+        .||+|.+.+.++.+.
T Consensus       200 ~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~g~~R~l~~~l~~~~  270 (310)
T 1ofh_A          200 TALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLM  270 (310)
T ss_dssp             CCCCHHHHHHHHHSSTTCHHHHHHHHHHHTTCEEEECHHHHHHHHHHHHHHHHHSCCCTTHHHHHHHHHHS
T ss_pred             CCcCHHHHHHHHHhhHHHHHHHHHHHHHhcCCeeccCHHHHHHHHHHhhhhcccccccCcHHHHHHHHHHH
Confidence            9999999998887           23344564  68999999999998        799999999999865

>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=99.23  E-value=1.4e-11  Score=95.65  Aligned_cols=104  Identities=19%  Similarity=0.138  Sum_probs=88.1

Q ss_pred             CcccccCcCCHHH-HHH-HHHHHHhccCCceEEEEeCCC---CCc-hhhhhc-ceeeEecCCCHHHHHHHHHHHHHH--c
Q 042716            1 IILCEADKLSTDA-LLY-MRWLLERYKGLNKVFFCCSDV---SKL-QPIKSL-CTVIQLLPPSKQEIVEVLEFIAEQ--E   71 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~-L~~~le~~~~~~~~Il~~n~~---~~i-~~l~SR-c~~i~~~~~~~~~i~~~l~~i~~~--e   71 (137)
                      |+|||+|.+.... ++. +..+++.. .++.||++||..   ..+ ++++|| |..+.|++++.+++..++...+.+  .
T Consensus       137 lilDEi~~l~~~~~~~~~l~~l~~~~-~~~~iI~~t~~~~~~~~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~~  215 (384)
T 2qby_B          137 IYLDEVDTLVKRRGGDIVLYQLLRSD-ANISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLI  215 (384)
T ss_dssp             EEEETTHHHHHSTTSHHHHHHHHTSS-SCEEEEEECSSTTTTTTSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHTSC
T ss_pred             EEEECHHHhccCCCCceeHHHHhcCC-cceEEEEEECCCchHhhhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhhcc
Confidence            5899999997653 666 66666654 678899999988   568 999999 589999999999999999998875  4


Q ss_pred             CCCCCHHHHHHHHHHcC---CcHHHHHHHHHHHHhcC
Q 042716           72 GIQLPHQLAEKIADNSK---NNLRQAIRSFEASRQMN  105 (137)
Q Consensus        72 gi~i~~~~l~~i~~~~~---gd~R~aln~L~~~~~~~  105 (137)
                      +..++++++..++..+.   ||+|.++++|+.+....
T Consensus       216 ~~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~~a~~~a  252 (384)
T 2qby_B          216 KGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQLA  252 (384)
T ss_dssp             TTSCCSHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHT
T ss_pred             cCCcCHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHh
Confidence            56889999999999988   99999999999887544

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

Probab=99.21  E-value=1.9e-11  Score=92.66  Aligned_cols=103  Identities=12%  Similarity=0.171  Sum_probs=86.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCC--------------------------CCCc-hh
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSD--------------------------VSKL-QP   42 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~--------------------------~~~i-~~   42 (137)
                      ++|||+|.++...|+.|++++++..           .++.||++||.                          ...+ ++
T Consensus       123 l~lDEi~~l~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~  202 (311)
T 4fcw_A          123 ILFDAIEKAHPDVFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPE  202 (311)
T ss_dssp             EEEETGGGSCHHHHHHHHHHHHHSEEECTTSCEEECTTEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHH
T ss_pred             EEEeChhhcCHHHHHHHHHHHhcCEEEcCCCCEEECCCcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHH
Confidence            5899999999999999999999865           35559999998                          3357 89


Q ss_pred             hhhcc-eeeEecCCCHHHHHHHHHHHHHHc---------CCCCCHHHHHHHHHHcC---CcHHHHHHHHHHHHh
Q 042716           43 IKSLC-TVIQLLPPSKQEIVEVLEFIAEQE---------GIQLPHQLAEKIADNSK---NNLRQAIRSFEASRQ  103 (137)
Q Consensus        43 l~SRc-~~i~~~~~~~~~i~~~l~~i~~~e---------gi~i~~~~l~~i~~~~~---gd~R~aln~L~~~~~  103 (137)
                      |.+|| .++.|.+|+.+++..++...+.+.         .+.++++++..++.++.   |+.|.+.+.++.+..
T Consensus       203 l~~R~~~~~~~~p~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~gn~R~L~~~i~~~~~  276 (311)
T 4fcw_A          203 FLNRLDEIVVFRPLTKEQIRQIVEIQMSYLRARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELE  276 (311)
T ss_dssp             HHTTCSEEEECCCCCHHHHHHHHHHHTHHHHHHHHTTTCEEEECHHHHHHHHHHSCBTTTBTTTHHHHHHHHTH
T ss_pred             HHhcCCeEEEeCCCCHHHHHHHHHHHHHHHHHHHHhCCcEEEeCHHHHHHHHHhCCCccCCchhHHHHHHHHHH
Confidence            99999 789999999999998887765542         45789999999999764   999999999987664

>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=99.16  E-value=2.4e-10  Score=87.79  Aligned_cols=103  Identities=13%  Similarity=0.104  Sum_probs=79.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc-------------cCCceEEEEeCCCC-Cc-hhhhhccee-eEecCCCHH-HHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERY-------------KGLNKVFFCCSDVS-KL-QPIKSLCTV-IQLLPPSKQ-EIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~-------------~~~~~~Il~~n~~~-~i-~~l~SRc~~-i~~~~~~~~-~i~~~   63 (137)
                      +||||+|.++...+++|+.++|+.             +.++.+|.++|... .+ ++|+|||.. +.|++|++. +...+
T Consensus       148 l~iDEi~~l~~~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~R~~~~~~l~~~~~~~~~~~i  227 (350)
T 1g8p_A          148 LYIDECNLLEDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLDRFGLSVEVLSPRDVETRVEV  227 (350)
T ss_dssp             EEETTGGGSCHHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHTTCSEEEECCCCCSHHHHHHH
T ss_pred             EEEeChhhCCHHHHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCCCCCCCCHHHHhhcceEEEcCCCCcHHHHHHH
Confidence            589999999999999999999973             12556777777644 68 999999965 999999654 33244


Q ss_pred             HHHH-----------------------------HHHcCCCCCHHHHHHHHHHcCC----cHHHHHHHHHHHHh
Q 042716           64 LEFI-----------------------------AEQEGIQLPHQLAEKIADNSKN----NLRQAIRSFEASRQ  103 (137)
Q Consensus        64 l~~i-----------------------------~~~egi~i~~~~l~~i~~~~~g----d~R~aln~L~~~~~  103 (137)
                      +...                             ...+++.++++++..+++.+.+    ++|.+.++++.+..
T Consensus       228 l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ls~~~~~~l~~~~~~~~~~~~R~~~~ll~~a~~  300 (350)
T 1g8p_A          228 IRRRDTYDADPKAFLEEWRPKDMDIRNQILEARERLPKVEAPNTALYDCAALCIALGSDGLRGELTLLRSARA  300 (350)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHGGGCBCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHHH
T ss_pred             HHHHHhcccCchhhccccccchHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHH
Confidence            4331                             3345678999999999998777    89999999986543

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=99.09  E-value=7.8e-10  Score=82.38  Aligned_cols=104  Identities=13%  Similarity=0.100  Sum_probs=82.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc-----------cCCceEEEEeCCC-------CCc-hhhhhcce--eeEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERY-----------KGLNKVFFCCSDV-------SKL-QPIKSLCT--VIQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~-----------~~~~~~Il~~n~~-------~~i-~~l~SRc~--~i~~~~~~~--   57 (137)
                      ++|||+|.++...|..|+.++++.           +.++++|++||..       ..+ ++|.+|+.  .+.++++..  
T Consensus       104 l~lDEi~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~~~~~~~~~~~~~~~L~~Rl~~~~i~lp~L~~R~  183 (265)
T 2bjv_A          104 LFLDELATAPMMVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLDALAFDVVQLPPLRERE  183 (265)
T ss_dssp             EEEESGGGSCHHHHHHHHHHHHHCEECCCCC--CEECCCEEEEEESSCHHHHHHHTSSCHHHHHHHCSEEEECCCGGGCH
T ss_pred             EEEechHhcCHHHHHHHHHHHHhCCeecCCCcccccCCeEEEEecCcCHHHHHHcCCccHHHHHhhcCcEEeCCChhhhh
Confidence            589999999999999999999963           3567899999985       247 89999984  577877776  


Q ss_pred             HHHHHH----HHHHHHHcCC----CCCHHHHHHHHHHc-CCcHHHHHHHHHHHHhc
Q 042716           58 QEIVEV----LEFIAEQEGI----QLPHQLAEKIADNS-KNNLRQAIRSFEASRQM  104 (137)
Q Consensus        58 ~~i~~~----l~~i~~~egi----~i~~~~l~~i~~~~-~gd~R~aln~L~~~~~~  104 (137)
                      +++...    +...+.+.|.    .++++++..+..+. .||+|.+.+.++.+...
T Consensus       184 ~di~~l~~~~l~~~~~~~~~~~~~~~~~~a~~~L~~~~~~gn~reL~~~l~~~~~~  239 (265)
T 2bjv_A          184 SDIMLMAEYFAIQMCREIKLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYR  239 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCSSCCCBCHHHHHHHHHSCCTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCCcccCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHh
Confidence            555544    4455566665    68999999998775 89999999999987643

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

Probab=99.08  E-value=5.4e-10  Score=87.99  Aligned_cols=101  Identities=11%  Similarity=0.104  Sum_probs=84.7

Q ss_pred             CcccccCcC-----------CHHHHHHHHHHHHhcc----CCceEEEEeCCCCCc-hhhhhcce-eeEecCCCHHHHHHH
Q 042716            1 IILCEADKL-----------STDALLYMRWLLERYK----GLNKVFFCCSDVSKL-QPIKSLCT-VIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l-----------~~~~~~~L~~~le~~~----~~~~~Il~~n~~~~i-~~l~SRc~-~i~~~~~~~~~i~~~   63 (137)
                      |||||+|.|           ....++.|+..++...    .++.||.+||.+..+ +++++||. .+.|+.|+.++...+
T Consensus       211 l~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~i  290 (389)
T 3vfd_A          211 IFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLL  290 (389)
T ss_dssp             EEEETGGGGC--------CTHHHHHHHHHHHHHHHC-----CEEEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHH
T ss_pred             EEEECchhhcccCCCccchHHHHHHHHHHHHhhcccccCCCCEEEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHH
Confidence            589999998           3445777888887543    346688889998889 99999994 799999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHH
Q 042716           64 LEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS  101 (137)
Q Consensus        64 l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~  101 (137)
                      +..++.+++..++++.+..++..+.|..+..++.|...
T Consensus       291 l~~~~~~~~~~l~~~~~~~la~~~~g~~~~~l~~L~~~  328 (389)
T 3vfd_A          291 LKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAKD  328 (389)
T ss_dssp             HHHHHTTSCCCSCHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            99999999999999999999999999888777666443

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

Probab=99.04  E-value=3.3e-09  Score=81.30  Aligned_cols=102  Identities=15%  Similarity=0.118  Sum_probs=80.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc-----------cCCceEEEEeCCCC-----Cc-hhhhhcce-eeEecCCCHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERY-----------KGLNKVFFCCSDVS-----KL-QPIKSLCT-VIQLLPPSKQEIVE   62 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~-----------~~~~~~Il~~n~~~-----~i-~~l~SRc~-~i~~~~~~~~~i~~   62 (137)
                      ++|||+|.+++..+++|+..+++.           +..+.++.++|...     .+ ++|+|||. .+.|.+|+.++...
T Consensus       113 l~iDEi~~~~~~~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~~~~~~~~l~~~l~~Rf~~~i~i~~p~~~~~~~  192 (331)
T 2r44_A          113 ILADEVNRSPAKVQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPVEQEGTYPLPEAQVDRFMMKIHLTYLDKESELE  192 (331)
T ss_dssp             EEEETGGGSCHHHHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTTCCSCCCCCCHHHHTTSSEEEECCCCCHHHHHH
T ss_pred             EEEEccccCCHHHHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCCcccCcccCCHHHHhheeEEEEcCCCCHHHHHH
Confidence            589999999999999999999974           23344555555322     38 99999997 59999999999999


Q ss_pred             HHHHHHHH----------------------cCCCCCHHHHHHHHHHc-----CC---------------cHHHHHHHHHH
Q 042716           63 VLEFIAEQ----------------------EGIQLPHQLAEKIADNS-----KN---------------NLRQAIRSFEA  100 (137)
Q Consensus        63 ~l~~i~~~----------------------egi~i~~~~l~~i~~~~-----~g---------------d~R~aln~L~~  100 (137)
                      +|+..+..                      .++.++++++.++++.+     .+               ++|.++++++.
T Consensus       193 il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~v~~~~~~~~~i~~~~~~~r~~~~~~~~~~~~~~~~~~s~R~~~~ll~~  272 (331)
T 2r44_A          193 VMRRVSNMNFNYQVQKIVSKNDVLEIRNEINKVTISESLEKYIIELVFATRFPAEYGLEAEASYILYGASTRAAINLNRV  272 (331)
T ss_dssp             HHHHHHCTTCCCCCCCCSCHHHHHHHHHHHHTCBCCHHHHHHHHHHHHHHHSGGGGTCHHHHHHEEECCCHHHHHHHHHH
T ss_pred             HHHhccccCcchhccccCCHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHhccccccccccccccccCcChhHHHHHHHH
Confidence            99877654                      37889999999988754     23               69999999886


Q ss_pred             HH
Q 042716          101 SR  102 (137)
Q Consensus       101 ~~  102 (137)
                      +.
T Consensus       273 a~  274 (331)
T 2r44_A          273 AK  274 (331)
T ss_dssp             HH
T ss_pred             HH
Confidence            55

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

Probab=99.04  E-value=1.3e-09  Score=92.43  Aligned_cols=102  Identities=15%  Similarity=0.198  Sum_probs=83.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHh-----------ccCCceEEEEeCCCCC------------c-hhhhhcc-eeeEecCC
Q 042716            1 IILCEADKLSTDALLYMRWLLER-----------YKGLNKVFFCCSDVSK------------L-QPIKSLC-TVIQLLPP   55 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~-----------~~~~~~~Il~~n~~~~------------i-~~l~SRc-~~i~~~~~   55 (137)
                      ++|||+|.++++.++.|+.++++           ...++.||++||....            + ++|++|| .++.|++|
T Consensus       583 l~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~~~~~f~p~l~~Rl~~~i~~~~l  662 (758)
T 3pxi_A          583 VLLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKVMGELKRAFRPEFINRIDEIIVFHSL  662 (758)
T ss_dssp             EEEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHHHHHHHHHSCHHHHTTSSEEEECC--
T ss_pred             EEEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHHHHHHHhhCCHHHHhhCCeEEecCCC
Confidence            58999999999999999999998           3457889999996543            7 8999999 89999999


Q ss_pred             CHHHHHHHHHHHHHH---------cCCCCCHHHHHHHHHH---cCCcHHHHHHHHHHHH
Q 042716           56 SKQEIVEVLEFIAEQ---------EGIQLPHQLAEKIADN---SKNNLRQAIRSFEASR  102 (137)
Q Consensus        56 ~~~~i~~~l~~i~~~---------egi~i~~~~l~~i~~~---~~gd~R~aln~L~~~~  102 (137)
                      +.+++..++...+.+         .++.++++++.++++.   ..|+.|.+-+.++...
T Consensus       663 ~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~L~~~i~~~v  721 (758)
T 3pxi_A          663 EKKHLTEIVSLMSDQLTKRLKEQDLSIELTDAAKAKVAEEGVDLEYGARPLRRAIQKHV  721 (758)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHGGGCCTTTTTTTHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCCeEEECHHHHHHHHHhCCCCCCCChHHHHHHHHHH
Confidence            999999888776654         2457899999999875   3578888888887554

>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=99.03  E-value=5.5e-10  Score=94.57  Aligned_cols=103  Identities=11%  Similarity=0.120  Sum_probs=85.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCCC-------------------------Cc-hhh
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDVS-------------------------KL-QPI   43 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~~-------------------------~i-~~l   43 (137)
                      ++|||+|.++++.++.|+.++|+..           .++.||++||...                         .+ ++|
T Consensus       561 l~lDEi~~~~~~~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l  640 (758)
T 1r6b_X          561 LLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEF  640 (758)
T ss_dssp             EEEETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHH
T ss_pred             EEEeCccccCHHHHHHHHHHhcCcEEEcCCCCEEecCCeEEEEecCcchhhhhhcccCccccchHHHHHHHHHHhcCHHH
Confidence            5899999999999999999999742           4577999998743                         56 899


Q ss_pred             hhcc-eeeEecCCCHHHHHHHHHHHHHHc---------CCCCCHHHHHHHHHHc---CCcHHHHHHHHHHHHh
Q 042716           44 KSLC-TVIQLLPPSKQEIVEVLEFIAEQE---------GIQLPHQLAEKIADNS---KNNLRQAIRSFEASRQ  103 (137)
Q Consensus        44 ~SRc-~~i~~~~~~~~~i~~~l~~i~~~e---------gi~i~~~~l~~i~~~~---~gd~R~aln~L~~~~~  103 (137)
                      ++|| .++.|++++.+++..++...+.+.         ++.++++++.++++.+   +++.|.+.+.++....
T Consensus       641 ~~R~~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~g~R~l~~~i~~~~~  713 (758)
T 1r6b_X          641 RNRLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAEKGYDRAMGARPMARVIQDNLK  713 (758)
T ss_dssp             HTTCSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHTTEEEEECHHHHHHHHHHHCBTTTBTTTHHHHHHHHHT
T ss_pred             HhhCCcceeeCCCCHHHHHHHHHHHHHHHHHHHHHCCcEEEeCHHHHHHHHHhCCCcCCCchHHHHHHHHHHH
Confidence            9999 789999999999999888776532         3578999999999876   5668888888776653

>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=99.02  E-value=1.7e-10  Score=94.88  Aligned_cols=102  Identities=19%  Similarity=0.215  Sum_probs=78.8

Q ss_pred             CcccccCcCCHH----HHHHHHHHHHhcc---------------CCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHH
Q 042716            1 IILCEADKLSTD----ALLYMRWLLERYK---------------GLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~----~~~~L~~~le~~~---------------~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i   60 (137)
                      ++|||+|.+...    .+++|+.+++...               .++.||++||....+ ++|++||.++.|++|+.++.
T Consensus       179 l~lDEid~l~~~~~~~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~ttN~~~~l~~aL~~R~~vi~~~~~~~~e~  258 (543)
T 3m6a_A          179 FLLDEIDKMSSDFRGDPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATANNLATIPGPLRDRMEIINIAGYTEIEK  258 (543)
T ss_dssp             EEEEESSSCC---------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEECSSTTTSCHHHHHHEEEEECCCCCHHHH
T ss_pred             EEEhhhhhhhhhhccCHHHHHHHHHhhhhcceeecccCCeeecccceEEEeccCccccCCHHHHhhcceeeeCCCCHHHH
Confidence            479999999887    4588999997532               456799999999999 99999999999999999999


Q ss_pred             HHHHHHHH-----HHc-----CCCCCHHHHHHHHHHcC--CcHHHHHHHHHHHH
Q 042716           61 VEVLEFIA-----EQE-----GIQLPHQLAEKIADNSK--NNLRQAIRSFEASR  102 (137)
Q Consensus        61 ~~~l~~i~-----~~e-----gi~i~~~~l~~i~~~~~--gd~R~aln~L~~~~  102 (137)
                      ..++....     ++.     ++.++++++..++..+.  |++|.+-+.++.+.
T Consensus       259 ~~Il~~~l~~~~~~~~~~~~~~i~i~~~~l~~l~~~~~~~~~vR~L~~~i~~~~  312 (543)
T 3m6a_A          259 LEIVKDHLLPKQIKEHGLKKSNLQLRDQAILDIIRYYTREAGVRSLERQLAAIC  312 (543)
T ss_dssp             HHHHHHTHHHHHHHHTTCCGGGCEECHHHHHHHHHHHCCCSSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCcccccCCHHHHHHHHHhCChhhchhHHHHHHHHHH
Confidence            88887654     233     45778999999887654  67888777776543

>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=99.02  E-value=5.6e-10  Score=86.06  Aligned_cols=103  Identities=22%  Similarity=0.210  Sum_probs=83.3

Q ss_pred             CcccccCcCC----HHHHHHHHHHHHhc-cCCceEEEEeCCCC---Cc-hhhhhcc--eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLS----TDALLYMRWLLERY-KGLNKVFFCCSDVS---KL-QPIKSLC--TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~----~~~~~~L~~~le~~-~~~~~~Il~~n~~~---~i-~~l~SRc--~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.+.    .+....|++.++.. ..+..+|++++..+   .+ +.++|||  ..+.|++++.+++..++...+.
T Consensus       132 lilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~  211 (386)
T 2qby_A          132 IVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQ  211 (386)
T ss_dssp             EEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGGGGGGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHHH
T ss_pred             EEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCChHhhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHHH
Confidence            5899999996    44566677777542 44677899998874   57 8999999  7899999999999999998876


Q ss_pred             HcC--CCCCHHHHHHHHHHcC---CcHHHHHHHHHHHHh
Q 042716           70 QEG--IQLPHQLAEKIADNSK---NNLRQAIRSFEASRQ  103 (137)
Q Consensus        70 ~eg--i~i~~~~l~~i~~~~~---gd~R~aln~L~~~~~  103 (137)
                      +.+  ..++++++..++..+.   ||+|.++++++.+..
T Consensus       212 ~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~a~~  250 (386)
T 2qby_A          212 MAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGE  250 (386)
T ss_dssp             HHBCSSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             hhccCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            543  6789999999999988   999999999987764

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

Probab=99.01  E-value=2e-09  Score=81.27  Aligned_cols=100  Identities=13%  Similarity=0.097  Sum_probs=82.8

Q ss_pred             CcccccCcCC-----------HHHHHHHHHHHHhccC-----CceEEEEeCCCCCc-hhhhhcc-eeeEecCCCHHHHHH
Q 042716            1 IILCEADKLS-----------TDALLYMRWLLERYKG-----LNKVFFCCSDVSKL-QPIKSLC-TVIQLLPPSKQEIVE   62 (137)
Q Consensus         1 iiiDEid~l~-----------~~~~~~L~~~le~~~~-----~~~~Il~~n~~~~i-~~l~SRc-~~i~~~~~~~~~i~~   62 (137)
                      ++|||+|.+.           ...++.|+..++.++.     ++.+|.+||.+..+ +++++|| ..+.|+.|+.++...
T Consensus       117 l~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~~~l~~~l~~R~~~~i~~~~p~~~~r~~  196 (297)
T 3b9p_A          117 IFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALRRFTKRVYVSLPDEQTREL  196 (297)
T ss_dssp             EEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC------CEEEEEEESCGGGBCHHHHHHCCEEEECCCCCHHHHHH
T ss_pred             EEeccHHHhccccccCcchHHHHHHHHHHHHHhcccccCCCCcEEEEeecCChhhCCHHHHhhCCeEEEeCCcCHHHHHH
Confidence            5899999983           4457788888887653     46688889999899 9999999 689999999999999


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHH-HHHHH
Q 042716           63 VLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAI-RSFEA  100 (137)
Q Consensus        63 ~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~al-n~L~~  100 (137)
                      .+...+.+.+..++++.+..++..+.|..+..+ ++++.
T Consensus       197 il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~l~~l~~~  235 (297)
T 3b9p_A          197 LLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAKD  235 (297)
T ss_dssp             HHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            999999999999999999999999999777555 44443

>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=99.01  E-value=2.7e-09  Score=83.33  Aligned_cols=99  Identities=10%  Similarity=-0.002  Sum_probs=80.4

Q ss_pred             CcccccCcCCH-----------HHHHHHHHHHHhc---cCCceEEEEeCCCCCc-hhhhhcc-eeeEecCCCHHHHHHHH
Q 042716            1 IILCEADKLST-----------DALLYMRWLLERY---KGLNKVFFCCSDVSKL-QPIKSLC-TVIQLLPPSKQEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l~~-----------~~~~~L~~~le~~---~~~~~~Il~~n~~~~i-~~l~SRc-~~i~~~~~~~~~i~~~l   64 (137)
                      |||||+|.|..           ..++.|+..++..   ..++.+|.+||.+..+ +++++|| ..+.|+.|+.++...++
T Consensus       147 l~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il  226 (355)
T 2qp9_X          147 IFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMF  226 (355)
T ss_dssp             EEEECGGGGTC------CTHHHHHHHHHHHHHHHCC---CCEEEEEEESCGGGSCHHHHHTCCEEEECCCCCHHHHHHHH
T ss_pred             EEEechHhhcccCCCCcchHHHHHHHHHHHHhhcccccCCCeEEEeecCCcccCCHHHHcccCEEEEeCCcCHHHHHHHH
Confidence            58999999973           2477788888743   4467788889999999 9999999 78999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHcCC-cHHHHHHHHH
Q 042716           65 EFIAEQEGIQLPHQLAEKIADNSKN-NLRQAIRSFE   99 (137)
Q Consensus        65 ~~i~~~egi~i~~~~l~~i~~~~~g-d~R~aln~L~   99 (137)
                      +..+.+.+..+++..+..|+..+.| ..|.+-++++
T Consensus       227 ~~~l~~~~~~~~~~~l~~la~~t~G~sg~dl~~l~~  262 (355)
T 2qp9_X          227 EINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVK  262 (355)
T ss_dssp             HHHHTTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             HHHHhhCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            9999888888899999999999988 3444444433

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=98.99  E-value=4.3e-09  Score=80.63  Aligned_cols=105  Identities=11%  Similarity=0.119  Sum_probs=82.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcce--eeEecCCC--H
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLCT--VIQLLPPS--K   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc~--~i~~~~~~--~   57 (137)
                      +||||+|.|+...|..|++++++..           .++++|++||..       ..+ ++|.+|+.  .+.++++.  .
T Consensus       100 L~LDEi~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~l~~~v~~g~fr~~L~~Rl~~~~i~lPpL~eR~  179 (304)
T 1ojl_A          100 LFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRR  179 (304)
T ss_dssp             EEEESCTTCCHHHHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSCHHHHHHHTSSCHHHHHHHSSEEEECCCSGGGG
T ss_pred             EEEeccccCCHHHHHHHHHHHhcCEeeecCCcccccCCeEEEEecCccHHHHHHhCCcHHHHHhhcCeeEEeccCHHHhH
Confidence            5899999999999999999999752           457899999976       246 78999974  46677777  4


Q ss_pred             HHHHHHHHH----HHHHcC---CCCCHHHHHHHHHHc-CCcHHHHHHHHHHHHhcC
Q 042716           58 QEIVEVLEF----IAEQEG---IQLPHQLAEKIADNS-KNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        58 ~~i~~~l~~----i~~~eg---i~i~~~~l~~i~~~~-~gd~R~aln~L~~~~~~~  105 (137)
                      +++...+..    .+.+.|   ..++++++..+..++ .||+|.+.|.++.+....
T Consensus       180 edi~~l~~~~l~~~~~~~~~~~~~~s~~a~~~L~~~~wpGnvReL~~~l~~~~~~~  235 (304)
T 1ojl_A          180 EDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLL  235 (304)
T ss_dssp             GGHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHHCCCSSHHHHHHHHHHHHHHHC
T ss_pred             hhHHHHHHHHHHHHHHHhccCccCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhC
Confidence            666655544    344444   578999999999997 999999999999877644

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=98.98  E-value=6.7e-10  Score=86.84  Aligned_cols=103  Identities=14%  Similarity=0.051  Sum_probs=79.7

Q ss_pred             CcccccCcCCHH--------------HHHHHHHHHHhcc---------------------CCceEEEEeCC---------
Q 042716            1 IILCEADKLSTD--------------ALLYMRWLLERYK---------------------GLNKVFFCCSD---------   36 (137)
Q Consensus         1 iiiDEid~l~~~--------------~~~~L~~~le~~~---------------------~~~~~Il~~n~---------   36 (137)
                      ++|||+|.+...              .|++|+.++|...                     .+..||+++|.         
T Consensus       141 l~iDEi~~l~~~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~  220 (376)
T 1um8_A          141 VFIDEIDKISRLSENRSITRDVSGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKK  220 (376)
T ss_dssp             EEEETGGGC--------------CHHHHHHHHHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTT
T ss_pred             EEEcCHHHHhhhcCCCceecccchHHHHHHHHHHhhccceecccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHH
Confidence            589999999888              8999999999541                     45567777762         


Q ss_pred             --------------------------------CCCc-hhhhhcc-eeeEecCCCHHHHHHHHHH----HHH---------
Q 042716           37 --------------------------------VSKL-QPIKSLC-TVIQLLPPSKQEIVEVLEF----IAE---------   69 (137)
Q Consensus        37 --------------------------------~~~i-~~l~SRc-~~i~~~~~~~~~i~~~l~~----i~~---------   69 (137)
                                                      ...+ ++|++|| .++.|++++.+++..++..    +.+         
T Consensus       221 R~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~~~p~l~~R~~~~i~~~~l~~~~l~~i~~~~~~~~~~~~~~~~~~~  300 (376)
T 1um8_A          221 RTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPELIGRLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMD  300 (376)
T ss_dssp             SCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTTCCHHHHTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTT
T ss_pred             HhcccccCCCchhhhccchhHHHhhcCHHHHhhcCCChHHhcCCCceeeccCCCHHHHHHHHhhhHHHHHHHHHHHHhhc
Confidence                                            1136 8999999 8899999999999988851    211         


Q ss_pred             HcCCCCCHHHHHHHHHHcC---CcHHHHHHHHHHHHh
Q 042716           70 QEGIQLPHQLAEKIADNSK---NNLRQAIRSFEASRQ  103 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~---gd~R~aln~L~~~~~  103 (137)
                      ..++.++++++.++++++.   |++|.+.+.++.+..
T Consensus       301 ~~~~~~~~~a~~~l~~~~~~~~~~~R~L~~~le~~~~  337 (376)
T 1um8_A          301 EVDLIFEEEAIKEIAQLALERKTGARGLRAIIEDFCL  337 (376)
T ss_dssp             TCEEEECHHHHHHHHHHHHHTTCTGGGHHHHHHHHHH
T ss_pred             CceEEECHHHHHHHHHHhcccccCcHHHHHHHHHHHH
Confidence            1246789999999999866   999999999997764

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

Probab=98.93  E-value=1.5e-09  Score=81.18  Aligned_cols=99  Identities=20%  Similarity=0.248  Sum_probs=74.2

Q ss_pred             CcccccCcC----------CHHHHHHHHHHHHhc---cCCceEEEEeCCCCCc-h-hhhhc-ceeeEecCCCH-HHHHHH
Q 042716            1 IILCEADKL----------STDALLYMRWLLERY---KGLNKVFFCCSDVSKL-Q-PIKSL-CTVIQLLPPSK-QEIVEV   63 (137)
Q Consensus         1 iiiDEid~l----------~~~~~~~L~~~le~~---~~~~~~Il~~n~~~~i-~-~l~SR-c~~i~~~~~~~-~~i~~~   63 (137)
                      ++|||+|.|          ....++.|...++..   ...+.+|.+||.+..+ + .+++| |..+.|++++. +++...
T Consensus       128 l~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~~l~~~~l~~rf~~~i~~p~l~~r~~i~~i  207 (272)
T 1d2n_A          128 VVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEA  207 (272)
T ss_dssp             EEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTTTSSEEEECCCEEEHHHHHHH
T ss_pred             EEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCEEEEEecCChhhcchhhhhcccceEEcCCCccHHHHHHHH
Confidence            589999998          455567777777642   2234466677777667 5 68999 68899988888 665555


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHcCC-----cHHHHHHHHHHHHhc
Q 042716           64 LEFIAEQEGIQLPHQLAEKIADNSKN-----NLRQAIRSFEASRQM  104 (137)
Q Consensus        64 l~~i~~~egi~i~~~~l~~i~~~~~g-----d~R~aln~L~~~~~~  104 (137)
                      +..    .+ .++++++..+++.+.|     |+|.++|+++.+...
T Consensus       208 ~~~----~~-~~~~~~~~~l~~~~~g~~~~g~ir~l~~~l~~a~~~  248 (272)
T 1d2n_A          208 LEL----LG-NFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQM  248 (272)
T ss_dssp             HHH----HT-CSCHHHHHHHHHHHTTSEEEECHHHHHHHHHHHTTS
T ss_pred             HHh----cC-CCCHHHHHHHHHHhcCCCccccHHHHHHHHHHHhhh
Confidence            543    32 5689999999999988     999999999988743

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

Probab=98.93  E-value=4.8e-09  Score=81.87  Aligned_cols=101  Identities=12%  Similarity=0.064  Sum_probs=80.3

Q ss_pred             CcccccCcCCH-----------HHHHHHHHHHHhc----cCCceEEEEeCCCCCc-hhhhhcce-eeEecCCCHHHHHHH
Q 042716            1 IILCEADKLST-----------DALLYMRWLLERY----KGLNKVFFCCSDVSKL-QPIKSLCT-VIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~-----------~~~~~L~~~le~~----~~~~~~Il~~n~~~~i-~~l~SRc~-~i~~~~~~~~~i~~~   63 (137)
                      |||||+|.|..           ..++.|+..++..    ..++.+|.+||.+..+ +++++||. .+.++.|+.++...+
T Consensus       180 l~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~i  259 (357)
T 3d8b_A          180 IFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQI  259 (357)
T ss_dssp             EEEETHHHHTBC------CHHHHHHHHHHHHHHC----CCCCEEEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHH
T ss_pred             EEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccccCCCCEEEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHH
Confidence            58999998832           3466777777742    3456788889998889 99999995 789999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHcCC-cHHHHHHHHHHH
Q 042716           64 LEFIAEQEGIQLPHQLAEKIADNSKN-NLRQAIRSFEAS  101 (137)
Q Consensus        64 l~~i~~~egi~i~~~~l~~i~~~~~g-d~R~aln~L~~~  101 (137)
                      +...+.++++.++++.+..++..+.| ..+.+-++++..
T Consensus       260 l~~~~~~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~~a  298 (357)
T 3d8b_A          260 VINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCREA  298 (357)
T ss_dssp             HHHHHHTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHHhhcCCCccHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence            99999999999999999999999988 444444444443

>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=98.92  E-value=6.8e-09  Score=79.75  Aligned_cols=100  Identities=10%  Similarity=-0.000  Sum_probs=81.2

Q ss_pred             CcccccCcCCH-----------HHHHHHHHHHHhc---cCCceEEEEeCCCCCc-hhhhhcc-eeeEecCCCHHHHHHHH
Q 042716            1 IILCEADKLST-----------DALLYMRWLLERY---KGLNKVFFCCSDVSKL-QPIKSLC-TVIQLLPPSKQEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l~~-----------~~~~~L~~~le~~---~~~~~~Il~~n~~~~i-~~l~SRc-~~i~~~~~~~~~i~~~l   64 (137)
                      |||||+|.|..           ..++.|+..++..   ..++.+|.+||.+..+ +++++|| ..+.|+.|+.++...++
T Consensus       114 l~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il  193 (322)
T 3eie_A          114 IFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMF  193 (322)
T ss_dssp             EEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTSCCCEEEEEEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHH
T ss_pred             EEechhhhhhccCCCCcchHHHHHHHHHHHHhccccccCCceEEEEecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHH
Confidence            58999999854           3367888888753   3456688888988899 9999999 67999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHcCC-cHHHHHHHHHH
Q 042716           65 EFIAEQEGIQLPHQLAEKIADNSKN-NLRQAIRSFEA  100 (137)
Q Consensus        65 ~~i~~~egi~i~~~~l~~i~~~~~g-d~R~aln~L~~  100 (137)
                      +..+.+.+..+++..+..++..+.| ..+.+-++++.
T Consensus       194 ~~~~~~~~~~~~~~~l~~la~~t~g~sg~di~~l~~~  230 (322)
T 3eie_A          194 EINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKD  230 (322)
T ss_dssp             HHHHTTCCCCCCHHHHHHHHHTTTTCCHHHHHHHHHH
T ss_pred             HHHhccCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            9999988888999999999999887 44444444443

>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=98.89  E-value=5.3e-09  Score=84.00  Aligned_cols=101  Identities=10%  Similarity=-0.003  Sum_probs=81.2

Q ss_pred             CcccccCcCC-----------HHHHHHHHHHHHhc---cCCceEEEEeCCCCCc-hhhhhcc-eeeEecCCCHHHHHHHH
Q 042716            1 IILCEADKLS-----------TDALLYMRWLLERY---KGLNKVFFCCSDVSKL-QPIKSLC-TVIQLLPPSKQEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l~-----------~~~~~~L~~~le~~---~~~~~~Il~~n~~~~i-~~l~SRc-~~i~~~~~~~~~i~~~l   64 (137)
                      |||||+|.|.           ...++.|+..++..   ..++.||.+||.+..+ +++++|| ..+.|+.|+.++...++
T Consensus       231 l~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il  310 (444)
T 2zan_A          231 IFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMF  310 (444)
T ss_dssp             EEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCSSCEEEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHH
T ss_pred             EEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccCCCCEEEEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHH
Confidence            5899999983           34567777777653   4567789999999899 9999999 58999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHcCC-cHHHHHHHHHHH
Q 042716           65 EFIAEQEGIQLPHQLAEKIADNSKN-NLRQAIRSFEAS  101 (137)
Q Consensus        65 ~~i~~~egi~i~~~~l~~i~~~~~g-d~R~aln~L~~~  101 (137)
                      ...+.+.+..+++..+..|+..+.| +.+.+-++++.+
T Consensus       311 ~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~a  348 (444)
T 2zan_A          311 RLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDA  348 (444)
T ss_dssp             HHHHTTSCEECCHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence            9988888888899999999999988 444444444443

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

Probab=98.85  E-value=2.6e-08  Score=76.74  Aligned_cols=100  Identities=10%  Similarity=-0.018  Sum_probs=79.6

Q ss_pred             CcccccCcCC-----------HHHHHHHHHHHHhc---cCCceEEEEeCCCCCc-hhhhhcc-eeeEecCCCHHHHHHHH
Q 042716            1 IILCEADKLS-----------TDALLYMRWLLERY---KGLNKVFFCCSDVSKL-QPIKSLC-TVIQLLPPSKQEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l~-----------~~~~~~L~~~le~~---~~~~~~Il~~n~~~~i-~~l~SRc-~~i~~~~~~~~~i~~~l   64 (137)
                      |||||+|.+.           ....+.|+..++..   ..++.+|.+||.+..+ +++++|| ..+.++.|+.++...++
T Consensus       109 l~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il  188 (322)
T 1xwi_A          109 IFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMF  188 (322)
T ss_dssp             EEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTTEEEEEEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHH
T ss_pred             EEeecHHHhccccccccchHHHHHHHHHHHHHhcccccCCCEEEEEecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHH
Confidence            5899999982           23466777777753   3456788889999999 9999999 78999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHcCCc-HHHHHHHHHH
Q 042716           65 EFIAEQEGIQLPHQLAEKIADNSKNN-LRQAIRSFEA  100 (137)
Q Consensus        65 ~~i~~~egi~i~~~~l~~i~~~~~gd-~R~aln~L~~  100 (137)
                      +..+.+.+..+++..+..+++.+.|- .+.+-++++.
T Consensus       189 ~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~  225 (322)
T 1xwi_A          189 KLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVRD  225 (322)
T ss_dssp             HHHHTTCCBCCCHHHHHHHHHTCTTCCHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            99888888888999999999998774 4444444443

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

Probab=98.84  E-value=4e-09  Score=90.64  Aligned_cols=103  Identities=13%  Similarity=0.182  Sum_probs=85.0

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCC--------------------------CCCc-hh
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSD--------------------------VSKL-QP   42 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~--------------------------~~~i-~~   42 (137)
                      +||||+|.++.+.++.|+.++++..           .++.||++||.                          ...+ ++
T Consensus       664 l~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~  743 (854)
T 1qvr_A          664 ILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPE  743 (854)
T ss_dssp             EEESSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHH
T ss_pred             EEEecccccCHHHHHHHHHHhccCceECCCCCEeccCCeEEEEecCcChHHHhhhcccccchHHHHHHHHHHHHhhCCHH
Confidence            5899999999999999999999653           35669999996                          2346 88


Q ss_pred             hhhcc-eeeEecCCCHHHHHHHHHHHHHH---------cCCCCCHHHHHHHHHHcC---CcHHHHHHHHHHHHh
Q 042716           43 IKSLC-TVIQLLPPSKQEIVEVLEFIAEQ---------EGIQLPHQLAEKIADNSK---NNLRQAIRSFEASRQ  103 (137)
Q Consensus        43 l~SRc-~~i~~~~~~~~~i~~~l~~i~~~---------egi~i~~~~l~~i~~~~~---gd~R~aln~L~~~~~  103 (137)
                      |++|| .++.|.||+.+++..++...+.+         .++.++++++..+++++.   |++|.+.+.++....
T Consensus       744 l~~Rl~~~i~~~pl~~edi~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~L~~~~~~~~gn~R~L~~~i~~~~~  817 (854)
T 1qvr_A          744 FLNRLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELE  817 (854)
T ss_dssp             HHHTCSBCCBCCCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHHHHCBTTTBTSTHHHHHHHHTH
T ss_pred             HHHhcCeEEeCCCCCHHHHHHHHHHHHHHHHHHHHhCCceEEECHHHHHHHHHcCCCCCCChHHHHHHHHHHHH
Confidence            99999 78999999999998888765542         135789999999999865   999999999887654

>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=98.79  E-value=1.2e-07  Score=69.74  Aligned_cols=103  Identities=13%  Similarity=0.083  Sum_probs=73.7

Q ss_pred             CcccccCcCC------------HHHHHHHHHHHHhc-----cCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHH
Q 042716            1 IILCEADKLS------------TDALLYMRWLLERY-----KGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQE   59 (137)
Q Consensus         1 iiiDEid~l~------------~~~~~~L~~~le~~-----~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~   59 (137)
                      ++|||+|.+.            ...+..|..+++..     ..++.+|.+||.+..+ +++++  |+ ..+.|+.|+.++
T Consensus       102 l~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~  181 (262)
T 2qz4_A          102 VYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQE  181 (262)
T ss_dssp             EEEECC-------------------CHHHHHHHHHHHTCCTTCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHH
T ss_pred             EEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCCCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHH
Confidence            5899999993            33455555555542     2356788888888889 99998  98 789999999999


Q ss_pred             HHHHHHHHHHHcCCCCCHHH-HHHHHHHcCCc-HHHHHHHHHHHHh
Q 042716           60 IVEVLEFIAEQEGIQLPHQL-AEKIADNSKNN-LRQAIRSFEASRQ  103 (137)
Q Consensus        60 i~~~l~~i~~~egi~i~~~~-l~~i~~~~~gd-~R~aln~L~~~~~  103 (137)
                      ...+++..+.+.++..+.+. ...++..+.|- .|.+.++++.+..
T Consensus       182 r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~~~a~~  227 (262)
T 2qz4_A          182 RREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICNEAAL  227 (262)
T ss_dssp             HHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence            99999999999999888764 47788887764 4566666665553

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=98.76  E-value=3.8e-08  Score=77.31  Aligned_cols=105  Identities=17%  Similarity=0.211  Sum_probs=82.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhccee--eEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLCTV--IQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc~~--i~~~~~~~--   57 (137)
                      +||||+|.|+...|..|++++++..           .++++|.+||..       ... ++|.+|+.+  +.++|+.+  
T Consensus       226 lfldei~~l~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~l~~~v~~g~fr~dL~~rl~~~~i~lPpLreR~  305 (368)
T 3dzd_A          226 LFLDEVGELDQRVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNKNLEEEIKKGNFREDLYYRLSVFQIYLPPLRERG  305 (368)
T ss_dssp             EEEETGGGSCHHHHHHHHHHHHHSEECCBTCCCBEECCCEEEEEESSCHHHHHHTTSSCHHHHHHHTSEEEECCCGGGST
T ss_pred             EEecChhhCCHHHHHHHHHHHHhCCcccCCCCcceeeeeEEEEecCCCHHHHHHcCCccHHHHHHhCCeEEeCCChhhch
Confidence            5899999999999999999999632           257799999866       235 789999854  66888877  


Q ss_pred             HHHHHHHHHH----HHHcC---CCCCHHHHHHHHHHc-CCcHHHHHHHHHHHHhcC
Q 042716           58 QEIVEVLEFI----AEQEG---IQLPHQLAEKIADNS-KNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        58 ~~i~~~l~~i----~~~eg---i~i~~~~l~~i~~~~-~gd~R~aln~L~~~~~~~  105 (137)
                      +++...+...    +.+.|   ..++++++..+..+. +||+|.+.|.++.+....
T Consensus       306 ~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpGNvreL~n~i~~~~~~~  361 (368)
T 3dzd_A          306 KDVILLAEYFLKKFAKEYKKNCFELSEETKEYLMKQEWKGNVRELKNLIERAVILC  361 (368)
T ss_dssp             THHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHTCCCTTHHHHHHHHHHHHHHTC
T ss_pred             hhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhCCCCcHHHHHHHHHHHHHHhC
Confidence            6766555443    44444   458999999999986 999999999999887654

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

Probab=98.74  E-value=4.9e-08  Score=73.05  Aligned_cols=100  Identities=17%  Similarity=0.211  Sum_probs=73.8

Q ss_pred             CcccccCcC-----------CHHHHHHHHHHHHhc-----cCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKL-----------STDALLYMRWLLERY-----KGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l-----------~~~~~~~L~~~le~~-----~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      ++|||+|.+           ....+..|..+++..     ..++.+|++||.+..+ +++++  |+ ..+.|++|+.++.
T Consensus       114 l~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r  193 (285)
T 3h4m_A          114 IFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGR  193 (285)
T ss_dssp             EEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSSSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHH
T ss_pred             EEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHH
Confidence            589999998           556677887777653     3456688888988889 99998  87 5899999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCC----cHHHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKN----NLRQAIRSFEAS  101 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~g----d~R~aln~L~~~  101 (137)
                      ..+++..+...++.- +..+..++..+.|    |++.+++.....
T Consensus       194 ~~il~~~~~~~~~~~-~~~~~~l~~~~~g~~~~~i~~l~~~a~~~  237 (285)
T 3h4m_A          194 LEILKIHTRKMNLAE-DVNLEEIAKMTEGCVGAELKAICTEAGMN  237 (285)
T ss_dssp             HHHHHHHHTTSCBCT-TCCHHHHHHHCTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCC-cCCHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence            999998877665542 2246777777766    555554444433

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=98.66  E-value=2.3e-08  Score=83.09  Aligned_cols=102  Identities=12%  Similarity=0.095  Sum_probs=77.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc---------------------cCCceEEEEeCCC--CCc-hhhhhcc----eeeEe
Q 042716            1 IILCEADKLSTDALLYMRWLLERY---------------------KGLNKVFFCCSDV--SKL-QPIKSLC----TVIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~---------------------~~~~~~Il~~n~~--~~i-~~l~SRc----~~i~~   52 (137)
                      +||||+|.|++..|+.|+++|++.                     +.++++|++||..  ..+ ++|++||    ..+.|
T Consensus       205 L~LDEi~~l~~~~q~~Ll~~Le~~~~~~~g~~~~~~~~~l~~~~~p~~~~vI~atn~~~~~~l~~~l~~R~~v~~i~i~l  284 (604)
T 3k1j_A          205 LFIDEIATLSLKMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNLDTVDKMHPALRSRIRGYGYEVYM  284 (604)
T ss_dssp             EEETTGGGSCHHHHHHHHHHHHHSEECCBCSCTTSGGGGCBCSCEECCCEEEEEECHHHHHHSCHHHHHHHHHHSEEEEC
T ss_pred             EEEechhhCCHHHHHHHHHHHHcCcEEecccccccccccCCCCccceeEEEEEecCHHHHhhcCHHHHHHhhccceEeec
Confidence            589999999999999999999943                     2356699999876  568 9999999    45666


Q ss_pred             cCC---CHHHHHHHHHHHHHHcC-----CCCCHHHHHHHHHHc---CC-------cHHHHHHHHHHHH
Q 042716           53 LPP---SKQEIVEVLEFIAEQEG-----IQLPHQLAEKIADNS---KN-------NLRQAIRSFEASR  102 (137)
Q Consensus        53 ~~~---~~~~i~~~l~~i~~~eg-----i~i~~~~l~~i~~~~---~g-------d~R~aln~L~~~~  102 (137)
                      +..   ..+.+..++..++++.+     ..++++++..+++++   .|       ++|.+.++++.+.
T Consensus       285 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ls~eAl~~Li~~~~r~~g~r~~l~~~~R~l~~llr~A~  352 (604)
T 3k1j_A          285 RTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEIVREAQKRAGRKGHLTLRLRDLGGIVRAAG  352 (604)
T ss_dssp             CSEEECCHHHHHHHHHHHHHHHHHHCSSCCBBHHHHHHHHHHHHHTTCSTTEEECCHHHHHHHHHHHH
T ss_pred             cccccCCHHHHHHHHHHHHHHHhhccCcccCCHHHHHHHHHHHhhhhccccccccCHHHHHHHHHHHH
Confidence            433   34456666655554332     578999999999876   56       5999999998655

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

Probab=98.55  E-value=6e-08  Score=83.39  Aligned_cols=100  Identities=14%  Similarity=0.162  Sum_probs=73.8

Q ss_pred             CcccccCcCC--------HHHHHHHHHHHHhccCCceEEEEeCCCC----Cc-hhhhhcceeeEecCCCHHHHHHHHHHH
Q 042716            1 IILCEADKLS--------TDALLYMRWLLERYKGLNKVFFCCSDVS----KL-QPIKSLCTVIQLLPPSKQEIVEVLEFI   67 (137)
Q Consensus         1 iiiDEid~l~--------~~~~~~L~~~le~~~~~~~~Il~~n~~~----~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i   67 (137)
                      +||||+|.|.        ..+++.|+..++  .+...+|.+||...    .+ ++|++||..+.|++|+.++...+|+.+
T Consensus       267 L~IDEi~~l~~~~~~~g~~~~~~~L~~~l~--~~~i~~I~at~~~~~~~~~~d~aL~rRf~~i~l~~p~~~e~~~iL~~~  344 (854)
T 1qvr_A          267 LFIDELHTVVGAGKAEGAVDAGNMLKPALA--RGELRLIGATTLDEYREIEKDPALERRFQPVYVDEPTVEETISILRGL  344 (854)
T ss_dssp             EEECCC-------------------HHHHH--TTCCCEEEEECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHHHHHHH
T ss_pred             EEEecHHHHhccCCccchHHHHHHHHHHHh--CCCeEEEEecCchHHhhhccCHHHHhCCceEEeCCCCHHHHHHHHHhh
Confidence            4789999997        455778899998  56778999988764    36 999999999999999999999999876


Q ss_pred             HH----HcCCCCCHHHHHHHHHHcCCc------HHHHHHHHHHHH
Q 042716           68 AE----QEGIQLPHQLAEKIADNSKNN------LRQAIRSFEASR  102 (137)
Q Consensus        68 ~~----~egi~i~~~~l~~i~~~~~gd------~R~aln~L~~~~  102 (137)
                      +.    ..++.++++++..++..+.|.      +++++.+++.+.
T Consensus       345 ~~~~~~~~~~~i~~~al~~~~~ls~r~i~~~~lp~kai~lldea~  389 (854)
T 1qvr_A          345 KEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAIDLIDEAA  389 (854)
T ss_dssp             HHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCTHHHHHHHHHHHH
T ss_pred             hhhhhhhcCCCCCHHHHHHHHHHHhhhcccccChHHHHHHHHHHH
Confidence            65    458899999999999877443      788888887655

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

Probab=98.49  E-value=4.2e-08  Score=79.21  Aligned_cols=93  Identities=15%  Similarity=0.146  Sum_probs=71.9

Q ss_pred             CCHHHHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCCHHHHHHHHHHHHHH----cCCCCCHH
Q 042716            9 LSTDALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQ----EGIQLPHQ   78 (137)
Q Consensus         9 l~~~~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~----egi~i~~~   78 (137)
                      .+..+++.|+..++  .+..++|.+||...     .+ +++++||..+.|++|+.++...+|..++.+    .|+.++++
T Consensus       275 ~~~~a~~~L~~~L~--~g~v~vI~at~~~e~~~~~~~~~al~~Rf~~i~v~~p~~e~~~~iL~~~~~~~~~~~~~~i~~~  352 (468)
T 3pxg_A          275 AAIDASNILKPSLA--RGELQCIGATTLDEYRKYIEKDAALERRFQPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDD  352 (468)
T ss_dssp             C--------CCCTT--SSSCEEEEECCTTTTHHHHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHH
T ss_pred             CchhHHHHHHHhhc--CCCEEEEecCCHHHHHHHhhcCHHHHHhCccceeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHH
Confidence            45667888999998  66788999998886     47 999999999999999999999999988776    78999999


Q ss_pred             HHHHHHHHcCCc------HHHHHHHHHHHHh
Q 042716           79 LAEKIADNSKNN------LRQAIRSFEASRQ  103 (137)
Q Consensus        79 ~l~~i~~~~~gd------~R~aln~L~~~~~  103 (137)
                      ++..++..+.+.      +++++++|+....
T Consensus       353 al~~l~~~s~~~~~~~~lp~~ai~ll~~a~~  383 (468)
T 3pxg_A          353 AIEAAVKLSDRYISDRFLPDKAIDLIDEAGS  383 (468)
T ss_dssp             HHHHHHHHHHHSSCCSCTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCcCCcHHHHHHHHHHH
Confidence            999999876543      4579988876653

>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=98.46  E-value=3.2e-07  Score=71.44  Aligned_cols=102  Identities=22%  Similarity=0.188  Sum_probs=77.2

Q ss_pred             CcccccCcCCH------HHHHHHHHHHHhcc-----CCceEEEEeCCCCCc-------hhhhhcc-eeeEecCCCHHHHH
Q 042716            1 IILCEADKLST------DALLYMRWLLERYK-----GLNKVFFCCSDVSKL-------QPIKSLC-TVIQLLPPSKQEIV   61 (137)
Q Consensus         1 iiiDEid~l~~------~~~~~L~~~le~~~-----~~~~~Il~~n~~~~i-------~~l~SRc-~~i~~~~~~~~~i~   61 (137)
                      |+|||+|.+..      +....|.+.+++.+     .+..+|++++.+.-.       +.+.+|. ..+.|++++.+++.
T Consensus       142 lvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~  221 (412)
T 1w5s_A          142 VILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELY  221 (412)
T ss_dssp             EEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHH
T ss_pred             EEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHH
Confidence            58999999853      56667777787654     455588888765421       3344553 34999999999999


Q ss_pred             HHHHHHHHHcCC--CCCHHHHHHHHHHcC------CcHHHHHHHHHHHH
Q 042716           62 EVLEFIAEQEGI--QLPHQLAEKIADNSK------NNLRQAIRSFEASR  102 (137)
Q Consensus        62 ~~l~~i~~~egi--~i~~~~l~~i~~~~~------gd~R~aln~L~~~~  102 (137)
                      ..+...+...+.  .++++++..++..+.      |++|.++++++.+.
T Consensus       222 ~ll~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~G~p~~~~~l~~~a~  270 (412)
T 1w5s_A          222 TILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMAC  270 (412)
T ss_dssp             HHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCCCChHHHHHHHHHHHHhccCCCcHHHHHHHHHHHH
Confidence            999887765433  578999999999999      99999999987643

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=98.43  E-value=2.2e-07  Score=70.30  Aligned_cols=76  Identities=17%  Similarity=0.284  Sum_probs=61.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHH--------hcc-----CCceEEEEeCCC-----------CCc-hhhhhcceeeEec--
Q 042716            1 IILCEADKLSTDALLYMRWLLE--------RYK-----GLNKVFFCCSDV-----------SKL-QPIKSLCTVIQLL--   53 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le--------~~~-----~~~~~Il~~n~~-----------~~i-~~l~SRc~~i~~~--   53 (137)
                      |+++|-..+..++++.++.+++        ++.     ..+|+|++||..           ... ++|+|||.+|+|.  
T Consensus       151 i~l~Ee~~~~~d~~~~lr~i~~G~~~~id~K~k~~~~v~~tPvIitsN~~i~~~~~g~~~s~~~~~~L~sR~~~f~F~~~  230 (267)
T 1u0j_A          151 VIWWEEGKMTAKVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRR  230 (267)
T ss_dssp             EEEECSCCEETTTHHHHHHHHTTCCEEC------CCEECCCCEEEEESSCTTCEEETTEEECTTHHHHHTTEEEEECCSC
T ss_pred             EEEeccccchhHHHHHHHHHhCCCcEEEecCcCCcccccCCCEEEEecCCcccccccCccchhhhHHHhhhEEEEECCCc
Confidence            3566777777888899999998        655     788999999982           245 8999999999999  


Q ss_pred             ------CCCHHHHHHHHHHHHHHcCCCCCH
Q 042716           54 ------PPSKQEIVEVLEFIAEQEGIQLPH   77 (137)
Q Consensus        54 ------~~~~~~i~~~l~~i~~~egi~i~~   77 (137)
                            +++++++..++.++ +.++.++++
T Consensus       231 ~p~~~~~lt~~~~~~f~~w~-~~~~~~~~~  259 (267)
T 1u0j_A          231 LDHDFGKVTKQEVKDFFRWA-KDHVVEVEH  259 (267)
T ss_dssp             CCTTSCCCCHHHHHHHHHHH-HHTCCCCCC
T ss_pred             CCcccCCCCHHHHHHHHHHH-HHcCCCCcc
Confidence                  89999999999966 888887654

>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=98.38  E-value=2.9e-07  Score=71.53  Aligned_cols=103  Identities=17%  Similarity=0.166  Sum_probs=75.8

Q ss_pred             CcccccCcCCHH--------------HHHHHHHHHHh---------------------ccCCceEEEEeCCC--------
Q 042716            1 IILCEADKLSTD--------------ALLYMRWLLER---------------------YKGLNKVFFCCSDV--------   37 (137)
Q Consensus         1 iiiDEid~l~~~--------------~~~~L~~~le~---------------------~~~~~~~Il~~n~~--------   37 (137)
                      +||||+|.+...              .|+.|+.+||.                     ...|..||++++..        
T Consensus       120 l~lDEid~l~~~~~~~~~~~~~~~~~~~~~Ll~~leg~~~~~~~~~~~~~~~~~~~~i~tsn~~~i~~g~~~~l~~~i~~  199 (363)
T 3hws_A          120 VYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEGTVAAVPPQGGRKHPQQEFLQVDTSKILFICGGAFAGLDKVISH  199 (363)
T ss_dssp             EEEECHHHHCCCSSCC---CHHHHHHHHHHHHHHHHCC----------------CCCCCTTSSEEEEEECCTTHHHHHHH
T ss_pred             EEEeChhhhcccccccccccccchHHHHHHHHHHhcCceeeccCccccccCCCceEEEECCCceEEecCCcHHHHHHHHH
Confidence            589999999866              89999999992                     12455677777743        


Q ss_pred             --CC-----------------------------------c-hhhhhcce-eeEecCCCHHHHHHHHHH----HH------
Q 042716           38 --SK-----------------------------------L-QPIKSLCT-VIQLLPPSKQEIVEVLEF----IA------   68 (137)
Q Consensus        38 --~~-----------------------------------i-~~l~SRc~-~i~~~~~~~~~i~~~l~~----i~------   68 (137)
                        .+                                   + ++|.+|+- ++.|.+|+.+++.+++..    +.      
T Consensus       200 ~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~~~~~~~l~~R~~~~~~~~pl~~~~~~~I~~~~~~~l~~~~~~~  279 (363)
T 3hws_A          200 RVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQAL  279 (363)
T ss_dssp             HHCCCC------------CCSCHHHHHHTCCHHHHHHHTCCHHHHTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHH
T ss_pred             hhhccccCCccccccccccchhhHHHHHhCCHHHHHHcCCCHHHhcccCeeeecCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence              12                                   7 89999995 566999999988777654    22      


Q ss_pred             -HHcC--CCCCHHHHHHHHHH---cCCcHHHHHHHHHHHHh
Q 042716           69 -EQEG--IQLPHQLAEKIADN---SKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        69 -~~eg--i~i~~~~l~~i~~~---~~gd~R~aln~L~~~~~  103 (137)
                       ...|  +.++++++..+++.   .+++.|.+-|.++....
T Consensus       280 ~~~~~~~l~~~~~a~~~L~~~~~~~~~gaR~L~~~ie~~~~  320 (363)
T 3hws_A          280 FNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALL  320 (363)
T ss_dssp             HHTTTCEEEECHHHHHHHHHHHHHTTCTTTTHHHHHHHHHH
T ss_pred             HHhcCceEEECHHHHHHHHHhhcCCccCchHHHHHHHHHHH
Confidence             2223  46899999999964   46777888888876654

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

Probab=98.35  E-value=3.7e-07  Score=77.26  Aligned_cols=99  Identities=14%  Similarity=0.198  Sum_probs=76.8

Q ss_pred             CcccccCcC---------CHHHHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCCHHHHHHHHH
Q 042716            1 IILCEADKL---------STDALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPSKQEIVEVLE   65 (137)
Q Consensus         1 iiiDEid~l---------~~~~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~~~~i~~~l~   65 (137)
                      +||||+|.|         ...+++.|...++  .+...+|.+||...     .+ ++|++||..+.|.+|+.++....+.
T Consensus       282 L~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~--~~~~~~I~at~~~~~~~~~~~d~aL~~Rf~~i~v~~p~~~e~~~il~  359 (758)
T 1r6b_X          282 LFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIIN  359 (758)
T ss_dssp             EEETTTTTTTTSCCSSSCHHHHHHHHSSCSS--SCCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHHH
T ss_pred             EEEechHHHhhcCCCCcchHHHHHHHHHHHh--CCCeEEEEEeCchHHhhhhhcCHHHHhCceEEEcCCCCHHHHHHHHH
Confidence            589999999         3344666777776  45677888888642     35 7899999999999999999999998


Q ss_pred             HHHHH----cCCCCCHHHHHHHHHHcCC------cHHHHHHHHHHH
Q 042716           66 FIAEQ----EGIQLPHQLAEKIADNSKN------NLRQAIRSFEAS  101 (137)
Q Consensus        66 ~i~~~----egi~i~~~~l~~i~~~~~g------d~R~aln~L~~~  101 (137)
                      .++..    .++.++++++..++..+.|      .+..++.+++.+
T Consensus       360 ~l~~~~~~~~~v~~~~~al~~~~~~s~~~i~~~~lp~~~i~lld~a  405 (758)
T 1r6b_X          360 GLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEA  405 (758)
T ss_dssp             HHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHhhhhcccccCchHHHHHHHHH
Confidence            87765    7899999999999887654      344667666544

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

Probab=98.35  E-value=1.3e-06  Score=64.42  Aligned_cols=101  Identities=13%  Similarity=0.086  Sum_probs=74.8

Q ss_pred             CcccccCcCCH--------------HHHHHHHHHHHhc--cCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLST--------------DALLYMRWLLERY--KGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~--------------~~~~~L~~~le~~--~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      ++|||+|.+..              ...+.++..++..  ..+..+|.+||.+..+ +.+++  |+ ..+.|+.|+.++.
T Consensus       108 l~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r  187 (257)
T 1lv7_A          108 IFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGR  187 (257)
T ss_dssp             EEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHH
T ss_pred             ehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCcccCCCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHH
Confidence            47899988743              3355666777643  3345688888998889 88887  76 5789999999998


Q ss_pred             HHHHHHHHHHcCCCCCHHH-HHHHHHHcCC-cHHHHHHHHHHHHh
Q 042716           61 VEVLEFIAEQEGIQLPHQL-AEKIADNSKN-NLRQAIRSFEASRQ  103 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~-l~~i~~~~~g-d~R~aln~L~~~~~  103 (137)
                      ..+++..+++.  .+++++ ...++..+.| +.|.+.++++.+..
T Consensus       188 ~~il~~~~~~~--~l~~~~~~~~la~~~~G~~~~dl~~l~~~a~~  230 (257)
T 1lv7_A          188 EQILKVHMRRV--PLAPDIDAAIIARGTPGFSGADLANLVNEAAL  230 (257)
T ss_dssp             HHHHHHHHTTS--CBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC--CCCccccHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            88888776554  344333 6778888999 89988888876654

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=98.31  E-value=5.1e-06  Score=65.47  Aligned_cols=106  Identities=14%  Similarity=0.147  Sum_probs=80.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcce--eeEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLCT--VIQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc~--~i~~~~~~~--   57 (137)
                      +||||++.|+.+.|..|++++++..           .++++|.+||..       ... ++|..|..  .+.++|+..  
T Consensus       235 lfldei~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~l~~~~~~g~fr~dl~~rl~~~~i~lPpLreR~  314 (387)
T 1ny5_A          235 LFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYRLGVIEIEIPPLRERK  314 (387)
T ss_dssp             EEEESGGGCCHHHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSCHHHHHHTTSSCHHHHHHHTTEEEECCCGGGCH
T ss_pred             EEEcChhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCCCCHHHHHHcCCccHHHHHhhcCCeecCCcchhcc
Confidence            5899999999999999999999732           367899999965       346 78888874  466666654  


Q ss_pred             HHHHHHHH----HHHHHcCC---CCCHHHHHHHHHHc-CCcHHHHHHHHHHHHhcCC
Q 042716           58 QEIVEVLE----FIAEQEGI---QLPHQLAEKIADNS-KNNLRQAIRSFEASRQMNY  106 (137)
Q Consensus        58 ~~i~~~l~----~i~~~egi---~i~~~~l~~i~~~~-~gd~R~aln~L~~~~~~~~  106 (137)
                      +++...+.    +.+.+.|.   .++++++..+..+. .||+|.+-|.++.+.....
T Consensus       315 ~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~l~~~~wpGNvreL~~~i~~~~~~~~  371 (387)
T 1ny5_A          315 EDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELKNVIERAVLFSE  371 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHHHHSCCTTHHHHHHHHHHHHHHHCC
T ss_pred             ccHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHHhCC
Confidence            56655444    34444453   37899999999774 9999999999998876543

>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=98.30  E-value=9.2e-07  Score=71.26  Aligned_cols=102  Identities=17%  Similarity=0.186  Sum_probs=74.9

Q ss_pred             CcccccCcCCH------------HHHHHHHHHHHhc----------cCCceEEEEe----CCCCCc-hhhhhccee-eEe
Q 042716            1 IILCEADKLST------------DALLYMRWLLERY----------KGLNKVFFCC----SDVSKL-QPIKSLCTV-IQL   52 (137)
Q Consensus         1 iiiDEid~l~~------------~~~~~L~~~le~~----------~~~~~~Il~~----n~~~~i-~~l~SRc~~-i~~   52 (137)
                      +++||+|.++.            +.|++|++++|..          ..+..||+++    +++..+ |.|++|+.+ +.|
T Consensus       254 l~~DEidki~~~~~~~~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dlipel~~R~~i~i~l  333 (444)
T 1g41_A          254 VFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLPIRVEL  333 (444)
T ss_dssp             EEEETGGGGSCCSSCSSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHTTCCEEEEC
T ss_pred             eeHHHHHHHhhccCCCCCCchHHHHHHHHHHHhcccccccccceecCCcEEEEeccccccCChhhcchHHhcccceeeeC
Confidence            47899999963            2589999999941          2345577776    234446 999999976 999


Q ss_pred             cCCCHHHHHHHHH-----------HHHHHcCC--CCCHHHHHHHHHH--------cCCcHHHHHHHHHHHH
Q 042716           53 LPPSKQEIVEVLE-----------FIAEQEGI--QLPHQLAEKIADN--------SKNNLRQAIRSFEASR  102 (137)
Q Consensus        53 ~~~~~~~i~~~l~-----------~i~~~egi--~i~~~~l~~i~~~--------~~gd~R~aln~L~~~~  102 (137)
                      ++++.++...++.           .....+|+  .++++++..|++.        -+...|.+-+.++.+.
T Consensus       334 ~~lt~~e~~~Il~~~~~~l~~q~~~~~~~~~~~l~~~~~al~~i~~~a~~~~~~t~~~GaR~L~~~ie~~~  404 (444)
T 1g41_A          334 TALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLM  404 (444)
T ss_dssp             CCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhHHHHHHHHhcccCceEEECHHHHHHHHHHHHHhccCCccCCchHHHHHHHHHH
Confidence            9999999998883           12223444  5889999999986        3577888777777554

>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=98.29  E-value=1.8e-06  Score=65.57  Aligned_cols=87  Identities=11%  Similarity=0.071  Sum_probs=65.0

Q ss_pred             CcccccCcCCHH--------------HHHHHHHHHHhc--cCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLSTD--------------ALLYMRWLLERY--KGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~--------------~~~~L~~~le~~--~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      +||||+|.|...              .++.|+..++..  ..++.+|.+||.+..+ +++++  |+ ..+.|+.|+.++.
T Consensus       112 l~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r  191 (301)
T 3cf0_A          112 LFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSR  191 (301)
T ss_dssp             EEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCTTSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHH
T ss_pred             EEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccCCCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHH
Confidence            589999988654              367888888743  3456788899999889 88888  88 5899999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcC
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSK   88 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~   88 (137)
                      ..+++..+++.++.- +-.+..++..+.
T Consensus       192 ~~il~~~l~~~~~~~-~~~~~~la~~~~  218 (301)
T 3cf0_A          192 VAILKANLRKSPVAK-DVDLEFLAKMTN  218 (301)
T ss_dssp             HHHHHHHHTTSCBCS-SCCHHHHHHTCS
T ss_pred             HHHHHHHHccCCCCc-cchHHHHHHHcC
Confidence            999998887776531 112445555443

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

Probab=98.29  E-value=2e-07  Score=64.47  Aligned_cols=62  Identities=11%  Similarity=0.108  Sum_probs=51.1

Q ss_pred             CcccccCcCCHH--------HHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCCHHHHHHHH
Q 042716            1 IILCEADKLSTD--------ALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPSKQEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l~~~--------~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~~~~i~~~l   64 (137)
                      ++|||+|.+...        .++.|+..++  ..+..+|+++|...     .+ ++++|||..+.|.+|+.++...+|
T Consensus       119 l~iDe~~~l~~~~~~~~~~~~~~~l~~~~~--~~~~~~i~~~~~~~~~~~~~~~~~l~~r~~~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          119 LFIDELHTMVGAGKADGAMDAGNMLKPALA--RGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             EEEETGGGGTT------CCCCHHHHHHHHH--TTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             EEEeCHHHHhccCcccchHHHHHHHHHhhc--cCCeEEEEeCCHHHHHHHHhcCHHHHHHhceeecCCCCHHHHHHHh
Confidence            589999999633        3788888887  56788999998875     68 999999999999999999876654

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

Probab=98.25  E-value=2.1e-06  Score=71.30  Aligned_cols=101  Identities=16%  Similarity=0.110  Sum_probs=69.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-------------CCceEEEEeCCCC-------------Cc-hhhhhcc-eeeEe
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-------------GLNKVFFCCSDVS-------------KL-QPIKSLC-TVIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-------------~~~~~Il~~n~~~-------------~i-~~l~SRc-~~i~~   52 (137)
                      ++|||+|.|++..|++|+..||+..             .++.+|.++|...             .+ ++|+||+ .++.+
T Consensus       395 l~IDEid~l~~~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaatNp~~G~~~~~~~~~~ni~l~~aLl~RFDl~~~~  474 (595)
T 3f9v_A          395 AVIDEIDKMRDEDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPKFGRYISERPVSDNINLPPTILSRFDLIFIL  474 (595)
T ss_dssp             ECCTTTTCCCSHHHHHHHHHHHSSSEEEESSSSEEEECCCCEEEEEECCTTCCSCTTSCSCTTTCSCSSSGGGCSCCEEE
T ss_pred             EEeehhhhCCHhHhhhhHHHHhCCEEEEecCCcEEEecCceEEEEEcCCcCCccCcccCchhccCCCHHHHhhCeEEEEe
Confidence            5899999999999999999999632             3456888888764             78 9999999 66777


Q ss_pred             cCCCHHHHHHHHHHHHHHc-------------------------CCCCCHHHHHHHHHH---------------cCCcHH
Q 042716           53 LPPSKQEIVEVLEFIAEQE-------------------------GIQLPHQLAEKIADN---------------SKNNLR   92 (137)
Q Consensus        53 ~~~~~~~i~~~l~~i~~~e-------------------------gi~i~~~~l~~i~~~---------------~~gd~R   92 (137)
                      .++++.+-...+.++....                         .-.+++++.+.+.+.               ..+++|
T Consensus       475 ~~~~~~e~~~i~~~il~~~~~~~~~~~l~~~~l~~~i~~ar~~~~p~ls~ea~~~l~~~y~~lR~~~~~~~~~~~~~s~R  554 (595)
T 3f9v_A          475 KDQPGEQDRELANYILDVHSGKSTKNIIDIDTLRKYIAYARKYVTPKITSEAKNLITDFFVEMRKKSSETPDSPILITPR  554 (595)
T ss_dssp             CCTTHHHHHHHHHHHHTTTCCCSSSSTTCCTTTHHHHHHHHHHHCCCCCCCTHHHHHHHHTTSSCSCCBCSSSCBCSSTT
T ss_pred             CCCCCHHHHHHHHHHHHHhhccccccCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHhhccCCCccccccHH
Confidence            6766655333333333221                         125566666666665               466777


Q ss_pred             HHHHHHHHH
Q 042716           93 QAIRSFEAS  101 (137)
Q Consensus        93 ~aln~L~~~  101 (137)
                      .+.+++..+
T Consensus       555 ~l~~lirla  563 (595)
T 3f9v_A          555 QLEALIRIS  563 (595)
T ss_dssp             TTTHHHHHH
T ss_pred             HHHHHHHHH
Confidence            777777644

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.22  E-value=1.3e-05  Score=60.73  Aligned_cols=99  Identities=15%  Similarity=0.117  Sum_probs=76.9

Q ss_pred             CcccccCcCCH-------HHHHHHHHHHHhccCCceEEEEeCCCC---------Cc-hhhhhcc-eeeEecCCCHHHHHH
Q 042716            1 IILCEADKLST-------DALLYMRWLLERYKGLNKVFFCCSDVS---------KL-QPIKSLC-TVIQLLPPSKQEIVE   62 (137)
Q Consensus         1 iiiDEid~l~~-------~~~~~L~~~le~~~~~~~~Il~~n~~~---------~i-~~l~SRc-~~i~~~~~~~~~i~~   62 (137)
                      |+|||+|.+..       +....|...++.. .++.+|+++....         .. .++..|. ..+++.+++.++...
T Consensus       132 lvlDe~~~~~~~~~~~~~~~~~~L~~~~~~~-~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~  210 (350)
T 2qen_A          132 VAFDEAQYLRFYGSRGGKELLALFAYAYDSL-PNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVE  210 (350)
T ss_dssp             EEEETGGGGGGBTTTTTHHHHHHHHHHHHHC-TTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHH
T ss_pred             EEEeCHHHHhccCccchhhHHHHHHHHHHhc-CCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHH
Confidence            58999999864       4566677777654 4778898886542         22 4566565 589999999999999


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHH
Q 042716           63 VLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEA  100 (137)
Q Consensus        63 ~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~  100 (137)
                      .+.......|..++++.+..+...++|.+..+..+...
T Consensus       211 ~l~~~~~~~~~~~~~~~~~~i~~~tgG~P~~l~~~~~~  248 (350)
T 2qen_A          211 FLKRGFREVNLDVPENEIEEAVELLDGIPGWLVVFGVE  248 (350)
T ss_dssp             HHHHHHHTTTCCCCHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            99888878888899999999999999999876555443

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

Probab=98.16  E-value=8.6e-06  Score=66.49  Aligned_cols=101  Identities=13%  Similarity=0.022  Sum_probs=73.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc---------CCceE-EEEeCCCCC---c-hhhhhcce-eeEecCCCH-HHHHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK---------GLNKV-FFCCSDVSK---L-QPIKSLCT-VIQLLPPSK-QEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~---------~~~~~-Il~~n~~~~---i-~~l~SRc~-~i~~~~~~~-~~i~~~l   64 (137)
                      ++|||++.+++..|++|+..|++..         ...+| |++||..+.   . +++.+|+. .+.+++|+. ++...++
T Consensus       113 L~IDEI~r~~~~~q~~LL~~lee~~v~i~G~~~~~~~~~iI~ATN~lpe~~~~~~aLldRF~~~i~v~~p~~~ee~~~IL  192 (500)
T 3nbx_X          113 VFLDEIWKAGPAILNTLLTAINERQFRNGAHVEKIPMRLLVAASNELPEADSSLEALYDRMLIRLWLDKVQDKANFRSML  192 (500)
T ss_dssp             EEEESGGGCCHHHHHHHHHHHHSSEEECSSSEEECCCCEEEEEESSCCCTTCTTHHHHTTCCEEEECCSCCCHHHHHHHH
T ss_pred             eeHHhHhhhcHHHHHHHHHHHHHHhccCCCCcCCcchhhhhhccccCCCccccHHHHHHHHHHHHHHHHhhhhhhHHHHH
Confidence            5899999999999999999998531         22345 777776543   4 79999974 588888887 4555555


Q ss_pred             HHHH-----------------------HHcCCCCCHHHHHHHHHHc----------CCcHHHHHHHHHHH
Q 042716           65 EFIA-----------------------EQEGIQLPHQLAEKIADNS----------KNNLRQAIRSFEAS  101 (137)
Q Consensus        65 ~~i~-----------------------~~egi~i~~~~l~~i~~~~----------~gd~R~aln~L~~~  101 (137)
                      ....                       ...++.+++++++++++..          +.+.|.++.++..+
T Consensus       193 ~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~v~v~d~v~e~i~~l~~~lr~~r~~~~iS~R~~~~llr~A  262 (500)
T 3nbx_X          193 TSQQDENDNPVPDALQVTDEEYERWQKEIGEITLPDHVFELIFMLRQQLDKLPDAPYVSDRRWKKAIRLL  262 (500)
T ss_dssp             TCCCCTTSCCSCTTTSBCHHHHHHHHHHHTTCBCCHHHHHHHHHHHHHHHHCSSSCCCCHHHHHHHHHHH
T ss_pred             hcccccCCCCCCccceecHHHHHHHHhcCCcccCchHHHHHHHHHHHHhhcCCCCCccchhHHHHHHHHH
Confidence            4321                       2347889999999988776          55889877776644

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

Probab=98.16  E-value=1.2e-06  Score=74.25  Aligned_cols=95  Identities=15%  Similarity=0.139  Sum_probs=72.1

Q ss_pred             cccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCCHHHHHHHHHHHHHH----c
Q 042716            2 ILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQ----E   71 (137)
Q Consensus         2 iiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~----e   71 (137)
                      |||    .+..+++.|+..++  .+..++|.+||...     .+ +++++||..+.|++|+.++...+|..++.+    .
T Consensus       272 fiD----~~~~~~~~L~~~l~--~~~v~~I~at~~~~~~~~~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~~~~~~~~  345 (758)
T 3pxi_A          272 FID----AAIDASNILKPSLA--RGELQCIGATTLDEYRKYIEKDAALERRFQPIQVDQPSVDESIQILQGLRDRYEAHH  345 (758)
T ss_dssp             EEC----C--------CCCTT--SSSCEEEEECCTTTTHHHHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTTTTSGGGS
T ss_pred             EEc----CchhHHHHHHHHHh--cCCEEEEeCCChHHHHHHhhccHHHHhhCcEEEeCCCCHHHHHHHHHHHHHHHHHhc
Confidence            566    45567888999998  66788999999887     57 999999999999999999999999977765    7


Q ss_pred             CCCCCHHHHHHHHHHcCC------cHHHHHHHHHHHH
Q 042716           72 GIQLPHQLAEKIADNSKN------NLRQAIRSFEASR  102 (137)
Q Consensus        72 gi~i~~~~l~~i~~~~~g------d~R~aln~L~~~~  102 (137)
                      ++.++++++..++..+.+      -++.++.++..+.
T Consensus       346 ~~~i~~~al~~~~~~s~~~i~~~~~p~~ai~ll~~a~  382 (758)
T 3pxi_A          346 RVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAG  382 (758)
T ss_dssp             SCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhhcccccCcCCcHHHHHHHHHH
Confidence            889999999999887643      3467777776553

>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=98.14  E-value=1.9e-06  Score=70.16  Aligned_cols=100  Identities=11%  Similarity=0.128  Sum_probs=72.6

Q ss_pred             CcccccCcCCH-----------HHHHHHHHHHHhcc--CCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHHHHH
Q 042716            1 IILCEADKLST-----------DALLYMRWLLERYK--GLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~-----------~~~~~L~~~le~~~--~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i~~~   63 (137)
                      +||||+|.|..           ..++.|+..++...  .++.+|.+||.+..+ +++++  |+ ..+.|+.|+.++...+
T Consensus       301 LfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~I  380 (489)
T 3hu3_A          301 IFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEI  380 (489)
T ss_dssp             EEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHH
T ss_pred             EEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHH
Confidence            58999987754           56888999999644  356688888888889 99999  55 4799999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHcCCc-HHHHHHHHHHH
Q 042716           64 LEFIAEQEGIQLPHQLAEKIADNSKNN-LRQAIRSFEAS  101 (137)
Q Consensus        64 l~~i~~~egi~i~~~~l~~i~~~~~gd-~R~aln~L~~~  101 (137)
                      |+..++..++..+ ..+..++..+.|- .+.+-++++.+
T Consensus       381 L~~~~~~~~l~~~-~~l~~la~~t~g~s~~dL~~L~~~A  418 (489)
T 3hu3_A          381 LQIHTKNMKLADD-VDLEQVANETHGHVGADLAALCSEA  418 (489)
T ss_dssp             HHHHTTTSCBCTT-CCHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             HHHHHhcCCCcch-hhHHHHHHHccCCcHHHHHHHHHHH
Confidence            9887766554422 2367778777763 33343443433

>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=98.12  E-value=5.4e-06  Score=67.29  Aligned_cols=100  Identities=15%  Similarity=0.144  Sum_probs=72.8

Q ss_pred             CcccccCcCCH--------------HHHHHHHHHHHhc--cCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLST--------------DALLYMRWLLERY--KGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~--------------~~~~~L~~~le~~--~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      |||||+|.+..              ..++.|+..++..  ..++.+|.+||.+..+ ++++.  |+ ..+.|+.|+.++.
T Consensus       112 LfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R  191 (476)
T 2ce7_A          112 VFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGR  191 (476)
T ss_dssp             EEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGGGTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHH
T ss_pred             EEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCCCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHH
Confidence            58999999843              2356777777643  3456788888888888 88875  76 4899999999998


Q ss_pred             HHHHHHHHHHcCCCCCHHH-HHHHHHHcCCcH-HHHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQL-AEKIADNSKNNL-RQAIRSFEASR  102 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~-l~~i~~~~~gd~-R~aln~L~~~~  102 (137)
                      ..+++..+++.+  +++++ +..++..+.|.. |.+.+++..+.
T Consensus       192 ~~Il~~~~~~~~--l~~~v~l~~la~~t~G~sgadL~~lv~~Aa  233 (476)
T 2ce7_A          192 KKILEIHTRNKP--LAEDVNLEIIAKRTPGFVGADLENLVNEAA  233 (476)
T ss_dssp             HHHHHHHHTTSC--BCTTCCHHHHHHTCTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCC--CcchhhHHHHHHhcCCCcHHHHHHHHHHHH
Confidence            888887766543  33333 777899888866 66777766544

>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=97.98  E-value=3.1e-07  Score=68.10  Aligned_cols=102  Identities=11%  Similarity=0.067  Sum_probs=68.8

Q ss_pred             CcccccCcCCHH---------------HHHHHHHHHHhccC---CceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHH
Q 042716            1 IILCEADKLSTD---------------ALLYMRWLLERYKG---LNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQ   58 (137)
Q Consensus         1 iiiDEid~l~~~---------------~~~~L~~~le~~~~---~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~   58 (137)
                      ++|||+|.|...               .++.|+..++.+..   .+.+|.++|.+..+ +++++  |+ ..+.|+.|+.+
T Consensus       107 l~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~  186 (268)
T 2r62_A          107 IFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFN  186 (268)
T ss_dssp             EEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCSCSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTT
T ss_pred             EEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccCCCCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHH
Confidence            589999999654               24556777765432   25577788888888 88988  54 67999999999


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-cHHHHHHHHHHHHh
Q 042716           59 EIVEVLEFIAEQEGIQLPHQLAEKIADNSKN-NLRQAIRSFEASRQ  103 (137)
Q Consensus        59 ~i~~~l~~i~~~egi~i~~~~l~~i~~~~~g-d~R~aln~L~~~~~  103 (137)
                      +....++..++..++. ++..+..++..+.| ..|.+.++++.+..
T Consensus       187 ~r~~il~~~~~~~~~~-~~~~~~~la~~~~g~~g~dl~~l~~~a~~  231 (268)
T 2r62_A          187 GRVEILKVHIKGVKLA-NDVNLQEVAKLTAGLAGADLANIINEAAL  231 (268)
T ss_dssp             THHHHHHHHTSSSCCC-SSCCTTTTTSSSCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCC-CccCHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            9999998876544332 22225667776665 34555555555543

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

Probab=97.89  E-value=0.00014  Score=55.08  Aligned_cols=88  Identities=15%  Similarity=0.186  Sum_probs=59.4

Q ss_pred             CcccccCcCCH-------------HHHHHHHHHHHh-------------ccCCceEEEEeCCCCCc-hhhhh--cceeeE
Q 042716            1 IILCEADKLST-------------DALLYMRWLLER-------------YKGLNKVFFCCSDVSKL-QPIKS--LCTVIQ   51 (137)
Q Consensus         1 iiiDEid~l~~-------------~~~~~L~~~le~-------------~~~~~~~Il~~n~~~~i-~~l~S--Rc~~i~   51 (137)
                      ++|||+|.+.+             ..++.|+.+++.             ...++.+|+|||.+..+ ++++.  |+..+-
T Consensus       103 l~iDEiD~~~~~~~~~~~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~R~d~~i  182 (293)
T 3t15_A          103 LFINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFY  182 (293)
T ss_dssp             EEEECCC--------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCCC--CHHHHHHHEEEEE
T ss_pred             EEEechhhhcCCCCCCccccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcccCCHHHhCCCCCceeE
Confidence            57999999865             234788888762             23467799999999999 88884  664332


Q ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCcH
Q 042716           52 LLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNS-KNNL   91 (137)
Q Consensus        52 ~~~~~~~~i~~~l~~i~~~egi~i~~~~l~~i~~~~-~gd~   91 (137)
                      + .|+.++...+++......++  +.+.+..+.... +.++
T Consensus       183 ~-~P~~~~r~~Il~~~~~~~~~--~~~~l~~~~~~~~~~~l  220 (293)
T 3t15_A          183 W-APTREDRIGVCTGIFRTDNV--PAEDVVKIVDNFPGQSI  220 (293)
T ss_dssp             E-CCCHHHHHHHHHHHHGGGCC--CHHHHHHHHHHSCSCCH
T ss_pred             e-CcCHHHHHHHHHHhccCCCC--CHHHHHHHhCCCCcccH
Confidence            3 46999999999988877655  566677766654 4455

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

Probab=97.87  E-value=5.2e-05  Score=60.41  Aligned_cols=95  Identities=16%  Similarity=0.278  Sum_probs=67.4

Q ss_pred             CcccccCcCCH-----------HH---HHHHHHHHHhcc--CCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLST-----------DA---LLYMRWLLERYK--GLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~-----------~~---~~~L~~~le~~~--~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      |||||+|.+..           ..   .+.|+.-|+...  .+..+|.+||.+..| ++|+-  |+ ..+.|+.|+.++.
T Consensus       245 IFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R  324 (405)
T 4b4t_J          245 IFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAAR  324 (405)
T ss_dssp             EEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTCCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHH
T ss_pred             EeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCCCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHH
Confidence            58999999842           12   344555565433  345588899999999 99985  77 6899999999999


Q ss_pred             HHHHHHHHHHcCCCCCHH-HHHHHHHHcCC----cHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQ-LAEKIADNSKN----NLRQAIRS   97 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~-~l~~i~~~~~g----d~R~aln~   97 (137)
                      ..+++..+++.++  +++ .+..+++.+.|    |++.+.+-
T Consensus       325 ~~Il~~~~~~~~l--~~dvdl~~lA~~t~G~SGADi~~l~~e  364 (405)
T 4b4t_J          325 AEILRIHSRKMNL--TRGINLRKVAEKMNGCSGADVKGVCTE  364 (405)
T ss_dssp             HHHHHHHHTTSBC--CSSCCHHHHHHHCCSCCHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCC--CccCCHHHHHHHCCCCCHHHHHHHHHH
Confidence            9999877765544  322 37788887665    66655543

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

Probab=97.86  E-value=3.7e-06  Score=58.02  Aligned_cols=54  Identities=15%  Similarity=0.145  Sum_probs=44.8

Q ss_pred             CcccccCcCC---------HHHHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCC
Q 042716            1 IILCEADKLS---------TDALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPS   56 (137)
Q Consensus         1 iiiDEid~l~---------~~~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~   56 (137)
                      ++|||+|.+.         ...++.|...++  ..++.+|+++|...     .+ ++++|||..+.+.+|+
T Consensus       119 l~iDe~~~l~~~~~~~~~~~~~~~~l~~~~~--~~~~~ii~~~~~~~~~~~~~~~~~l~~R~~~i~i~~p~  187 (187)
T 2p65_A          119 MFIDEIHTVVGAGAVAEGALDAGNILKPMLA--RGELRCIGATTVSEYRQFIEKDKALERRFQQILVEQPS  187 (187)
T ss_dssp             EEETTGGGGSSSSSSCTTSCCTHHHHHHHHH--TTCSCEEEEECHHHHHHHTTTCHHHHHHEEEEECCSCC
T ss_pred             EEEeCHHHhcccccccccchHHHHHHHHHHh--cCCeeEEEecCHHHHHHHHhccHHHHHhcCcccCCCCC
Confidence            5899999997         455778888887  56788999998775     57 9999999999998875

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=97.77  E-value=0.00012  Score=55.38  Aligned_cols=98  Identities=17%  Similarity=0.154  Sum_probs=73.6

Q ss_pred             CcccccCcCCH----HHHHHHHHHHHhccCCceEEEEeCCCC---------Cc-hhhhhcc-eeeEecCCCHHHHHHHHH
Q 042716            1 IILCEADKLST----DALLYMRWLLERYKGLNKVFFCCSDVS---------KL-QPIKSLC-TVIQLLPPSKQEIVEVLE   65 (137)
Q Consensus         1 iiiDEid~l~~----~~~~~L~~~le~~~~~~~~Il~~n~~~---------~i-~~l~SRc-~~i~~~~~~~~~i~~~l~   65 (137)
                      ++|||+|.+..    +....|....+.. .+..+|++++...         .. .++..|. ..+.+.+++.+++...+.
T Consensus       141 lvlDe~~~~~~~~~~~~~~~l~~~~~~~-~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~  219 (357)
T 2fna_A          141 IVLDEAQELVKLRGVNLLPALAYAYDNL-KRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLR  219 (357)
T ss_dssp             EEEETGGGGGGCTTCCCHHHHHHHHHHC-TTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHH
T ss_pred             EEEECHHHhhccCchhHHHHHHHHHHcC-CCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHH
Confidence            58999999864    3355666666653 3678999987642         22 3566675 689999999999999998


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHH
Q 042716           66 FIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS  101 (137)
Q Consensus        66 ~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~  101 (137)
                      ......|...++.  ..+...++|.+..+..+...+
T Consensus       220 ~~~~~~~~~~~~~--~~i~~~t~G~P~~l~~~~~~~  253 (357)
T 2fna_A          220 RGFQEADIDFKDY--EVVYEKIGGIPGWLTYFGFIY  253 (357)
T ss_dssp             HHHHHHTCCCCCH--HHHHHHHCSCHHHHHHHHHHH
T ss_pred             HHHHHcCCCCCcH--HHHHHHhCCCHHHHHHHHHHH
Confidence            8777778777654  889999999998876665544

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

Probab=97.73  E-value=0.00013  Score=54.32  Aligned_cols=100  Identities=14%  Similarity=0.149  Sum_probs=67.2

Q ss_pred             CcccccCcCC-----------HHHHHHHHHHHHhccC----C-ceEEEEeCCCCCc-hhhhhcc---eeeEecCCCHHHH
Q 042716            1 IILCEADKLS-----------TDALLYMRWLLERYKG----L-NKVFFCCSDVSKL-QPIKSLC---TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~-----------~~~~~~L~~~le~~~~----~-~~~Il~~n~~~~i-~~l~SRc---~~i~~~~~~~~~i   60 (137)
                      +++||+|.+.           ...+..+...+.+..+    . ..++.++|.+..+ +++++|+   ..+.|+.|+.++.
T Consensus       136 ~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r  215 (278)
T 1iy2_A          136 VFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGR  215 (278)
T ss_dssp             EEEETHHHHHCC--------CHHHHHHHHHHHHHHTTCCTTCCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHH
T ss_pred             EehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCCCCCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHH
Confidence            4789998762           2234444555544332    2 2355566777778 8998844   5799999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHH-HHHHHHHcCCcH-HHHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQL-AEKIADNSKNNL-RQAIRSFEASR  102 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~-l~~i~~~~~gd~-R~aln~L~~~~  102 (137)
                      ..+++..++  +..+++++ +..++..+.|.. |.+.++++.+.
T Consensus       216 ~~il~~~~~--~~~~~~~~~~~~la~~~~G~~~~dl~~l~~~a~  257 (278)
T 1iy2_A          216 EQILRIHAR--GKPLAEDVDLALLAKRTPGFVGADLENLLNEAA  257 (278)
T ss_dssp             HHHHHHHHT--TSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHc--cCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            998887653  45565554 788999998866 66666666554

>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=97.72  E-value=9e-05  Score=54.38  Aligned_cols=100  Identities=12%  Similarity=0.146  Sum_probs=65.6

Q ss_pred             CcccccCcCCH-----------HH---HHHHHHHHHhccC-Cc-eEEEEeCCCCCc-hhhhhcc---eeeEecCCCHHHH
Q 042716            1 IILCEADKLST-----------DA---LLYMRWLLERYKG-LN-KVFFCCSDVSKL-QPIKSLC---TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~-----------~~---~~~L~~~le~~~~-~~-~~Il~~n~~~~i-~~l~SRc---~~i~~~~~~~~~i   60 (137)
                      +++||+|.+..           ..   .+.++..++.... .. .++.++|.+..+ +++++|+   ..+.|+.|+.++.
T Consensus       112 ~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r  191 (254)
T 1ixz_A          112 VFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGR  191 (254)
T ss_dssp             EEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHH
T ss_pred             EEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCCCCCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHH
Confidence            47899987731           11   3344444443222 22 344556777678 9999854   5799999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHH-HHHHHHHcCCcH-HHHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQL-AEKIADNSKNNL-RQAIRSFEASR  102 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~-l~~i~~~~~gd~-R~aln~L~~~~  102 (137)
                      ..+++..+  +++.+++++ +..++..+.|.. |.+.++++.+.
T Consensus       192 ~~il~~~~--~~~~~~~~~~~~~la~~~~G~~~~dl~~~~~~a~  233 (254)
T 1ixz_A          192 EQILRIHA--RGKPLAEDVDLALLAKRTPGFVGADLENLLNEAA  233 (254)
T ss_dssp             HHHHHHHH--TTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHH--cCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            99888665  455565554 788999988855 66666666544

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.66  E-value=4e-05  Score=51.96  Aligned_cols=55  Identities=11%  Similarity=0.100  Sum_probs=45.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCC-------Cc-hhhhhcce--eeEecCC
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVS-------KL-QPIKSLCT--VIQLLPP   55 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~-------~i-~~l~SRc~--~i~~~~~   55 (137)
                      ++|||+|.|+...|..|+..++..+.++++|++||.+.       .+ +.|..|+.  .+.++|+
T Consensus        80 l~ldei~~l~~~~q~~Ll~~l~~~~~~~~~I~~t~~~~~~~~~~~~~~~~L~~rl~~~~i~lPpL  144 (145)
T 3n70_A           80 LVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDTSLVELAASNHIIAELYYCFAMTQIACLPL  144 (145)
T ss_dssp             EEEECGGGSCHHHHHHHHHHHHSSSCSSCEEEEESSCHHHHHHHSCCCHHHHHHHHHHEEECCCC
T ss_pred             EEEcChHHCCHHHHHHHHHHHhhcCCCEEEEEECCcCHHHHHHcCCCCHHHHHHhcCCEEeCCCC
Confidence            58999999999999999999988788899999999762       46 78888864  4555554

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

Probab=97.64  E-value=0.00018  Score=57.83  Aligned_cols=95  Identities=12%  Similarity=0.194  Sum_probs=67.6

Q ss_pred             CcccccCcCCH-----------H---HHHHHHHHHHhccC--CceEEEEeCCCCCc-hhhhhc--c-eeeEecCCCHHHH
Q 042716            1 IILCEADKLST-----------D---ALLYMRWLLERYKG--LNKVFFCCSDVSKL-QPIKSL--C-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~-----------~---~~~~L~~~le~~~~--~~~~Il~~n~~~~i-~~l~SR--c-~~i~~~~~~~~~i   60 (137)
                      |||||+|.+..           .   ..+.|+..|+....  ++.+|.+||.+..| ++|+.+  + ..+.|+.|+.++.
T Consensus       278 ifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R  357 (437)
T 4b4t_L          278 IFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGR  357 (437)
T ss_dssp             EEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSCTTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHH
T ss_pred             eeeecccccccccccCCCCcchHHHHHHHHHHHHhhcccCCCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHH
Confidence            58999998832           1   23456666764433  45689999999999 999765  4 5799999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCC----cHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKN----NLRQAIR   96 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~g----d~R~aln   96 (137)
                      ..+++..+.+..+. ++-.+..++..+.|    |++.+.+
T Consensus       358 ~~Il~~~~~~~~~~-~d~dl~~lA~~t~G~sGADi~~l~~  396 (437)
T 4b4t_L          358 LEIFKIHTAKVKKT-GEFDFEAAVKMSDGFNGADIRNCAT  396 (437)
T ss_dssp             HHHHHHHHHTSCBC-SCCCHHHHHHTCCSCCHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCC-cccCHHHHHHhCCCCCHHHHHHHHH
Confidence            99998877665432 12236778887665    6666554

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

Probab=97.61  E-value=0.00055  Score=54.96  Aligned_cols=95  Identities=14%  Similarity=0.239  Sum_probs=65.7

Q ss_pred             CcccccCcCCH-----------HH---HHHHHHHHHhcc--CCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLST-----------DA---LLYMRWLLERYK--GLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~-----------~~---~~~L~~~le~~~--~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      |||||+|.+..           ..   ...|+..++-..  .++.+|.+||.+..| ++|+-  |+ ..+.|+.|+.++.
T Consensus       279 IfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R  358 (437)
T 4b4t_I          279 VFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTK  358 (437)
T ss_dssp             EEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCCSSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHH
T ss_pred             EEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHH
Confidence            58999998832           12   334455555333  345688899999999 99986  77 5799999999999


Q ss_pred             HHHHHHHHHHcCCCCCHH-HHHHHHHHcCC----cHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQ-LAEKIADNSKN----NLRQAIRS   97 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~-~l~~i~~~~~g----d~R~aln~   97 (137)
                      ..+++..+.+..+  +++ .+..++..+.|    |++.+.+-
T Consensus       359 ~~Il~~~l~~~~l--~~dvdl~~LA~~T~GfSGADI~~l~~e  398 (437)
T 4b4t_I          359 KKILGIHTSKMNL--SEDVNLETLVTTKDDLSGADIQAMCTE  398 (437)
T ss_dssp             HHHHHHHHTTSCB--CSCCCHHHHHHHCCSCCHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCC--CCcCCHHHHHHhCCCCCHHHHHHHHHH
Confidence            9999877765543  332 36777877654    66655543

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

Probab=97.56  E-value=0.00015  Score=58.29  Aligned_cols=94  Identities=17%  Similarity=0.242  Sum_probs=66.3

Q ss_pred             CcccccCcCCH-----------HH---HHHHHHHHHhccC--CceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLST-----------DA---LLYMRWLLERYKG--LNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~-----------~~---~~~L~~~le~~~~--~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      |||||+|.+..           ..   ...|+..|+.+..  ++.+|.+||.+..| ++|+.  |+ ..+.|+.|+.++.
T Consensus       278 ifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~~~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R  357 (434)
T 4b4t_M          278 IFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSR  357 (434)
T ss_dssp             EEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTSCSSCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHH
T ss_pred             EeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhccCCCCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHH
Confidence            58999998721           12   3345666664433  34577889999999 99976  77 5799999999999


Q ss_pred             HHHHHHHHHHcCCCCCHH-HHHHHHHHcCC----cHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQ-LAEKIADNSKN----NLRQAIR   96 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~-~l~~i~~~~~g----d~R~aln   96 (137)
                      ..+++..+++..+.  ++ .+..++..+.|    |++.+.+
T Consensus       358 ~~Il~~~~~~~~~~--~dvdl~~lA~~t~G~sGADi~~l~~  396 (434)
T 4b4t_M          358 AQILQIHSRKMTTD--DDINWQELARSTDEFNGAQLKAVTV  396 (434)
T ss_dssp             HHHHHHHHHHSCBC--SCCCHHHHHHHCSSCCHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCC--CcCCHHHHHHhCCCCCHHHHHHHHH
Confidence            99998887766442  22 26778877665    6666554

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

Probab=97.55  E-value=5.5e-05  Score=61.74  Aligned_cols=101  Identities=11%  Similarity=0.109  Sum_probs=67.8

Q ss_pred             CcccccCcCCH-----------HHH---HHHHHHHHhccC--CceEEEEeCCCCCc-hhhhhcc---eeeEecCCCHHHH
Q 042716            1 IILCEADKLST-----------DAL---LYMRWLLERYKG--LNKVFFCCSDVSKL-QPIKSLC---TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~-----------~~~---~~L~~~le~~~~--~~~~Il~~n~~~~i-~~l~SRc---~~i~~~~~~~~~i   60 (137)
                      ++|||+|.+..           +..   +.|+..++....  ...++.++|.+..+ +++++++   ..+.|+.|+.++.
T Consensus       127 l~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R  206 (499)
T 2dhr_A          127 VFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGR  206 (499)
T ss_dssp             EEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCSSCCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHH
T ss_pred             EEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcccccCccEEEEEecCChhhcCcccccccccceEEecCCCCHHHH
Confidence            47999998842           222   344444442222  23355556666668 8999865   4799999999998


Q ss_pred             HHHHHHHHHHcCCCCCHHH-HHHHHHHcCCcH-HHHHHHHHHHHh
Q 042716           61 VEVLEFIAEQEGIQLPHQL-AEKIADNSKNNL-RQAIRSFEASRQ  103 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~-l~~i~~~~~gd~-R~aln~L~~~~~  103 (137)
                      ..+++..+  .++.+++++ +..++..+.|.. |.+-|++..+..
T Consensus       207 ~~IL~~~~--~~~~l~~dv~l~~lA~~t~G~~gadL~~lv~~Aa~  249 (499)
T 2dhr_A          207 EQILRIHA--RGKPLAEDVDLALLAKRTPGFVGADLENLLNEAAL  249 (499)
T ss_dssp             HHHHHHTT--SSSCCCCSSTTHHHHTTSCSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--hcCCCChHHHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence            88887654  355666554 788999998876 777777775543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.54  E-value=7.1e-05  Score=50.65  Aligned_cols=55  Identities=13%  Similarity=0.286  Sum_probs=43.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc-cCCceEEEEeCCCC-C----c-hhhhhcce--eeEecCC
Q 042716            1 IILCEADKLSTDALLYMRWLLERY-KGLNKVFFCCSDVS-K----L-QPIKSLCT--VIQLLPP   55 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~-~~~~~~Il~~n~~~-~----i-~~l~SRc~--~i~~~~~   55 (137)
                      ++|||+|.++...|..|+..+++. +.++++|++||... .    + +.|..|+.  .+.++++
T Consensus        79 l~lDei~~l~~~~q~~Ll~~l~~~~~~~~~iI~~tn~~~~~~~~~~~~~L~~rl~~~~i~lPpL  142 (143)
T 3co5_A           79 LYVGDIAQYSRNIQTGITFIIGKAERCRVRVIASCSYAAGSDGISCEEKLAGLFSESVVRIPPL  142 (143)
T ss_dssp             EEEEECTTCCHHHHHHHHHHHHHHTTTTCEEEEEEEECTTTC--CHHHHHHHHSSSEEEEECCC
T ss_pred             EEEeChHHCCHHHHHHHHHHHHhCCCCCEEEEEecCCCHHHHHhCccHHHHHHhcCcEEeCCCC
Confidence            589999999999999999999975 35688999998552 2    7 78888864  4555554

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

Probab=97.48  E-value=0.00034  Score=56.62  Aligned_cols=94  Identities=17%  Similarity=0.234  Sum_probs=65.2

Q ss_pred             CcccccCcCCH-----------HH---HHHHHHHHHhcc--CCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLST-----------DA---LLYMRWLLERYK--GLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~-----------~~---~~~L~~~le~~~--~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      |||||+|.+..           ..   ...|+.-|+...  .++.+|.+||.+..| ++|+-  |+ ..+.|+.|+.++.
T Consensus       306 IfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R  385 (467)
T 4b4t_H          306 IFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGR  385 (467)
T ss_dssp             EEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCCTTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHH
T ss_pred             EeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCCCCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHH
Confidence            58999998842           12   334445554332  344578889999999 88875  87 6899999999999


Q ss_pred             HHHHHHHHHHcCCCCCHH-HHHHHHHHcCC----cHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQ-LAEKIADNSKN----NLRQAIR   96 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~-~l~~i~~~~~g----d~R~aln   96 (137)
                      ..+++..+++..+  +++ .+..+++.+.|    |++.+.+
T Consensus       386 ~~Ilk~~l~~~~l--~~dvdl~~LA~~T~GfSGADI~~l~~  424 (467)
T 4b4t_H          386 ANIFRIHSKSMSV--ERGIRWELISRLCPNSTGAELRSVCT  424 (467)
T ss_dssp             HHHHHHHHTTSCB--CSSCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             HHHHHHHhcCCCC--CCCCCHHHHHHHCCCCCHHHHHHHHH
Confidence            9999877765443  322 26778887765    6666554

>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family; helicase, MCM homolog, DNA replication, ATP-binding, DNA-binding; 1.90A {Methanopyrus kandleri AV19}

Probab=97.37  E-value=0.00087  Score=54.60  Aligned_cols=85  Identities=12%  Similarity=0.068  Sum_probs=60.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc---------cCCceEEEEeCCCC-----------Cc-hhhhhcc-eeeEe-c----
Q 042716            1 IILCEADKLSTDALLYMRWLLERY---------KGLNKVFFCCSDVS-----------KL-QPIKSLC-TVIQL-L----   53 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~---------~~~~~~Il~~n~~~-----------~i-~~l~SRc-~~i~~-~----   53 (137)
                      +++||++.|.+..|.+|+..||+-         +..+.+|.++|..+           .+ +++.||+ .++-. .    
T Consensus       304 l~lDEIn~~~~~~qsaLlEaMEe~~VtI~G~~lparf~VIAA~NP~~~yd~~~s~~~~~Lp~alLDRFDLi~i~~d~pd~  383 (506)
T 3f8t_A          304 LAVDHLEGAPEPHRWALMEAMDKGTVTVDGIALNARCAVLAAINPGEQWPSDPPIARIDLDQDFLSHFDLIAFLGVDPRP  383 (506)
T ss_dssp             EEEECCTTCCHHHHHHHHHHHHHSEEEETTEEEECCCEEEEEECCCC--CCSCGGGGCCSCHHHHTTCSEEEETTC----
T ss_pred             eehHhhhhCCHHHHHHHHHHHhCCcEEECCEEcCCCeEEEEEeCcccccCCCCCccccCCChHHhhheeeEEEecCCCCh
Confidence            479999999999999999999963         45667777788653           78 9999998 43332 2    


Q ss_pred             ---------CCCHHHHHHHHHHHHH--HcCCCCCHHHHHHHHHH
Q 042716           54 ---------PPSKQEIVEVLEFIAE--QEGIQLPHQLAEKIADN   86 (137)
Q Consensus        54 ---------~~~~~~i~~~l~~i~~--~egi~i~~~~l~~i~~~   86 (137)
                               .++.+.+.+++.. ++  .-...+++++.++|.+.
T Consensus       384 e~d~e~~~~~ls~e~L~~yi~~-ar~~~~~p~ls~ea~~yI~~~  426 (506)
T 3f8t_A          384 GEPEEQDTEVPSYTLLRRYLLY-AIREHPAPELTEEARKRLEHW  426 (506)
T ss_dssp             ----------CCHHHHHHHHHH-HHHHCSCCEECHHHHHHHHHH
T ss_pred             hHhhcccCCCCCHHHHHHHHHH-HHhcCCCceeCHHHHHHHHHH
Confidence                     2334455555544 44  22677889888777653

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

Probab=97.30  E-value=0.00052  Score=54.99  Aligned_cols=94  Identities=13%  Similarity=0.184  Sum_probs=64.7

Q ss_pred             CcccccCcCCH-----------H---HHHHHHHHHHhcc--CCceEEEEeCCCCCc-hhhhh--cc-eeeEec-CCCHHH
Q 042716            1 IILCEADKLST-----------D---ALLYMRWLLERYK--GLNKVFFCCSDVSKL-QPIKS--LC-TVIQLL-PPSKQE   59 (137)
Q Consensus         1 iiiDEid~l~~-----------~---~~~~L~~~le~~~--~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~-~~~~~~   59 (137)
                      +||||+|.+..           .   ..+.|+..|+...  .++.+|.+||.+..| ++|+-  |+ ..+.|+ .|+.++
T Consensus       269 ifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~  348 (428)
T 4b4t_K          269 IFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRE  348 (428)
T ss_dssp             EEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCSSCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHH
T ss_pred             eechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHH
Confidence            57899997621           1   2455666676543  345688899999999 99986  66 468895 678888


Q ss_pred             HHHHHHHHHHHcCCCCCHH-HHHHHHHHcCC----cHHHHHH
Q 042716           60 IVEVLEFIAEQEGIQLPHQ-LAEKIADNSKN----NLRQAIR   96 (137)
Q Consensus        60 i~~~l~~i~~~egi~i~~~-~l~~i~~~~~g----d~R~aln   96 (137)
                      ...+++..+.+.++  .++ .+..++..+.|    |++.+.+
T Consensus       349 R~~Il~~~~~~~~l--~~~~dl~~lA~~t~G~sgadi~~l~~  388 (428)
T 4b4t_K          349 RRLIFGTIASKMSL--APEADLDSLIIRNDSLSGAVIAAIMQ  388 (428)
T ss_dssp             HHHHHHHHHHSSCB--CTTCCHHHHHHHTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCC--CcccCHHHHHHHCCCCCHHHHHHHHH
Confidence            88888877766544  322 36778877655    6666554

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.80  E-value=0.00072  Score=46.21  Aligned_cols=48  Identities=8%  Similarity=0.252  Sum_probs=37.1

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccC-Cce-EEEEeCCCCC-c---hhhhhcce
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKG-LNK-VFFCCSDVSK-L---QPIKSLCT   48 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~-~~~-~Il~~n~~~~-i---~~l~SRc~   48 (137)
                      ++|||++.+....+..|+.+++.... +.. +|++++.++. +   ++|+||+.
T Consensus        87 LilDE~~~~~~~~~~~l~~li~~~~~~g~~~iiits~~~p~~l~~~~~L~SRl~  140 (149)
T 2kjq_A           87 LAVDQVEKLGNEEQALLFSIFNRFRNSGKGFLLLGSEYTPQQLVIREDLRTRMA  140 (149)
T ss_dssp             EEEESTTCCCSHHHHHHHHHHHHHHHHTCCEEEEEESSCTTTSSCCHHHHHHGG
T ss_pred             EEEeCccccChHHHHHHHHHHHHHHHcCCcEEEEECCCCHHHccccHHHHHHHh
Confidence            48999999988889999999886433 344 8888886543 3   89999974

>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=96.80  E-value=0.00094  Score=57.39  Aligned_cols=88  Identities=13%  Similarity=0.186  Sum_probs=61.7

Q ss_pred             CcccccCcCCHH-----------HHHHHHHHHHhccC--CceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHHHHH
Q 042716            1 IILCEADKLSTD-----------ALLYMRWLLERYKG--LNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~~-----------~~~~L~~~le~~~~--~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i~~~   63 (137)
                      |||||+|.+.+.           ..+.|+..|+....  ++.+|.+||.+..| ++|+.  |+ ..+.|+.|+.++...+
T Consensus       301 IfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~I  380 (806)
T 3cf2_A          301 IFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEI  380 (806)
T ss_dssp             EEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHH
T ss_pred             EEEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHH
Confidence            589999999532           25667777776543  44577888999999 99998  76 5799999999999888


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHcCC
Q 042716           64 LEFIAEQEGIQLPHQLAEKIADNSKN   89 (137)
Q Consensus        64 l~~i~~~egi~i~~~~l~~i~~~~~g   89 (137)
                      |+..+++..+. ++-.+..++..+.|
T Consensus       381 L~~~l~~~~~~-~dvdl~~lA~~T~G  405 (806)
T 3cf2_A          381 LQIHTKNMKLA-DDVDLEQVANETHG  405 (806)
T ss_dssp             HHHTCSSSEEC-TTCCHHHHHHHCCS
T ss_pred             HHHHhcCCCCC-cccCHHHHHHhcCC
Confidence            87655433222 11225666766543

>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=96.07  E-value=0.0016  Score=55.89  Aligned_cols=96  Identities=11%  Similarity=0.077  Sum_probs=50.8

Q ss_pred             CcccccCcCCHH--------------HHHHHHHHHHhccCC--ceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLSTD--------------ALLYMRWLLERYKGL--NKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~--------------~~~~L~~~le~~~~~--~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      |||||+|.+...              ..+.|+..|+.....  +.+|.+||.+..| ++++-  |+ ..+.|+.|+.++.
T Consensus       574 ifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~~~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R  653 (806)
T 3cf2_A          574 LFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSR  653 (806)
T ss_dssp             EECSCGGGCC--------------CHHHHHHHHHHHSSCSSSSEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHH
T ss_pred             eechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHH
Confidence            589999998432              145677778755443  3455567888889 88875  77 5789999999988


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHH----cCCcHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADN----SKNNLRQAIRS   97 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~----~~gd~R~aln~   97 (137)
                      ..+++...++..+.- +-.+..+++.    +..|+..+.+.
T Consensus       654 ~~il~~~l~~~~~~~-~~dl~~la~~t~g~SGadi~~l~~~  693 (806)
T 3cf2_A          654 VAILKANLRKSPVAK-DVDLEFLAKMTNGFSGADLTEICQR  693 (806)
T ss_dssp             HHTTTTTSSCC--CC-C----------------CHHHHHHH
T ss_pred             HHHHHHHhcCCCCCC-CCCHHHHHHhCCCCCHHHHHHHHHH
Confidence            888876655443321 1124455543    55677766543

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=95.93  E-value=0.011  Score=40.68  Aligned_cols=39  Identities=10%  Similarity=0.137  Sum_probs=31.9

Q ss_pred             CcccccC--cCCHHHHHHHHHHHHhcc-CCceEEEEeCCCCC
Q 042716            1 IILCEAD--KLSTDALLYMRWLLERYK-GLNKVFFCCSDVSK   39 (137)
Q Consensus         1 iiiDEid--~l~~~~~~~L~~~le~~~-~~~~~Il~~n~~~~   39 (137)
                      ++|||++  .+++..+..|..+++... .+..+|++||.+..
T Consensus       104 lilDE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~~~~  145 (180)
T 3ec2_A          104 LVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNYSLQ  145 (180)
T ss_dssp             EEEETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCCCSC
T ss_pred             EEEeCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCCChh
Confidence            5899998  678888899999887653 56789999998854

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=95.79  E-value=0.0065  Score=44.26  Aligned_cols=56  Identities=16%  Similarity=0.073  Sum_probs=37.8

Q ss_pred             CcccccCcCCHHH-HHHHHHHHHhcc-------------CCceEEEEeCCCC---Cc-hhhhhcceeeEecCCC
Q 042716            1 IILCEADKLSTDA-LLYMRWLLERYK-------------GLNKVFFCCSDVS---KL-QPIKSLCTVIQLLPPS   56 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~L~~~le~~~-------------~~~~~Il~~n~~~---~i-~~l~SRc~~i~~~~~~   56 (137)
                      ++|||+|.-.... ...++.+++-.+             ...|+|+|||...   .. +.|.||+..+.|+.+-
T Consensus       107 iiLDEad~~~~~~~d~~lrn~ldG~~~~iD~Khr~~~~~~~~PlIITtN~~~~~~~~~~~L~SRi~~f~F~~~~  180 (212)
T 1tue_A          107 AMLDDATTTCWTYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLESRITVFEFPNAF  180 (212)
T ss_dssp             EEEEEECHHHHHHHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHTSCEEEECCSCC
T ss_pred             EEEECCCchhHHHHHHHHHHHhCCCcccHHHhhcCccccCCCCEEEecCCCcccccchhhhhhhEEEEEcCCCC
Confidence            4789998422112 345677776532             1358999999853   34 8999999999998443

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=95.79  E-value=0.018  Score=40.33  Aligned_cols=64  Identities=25%  Similarity=0.301  Sum_probs=48.0

Q ss_pred             Cccccc---CcCCHHHHHHHHHHHHhccCCceEEEEeC--CCCCc-hhhhhc--ceeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEA---DKLSTDALLYMRWLLERYKGLNKVFFCCS--DVSKL-QPIKSL--CTVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEi---d~l~~~~~~~L~~~le~~~~~~~~Il~~n--~~~~i-~~l~SR--c~~i~~~~~~~~~i~~~l~~   66 (137)
                      +++||+   ..++...++.+...+++  .++.+|+++.  +...+ ..+.+|  |.++.|.+.+.+++...+.+
T Consensus       103 lilDEigp~~~ld~~~~~~l~~~l~~--~~~~~i~~~H~~h~~~~~~~i~~r~~~~i~~~~~~~r~~~~~~l~~  174 (178)
T 1ye8_A          103 IIIDEIGKMELFSKKFRDLVRQIMHD--PNVNVVATIPIRDVHPLVKEIRRLPGAVLIELTPENRDVILEDILS  174 (178)
T ss_dssp             EEECCCSTTGGGCHHHHHHHHHHHTC--TTSEEEEECCSSCCSHHHHHHHTCTTCEEEECCTTTTTTHHHHHHH
T ss_pred             EEEeCCCCcccCCHHHHHHHHHHHhc--CCCeEEEEEccCCCchHHHHHHhcCCcEEEEecCcCHHHHHHHHHH
Confidence            478995   45678889999999985  3444777773  34445 889999  89999999988777666543

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=94.31  E-value=0.03  Score=39.33  Aligned_cols=53  Identities=23%  Similarity=0.239  Sum_probs=39.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCC------Cc-hhhhhcc-eeeEecCCC
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVS------KL-QPIKSLC-TVIQLLPPS   56 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~------~i-~~l~SRc-~~i~~~~~~   56 (137)
                      |+|||++.++++....|..+.++   +.++++++...+      .. +.|.+++ .+.+++...
T Consensus        80 viIDE~Q~~~~~~~~~l~~l~~~---~~~Vi~~Gl~~~f~~~~f~~~~~ll~~ad~v~~l~~ic  140 (184)
T 2orw_A           80 VFIDEVQFFNPSLFEVVKDLLDR---GIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKKAVC  140 (184)
T ss_dssp             EEECCGGGSCTTHHHHHHHHHHT---TCEEEEEEESBCTTSCBCHHHHHHHHHCSEEEECCBCC
T ss_pred             EEEECcccCCHHHHHHHHHHHHC---CCCEEEEeeccccccCCccchHHHHHHhhheEEeeeec
Confidence            58999999988888888888873   778888876443      34 7788888 455665543

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

Probab=94.17  E-value=0.079  Score=50.92  Aligned_cols=70  Identities=16%  Similarity=0.275  Sum_probs=53.6

Q ss_pred             CcccccCcCCHH------HHHHHHHHHHhcc------------CCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCC
Q 042716            1 IILCEADKLSTD------ALLYMRWLLERYK------------GLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPS   56 (137)
Q Consensus         1 iiiDEid~l~~~------~~~~L~~~le~~~------------~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~   56 (137)
                      +||||+|.-..+      ....|+..+|...            .++.||.+||.+.     .| +.+++||.++.++.|+
T Consensus      1340 lFiDEinmp~~d~yg~q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllRrf~vi~i~~P~ 1419 (2695)
T 4akg_A         1340 LFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYLGYPS 1419 (2695)
T ss_dssp             EEEETTTCSCCCSSSCCHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHTTEEEEECCCCT
T ss_pred             EEecccccccccccCchhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhheeeEEEeCCCC
Confidence            478998876433      5777888887310            1346788888774     48 9999999999999999


Q ss_pred             HHHHHHHHHHHHHH
Q 042716           57 KQEIVEVLEFIAEQ   70 (137)
Q Consensus        57 ~~~i~~~l~~i~~~   70 (137)
                      .+++..++..+...
T Consensus      1420 ~~~l~~I~~~il~~ 1433 (2695)
T 4akg_A         1420 GKSLSQIYEIYYKA 1433 (2695)
T ss_dssp             TTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999998887653

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=93.76  E-value=0.012  Score=42.18  Aligned_cols=55  Identities=15%  Similarity=0.149  Sum_probs=37.5

Q ss_pred             CcccccCcC--CH-HH--HHHHHHHHHhccC-CceEEEEeCCCCCc-hhhhhcce-eeEecCC
Q 042716            1 IILCEADKL--ST-DA--LLYMRWLLERYKG-LNKVFFCCSDVSKL-QPIKSLCT-VIQLLPP   55 (137)
Q Consensus         1 iiiDEid~l--~~-~~--~~~L~~~le~~~~-~~~~Il~~n~~~~i-~~l~SRc~-~i~~~~~   55 (137)
                      ++|||||.+  .. +.  ...++..++.... ...+||+++.+..+ .+|++|+. .++|.++
T Consensus        91 liIDEAq~l~~~~~~~~e~~rll~~l~~~r~~~~~iil~tq~~~~l~~~lr~ri~~~~~l~~~  153 (199)
T 2r2a_A           91 VIVDEAQDVWPARSAGSKIPENVQWLNTHRHQGIDIFVLTQGPKLLDQNLRTLVRKHYHIASN  153 (199)
T ss_dssp             EEETTGGGTSBCCCTTCCCCHHHHGGGGTTTTTCEEEEEESCGGGBCHHHHTTEEEEEEEEEC
T ss_pred             EEEEChhhhccCccccchhHHHHHHHHhcCcCCeEEEEECCCHHHHhHHHHHHhheEEEEcCc
Confidence            589999999  32 11  1134455554433 34589999998889 99999985 5777664

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=92.82  E-value=0.36  Score=37.35  Aligned_cols=83  Identities=13%  Similarity=0.206  Sum_probs=55.5

Q ss_pred             CcccccCcCC----HHHHHHHHHHHHhccC-CceEEEEeCCCCCc-h--------hhhhcceeeEecCCCHHHHHHHHHH
Q 042716            1 IILCEADKLS----TDALLYMRWLLERYKG-LNKVFFCCSDVSKL-Q--------PIKSLCTVIQLLPPSKQEIVEVLEF   66 (137)
Q Consensus         1 iiiDEid~l~----~~~~~~L~~~le~~~~-~~~~Il~~n~~~~i-~--------~l~SRc~~i~~~~~~~~~i~~~l~~   66 (137)
                      +++||+|.+.    +.....+...+.+..+ ++.++++|-++..+ .        ++.+.|...-|-+.+.+++.. +  
T Consensus       266 i~iDEa~~~~~~~~~~~~~~l~~~~~~~Rk~g~~~~~~tQ~~~d~~~~~~~~~~~~il~n~~~~i~l~~~~~~~~~-~--  342 (392)
T 4ag6_A          266 LVVDEAWMLVDPQTPQAIAFLRDTSKRIRKYNGSLIVISQNVIDFLAPEVQRYGQALLDNPTYKLLLAQGEKDLEA-I--  342 (392)
T ss_dssp             EEETTGGGGCCTTCTHHHHHHHHHHHHGGGGTCEEEEEESCGGGGGSTTTHHHHHHHHHSCSEEEECSCCHHHHHH-H--
T ss_pred             EEEecHHHHhCcCchHHHHHHHHHHHHhhhhCeEEEEEcCCHHHhhChhhHHHHHHHHHhhhhhheeCCChhhHHH-H--
Confidence            5799999996    3456667777766544 56688888877665 2        788999765555666665333 2  


Q ss_pred             HHHHcCCCCCHHHHHHHHHHcCC
Q 042716           67 IAEQEGIQLPHQLAEKIADNSKN   89 (137)
Q Consensus        67 i~~~egi~i~~~~l~~i~~~~~g   89 (137)
                       ++.  +.+++...+.|.....|
T Consensus       343 -~~~--~~ls~~e~~~l~~~~~G  362 (392)
T 4ag6_A          343 -TTL--MNLSEAEHDLLVNAKRG  362 (392)
T ss_dssp             -HHH--TTCCHHHHHHHHTCCTT
T ss_pred             -HHH--hCCCHHHHHhccCCCCc
Confidence             222  34788887777765555

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

Probab=92.64  E-value=0.35  Score=35.85  Aligned_cols=70  Identities=11%  Similarity=0.110  Sum_probs=45.2

Q ss_pred             CcccccCcCCHH-----------HHHHHHHHHHhcc-C-CceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHHHHH
Q 042716            1 IILCEADKLSTD-----------ALLYMRWLLERYK-G-LNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~~-----------~~~~L~~~le~~~-~-~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i~~~   63 (137)
                      +++||+|.+...           ..+.++..|.-.. . ...++.++|.+..+ ++++.  |+ ..+.|+.|+.++...+
T Consensus       107 ~~~Deid~~~~~r~~~~~~~~~~~~~~~l~~Lsgg~~~~~~i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~i  186 (274)
T 2x8a_A          107 IFFDEVDALCPRRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAI  186 (274)
T ss_dssp             EEEETCTTTCC---------CTTHHHHHHHHHHTCCSTTCEEEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHH
T ss_pred             EeeehhhhhhcccCCCcchHHHHHHHHHHHhhhcccccCCEEEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHH
Confidence            478999987421           1233344443211 1 22355566777778 88875  76 6789999999999999


Q ss_pred             HHHHHHH
Q 042716           64 LEFIAEQ   70 (137)
Q Consensus        64 l~~i~~~   70 (137)
                      ++..++.
T Consensus       187 l~~~~~~  193 (274)
T 2x8a_A          187 LKTITKN  193 (274)
T ss_dssp             HHHHTTT
T ss_pred             HHHHHhc
Confidence            9887654

>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=91.33  E-value=1.9  Score=41.75  Aligned_cols=98  Identities=19%  Similarity=0.161  Sum_probs=63.4

Q ss_pred             CcccccCcCCHHHHHHH-------HHHHHhc-------------cCCceEEEEeCCC----CCc-hhhhhcceeeEecCC
Q 042716            1 IILCEADKLSTDALLYM-------RWLLERY-------------KGLNKVFFCCSDV----SKL-QPIKSLCTVIQLLPP   55 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L-------~~~le~~-------------~~~~~~Il~~n~~----~~i-~~l~SRc~~i~~~~~   55 (137)
                      +++||++++..+...++       ...+.+.             ++++.+++|.|..    ..+ +.|++||..+.+..|
T Consensus       701 ~~~DE~nr~~~evLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy~g~~eLP~~Lk~~Fr~v~m~~P  780 (2695)
T 4akg_A          701 GCFDEFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKKSFREFSMKSP  780 (2695)
T ss_dssp             EEEETTTSSCHHHHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCSSSSCCCCHHHHTTEEEEECCCC
T ss_pred             eeehhhhhcChHHHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCccCcccccHHHHhheEEEEeeCC
Confidence            36899999999987776       3333222             1234456666632    348 899999999999999


Q ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHH-------------HcCCcHHHHHHHHHHH
Q 042716           56 SKQEIVEVLEFIAEQEGIQLPHQLAEKIAD-------------NSKNNLRQAIRSFEAS  101 (137)
Q Consensus        56 ~~~~i~~~l~~i~~~egi~i~~~~l~~i~~-------------~~~gd~R~aln~L~~~  101 (137)
                      +.+.+..++..   ..|+.........++.             +.+..+|.+...|..+
T Consensus       781 d~~~i~ei~l~---s~Gf~~a~~la~kiv~~~~l~~e~ls~q~hydfglRalksvL~~a  836 (2695)
T 4akg_A          781 QSGTIAEMILQ---IMGFEDSKSLASKIVHFLELLSSKCSSMNHYHFGLRTLKGVLRNC  836 (2695)
T ss_dssp             CHHHHHHHHHH---HHHCSSHHHHHHHHHHHHHHHHHHSCCCTTCCCSHHHHHHHHHHH
T ss_pred             CHHHHHHHHHH---hcCCCchHHHHHHHHHHHHHHHHHhCcCCcccccHHHHHHHHHHH
Confidence            99988877543   3566555444443332             1234677777666544

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=89.22  E-value=0.32  Score=34.08  Aligned_cols=45  Identities=20%  Similarity=0.269  Sum_probs=28.9

Q ss_pred             CcccccCcCC--HHHHHHHHHHHHhccCCceEEEEeCCCC-Cchhhhh
Q 042716            1 IILCEADKLS--TDALLYMRWLLERYKGLNKVFFCCSDVS-KLQPIKS   45 (137)
Q Consensus         1 iiiDEid~l~--~~~~~~L~~~le~~~~~~~~Il~~n~~~-~i~~l~S   45 (137)
                      +|+||+|.+.  .+....+..++...+.+.++++.+..++ .+..+..
T Consensus       162 lViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~  209 (220)
T 1t6n_A          162 FILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCR  209 (220)
T ss_dssp             EEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHH
T ss_pred             EEEcCHHHHhcccCcHHHHHHHHHhCCCcCeEEEEEeecCHHHHHHHH
Confidence            5899999984  3455667777776666677666655544 4443433

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=88.69  E-value=2.2  Score=34.43  Aligned_cols=92  Identities=15%  Similarity=0.160  Sum_probs=56.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCchhhhhcceeeE-ecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQ-LLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i~~l~SRc~~i~-~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +++|+++..         ..++..+.++++|+||.+..-..........+. ..+++.++....+...+....-. .++.
T Consensus       240 LVLDdv~~~---------~~l~~l~~~~~ilvTsR~~~~~~~~~~~~~~v~~l~~L~~~ea~~L~~~~~~~~~~~-~~~~  309 (591)
T 1z6t_A          240 LILDDVWDS---------WVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKAD-LPEQ  309 (591)
T ss_dssp             EEEEEECCH---------HHHHTTCSSCEEEEEESCGGGGTTCCSCEEEEECCSSCCHHHHHHHHHHHHTSCGGG-SCTH
T ss_pred             EEEeCCCCH---------HHHHHhcCCCeEEEECCCcHHHHhcCCCceEeecCCCCCHHHHHHHHHHHhCCCccc-ccHH
Confidence            478888752         123334667889998887643222222222222 25899999999888766431111 1456


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      +..|++.++|.+-.+--+...+.
T Consensus       310 ~~~i~~~~~G~PLal~~~a~~l~  332 (591)
T 1z6t_A          310 AHSIIKECKGSPLVVSLIGALLR  332 (591)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCcHHHHHHHHHHh
Confidence            78999999998876655544443

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=88.61  E-value=0.18  Score=34.95  Aligned_cols=37  Identities=11%  Similarity=-0.076  Sum_probs=23.3

Q ss_pred             CcccccCcCCHH--HHHHHH-HHHHhc-cCCceEEEEeCCC
Q 042716            1 IILCEADKLSTD--ALLYMR-WLLERY-KGLNKVFFCCSDV   37 (137)
Q Consensus         1 iiiDEid~l~~~--~~~~L~-~~le~~-~~~~~~Il~~n~~   37 (137)
                      ++|||++.....  .+..++ .+++.. ..+.++|++||..
T Consensus       119 lilDei~~~~~~~~~~~~ll~~~l~~~~~~~~~~i~tsn~~  159 (202)
T 2w58_A          119 LMLDDLGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNFD  159 (202)
T ss_dssp             EEEEEECCC---CCGGGTTHHHHHHHHHHTTCCEEEEESSC
T ss_pred             EEEcCCCCCcCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCC
Confidence            589999775443  355344 466543 4567899999965

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=87.46  E-value=0.67  Score=37.54  Aligned_cols=87  Identities=13%  Similarity=0.105  Sum_probs=53.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCchhhhhcceeeEecCCCHHHHHHHHHHHHHHcCC-CCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGI-QLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi-~i~~~~   79 (137)
                      |++|+++....-   .+.   .  ..++++|+||.+..-..........+++++++.++....+...+..... .-.++.
T Consensus       247 lVLDdv~~~~~~---~~~---~--~~gs~ilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~  318 (549)
T 2a5y_B          247 FVFDDVVQEETI---RWA---Q--ELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDV  318 (549)
T ss_dssp             EEEEEECCHHHH---HHH---H--HTTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHH
T ss_pred             EEEECCCCchhh---ccc---c--cCCCEEEEEcCCHHHHHHcCCCCeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHH
Confidence            478888873221   222   1  1577888888764322322223357999999999999888775422211 111345


Q ss_pred             HHHHHHHcCCcHHHHH
Q 042716           80 AEKIADNSKNNLRQAI   95 (137)
Q Consensus        80 l~~i~~~~~gd~R~al   95 (137)
                      ...|++.|+|-+-.+.
T Consensus       319 ~~~I~~~c~GlPLAl~  334 (549)
T 2a5y_B          319 LNKTIELSSGNPATLM  334 (549)
T ss_dssp             HHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHhCCChHHHH
Confidence            7789999999775544

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=85.83  E-value=0.27  Score=33.99  Aligned_cols=38  Identities=24%  Similarity=0.305  Sum_probs=25.5

Q ss_pred             CcccccCcCCH-HHHHHHHHHHHhccCCceEEEEeCCCC
Q 042716            1 IILCEADKLST-DALLYMRWLLERYKGLNKVFFCCSDVS   38 (137)
Q Consensus         1 iiiDEid~l~~-~~~~~L~~~le~~~~~~~~Il~~n~~~   38 (137)
                      +|+||+|.+.. +....+..++...+.+.++++.+...+
T Consensus       150 lViDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~  188 (206)
T 1vec_A          150 IVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFP  188 (206)
T ss_dssp             EEEETHHHHTSTTTHHHHHHHHHHSCTTCEEEEEESCCC
T ss_pred             EEEEChHHhHhhCcHHHHHHHHHhCCccceEEEEEeeCC
Confidence            58999998754 345566777776666677666555544

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=85.73  E-value=6.8  Score=34.00  Aligned_cols=87  Identities=15%  Similarity=0.206  Sum_probs=56.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCchhhhhcceeeEecC-CCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLP-PSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i~~l~SRc~~i~~~~-~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +|||+++..         ..++....++++|+||.+..-..........+++.+ ++.++....+...+....-.. ++.
T Consensus       240 lvlDd~~~~---------~~~~~~~~~~~ilvTtR~~~~~~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~~-~~~  309 (1249)
T 3sfz_A          240 LILDDVWDP---------WVLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDL-PAE  309 (1249)
T ss_dssp             EEEESCCCH---------HHHTTTCSSCEEEEEESSTTTTTTCCSCBCCEECCSSCCHHHHHHHHHHHHTSCSTTC-CTH
T ss_pred             EEEecCCCH---------HHHHhhcCCCEEEEEcCCHHHHHhhcCCceEEEecCCCCHHHHHHHHHHhhCCChhhC-cHH
Confidence            478888753         123334567889999887643233333446788886 999999998887664332222 346


Q ss_pred             HHHHHHHcCCcHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRS   97 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~   97 (137)
                      ...|++.++|-+-.+.-.
T Consensus       310 ~~~i~~~~~glPLal~~~  327 (1249)
T 3sfz_A          310 AHSIIKECKGSPLVVSLI  327 (1249)
T ss_dssp             HHHHHHHTTTCHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHH
Confidence            788999999876544433

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=85.59  E-value=0.61  Score=33.30  Aligned_cols=37  Identities=14%  Similarity=0.262  Sum_probs=20.9

Q ss_pred             CcccccCcCCHHH--H-HHHHHHHHhccCCceEE-EEeCCCC
Q 042716            1 IILCEADKLSTDA--L-LYMRWLLERYKGLNKVF-FCCSDVS   38 (137)
Q Consensus         1 iiiDEid~l~~~~--~-~~L~~~le~~~~~~~~I-l~~n~~~   38 (137)
                      +||||+|.++-..  . ..+..++...+ +.+++ ++++-+.
T Consensus       180 lVlDEah~~~~~~~~~~~~l~~i~~~~~-~~~~il~SAT~~~  220 (235)
T 3llm_A          180 VIVDEIHERDINTDFLLVVLRDVVQAYP-EVRIVLMSATIDT  220 (235)
T ss_dssp             EEECCTTSCCHHHHHHHHHHHHHHHHCT-TSEEEEEECSSCC
T ss_pred             EEEECCccCCcchHHHHHHHHHHHhhCC-CCeEEEEecCCCH
Confidence            5899999964433  2 34555665544 45544 4444433

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=84.95  E-value=0.28  Score=37.01  Aligned_cols=37  Identities=14%  Similarity=0.022  Sum_probs=22.0

Q ss_pred             CcccccCcC--CHHHHHHH-HHHHHhc-cCCceEEEEeCCC
Q 042716            1 IILCEADKL--STDALLYM-RWLLERY-KGLNKVFFCCSDV   37 (137)
Q Consensus         1 iiiDEid~l--~~~~~~~L-~~~le~~-~~~~~~Il~~n~~   37 (137)
                      +||||++..  +...+..| ..+++.. ..+.++|++||.+
T Consensus       218 LiiDdig~~~~~~~~~~~ll~~ll~~r~~~~~~~IitSN~~  258 (308)
T 2qgz_A          218 LILDDIGAEQATSWVRDEVLQVILQYRMLEELPTFFTSNYS  258 (308)
T ss_dssp             EEEETCCC------CTTTTHHHHHHHHHHHTCCEEEEESSC
T ss_pred             EEEcCCCCCCCCHHHHHHHHHHHHHHHHHCCCcEEEECCCC
Confidence            589999654  43334434 3466643 3467899999954

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=84.80  E-value=6.6  Score=38.83  Aligned_cols=102  Identities=14%  Similarity=0.179  Sum_probs=68.0

Q ss_pred             CcccccCcCCHH------HHHHHHHHHHhc------------cCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCC
Q 042716            1 IILCEADKLSTD------ALLYMRWLLERY------------KGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPS   56 (137)
Q Consensus         1 iiiDEid~l~~~------~~~~L~~~le~~------------~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~   56 (137)
                      +||||++.-..+      ....|+-.++..            ..++.||.++|.+.     .+ +.+.+|+.++.+..|+
T Consensus      1378 lFiDDiNmp~~D~yGtQ~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp~~gGr~~l~~Rf~r~F~vi~i~~ps 1457 (3245)
T 3vkg_A         1378 VFCDEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLRHAPILLVDFPS 1457 (3245)
T ss_dssp             EEETTTTCCCCCTTSCCHHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECCTTSTTCCCCCHHHHTTCCEEECCCCC
T ss_pred             EEecccCCCCccccccccHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCCCCCCCccCCHHHHhhceEEEeCCCC
Confidence            468999876543      567788888742            12455788888763     38 9999999999999999


Q ss_pred             HHHHHHHHHHHHHHc-CC-----CCCHHHHHHHHH---------------HcCCcHHHHHHHHHHHH
Q 042716           57 KQEIVEVLEFIAEQE-GI-----QLPHQLAEKIAD---------------NSKNNLRQAIRSFEASR  102 (137)
Q Consensus        57 ~~~i~~~l~~i~~~e-gi-----~i~~~~l~~i~~---------------~~~gd~R~aln~L~~~~  102 (137)
                      .+++..+...+...- +.     .+.+..+...++               +.--++|.+.+.+|.+.
T Consensus      1458 ~esL~~If~til~~~l~~~p~l~~~~~~lv~ati~ly~~v~~~~lp~~k~HY~FnLRDLsrv~qGll 1524 (3245)
T 3vkg_A         1458 TSSLTQIYGTFNRALMKLLPNLRSFADNLTDAMVEFYSESQKRFTPDIQAHYIYSPRELSRWDRALL 1524 (3245)
T ss_dssp             HHHHHHHHHHHHHHHTTSCGGGTTSHHHHHHHHHHHHHHHHHHSCTTTSTTCCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCccccHHHHHHHHHHHH
Confidence            999888876654421 10     112333333332               34458888888888654

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=84.46  E-value=0.3  Score=33.75  Aligned_cols=39  Identities=15%  Similarity=0.128  Sum_probs=25.7

Q ss_pred             CcccccCcCCHHH-HHHHHHHHHhccCCceEEEEeCCCCC
Q 042716            1 IILCEADKLSTDA-LLYMRWLLERYKGLNKVFFCCSDVSK   39 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~L~~~le~~~~~~~~Il~~n~~~~   39 (137)
                      +|+||+|.+.... ...+..++...+.+.++++.+...+.
T Consensus       148 iViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~  187 (207)
T 2gxq_A          148 AVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPS  187 (207)
T ss_dssp             EEEESHHHHHHTTCHHHHHHHHHTSCTTSEEEEECSSCCH
T ss_pred             EEEEChhHhhccchHHHHHHHHHhCCccCeEEEEEEecCH
Confidence            5899999885443 45566677666666776666655543

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=84.24  E-value=0.34  Score=33.97  Aligned_cols=45  Identities=13%  Similarity=0.190  Sum_probs=28.0

Q ss_pred             CcccccCcCCHHH-HHHHHHHHHhccCCceEEEEeCCCC-Cchhhhh
Q 042716            1 IILCEADKLSTDA-LLYMRWLLERYKGLNKVFFCCSDVS-KLQPIKS   45 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~L~~~le~~~~~~~~Il~~n~~~-~i~~l~S   45 (137)
                      +|+||+|.+.... ...+..++...+.+.++++.+...+ .+..+.+
T Consensus       159 iViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~lSAT~~~~~~~~~~  205 (224)
T 1qde_A          159 FILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTT  205 (224)
T ss_dssp             EEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHH
T ss_pred             EEEcChhHHhhhhhHHHHHHHHHhCCccCeEEEEEeecCHHHHHHHH
Confidence            5899999986543 4456777776666776666555444 3433333

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=84.07  E-value=0.72  Score=33.78  Aligned_cols=34  Identities=6%  Similarity=-0.013  Sum_probs=22.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCC
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDV   37 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~   37 (137)
                      +|+||+|.+...   .+..++.......++++.|-.+
T Consensus       229 vIiDEaH~~~~~---~~~~il~~~~~~~~~l~lSATp  262 (282)
T 1rif_A          229 MMNDECHLATGK---SISSIISGLNNCMFKFGLSGSL  262 (282)
T ss_dssp             EEEETGGGCCHH---HHHHHTTTCTTCCEEEEECSSC
T ss_pred             EEEECCccCCcc---cHHHHHHHhhcCCeEEEEeCCC
Confidence            589999999965   5556666554455655555444

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=83.41  E-value=0.38  Score=34.15  Aligned_cols=38  Identities=16%  Similarity=0.204  Sum_probs=25.4

Q ss_pred             CcccccCcCCHHH-HHHHHHHHHhccCCceEEEEeCCCC
Q 042716            1 IILCEADKLSTDA-LLYMRWLLERYKGLNKVFFCCSDVS   38 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~L~~~le~~~~~~~~Il~~n~~~   38 (137)
                      +++||+|.+.... ...+..+++..+...++++.+...+
T Consensus       175 lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~  213 (236)
T 2pl3_A          175 LVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQT  213 (236)
T ss_dssp             EEETTHHHHHHTTTHHHHHHHHHTSCTTSEEEEEESSCC
T ss_pred             EEEeChHHHhcCCcHHHHHHHHHhCCCCCeEEEEEeeCC
Confidence            5899999885433 5567777777666776555554443

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=82.80  E-value=0.44  Score=33.61  Aligned_cols=38  Identities=16%  Similarity=0.140  Sum_probs=25.4

Q ss_pred             CcccccCcCCHHH-HHHHHHHHHhccCCceEEEEeCCCC
Q 042716            1 IILCEADKLSTDA-LLYMRWLLERYKGLNKVFFCCSDVS   38 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~L~~~le~~~~~~~~Il~~n~~~   38 (137)
                      +|+||+|.+.... ...+..++...+.+.++++.+...+
T Consensus       171 lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~  209 (228)
T 3iuy_A          171 LVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWP  209 (228)
T ss_dssp             EEECCHHHHHHTTCHHHHHHHHHHSCSSCEEEEEESCCC
T ss_pred             EEEECHHHHhccchHHHHHHHHHhCCcCCeEEEEEeeCC
Confidence            5899999986543 5556677777666777666554443

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=82.63  E-value=0.42  Score=33.54  Aligned_cols=45  Identities=16%  Similarity=0.225  Sum_probs=27.7

Q ss_pred             CcccccCcCCHHH-HHHHHHHHHhccCCceEEEEeCCC-CCchhhhh
Q 042716            1 IILCEADKLSTDA-LLYMRWLLERYKGLNKVFFCCSDV-SKLQPIKS   45 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~L~~~le~~~~~~~~Il~~n~~-~~i~~l~S   45 (137)
                      +++||+|.+.... ...+..+++..+.+.++++.+... ..+..+..
T Consensus       154 lViDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~  200 (219)
T 1q0u_A          154 LVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLK  200 (219)
T ss_dssp             EEECSHHHHHHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHH
T ss_pred             EEEcCchHHhhhChHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHH
Confidence            5899999986543 455677777666666655554444 44533333

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=81.31  E-value=0.73  Score=34.42  Aligned_cols=38  Identities=11%  Similarity=0.032  Sum_probs=26.0

Q ss_pred             CcccccCcCCH--HHHHHHHHHHHhccCCceEEEEeCCCC
Q 042716            1 IILCEADKLST--DALLYMRWLLERYKGLNKVFFCCSDVS   38 (137)
Q Consensus         1 iiiDEid~l~~--~~~~~L~~~le~~~~~~~~Il~~n~~~   38 (137)
                      +||||+|.|..  +....+..++...+.++.+++.+...+
T Consensus       239 lVlDEad~l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~  278 (300)
T 3fmo_B          239 FVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFE  278 (300)
T ss_dssp             EEETTHHHHHHSTTHHHHHHHHHTTSCTTCEEEEEESCCC
T ss_pred             EEEeCHHHHhhccCcHHHHHHHHHhCCCCCEEEEEeccCC
Confidence            58999999864  445556677776666777666655444

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=80.62  E-value=0.53  Score=33.60  Aligned_cols=38  Identities=13%  Similarity=0.182  Sum_probs=25.2

Q ss_pred             CcccccCcCCHHH-HHHHHHHHHhccCCceEEEEeCCCC
Q 042716            1 IILCEADKLSTDA-LLYMRWLLERYKGLNKVFFCCSDVS   38 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~L~~~le~~~~~~~~Il~~n~~~   38 (137)
                      +|+||+|.+.... ...+..++...+.+.++++.+...+
T Consensus       177 lViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT~~  215 (237)
T 3bor_A          177 FVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMP  215 (237)
T ss_dssp             EEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCC
T ss_pred             EEECCchHhhccCcHHHHHHHHHhCCCCCeEEEEEEecC
Confidence            5899999885432 4456667776666777666655544

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=80.28  E-value=0.65  Score=37.75  Aligned_cols=37  Identities=19%  Similarity=0.165  Sum_probs=19.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCC
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDV   37 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~   37 (137)
                      ||+||+|++.......+..+++..+....+.|+++..
T Consensus       306 vIiDEaH~~~~~~~~~~~~il~~~~~~~~l~lTATP~  342 (590)
T 3h1t_A          306 IIIDECHRGSARDNSNWREILEYFEPAFQIGMTATPL  342 (590)
T ss_dssp             EEESCCC---------CHHHHHHSTTSEEEEEESSCS
T ss_pred             EEEECCccccccchHHHHHHHHhCCcceEEEeccccc
Confidence            5899999997765566777777766555566666643

---

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	137
d1njfa_	239	c.37.1.20 (A:) delta prime subunit of DNA polymera	4e-07
d1iqpa2	231	c.37.1.20 (A:2-232) Replication factor C {Archaeon	9e-05
d1sxjd2	237	c.37.1.20 (D:26-262) Replication factor C2 {Baker'	0.002
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	0.004

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 239

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]

 Score = 45.1 bits (106), Expect = 4e-07
 Identities = 23/100 (23%), Positives = 39/100 (39%), Gaps = 1/100 (1%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
            ++ E   LS  +   +   LE      K     +D  KL   I S C    L     ++
Sbjct: 119 YLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQ 178

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFE 99
           I   LE I  +E I    +  + +A  ++ +LR A+   +
Sbjct: 179 IRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTD 218

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 231

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]

 Score = 38.4 bits (88), Expect = 9e-05
 Identities = 31/106 (29%), Positives = 59/106 (55%), Gaps = 1/106 (0%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
           I L EAD L+ DA   +R  +E +    +    C+  SK+ +PI+S C + +  P   ++
Sbjct: 113 IFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDED 172

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMN 105
           I + L +IAE EG++L  +  + I   ++ ++R+AI   +A+  ++
Sbjct: 173 IAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALD 218

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 237

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]

 Score = 34.7 bits (78), Expect = 0.002
 Identities = 31/115 (26%), Positives = 59/115 (51%), Gaps = 1/115 (0%)

Query: 1   IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQP-IKSLCTVIQLLPPSKQE 59
           IIL EAD ++ DA   +R  +E Y G+ +    C+ V+++   + S C+  +        
Sbjct: 112 IILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASN 171

Query: 60  IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVI 114
            ++ L FI+EQE ++    + E+I D S  +LR+ I   +++ +      +G+ I
Sbjct: 172 AIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNI 226

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 253

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]

 Score = 33.6 bits (75), Expect = 0.004
 Identities = 19/98 (19%), Positives = 37/98 (37%), Gaps = 2/98 (2%)

Query: 27  LNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADN 86
              +     ++ K++P   +C  IQ   P    I   L  IA +E  +L   + +++   
Sbjct: 156 PLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQT 215

Query: 87  SKNNLRQAIRSFEASRQMNYPFVEGQV--ILTGWEDDI 122
           ++ ++RQ I                 +  I   WE +I
Sbjct: 216 TRGDIRQVINLLSTISTTTKTINHENINEISKAWEKNI 253

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	137
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.93
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.91
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.9
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.89
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.89
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.88
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.87
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.77
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.72
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.63
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.62
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.23
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.66
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.59
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.46
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	98.34
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.22
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.06
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.99
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.93
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.8
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.74
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	97.71
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.47
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.28
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	97.16
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.38
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	96.33
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	95.91
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	94.83
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	93.25
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	88.78
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	86.67
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	86.54
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	85.96
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	85.48
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	85.02
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	84.96
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	84.76
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	83.31
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	81.41
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	81.11

>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=99.93  E-value=3.1e-26  Score=168.92  Aligned_cols=105  Identities=22%  Similarity=0.224  Sum_probs=100.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.++|++|+++||+|+.+++||++||+.+++ ++|+|||..++|++|+.+++.+++.+++++||+.+++++
T Consensus       119 iiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~~~i~~~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~~~~~~~  198 (239)
T d1njfa_         119 YLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRA  198 (239)
T ss_dssp             EEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHH
T ss_pred             EEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCCccccChhHhhhhcccccccCcHHHhhhHHHHHHhhhccCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcC
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMN  105 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~  105 (137)
                      ++.++..++||+|+|+|+|+.+...+
T Consensus       199 l~~i~~~s~Gd~R~ain~l~~~~~~~  224 (239)
T d1njfa_         199 LQLLARAAEGSLRDALSLTDQAIASG  224 (239)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhC
Confidence            99999999999999999998765443

>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=99.91  E-value=6.5e-25  Score=159.74  Aligned_cols=109  Identities=23%  Similarity=0.393  Sum_probs=103.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+..+|++|++.+|+++.+++|+++|++..++ ++|+|||..++|++|+.+++.++|..++++||+.+++++
T Consensus       105 iiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~~~~~~~~~i~~~l~~i~~~e~~~i~~~~  184 (224)
T d1sxjb2         105 VILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDG  184 (224)
T ss_dssp             EEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHH
T ss_pred             EEEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHHHhhhcccchhhhHHHHHHHHHhcccCCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFV  109 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~  109 (137)
                      ++.|++.++||+|.|++.||.+......++
T Consensus       185 l~~I~~~s~Gd~R~ai~~Lq~~~~~~~~i~  214 (224)
T d1sxjb2         185 LEAIIFTAEGDMRQAINNLQSTVAGHGLVN  214 (224)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHSSBC
T ss_pred             HHHHHHHcCCcHHHHHHHHHHHHHcCCCcC
Confidence            999999999999999999998875544444

>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=99.90  E-value=1.1e-24  Score=157.96  Aligned_cols=94  Identities=19%  Similarity=0.229  Sum_probs=89.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+.++|++|+++||+|+.++.|||+|++++++ +||+|||+.++|.+|+.+++..+|+     +++.+++++
T Consensus       112 iIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~tI~SRc~~i~~~~~~~~~~~~~L~-----~~~~~~~~~  186 (207)
T d1a5ta2         112 VWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLS-----REVTMSQDA  186 (207)
T ss_dssp             EEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHH-----HHCCCCHHH
T ss_pred             EEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChhhhhhhhcceeEEEecCCCCHHHHHHHHH-----HcCCCCHHH
Confidence            5899999999999999999999999999999999999999 9999999999999999999999985     467789999


Q ss_pred             HHHHHHHcCCcHHHHHHHHH
Q 042716           80 AEKIADNSKNNLRQAIRSFE   99 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~   99 (137)
                      +..+++.++||+|.|+++||
T Consensus       187 ~~~i~~~s~Gs~r~al~~le  206 (207)
T d1a5ta2         187 LLAALRLSAGSPGAALALFQ  206 (207)
T ss_dssp             HHHHHHHTTTCHHHHHHTTS
T ss_pred             HHHHHHHcCCCHHHHHHHhC
Confidence            99999999999999999886

>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=99.89  E-value=1.4e-23  Score=152.49  Aligned_cols=104  Identities=21%  Similarity=0.357  Sum_probs=100.4

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      ++|||+|.++..+|++|++++|+++.++.|+++||.+.++ ++|+|||..++|++|+.+++.++|.+++.+||+.+++++
T Consensus       103 iiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~~~~~~~~i~~~l~~I~~~e~i~i~~~~  182 (227)
T d1sxjc2         103 IILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNA  182 (227)
T ss_dssp             EEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTCCBCHHH
T ss_pred             EEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhhhccccccccccccccccccccccccCCHHH
Confidence            5899999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM  104 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~  104 (137)
                      ++.|++.++||+|.|+|.||.+...
T Consensus       183 l~~i~~~s~Gd~R~ain~Lq~~~~~  207 (227)
T d1sxjc2         183 EKALIELSNGDMRRVLNVLQSCKAT  207 (227)
T ss_dssp             HHHHHHHHTTCHHHHHHHTTTTTTT
T ss_pred             HHHHHHHcCCcHHHHHHHHHHHHHh
Confidence            9999999999999999999987643

>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=99.89  E-value=2.2e-23  Score=152.82  Aligned_cols=106  Identities=32%  Similarity=0.506  Sum_probs=99.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCC-HH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLP-HQ   78 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~-~~   78 (137)
                      ++|||+|.|+.++++.|++++|+++.+++||++||+..++ ++|+|||..++|++|+.+++.++|..++.+||+.++ ++
T Consensus       135 iiide~d~l~~~~~~~l~~~~e~~~~~~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~~~~~~~  214 (252)
T d1sxje2         135 VIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKD  214 (252)
T ss_dssp             EEEECTTSSCHHHHHHHHHHHHHSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSH
T ss_pred             EEeccccccccccchhhhcccccccccccceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCCCCCcHH
Confidence            4789999999999999999999999999999999999999 999999999999999999999999999999999885 67


Q ss_pred             HHHHHHHHcCCcHHHHHHHHHHHHhcCC
Q 042716           79 LAEKIADNSKNNLRQAIRSFEASRQMNY  106 (137)
Q Consensus        79 ~l~~i~~~~~gd~R~aln~L~~~~~~~~  106 (137)
                      +++.|+..++||+|+|+|.||.+...+.
T Consensus       215 ~l~~i~~~s~Gd~R~ai~~Lq~~~~~~~  242 (252)
T d1sxje2         215 ILKRIAQASNGNLRVSLLMLESMALNNE  242 (252)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHTHHHHTTT
T ss_pred             HHHHHHHHcCCcHHHHHHHHHHHHHcCC
Confidence            8899999999999999999998886543

>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=99.88  E-value=5.9e-23  Score=149.30  Aligned_cols=104  Identities=29%  Similarity=0.527  Sum_probs=99.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +||||+|.|+..+++++++++++++.++.||++++...++ ++|+|||..++|++|+.+++.++|..++++||+.+++++
T Consensus       112 iiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i~f~~~~~~~~~~~L~~i~~~e~i~i~~~~  191 (237)
T d1sxjd2         112 IILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENVKCDDGV  191 (237)
T ss_dssp             EEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHH
T ss_pred             EEEecccccCHHHHHHHhhccccccccccccccccccccccccccchhhhhccccccccccchhhhhhhhhhcCcCCHHH
Confidence            5899999999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQM  104 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~  104 (137)
                      ++.|++.++||+|.|+|.||.+...
T Consensus       192 l~~ia~~s~gd~R~ai~~L~~~~~~  216 (237)
T d1sxjd2         192 LERILDISAGDLRRGITLLQSASKG  216 (237)
T ss_dssp             HHHHHHHTSSCHHHHHHHHHHTHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHh
Confidence            9999999999999999999987543

>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=99.87  E-value=1.7e-22  Score=147.13  Aligned_cols=113  Identities=28%  Similarity=0.502  Sum_probs=105.6

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~~~   79 (137)
                      +++||+|.+....+++|+++++++..++.||++||..+++ ++|+|||..+.|.+++.+++..+|..+++++|+++++++
T Consensus       113 ilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~e~i~i~~~~  192 (231)
T d1iqpa2         113 IFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEG  192 (231)
T ss_dssp             EEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTTCEECHHH
T ss_pred             EeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccccccccccchhhHHHHHHHHHHHhCCCCCHHH
Confidence            5789999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHHhcCCCcccCcc
Q 042716           80 AEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQV  113 (137)
Q Consensus        80 l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~~~  113 (137)
                      ++.|++.++||+|.|+|.||.+...+..++.+.+
T Consensus       193 l~~I~~~~~gdiR~ai~~Lq~~~~~~~~it~e~v  226 (231)
T d1iqpa2         193 LQAILYIAEGDMRRAINILQAAAALDKKITDENV  226 (231)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTCSEECHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHcCCCcCHHHH
Confidence            9999999999999999999998876655654433

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.77  E-value=9.3e-20  Score=131.18  Aligned_cols=102  Identities=14%  Similarity=0.143  Sum_probs=73.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCc-hhhhhcceeeEecCCCHHH--HHHHHHHHHHH-----cC
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE--IVEVLEFIAEQ-----EG   72 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~SRc~~i~~~~~~~~~--i~~~l~~i~~~-----eg   72 (137)
                      +||||+|+|+.++|++|+++||+|++++.|||+|+++.++ +||+|||+.++|++|++..  ....+....+.     .+
T Consensus        83 iIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~TI~SRC~~i~~~~p~~~~~~~~~~~~~~~~~~~~~~~~  162 (198)
T d2gnoa2          83 VIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVPKEFRDLVKEKIGDLWEELPLLERD  162 (198)
T ss_dssp             EEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCHHHHHHHHHHHTTHHHHCGGGGTC
T ss_pred             EEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChhhCHHHHhcceEEEeCCCchHHHHHHHHHHHHHHHHHHHHhcc
Confidence            5899999999999999999999999999999999999999 9999999999998776432  11111111111     12


Q ss_pred             CCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           73 IQLPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        73 i~i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      .....+++..+++...| +|.++++++....
T Consensus       163 ~~~~~~~~~~~~~~~~~-~~~~l~~ld~~~~  192 (198)
T d2gnoa2         163 FKTALEAYKLGAEKLSG-LMESLKVLETEKL  192 (198)
T ss_dssp             HHHHHHHHHHHHHHHHH-HHHHHHHSCHHHH
T ss_pred             ccCCHHHHHHHHHHhhC-HHHHHHHHHHHHH
Confidence            22233444555555544 7777777665554

>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=99.72  E-value=6.8e-18  Score=123.37  Aligned_cols=111  Identities=20%  Similarity=0.282  Sum_probs=97.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc-cCCceEEEEeCCCCC-c-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcCCCCCH
Q 042716            1 IILCEADKLSTDALLYMRWLLERY-KGLNKVFFCCSDVSK-L-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGIQLPH   77 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~-~~~~~~Il~~n~~~~-i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi~i~~   77 (137)
                      +++||+|.++..+++.+..+++.. ....+++++||+... . ++++|||..++|.+|+.+++..++..++.+||+.+++
T Consensus       127 i~ide~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~  206 (253)
T d1sxja2         127 IIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDP  206 (253)
T ss_dssp             EEECSGGGCCTTSTTHHHHHHHHHHHCSSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCT
T ss_pred             EEeeeccccccchhhhhHHHhhhhcccccccccccccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCCH
Confidence            479999999999988888887753 455678899887653 4 9999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCcHHHHHHHHHHHHhcCCCcccC
Q 042716           78 QLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEG  111 (137)
Q Consensus        78 ~~l~~i~~~~~gd~R~aln~L~~~~~~~~~~~~~  111 (137)
                      +++..|++.++||+|.+++.||++......++.+
T Consensus       207 ~~l~~i~~~s~GDiR~ai~~L~~~~~~~~~i~~~  240 (253)
T d1sxja2         207 NVIDRLIQTTRGDIRQVINLLSTISTTTKTINHE  240 (253)
T ss_dssp             THHHHHHHHTTTCHHHHHHHHTHHHHHSSCCCTT
T ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCCHH
Confidence            9999999999999999999999988766555543

>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=99.63  E-value=3.1e-15  Score=108.60  Aligned_cols=103  Identities=17%  Similarity=0.156  Sum_probs=93.3

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc------------------cCCceEEEEeCCCCCc--hhhhhcceeeEecCCCHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERY------------------KGLNKVFFCCSDVSKL--QPIKSLCTVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~------------------~~~~~~Il~~n~~~~i--~~l~SRc~~i~~~~~~~~~i   60 (137)
                      ++|||+|.+++..++.++..+|..                  .+++.|+++|++++..  +.++++|..++|.+|+.+++
T Consensus        91 ~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  170 (239)
T d1ixsb2          91 LFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEEL  170 (239)
T ss_dssp             EEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTTCCCEEEEECCCCEEEEEESCCSSCSCGGGGGCSEEEECCCCCHHHH
T ss_pred             eeeecccccchhHHHhhhhhhhhhhhhhhhccchhhhhcccCCCCEEEEeeccCcccccchhhcccceeeEeeccChhhh
Confidence            479999999999999999999863                  2345688889988775  88888999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~~  103 (137)
                      ..++..++.++++.++++.+..+++.++||+|.++|.|+.+..
T Consensus       171 ~~i~~~~~~~~~i~~~~~~l~~ia~~s~gd~R~a~~~l~~~~~  213 (239)
T d1ixsb2         171 AQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRD  213 (239)
T ss_dssp             HHHHHHHHGGGCCCBCHHHHHHHHHHTTSSHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHhCCccchHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999998763

>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=99.62  E-value=2.9e-15  Score=108.60  Aligned_cols=102  Identities=20%  Similarity=0.230  Sum_probs=93.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc------------------CCceEEEEeCCCCCc-hhhhhcce-eeEecCCCHHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK------------------GLNKVFFCCSDVSKL-QPIKSLCT-VIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~------------------~~~~~Il~~n~~~~i-~~l~SRc~-~i~~~~~~~~~i   60 (137)
                      +++||+|.+.+..+++++..+|...                  .++.||++||+...+ +++++||. ++.|++|+.+++
T Consensus        90 ~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~at~~~~~~~~~~~~r~~~~~~~~~~~~~~~  169 (238)
T d1in4a2          90 LFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKEL  169 (238)
T ss_dssp             EEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHH
T ss_pred             hHHHHHHHhhhHHHhhcccceeeeeeeeeecCcccccccccCCCCeEEEEecCCCccccccceeeeeEEEEecCCCHHHH
Confidence            4799999999999999999998753                  356799999999998 99999985 689999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      ..+++.++..+++.++++++..+++.++||+|.++|+|+.+.
T Consensus       170 ~~~l~~~~~~~~~~~~~~~l~~i~~~s~gd~R~ai~~l~~~~  211 (238)
T d1in4a2         170 KEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVR  211 (238)
T ss_dssp             HHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHhhhhccchhhHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999998664

>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=99.23  E-value=6.1e-11  Score=85.15  Aligned_cols=100  Identities=8%  Similarity=0.178  Sum_probs=83.3

Q ss_pred             CcccccCcCC--HHHHHHHHHHHHhcc-CCceEEEEeCCCCC----c-hhhhhcc---eeeEecCCCHHHHHHHHHHHHH
Q 042716            1 IILCEADKLS--TDALLYMRWLLERYK-GLNKVFFCCSDVSK----L-QPIKSLC---TVIQLLPPSKQEIVEVLEFIAE   69 (137)
Q Consensus         1 iiiDEid~l~--~~~~~~L~~~le~~~-~~~~~Il~~n~~~~----i-~~l~SRc---~~i~~~~~~~~~i~~~l~~i~~   69 (137)
                      ++|||+|.+.  +..+..|..+++... .+.++|++++.++.    + ++|+||+   .++.++ |++++..++|++.+.
T Consensus       101 l~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i~-p~d~~~~~iL~~~a~  179 (213)
T d1l8qa2         101 LLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIE-LDNKTRFKIIKEKLK  179 (213)
T ss_dssp             EEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECC-CCHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHHHhhCceEEEEC-CCcHHHHHHHHHHHH
Confidence            5899999995  566888999998744 66779999987753    5 8999996   688885 678889999999999


Q ss_pred             HcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH
Q 042716           70 QEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        70 ~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~~  102 (137)
                      .+|+.++++++.+|++++ +|+|.+...|..+.
T Consensus       180 ~rgl~l~~~v~~yl~~~~-~~~R~L~~~l~~l~  211 (213)
T d1l8qa2         180 EFNLELRKEVIDYLLENT-KNVREIEGKIKLIK  211 (213)
T ss_dssp             HTTCCCCHHHHHHHHHHC-SSHHHHHHHHHHHH
T ss_pred             HcCCCCCHHHHHHHHHhc-CcHHHHHHHHHHhh
Confidence            999999999999999998 57887777666554

>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=98.66  E-value=5.1e-08  Score=70.06  Aligned_cols=102  Identities=21%  Similarity=0.173  Sum_probs=79.0

Q ss_pred             cccccCcC------CHHHHHHHHHHHHhcc-----CCceEEEEeCCCCC------c-hhhhhc-ceeeEecCCCHHHHHH
Q 042716            2 ILCEADKL------STDALLYMRWLLERYK-----GLNKVFFCCSDVSK------L-QPIKSL-CTVIQLLPPSKQEIVE   62 (137)
Q Consensus         2 iiDEid~l------~~~~~~~L~~~le~~~-----~~~~~Il~~n~~~~------i-~~l~SR-c~~i~~~~~~~~~i~~   62 (137)
                      ++||+|.+      ..+....|..+++...     ....+|++++....      . +.+++| +..+.|++++.+++..
T Consensus       137 iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~  216 (287)
T d1w5sa2         137 ILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYT  216 (287)
T ss_dssp             EEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHH
T ss_pred             ceeEEEEeccccccchhHHHHHHHHHHhcchhhcccceeEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHH
Confidence            56777766      4556777777777643     34558888876642      3 577776 6899999999999999


Q ss_pred             HHHHHHHHcCC--CCCHHHHHHHHHHc------CCcHHHHHHHHHHHHh
Q 042716           63 VLEFIAEQEGI--QLPHQLAEKIADNS------KNNLRQAIRSFEASRQ  103 (137)
Q Consensus        63 ~l~~i~~~egi--~i~~~~l~~i~~~~------~gd~R~aln~L~~~~~  103 (137)
                      +++..++..+.  .++++++..+++.+      .||+|.|+++|+.+..
T Consensus       217 Il~~r~~~~~~~~~~~~~al~~ia~~~~~~~~~~gd~R~ai~~l~~a~~  265 (287)
T d1w5sa2         217 ILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACE  265 (287)
T ss_dssp             HHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHHH
T ss_pred             HHhhhHHHhhccCCCCHHHHHHHHHHHhccccCCCCHHHHHHHHHHHHH
Confidence            99998876544  48999999999865      7999999999987653

>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=98.59  E-value=2.2e-07  Score=66.28  Aligned_cols=102  Identities=21%  Similarity=0.179  Sum_probs=80.2

Q ss_pred             cccccCcCCHHHHHHHHHHHHhc----cCCceEEEEeCCCC---Cc-hhhhhcc--eeeEecCCCHHHHHHHHHHHHHHc
Q 042716            2 ILCEADKLSTDALLYMRWLLERY----KGLNKVFFCCSDVS---KL-QPIKSLC--TVIQLLPPSKQEIVEVLEFIAEQE   71 (137)
Q Consensus         2 iiDEid~l~~~~~~~L~~~le~~----~~~~~~Il~~n~~~---~i-~~l~SRc--~~i~~~~~~~~~i~~~l~~i~~~e   71 (137)
                      ++|++|.+....++.+...++..    .....+|++++...   .+ +.++||+  ..+.|.+++.+++..++.+.++..
T Consensus       129 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~~~~  208 (276)
T d1fnna2         129 VLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAG  208 (276)
T ss_dssp             EEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHH
T ss_pred             chhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchhhhhhcchhhhhhhcchhccccchhHHHHHHHHHHHHHHh
Confidence            57899999888877776665432    33456888888753   57 8999998  459999999999999999887763


Q ss_pred             --CCCCCHHHHHHHHHH---------cCCcHHHHHHHHHHHHh
Q 042716           72 --GIQLPHQLAEKIADN---------SKNNLRQAIRSFEASRQ  103 (137)
Q Consensus        72 --gi~i~~~~l~~i~~~---------~~gd~R~aln~L~~~~~  103 (137)
                        +..+++++++.++..         +.||+|.++++|+.+..
T Consensus       209 ~~~~~~~~~~l~~ia~~~~~~~~~~~~~G~~R~a~~ll~~a~~  251 (276)
T d1fnna2         209 LAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAY  251 (276)
T ss_dssp             BCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHH
T ss_pred             cccccccHHHHHHHHHHhhhhhhhhhcCCCHHHHHHHHHHHHH
Confidence              345899999999875         47999999999987654

>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=98.46  E-value=1.3e-07  Score=68.89  Aligned_cols=95  Identities=12%  Similarity=0.126  Sum_probs=69.2

Q ss_pred             CcccccCcCCHH--------------HHHHHHHHHHhccCC--ceEEEEeCCCCCc-hhhh--hcc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLSTD--------------ALLYMRWLLERYKGL--NKVFFCCSDVSKL-QPIK--SLC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~--------------~~~~L~~~le~~~~~--~~~Il~~n~~~~i-~~l~--SRc-~~i~~~~~~~~~i   60 (137)
                      |+|||+|.+...              ..+.|+..|+....+  +.+|.+||++..+ ++++  +|+ ..+.|++|+.++.
T Consensus       105 i~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR  184 (247)
T d1ixza_         105 VFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGR  184 (247)
T ss_dssp             EEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHH
T ss_pred             EEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHH
Confidence            579999987221              245677778755443  3466789999999 9897  577 5899999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCC----cHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKN----NLRQAIR   96 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~g----d~R~aln   96 (137)
                      ...++..+.+.+.. .+..+..+++.+.|    |++.+++
T Consensus       185 ~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~lv~  223 (247)
T d1ixza_         185 EQILRIHARGKPLA-EDVDLALLAKRTPGFVGADLENLLN  223 (247)
T ss_dssp             HHHHHHHHTTSCBC-TTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             HHHHHHHhcccCCc-cccCHHHHHHHCCCCCHHHHHHHHH
Confidence            99999888766543 33347788888776    6666655

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.34  E-value=3.3e-06  Score=61.15  Aligned_cols=106  Identities=14%  Similarity=0.150  Sum_probs=79.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC-------CCc-hhhhhcc--eeeEecCCCH--
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV-------SKL-QPIKSLC--TVIQLLPPSK--   57 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~-------~~i-~~l~SRc--~~i~~~~~~~--   57 (137)
                      ++|||+|.|+...|..|+..+++..           .++++|++++.+       ..+ +.|..|+  ..+.++|+.+  
T Consensus        98 L~l~~i~~L~~~~Q~~L~~~l~~~~~~~~~~~~~~~~~~RlI~~s~~~l~~l~~~~~f~~~L~~~l~~~~i~lPpLreR~  177 (247)
T d1ny5a2          98 LFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYRLGVIEIEIPPLRERK  177 (247)
T ss_dssp             EEEESGGGCCHHHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSCHHHHHHTTSSCHHHHHHHTTEEEECCCGGGCH
T ss_pred             EEEeChHhCCHHHHHHHHHHHHhCCEEECCCCCceecCeEEEEecCCCHHHHHHcCCCcHHHHhhcCeeeecCCChhhch
Confidence            4799999999999999999998532           256799998865       236 7888886  4567777753  


Q ss_pred             HHHHHHH----HHHHHHcCC---CCCHHHHHHHHHHc-CCcHHHHHHHHHHHHhcCC
Q 042716           58 QEIVEVL----EFIAEQEGI---QLPHQLAEKIADNS-KNNLRQAIRSFEASRQMNY  106 (137)
Q Consensus        58 ~~i~~~l----~~i~~~egi---~i~~~~l~~i~~~~-~gd~R~aln~L~~~~~~~~  106 (137)
                      +++...+    ...+.+.|.   .++++++..+..+. .||+|++-+.++.+...+.
T Consensus       178 ~Di~~l~~~~l~~~~~~~~~~~~~ls~~al~~L~~~~WPGNl~EL~~~l~~a~~~~~  234 (247)
T d1ny5a2         178 EDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELKNVIERAVLFSE  234 (247)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHHHHSCCTTHHHHHHHHHHHHHHHCC
T ss_pred             hhHhhhhhhhhhhhhhhcCCCCCCCCHHHHHHHHhCCCCCHHHHHHHHHHHHHHhCC
Confidence            5665444    445555554   37899999998874 8999999999998876553

>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=98.22  E-value=1.9e-06  Score=62.89  Aligned_cols=98  Identities=14%  Similarity=0.113  Sum_probs=68.1

Q ss_pred             CcccccCcCCH-----------H---HHHHHHHHHHhccC--CceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLST-----------D---ALLYMRWLLERYKG--LNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~-----------~---~~~~L~~~le~~~~--~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      ++|||+|.+..           .   ..+.|+..++....  ++.+|.+||++..+ ++++.  |+ ..+.|++|+.++.
T Consensus       108 l~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R  187 (256)
T d1lv7a_         108 IFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGR  187 (256)
T ss_dssp             EEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHH
T ss_pred             EEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHH
Confidence            47899998632           1   23557777775443  34577789999999 88873  77 6899999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCC-cHHHHHHHHH
Q 042716           61 VEVLEFIAEQEGIQLPHQLAEKIADNSKN-NLRQAIRSFE   99 (137)
Q Consensus        61 ~~~l~~i~~~egi~i~~~~l~~i~~~~~g-d~R~aln~L~   99 (137)
                      ..+++....+.++. ++..+..+++.++| ..+.+-++++
T Consensus       188 ~~il~~~l~~~~~~-~~~~~~~la~~t~G~s~adi~~l~~  226 (256)
T d1lv7a_         188 EQILKVHMRRVPLA-PDIDAAIIARGTPGFSGADLANLVN  226 (256)
T ss_dssp             HHHHHHHHTTSCBC-TTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             HHHHHHhccCCCcC-cccCHHHHHHhCCCCCHHHHHHHHH
Confidence            99998887666554 33456778877654 3333334443

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.06  E-value=1.3e-05  Score=58.81  Aligned_cols=101  Identities=14%  Similarity=0.186  Sum_probs=78.7

Q ss_pred             CcccccCcCC---------HHHHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCCHHHHHHHHH
Q 042716            1 IILCEADKLS---------TDALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPSKQEIVEVLE   65 (137)
Q Consensus         1 iiiDEid~l~---------~~~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~~~~i~~~l~   65 (137)
                      +||||+|.|.         ..+.+.|...+.  .+..++|.+|+...     .- ++|..|+..+++.+|+.++...+|.
T Consensus       114 lfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~--rg~i~vIgatT~eey~~~~e~d~al~rrF~~I~V~Eps~e~t~~IL~  191 (268)
T d1r6bx2         114 LFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIIN  191 (268)
T ss_dssp             EEETTTTTTTTSCCSSSCHHHHHHHHSSCSS--SCCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHHH
T ss_pred             EEecchHHHhcCCCCCCccccHHHHhhHHHh--CCCCeEEEeCCHHHHHHHHhhcHHHHhhhcccccCCCCHHHHHHHHH
Confidence            4799999993         234666666776  66788999887442     23 7899999999999999999999887


Q ss_pred             HHH----HHcCCCCCHHHHHHHHHHcC------CcHHHHHHHHHHHHh
Q 042716           66 FIA----EQEGIQLPHQLAEKIADNSK------NNLRQAIRSFEASRQ  103 (137)
Q Consensus        66 ~i~----~~egi~i~~~~l~~i~~~~~------gd~R~aln~L~~~~~  103 (137)
                      ...    ...++.++++++..+++.+.      .=+.+|+.+|+.+..
T Consensus       192 ~~~~~~e~~h~v~~~~~al~~~v~ls~ryi~~~~~PdKAIdllDea~a  239 (268)
T d1r6bx2         192 GLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGA  239 (268)
T ss_dssp             HHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHHHHHHH
T ss_pred             HhhHHHhccCCEEeChHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHH
Confidence            644    46789999999999887653      458899999986653

>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=97.99  E-value=7.2e-06  Score=59.45  Aligned_cols=95  Identities=13%  Similarity=0.189  Sum_probs=67.3

Q ss_pred             CcccccCcCCHHH-----------HHHHHHHHHhcc--CCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHHHHH
Q 042716            1 IILCEADKLSTDA-----------LLYMRWLLERYK--GLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~~~~-----------~~~L~~~le~~~--~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i~~~   63 (137)
                      ++|||+|.+....           ...++..++...  .++.+|.+||++..+ ++++.  |+ ..+.|+.|+.++...+
T Consensus       101 l~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~i  180 (258)
T d1e32a2         101 IFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEI  180 (258)
T ss_dssp             EEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHH
T ss_pred             EEehhhhhhccCCCCCCCchHHHHHHHhccccccccccCCccEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHH
Confidence            5799999995332           334444444332  334578889999999 99987  77 7899999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHcCC----cHHHHHH
Q 042716           64 LEFIAEQEGIQLPHQLAEKIADNSKN----NLRQAIR   96 (137)
Q Consensus        64 l~~i~~~egi~i~~~~l~~i~~~~~g----d~R~aln   96 (137)
                      ++....+..+. ++..+..|++.+.|    |++.+++
T Consensus       181 l~~~l~~~~~~-~~~~~~~la~~t~G~s~adl~~lv~  216 (258)
T d1e32a2         181 LQIHTKNMKLA-DDVDLEQVANETHGHVGADLAALCS  216 (258)
T ss_dssp             HHHTTTTSCBC-TTCCHHHHHHHCTTCCHHHHHHHHH
T ss_pred             hhhhccCcccc-cccchhhhhhcccCCCHHHHHHHHH
Confidence            98877654332 22247788888776    6665554

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.93  E-value=1.6e-05  Score=59.33  Aligned_cols=87  Identities=13%  Similarity=0.229  Sum_probs=67.5

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhcc-----------CCceEEEEeCCC--------------------------CCc-hh
Q 042716            1 IILCEADKLSTDALLYMRWLLERYK-----------GLNKVFFCCSDV--------------------------SKL-QP   42 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~-----------~~~~~Il~~n~~--------------------------~~i-~~   42 (137)
                      |++||+|.++++.++.|+.++++..           .++.||++||--                          ..+ |.
T Consensus       129 vl~DEieK~~~~v~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~tsnlG~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~pE  208 (315)
T d1qvra3         129 ILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPE  208 (315)
T ss_dssp             EEESSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHH
T ss_pred             EEEehHhhcCHHHHHHHHHHhccCceeCCCCcEecCcceEEEEecccChHHHhhhcccccchhhhhHHHHHHHHhhcCHH
Confidence            5799999999999999999998741           355688888831                          336 89


Q ss_pred             hhhcce-eeEecCCCHHHHHHHHHHHH-------HHcC--CCCCHHHHHHHHHHc
Q 042716           43 IKSLCT-VIQLLPPSKQEIVEVLEFIA-------EQEG--IQLPHQLAEKIADNS   87 (137)
Q Consensus        43 l~SRc~-~i~~~~~~~~~i~~~l~~i~-------~~eg--i~i~~~~l~~i~~~~   87 (137)
                      +.+|+- ++.|.+++.+++.+++....       ...+  +.++++++.+|++.+
T Consensus       209 flnRid~Ii~F~~L~~~~~~~I~~~~l~~l~~rl~~~~i~l~i~~~~~~~L~~~~  263 (315)
T d1qvra3         209 FLNRLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDFLAERG  263 (315)
T ss_dssp             HHHTCSBCCBCCCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHHHH
T ss_pred             HHhcCCeeeeccchhhhhhHHHHHHHHHHHHHHHHhccccccccHHHHHHHHHhC
Confidence            999995 67899999999887764322       2333  468899999999873

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.80  E-value=3.2e-05  Score=59.38  Aligned_cols=101  Identities=13%  Similarity=0.149  Sum_probs=74.3

Q ss_pred             CcccccCcCCH--------HHHHHHHHHHHhccCCceEEEEeCCCC--Cc---hhhhhcceeeEecCCCHHHHHHHHHHH
Q 042716            1 IILCEADKLST--------DALLYMRWLLERYKGLNKVFFCCSDVS--KL---QPIKSLCTVIQLLPPSKQEIVEVLEFI   67 (137)
Q Consensus         1 iiiDEid~l~~--------~~~~~L~~~le~~~~~~~~Il~~n~~~--~i---~~l~SRc~~i~~~~~~~~~i~~~l~~i   67 (137)
                      +||||+|.|..        ++.+.|...+.  .+..++|.+|+...  ++   ++|..|++.+.+.+|+.++...+|..+
T Consensus       119 lfide~h~l~~~g~~~g~~d~a~~Lkp~L~--rg~~~~I~~tT~~ey~~~e~d~al~rrF~~v~v~ep~~~~~~~il~~~  196 (387)
T d1qvra2         119 LFIDELHTVVGAGKAEGAVDAGNMLKPALA--RGELRLIGATTLDEYREIEKDPALERRFQPVYVDEPTVEETISILRGL  196 (387)
T ss_dssp             EEECCC-------------------HHHHH--TTCCCEEEEECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHHHHHHH
T ss_pred             EEeccHHHHhcCCCCCCcccHHHHHHHHHh--CCCcceeeecCHHHHHHhcccHHHHHhcccccCCCCcHHHHHHHHHHH
Confidence            48999999932        34688888998  67888999997441  22   799999999999999999999998765


Q ss_pred             H----HHcCCCCCHHHHHHHHHHcC------CcHHHHHHHHHHHHh
Q 042716           68 A----EQEGIQLPHQLAEKIADNSK------NNLRQAIRSFEASRQ  103 (137)
Q Consensus        68 ~----~~egi~i~~~~l~~i~~~~~------gd~R~aln~L~~~~~  103 (137)
                      .    ...|+.++++++...++.|.      .=+.+|+.+|+.+..
T Consensus       197 ~~~~e~~h~v~~~~~ai~~~v~ls~ryi~~r~~PdKAidlld~a~a  242 (387)
T d1qvra2         197 KEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAIDLIDEAAA  242 (387)
T ss_dssp             HHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCTHHHHHHHHHHHHH
T ss_pred             HHHHHhccCCcccHHHHHHHHHhcccccccccChhhHHHHHHHHHH
Confidence            5    35599999999999888653      568999999997653

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.74  E-value=0.00012  Score=54.42  Aligned_cols=87  Identities=13%  Similarity=0.166  Sum_probs=66.7

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhc-----------cCCceEEEEeCCCC-------------------------Cc-hhh
Q 042716            1 IILCEADKLSTDALLYMRWLLERY-----------KGLNKVFFCCSDVS-------------------------KL-QPI   43 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~-----------~~~~~~Il~~n~~~-------------------------~i-~~l   43 (137)
                      +++||+|.++++.++.|+.++++.           -.++.+|+|+|-..                         .+ |.+
T Consensus       125 vl~DeieKa~~~V~~~lLqild~G~ltd~~Gr~vdf~n~iiI~Tsnig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEf  204 (315)
T d1r6bx3         125 LLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEF  204 (315)
T ss_dssp             EEEETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHH
T ss_pred             hhhcccccccchHhhhhHHhhccceecCCCCCccCccceEEEeccchhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHH
Confidence            579999999999999999999862           24667899988321                         25 788


Q ss_pred             hhcc-eeeEecCCCHHHHHHHHHHHH-------HHcC--CCCCHHHHHHHHHHc
Q 042716           44 KSLC-TVIQLLPPSKQEIVEVLEFIA-------EQEG--IQLPHQLAEKIADNS   87 (137)
Q Consensus        44 ~SRc-~~i~~~~~~~~~i~~~l~~i~-------~~eg--i~i~~~~l~~i~~~~   87 (137)
                      .+|+ .++.|.+++.+++.+++....       ...+  +.++++++.+++..+
T Consensus       205 lnRid~ii~f~~l~~~~~~~I~~~~l~~~~~~l~~~~i~l~~~~~a~~~l~~~~  258 (315)
T d1r6bx3         205 RNRLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAEKG  258 (315)
T ss_dssp             HTTCSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHTTEEEEECHHHHHHHHHHH
T ss_pred             HhhhhhhhcccchhhhHHHHHHHHHHHHHHHHHHhcCcchhhHHHHHHHHHHhC
Confidence            8998 589999999998887654322       2333  467899999998763

>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=97.71  E-value=7.1e-07  Score=68.28  Aligned_cols=102  Identities=15%  Similarity=-0.015  Sum_probs=71.2

Q ss_pred             CcccccCcCCHHHHHHHHHHHHh------ccCCceEEEEeCCCC-Cc-hhhhhcceeeEecCCCHHHHHHHHHHHHHHcC
Q 042716            1 IILCEADKLSTDALLYMRWLLER------YKGLNKVFFCCSDVS-KL-QPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEG   72 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~------~~~~~~~Il~~n~~~-~i-~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~eg   72 (137)
                      +++||+|+|.....+..-..+++      .....|+|+|||+.. .+ .++|.++.++.+.++.......++..+++++.
T Consensus       224 ~~~DeiD~l~~~~dg~~~~~~~~~~~~~~~~~~~p~i~ttN~~~~~~~r~~Rf~~~i~~~~~~~~~~~~~~l~~i~~~~~  303 (362)
T d1svma_         224 QGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRI  303 (362)
T ss_dssp             SHHHHHHTTHHHHHCSSCEEECCSSSCCEEECCCCEEEEECSCCCCHHHHTTEEEEEECCCCHHHHHHHHTCTHHHHTTC
T ss_pred             EEEehHhhcccccCCcchhhhhhhhhchhhhccCCceeecccccccccccccCceEEeecCCCcHHHHHHHHHHHhcccC
Confidence            46788888754332221111111      112346999999764 35 78888899888888888888888999999999


Q ss_pred             CCCCHHHHHHHH-HHcCCcHHHHHHHHHHHH
Q 042716           73 IQLPHQLAEKIA-DNSKNNLRQAIRSFEASR  102 (137)
Q Consensus        73 i~i~~~~l~~i~-~~~~gd~R~aln~L~~~~  102 (137)
                      +..+.+.+..++ ..+++|++.+++.+...+
T Consensus       304 l~~~~~~L~~li~~~s~~D~~~~i~~~~~~~  334 (362)
T d1svma_         304 IQSGIALLLMLIWYRPVAEFAQSIQSRIVEW  334 (362)
T ss_dssp             TTCHHHHHHHHHHHSCGGGSCGGGHHHHHHH
T ss_pred             CCCCHHHHHHHccCCCHHHHHHHHHHHHHHH
Confidence            999888877755 556778999888775444

>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=97.47  E-value=1.4e-05  Score=58.13  Aligned_cols=70  Identities=11%  Similarity=0.092  Sum_probs=49.5

Q ss_pred             CcccccCcCCHH--------------HHHHHHHHHHhc--cCCceEEEEeCCCCCc-hhhhh--cc-eeeEecCCCHHHH
Q 042716            1 IILCEADKLSTD--------------ALLYMRWLLERY--KGLNKVFFCCSDVSKL-QPIKS--LC-TVIQLLPPSKQEI   60 (137)
Q Consensus         1 iiiDEid~l~~~--------------~~~~L~~~le~~--~~~~~~Il~~n~~~~i-~~l~S--Rc-~~i~~~~~~~~~i   60 (137)
                      ++|||+|.+...              ..+.|+..++..  ..+..+|.+||.+..| +++++  |+ ..++|++|+.++.
T Consensus       104 l~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R  183 (265)
T d1r7ra3         104 LFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSR  183 (265)
T ss_dssp             EEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHH
T ss_pred             eeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHH
Confidence            479999988532              124455555432  2245688888999999 89875  66 5799999999999


Q ss_pred             HHHHHHHHHH
Q 042716           61 VEVLEFIAEQ   70 (137)
Q Consensus        61 ~~~l~~i~~~   70 (137)
                      ...++..+++
T Consensus       184 ~~il~~~l~~  193 (265)
T d1r7ra3         184 VAILKANLRK  193 (265)
T ss_dssp             HHHHHHHTTC
T ss_pred             HHHHHHHhcc
Confidence            9999876543

>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=97.28  E-value=0.00018  Score=51.50  Aligned_cols=97  Identities=16%  Similarity=0.190  Sum_probs=64.3

Q ss_pred             CcccccCcCC----------HHHHHHHHHHHHhccCC---ceEEEEeCCCCCc-h-hhhhcc-eeeEecCCC-HHHHHHH
Q 042716            1 IILCEADKLS----------TDALLYMRWLLERYKGL---NKVFFCCSDVSKL-Q-PIKSLC-TVIQLLPPS-KQEIVEV   63 (137)
Q Consensus         1 iiiDEid~l~----------~~~~~~L~~~le~~~~~---~~~Il~~n~~~~i-~-~l~SRc-~~i~~~~~~-~~~i~~~   63 (137)
                      ++|||+|.+.          ....++|+..++.....   +.+|.+||.+..+ + .+++|+ ..+.|+.++ .+++.++
T Consensus       104 l~iDEid~l~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~tTn~~~~ld~~~~~~rF~~~i~~P~~~~r~~il~~  183 (246)
T d1d2na_         104 VVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEA  183 (246)
T ss_dssp             EEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTTTSSEEEECCCEEEHHHHHHH
T ss_pred             eehhhhhhHhhhcccccchhHHHHHHHHHHhcCCCccccceeeeeccCChhhccchhhcCccceEEecCCchhHHHHHHH
Confidence            5899999862          33356777777765432   3466788887777 5 477787 457775544 3455555


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHcCC-----cHHHHHHHHHHHH
Q 042716           64 LEFIAEQEGIQLPHQLAEKIADNSKN-----NLRQAIRSFEASR  102 (137)
Q Consensus        64 l~~i~~~egi~i~~~~l~~i~~~~~g-----d~R~aln~L~~~~  102 (137)
                      +...     ..+++.....+++...|     +++.+++.++...
T Consensus       184 l~~~-----~~~~~~~~~~i~~~~~g~~~~~~ik~ll~~ie~a~  222 (246)
T d1d2na_         184 LELL-----GNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSL  222 (246)
T ss_dssp             HHHH-----TCSCHHHHHHHHHHHTTSEEEECHHHHHHHHHHHT
T ss_pred             HHhc-----cCCChHHHHHHHHHcCCCccchhHHHHHHHHHHHH
Confidence            5432     24577778888888776     4888988887664

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=97.16  E-value=0.0029  Score=46.43  Aligned_cols=102  Identities=13%  Similarity=0.172  Sum_probs=62.9

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCC-----------ceEEE--EeCCC-CCc-hhhhhcce-eeEecCCCHHHHH-HH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGL-----------NKVFF--CCSDV-SKL-QPIKSLCT-VIQLLPPSKQEIV-EV   63 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~-----------~~~Il--~~n~~-~~i-~~l~SRc~-~i~~~~~~~~~i~-~~   63 (137)
                      ++|||++.+.+..+++|+..||+..-.           ++|++  ++|.. .++ +++++|+. .+.+..+.+.+.. ..
T Consensus       131 l~iDEi~~~~~~~~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~~l~~~llDRf~~~i~v~~~~~~~~~~~~  210 (333)
T d1g8pa_         131 LYIDECNLLEDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLDRFGLSVEVLSPRDVETRVEV  210 (333)
T ss_dssp             EEETTGGGSCHHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHTTCSEEEECCCCCSHHHHHHH
T ss_pred             eecccHHHHHHHHHHHHhhhhcCCeEEecccCceecCCCCEEEEEecCccccccccchhhhhcceeeccCcchhhHHHHH
Confidence            479999999999999999999975311           22333  33433 358 99999985 4777766542211 11


Q ss_pred             HH-----------------------------HHHHHcCCCCCHHHHHHHHHHc---C-CcHHHHHHHHHHHH
Q 042716           64 LE-----------------------------FIAEQEGIQLPHQLAEKIADNS---K-NNLRQAIRSFEASR  102 (137)
Q Consensus        64 l~-----------------------------~i~~~egi~i~~~~l~~i~~~~---~-gd~R~aln~L~~~~  102 (137)
                      +.                             ....-..+.++++....+....   . -++|....+++.+.
T Consensus       211 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~v~~~~~~~~~~~~~~~~~~~~S~R~~~~llrvAr  282 (333)
T d1g8pa_         211 IRRRDTYDADPKAFLEEWRPKDMDIRNQILEARERLPKVEAPNTALYDCAALCIALGSDGLRGELTLLRSAR  282 (333)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHGGGCBCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHH
T ss_pred             HHhhhhcccChHHHHHHHHHHHHHHHHHHHHHhhcccceecCHHHHHHHHHHHHHcCCCChHHHHHHHHHHH
Confidence            10                             0011123566666666655432   2 27898888887654

>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=96.38  E-value=0.0017  Score=47.61  Aligned_cols=64  Identities=16%  Similarity=0.125  Sum_probs=45.5

Q ss_pred             CcccccCcCCHH------------HHHHHHHHHHhc----------cCCceEEEEe----CCCCCc-hhhhhcc-eeeEe
Q 042716            1 IILCEADKLSTD------------ALLYMRWLLERY----------KGLNKVFFCC----SDVSKL-QPIKSLC-TVIQL   52 (137)
Q Consensus         1 iiiDEid~l~~~------------~~~~L~~~le~~----------~~~~~~Il~~----n~~~~i-~~l~SRc-~~i~~   52 (137)
                      |+|||+|++++.            -++.|+..++-.          ..+..||++.    +.+..+ |.++.|. ..+.|
T Consensus       119 If~DEIdki~~~~~~~~~~~~~~gv~~~LL~~~dg~~~~~~~~~i~~s~ilfi~~ga~~~~~~~~~~p~l~~R~~~~i~~  198 (309)
T d1ofha_         119 VFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLPIRVEL  198 (309)
T ss_dssp             EEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHHTCCEEEEC
T ss_pred             EEehhhhhhhhhccCcccchhhhHHHHHhhHHhcCCEEecCCeEEEccceeEEeccchhhcCcccchhhhhhhhheeeec
Confidence            589999998643            467788888731          1123355442    334457 9999998 67999


Q ss_pred             cCCCHHHHHHHH
Q 042716           53 LPPSKQEIVEVL   64 (137)
Q Consensus        53 ~~~~~~~i~~~l   64 (137)
                      .+|+..+...++
T Consensus       199 ~~~~~~~~~~Il  210 (309)
T d1ofha_         199 TALSAADFERIL  210 (309)
T ss_dssp             CCCCHHHHHHHH
T ss_pred             cCCCHHHHHHHH
Confidence            999999888775

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=96.33  E-value=0.0008  Score=46.76  Aligned_cols=62  Identities=11%  Similarity=0.108  Sum_probs=49.1

Q ss_pred             CcccccCcCCHH--------HHHHHHHHHHhccCCceEEEEeCCCC-----Cc-hhhhhcceeeEecCCCHHHHHHHH
Q 042716            1 IILCEADKLSTD--------ALLYMRWLLERYKGLNKVFFCCSDVS-----KL-QPIKSLCTVIQLLPPSKQEIVEVL   64 (137)
Q Consensus         1 iiiDEid~l~~~--------~~~~L~~~le~~~~~~~~Il~~n~~~-----~i-~~l~SRc~~i~~~~~~~~~i~~~l   64 (137)
                      +||||+|.+...        +.+.|...++  .+...+|.+|+...     .- ++|.+|+..+++..|+.++...+|
T Consensus       119 LfIDeih~l~~~g~~~g~~d~~~~Lkp~L~--rg~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         119 LFIDELHTMVGAGKADGAMDAGNMLKPALA--RGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             EEEETGGGGTT------CCCCHHHHHHHHH--TTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             EEcchHHHHhcCCCCCCcccHHHHHHHHHh--CCCceEEecCCHHHHHHHHHcCHHHHhcCCEeecCCCCHHHHHHHh
Confidence            489999999433        2588899998  67888999887542     23 899999999999999999876554

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=95.91  E-value=0.0096  Score=44.68  Aligned_cols=47  Identities=15%  Similarity=0.195  Sum_probs=36.8

Q ss_pred             c-hhhhhcc-eeeEecCCCHHHHHHHHH-----------HHHHHcCC--CCCHHHHHHHHHH
Q 042716           40 L-QPIKSLC-TVIQLLPPSKQEIVEVLE-----------FIAEQEGI--QLPHQLAEKIADN   86 (137)
Q Consensus        40 i-~~l~SRc-~~i~~~~~~~~~i~~~l~-----------~i~~~egi--~i~~~~l~~i~~~   86 (137)
                      + |.++.|. .++.|++++.+++..++.           ...+.+|+  .++++++.+|++.
T Consensus       252 f~PEf~gRi~~iv~f~~L~~~~l~~Il~~~~~~l~kq~~~~l~~~gi~L~~td~a~~~la~~  313 (364)
T d1um8a_         252 LIPELIGRLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQL  313 (364)
T ss_dssp             CCHHHHTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHH
T ss_pred             hHHHHHHHhcchhhHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHh
Confidence            5 7788888 579999999999988874           22344566  4679999999985

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=94.83  E-value=0.04  Score=37.75  Aligned_cols=98  Identities=17%  Similarity=0.116  Sum_probs=64.8

Q ss_pred             CcccccCcCCHHH----HHHHHHHHHhccCCceEEEEeCCCCC---------c-hhhhh-cceeeEecCCCHHHHHHHHH
Q 042716            1 IILCEADKLSTDA----LLYMRWLLERYKGLNKVFFCCSDVSK---------L-QPIKS-LCTVIQLLPPSKQEIVEVLE   65 (137)
Q Consensus         1 iiiDEid~l~~~~----~~~L~~~le~~~~~~~~Il~~n~~~~---------i-~~l~S-Rc~~i~~~~~~~~~i~~~l~   65 (137)
                      +++||+|.+....    ...|...... .....+++++.....         . .++.. +...+.+.+++.++..+.+.
T Consensus       140 i~id~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~  218 (283)
T d2fnaa2         140 IVLDEAQELVKLRGVNLLPALAYAYDN-LKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLR  218 (283)
T ss_dssp             EEEETGGGGGGCTTCCCHHHHHHHHHH-CTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHH
T ss_pred             cccchhhhhcccchHHHHHHHHHHHHh-hhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHH
Confidence            4688888874433    4455555543 345566666654321         1 12223 34679999999999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHH
Q 042716           66 FIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS  101 (137)
Q Consensus        66 ~i~~~egi~i~~~~l~~i~~~~~gd~R~aln~L~~~  101 (137)
                      +.+...|++.++  +..+.+.++|.+..+--+...+
T Consensus       219 ~~~~~~~~~~~~--~~~i~~~~~G~P~~L~~~~~~~  252 (283)
T d2fnaa2         219 RGFQEADIDFKD--YEVVYEKIGGIPGWLTYFGFIY  252 (283)
T ss_dssp             HHHHHHTCCCCC--HHHHHHHHCSCHHHHHHHHHHH
T ss_pred             hhhhhcCCCHHH--HHHHHHHhCCCHHHHHHHHHHH
Confidence            988888876654  7899999999997544333333

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

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: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=93.25  E-value=0.045  Score=38.98  Aligned_cols=86  Identities=14%  Similarity=0.206  Sum_probs=55.8

Q ss_pred             CcccccCcCCHHHHHHHHHHHHhccCCceEEEEeCCCCCchhhhhcceeeEecCCCHHHHHHHHHHHHHHcCC-CCCHHH
Q 042716            1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQPIKSLCTVIQLLPPSKQEIVEVLEFIAEQEGI-QLPHQL   79 (137)
Q Consensus         1 iiiDEid~l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i~~l~SRc~~i~~~~~~~~~i~~~l~~i~~~egi-~i~~~~   79 (137)
                      +++|+++..  ...   .. ..  ..++++|+||++..-...+.+++..+++++++.++....+...+..... .-.++.
T Consensus       139 lVLDDv~~~--~~~---~~-~~--~~~srilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~  210 (277)
T d2a5yb3         139 FVFDDVVQE--ETI---RW-AQ--ELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDV  210 (277)
T ss_dssp             EEEEEECCH--HHH---HH-HH--HTTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHH
T ss_pred             EecchhhHH--hhh---hh-hc--ccCceEEEEeehHHHHHhcCCCCceEECCCCCHHHHHHHHHHHhCCccCchhhHHH
Confidence            467877742  222   21 22  3356788888766333777788889999999999999988654322211 112455


Q ss_pred             HHHHHHHcCCcHHHH
Q 042716           80 AEKIADNSKNNLRQA   94 (137)
Q Consensus        80 l~~i~~~~~gd~R~a   94 (137)
                      ...|++.|+|.+-.+
T Consensus       211 ~~~iv~~c~GlPLAl  225 (277)
T d2a5yb3         211 LNKTIELSSGNPATL  225 (277)
T ss_dssp             HHHHHHHHTTCHHHH
T ss_pred             HHHHHHHhCCCHHHH
Confidence            688999999987443

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=88.78  E-value=0.24  Score=34.72  Aligned_cols=40  Identities=15%  Similarity=0.140  Sum_probs=33.7

Q ss_pred             CcccccCc-CCHHHHHHHHHHHHhccCCceEEEEeCCCCCc
Q 042716            1 IILCEADK-LSTDALLYMRWLLERYKGLNKVFFCCSDVSKL   40 (137)
Q Consensus         1 iiiDEid~-l~~~~~~~L~~~le~~~~~~~~Il~~n~~~~i   40 (137)
                      ++|||+|. |++..+..|...+++...++.||+||-++.-+
T Consensus       245 ~~iDEpe~~Lhp~~~~~l~~~l~~~~~~~QviitTHsp~~~  285 (308)
T d1e69a_         245 YVLDEVDSPLDDYNAERFKRLLKENSKHTQFIVITHNKIVM  285 (308)
T ss_dssp             EEEESCCSSCCHHHHHHHHHHHHHHTTTSEEEEECCCTTGG
T ss_pred             hhhhhccccCCHHHHHHHHHHHHHhccCCEEEEEECCHHHH
Confidence            46899995 79999999999999888888899888776544

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=86.67  E-value=1.1  Score=33.94  Aligned_cols=86  Identities=20%  Similarity=0.272  Sum_probs=57.9

Q ss_pred             cccccCcCC------------HHHHHHHHHHHHhccC--------CceEEEEeCC------CCCc-hhhhhcc-eeeEec
Q 042716            2 ILCEADKLS------------TDALLYMRWLLERYKG--------LNKVFFCCSD------VSKL-QPIKSLC-TVIQLL   53 (137)
Q Consensus         2 iiDEid~l~------------~~~~~~L~~~le~~~~--------~~~~Il~~n~------~~~i-~~l~SRc-~~i~~~   53 (137)
                      ++||+|...            .+.+..++..+|-..-        ..++.+++..      ++.+ |.|..|. .++.|.
T Consensus       254 ~~dei~k~~~~~~~~g~d~~~eg~~~~ll~~~e~~~v~~~~~~~~~~~~l~i~~~~~~~~~~~gliPEliGRlPi~v~L~  333 (443)
T d1g41a_         254 FIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLPIRVELT  333 (443)
T ss_dssp             EEETGGGGSCCSSCSSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHTTCCEEEECC
T ss_pred             ccchhhhhhhcccCCCCCcccchhhhhhhhhccccccccccccccccchhhccccchhhcccccchhhhccceEEEEEcc
Confidence            567777652            3347778888874221        1122233322      2347 9999997 679999


Q ss_pred             CCCHHHHHHHHHH-----------HHHHcCCCC--CHHHHHHHHHHc
Q 042716           54 PPSKQEIVEVLEF-----------IAEQEGIQL--PHQLAEKIADNS   87 (137)
Q Consensus        54 ~~~~~~i~~~l~~-----------i~~~egi~i--~~~~l~~i~~~~   87 (137)
                      +++.+++.++|..           ....+|+++  +++++..|++.+
T Consensus       334 ~L~~~dL~rILtEPknsLikQy~~lf~~~gv~L~ft~~al~~iA~~A  380 (443)
T d1g41a_         334 ALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAA  380 (443)
T ss_dssp             CCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHhhhhhHHHHHHHHHhhcCcEEEEcHHHHHHHHHHH
Confidence            9999999998842           234567765  799999998765

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {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: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=86.54  E-value=0.083  Score=34.97  Aligned_cols=45  Identities=13%  Similarity=0.098  Sum_probs=23.5

Q ss_pred             CcccccCcCCHHH-HHHHHHHHHhccCCceEEEEeCCCCCc-hhhhh
Q 042716            1 IILCEADKLSTDA-LLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKS   45 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~L~~~le~~~~~~~~Il~~n~~~~i-~~l~S   45 (137)
                      +|+||+|.+..+. ...+.........+.++++.+-.+... ..+..
T Consensus       129 vIiDE~H~~~~~~~~~~~~~~~~~~~~~~~~l~~SATp~~~~~~~~~  175 (200)
T d1wp9a1         129 IVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIME  175 (200)
T ss_dssp             EEEETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEESCSCSSHHHHHH
T ss_pred             EEEEehhhhhcchhHHHHHHHHHhcCCCCcEEEEEecCCCcHHHHHH
Confidence            5899999986543 333333333334455555544445443 43433

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {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: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.96  E-value=0.23  Score=33.39  Aligned_cols=46  Identities=13%  Similarity=0.150  Sum_probs=31.6

Q ss_pred             CcccccCcCCHH-HHHHHHHHHHhccCCceEEEEeCCCC-Cchhhhhc
Q 042716            1 IILCEADKLSTD-ALLYMRWLLERYKGLNKVFFCCSDVS-KLQPIKSL   46 (137)
Q Consensus         1 iiiDEid~l~~~-~~~~L~~~le~~~~~~~~Il~~n~~~-~i~~l~SR   46 (137)
                      +++||+|.|-.. -...+..+++..+..+.+++.+...+ .+..+..+
T Consensus       147 lV~DEaD~l~~~~f~~~v~~I~~~l~~~~Q~il~SATl~~~v~~~~~~  194 (206)
T d1s2ma1         147 FIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVK  194 (206)
T ss_dssp             EEEESHHHHSSHHHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHH
T ss_pred             EEeechhhhhhhhhHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHH
Confidence            579999998654 47778888888877777777665443 34334443

>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=85.48  E-value=0.23  Score=36.34  Aligned_cols=59  Identities=8%  Similarity=-0.041  Sum_probs=32.3

Q ss_pred             CcccccCcCCHHH------------HHHHHHHHHhc--cCCceEEEEeCCCCCc-hhhh------hcc-eeeEecCCCHH
Q 042716            1 IILCEADKLSTDA------------LLYMRWLLERY--KGLNKVFFCCSDVSKL-QPIK------SLC-TVIQLLPPSKQ   58 (137)
Q Consensus         1 iiiDEid~l~~~~------------~~~L~~~le~~--~~~~~~Il~~n~~~~i-~~l~------SRc-~~i~~~~~~~~   58 (137)
                      +||||+|.+.+..            .+.|+.-|+-+  ..++.+|.+|| +..+ ++|-      +|+ ..+.+.+|+.+
T Consensus       186 lf~DEid~~~~~r~~~~~~~~~~r~v~~lL~e~dg~~~~~~v~viaatN-~~~~~~~i~~~~~r~~Rf~~~v~v~~pd~~  264 (321)
T d1w44a_         186 IVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLN-PTSNDDKIVELVKEASRSNSTSLVISTDVD  264 (321)
T ss_dssp             EEEECCTTTC-----------CCHHHHHHHHHHHHHHHHHTCEEEEECC-CCCCCHHHHHHHHHHHHHSCSEEEEECSST
T ss_pred             EEeehhhhhccccccCCCCCcchhhhhhhhhhccccccCCCeEEEEeCC-CcccccchhhhhhccCcccceeecCCCChH
Confidence            5899999994432            24555555432  23455565665 5444 4443      454 45666666665


Q ss_pred             HH
Q 042716           59 EI   60 (137)
Q Consensus        59 ~i   60 (137)
                      .-
T Consensus       265 ~r  266 (321)
T d1w44a_         265 GE  266 (321)
T ss_dssp             TE
T ss_pred             HH
Confidence            43

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=85.02  E-value=0.76  Score=29.10  Aligned_cols=59  Identities=24%  Similarity=0.282  Sum_probs=38.8

Q ss_pred             CcccccCcC---CHHHHHHHHHHHHhccCCceEEEEeCCCCC--c-hhhhhc--ceeeEecCCCHHHHH
Q 042716            1 IILCEADKL---STDALLYMRWLLERYKGLNKVFFCCSDVSK--L-QPIKSL--CTVIQLLPPSKQEIV   61 (137)
Q Consensus         1 iiiDEid~l---~~~~~~~L~~~le~~~~~~~~Il~~n~~~~--i-~~l~SR--c~~i~~~~~~~~~i~   61 (137)
                      +++||++..   +.+...+|+++++  ...+.+++++.....  + ..+..+  ..++.+.+.+.+.+.
T Consensus       103 lllDE~~~~~~~~~~~~~~l~~~l~--~~~~~il~~~h~~~~~~~~~~i~~~~~~~i~~v~~~nrd~~~  169 (178)
T d1ye8a1         103 IIIDEIGKMELFSKKFRDLVRQIMH--DPNVNVVATIPIRDVHPLVKEIRRLPGAVLIELTPENRDVIL  169 (178)
T ss_dssp             EEECCCSTTGGGCHHHHHHHHHHHT--CTTSEEEEECCSSCCSHHHHHHHTCTTCEEEECCTTTTTTHH
T ss_pred             eeecCCCccchhhHHHHHHHHHHhc--cCCCEEEEEEccHHHHHhhceEEEEeCCEEEEECCccHHHHH
Confidence            478998765   5666888899988  445677887766543  3 555554  367777666644433

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.96  E-value=0.15  Score=34.96  Aligned_cols=46  Identities=11%  Similarity=0.179  Sum_probs=32.8

Q ss_pred             CcccccCcCCHHH-HHHHHHHHHhccCCceEEEEeCCCCC-chhhhhc
Q 042716            1 IILCEADKLSTDA-LLYMRWLLERYKGLNKVFFCCSDVSK-LQPIKSL   46 (137)
Q Consensus         1 iiiDEid~l~~~~-~~~L~~~le~~~~~~~~Il~~n~~~~-i~~l~SR   46 (137)
                      +++||||.|.... ++.+..+++..+.+..+++.+...++ +..+..+
T Consensus       159 lVlDEaD~ll~~~f~~~~~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~  206 (218)
T d2g9na1         159 FVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKK  206 (218)
T ss_dssp             EEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHH
T ss_pred             EEeeecchhhcCchHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHH
Confidence            5899999997654 77788888888888888777665543 4334333

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.76  E-value=0.16  Score=34.30  Aligned_cols=37  Identities=22%  Similarity=0.275  Sum_probs=26.6

Q ss_pred             CcccccCcCCHH-HHHHHHHHHHhccCCceEEEEeCCC
Q 042716            1 IILCEADKLSTD-ALLYMRWLLERYKGLNKVFFCCSDV   37 (137)
Q Consensus         1 iiiDEid~l~~~-~~~~L~~~le~~~~~~~~Il~~n~~   37 (137)
                      +++||||.|... -...+..+++..+++..+++.+...
T Consensus       150 lVlDEaD~ll~~~f~~~i~~I~~~~~~~~Q~~l~SAT~  187 (206)
T d1veca_         150 IVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATF  187 (206)
T ss_dssp             EEEETHHHHTSTTTHHHHHHHHHHSCTTCEEEEEESCC
T ss_pred             EEEeccccccccchHHHHHHHHHhCCCCCEEEEEEecC
Confidence            589999988543 4667888888877777766655443

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=83.31  E-value=0.32  Score=32.22  Aligned_cols=37  Identities=14%  Similarity=0.142  Sum_probs=23.4

Q ss_pred             CcccccCcCCHH----HHHHHHHHHHhccCCceEEEEeCCC
Q 042716            1 IILCEADKLSTD----ALLYMRWLLERYKGLNKVFFCCSDV   37 (137)
Q Consensus         1 iiiDEid~l~~~----~~~~L~~~le~~~~~~~~Il~~n~~   37 (137)
                      ||+||+|.+...    ....+...+.+..+++++++.+-..
T Consensus       142 ii~DE~h~~~~~~r~~~~~~~l~~i~~~~~~~~~l~lSATl  182 (202)
T d2p6ra3         142 LVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATA  182 (202)
T ss_dssp             EEETTGGGGGCTTTHHHHHHHHHHHHHHCTTCEEEEEECCC
T ss_pred             ccccHHHHhcccccchHHHHHHHHHHhcCCCCcEEEEcCCC
Confidence            589999998533    2344555565556677776655443

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=81.41  E-value=0.23  Score=33.46  Aligned_cols=37  Identities=16%  Similarity=0.271  Sum_probs=27.3

Q ss_pred             CcccccCcC-CHHHHHHHHHHHHhccCCceEEEEeCCC
Q 042716            1 IILCEADKL-STDALLYMRWLLERYKGLNKVFFCCSDV   37 (137)
Q Consensus         1 iiiDEid~l-~~~~~~~L~~~le~~~~~~~~Il~~n~~   37 (137)
                      +++||+|.| +.+....+.++++..+.++.+++.+...
T Consensus       149 lViDEad~l~~~~~~~~i~~I~~~~~~~~Q~i~~SAT~  186 (208)
T d1hv8a1         149 FILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATM  186 (208)
T ss_dssp             EEEETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECSSC
T ss_pred             EEEEChHHhhcCCChHHHHHHHHhCCCCCeEEEEEccC
Confidence            589999986 4445667888888877778877766443

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {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: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.11  E-value=0.19  Score=34.21  Aligned_cols=47  Identities=13%  Similarity=0.142  Sum_probs=32.3

Q ss_pred             CcccccCcCCHH-HHHHHHHHHHhccCCceEEEEeCCCC-Cchhhhhcc
Q 042716            1 IILCEADKLSTD-ALLYMRWLLERYKGLNKVFFCCSDVS-KLQPIKSLC   47 (137)
Q Consensus         1 iiiDEid~l~~~-~~~~L~~~le~~~~~~~~Il~~n~~~-~i~~l~SRc   47 (137)
                      +++||+|.|... -...+..+++..+.++.+++.+...+ ++..+..|.
T Consensus       155 lVlDEad~lld~~f~~~v~~I~~~~~~~~Q~vl~SAT~~~~v~~l~~~~  203 (212)
T d1qdea_         155 FILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKF  203 (212)
T ss_dssp             EEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHH
T ss_pred             EeehhhhhhcccchHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHH
Confidence            579999999655 36778888888777777666655443 344455443