Psyllid ID: psy5642

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------
Protein Sequence
MEDLGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK
Secondary Structure (PSIPRED)
cccccccccEEEEcccccccccHHHHHHHHHHHHHHHHHccccEEEEEcccccccccccccccccccHHHHHHHHHHHHHHcccccccEEEEEEcccccccccccccccccccEEEcccccHHHHHHHHHHHHccccccccccHHHHHHHccccccccHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHccccccHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccEEEEccHHHHHHHHcccHHHHHHHHHHHHHcccEEEEEEcHHHHccccccccccccccHHHHHHHHHHHHHccccccccEEEEEEccccccccHHHcccccccEEEEEccccHHHHHHHHHHHHccccccccccHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHccccccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
medlggltEVVESIGPELFRKYVGESERCVRDVFKRArqvspsviffdeldslagergdggggggsNVQERVLAQMLTEmdgivplnnVTIVaatnrpdridkallrpgrldrliyvplpddlTRAAILKIRLarsplgedvCVEELVRLtegysgaeqSLSKHRAkkirprresnpgppackpsivAVCDEAALSALENNLEAAYVSHQDFLTALqlvkprtppqlIKLYENYIKK
Flexible Loop (DISEMBL)
medlggltevvesigpelfrkyvgesERCVRDVFkrarqvspsvifFDELDSLAGErgdggggggSNVQERVLAQMLTEMDGIVPLNNVTIvaatnrpdridkallrpgrldrliyvplpddlTRAAILKIRlarsplgedvCVEELVRLtegysgaeqslskhrakkirprresnpgppacKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALqlvkprtppqliklyenyikk
Low Complexity Region (SEG)
MEDLGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAgergdggggggSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDeaalsalennleaaYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK
Disordered region (IsUnstruct)
*******TEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDEL**********************LAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEG*******************************SIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENY***
Disordered Region (DISOPRED)
**DLGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSL******************VLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLV******QLIKLYENYIK*
Disordered Region (DISEMBL)
MEDLGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGE*********SNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEG**************************PACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK
Disordered Region (DISPRO)
******LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGE*********SNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIK*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEDLGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK
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	237	2.2.26 [Sep-21-2011]
Q3UMC0	893	Spermatogenesis-associate	yes	N/A	0.818	0.217	0.529	6e-58
Q8NB90	893	Spermatogenesis-associate	yes	N/A	0.818	0.217	0.524	3e-56
Q07590	780	Protein SAV OS=Sulfolobus	yes	N/A	0.877	0.266	0.436	5e-45
O28972	733	Cell division cycle prote	yes	N/A	0.810	0.261	0.451	3e-44
Q9LET7	1022	Calmodulin-interacting pr	yes	N/A	0.751	0.174	0.449	5e-44
O60058	809	ATPase family gene 2 prot	yes	N/A	0.789	0.231	0.431	9e-42
O05209	745	VCP-like ATPase OS=Thermo	yes	N/A	0.789	0.251	0.396	1e-41
Q7KN62	801	Transitional endoplasmic	no	N/A	0.666	0.197	0.522	1e-39
Q9LZF6	810	Cell division control pro	no	N/A	0.645	0.188	0.532	6e-39
Q96372	805	Cell division cycle prote	N/A	N/A	0.645	0.190	0.525	3e-38

>sp|Q3UMC0|SPAT5_MOUSE Spermatogenesis-associated protein 5 OS=Mus musculus GN=Spata5 PE=2 SV=2

 Score =  223 bits (569), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 118/223 (52%), Positives = 148/223 (66%), Gaps = 29/223 (13%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPEL  KYVGESER VR++F++AR V+PS+IFFDELD+LA ERG   G G  NV +RVLA
Sbjct: 694 GPELMNKYVGESERAVREIFRKARAVAPSIIFFDELDALAVERGSSSGAG--NVADRVLA 751

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTEMDGI  L NVT++AATNRPDRIDKAL+RPGR+DR+IYVPLPD  TR  IL ++  
Sbjct: 752 QLLTEMDGIEQLKNVTVLAATNRPDRIDKALMRPGRIDRIIYVPLPDAATRREILNLQFH 811

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             P+  +V ++ELV  T+ YSGAE                           I+AVC EAA
Sbjct: 812 SMPISNEVDLDELVLQTDTYSGAE---------------------------IIAVCKEAA 844

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           L ALE N++A  +  + F  AL +V PR P  L + YE+Y +K
Sbjct: 845 LLALEENIKADCIMKRHFTQALSIVTPRIPESLRRFYEDYQEK 887

May be involved in morphological and functional mitochondrial transformations during spermatogenesis.
Mus musculus (taxid: 10090)

>sp|Q8NB90|SPAT5_HUMAN Spermatogenesis-associated protein 5 OS=Homo sapiens GN=SPATA5 PE=1 SV=3

 Score =  218 bits (555), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 117/223 (52%), Positives = 146/223 (65%), Gaps = 29/223 (13%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPEL  KYVGESER VR+ F++AR V+PS+IFFDELD+LA ERG   G G  NV +RVLA
Sbjct: 694 GPELMNKYVGESERAVRETFRKARAVAPSIIFFDELDALAVERGSSLGAG--NVADRVLA 751

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTEMDGI  L +VTI+AATNRPDRIDKAL+RPGR+DR+IYVPLPD  TR  I K++  
Sbjct: 752 QLLTEMDGIEQLKDVTILAATNRPDRIDKALMRPGRIDRIIYVPLPDAATRREIFKLQFH 811

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             P+  +V ++EL+  T+ YSGAE                           IVAVC EAA
Sbjct: 812 SMPVSNEVDLDELILQTDAYSGAE---------------------------IVAVCREAA 844

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           L ALE +++A  +  + F  AL  V PR P  L + YE+Y +K
Sbjct: 845 LLALEEDIQANLIMKRHFTQALSTVTPRIPESLRRFYEDYQEK 887

May be involved in morphological and functional mitochondrial transformations during spermatogenesis.

Homo sapiens (taxid: 9606)

>sp|Q07590|SAV_SULAC Protein SAV OS=Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) GN=sav PE=3 SV=2

 Score =  181 bits (458), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 103/236 (43%), Positives = 139/236 (58%), Gaps = 28/236 (11%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPE+  K+VGESE+ +R++F++ARQ +P+VIFFDE+DS+A  RG     G   V ER++ 
Sbjct: 554 GPEILSKWVGESEKAIREIFRKARQAAPTVIFFDEIDSIAPIRGLSTDSG---VTERIVN 610

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+L EMDGIVPLN V I+AATNRPD +D ALLRPGR DRLIYVP PD   R  ILK+   
Sbjct: 611 QLLAEMDGIVPLNKVVIIAATNRPDILDPALLRPGRFDRLIYVPPPDKTARFEILKVHTK 670

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             PL EDV +E++    EGY+GA+   +  R   I   R           SI ++CD+ +
Sbjct: 671 NVPLAEDVSLEDIAEKAEGYTGADLE-ALVREATINAMR-----------SIYSMCDKQS 718

Query: 195 LSALENNLE-------------AAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
               + N+E             +  VS +DF  AL +VK       I+ YE + K+
Sbjct: 719 RDECKGNMECYQKHIKECMNKTSFKVSKEDFEKALNVVKASLTQADIQRYERFSKE 774

Not yet known, shows ATPase activity.

Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (taxid: 330779)

>sp|O28972|Y1297_ARCFU Cell division cycle protein 48 homolog AF_1297 OS=Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) GN=AF_1297 PE=3 SV=1

 Score =  178 bits (451), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 106/235 (45%), Positives = 139/235 (59%), Gaps = 43/235 (18%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPEL  K+VGESE+ VR++F++ARQV+P VIFFDE+DSLA  RG   G G S+V ERV++
Sbjct: 522 GPELLSKWVGESEKHVREMFRKARQVAPCVIFFDEIDSLAPRRG---GIGDSHVTERVVS 578

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTE+DG+  L +V ++AATNRPD ID ALLRPGRL+R IY+P PD   R  I KI L 
Sbjct: 579 QLLTELDGLEELKDVVVIAATNRPDMIDPALLRPGRLERHIYIPPPDKKARVEIFKIHLR 638

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             PL +DV +EEL   TEGYSGA+                           I AVC EA 
Sbjct: 639 GKPLADDVNIEELAEKTEGYSGAD---------------------------IEAVCREAG 671

Query: 195 LSAL----------ENNLEAA---YVSHQDFLTALQLVKPRTPPQLIKLYENYIK 236
           + A+          E   EAA    ++ + F  AL+ V+P    + ++ YE  I+
Sbjct: 672 MLAIRELIKPGMTREEAKEAAKKLKITKKHFEEALKKVRPSLTKEDVEKYEKLIE 726

Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (taxid: 224325)

>sp|Q9LET7|CI111_ARATH Calmodulin-interacting protein 111 OS=Arabidopsis thaliana GN=CIP111 PE=1 SV=1

 Score =  177 bits (449), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 93/207 (44%), Positives = 130/207 (62%), Gaps = 29/207 (14%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPELF K+VGESE+ VR +F +AR  +PS+IFFDE+DSLA  RG    G   +V +RV++
Sbjct: 791 GPELFSKWVGESEKAVRSLFAKARANAPSIIFFDEIDSLASIRGKENDG--VSVSDRVMS 848

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+L E+DG+     VT++AATNRPD+ID ALLRPGR DRL+YV  P++  R AILKI L 
Sbjct: 849 QLLVELDGLHQRVGVTVIAATNRPDKIDSALLRPGRFDRLLYVGPPNETDREAILKIHLR 908

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
           + P   D+C++EL  +T+GY+GA+ SL                           +C EAA
Sbjct: 909 KIPCSSDICLKELASITKGYTGADISL---------------------------ICREAA 941

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKP 221
           ++ALE +LE   +S +    A+  ++P
Sbjct: 942 IAALEESLEMEEISMRHLKAAISQIEP 968

Arabidopsis thaliana (taxid: 3702)

>sp|O60058|AFG2_SCHPO ATPase family gene 2 protein OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=afg2 PE=3 SV=1

 Score =  170 bits (430), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 95/220 (43%), Positives = 128/220 (58%), Gaps = 33/220 (15%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPELF K+VGESER VR VF++ARQ SPSVIFFDE+D+L   RG+       N  +RV+A
Sbjct: 615 GPELFDKFVGESERAVRQVFQKARQASPSVIFFDEIDALTANRGE------DNSSDRVVA 668

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
            +L E+DGI  L NV ++AATNRPD ID AL+RPGRLDRL+YV  P+   R  I+KI+  
Sbjct: 669 ALLNELDGIEALRNVLVLAATNRPDMIDPALMRPGRLDRLLYVGPPNFEARKQIVKIQAE 728

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
           +    EDV ++ +   TEG SGAE                           +VA+C EA 
Sbjct: 729 KMKFAEDVDLDLIAEKTEGCSGAE---------------------------VVALCQEAG 761

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENY 234
           L A+  +LEA  +    F TAL  ++      +++ Y ++
Sbjct: 762 LIAMHEDLEAKEICQAHFKTALLALRKAITRDMLEYYASF 801

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

>sp|O05209|VAT_THEAC VCP-like ATPase OS=Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) GN=vat PE=1 SV=1

 Score =  169 bits (428), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 86/217 (39%), Positives = 129/217 (59%), Gaps = 30/217 (13%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPE+  K+VGESE+ +R++FK+A+QV+P+++F DE+DS+A  RG     G   V ER++ 
Sbjct: 534 GPEVLSKWVGESEKAIREIFKKAKQVAPAIVFLDEIDSIAPRRGTTSDSG---VTERIVN 590

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LT +DGI  +N V ++ ATNRPD +D ALLR GR D+LIY+P PD   R +ILK+   
Sbjct: 591 QLLTSLDGIEVMNGVVVIGATNRPDIMDPALLRAGRFDKLIYIPPPDKEARLSILKVHTK 650

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             PL  DV + ++ + TEGY GA+                           +  +C EA 
Sbjct: 651 NMPLAPDVDLNDIAQRTEGYVGAD---------------------------LENLCREAG 683

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLY 231
           ++A   N +A  VS ++FL AL+ ++P    ++IK Y
Sbjct: 684 MNAYRENPDATSVSQKNFLDALKTIRPSVDEEVIKFY 720

Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) (taxid: 273075)

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

 Score =  163 bits (412), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 83/159 (52%), Positives = 111/159 (69%), Gaps = 1/159 (0%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPEL   + GESE  VRD+F +AR  +P V+FFDELDS+A  RG G  G      +RV+ 
Sbjct: 541 GPELLTMWFGESEANVRDIFDKARSAAPCVLFFDELDSIAKARG-GNVGDAGGAADRVIN 599

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTEMDG+    NV I+ ATNRPD ID A+LRPGRLD+LIY+PLPDD +R AILK  L 
Sbjct: 600 QILTEMDGMGAKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDDKSREAILKANLR 659

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRR 173
           +SPL ++V +  + ++T+G+SGA+ +    RA K+  R+
Sbjct: 660 KSPLAKEVDLTYIAKVTQGFSGADLTEICQRACKLAIRQ 698

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

Drosophila melanogaster (taxid: 7227)

>sp|Q9LZF6|CD48E_ARATH Cell division control protein 48 homolog E OS=Arabidopsis thaliana GN=CDC48E PE=1 SV=2

 Score =  160 bits (406), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 82/154 (53%), Positives = 107/154 (69%), Gaps = 1/154 (0%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPEL   + GESE  VR++F +ARQ +P V+FFDELDS+A +RG+  G  G    +RVL 
Sbjct: 547 GPELLTMWFGESEANVREIFDKARQSAPCVLFFDELDSIATQRGNSAGDAGG-AADRVLN 605

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTEMDG+     V I+ ATNRPD ID ALLRPGRLD+LIY+PLPD+ +R  I K  L 
Sbjct: 606 QLLTEMDGMNAKKTVFIIGATNRPDIIDSALLRPGRLDQLIYIPLPDEDSRLNIFKACLR 665

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKK 168
           +SP+ +DV V  L + T+G+SGA+ +    RA K
Sbjct: 666 KSPVAKDVDVTALAKYTQGFSGADITEICQRACK 699

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  158 bits (400), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 81/154 (52%), Positives = 106/154 (68%), Gaps = 1/154 (0%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPEL   + GESE  VR++F +ARQ +P V+FFDELDS+A +RG   G  G    +RVL 
Sbjct: 548 GPELLTMWFGESEANVREIFDKARQSAPCVLFFDELDSIATQRGSSSGDAGG-AADRVLN 606

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTEMDG+     V I+ ATNRPD ID ALLRPGRLD+LIY+PLPD+ +R  I K  L 
Sbjct: 607 QLLTEMDGMNAKKTVFIIGATNRPDIIDPALLRPGRLDQLIYIPLPDEDSRHQIFKACLR 666

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKK 168
           +SPL +D+ +  L + T+G+SGA+ +    RA K
Sbjct: 667 KSPLSKDIDLRALAKHTQGFSGADVTEICQRACK 700

Probably functions in cell division and growth processes.

Capsicum annuum (taxid: 4072)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	237
328787695	793	PREDICTED: spermatogenesis-associated pr	0.822	0.245	0.556	6e-63
380011891	792	PREDICTED: spermatogenesis-associated pr	0.822	0.246	0.556	1e-62
270006246	758	hypothetical protein TcasGA2_TC008415 [T	0.810	0.253	0.565	2e-62
91081693	696	PREDICTED: similar to spermatogenesis as	0.810	0.275	0.565	2e-62
383865969	796	PREDICTED: spermatogenesis-associated pr	0.822	0.244	0.547	7e-62
194761322	796	GF15657 [Drosophila ananassae] gi|190616	0.822	0.244	0.556	2e-60
195114758	802	GI14498 [Drosophila mojavensis] gi|19391	0.822	0.243	0.551	2e-60
350403271	797	PREDICTED: spermatogenesis-associated pr	0.822	0.244	0.533	3e-60
340728362	797	PREDICTED: spermatogenesis-associated pr	0.822	0.244	0.533	5e-60
194861081	799	GG10242 [Drosophila erecta] gi|190661578	0.827	0.245	0.544	1e-59

>gi|328787695|ref|XP_625214.3| PREDICTED: spermatogenesis-associated protein 5-like [Apis mellifera]

 Score =  246 bits (628), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 124/223 (55%), Positives = 153/223 (68%), Gaps = 28/223 (12%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPELF K+VGESE+ VR+VF++ARQVSPS+IF DE+D+L GER      G SNVQERVLA
Sbjct: 597 GPELFSKWVGESEKAVREVFRKARQVSPSIIFIDEIDALGGERSSSVTAG-SNVQERVLA 655

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTE+DG+  L +VT+VAATNRPD+IDKALLRPGRLDR+IYVPLPD  TR  I  I+L 
Sbjct: 656 QLLTELDGVTALGSVTLVAATNRPDKIDKALLRPGRLDRIIYVPLPDYETRQEIFDIKLR 715

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             P+ EDV +++LV LTEGYSGAE                           I A+C EAA
Sbjct: 716 NMPIAEDVQIQDLVDLTEGYSGAE---------------------------IQAICHEAA 748

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           + ALE +L A  ++ + F  AL ++ PRTPP LI LY +YI K
Sbjct: 749 IKALEEDLNATIITKEHFKAALAIITPRTPPSLINLYNDYINK 791

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380011891|ref|XP_003690027.1| PREDICTED: spermatogenesis-associated protein 5-like [Apis florea]

 Score =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 124/223 (55%), Positives = 153/223 (68%), Gaps = 28/223 (12%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPELF K+VGESE+ VR+VF++ARQVSPS+IF DE+D+L GER      G SNVQERVLA
Sbjct: 596 GPELFSKWVGESEKAVREVFRKARQVSPSIIFIDEIDALGGERSSSVTTG-SNVQERVLA 654

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTE+DG+  L +VT+VAATNRPD+IDKALLRPGRLDR+IYVPLPD  TR  I  I+L 
Sbjct: 655 QLLTELDGVTALGSVTLVAATNRPDKIDKALLRPGRLDRIIYVPLPDYETRQEIFDIKLR 714

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             P+ EDV +++LV LTEGYSGAE                           I A+C EAA
Sbjct: 715 NMPIAEDVQIQDLVDLTEGYSGAE---------------------------IQAICHEAA 747

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           + ALE +L A  ++ + F  AL ++ PRTPP LI LY +YI K
Sbjct: 748 IKALEEDLNATIITKEHFKAALAIITPRTPPSLINLYNDYINK 790

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270006246|gb|EFA02694.1| hypothetical protein TcasGA2_TC008415 [Tribolium castaneum]

 Score =  244 bits (624), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 126/223 (56%), Positives = 161/223 (72%), Gaps = 31/223 (13%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPELF K+VGESE+ VR+VF++ARQV+PSVIFFDE+D+L GER     G  ++VQERVLA
Sbjct: 565 GPELFSKWVGESEKAVREVFRKARQVAPSVIFFDEIDALGGERS---SGSSTSVQERVLA 621

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTE+DG+ PL +VT++AATNRPDRIDKALLRPGRLDR++YVPLPDD TR  I K++L 
Sbjct: 622 QLLTELDGVSPLGDVTVLAATNRPDRIDKALLRPGRLDRIVYVPLPDDDTRREIFKLKLG 681

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
           + P+  +V VEELVRLT GYSGAE                           + AVC EAA
Sbjct: 682 KMPVC-NVDVEELVRLTPGYSGAE---------------------------VNAVCHEAA 713

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           + ALE++L+A +V  + F  AL +VKPRTP  LI+LY++Y+ K
Sbjct: 714 MMALEDSLDARFVEKRHFEKALTIVKPRTPDSLIQLYQDYLNK 756

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91081693|ref|XP_970788.1| PREDICTED: similar to spermatogenesis associated 5 [Tribolium castaneum]

 Score =  244 bits (623), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 126/223 (56%), Positives = 161/223 (72%), Gaps = 31/223 (13%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPELF K+VGESE+ VR+VF++ARQV+PSVIFFDE+D+L GER     G  ++VQERVLA
Sbjct: 503 GPELFSKWVGESEKAVREVFRKARQVAPSVIFFDEIDALGGERS---SGSSTSVQERVLA 559

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTE+DG+ PL +VT++AATNRPDRIDKALLRPGRLDR++YVPLPDD TR  I K++L 
Sbjct: 560 QLLTELDGVSPLGDVTVLAATNRPDRIDKALLRPGRLDRIVYVPLPDDDTRREIFKLKLG 619

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
           + P+  +V VEELVRLT GYSGAE                           + AVC EAA
Sbjct: 620 KMPVC-NVDVEELVRLTPGYSGAE---------------------------VNAVCHEAA 651

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           + ALE++L+A +V  + F  AL +VKPRTP  LI+LY++Y+ K
Sbjct: 652 MMALEDSLDARFVEKRHFEKALTIVKPRTPDSLIQLYQDYLNK 694

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383865969|ref|XP_003708444.1| PREDICTED: spermatogenesis-associated protein 5-like [Megachile rotundata]

 Score =  242 bits (618), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 122/223 (54%), Positives = 154/223 (69%), Gaps = 28/223 (12%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPELF K+VGESE+ VR+VF++ARQVSPS++F DE+D+L GER       GSNVQERVLA
Sbjct: 600 GPELFSKWVGESEKAVREVFRKARQVSPSIVFIDEIDALGGERS-SSSNTGSNVQERVLA 658

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTE+DG+  L +VT+VAATNRPD+IDKALLRPGRLDR+IYVPLPD  TR  I  I+L 
Sbjct: 659 QLLTELDGVSALGSVTLVAATNRPDKIDKALLRPGRLDRIIYVPLPDYDTRQEIFDIKLR 718

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             P+ EDV +++LV LTEGYSGAE                           I A+C EAA
Sbjct: 719 NMPINEDVRIQDLVELTEGYSGAE---------------------------IQAICHEAA 751

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           + ALE +L A+ ++ + F  AL L+ PRTPP LI +Y +Y+ K
Sbjct: 752 MKALEEDLNASIITKEHFKAALALIIPRTPPSLINIYNDYLNK 794

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194761322|ref|XP_001962878.1| GF15657 [Drosophila ananassae] gi|190616575|gb|EDV32099.1| GF15657 [Drosophila ananassae]

 Score =  238 bits (607), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 124/223 (55%), Positives = 155/223 (69%), Gaps = 28/223 (12%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPELF  +VGESER VR+VF+RARQV+P+++FFDE+D++ GER DG  G  S+V+ERVL 
Sbjct: 602 GPELFSMWVGESERAVREVFRRARQVAPAIVFFDEIDAIGGERADGDSGS-SSVKERVLT 660

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTEMDG+  L NVTIVAATNRPD IDKALLRPGR+DR++YV LP    R  ILKI+L 
Sbjct: 661 QLLTEMDGVEALQNVTIVAATNRPDMIDKALLRPGRIDRILYVGLPKAEARREILKIKLR 720

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             PL + V +E+LV+LT+GYSGAE                           I AVC EAA
Sbjct: 721 AMPLADGVDMEKLVQLTDGYSGAE---------------------------IQAVCHEAA 753

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           L ALE + EA +V   DF  AL+ V PRT P+L+KLYE+Y+K+
Sbjct: 754 LRALEQSFEAEHVQWADFEHALKAVPPRTSPELLKLYEDYLKR 796

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195114758|ref|XP_002001934.1| GI14498 [Drosophila mojavensis] gi|193912509|gb|EDW11376.1| GI14498 [Drosophila mojavensis]

 Score =  238 bits (607), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 123/223 (55%), Positives = 156/223 (69%), Gaps = 28/223 (12%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPELF  +VGESER VR+VF++ARQV+P+++FFDE+D++ GER +G  GG S+V+ERVL 
Sbjct: 608 GPELFSMWVGESERAVREVFRKARQVAPAIVFFDEIDAIGGERSEGSAGG-SSVKERVLT 666

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTE+DG+  L+NVTIVAATNRPD IDKALLRPGR+DR+ YV LP+   R  IL I+L 
Sbjct: 667 QLLTELDGVDALHNVTIVAATNRPDMIDKALLRPGRIDRVCYVGLPEAAARREILLIKLR 726

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             PL EDV V++LV LTEGYSGAE                           I AVC EAA
Sbjct: 727 PMPLAEDVIVDQLVELTEGYSGAE---------------------------IQAVCHEAA 759

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           LSALE + EA  V  + F +AL  VKPRT P+L++LY+ Y++K
Sbjct: 760 LSALEQSFEAELVHWRHFESALATVKPRTSPELLRLYQEYMQK 802

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350403271|ref|XP_003486751.1| PREDICTED: spermatogenesis-associated protein 5-like [Bombus impatiens]

 Score =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 119/223 (53%), Positives = 150/223 (67%), Gaps = 28/223 (12%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPELF K+VGESE+ VR+VF++ARQVSPS++F DE+D+L  ERG     G SNVQERVLA
Sbjct: 601 GPELFSKWVGESEKAVREVFRKARQVSPSIVFIDEIDALGSERGSSSSAG-SNVQERVLA 659

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTE+DG+  L +VT+VAATNRPD+IDKALLRPGRLDR+IYV LPD   R  I  I+L 
Sbjct: 660 QLLTELDGVTALGSVTLVAATNRPDKIDKALLRPGRLDRIIYVALPDYEARQEIFDIKLR 719

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             P+ EDV +++LV LTEGYSGAE                           I A+C EAA
Sbjct: 720 NMPIAEDVHIQDLVDLTEGYSGAE---------------------------IQAICHEAA 752

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           + ALE +L A+ ++ + F  AL ++ PRTP  LI LY  Y+ K
Sbjct: 753 IKALEEDLNASIITKEHFKAALAIITPRTPASLINLYNEYMNK 795

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340728362|ref|XP_003402494.1| PREDICTED: spermatogenesis-associated protein 5-like [Bombus terrestris]

 Score =  236 bits (603), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 119/223 (53%), Positives = 149/223 (66%), Gaps = 28/223 (12%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPELF K+VGESE+ VR+VF++ARQVSPS++F DE+D+L  ERG     G SNVQERVLA
Sbjct: 601 GPELFSKWVGESEKAVREVFRKARQVSPSIVFIDEIDALGSERGSSSSAG-SNVQERVLA 659

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTE+DG+  L +VT+VAATNRPD+IDKALLRPGRLDR+IYV LPD   R  I  I+L 
Sbjct: 660 QLLTELDGVTALGSVTLVAATNRPDKIDKALLRPGRLDRIIYVALPDYEARQEIFDIKLR 719

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             P+ EDV +++LV LTEGYSGAE                           I A+C EAA
Sbjct: 720 NMPIAEDVHIQDLVDLTEGYSGAE---------------------------IQAICHEAA 752

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           + ALE +L A  ++ + F  AL ++ PRTP  LI LY  Y+ K
Sbjct: 753 IKALEEDLNATIITKEHFKAALAIITPRTPASLINLYNEYMNK 795

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194861081|ref|XP_001969711.1| GG10242 [Drosophila erecta] gi|190661578|gb|EDV58770.1| GG10242 [Drosophila erecta]

 Score =  235 bits (599), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 122/224 (54%), Positives = 153/224 (68%), Gaps = 28/224 (12%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDG-GGGGGSNVQERVL 73
           GPELF  +VGESER VR+VF++ARQV+P+++FFDE+D++ GER +G G G G++V+ERVL
Sbjct: 602 GPELFSMWVGESERAVREVFRKARQVAPAIVFFDEIDAIGGERSEGEGSGSGASVKERVL 661

Query: 74  AQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
            Q+LTE+DG+  L NVTIVAATNRPD IDKALLRPGR+DR++YV LP    R  IL+I+L
Sbjct: 662 TQLLTELDGVETLQNVTIVAATNRPDMIDKALLRPGRIDRILYVGLPQCEARREILRIKL 721

Query: 134 ARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEA 193
              P   DV +E LV+LTEGYSGAE                           I AVC EA
Sbjct: 722 RAMPTSNDVDMERLVQLTEGYSGAE---------------------------IQAVCHEA 754

Query: 194 ALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           AL ALE + EA  V   DF  AL+ V PRT P+L+KLYE Y+K+
Sbjct: 755 ALRALEQSFEAEDVKWTDFEHALKAVPPRTSPELLKLYEEYLKR 798

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	237
FB|FBgn0032450	799	CG5776 [Drosophila melanogaste	0.641	0.190	0.581	1.6e-48
MGI|MGI:1927170	893	Spata5 "spermatogenesis associ	0.599	0.159	0.611	5.6e-46
UNIPROTKB|E2RC37	893	SPATA5 "Uncharacterized protei	0.599	0.159	0.618	4.9e-45
UNIPROTKB|Q8NB90	893	SPATA5 "Spermatogenesis-associ	0.599	0.159	0.604	5.3e-45
WB|WBGene00010562	724	cdc-48.3 [Caenorhabditis elega	0.594	0.194	0.524	6.8e-38
DICTYBASE|DDB_G0278435	886	DDB_G0278435 "AAA ATPase domai	0.590	0.158	0.562	2.6e-37
TAIR|locus:2103555	1022	CIP111 "Cam interacting protei	0.611	0.141	0.530	9.1e-36
ZFIN|ZDB-GENE-060312-22	805	zgc:136908 "zgc:136908" [Danio	0.662	0.195	0.506	1.4e-35
UNIPROTKB|H9KYT1	538	LOC430766 "Uncharacterized pro	0.662	0.291	0.5	1.9e-35
UNIPROTKB|G3X757	806	VCP "Transitional endoplasmic	0.662	0.194	0.506	7.8e-35

FB|FBgn0032450 CG5776 [Drosophila melanogaster (taxid:7227)]

 Score = 444 (161.4 bits), Expect = 1.6e-48, Sum P(2) = 1.6e-48
 Identities = 89/153 (58%), Positives = 113/153 (73%)

Query:    15 GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXX-SNVQERVL 73
             GPELF  +VGESER VR+VF++ARQV+P+++FFDE+D++             S+V+ERVL
Sbjct:   602 GPELFSMWVGESERAVREVFRKARQVAPAIVFFDEIDAIGGERSEGDGSSSGSSVKERVL 661

Query:    74 AQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
              Q+LTE+DG+  L NVTIVAATNRPD IDKALLRPGR+DR++YV LP    R  ILKI+L
Sbjct:   662 TQLLTELDGVEALQNVTIVAATNRPDMIDKALLRPGRIDRILYVGLPQCEARREILKIKL 721

Query:   134 ARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA 166
                P+  DV +E+LV+LTEGYSGAE     H A
Sbjct:   722 RAMPISNDVDMEKLVQLTEGYSGAEIQAVCHEA 754

GO:0016887 "ATPase activity" evidence=ISS

GO:0005783 "endoplasmic reticulum" evidence=ISS

GO:0005524 "ATP binding" evidence=IEA

MGI|MGI:1927170 Spata5 "spermatogenesis associated 5" [Mus musculus (taxid:10090)]

 Score = 445 (161.7 bits), Expect = 5.6e-46, Sum P(2) = 5.6e-46
 Identities = 88/144 (61%), Positives = 109/144 (75%)

Query:    15 GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
             GPEL  KYVGESER VR++F++AR V+PS+IFFDELD+LA            NV +RVLA
Sbjct:   694 GPELMNKYVGESERAVREIFRKARAVAPSIIFFDELDALAVERGSSSGA--GNVADRVLA 751

Query:    75 QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
             Q+LTEMDGI  L NVT++AATNRPDRIDKAL+RPGR+DR+IYVPLPD  TR  IL ++  
Sbjct:   752 QLLTEMDGIEQLKNVTVLAATNRPDRIDKALMRPGRIDRIIYVPLPDAATRREILNLQFH 811

Query:   135 RSPLGEDVCVEELVRLTEGYSGAE 158
               P+  +V ++ELV  T+ YSGAE
Sbjct:   812 SMPISNEVDLDELVLQTDTYSGAE 835

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

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

GO:0030154 "cell differentiation" evidence=IEA

UNIPROTKB|E2RC37 SPATA5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 446 (162.1 bits), Expect = 4.9e-45, Sum P(2) = 4.9e-45
 Identities = 89/144 (61%), Positives = 109/144 (75%)

Query:    15 GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
             GPEL  KYVGESER VR++F++AR VSPS+IFFDELD+LA            NV +RVLA
Sbjct:   694 GPELMNKYVGESERAVREIFRKARAVSPSIIFFDELDALAIERGSSSGA--GNVADRVLA 751

Query:    75 QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
             Q+LTEMDGI  L +VTI+AATNRPDRIDKAL+RPGR+DR+IYVPLPD  TR  IL ++  
Sbjct:   752 QLLTEMDGIEQLKDVTILAATNRPDRIDKALMRPGRIDRIIYVPLPDAATRREILNLQFH 811

Query:   135 RSPLGEDVCVEELVRLTEGYSGAE 158
               P+  DV ++EL+  T+ YSGAE
Sbjct:   812 SMPISNDVNLDELIFQTDTYSGAE 835

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|Q8NB90 SPATA5 "Spermatogenesis-associated protein 5" [Homo sapiens (taxid:9606)]

 Score = 438 (159.2 bits), Expect = 5.3e-45, Sum P(2) = 5.3e-45
 Identities = 87/144 (60%), Positives = 108/144 (75%)

Query:    15 GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
             GPEL  KYVGESER VR+ F++AR V+PS+IFFDELD+LA            NV +RVLA
Sbjct:   694 GPELMNKYVGESERAVRETFRKARAVAPSIIFFDELDALAVERGSSLGA--GNVADRVLA 751

Query:    75 QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
             Q+LTEMDGI  L +VTI+AATNRPDRIDKAL+RPGR+DR+IYVPLPD  TR  I K++  
Sbjct:   752 QLLTEMDGIEQLKDVTILAATNRPDRIDKALMRPGRIDRIIYVPLPDAATRREIFKLQFH 811

Query:   135 RSPLGEDVCVEELVRLTEGYSGAE 158
               P+  +V ++EL+  T+ YSGAE
Sbjct:   812 SMPVSNEVDLDELILQTDAYSGAE 835

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

GO:0005524 "ATP binding" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0030154 "cell differentiation" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

WB|WBGene00010562 cdc-48.3 [Caenorhabditis elegans (taxid:6239)]

 Score = 386 (140.9 bits), Expect = 6.8e-38, Sum P(2) = 6.8e-38
 Identities = 76/145 (52%), Positives = 106/145 (73%)

Query:    15 GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
             GPELF K+VG+SE+ +RD+F RARQV+P+++FFDE+D++            S V +RVLA
Sbjct:   526 GPELFSKWVGDSEKAIRDLFSRARQVAPTIVFFDEIDAVGSSRGSEKS---SGVSDRVLA 582

Query:    75 QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
             Q+LTE+DG+   + V ++AATNRPD++D ALLRPGRLDR IYV LP ++TR AIL++R  
Sbjct:   583 QLLTELDGLEKSSRVILLAATNRPDQLDSALLRPGRLDRAIYVGLPCEVTRRAILEMRTK 642

Query:   135 RSPLGEDV-CVEELVRLTEGYSGAE 158
             +    + V  +++LV  T GYSGAE
Sbjct:   643 KMKFDDTVRTIDKLVEKTSGYSGAE 667

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0007091 "metaphase/anaphase transition of mitotic cell cycle" evidence=IMP

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0007067 "mitosis" evidence=IMP

GO:0019901 "protein kinase binding" evidence=IPI

GO:0016887 "ATPase activity" evidence=IDA

GO:0006469 "negative regulation of protein kinase activity" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006200 "ATP catabolic process" evidence=IDA

DICTYBASE|DDB_G0278435 DDB_G0278435 "AAA ATPase domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 398 (145.2 bits), Expect = 2.6e-37, Sum P(2) = 2.6e-37
 Identities = 81/144 (56%), Positives = 101/144 (70%)

Query:    15 GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
             GPEL  K+VGESER VRD+FK+ARQ SPS++FFDE+D LA           S   ERV++
Sbjct:   689 GPELLSKWVGESERAVRDIFKKARQNSPSILFFDEIDGLAISRSGEG----SGAVERVVS 744

Query:    75 QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
             Q+LTEMDGI PL NVTI+ ATNRPD IDKA+LR GR+DR++Y+  PD   R  I  I L 
Sbjct:   745 QLLTEMDGIQPLTNVTIIGATNRPDIIDKAILRAGRIDRILYISPPDLDARKEIFNIHLK 804

Query:   135 RSPLGEDVCVEELVRLTEGYSGAE 158
             + P   D+ + +L  LT+GYSGAE
Sbjct:   805 KVPHSSDIDINQLSILTDGYSGAE 828

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

GO:0005524 "ATP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0016887 "ATPase activity" evidence=ISS

GO:0006200 "ATP catabolic process" evidence=ISS

TAIR|locus:2103555 CIP111 "Cam interacting protein 111" [Arabidopsis thaliana (taxid:3702)]

 Score = 397 (144.8 bits), Expect = 9.1e-36, P = 9.1e-36
 Identities = 78/147 (53%), Positives = 106/147 (72%)

Query:    15 GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
             GPELF K+VGESE+ VR +F +AR  +PS+IFFDE+DSLA            +V +RV++
Sbjct:   791 GPELFSKWVGESEKAVRSLFAKARANAPSIIFFDEIDSLASIRGKENDGV--SVSDRVMS 848

Query:    75 QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
             Q+L E+DG+     VT++AATNRPD+ID ALLRPGR DRL+YV  P++  R AILKI L 
Sbjct:   849 QLLVELDGLHQRVGVTVIAATNRPDKIDSALLRPGRFDRLLYVGPPNETDREAILKIHLR 908

Query:   135 RSPLGEDVCVEELVRLTEGYSGAEQSL 161
             + P   D+C++EL  +T+GY+GA+ SL
Sbjct:   909 KIPCSSDICLKELASITKGYTGADISL 935

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0005516 "calmodulin binding" evidence=IDA;TAS

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

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

 Score = 381 (139.2 bits), Expect = 1.4e-35, Sum P(2) = 1.4e-35
 Identities = 80/158 (50%), Positives = 106/158 (67%)

Query:    15 GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
             GPEL   + GESE  VRDVF +ARQ +P ++FFDELDS+A               +RV+ 
Sbjct:   546 GPELLTMWFGESEANVRDVFDKARQAAPCILFFDELDSIAKARGGGAGDA-GGAADRVIN 604

Query:    75 QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
             Q+LTEMDG+    NV I+ ATNRPD ID A+LRPGRLD+LIY+PLPD  +R AIL+  L 
Sbjct:   605 QILTEMDGMTNKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDMPSRTAILRANLR 664

Query:   135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPR 172
             +SP+ +DV +  L ++TEG+SGA+ +    RA K+  R
Sbjct:   665 KSPVAKDVDLMYLSKITEGFSGADLTEICQRACKLAIR 702

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

GO:0005524 "ATP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|H9KYT1 LOC430766 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 383 (139.9 bits), Expect = 1.9e-35, P = 1.9e-35
 Identities = 79/158 (50%), Positives = 107/158 (67%)

Query:    15 GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
             GPEL   + GESE  VR++F +ARQ +P V+FFDELDS+A               +RV+ 
Sbjct:   276 GPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDG-GGAADRVIN 334

Query:    75 QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
             Q+LTEMDG+    NV I+ ATNRPD ID A+LRPGRLD+LIY+PLPD+ +R AILK  L 
Sbjct:   335 QILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLR 394

Query:   135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPR 172
             +SP+ +DV ++ L ++T G+SGA+ +    RA K+  R
Sbjct:   395 KSPVAKDVDLDFLAKMTNGFSGADLTEICQRACKLAIR 432

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

GO:0005524 "ATP binding" evidence=IEA

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

 Score = 386 (140.9 bits), Expect = 7.8e-35, P = 7.8e-35
 Identities = 80/158 (50%), Positives = 107/158 (67%)

Query:    15 GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
             GPEL   + GESE  VR++F +ARQ +P V+FFDELDS+A               +RV+ 
Sbjct:   544 GPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDG-GGAADRVIN 602

Query:    75 QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
             Q+LTEMDG+    NV I+ ATNRPD ID A+LRPGRLD+LIY+PLPD+ +R AILK  L 
Sbjct:   603 QILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLR 662

Query:   135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPR 172
             +SP+ +DV +E L ++T G+SGA+ +    RA K+  R
Sbjct:   663 KSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIR 700

GO:0070842 "aggresome assembly" evidence=IEA

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

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

GO:0031593 "polyubiquitin binding" evidence=IEA

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

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

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

GO:0019903 "protein phosphatase binding" evidence=IEA

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

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

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

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q58556	Y1156_METJA	No assigned EC number	0.5277	0.5949	0.1561	yes	N/A
P46468	CDAT_PLAF7	No assigned EC number	0.5277	0.5949	0.1147	yes	N/A
P46462	TERA_RAT	No assigned EC number	0.5419	0.6497	0.1910	yes	N/A
Q3UMC0	SPAT5_MOUSE	No assigned EC number	0.5291	0.8185	0.2172	yes	N/A
Q8NB90	SPAT5_HUMAN	No assigned EC number	0.5246	0.8185	0.2172	yes	N/A
Q7ZU99	TERA_DANRE	No assigned EC number	0.5316	0.6624	0.1947	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	237
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	2e-57
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	2e-57
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	4e-54
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	4e-54
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	2e-49
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	7e-42
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	6e-39
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	5e-38
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	8e-37
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	1e-36
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	7e-36
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	3e-33
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	4e-33
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	8e-31
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	5e-23
COG1223	368	COG1223, COG1223, Predicted ATPase (AAA+ superfami	6e-23
CHL00195	489	CHL00195, ycf46, Ycf46; Provisional	7e-13
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	5e-12
smart00382	148	smart00382, AAA, ATPases associated with a variety	2e-10

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

 Score =  187 bits (476), Expect = 2e-57
 Identities = 84/206 (40%), Positives = 119/206 (57%), Gaps = 30/206 (14%)

Query: 14  IGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVL 73
           +G EL +KY+GE  R VR++F+ AR+ +PS+IF DE+D++  +R D G  G   VQ R +
Sbjct: 217 VGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQ-RTM 275

Query: 74  AQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
            ++L ++DG  P  NV ++ ATNRPD +D ALLRPGR DR I  PLPD+  RA ILKI  
Sbjct: 276 LELLNQLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHT 335

Query: 134 ARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEA 193
            +  L +DV +E L RLTEG+SGA+                           + A+C EA
Sbjct: 336 RKMNLADDVDLELLARLTEGFSGAD---------------------------LKAICTEA 368

Query: 194 ALSALENNLEAAYVSHQDFLTALQLV 219
            + A+        V+ +DFL A++ V
Sbjct: 369 GMFAIRE--RRDEVTMEDFLKAVEKV 392

Length = 406

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

 Score =  186 bits (475), Expect = 2e-57
 Identities = 88/207 (42%), Positives = 122/207 (58%), Gaps = 30/207 (14%)

Query: 14  IGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVL 73
           +G EL +K++GE  R VR++F+ AR+ +PS+IF DE+D++A +R D G  G   VQ R L
Sbjct: 197 VGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQ-RTL 255

Query: 74  AQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
            Q+L EMDG  P  NV I+AATNR D +D A+LRPGR DR+I VPLPD+  R  ILKI  
Sbjct: 256 MQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHT 315

Query: 134 ARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEA 193
            +  L +DV +EEL  LTEG SGA+                           + A+C EA
Sbjct: 316 RKMNLADDVDLEELAELTEGASGAD---------------------------LKAICTEA 348

Query: 194 ALSALENNLEAAYVSHQDFLTALQLVK 220
            + A+ ++     V+ +DFL A++ V 
Sbjct: 349 GMFAIRDDRT--EVTMEDFLKAIEKVM 373

Length = 389

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

 Score =  180 bits (459), Expect = 4e-54
 Identities = 98/214 (45%), Positives = 124/214 (57%), Gaps = 34/214 (15%)

Query: 10  VVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQ 69
            +   G EL  K+VGESE+ +R++F++AR+++PS+IF DE+DSLA  RG    G G    
Sbjct: 304 FISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSG---- 359

Query: 70  ERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAIL 129
            RV+ Q+LTE+DGI     V ++AATNRPD +D ALLRPGR DRLIYVPLPD   R  I 
Sbjct: 360 RRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIF 419

Query: 130 KIRLARS--PLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIV 187
           KI L     PL EDV +EEL  +TEGYSGA+                           I 
Sbjct: 420 KIHLRDKKPPLAEDVDLEELAEITEGYSGAD---------------------------IA 452

Query: 188 AVCDEAALSALENNLEAAYVSHQDFLTALQLVKP 221
           A+  EAAL AL        V+  DFL AL+ +KP
Sbjct: 453 ALVREAALEALREAR-RREVTLDDFLDALKKIKP 485

Length = 494

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

 Score =  184 bits (468), Expect = 4e-54
 Identities = 100/238 (42%), Positives = 136/238 (57%), Gaps = 46/238 (19%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPE+  K+VGESE+ +R++F++ARQ +P++IFFDE+D++A  RG       ++V +R++ 
Sbjct: 520 GPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARG---ARFDTSVTDRIVN 576

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTEMDGI  L+NV ++AATNRPD +D ALLRPGR DRLI VP PD+  R  I KI   
Sbjct: 577 QLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTR 636

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             PL EDV +EEL  +TEGY+GA+                           I AVC EAA
Sbjct: 637 SMPLAEDVDLEELAEMTEGYTGAD---------------------------IEAVCREAA 669

Query: 195 LSAL----------------ENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIK 236
           ++AL                E  L+   V  + FL AL+ VKP    + +  YE   K
Sbjct: 670 MAALRESIGSPAKEKLEVGEEEFLKDLKVEMRHFLEALKKVKPSVSKEDMLRYERLAK 727

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

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

 Score =  165 bits (419), Expect = 2e-49
 Identities = 88/207 (42%), Positives = 121/207 (58%), Gaps = 30/207 (14%)

Query: 14  IGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVL 73
           +G EL RKY+GE  R VR++F+ A++ +PS+IF DE+D++A +R D G  G   VQ R L
Sbjct: 188 VGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQ-RTL 246

Query: 74  AQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
            Q+L E+DG  P  NV ++AATNRPD +D ALLRPGR DR+I VPLPD   R  ILKI  
Sbjct: 247 MQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHT 306

Query: 134 ARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEA 193
            +  L EDV +E + ++TEG SGA+                           + A+C EA
Sbjct: 307 RKMKLAEDVDLEAIAKMTEGASGAD---------------------------LKAICTEA 339

Query: 194 ALSALENNLEAAYVSHQDFLTALQLVK 220
            + A+    E  YV+  DF+ A++ V 
Sbjct: 340 GMFAIRE--ERDYVTMDDFIKAVEKVL 364

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

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

 Score =  148 bits (375), Expect = 7e-42
 Identities = 63/136 (46%), Positives = 89/136 (65%), Gaps = 3/136 (2%)

Query: 23  VGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG 82
           VG S   VRD+F++A++ +P +IF DE+D++  +RG  G GGG++ +E+ L Q+L EMDG
Sbjct: 131 VGASR--VRDLFEQAKKNAPCIIFIDEIDAVGRQRG-AGLGGGNDEREQTLNQLLVEMDG 187

Query: 83  IVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDV 142
                 V ++AATNRPD +D ALLRPGR DR + V LPD   R  ILK+      L  DV
Sbjct: 188 FGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDV 247

Query: 143 CVEELVRLTEGYSGAE 158
            ++ + R T G+SGA+
Sbjct: 248 DLKAVARRTPGFSGAD 263

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

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

 Score =  138 bits (350), Expect = 6e-39
 Identities = 73/188 (38%), Positives = 101/188 (53%), Gaps = 28/188 (14%)

Query: 14  IGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVL 73
           +G E  +KY+GE  R VRDVF+ AR+ +PS+IF DE+DS+A +R D   G    VQ R+L
Sbjct: 211 VGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQ-RIL 269

Query: 74  AQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
            ++L +MDG     NV ++ ATNR D +D ALLRPGRLDR I  PLPD   +  I +   
Sbjct: 270 LELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTIT 329

Query: 134 ARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEA 193
           ++  L E+V +E+ V   E  S A+                           I A+C EA
Sbjct: 330 SKMNLSEEVDLEDFVSRPEKISAAD---------------------------IAAICQEA 362

Query: 194 ALSALENN 201
            + A+  N
Sbjct: 363 GMQAVRKN 370

Length = 398

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

 Score =  139 bits (352), Expect = 5e-38
 Identities = 67/144 (46%), Positives = 91/144 (63%), Gaps = 1/144 (0%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           G E    +VG     VRD+FK+A++ SP ++F DE+D++  +RG  G GGG++ +E+ L 
Sbjct: 249 GSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRG-AGIGGGNDEREQTLN 307

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTEMDG      V ++AATNR D +D ALLRPGR DR I V LPD   R  ILK+   
Sbjct: 308 QLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHAR 367

Query: 135 RSPLGEDVCVEELVRLTEGYSGAE 158
              L  DV +E + R T G+SGA+
Sbjct: 368 NKKLSPDVSLELIARRTPGFSGAD 391

Length = 638

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

 Score =  135 bits (342), Expect = 8e-37
 Identities = 65/138 (47%), Positives = 92/138 (66%), Gaps = 1/138 (0%)

Query: 22  YVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD 81
           +VG     VRD+F++A++ +P +IF DE+D++  +RG  G GGG++ +E+ L Q+L EMD
Sbjct: 223 FVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRG-AGLGGGNDEREQTLNQLLVEMD 281

Query: 82  GIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGED 141
           G      V ++AATNRPD +D ALLRPGR DR I V LPD   R  ILK+     PL ED
Sbjct: 282 GFGGNEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAED 341

Query: 142 VCVEELVRLTEGYSGAEQ 159
           V ++++ R T G+SGA+ 
Sbjct: 342 VDLKKIARGTPGFSGADL 359

Length = 596

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

 Score =  136 bits (343), Expect = 1e-36
 Identities = 80/207 (38%), Positives = 118/207 (57%), Gaps = 14/207 (6%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPE+  KY GESE  +R++FK A + +PS+IF DE+D++A +R +  G     V++RV+A
Sbjct: 245 GPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTG----EVEKRVVA 300

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LT MDG+     V ++ ATNRPD +D AL RPGR DR I + +PD   R  ILK+   
Sbjct: 301 QLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTR 360

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             PL EDV +++L  +T G+ GA+ +     A     RR    G       I    +E  
Sbjct: 361 NMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREG------KINFEAEEIP 414

Query: 195 LSALENNLEAAYVSHQDFLTALQLVKP 221
              L+       V+ +DF+ AL++V+P
Sbjct: 415 AEVLKE----LKVTMKDFMEALKMVEP 437

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

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

 Score =  123 bits (310), Expect = 7e-36
 Identities = 56/106 (52%), Positives = 76/106 (71%), Gaps = 6/106 (5%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           G EL  KYVGESE+ +R++F+ A++++P VIF DE+D+LAG RG GG         RV+ 
Sbjct: 31  GSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSGGDS----ESRRVVN 86

Query: 75  QMLTEMDGI-VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPL 119
           Q+LTE+DG    L+ V ++AATNRPD++D ALLR GR DR+I  PL
Sbjct: 87  QLLTELDGFTSSLSKVIVIAATNRPDKLDPALLR-GRFDRIIEFPL 131

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

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

 Score =  126 bits (317), Expect = 3e-33
 Identities = 64/144 (44%), Positives = 91/144 (63%), Gaps = 1/144 (0%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           G +    +VG     VRD+F++A++ +P +IF DE+D++  +RG  G GGG + +E+ L 
Sbjct: 218 GSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRG-AGLGGGHDEREQTLN 276

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           QML EMDG      + ++AATNRPD +D ALLRPGR DR + V LPD   R  ILK+ + 
Sbjct: 277 QMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMR 336

Query: 135 RSPLGEDVCVEELVRLTEGYSGAE 158
           R PL  D+    + R T G+SGA+
Sbjct: 337 RVPLAPDIDAAIIARGTPGFSGAD 360

Length = 644

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

 Score =  123 bits (311), Expect = 4e-33
 Identities = 68/203 (33%), Positives = 110/203 (54%), Gaps = 32/203 (15%)

Query: 14  IGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVL 73
           +G EL +KY+G+  + VR++F+ A + +PS++F DE+D++  +R D   GG   +Q R +
Sbjct: 249 VGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQ-RTM 307

Query: 74  AQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
            ++L ++DG     +V ++ ATNR + +D AL+RPGR+DR I  P PD+ T+  I +I  
Sbjct: 308 LELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHT 367

Query: 134 ARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEA 193
           ++  L EDV +EE +   +  SGA+                           I A+C EA
Sbjct: 368 SKMTLAEDVDLEEFIMAKDELSGAD---------------------------IKAICTEA 400

Query: 194 ALSAL-ENNLEAAYVSHQDFLTA 215
            L AL E  ++   V+  DF  A
Sbjct: 401 GLLALRERRMK---VTQADFRKA 420

Length = 438

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

 Score =  118 bits (297), Expect = 8e-31
 Identities = 62/132 (46%), Positives = 82/132 (62%), Gaps = 8/132 (6%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQE 70
           GPEL  KYVGE+ER +R +F+RAR+      P ++FFDE+DSL   RG G     S+V+ 
Sbjct: 259 GPELLNKYVGETERQIRLIFQRAREKASEGRPVIVFFDEMDSLFRTRGSGVS---SDVET 315

Query: 71  RVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILK 130
            V+ Q+L E+DG+  L+NV ++ A+NR D ID A+LRPGRLD  I +  PD    A I  
Sbjct: 316 TVVPQLLAEIDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFA 375

Query: 131 IRLARS-PLGED 141
             L    PL ED
Sbjct: 376 KYLTDDLPLPED 387

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

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

 Score = 96.4 bits (240), Expect = 5e-23
 Identities = 79/211 (37%), Positives = 106/211 (50%), Gaps = 36/211 (17%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPE+  KYVGESE  +R++F+ A +++PS+IF DE+D+LA +R    G     V+ RV+A
Sbjct: 50  GPEILSKYVGESELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQGE----VERRVVA 105

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+L  MDG +    V ++ ATNRPD +D A  RPGR DR I V LPD+  R  IL+I   
Sbjct: 106 QLLALMDG-LKRGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHTR 164

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
              LG     + L   T G SGA+                           + A+  EAA
Sbjct: 165 LMFLGPPGTGKTLAARTVGKSGAD---------------------------LGALAKEAA 197

Query: 195 LSALEN----NLEAAYVSHQDFLTALQLVKP 221
           L  L        E   V+  DF  AL+ V P
Sbjct: 198 LRELRRAIDLVGEYIGVTEDDFEEALKKVLP 228

Length = 494

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

 Score = 95.3 bits (237), Expect = 6e-23
 Identities = 52/143 (36%), Positives = 81/143 (56%), Gaps = 5/143 (3%)

Query: 16  PELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQ 75
            EL  ++VG+  R + ++++RAR+ +P ++F DELD++A +R      G  +V E V A 
Sbjct: 185 TELIGEHVGDGARRIHELYERARKAAPCIVFIDELDAIALDRRYQELRG--DVSEIVNA- 241

Query: 76  MLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR 135
           +LTE+DGI     V  +AATNRP+ +D A+    R +  I   LP+D  R  IL+    +
Sbjct: 242 LLTELDGIKENEGVVTIAATNRPELLDPAI--RSRFEEEIEFKLPNDEERLEILEYYAKK 299

Query: 136 SPLGEDVCVEELVRLTEGYSGAE 158
            PL  D  +  L   T+G SG +
Sbjct: 300 FPLPVDADLRYLAAKTKGMSGRD 322

Length = 368

>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional

 Score = 67.0 bits (164), Expect = 7e-13
 Identities = 47/144 (32%), Positives = 73/144 (50%), Gaps = 9/144 (6%)

Query: 18  LFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQML 77
           LF   VGESE  +R + + A  +SP +++ DE+D         G  G +N   RVLA  +
Sbjct: 295 LFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKGDSGTTN---RVLATFI 351

Query: 78  TEM-DGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS 136
           T + +   P   V +VA  N  D +   +LR GR D + ++ LP    R  I KI L + 
Sbjct: 352 TWLSEKKSP---VFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKF 408

Query: 137 -PLG-EDVCVEELVRLTEGYSGAE 158
            P   +   +++L +L+  +SGAE
Sbjct: 409 RPKSWKKYDIKKLSKLSNKFSGAE 432

Length = 489

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

 Score = 61.4 bits (149), Expect = 5e-12
 Identities = 32/113 (28%), Positives = 46/113 (40%), Gaps = 14/113 (12%)

Query: 10  VVESIGPELFRKYVGESER---CVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGS 66
            +     +L    V         VR +F+ A +  P V+F DE+DSL+            
Sbjct: 50  FLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRG---------- 99

Query: 67  NVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPL 119
             Q  +L  + T  D  +   NV ++ ATNRP   D       RLD  I +PL
Sbjct: 100 -AQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151

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

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

 Score = 57.0 bits (137), Expect = 2e-10
 Identities = 29/121 (23%), Positives = 47/121 (38%), Gaps = 10/121 (8%)

Query: 1   MEDLGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDG 60
            ED+         +     +K  G  E  +R     AR++ P V+  DE+ SL     + 
Sbjct: 38  GEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDVLILDEITSLLDAEQE- 96

Query: 61  GGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLP 120
                      +L + L  +  +    N+T++  TN    +  ALLR  R DR I + L 
Sbjct: 97  --------ALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLI 147

Query: 121 D 121
            
Sbjct: 148 L 148

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Length = 148

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	237
KOG0730|consensus	693		100.0
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	100.0
KOG0738|consensus	491		100.0
KOG0733|consensus	802		100.0
KOG0736|consensus	953		100.0
KOG0739|consensus	439		100.0
KOG0733|consensus	802		100.0
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	100.0
CHL00195	489	ycf46 Ycf46; Provisional	100.0
KOG0734|consensus	752		100.0
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	100.0
KOG0728|consensus	404		100.0
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.97
KOG0735|consensus	952		99.97
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.97
KOG0737|consensus	386		99.97
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.97
KOG0731|consensus	774		99.97
KOG0740|consensus	428		99.97
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.97
KOG0730|consensus	693		99.96
KOG0727|consensus	408		99.96
KOG0726|consensus	440		99.96
KOG0652|consensus	424		99.96
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.96
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.96
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.96
KOG0729|consensus	435		99.96
CHL00206	2281	ycf2 Ycf2; Provisional	99.96
KOG0741|consensus	744		99.95
CHL00176	638	ftsH cell division protein; Validated	99.95
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.94
KOG0732|consensus	1080		99.94
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.93
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.93
KOG0651|consensus	388		99.93
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.92
KOG0735|consensus	952		99.83
KOG0736|consensus	953		99.81
KOG0744|consensus	423		99.76
PF00004	132	AAA: ATPase family associated with various cellula	99.65
KOG0742|consensus	630		99.65
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.64
KOG0743|consensus	457		99.44
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.4
CHL00181	287	cbbX CbbX; Provisional	99.37
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.37
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.26
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.26
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.17
PRK10865	857	protein disaggregation chaperone; Provisional	99.09
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.06
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.02
CHL00095	821	clpC Clp protease ATP binding subunit	98.97
PRK00149	450	dnaA chromosomal replication initiation protein; R	98.76
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.76
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.74
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.66
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.62
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.6
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	98.57
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	98.57
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.54
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	98.52
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	98.49
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.49
PRK14086	617	dnaA chromosomal replication initiation protein; P	98.48
PRK12422	445	chromosomal replication initiation protein; Provis	98.46
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.36
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.29
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.27
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	98.26
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	98.24
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.23
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.21
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.21
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.2
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.19
PRK04132	846	replication factor C small subunit; Provisional	98.18
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	98.17
PRK04195	482	replication factor C large subunit; Provisional	98.14
PRK12402	337	replication factor C small subunit 2; Reviewed	98.12
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	98.1
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.1
KOG2004|consensus	906		98.09
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.09
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.07
PRK13342	413	recombination factor protein RarA; Reviewed	98.06
PRK08727	233	hypothetical protein; Validated	98.05
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.05
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.01
PRK06893	229	DNA replication initiation factor; Validated	97.99
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	97.99
PF09336	62	Vps4_C: Vps4 C terminal oligomerisation domain; In	97.99
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.99
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.95
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.94
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	97.94
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.93
PHA02544	316	44 clamp loader, small subunit; Provisional	97.93
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	97.92
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.92
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.89
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.85
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.85
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.84
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.81
COG2256	436	MGS1 ATPase related to the helicase subunit of the	97.81
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.8
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.8
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.79
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	97.78
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.77
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.75
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.75
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.74
PRK13341	725	recombination factor protein RarA/unknown domain f	97.73
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.73
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.72
PRK09087	226	hypothetical protein; Validated	97.7
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	97.7
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.68
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.67
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.67
PRK05642	234	DNA replication initiation factor; Validated	97.67
CHL00195	489	ycf46 Ycf46; Provisional	97.65
PRK08084	235	DNA replication initiation factor; Provisional	97.64
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	97.64
PLN03025	319	replication factor C subunit; Provisional	97.63
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.63
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.62
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.61
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.57
KOG1514|consensus	767		97.57
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.54
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	97.53
KOG0741|consensus	744		97.53
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.51
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.51
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	97.5
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	97.5
smart00350	509	MCM minichromosome maintenance proteins.	97.45
KOG2028|consensus	554		97.42
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.41
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.41
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.39
PRK06620	214	hypothetical protein; Validated	97.32
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.3
KOG0989|consensus	346		97.3
PRK06964	342	DNA polymerase III subunit delta'; Validated	97.28
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	97.28
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	97.26
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.26
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	97.24
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.23
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	97.21
PRK07993	334	DNA polymerase III subunit delta'; Validated	97.19
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.17
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.15
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	97.07
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.03
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	97.01
PRK08769	319	DNA polymerase III subunit delta'; Validated	96.97
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	96.96
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.93
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.87
CHL00095	821	clpC Clp protease ATP binding subunit	96.84
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	96.83
COG0714	329	MoxR-like ATPases [General function prediction onl	96.79
PRK05564	313	DNA polymerase III subunit delta'; Validated	96.79
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	96.68
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.65
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	96.46
smart00382	148	AAA ATPases associated with a variety of cellular	96.46
KOG2680|consensus	454		96.45
PRK10865	857	protein disaggregation chaperone; Provisional	96.34
PRK07399	314	DNA polymerase III subunit delta'; Validated	96.33
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	96.32
PRK08058	329	DNA polymerase III subunit delta'; Validated	96.28
PHA02244	383	ATPase-like protein	96.25
KOG1051|consensus	898		96.17
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.16
PRK06581	263	DNA polymerase III subunit delta'; Validated	96.08
KOG2227|consensus	529		96.01
PRK07276	290	DNA polymerase III subunit delta'; Validated	95.97
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	95.94
KOG2035|consensus	351		95.67
PRK13531	498	regulatory ATPase RavA; Provisional	95.47
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	95.44
PRK08485	206	DNA polymerase III subunit delta'; Validated	95.39
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	95.23
PRK08699	325	DNA polymerase III subunit delta'; Validated	95.21
KOG0745|consensus	564		95.15
KOG1942|consensus	456		95.14
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	95.07
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	94.88
PRK05917	290	DNA polymerase III subunit delta'; Validated	94.81
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	94.71
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	94.68
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	94.65
PRK09862	506	putative ATP-dependent protease; Provisional	94.54
PF05729	166	NACHT: NACHT domain	94.39
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	94.31
KOG2228|consensus	408		93.83
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	93.7
COG4565	224	CitB Response regulator of citrate/malate metaboli	93.61
PF13304	303	AAA_21: AAA domain; PDB: 3QKS_B 1US8_B 1F2U_B 1F2T	93.02
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	92.82
PRK07132	299	DNA polymerase III subunit delta'; Validated	92.79
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	92.74
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	92.68
PRK10365	441	transcriptional regulatory protein ZraR; Provision	92.64
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	92.63
PF12846	304	AAA_10: AAA-like domain	92.56
PRK05818	261	DNA polymerase III subunit delta'; Validated	92.31
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	92.18
KOG1969|consensus	877		92.03
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	91.83
COG1067	647	LonB Predicted ATP-dependent protease [Posttransla	91.71
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	91.69
PRK15115	444	response regulator GlrR; Provisional	91.58
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	91.39
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	90.94
COG1221	403	PspF Transcriptional regulators containing an AAA-	90.87
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	90.86
PRK13765	637	ATP-dependent protease Lon; Provisional	90.65
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	90.23
PRK05022	509	anaerobic nitric oxide reductase transcription reg	89.81
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	89.65
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	89.53
PRK11608	326	pspF phage shock protein operon transcriptional ac	89.48
PF13173	128	AAA_14: AAA domain	89.23
PF14516	331	AAA_35: AAA-like domain	88.54
PRK14700	300	recombination factor protein RarA; Provisional	88.14
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	87.49
PF07726	131	AAA_3: ATPase family associated with various cellu	87.05
COG2204	464	AtoC Response regulator containing CheY-like recei	86.65
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	86.25
PRK08116	268	hypothetical protein; Validated	85.9
PRK07452	326	DNA polymerase III subunit delta; Validated	83.56
KOG1051|consensus	898		83.54
TIGR01128	302	holA DNA polymerase III, delta subunit. subunit ar	83.34
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	82.66
PRK04841	903	transcriptional regulator MalT; Provisional	82.55
KOG1968|consensus	871		81.93
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	81.92
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	81.81
KOG0478|consensus	804		81.6
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	81.41
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	81.35
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	81.15
PRK05574	340	holA DNA polymerase III subunit delta; Reviewed	81.13
PRK15424	538	propionate catabolism operon regulatory protein Pr	80.88
KOG0990|consensus	360		80.21

>KOG0730|consensus

Probab=100.00  E-value=1e-42  Score=312.66  Aligned_cols=202  Identities=56%  Similarity=0.898  Sum_probs=193.8

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      -+.++|+.|++.+|+++|+|++++.++++|++|++.+||||||||||+++..|+++..    ....|++++||++||++.
T Consensus       491 e~~~nFlsvkgpEL~sk~vGeSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~~~----~v~~RVlsqLLtEmDG~e  566 (693)
T KOG0730|consen  491 EAGMNFLSVKGPELFSKYVGESERAIREVFRKARQVAPCIIFFDEIDALAGSRGGSSS----GVTDRVLSQLLTEMDGLE  566 (693)
T ss_pred             hhcCCeeeccCHHHHHHhcCchHHHHHHHHHHHhhcCCeEEehhhHHhHhhccCCCcc----chHHHHHHHHHHHccccc
Confidence            4678999999999999999999999999999999999999999999999999974442    667999999999999999


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhH
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      ...+|+|||+||+|+.||+|++||||||+.|+||+||.+.|.+||+.+++++++.+++|+.+||++|+||||+|      
T Consensus       567 ~~k~V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~vdl~~La~~T~g~SGAe------  640 (693)
T KOG0730|consen  567 ALKNVLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKMPFSEDVDLEELAQATEGYSGAE------  640 (693)
T ss_pred             ccCcEEEEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhcCCCCccccHHHHHHHhccCChHH------
Confidence            88899999999999999999999999999999999999999999999999999999999999999999999999      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCCCHHHHHHHHHHhhC
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK  237 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~~~~~~~~~~~~~~~  237 (237)
                                           |.++|++|...++++......|+.++|.+|++..+|+.+...++.|++|.++
T Consensus       641 ---------------------l~~lCq~A~~~a~~e~i~a~~i~~~hf~~al~~~r~s~~~~~~~~Ye~fa~~  692 (693)
T KOG0730|consen  641 ---------------------IVAVCQEAALLALRESIEATEITWQHFEEALKAVRPSLTSELLEKYEDFAAR  692 (693)
T ss_pred             ---------------------HHHHHHHHHHHHHHHhcccccccHHHHHHHHHhhcccCCHHHHHHHHHHhhc
Confidence                                 9999999999999999999999999999999999999999999999999864

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

Probab=100.00  E-value=3.3e-40  Score=278.93  Aligned_cols=189  Identities=43%  Similarity=0.724  Sum_probs=177.3

Q ss_pred             cCCCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC
Q psy5642           3 DLGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG   82 (237)
Q Consensus         3 ~~~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~   82 (237)
                      +...++.||.|.+|+|..+|+|++.+.+|++|..|+.++||||||||||++..+|-+++.++ +.-.++++-+||++||+
T Consensus       206 A~~T~AtFIrvvgSElVqKYiGEGaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~g-DrEVQRTmleLL~qlDG  284 (406)
T COG1222         206 ANQTDATFIRVVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSG-DREVQRTMLELLNQLDG  284 (406)
T ss_pred             HhccCceEEEeccHHHHHHHhccchHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCc-hHHHHHHHHHHHHhccC
Confidence            35678999999999999999999999999999999999999999999999999998877654 44567889999999999


Q ss_pred             CCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccch
Q psy5642          83 IVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLS  162 (237)
Q Consensus        83 ~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~  162 (237)
                      +...++|-||++||+++-|||||+||||||+.|+||+|+.+.|.+||+.|.+++.+..+++|+.||..|+|+||+|    
T Consensus       285 FD~~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~g~sGAd----  360 (406)
T COG1222         285 FDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGAD----  360 (406)
T ss_pred             CCCCCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcCCCchHH----
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999    


Q ss_pred             hHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCC
Q psy5642         163 KHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKP  221 (237)
Q Consensus       163 ~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p  221 (237)
                                             |+++|.+|.+.++++.  ...|+++||..|.+.+..
T Consensus       361 -----------------------lkaictEAGm~AiR~~--R~~Vt~~DF~~Av~KV~~  394 (406)
T COG1222         361 -----------------------LKAICTEAGMFAIRER--RDEVTMEDFLKAVEKVVK  394 (406)
T ss_pred             -----------------------HHHHHHHHhHHHHHhc--cCeecHHHHHHHHHHHHh
Confidence                                   9999999999999987  567999999999886543

>KOG0738|consensus

Probab=100.00  E-value=5.9e-40  Score=279.37  Aligned_cols=200  Identities=40%  Similarity=0.622  Sum_probs=184.8

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      -|+..|++|+.+.|.|||-|++++.+|-+|+.|+.++|++|||||||+|+..|+.++   ..+.++++.++||.+||++.
T Consensus       268 Ec~tTFFNVSsstltSKwRGeSEKlvRlLFemARfyAPStIFiDEIDslcs~RG~s~---EHEaSRRvKsELLvQmDG~~  344 (491)
T KOG0738|consen  268 ECGTTFFNVSSSTLTSKWRGESEKLVRLLFEMARFYAPSTIFIDEIDSLCSQRGGSS---EHEASRRVKSELLVQMDGVQ  344 (491)
T ss_pred             hhcCeEEEechhhhhhhhccchHHHHHHHHHHHHHhCCceeehhhHHHHHhcCCCcc---chhHHHHHHHHHHHHhhccc
Confidence            367899999999999999999999999999999999999999999999999998875   46778999999999999986


Q ss_pred             CC-CC---EEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCccccc
Q psy5642          85 PL-NN---VTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQS  160 (237)
Q Consensus        85 ~~-~~---v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~  160 (237)
                      .. .+   |+|+|+||.||+||+|++|  ||.+.|++|+|+.+.|..+|+..++..+...++++..||.+++||||+|  
T Consensus       345 ~t~e~~k~VmVLAATN~PWdiDEAlrR--RlEKRIyIPLP~~~~R~~Li~~~l~~~~~~~~~~~~~lae~~eGySGaD--  420 (491)
T KOG0738|consen  345 GTLENSKVVMVLAATNFPWDIDEALRR--RLEKRIYIPLPDAEARSALIKILLRSVELDDPVNLEDLAERSEGYSGAD--  420 (491)
T ss_pred             cccccceeEEEEeccCCCcchHHHHHH--HHhhheeeeCCCHHHHHHHHHHhhccccCCCCccHHHHHHHhcCCChHH--
Confidence            52 23   9999999999999999999  9999999999999999999999999999999999999999999999999  


Q ss_pred             chhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccc---------------cCCccHHHHHHHHhhcCCCCCH
Q psy5642         161 LSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLE---------------AAYVSHQDFLTALQLVKPRTPP  225 (237)
Q Consensus       161 ~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~---------------~~~v~~~df~~al~~~~p~~~~  225 (237)
                                               |.++|++|.+..+++...               ..+|+..||+.|++..+|+++.
T Consensus       421 -------------------------I~nvCreAsm~~mRR~i~g~~~~ei~~lakE~~~~pv~~~Dfe~Al~~v~pSvs~  475 (491)
T KOG0738|consen  421 -------------------------ITNVCREASMMAMRRKIAGLTPREIRQLAKEEPKMPVTNEDFEEALRKVRPSVSA  475 (491)
T ss_pred             -------------------------HHHHHHHHHHHHHHHHHhcCCcHHhhhhhhhccccccchhhHHHHHHHcCcCCCH
Confidence                                     999999999988875321               2479999999999999999999


Q ss_pred             HHHHHHHHHhh
Q psy5642         226 QLIKLYENYIK  236 (237)
Q Consensus       226 ~~~~~~~~~~~  236 (237)
                      .++.+|++|-.
T Consensus       476 ~d~~k~ekW~~  486 (491)
T KOG0738|consen  476 ADLEKYEKWMD  486 (491)
T ss_pred             HHHHHHHHHHH
Confidence            99999999975

>KOG0733|consensus

Probab=100.00  E-value=4.9e-39  Score=286.26  Aligned_cols=202  Identities=46%  Similarity=0.727  Sum_probs=182.5

Q ss_pred             CCCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           4 LGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         4 ~~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      +-+++.||.|++.+|+++|+|++++.+|.+|.+|+..+||||||||+|+|++.|+...    ++...+++++||++||++
T Consensus       567 NEag~NFisVKGPELlNkYVGESErAVR~vFqRAR~saPCVIFFDEiDaL~p~R~~~~----s~~s~RvvNqLLtElDGl  642 (802)
T KOG0733|consen  567 NEAGANFISVKGPELLNKYVGESERAVRQVFQRARASAPCVIFFDEIDALVPRRSDEG----SSVSSRVVNQLLTELDGL  642 (802)
T ss_pred             hhccCceEeecCHHHHHHHhhhHHHHHHHHHHHhhcCCCeEEEecchhhcCcccCCCC----chhHHHHHHHHHHHhccc
Confidence            4467899999999999999999999999999999999999999999999999998776    345589999999999999


Q ss_pred             CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHc--CCCCCchhhHHHHHHHCC--CCCcccc
Q psy5642          84 VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA--RSPLGEDVCVEELVRLTE--GYSGAEQ  159 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~--~~~~~~~~~~~~la~~t~--g~s~~Dl  159 (237)
                      ..+.+|+|||+||+|+-||||++||||||+.++++.|+.++|.+||+.+++  +.++..++|+++||..+.  ||||+| 
T Consensus       643 ~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVdl~eia~~~~c~gftGAD-  721 (802)
T KOG0733|consen  643 EERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEERVAILKTITKNTKPPLSSDVDLDEIARNTKCEGFTGAD-  721 (802)
T ss_pred             ccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHHHHHHHHHhccCCCCCCcccCHHHHhhcccccCCchhh-
Confidence            988899999999999999999999999999999999999999999999999  777889999999999877  999999 


Q ss_pred             cchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccc--------------cCCccHHHHHHHHhhcCCCCCH
Q psy5642         160 SLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLE--------------AAYVSHQDFLTALQLVKPRTPP  225 (237)
Q Consensus       160 ~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~--------------~~~v~~~df~~al~~~~p~~~~  225 (237)
                                                |..+|++|.+.++++...              ...++..+|.+|++.++|+++.
T Consensus       722 --------------------------LaaLvreAsi~AL~~~~~~~~~~~~~~~~~~~~~~~t~~hF~eA~~~i~pSv~~  775 (802)
T KOG0733|consen  722 --------------------------LAALVREASILALRESLFEIDSSEDDVTVRSSTIIVTYKHFEEAFQRIRPSVSE  775 (802)
T ss_pred             --------------------------HHHHHHHHHHHHHHHHHhhccccCcccceeeeeeeecHHHHHHHHHhcCCCccH
Confidence                                      777887777777654321              2247888999999999999999


Q ss_pred             HHHHHHHHHhh
Q psy5642         226 QLIKLYENYIK  236 (237)
Q Consensus       226 ~~~~~~~~~~~  236 (237)
                      ++-..|..-.|
T Consensus       776 ~dr~~Yd~l~k  786 (802)
T KOG0733|consen  776 RDRKKYDRLNK  786 (802)
T ss_pred             HHHHHHHHHhh
Confidence            99999886554

>KOG0736|consensus

Probab=100.00  E-value=2.3e-37  Score=281.34  Aligned_cols=202  Identities=40%  Similarity=0.671  Sum_probs=186.1

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      +.+.|+.|++.+|.+.|+|++++|+|++|++|+..+||||||||+|.++++|+.+++++  ..-.|++++||.+||++..
T Consensus       729 csL~FlSVKGPELLNMYVGqSE~NVR~VFerAR~A~PCVIFFDELDSlAP~RG~sGDSG--GVMDRVVSQLLAELDgls~  806 (953)
T KOG0736|consen  729 CSLNFLSVKGPELLNMYVGQSEENVREVFERARSAAPCVIFFDELDSLAPNRGRSGDSG--GVMDRVVSQLLAELDGLSD  806 (953)
T ss_pred             ceeeEEeecCHHHHHHHhcchHHHHHHHHHHhhccCCeEEEeccccccCccCCCCCCcc--ccHHHHHHHHHHHhhcccC
Confidence            56889999999999999999999999999999999999999999999999999988754  4567999999999999985


Q ss_pred             --CCCEEEEEEeCCCCccchhccCCCCcccEEEecCC-CHHHHHHHHHHHHcCCCCCchhhHHHHHHHCC-CCCcccccc
Q psy5642          86 --LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLP-DDLTRAAILKIRLARSPLGEDVCVEELVRLTE-GYSGAEQSL  161 (237)
Q Consensus        86 --~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P-~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~-g~s~~Dl~~  161 (237)
                        ...|+|||+||+|+.|||+|+||||||+.++++.+ +.+.+..+|+...++..+++++++.++|++|+ .|||+|   
T Consensus       807 ~~s~~VFViGATNRPDLLDpALLRPGRFDKLvyvG~~~d~esk~~vL~AlTrkFkLdedVdL~eiAk~cp~~~TGAD---  883 (953)
T KOG0736|consen  807 SSSQDVFVIGATNRPDLLDPALLRPGRFDKLVYVGPNEDAESKLRVLEALTRKFKLDEDVDLVEIAKKCPPNMTGAD---  883 (953)
T ss_pred             CCCCceEEEecCCCccccChhhcCCCccceeEEecCCccHHHHHHHHHHHHHHccCCCCcCHHHHHhhCCcCCchhH---
Confidence              44699999999999999999999999999999998 77899999999999999999999999999996 899999   


Q ss_pred             hhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc---------------ccCCccHHHHHHHHhhcCCCCCHH
Q psy5642         162 SKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL---------------EAAYVSHQDFLTALQLVKPRTPPQ  226 (237)
Q Consensus       162 ~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~---------------~~~~v~~~df~~al~~~~p~~~~~  226 (237)
                                              +.++|.+|.+.|+++..               ....|+++||.+|+++++|+.|++
T Consensus       884 ------------------------lYsLCSdA~l~AikR~i~~ie~g~~~~~e~~~~~v~V~~eDflks~~~l~PSvS~~  939 (953)
T KOG0736|consen  884 ------------------------LYSLCSDAMLAAIKRTIHDIESGTISEEEQESSSVRVTMEDFLKSAKRLQPSVSEQ  939 (953)
T ss_pred             ------------------------HHHHHHHHHHHHHHHHHHHhhhccccccccCCceEEEEHHHHHHHHHhcCCcccHH
Confidence                                    99999999998887632               134799999999999999999999


Q ss_pred             HHHHHHHHhh
Q psy5642         227 LIKLYENYIK  236 (237)
Q Consensus       227 ~~~~~~~~~~  236 (237)
                      ++..|+..+.
T Consensus       940 EL~~ye~vr~  949 (953)
T KOG0736|consen  940 ELLRYEMVRA  949 (953)
T ss_pred             HHHHHHHHHH
Confidence            9999998664

>KOG0739|consensus

Probab=100.00  E-value=2e-37  Score=256.37  Aligned_cols=224  Identities=31%  Similarity=0.511  Sum_probs=194.4

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      ++..|+.|+.|+|.++|+|++++.++.+|+.|+.+.|+||||||||.+|..|+.+.    ++.++++..+||.+|++.-.
T Consensus       190 AnSTFFSvSSSDLvSKWmGESEkLVknLFemARe~kPSIIFiDEiDslcg~r~enE----seasRRIKTEfLVQMqGVG~  265 (439)
T KOG0739|consen  190 ANSTFFSVSSSDLVSKWMGESEKLVKNLFEMARENKPSIIFIDEIDSLCGSRSENE----SEASRRIKTEFLVQMQGVGN  265 (439)
T ss_pred             cCCceEEeehHHHHHHHhccHHHHHHHHHHHHHhcCCcEEEeehhhhhccCCCCCc----hHHHHHHHHHHHHhhhcccc
Confidence            46889999999999999999999999999999999999999999999999887765    56779999999999999865


Q ss_pred             C-CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchh
Q psy5642          86 L-NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSK  163 (237)
Q Consensus        86 ~-~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~  163 (237)
                      + .+|+|+|+||.||.+|.+|+|  ||++.|++|+|+...|..+++.++...+.. .+.|+.+|+.+|+||||+||+.++
T Consensus       266 d~~gvLVLgATNiPw~LDsAIRR--RFekRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d~~eL~~kTeGySGsDisivV  343 (439)
T KOG0739|consen  266 DNDGVLVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEGYSGSDISIVV  343 (439)
T ss_pred             CCCceEEEecCCCchhHHHHHHH--HhhcceeccCCcHHHhhhhheeccCCCccccchhhHHHHHhhcCCCCcCceEEEe
Confidence            3 469999999999999999999  999999999999999999999999888766 889999999999999999999998


Q ss_pred             HHhhhhccccCC------------------CCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCCCH
Q psy5642         164 HRAKKIRPRRES------------------NPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPP  225 (237)
Q Consensus       164 ~~a~~~~~~~~~------------------~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~~~  225 (237)
                      +.|+- .+.|..                  .+--.+|.++....+++..+.-..+.+-+++||+.||..+|...+|++..
T Consensus       344 rDalm-ePvRkvqsAthFk~v~~~s~~~~~~~lltpcspgd~ga~em~w~dv~~dkl~eP~vt~~D~~k~l~~tkPTvn~  422 (439)
T KOG0739|consen  344 RDALM-EPVRKVQSATHFKKVSGPSNPSEVDDLLTPCSPGDPGAIEMSWMDVPADKLLEPPVTMRDFLKSLSRTKPTVNE  422 (439)
T ss_pred             hhhhh-hhHHHhhhhhhhhccCCCCChhhhccccCCCCCCCcchhhhhhccCCHhhccCCCccHHHHHHHHhhcCCCCCH
Confidence            77752 122211                  12234566666666666666655566667899999999999999999999


Q ss_pred             HHHHHHHHHhh
Q psy5642         226 QLIKLYENYIK  236 (237)
Q Consensus       226 ~~~~~~~~~~~  236 (237)
                      .++.+.++|++
T Consensus       423 ~Dl~k~~~Ft~  433 (439)
T KOG0739|consen  423 DDLLKHEKFTE  433 (439)
T ss_pred             HHHHHHHHHHH
Confidence            99999999986

>KOG0733|consensus

Probab=100.00  E-value=6.3e-37  Score=272.84  Aligned_cols=226  Identities=29%  Similarity=0.448  Sum_probs=187.8

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      ..+||+.|.+.++.+.+.|+++++|+++|+.|+.++|||+||||||++.++|...+    .+..++++.+|++.||++..
T Consensus       247 l~vPf~~isApeivSGvSGESEkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~aq----reMErRiVaQLlt~mD~l~~  322 (802)
T KOG0733|consen  247 LGVPFLSISAPEIVSGVSGESEKKIRELFDQAKSNAPCIVFIDEIDAITPKREEAQ----REMERRIVAQLLTSMDELSN  322 (802)
T ss_pred             cCCceEeecchhhhcccCcccHHHHHHHHHHHhccCCeEEEeecccccccchhhHH----HHHHHHHHHHHHHhhhcccc
Confidence            46899999999999999999999999999999999999999999999999987744    57789999999999999865


Q ss_pred             C----CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccc
Q psy5642          86 L----NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSL  161 (237)
Q Consensus        86 ~----~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~  161 (237)
                      .    .+|+|||+||+|+.||++|||+||||+.|.+..|+..+|++||+.+.+++.+..++++.+||..|+||+|+||+.
T Consensus       323 ~~~~g~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~d~~qlA~lTPGfVGADL~A  402 (802)
T KOG0733|consen  323 EKTKGDPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSGDFDFKQLAKLTPGFVGADLMA  402 (802)
T ss_pred             cccCCCCeEEEecCCCCcccCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCCCcCHHHHHhcCCCccchhHHH
Confidence            4    469999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHhhhhccccCCCCCCC---CC---ch-----------------------hHHHHHHHHHHHHHH----hccccCCcc
Q psy5642         162 SKHRAKKIRPRRESNPGPP---AC---KP-----------------------SIVAVCDEAALSALE----NNLEAAYVS  208 (237)
Q Consensus       162 ~~~~a~~~~~~~~~~~~~~---~~---~~-----------------------~i~~~~~~a~~~~~~----~~~~~~~v~  208 (237)
                      ++..|...+..|..+....   ..   +.                       .+.++++++..+...    +......|+
T Consensus       403 L~~~Aa~vAikR~ld~~~~p~~~~~~~ed~~~~~~~~d~S~i~~~~~~~~~~~ld~v~~~~i~~~~d~~S~E~~~~L~i~  482 (802)
T KOG0733|consen  403 LCREAAFVAIKRILDQSSSPLTKVPISEDSSNKDAEEDQSSIKITSNAERPLELDRVVQDAILNNPDPLSKELLEGLSIK  482 (802)
T ss_pred             HHHHHHHHHHHHHhhcccCccccCCccccccCCCccchhhhhhcCCcccccccHHHHHHHHHHhCCCCcChHHhccceec
Confidence            9999998888877542110   00   00                       122333333322211    223356799


Q ss_pred             HHHHHHHHhhcCCC-----------CCHHHHHHHHHHh
Q psy5642         209 HQDFLTALQLVKPR-----------TPPQLIKLYENYI  235 (237)
Q Consensus       209 ~~df~~al~~~~p~-----------~~~~~~~~~~~~~  235 (237)
                      .+||..|+..++|+           ++|++++.+++.+
T Consensus       483 ~eDF~~Al~~iQPSakREGF~tVPdVtW~dIGaL~~vR  520 (802)
T KOG0733|consen  483 FEDFEEALSKIQPSAKREGFATVPDVTWDDIGALEEVR  520 (802)
T ss_pred             HHHHHHHHHhcCcchhcccceecCCCChhhcccHHHHH
Confidence            99999999999987           4556666665544

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=100.00  E-value=3.5e-34  Score=272.22  Aligned_cols=202  Identities=49%  Similarity=0.809  Sum_probs=182.0

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+++|+.+++++++++|+|+++++++.+|..|+..+||||||||+|.+++.++....   .....++++.|+..|+++..
T Consensus       511 ~~~~fi~v~~~~l~~~~vGese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~~---~~~~~~~~~~lL~~ldg~~~  587 (733)
T TIGR01243       511 SGANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFD---TSVTDRIVNQLLTEMDGIQE  587 (733)
T ss_pred             cCCCEEEEehHHHhhcccCcHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCCCCC---ccHHHHHHHHHHHHhhcccC
Confidence            457899999999999999999999999999999999999999999999998765432   23557899999999999888


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      .++++||+|||+|+.||++++||||||..|++++|+.++|.+||+.++++.++..++++..+|..|+||||+|       
T Consensus       588 ~~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~~l~~la~~t~g~sgad-------  660 (733)
T TIGR01243       588 LSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGAD-------  660 (733)
T ss_pred             CCCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHcCCCCHHH-------
Confidence            7899999999999999999999999999999999999999999999999988888999999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc----------------ccCCccHHHHHHHHhhcCCCCCHHHHH
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL----------------EAAYVSHQDFLTALQLVKPRTPPQLIK  229 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~----------------~~~~v~~~df~~al~~~~p~~~~~~~~  229 (237)
                                          |.++|++|...++.+..                ....|+.+||..|++.++|++++++++
T Consensus       661 --------------------i~~~~~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~f~~al~~~~ps~~~~~~~  720 (733)
T TIGR01243       661 --------------------IEAVCREAAMAALRESIGSPAKEKLEVGEEEFLKDLKVEMRHFLEALKKVKPSVSKEDML  720 (733)
T ss_pred             --------------------HHHHHHHHHHHHHHHHhhhccchhhhcccccccccCcccHHHHHHHHHHcCCCCCHHHHH
Confidence                                77777777776665321                124799999999999999999999999


Q ss_pred             HHHHHhhC
Q psy5642         230 LYENYIKK  237 (237)
Q Consensus       230 ~~~~~~~~  237 (237)
                      .|++|.++
T Consensus       721 ~~~~~~~~  728 (733)
T TIGR01243       721 RYERLAKE  728 (733)
T ss_pred             HHHHHHHH
Confidence            99999863

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=100.00  E-value=1.2e-33  Score=255.02  Aligned_cols=196  Identities=29%  Similarity=0.395  Sum_probs=175.7

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+++|+.+++++++++|+|+++++++.+|..|+.++||||||||+|.++..+...++   +....++++.|+.+|++  .
T Consensus       283 ~~~~~~~l~~~~l~~~~vGese~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~~~~d---~~~~~rvl~~lL~~l~~--~  357 (489)
T CHL00195        283 WQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKGD---SGTTNRVLATFITWLSE--K  357 (489)
T ss_pred             hCCCEEEEEhHHhcccccChHHHHHHHHHHHHHhcCCcEEEehhhhhhhccccCCCC---chHHHHHHHHHHHHHhc--C
Confidence            367899999999999999999999999999999999999999999999876543322   34557899999999986  4


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC--chhhHHHHHHHCCCCCcccccchh
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG--EDVCVEELVRLTEGYSGAEQSLSK  163 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~--~~~~~~~la~~t~g~s~~Dl~~~~  163 (237)
                      ..+|+||||||+++.||++++|+||||..++++.|+.++|.+||+.++.+....  .+.++..+|..|+||||+|     
T Consensus       358 ~~~V~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfSGAd-----  432 (489)
T CHL00195        358 KSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSGAE-----  432 (489)
T ss_pred             CCceEEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCCHHH-----
Confidence            468999999999999999999999999999999999999999999999886533  5789999999999999999     


Q ss_pred             HHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCC--CCHHHHHHHHHHhh
Q psy5642         164 HRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPR--TPPQLIKLYENYIK  236 (237)
Q Consensus       164 ~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~--~~~~~~~~~~~~~~  236 (237)
                                            |.++|.+|...+..++   .+++.+||..|++.+.|.  +..+.++.+++|..
T Consensus       433 ----------------------I~~lv~eA~~~A~~~~---~~lt~~dl~~a~~~~~Pls~~~~e~i~~~~~Wa~  482 (489)
T CHL00195        433 ----------------------IEQSIIEAMYIAFYEK---REFTTDDILLALKQFIPLAQTEKEQIEALQNWAS  482 (489)
T ss_pred             ----------------------HHHHHHHHHHHHHHcC---CCcCHHHHHHHHHhcCCCcccCHHHHHHHHHHHH
Confidence                                  9999999988887665   569999999999999998  58899999999986

>KOG0734|consensus

Probab=100.00  E-value=4.3e-34  Score=251.57  Aligned_cols=180  Identities=37%  Similarity=0.586  Sum_probs=168.9

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      ++.||+...+|++--.|+|.+.+.+|++|..|++.+||||||||||++..+|.....    -..+.++++||..||++..
T Consensus       361 A~VPFF~~sGSEFdEm~VGvGArRVRdLF~aAk~~APcIIFIDEiDavG~kR~~~~~----~y~kqTlNQLLvEmDGF~q  436 (752)
T KOG0734|consen  361 AGVPFFYASGSEFDEMFVGVGARRVRDLFAAAKARAPCIIFIDEIDAVGGKRNPSDQ----HYAKQTLNQLLVEMDGFKQ  436 (752)
T ss_pred             cCCCeEeccccchhhhhhcccHHHHHHHHHHHHhcCCeEEEEechhhhcccCCccHH----HHHHHHHHHHHHHhcCcCc
Confidence            578999999999999999999999999999999999999999999999999877653    2668999999999999999


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      +.+|+|||+||.|+.+|+||.||||||.+|.+|.||...|.+||+.|+.+.+...++|+.-||.-|.||+|+|       
T Consensus       437 NeGiIvigATNfpe~LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~ki~~~~~VD~~iiARGT~GFsGAd-------  509 (752)
T KOG0734|consen  437 NEGIIVIGATNFPEALDKALTRPGRFDRHVTVPLPDVRGRTEILKLYLSKIPLDEDVDPKIIARGTPGFSGAD-------  509 (752)
T ss_pred             CCceEEEeccCChhhhhHHhcCCCccceeEecCCCCcccHHHHHHHHHhcCCcccCCCHhHhccCCCCCchHH-------
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhh
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQL  218 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~  218 (237)
                                          |+++++.|+..+..++  ...|++.+++-|-..
T Consensus       510 --------------------LaNlVNqAAlkAa~dg--a~~VtM~~LE~akDr  540 (752)
T KOG0734|consen  510 --------------------LANLVNQAALKAAVDG--AEMVTMKHLEFAKDR  540 (752)
T ss_pred             --------------------HHHHHHHHHHHHHhcC--cccccHHHHhhhhhh
Confidence                                9999999999999888  456889999887543

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

Probab=100.00  E-value=2.7e-32  Score=249.28  Aligned_cols=192  Identities=51%  Similarity=0.812  Sum_probs=176.7

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+.+|+.++++++.++|+|+++++++.+|..|+..+||||||||+|.+++.+..+...    ...+++++++.+|+++..
T Consensus       300 ~~~~fi~v~~~~l~sk~vGesek~ir~~F~~A~~~~p~iiFiDEiDs~~~~r~~~~~~----~~~r~~~~lL~~~d~~e~  375 (494)
T COG0464         300 SRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDG----SGRRVVGQLLTELDGIEK  375 (494)
T ss_pred             CCCeEEEeeCHHHhccccchHHHHHHHHHHHHHcCCCcEEEEEchhhhhccCCCCCch----HHHHHHHHHHHHhcCCCc
Confidence            4789999999999999999999999999999999999999999999999998765532    226999999999999999


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCC--CchhhHHHHHHHCCCCCcccccchh
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPL--GEDVCVEELVRLTEGYSGAEQSLSK  163 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~--~~~~~~~~la~~t~g~s~~Dl~~~~  163 (237)
                      ..+|+||++||.|+.+|++++||||||..++|++|+..+|.+||+.++.....  ..+.++..++..|+||+|+|     
T Consensus       376 ~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~~sgad-----  450 (494)
T COG0464         376 AEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGAD-----  450 (494)
T ss_pred             cCceEEEecCCCccccCHhhcccCccceEeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhcCCCHHH-----
Confidence            88999999999999999999999999999999999999999999999985543  47899999999999999999     


Q ss_pred             HHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCCCHHHHHHHHHHhh
Q psy5642         164 HRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIK  236 (237)
Q Consensus       164 ~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~~~~~~~~~~~~~~  236 (237)
                                            |.++|++|...+..+.. ...++.+||..|++..+|++.      |++| +
T Consensus       451 ----------------------i~~i~~ea~~~~~~~~~-~~~~~~~~~~~a~~~~~p~~~------~~~~-~  493 (494)
T COG0464         451 ----------------------IAALVREAALEALREAR-RREVTLDDFLDALKKIKPSVT------YEEW-K  493 (494)
T ss_pred             ----------------------HHHHHHHHHHHHHHHhc-cCCccHHHHHHHHHhcCCCCC------hhhc-c
Confidence                                  99999999999988764 457999999999999999988      8888 5

>KOG0728|consensus

Probab=100.00  E-value=1.9e-32  Score=222.41  Aligned_cols=201  Identities=35%  Similarity=0.591  Sum_probs=181.0

Q ss_pred             CCCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           4 LGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         4 ~~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      -+..|.||.|++|+|..+|+|++.+.++++|-.|+.++|+|||+||||++...|..++..+ ++..+++.-+||+++|++
T Consensus       203 hht~c~firvsgselvqk~igegsrmvrelfvmarehapsiifmdeidsigs~r~e~~~gg-dsevqrtmlellnqldgf  281 (404)
T KOG0728|consen  203 HHTDCTFIRVSGSELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSSRVESGSGG-DSEVQRTMLELLNQLDGF  281 (404)
T ss_pred             hhcceEEEEechHHHHHHHhhhhHHHHHHHHHHHHhcCCceEeeecccccccccccCCCCc-cHHHHHHHHHHHHhcccc
Confidence            4678999999999999999999999999999999999999999999999998887665543 455678888999999999


Q ss_pred             CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchh
Q psy5642          84 VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSK  163 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~  163 (237)
                      ....+|-||.+||+.+-+||+++||||+|+.|+||+|+.+.|.+||+.+-+++.+-...++..+|.+..|.||++     
T Consensus       282 eatknikvimatnridild~allrpgridrkiefp~p~e~ar~~ilkihsrkmnl~rgi~l~kiaekm~gasgae-----  356 (404)
T KOG0728|consen  282 EATKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAEKMPGASGAE-----  356 (404)
T ss_pred             ccccceEEEEeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHHhhhhhchhcccCHHHHHHhCCCCccch-----
Confidence            999999999999999999999999999999999999999999999999999999989999999999999999999     


Q ss_pred             HHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCCCHHHHHHHHHH
Q psy5642         164 HRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENY  234 (237)
Q Consensus       164 ~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~~~~~~~~~~~~  234 (237)
                                            ++.+|.+|.+.+.++.  ..+||++||+-|+...-...+......-+=|
T Consensus       357 ----------------------vk~vcteagm~alrer--rvhvtqedfemav~kvm~k~~e~nms~~kl~  403 (404)
T KOG0728|consen  357 ----------------------VKGVCTEAGMYALRER--RVHVTQEDFEMAVAKVMQKDSEKNMSIKKLW  403 (404)
T ss_pred             ----------------------hhhhhhhhhHHHHHHh--hccccHHHHHHHHHHHHhccccccchHHHhh
Confidence                                  9999999999999876  5789999999998876554555554444444

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

Probab=99.97  E-value=2.1e-30  Score=229.30  Aligned_cols=186  Identities=40%  Similarity=0.642  Sum_probs=168.3

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+.+|+.+.++.+.++|.|++++.++.+|..|...+|+||||||+|.++..+.+.... .+...++++..++.+++++..
T Consensus       203 l~~~fi~i~~s~l~~k~~ge~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~~~~~-~d~~~~r~l~~LL~~ld~~~~  281 (398)
T PTZ00454        203 TTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTG-ADREVQRILLELLNQMDGFDQ  281 (398)
T ss_pred             cCCCEEEEehHHHHHHhcchhHHHHHHHHHHHHhcCCeEEEEECHhhhccccccccCC-ccHHHHHHHHHHHHHhhccCC
Confidence            3568999999999999999999999999999999999999999999999877543322 233456888999999999877


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      ..++.||+|||+++.+|++++||||||..|+|++|+.++|..||+.++.+.++..+.++.++|..|+||||+|       
T Consensus       282 ~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~dvd~~~la~~t~g~sgaD-------  354 (398)
T PTZ00454        282 TTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAAD-------  354 (398)
T ss_pred             CCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCcccCHHHHHHHcCCCCHHH-------
Confidence            7889999999999999999999999999999999999999999999999988888999999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCC
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKP  221 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p  221 (237)
                                          |.++|.+|.+.++.++  ...|+.+||..|++....
T Consensus       355 --------------------I~~l~~eA~~~A~r~~--~~~i~~~df~~A~~~v~~  388 (398)
T PTZ00454        355 --------------------IAAICQEAGMQAVRKN--RYVILPKDFEKGYKTVVR  388 (398)
T ss_pred             --------------------HHHHHHHHHHHHHHcC--CCccCHHHHHHHHHHHHh
Confidence                                9999999999999887  457999999999998644

>KOG0735|consensus

Probab=99.97  E-value=7.7e-31  Score=237.26  Aligned_cols=151  Identities=47%  Similarity=0.782  Sum_probs=143.4

Q ss_pred             CCCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           4 LGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         4 ~~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      +.+++.||.|++.+|.+||+|.+++++|++|++|+..+||||||||+|.++++|+-+..    ....|+++++|++||+.
T Consensus       723 ~~~~~~fisvKGPElL~KyIGaSEq~vR~lF~rA~~a~PCiLFFDEfdSiAPkRGhDsT----GVTDRVVNQlLTelDG~  798 (952)
T KOG0735|consen  723 SNSNLRFISVKGPELLSKYIGASEQNVRDLFERAQSAKPCILFFDEFDSIAPKRGHDST----GVTDRVVNQLLTELDGA  798 (952)
T ss_pred             hhCCeeEEEecCHHHHHHHhcccHHHHHHHHHHhhccCCeEEEeccccccCcccCCCCC----CchHHHHHHHHHhhccc
Confidence            46789999999999999999999999999999999999999999999999999976653    44589999999999999


Q ss_pred             CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCccc
Q psy5642          84 VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~D  158 (237)
                      ..-.+|+|+|+|++|+.||||++||||+|+.++-+.|+..+|.+|++.+-.......++|++-+|.+|+||||+|
T Consensus       799 Egl~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s~~~~~~vdl~~~a~~T~g~tgAD  873 (952)
T KOG0735|consen  799 EGLDGVYILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSNSLLKDTDVDLECLAQKTDGFTGAD  873 (952)
T ss_pred             cccceEEEEEecCCccccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhhccCCccccchHHHhhhcCCCchhh
Confidence            888899999999999999999999999999999999999999999999999888889999999999999999999

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

Probab=99.97  E-value=1.5e-30  Score=212.11  Aligned_cols=184  Identities=30%  Similarity=0.444  Sum_probs=164.3

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      -.+.||+-|++.+|.+.|+|++.+.++.+|++|...+|||+||||+|+++-+|.-.+.   .....+++|.||+.||++.
T Consensus       174 e~kvp~l~vkat~liGehVGdgar~Ihely~rA~~~aPcivFiDE~DAiaLdRryQel---RGDVsEiVNALLTelDgi~  250 (368)
T COG1223         174 EAKVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCIVFIDELDAIALDRRYQEL---RGDVSEIVNALLTELDGIK  250 (368)
T ss_pred             ccCCceEEechHHHHHHHhhhHHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhhHHHh---cccHHHHHHHHHHhccCcc
Confidence            3578999999999999999999999999999999999999999999999988876554   2345789999999999999


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhH
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      .+.+|+.|++||+|+.+|+++++  ||...|+|.+|+.++|.+|++.++++.+++-+.++..++.+|.||||+|      
T Consensus       251 eneGVvtIaaTN~p~~LD~aiRs--RFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~~~~~~~~t~g~SgRd------  322 (368)
T COG1223         251 ENEGVVTIAATNRPELLDPAIRS--RFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGMSGRD------  322 (368)
T ss_pred             cCCceEEEeecCChhhcCHHHHh--hhhheeeeeCCChHHHHHHHHHHHHhCCCccccCHHHHHHHhCCCCchh------
Confidence            88899999999999999999999  9999999999999999999999999999998999999999999999999      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHH-HHHHHHHHHHHhccccCCccHHHHHHHHhhcCCC
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVA-VCDEAALSALENNLEAAYVSHQDFLTALQLVKPR  222 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~-~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~  222 (237)
                                           |+. +...|...++.++  .-.|+.+||..|+++.++.
T Consensus       323 ---------------------ikekvlK~aLh~Ai~ed--~e~v~~edie~al~k~r~~  358 (368)
T COG1223         323 ---------------------IKEKVLKTALHRAIAED--REKVEREDIEKALKKERKR  358 (368)
T ss_pred             ---------------------HHHHHHHHHHHHHHHhc--hhhhhHHHHHHHHHhhccc
Confidence                                 654 4455556666666  3358999999999976553

>KOG0737|consensus

Probab=99.97  E-value=1.3e-30  Score=221.64  Aligned_cols=184  Identities=33%  Similarity=0.544  Sum_probs=164.6

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      +++.|++|+.+.+.++|+|++++.++.+|..|...+||||||||+|.++..|..+    ..+....+.++|+..+|++.+
T Consensus       151 aga~fInv~~s~lt~KWfgE~eKlv~AvFslAsKl~P~iIFIDEvds~L~~R~s~----dHEa~a~mK~eFM~~WDGl~s  226 (386)
T KOG0737|consen  151 AGANFINVSVSNLTSKWFGEAQKLVKAVFSLASKLQPSIIFIDEVDSFLGQRRST----DHEATAMMKNEFMALWDGLSS  226 (386)
T ss_pred             cCCCcceeeccccchhhHHHHHHHHHHHHhhhhhcCcceeehhhHHHHHhhcccc----hHHHHHHHHHHHHHHhccccC
Confidence            5789999999999999999999999999999999999999999999999998432    357778999999999999988


Q ss_pred             CCC--EEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchh
Q psy5642          86 LNN--VTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSK  163 (237)
Q Consensus        86 ~~~--v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~  163 (237)
                      +++  |+|+|+||+|.++|.|++|  |+.+.++|+.|+..+|++||+.+|++.++.+++|+.++|..|+||||+|     
T Consensus       227 ~~~~rVlVlgATNRP~DlDeAiiR--R~p~rf~V~lP~~~qR~kILkviLk~e~~e~~vD~~~iA~~t~GySGSD-----  299 (386)
T KOG0737|consen  227 KDSERVLVLGATNRPFDLDEAIIR--RLPRRFHVGLPDAEQRRKILKVILKKEKLEDDVDLDEIAQMTEGYSGSD-----  299 (386)
T ss_pred             CCCceEEEEeCCCCCccHHHHHHH--hCcceeeeCCCchhhHHHHHHHHhcccccCcccCHHHHHHhcCCCcHHH-----
Confidence            665  9999999999999999999  9999999999999999999999999999999999999999999999999     


Q ss_pred             HHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccc--------------------------cCCccHHHHHHHHh
Q psy5642         164 HRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLE--------------------------AAYVSHQDFLTALQ  217 (237)
Q Consensus       164 ~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~--------------------------~~~v~~~df~~al~  217 (237)
                                            |.++|..|+...+++-..                          -++++++||..|+.
T Consensus       300 ----------------------LkelC~~Aa~~~ire~~~~~~~~~d~d~~~~d~~~~~~~~~~~~~r~l~~eDf~~a~~  357 (386)
T KOG0737|consen  300 ----------------------LKELCRLAALRPIRELLVSETGLLDLDKAIADLKPTQAAASSCLLRPLEQEDFPKAIN  357 (386)
T ss_pred             ----------------------HHHHHHHHhHhHHHHHHHhcccchhhhhhhhhccCCcccccccccCcccHHHHHHHHH
Confidence                                  777777777666543110                          26789999999988


Q ss_pred             hcCCC
Q psy5642         218 LVKPR  222 (237)
Q Consensus       218 ~~~p~  222 (237)
                      .+-++
T Consensus       358 ~v~~~  362 (386)
T KOG0737|consen  358 RVSAS  362 (386)
T ss_pred             hhhhH
Confidence            66555

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.97  E-value=7.3e-30  Score=226.31  Aligned_cols=190  Identities=45%  Similarity=0.746  Sum_probs=170.8

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+|+.++++++.++|.|++++.++.+|+.|...+|+||||||+|.++..+.+...++ +...++.+..++..++++...
T Consensus       190 ~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~~-~~~~~~~l~~lL~~ld~~~~~  268 (389)
T PRK03992        190 NATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSG-DREVQRTLMQLLAEMDGFDPR  268 (389)
T ss_pred             CCCEEEeehHHHhHhhccchHHHHHHHHHHHHhcCCeEEEEechhhhhcccccCCCCc-cHHHHHHHHHHHHhccccCCC
Confidence            4689999999999999999999999999999999999999999999998776544332 234467778899999988777


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      +++.||+|||+++.+|++++||||||..|+|++|+.++|.+||+.++++..+..+.++..+|..|+||+|+|        
T Consensus       269 ~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~~~~~la~~t~g~sgad--------  340 (389)
T PRK03992        269 GNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGAD--------  340 (389)
T ss_pred             CCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCcCCHHHHHHHcCCCCHHH--------
Confidence            789999999999999999999999999999999999999999999999888878899999999999999999        


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCCCHH
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQ  226 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~~~~  226 (237)
                                         |.++|.+|...+++++  ...|+.+||.+|+..++|+...+
T Consensus       341 -------------------l~~l~~eA~~~a~~~~--~~~i~~~d~~~A~~~~~~~~~~~  379 (389)
T PRK03992        341 -------------------LKAICTEAGMFAIRDD--RTEVTMEDFLKAIEKVMGKEEKD  379 (389)
T ss_pred             -------------------HHHHHHHHHHHHHHcC--CCCcCHHHHHHHHHHHhcccccc
Confidence                               9999999999998886  45699999999999999876544

>KOG0731|consensus

Probab=99.97  E-value=4.8e-30  Score=236.85  Aligned_cols=184  Identities=42%  Similarity=0.684  Sum_probs=169.3

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      +++||+.+++|++...++|....+++++|..|+.++||||||||||++...+.+....+.+.....++++||..||++..
T Consensus       368 AgVPF~svSGSEFvE~~~g~~asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~  447 (774)
T KOG0731|consen  368 AGVPFFSVSGSEFVEMFVGVGASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFET  447 (774)
T ss_pred             cCCceeeechHHHHHHhcccchHHHHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcC
Confidence            68999999999999999999999999999999999999999999999999886322333344557889999999999998


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      ...|+|+++||+++-+|++++||||||++|+++.|+...|.+|++.|++..+.. .+.+|..+|..|+||+|+|      
T Consensus       448 ~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~a~~t~gf~gad------  521 (774)
T KOG0731|consen  448 SKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKLASLTPGFSGAD------  521 (774)
T ss_pred             CCcEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHHHHhcCCCCcHHH------
Confidence            888999999999999999999999999999999999999999999999998885 8899999999999999999      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhh
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQL  218 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~  218 (237)
                                           |+++|.+|++.+.++.  ...|+..||..|++.
T Consensus       522 ---------------------l~n~~neaa~~a~r~~--~~~i~~~~~~~a~~R  552 (774)
T KOG0731|consen  522 ---------------------LANLCNEAALLAARKG--LREIGTKDLEYAIER  552 (774)
T ss_pred             ---------------------HHhhhhHHHHHHHHhc--cCccchhhHHHHHHH
Confidence                                 9999999999999887  456999999999993

>KOG0740|consensus

Probab=99.97  E-value=2.7e-30  Score=226.17  Aligned_cols=199  Identities=37%  Similarity=0.576  Sum_probs=176.2

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      =+++.|+.+++++|.++|+|++++.+|.+|..|+..+|+|+||||+|.++..|.+..    .+...++..+++.++++..
T Consensus       209 E~~atff~iSassLtsK~~Ge~eK~vralf~vAr~~qPsvifidEidslls~Rs~~e----~e~srr~ktefLiq~~~~~  284 (428)
T KOG0740|consen  209 ESGATFFNISASSLTSKYVGESEKLVRALFKVARSLQPSVIFIDEIDSLLSKRSDNE----HESSRRLKTEFLLQFDGKN  284 (428)
T ss_pred             hhcceEeeccHHHhhhhccChHHHHHHHHHHHHHhcCCeEEEechhHHHHhhcCCcc----cccchhhhhHHHhhhcccc
Confidence            467899999999999999999999999999999999999999999999999985544    3444788999999888765


Q ss_pred             C--CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccc
Q psy5642          85 P--LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSL  161 (237)
Q Consensus        85 ~--~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~  161 (237)
                      .  .++|+||||||.||++|.+++|  ||.+.+++|.|+.+.|..+|+.++...+.. .+.+++.+++.|+||+++|   
T Consensus       285 s~~~drvlvigaTN~P~e~Dea~~R--rf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~~~Tegysgsd---  359 (428)
T KOG0740|consen  285 SAPDDRVLVIGATNRPWELDEAARR--RFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLAKVTEGYSGSD---  359 (428)
T ss_pred             CCCCCeEEEEecCCCchHHHHHHHH--HhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCccccc---
Confidence            4  4579999999999999999999  999999999999999999999999887554 7899999999999999999   


Q ss_pred             hhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc-----------ccCCccHHHHHHHHhhcCCCCCHHHHHH
Q psy5642         162 SKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL-----------EAAYVSHQDFLTALQLVKPRTPPQLIKL  230 (237)
Q Consensus       162 ~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~-----------~~~~v~~~df~~al~~~~p~~~~~~~~~  230 (237)
                                              |.++|.+|++...+...           ..++++..||..|++.++|+++.+.++.
T Consensus       360 ------------------------i~~l~kea~~~p~r~~~~~~~~~~~~~~~~r~i~~~df~~a~~~i~~~~s~~~l~~  415 (428)
T KOG0740|consen  360 ------------------------ITALCKEAAMGPLRELGGTTDLEFIDADKIRPITYPDFKNAFKNIKPSVSLEGLEK  415 (428)
T ss_pred             ------------------------HHHHHHHhhcCchhhcccchhhhhcchhccCCCCcchHHHHHHhhccccCccccch
Confidence                                    88888888865544321           2458999999999999999999999999


Q ss_pred             HHHHhh
Q psy5642         231 YENYIK  236 (237)
Q Consensus       231 ~~~~~~  236 (237)
                      |.+|-+
T Consensus       416 ~~~~~~  421 (428)
T KOG0740|consen  416 YEKWDK  421 (428)
T ss_pred             hHHHhh
Confidence            999965

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

Probab=99.97  E-value=5.3e-30  Score=232.68  Aligned_cols=184  Identities=40%  Similarity=0.650  Sum_probs=170.2

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      -++.||+.+++|++...|+|-+...+|++|.+|++++||||||||+|++...|+... .+.......+++++|.+||++.
T Consensus       206 EA~VPFf~iSGS~FVemfVGvGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~g~-GggnderEQTLNQlLvEmDGF~  284 (596)
T COG0465         206 EAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGL-GGGNDEREQTLNQLLVEMDGFG  284 (596)
T ss_pred             ccCCCceeccchhhhhhhcCCCcHHHHHHHHHhhccCCCeEEEehhhhcccccCCCC-CCCchHHHHHHHHHHhhhccCC
Confidence            367899999999999999999999999999999999999999999999999987652 2223344679999999999999


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhH
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      .+..|+||++||+|+-+|+||+||||||++|.++.||...|++|++.++++.++..++++..+|..|.||+|+|      
T Consensus       285 ~~~gviviaaTNRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~~~Vdl~~iAr~tpGfsGAd------  358 (596)
T COG0465         285 GNEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTPGFSGAD------  358 (596)
T ss_pred             CCCceEEEecCCCcccchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCCCcCCHHHHhhhCCCcccch------
Confidence            88899999999999999999999999999999999999999999999999999999999999999999999999      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhh
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQL  218 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~  218 (237)
                                           +.+++++|++.+.+.+  ...+++.||.+|...
T Consensus       359 ---------------------L~nl~NEAal~aar~n--~~~i~~~~i~ea~dr  389 (596)
T COG0465         359 ---------------------LANLLNEAALLAARRN--KKEITMRDIEEAIDR  389 (596)
T ss_pred             ---------------------HhhhHHHHHHHHHHhc--CeeEeccchHHHHHH
Confidence                                 9999999999999888  567999999999875

>KOG0730|consensus

Probab=99.96  E-value=1.9e-29  Score=227.30  Aligned_cols=189  Identities=38%  Similarity=0.557  Sum_probs=173.3

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcC-CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVS-PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~-P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      +++++.++++.+++++.|+++++++++|+.|..++ |++|||||+|.+++++.....     ...++.++++++++++..
T Consensus       243 ~a~~~~i~~peli~k~~gEte~~LR~~f~~a~k~~~psii~IdEld~l~p~r~~~~~-----~e~Rv~sqlltL~dg~~~  317 (693)
T KOG0730|consen  243 GAFLFLINGPELISKFPGETESNLRKAFAEALKFQVPSIIFIDELDALCPKREGADD-----VESRVVSQLLTLLDGLKP  317 (693)
T ss_pred             CceeEecccHHHHHhcccchHHHHHHHHHHHhccCCCeeEeHHhHhhhCCcccccch-----HHHHHHHHHHHHHhhCcC
Confidence            47899999999999999999999999999999999 999999999999998876542     458999999999999988


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      .++++||++||+|..||++++| ||||+.+++..|+..+|.+|++.+.++++...+.++.++|..|+||+|+|       
T Consensus       318 ~~~vivl~atnrp~sld~alRR-gRfd~ev~IgiP~~~~RldIl~~l~k~~~~~~~~~l~~iA~~thGyvGaD-------  389 (693)
T KOG0730|consen  318 DAKVIVLAATNRPDSLDPALRR-GRFDREVEIGIPGSDGRLDILRVLTKKMNLLSDVDLEDIAVSTHGYVGAD-------  389 (693)
T ss_pred             cCcEEEEEecCCccccChhhhc-CCCcceeeecCCCchhHHHHHHHHHHhcCCcchhhHHHHHHHccchhHHH-------
Confidence            8899999999999999999999 99999999999999999999999999999888899999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCC-----------CCHHHHHHHHHH
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPR-----------TPPQLIKLYENY  234 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~-----------~~~~~~~~~~~~  234 (237)
                                          +.++|.+|...+.++       +.++|..|+...+|+           +++++|+.+++.
T Consensus       390 --------------------L~~l~~ea~~~~~r~-------~~~~~~~A~~~i~psa~Re~~ve~p~v~W~dIGGlE~l  442 (693)
T KOG0730|consen  390 --------------------LAALCREASLQATRR-------TLEIFQEALMGIRPSALREILVEMPNVSWDDIGGLEEL  442 (693)
T ss_pred             --------------------HHHHHHHHHHHHhhh-------hHHHHHHHHhcCCchhhhheeccCCCCChhhccCHHHH
Confidence                                999999999999888       678899998888866           566677766655


Q ss_pred             h
Q psy5642         235 I  235 (237)
Q Consensus       235 ~  235 (237)
                      +
T Consensus       443 K  443 (693)
T KOG0730|consen  443 K  443 (693)
T ss_pred             H
Confidence            4

>KOG0727|consensus

Probab=99.96  E-value=2e-29  Score=205.13  Aligned_cols=186  Identities=39%  Similarity=0.642  Sum_probs=173.1

Q ss_pred             CCCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           4 LGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         4 ~~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      .+..+.||.|.+|++..+|.|++++.++++|..|+.++|+||||||+|+++.+|-+.+... +...++++-+||++||++
T Consensus       211 ~~t~a~firvvgsefvqkylgegprmvrdvfrlakenapsiifideidaiatkrfdaqtga-drevqril~ellnqmdgf  289 (408)
T KOG0727|consen  211 NHTTAAFIRVVGSEFVQKYLGEGPRMVRDVFRLAKENAPSIIFIDEIDAIATKRFDAQTGA-DREVQRILIELLNQMDGF  289 (408)
T ss_pred             hccchheeeeccHHHHHHHhccCcHHHHHHHHHHhccCCcEEEeehhhhHhhhhccccccc-cHHHHHHHHHHHHhccCc
Confidence            4567889999999999999999999999999999999999999999999998887766543 345579999999999999


Q ss_pred             CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchh
Q psy5642          84 VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSK  163 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~  163 (237)
                      ....+|-||.+||+.+.+||+++||||.|+.|+||+|+.-|++-++.....++.+..++|++++..+-+..|++|     
T Consensus       290 dq~~nvkvimatnradtldpallrpgrldrkiefplpdrrqkrlvf~titskm~ls~~vdle~~v~rpdkis~ad-----  364 (408)
T KOG0727|consen  290 DQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFSTITSKMNLSDEVDLEDLVARPDKISGAD-----  364 (408)
T ss_pred             CcccceEEEEecCcccccCHhhcCCccccccccCCCCchhhhhhhHHhhhhcccCCcccCHHHHhcCccccchhh-----
Confidence            998899999999999999999999999999999999999999999999999999999999999999999999999     


Q ss_pred             HHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhc
Q psy5642         164 HRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLV  219 (237)
Q Consensus       164 ~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~  219 (237)
                                            |.++|++|.+.+++++  ...|...||++|.+..
T Consensus       365 ----------------------i~aicqeagm~avr~n--ryvvl~kd~e~ay~~~  396 (408)
T KOG0727|consen  365 ----------------------INAICQEAGMLAVREN--RYVVLQKDFEKAYKTV  396 (408)
T ss_pred             ----------------------HHHHHHHHhHHHHHhc--ceeeeHHHHHHHHHhh
Confidence                                  9999999999999988  6679999999997754

>KOG0726|consensus

Probab=99.96  E-value=4.5e-30  Score=212.34  Aligned_cols=183  Identities=38%  Similarity=0.675  Sum_probs=168.5

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      -+.|+.|-+|+|..+|.|++.+.+|.+|..|..++|+|+||||||++..+|-++.+.+.. ..++..-+||+++|++..+
T Consensus       244 SATFlRvvGseLiQkylGdGpklvRqlF~vA~e~apSIvFiDEIdAiGtKRyds~Sgger-EiQrtmLELLNQldGFdsr  322 (440)
T KOG0726|consen  244 SATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGER-EIQRTMLELLNQLDGFDSR  322 (440)
T ss_pred             chhhhhhhhHHHHHHHhccchHHHHHHHHHHHhcCCceEEeehhhhhccccccCCCccHH-HHHHHHHHHHHhccCcccc
Confidence            467899999999999999999999999999999999999999999999998876655543 3456667999999999998


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      +.|-||.+||..+.+||+++||||+|+.|+|+.||...+..||..+..++-+..+++++++...-..+||+|        
T Consensus       323 gDvKvimATnrie~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~IHTs~Mtl~~dVnle~li~~kddlSGAd--------  394 (440)
T KOG0726|consen  323 GDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKKIFQIHTSRMTLAEDVNLEELIMTKDDLSGAD--------  394 (440)
T ss_pred             CCeEEEEecccccccCHhhcCCCccccccccCCCchhhhceeEEEeecccchhccccHHHHhhccccccccc--------
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999        


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhc
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLV  219 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~  219 (237)
                                         |+++|.+|.+-+.++.  ...|+.+||..|.+.+
T Consensus       395 -------------------IkAictEaGllAlRer--Rm~vt~~DF~ka~e~V  426 (440)
T KOG0726|consen  395 -------------------IKAICTEAGLLALRER--RMKVTMEDFKKAKEKV  426 (440)
T ss_pred             -------------------HHHHHHHHhHHHHHHH--HhhccHHHHHHHHHHH
Confidence                               9999999999999887  4569999999997753

>KOG0652|consensus

Probab=99.96  E-value=2.6e-29  Score=205.25  Aligned_cols=187  Identities=37%  Similarity=0.633  Sum_probs=172.6

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      -.+..|+.+-+.+|...|+|++.+.++++|..|+..+|+||||||+|++..+|-++...+ +...+++.-+||+++|++.
T Consensus       228 qT~aTFLKLAgPQLVQMfIGdGAkLVRDAFaLAKEkaP~IIFIDElDAIGtKRfDSek~G-DREVQRTMLELLNQLDGFs  306 (424)
T KOG0652|consen  228 QTNATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKAG-DREVQRTMLELLNQLDGFS  306 (424)
T ss_pred             hccchHHHhcchHHHhhhhcchHHHHHHHHHHhhccCCeEEEEechhhhccccccccccc-cHHHHHHHHHHHHhhcCCC
Confidence            346778889999999999999999999999999999999999999999999988776554 3455688889999999999


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhH
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      +..+|-||++||+.+-+||+++|+||.|+.|+||.|+.+.|..|++.+-+++....+++|++||.-|++|.|+.      
T Consensus       307 s~~~vKviAATNRvDiLDPALlRSGRLDRKIEfP~Pne~aRarIlQIHsRKMnv~~DvNfeELaRsTddFNGAQ------  380 (424)
T KOG0652|consen  307 SDDRVKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARILQIHSRKMNVSDDVNFEELARSTDDFNGAQ------  380 (424)
T ss_pred             CccceEEEeecccccccCHHHhhcccccccccCCCCChHHHHHHHHHhhhhcCCCCCCCHHHHhhcccccCchh------
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCC
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKP  221 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p  221 (237)
                                           .+++|-+|.+.+.+++  ...|+.+||.+++.+.+.
T Consensus       381 ---------------------cKAVcVEAGMiALRr~--atev~heDfmegI~eVqa  414 (424)
T KOG0652|consen  381 ---------------------CKAVCVEAGMIALRRG--ATEVTHEDFMEGILEVQA  414 (424)
T ss_pred             ---------------------heeeehhhhHHHHhcc--cccccHHHHHHHHHHHHH
Confidence                                 9999999999999988  557999999999876543

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.96  E-value=1.2e-28  Score=224.98  Aligned_cols=185  Identities=39%  Similarity=0.628  Sum_probs=165.3

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+.+|+.++++++.+.|.|.+.+.++.+|..|+..+||||||||+|.++..+...... .......+++.|+..|+++..
T Consensus       112 ~~~~~~~i~~~~~~~~~~g~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~~~~-~~~~~~~~~~~lL~~~d~~~~  190 (495)
T TIGR01241       112 AGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGG-GNDEREQTLNQLLVEMDGFGT  190 (495)
T ss_pred             cCCCeeeccHHHHHHHHhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhccccCcCC-ccHHHHHHHHHHHhhhccccC
Confidence            4678999999999999999999999999999999999999999999999877553211 123346788999999999888


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      .++++||+|||+|+.||++++||||||..|+++.|+.++|.+||+.+++..+...+.++..+|..|.||+|+|       
T Consensus       191 ~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgad-------  263 (495)
T TIGR01241       191 NTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGAD-------  263 (495)
T ss_pred             CCCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCCcchhHHHHHHhCCCCCHHH-------
Confidence            7889999999999999999999999999999999999999999999999887777899999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcC
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVK  220 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~  220 (237)
                                          |.+++++|...+.+++  ...|+.+||..|++...
T Consensus       264 --------------------l~~l~~eA~~~a~~~~--~~~i~~~~l~~a~~~~~  296 (495)
T TIGR01241       264 --------------------LANLLNEAALLAARKN--KTEITMNDIEEAIDRVI  296 (495)
T ss_pred             --------------------HHHHHHHHHHHHHHcC--CCCCCHHHHHHHHHHHh
Confidence                                9999999988877765  45799999999999764

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.

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

Probab=99.96  E-value=2.2e-28  Score=218.04  Aligned_cols=184  Identities=36%  Similarity=0.644  Sum_probs=165.4

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      ..+|+.+.++++.++|.|++.+.++.+|..|...+||||||||+|.++..+......+ .....+.+..++..++++...
T Consensus       242 ~~~fi~V~~seL~~k~~Ge~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~~~sgg-~~e~qr~ll~LL~~Ldg~~~~  320 (438)
T PTZ00361        242 SATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGG-EKEIQRTMLELLNQLDGFDSR  320 (438)
T ss_pred             CCCEEEEecchhhhhhcchHHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCCCCCcc-cHHHHHHHHHHHHHHhhhccc
Confidence            4578999999999999999999999999999999999999999999998775443322 234457778899999988777


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      .++.||+|||+++.+|++++||||||..|+|+.|+.++|.+||+.++.+..+..+.++..++..|+||||+|        
T Consensus       321 ~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dvdl~~la~~t~g~sgAd--------  392 (438)
T PTZ00361        321 GDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGAD--------  392 (438)
T ss_pred             CCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCcCHHHHHHhcCCCCHHH--------
Confidence            789999999999999999999999999999999999999999999999988888999999999999999999        


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcC
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVK  220 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~  220 (237)
                                         |.++|.+|...+..++  ...|+.+||..|++.+.
T Consensus       393 -------------------I~~i~~eA~~~Alr~~--r~~Vt~~D~~~A~~~v~  425 (438)
T PTZ00361        393 -------------------IKAICTEAGLLALRER--RMKVTQADFRKAKEKVL  425 (438)
T ss_pred             -------------------HHHHHHHHHHHHHHhc--CCccCHHHHHHHHHHHH
Confidence                               9999999999999887  45699999999998753

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.96  E-value=4.6e-28  Score=226.64  Aligned_cols=186  Identities=40%  Similarity=0.641  Sum_probs=167.8

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+.+|+.++++++...+.|.+...++.+|..|+..+||||||||+|.++..+...... .......+++.+|..|+++..
T Consensus       209 ~~~~f~~is~~~~~~~~~g~~~~~~~~~f~~a~~~~P~IifIDEiD~l~~~r~~~~~g-~~~~~~~~ln~lL~~mdg~~~  287 (644)
T PRK10733        209 AKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGG-GHDEREQTLNQMLVEMDGFEG  287 (644)
T ss_pred             cCCCEEEEehHHhHHhhhcccHHHHHHHHHHHHhcCCcEEEehhHhhhhhccCCCCCC-CchHHHHHHHHHHHhhhcccC
Confidence            4578999999999999999999999999999999999999999999999877653221 233446789999999999988


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      ..+++||+|||+|+.||++++||||||+.|+|+.|+.++|.+||+.++++.++..+.++..+|..|.||||+|       
T Consensus       288 ~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~~~d~~~la~~t~G~sgad-------  360 (644)
T PRK10733        288 NEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGAD-------  360 (644)
T ss_pred             CCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCCCcCCHHHHHhhCCCCCHHH-------
Confidence            7889999999999999999999999999999999999999999999999998888999999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCC
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKP  221 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p  221 (237)
                                          |.++|++|...+.+.+  ...++..||..|+..+.+
T Consensus       361 --------------------l~~l~~eAa~~a~r~~--~~~i~~~d~~~a~~~v~~  394 (644)
T PRK10733        361 --------------------LANLVNEAALFAARGN--KRVVSMVEFEKAKDKIMM  394 (644)
T ss_pred             --------------------HHHHHHHHHHHHHHcC--CCcccHHHHHHHHHHHhc
Confidence                                9999999999988776  456999999999987654

>KOG0729|consensus

Probab=99.96  E-value=1.7e-28  Score=200.99  Aligned_cols=186  Identities=41%  Similarity=0.666  Sum_probs=171.6

Q ss_pred             CCCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           4 LGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         4 ~~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      ....+-||.|-+|+|..+|+|++.+.++++|+.|+...-|||||||+|++.+.|-+.+..+ ++..+++.-+++++||++
T Consensus       233 nrtdacfirvigselvqkyvgegarmvrelf~martkkaciiffdeidaiggarfddg~gg-dnevqrtmleli~qldgf  311 (435)
T KOG0729|consen  233 NRTDACFIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAIGGARFDDGAGG-DNEVQRTMLELINQLDGF  311 (435)
T ss_pred             cccCceEEeehhHHHHHHHhhhhHHHHHHHHHHhcccceEEEEeeccccccCccccCCCCC-cHHHHHHHHHHHHhccCC
Confidence            4556789999999999999999999999999999999999999999999998887765443 566678889999999999


Q ss_pred             CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchh
Q psy5642          84 VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSK  163 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~  163 (237)
                      ..+++|-|+.+||+|+.+||+++||||+|+.++|.+|+.+.|..||+.+.+.+.+..+.-|+-||..|..-||+|     
T Consensus       312 dprgnikvlmatnrpdtldpallrpgrldrkvef~lpdlegrt~i~kihaksmsverdir~ellarlcpnstgae-----  386 (435)
T KOG0729|consen  312 DPRGNIKVLMATNRPDTLDPALLRPGRLDRKVEFGLPDLEGRTHIFKIHAKSMSVERDIRFELLARLCPNSTGAE-----  386 (435)
T ss_pred             CCCCCeEEEeecCCCCCcCHhhcCCcccccceeccCCcccccceeEEEeccccccccchhHHHHHhhCCCCcchH-----
Confidence            999999999999999999999999999999999999999999999999999999989999999999999999999     


Q ss_pred             HHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhc
Q psy5642         164 HRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLV  219 (237)
Q Consensus       164 ~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~  219 (237)
                                            |..+|.+|.+.+++..  ....|..||+.|+...
T Consensus       387 ----------------------irsvcteagmfairar--rk~atekdfl~av~kv  418 (435)
T KOG0729|consen  387 ----------------------IRSVCTEAGMFAIRAR--RKVATEKDFLDAVNKV  418 (435)
T ss_pred             ----------------------HHHHHHHhhHHHHHHH--hhhhhHHHHHHHHHHH
Confidence                                  9999999999998866  4568999999998754

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.96  E-value=4.7e-28  Score=237.88  Aligned_cols=177  Identities=15%  Similarity=0.204  Sum_probs=147.6

Q ss_pred             CCceEEEEEecccccccc-----------------------------------------cChHHH--HHHHHHHHHHhcC
Q psy5642           5 GGLTEVVESIGPELFRKY-----------------------------------------VGESER--CVRDVFKRARQVS   41 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~-----------------------------------------~g~~~~--~l~~~f~~a~~~~   41 (237)
                      -+++||+.|+++++++++                                         ++.++.  .++.+|+.|++++
T Consensus      1653 es~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~~~~e~~e~~n~~~~~m~~~e~~~rIr~lFelARk~S 1732 (2281)
T CHL00206       1653 NSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDLDTELLTMMNALTMDMMPKIDRFYITLQFELAKAMS 1732 (2281)
T ss_pred             hcCCceEEEEHHHHhhcccccccccccccccccccccccccccccchhhhhhcchhhhhhhhhhhHHHHHHHHHHHHHCC
Confidence            467899999999998765                                         222333  4899999999999


Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC---CCCCEEEEEEeCCCCccchhccCCCCcccEEEec
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV---PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVP  118 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~  118 (237)
                      ||||||||||+++.+...          ...++.|+++|++..   ...+|+||||||+|+.||||++||||||+.|+++
T Consensus      1733 PCIIFIDEIDaL~~~ds~----------~ltL~qLLneLDg~~~~~s~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir 1802 (2281)
T CHL00206       1733 PCIIWIPNIHDLNVNESN----------YLSLGLLVNSLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIR 1802 (2281)
T ss_pred             CeEEEEEchhhcCCCccc----------eehHHHHHHHhccccccCCCCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeC
Confidence            999999999999876211          124788999999753   3457999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHH--cCCCCC-chhhHHHHHHHCCCCCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHH
Q psy5642         119 LPDDLTRAAILKIRL--ARSPLG-EDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAAL  195 (237)
Q Consensus       119 ~P~~~~R~~il~~~l--~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~  195 (237)
                      .|+.++|++++..++  ++..+. ...++..+|..|.||||+|                           |+++|.+|+.
T Consensus      1803 ~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA~~T~GfSGAD---------------------------LanLvNEAal 1855 (2281)
T CHL00206       1803 RLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARD---------------------------LVALTNEALS 1855 (2281)
T ss_pred             CCCchhHHHHHHHHHhhcCCCCCcccccHHHHHHhCCCCCHHH---------------------------HHHHHHHHHH
Confidence            999999999998654  334443 3368999999999999999                           9999999999


Q ss_pred             HHHHhccccCCccHHHHHHHHhhcC
Q psy5642         196 SALENNLEAAYVSHQDFLTALQLVK  220 (237)
Q Consensus       196 ~~~~~~~~~~~v~~~df~~al~~~~  220 (237)
                      .++.++  ...|+.++|..|+....
T Consensus      1856 iAirq~--ks~Id~~~I~~Al~Rq~ 1878 (2281)
T CHL00206       1856 ISITQK--KSIIDTNTIRSALHRQT 1878 (2281)
T ss_pred             HHHHcC--CCccCHHHHHHHHHHHH
Confidence            999887  55699999999988654

>KOG0741|consensus

Probab=99.95  E-value=1.5e-28  Score=216.49  Aligned_cols=203  Identities=38%  Similarity=0.589  Sum_probs=162.3

Q ss_pred             EecccccccccChHHHHHHHHHHHHHhcC--------CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642          13 SIGPELFRKYVGESERCVRDVFKRARQVS--------PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus        13 v~~s~l~~~~~g~~~~~l~~~f~~a~~~~--------P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      |++.++.+||+|+++.++|++|..|.+.+        =-||+|||||++|.+|++...++  .....++++||.-||+..
T Consensus       288 VNGPeIL~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEiDAICKqRGS~~g~T--GVhD~VVNQLLsKmDGVe  365 (744)
T KOG0741|consen  288 VNGPEILNKYVGESEENVRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAGST--GVHDTVVNQLLSKMDGVE  365 (744)
T ss_pred             cCcHHHHHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEEEehhhHHHHHhcCCCCCCC--CccHHHHHHHHHhcccHH
Confidence            77889999999999999999999997532        23999999999999998765532  344789999999999999


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCC----CCchhhHHHHHHHCCCCCccccc
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSP----LGEDVCVEELVRLTEGYSGAEQS  160 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~----~~~~~~~~~la~~t~g~s~~Dl~  160 (237)
                      .-++|+|||-||+.+.||+||+|||||.-++++.+||++.|.+||+.+.+++.    +..++|+.+||.+|..|||++|+
T Consensus       366 qLNNILVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gRlQIl~IHT~rMre~~~l~~dVdl~elA~lTKNfSGAEle  445 (744)
T KOG0741|consen  366 QLNNILVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGRLQILKIHTKRMRENNKLSADVDLKELAALTKNFSGAELE  445 (744)
T ss_pred             hhhcEEEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCceEEEEhhhhhhhhcCCCCCCcCHHHHHHHhcCCchhHHH
Confidence            88999999999999999999999999999999999999999999998887653    44899999999999999999955


Q ss_pred             chhHHhhhhccccCCCCCCCCCchhHHHHHHHHH-HHHHHhccccCCccHHHHHHHHhhcCCC--CCHHHHHHHH
Q psy5642         161 LSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA-LSALENNLEAAYVSHQDFLTALQLVKPR--TPPQLIKLYE  232 (237)
Q Consensus       161 ~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~-~~~~~~~~~~~~v~~~df~~al~~~~p~--~~~~~~~~~~  232 (237)
                      -+++.|.+.+-.|               .+..-. ...-....+...|+.+||..||..++|+  ++.++++.+.
T Consensus       446 glVksA~S~A~nR---------------~vk~~~~~~~~~~~~e~lkV~r~DFl~aL~dVkPAFG~see~l~~~~  505 (744)
T KOG0741|consen  446 GLVKSAQSFAMNR---------------HVKAGGKVEVDPVAIENLKVTRGDFLNALEDVKPAFGISEEDLERFV  505 (744)
T ss_pred             HHHHHHHHHHHHh---------------hhccCcceecCchhhhheeecHHHHHHHHHhcCcccCCCHHHHHHHH
Confidence            5555444333111               111000 0000112234679999999999999999  4888887754

>CHL00176 ftsH cell division protein; Validated

Probab=99.95  E-value=4.8e-27  Score=218.19  Aligned_cols=184  Identities=40%  Similarity=0.637  Sum_probs=164.8

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+.||+.++++++...+.|.+...++.+|..|+..+||||||||+|.++..++..... .......+++.|+..++++..
T Consensus       240 ~~~p~i~is~s~f~~~~~g~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~-~~~e~~~~L~~LL~~~dg~~~  318 (638)
T CHL00176        240 AEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGG-GNDEREQTLNQLLTEMDGFKG  318 (638)
T ss_pred             hCCCeeeccHHHHHHHhhhhhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCCCCC-CcHHHHHHHHHHHhhhccccC
Confidence            4679999999999999999999999999999999999999999999999776543322 233456788999999999887


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      +.+++||++||+++.+|++++||||||.+|++++|+.++|.+||+.+++......+.++..+|..|.||+|+|       
T Consensus       319 ~~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~~~d~~l~~lA~~t~G~sgaD-------  391 (638)
T CHL00176        319 NKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGAD-------  391 (638)
T ss_pred             CCCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhcccchhHHHHHHHhcCCCCCHHH-------
Confidence            7889999999999999999999999999999999999999999999999877778899999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhc
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLV  219 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~  219 (237)
                                          |.+++++|+..+.+++  ...|+.+||..|+..+
T Consensus       392 --------------------L~~lvneAal~a~r~~--~~~It~~dl~~Ai~rv  423 (638)
T CHL00176        392 --------------------LANLLNEAAILTARRK--KATITMKEIDTAIDRV  423 (638)
T ss_pred             --------------------HHHHHHHHHHHHHHhC--CCCcCHHHHHHHHHHH
Confidence                                9999999988887766  4569999999999875

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.94  E-value=2.4e-26  Score=202.62  Aligned_cols=183  Identities=46%  Similarity=0.791  Sum_probs=162.7

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+|+.+.++++...|.|++...++.+|..|+...|+||||||+|.++..+.....++ ....++.+..++..++++...
T Consensus       181 ~~~~~~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~-~~~~~~~l~~ll~~ld~~~~~  259 (364)
T TIGR01242       181 NATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSG-DREVQRTLMQLLAELDGFDPR  259 (364)
T ss_pred             CCCEEecchHHHHHHhhhHHHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCc-cHHHHHHHHHHHHHhhCCCCC
Confidence            4578899999999999999999999999999999999999999999987765443322 234456778888889887767


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      +++.||+|||+++.+|++++|||||+..|+|+.|+.++|.+||+.++.+..+..+.++..++..|+||+|+|        
T Consensus       260 ~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~~~~la~~t~g~sg~d--------  331 (364)
T TIGR01242       260 GNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGAD--------  331 (364)
T ss_pred             CCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccCCHHHHHHHcCCCCHHH--------
Confidence            789999999999999999999999999999999999999999999998888777789999999999999999        


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhc
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLV  219 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~  219 (237)
                                         |.++|.+|+..++.++  ...|+.+||..|++.+
T Consensus       332 -------------------l~~l~~~A~~~a~~~~--~~~i~~~d~~~a~~~~  363 (364)
T TIGR01242       332 -------------------LKAICTEAGMFAIREE--RDYVTMDDFIKAVEKV  363 (364)
T ss_pred             -------------------HHHHHHHHHHHHHHhC--CCccCHHHHHHHHHHh
Confidence                               9999999999998876  4579999999999864

Many proteins may score above the trusted cutoff because an internal

>KOG0732|consensus

Probab=99.94  E-value=3.4e-26  Score=216.49  Aligned_cols=191  Identities=37%  Similarity=0.587  Sum_probs=170.0

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      ..+.-|+.-++.+..++|+|+.+++++.+|+.|+.++|+|||+||||-|++.++....    .....+++.||..|+++.
T Consensus       327 ~~kisffmrkgaD~lskwvgEaERqlrllFeeA~k~qPSIIffdeIdGlapvrSskqE----qih~SIvSTLLaLmdGld  402 (1080)
T KOG0732|consen  327 NRKISFFMRKGADCLSKWVGEAERQLRLLFEEAQKTQPSIIFFDEIDGLAPVRSSKQE----QIHASIVSTLLALMDGLD  402 (1080)
T ss_pred             ccccchhhhcCchhhccccCcHHHHHHHHHHHHhccCceEEeccccccccccccchHH----HhhhhHHHHHHHhccCCC
Confidence            3467788889999999999999999999999999999999999999999999866543    233678999999999999


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchh
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSK  163 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~  163 (237)
                      .++.|+|||+||+|+.+|+++|||||||+.++|++|+.++|.+|+..+.++-... ....+..+|..|.||.|+|     
T Consensus       403 sRgqVvvigATnRpda~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrkw~~~i~~~l~~~la~~t~gy~gaD-----  477 (1080)
T KOG0732|consen  403 SRGQVVVIGATNRPDAIDPALRRPGRFDREFYFPLPDVDARAKILDIHTRKWEPPISRELLLWLAEETSGYGGAD-----  477 (1080)
T ss_pred             CCCceEEEcccCCccccchhhcCCcccceeEeeeCCchHHHHHHHHHhccCCCCCCCHHHHHHHHHhccccchHH-----
Confidence            9999999999999999999999999999999999999999999999988776533 6677889999999999999     


Q ss_pred             HHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccc--------------cCCccHHHHHHHHhhcCCCCCHH
Q psy5642         164 HRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLE--------------AAYVSHQDFLTALQLVKPRTPPQ  226 (237)
Q Consensus       164 ~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~--------------~~~v~~~df~~al~~~~p~~~~~  226 (237)
                                            |+++|.+|++.++.+...              ...|...||..|+..+.|+..+.
T Consensus       478 ----------------------lkaLCTeAal~~~~r~~Pq~y~s~~kl~~d~~~ikV~~~~f~~A~~~i~ps~~R~  532 (1080)
T KOG0732|consen  478 ----------------------LKALCTEAALIALRRSFPQIYSSSDKLLIDVALIKVEVRDFVEAMSRITPSSRRS  532 (1080)
T ss_pred             ----------------------HHHHHHHHhhhhhccccCeeecccccccccchhhhhhhHhhhhhhhccCCCCCcc
Confidence                                  999999999999876432              23588999999999999987763

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

Probab=99.93  E-value=3.5e-25  Score=190.37  Aligned_cols=155  Identities=20%  Similarity=0.249  Sum_probs=126.3

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhc-----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHh
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQV-----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEM   80 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~-----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l   80 (237)
                      .+++|+.+++.+|+++|+|+++++|+.+|..|...     +||||||||||.+++.++..+.   ....+.+..+|++.+
T Consensus       172 lg~~~i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~~g~r~~~~~---tv~~qiV~~tLLnl~  248 (413)
T PLN00020        172 MGIEPIVMSAGELESENAGEPGKLIRQRYREAADIIKKKGKMSCLFINDLDAGAGRFGTTQY---TVNNQMVNGTLMNIA  248 (413)
T ss_pred             cCCCeEEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhhccCCCeEEEEehhhhcCCCCCCCCc---chHHHHHHHHHHHHh
Confidence            46789999999999999999999999999999864     6999999999999998863321   112234458999998


Q ss_pred             cCC------------CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHH
Q psy5642          81 DGI------------VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELV  148 (237)
Q Consensus        81 ~~~------------~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la  148 (237)
                      |+.            ....+|+||+|||+|+.||++|+||||||+.+  ..|+.++|.+||+.++++..+. ..++..|+
T Consensus       249 D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd~LDpALlRpGRfDk~i--~lPd~e~R~eIL~~~~r~~~l~-~~dv~~Lv  325 (413)
T PLN00020        249 DNPTNVSLGGDWREKEEIPRVPIIVTGNDFSTLYAPLIRDGRMEKFY--WAPTREDRIGVVHGIFRDDGVS-REDVVKLV  325 (413)
T ss_pred             cCCccccccccccccccCCCceEEEeCCCcccCCHhHcCCCCCCcee--CCCCHHHHHHHHHHHhccCCCC-HHHHHHHH
Confidence            863            23457999999999999999999999999965  5899999999999999987764 67888888


Q ss_pred             HHCCC----CCcccccchhHHh
Q psy5642         149 RLTEG----YSGAEQSLSKHRA  166 (237)
Q Consensus       149 ~~t~g----~s~~Dl~~~~~~a  166 (237)
                      ..+.|    |.|+--..+++++
T Consensus       326 ~~f~gq~~Df~GAlrar~yd~~  347 (413)
T PLN00020        326 DTFPGQPLDFFGALRARVYDDE  347 (413)
T ss_pred             HcCCCCCchhhhHHHHHHHHHH
Confidence            87765    4555546666666

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.93  E-value=4.1e-25  Score=199.78  Aligned_cols=204  Identities=34%  Similarity=0.502  Sum_probs=165.3

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      ....|+.++++++.++|.|++++.++.+|+.|+..    .|+||||||+|.++.+++....   +....++++.|+++|+
T Consensus       250 ~~~~fl~v~~~eLl~kyvGete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s---~d~e~~il~~LL~~LD  326 (512)
T TIGR03689       250 DKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVS---SDVETTVVPQLLSELD  326 (512)
T ss_pred             CceeEEeccchhhcccccchHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCcc---chHHHHHHHHHHHHhc
Confidence            45678899999999999999999999999999874    6999999999999988754332   2344688999999999


Q ss_pred             CCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC-CCCchhhHHHHHHHCCCCCccccc
Q psy5642          82 GIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS-PLGEDVCVEELVRLTEGYSGAEQS  160 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~-~~~~~~~~~~la~~t~g~s~~Dl~  160 (237)
                      ++...++++||+|||+++.||++++||||||.+|+|++|+.++|.+||+.++... ++      ...+..+.|++++++.
T Consensus       327 gl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~~l~l------~~~l~~~~g~~~a~~~  400 (512)
T TIGR03689       327 GVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTDSLPL------DADLAEFDGDREATAA  400 (512)
T ss_pred             ccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhccCCc------hHHHHHhcCCCHHHHH
Confidence            9988788999999999999999999999999999999999999999999998642 22      2334557899999999


Q ss_pred             chhHHhhhhccccC-----------------CCCCCCCCchhHHHHHHHHHHHHHHhccc--cCCccHHHHHHHHhh
Q psy5642         161 LSKHRAKKIRPRRE-----------------SNPGPPACKPSIVAVCDEAALSALENNLE--AAYVSHQDFLTALQL  218 (237)
Q Consensus       161 ~~~~~a~~~~~~~~-----------------~~~~~~~~~~~i~~~~~~a~~~~~~~~~~--~~~v~~~df~~al~~  218 (237)
                      .+++++....-.+.                 ..-.+-.+..-|+++|..|...++++...  ...++.+|+..|+..
T Consensus       401 al~~~av~~~~a~~~~~~~l~~~~~~g~~~~l~~~d~~sGa~i~~iv~~a~~~ai~~~~~~~~~~~~~~~l~~a~~~  477 (512)
T TIGR03689       401 ALIQRAVDHLYATSEENRYVEVTYANGSTEVLYFKDFVSGAMIANIVDRAKKRAIKDHITGGQVGLRIEHLLAAVLD  477 (512)
T ss_pred             HHHHHHHHHHhhhhcccceeEEEecCCceeeEeecccccHHHHHHHHHHHHHHHHHHHHhcCCcCcCHHHHHHHHHH
Confidence            99888744322211                 01123344667899999999988887532  357999999999874

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.

>KOG0651|consensus

Probab=99.93  E-value=5e-26  Score=189.59  Aligned_cols=184  Identities=38%  Similarity=0.683  Sum_probs=163.4

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      .+.|+.+..+.+.++|+||+.+.|++.|..|+.+.|||||+||||++.+.+.+...+. ....++++=+|+++|+++...
T Consensus       191 g~nfl~v~ss~lv~kyiGEsaRlIRemf~yA~~~~pciifmdeiDAigGRr~se~Ts~-dreiqrTLMeLlnqmdgfd~l  269 (388)
T KOG0651|consen  191 GVNFLKVVSSALVDKYIGESARLIRDMFRYAREVIPCIIFMDEIDAIGGRRFSEGTSS-DREIQRTLMELLNQMDGFDTL  269 (388)
T ss_pred             CCceEEeeHhhhhhhhcccHHHHHHHHHHHHhhhCceEEeehhhhhhccEEeccccch-hHHHHHHHHHHHHhhccchhc
Confidence            5679999999999999999999999999999999999999999999998885544332 334467778888999999888


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      ++|-+|.|||+|+.|||+|+||||.|+.+++|.|+...|..|++.+-.........+.+.+.+.++||.|+|        
T Consensus       270 ~rVk~ImatNrpdtLdpaLlRpGRldrk~~iPlpne~~r~~I~Kih~~~i~~~Geid~eaivK~~d~f~gad--------  341 (388)
T KOG0651|consen  270 HRVKTIMATNRPDTLDPALLRPGRLDRKVEIPLPNEQARLGILKIHVQPIDFHGEIDDEAILKLVDGFNGAD--------  341 (388)
T ss_pred             ccccEEEecCCccccchhhcCCccccceeccCCcchhhceeeEeeccccccccccccHHHHHHHHhccChHH--------
Confidence            999999999999999999999999999999999999999999998888776667889999999999999999        


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcC
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVK  220 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~  220 (237)
                                         +.+.|.+|...++++.  ...+-.+||..++.+..
T Consensus       342 -------------------~rn~~tEag~Fa~~~~--~~~vl~Ed~~k~vrk~~  374 (388)
T KOG0651|consen  342 -------------------LRNVCTEAGMFAIPEE--RDEVLHEDFMKLVRKQA  374 (388)
T ss_pred             -------------------Hhhhcccccccccchh--hHHHhHHHHHHHHHHHH
Confidence                               9999999998887776  33577899999987654

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.92  E-value=5.3e-24  Score=202.70  Aligned_cols=189  Identities=42%  Similarity=0.694  Sum_probs=163.9

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+|+.++++++.++|.|++++.++.+|+.|....|+||||||+|.++..+....    .....++++.|+..|+++...
T Consensus       237 ~~~~i~i~~~~i~~~~~g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~~~----~~~~~~~~~~Ll~~ld~l~~~  312 (733)
T TIGR01243       237 GAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVT----GEVEKRVVAQLLTLMDGLKGR  312 (733)
T ss_pred             CCeEEEEecHHHhcccccHHHHHHHHHHHHHHhcCCcEEEeehhhhhcccccCCc----chHHHHHHHHHHHHhhccccC
Confidence            4679999999999999999999999999999999999999999999998765432    234468899999999998877


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      ++++||++||.++.+|++++++|||+..++++.|+.++|.+||+.+.+..++..+.++..++..|+||+++|        
T Consensus       313 ~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~~d~~l~~la~~t~G~~gad--------  384 (733)
T TIGR01243       313 GRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGAD--------  384 (733)
T ss_pred             CCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCccccCHHHHHHhCCCCCHHH--------
Confidence            889999999999999999999999999999999999999999999998888778899999999999999999        


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhc-----------------cccCCccHHHHHHHHhhcCCCCCHH
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENN-----------------LEAAYVSHQDFLTALQLVKPRTPPQ  226 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~-----------------~~~~~v~~~df~~al~~~~p~~~~~  226 (237)
                                         +..++..|...++.+.                 .....++.+||..|++..+|+..++
T Consensus       385 -------------------l~~l~~~a~~~al~r~~~~~~~~~~~~~i~~~~~~~~~v~~~df~~Al~~v~ps~~~~  442 (733)
T TIGR01243       385 -------------------LAALAKEAAMAALRRFIREGKINFEAEEIPAEVLKELKVTMKDFMEALKMVEPSAIRE  442 (733)
T ss_pred             -------------------HHHHHHHHHHHHHHHHhhccccccccccccchhcccccccHHHHHHHHhhccccccch
Confidence                               6666666665554431                 1234689999999999999986543

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.

>KOG0735|consensus

Probab=99.83  E-value=9.7e-20  Score=165.71  Aligned_cols=189  Identities=21%  Similarity=0.262  Sum_probs=147.9

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHH-hcCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTE-MDGIVP   85 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~-l~~~~~   85 (237)
                      -+|+..++|+.+-.+.....++.++.+|..|.+++|+||++|++|.|+....  ..++........+..++++ +..+.+
T Consensus       460 ~~hv~~v~Cs~l~~~~~e~iQk~l~~vfse~~~~~PSiIvLDdld~l~~~s~--~e~~q~~~~~~rla~flnqvi~~y~~  537 (952)
T KOG0735|consen  460 IAHVEIVSCSTLDGSSLEKIQKFLNNVFSEALWYAPSIIVLDDLDCLASASS--NENGQDGVVSERLAAFLNQVIKIYLK  537 (952)
T ss_pred             ceEEEEEechhccchhHHHHHHHHHHHHHHHHhhCCcEEEEcchhhhhccCc--ccCCcchHHHHHHHHHHHHHHHHHHc
Confidence            4789999999999999999999999999999999999999999999998322  2222233334455556644 444444


Q ss_pred             CC-CEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchh
Q psy5642          86 LN-NVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSK  163 (237)
Q Consensus        86 ~~-~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~  163 (237)
                      ++ .+.||||.+..+.+++-|..|++|+.++.+++|+..+|.+||+..+++.... ...+++-++.+|+||.+.||..++
T Consensus       538 ~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~R~~IL~~~~s~~~~~~~~~dLd~ls~~TEGy~~~DL~ifV  617 (952)
T KOG0735|consen  538 RNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAVTRRKEILTTIFSKNLSDITMDDLDFLSVKTEGYLATDLVIFV  617 (952)
T ss_pred             cCcEEEEEEechhhhhcChhhcCccceEEEEecCCcchhHHHHHHHHHHHhhhhhhhhHHHHHHHHhcCCccchhHHHHH
Confidence            44 5899999999999999999999999999999999999999999999876533 445555599999999999966655


Q ss_pred             HHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHh--ccccCCccHHHHHHHHhhcCCCCC
Q psy5642         164 HRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALEN--NLEAAYVSHQDFLTALQLVKPRTP  224 (237)
Q Consensus       164 ~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~--~~~~~~v~~~df~~al~~~~p~~~  224 (237)
                      +||                           ...++.+  ...+..++.++|.++|+.+.|.+.
T Consensus       618 eRa---------------------------i~~a~leris~~~klltke~f~ksL~~F~P~aL  653 (952)
T KOG0735|consen  618 ERA---------------------------IHEAFLERISNGPKLLTKELFEKSLKDFVPLAL  653 (952)
T ss_pred             HHH---------------------------HHHHHHHHhccCcccchHHHHHHHHHhcChHHh
Confidence            555                           3333322  111337999999999999888643

>KOG0736|consensus

Probab=99.81  E-value=9e-20  Score=167.14  Aligned_cols=212  Identities=22%  Similarity=0.260  Sum_probs=164.5

Q ss_pred             CCCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc--
Q psy5642           4 LGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD--   81 (237)
Q Consensus         4 ~~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~--   81 (237)
                      +.-++|+++++|+++.+...+.++..+..+|.+|+..+|+|||+-++|.+..+..+..       ..++...+-..+.  
T Consensus       453 s~lg~h~~evdc~el~~~s~~~~etkl~~~f~~a~~~~pavifl~~~dvl~id~dgge-------d~rl~~~i~~~ls~e  525 (953)
T KOG0736|consen  453 SELGLHLLEVDCYELVAESASHTETKLQAIFSRARRCSPAVLFLRNLDVLGIDQDGGE-------DARLLKVIRHLLSNE  525 (953)
T ss_pred             HHhCCceEeccHHHHhhcccchhHHHHHHHHHHHhhcCceEEEEeccceeeecCCCch-------hHHHHHHHHHHHhcc
Confidence            3457899999999999999999999999999999999999999999999985543321       1455555544444  


Q ss_pred             CC-CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCccccc
Q psy5642          82 GI-VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQS  160 (237)
Q Consensus        82 ~~-~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~  160 (237)
                      .. ....+++||+||++.+.||+.+++  .|-++|.++.|+.+||.+||++++....+..++.+..+|.+|.||+.+|++
T Consensus       526 ~~~~~~~~~ivv~t~~s~~~lp~~i~~--~f~~ei~~~~lse~qRl~iLq~y~~~~~~n~~v~~k~~a~~t~gfs~~~L~  603 (953)
T KOG0736|consen  526 DFKFSCPPVIVVATTSSIEDLPADIQS--LFLHEIEVPALSEEQRLEILQWYLNHLPLNQDVNLKQLARKTSGFSFGDLE  603 (953)
T ss_pred             cccCCCCceEEEEeccccccCCHHHHH--hhhhhccCCCCCHHHHHHHHHHHHhccccchHHHHHHHHHhcCCCCHHHHH
Confidence            22 234579999999999999999999  999999999999999999999999999999999999999999999999988


Q ss_pred             chhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhc---cccCCccHHHHHHHHhhcC------------CCCCH
Q psy5642         161 LSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENN---LEAAYVSHQDFLTALQLVK------------PRTPP  225 (237)
Q Consensus       161 ~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~---~~~~~v~~~df~~al~~~~------------p~~~~  225 (237)
                      .++.++...+..|            +++---.-......++   .....++++||..|+..++            |.++|
T Consensus       604 ~l~~~~s~~~~~~------------i~~~~l~g~~~~~~~~~~~~~~~~l~~edf~kals~~~~~fs~aiGAPKIPnV~W  671 (953)
T KOG0736|consen  604 ALVAHSSLAAKTR------------IKNKGLAGGLQEEDEGELCAAGFLLTEEDFDKALSRLQKEFSDAIGAPKIPNVSW  671 (953)
T ss_pred             HHhcCchHHHHHH------------HHhhcccccchhccccccccccceecHHHHHHHHHHHHHhhhhhcCCCCCCccch
Confidence            8877763222211            1110000000000111   1235799999999998544            88999


Q ss_pred             HHHHHHHHHhh
Q psy5642         226 QLIKLYENYIK  236 (237)
Q Consensus       226 ~~~~~~~~~~~  236 (237)
                      ++++.+++.++
T Consensus       672 dDVGGLeevK~  682 (953)
T KOG0736|consen  672 DDVGGLEEVKT  682 (953)
T ss_pred             hcccCHHHHHH
Confidence            99999998764

>KOG0744|consensus

Probab=99.76  E-value=3.3e-18  Score=143.84  Aligned_cols=133  Identities=28%  Similarity=0.387  Sum_probs=120.7

Q ss_pred             CCcCCCceEEEEEecccccccccChHHHHHHHHHHHHHhcC---C--eEEEEccccccccccCCCCCCCCCchHHHHHHH
Q psy5642           1 MEDLGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVS---P--SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQ   75 (237)
Q Consensus         1 ~~~~~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~---P--~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~   75 (237)
                      +++.+....+++++++.||+||++|+.|.+.++|+.....-   .  ..++|||+++|+..|.+....+.+...-|+++.
T Consensus       205 ~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLIDEVESLa~aR~s~~S~~EpsDaIRvVNa  284 (423)
T KOG0744|consen  205 TNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVLIDEVESLAAARTSASSRNEPSDAIRVVNA  284 (423)
T ss_pred             ecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEeHHHHHHHHHHHhhhcCCCCchHHHHHHH
Confidence            35678899999999999999999999999999999988742   2  267899999999988776666677788999999


Q ss_pred             HHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcC
Q psy5642          76 MLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR  135 (237)
Q Consensus        76 ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~  135 (237)
                      +|++||.+++.++|++++|+|-.+.||.|+..  |-|-..++++|+...|.+|++.++..
T Consensus       285 lLTQlDrlK~~~NvliL~TSNl~~siD~AfVD--RADi~~yVG~Pt~~ai~~IlkscieE  342 (423)
T KOG0744|consen  285 LLTQLDRLKRYPNVLILATSNLTDSIDVAFVD--RADIVFYVGPPTAEAIYEILKSCIEE  342 (423)
T ss_pred             HHHHHHHhccCCCEEEEeccchHHHHHHHhhh--HhhheeecCCccHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999  99999999999999999999987753

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

Probab=99.65  E-value=1.6e-15  Score=114.06  Aligned_cols=108  Identities=41%  Similarity=0.660  Sum_probs=95.3

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcC-CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVS-PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~-P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      +.++++++++.+.+.+.+++.+.++.+|..++... |+||+|||+|.++......    .......++..++..++....
T Consensus        23 ~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~vl~iDe~d~l~~~~~~~----~~~~~~~~~~~L~~~l~~~~~   98 (132)
T PF00004_consen   23 GFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKSAKPCVLFIDEIDKLFPKSQPS----SSSFEQRLLNQLLSLLDNPSS   98 (132)
T ss_dssp             TSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGTSHHCSTS----SSHHHHHHHHHHHHHHHTTTT
T ss_pred             ccccccccccccccccccccccccccccccccccccceeeeeccchhcccccccc----cccccccccceeeeccccccc
Confidence            57899999999999999999999999999999987 9999999999999887211    245668899999999999876


Q ss_pred             C-CCEEEEEEeCCCCccchhccCCCCcccEEEecC
Q psy5642          86 L-NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPL  119 (237)
Q Consensus        86 ~-~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~  119 (237)
                      . ++++||+|||.++.+++++++ +||+..|+++.
T Consensus        99 ~~~~~~vI~ttn~~~~i~~~l~~-~rf~~~i~~~~  132 (132)
T PF00004_consen   99 KNSRVIVIATTNSPDKIDPALLR-SRFDRRIEFPL  132 (132)
T ss_dssp             TSSSEEEEEEESSGGGSCHHHHS-TTSEEEEEE-S
T ss_pred             ccccceeEEeeCChhhCCHhHHh-CCCcEEEEcCC
Confidence            5 569999999999999999997 79999999874

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 ....

>KOG0742|consensus

Probab=99.65  E-value=1.7e-15  Score=131.07  Aligned_cols=128  Identities=28%  Similarity=0.442  Sum_probs=108.0

Q ss_pred             ChHHHHHHHHHHHHHhcCCe-EEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          24 GESERCVRDVFKRARQVSPS-VIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        24 g~~~~~l~~~f~~a~~~~P~-il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      .++...|+++|++|+..... +|||||.|.++..|+....   ++..+..++.||--...  .+..++++.+||.|.++|
T Consensus       425 ~qaVTkiH~lFDWakkS~rGLllFIDEADAFLceRnktym---SEaqRsaLNAlLfRTGd--qSrdivLvlAtNrpgdlD  499 (630)
T KOG0742|consen  425 AQAVTKIHKLFDWAKKSRRGLLLFIDEADAFLCERNKTYM---SEAQRSALNALLFRTGD--QSRDIVLVLATNRPGDLD  499 (630)
T ss_pred             hHHHHHHHHHHHHHhhcccceEEEehhhHHHHHHhchhhh---cHHHHHHHHHHHHHhcc--cccceEEEeccCCccchh
Confidence            37789999999999987655 8899999999999887763   56777888888876655  345799999999999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC---------------------------chhhHHHHHHHCCCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG---------------------------EDVCVEELVRLTEGYS  155 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~---------------------------~~~~~~~la~~t~g~s  155 (237)
                      .++-.  |||.+|+||+|..++|..||..|+.++...                           .+.-+++.|.+|+|||
T Consensus       500 sAV~D--Ride~veFpLPGeEERfkll~lYlnkyi~~~~~~~~~~~~~~lfkk~sQ~i~l~~~~t~~~~~EaAkkTeGfS  577 (630)
T KOG0742|consen  500 SAVND--RIDEVVEFPLPGEEERFKLLNLYLNKYILKPATSGKPGKWSHLFKKESQRIKLAGFDTGRKCSEAAKKTEGFS  577 (630)
T ss_pred             HHHHh--hhhheeecCCCChHHHHHHHHHHHHHHhcCcCCCCCCchhhHHHhhhhheeeeccchHHHHHHHHHHhccCCc
Confidence            99999  999999999999999999999998765321                           1234578899999999


Q ss_pred             ccc
Q psy5642         156 GAE  158 (237)
Q Consensus       156 ~~D  158 (237)
                      |++
T Consensus       578 GRE  580 (630)
T KOG0742|consen  578 GRE  580 (630)
T ss_pred             HHH
Confidence            999

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

Probab=99.64  E-value=7e-15  Score=134.69  Aligned_cols=182  Identities=43%  Similarity=0.619  Sum_probs=162.9

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNN   88 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~   88 (237)
                      +++.+++....++|.|+++.+++.+|..+...+|+++++|++|.+.+.+...    ......++++.++..+++.. ...
T Consensus        44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ii~~d~~~~~~~~~~~~----~~~~~~~v~~~l~~~~d~~~-~~~  118 (494)
T COG0464          44 EFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSD----QGEVERRVVAQLLALMDGLK-RGQ  118 (494)
T ss_pred             cccccCcchhhhhhhhHHHHHHHHHHHHHHHhCCCeEeechhhhcccCcccc----ccchhhHHHHHHHHhccccc-CCc
Confidence            3477889999999999999999999999999999999999999999988772    23455789999999999988 444


Q ss_pred             EEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHhhh
Q psy5642          89 VTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKK  168 (237)
Q Consensus        89 v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a~~  168 (237)
                      +++++.+|.+..+++++++||||+..+.++.|+...|.+++...........+.++..++..+.||+++|          
T Consensus       119 v~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~----------  188 (494)
T COG0464         119 VIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGAD----------  188 (494)
T ss_pred             eEEEeecCCccccChhHhCccccceeeecCCCCHHHHHHHHHHHHhcCCCcccccHHHHHHhcCCccHHH----------
Confidence            9999999999999999999999999999999999999999999998888777899999999999999999          


Q ss_pred             hccccCCCCCCCCCchhHHHHHHHHHHHHHHhc----cccCCccHHHHHHHHhhcCCC
Q psy5642         169 IRPRRESNPGPPACKPSIVAVCDEAALSALENN----LEAAYVSHQDFLTALQLVKPR  222 (237)
Q Consensus       169 ~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~----~~~~~v~~~df~~al~~~~p~  222 (237)
                                       +..++.++...+..+.    .....++.++|.++++.+.|+
T Consensus       189 -----------------~~~l~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~l~~~~~~  229 (494)
T COG0464         189 -----------------LGALAKEAALRELRRAIDLVGEYIGVTEDDFEEALKKVLPS  229 (494)
T ss_pred             -----------------HHHHHHHHHHHHHHhhhccCcccccccHHHHHHHHHhcCcc
Confidence                             8889988888777775    456679999999999998763

>KOG0743|consensus

Probab=99.44  E-value=3.2e-13  Score=118.61  Aligned_cols=125  Identities=23%  Similarity=0.320  Sum_probs=94.1

Q ss_pred             HHHHHHHHHhcCCeEEEEccccccccccCCCCCC--CCC-chHHHHHHHHHHHhcCCCCCC--CEEEEEEeCCCCccchh
Q psy5642          30 VRDVFKRARQVSPSVIFFDELDSLAGERGDGGGG--GGS-NVQERVLAQMLTEMDGIVPLN--NVTIVAATNRPDRIDKA  104 (237)
Q Consensus        30 l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~--~~~-~~~~~~~~~ll~~l~~~~~~~--~v~vI~ttn~~~~ld~a  104 (237)
                      |+.++..+..  .+||+|+|||.-+.-+......  ... ....-+++.||+.+|+++...  -.|||+|||+++.||||
T Consensus       277 Lr~LL~~t~~--kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPA  354 (457)
T KOG0743|consen  277 LRHLLLATPN--KSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPA  354 (457)
T ss_pred             HHHHHHhCCC--CcEEEEeecccccccccccccccccccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHh
Confidence            8888876664  5899999999966433322211  111 123467899999999999866  58899999999999999


Q ss_pred             ccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCC--CCCccc
Q psy5642         105 LLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTE--GYSGAE  158 (237)
Q Consensus       105 l~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~--g~s~~D  158 (237)
                      |+||||.|.+|++++++.++-..+++.|+....  +..-++++...-+  -.||+|
T Consensus       355 LlRpGRmDmhI~mgyCtf~~fK~La~nYL~~~~--~h~L~~eie~l~~~~~~tPA~  408 (457)
T KOG0743|consen  355 LLRPGRMDMHIYMGYCTFEAFKTLASNYLGIEE--DHRLFDEIERLIEETEVTPAQ  408 (457)
T ss_pred             hcCCCcceeEEEcCCCCHHHHHHHHHHhcCCCC--CcchhHHHHHHhhcCccCHHH
Confidence            999999999999999999999999999997643  1233333433333  468988

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

Probab=99.40  E-value=5.1e-12  Score=120.72  Aligned_cols=140  Identities=21%  Similarity=0.297  Sum_probs=110.5

Q ss_pred             CceEEEEEeccccc--ccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           6 GLTEVVESIGPELF--RKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         6 ~~~~~i~v~~s~l~--~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      .+.+++.++++.+.  .+|.|+.++.++++|+.++...|+||||||+|.|++.+...+.   +   ..+.+.|...+.  
T Consensus       237 ~~~~~~~~~~~~l~a~~~~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~~~---~---~~~~~~L~~~l~--  308 (731)
T TIGR02639       237 KNAKIYSLDMGSLLAGTKYRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGATSGG---S---MDASNLLKPALS--  308 (731)
T ss_pred             cCCeEEEecHHHHhhhccccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCCCCc---c---HHHHHHHHHHHh--
Confidence            46789999999887  6899999999999999999888999999999999876543221   1   112333444443  


Q ss_pred             CCCCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC----CCC-chhhHHHHHHHCCC
Q psy5642          84 VPLNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS----PLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~----~~~-~~~~~~~la~~t~g  153 (237)
                        ++.+.+||+|+..+     ..|+++.|  ||. .|+++.|+.+++.+||+.+...+    .+. .+..+..++..+..
T Consensus       309 --~g~i~~IgaTt~~e~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~ls~r  383 (731)
T TIGR02639       309 --SGKLRCIGSTTYEEYKNHFEKDRALSR--RFQ-KIDVGEPSIEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSAR  383 (731)
T ss_pred             --CCCeEEEEecCHHHHHHHhhhhHHHHH--hCc-eEEeCCCCHHHHHHHHHHHHHHHHhccCcccCHHHHHHHHHhhhc
Confidence              36899999999633     67999999  997 69999999999999999766543    222 67888889999988


Q ss_pred             CCccc
Q psy5642         154 YSGAE  158 (237)
Q Consensus       154 ~s~~D  158 (237)
                      |-+..
T Consensus       384 yi~~r  388 (731)
T TIGR02639       384 YINDR  388 (731)
T ss_pred             ccccc
Confidence            88775

>CHL00181 cbbX CbbX; Provisional

Probab=99.37  E-value=1.2e-11  Score=105.76  Aligned_cols=118  Identities=18%  Similarity=0.262  Sum_probs=93.6

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+++++++++|.+.|+|++....+.+|+.|.   ++||||||+|.++..++.      ......+...|+..|+..  .
T Consensus        91 ~~~~~~v~~~~l~~~~~g~~~~~~~~~l~~a~---ggVLfIDE~~~l~~~~~~------~~~~~e~~~~L~~~me~~--~  159 (287)
T CHL00181         91 KGHLLTVTRDDLVGQYIGHTAPKTKEVLKKAM---GGVLFIDEAYYLYKPDNE------RDYGSEAIEILLQVMENQ--R  159 (287)
T ss_pred             CCceEEecHHHHHHHHhccchHHHHHHHHHcc---CCEEEEEccchhccCCCc------cchHHHHHHHHHHHHhcC--C
Confidence            34799999999999999999888888888764   589999999999754321      123467788888888863  3


Q ss_pred             CCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCC
Q psy5642          87 NNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSP  137 (237)
Q Consensus        87 ~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~  137 (237)
                      ++++||++++...     .++|++++  ||+.+|+|+.++.+++.+|++.++.+..
T Consensus       160 ~~~~vI~ag~~~~~~~~~~~np~L~s--R~~~~i~F~~~t~~el~~I~~~~l~~~~  213 (287)
T CHL00181        160 DDLVVIFAGYKDRMDKFYESNPGLSS--RIANHVDFPDYTPEELLQIAKIMLEEQQ  213 (287)
T ss_pred             CCEEEEEeCCcHHHHHHHhcCHHHHH--hCCceEEcCCcCHHHHHHHHHHHHHHhc
Confidence            5677777765321     23599999  9999999999999999999999997654

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.37  E-value=1.5e-11  Score=103.77  Aligned_cols=129  Identities=19%  Similarity=0.232  Sum_probs=97.2

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      ..++++++++++.+.|+|++...++.+|+.|.   ++||||||+|.|.....       .......+..++..|+..  .
T Consensus        74 ~~~~v~~~~~~l~~~~~g~~~~~~~~~~~~a~---~~VL~IDE~~~L~~~~~-------~~~~~~~i~~Ll~~~e~~--~  141 (261)
T TIGR02881        74 KGHLIEVERADLVGEYIGHTAQKTREVIKKAL---GGVLFIDEAYSLARGGE-------KDFGKEAIDTLVKGMEDN--R  141 (261)
T ss_pred             CCceEEecHHHhhhhhccchHHHHHHHHHhcc---CCEEEEechhhhccCCc-------cchHHHHHHHHHHHHhcc--C
Confidence            45789999999999999999999999998874   58999999999963211       123356778888888874  3


Q ss_pred             CCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHH
Q psy5642          87 NNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVR  149 (237)
Q Consensus        87 ~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~  149 (237)
                      .++++|+++...+     .++|++++  ||+..|+|+.++.+++.+|++.++...... ++..+..++.
T Consensus       142 ~~~~vila~~~~~~~~~~~~~p~L~s--Rf~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~a~~~l~~  208 (261)
T TIGR02881       142 NEFVLILAGYSDEMDYFLSLNPGLRS--RFPISIDFPDYTVEELMEIAERMVKEREYKLTEEAKWKLRE  208 (261)
T ss_pred             CCEEEEecCCcchhHHHHhcChHHHh--ccceEEEECCCCHHHHHHHHHHHHHHcCCccCHHHHHHHHH
Confidence            4566666554322     36889999  999999999999999999999998765443 3344444443

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

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

Probab=99.26  E-value=4.3e-11  Score=113.91  Aligned_cols=140  Identities=19%  Similarity=0.277  Sum_probs=104.5

Q ss_pred             CceEEEEEeccccc--ccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           6 GLTEVVESIGPELF--RKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         6 ~~~~~i~v~~s~l~--~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      .++.++.++...+.  .+|.|+.+..++.+|..+....|+||||||+|.|++.+...+.   .   ..+.+.|...+.  
T Consensus       241 ~~~~~~~l~~~~llaG~~~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~~~~g---~---~d~~nlLkp~L~--  312 (758)
T PRK11034        241 ADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGG---Q---VDAANLIKPLLS--  312 (758)
T ss_pred             cCCeEEeccHHHHhcccchhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCCCCCc---H---HHHHHHHHHHHh--
Confidence            35667777776666  5789999999999999999888999999999999877643221   1   223333333333  


Q ss_pred             CCCCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-----chhhHHHHHHHCCC
Q psy5642          84 VPLNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-----EDVCVEELVRLTEG  153 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-----~~~~~~~la~~t~g  153 (237)
                        ++.+.+||+|+.++     ..|++|.|  ||+ .|.++.|+.+++..||+.+..++...     .+..+..++..+..
T Consensus       313 --~g~i~vIgATt~~E~~~~~~~D~AL~r--RFq-~I~v~ePs~~~~~~IL~~~~~~ye~~h~v~i~~~al~~a~~ls~r  387 (758)
T PRK11034        313 --SGKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVK  387 (758)
T ss_pred             --CCCeEEEecCChHHHHHHhhccHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHHHhhhccCCCcCHHHHHHHHHHhhc
Confidence              47899999999865     57999999  996 69999999999999999877655433     45556666666666


Q ss_pred             CCccc
Q psy5642         154 YSGAE  158 (237)
Q Consensus       154 ~s~~D  158 (237)
                      |.+..
T Consensus       388 yi~~r  392 (758)
T PRK11034        388 YINDR  392 (758)
T ss_pred             cccCc
Confidence            65443

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.26  E-value=1.5e-10  Score=98.78  Aligned_cols=118  Identities=17%  Similarity=0.291  Sum_probs=94.6

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCC
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLN   87 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~   87 (237)
                      .+++.++++++.+.|.|++...++.+|+.|.   +++|||||++.+...+..      ......+...|+..|+..  ..
T Consensus        91 ~~~v~v~~~~l~~~~~g~~~~~~~~~~~~a~---~gvL~iDEi~~L~~~~~~------~~~~~~~~~~Ll~~le~~--~~  159 (284)
T TIGR02880        91 GHLVSVTRDDLVGQYIGHTAPKTKEILKRAM---GGVLFIDEAYYLYRPDNE------RDYGQEAIEILLQVMENQ--RD  159 (284)
T ss_pred             ceEEEecHHHHhHhhcccchHHHHHHHHHcc---CcEEEEechhhhccCCCc------cchHHHHHHHHHHHHhcC--CC
Confidence            4799999999999999999999999998874   489999999998654321      233466778888888863  35


Q ss_pred             CEEEEEEeCCC--C---ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCC
Q psy5642          88 NVTIVAATNRP--D---RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPL  138 (237)
Q Consensus        88 ~v~vI~ttn~~--~---~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~  138 (237)
                      +++||++++..  +   .++|++++  ||...|+||.++.+++..|++.++.+...
T Consensus       160 ~~~vI~a~~~~~~~~~~~~np~L~s--R~~~~i~fp~l~~edl~~I~~~~l~~~~~  213 (284)
T TIGR02880       160 DLVVILAGYKDRMDSFFESNPGFSS--RVAHHVDFPDYSEAELLVIAGLMLKEQQY  213 (284)
T ss_pred             CEEEEEeCCcHHHHHHHhhCHHHHh--hCCcEEEeCCcCHHHHHHHHHHHHHHhcc
Confidence            67777776642  2   24799999  99999999999999999999999987543

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.17  E-value=6.1e-10  Score=107.76  Aligned_cols=139  Identities=23%  Similarity=0.288  Sum_probs=108.4

Q ss_pred             CceEEEEEeccccc--ccccChHHHHHHHHHHHHHh-cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC
Q psy5642           6 GLTEVVESIGPELF--RKYVGESERCVRDVFKRARQ-VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG   82 (237)
Q Consensus         6 ~~~~~i~v~~s~l~--~~~~g~~~~~l~~~f~~a~~-~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~   82 (237)
                      .+.+++.++.+.+.  ++|.|+.+..++.+|+.++. ..++||||||++.+++.++..+..       ...+.|+..+  
T Consensus       242 ~~~~i~~l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~~~-------d~~n~Lkp~l--  312 (852)
T TIGR03345       242 RNVRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAGQG-------DAANLLKPAL--  312 (852)
T ss_pred             cCCeEEEeehhhhhcccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCccccc-------cHHHHhhHHh--
Confidence            45678888888876  47999999999999999975 468999999999998766432211       1223344433  


Q ss_pred             CCCCCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCC----CC-chhhHHHHHHHCC
Q psy5642          83 IVPLNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSP----LG-EDVCVEELVRLTE  152 (237)
Q Consensus        83 ~~~~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~----~~-~~~~~~~la~~t~  152 (237)
                        .++.+.+||+|+..+     .+|++|.|  ||. .|.|+.|+.+++..||+.+...+.    +. .+..+..++..+.
T Consensus       313 --~~G~l~~IgaTT~~e~~~~~~~d~AL~r--Rf~-~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~  387 (852)
T TIGR03345       313 --ARGELRTIAATTWAEYKKYFEKDPALTR--RFQ-VVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSH  387 (852)
T ss_pred             --hCCCeEEEEecCHHHHhhhhhccHHHHH--hCe-EEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHcc
Confidence              347899999999743     58999999  996 799999999999999887665433    22 6888999999999


Q ss_pred             CCCccc
Q psy5642         153 GYSGAE  158 (237)
Q Consensus       153 g~s~~D  158 (237)
                      +|.+.-
T Consensus       388 ryi~~r  393 (852)
T TIGR03345       388 RYIPGR  393 (852)
T ss_pred             cccccc
Confidence            998876

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.09  E-value=1.1e-09  Score=106.31  Aligned_cols=136  Identities=24%  Similarity=0.283  Sum_probs=105.2

Q ss_pred             ceEEEEEeccccc--ccccChHHHHHHHHHHHHHh-cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           7 LTEVVESIGPELF--RKYVGESERCVRDVFKRARQ-VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         7 ~~~~i~v~~s~l~--~~~~g~~~~~l~~~f~~a~~-~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      +.+++.++.+.+.  .+|.|+.++.++.+|+.+.. ..|+||||||+|.|++.+++.+..       ...+.|...+   
T Consensus       234 ~~~~~~l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~~~-------d~~~~lkp~l---  303 (857)
T PRK10865        234 GRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAM-------DAGNMLKPAL---  303 (857)
T ss_pred             CCEEEEEehhhhhhccchhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCccch-------hHHHHhcchh---
Confidence            6788999888876  67999999999999998754 578999999999998765433221       1122222222   


Q ss_pred             CCCCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-----chhhHHHHHHHCCC
Q psy5642          84 VPLNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-----EDVCVEELVRLTEG  153 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-----~~~~~~~la~~t~g  153 (237)
                       .++.+.+||+|+..+     ++|+++.|  ||+ .|.++.|+.+++..||+.+..++...     .+..+...+..+++
T Consensus       304 -~~g~l~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~eP~~~~~~~iL~~l~~~~e~~~~v~~~d~a~~~a~~ls~r  379 (857)
T PRK10865        304 -ARGELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAILRGLKERYELHHHVQITDPAIVAAATLSHR  379 (857)
T ss_pred             -hcCCCeEEEcCCCHHHHHHhhhcHHHHh--hCC-EEEeCCCCHHHHHHHHHHHhhhhccCCCCCcCHHHHHHHHHHhhc
Confidence             457899999999876     58999999  998 58999999999999999887654322     56667777788888


Q ss_pred             CCc
Q psy5642         154 YSG  156 (237)
Q Consensus       154 ~s~  156 (237)
                      |..
T Consensus       380 y~~  382 (857)
T PRK10865        380 YIA  382 (857)
T ss_pred             ccc
Confidence            884

>TIGR00763 lon ATP-dependent protease La

Probab=99.06  E-value=3.5e-09  Score=102.00  Aligned_cols=140  Identities=21%  Similarity=0.262  Sum_probs=95.5

Q ss_pred             ceEEEEEeccccc---------ccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHH
Q psy5642           7 LTEVVESIGPELF---------RKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQML   77 (237)
Q Consensus         7 ~~~~i~v~~s~l~---------~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll   77 (237)
                      +.+|+.+++..+.         ..|+|.....+...|..+....| ||+|||+|.+.....++           ..+.|+
T Consensus       372 ~~~~~~i~~~~~~~~~~i~g~~~~~~g~~~g~i~~~l~~~~~~~~-villDEidk~~~~~~~~-----------~~~aLl  439 (775)
T TIGR00763       372 NRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAKTKNP-LFLLDEIDKIGSSFRGD-----------PASALL  439 (775)
T ss_pred             cCCeEEEeCCCcccHHHHcCCCCceeCCCCchHHHHHHHhCcCCC-EEEEechhhcCCccCCC-----------HHHHHH
Confidence            3466666554332         46788888888889998877666 89999999998532111           134555


Q ss_pred             HHhcC-----CC--------CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHc-----CCCCC
Q psy5642          78 TEMDG-----IV--------PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA-----RSPLG  139 (237)
Q Consensus        78 ~~l~~-----~~--------~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~-----~~~~~  139 (237)
                      ..|+.     +.        ..+++++|+|||.++.+|+++++  ||+ .|+|+.|+.+++.+|++.++.     ...+.
T Consensus       440 ~~ld~~~~~~f~d~~~~~~~d~s~v~~I~TtN~~~~i~~~L~~--R~~-vi~~~~~~~~e~~~I~~~~l~~~~~~~~~l~  516 (775)
T TIGR00763       440 EVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSIDTIPRPLLD--RME-VIELSGYTEEEKLEIAKKYLIPKALEDHGLK  516 (775)
T ss_pred             HhcCHHhcCccccccCCceeccCCEEEEEecCCchhCCHHHhC--Cee-EEecCCCCHHHHHHHHHHHHHHHHHHHcCCC
Confidence            55542     11        12478999999999999999999  996 799999999999999987762     11221


Q ss_pred             ------chhhHHHHHH-HCCCCCcccccc
Q psy5642         140 ------EDVCVEELVR-LTEGYSGAEQSL  161 (237)
Q Consensus       140 ------~~~~~~~la~-~t~g~s~~Dl~~  161 (237)
                            .+..+..++. .|..+..++|+.
T Consensus       517 ~~~~~~~~~~l~~i~~~~~~e~g~R~l~r  545 (775)
T TIGR00763       517 PDELKITDEALLLLIKYYTREAGVRNLER  545 (775)
T ss_pred             cceEEECHHHHHHHHHhcChhcCChHHHH
Confidence                  3445565655 333455555333

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.02  E-value=2e-09  Score=104.63  Aligned_cols=150  Identities=21%  Similarity=0.271  Sum_probs=112.5

Q ss_pred             CceEEEEEeccccc--ccccChHHHHHHHHHHHHHhc-CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC
Q psy5642           6 GLTEVVESIGPELF--RKYVGESERCVRDVFKRARQV-SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG   82 (237)
Q Consensus         6 ~~~~~i~v~~s~l~--~~~~g~~~~~l~~~f~~a~~~-~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~   82 (237)
                      .+.+++.++...+.  .+|.|+.++.++.+|+.+... .|+||||||+|.|++.+...+.       ....+.|...   
T Consensus       228 ~~~~~~~l~~~~l~a~~~~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~~-------~d~~~~Lk~~---  297 (852)
T TIGR03346       228 KNKRLLALDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGA-------MDAGNMLKPA---  297 (852)
T ss_pred             cCCeEEEeeHHHHhhcchhhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcch-------hHHHHHhchh---
Confidence            36788888888775  679999999999999999764 6999999999999875433221       1122223222   


Q ss_pred             CCCCCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-----chhhHHHHHHHCC
Q psy5642          83 IVPLNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-----EDVCVEELVRLTE  152 (237)
Q Consensus        83 ~~~~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-----~~~~~~~la~~t~  152 (237)
                       ..++.+.+||+|+..+     .+|+++.|  ||. .|.++.|+.+++..||+.+..++...     .+..+..++..++
T Consensus       298 -l~~g~i~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~iL~~~~~~~e~~~~v~~~d~~i~~~~~ls~  373 (852)
T TIGR03346       298 -LARGELHCIGATTLDEYRKYIEKDAALER--RFQ-PVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSH  373 (852)
T ss_pred             -hhcCceEEEEeCcHHHHHHHhhcCHHHHh--cCC-EEEeCCCCHHHHHHHHHHHHHHhccccCCCCCHHHHHHHHHhcc
Confidence             2447899999999864     57999999  997 58999999999999999887665432     5678888899999


Q ss_pred             CCCccc------ccchhHHhhhh
Q psy5642         153 GYSGAE------QSLSKHRAKKI  169 (237)
Q Consensus       153 g~s~~D------l~~~~~~a~~~  169 (237)
                      +|.+.-      |..+...|..+
T Consensus       374 ~yi~~r~lPdkAidlld~a~a~~  396 (852)
T TIGR03346       374 RYITDRFLPDKAIDLIDEAAARI  396 (852)
T ss_pred             ccccccCCchHHHHHHHHHHHHH
Confidence            998763      44444444433

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.97  E-value=1.9e-09  Score=104.34  Aligned_cols=150  Identities=21%  Similarity=0.269  Sum_probs=112.5

Q ss_pred             CceEEEEEeccccc--ccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           6 GLTEVVESIGPELF--RKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         6 ~~~~~i~v~~s~l~--~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      .+.+++.++.+.+.  ++|.|+.+..++.+|+.++...|+||||||+|.|++.+...+..       .+.+.|...+.  
T Consensus       234 ~~~~i~~l~~~~l~ag~~~~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g~~-------~~a~lLkp~l~--  304 (821)
T CHL00095        234 EDKLVITLDIGLLLAGTKYRGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEGAI-------DAANILKPALA--  304 (821)
T ss_pred             cCCeEEEeeHHHHhccCCCccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCCcc-------cHHHHhHHHHh--
Confidence            46789999998887  68999999999999999998889999999999998765433211       12222333333  


Q ss_pred             CCCCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcC----CCC-CchhhHHHHHHHCCC
Q psy5642          84 VPLNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR----SPL-GEDVCVEELVRLTEG  153 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~----~~~-~~~~~~~~la~~t~g  153 (237)
                        ++.+.+||+|+..+     ..|+++.+  ||.. |.++.|+.++...|++.....    +.+ -++..+..++..+.+
T Consensus       305 --rg~l~~IgaTt~~ey~~~ie~D~aL~r--Rf~~-I~v~ep~~~e~~aILr~l~~~~e~~~~v~i~deal~~i~~ls~~  379 (821)
T CHL00095        305 --RGELQCIGATTLDEYRKHIEKDPALER--RFQP-VYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQ  379 (821)
T ss_pred             --CCCcEEEEeCCHHHHHHHHhcCHHHHh--cceE-EecCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhc
Confidence              46789999999764     57999999  9974 899999999999999865432    222 267778889999999


Q ss_pred             CCccc------ccchhHHhhhh
Q psy5642         154 YSGAE------QSLSKHRAKKI  169 (237)
Q Consensus       154 ~s~~D------l~~~~~~a~~~  169 (237)
                      |.+..      |..+...+..+
T Consensus       380 yi~~r~lPdkaidlld~a~a~~  401 (821)
T CHL00095        380 YIADRFLPDKAIDLLDEAGSRV  401 (821)
T ss_pred             cCccccCchHHHHHHHHHHHHH
Confidence            98763      44444444433

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=98.76  E-value=9.9e-08  Score=86.66  Aligned_cols=131  Identities=19%  Similarity=0.314  Sum_probs=86.7

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +..++++.+.++.+.+.+........-|..... .+.+|+|||++.+..++             .....++..++.....
T Consensus       178 ~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~-~~dlLiiDDi~~l~~~~-------------~~~~~l~~~~n~l~~~  243 (450)
T PRK00149        178 NAKVVYVTSEKFTNDFVNALRNNTMEEFKEKYR-SVDVLLIDDIQFLAGKE-------------RTQEEFFHTFNALHEA  243 (450)
T ss_pred             CCeEEEEEHHHHHHHHHHHHHcCcHHHHHHHHh-cCCEEEEehhhhhcCCH-------------HHHHHHHHHHHHHHHC
Confidence            567888888887766554443322233333222 57899999999985432             1122344444333333


Q ss_pred             CCEEEEEEeCCCCc---cchhccCCCCcc--cEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642          87 NNVTIVAATNRPDR---IDKALLRPGRLD--RLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        87 ~~v~vI~ttn~~~~---ld~al~r~gRf~--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +..+||++...|..   +++.+++  ||.  ..+++..|+.++|..||+..+...+.. ++..+..||..+.|
T Consensus       244 ~~~iiits~~~p~~l~~l~~~l~S--Rl~~gl~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~  314 (450)
T PRK00149        244 GKQIVLTSDRPPKELPGLEERLRS--RFEWGLTVDIEPPDLETRIAILKKKAEEEGIDLPDEVLEFIAKNITS  314 (450)
T ss_pred             CCcEEEECCCCHHHHHHHHHHHHh--HhcCCeeEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHcCcCC
Confidence            44566666666665   6789999  996  589999999999999999988765543 56667778877643

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.76  E-value=1.4e-07  Score=84.45  Aligned_cols=141  Identities=18%  Similarity=0.269  Sum_probs=88.3

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +..++++++.++...+.+.....-..-|..... .+.+|+|||++.+....             .....++..++.....
T Consensus       166 ~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~-~~dlLiiDDi~~l~~~~-------------~~~~~l~~~~n~~~~~  231 (405)
T TIGR00362       166 NAKVVYVSSEKFTNDFVNALRNNKMEEFKEKYR-SVDLLLIDDIQFLAGKE-------------RTQEEFFHTFNALHEN  231 (405)
T ss_pred             CCcEEEEEHHHHHHHHHHHHHcCCHHHHHHHHH-hCCEEEEehhhhhcCCH-------------HHHHHHHHHHHHHHHC
Confidence            567788888877655443322111112222222 46799999999985432             1122333444333233


Q ss_pred             CCEEEEEEeCCCCc---cchhccCCCCcc--cEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccccc
Q psy5642          87 NNVTIVAATNRPDR---IDKALLRPGRLD--RLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQS  160 (237)
Q Consensus        87 ~~v~vI~ttn~~~~---ld~al~r~gRf~--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~  160 (237)
                      +..+||++...|..   +++.+++  ||.  ..++++.|+.++|..||+..+...+.. ++..+..||....| +.++|+
T Consensus       232 ~~~iiits~~~p~~l~~l~~~l~S--Rl~~g~~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~-~~r~l~  308 (405)
T TIGR00362       232 GKQIVLTSDRPPKELPGLEERLRS--RFEWGLVVDIEPPDLETRLAILQKKAEEEGLELPDEVLEFIAKNIRS-NVRELE  308 (405)
T ss_pred             CCCEEEecCCCHHHHhhhhhhhhh--hccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHH
Confidence            44566666666665   5688998  996  479999999999999999998766554 66777888877654 445544


Q ss_pred             chhH
Q psy5642         161 LSKH  164 (237)
Q Consensus       161 ~~~~  164 (237)
                      -++.
T Consensus       309 ~~l~  312 (405)
T TIGR00362       309 GALN  312 (405)
T ss_pred             HHHH
Confidence            3333

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).

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.74  E-value=2.3e-07  Score=82.70  Aligned_cols=138  Identities=13%  Similarity=0.108  Sum_probs=88.4

Q ss_pred             ceEEEEEeccccccc----------c-------cC-hHHHHHHHHHHHHHh-cCCeEEEEccccccccccCCCCCCCCCc
Q psy5642           7 LTEVVESIGPELFRK----------Y-------VG-ESERCVRDVFKRARQ-VSPSVIFFDELDSLAGERGDGGGGGGSN   67 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~----------~-------~g-~~~~~l~~~f~~a~~-~~P~il~iDeid~l~~~~~~~~~~~~~~   67 (237)
                      ++.+++++|....+.          .       .| .....+..+++.... ..+.||+|||+|.+.... .        
T Consensus        85 ~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~-~--------  155 (394)
T PRK00411         85 KVVYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKE-G--------  155 (394)
T ss_pred             CcEEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccC-C--------
Confidence            577888888654321          1       11 123344444444443 356899999999997221 1        


Q ss_pred             hHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCC---ccchhccCCCCcc-cEEEecCCCHHHHHHHHHHHHcCC---CCCc
Q psy5642          68 VQERVLAQMLTEMDGIVPLNNVTIVAATNRPD---RIDKALLRPGRLD-RLIYVPLPDDLTRAAILKIRLARS---PLGE  140 (237)
Q Consensus        68 ~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~---~ld~al~r~gRf~-~~i~~~~P~~~~R~~il~~~l~~~---~~~~  140 (237)
                        ...+..++..++... ..++.+|+++|.+.   .+++.+.+  ||. ..|+|++++.++..+||+..+...   ..-.
T Consensus       156 --~~~l~~l~~~~~~~~-~~~v~vI~i~~~~~~~~~l~~~~~s--~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~  230 (394)
T PRK00411        156 --NDVLYSLLRAHEEYP-GARIGVIGISSDLTFLYILDPRVKS--VFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVD  230 (394)
T ss_pred             --chHHHHHHHhhhccC-CCeEEEEEEECCcchhhhcCHHHHh--cCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCC
Confidence              135666776666543 23788889888764   56777777  774 578999999999999999887532   1124


Q ss_pred             hhhHHHHHHHCCCCCcccc
Q psy5642         141 DVCVEELVRLTEGYSGAEQ  159 (237)
Q Consensus       141 ~~~~~~la~~t~g~s~~Dl  159 (237)
                      +..++.++..+.+. .+|+
T Consensus       231 ~~~l~~i~~~~~~~-~Gd~  248 (394)
T PRK00411        231 DEVLDLIADLTARE-HGDA  248 (394)
T ss_pred             HhHHHHHHHHHHHh-cCcH
Confidence            56667777777553 3353

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.66  E-value=1.2e-06  Score=77.23  Aligned_cols=94  Identities=21%  Similarity=0.286  Sum_probs=66.4

Q ss_pred             HHHHHHHHHHHHh-cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC-CCCCCEEEEEEeCCCC---cc
Q psy5642          27 ERCVRDVFKRARQ-VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI-VPLNNVTIVAATNRPD---RI  101 (237)
Q Consensus        27 ~~~l~~~f~~a~~-~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-~~~~~v~vI~ttn~~~---~l  101 (237)
                      .+.+..++..... ..|.||+|||+|.+....            ..++..++...+.. ....++.+|+++|.++   .+
T Consensus       114 ~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~------------~~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~~~~~l  181 (365)
T TIGR02928       114 SEVFRRLYKELNERGDSLIIVLDEIDYLVGDD------------DDLLYQLSRARSNGDLDNAKVGVIGISNDLKFRENL  181 (365)
T ss_pred             HHHHHHHHHHHHhcCCeEEEEECchhhhccCC------------cHHHHhHhccccccCCCCCeEEEEEEECCcchHhhc
Confidence            3445666665543 357899999999997221            12445555442211 1235789999999886   57


Q ss_pred             chhccCCCCcc-cEEEecCCCHHHHHHHHHHHHc
Q psy5642         102 DKALLRPGRLD-RLIYVPLPDDLTRAAILKIRLA  134 (237)
Q Consensus       102 d~al~r~gRf~-~~i~~~~P~~~~R~~il~~~l~  134 (237)
                      ++.+.+  ||. ..|+|++++.++..+|++..+.
T Consensus       182 ~~~~~s--~~~~~~i~f~p~~~~e~~~il~~r~~  213 (365)
T TIGR02928       182 DPRVKS--SLCEEEIIFPPYDAEELRDILENRAE  213 (365)
T ss_pred             CHHHhc--cCCcceeeeCCCCHHHHHHHHHHHHH
Confidence            888888  885 6799999999999999998875

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.62  E-value=7.7e-07  Score=77.57  Aligned_cols=68  Identities=16%  Similarity=0.131  Sum_probs=58.2

Q ss_pred             CEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          88 NVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        88 ~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      ++.+|++|+.+..+++++++  ||...+.++.|+.+++.++++......... ++..+..++..+.|.. +.
T Consensus       150 ~~~li~at~~~~~l~~~L~s--Rf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~p-R~  218 (328)
T PRK00080        150 PFTLIGATTRAGLLTSPLRD--RFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTP-RI  218 (328)
T ss_pred             CceEEeecCCcccCCHHHHH--hcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCc-hH
Confidence            47889999999999999999  999999999999999999999888766554 5667888999988754 44

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.60  E-value=1e-06  Score=75.80  Aligned_cols=100  Identities=20%  Similarity=0.227  Sum_probs=74.4

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC----------------CCCCEEEEEEeCCCCccchh
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV----------------PLNNVTIVAATNRPDRIDKA  104 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~----------------~~~~v~vI~ttn~~~~ld~a  104 (237)
                      .+.+|||||+|.+....               ...|...+++..                ...++.+|++|+.+..++++
T Consensus        81 ~~~vl~iDEi~~l~~~~---------------~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li~~t~~~~~l~~~  145 (305)
T TIGR00635        81 EGDVLFIDEIHRLSPAV---------------EELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSP  145 (305)
T ss_pred             cCCEEEEehHhhhCHHH---------------HHHhhHHHhhhheeeeeccCccccceeecCCCeEEEEecCCccccCHH
Confidence            57899999999884321               122333332211                11348899999999999999


Q ss_pred             ccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642         105 LLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus       105 l~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      +++  ||...+.+++|+.++..++++......... ++..+..++..+.|+. +.
T Consensus       146 l~s--R~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~p-R~  197 (305)
T TIGR00635       146 LRD--RFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTP-RI  197 (305)
T ss_pred             HHh--hcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCc-ch
Confidence            999  999899999999999999999887654443 5667788999988855 44

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

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

Probab=98.57  E-value=3.1e-07  Score=85.27  Aligned_cols=173  Identities=21%  Similarity=0.295  Sum_probs=117.7

Q ss_pred             ccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC---------C----CCC
Q psy5642          20 RKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG---------I----VPL   86 (237)
Q Consensus        20 ~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~----~~~   86 (237)
                      --|+|..+..+-.-+..|+...| +++|||||.+..+-.++.           .+.||.-||-         +    ..-
T Consensus       397 RTYIGamPGrIiQ~mkka~~~NP-v~LLDEIDKm~ss~rGDP-----------aSALLEVLDPEQN~~F~DhYLev~yDL  464 (782)
T COG0466         397 RTYIGAMPGKIIQGMKKAGVKNP-VFLLDEIDKMGSSFRGDP-----------ASALLEVLDPEQNNTFSDHYLEVPYDL  464 (782)
T ss_pred             ccccccCChHHHHHHHHhCCcCC-eEEeechhhccCCCCCCh-----------HHHHHhhcCHhhcCchhhccccCccch
Confidence            35899999999999999999888 999999999975533221           3455555542         1    122


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      ++|++|+|+|+.+.||..|+.  |.. +|.++--+..+..+|.+.||=...           -+.+|+...++...-...
T Consensus       465 S~VmFiaTANsl~tIP~PLlD--RME-iI~lsgYt~~EKl~IAk~~LiPk~-----------~~~~gL~~~el~i~d~ai  530 (782)
T COG0466         465 SKVMFIATANSLDTIPAPLLD--RME-VIRLSGYTEDEKLEIAKRHLIPKQ-----------LKEHGLKKGELTITDEAI  530 (782)
T ss_pred             hheEEEeecCccccCChHHhc--cee-eeeecCCChHHHHHHHHHhcchHH-----------HHHcCCCccceeecHHHH
Confidence            479999999999999999999  996 699999999999999998874221           122344444433333333


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccC-CccHHHHHHHHhh
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAA-YVSHQDFLTALQL  218 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~-~v~~~df~~al~~  218 (237)
                      ..+........+.+.....|..+|++++..-+....... .++..++..-|..
T Consensus       531 ~~iI~~YTREAGVR~LeR~i~ki~RK~~~~i~~~~~k~~~~i~~~~l~~yLG~  583 (782)
T COG0466         531 KDIIRYYTREAGVRNLEREIAKICRKAAKKILLKKEKSIVKIDEKNLKKYLGV  583 (782)
T ss_pred             HHHHHHHhHhhhhhHHHHHHHHHHHHHHHHHHhcCcccceeeCHHHHHHHhCC
Confidence            333333333333333444578888888887776554443 6777777776653

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

Probab=98.57  E-value=6.5e-07  Score=84.79  Aligned_cols=149  Identities=21%  Similarity=0.289  Sum_probs=110.8

Q ss_pred             ceEEEEEeccccc--ccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCC-CCCCchHHHHHHHHHHHhcCC
Q psy5642           7 LTEVVESIGPELF--RKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGG-GGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         7 ~~~~i~v~~s~l~--~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~-~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      +..++.++-..|.  .+|.|+.+..++.+.+..+...+.||||||++.+.+..+..+. .+       ..+.|.-.|   
T Consensus       226 ~~~i~sLD~g~LvAGakyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~a~D-------AaNiLKPaL---  295 (786)
T COG0542         226 DKRIYSLDLGSLVAGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMD-------AANLLKPAL---  295 (786)
T ss_pred             CCEEEEecHHHHhccccccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcccccccc-------hhhhhHHHH---
Confidence            4455666665543  6899999999999999999988999999999999988766442 11       122233333   


Q ss_pred             CCCCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-----chhhHHHHHHHCCC
Q psy5642          84 VPLNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-----EDVCVEELVRLTEG  153 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-----~~~~~~~la~~t~g  153 (237)
                       .++.+-+||+|...+     +-|+||-|  ||.. |.+..|+.++-..||+.+-.++...     .+..+...+..+..
T Consensus       296 -ARGeL~~IGATT~~EYRk~iEKD~AL~R--RFQ~-V~V~EPs~e~ti~ILrGlk~~yE~hH~V~i~D~Al~aAv~LS~R  371 (786)
T COG0542         296 -ARGELRCIGATTLDEYRKYIEKDAALER--RFQK-VLVDEPSVEDTIAILRGLKERYEAHHGVRITDEALVAAVTLSDR  371 (786)
T ss_pred             -hcCCeEEEEeccHHHHHHHhhhchHHHh--cCce-eeCCCCCHHHHHHHHHHHHHHHHHccCceecHHHHHHHHHHHHh
Confidence             236788999998755     56999999  9975 9999999999999999877665433     67778888888888


Q ss_pred             CCccc------ccchhHHhhhh
Q psy5642         154 YSGAE------QSLSKHRAKKI  169 (237)
Q Consensus       154 ~s~~D------l~~~~~~a~~~  169 (237)
                      |-+.-      |..+...|.++
T Consensus       372 YI~dR~LPDKAIDLiDeA~a~~  393 (786)
T COG0542         372 YIPDRFLPDKAIDLLDEAGARV  393 (786)
T ss_pred             hcccCCCCchHHHHHHHHHHHH
Confidence            87733      44444444443

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.54  E-value=6.3e-07  Score=81.12  Aligned_cols=136  Identities=13%  Similarity=0.227  Sum_probs=84.7

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +..++++++.++...+.......-..-|.......|.+|+|||++.+.....             ....+...++.+...
T Consensus       160 ~~~v~yi~~~~f~~~~~~~~~~~~~~~f~~~~~~~~dvLlIDDi~~l~~~~~-------------~q~elf~~~n~l~~~  226 (440)
T PRK14088        160 DLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDVLLIDDVQFLIGKTG-------------VQTELFHTFNELHDS  226 (440)
T ss_pred             CCeEEEEEHHHHHHHHHHHHhcccHHHHHHHHHhcCCEEEEechhhhcCcHH-------------HHHHHHHHHHHHHHc
Confidence            4577888888776554332211111123333334688999999998854321             112233333333333


Q ss_pred             CCEEEEEEeCCCCc---cchhccCCCCcc--cEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          87 NNVTIVAATNRPDR---IDKALLRPGRLD--RLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        87 ~~v~vI~ttn~~~~---ld~al~r~gRf~--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      +..+||++.+.|..   +.+.+++  ||.  .++.+.+|+.+.|..|++..+...++. ++..+..||....| +.++
T Consensus       227 ~k~iIitsd~~p~~l~~l~~rL~S--R~~~gl~v~i~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~~~-~~R~  301 (440)
T PRK14088        227 GKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETRKKIARKMLEIEHGELPEEVLNFVAENVDD-NLRR  301 (440)
T ss_pred             CCeEEEECCCCHHHHHHHHHHHhh--HHhcCceEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhcccc-CHHH
Confidence            45566666667775   4577888  884  678999999999999999988755443 56667778877654 3344

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

Probab=98.52  E-value=2.5e-06  Score=82.23  Aligned_cols=159  Identities=19%  Similarity=0.295  Sum_probs=100.9

Q ss_pred             cccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC-------------CCCC
Q psy5642          21 KYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI-------------VPLN   87 (237)
Q Consensus        21 ~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-------------~~~~   87 (237)
                      .|.|.....+...+..+....| ||+|||+|.+......           ...+.|+..++.-             ..-+
T Consensus       397 ~~~g~~~G~~~~~l~~~~~~~~-villDEidk~~~~~~g-----------~~~~aLlevld~~~~~~~~d~~~~~~~dls  464 (784)
T PRK10787        397 TYIGSMPGKLIQKMAKVGVKNP-LFLLDEIDKMSSDMRG-----------DPASALLEVLDPEQNVAFSDHYLEVDYDLS  464 (784)
T ss_pred             ccCCCCCcHHHHHHHhcCCCCC-EEEEEChhhcccccCC-----------CHHHHHHHHhccccEEEEecccccccccCC
Confidence            4677776777777777665555 8999999998654211           1245666666531             1226


Q ss_pred             CEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcC-----CCCC------chhhHHHHHHH-CCCCC
Q psy5642          88 NVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR-----SPLG------EDVCVEELVRL-TEGYS  155 (237)
Q Consensus        88 ~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~-----~~~~------~~~~~~~la~~-t~g~s  155 (237)
                      ++++|+|+|.. .||++|++  ||. .|.++.++.++..+|.+.++-.     ....      .+..+..++.. +..|.
T Consensus       465 ~v~~i~TaN~~-~i~~aLl~--R~~-ii~~~~~t~eek~~Ia~~~L~~k~~~~~~l~~~~l~i~~~ai~~ii~~yt~e~G  540 (784)
T PRK10787        465 DVMFVATSNSM-NIPAPLLD--RME-VIRLSGYTEDEKLNIAKRHLLPKQIERNALKKGELTVDDSAIIGIIRYYTREAG  540 (784)
T ss_pred             ceEEEEcCCCC-CCCHHHhc--cee-eeecCCCCHHHHHHHHHHhhhHHHHHHhCCCCCeEEECHHHHHHHHHhCCcccC
Confidence            79999999987 59999999  996 7999999999999999987741     1111      33344455531 12222


Q ss_pred             cccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhc-cccCCccHHHHHHHHhh
Q psy5642         156 GAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENN-LEAAYVSHQDFLTALQL  218 (237)
Q Consensus       156 ~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~-~~~~~v~~~df~~al~~  218 (237)
                      .+.|+..                       |..+++......+..+ .....|+.+++...|..
T Consensus       541 aR~LeR~-----------------------I~~i~r~~l~~~~~~~~~~~v~v~~~~~~~~lg~  581 (784)
T PRK10787        541 VRSLERE-----------------------ISKLCRKAVKQLLLDKSLKHIEINGDNLHDYLGV  581 (784)
T ss_pred             CcHHHHH-----------------------HHHHHHHHHHHHHhcCCCceeeecHHHHHHHhCC
Confidence            3332222                       4445555444443332 23457888988888763

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=98.49  E-value=1.2e-06  Score=81.10  Aligned_cols=95  Identities=24%  Similarity=0.193  Sum_probs=75.0

Q ss_pred             EEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhHHhh
Q psy5642          89 VTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKHRAK  167 (237)
Q Consensus        89 v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~~a~  167 (237)
                      .++++||+.|+.+++++++  |+. .++|+.++.+++.+|++..+++.... ++..++.++..+.  .+++         
T Consensus       235 rlI~ATt~~p~~L~paLrs--R~~-~I~f~pL~~eei~~Il~~~a~k~~i~is~~al~~I~~y~~--n~Re---------  300 (531)
T TIGR02902       235 RLIGATTRNPEEIPPALRS--RCV-EIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYAS--NGRE---------  300 (531)
T ss_pred             EEEEEecCCcccCChHHhh--hhh-eeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhh--hHHH---------
Confidence            5667778889999999999  985 68899999999999999999876654 5556666666553  5677         


Q ss_pred             hhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHh
Q psy5642         168 KIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQ  217 (237)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~  217 (237)
                                        +.++++.|...+..++  ...|+.+|+..++.
T Consensus       301 ------------------l~nll~~Aa~~A~~~~--~~~It~~dI~~vl~  330 (531)
T TIGR02902       301 ------------------AVNIVQLAAGIALGEG--RKRILAEDIEWVAE  330 (531)
T ss_pred             ------------------HHHHHHHHHHHHhhCC--CcEEcHHHHHHHhC
Confidence                              8888888877665544  34699999999987

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.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.49  E-value=4.5e-06  Score=79.86  Aligned_cols=148  Identities=16%  Similarity=0.190  Sum_probs=99.7

Q ss_pred             ceEEEEEeccccccccc----------------C-hHHHHHHHHHHHHHh--cCCeEEEEccccccccccCCCCCCCCCc
Q psy5642           7 LTEVVESIGPELFRKYV----------------G-ESERCVRDVFKRARQ--VSPSVIFFDELDSLAGERGDGGGGGGSN   67 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~----------------g-~~~~~l~~~f~~a~~--~~P~il~iDeid~l~~~~~~~~~~~~~~   67 (237)
                      .+.+++|+|..+.+.+.                | .+...+..+|.....  ..+.||+|||||.|....          
T Consensus       816 ~f~vVYINCm~Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~----------  885 (1164)
T PTZ00112        816 SFNVFEINGMNVVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKT----------  885 (1164)
T ss_pred             CceEEEEeCCccCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccH----------
Confidence            36788999965433321                1 234567777776532  246799999999996531          


Q ss_pred             hHHHHHHHHHHHhcCCCCCCCEEEEEEeCC---CCccchhccCCCCccc-EEEecCCCHHHHHHHHHHHHcCCC-CCchh
Q psy5642          68 VQERVLAQMLTEMDGIVPLNNVTIVAATNR---PDRIDKALLRPGRLDR-LIYVPLPDDLTRAAILKIRLARSP-LGEDV  142 (237)
Q Consensus        68 ~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~---~~~ld~al~r~gRf~~-~i~~~~P~~~~R~~il~~~l~~~~-~~~~~  142 (237)
                        +.++-.|..+...  ...+++|||.+|.   ++.+++.+++  ||.. .|.|++++.++..+||+..+.... .-.+.
T Consensus       886 --QDVLYnLFR~~~~--s~SKLiLIGISNdlDLperLdPRLRS--RLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDd  959 (1164)
T PTZ00112        886 --QKVLFTLFDWPTK--INSKLVLIAISNTMDLPERLIPRCRS--RLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHT  959 (1164)
T ss_pred             --HHHHHHHHHHhhc--cCCeEEEEEecCchhcchhhhhhhhh--ccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHH
Confidence              3455556665442  3457999999986   5677888888  7753 488899999999999998887532 22556


Q ss_pred             hHHHHHHHCCCCCcccccchhHHhhhhcc
Q psy5642         143 CVEELVRLTEGYSGAEQSLSKHRAKKIRP  171 (237)
Q Consensus       143 ~~~~la~~t~g~s~~Dl~~~~~~a~~~~~  171 (237)
                      .+.-+|.+.. ...+|++..++.++.+..
T Consensus       960 AIELIArkVA-q~SGDARKALDILRrAgE  987 (1164)
T PTZ00112        960 AIQLCARKVA-NVSGDIRKALQICRKAFE  987 (1164)
T ss_pred             HHHHHHHhhh-hcCCHHHHHHHHHHHHHh
Confidence            6666777554 446787766666555543

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=98.48  E-value=3.2e-06  Score=78.62  Aligned_cols=139  Identities=16%  Similarity=0.227  Sum_probs=88.5

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +..++++.+.+|...+...........|..-. ..+.+|+||||+.+..+..          .+..+-.+++.+.+   .
T Consensus       344 g~~V~Yitaeef~~el~~al~~~~~~~f~~~y-~~~DLLlIDDIq~l~gke~----------tqeeLF~l~N~l~e---~  409 (617)
T PRK14086        344 GTRVRYVSSEEFTNEFINSIRDGKGDSFRRRY-REMDILLVDDIQFLEDKES----------TQEEFFHTFNTLHN---A  409 (617)
T ss_pred             CCeEEEeeHHHHHHHHHHHHHhccHHHHHHHh-hcCCEEEEehhccccCCHH----------HHHHHHHHHHHHHh---c
Confidence            46778888888877666544443333454333 3578999999999865421          12223334444432   2


Q ss_pred             CCEEEEEEeCCCC---ccchhccCCCCcc--cEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccccc
Q psy5642          87 NNVTIVAATNRPD---RIDKALLRPGRLD--RLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQS  160 (237)
Q Consensus        87 ~~v~vI~ttn~~~---~ld~al~r~gRf~--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~  160 (237)
                      ++-+||.+...|.   .+++.|++  ||.  .++.+..|+.+.|..||+.......+. ++..+..|+.+.++ +.++|+
T Consensus       410 gk~IIITSd~~P~eL~~l~~rL~S--Rf~~GLvv~I~~PD~EtR~aIL~kka~~r~l~l~~eVi~yLa~r~~r-nvR~Le  486 (617)
T PRK14086        410 NKQIVLSSDRPPKQLVTLEDRLRN--RFEWGLITDVQPPELETRIAILRKKAVQEQLNAPPEVLEFIASRISR-NIRELE  486 (617)
T ss_pred             CCCEEEecCCChHhhhhccHHHHh--hhhcCceEEcCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhccC-CHHHHH
Confidence            3334443333344   56889999  994  677999999999999999988776665 56667777777643 344433


Q ss_pred             ch
Q psy5642         161 LS  162 (237)
Q Consensus       161 ~~  162 (237)
                      -+
T Consensus       487 ga  488 (617)
T PRK14086        487 GA  488 (617)
T ss_pred             HH
Confidence            33

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=98.46  E-value=2e-06  Score=77.86  Aligned_cols=129  Identities=9%  Similarity=0.204  Sum_probs=77.2

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCC
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLN   87 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~   87 (237)
                      ..++++.+..+...+.......-...|.... ..+.+|+|||++.+.+...          .+..+-.+++.+.   ..+
T Consensus       170 ~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~-~~~dvLiIDDiq~l~~k~~----------~qeelf~l~N~l~---~~~  235 (445)
T PRK12422        170 GKILYVRSELFTEHLVSAIRSGEMQRFRQFY-RNVDALFIEDIEVFSGKGA----------TQEEFFHTFNSLH---TEG  235 (445)
T ss_pred             CCEEEeeHHHHHHHHHHHHhcchHHHHHHHc-ccCCEEEEcchhhhcCChh----------hHHHHHHHHHHHH---HCC
Confidence            5566777665544332221111111233322 3577999999998754321          1222223333322   223


Q ss_pred             CEEEEEEeCCCC---ccchhccCCCCcc--cEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642          88 NVTIVAATNRPD---RIDKALLRPGRLD--RLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus        88 ~v~vI~ttn~~~---~ld~al~r~gRf~--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      +.+|++++..|.   .+++.+++  ||.  ..+.+..|+.+.|..||+......++. ++..+..+|....
T Consensus       236 k~IIlts~~~p~~l~~l~~rL~S--R~~~Gl~~~l~~pd~e~r~~iL~~k~~~~~~~l~~evl~~la~~~~  304 (445)
T PRK12422        236 KLIVISSTCAPQDLKAMEERLIS--RFEWGIAIPLHPLTKEGLRSFLERKAEALSIRIEETALDFLIEALS  304 (445)
T ss_pred             CcEEEecCCCHHHHhhhHHHHHh--hhcCCeEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcC
Confidence            445555555554   56799999  996  789999999999999999988766554 5556666777554

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.36  E-value=7e-06  Score=77.73  Aligned_cols=122  Identities=19%  Similarity=0.197  Sum_probs=92.0

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      .+++++.++-      .+...++.+++.+..    ....|+||||+|.|..               ...+.||..|++. 
T Consensus        89 DviEIDAas~------rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~---------------~A~NALLKtLEEP-  146 (830)
T PRK07003         89 DYVEMDAASN------RGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTN---------------HAFNAMLKTLEEP-  146 (830)
T ss_pred             eEEEeccccc------ccHHHHHHHHHHHHhccccCCceEEEEeChhhCCH---------------HHHHHHHHHHHhc-
Confidence            4677766531      234456666666553    2346999999999832               3467888888883 


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCc
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSG  156 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~  156 (237)
                       ..++.+|.+||+++.|.+.|++  |+ ..+.|..++.++..+.|+..+...++. .+..+..|+..+.|-..
T Consensus       147 -P~~v~FILaTtd~~KIp~TIrS--RC-q~f~Fk~Ls~eeIv~~L~~Il~~EgI~id~eAL~lIA~~A~GsmR  215 (830)
T PRK07003        147 -PPHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPAGHIVSHLERILGEERIAFEPQALRLLARAAQGSMR  215 (830)
T ss_pred             -CCCeEEEEEECChhhccchhhh--he-EEEecCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHH
Confidence             4578999999999999999999  98 469999999999999999988766554 66778888888877543

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.29  E-value=8e-06  Score=76.29  Aligned_cols=120  Identities=18%  Similarity=0.208  Sum_probs=88.5

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      .++++++..-      .+...++++.+.+..    ....|++|||+|.+..               ...+.||..|++  
T Consensus        94 DviEIdAas~------~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~---------------~AaNALLKTLEE--  150 (700)
T PRK12323         94 DYIEMDAASN------RGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTN---------------HAFNAMLKTLEE--  150 (700)
T ss_pred             cceEeccccc------CCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCH---------------HHHHHHHHhhcc--
Confidence            5777777521      224455566555543    2356999999999832               346889998888  


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCC
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGY  154 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~  154 (237)
                      ...++++|.+|++++.|.+.|++  |. ..+.|+.++.++..+.|+..+...++. .+..+..|+..+.|-
T Consensus       151 PP~~v~FILaTtep~kLlpTIrS--RC-q~f~f~~ls~eei~~~L~~Il~~Egi~~d~eAL~~IA~~A~Gs  218 (700)
T PRK12323        151 PPEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALRLLAQAAQGS  218 (700)
T ss_pred             CCCCceEEEEeCChHhhhhHHHH--HH-HhcccCCCChHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCC
Confidence            44678899999999999999999  98 569999999999999999888665544 344567777776653

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.27  E-value=2.2e-05  Score=68.92  Aligned_cols=119  Identities=19%  Similarity=0.276  Sum_probs=86.3

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      .++.+++..      +.+...++.+++.+...    ..-||+|||+|.+..               ...+.++..+++. 
T Consensus        87 ~~~~~~~~~------~~~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~~---------------~~~~~Ll~~le~~-  144 (355)
T TIGR02397        87 DVIEIDAAS------NNGVDDIREILDNVKYAPSSGKYKVYIIDEVHMLSK---------------SAFNALLKTLEEP-  144 (355)
T ss_pred             CEEEeeccc------cCCHHHHHHHHHHHhcCcccCCceEEEEeChhhcCH---------------HHHHHHHHHHhCC-
Confidence            455665542      12345677888877653    234999999988732               2456788888763 


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                       ...+++|.+|++++.+.+.+++  |+. .+++++|+..+...+++..+...+.. ++..+..++..+.|
T Consensus       145 -~~~~~lIl~~~~~~~l~~~l~s--r~~-~~~~~~~~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g  210 (355)
T TIGR02397       145 -PEHVVFILATTEPHKIPATILS--RCQ-RFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAADG  210 (355)
T ss_pred             -ccceeEEEEeCCHHHHHHHHHh--hee-EEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence             3467778888889999999999  884 68999999999999999988766544 45666777776654

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=98.26  E-value=1.9e-05  Score=73.52  Aligned_cols=125  Identities=20%  Similarity=0.265  Sum_probs=93.0

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG   82 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~   82 (237)
                      ...+++++++.      +.+...++.+.+.+...    ..-|++|||+|.+..               ...+.|+..+++
T Consensus        87 ~~dv~eidaas------~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~---------------~a~naLLKtLEe  145 (559)
T PRK05563         87 LMDVIEIDAAS------NNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLST---------------GAFNALLKTLEE  145 (559)
T ss_pred             CCCeEEeeccc------cCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCH---------------HHHHHHHHHhcC
Confidence            34567777642      24566788888887652    245999999998832               246788888887


Q ss_pred             CCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          83 IVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        83 ~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      .  ...+++|.+|+.+..+++.|++  |+. .+.|+.|+..+....++..+...+.. .+..+..++..+.| +.++
T Consensus       146 p--p~~~ifIlatt~~~ki~~tI~S--Rc~-~~~f~~~~~~ei~~~L~~i~~~egi~i~~~al~~ia~~s~G-~~R~  216 (559)
T PRK05563        146 P--PAHVIFILATTEPHKIPATILS--RCQ-RFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAAEG-GMRD  216 (559)
T ss_pred             C--CCCeEEEEEeCChhhCcHHHHh--Hhe-EEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHH
Confidence            3  3567777777889999999999  885 58999999999999999988776654 45667778887765 5555

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

Probab=98.24  E-value=3.9e-05  Score=68.84  Aligned_cols=149  Identities=18%  Similarity=0.211  Sum_probs=93.0

Q ss_pred             ceEEEEEeccccc-ccccChH-HHHHHHHHHHH----HhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHh
Q psy5642           7 LTEVVESIGPELF-RKYVGES-ERCVRDVFKRA----RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEM   80 (237)
Q Consensus         7 ~~~~i~v~~s~l~-~~~~g~~-~~~l~~~f~~a----~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l   80 (237)
                      +.||+.++++.+. ..|+|+. +..+..++..+    ....++||||||+|.+...+.+.+ .+.+.....+.+.||..|
T Consensus       133 ~~pf~~id~~~l~~~gyvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~~~~~~~-~~~d~s~~~vQ~~LL~~L  211 (412)
T PRK05342        133 DVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARKSENPS-ITRDVSGEGVQQALLKIL  211 (412)
T ss_pred             CCCceecchhhcccCCcccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhccccCCCC-cCCCcccHHHHHHHHHHH
Confidence            5789999998875 4688865 44556665532    234789999999999987633211 111111135678888888


Q ss_pred             cCCC-----------CCCCEEEEEEeCCCC--------------------------------------------------
Q psy5642          81 DGIV-----------PLNNVTIVAATNRPD--------------------------------------------------   99 (237)
Q Consensus        81 ~~~~-----------~~~~v~vI~ttn~~~--------------------------------------------------   99 (237)
                      ++..           ...+.++|.|+|-..                                                  
T Consensus       212 eg~~~~v~~~gg~~~~~~~~~~i~t~nilfi~~Gaf~g~~~~~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~dL~  291 (412)
T PRK05342        212 EGTVASVPPQGGRKHPQQEFIQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLI  291 (412)
T ss_pred             hcCeEEeCCCCCcCcCCCCeEEeccCCceeeecccccCcHHHHHHHHhhcccCCccccccccccchhHHHHHhcCHHHHH
Confidence            7531           011245666655400                                                  


Q ss_pred             --ccchhccCCCCcccEEEecCCCHHHHHHHHHH----HHc-------CCCCC---chhhHHHHHHH--CCCCCccc
Q psy5642         100 --RIDKALLRPGRLDRLIYVPLPDDLTRAAILKI----RLA-------RSPLG---EDVCVEELVRL--TEGYSGAE  158 (237)
Q Consensus       100 --~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~----~l~-------~~~~~---~~~~~~~la~~--t~g~s~~D  158 (237)
                        .+.|+++.  |++.++.|...+.++..+|+..    +++       ...+.   .+..+..||++  ..+|..+-
T Consensus       292 ~~gf~PEflg--Rld~iv~f~~L~~~~L~~Il~~~~~~l~~q~~~~l~~~~i~L~~t~~al~~Ia~~~~~~~~GAR~  366 (412)
T PRK05342        292 KFGLIPEFIG--RLPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARG  366 (412)
T ss_pred             HHhhhHHHhC--CCCeeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHhCCCCCCCCch
Confidence              13566666  9999999999999999999972    332       22222   55666777775  34555555

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.23  E-value=2.4e-05  Score=71.10  Aligned_cols=136  Identities=14%  Similarity=0.193  Sum_probs=82.9

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHH--hcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRAR--QVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~--~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      .+..++++.+.++...+........ ..+...+  ...+.+|+|||++.+..+.          .....+-.+++.+.. 
T Consensus       170 ~~~~v~yv~~~~f~~~~~~~l~~~~-~~~~~~~~~~~~~dvLiIDDiq~l~~k~----------~~~e~lf~l~N~~~~-  237 (450)
T PRK14087        170 SDLKVSYMSGDEFARKAVDILQKTH-KEIEQFKNEICQNDVLIIDDVQFLSYKE----------KTNEIFFTIFNNFIE-  237 (450)
T ss_pred             CCCeEEEEEHHHHHHHHHHHHHHhh-hHHHHHHHHhccCCEEEEeccccccCCH----------HHHHHHHHHHHHHHH-
Confidence            3567788888887766554433211 1122221  2356799999999885432          112333444444333 


Q ss_pred             CCCCCEEEEEEeCCCCc---cchhccCCCCcc--cEEEecCCCHHHHHHHHHHHHcCCCC---CchhhHHHHHHHCCCCC
Q psy5642          84 VPLNNVTIVAATNRPDR---IDKALLRPGRLD--RLIYVPLPDDLTRAAILKIRLARSPL---GEDVCVEELVRLTEGYS  155 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~~---ld~al~r~gRf~--~~i~~~~P~~~~R~~il~~~l~~~~~---~~~~~~~~la~~t~g~s  155 (237)
                        .++-+|+.+...|+.   +++.+++  ||.  ..+.+..|+.++|.+||+..+...+.   -++..+..||..+.| +
T Consensus       238 --~~k~iIltsd~~P~~l~~l~~rL~S--R~~~Gl~~~L~~pd~e~r~~iL~~~~~~~gl~~~l~~evl~~Ia~~~~g-d  312 (450)
T PRK14087        238 --NDKQLFFSSDKSPELLNGFDNRLIT--RFNMGLSIAIQKLDNKTATAIIKKEIKNQNIKQEVTEEAINFISNYYSD-D  312 (450)
T ss_pred             --cCCcEEEECCCCHHHHhhccHHHHH--HHhCCceeccCCcCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHccCC-C
Confidence              234344444444554   4789999  995  77889999999999999998876543   255666667776654 4


Q ss_pred             ccc
Q psy5642         156 GAE  158 (237)
Q Consensus       156 ~~D  158 (237)
                      ++.
T Consensus       313 ~R~  315 (450)
T PRK14087        313 VRK  315 (450)
T ss_pred             HHH
Confidence            444

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.21  E-value=3e-05  Score=70.80  Aligned_cols=118  Identities=14%  Similarity=0.144  Sum_probs=85.2

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      .++.++++.-      .+...++.+.+.+...    ...||+|||+|.+..               ...+.|+..++.. 
T Consensus        87 dv~el~aa~~------~gid~iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt~---------------~a~~~LLk~LE~p-  144 (472)
T PRK14962         87 DVIELDAASN------RGIDEIRKIRDAVGYRPMEGKYKVYIIDEVHMLTK---------------EAFNALLKTLEEP-  144 (472)
T ss_pred             ccEEEeCccc------CCHHHHHHHHHHHhhChhcCCeEEEEEEChHHhHH---------------HHHHHHHHHHHhC-
Confidence            5666766421      1234566666665532    346999999998832               2356778888773 


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                       .+.+++|++|+.+..+++++++  |+. .++|..|+.++...+++..+...+.. .+..+..|+..+.
T Consensus       145 -~~~vv~Ilattn~~kl~~~L~S--R~~-vv~f~~l~~~el~~~L~~i~~~egi~i~~eal~~Ia~~s~  209 (472)
T PRK14962        145 -PSHVVFVLATTNLEKVPPTIIS--RCQ-VIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIAKRAS  209 (472)
T ss_pred             -CCcEEEEEEeCChHhhhHHHhc--CcE-EEEECCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhC
Confidence             3567788888888999999999  985 79999999999999999888655443 5666777888654

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.21  E-value=2.8e-05  Score=71.44  Aligned_cols=124  Identities=15%  Similarity=0.204  Sum_probs=92.8

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      ..++++++..      ..+...++.+++.+...    ...|++|||+|.+..               ...+.|+..|+. 
T Consensus        97 ~Dv~eidaas------~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~---------------~a~naLLk~LEe-  154 (507)
T PRK06645         97 PDIIEIDAAS------KTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSK---------------GAFNALLKTLEE-  154 (507)
T ss_pred             CcEEEeeccC------CCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCH---------------HHHHHHHHHHhh-
Confidence            3566666642      12456778888877643    245999999988732               346778888886 


Q ss_pred             CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          84 VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                       ....+++|++|+.++.+++.+++  |. ..++|+.++.++...+++..+...+.. .+..+..++..+.| +.++
T Consensus       155 -pp~~~vfI~aTte~~kI~~tI~S--Rc-~~~ef~~ls~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~G-slR~  225 (507)
T PRK06645        155 -PPPHIIFIFATTEVQKIPATIIS--RC-QRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIAYKSEG-SARD  225 (507)
T ss_pred             -cCCCEEEEEEeCChHHhhHHHHh--cc-eEEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHH
Confidence             34567778788889999999998  88 469999999999999999999876654 55667888888876 6666

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.20  E-value=1.4e-05  Score=65.58  Aligned_cols=125  Identities=18%  Similarity=0.264  Sum_probs=73.9

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCC
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLN   87 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~   87 (237)
                      .++++++|+++....        ..++....  .+.+|+|||+|.+....         .. ...+..++..+..   .+
T Consensus        67 ~~~~~i~~~~~~~~~--------~~~~~~~~--~~~lLvIDdi~~l~~~~---------~~-~~~L~~~l~~~~~---~~  123 (226)
T TIGR03420        67 KSAIYLPLAELAQAD--------PEVLEGLE--QADLVCLDDVEAIAGQP---------EW-QEALFHLYNRVRE---AG  123 (226)
T ss_pred             CcEEEEeHHHHHHhH--------HHHHhhcc--cCCEEEEeChhhhcCCh---------HH-HHHHHHHHHHHHH---cC
Confidence            467788888775432        23333332  34699999999874321         00 1223333333322   22


Q ss_pred             CEEEEEEeCCCCccc---hhccCCCCc--ccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          88 NVTIVAATNRPDRID---KALLRPGRL--DRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        88 ~v~vI~ttn~~~~ld---~al~r~gRf--~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      ..+|+.++..+..++   +.+.+  ||  ...+.++.|+.+++..+++.+....+.. ++..+..|+.. -+-++++
T Consensus       124 ~~iIits~~~~~~~~~~~~~L~~--r~~~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~l~~L~~~-~~gn~r~  197 (226)
T TIGR03420       124 GRLLIAGRAAPAQLPLRLPDLRT--RLAWGLVFQLPPLSDEEKIAALQSRAARRGLQLPDEVADYLLRH-GSRDMGS  197 (226)
T ss_pred             CeEEEECCCChHHCCcccHHHHH--HHhcCeeEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHh-ccCCHHH
Confidence            344444444454443   77787  76  4789999999999999999877655443 45556666663 3444555

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.19  E-value=2.3e-05  Score=69.35  Aligned_cols=111  Identities=15%  Similarity=0.243  Sum_probs=82.1

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+.+.+...    ...|++|||+|.+..               ...+.++..++..  ...+.+|.+|+.++.+.
T Consensus       101 v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~---------------~a~naLLk~lEe~--~~~~~fIl~t~~~~~l~  163 (363)
T PRK14961        101 VEEMREILDNIYYSPSKSRFKVYLIDEVHMLSR---------------HSFNALLKTLEEP--PQHIKFILATTDVEKIP  163 (363)
T ss_pred             HHHHHHHHHHHhcCcccCCceEEEEEChhhcCH---------------HHHHHHHHHHhcC--CCCeEEEEEcCChHhhh
Confidence            45567777665432    235999999998721               2356788888873  34677777888899999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      +.+++  |+ ..++|++|+.++..++++..+...+.. ++..+..++..+.| ++++
T Consensus       164 ~tI~S--Rc-~~~~~~~l~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s~G-~~R~  216 (363)
T PRK14961        164 KTILS--RC-LQFKLKIISEEKIFNFLKYILIKESIDTDEYALKLIAYHAHG-SMRD  216 (363)
T ss_pred             HHHHh--hc-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHH
Confidence            99998  88 479999999999999999988776543 55677778887755 4444

>PRK04132 replication factor C small subunit; Provisional

Probab=98.18  E-value=4.5e-05  Score=73.66  Aligned_cols=121  Identities=17%  Similarity=0.207  Sum_probs=92.4

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcC------CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHh
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVS------PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEM   80 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~------P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l   80 (237)
                      +.+++++++++-.+      ...++.+...+....      ..|++|||+|.+..               ...+.|+..|
T Consensus       596 ~~~~lElNASd~rg------id~IR~iIk~~a~~~~~~~~~~KVvIIDEaD~Lt~---------------~AQnALLk~l  654 (846)
T PRK04132        596 RHNFLELNASDERG------INVIREKVKEFARTKPIGGASFKIIFLDEADALTQ---------------DAQQALRRTM  654 (846)
T ss_pred             cCeEEEEeCCCccc------HHHHHHHHHHHHhcCCcCCCCCEEEEEECcccCCH---------------HHHHHHHHHh
Confidence            35799999997543      346666665544333      25999999999932               2357788888


Q ss_pred             cCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642          81 DGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        81 ~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +..  .+++.+|.+||+++.+.++|++  |. ..+.|+.|+.++-...|+......++. ++..+..++..+.|
T Consensus       655 Eep--~~~~~FILi~N~~~kIi~tIrS--RC-~~i~F~~ls~~~i~~~L~~I~~~Egi~i~~e~L~~Ia~~s~G  723 (846)
T PRK04132        655 EMF--SSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEG  723 (846)
T ss_pred             hCC--CCCeEEEEEeCChhhCchHHhh--hc-eEEeCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCC
Confidence            873  3578899999999999999999  86 579999999999999999887765543 56677788877765

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=98.17  E-value=2.8e-05  Score=75.26  Aligned_cols=130  Identities=15%  Similarity=0.131  Sum_probs=87.2

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      ....|+++++..-.  .+.+.......++.........|+||||+|.|..               ...+.||+.|++.  
T Consensus        87 ~~~dv~eidaas~~--~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~---------------~a~NaLLK~LEEp--  147 (824)
T PRK07764         87 GSLDVTEIDAASHG--GVDDARELRERAFFAPAESRYKIFIIDEAHMVTP---------------QGFNALLKIVEEP--  147 (824)
T ss_pred             CCCcEEEecccccC--CHHHHHHHHHHHHhchhcCCceEEEEechhhcCH---------------HHHHHHHHHHhCC--
Confidence            34557777664321  1222222222222222233456999999999833               3467899999984  


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      ...+++|++|+.++.|.+.|++  |. .++.|..++.++-..+|+..+...++. .+..+..++..+.| +.++
T Consensus       148 P~~~~fIl~tt~~~kLl~TIrS--Rc-~~v~F~~l~~~~l~~~L~~il~~EGv~id~eal~lLa~~sgG-dlR~  217 (824)
T PRK07764        148 PEHLKFIFATTEPDKVIGTIRS--RT-HHYPFRLVPPEVMRGYLERICAQEGVPVEPGVLPLVIRAGGG-SVRD  217 (824)
T ss_pred             CCCeEEEEEeCChhhhhHHHHh--he-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHH
Confidence            3577788888888999999998  87 469999999999999999888766554 44556667776654 4444

>PRK04195 replication factor C large subunit; Provisional

Probab=98.14  E-value=0.00014  Score=66.72  Aligned_cols=130  Identities=16%  Similarity=0.192  Sum_probs=87.1

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHHhc------CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRARQV------SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~------~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      .+++++++++..+      ...++.+...+...      .+.+|+|||+|.+.....           ......++..+.
T Consensus        65 ~~~ielnasd~r~------~~~i~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~~~d-----------~~~~~aL~~~l~  127 (482)
T PRK04195         65 WEVIELNASDQRT------ADVIERVAGEAATSGSLFGARRKLILLDEVDGIHGNED-----------RGGARAILELIK  127 (482)
T ss_pred             CCEEEEccccccc------HHHHHHHHHHhhccCcccCCCCeEEEEecCcccccccc-----------hhHHHHHHHHHH
Confidence            4677888876542      23445554444332      477999999999865211           123455666665


Q ss_pred             CCCCCCCEEEEEEeCCCCccch-hccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccc
Q psy5642          82 GIVPLNNVTIVAATNRPDRIDK-ALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQ  159 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn~~~~ld~-al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl  159 (237)
                      .    .+..+|.++|.+..++. .+++  |. ..|.|+.|+..+...+|+..+...+.. .+..+..|+..+    ++|+
T Consensus       128 ~----~~~~iIli~n~~~~~~~k~Lrs--r~-~~I~f~~~~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~~s----~GDl  196 (482)
T PRK04195        128 K----AKQPIILTANDPYDPSLRELRN--AC-LMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERS----GGDL  196 (482)
T ss_pred             c----CCCCEEEeccCccccchhhHhc--cc-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc----CCCH
Confidence            4    23456778899998887 5665  44 579999999999999999988766554 566788888876    4575


Q ss_pred             cchhHH
Q psy5642         160 SLSKHR  165 (237)
Q Consensus       160 ~~~~~~  165 (237)
                      ..++..
T Consensus       197 R~ain~  202 (482)
T PRK04195        197 RSAIND  202 (482)
T ss_pred             HHHHHH
Confidence            554443

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.12  E-value=0.00015  Score=63.02  Aligned_cols=99  Identities=14%  Similarity=0.201  Sum_probs=68.6

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCC
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPD  121 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~  121 (237)
                      +.+|+|||+|.+..               .....|...++...  ....+|.+++.+..+.+.+++  |+ ..+.+.+|+
T Consensus       126 ~~vlilDe~~~l~~---------------~~~~~L~~~le~~~--~~~~~Il~~~~~~~~~~~L~s--r~-~~v~~~~~~  185 (337)
T PRK12402        126 YKTILLDNAEALRE---------------DAQQALRRIMEQYS--RTCRFIIATRQPSKLIPPIRS--RC-LPLFFRAPT  185 (337)
T ss_pred             CcEEEEeCcccCCH---------------HHHHHHHHHHHhcc--CCCeEEEEeCChhhCchhhcC--Cc-eEEEecCCC
Confidence            45999999998732               12334555555533  234456667777788888888  76 468999999


Q ss_pred             HHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhH
Q psy5642         122 DLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus       122 ~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      .++...+++..+...+.. ++..+..++..+    ++|+..++.
T Consensus       186 ~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~----~gdlr~l~~  225 (337)
T PRK12402        186 DDELVDVLESIAEAEGVDYDDDGLELIAYYA----GGDLRKAIL  225 (337)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc----CCCHHHHHH
Confidence            999999999988766654 566777777765    566444333

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.10  E-value=2.6e-05  Score=71.88  Aligned_cols=123  Identities=18%  Similarity=0.229  Sum_probs=89.4

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      .+++++++.      ..+...++.+.+.+...    ...|++|||+|.+..               ...+.|+..|+.. 
T Consensus        89 d~~eidaas------~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls~---------------~a~naLLk~LEep-  146 (509)
T PRK14958         89 DLFEVDAAS------RTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLSG---------------HSFNALLKTLEEP-  146 (509)
T ss_pred             eEEEEcccc------cCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcCH---------------HHHHHHHHHHhcc-
Confidence            477787652      12344566666655431    235999999999843               2367888888884 


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                       ...+.+|.+|+.+..+++.|++  |. ..++|..++..+-...++..+...+.. .+..+..++..+.| +.++
T Consensus       147 -p~~~~fIlattd~~kl~~tI~S--Rc-~~~~f~~l~~~~i~~~l~~il~~egi~~~~~al~~ia~~s~G-slR~  216 (509)
T PRK14958        147 -PSHVKFILATTDHHKLPVTVLS--RC-LQFHLAQLPPLQIAAHCQHLLKEENVEFENAALDLLARAANG-SVRD  216 (509)
T ss_pred             -CCCeEEEEEECChHhchHHHHH--Hh-hhhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-cHHH
Confidence             3567788888889999999998  88 468999999999888888888766554 55667778887754 5556

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.10  E-value=1.7e-05  Score=70.70  Aligned_cols=109  Identities=16%  Similarity=0.207  Sum_probs=79.1

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+++.+...    ...|++|||+|.+..               ...+.|+..|++.  ..++++|.+|++++.+.
T Consensus        99 i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~---------------~aanaLLk~LEep--~~~~~fIL~a~~~~~ll  161 (394)
T PRK07940         99 VDEVRELVTIAARRPSTGRWRIVVIEDADRLTE---------------RAANALLKAVEEP--PPRTVWLLCAPSPEDVL  161 (394)
T ss_pred             HHHHHHHHHHHHhCcccCCcEEEEEechhhcCH---------------HHHHHHHHHhhcC--CCCCeEEEEECChHHCh
Confidence            44578888877652    235999999999933               2357788888873  34555666666699999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccc
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQ  159 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl  159 (237)
                      |.|++  |+ ..++|+.|+.++..++|....   +. +......++..+.|..+..+
T Consensus       162 pTIrS--Rc-~~i~f~~~~~~~i~~~L~~~~---~~-~~~~a~~la~~s~G~~~~A~  211 (394)
T PRK07940        162 PTIRS--RC-RHVALRTPSVEAVAEVLVRRD---GV-DPETARRAARASQGHIGRAR  211 (394)
T ss_pred             HHHHh--hC-eEEECCCCCHHHHHHHHHHhc---CC-CHHHHHHHHHHcCCCHHHHH
Confidence            99999  98 479999999999887776322   23 34556778888888776553

>KOG2004|consensus

Probab=98.09  E-value=1.1e-05  Score=75.08  Aligned_cols=100  Identities=27%  Similarity=0.409  Sum_probs=78.7

Q ss_pred             ccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC---------C----CCC
Q psy5642          20 RKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG---------I----VPL   86 (237)
Q Consensus        20 ~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~----~~~   86 (237)
                      --|+|.++..+-..+..++...| +++|||+|.+..  +-.++.         .+.||..||-         +    ..-
T Consensus       485 RTYVGAMPGkiIq~LK~v~t~NP-liLiDEvDKlG~--g~qGDP---------asALLElLDPEQNanFlDHYLdVp~DL  552 (906)
T KOG2004|consen  485 RTYVGAMPGKIIQCLKKVKTENP-LILIDEVDKLGS--GHQGDP---------ASALLELLDPEQNANFLDHYLDVPVDL  552 (906)
T ss_pred             eeeeccCChHHHHHHHhhCCCCc-eEEeehhhhhCC--CCCCCh---------HHHHHHhcChhhccchhhhccccccch
Confidence            35899999999999999998888 999999999972  222211         2445554442         1    123


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHc
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA  134 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~  134 (237)
                      ++|++|+|+|..+.||+.|+.  |.. +|+++--..++...|-+.||-
T Consensus       553 SkVLFicTAN~idtIP~pLlD--RME-vIelsGYv~eEKv~IA~~yLi  597 (906)
T KOG2004|consen  553 SKVLFICTANVIDTIPPPLLD--RME-VIELSGYVAEEKVKIAERYLI  597 (906)
T ss_pred             hheEEEEeccccccCChhhhh--hhh-eeeccCccHHHHHHHHHHhhh
Confidence            579999999999999999999  996 699999999999999998874

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.09  E-value=3.1e-05  Score=70.31  Aligned_cols=108  Identities=12%  Similarity=0.127  Sum_probs=83.0

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+.+.+..    ....|++|||+|.+..               ...+.||..|++  ...++++|++|+.+..|+
T Consensus       103 Vd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~---------------~A~NALLKtLEE--Pp~~viFILaTte~~kI~  165 (484)
T PRK14956        103 IENIRELRDNVKFAPMGGKYKVYIIDEVHMLTD---------------QSFNALLKTLEE--PPAHIVFILATTEFHKIP  165 (484)
T ss_pred             HHHHHHHHHHHHhhhhcCCCEEEEEechhhcCH---------------HHHHHHHHHhhc--CCCceEEEeecCChhhcc
Confidence            4455666555542    2456999999999832               356888888877  446788999999999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGY  154 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~  154 (237)
                      +.|++  |.. .+.|..++.++-.+.++..+...++. .+..+..+|..+.|-
T Consensus       166 ~TI~S--RCq-~~~f~~ls~~~i~~~L~~i~~~Egi~~e~eAL~~Ia~~S~Gd  215 (484)
T PRK14956        166 ETILS--RCQ-DFIFKKVPLSVLQDYSEKLCKIENVQYDQEGLFWIAKKGDGS  215 (484)
T ss_pred             HHHHh--hhh-eeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCh
Confidence            99999  985 58999999999999999888766554 566778888877764

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.07  E-value=9.8e-05  Score=67.50  Aligned_cols=127  Identities=13%  Similarity=0.141  Sum_probs=95.7

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      ....++++++++-      .+...++.+.+.+...    ..-|++|||+|.+..               ...+.|+..|+
T Consensus        83 ~~~Dv~eidaas~------~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls~---------------~A~NaLLK~LE  141 (491)
T PRK14964         83 NHPDVIEIDAASN------TSVDDIKVILENSCYLPISSKFKVYIIDEVHMLSN---------------SAFNALLKTLE  141 (491)
T ss_pred             CCCCEEEEecccC------CCHHHHHHHHHHHHhccccCCceEEEEeChHhCCH---------------HHHHHHHHHHh
Confidence            3456788888632      2356677777777543    345999999988732               34678899999


Q ss_pred             CCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccc
Q psy5642          82 GIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQ  159 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl  159 (237)
                      +.  ...+.+|.+|+.+..+++.+++  |+. .++|..++.++....++..+.+.+.. .+..+..++..+.| +.+++
T Consensus       142 eP--p~~v~fIlatte~~Kl~~tI~S--Rc~-~~~f~~l~~~el~~~L~~ia~~Egi~i~~eAL~lIa~~s~G-slR~a  214 (491)
T PRK14964        142 EP--APHVKFILATTEVKKIPVTIIS--RCQ-RFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLIAENSSG-SMRNA  214 (491)
T ss_pred             CC--CCCeEEEEEeCChHHHHHHHHH--hhe-eeecccccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHH
Confidence            83  3567788888889999999999  884 59999999999999999988776654 66778888888865 55663

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.06  E-value=0.00021  Score=64.31  Aligned_cols=116  Identities=21%  Similarity=0.306  Sum_probs=78.3

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG   82 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~   82 (237)
                      +.+|+.+++...       +...++.+++.+..    ..+.||||||+|.+..               .....|+..+++
T Consensus        61 ~~~~~~l~a~~~-------~~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~~---------------~~q~~LL~~le~  118 (413)
T PRK13342         61 DAPFEALSAVTS-------GVKDLREVIEEARQRRSAGRRTILFIDEIHRFNK---------------AQQDALLPHVED  118 (413)
T ss_pred             CCCEEEEecccc-------cHHHHHHHHHHHHHhhhcCCceEEEEechhhhCH---------------HHHHHHHHHhhc
Confidence            346777776532       34566777777643    2568999999998732               123455666654


Q ss_pred             CCCCCCEEEEEEeC-C-CCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC--CC-C-chhhHHHHHHHC
Q psy5642          83 IVPLNNVTIVAATN-R-PDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS--PL-G-EDVCVEELVRLT  151 (237)
Q Consensus        83 ~~~~~~v~vI~ttn-~-~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~--~~-~-~~~~~~~la~~t  151 (237)
                          +.+++|++|+ . ...+++++++  |+ ..+.++.|+.++...+++..+...  +. . .+..+..++..+
T Consensus       119 ----~~iilI~att~n~~~~l~~aL~S--R~-~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s  186 (413)
T PRK13342        119 ----GTITLIGATTENPSFEVNPALLS--RA-QVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLA  186 (413)
T ss_pred             ----CcEEEEEeCCCChhhhccHHHhc--cc-eeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhC
Confidence                4567776653 3 4489999999  98 679999999999999999877542  11 1 445566677665

>PRK08727 hypothetical protein; Validated

Probab=98.05  E-value=9.1e-05  Score=61.48  Aligned_cols=106  Identities=28%  Similarity=0.400  Sum_probs=67.8

Q ss_pred             HHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCcc---chhcc
Q psy5642          30 VRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRI---DKALL  106 (237)
Q Consensus        30 l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~l---d~al~  106 (237)
                      +.++++...  +..+|+|||++.+.....          ....+-.+++.+..   .+.-+|+.+...|..+   +++++
T Consensus        84 ~~~~~~~l~--~~dlLiIDDi~~l~~~~~----------~~~~lf~l~n~~~~---~~~~vI~ts~~~p~~l~~~~~dL~  148 (233)
T PRK08727         84 LRDALEALE--GRSLVALDGLESIAGQRE----------DEVALFDFHNRARA---AGITLLYTARQMPDGLALVLPDLR  148 (233)
T ss_pred             HHHHHHHHh--cCCEEEEeCcccccCChH----------HHHHHHHHHHHHHH---cCCeEEEECCCChhhhhhhhHHHH
Confidence            344444433  457999999998864321          12233344444432   2222344444467766   69999


Q ss_pred             CCCCc--ccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642         107 RPGRL--DRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus       107 r~gRf--~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      +  ||  ...+.++.|+.++|.++++......++. ++..+..|+..++
T Consensus       149 S--Rl~~~~~~~l~~~~~e~~~~iL~~~a~~~~l~l~~e~~~~La~~~~  195 (233)
T PRK08727        149 S--RLAQCIRIGLPVLDDVARAAVLRERAQRRGLALDEAAIDWLLTHGE  195 (233)
T ss_pred             H--HHhcCceEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCC
Confidence            9  98  5678999999999999999866544443 6667777888764

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.05  E-value=6.8e-05  Score=70.34  Aligned_cols=124  Identities=13%  Similarity=0.158  Sum_probs=91.6

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      ..++++++++-      .+...+|.+.+.+..    ....|++|||+|.+..               ...+.|+..|+..
T Consensus        87 pDviEIDAAs~------~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~---------------~A~NALLKtLEEP  145 (702)
T PRK14960         87 IDLIEIDAASR------TKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLST---------------HSFNALLKTLEEP  145 (702)
T ss_pred             CceEEeccccc------CCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCH---------------HHHHHHHHHHhcC
Confidence            36777777532      124556777666543    2346999999998832               2467788888873


Q ss_pred             CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          84 VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                        .+.+.+|++|+.+..+++.+++  |+. .++|..++..+-...++..+.+.+.. .+..+..++..+.| +.++
T Consensus       146 --P~~v~FILaTtd~~kIp~TIlS--RCq-~feFkpLs~eEI~k~L~~Il~kEgI~id~eAL~~IA~~S~G-dLRd  215 (702)
T PRK14960        146 --PEHVKFLFATTDPQKLPITVIS--RCL-QFTLRPLAVDEITKHLGAILEKEQIAADQDAIWQIAESAQG-SLRD  215 (702)
T ss_pred             --CCCcEEEEEECChHhhhHHHHH--hhh-eeeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHH
Confidence              3567788888899999999998  884 69999999999999999988776654 56778888887765 4444

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.01  E-value=4.9e-05  Score=71.51  Aligned_cols=122  Identities=17%  Similarity=0.227  Sum_probs=88.6

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      .|++++++.-      .+...++.+.+.+..    ...-|++|||+|.+..               ...+.||..|++  
T Consensus        89 D~ieidaas~------~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~---------------~a~NALLKtLEE--  145 (647)
T PRK07994         89 DLIEIDAASR------TKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSR---------------HSFNALLKTLEE--  145 (647)
T ss_pred             Cceeeccccc------CCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCH---------------HHHHHHHHHHHc--
Confidence            4666766431      123445555555443    2345999999999832               357889999998  


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCc
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSG  156 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~  156 (237)
                      ..+++.+|.+|+.++.|.+.|++  |. ..++|+.++.++-...|+..+...++. .+..+..++..+.|-..
T Consensus       146 Pp~~v~FIL~Tt~~~kLl~TI~S--RC-~~~~f~~Ls~~ei~~~L~~il~~e~i~~e~~aL~~Ia~~s~Gs~R  215 (647)
T PRK07994        146 PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRQQLEHILQAEQIPFEPRALQLLARAADGSMR  215 (647)
T ss_pred             CCCCeEEEEecCCccccchHHHh--hh-eEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHH
Confidence            44578888888999999999999  96 679999999999999999888655543 55667778877766433

>PRK06893 DNA replication initiation factor; Validated

Probab=97.99  E-value=6.9e-05  Score=62.04  Aligned_cols=99  Identities=11%  Similarity=0.200  Sum_probs=66.1

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCC-CEEEEEEeCCCCccc---hhccCCCCcccEEE
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLN-NVTIVAATNRPDRID---KALLRPGRLDRLIY  116 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~-~v~vI~ttn~~~~ld---~al~r~gRf~~~i~  116 (237)
                      ++.+|+|||++.+.++..          ....+-.+++.+   ...+ .+++++++..|..++   +.+++..++...+.
T Consensus        91 ~~dlLilDDi~~~~~~~~----------~~~~l~~l~n~~---~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~  157 (229)
T PRK06893         91 QQDLVCLDDLQAVIGNEE----------WELAIFDLFNRI---KEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQ  157 (229)
T ss_pred             cCCEEEEeChhhhcCChH----------HHHHHHHHHHHH---HHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeee
Confidence            467999999999864321          122233344433   2223 355666666788776   88998222357899


Q ss_pred             ecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642         117 VPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus       117 ~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      ++.|+.++|.+||+.......+. ++..+..|+.+.+
T Consensus       158 l~~pd~e~~~~iL~~~a~~~~l~l~~~v~~~L~~~~~  194 (229)
T PRK06893        158 LNDLTDEQKIIVLQRNAYQRGIELSDEVANFLLKRLD  194 (229)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcc
Confidence            99999999999999877655544 5666677777664

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

Probab=97.99  E-value=0.00019  Score=64.31  Aligned_cols=149  Identities=16%  Similarity=0.234  Sum_probs=94.1

Q ss_pred             ceEEEEEeccccc-ccccChH-HHHHHHHHHHH----HhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHh
Q psy5642           7 LTEVVESIGPELF-RKYVGES-ERCVRDVFKRA----RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEM   80 (237)
Q Consensus         7 ~~~~i~v~~s~l~-~~~~g~~-~~~l~~~f~~a----~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l   80 (237)
                      +.+|..++++.+. ..|+|.. +..+..++..+    ....|+||||||+|.+...+.+.+- +.......+.+.||+.|
T Consensus       141 ~~pf~~~da~~L~~~gyvG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~~~~~~s~-~~dvsg~~vq~~LL~iL  219 (413)
T TIGR00382       141 NVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSI-TRDVSGEGVQQALLKII  219 (413)
T ss_pred             CCCeEEechhhccccccccccHHHHHHHHHHhCcccHHhcccceEEecccchhchhhccccc-cccccchhHHHHHHHHh
Confidence            4688889988875 3588874 55666666543    2347899999999999875432211 00111124667778877


Q ss_pred             cCCCC-----------CCCEEEEEEeCCC---------------------------C-----------------------
Q psy5642          81 DGIVP-----------LNNVTIVAATNRP---------------------------D-----------------------   99 (237)
Q Consensus        81 ~~~~~-----------~~~v~vI~ttn~~---------------------------~-----------------------   99 (237)
                      ++...           ..+.++|.|+|-.                           +                       
T Consensus       220 eG~~~~v~~~~gr~~~~~~~i~i~TsNilfi~~Gaf~g~~~i~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~dl~~~  299 (413)
T TIGR00382       220 EGTVANVPPQGGRKHPYQEFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKF  299 (413)
T ss_pred             hccceecccCCCccccCCCeEEEEcCCceeeecccccChHHHHHHHhhhccccccccccccchhhHHHHHHHHHHHHHHH
Confidence            65421           1246788887761                           0                       


Q ss_pred             ccchhccCCCCcccEEEecCCCHHHHHHHHHHH----HcC-------CCCC---chhhHHHHHHHC--CCCCccc
Q psy5642         100 RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIR----LAR-------SPLG---EDVCVEELVRLT--EGYSGAE  158 (237)
Q Consensus       100 ~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~----l~~-------~~~~---~~~~~~~la~~t--~g~s~~D  158 (237)
                      .+.|+++.  |++.++.|...+.++..+|+...    ++.       ..+.   .+..+..||++.  .+|..+-
T Consensus       300 g~~PEflg--Rld~Iv~f~pL~~~~L~~Il~~~~n~l~kq~~~~l~~~gi~L~~t~~a~~~Ia~~~~~~~~GAR~  372 (413)
T TIGR00382       300 GLIPEFIG--RLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARG  372 (413)
T ss_pred             hhHHHHhC--CCCeEeecCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCeEEEECHHHHHHHHHhCCCCCCCchH
Confidence            14467776  99999999999999999998652    221       1221   456677777763  3455555

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.

>PF09336 Vps4_C: Vps4 C terminal oligomerisation domain; InterPro: IPR015415 This domain is found at the C-terminal of ATPase proteins involved in vacuolar sorting

Probab=97.99  E-value=4.1e-06  Score=54.71  Aligned_cols=34  Identities=32%  Similarity=0.518  Sum_probs=30.5

Q ss_pred             cCCccHHHHHHHHhhcCCCCCHHHHHHHHHHhhC
Q psy5642         204 AAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK  237 (237)
Q Consensus       204 ~~~v~~~df~~al~~~~p~~~~~~~~~~~~~~~~  237 (237)
                      .++|+.+||..||+..+|+++.+++++|++|.++
T Consensus        27 ~p~it~~DF~~Al~~~kpSVs~~dl~~ye~w~~~   60 (62)
T PF09336_consen   27 EPPITMEDFEEALKKVKPSVSQEDLKKYEEWTKE   60 (62)
T ss_dssp             HHHBCHHHHHHHHHTCGGSS-HHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence            4479999999999999999999999999999873

It forms an alpha helix structure and is required for oligomerisation []. ; PDB: 1XWI_A 3EIH_C 2QPA_C 3EIE_A 2RKO_A 2QP9_X 3MHV_C 3CF3_C 3CF1_A 3CF2_A ....

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.99  E-value=8.1e-05  Score=69.84  Aligned_cols=122  Identities=21%  Similarity=0.252  Sum_probs=89.3

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHhcCC-----eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQVSP-----SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P-----~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      .++++++..-      .+...++++.+.+.. .|     -|++|||+|.+..               ...+.|+..|++ 
T Consensus        94 D~~eldaas~------~~Vd~iReli~~~~~-~p~~g~~KV~IIDEvh~Ls~---------------~a~NaLLKtLEE-  150 (618)
T PRK14951         94 DYTELDAASN------RGVDEVQQLLEQAVY-KPVQGRFKVFMIDEVHMLTN---------------TAFNAMLKTLEE-  150 (618)
T ss_pred             ceeecCcccc------cCHHHHHHHHHHHHh-CcccCCceEEEEEChhhCCH---------------HHHHHHHHhccc-
Confidence            4666665421      234567777776654 33     4999999999833               236778888887 


Q ss_pred             CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          84 VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                       ....+.+|.+|+.++.+.+.+++  |. ..++|..++.++....|+..+...++. .+..+..|+..+.| +.++
T Consensus       151 -PP~~~~fIL~Ttd~~kil~TIlS--Rc-~~~~f~~Ls~eei~~~L~~i~~~egi~ie~~AL~~La~~s~G-slR~  221 (618)
T PRK14951        151 -PPEYLKFVLATTDPQKVPVTVLS--RC-LQFNLRPMAPETVLEHLTQVLAAENVPAEPQALRLLARAARG-SMRD  221 (618)
T ss_pred             -CCCCeEEEEEECCchhhhHHHHH--hc-eeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHH
Confidence             33567788888889999999998  87 579999999999999999888766654 45667788887765 4444

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.95  E-value=0.00026  Score=65.33  Aligned_cols=110  Identities=19%  Similarity=0.292  Sum_probs=82.3

Q ss_pred             HHHHHHHHHHHHhcCC-----eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCcc
Q psy5642          27 ERCVRDVFKRARQVSP-----SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRI  101 (237)
Q Consensus        27 ~~~l~~~f~~a~~~~P-----~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~l  101 (237)
                      -..++.+...+.. .|     -|++|||+|.+.               ....+.|+..|+..  ...+.+|.+|+.+..+
T Consensus        99 Id~IRelie~~~~-~P~~~~~KVvIIDEad~Lt---------------~~A~NALLK~LEEp--p~~t~FIL~ttd~~kL  160 (535)
T PRK08451         99 IDDIRELIEQTKY-KPSMARFKIFIIDEVHMLT---------------KEAFNALLKTLEEP--PSYVKFILATTDPLKL  160 (535)
T ss_pred             HHHHHHHHHHHhh-CcccCCeEEEEEECcccCC---------------HHHHHHHHHHHhhc--CCceEEEEEECChhhC
Confidence            4566666665443 33     499999998872               23467889999884  3457777778889999


Q ss_pred             chhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642         102 DKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus       102 d~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      .+.|++  |. ..++|.+++.++-...++..+...+.. .+..+..++..+.| +.++
T Consensus       161 ~~tI~S--Rc-~~~~F~~Ls~~ei~~~L~~Il~~EGi~i~~~Al~~Ia~~s~G-dlR~  214 (535)
T PRK08451        161 PATILS--RT-QHFRFKQIPQNSIISHLKTILEKEGVSYEPEALEILARSGNG-SLRD  214 (535)
T ss_pred             chHHHh--hc-eeEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-cHHH
Confidence            999999  85 579999999999999999888766554 55677778887665 5555

>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=97.94  E-value=1.4e-05  Score=65.71  Aligned_cols=131  Identities=20%  Similarity=0.292  Sum_probs=74.3

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+..++++++.++...+.......-..-|..-. ....+|+|||++.+..+             ......+...++....
T Consensus        63 ~~~~v~y~~~~~f~~~~~~~~~~~~~~~~~~~~-~~~DlL~iDDi~~l~~~-------------~~~q~~lf~l~n~~~~  128 (219)
T PF00308_consen   63 PGKRVVYLSAEEFIREFADALRDGEIEEFKDRL-RSADLLIIDDIQFLAGK-------------QRTQEELFHLFNRLIE  128 (219)
T ss_dssp             TTS-EEEEEHHHHHHHHHHHHHTTSHHHHHHHH-CTSSEEEEETGGGGTTH-------------HHHHHHHHHHHHHHHH
T ss_pred             ccccceeecHHHHHHHHHHHHHcccchhhhhhh-hcCCEEEEecchhhcCc-------------hHHHHHHHHHHHHHHh
Confidence            345566666666654433322221111122111 24579999999998543             1223444444444434


Q ss_pred             CCCEEEEEEeCCCCc---cchhccCCCCcc--cEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642          86 LNNVTIVAATNRPDR---IDKALLRPGRLD--RLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~---ld~al~r~gRf~--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      .++-+|+.+-..|..   +++.+++  ||.  ..+.+..|+.+.|..|++......+.. ++..+..|+...+
T Consensus       129 ~~k~li~ts~~~P~~l~~~~~~L~S--Rl~~Gl~~~l~~pd~~~r~~il~~~a~~~~~~l~~~v~~~l~~~~~  199 (219)
T PF00308_consen  129 SGKQLILTSDRPPSELSGLLPDLRS--RLSWGLVVELQPPDDEDRRRILQKKAKERGIELPEEVIEYLARRFR  199 (219)
T ss_dssp             TTSEEEEEESS-TTTTTTS-HHHHH--HHHCSEEEEE----HHHHHHHHHHHHHHTT--S-HHHHHHHHHHTT
T ss_pred             hCCeEEEEeCCCCccccccChhhhh--hHhhcchhhcCCCCHHHHHHHHHHHHHHhCCCCcHHHHHHHHHhhc
Confidence            456666666666765   4688888  986  488999999999999999988776665 5666666777753

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.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=97.94  E-value=0.00016  Score=57.87  Aligned_cols=102  Identities=14%  Similarity=0.226  Sum_probs=75.6

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+.+.+...    .+.|++|||+|.+..               ...+.|+..|+..  ....++|.+|+++..+.
T Consensus        78 ~~~i~~i~~~~~~~~~~~~~kviiide~~~l~~---------------~~~~~Ll~~le~~--~~~~~~il~~~~~~~l~  140 (188)
T TIGR00678        78 VDQVRELVEFLSRTPQESGRRVVIIEDAERMNE---------------AAANALLKTLEEP--PPNTLFILITPSPEKLL  140 (188)
T ss_pred             HHHHHHHHHHHccCcccCCeEEEEEechhhhCH---------------HHHHHHHHHhcCC--CCCeEEEEEECChHhCh
Confidence            45666666666542    356999999988833               2356788888873  34566777788889999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEG  153 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g  153 (237)
                      +++++  |+. .++|++|+.++..++++..    +. .+..+..++..+.|
T Consensus       141 ~~i~s--r~~-~~~~~~~~~~~~~~~l~~~----gi-~~~~~~~i~~~~~g  183 (188)
T TIGR00678       141 PTIRS--RCQ-VLPFPPLSEEALLQWLIRQ----GI-SEEAAELLLALAGG  183 (188)
T ss_pred             HHHHh--hcE-EeeCCCCCHHHHHHHHHHc----CC-CHHHHHHHHHHcCC
Confidence            99999  884 7999999999999888876    23 34557777777765

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.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.93  E-value=0.00015  Score=68.00  Aligned_cols=118  Identities=17%  Similarity=0.267  Sum_probs=88.3

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHhcCC-----eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQVSP-----SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P-----~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      .++++++..-      .+...++.+.+.+.. .|     -|++|||+|.+..               ...+.|+..|+. 
T Consensus        89 d~~eid~~s~------~~v~~ir~l~~~~~~-~p~~~~~KVvIIdev~~Lt~---------------~a~naLLk~LEe-  145 (576)
T PRK14965         89 DVFEIDGASN------TGVDDIRELRENVKY-LPSRSRYKIFIIDEVHMLST---------------NAFNALLKTLEE-  145 (576)
T ss_pred             CeeeeeccCc------cCHHHHHHHHHHHHh-ccccCCceEEEEEChhhCCH---------------HHHHHHHHHHHc-
Confidence            4566665431      234567777777654 34     4999999988732               246789999988 


Q ss_pred             CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642          84 VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                       ...++++|.+|+.++.|++.|++  |.. .++|..++..+-...+...+...+.. .+..+..++..+.|
T Consensus       146 -pp~~~~fIl~t~~~~kl~~tI~S--Rc~-~~~f~~l~~~~i~~~L~~i~~~egi~i~~~al~~la~~a~G  212 (576)
T PRK14965        146 -PPPHVKFIFATTEPHKVPITILS--RCQ-RFDFRRIPLQKIVDRLRYIADQEGISISDAALALVARKGDG  212 (576)
T ss_pred             -CCCCeEEEEEeCChhhhhHHHHH--hhh-hhhcCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Confidence             34578888888999999999998  874 69999999999999999888776654 56677778887765

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.93  E-value=0.00012  Score=63.29  Aligned_cols=104  Identities=17%  Similarity=0.213  Sum_probs=66.6

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHHh-cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRARQ-VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~-~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      .+++++++++  +. .......+......... ..+.+|+|||+|.+...              .....+...++..  .
T Consensus        69 ~~~~~i~~~~--~~-~~~i~~~l~~~~~~~~~~~~~~vliiDe~d~l~~~--------------~~~~~L~~~le~~--~  129 (316)
T PHA02544         69 AEVLFVNGSD--CR-IDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLGLA--------------DAQRHLRSFMEAY--S  129 (316)
T ss_pred             ccceEeccCc--cc-HHHHHHHHHHHHHhhcccCCCeEEEEECcccccCH--------------HHHHHHHHHHHhc--C
Confidence            4677777776  22 22222223322222211 25789999999887211              1123344445553  2


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHH
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL  133 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l  133 (237)
                      +++.+|.|||.+..+++++++  ||. .+.++.|+.+++..+++.++
T Consensus       130 ~~~~~Ilt~n~~~~l~~~l~s--R~~-~i~~~~p~~~~~~~il~~~~  173 (316)
T PHA02544        130 KNCSFIITANNKNGIIEPLRS--RCR-VIDFGVPTKEEQIEMMKQMI  173 (316)
T ss_pred             CCceEEEEcCChhhchHHHHh--hce-EEEeCCCCHHHHHHHHHHHH
Confidence            456788899999999999999  996 68999999999998877543

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

Probab=97.92  E-value=0.00016  Score=60.95  Aligned_cols=85  Identities=16%  Similarity=0.185  Sum_probs=67.1

Q ss_pred             hccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCC-----CchhhHHHHHHHCCCCCcccccchhHHhhhhccccCCCCC
Q psy5642         104 ALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPL-----GEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPG  178 (237)
Q Consensus       104 al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~-----~~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~  178 (237)
                      .+.+  |+...+++++.+.++-.+++...+...+.     -.+..+..++..|.|+ ++.                    
T Consensus       178 ~l~~--r~~~~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~-p~~--------------------  234 (269)
T TIGR03015       178 QLRQ--RIIASCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGI-PRL--------------------  234 (269)
T ss_pred             HHHh--heeeeeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCc-ccH--------------------
Confidence            3555  78888999999999999999988864331     2567788888888887 566                    


Q ss_pred             CCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcC
Q psy5642         179 PPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVK  220 (237)
Q Consensus       179 ~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~  220 (237)
                             |..++..+...+..++  ...|+.+++..++..++
T Consensus       235 -------i~~l~~~~~~~a~~~~--~~~i~~~~v~~~~~~~~  267 (269)
T TIGR03015       235 -------INILCDRLLLSAFLEE--KREIGGEEVREVIAEID  267 (269)
T ss_pred             -------HHHHHHHHHHHHHHcC--CCCCCHHHHHHHHHHhh
Confidence                   8888888888887766  45799999999988764

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.

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

Probab=97.92  E-value=0.00022  Score=63.53  Aligned_cols=131  Identities=20%  Similarity=0.317  Sum_probs=91.1

Q ss_pred             CCCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           4 LGGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         4 ~~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      .+.+..++++...+++..++.....+=..-|..-+  +-.+|+|||++.+.++...             ..+|-..+..+
T Consensus       140 ~~~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~y--~~dlllIDDiq~l~gk~~~-------------qeefFh~FN~l  204 (408)
T COG0593         140 NGPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKY--SLDLLLIDDIQFLAGKERT-------------QEEFFHTFNAL  204 (408)
T ss_pred             hCCCceEEeccHHHHHHHHHHHHHhhhHHHHHHhh--ccCeeeechHhHhcCChhH-------------HHHHHHHHHHH
Confidence            34566788888887777666665555555565555  4569999999999776322             23344444444


Q ss_pred             CCCCCEEEEEEeCCCCccc---hhccCCCCcc--cEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHC
Q psy5642          84 VPLNNVTIVAATNRPDRID---KALLRPGRLD--RLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLT  151 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~~ld---~al~r~gRf~--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t  151 (237)
                      ...++-+|+.+-..|.+++   +.|++  ||.  .++.+.+|+.+.|..||+......++. ++.-+.-+|...
T Consensus       205 ~~~~kqIvltsdr~P~~l~~~~~rL~S--R~~~Gl~~~I~~Pd~e~r~aiL~kka~~~~~~i~~ev~~~la~~~  276 (408)
T COG0593         205 LENGKQIVLTSDRPPKELNGLEDRLRS--RLEWGLVVEIEPPDDETRLAILRKKAEDRGIEIPDEVLEFLAKRL  276 (408)
T ss_pred             HhcCCEEEEEcCCCchhhccccHHHHH--HHhceeEEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHh
Confidence            4445556666667787665   89999  996  677999999999999999977666655 566666677665

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.89  E-value=0.00033  Score=64.51  Aligned_cols=119  Identities=19%  Similarity=0.259  Sum_probs=85.7

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      .+++++++.      ..+...++.+.+.+..    ..+.||+|||+|.+.               ....+.|+..|+.. 
T Consensus        86 dv~el~~~~------~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls---------------~~a~naLLk~LEep-  143 (504)
T PRK14963         86 DVLEIDAAS------NNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMS---------------KSAFNALLKTLEEP-  143 (504)
T ss_pred             ceEEecccc------cCCHHHHHHHHHHHhhccccCCCeEEEEECccccC---------------HHHHHHHHHHHHhC-
Confidence            366666642      1224456666555443    246699999998652               23467788888873 


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                       ...+++|.+|+.+..+.+.+++  |+. .+.|+.|+.++-...++..+...+.. .+..+..++..+.|
T Consensus       144 -~~~t~~Il~t~~~~kl~~~I~S--Rc~-~~~f~~ls~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~G  209 (504)
T PRK14963        144 -PEHVIFILATTEPEKMPPTILS--RTQ-HFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLVARLADG  209 (504)
T ss_pred             -CCCEEEEEEcCChhhCChHHhc--ceE-EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence             3467788888999999999998  875 69999999999999999988776654 55667777776653

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.85  E-value=0.00021  Score=67.57  Aligned_cols=123  Identities=20%  Similarity=0.245  Sum_probs=89.3

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      .+++++++.      +.+...++++++.+...    ...|++|||+|.+.               ....+.|+..|+.. 
T Consensus        89 DvlEidaAs------~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls---------------~~A~NALLKtLEEP-  146 (709)
T PRK08691         89 DLLEIDAAS------NTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLS---------------KSAFNAMLKTLEEP-  146 (709)
T ss_pred             ceEEEeccc------cCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccC---------------HHHHHHHHHHHHhC-
Confidence            455666542      12345677887766432    34699999998762               23467888888873 


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                       .+.+.+|.+|+.+..+.+.+++  |+ ..+.|+.++.++-...|+..+...++. .+..+..|+..+.| +.++
T Consensus       147 -p~~v~fILaTtd~~kL~~TIrS--RC-~~f~f~~Ls~eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A~G-slRd  216 (709)
T PRK08691        147 -PEHVKFILATTDPHKVPVTVLS--RC-LQFVLRNMTAQQVADHLAHVLDSEKIAYEPPALQLLGRAAAG-SMRD  216 (709)
T ss_pred             -CCCcEEEEEeCCccccchHHHH--HH-hhhhcCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCC-CHHH
Confidence             3567888888999999999998  88 458999999999999999998876654 55667788887743 4444

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.85  E-value=0.00047  Score=66.78  Aligned_cols=107  Identities=18%  Similarity=0.249  Sum_probs=79.9

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...+|.+.+.+..    ....|++|||+|.+.               ....+.||..|+.  ...++.+|++|+.+..|.
T Consensus       101 VDdIReLie~v~~~P~~gk~KViIIDEAh~LT---------------~eAqNALLKtLEE--PP~~vrFILaTTe~~kLl  163 (944)
T PRK14949        101 VDDTRELLDNVQYRPSRGRFKVYLIDEVHMLS---------------RSSFNALLKTLEE--PPEHVKFLLATTDPQKLP  163 (944)
T ss_pred             HHHHHHHHHHHHhhhhcCCcEEEEEechHhcC---------------HHHHHHHHHHHhc--cCCCeEEEEECCCchhch
Confidence            3445555555442    234599999999982               3457889999998  345677888888999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +.|++  |. ..+.|+.++.++-...|+..+...++. .+..+..|+..+.|
T Consensus       164 ~TIlS--RC-q~f~fkpLs~eEI~~~L~~il~~EgI~~edeAL~lIA~~S~G  212 (944)
T PRK14949        164 VTVLS--RC-LQFNLKSLTQDEIGTQLNHILTQEQLPFEAEALTLLAKAANG  212 (944)
T ss_pred             HHHHH--hh-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            99998  87 569999999999999999888664443 45567777777655

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.84  E-value=0.00033  Score=64.31  Aligned_cols=107  Identities=17%  Similarity=0.206  Sum_probs=77.2

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+.+.+...    .+.|++|||+|.+..               ...+.|+..|+..  ...+++|.+|+.++.++
T Consensus       101 vd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~---------------~a~naLLk~LEep--p~~~v~Il~tt~~~kl~  163 (486)
T PRK14953        101 IDDIRALRDAVSYTPIKGKYKVYIIDEAHMLTK---------------EAFNALLKTLEEP--PPRTIFILCTTEYDKIP  163 (486)
T ss_pred             HHHHHHHHHHHHhCcccCCeeEEEEEChhhcCH---------------HHHHHHHHHHhcC--CCCeEEEEEECCHHHHH
Confidence            34455665555432    356999999997732               2356788888873  34556666677788999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +++++  |+. .+.|+.|+.++...+++..+...+.. .+..+..++..+.|
T Consensus       164 ~tI~S--Rc~-~i~f~~ls~~el~~~L~~i~k~egi~id~~al~~La~~s~G  212 (486)
T PRK14953        164 PTILS--RCQ-RFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQASEG  212 (486)
T ss_pred             HHHHH--hce-EEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            99998  875 69999999999999999988876654 45566677776553

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.81  E-value=0.00045  Score=64.50  Aligned_cols=124  Identities=17%  Similarity=0.259  Sum_probs=88.7

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      ..+++++++.-      .+-..++.+.+.+...    ...|++|||+|.+..               ...+.|+..|+. 
T Consensus        88 ~DiieIdaas~------igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~---------------~A~NaLLKtLEE-  145 (605)
T PRK05896         88 VDIVELDAASN------NGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLST---------------SAWNALLKTLEE-  145 (605)
T ss_pred             CceEEeccccc------cCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCH---------------HHHHHHHHHHHh-
Confidence            35666766431      1234566666666542    234999999998832               235788888888 


Q ss_pred             CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          84 VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                       ....+++|.+|+.+..+.+.+++  |+. .++|+.|+..+....++..+...+.. ++..+..++..+.| +.++
T Consensus       146 -Pp~~tvfIL~Tt~~~KLl~TI~S--Rcq-~ieF~~Ls~~eL~~~L~~il~kegi~Is~eal~~La~lS~G-dlR~  216 (605)
T PRK05896        146 -PPKHVVFIFATTEFQKIPLTIIS--RCQ-RYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKIADLADG-SLRD  216 (605)
T ss_pred             -CCCcEEEEEECCChHhhhHHHHh--hhh-hcccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-cHHH
Confidence             33567788888889999999999  886 69999999999999999888766543 45667777777755 3444

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

Probab=97.81  E-value=0.00021  Score=62.84  Aligned_cols=99  Identities=18%  Similarity=0.319  Sum_probs=74.0

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcC----CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVS----PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~----P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      .+++|..+++-.       .+.+.++.+|+.|+...    ..|||+|||+.|...               ....||..++
T Consensus        72 ~~~~f~~~sAv~-------~gvkdlr~i~e~a~~~~~~gr~tiLflDEIHRfnK~---------------QQD~lLp~vE  129 (436)
T COG2256          72 TNAAFEALSAVT-------SGVKDLREIIEEARKNRLLGRRTILFLDEIHRFNKA---------------QQDALLPHVE  129 (436)
T ss_pred             hCCceEEecccc-------ccHHHHHHHHHHHHHHHhcCCceEEEEehhhhcChh---------------hhhhhhhhhc
Confidence            355666666632       35899999999996542    589999999998432               2345666666


Q ss_pred             CCCCCCCEEEEEEe-CCCC-ccchhccCCCCcccEEEecCCCHHHHHHHHHHHH
Q psy5642          82 GIVPLNNVTIVAAT-NRPD-RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL  133 (237)
Q Consensus        82 ~~~~~~~v~vI~tt-n~~~-~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l  133 (237)
                      .    +.|++||+| -+|. .+.++|++  |. .++++.+.+.++-..+++..+
T Consensus       130 ~----G~iilIGATTENPsF~ln~ALlS--R~-~vf~lk~L~~~di~~~l~ra~  176 (436)
T COG2256         130 N----GTIILIGATTENPSFELNPALLS--RA-RVFELKPLSSEDIKKLLKRAL  176 (436)
T ss_pred             C----CeEEEEeccCCCCCeeecHHHhh--hh-heeeeecCCHHHHHHHHHHHH
Confidence            5    677777766 4455 99999999  87 468999999999999998833

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.80  E-value=0.00043  Score=64.76  Aligned_cols=121  Identities=17%  Similarity=0.157  Sum_probs=86.0

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      +...+++++++.-.      +...++.+-+.+..    ...-|++|||+|.+..               ...+.||..|+
T Consensus        85 ~~~dvieidaas~~------gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~---------------~A~NALLK~LE  143 (584)
T PRK14952         85 GSIDVVELDAASHG------GVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTT---------------AGFNALLKIVE  143 (584)
T ss_pred             CCceEEEecccccc------CHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCH---------------HHHHHHHHHHh
Confidence            34667788775321      24445555555433    2335999999998832               24678899998


Q ss_pred             CCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642          82 GIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      .  ....+++|.+|+.++.+.+.|++  |. ..++|..++.++-.+.+...+...+.. .+..+..++..+.
T Consensus       144 E--pp~~~~fIL~tte~~kll~TI~S--Rc-~~~~F~~l~~~~i~~~L~~i~~~egi~i~~~al~~Ia~~s~  210 (584)
T PRK14952        144 E--PPEHLIFIFATTEPEKVLPTIRS--RT-HHYPFRLLPPRTMRALIARICEQEGVVVDDAVYPLVIRAGG  210 (584)
T ss_pred             c--CCCCeEEEEEeCChHhhHHHHHH--hc-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            8  44578888888889999999999  85 579999999999999999888766543 4455555666543

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.80  E-value=0.00017  Score=67.62  Aligned_cols=93  Identities=22%  Similarity=0.298  Sum_probs=73.0

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P  120 (237)
                      ...||+|||+|.+..               ...+.|+..|+.  ...++++|++|+.+..+.+.|++  |+. .|.|+.+
T Consensus       119 ~~kVIIIDEad~Lt~---------------~a~naLLk~LEE--P~~~~ifILaTt~~~kll~TI~S--Rcq-~i~F~pL  178 (624)
T PRK14959        119 RYKVFIIDEAHMLTR---------------EAFNALLKTLEE--PPARVTFVLATTEPHKFPVTIVS--RCQ-HFTFTRL  178 (624)
T ss_pred             CceEEEEEChHhCCH---------------HHHHHHHHHhhc--cCCCEEEEEecCChhhhhHHHHh--hhh-ccccCCC
Confidence            456999999999832               346788888887  33578888899999999999998  875 6899999


Q ss_pred             CHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         121 DDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       121 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +.++-..+|+..+...... .+..+..++..+.|
T Consensus       179 s~~eL~~~L~~il~~egi~id~eal~lIA~~s~G  212 (624)
T PRK14959        179 SEAGLEAHLTKVLGREGVDYDPAAVRLIARRAAG  212 (624)
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            9999999999888766543 55667777776654

>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=97.79  E-value=0.00012  Score=59.96  Aligned_cols=122  Identities=19%  Similarity=0.283  Sum_probs=75.6

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC--
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV--   84 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--   84 (237)
                      +.+|...++..+.      ....+..++...+  ...|||||||+.+..               .+-..|+..|++..  
T Consensus        75 ~~~~~~~sg~~i~------k~~dl~~il~~l~--~~~ILFIDEIHRlnk---------------~~qe~LlpamEd~~id  131 (233)
T PF05496_consen   75 GVNFKITSGPAIE------KAGDLAAILTNLK--EGDILFIDEIHRLNK---------------AQQEILLPAMEDGKID  131 (233)
T ss_dssp             T--EEEEECCC--------SCHHHHHHHHT----TT-EEEECTCCC--H---------------HHHHHHHHHHHCSEEE
T ss_pred             CCCeEeccchhhh------hHHHHHHHHHhcC--CCcEEEEechhhccH---------------HHHHHHHHHhccCeEE
Confidence            3455556654321      1334444444433  467999999999832               23445566665432  


Q ss_pred             ------C--------CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHH
Q psy5642          85 ------P--------LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVR  149 (237)
Q Consensus        85 ------~--------~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~  149 (237)
                            .        -.+..+||+|+....+.+.++.  ||..+..+..-+.++-..|++.....+.+. .+....++|.
T Consensus       132 iiiG~g~~ar~~~~~l~~FTligATTr~g~ls~pLrd--RFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~i~~~~~~~Ia~  209 (233)
T PF05496_consen  132 IIIGKGPNARSIRINLPPFTLIGATTRAGLLSSPLRD--RFGIVLRLEFYSEEELAKIVKRSARILNIEIDEDAAEEIAR  209 (233)
T ss_dssp             EEBSSSSS-BEEEEE----EEEEEESSGCCTSHCCCT--TSSEEEE----THHHHHHHHHHCCHCTT-EE-HHHHHHHHH
T ss_pred             EEeccccccceeeccCCCceEeeeeccccccchhHHh--hcceecchhcCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHH
Confidence                  1        1358899999999999999999  999988999999999999999877766665 5667778888


Q ss_pred             HCCC
Q psy5642         150 LTEG  153 (237)
Q Consensus       150 ~t~g  153 (237)
                      ++.|
T Consensus       210 rsrG  213 (233)
T PF05496_consen  210 RSRG  213 (233)
T ss_dssp             CTTT
T ss_pred             hcCC
Confidence            8865

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.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=97.78  E-value=0.00091  Score=60.88  Aligned_cols=93  Identities=14%  Similarity=0.173  Sum_probs=72.4

Q ss_pred             cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecC
Q psy5642          40 VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPL  119 (237)
Q Consensus        40 ~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~  119 (237)
                      ....|++|||+|.+..               ...+.|+..|+..  .+.+++|++|+.+..+.+.|++  |+. .++|+.
T Consensus       120 ~~~kvvIIdead~lt~---------------~~~n~LLk~lEep--~~~~~~Il~t~~~~kl~~tI~s--Rc~-~v~f~~  179 (451)
T PRK06305        120 SRYKIYIIDEVHMLTK---------------EAFNSLLKTLEEP--PQHVKFFLATTEIHKIPGTILS--RCQ-KMHLKR  179 (451)
T ss_pred             CCCEEEEEecHHhhCH---------------HHHHHHHHHhhcC--CCCceEEEEeCChHhcchHHHH--hce-EEeCCC
Confidence            3567999999988832               2357888888883  3577777888889999999999  885 699999


Q ss_pred             CCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642         120 PDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus       120 P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      ++.++-...++..+...+.. ....+..|+..+.
T Consensus       180 l~~~el~~~L~~~~~~eg~~i~~~al~~L~~~s~  213 (451)
T PRK06305        180 IPEETIIDKLALIAKQEGIETSREALLPIARAAQ  213 (451)
T ss_pred             CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            99999999999887765543 4556777777664

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.77  E-value=0.00097  Score=62.99  Aligned_cols=59  Identities=17%  Similarity=0.176  Sum_probs=43.5

Q ss_pred             EEEEE-EeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHH
Q psy5642          89 VTIVA-ATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRL  150 (237)
Q Consensus        89 v~vI~-ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~  150 (237)
                      +++|+ ||+.++.+++++++  ||. .+++++++.++...|++..+...... ++..+..|+..
T Consensus       324 ~VLI~aTt~~~~~l~~aLrS--R~~-~i~~~pls~edi~~Il~~~a~~~~v~ls~eal~~L~~y  384 (615)
T TIGR02903       324 FVLIGATTRDPEEINPALRS--RCA-EVFFEPLTPEDIALIVLNAAEKINVHLAAGVEELIARY  384 (615)
T ss_pred             EEEEEeccccccccCHHHHh--cee-EEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHC
Confidence            45554 56779999999999  997 57899999999999999988765432 33444444443

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.

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.75  E-value=0.00084  Score=62.69  Aligned_cols=111  Identities=16%  Similarity=0.176  Sum_probs=82.2

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      -..++.+.+.+..    ...-|++|||+|.+.               ....+.|+..++.  ....+++|++|+.+..+.
T Consensus       101 vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls---------------~~a~naLLK~LEe--pp~~~vfI~~tte~~kL~  163 (563)
T PRK06647        101 VQDVRQIKEEIMFPPASSRYRVYIIDEVHMLS---------------NSAFNALLKTIEE--PPPYIVFIFATTEVHKLP  163 (563)
T ss_pred             HHHHHHHHHHHHhchhcCCCEEEEEEChhhcC---------------HHHHHHHHHhhcc--CCCCEEEEEecCChHHhH
Confidence            4455566554443    245599999998872               2346788888887  345778888888899999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      ++|++  |+. .++|..|+.++...+++..+...+.. .+..+..|+..+.| +.++
T Consensus       164 ~tI~S--Rc~-~~~f~~l~~~el~~~L~~i~~~egi~id~eAl~lLa~~s~G-dlR~  216 (563)
T PRK06647        164 ATIKS--RCQ-HFNFRLLSLEKIYNMLKKVCLEDQIKYEDEALKWIAYKSTG-SVRD  216 (563)
T ss_pred             HHHHH--hce-EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHH
Confidence            99999  986 58999999999999999887665543 56677778887765 4555

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.75  E-value=0.00052  Score=64.43  Aligned_cols=123  Identities=20%  Similarity=0.216  Sum_probs=89.3

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      .++++++..-      .+...++.+.+.+...    ...|++|||+|.+..               ...+.|+..|++. 
T Consensus       102 Dv~e~~a~s~------~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~---------------~a~naLLKtLEeP-  159 (598)
T PRK09111        102 DVLEMDAASH------TGVDDIREIIESVRYRPVSARYKVYIIDEVHMLST---------------AAFNALLKTLEEP-  159 (598)
T ss_pred             ceEEeccccc------CCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCH---------------HHHHHHHHHHHhC-
Confidence            4566665421      1245677787777643    346999999988832               3467888888883 


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                       ...+.+|.+|+.++.+.+.|++  |.. .++|..|+.++-..+++..+.+.+.. .+..+..++..+.| +.++
T Consensus       160 -p~~~~fIl~tte~~kll~tI~S--Rcq-~~~f~~l~~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~G-dlr~  229 (598)
T PRK09111        160 -PPHVKFIFATTEIRKVPVTVLS--RCQ-RFDLRRIEADVLAAHLSRIAAKEGVEVEDEALALIARAAEG-SVRD  229 (598)
T ss_pred             -CCCeEEEEEeCChhhhhHHHHh--hee-EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHH
Confidence             3467777778888889999998  874 69999999999999999988776654 45667777887765 4555

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.74  E-value=0.00039  Score=57.24  Aligned_cols=92  Identities=17%  Similarity=0.207  Sum_probs=57.3

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCC-CC--ccchhccCCCCc--ccEE
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNR-PD--RIDKALLRPGRL--DRLI  115 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~-~~--~ld~al~r~gRf--~~~i  115 (237)
                      .+.+|+|||+|.+...            ...   .+...++.....+..++|.|++. |.  .+.+.+++  ||  ...+
T Consensus        90 ~~~~liiDdi~~l~~~------------~~~---~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~s--r~~~~~~i  152 (227)
T PRK08903         90 EAELYAVDDVERLDDA------------QQI---ALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRT--RLGWGLVY  152 (227)
T ss_pred             cCCEEEEeChhhcCch------------HHH---HHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHH--HHhcCeEE
Confidence            4679999999986221            122   23333433323344334445443 22  34577777  87  4789


Q ss_pred             EecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHH
Q psy5642         116 YVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVR  149 (237)
Q Consensus       116 ~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~  149 (237)
                      .+++|+..++..+++.+.....+. ++..+..|+.
T Consensus       153 ~l~pl~~~~~~~~l~~~~~~~~v~l~~~al~~L~~  187 (227)
T PRK08903        153 ELKPLSDADKIAALKAAAAERGLQLADEVPDYLLT  187 (227)
T ss_pred             EecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            999999999999999877665554 4555666666

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

Probab=97.73  E-value=0.00047  Score=66.06  Aligned_cols=123  Identities=20%  Similarity=0.258  Sum_probs=76.7

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHh-----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQ-----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~-----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      +.+|+.++++.-       +.+.++..+..+..     ..+.+|||||+|.+...               ....|+..++
T Consensus        77 ~~~f~~lna~~~-------~i~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~---------------qQdaLL~~lE  134 (725)
T PRK13341         77 RAHFSSLNAVLA-------GVKDLRAEVDRAKERLERHGKRTILFIDEVHRFNKA---------------QQDALLPWVE  134 (725)
T ss_pred             cCcceeehhhhh-------hhHHHHHHHHHHHHHhhhcCCceEEEEeChhhCCHH---------------HHHHHHHHhc
Confidence            345666666421       12334455554421     24679999999988321               1234555554


Q ss_pred             CCCCCCCEEEEEEeC-CC-CccchhccCCCCcccEEEecCCCHHHHHHHHHHHHc-------CCCCC-chhhHHHHHHHC
Q psy5642          82 GIVPLNNVTIVAATN-RP-DRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA-------RSPLG-EDVCVEELVRLT  151 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn-~~-~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~-------~~~~~-~~~~~~~la~~t  151 (237)
                      +    +.+++|++|+ .+ ..+++++++  |. ..+.|++++.+++..+++..+.       ...+. ++..+..|+..+
T Consensus       135 ~----g~IiLI~aTTenp~~~l~~aL~S--R~-~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s  207 (725)
T PRK13341        135 N----GTITLIGATTENPYFEVNKALVS--RS-RLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVA  207 (725)
T ss_pred             C----ceEEEEEecCCChHhhhhhHhhc--cc-cceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhC
Confidence            3    5677776653 33 478999998  75 4699999999999999998886       22222 455566677654


Q ss_pred             CCCCcccccch
Q psy5642         152 EGYSGAEQSLS  162 (237)
Q Consensus       152 ~g~s~~Dl~~~  162 (237)
                          ++|+..+
T Consensus       208 ----~GD~R~l  214 (725)
T PRK13341        208 ----NGDARSL  214 (725)
T ss_pred             ----CCCHHHH
Confidence                5564443

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.73  E-value=0.00061  Score=60.28  Aligned_cols=106  Identities=13%  Similarity=0.159  Sum_probs=78.6

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+++.+...    .+.||+|||+|.+..               ...+.++..+++.  ....++|.+|+.+..+.
T Consensus        90 ~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~~---------------~~~~~ll~~le~~--~~~~~~Il~~~~~~kl~  152 (367)
T PRK14970         90 VDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSS---------------AAFNAFLKTLEEP--PAHAIFILATTEKHKII  152 (367)
T ss_pred             HHHHHHHHHHHhhccccCCcEEEEEeChhhcCH---------------HHHHHHHHHHhCC--CCceEEEEEeCCcccCC
Confidence            46777888876542    346999999987732               2356777777762  34566677778889999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      +++++  |+. .++++.|+.++...++...+...+.. ++..+..++..+.
T Consensus       153 ~~l~s--r~~-~v~~~~~~~~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~  200 (367)
T PRK14970        153 PTILS--RCQ-IFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKAD  200 (367)
T ss_pred             HHHHh--cce-eEecCCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCC
Confidence            99998  774 68999999999999999888766653 5667777777654

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

Probab=97.72  E-value=0.00056  Score=60.55  Aligned_cols=80  Identities=24%  Similarity=0.302  Sum_probs=61.6

Q ss_pred             cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCC---ccchhccCCCCcc-cEE
Q psy5642          40 VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPD---RIDKALLRPGRLD-RLI  115 (237)
Q Consensus        40 ~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~---~ld~al~r~gRf~-~~i  115 (237)
                      ..+.||++||+|.|.....            .++-.|+..-+..  ..++.+|+.+|..+   .+|+.+.+  +|. ..|
T Consensus       122 ~~~~IvvLDEid~L~~~~~------------~~LY~L~r~~~~~--~~~v~vi~i~n~~~~~~~ld~rv~s--~l~~~~I  185 (366)
T COG1474         122 GKTVIVILDEVDALVDKDG------------EVLYSLLRAPGEN--KVKVSIIAVSNDDKFLDYLDPRVKS--SLGPSEI  185 (366)
T ss_pred             CCeEEEEEcchhhhccccc------------hHHHHHHhhcccc--ceeEEEEEEeccHHHHHHhhhhhhh--ccCccee
Confidence            3567999999999977642            3455555555554  45799999999864   78999998  763 558


Q ss_pred             EecCCCHHHHHHHHHHHHcC
Q psy5642         116 YVPLPDDLTRAAILKIRLAR  135 (237)
Q Consensus       116 ~~~~P~~~~R~~il~~~l~~  135 (237)
                      .|++-+.+|-.+|++.....
T Consensus       186 ~F~pY~a~el~~Il~~R~~~  205 (366)
T COG1474         186 VFPPYTAEELYDILRERVEE  205 (366)
T ss_pred             eeCCCCHHHHHHHHHHHHHh
Confidence            99999999999999987753

>PRK09087 hypothetical protein; Validated

Probab=97.70  E-value=0.00034  Score=57.79  Aligned_cols=92  Identities=16%  Similarity=0.201  Sum_probs=64.3

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCcc---chhccCCCCcc--cEEEe
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRI---DKALLRPGRLD--RLIYV  117 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~l---d~al~r~gRf~--~~i~~  117 (237)
                      .+|+|||++.+..+             +.   .|...++.....++.+||+++..|..+   .+.+++  ||.  ..+++
T Consensus        89 ~~l~iDDi~~~~~~-------------~~---~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~S--Rl~~gl~~~l  150 (226)
T PRK09087         89 GPVLIEDIDAGGFD-------------ET---GLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKS--RLKAATVVEI  150 (226)
T ss_pred             CeEEEECCCCCCCC-------------HH---HHHHHHHHHHhCCCeEEEECCCChHHhccccccHHH--HHhCCceeec
Confidence            47999999976211             11   233333333333556677776666533   678999  995  78999


Q ss_pred             cCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642         118 PLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus       118 ~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      ..|+.+.|.++++..+...... ++..+..|+.+..
T Consensus       151 ~~pd~e~~~~iL~~~~~~~~~~l~~ev~~~La~~~~  186 (226)
T PRK09087        151 GEPDDALLSQVIFKLFADRQLYVDPHVVYYLVSRME  186 (226)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhh
Confidence            9999999999999999776554 6677777887775

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=97.70  E-value=0.0016  Score=62.09  Aligned_cols=107  Identities=16%  Similarity=0.310  Sum_probs=82.2

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+.+.+...    ...|++|||+|.+..               ...+.|+..|+.  ....+++|.+|+.++.|+
T Consensus       100 vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~---------------~A~NALLKtLEE--PP~~tifILaTte~~KLl  162 (725)
T PRK07133        100 VDEIRELIENVKNLPTQSKYKIYIIDEVHMLSK---------------SAFNALLKTLEE--PPKHVIFILATTEVHKIP  162 (725)
T ss_pred             HHHHHHHHHHHHhchhcCCCEEEEEEChhhCCH---------------HHHHHHHHHhhc--CCCceEEEEEcCChhhhh
Confidence            55577887777653    345999999998732               246788999988  345778888888999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +.|++  |+. .+.|..|+.++....|+..+...+.. .+..+..+|..+.|
T Consensus       163 ~TI~S--Rcq-~ieF~~L~~eeI~~~L~~il~kegI~id~eAl~~LA~lS~G  211 (725)
T PRK07133        163 LTILS--RVQ-RFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLSSG  211 (725)
T ss_pred             HHHHh--hce-eEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            99999  985 79999999999999999887766554 34456677776653

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

Probab=97.68  E-value=0.00066  Score=65.39  Aligned_cols=138  Identities=16%  Similarity=0.177  Sum_probs=85.8

Q ss_pred             eEEEEEecccccc-----c-------ccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHH
Q psy5642           8 TEVVESIGPELFR-----K-------YVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQ   75 (237)
Q Consensus         8 ~~~i~v~~s~l~~-----~-------~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~   75 (237)
                      .+|+.++++++..     +       |+|...  -..+.+..+....+||||||+|.+.+               .+.+.
T Consensus       514 ~~~i~id~se~~~~~~~~~LiG~~~gyvg~~~--~g~L~~~v~~~p~sVlllDEieka~~---------------~v~~~  576 (758)
T PRK11034        514 IELLRFDMSEYMERHTVSRLIGAPPGYVGFDQ--GGLLTDAVIKHPHAVLLLDEIEKAHP---------------DVFNL  576 (758)
T ss_pred             CCcEEeechhhcccccHHHHcCCCCCcccccc--cchHHHHHHhCCCcEEEeccHhhhhH---------------HHHHH
Confidence            5788888876533     1       222110  11222333455568999999999832               36777


Q ss_pred             HHHHhcCCC---------CCCCEEEEEEeCCC-------------------------CccchhccCCCCcccEEEecCCC
Q psy5642          76 MLTEMDGIV---------PLNNVTIVAATNRP-------------------------DRIDKALLRPGRLDRLIYVPLPD  121 (237)
Q Consensus        76 ll~~l~~~~---------~~~~v~vI~ttn~~-------------------------~~ld~al~r~gRf~~~i~~~~P~  121 (237)
                      |++.|++-.         .-.++++|+|||.-                         ..+.|.++.  |+|.+|.|++.+
T Consensus       577 LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~g~~~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~--Rid~ii~f~~L~  654 (758)
T PRK11034        577 LLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLS  654 (758)
T ss_pred             HHHHHhcCeeecCCCceecCCCcEEEEeCCcCHHHHhhcccCcccchhhHHHHHHHHHhcCHHHHc--cCCEEEEcCCCC
Confidence            888776321         11368899999932                         125678888  999999999999


Q ss_pred             HHHHHHHHHHHHcC-------CCCC---chhhHHHHHHHC--CCCCcccccchhH
Q psy5642         122 DLTRAAILKIRLAR-------SPLG---EDVCVEELVRLT--EGYSGAEQSLSKH  164 (237)
Q Consensus       122 ~~~R~~il~~~l~~-------~~~~---~~~~~~~la~~t--~g~s~~Dl~~~~~  164 (237)
                      .++..+|+..++..       .++.   .+..+..|+...  ..|..+.|..+++
T Consensus       655 ~~~l~~I~~~~l~~~~~~l~~~~i~l~~~~~~~~~l~~~~~~~~~GAR~l~r~i~  709 (758)
T PRK11034        655 TDVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPMARVIQ  709 (758)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCceECHHHHHHHHHhCCCCCCCCchHHHHHH
Confidence            99999999876642       1222   455556666543  2344555333333

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.67  E-value=0.00065  Score=57.37  Aligned_cols=75  Identities=23%  Similarity=0.305  Sum_probs=54.9

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC--------------CCCCEEEEEEeCCCC-----cc
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV--------------PLNNVTIVAATNRPD-----RI  101 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--------------~~~~v~vI~ttn~~~-----~l  101 (237)
                      .+.+|+|||++.+-+               .+.+.|+..|++-.              ...+..||+|+|...     .+
T Consensus       105 ~g~~lllDEi~r~~~---------------~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~~~g~~~l  169 (262)
T TIGR02640       105 EGFTLVYDEFTRSKP---------------ETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVEYAGVHET  169 (262)
T ss_pred             cCCEEEEcchhhCCH---------------HHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCccccceecc
Confidence            457999999998622               23455555554311              112567999999753     67


Q ss_pred             chhccCCCCcccEEEecCCCHHHHHHHHHHHH
Q psy5642         102 DKALLRPGRLDRLIYVPLPDDLTRAAILKIRL  133 (237)
Q Consensus       102 d~al~r~gRf~~~i~~~~P~~~~R~~il~~~l  133 (237)
                      ++++++  || ..+++++|+.++-.+|++...
T Consensus       170 ~~aL~~--R~-~~i~i~~P~~~~e~~Il~~~~  198 (262)
T TIGR02640       170 QDALLD--RL-ITIFMDYPDIDTETAILRAKT  198 (262)
T ss_pred             cHHHHh--hc-EEEECCCCCHHHHHHHHHHhh
Confidence            999999  99 579999999999999998875

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

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.67  E-value=0.0005  Score=63.78  Aligned_cols=119  Identities=18%  Similarity=0.286  Sum_probs=86.3

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      .+++++++.      ..+...++.+.+.+...    ...|++|||+|.+..               ...+.|+..|++  
T Consensus        89 d~~ei~~~~------~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~---------------~a~naLLK~LEe--  145 (527)
T PRK14969         89 DLIEVDAAS------NTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSK---------------SAFNAMLKTLEE--  145 (527)
T ss_pred             ceeEeeccc------cCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCCH---------------HHHHHHHHHHhC--
Confidence            456666542      12355677777776542    235999999988732               346789999988  


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      ..+.+.+|.+|++++.+.+.+++  |. ..++|+.|+.++-...+...+...+.. .+..+..++..+.|
T Consensus       146 pp~~~~fIL~t~d~~kil~tI~S--Rc-~~~~f~~l~~~~i~~~L~~il~~egi~~~~~al~~la~~s~G  212 (527)
T PRK14969        146 PPEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAAAG  212 (527)
T ss_pred             CCCCEEEEEEeCChhhCchhHHH--HH-HHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            34577788888889999999998  87 579999999999999999888665544 45566777776643

>PRK05642 DNA replication initiation factor; Validated

Probab=97.67  E-value=0.00077  Score=55.98  Aligned_cols=95  Identities=18%  Similarity=0.233  Sum_probs=63.4

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCcc---chhccCCCCcc--cEEEe
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRI---DKALLRPGRLD--RLIYV  117 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~l---d~al~r~gRf~--~~i~~  117 (237)
                      .+|+|||++.+....             .....|.+.++.....++.++|+++..|..+   .+.+++  ||.  ..+.+
T Consensus        99 d~LiiDDi~~~~~~~-------------~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~S--Rl~~gl~~~l  163 (234)
T PRK05642         99 ELVCLDDLDVIAGKA-------------DWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKS--RLTLALVFQM  163 (234)
T ss_pred             CEEEEechhhhcCCh-------------HHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHH--HHhcCeeeec
Confidence            589999999874432             1123344444444444567788777777644   688999  994  67788


Q ss_pred             cCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642         118 PLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus       118 ~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      ..|+.++|..+++......++. ++..+..|+...+
T Consensus       164 ~~~~~e~~~~il~~ka~~~~~~l~~ev~~~L~~~~~  199 (234)
T PRK05642        164 RGLSDEDKLRALQLRASRRGLHLTDEVGHFILTRGT  199 (234)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcC
Confidence            9999999999999655444333 5555666666553

>CHL00195 ycf46 Ycf46; Provisional

Probab=97.65  E-value=0.00082  Score=61.65  Aligned_cols=121  Identities=16%  Similarity=0.207  Sum_probs=81.6

Q ss_pred             HHHHHHHHHHHhcC---CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchh
Q psy5642          28 RCVRDVFKRARQVS---PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKA  104 (237)
Q Consensus        28 ~~l~~~f~~a~~~~---P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~a  104 (237)
                      +.-..+++......   |+|++|.|++.++.+          ....+.+..+...+..   .++.+|+.+.  ...+|+.
T Consensus        65 ~~p~~al~~i~~~~~~~~~~~vl~d~h~~~~~----------~~~~r~l~~l~~~~~~---~~~~~i~~~~--~~~~p~e  129 (489)
T CHL00195         65 RNPLQALEFIEKLTPETPALFLLKDFNRFLND----------ISISRKLRNLSRILKT---QPKTIIIIAS--ELNIPKE  129 (489)
T ss_pred             ccHHHHHHHHHhcCCCCCcEEEEecchhhhcc----------hHHHHHHHHHHHHHHh---CCCEEEEEcC--CCCCCHH
Confidence            34445555555443   789999999999832          1123444444444444   2344444443  3678888


Q ss_pred             ccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhHHh
Q psy5642         105 LLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus       105 l~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      |.+   +-.++++|+|+.++...+++.+....+.. .+.++..++..+.|+|..+++.+...+
T Consensus       130 l~~---~~~~~~~~lP~~~ei~~~l~~~~~~~~~~~~~~~~~~l~~~~~gls~~~~~~~~~~~  189 (489)
T CHL00195        130 LKD---LITVLEFPLPTESEIKKELTRLIKSLNIKIDSELLENLTRACQGLSLERIRRVLSKI  189 (489)
T ss_pred             HHh---ceeEEeecCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            886   33578999999999999998887654433 678889999999999999955555443

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.64  E-value=0.00042  Score=57.60  Aligned_cols=95  Identities=15%  Similarity=0.212  Sum_probs=62.6

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCC-EEEEEEeCCCCc---cchhccCCCCcc--cEEE
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNN-VTIVAATNRPDR---IDKALLRPGRLD--RLIY  116 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~-v~vI~ttn~~~~---ld~al~r~gRf~--~~i~  116 (237)
                      .+|+|||++.+..+.         .. ...+-.+++.+.   ..++ -+++.+++.|..   +.+.+++  |+.  .++.
T Consensus        99 dlliiDdi~~~~~~~---------~~-~~~lf~l~n~~~---e~g~~~li~ts~~~p~~l~~~~~~L~S--Rl~~g~~~~  163 (235)
T PRK08084         99 SLVCIDNIECIAGDE---------LW-EMAIFDLYNRIL---ESGRTRLLITGDRPPRQLNLGLPDLAS--RLDWGQIYK  163 (235)
T ss_pred             CEEEEeChhhhcCCH---------HH-HHHHHHHHHHHH---HcCCCeEEEeCCCChHHcCcccHHHHH--HHhCCceee
Confidence            589999999885431         11 222333333322   2244 344445555555   5799999  996  8899


Q ss_pred             ecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642         117 VPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus       117 ~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      +..|+.++|.++++......++. ++.-+..|+.+.+
T Consensus       164 l~~~~~~~~~~~l~~~a~~~~~~l~~~v~~~L~~~~~  200 (235)
T PRK08084        164 LQPLSDEEKLQALQLRARLRGFELPEDVGRFLLKRLD  200 (235)
T ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhhc
Confidence            99999999999999866554444 5666677777664

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=97.64  E-value=0.0016  Score=56.97  Aligned_cols=147  Identities=14%  Similarity=0.093  Sum_probs=91.0

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-----------CCCCEEEEEEeCCCC-ccchhccCCCC
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-----------PLNNVTIVAATNRPD-RIDKALLRPGR  110 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vI~ttn~~~-~ld~al~r~gR  110 (237)
                      .+||+||++.+-               ..+.+.++..|+.-.           ...++++|+|+|-.+ .+++++..  |
T Consensus       130 GiL~lDEInrl~---------------~~~q~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP~e~~l~~aLld--R  192 (334)
T PRK13407        130 GYLYIDEVNLLE---------------DHIVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEGELRPQLLD--R  192 (334)
T ss_pred             CeEEecChHhCC---------------HHHHHHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCcccCCCCHHHHh--h
Confidence            599999999872               245666677665321           123689999988644 68999999  9


Q ss_pred             cccEEEecCCCH-HHHHHHHHHHHcCCC--C--------C---chhhHHHHHHHCCCCCccc--ccchhHHhhhhccccC
Q psy5642         111 LDRLIYVPLPDD-LTRAAILKIRLARSP--L--------G---EDVCVEELVRLTEGYSGAE--QSLSKHRAKKIRPRRE  174 (237)
Q Consensus       111 f~~~i~~~~P~~-~~R~~il~~~l~~~~--~--------~---~~~~~~~la~~t~g~s~~D--l~~~~~~a~~~~~~~~  174 (237)
                      |...+.+++|.. ++|.++++.......  .        .   ...++...-.....-.-.|  +..+++-+......  
T Consensus       193 F~~~v~v~~~~~~~e~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~a~~~~~~V~v~~~~~~yi~~l~~~~~~~--  270 (334)
T PRK13407        193 FGLSVEVRSPRDVETRVEVIRRRDAYDADHDAFMAKWGAEDMQLRGRILGARARLPQLKTPNTVLHDCAALCIALGSD--  270 (334)
T ss_pred             cceEEEcCCCCcHHHHHHHHHHhhcccccchhhhccccccccCCHHHHHHHHHhcCCcccCHHHHHHHHHHHHHHCCC--
Confidence            999999999966 899999987543211  0        0   1122222223333333222  44444444433321  


Q ss_pred             CCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHh
Q psy5642         175 SNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQ  217 (237)
Q Consensus       175 ~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~  217 (237)
                             .+.+-..+++.|...++.++  ...|+.+|+..+..
T Consensus       271 -------s~Ra~i~l~~aA~a~A~l~G--r~~V~~~Di~~~~~  304 (334)
T PRK13407        271 -------GLRGELTLLRAARALAAFEG--AEAVGRSHLRSVAT  304 (334)
T ss_pred             -------CchHHHHHHHHHHHHHHHcC--CCeeCHHHHHHHHH
Confidence                   12223346777777777777  44699999977653

>PLN03025 replication factor C subunit; Provisional

Probab=97.63  E-value=0.00053  Score=59.58  Aligned_cols=92  Identities=14%  Similarity=0.161  Sum_probs=68.4

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P  120 (237)
                      .+.|++|||+|.+...               ..+.|+..++...  ....+|.+||.++.+.++|++  |. ..+.|+.|
T Consensus        99 ~~kviiiDE~d~lt~~---------------aq~aL~~~lE~~~--~~t~~il~~n~~~~i~~~L~S--Rc-~~i~f~~l  158 (319)
T PLN03025         99 RHKIVILDEADSMTSG---------------AQQALRRTMEIYS--NTTRFALACNTSSKIIEPIQS--RC-AIVRFSRL  158 (319)
T ss_pred             CeEEEEEechhhcCHH---------------HHHHHHHHHhccc--CCceEEEEeCCccccchhHHH--hh-hcccCCCC
Confidence            3579999999998432               1344556665532  234567788888999999998  87 47999999


Q ss_pred             CHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642         121 DDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus       121 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      +.++....++..+...+.. .+..+..++..+.
T Consensus       159 ~~~~l~~~L~~i~~~egi~i~~~~l~~i~~~~~  191 (319)
T PLN03025        159 SDQEILGRLMKVVEAEKVPYVPEGLEAIIFTAD  191 (319)
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            9999999999988766554 5666777777664

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.63  E-value=0.00059  Score=58.76  Aligned_cols=91  Identities=18%  Similarity=0.231  Sum_probs=67.0

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCC
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPD  121 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~  121 (237)
                      +.+|+|||+|.+...               ....|+..++...  .+..+|.++|.+..+.+.+.+  |+. .++++.|+
T Consensus       103 ~~vviiDe~~~l~~~---------------~~~~L~~~le~~~--~~~~lIl~~~~~~~l~~~l~s--r~~-~~~~~~l~  162 (319)
T PRK00440        103 FKIIFLDEADNLTSD---------------AQQALRRTMEMYS--QNTRFILSCNYSSKIIDPIQS--RCA-VFRFSPLK  162 (319)
T ss_pred             ceEEEEeCcccCCHH---------------HHHHHHHHHhcCC--CCCeEEEEeCCccccchhHHH--Hhh-eeeeCCCC
Confidence            569999999888321               1345666666543  234566677888888888988  876 59999999


Q ss_pred             HHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642         122 DLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus       122 ~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      .++...+++.++...+.. .+..+..++..+.
T Consensus       163 ~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~  194 (319)
T PRK00440        163 KEAVAERLRYIAENEGIEITDDALEAIYYVSE  194 (319)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            999999999988776654 5667777877654

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.62  E-value=0.0015  Score=60.70  Aligned_cols=105  Identities=17%  Similarity=0.251  Sum_probs=77.9

Q ss_pred             HHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccch
Q psy5642          28 RCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDK  103 (237)
Q Consensus        28 ~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~  103 (237)
                      ..++.+.+.+..    ...-|++|||+|.+..               ...+.|+..|++  ..+.+.+|++|+.+..+.+
T Consensus       102 d~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~---------------~a~naLLK~LEe--pp~~v~fIL~Ttd~~kil~  164 (546)
T PRK14957        102 EETKEILDNIQYMPSQGRYKVYLIDEVHMLSK---------------QSFNALLKTLEE--PPEYVKFILATTDYHKIPV  164 (546)
T ss_pred             HHHHHHHHHHHhhhhcCCcEEEEEechhhccH---------------HHHHHHHHHHhc--CCCCceEEEEECChhhhhh
Confidence            345566655543    2345999999988732               346788999987  3356777777788999999


Q ss_pred             hccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642         104 ALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus       104 al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      .|++  |. ..++|..++.++-...++..+...+.. .+..+..++..+.
T Consensus       165 tI~S--Rc-~~~~f~~Ls~~eI~~~L~~il~~egi~~e~~Al~~Ia~~s~  211 (546)
T PRK14957        165 TILS--RC-IQLHLKHISQADIKDQLKIILAKENINSDEQSLEYIAYHAK  211 (546)
T ss_pred             hHHH--he-eeEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            9998  87 579999999999999999888766544 5566677777664

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.61  E-value=0.00064  Score=59.32  Aligned_cols=104  Identities=17%  Similarity=0.309  Sum_probs=76.0

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...+|.+.+.+..    ...-|++||++|.+..               ...+.||..|++  +..++++|.+|++++.+.
T Consensus        88 id~iR~l~~~~~~~~~~~~~kv~iI~~a~~m~~---------------~aaNaLLK~LEE--Pp~~~~fiL~t~~~~~ll  150 (328)
T PRK05707         88 VDQVRELVSFVVQTAQLGGRKVVLIEPAEAMNR---------------NAANALLKSLEE--PSGDTVLLLISHQPSRLL  150 (328)
T ss_pred             HHHHHHHHHHHhhccccCCCeEEEECChhhCCH---------------HHHHHHHHHHhC--CCCCeEEEEEECChhhCc
Confidence            4556666555544    2355899999999833               357899999999  446888999999999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEG  153 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g  153 (237)
                      |.|++  |... +.|+.|+.++-.+.|......   ..+.....++..+.|
T Consensus       151 ~TI~S--Rc~~-~~~~~~~~~~~~~~L~~~~~~---~~~~~~~~~l~la~G  195 (328)
T PRK05707        151 PTIKS--RCQQ-QACPLPSNEESLQWLQQALPE---SDERERIELLTLAGG  195 (328)
T ss_pred             HHHHh--hcee-eeCCCcCHHHHHHHHHHhccc---CChHHHHHHHHHcCC
Confidence            99999  9865 999999999888888765421   123344455555555

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

Probab=97.57  E-value=0.0015  Score=63.11  Aligned_cols=132  Identities=18%  Similarity=0.201  Sum_probs=84.8

Q ss_pred             eEEEEEeccccccc------------ccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHH
Q psy5642           8 TEVVESIGPELFRK------------YVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQ   75 (237)
Q Consensus         8 ~~~i~v~~s~l~~~------------~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~   75 (237)
                      .+++.++++++..+            |+|..+  -..+.+..+....+||+|||+|.+.+               .+.+.
T Consensus       510 ~~~~~~d~se~~~~~~~~~lig~~~gyvg~~~--~~~l~~~~~~~p~~VvllDEieka~~---------------~~~~~  572 (731)
T TIGR02639       510 VHLERFDMSEYMEKHTVSRLIGAPPGYVGFEQ--GGLLTEAVRKHPHCVLLLDEIEKAHP---------------DIYNI  572 (731)
T ss_pred             CCeEEEeCchhhhcccHHHHhcCCCCCcccch--hhHHHHHHHhCCCeEEEEechhhcCH---------------HHHHH
Confidence            46777777765432            333211  12233444556678999999997732               35677


Q ss_pred             HHHHhcCCC---------CCCCEEEEEEeCCCC-------------------------ccchhccCCCCcccEEEecCCC
Q psy5642          76 MLTEMDGIV---------PLNNVTIVAATNRPD-------------------------RIDKALLRPGRLDRLIYVPLPD  121 (237)
Q Consensus        76 ll~~l~~~~---------~~~~v~vI~ttn~~~-------------------------~ld~al~r~gRf~~~i~~~~P~  121 (237)
                      |++.|++-.         .-.+.++|+|||...                         .+.|.++.  |||.+|.|.+.+
T Consensus       573 Ll~~ld~g~~~d~~g~~vd~~~~iii~Tsn~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef~~--Rid~Vi~F~pLs  650 (731)
T TIGR02639       573 LLQVMDYATLTDNNGRKADFRNVILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRN--RLDAIIHFNPLS  650 (731)
T ss_pred             HHHhhccCeeecCCCcccCCCCCEEEECCCcchhhhhhccCCcchhhhHHHHHHHHHhhcChHHHh--cCCeEEEcCCCC
Confidence            788776521         123588999998642                         24677877  999999999999


Q ss_pred             HHHHHHHHHHHHcCC-------C--CC-chhhHHHHHHHC--CCCCccc
Q psy5642         122 DLTRAAILKIRLARS-------P--LG-EDVCVEELVRLT--EGYSGAE  158 (237)
Q Consensus       122 ~~~R~~il~~~l~~~-------~--~~-~~~~~~~la~~t--~g~s~~D  158 (237)
                      .++..+|++..+...       .  +. .+..++.|+...  ..|..+.
T Consensus       651 ~e~l~~Iv~~~L~~l~~~l~~~~~~l~i~~~a~~~La~~~~~~~~GaR~  699 (731)
T TIGR02639       651 EEVLEKIVQKFVDELSKQLNEKNIKLELTDDAKKYLAEKGYDEEFGARP  699 (731)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCeEEeCHHHHHHHHHhCCCcccCchH
Confidence            999999999877531       1  11 455566677642  3444555

>KOG1514|consensus

Probab=97.57  E-value=0.00091  Score=62.61  Aligned_cols=149  Identities=21%  Similarity=0.230  Sum_probs=93.9

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccC---CCCcc-cEEE
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLR---PGRLD-RLIY  116 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r---~gRf~-~~i~  116 (237)
                      .|+||+|||+|.|+...            +.++-.|.+|...  ++.+++||+.+|..+ +|+.++-   ..|.+ ..|.
T Consensus       508 ~~~VvLiDElD~Lvtr~------------QdVlYn~fdWpt~--~~sKLvvi~IaNTmd-lPEr~l~nrvsSRlg~tRi~  572 (767)
T KOG1514|consen  508 STTVVLIDELDILVTRS------------QDVLYNIFDWPTL--KNSKLVVIAIANTMD-LPERLLMNRVSSRLGLTRIC  572 (767)
T ss_pred             CCEEEEeccHHHHhccc------------HHHHHHHhcCCcC--CCCceEEEEeccccc-CHHHHhccchhhhccceeee
Confidence            58899999999998753            5677788887766  456788888888744 4444432   11443 4578


Q ss_pred             ecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHH
Q psy5642         117 VPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALS  196 (237)
Q Consensus       117 ~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~  196 (237)
                      |.+-+.+|-.+|+...|.....-....++-+|.+. +-..+|.+.                        --.+|+.|...
T Consensus       573 F~pYth~qLq~Ii~~RL~~~~~f~~~aielvarkV-AavSGDaRr------------------------aldic~RA~Ei  627 (767)
T KOG1514|consen  573 FQPYTHEQLQEIISARLKGLDAFENKAIELVARKV-AAVSGDARR------------------------ALDICRRAAEI  627 (767)
T ss_pred             cCCCCHHHHHHHHHHhhcchhhcchhHHHHHHHHH-HhccccHHH------------------------HHHHHHHHHHH
Confidence            88889999999999999876433333443344444 444455222                        22445555554


Q ss_pred             HHHhcc-----ccCCccHHHHHHHHhhcCCCCCHHHHH
Q psy5642         197 ALENNL-----EAAYVSHQDFLTALQLVKPRTPPQLIK  229 (237)
Q Consensus       197 ~~~~~~-----~~~~v~~~df~~al~~~~p~~~~~~~~  229 (237)
                      +-.+..     ....|+.-++.+|+..+..+..-..+.
T Consensus       628 a~~~~~~~k~~~~q~v~~~~v~~Ai~em~~~~~~~~i~  665 (767)
T KOG1514|consen  628 AEERNVKGKLAVSQLVGILHVMEAINEMLASPYIKALK  665 (767)
T ss_pred             hhhhcccccccccceeehHHHHHHHHHHhhhhHHHHhc
Confidence            444332     124567778888877776655444443

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.54  E-value=0.00062  Score=59.93  Aligned_cols=93  Identities=13%  Similarity=0.137  Sum_probs=68.1

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P  120 (237)
                      ..-|++|||+|.+..               ...+.||..|++.  ..+.++|..|+.++.+.+.+++  |+ ..+.|++|
T Consensus       141 ~~rVviIDeAd~l~~---------------~aanaLLk~LEEp--p~~~~fiLit~~~~~llptIrS--Rc-~~i~l~pl  200 (351)
T PRK09112        141 NWRIVIIDPADDMNR---------------NAANAILKTLEEP--PARALFILISHSSGRLLPTIRS--RC-QPISLKPL  200 (351)
T ss_pred             CceEEEEEchhhcCH---------------HHHHHHHHHHhcC--CCCceEEEEECChhhccHHHHh--hc-cEEEecCC
Confidence            456999999999832               2367788888873  3456667777889999999999  88 58999999


Q ss_pred             CHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCC
Q psy5642         121 DDLTRAAILKIRLARSPLGEDVCVEELVRLTEGY  154 (237)
Q Consensus       121 ~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~  154 (237)
                      +.++-..+|......... .+..+..++..+.|-
T Consensus       201 ~~~~~~~~L~~~~~~~~~-~~~~~~~i~~~s~G~  233 (351)
T PRK09112        201 DDDELKKALSHLGSSQGS-DGEITEALLQRSKGS  233 (351)
T ss_pred             CHHHHHHHHHHhhcccCC-CHHHHHHHHHHcCCC
Confidence            999999999874332221 234456666666543

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=97.53  E-value=0.0014  Score=58.64  Aligned_cols=84  Identities=21%  Similarity=0.325  Sum_probs=61.9

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC--------CCCCEEEEEEeC----CCCccchhccCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV--------PLNNVTIVAATN----RPDRIDKALLRP  108 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--------~~~~v~vI~ttn----~~~~ld~al~r~  108 (237)
                      +..||||||+|.++......+.   +....-+...||..+++..        ..++|++|++-.    .|++|=|.|.. 
T Consensus       247 ~~GIVfiDEiDKIa~~~~~~~~---DvS~eGVQ~~LLkilEGt~v~~k~~~v~T~~ILFI~~GAF~~~kp~DlIPEl~G-  322 (441)
T TIGR00390       247 QSGIIFIDEIDKIAKKGESSGA---DVSREGVQRDLLPIVEGSTVNTKYGMVKTDHILFIAAGAFQLAKPSDLIPELQG-  322 (441)
T ss_pred             cCCEEEEEchhhhcccCCCCCC---CCCccchhccccccccCceeeecceeEECCceeEEecCCcCCCChhhccHHHhC-
Confidence            4589999999999976532211   1112346777888887632        345788998865    46677777776 


Q ss_pred             CCcccEEEecCCCHHHHHHHH
Q psy5642         109 GRLDRLIYVPLPDDLTRAAIL  129 (237)
Q Consensus       109 gRf~~~i~~~~P~~~~R~~il  129 (237)
                       ||.-++.+..++.++-..||
T Consensus       323 -R~Pi~v~L~~L~~edL~rIL  342 (441)
T TIGR00390       323 -RFPIRVELQALTTDDFERIL  342 (441)
T ss_pred             -ccceEEECCCCCHHHHHHHh
Confidence             99999999999999998888

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.

>KOG0741|consensus

Probab=97.53  E-value=0.00053  Score=62.39  Aligned_cols=119  Identities=17%  Similarity=0.213  Sum_probs=87.3

Q ss_pred             CCceEEEEE-ecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           5 GGLTEVVES-IGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         5 ~~~~~~i~v-~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      .+..||+.+ ++.++.+......-..++++|+-|++..-+||++|+++.|.---.     -...+++.++..|+..+...
T Consensus       561 ~S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYkS~lsiivvDdiErLiD~vp-----IGPRfSN~vlQaL~VllK~~  635 (744)
T KOG0741|consen  561 SSDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKSPLSIIVVDDIERLLDYVP-----IGPRFSNLVLQALLVLLKKQ  635 (744)
T ss_pred             hcCCCeEEEeChHHccCccHHHHHHHHHHHHHHhhcCcceEEEEcchhhhhcccc-----cCchhhHHHHHHHHHHhccC
Confidence            356788875 556676666667778899999999999899999999999863211     12356678899999999988


Q ss_pred             CCCC-CEEEEEEeCCCCccch-hccCCCCcccEEEecCCCH-HHHHHHHH
Q psy5642          84 VPLN-NVTIVAATNRPDRIDK-ALLRPGRLDRLIYVPLPDD-LTRAAILK  130 (237)
Q Consensus        84 ~~~~-~v~vI~ttn~~~~ld~-al~r~gRf~~~i~~~~P~~-~~R~~il~  130 (237)
                      .+.+ +.+|++||+..+-|.+ .+..  +|+..+++|..+. ++-.+++.
T Consensus       636 ppkg~kLli~~TTS~~~vL~~m~i~~--~F~~~i~Vpnl~~~~~~~~vl~  683 (744)
T KOG0741|consen  636 PPKGRKLLIFGTTSRREVLQEMGILD--CFSSTIHVPNLTTGEQLLEVLE  683 (744)
T ss_pred             CCCCceEEEEecccHHHHHHHcCHHH--hhhheeecCccCchHHHHHHHH
Confidence            7765 5888888887665533 3455  8999999998755 55555554

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.51  E-value=0.004  Score=58.88  Aligned_cols=109  Identities=17%  Similarity=0.216  Sum_probs=81.6

Q ss_pred             hHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCc
Q psy5642          25 ESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDR  100 (237)
Q Consensus        25 ~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~  100 (237)
                      .+...++.+.+.+...    ..-|++|||+|.+..               ...+.|+..|++  ....+++|++|++++.
T Consensus       101 ~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~---------------~a~naLLK~LEe--Pp~~tvfIL~t~~~~~  163 (620)
T PRK14948        101 TGVDNIRELIERAQFAPVQARWKVYVIDECHMLST---------------AAFNALLKTLEE--PPPRVVFVLATTDPQR  163 (620)
T ss_pred             CCHHHHHHHHHHHhhChhcCCceEEEEECccccCH---------------HHHHHHHHHHhc--CCcCeEEEEEeCChhh
Confidence            4467888888877642    235999999998822               346788999987  3456788888888999


Q ss_pred             cchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         101 IDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       101 ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +-+.|++  |.. .++|+.++.++-...+.....+.+.. ....+..++..+.|
T Consensus       164 llpTIrS--Rc~-~~~f~~l~~~ei~~~L~~ia~kegi~is~~al~~La~~s~G  214 (620)
T PRK14948        164 VLPTIIS--RCQ-RFDFRRIPLEAMVQHLSEIAEKESIEIEPEALTLVAQRSQG  214 (620)
T ss_pred             hhHHHHh--hee-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Confidence            9999998  874 58999999988888888777665443 34557777777654

>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=97.51  E-value=0.00035  Score=52.13  Aligned_cols=95  Identities=32%  Similarity=0.442  Sum_probs=62.3

Q ss_pred             ceEEEEEecccccccccChHHHH---HHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERC---VRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~---l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      +.+++.++++.............   ....+..+....+.+|++||++.+..               .....++..+...
T Consensus        47 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lilDe~~~~~~---------------~~~~~~~~~i~~~  111 (151)
T cd00009          47 GAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSR---------------GAQNALLRVLETL  111 (151)
T ss_pred             CCCeEEEehhhhhhhhHHHHHhhhhhHhHHHHhhccCCCeEEEEeChhhhhH---------------HHHHHHHHHHHhc
Confidence            46788888877665544433332   12333444455789999999998711               1234455555444


Q ss_pred             CC----CCCEEEEEEeCCCC--ccchhccCCCCcccEEEec
Q psy5642          84 VP----LNNVTIVAATNRPD--RIDKALLRPGRLDRLIYVP  118 (237)
Q Consensus        84 ~~----~~~v~vI~ttn~~~--~ld~al~r~gRf~~~i~~~  118 (237)
                      ..    ..++.+|++++...  .+++.+..  ||+.+++++
T Consensus       112 ~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~--r~~~~i~~~  150 (151)
T cd00009         112 NDLRIDRENVRVIGATNRPLLGDLDRALYD--RLDIRIVIP  150 (151)
T ss_pred             CceeccCCCeEEEEecCccccCCcChhHHh--hhccEeecC
Confidence            32    35788899998877  78888888  998888776

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.

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

Probab=97.50  E-value=0.0015  Score=58.46  Aligned_cols=84  Identities=21%  Similarity=0.362  Sum_probs=62.6

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC--------CCCCCEEEEEEeC----CCCccchhccCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI--------VPLNNVTIVAATN----RPDRIDKALLRP  108 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~--------~~~~~v~vI~ttn----~~~~ld~al~r~  108 (237)
                      +-.||||||||.++...++.+   .+....-+...||..+++.        ...++|++|++-.    .|++|=|.|.. 
T Consensus       249 ~~GIVfiDEiDKIa~~~~~~~---~DvS~eGVQ~~LLki~EG~~v~~k~~~i~T~~ILFI~~GAF~~~kp~DlIPEl~G-  324 (443)
T PRK05201        249 QNGIVFIDEIDKIAARGGSSG---PDVSREGVQRDLLPLVEGSTVSTKYGMVKTDHILFIASGAFHVSKPSDLIPELQG-  324 (443)
T ss_pred             cCCEEEEEcchhhcccCCCCC---CCCCccchhcccccccccceeeecceeEECCceeEEecCCcCCCChhhccHHHhC-
Confidence            458999999999997654321   1112244677788888773        2345788888764    46777788887 


Q ss_pred             CCcccEEEecCCCHHHHHHHH
Q psy5642         109 GRLDRLIYVPLPDDLTRAAIL  129 (237)
Q Consensus       109 gRf~~~i~~~~P~~~~R~~il  129 (237)
                       ||.-++.+..++.++-..||
T Consensus       325 -R~Pi~v~L~~L~~~dL~~IL  344 (443)
T PRK05201        325 -RFPIRVELDALTEEDFVRIL  344 (443)
T ss_pred             -ccceEEECCCCCHHHHHHHh
Confidence             99999999999999998888

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=97.50  E-value=0.0029  Score=55.44  Aligned_cols=148  Identities=13%  Similarity=0.103  Sum_probs=87.7

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-----------CCCCEEEEEEeCCCC-ccchhccCCC
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-----------PLNNVTIVAATNRPD-RIDKALLRPG  109 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vI~ttn~~~-~ld~al~r~g  109 (237)
                      ..+|||||++.+-               ..+.+.|+..|+.-.           ...++++|+|.|-.+ .+++++..  
T Consensus       132 ~GvL~lDEi~~L~---------------~~~Q~~Ll~~l~~g~~~v~r~G~~~~~~~r~iviat~np~eg~l~~~Lld--  194 (337)
T TIGR02030       132 RGILYIDEVNLLE---------------DHLVDVLLDVAASGWNVVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--  194 (337)
T ss_pred             CCEEEecChHhCC---------------HHHHHHHHHHHHhCCeEEEECCEEEEcCCCEEEEeccccccCCCCHHHHh--
Confidence            4799999999872               234556666664311           123588888888544 69999999  


Q ss_pred             CcccEEEecCCCH-HHHHHHHHHHHcCC--CCC--------c---hhhHHHHHHHCCCCCccc--ccchhHHhhhhcccc
Q psy5642         110 RLDRLIYVPLPDD-LTRAAILKIRLARS--PLG--------E---DVCVEELVRLTEGYSGAE--QSLSKHRAKKIRPRR  173 (237)
Q Consensus       110 Rf~~~i~~~~P~~-~~R~~il~~~l~~~--~~~--------~---~~~~~~la~~t~g~s~~D--l~~~~~~a~~~~~~~  173 (237)
                      ||...+.+++|.. ++|.+|++......  +..        .   ...+...-+....-.-.|  +..+++-+...... 
T Consensus       195 Rf~l~i~l~~p~~~eer~eIL~~~~~~~~~~~~~~~~~~~e~~~~~~~I~~a~~~~~~V~v~d~~~~~i~~l~~~~~~~-  273 (337)
T TIGR02030       195 RFGLHAEIRTVRDVELRVEIVERRTEYDADPHAFCEKWQTEQEALQAKIVNAQNLLPQVTIPYDVLVKVAELCAELDVD-  273 (337)
T ss_pred             hcceEEECCCCCCHHHHHHHHHhhhhcccCchhhhhhhhhhhhcCHHHHHHHHHHhccCcCCHHHHHHHHHHHHHHCCC-
Confidence            9999999999976 89999998754321  000        0   011111111112211111  33344434332211 


Q ss_pred             CCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHh
Q psy5642         174 ESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQ  217 (237)
Q Consensus       174 ~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~  217 (237)
                              ++.+-..+++-|...+..++  ...|+.+|+..+..
T Consensus       274 --------s~Ra~i~l~raArA~Aal~G--R~~V~~dDv~~~a~  307 (337)
T TIGR02030       274 --------GLRGELTLNRAAKALAAFEG--RTEVTVDDIRRVAV  307 (337)
T ss_pred             --------CCcHHHHHHHHHHHHHHHcC--CCCCCHHHHHHHHH
Confidence                    12235566666777777666  45699999998865

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.

>smart00350 MCM minichromosome maintenance proteins

Probab=97.45  E-value=0.0029  Score=58.54  Aligned_cols=160  Identities=15%  Similarity=0.136  Sum_probs=94.7

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-----------CCCCEEEEEEeCCCC-----------
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-----------PLNNVTIVAATNRPD-----------   99 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vI~ttn~~~-----------   99 (237)
                      ..+++|||+|.+-.               .....|+..|++-.           -..+..||||+|-..           
T Consensus       301 ~Gil~iDEi~~l~~---------------~~q~~L~e~me~~~i~i~k~G~~~~l~~~~~viAa~NP~~g~y~~~~~~~~  365 (509)
T smart00350      301 NGVCCIDEFDKMDD---------------SDRTAIHEAMEQQTISIAKAGITTTLNARCSVLAAANPIGGRYDPKLTPEE  365 (509)
T ss_pred             CCEEEEechhhCCH---------------HHHHHHHHHHhcCEEEEEeCCEEEEecCCcEEEEEeCCCCcccCCCcChhh
Confidence            46899999988732               23444555554321           123688999999643           


Q ss_pred             --ccchhccCCCCcccEEEe-cCCCHHHHHHHHHHHHcCCCC------------CchhhHHH---HHHH-C-CCCCcccc
Q psy5642         100 --RIDKALLRPGRLDRLIYV-PLPDDLTRAAILKIRLARSPL------------GEDVCVEE---LVRL-T-EGYSGAEQ  159 (237)
Q Consensus       100 --~ld~al~r~gRf~~~i~~-~~P~~~~R~~il~~~l~~~~~------------~~~~~~~~---la~~-t-~g~s~~Dl  159 (237)
                        .+++++++  |||..+.+ +.|+.+...+|.++.+..+..            -+...+..   .|+. . .-++..-.
T Consensus       366 n~~l~~~lLs--RFdLi~~~~d~~~~~~d~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~l~~yi~~ar~~~~P~ls~~~~  443 (509)
T smart00350      366 NIDLPAPILS--RFDLLFVVLDEVDEERDRELAKHVVDLHRYSHPEPDEADEVPISQEFLRKYIAYAREKIKPKLSEEAA  443 (509)
T ss_pred             ccCCChHHhC--ceeeEEEecCCCChHHHHHHHHHHHHhhcccCccccccccccCCHHHHHHHHHHHHhcCCCCCCHHHH
Confidence              69999999  99986555 689999999999986643210            01112222   2332 1 22333334


Q ss_pred             cchhHHhhhhccccCCC---CCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcC
Q psy5642         160 SLSKHRAKKIRPRRESN---PGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVK  220 (237)
Q Consensus       160 ~~~~~~a~~~~~~~~~~---~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~  220 (237)
                      ..+++.+...+......   .....+...+..+++-|-..|..+.  ...|+.+|+..|++-+.
T Consensus       444 ~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~--r~~V~~~Dv~~ai~l~~  505 (509)
T smart00350      444 EKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRL--SDVVEEADVEEAIRLLR  505 (509)
T ss_pred             HHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcC--CCccCHHHHHHHHHHHH
Confidence            44555554444322111   1233444556666666666665554  34699999999987654

>KOG2028|consensus

Probab=97.42  E-value=0.0039  Score=54.63  Aligned_cols=97  Identities=24%  Similarity=0.416  Sum_probs=69.2

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHhc-----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQV-----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~-----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      .|++++..+       .+.+-+|++|+.++..     ..+|||||||+.+....               ...||-.++. 
T Consensus       192 rfvelSAt~-------a~t~dvR~ife~aq~~~~l~krkTilFiDEiHRFNksQ---------------QD~fLP~VE~-  248 (554)
T KOG2028|consen  192 RFVELSATN-------AKTNDVRDIFEQAQNEKSLTKRKTILFIDEIHRFNKSQ---------------QDTFLPHVEN-  248 (554)
T ss_pred             EEEEEeccc-------cchHHHHHHHHHHHHHHhhhcceeEEEeHHhhhhhhhh---------------hhcccceecc-
Confidence            366666643       2478899999999863     57899999999984321               2234444433 


Q ss_pred             CCCCCEEEEEEe-CCCC-ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHc
Q psy5642          84 VPLNNVTIVAAT-NRPD-RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA  134 (237)
Q Consensus        84 ~~~~~v~vI~tt-n~~~-~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~  134 (237)
                         +.|++||+| -+|+ .+..+|++  |. .++.+.......-..||..-+.
T Consensus       249 ---G~I~lIGATTENPSFqln~aLlS--RC-~VfvLekL~~n~v~~iL~raia  295 (554)
T KOG2028|consen  249 ---GDITLIGATTENPSFQLNAALLS--RC-RVFVLEKLPVNAVVTILMRAIA  295 (554)
T ss_pred             ---CceEEEecccCCCccchhHHHHh--cc-ceeEeccCCHHHHHHHHHHHHH
Confidence               678888776 3454 88999998  76 4688888888888899887443

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.41  E-value=0.0015  Score=57.79  Aligned_cols=103  Identities=16%  Similarity=0.133  Sum_probs=73.7

Q ss_pred             HHHHHHHHHHH----hcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccch
Q psy5642          28 RCVRDVFKRAR----QVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDK  103 (237)
Q Consensus        28 ~~l~~~f~~a~----~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~  103 (237)
                      ..++.+-+.+.    ...|-|++|||+|.+.               ....+.|+..+++  ...+.++|.+|+.++.+.+
T Consensus       124 dqiR~l~~~~~~~~~~~~~kVviIDead~m~---------------~~aanaLLK~LEe--pp~~~~~IL~t~~~~~llp  186 (365)
T PRK07471        124 DEVRELISFFGLTAAEGGWRVVIVDTADEMN---------------ANAANALLKVLEE--PPARSLFLLVSHAPARLLP  186 (365)
T ss_pred             HHHHHHHHHhCcCcccCCCEEEEEechHhcC---------------HHHHHHHHHHHhc--CCCCeEEEEEECCchhchH
Confidence            44555555444    2357899999999872               2357889999987  3356778889999999999


Q ss_pred             hccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCC
Q psy5642         104 ALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEG  153 (237)
Q Consensus       104 al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g  153 (237)
                      .+++  |.. .+.|+.|+.++-.++|......   ..+..+..++..+.|
T Consensus       187 ti~S--Rc~-~i~l~~l~~~~i~~~L~~~~~~---~~~~~~~~l~~~s~G  230 (365)
T PRK07471        187 TIRS--RCR-KLRLRPLAPEDVIDALAAAGPD---LPDDPRAALAALAEG  230 (365)
T ss_pred             Hhhc--cce-EEECCCCCHHHHHHHHHHhccc---CCHHHHHHHHHHcCC
Confidence            9998  875 6999999999999999875422   122233455555554

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

Probab=97.41  E-value=0.00069  Score=62.11  Aligned_cols=138  Identities=20%  Similarity=0.252  Sum_probs=103.2

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      ....++++|+..=      .+-..+|.+-+.+..    ...-|.+|||++-|.               ....+.||..++
T Consensus        86 ~~~DviEiDaASn------~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS---------------~~afNALLKTLE  144 (515)
T COG2812          86 SLIDVIEIDAASN------TGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLS---------------KQAFNALLKTLE  144 (515)
T ss_pred             Ccccchhhhhhhc------cChHHHHHHHHHhccCCccccceEEEEecHHhhh---------------HHHHHHHhcccc
Confidence            3455666666422      246667777777664    234599999999883               345789999999


Q ss_pred             CCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccccc
Q psy5642          82 GIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQS  160 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~  160 (237)
                      +  +..+|++|.+|..+..+|+.+++  |.. .+.|...+.++....|...+.+..+. .+..+.-+|...+| +.+|..
T Consensus       145 E--PP~hV~FIlATTe~~Kip~TIlS--Rcq-~f~fkri~~~~I~~~L~~i~~~E~I~~e~~aL~~ia~~a~G-s~RDal  218 (515)
T COG2812         145 E--PPSHVKFILATTEPQKIPNTILS--RCQ-RFDFKRLDLEEIAKHLAAILDKEGINIEEDALSLIARAAEG-SLRDAL  218 (515)
T ss_pred             c--CccCeEEEEecCCcCcCchhhhh--ccc-cccccCCCHHHHHHHHHHHHHhcCCccCHHHHHHHHHHcCC-ChhhHH
Confidence            8  55689999999999999999999  986 48999999999999999999887776 56677778888876 446644


Q ss_pred             chhHHhhhhc
Q psy5642         161 LSKHRAKKIR  170 (237)
Q Consensus       161 ~~~~~a~~~~  170 (237)
                      .+.+.+....
T Consensus       219 slLDq~i~~~  228 (515)
T COG2812         219 SLLDQAIAFG  228 (515)
T ss_pred             HHHHHHHHcc
Confidence            5555554443

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.39  E-value=0.0033  Score=59.14  Aligned_cols=111  Identities=18%  Similarity=0.207  Sum_probs=79.3

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+.+.+...    ...|++|||+|.+..               ...+.|+..|++..  ...++|.+++.++.+.
T Consensus       102 vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~---------------~a~naLLk~LEepp--~~tv~Il~t~~~~kll  164 (585)
T PRK14950        102 VDDAREIIERVQFRPALARYKVYIIDEVHMLST---------------AAFNALLKTLEEPP--PHAIFILATTEVHKVP  164 (585)
T ss_pred             HHHHHHHHHHHhhCcccCCeEEEEEeChHhCCH---------------HHHHHHHHHHhcCC--CCeEEEEEeCChhhhh
Confidence            34456655554432    345999999988732               34677888888843  4567777778888899


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      +.+++  |+. .++|+.++..+...+++..+...+.. .+..+..++..+.| +.++
T Consensus       165 ~tI~S--R~~-~i~f~~l~~~el~~~L~~~a~~egl~i~~eal~~La~~s~G-dlr~  217 (585)
T PRK14950        165 ATILS--RCQ-RFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIARAATG-SMRD  217 (585)
T ss_pred             HHHHh--ccc-eeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHH
Confidence            99988  875 58999999999999999888766543 45567777777755 4444

>PRK06620 hypothetical protein; Validated

Probab=97.32  E-value=0.0024  Score=52.35  Aligned_cols=89  Identities=11%  Similarity=0.216  Sum_probs=62.4

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCc--cchhccCCCCcc--cEEEe
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDR--IDKALLRPGRLD--RLIYV  117 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~--ld~al~r~gRf~--~~i~~  117 (237)
                      ..+|+|||+|.+       +        ...+-.+.+.+.   ..++.++|+++..|..  + +++++  |+.  .++.+
T Consensus        86 ~d~lliDdi~~~-------~--------~~~lf~l~N~~~---e~g~~ilits~~~p~~l~l-~~L~S--Rl~~gl~~~l  144 (214)
T PRK06620         86 YNAFIIEDIENW-------Q--------EPALLHIFNIIN---EKQKYLLLTSSDKSRNFTL-PDLSS--RIKSVLSILL  144 (214)
T ss_pred             CCEEEEeccccc-------h--------HHHHHHHHHHHH---hcCCEEEEEcCCCccccch-HHHHH--HHhCCceEee
Confidence            468999999943       0        122334444443   3356778888777665  5 78999  985  46899


Q ss_pred             cCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHC
Q psy5642         118 PLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLT  151 (237)
Q Consensus       118 ~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t  151 (237)
                      ..|+.+.+..+++......++. ++..+.-|+...
T Consensus       145 ~~pd~~~~~~~l~k~~~~~~l~l~~ev~~~L~~~~  179 (214)
T PRK06620        145 NSPDDELIKILIFKHFSISSVTISRQIIDFLLVNL  179 (214)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence            9999999999999887755443 566667777766

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.30  E-value=0.0027  Score=62.15  Aligned_cols=132  Identities=23%  Similarity=0.265  Sum_probs=82.9

Q ss_pred             ceEEEEEeccccccc------------ccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHH
Q psy5642           7 LTEVVESIGPELFRK------------YVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA   74 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~------------~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~   74 (237)
                      ...++.++++++...            |+|..+..  .+....+...++||+|||+|..-               ..+.+
T Consensus       624 ~~~~~~~dmse~~~~~~~~~l~g~~~gyvg~~~~g--~L~~~v~~~p~svvllDEieka~---------------~~v~~  686 (852)
T TIGR03345       624 EQNLITINMSEFQEAHTVSRLKGSPPGYVGYGEGG--VLTEAVRRKPYSVVLLDEVEKAH---------------PDVLE  686 (852)
T ss_pred             CcceEEEeHHHhhhhhhhccccCCCCCcccccccc--hHHHHHHhCCCcEEEEechhhcC---------------HHHHH
Confidence            456778887765322            44432211  12344455677999999998642               24567


Q ss_pred             HHHHHhcCCC---------CCCCEEEEEEeCCCC-----------------------------ccchhccCCCCcccEEE
Q psy5642          75 QMLTEMDGIV---------PLNNVTIVAATNRPD-----------------------------RIDKALLRPGRLDRLIY  116 (237)
Q Consensus        75 ~ll~~l~~~~---------~~~~v~vI~ttn~~~-----------------------------~ld~al~r~gRf~~~i~  116 (237)
                      .|++.++.-.         .-.+.++|.|||...                             .+.|+++.  |++ +|.
T Consensus       687 ~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSNlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEfln--Ri~-iI~  763 (852)
T TIGR03345       687 LFYQVFDKGVMEDGEGREIDFKNTVILLTSNAGSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLG--RMT-VIP  763 (852)
T ss_pred             HHHHHhhcceeecCCCcEEeccccEEEEeCCCchHHHHHhccCcccCcchHHHHHHHHHHHHHhccHHHhc--cee-EEE
Confidence            7777776422         114688999988522                             14577777  897 899


Q ss_pred             ecCCCHHHHHHHHHHHHcCC--------CCC---chhhHHHHHHHCCC--CCccc
Q psy5642         117 VPLPDDLTRAAILKIRLARS--------PLG---EDVCVEELVRLTEG--YSGAE  158 (237)
Q Consensus       117 ~~~P~~~~R~~il~~~l~~~--------~~~---~~~~~~~la~~t~g--~s~~D  158 (237)
                      |.+.+.++-..|+...+...        +..   .+..++.|+..+.+  |..+.
T Consensus       764 F~pLs~e~l~~Iv~~~L~~l~~rl~~~~gi~l~i~d~a~~~La~~g~~~~~GAR~  818 (852)
T TIGR03345       764 YLPLDDDVLAAIVRLKLDRIARRLKENHGAELVYSEALVEHIVARCTEVESGARN  818 (852)
T ss_pred             eCCCCHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHHHHHHcCCCCCChHH
Confidence            99999999999998766431        221   44556667776533  34444

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.

>KOG0989|consensus

Probab=97.30  E-value=0.0021  Score=54.82  Aligned_cols=125  Identities=17%  Similarity=0.207  Sum_probs=86.4

Q ss_pred             EEEEEecccccccccC-hHHHHHHHHHHHHHh--cCC----eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           9 EVVESIGPELFRKYVG-ESERCVRDVFKRARQ--VSP----SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g-~~~~~l~~~f~~a~~--~~P----~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      .+++...|+..++.++ +.-++..++-..-..  ..|    -|++|||+|.+..               ..-+.|...|+
T Consensus        90 rvl~lnaSderGisvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmts---------------daq~aLrr~mE  154 (346)
T KOG0989|consen   90 RVLELNASDERGISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTS---------------DAQAALRRTME  154 (346)
T ss_pred             chhhhcccccccccchhhhhcCHHHHhhccccccCCCCCcceEEEEechhhhhH---------------HHHHHHHHHHh
Confidence            3445555655555433 333333333332211  122    4999999999843               24567788888


Q ss_pred             CCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642          82 GIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      ..  ...+.+|..||+++.|+..+.+  |..+ +.|+....+....-|+....+..++ .+..+..++..++|
T Consensus       155 ~~--s~~trFiLIcnylsrii~pi~S--RC~K-frFk~L~d~~iv~rL~~Ia~~E~v~~d~~al~~I~~~S~G  222 (346)
T KOG0989|consen  155 DF--SRTTRFILICNYLSRIIRPLVS--RCQK-FRFKKLKDEDIVDRLEKIASKEGVDIDDDALKLIAKISDG  222 (346)
T ss_pred             cc--ccceEEEEEcCChhhCChHHHh--hHHH-hcCCCcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Confidence            83  3578899999999999999999  9876 8888888888888888888777766 66677778886654

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=97.28  E-value=0.00072  Score=59.26  Aligned_cols=86  Identities=19%  Similarity=0.236  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      -..++.+.+.+...    .--|++||++|.+..               ...|.||+.|++  +..++++|.+|++++.|.
T Consensus       114 idqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~---------------~AaNaLLKtLEE--Pp~~t~fiL~t~~~~~LL  176 (342)
T PRK06964        114 IEQVRALLDFCGVGTHRGGARVVVLYPAEALNV---------------AAANALLKTLEE--PPPGTVFLLVSARIDRLL  176 (342)
T ss_pred             HHHHHHHHHHhccCCccCCceEEEEechhhcCH---------------HHHHHHHHHhcC--CCcCcEEEEEECChhhCc
Confidence            45666666655432    234999999999833               357899999998  557899999999999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHH
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIR  132 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~  132 (237)
                      |.|++  |. ..+.|++|+.++..+.|...
T Consensus       177 pTI~S--Rc-q~i~~~~~~~~~~~~~L~~~  203 (342)
T PRK06964        177 PTILS--RC-RQFPMTVPAPEAAAAWLAAQ  203 (342)
T ss_pred             HHHHh--cC-EEEEecCCCHHHHHHHHHHc
Confidence            99999  98 47999999999988888753

>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=97.28  E-value=0.002  Score=52.38  Aligned_cols=119  Identities=20%  Similarity=0.282  Sum_probs=70.7

Q ss_pred             ChHHHHHHHHHHHHHhcC-CeEEEEccccccc-cccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCcc
Q psy5642          24 GESERCVRDVFKRARQVS-PSVIFFDELDSLA-GERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRI  101 (237)
Q Consensus        24 g~~~~~l~~~f~~a~~~~-P~il~iDeid~l~-~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~l  101 (237)
                      ......+..+++...... +.||+|||++.+. ...  .        ...++..+.+.++......++.+|.+++.....
T Consensus       100 ~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~--~--------~~~~~~~l~~~~~~~~~~~~~~~v~~~S~~~~~  169 (234)
T PF01637_consen  100 EDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASE--E--------DKDFLKSLRSLLDSLLSQQNVSIVITGSSDSLM  169 (234)
T ss_dssp             GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTT--T--------THHHHHHHHHHHHH----TTEEEEEEESSHHHH
T ss_pred             hhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhccc--c--------hHHHHHHHHHHHhhccccCCceEEEECCchHHH
Confidence            345677788888877653 4899999999998 221  1        145667777777775555666666666553322


Q ss_pred             c------hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCC-C-CchhhHHHHHHHCCCCC
Q psy5642         102 D------KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSP-L-GEDVCVEELVRLTEGYS  155 (237)
Q Consensus       102 d------~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~-~-~~~~~~~~la~~t~g~s  155 (237)
                      .      ..+..  |+.. +.+++.+.++..++++..+.... + .++.++..+...|.|+.
T Consensus       170 ~~~~~~~~~~~~--~~~~-~~l~~l~~~e~~~~~~~~~~~~~~~~~~~~~~~~i~~~~gG~P  228 (234)
T PF01637_consen  170 EEFLDDKSPLFG--RFSH-IELKPLSKEEAREFLKELFKELIKLPFSDEDIEEIYSLTGGNP  228 (234)
T ss_dssp             HHTT-TTSTTTT-----E-EEE----HHHHHHHHHHHHHCC------HHHHHHHHHHHTT-H
T ss_pred             HHhhcccCcccc--ccce-EEEeeCCHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHhCCCH
Confidence            2      22333  7777 99999999999999999876652 1 26888999999998864

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

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

Probab=97.26  E-value=0.0019  Score=55.94  Aligned_cols=97  Identities=23%  Similarity=0.362  Sum_probs=69.2

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC--------CCCCCEEEEEEe---
Q psy5642          27 ERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI--------VPLNNVTIVAAT---   95 (237)
Q Consensus        27 ~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~--------~~~~~v~vI~tt---   95 (237)
                      +..-+.+.+.|..  -.||||||||.++...+..+.   +....-+...+|-.+.+.        ...+.|++||+-   
T Consensus       238 e~i~~eAi~~aE~--~GIvFIDEIDKIa~~~~~g~~---dvSREGVQRDlLPlvEGstV~TKyG~VkTdHILFIasGAFh  312 (444)
T COG1220         238 EEIKQEAIDAAEQ--NGIVFIDEIDKIAKRGGSGGP---DVSREGVQRDLLPLVEGSTVSTKYGPVKTDHILFIASGAFH  312 (444)
T ss_pred             HHHHHHHHHHHHh--cCeEEEehhhHHHhcCCCCCC---CcchhhhcccccccccCceeeccccccccceEEEEecCcee
Confidence            4444555555554  479999999999987653221   112234556677776653        234569999985   


Q ss_pred             -CCCCccchhccCCCCcccEEEecCCCHHHHHHHHH
Q psy5642          96 -NRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILK  130 (237)
Q Consensus        96 -n~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~  130 (237)
                       ..|++|=|.|..  ||.-.|++...+.++-..||.
T Consensus       313 ~sKPSDLiPELQG--RfPIRVEL~~Lt~~Df~rILt  346 (444)
T COG1220         313 VAKPSDLIPELQG--RFPIRVELDALTKEDFERILT  346 (444)
T ss_pred             cCChhhcChhhcC--CCceEEEcccCCHHHHHHHHc
Confidence             568888888887  999999999999999998883

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.26  E-value=0.0031  Score=54.95  Aligned_cols=86  Identities=13%  Similarity=0.234  Sum_probs=67.7

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...+|.+-+.+..    ..--|++||++|.+..               ...+.||..|++  +..++++|.+|++++.|.
T Consensus        89 id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~---------------~AaNaLLKtLEE--Pp~~~~fiL~t~~~~~ll  151 (325)
T PRK06871         89 VDQVREINEKVSQHAQQGGNKVVYIQGAERLTE---------------AAANALLKTLEE--PRPNTYFLLQADLSAALL  151 (325)
T ss_pred             HHHHHHHHHHHhhccccCCceEEEEechhhhCH---------------HHHHHHHHHhcC--CCCCeEEEEEECChHhCc
Confidence            4555555555443    2345999999999833               357899999999  556889999999999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHH
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIR  132 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~  132 (237)
                      |.|++  |.. .+.|++|+.++-.+.|...
T Consensus       152 pTI~S--RC~-~~~~~~~~~~~~~~~L~~~  178 (325)
T PRK06871        152 PTIYS--RCQ-TWLIHPPEEQQALDWLQAQ  178 (325)
T ss_pred             hHHHh--hce-EEeCCCCCHHHHHHHHHHH
Confidence            99999  875 5899999999888888764

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=97.24  E-value=0.0078  Score=52.90  Aligned_cols=148  Identities=11%  Similarity=0.072  Sum_probs=88.7

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC-----------CCCCCEEEEEEeCCCC-ccchhccCCC
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI-----------VPLNNVTIVAATNRPD-RIDKALLRPG  109 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-----------~~~~~v~vI~ttn~~~-~ld~al~r~g  109 (237)
                      ..+||+||++.+-+               .+.+.|+..|+.-           ....++++|+|.|-.+ .+++++..  
T Consensus       145 ~GiL~lDEInrL~~---------------~~Q~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np~eg~l~~~Lld--  207 (350)
T CHL00081        145 RGILYVDEVNLLDD---------------HLVDILLDSAASGWNTVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--  207 (350)
T ss_pred             CCEEEecChHhCCH---------------HHHHHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCcccCCCCHHHHH--
Confidence            46999999998833               3445566665431           1123688888888544 69999999  


Q ss_pred             CcccEEEecCCC-HHHHHHHHHHHHcCCCCC-------------chhhHHHHHHHCCCCCccc--ccchhHHhhhhcccc
Q psy5642         110 RLDRLIYVPLPD-DLTRAAILKIRLARSPLG-------------EDVCVEELVRLTEGYSGAE--QSLSKHRAKKIRPRR  173 (237)
Q Consensus       110 Rf~~~i~~~~P~-~~~R~~il~~~l~~~~~~-------------~~~~~~~la~~t~g~s~~D--l~~~~~~a~~~~~~~  173 (237)
                      ||...+.+.+|+ .+.|.+|++.........             ...++...-+....-...|  +..+++-+.....  
T Consensus       208 Rf~l~i~l~~~~~~~~e~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~ar~~~~~V~v~~~~~~yi~~l~~~~~~--  285 (350)
T CHL00081        208 RFGMHAEIRTVKDPELRVKIVEQRTSFDKNPQEFREKYEESQEELRSKIVAAQNLLPKVEIDYDLRVKISQICSELDV--  285 (350)
T ss_pred             HhCceeecCCCCChHHHHHHHHhhhccccChhhhhhhhccccccCHHHHHHHHHhcCCCccCHHHHHHHHHHHHHHCC--
Confidence            999999999997 599999998754311000             0111211222222222222  4444444433321  


Q ss_pred             CCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHh
Q psy5642         174 ESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQ  217 (237)
Q Consensus       174 ~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~  217 (237)
                             .++.+-..+++-|...+.-++  ...|+.+|+..+..
T Consensus       286 -------~s~Ra~i~l~raArA~Aal~G--R~~V~pdDv~~~a~  320 (350)
T CHL00081        286 -------DGLRGDIVTNRAAKALAAFEG--RTEVTPKDIFKVIT  320 (350)
T ss_pred             -------CCChHHHHHHHHHHHHHHHcC--CCCCCHHHHHHHHH
Confidence                   122235555666666666666  44699999998865

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.23  E-value=0.0096  Score=56.23  Aligned_cols=107  Identities=13%  Similarity=0.128  Sum_probs=77.6

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+.+.+..    ...-|++|||+|.+..               ...+.|+..|+...  ...++|.+|+.+..|.
T Consensus       109 vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~---------------~a~naLLK~LEePp--~~tv~IL~t~~~~kLl  171 (620)
T PRK14954        109 VDDIRQLRENVRYGPQKGRYRVYIIDEVHMLST---------------AAFNAFLKTLEEPP--PHAIFIFATTELHKIP  171 (620)
T ss_pred             HHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCH---------------HHHHHHHHHHhCCC--CCeEEEEEeCChhhhh
Confidence            4556666555532    2345999999988832               23678999998843  4566666777789999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +.|++  |. ..++|..++.++-...++..+...+.. .+..+..++..+.|
T Consensus       172 ~TI~S--Rc-~~vef~~l~~~ei~~~L~~i~~~egi~I~~eal~~La~~s~G  220 (620)
T PRK14954        172 ATIAS--RC-QRFNFKRIPLDEIQSQLQMICRAEGIQIDADALQLIARKAQG  220 (620)
T ss_pred             HHHHh--hc-eEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCC
Confidence            99998  77 479999999999988888887765543 56677778877754

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

Probab=97.21  E-value=0.0095  Score=50.51  Aligned_cols=96  Identities=20%  Similarity=0.263  Sum_probs=73.5

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC----------------CCCCEEEEEEeCCCCccchhc
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV----------------PLNNVTIVAATNRPDRIDKAL  105 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~----------------~~~~v~vI~ttn~~~~ld~al  105 (237)
                      ..|||||||+.+.+.-            .+   .|...|+.+.                .-.+.-+||+|.+...+...|
T Consensus       104 ~DVLFIDEIHrl~~~v------------EE---~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTLIGATTr~G~lt~PL  168 (332)
T COG2255         104 GDVLFIDEIHRLSPAV------------EE---VLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTLIGATTRAGMLTNPL  168 (332)
T ss_pred             CCeEEEehhhhcChhH------------HH---HhhhhhhheeEEEEEccCCccceEeccCCCeeEeeeccccccccchh
Confidence            4699999999984431            22   2333344332                113588999999999999999


Q ss_pred             cCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCC
Q psy5642         106 LRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGY  154 (237)
Q Consensus       106 ~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~  154 (237)
                      +.  ||..+..+..-+.++-.+|++..-..+... .+....++|.++.|-
T Consensus       169 rd--RFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~~~a~eIA~rSRGT  216 (332)
T COG2255         169 RD--RFGIIQRLEFYTVEELEEIVKRSAKILGIEIDEEAALEIARRSRGT  216 (332)
T ss_pred             HH--hcCCeeeeecCCHHHHHHHHHHHHHHhCCCCChHHHHHHHHhccCC
Confidence            99  999999999999999999999877666555 566777899988773

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=97.19  E-value=0.0028  Score=55.45  Aligned_cols=85  Identities=20%  Similarity=0.277  Sum_probs=66.4

Q ss_pred             HHHHHHHHHHHH----hcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRAR----QVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~----~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...+|.+-+.+.    ....-|++||++|.+..               ...|.||+.|++  +..+.++|.+|++++.|.
T Consensus        90 idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~---------------~AaNaLLKtLEE--Pp~~t~fiL~t~~~~~lL  152 (334)
T PRK07993         90 VDAVREVTEKLYEHARLGGAKVVWLPDAALLTD---------------AAANALLKTLEE--PPENTWFFLACREPARLL  152 (334)
T ss_pred             HHHHHHHHHHHhhccccCCceEEEEcchHhhCH---------------HHHHHHHHHhcC--CCCCeEEEEEECChhhCh
Confidence            344444444443    33455999999999833               357999999999  557899999999999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHH
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKI  131 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~  131 (237)
                      |.|++  |.. .+.|+.|+.++..+.|..
T Consensus       153 pTIrS--RCq-~~~~~~~~~~~~~~~L~~  178 (334)
T PRK07993        153 ATLRS--RCR-LHYLAPPPEQYALTWLSR  178 (334)
T ss_pred             HHHHh--ccc-cccCCCCCHHHHHHHHHH
Confidence            99999  987 489999999888877754

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.17  E-value=0.0039  Score=55.90  Aligned_cols=107  Identities=13%  Similarity=0.073  Sum_probs=75.6

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+.+.+...    ...|++|||+|.+..               ...+.|+..+++.  ....++|.+|+.+..+.
T Consensus       109 id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~---------------~~~~~LLk~LEep--~~~t~~Il~t~~~~kl~  171 (397)
T PRK14955        109 VDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSI---------------AAFNAFLKTLEEP--PPHAIFIFATTELHKIP  171 (397)
T ss_pred             HHHHHHHHHHHhhchhcCCeEEEEEeChhhCCH---------------HHHHHHHHHHhcC--CCCeEEEEEeCChHHhH
Confidence            45566665555321    235999999988832               2356778888763  34566666777788999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +.+++  |.. .++|+.++.++-...++..+...+.. .+..+..++..+.|
T Consensus       172 ~tl~s--R~~-~v~f~~l~~~ei~~~l~~~~~~~g~~i~~~al~~l~~~s~g  220 (397)
T PRK14955        172 ATIAS--RCQ-RFNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRKAQG  220 (397)
T ss_pred             HHHHH--HHH-HhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            99998  875 69999999999998888888665543 56667777776643

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

Probab=97.15  E-value=0.0052  Score=52.60  Aligned_cols=151  Identities=18%  Similarity=0.238  Sum_probs=92.8

Q ss_pred             HHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCC--ccchhc
Q psy5642          28 RCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPD--RIDKAL  105 (237)
Q Consensus        28 ~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~--~ld~al  105 (237)
                      +.-..+....+..++-+|+|||++.++.....         .++.+-.+|..|.+-. .=.++.+||-.-..  .-|+-+
T Consensus       132 ~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~---------~qr~~Ln~LK~L~NeL-~ipiV~vGt~~A~~al~~D~QL  201 (302)
T PF05621_consen  132 KLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYR---------KQREFLNALKFLGNEL-QIPIVGVGTREAYRALRTDPQL  201 (302)
T ss_pred             HHHHHHHHHHHHcCCcEEEeechHHHhcccHH---------HHHHHHHHHHHHhhcc-CCCeEEeccHHHHHHhccCHHH
Confidence            33344456667778899999999998764322         1333334444443311 12466677644333  336777


Q ss_pred             cCCCCcccEEEecCCC-HHHHHHHHHHHHcCCCCC--c---hhh-HHHHHHHCCCCCcccccchhHHhhhhccccCCCCC
Q psy5642         106 LRPGRLDRLIYVPLPD-DLTRAAILKIRLARSPLG--E---DVC-VEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPG  178 (237)
Q Consensus       106 ~r~gRf~~~i~~~~P~-~~~R~~il~~~l~~~~~~--~---~~~-~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~  178 (237)
                      -+  ||+. +.+|... .++...++..+-..+++.  +   +.. ...+-..|+|.+| +                    
T Consensus       202 a~--RF~~-~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG-~--------------------  257 (302)
T PF05621_consen  202 AS--RFEP-FELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIG-E--------------------  257 (302)
T ss_pred             Hh--ccCC-ccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchH-H--------------------
Confidence            77  9975 7778663 346667777776666654  2   222 2456677777766 4                    


Q ss_pred             CCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCC
Q psy5642         179 PPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPR  222 (237)
Q Consensus       179 ~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~  222 (237)
                             +.+++..|+..++..+.+  .||.+.+.. +.-+.|+
T Consensus       258 -------l~~ll~~aA~~AI~sG~E--~It~~~l~~-~~~~~ps  291 (302)
T PF05621_consen  258 -------LSRLLNAAAIAAIRSGEE--RITREILDK-IDWVPPS  291 (302)
T ss_pred             -------HHHHHHHHHHHHHhcCCc--eecHHHHhh-CCCcChh
Confidence                   788899999999988844  477666654 3334443

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

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

Probab=97.07  E-value=0.011  Score=51.62  Aligned_cols=160  Identities=22%  Similarity=0.272  Sum_probs=98.7

Q ss_pred             hHHHHHHHHHHHHHh-cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeC-------
Q psy5642          25 ESERCVRDVFKRARQ-VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATN-------   96 (237)
Q Consensus        25 ~~~~~l~~~f~~a~~-~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn-------   96 (237)
                      +..+.+.++.++-++ .-|.||||||++-|--               +..+-|-..|..  .-.+|+++||-.       
T Consensus       274 ~vn~~V~~~ieeGkAElVpGVLFIDEvHmLDI---------------E~FsFlnrAlEs--e~aPIii~AtNRG~~kiRG  336 (450)
T COG1224         274 EVNEKVKKWIEEGKAELVPGVLFIDEVHMLDI---------------ECFSFLNRALES--ELAPIIILATNRGMTKIRG  336 (450)
T ss_pred             HHHHHHHHHHhcCcEEeecceEEEechhhhhH---------------HHHHHHHHHhhc--ccCcEEEEEcCCceeeecc
Confidence            344445555555443 3599999999988721               223333333444  223555544422       


Q ss_pred             ----CCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhHHhhhhcc
Q psy5642          97 ----RPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKHRAKKIRP  171 (237)
Q Consensus        97 ----~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~  171 (237)
                          .|..||..++.  |. .+|...+-+.++.++|++.......+. .+..++.|+...+.-|-+-             
T Consensus       337 Td~~sPhGIP~DlLD--Rl-lII~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRY-------------  400 (450)
T COG1224         337 TDIESPHGIPLDLLD--RL-LIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRY-------------  400 (450)
T ss_pred             cCCcCCCCCCHhhhh--he-eEEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHH-------------
Confidence                35577888887  76 356666778899999999887665554 5667777777665333333             


Q ss_pred             ccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCC-CHHHHHHHHH
Q psy5642         172 RRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRT-PPQLIKLYEN  233 (237)
Q Consensus       172 ~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~-~~~~~~~~~~  233 (237)
                                    -.++...|...+.+++  ...|..+|...|-..|.... |-+.++++++
T Consensus       401 --------------a~qLL~pa~iiA~~rg--~~~V~~~dVe~a~~lF~D~krSv~~v~~~~~  447 (450)
T COG1224         401 --------------AVQLLTPASIIAKRRG--SKRVEVEDVERAKELFLDVKRSVEYVEKYEG  447 (450)
T ss_pred             --------------HHHhccHHHHHHHHhC--CCeeehhHHHHHHHHHhhHHHHHHHHHHHHh
Confidence                          3355566667776665  34588899999988776532 4455555543

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.03  E-value=0.017  Score=56.72  Aligned_cols=109  Identities=23%  Similarity=0.293  Sum_probs=71.2

Q ss_pred             ceEEEEEecccccccc------------cChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHH
Q psy5642           7 LTEVVESIGPELFRKY------------VGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA   74 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~------------~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~   74 (237)
                      ..+++.++++.+....            +|-.+  -..+....+....+||+|||+|.+-               ..+.+
T Consensus       623 ~~~~i~~d~s~~~~~~~~~~l~g~~~g~~g~~~--~g~l~~~v~~~p~~vlllDeieka~---------------~~v~~  685 (852)
T TIGR03346       623 EDAMVRIDMSEYMEKHSVARLIGAPPGYVGYEE--GGQLTEAVRRKPYSVVLFDEVEKAH---------------PDVFN  685 (852)
T ss_pred             CCcEEEEechhhcccchHHHhcCCCCCccCccc--ccHHHHHHHcCCCcEEEEeccccCC---------------HHHHH
Confidence            4578888887654321            11111  0122333344455699999999762               24567


Q ss_pred             HHHHHhcCCC---------CCCCEEEEEEeCCCCc-------------------------cchhccCCCCcccEEEecCC
Q psy5642          75 QMLTEMDGIV---------PLNNVTIVAATNRPDR-------------------------IDKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus        75 ~ll~~l~~~~---------~~~~v~vI~ttn~~~~-------------------------ld~al~r~gRf~~~i~~~~P  120 (237)
                      .|++.|+.-.         .-.+.+||+|||....                         +.|.|..  |+|.++.|.++
T Consensus       686 ~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~g~~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel~~--Rid~IivF~PL  763 (852)
T TIGR03346       686 VLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELAGGDDYEEMREAVMEVLRAHFRPEFLN--RIDEIVVFHPL  763 (852)
T ss_pred             HHHHHHhcCceecCCCeEEecCCcEEEEeCCcchHhHhhhcccccHHHHHHHHHHHHHhhcCHHHhc--CcCeEEecCCc
Confidence            7777775421         1245789999998322                         3466776  99999999999


Q ss_pred             CHHHHHHHHHHHHc
Q psy5642         121 DDLTRAAILKIRLA  134 (237)
Q Consensus       121 ~~~~R~~il~~~l~  134 (237)
                      +.+...+|+...+.
T Consensus       764 ~~e~l~~I~~l~L~  777 (852)
T TIGR03346       764 GREQIARIVEIQLG  777 (852)
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999999987664

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.

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=97.01  E-value=0.0026  Score=55.17  Aligned_cols=114  Identities=18%  Similarity=0.149  Sum_probs=72.0

Q ss_pred             ceEEEEEeccccccc--ccChHHH----------HHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHH
Q psy5642           7 LTEVVESIGPELFRK--YVGESER----------CVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA   74 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~--~~g~~~~----------~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~   74 (237)
                      +.+++.|.++...+.  ++|...-          .....+-+|.. .+++|++||+|..-++            ....++
T Consensus        89 ~~~~~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f~~GpL~~A~~-~g~illlDEin~a~p~------------~~~~L~  155 (327)
T TIGR01650        89 NWPCVRVNLDSHVSRIDLVGKDAIVLKDGKQITEFRDGILPWALQ-HNVALCFDEYDAGRPD------------VMFVIQ  155 (327)
T ss_pred             CCCeEEEEecCCCChhhcCCCceeeccCCcceeEEecCcchhHHh-CCeEEEechhhccCHH------------HHHHHH
Confidence            456777766554444  4443211          11123445554 5789999999987221            123344


Q ss_pred             HHHHH-----hcC----CCCCCCEEEEEEeCCCC------------ccchhccCCCCcccEEEecCCCHHHHHHHHHHHH
Q psy5642          75 QMLTE-----MDG----IVPLNNVTIVAATNRPD------------RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL  133 (237)
Q Consensus        75 ~ll~~-----l~~----~~~~~~v~vI~ttn~~~------------~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l  133 (237)
                      .+|+.     +.+    +.....+.||||.|..+            .++++++.  ||-..+.+++|+.++-.+|+....
T Consensus       156 ~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~Gd~~G~y~Gt~~l~~A~lD--RF~i~~~~~Yp~~e~E~~Il~~~~  233 (327)
T TIGR01650       156 RVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLGDTTGLYHGTQQINQAQMD--RWSIVTTLNYLEHDNEAAIVLAKA  233 (327)
T ss_pred             HHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcCCCCcceeeeecCCHHHHh--heeeEeeCCCCCHHHHHHHHHhhc
Confidence            44442     111    11223588999999754            56899999  998888999999999999998765


Q ss_pred             cC
Q psy5642         134 AR  135 (237)
Q Consensus       134 ~~  135 (237)
                      ..
T Consensus       234 ~~  235 (327)
T TIGR01650       234 KG  235 (327)
T ss_pred             cC
Confidence            43

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.

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=96.97  E-value=0.0071  Score=52.57  Aligned_cols=106  Identities=16%  Similarity=0.255  Sum_probs=76.2

Q ss_pred             HHHHHHHHHHHHHhcC----CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCcc
Q psy5642          26 SERCVRDVFKRARQVS----PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRI  101 (237)
Q Consensus        26 ~~~~l~~~f~~a~~~~----P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~l  101 (237)
                      +...+|.+.+.+....    --|++||++|.+..               ...|.||+.|++  +..++++|.+|++++.|
T Consensus        94 ~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~---------------~AaNaLLKtLEE--Pp~~~~fiL~~~~~~~l  156 (319)
T PRK08769         94 VIEQVREISQKLALTPQYGIAQVVIVDPADAINR---------------AACNALLKTLEE--PSPGRYLWLISAQPARL  156 (319)
T ss_pred             cHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCH---------------HHHHHHHHHhhC--CCCCCeEEEEECChhhC
Confidence            3566777776665532    24999999999832               357899999999  44678888899999999


Q ss_pred             chhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCc
Q psy5642         102 DKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSG  156 (237)
Q Consensus       102 d~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~  156 (237)
                      .|.|++  |.. .+.|+.|+.++-.+.|...    +. ...+...++..+.|-.+
T Consensus       157 LpTIrS--RCq-~i~~~~~~~~~~~~~L~~~----~~-~~~~a~~~~~l~~G~p~  203 (319)
T PRK08769        157 PATIRS--RCQ-RLEFKLPPAHEALAWLLAQ----GV-SERAAQEALDAARGHPG  203 (319)
T ss_pred             chHHHh--hhe-EeeCCCcCHHHHHHHHHHc----CC-ChHHHHHHHHHcCCCHH
Confidence            999999  986 5899999998777777542    22 22334455666655433

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=96.96  E-value=0.0051  Score=58.08  Aligned_cols=115  Identities=17%  Similarity=0.206  Sum_probs=66.5

Q ss_pred             CEEEEEEeCCC--CccchhccCCCCcc---cEEEec--CC-CHHHHHHHHHHHHc---CCCCCchhhHHHHHHHCCCCCc
Q psy5642          88 NVTIVAATNRP--DRIDKALLRPGRLD---RLIYVP--LP-DDLTRAAILKIRLA---RSPLGEDVCVEELVRLTEGYSG  156 (237)
Q Consensus        88 ~v~vI~ttn~~--~~ld~al~r~gRf~---~~i~~~--~P-~~~~R~~il~~~l~---~~~~~~~~~~~~la~~t~g~s~  156 (237)
                      ++.+|+++|..  ..+++.++.  ||+   ..++|+  .| +.+.|..+++....   +.+..+            .++.
T Consensus       268 dvrvIa~~~~~~l~~l~~~l~~--rf~~y~v~v~~~~~~~~~~e~~~~~~~~i~~~~~r~G~l~------------~~s~  333 (608)
T TIGR00764       268 DFILVASGNLDDLEGMHPALRS--RIRGYGYEVYMKDTMPDTPENRDKLVQFVAQEVKKDGRIP------------HFTR  333 (608)
T ss_pred             ceEEEEECCHHHHhhcCHHHHH--HhcCCeEEEEeeccCCCCHHHHHHHHHHHHHHHHHhCCCC------------cCCH
Confidence            57889998864  689999999  999   666664  34 45666665554332   221111            2222


Q ss_pred             ccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCC
Q psy5642         157 AEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKP  221 (237)
Q Consensus       157 ~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p  221 (237)
                      .-++.+++.+.+.+..|.   ....+...|.++++.|...+..++  ...|+.+|+.+|++..+.
T Consensus       334 ~Av~~Li~~~~R~ag~r~---~lsl~~R~L~~llR~A~~iA~~~~--~~~I~~ehV~~Ai~~~~~  393 (608)
T TIGR00764       334 DAVEEIVREAQRRAGRKD---HLTLRLRELGGLVRAAGDIAKSSG--KVYVTAEHVLKAKKLAKT  393 (608)
T ss_pred             HHHHHHHHHHHHHHhccc---ccCCCHHHHHHHHHHHHHHHHhcC--CceecHHHHHHHHHHHHH
Confidence            223333333332221111   111222338899999866555444  457999999999887654

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

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.93  E-value=0.0049  Score=53.55  Aligned_cols=85  Identities=15%  Similarity=0.214  Sum_probs=66.7

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...+|.+-+.+...    .--|++||++|.+..               ...|.||+.|++  +..++++|.+|++++.|.
T Consensus        90 vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~---------------~AaNaLLKtLEE--Pp~~t~fiL~t~~~~~lL  152 (319)
T PRK06090         90 VEQIRQCNRLAQESSQLNGYRLFVIEPADAMNE---------------SASNALLKTLEE--PAPNCLFLLVTHNQKRLL  152 (319)
T ss_pred             HHHHHHHHHHHhhCcccCCceEEEecchhhhCH---------------HHHHHHHHHhcC--CCCCeEEEEEECChhhCh
Confidence            44555555444432    245999999999832               357899999999  556899999999999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHH
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKI  131 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~  131 (237)
                      |.|++  |.. .+.|+.|+.++..+.|..
T Consensus       153 pTI~S--RCq-~~~~~~~~~~~~~~~L~~  178 (319)
T PRK06090        153 PTIVS--RCQ-QWVVTPPSTAQAMQWLKG  178 (319)
T ss_pred             HHHHh--cce-eEeCCCCCHHHHHHHHHH
Confidence            99999  986 699999999988887764

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.87  E-value=0.014  Score=55.22  Aligned_cols=107  Identities=13%  Similarity=0.193  Sum_probs=80.1

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+.+.+...    ..-|++|||+|.+..               ...+.|+..|+...  ...++|.+|+.+..|-
T Consensus       103 vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls~---------------~a~naLLK~LEepp--~~tifIL~tt~~~kIl  165 (614)
T PRK14971        103 VDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLSQ---------------AAFNAFLKTLEEPP--SYAIFILATTEKHKIL  165 (614)
T ss_pred             HHHHHHHHHHHhhCcccCCcEEEEEECcccCCH---------------HHHHHHHHHHhCCC--CCeEEEEEeCCchhch
Confidence            46677777766543    233999999988822               34678999999843  4666777777789999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +.|++  |.. .++|..++..+-...++..+...++. ....+..|+..+.|
T Consensus       166 ~tI~S--Rc~-iv~f~~ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~g  214 (614)
T PRK14971        166 PTILS--RCQ-IFDFNRIQVADIVNHLQYVASKEGITAEPEALNVIAQKADG  214 (614)
T ss_pred             HHHHh--hhh-eeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            99998  874 69999999999999999888776654 44557778877743

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.84  E-value=0.027  Score=55.18  Aligned_cols=110  Identities=22%  Similarity=0.294  Sum_probs=73.4

Q ss_pred             ceEEEEEeccccccc------------ccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHH
Q psy5642           7 LTEVVESIGPELFRK------------YVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA   74 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~------------~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~   74 (237)
                      ..+++.++.+++...            |+|-.+  ...+.+..+....+||+|||+|...               ..+.+
T Consensus       567 ~~~~~~~d~s~~~~~~~~~~l~g~~~gyvg~~~--~~~l~~~~~~~p~~VvllDeieka~---------------~~v~~  629 (821)
T CHL00095        567 EDAMIRLDMSEYMEKHTVSKLIGSPPGYVGYNE--GGQLTEAVRKKPYTVVLFDEIEKAH---------------PDIFN  629 (821)
T ss_pred             ccceEEEEchhccccccHHHhcCCCCcccCcCc--cchHHHHHHhCCCeEEEECChhhCC---------------HHHHH
Confidence            456777877765321            222111  1234444555555899999999762               24677


Q ss_pred             HHHHHhcCCC---------CCCCEEEEEEeCCCCc-------------------------------------cchhccCC
Q psy5642          75 QMLTEMDGIV---------PLNNVTIVAATNRPDR-------------------------------------IDKALLRP  108 (237)
Q Consensus        75 ~ll~~l~~~~---------~~~~v~vI~ttn~~~~-------------------------------------ld~al~r~  108 (237)
                      .|++.|+.-.         .-++.++|.|||....                                     +.|.++. 
T Consensus       630 ~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~pefln-  708 (821)
T CHL00095        630 LLLQILDDGRLTDSKGRTIDFKNTLIIMTSNLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLN-  708 (821)
T ss_pred             HHHHHhccCceecCCCcEEecCceEEEEeCCcchHHHHhhccccCCcccccccccccHHHHHHHHHHHHHHhcCHHHhc-
Confidence            7888877521         1246899999986321                                     2356777 


Q ss_pred             CCcccEEEecCCCHHHHHHHHHHHHcC
Q psy5642         109 GRLDRLIYVPLPDDLTRAAILKIRLAR  135 (237)
Q Consensus       109 gRf~~~i~~~~P~~~~R~~il~~~l~~  135 (237)
                       |+|.+|.|.+.+.++-.+|+...+..
T Consensus       709 -Rid~ii~F~pL~~~~l~~Iv~~~l~~  734 (821)
T CHL00095        709 -RLDEIIVFRQLTKNDVWEIAEIMLKN  734 (821)
T ss_pred             -cCCeEEEeCCCCHHHHHHHHHHHHHH
Confidence             99999999999999999999877653

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=96.83  E-value=0.013  Score=55.10  Aligned_cols=149  Identities=15%  Similarity=0.136  Sum_probs=88.3

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-----------CCCCEEEEEEeCCCC---ccchhccCC
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-----------PLNNVTIVAATNRPD---RIDKALLRP  108 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vI~ttn~~~---~ld~al~r~  108 (237)
                      .+|||||++.+-.               .+.+.|+..|+.-.           ...++.||+|+|..+   .+++++.. 
T Consensus        86 GvL~lDEi~rl~~---------------~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~Lld-  149 (589)
T TIGR02031        86 GVLYVDMANLLDD---------------GLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLD-  149 (589)
T ss_pred             CcEeccchhhCCH---------------HHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHH-
Confidence            5999999998832               35666777775321           113588999988765   79999999 


Q ss_pred             CCcccEEEecC-CCHHHHHHHHHHHHcCCC----CCchhhHHHHHH---HCCCCC--cccccchhHHhhhhccccCCCCC
Q psy5642         109 GRLDRLIYVPL-PDDLTRAAILKIRLARSP----LGEDVCVEELVR---LTEGYS--GAEQSLSKHRAKKIRPRRESNPG  178 (237)
Q Consensus       109 gRf~~~i~~~~-P~~~~R~~il~~~l~~~~----~~~~~~~~~la~---~t~g~s--~~Dl~~~~~~a~~~~~~~~~~~~  178 (237)
                       ||..+|.+.. |+..+|.+|++..+....    ........++..   ......  ...+..++..+..+...      
T Consensus       150 -Rf~l~v~~~~~~~~~er~eil~~~~~~~~~~~~~~~~~~~~~i~~ar~~~~~V~i~~~~~~~l~~~~~~~gv~------  222 (589)
T TIGR02031       150 -RLALHVSLEDVASQDLRVEIVRRERCNEVFRMNDELELLRGQIEAARELLPQVTISAEQVKELVLTAASLGIS------  222 (589)
T ss_pred             -hccCeeecCCCCCHHHHHHHHHHHHHhhhhhcchhhHHHHHHHHHHHHhcCCccCCHHHHHHHHHHHHHcCCC------
Confidence             9999888876 477889999988763221    111122222221   112222  22244555555433321      


Q ss_pred             CCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhc
Q psy5642         179 PPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLV  219 (237)
Q Consensus       179 ~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~  219 (237)
                         ....-..+++-|...+.-++  ...|+.+|+..|+.-+
T Consensus       223 ---s~Ra~i~~~r~ArA~Aal~g--r~~V~~~Dv~~a~~lv  258 (589)
T TIGR02031       223 ---GHRADLFAVRAAKAHAALHG--RTEVTEEDLKLAVELV  258 (589)
T ss_pred             ---CccHHHHHHHHHHHHHHHhC--CCCCCHHHHHHHHHHH
Confidence               01113344455555555555  4569999999997643

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.

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

Probab=96.79  E-value=0.0041  Score=54.24  Aligned_cols=74  Identities=23%  Similarity=0.313  Sum_probs=54.1

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC----------CCCCCCEEEEEEeC-----CCCccchhccC
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG----------IVPLNNVTIVAATN-----RPDRIDKALLR  107 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~----------~~~~~~v~vI~ttn-----~~~~ld~al~r  107 (237)
                      +|+++|||+..-               ..+.+.|+..|+.          +.-....+||+|.|     ....+++++++
T Consensus       114 ~ill~DEInra~---------------p~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~g~~~l~eA~ld  178 (329)
T COG0714         114 VILLLDEINRAP---------------PEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEGTYPLPEALLD  178 (329)
T ss_pred             eEEEEeccccCC---------------HHHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccCCCcCCCHHHHh
Confidence            499999997652               2456777777765          22235689999999     66789999999


Q ss_pred             CCCcccEEEecCC-CHHHHHHHHHHHH
Q psy5642         108 PGRLDRLIYVPLP-DDLTRAAILKIRL  133 (237)
Q Consensus       108 ~gRf~~~i~~~~P-~~~~R~~il~~~l  133 (237)
                        ||-..+++++| +..+...++....
T Consensus       179 --Rf~~~~~v~yp~~~~e~~~i~~~~~  203 (329)
T COG0714         179 --RFLLRIYVDYPDSEEEERIILARVG  203 (329)
T ss_pred             --hEEEEEecCCCCchHHHHHHHHhCc
Confidence              99989999999 5545555554443

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=96.79  E-value=0.013  Score=50.82  Aligned_cols=104  Identities=11%  Similarity=0.221  Sum_probs=73.9

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+.+.+...    ..-|++||++|.+.               ....+.|+..|++  +..++++|.+|++++.+.
T Consensus        75 v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~---------------~~a~naLLK~LEe--pp~~t~~il~~~~~~~ll  137 (313)
T PRK05564         75 VDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMT---------------EQAQNAFLKTIEE--PPKGVFIILLCENLEQIL  137 (313)
T ss_pred             HHHHHHHHHHHhcCcccCCceEEEEechhhcC---------------HHHHHHHHHHhcC--CCCCeEEEEEeCChHhCc
Confidence            34577776655432    34599999998872               2346889999998  445667777778899999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEG  153 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g  153 (237)
                      +.+++  |.. .++|+.|+.++-..++...+..  . .......++..+.|
T Consensus       138 ~TI~S--Rc~-~~~~~~~~~~~~~~~l~~~~~~--~-~~~~~~~l~~~~~g  182 (313)
T PRK05564        138 DTIKS--RCQ-IYKLNRLSKEEIEKFISYKYND--I-KEEEKKSAIAFSDG  182 (313)
T ss_pred             HHHHh--hce-eeeCCCcCHHHHHHHHHHHhcC--C-CHHHHHHHHHHcCC
Confidence            99999  874 7999999999988888765532  1 23445556666655

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

Probab=96.68  E-value=0.045  Score=45.59  Aligned_cols=129  Identities=21%  Similarity=0.239  Sum_probs=85.1

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHh-cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQ-VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-   84 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~-~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-   84 (237)
                      ++.+|+|...+|.+         |-++++..+. ..+-|||+||+-   ....+           .--..|...|++-. 
T Consensus        80 GLRlIev~k~~L~~---------l~~l~~~l~~~~~kFIlf~DDLs---Fe~~d-----------~~yk~LKs~LeGgle  136 (249)
T PF05673_consen   80 GLRLIEVSKEDLGD---------LPELLDLLRDRPYKFILFCDDLS---FEEGD-----------TEYKALKSVLEGGLE  136 (249)
T ss_pred             CceEEEECHHHhcc---------HHHHHHHHhcCCCCEEEEecCCC---CCCCc-----------HHHHHHHHHhcCccc
Confidence            47788888877654         4556666553 356799999853   22111           11345555566532 


Q ss_pred             -CCCCEEEEEEeCCCCccchhccC---------------------CCCcccEEEecCCCHHHHHHHHHHHHcCCCCCch-
Q psy5642          85 -PLNNVTIVAATNRPDRIDKALLR---------------------PGRLDRLIYVPLPDDLTRAAILKIRLARSPLGED-  141 (237)
Q Consensus        85 -~~~~v~vI~ttn~~~~ld~al~r---------------------~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~-  141 (237)
                       ...+|++.||+|+-..|++....                     ..||..+|.|..|+.++=.+|.+.++..+++.-+ 
T Consensus       137 ~~P~NvliyATSNRRHLv~E~~~d~~~~~~~eih~~d~~eEklSLsDRFGL~l~F~~~~q~~YL~IV~~~~~~~g~~~~~  216 (249)
T PF05673_consen  137 ARPDNVLIYATSNRRHLVPESFSDREDIQDDEIHPSDTIEEKLSLSDRFGLWLSFYPPDQEEYLAIVRHYAERYGLELDE  216 (249)
T ss_pred             cCCCcEEEEEecchhhccchhhhhccCCCccccCcchHHHHHHhHHHhCCcEEEecCCCHHHHHHHHHHHHHHcCCCCCH
Confidence             24579999999987766554332                     1289999999999999999999999987776522 


Q ss_pred             hhHHH----HHHHCCCCCccc
Q psy5642         142 VCVEE----LVRLTEGYSGAE  158 (237)
Q Consensus       142 ~~~~~----la~~t~g~s~~D  158 (237)
                      ..+..    -|..-.|.||+-
T Consensus       217 e~l~~~Al~wa~~rg~RSGRt  237 (249)
T PF05673_consen  217 EELRQEALQWALRRGGRSGRT  237 (249)
T ss_pred             HHHHHHHHHHHHHcCCCCHHH
Confidence            33322    233445777776

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

Probab=96.65  E-value=0.0097  Score=53.84  Aligned_cols=74  Identities=23%  Similarity=0.318  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHhc--CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc--------------------CCCCC
Q psy5642          29 CVRDVFKRARQV--SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD--------------------GIVPL   86 (237)
Q Consensus        29 ~l~~~f~~a~~~--~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~--------------------~~~~~   86 (237)
                      .+.+++..|+..  .|++|+|||++.....              ++...++..|+                    .+.-.
T Consensus       258 ~f~~~~~~A~~~p~~~~vliIDEINRani~--------------kiFGel~~lLE~~~rg~~~~v~l~y~e~d~e~f~iP  323 (459)
T PRK11331        258 IFYNFCQQAKEQPEKKYVFIIDEINRANLS--------------KVFGEVMMLMEHDKRGENWSVPLTYSENDEERFYVP  323 (459)
T ss_pred             hHHHHHHHHHhcccCCcEEEEehhhccCHH--------------HhhhhhhhhccccccccccceeeeccccccccccCC
Confidence            345566677653  5899999999864322              22333333332                    12234


Q ss_pred             CCEEEEEEeCCCC----ccchhccCCCCcccEEEecC
Q psy5642          87 NNVTIVAATNRPD----RIDKALLRPGRLDRLIYVPL  119 (237)
Q Consensus        87 ~~v~vI~ttn~~~----~ld~al~r~gRf~~~i~~~~  119 (237)
                      .++.||||+|..+    .+|.|++|  ||.. |++.+
T Consensus       324 ~Nl~IIgTMNt~Drs~~~lD~AlrR--RF~f-i~i~p  357 (459)
T PRK11331        324 ENVYIIGLMNTADRSLAVVDYALRR--RFSF-IDIEP  357 (459)
T ss_pred             CCeEEEEecCccccchhhccHHHHh--hhhe-EEecC
Confidence            5799999999988    89999999  9964 77765

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=96.46  E-value=0.049  Score=51.81  Aligned_cols=75  Identities=23%  Similarity=0.367  Sum_probs=55.6

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-----------CCCCEEEEEEeCCC-CccchhccCCCC
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-----------PLNNVTIVAATNRP-DRIDKALLRPGR  110 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vI~ttn~~-~~ld~al~r~gR  110 (237)
                      .||||||++.+-.               .+.+.|+..|+.-.           ...++.+|+|+|.. ..++++|+.  |
T Consensus       128 GiL~lDEi~~l~~---------------~~q~~Ll~~le~g~~~v~r~g~~~~~~~~~~lIat~np~eg~l~~~L~d--R  190 (633)
T TIGR02442       128 GILYIDEVNLLDD---------------HLVDVLLDAAAMGVNRVEREGLSVSHPARFVLIGTMNPEEGDLRPQLLD--R  190 (633)
T ss_pred             CeEEeChhhhCCH---------------HHHHHHHHHHhcCCEEEEECCceeeecCCeEEEEecCCCCCCCCHHHHh--h
Confidence            5999999998832               35666777765321           11358999998853 368999999  9


Q ss_pred             cccEEEecCC-CHHHHHHHHHHHHc
Q psy5642         111 LDRLIYVPLP-DDLTRAAILKIRLA  134 (237)
Q Consensus       111 f~~~i~~~~P-~~~~R~~il~~~l~  134 (237)
                      |+..|.++.| +.++|.++++..+.
T Consensus       191 ~~l~i~v~~~~~~~~~~~il~~~~~  215 (633)
T TIGR02442       191 FGLCVDVAAPRDPEERVEIIRRRLA  215 (633)
T ss_pred             cceEEEccCCCchHHHHHHHHHHHh
Confidence            9999999988 46788899886553

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.

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.46  E-value=0.021  Score=41.83  Aligned_cols=87  Identities=29%  Similarity=0.329  Sum_probs=55.3

Q ss_pred             cChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCC-CCcc
Q psy5642          23 VGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNR-PDRI  101 (237)
Q Consensus        23 ~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~-~~~l  101 (237)
                      .......++.++..+....|.+|+|||++.+........         .................+..+|+++|. ....
T Consensus        60 ~~~~~~~~~~~~~~~~~~~~~viiiDei~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~  130 (148)
T smart00382       60 SGSGELRLRLALALARKLKPDVLILDEITSLLDAEQEAL---------LLLLEELRLLLLLKSEKNLTVILTTNDEKDLG  130 (148)
T ss_pred             CCCHHHHHHHHHHHHHhcCCCEEEEECCcccCCHHHHHH---------HHhhhhhHHHHHHHhcCCCEEEEEeCCCccCc
Confidence            345677888999999998889999999999865421100         000000001111112346778888886 5566


Q ss_pred             chhccCCCCcccEEEecCC
Q psy5642         102 DKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus       102 d~al~r~gRf~~~i~~~~P  120 (237)
                      +..+++  |++..+.+..+
T Consensus       131 ~~~~~~--~~~~~~~~~~~  147 (148)
T smart00382      131 PALLRR--RFDRRIVLLLI  147 (148)
T ss_pred             hhhhhh--ccceEEEecCC
Confidence            667776  99998888765

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.

>KOG2680|consensus

Probab=96.45  E-value=0.13  Score=44.29  Aligned_cols=143  Identities=22%  Similarity=0.303  Sum_probs=83.5

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEE---------eC--CCCccchhccCCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAA---------TN--RPDRIDKALLRPG  109 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~t---------tn--~~~~ld~al~r~g  109 (237)
                      -|.+|||||++-|--.               -.+-|-..+.+  .-.++++++|         ||  +|..||-.++.  
T Consensus       288 vpGVLFIDEvHMLDIE---------------cFsFlNrAlE~--d~~PiiimaTNrgit~iRGTn~~SphGiP~D~lD--  348 (454)
T KOG2680|consen  288 VPGVLFIDEVHMLDIE---------------CFSFLNRALEN--DMAPIIIMATNRGITRIRGTNYRSPHGIPIDLLD--  348 (454)
T ss_pred             ccceEEEeeehhhhhH---------------HHHHHHHHhhh--ccCcEEEEEcCCceEEeecCCCCCCCCCcHHHhh--
Confidence            4999999999887221               11112222333  1234555444         33  35578888887  


Q ss_pred             CcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhHHhhhhccccCCCCCCCCCchhHHH
Q psy5642         110 RLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVA  188 (237)
Q Consensus       110 Rf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~  188 (237)
                      |. .+|.-.+-+.++-..||+.......+. .+..++-|....+.-+-+-                           -.+
T Consensus       349 R~-lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRY---------------------------ai~  400 (454)
T KOG2680|consen  349 RM-LIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRY---------------------------AIH  400 (454)
T ss_pred             hh-heeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHH---------------------------HHH
Confidence            76 356666678899999999877654433 3333333433332222222                           234


Q ss_pred             HHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCC-CHHHHHHHH
Q psy5642         189 VCDEAALSALENNLEAAYVSHQDFLTALQLVKPRT-PPQLIKLYE  232 (237)
Q Consensus       189 ~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~-~~~~~~~~~  232 (237)
                      +...+...+.++.  ...+..+|+..+.+.|-... +.+++.++.
T Consensus       401 Lit~a~~~~~krk--~~~v~~~di~r~y~LFlD~~Rs~~yl~E~~  443 (454)
T KOG2680|consen  401 LITAASLVCLKRK--GKVVEVDDIERVYRLFLDEKRSMKYLTEYQ  443 (454)
T ss_pred             HHHHHHHHHHHhc--CceeehhHHHHHHHHHhhhhhhhHHHHHhh
Confidence            5566677777776  44577899999988776553 455555543

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.34  E-value=0.041  Score=54.10  Aligned_cols=109  Identities=24%  Similarity=0.348  Sum_probs=70.0

Q ss_pred             ceEEEEEeccccccc------------ccChHHHHHHHHHHHHHhcCC-eEEEEccccccccccCCCCCCCCCchHHHHH
Q psy5642           7 LTEVVESIGPELFRK------------YVGESERCVRDVFKRARQVSP-SVIFFDELDSLAGERGDGGGGGGSNVQERVL   73 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~------------~~g~~~~~l~~~f~~a~~~~P-~il~iDeid~l~~~~~~~~~~~~~~~~~~~~   73 (237)
                      +-+++.++++.+...            |+|..+   ...+..+....| ++|+|||+|.+-               ..+.
T Consensus       626 ~~~~i~id~se~~~~~~~~~LiG~~pgy~g~~~---~g~l~~~v~~~p~~vLllDEieka~---------------~~v~  687 (857)
T PRK10865        626 DDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEE---GGYLTEAVRRRPYSVILLDEVEKAH---------------PDVF  687 (857)
T ss_pred             CCcEEEEEhHHhhhhhhHHHHhCCCCcccccch---hHHHHHHHHhCCCCeEEEeehhhCC---------------HHHH
Confidence            346788888776432            111111   112333333344 899999998762               2356


Q ss_pred             HHHHHHhcCCC---------CCCCEEEEEEeCCCC-------------------------ccchhccCCCCcccEEEecC
Q psy5642          74 AQMLTEMDGIV---------PLNNVTIVAATNRPD-------------------------RIDKALLRPGRLDRLIYVPL  119 (237)
Q Consensus        74 ~~ll~~l~~~~---------~~~~v~vI~ttn~~~-------------------------~ld~al~r~gRf~~~i~~~~  119 (237)
                      +.|++.|+.-.         .-.+.++|+|||...                         .+.|+++.  |+|.++.|.+
T Consensus       688 ~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TSN~g~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PELln--Rld~iivF~P  765 (857)
T PRK10865        688 NILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFIN--RIDEVVVFHP  765 (857)
T ss_pred             HHHHHHHhhCceecCCceEEeecccEEEEeCCcchHHHHHhccccchHHHHHHHHHHHcccccHHHHH--hCCeeEecCC
Confidence            66777665311         123567899998731                         24468888  9999999999


Q ss_pred             CCHHHHHHHHHHHHcC
Q psy5642         120 PDDLTRAAILKIRLAR  135 (237)
Q Consensus       120 P~~~~R~~il~~~l~~  135 (237)
                      ++.+....|++.++..
T Consensus       766 L~~edl~~Iv~~~L~~  781 (857)
T PRK10865        766 LGEQHIASIAQIQLQR  781 (857)
T ss_pred             CCHHHHHHHHHHHHHH
Confidence            9999999998877754

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=96.33  E-value=0.017  Score=50.16  Aligned_cols=104  Identities=14%  Similarity=0.215  Sum_probs=74.2

Q ss_pred             HHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccch
Q psy5642          28 RCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDK  103 (237)
Q Consensus        28 ~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~  103 (237)
                      ..++++-+.+...    ..-|++||++|.+..               ...+.||..|++..   +.++|.+|++++.|-+
T Consensus       107 d~ir~i~~~l~~~p~~~~~kVvII~~ae~m~~---------------~aaNaLLK~LEEPp---~~~fILi~~~~~~Ll~  168 (314)
T PRK07399        107 EQIREIKRFLSRPPLEAPRKVVVIEDAETMNE---------------AAANALLKTLEEPG---NGTLILIAPSPESLLP  168 (314)
T ss_pred             HHHHHHHHHHccCcccCCceEEEEEchhhcCH---------------HHHHHHHHHHhCCC---CCeEEEEECChHhCcH
Confidence            3566666655542    356999999988732               34788999999853   3457778889999999


Q ss_pred             hccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCC
Q psy5642         104 ALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGY  154 (237)
Q Consensus       104 al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~  154 (237)
                      .|++  |. ..+.|+.|+.++-.++|........  .+.+...++..+.|-
T Consensus       169 TI~S--Rc-q~i~f~~l~~~~~~~~L~~~~~~~~--~~~~~~~l~~~a~Gs  214 (314)
T PRK07399        169 TIVS--RC-QIIPFYRLSDEQLEQVLKRLGDEEI--LNINFPELLALAQGS  214 (314)
T ss_pred             HHHh--hc-eEEecCCCCHHHHHHHHHHhhcccc--chhHHHHHHHHcCCC
Confidence            9999  87 4699999999999999987643221  122345666665543

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=96.32  E-value=0.057  Score=48.18  Aligned_cols=90  Identities=19%  Similarity=0.301  Sum_probs=64.0

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC---------CC--CCCCEEEEEEeCCC-CccchhccCCC
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG---------IV--PLNNVTIVAATNRP-DRIDKALLRPG  109 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~~--~~~~v~vI~ttn~~-~~ld~al~r~g  109 (237)
                      ..|||+||+-.|-               ..++..||+.+..         +.  ..-++++|||.|-. .+|-+-|+.  
T Consensus       145 RGIlYvDEvnlL~---------------d~lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNPEeGeLrpqLlD--  207 (423)
T COG1239         145 RGILYVDEVNLLD---------------DHLVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPEEGELRPQLLD--  207 (423)
T ss_pred             CCEEEEecccccc---------------HHHHHHHHHHHHhCCceeeeCceeeccCccEEEEeecCccccccchhhHh--
Confidence            3599999997761               3567777776643         11  12359999999973 388899999  


Q ss_pred             CcccEEEecCC-CHHHHHHHHHHHHcCCCCCchhhHHHHHH
Q psy5642         110 RLDRLIYVPLP-DDLTRAAILKIRLARSPLGEDVCVEELVR  149 (237)
Q Consensus       110 Rf~~~i~~~~P-~~~~R~~il~~~l~~~~~~~~~~~~~la~  149 (237)
                      ||...|.+.+| +.++|.+|.+.-+... ..++..++.++.
T Consensus       208 Rfg~~v~~~~~~~~~~rv~Ii~r~~~f~-~~Pe~f~~~~~~  247 (423)
T COG1239         208 RFGLEVDTHYPLDLEERVEIIRRRLAFE-AVPEAFLEKYAD  247 (423)
T ss_pred             hhcceeeccCCCCHHHHHHHHHHHHHhh-cCcHHHHHHHHH
Confidence            99999999988 7789999999766542 234444444433

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=96.28  E-value=0.016  Score=50.56  Aligned_cols=85  Identities=13%  Similarity=0.154  Sum_probs=64.5

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+.+.+..    ...-|++|||+|.+.               ....+.|+..|++  +.+++++|.+|+.++.|.
T Consensus        92 id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~---------------~~a~NaLLK~LEE--Pp~~~~~Il~t~~~~~ll  154 (329)
T PRK08058         92 KDQIRYLKEEFSKSGVESNKKVYIIEHADKMT---------------ASAANSLLKFLEE--PSGGTTAILLTENKHQIL  154 (329)
T ss_pred             HHHHHHHHHHHhhCCcccCceEEEeehHhhhC---------------HHHHHHHHHHhcC--CCCCceEEEEeCChHhCc
Confidence            3456666655542    234599999998872               2357889999998  445777888999999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHH
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKI  131 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~  131 (237)
                      +.|++  |.. .++|+.|+.++-.+.|+.
T Consensus       155 ~TIrS--Rc~-~i~~~~~~~~~~~~~L~~  180 (329)
T PRK08058        155 PTILS--RCQ-VVEFRPLPPESLIQRLQE  180 (329)
T ss_pred             HHHHh--hce-eeeCCCCCHHHHHHHHHH
Confidence            99999  875 699999999887777753

>PHA02244 ATPase-like protein

Probab=96.25  E-value=0.038  Score=48.88  Aligned_cols=64  Identities=22%  Similarity=0.330  Sum_probs=44.8

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc--------CC-CCCCCEEEEEEeCCC-----------Cc
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD--------GI-VPLNNVTIVAATNRP-----------DR  100 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~--------~~-~~~~~v~vI~ttn~~-----------~~  100 (237)
                      ...+|+|||++.+.+.               +...|...++        +. ....++.+|+|+|.+           ..
T Consensus       180 ~GgvLiLDEId~a~p~---------------vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~~~~G~~~~y~G~k~  244 (383)
T PHA02244        180 KGGLFFIDEIDASIPE---------------ALIIINSAIANKFFDFADERVTAHEDFRVISAGNTLGKGADHIYVARNK  244 (383)
T ss_pred             cCCEEEEeCcCcCCHH---------------HHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCCCccCcccccCCCcc
Confidence            5789999999987332               2333333333        11 123468999999973           57


Q ss_pred             cchhccCCCCcccEEEecCCCH
Q psy5642         101 IDKALLRPGRLDRLIYVPLPDD  122 (237)
Q Consensus       101 ld~al~r~gRf~~~i~~~~P~~  122 (237)
                      ++++++.  ||- .|++++|+.
T Consensus       245 L~~AllD--RFv-~I~~dyp~~  263 (383)
T PHA02244        245 IDGATLD--RFA-PIEFDYDEK  263 (383)
T ss_pred             cCHHHHh--hcE-EeeCCCCcH
Confidence            8999999  996 699999983

>KOG1051|consensus

Probab=96.17  E-value=0.03  Score=54.59  Aligned_cols=116  Identities=21%  Similarity=0.181  Sum_probs=81.6

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHh-cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQ-VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~-~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      ++.++.+..---..++.|+.+..++.+...+.. ....||+|||++-+.....+.+       ....++.|...+.    
T Consensus       245 ~l~~l~~g~l~aGa~~rge~E~rlk~l~k~v~~~~~gvILfigelh~lvg~g~~~~-------~~d~~nlLkp~L~----  313 (898)
T KOG1051|consen  245 KLIALDFGSLVAGAKRRGEFEERLKELLKEVESGGGGVILFLGELHWLVGSGSNYG-------AIDAANLLKPLLA----  313 (898)
T ss_pred             ceEEEEhhhcccCcccchHHHHHHHHHHHHHhcCCCcEEEEecceeeeecCCCcch-------HHHHHHhhHHHHh----
Confidence            344444444345567889999999999999984 4567999999999987765411       1222333333332    


Q ss_pred             CCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC
Q psy5642          86 LNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS  136 (237)
Q Consensus        86 ~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~  136 (237)
                      ++.+.+||||..-.     .-||++-+  ||+. +.++.|+.+.-..||+.+-..+
T Consensus       314 rg~l~~IGatT~e~Y~k~iekdPalEr--rw~l-~~v~~pS~~~~~~iL~~l~~~~  366 (898)
T KOG1051|consen  314 RGGLWCIGATTLETYRKCIEKDPALER--RWQL-VLVPIPSVENLSLILPGLSERY  366 (898)
T ss_pred             cCCeEEEecccHHHHHHHHhhCcchhh--Ccce-eEeccCcccchhhhhhhhhhhh
Confidence            35599999998533     45999999  9986 8899999888777777666553

>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=96.16  E-value=0.015  Score=45.43  Aligned_cols=74  Identities=22%  Similarity=0.299  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+.+.+...    ..-|++||++|.+..               ...+.||..|++  ...++++|.+|++++.|.
T Consensus        84 i~~ir~i~~~~~~~~~~~~~KviiI~~ad~l~~---------------~a~NaLLK~LEe--pp~~~~fiL~t~~~~~il  146 (162)
T PF13177_consen   84 IDQIREIIEFLSLSPSEGKYKVIIIDEADKLTE---------------EAQNALLKTLEE--PPENTYFILITNNPSKIL  146 (162)
T ss_dssp             HHHHHHHHHHCTSS-TTSSSEEEEEETGGGS-H---------------HHHHHHHHHHHS--TTTTEEEEEEES-GGGS-
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEEeehHhhhhH---------------HHHHHHHHHhcC--CCCCEEEEEEECChHHCh
Confidence            46666666666543    355999999998833               457999999999  446899999999999999


Q ss_pred             hhccCCCCcccEEEecCC
Q psy5642         103 KALLRPGRLDRLIYVPLP  120 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P  120 (237)
                      +.+++  |.- .+.|+.+
T Consensus       147 ~TI~S--Rc~-~i~~~~l  161 (162)
T PF13177_consen  147 PTIRS--RCQ-VIRFRPL  161 (162)
T ss_dssp             HHHHT--TSE-EEEE---
T ss_pred             HHHHh--hce-EEecCCC
Confidence            99999  874 4666543

...

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=96.08  E-value=0.048  Score=45.39  Aligned_cols=92  Identities=13%  Similarity=0.007  Sum_probs=70.6

Q ss_pred             HHHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCcc
Q psy5642          26 SERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRI  101 (237)
Q Consensus        26 ~~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~l  101 (237)
                      +...+|.+-..+..    ...-|++|+++|.+..               ...+.||..|++  +..++++|.+|..++.+
T Consensus        70 ~IdqIReL~~~l~~~p~~g~~KViII~~ae~mt~---------------~AANALLKtLEE--PP~~t~fILit~~~~~L  132 (263)
T PRK06581         70 SIEQIRKLQDFLSKTSAISGYKVAIIYSAELMNL---------------NAANSCLKILED--APKNSYIFLITSRAASI  132 (263)
T ss_pred             cHHHHHHHHHHHhhCcccCCcEEEEEechHHhCH---------------HHHHHHHHhhcC--CCCCeEEEEEeCChhhC
Confidence            35556665555543    2345999999999833               357899999999  55678888888999999


Q ss_pred             chhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCC
Q psy5642         102 DKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSP  137 (237)
Q Consensus       102 d~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~  137 (237)
                      .|.+++  |.. .+.++.|+...-.+++...+....
T Consensus       133 LpTIrS--RCq-~i~~~~p~~~~~~e~~~~~~~p~~  165 (263)
T PRK06581        133 ISTIRS--RCF-KINVRSSILHAYNELYSQFIQPIA  165 (263)
T ss_pred             chhHhh--ceE-EEeCCCCCHHHHHHHHHHhccccc
Confidence            999999  875 589999999888888777776543

>KOG2227|consensus

Probab=96.01  E-value=0.025  Score=50.99  Aligned_cols=111  Identities=21%  Similarity=0.269  Sum_probs=77.8

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccC----CCCcccEEEe
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLR----PGRLDRLIYV  117 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r----~gRf~~~i~~  117 (237)
                      +-+|++||+|.|+..+            +.++-.+- ++..+ ...++++||.+|..+.=|..|-|    -+.--..+.|
T Consensus       257 ~~llVlDEmD~L~tr~------------~~vLy~lF-ewp~l-p~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F  322 (529)
T KOG2227|consen  257 MLLLVLDEMDHLITRS------------QTVLYTLF-EWPKL-PNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVF  322 (529)
T ss_pred             eEEEEechhhHHhhcc------------cceeeeeh-hcccC-CcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeee
Confidence            7799999999998432            12222222 22332 34689999999998877766654    1223578899


Q ss_pred             cCCCHHHHHHHHHHHHcCCCCC--chhhHHHHHHHCCCCCcccccchhHHhh
Q psy5642         118 PLPDDLTRAAILKIRLARSPLG--EDVCVEELVRLTEGYSGAEQSLSKHRAK  167 (237)
Q Consensus       118 ~~P~~~~R~~il~~~l~~~~~~--~~~~~~~la~~t~g~s~~Dl~~~~~~a~  167 (237)
                      ++-+.+|..+||+..+...+..  ....+.-+|.+..|.|| |+..+.+.+.
T Consensus       323 ~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~SG-DlRkaLdv~R  373 (529)
T KOG2227|consen  323 PPYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAPSG-DLRKALDVCR  373 (529)
T ss_pred             cCCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccCch-hHHHHHHHHH
Confidence            9999999999999999876654  34567778888888776 6666555554

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=95.97  E-value=0.033  Score=47.76  Aligned_cols=82  Identities=16%  Similarity=0.295  Sum_probs=60.0

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      -..+|.+...+...    ..-|++||++|.+..               ...|.||+.|++  +..+.++|.+|++++.|-
T Consensus        86 idqIR~l~~~~~~~p~~~~~kV~II~~ad~m~~---------------~AaNaLLKtLEE--Pp~~t~~iL~t~~~~~lL  148 (290)
T PRK07276         86 TDTIRELVKNFSQSGYEGKQQVFIIKDADKMHV---------------NAANSLLKVIEE--PQSEIYIFLLTNDENKVL  148 (290)
T ss_pred             HHHHHHHHHHHhhCcccCCcEEEEeehhhhcCH---------------HHHHHHHHHhcC--CCCCeEEEEEECChhhCc
Confidence            45566655555432    335999999999833               347899999999  556789999999999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHH
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAIL  129 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il  129 (237)
                      |.|++  |.. .|.|+. +.++-.+++
T Consensus       149 pTI~S--Rcq-~i~f~~-~~~~~~~~L  171 (290)
T PRK07276        149 PTIKS--RTQ-IFHFPK-NEAYLIQLL  171 (290)
T ss_pred             hHHHH--cce-eeeCCC-cHHHHHHHH
Confidence            99999  985 577865 444444444

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

Probab=95.94  E-value=0.022  Score=49.00  Aligned_cols=102  Identities=22%  Similarity=0.258  Sum_probs=72.3

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG   82 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~   82 (237)
                      ...++++.+++..+.-  -....++.+-+.....    ..-|++|||+|.+..               ...+.++..+..
T Consensus        73 ~~d~lel~~s~~~~~~--i~~~~vr~~~~~~~~~~~~~~~kviiidead~mt~---------------~A~nallk~lEe  135 (325)
T COG0470          73 HPDFLELNPSDLRKID--IIVEQVRELAEFLSESPLEGGYKVVIIDEADKLTE---------------DAANALLKTLEE  135 (325)
T ss_pred             CCceEEecccccCCCc--chHHHHHHHHHHhccCCCCCCceEEEeCcHHHHhH---------------HHHHHHHHHhcc
Confidence            4578889998776542  2344455554444433    356999999999854               246778888887


Q ss_pred             CCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHH
Q psy5642          83 IVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILK  130 (237)
Q Consensus        83 ~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~  130 (237)
                        ...+..+|.+||.++.+-+.|++  |.. .+.|+.|+...+.....
T Consensus       136 --p~~~~~~il~~n~~~~il~tI~S--Rc~-~i~f~~~~~~~~i~~~e  178 (325)
T COG0470         136 --PPKNTRFILITNDPSKILPTIRS--RCQ-RIRFKPPSRLEAIAWLE  178 (325)
T ss_pred             --CCCCeEEEEEcCChhhccchhhh--cce-eeecCCchHHHHHHHhh
Confidence              44678899999999999999998  874 58888766655555544

>KOG2035|consensus

Probab=95.67  E-value=0.11  Score=44.20  Aligned_cols=124  Identities=17%  Similarity=0.242  Sum_probs=87.3

Q ss_pred             EEEecccccccccChHHHHHHHHHHHHHhcCC---------eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642          11 VESIGPELFRKYVGESERCVRDVFKRARQVSP---------SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus        11 i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P---------~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      +++.+|+-..    .-.--++++.....+.+|         -+++|-|+|.|..+               ....|-..|+
T Consensus        92 lEitPSDaG~----~DRvViQellKevAQt~qie~~~qr~fKvvvi~ead~LT~d---------------AQ~aLRRTME  152 (351)
T KOG2035|consen   92 LEITPSDAGN----YDRVVIQELLKEVAQTQQIETQGQRPFKVVVINEADELTRD---------------AQHALRRTME  152 (351)
T ss_pred             EEeChhhcCc----ccHHHHHHHHHHHHhhcchhhccccceEEEEEechHhhhHH---------------HHHHHHHHHH
Confidence            5566665322    224556666666655443         28999999988443               2344555555


Q ss_pred             CCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          82 GIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      .+.  +++-+|..+|+.+.+=+++++  |. ..|.+|.|+.++...++...+.+..+. +...+..+|++++|--.+-
T Consensus       153 kYs--~~~RlIl~cns~SriIepIrS--RC-l~iRvpaps~eeI~~vl~~v~~kE~l~lp~~~l~rIa~kS~~nLRrA  225 (351)
T KOG2035|consen  153 KYS--SNCRLILVCNSTSRIIEPIRS--RC-LFIRVPAPSDEEITSVLSKVLKKEGLQLPKELLKRIAEKSNRNLRRA  225 (351)
T ss_pred             HHh--cCceEEEEecCcccchhHHhh--he-eEEeCCCCCHHHHHHHHHHHHHHhcccCcHHHHHHHHHHhcccHHHH
Confidence            543  466788889999999999998  64 359999999999999999999877766 6677788888876544443

>PRK13531 regulatory ATPase RavA; Provisional

Probab=95.47  E-value=0.33  Score=44.55  Aligned_cols=149  Identities=13%  Similarity=0.127  Sum_probs=80.6

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC--------CCCCEEEEEEeCCCC---ccchhccCCCCc
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV--------PLNNVTIVAATNRPD---RIDKALLRPGRL  111 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--------~~~~v~vI~ttn~~~---~ld~al~r~gRf  111 (237)
                      .+||+|||..+.               ..+.+.|+..|.+-.        .-+..+++++||...   ...+++..  ||
T Consensus       109 ~lLfLDEI~ras---------------p~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN~LPE~g~~leAL~D--RF  171 (498)
T PRK13531        109 EIVFLDEIWKAG---------------PAILNTLLTAINERRFRNGAHEEKIPMRLLVTASNELPEADSSLEALYD--RM  171 (498)
T ss_pred             cEEeecccccCC---------------HHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECCCCcccCCchHHhHh--hE
Confidence            399999996431               356788888884321        111234444446321   12248999  99


Q ss_pred             ccEEEecCCC-HHHHHHHHHHHHc--CCCC-----CchhhHHHHHHHCCCCCccc--ccchhHHhhhhccccCCCCCCCC
Q psy5642         112 DRLIYVPLPD-DLTRAAILKIRLA--RSPL-----GEDVCVEELVRLTEGYSGAE--QSLSKHRAKKIRPRRESNPGPPA  181 (237)
Q Consensus       112 ~~~i~~~~P~-~~~R~~il~~~l~--~~~~-----~~~~~~~~la~~t~g~s~~D--l~~~~~~a~~~~~~~~~~~~~~~  181 (237)
                      -..+.+++|+ .++-.++|.....  ..+.     -+..++..+-.......-.|  ++.+++-...+...+.   ....
T Consensus       172 liri~vp~l~~~~~e~~lL~~~~~~~~~~~~~~~vis~eel~~lq~~v~~V~v~d~v~eyI~~L~~~lr~~r~---~~~~  248 (498)
T PRK13531        172 LIRLWLDKVQDKANFRSMLTSQQDENDNPVPASLQITDEEYQQWQKEIGKITLPDHVFELIFQLRQQLDALPN---APYV  248 (498)
T ss_pred             EEEEECCCCCchHHHHHHHHcccccccCCCcccCCCCHHHHHHHHHHhcceeCCHHHHHHHHHHHHHHhcCCC---CCCc
Confidence            8889999997 4565777765322  1111     12344444444444433333  2222222211111110   1124


Q ss_pred             CchhHHHHHHHHHHHHHHhccccCCccHHHHH
Q psy5642         182 CKPSIVAVCDEAALSALENNLEAAYVSHQDFL  213 (237)
Q Consensus       182 ~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~  213 (237)
                      ++.+-..++.-+...|+-++  ...|+.+|+.
T Consensus       249 SpR~~~~l~~~akA~A~l~G--R~~V~p~Dv~  278 (498)
T PRK13531        249 SDRRWKKAIRLLQASAFFSG--RDAIAPIDLI  278 (498)
T ss_pred             CcHHHHHHHHHHHHHHHHCC--CCCCCHHHHH
Confidence            55557777777777777776  4457788888

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

Probab=95.44  E-value=0.33  Score=40.49  Aligned_cols=129  Identities=22%  Similarity=0.208  Sum_probs=84.3

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhc-CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQV-SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~-~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      ...+++|+..++.+         +-.+++..+.. ++-|||.||+-   ...   +    ..    --..|-..|++-..
T Consensus       113 glrLVEV~k~dl~~---------Lp~l~~~Lr~~~~kFIlFcDDLS---Fe~---g----d~----~yK~LKs~LeG~ve  169 (287)
T COG2607         113 GLRLVEVDKEDLAT---------LPDLVELLRARPEKFILFCDDLS---FEE---G----DD----AYKALKSALEGGVE  169 (287)
T ss_pred             CCeEEEEcHHHHhh---------HHHHHHHHhcCCceEEEEecCCC---CCC---C----ch----HHHHHHHHhcCCcc
Confidence            45688888877754         45666666653 46799999851   111   1    11    12334444554322


Q ss_pred             --CCCEEEEEEeCCCCccchhcc--------------------CCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCc-h-
Q psy5642          86 --LNNVTIVAATNRPDRIDKALL--------------------RPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGE-D-  141 (237)
Q Consensus        86 --~~~v~vI~ttn~~~~ld~al~--------------------r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~-~-  141 (237)
                        ..+|++-||+|+-..|++.+.                    =+.||...+.|.+|+.++=..|+..+.+...++- + 
T Consensus       170 ~rP~NVl~YATSNRRHLl~e~~~dn~~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~~~~l~~~~e  249 (287)
T COG2607         170 GRPANVLFYATSNRRHLLPEDMKDNEGSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDEYLKIVDHYAKHFGLDISDE  249 (287)
T ss_pred             cCCCeEEEEEecCCcccccHhhhhCCCcccccChhHHHHHhhchhhhcceeecccCCCHHHHHHHHHHHHHHcCCCCCHH
Confidence              347999999999777663222                    1238999999999999999999999998887762 3 


Q ss_pred             -hhHHHHHHHC--CCCCccc
Q psy5642         142 -VCVEELVRLT--EGYSGAE  158 (237)
Q Consensus       142 -~~~~~la~~t--~g~s~~D  158 (237)
                       .+.+.+.+.|  .|-||+-
T Consensus       250 ~l~~eAl~WAt~rg~RSGR~  269 (287)
T COG2607         250 ELHAEALQWATTRGGRSGRV  269 (287)
T ss_pred             HHHHHHHHHHHhcCCCccHh
Confidence             3444454444  4566665

>PRK08485 DNA polymerase III subunit delta'; Validated

Probab=95.39  E-value=0.1  Score=42.08  Aligned_cols=106  Identities=15%  Similarity=0.075  Sum_probs=72.8

Q ss_pred             HHHHHHHHHHHHHhc-CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchh
Q psy5642          26 SERCVRDVFKRARQV-SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKA  104 (237)
Q Consensus        26 ~~~~l~~~f~~a~~~-~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~a  104 (237)
                      +...+|.+.+.+... ...-++|+++|.+.               ....+.||..+++  +..++++|..|..+..+.|.
T Consensus        38 ~Vd~iReii~~~~~~~~~~k~iI~~a~~l~---------------~~A~NaLLK~LEE--Pp~~~~fiL~t~~~~~llpT  100 (206)
T PRK08485         38 KIEDAKEVIAEAYIAESEEKIIVIAAPSYG---------------IEAQNALLKILEE--PPKNICFIIVAKSKNLLLPT  100 (206)
T ss_pred             CHHHHHHHHHHHhhCCCCcEEEEEchHhhC---------------HHHHHHHHHHhcC--CCCCeEEEEEeCChHhCchH
Confidence            355666666666542 12344577887763               3457899999999  55678888888889999999


Q ss_pred             ccCCCCccc------------EEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHC
Q psy5642         105 LLRPGRLDR------------LIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLT  151 (237)
Q Consensus       105 l~r~gRf~~------------~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t  151 (237)
                      +++  |...            .+.+...+.++-.+.++. +.+.... .......++...
T Consensus       101 I~S--Rc~~~~~~~~~~~~~l~l~l~~l~~~~i~~~L~~-~~ke~~~~~~ea~~lIa~la  157 (206)
T PRK08485        101 IRS--RLIIEKRKQKKPVKPLDLDLKKLDLKDIYEFLKE-LEKENKLSKEELKELIESLL  157 (206)
T ss_pred             HHh--hheeccccccccccccccccCCCCHHHHHHHHHH-HHHcccccHHHHHHHHHHHH
Confidence            998  8653            577888899999999988 4443332 333344444443

>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=95.23  E-value=0.066  Score=42.26  Aligned_cols=93  Identities=15%  Similarity=0.157  Sum_probs=56.4

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHH----HhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRA----RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a----~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      ...+++.++++.+..  -++....+..++..+    ......||+|||||...+....    +.+.....+.+.||+.|+
T Consensus        31 ~~~~~~~~d~s~~~~--~~~~~~~~~~l~~~~~~~v~~~~~gVVllDEidKa~~~~~~----~~~v~~~~V~~~LL~~le  104 (171)
T PF07724_consen   31 SERPLIRIDMSEYSE--GDDVESSVSKLLGSPPGYVGAEEGGVVLLDEIDKAHPSNSG----GADVSGEGVQNSLLQLLE  104 (171)
T ss_dssp             SCCEEEEEEGGGHCS--HHHCSCHCHHHHHHTTCHHHHHHHTEEEEETGGGCSHTTTT----CSHHHHHHHHHHHHHHHH
T ss_pred             CccchHHHhhhcccc--cchHHhhhhhhhhcccceeeccchhhhhhHHHhhccccccc----cchhhHHHHHHHHHHHhc
Confidence            456899999998877  122233333333322    1112349999999999875111    123344677888888886


Q ss_pred             CCC---------CCCCEEEEEEeCCCCccchh
Q psy5642          82 GIV---------PLNNVTIVAATNRPDRIDKA  104 (237)
Q Consensus        82 ~~~---------~~~~v~vI~ttn~~~~ld~a  104 (237)
                      +-.         .-+++++|+|+|--......
T Consensus       105 ~g~~~d~~g~~vd~~n~ifI~Tsn~~~~~~~~  136 (171)
T PF07724_consen  105 GGTLTDSYGRTVDTSNIIFIMTSNFGAEEIID  136 (171)
T ss_dssp             HSEEEETTCCEEEGTTEEEEEEESSSTHHHHH
T ss_pred             ccceecccceEEEeCCceEEEecccccchhhh
Confidence            321         12469999999976544333

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 ....

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=95.21  E-value=0.068  Score=46.63  Aligned_cols=86  Identities=15%  Similarity=0.234  Sum_probs=64.7

Q ss_pred             HHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCcc
Q psy5642          26 SERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRI  101 (237)
Q Consensus        26 ~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~l  101 (237)
                      +...+|.+.+.+...    ..-|++||+++.+-.               ...+.++..|+...  .++.+|.+|++++.+
T Consensus        94 ~id~iR~l~~~~~~~p~~~~~kV~iiEp~~~Ld~---------------~a~naLLk~LEep~--~~~~~Ilvth~~~~l  156 (325)
T PRK08699         94 KIDAVREIIDNVYLTSVRGGLRVILIHPAESMNL---------------QAANSLLKVLEEPP--PQVVFLLVSHAADKV  156 (325)
T ss_pred             CHHHHHHHHHHHhhCcccCCceEEEEechhhCCH---------------HHHHHHHHHHHhCc--CCCEEEEEeCChHhC
Confidence            466777777777642    344999999988832               34677888888753  346677799999999


Q ss_pred             chhccCCCCcccEEEecCCCHHHHHHHHHH
Q psy5642         102 DKALLRPGRLDRLIYVPLPDDLTRAAILKI  131 (237)
Q Consensus       102 d~al~r~gRf~~~i~~~~P~~~~R~~il~~  131 (237)
                      .+.+++  |.. .+.|+.|+.++..+.|..
T Consensus       157 l~ti~S--Rc~-~~~~~~~~~~~~~~~L~~  183 (325)
T PRK08699        157 LPTIKS--RCR-KMVLPAPSHEEALAYLRE  183 (325)
T ss_pred             hHHHHH--Hhh-hhcCCCCCHHHHHHHHHh
Confidence            999998  874 589999999988777754

>KOG0745|consensus

Probab=95.15  E-value=0.061  Score=48.28  Aligned_cols=110  Identities=23%  Similarity=0.337  Sum_probs=71.5

Q ss_pred             ceEEEEEeccccc-ccccC-hHHHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHh
Q psy5642           7 LTEVVESIGPELF-RKYVG-ESERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEM   80 (237)
Q Consensus         7 ~~~~i~v~~s~l~-~~~~g-~~~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l   80 (237)
                      +.||...||..|. ..|+| +.+..|.+++..|..    .+..|+||||+|.+.....+.... -+....-+...||..+
T Consensus       251 dVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGIVflDEvDKi~~~~~~i~~~-RDVsGEGVQQaLLKll  329 (564)
T KOG0745|consen  251 DVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEVDKITKKAESIHTS-RDVSGEGVQQALLKLL  329 (564)
T ss_pred             CCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCeEEEehhhhhcccCcccccc-ccccchhHHHHHHHHh
Confidence            6799999998864 57888 568889999988753    367899999999998443332211 0111145667788877


Q ss_pred             cCCC-----------CC--------CCEEEEEEeCCCCccchhccCCCCc-ccEEEecCC
Q psy5642          81 DGIV-----------PL--------NNVTIVAATNRPDRIDKALLRPGRL-DRLIYVPLP  120 (237)
Q Consensus        81 ~~~~-----------~~--------~~v~vI~ttn~~~~ld~al~r~gRf-~~~i~~~~P  120 (237)
                      ++..           .+        .+|++|+.-.. ..||.-+-|  |. |..+=|..|
T Consensus       330 EGtvVnVpeK~~~~~~rgd~vqiDTtnILFiasGAF-~~Ldk~I~r--R~~d~slGFg~~  386 (564)
T KOG0745|consen  330 EGTVVNVPEKGSRRKPRGDTVQIDTTNILFIASGAF-VGLDKIISR--RLDDKSLGFGAP  386 (564)
T ss_pred             cccEEcccCCCCCCCCCCCeEEEeccceEEEecccc-cchHHHHHH--hhcchhcccCCC
Confidence            6531           11        23555544433 467777777  76 456667777

>KOG1942|consensus

Probab=95.14  E-value=0.34  Score=41.65  Aligned_cols=113  Identities=26%  Similarity=0.408  Sum_probs=65.6

Q ss_pred             ccccccChHHHHHHHHHHHHHh-cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeC
Q psy5642          18 LFRKYVGESERCVRDVFKRARQ-VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATN   96 (237)
Q Consensus        18 l~~~~~g~~~~~l~~~f~~a~~-~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn   96 (237)
                      +..+..|+.-+.+.+..+.-.+ .-|.+|||||++-|-               .+....|-..+..  +-.++ ||++||
T Consensus       272 ITdkLR~eiNkvVn~Yid~GvAElvPGVLFIDEVhMLD---------------iEcFTyL~kalES--~iaPi-vifAsN  333 (456)
T KOG1942|consen  272 ITDKLRGEINKVVNKYIDQGVAELVPGVLFIDEVHMLD---------------IECFTYLHKALES--PIAPI-VIFASN  333 (456)
T ss_pred             hHHHHHHHHHHHHHHHHhcchhhhcCcceEeeehhhhh---------------hHHHHHHHHHhcC--CCCce-EEEecC
Confidence            3444455555666666665543 469999999998771               1233333344544  22344 444444


Q ss_pred             C-------------CCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHC
Q psy5642          97 R-------------PDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLT  151 (237)
Q Consensus        97 ~-------------~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t  151 (237)
                      +             |..+|+.++.  |.= +|..-.-+.++-++|++.......+. .+..+.-++...
T Consensus       334 rG~~~irGt~d~~sPhGip~dllD--Rl~-Iirt~~y~~~e~r~Ii~~Ra~~E~l~~~e~a~~~l~~~g  399 (456)
T KOG1942|consen  334 RGMCTIRGTEDILSPHGIPPDLLD--RLL-IIRTLPYDEEEIRQIIKIRAQVEGLQVEEEALDLLAEIG  399 (456)
T ss_pred             CcceeecCCcCCCCCCCCCHHHhh--hee-EEeeccCCHHHHHHHHHHHHhhhcceecHHHHHHHHhhc
Confidence            2             4567778777  763 34333446677778888777655554 555666666544

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

Probab=95.07  E-value=0.023  Score=42.80  Aligned_cols=54  Identities=28%  Similarity=0.453  Sum_probs=37.8

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-----------CCC------CEEEEEEeCCCC----
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-----------PLN------NVTIVAATNRPD----   99 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~------~v~vI~ttn~~~----   99 (237)
                      .+++++|||++..-               ..+...|+..+++-.           ...      +..+|+|+|...    
T Consensus        65 ~~~il~lDEin~a~---------------~~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~  129 (139)
T PF07728_consen   65 KGGILVLDEINRAP---------------PEVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRK  129 (139)
T ss_dssp             EEEEEEESSCGG-----------------HHHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TT
T ss_pred             ceeEEEECCcccCC---------------HHHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcC
Confidence            58899999998752               245666666665421           011      389999999998    


Q ss_pred             ccchhccCCCCc
Q psy5642         100 RIDKALLRPGRL  111 (237)
Q Consensus       100 ~ld~al~r~gRf  111 (237)
                      .+++++++  ||
T Consensus       130 ~l~~al~~--Rf  139 (139)
T PF07728_consen  130 ELSPALLD--RF  139 (139)
T ss_dssp             TTCHHHHT--T-
T ss_pred             cCCHHHHh--hC
Confidence            99999999  98

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

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=94.88  E-value=0.53  Score=44.37  Aligned_cols=66  Identities=17%  Similarity=0.089  Sum_probs=48.5

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-----------CCCCEEEEEEeCCC---CccchhccC
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-----------PLNNVTIVAATNRP---DRIDKALLR  107 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vI~ttn~~---~~ld~al~r  107 (237)
                      ..|||+||+..+-               ..+++.|++-|+.=.           -..++++|||-|..   ..++++++.
T Consensus        94 ~GvL~lDe~n~~~---------------~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~~~L~~~lLD  158 (584)
T PRK13406         94 GGVLVLAMAERLE---------------PGTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEEDERAPAALAD  158 (584)
T ss_pred             CCEEEecCcccCC---------------HHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcccCCCHHhHh
Confidence            3699999987762               467888888886521           11358889973322   358999999


Q ss_pred             CCCcccEEEecCCCHHH
Q psy5642         108 PGRLDRLIYVPLPDDLT  124 (237)
Q Consensus       108 ~gRf~~~i~~~~P~~~~  124 (237)
                        ||+..|.++.|+..+
T Consensus       159 --Rf~l~v~v~~~~~~~  173 (584)
T PRK13406        159 --RLAFHLDLDGLALRD  173 (584)
T ss_pred             --heEEEEEcCCCChHH
Confidence              999999999987654

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=94.81  E-value=0.21  Score=42.88  Aligned_cols=74  Identities=16%  Similarity=0.273  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      -..++.+-..+...    ..-|++|+++|.+..               ...+.||..|++  +..++++|..|++++.+.
T Consensus        77 idqiR~l~~~~~~~p~e~~~kv~ii~~ad~mt~---------------~AaNaLLK~LEE--Pp~~~~fiL~~~~~~~ll  139 (290)
T PRK05917         77 IETPRAIKKQIWIHPYESPYKIYIIHEADRMTL---------------DAISAFLKVLED--PPQHGVIILTSAKPQRLP  139 (290)
T ss_pred             HHHHHHHHHHHhhCccCCCceEEEEechhhcCH---------------HHHHHHHHHhhc--CCCCeEEEEEeCChhhCc
Confidence            44455555554432    235999999999843               347899999999  556889999999999999


Q ss_pred             hhccCCCCcccEEEecCC
Q psy5642         103 KALLRPGRLDRLIYVPLP  120 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P  120 (237)
                      |.+++  |.. .+.|+.+
T Consensus       140 ~TI~S--Rcq-~~~~~~~  154 (290)
T PRK05917        140 PTIRS--RSL-SIHIPME  154 (290)
T ss_pred             HHHHh--cce-EEEccch
Confidence            99999  875 4667654

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=94.71  E-value=1.1  Score=37.61  Aligned_cols=140  Identities=19%  Similarity=0.167  Sum_probs=85.8

Q ss_pred             HHHHHHHHHHHHhc-CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCc-cc--
Q psy5642          27 ERCVRDVFKRARQV-SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDR-ID--  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~-~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~-ld--  102 (237)
                      ++.-+.+....++. .|-++++||++.+..+-            -+.+.-|.+.-.+....-+|+.||=..--.. .-  
T Consensus       116 e~~~~~L~al~~~g~r~v~l~vdEah~L~~~~------------le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~  183 (269)
T COG3267         116 EQIDRELAALVKKGKRPVVLMVDEAHDLNDSA------------LEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPV  183 (269)
T ss_pred             HHHHHHHHHHHHhCCCCeEEeehhHhhhChhH------------HHHHHHHHhhcccccCceeeeecCCcccchhhchHH
Confidence            33444444444443 56899999999985431            1223333333233222223666654321110 11  


Q ss_pred             -hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCC----CchhhHHHHHHHCCCCCcccccchhHHhhhhccccCCCC
Q psy5642         103 -KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPL----GEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNP  177 (237)
Q Consensus       103 -~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~----~~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~  177 (237)
                       ..+..  |++..|++++.+.++-...+++.++.-..    .++..+..+...+.| .|+-                   
T Consensus       184 l~e~~~--R~~ir~~l~P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg-~P~l-------------------  241 (269)
T COG3267         184 LRELEQ--RIDIRIELPPLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQG-IPRL-------------------  241 (269)
T ss_pred             HHhhhh--eEEEEEecCCcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhcc-chHH-------------------
Confidence             23334  77777888999999999999999876533    367778888888888 5666                   


Q ss_pred             CCCCCchhHHHHHHHHHHHHHHhccccCCccHH
Q psy5642         178 GPPACKPSIVAVCDEAALSALENNLEAAYVSHQ  210 (237)
Q Consensus       178 ~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~  210 (237)
                              |.++|..|...++..+  +..|+..
T Consensus       242 --------in~~~~~Al~~a~~a~--~~~v~~a  264 (269)
T COG3267         242 --------INNLATLALDAAYSAG--EDGVSEA  264 (269)
T ss_pred             --------HHHHHHHHHHHHHHcC--CCccchh
Confidence                    8888998888888776  3345444

>TIGR00368 Mg chelatase-related protein

Probab=94.68  E-value=0.5  Score=43.74  Aligned_cols=65  Identities=26%  Similarity=0.348  Sum_probs=45.6

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-----------CCCCEEEEEEeCCC-----C------
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-----------PLNNVTIVAATNRP-----D------   99 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vI~ttn~~-----~------   99 (237)
                      ..+|||||++.+-               ..+...|++.|+.-.           ...++.+|+++|.-     .      
T Consensus       296 ~GvLfLDEi~e~~---------------~~~~~~L~~~LE~~~v~i~r~g~~~~~pa~frlIaa~Npcpcg~~~~~~~~c  360 (499)
T TIGR00368       296 NGVLFLDELPEFK---------------RSVLDALREPIEDGSISISRASAKIFYPARFQLVAAMNPCPCGHYGGKNTHC  360 (499)
T ss_pred             CCeEecCChhhCC---------------HHHHHHHHHHHHcCcEEEEecCcceeccCCeEEEEecCCcccCcCCCCcccc
Confidence            4799999998762               234555555554321           12368899999852     1      


Q ss_pred             ------------ccchhccCCCCcccEEEecCCCHH
Q psy5642         100 ------------RIDKALLRPGRLDRLIYVPLPDDL  123 (237)
Q Consensus       100 ------------~ld~al~r~gRf~~~i~~~~P~~~  123 (237)
                                  .+...|+.  |||..+.++.++..
T Consensus       361 ~c~~~~~~~y~~~is~pllD--R~dl~~~~~~~~~~  394 (499)
T TIGR00368       361 RCSPQQISRYWNKLSGPFLD--RIDLSVEVPLLPPE  394 (499)
T ss_pred             cCCHHHHHHHhhhccHhHHh--hCCEEEEEcCCCHH
Confidence                        58889999  99999999987543

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

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

Probab=94.65  E-value=0.21  Score=48.27  Aligned_cols=105  Identities=21%  Similarity=0.269  Sum_probs=71.8

Q ss_pred             HHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC--C-C------CCEEEEEEeCCCC--------
Q psy5642          37 ARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV--P-L------NNVTIVAATNRPD--------   99 (237)
Q Consensus        37 a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--~-~------~~v~vI~ttn~~~--------   99 (237)
                      .+....|||+|||||.--               ..+.+.||+.||.=.  . .      .+.++|+|||-=.        
T Consensus       589 VRr~PySViLlDEIEKAH---------------pdV~nilLQVlDdGrLTD~~Gr~VdFrNtiIImTSN~Gs~~i~~~~~  653 (786)
T COG0542         589 VRRKPYSVILLDEIEKAH---------------PDVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNAGSEEILRDAD  653 (786)
T ss_pred             hhcCCCeEEEechhhhcC---------------HHHHHHHHHHhcCCeeecCCCCEEecceeEEEEecccchHHHHhhcc
Confidence            344456899999998752               357899999997522  1 1      2589999998532        


Q ss_pred             --------------------ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC-------CCC---chhhHHHHHH
Q psy5642         100 --------------------RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS-------PLG---EDVCVEELVR  149 (237)
Q Consensus       100 --------------------~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~-------~~~---~~~~~~~la~  149 (237)
                                          ...|+++.  |+|.+|.|.+.+.+.-.+|+..++...       .+.   ++.....|+.
T Consensus       654 ~~~~~~~~~~~~~v~~~l~~~F~PEFLN--Rid~II~F~~L~~~~l~~Iv~~~L~~l~~~L~~~~i~l~~s~~a~~~l~~  731 (786)
T COG0542         654 GDDFADKEALKEAVMEELKKHFRPEFLN--RIDEIIPFNPLSKEVLERIVDLQLNRLAKRLAERGITLELSDEAKDFLAE  731 (786)
T ss_pred             ccccchhhhHHHHHHHHHHhhCCHHHHh--hcccEEeccCCCHHHHHHHHHHHHHHHHHHHHhCCceEEECHHHHHHHHH
Confidence                                12467777  999999999999999999998777532       221   4445556666


Q ss_pred             HCC--CCCccc
Q psy5642         150 LTE--GYSGAE  158 (237)
Q Consensus       150 ~t~--g~s~~D  158 (237)
                      +.-  .|.++-
T Consensus       732 ~gyd~~~GARp  742 (786)
T COG0542         732 KGYDPEYGARP  742 (786)
T ss_pred             hccCCCcCchH
Confidence            552  344444

>PRK09862 putative ATP-dependent protease; Provisional

Probab=94.54  E-value=0.77  Score=42.54  Aligned_cols=65  Identities=28%  Similarity=0.416  Sum_probs=46.9

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-----------CCCCEEEEEEeCCCC-----------
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-----------PLNNVTIVAATNRPD-----------   99 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vI~ttn~~~-----------   99 (237)
                      ..+|||||++.+-               ..+...|++.|+.-.           ...++.+|+|+|...           
T Consensus       295 gGvLfLDEi~e~~---------------~~~~~~L~~~LE~g~v~I~r~g~~~~~pa~f~lIAa~NP~pcG~~~~~~c~c  359 (506)
T PRK09862        295 NGVLFLDELPEFE---------------RRTLDALREPIESGQIHLSRTRAKITYPARFQLVAAMNPSPTGHYQGNHNRC  359 (506)
T ss_pred             CCEEecCCchhCC---------------HHHHHHHHHHHHcCcEEEecCCcceeccCCEEEEEeecCccceecCCCCCCc
Confidence            3699999997751               345666666663321           123589999999742           


Q ss_pred             ----------ccchhccCCCCcccEEEecCCCHH
Q psy5642         100 ----------RIDKALLRPGRLDRLIYVPLPDDL  123 (237)
Q Consensus       100 ----------~ld~al~r~gRf~~~i~~~~P~~~  123 (237)
                                .++..++.  |||..+.++.|+..
T Consensus       360 ~~~~~~~Y~~~ls~plLD--RfdL~v~v~~~~~~  391 (506)
T PRK09862        360 TPEQTLRYLNRLSGPFLD--RFDLSLEIPLPPPG  391 (506)
T ss_pred             CHHHHHHHHhhCCHhHHh--hccEEEEeCCCCHH
Confidence                      47789999  99999999999754

>PF05729 NACHT: NACHT domain

Probab=94.39  E-value=0.33  Score=36.94  Aligned_cols=86  Identities=10%  Similarity=0.172  Sum_probs=49.0

Q ss_pred             HhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCC--CCccchhccCCCCcccEE
Q psy5642          38 RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNR--PDRIDKALLRPGRLDRLI  115 (237)
Q Consensus        38 ~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~--~~~ld~al~r~gRf~~~i  115 (237)
                      ....+.+|+||.+|.+.......       ........+...+.... ..++-+|.|++.  ...+...+..    ...+
T Consensus        78 ~~~~~~llilDglDE~~~~~~~~-------~~~~~~~~l~~l~~~~~-~~~~~liit~r~~~~~~~~~~~~~----~~~~  145 (166)
T PF05729_consen   78 EKNKRVLLILDGLDELEEQDQSQ-------ERQRLLDLLSQLLPQAL-PPGVKLIITSRPRAFPDLRRRLKQ----AQIL  145 (166)
T ss_pred             HcCCceEEEEechHhcccchhhh-------HHHHHHHHHHHHhhhcc-CCCCeEEEEEcCChHHHHHHhcCC----CcEE
Confidence            34567899999999997643220       01222333334444311 123334444432  2123333332    1578


Q ss_pred             EecCCCHHHHHHHHHHHHcC
Q psy5642         116 YVPLPDDLTRAAILKIRLAR  135 (237)
Q Consensus       116 ~~~~P~~~~R~~il~~~l~~  135 (237)
                      .+...+.+++.++++.+++.
T Consensus       146 ~l~~~~~~~~~~~~~~~f~~  165 (166)
T PF05729_consen  146 ELEPFSEEDIKQYLRKYFSN  165 (166)
T ss_pred             EECCCCHHHHHHHHHHHhhc
Confidence            99999999999999998864

>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=94.31  E-value=0.15  Score=44.97  Aligned_cols=89  Identities=27%  Similarity=0.399  Sum_probs=51.4

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeC------------CCCccchhccCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATN------------RPDRIDKALLRP  108 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn------------~~~~ld~al~r~  108 (237)
                      -|.||||||++-|--               +..+.|-..|+.  .-.++ ||.+||            .|..||..++. 
T Consensus       278 vpGVLFIDEvHmLDi---------------EcFsfLnralEs--~~sPi-iIlATNRg~~~irGt~~~sphGiP~DlLD-  338 (398)
T PF06068_consen  278 VPGVLFIDEVHMLDI---------------ECFSFLNRALES--ELSPI-IILATNRGITKIRGTDIISPHGIPLDLLD-  338 (398)
T ss_dssp             EE-EEEEESGGGSBH---------------HHHHHHHHHHTS--TT--E-EEEEES-SEEE-BTTS-EEETT--HHHHT-
T ss_pred             ecceEEecchhhccH---------------HHHHHHHHHhcC--CCCcE-EEEecCceeeeccCccCcCCCCCCcchHh-
Confidence            399999999998822               223333334544  22345 555555            46678888888 


Q ss_pred             CCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHH
Q psy5642         109 GRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRL  150 (237)
Q Consensus       109 gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~  150 (237)
                       |+ .+|...+.+.++-.+|++.......+. .+..+..|+..
T Consensus       339 -Rl-lII~t~py~~~ei~~Il~iR~~~E~v~i~~~al~~L~~i  379 (398)
T PF06068_consen  339 -RL-LIIRTKPYSEEEIKQILKIRAKEEDVEISEDALDLLTKI  379 (398)
T ss_dssp             -TE-EEEEE----HHHHHHHHHHHHHHCT--B-HHHHHHHHHH
T ss_pred             -hc-EEEECCCCCHHHHHHHHHhhhhhhcCcCCHHHHHHHHHH
Confidence             87 468888889999999999988766655 44445544443

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.

>KOG2228|consensus

Probab=93.83  E-value=0.37  Score=42.08  Aligned_cols=99  Identities=15%  Similarity=0.233  Sum_probs=65.4

Q ss_pred             cccChHHHHHHHHHHHHHhc-----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEe
Q psy5642          21 KYVGESERCVRDVFKRARQV-----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAAT   95 (237)
Q Consensus        21 ~~~g~~~~~l~~~f~~a~~~-----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~tt   95 (237)
                      +..|....++.+++...+..     .|.|.++||+|.+++...           +.++-.+.+.-+.  .+.+|.|||.|
T Consensus       112 k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~r-----------QtllYnlfDisqs--~r~Piciig~T  178 (408)
T KOG2228|consen  112 KSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSR-----------QTLLYNLFDISQS--ARAPICIIGVT  178 (408)
T ss_pred             eeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchh-----------hHHHHHHHHHHhh--cCCCeEEEEee
Confidence            44555666777777666542     355777889999976420           2233333333332  24589999999


Q ss_pred             CCCC---ccchhccCCCCcccE-EEecCC-CHHHHHHHHHHHHc
Q psy5642          96 NRPD---RIDKALLRPGRLDRL-IYVPLP-DDLTRAAILKIRLA  134 (237)
Q Consensus        96 n~~~---~ld~al~r~gRf~~~-i~~~~P-~~~~R~~il~~~l~  134 (237)
                      .+.+   .+...+.+  ||.+. |+++.| ..++-..+++..+.
T Consensus       179 trld~lE~LEKRVKS--RFshr~I~m~~~~~l~~yv~l~r~ll~  220 (408)
T KOG2228|consen  179 TRLDILELLEKRVKS--RFSHRVIFMLPSLPLGDYVDLYRKLLS  220 (408)
T ss_pred             ccccHHHHHHHHHHh--hcccceeeccCCCChHHHHHHHHHHhc
Confidence            8866   55678888  99766 666655 67888889988873

>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=93.70  E-value=0.13  Score=41.18  Aligned_cols=68  Identities=18%  Similarity=0.163  Sum_probs=43.0

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P  120 (237)
                      ..++|+|||+..+++.+......         ....++.+.... ..+.-+|.+|-++..+|+.+++  +.+..+.+..+
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~---------~~~~~~~l~~hR-h~g~diiliTQ~~~~id~~ir~--lve~~~~~~k~  146 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKK---------VPEIIEFLAQHR-HYGWDIILITQSPSQIDKFIRD--LVEYHYHCRKL  146 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T-------------HHHHGGGGCC-CTT-EEEEEES-GGGB-HHHHC--CEEEEEEEEE-
T ss_pred             CCcEEEEECChhhcCCCcccccc---------chHHHHHHHHhC-cCCcEEEEEeCCHHHHhHHHHH--HHheEEEEEee
Confidence            57899999999999887663210         123345554432 2467899999999999999998  99888887655

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.

>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

Probab=93.61  E-value=2  Score=35.10  Aligned_cols=150  Identities=14%  Similarity=0.151  Sum_probs=84.3

Q ss_pred             HHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccC
Q psy5642          28 RCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLR  107 (237)
Q Consensus        28 ~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r  107 (237)
                      .++.++-......+|.+|++|.-   +++.++              -.||.++.+......|+||-+++..+-+-.+++-
T Consensus        33 ~~~~ea~~~i~~~~pDLILLDiY---mPd~~G--------------i~lL~~ir~~~~~~DVI~iTAA~d~~tI~~alr~   95 (224)
T COG4565          33 GTLEEAKMIIEEFKPDLILLDIY---MPDGNG--------------IELLPELRSQHYPVDVIVITAASDMETIKEALRY   95 (224)
T ss_pred             ccHHHHHHHHHhhCCCEEEEeec---cCCCcc--------------HHHHHHHHhcCCCCCEEEEeccchHHHHHHHHhc
Confidence            34455555666778999999873   444322              3577777776555689999999999999999986


Q ss_pred             CCCcccEE-EecCCCHHHHHHHHHHHHcCCCCC---chhhHHHHHHHCCCCCcccccchhHHhhhhccccCCCCCCCCCc
Q psy5642         108 PGRLDRLI-YVPLPDDLTRAAILKIRLARSPLG---EDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACK  183 (237)
Q Consensus       108 ~gRf~~~i-~~~~P~~~~R~~il~~~l~~~~~~---~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~  183 (237)
                       |-||..| .|...-.+++..=++.+-..+...   +...++++-.   +.+..+                   .....+
T Consensus        96 -Gv~DYLiKPf~~eRl~~aL~~y~~~r~~l~~~~~~sQ~~lD~l~~---~~~k~~-------------------~~~~LP  152 (224)
T COG4565          96 -GVVDYLIKPFTFERLQQALTRYRQKRHALESHQQLSQKELDQLFN---IQSKEQ-------------------PPDDLP  152 (224)
T ss_pred             -CchhheecceeHHHHHHHHHHHHHHHHHHhhhcccCHHHHHHHHh---cccccc-------------------CcccCC
Confidence             8898766 233333333333333222211111   2223333322   222211                   112223


Q ss_pred             hhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhc
Q psy5642         184 PSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLV  219 (237)
Q Consensus       184 ~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~  219 (237)
                      .||....-......+..  ...+.|.+++-+++..-
T Consensus       153 kGi~~~Tl~~i~~~~~~--~~~~~Taeela~~~giS  186 (224)
T COG4565         153 KGLDELTLQKVREALKE--PDQELTAEELAQALGIS  186 (224)
T ss_pred             CCcCHHHHHHHHHHHhC--cCCccCHHHHHHHhCcc
Confidence            34666555555555552  24567888888776643

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

Probab=93.02  E-value=0.2  Score=40.51  Aligned_cols=66  Identities=12%  Similarity=0.246  Sum_probs=37.8

Q ss_pred             ccChHHHHHHHHHHHHHhcCC--eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCC
Q psy5642          22 YVGESERCVRDVFKRARQVSP--SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPD   99 (237)
Q Consensus        22 ~~g~~~~~l~~~f~~a~~~~P--~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~   99 (237)
                      ..|.+.+.+-.++.......+  .+|+|||.|.-+..          .    ....++..+..... .++-||.||++|.
T Consensus       236 ~~S~G~~~~l~l~~~l~~~~~~~~illiDEpE~~LHp----------~----~q~~l~~~l~~~~~-~~~QviitTHSp~  300 (303)
T PF13304_consen  236 SLSSGEKRLLSLLSLLLSAKKNGSILLIDEPENHLHP----------S----WQRKLIELLKELSK-KNIQVIITTHSPF  300 (303)
T ss_dssp             ---HHHHHHHHHHHHHHTTTTT-SEEEEESSSTTSSH----------H----HHHHHHHHHHHTGG-GSSEEEEEES-GG
T ss_pred             cCCHHHHHHHHHHHHHhCcCCCCeEEEecCCcCCCCH----------H----HHHHHHHHHHhhCc-cCCEEEEeCccch
Confidence            347777777555555554433  89999999986653          2    23333344433322 4677899999987


Q ss_pred             ccc
Q psy5642         100 RID  102 (237)
Q Consensus       100 ~ld  102 (237)
                      -||
T Consensus       301 ild  303 (303)
T PF13304_consen  301 ILD  303 (303)
T ss_dssp             G--
T ss_pred             hcC
Confidence            554

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=92.82  E-value=0.14  Score=46.27  Aligned_cols=69  Identities=26%  Similarity=0.364  Sum_probs=38.1

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-----C----CCCEEEEEEeCCC-------Cccchh
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-----P----LNNVTIVAATNRP-------DRIDKA  104 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----~----~~~v~vI~ttn~~-------~~ld~a  104 (237)
                      ...+|||||+|.+-.               .+...|+..++.-.     .    ..++-+|+||+..       ..+.+.
T Consensus       233 ~~gtl~l~~i~~l~~---------------~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~~~~~  297 (445)
T TIGR02915       233 HGGTLFLDEIGDLPL---------------NLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIAEGTFRED  297 (445)
T ss_pred             CCCEEEEechhhCCH---------------HHHHHHHHHHhhCeEEeCCCCceeeeceEEEEecCCCHHHHHHcCCccHH
Confidence            357999999999832               23445555554311     0    1247788888753       123333


Q ss_pred             ccCCCCcccEEEecCCCHHHHHH
Q psy5642         105 LLRPGRLDRLIYVPLPDDLTRAA  127 (237)
Q Consensus       105 l~r~gRf~~~i~~~~P~~~~R~~  127 (237)
                      +..  |+. .+.+..|...+|.+
T Consensus       298 L~~--~l~-~~~i~lPpLr~R~~  317 (445)
T TIGR02915       298 LFY--RIA-EISITIPPLRSRDG  317 (445)
T ss_pred             HHH--Hhc-cceecCCCchhchh
Confidence            333  432 25566666666654

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).

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=92.79  E-value=0.31  Score=42.05  Aligned_cols=84  Identities=12%  Similarity=0.227  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHhc-----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          28 RCVRDVFKRARQV-----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        28 ~~l~~~f~~a~~~-----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ..++.+.+.....     ..-|++||++|.+.               ....+.|+..|++  +...+++|.+|+.++.+-
T Consensus        72 d~Ir~l~~~~~~~~~~~~~~KvvII~~~e~m~---------------~~a~NaLLK~LEE--Pp~~t~~il~~~~~~kll  134 (299)
T PRK07132         72 SEFLSAINKLYFSSFVQSQKKILIIKNIEKTS---------------NSLLNALLKTIEE--PPKDTYFLLTTKNINKVL  134 (299)
T ss_pred             HHHHHHHHHhccCCcccCCceEEEEecccccC---------------HHHHHHHHHHhhC--CCCCeEEEEEeCChHhCh
Confidence            4555555555322     34599999987662               2356889999999  445677777777889999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHH
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKI  131 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~  131 (237)
                      +.+++  |.. .+++++|+.++-.+.|..
T Consensus       135 ~TI~S--Rc~-~~~f~~l~~~~l~~~l~~  160 (299)
T PRK07132        135 PTIVS--RCQ-VFNVKEPDQQKILAKLLS  160 (299)
T ss_pred             HHHHh--CeE-EEECCCCCHHHHHHHHHH
Confidence            99998  764 699999998887776654

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=92.74  E-value=0.54  Score=44.78  Aligned_cols=106  Identities=14%  Similarity=0.208  Sum_probs=55.1

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHH------------HhcCCeEEEEccccccccccCCCCCCCCCchHHHH
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRA------------RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERV   72 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a------------~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~   72 (237)
                      .+..||+.|+|..+-.      +..-..+|...            ......+|||||++.+-.               .+
T Consensus       374 r~~~pfv~vnc~~~~~------~~~~~elfg~~~~~~~~~~~g~~~~a~~GtL~ldei~~l~~---------------~~  432 (638)
T PRK11388        374 RAAGPYIAVNCQLYPD------EALAEEFLGSDRTDSENGRLSKFELAHGGTLFLEKVEYLSP---------------EL  432 (638)
T ss_pred             ccCCCeEEEECCCCCh------HHHHHHhcCCCCcCccCCCCCceeECCCCEEEEcChhhCCH---------------HH
Confidence            3567999999986631      11112233211            012357999999999832               23


Q ss_pred             HHHHHHHhcCCC--C-C------CCEEEEEEeCCCCccchhccCCCCccc-------EEEecCCCHHHHH----HHHHHH
Q psy5642          73 LAQMLTEMDGIV--P-L------NNVTIVAATNRPDRIDKALLRPGRLDR-------LIYVPLPDDLTRA----AILKIR  132 (237)
Q Consensus        73 ~~~ll~~l~~~~--~-~------~~v~vI~ttn~~~~ld~al~r~gRf~~-------~i~~~~P~~~~R~----~il~~~  132 (237)
                      ...|+..++.-.  . .      -++-+|+||+..  +. .+...|+|..       .+.+..|..-+|.    .++..+
T Consensus       433 Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~t~~~--l~-~~~~~~~f~~dL~~~l~~~~i~lPpLreR~~Di~~L~~~~  509 (638)
T PRK11388        433 QSALLQVLKTGVITRLDSRRLIPVDVRVIATTTAD--LA-MLVEQNRFSRQLYYALHAFEITIPPLRMRREDIPALVNNK  509 (638)
T ss_pred             HHHHHHHHhcCcEEeCCCCceEEeeEEEEEeccCC--HH-HHHhcCCChHHHhhhhceeEEeCCChhhhhhHHHHHHHHH
Confidence            344555554311  0 0      146788888853  22 2222345521       3556666665553    344455


Q ss_pred             Hc
Q psy5642         133 LA  134 (237)
Q Consensus       133 l~  134 (237)
                      +.
T Consensus       510 l~  511 (638)
T PRK11388        510 LR  511 (638)
T ss_pred             HH
Confidence            54

>TIGR01817 nifA Nif-specific regulatory protein

Probab=92.68  E-value=0.54  Score=43.81  Aligned_cols=105  Identities=19%  Similarity=0.250  Sum_probs=55.0

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHH---------------HhcCCeEEEEccccccccccCCCCCCCCCchHH
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRA---------------RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQE   70 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a---------------~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~   70 (237)
                      .+.||+.|+|..+-...      .-..+|...               ......+|||||+|.+-.               
T Consensus       246 ~~~pfv~i~c~~~~~~~------~~~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L~~---------------  304 (534)
T TIGR01817       246 AKRPFVKVNCAALSETL------LESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISP---------------  304 (534)
T ss_pred             CCCCeEEeecCCCCHHH------HHHHHcCCCCCccCCCCcCCCCcccccCCCeEEEechhhCCH---------------
Confidence            56799999998763211      111122111               112357999999999832               


Q ss_pred             HHHHHHHHHhcCCC--C-------CCCEEEEEEeCCCCccchhccCCCCcc---------cEEEecCCC--HHHHHHHHH
Q psy5642          71 RVLAQMLTEMDGIV--P-------LNNVTIVAATNRPDRIDKALLRPGRLD---------RLIYVPLPD--DLTRAAILK  130 (237)
Q Consensus        71 ~~~~~ll~~l~~~~--~-------~~~v~vI~ttn~~~~ld~al~r~gRf~---------~~i~~~~P~--~~~R~~il~  130 (237)
                      .+...|+..++.-.  .       ..++-+|+||+..  +...+ ..|+|.         ..|.+|+..  .++...|++
T Consensus       305 ~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~s~~~--l~~~~-~~~~f~~~L~~rl~~~~i~lPpLreR~eDi~~L~~  381 (534)
T TIGR01817       305 AFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRD--LEEAV-AKGEFRADLYYRINVVPIFLPPLRERREDIPLLAE  381 (534)
T ss_pred             HHHHHHHHHHhcCcEEECCCCceEeecEEEEEeCCCC--HHHHH-HcCCCCHHHHHHhcCCeeeCCCcccccccHHHHHH
Confidence            23455555554321  0       1147788888743  22222 234552         345555443  244556666


Q ss_pred             HHHc
Q psy5642         131 IRLA  134 (237)
Q Consensus       131 ~~l~  134 (237)
                      +++.
T Consensus       382 ~~l~  385 (534)
T TIGR01817       382 AFLE  385 (534)
T ss_pred             HHHH
Confidence            6664

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.

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=92.64  E-value=0.1  Score=47.13  Aligned_cols=105  Identities=17%  Similarity=0.248  Sum_probs=55.7

Q ss_pred             CCceEEEEEecccccccccChHHHHHHH-HHHHH---------------HhcCCeEEEEccccccccccCCCCCCCCCch
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRD-VFKRA---------------RQVSPSVIFFDELDSLAGERGDGGGGGGSNV   68 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~-~f~~a---------------~~~~P~il~iDeid~l~~~~~~~~~~~~~~~   68 (237)
                      ....||+.++|+.+..       ..+.. +|...               ....+++|||||+|.+...            
T Consensus       188 ~~~~~~i~~~c~~~~~-------~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ldei~~l~~~------------  248 (441)
T PRK10365        188 RSEKPLVTLNCAALNE-------SLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPM------------  248 (441)
T ss_pred             CCCCCeeeeeCCCCCH-------HHHHHHhcCCCCCCcCCCCcCCCCceeECCCCEEEEeccccCCHH------------
Confidence            3567999999987642       12211 22211               1224679999999998432            


Q ss_pred             HHHHHHHHHHHhcCCC-----C----CCCEEEEEEeCCCCccchhccCCCCccc-------EEEecCCCHHHHH----HH
Q psy5642          69 QERVLAQMLTEMDGIV-----P----LNNVTIVAATNRPDRIDKALLRPGRLDR-------LIYVPLPDDLTRA----AI  128 (237)
Q Consensus        69 ~~~~~~~ll~~l~~~~-----~----~~~v~vI~ttn~~~~ld~al~r~gRf~~-------~i~~~~P~~~~R~----~i  128 (237)
                         +...++..++.-.     .    ..++.+|+||+.+-  . ....+|+|..       .+.+..|..-+|.    .+
T Consensus       249 ---~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~~--~-~~~~~~~~~~~l~~~l~~~~i~~ppLreR~~Di~~l  322 (441)
T PRK10365        249 ---MQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDL--A-AEVNAGRFRQDLYYRLNVVAIEVPSLRQRREDIPLL  322 (441)
T ss_pred             ---HHHHHHHHHccCcEEeCCCCceeeeceEEEEeCCCCH--H-HHHHcCCchHHHHHHhccceecCCChhhcchhHHHH
Confidence               2344555554321     0    11466787776522  2 2233456642       3556666655553    34


Q ss_pred             HHHHHc
Q psy5642         129 LKIRLA  134 (237)
Q Consensus       129 l~~~l~  134 (237)
                      ++.++.
T Consensus       323 ~~~~l~  328 (441)
T PRK10365        323 AGHFLQ  328 (441)
T ss_pred             HHHHHH
Confidence            555554

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=92.63  E-value=0.17  Score=45.96  Aligned_cols=106  Identities=18%  Similarity=0.209  Sum_probs=54.7

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHH---------------HHhcCCeEEEEccccccccccCCCCCCCCCchHH
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKR---------------ARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQE   70 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~---------------a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~   70 (237)
                      .+.+|+.++|..+-..+.      -..+|..               ......++|||||+|.+-..              
T Consensus       184 ~~~~~~~~~c~~~~~~~~------~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l~~~--------------  243 (463)
T TIGR01818       184 ANGPFIALNMAAIPKDLI------ESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMPLD--------------  243 (463)
T ss_pred             CCCCeEEEeCCCCCHHHH------HHHhcCCCCCCCCCcccCCCCcEEECCCCeEEEEchhhCCHH--------------
Confidence            567999999987632111      1111110               11123678999999998332              


Q ss_pred             HHHHHHHHHhcCCC---------CCCCEEEEEEeCCCC-------ccchhccCCCCcc-cEEEecCCC--HHHHHHHHHH
Q psy5642          71 RVLAQMLTEMDGIV---------PLNNVTIVAATNRPD-------RIDKALLRPGRLD-RLIYVPLPD--DLTRAAILKI  131 (237)
Q Consensus        71 ~~~~~ll~~l~~~~---------~~~~v~vI~ttn~~~-------~ld~al~r~gRf~-~~i~~~~P~--~~~R~~il~~  131 (237)
                       +...|+..++.-.         ...++-+|+||+..-       .+.+.+..  |+. ..|++|+..  .++...++..
T Consensus       244 -~q~~ll~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~f~~~L~~--rl~~~~i~lPpLr~R~~Di~~l~~~  320 (463)
T TIGR01818       244 -AQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFREDLFH--RLNVIRIHLPPLRERREDIPRLARH  320 (463)
T ss_pred             -HHHHHHHHHhcCcEEECCCCceeeeeeEEEEeCCCCHHHHHHcCCcHHHHHH--HhCcceecCCCcccchhhHHHHHHH
Confidence             2344555544311         012467788876431       22233333  332 355555544  4556666666


Q ss_pred             HHc
Q psy5642         132 RLA  134 (237)
Q Consensus       132 ~l~  134 (237)
                      ++.
T Consensus       321 ~l~  323 (463)
T TIGR01818       321 FLA  323 (463)
T ss_pred             HHH
Confidence            654

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.

>PF12846 AAA_10: AAA-like domain

Probab=92.56  E-value=0.49  Score=39.83  Aligned_cols=109  Identities=18%  Similarity=0.182  Sum_probs=67.8

Q ss_pred             ceEEEEEecccccccccChH----HHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHH
Q psy5642           7 LTEVVESIGPELFRKYVGES----ERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLT   78 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~----~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~   78 (237)
                      +..++.++.+.+...-....    -..+..++..+..    ..|.++++||++.+......          ...+..++.
T Consensus       178 ~~~~iv~dl~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iDEa~~~~~~~~~----------~~~~~~~~~  247 (304)
T PF12846_consen  178 DGRIIVFDLSGLSDSAQKVFRAVLLLLLSWIYRRIRARSNRGRPKIIVIDEAHNFLSNPSG----------AEFLDELLR  247 (304)
T ss_pred             cCCeeEEecccccccchhhHHHHHHHHHHHHHHhhcccccCCceEEEEeCCccccccccch----------hhhhhHHHH
Confidence            34566666666655511111    2222223333333    46899999999998776311          223444444


Q ss_pred             HhcCCCCCCCEEEEEEeCCCCccc-----hhccCCCCcccEEEecCCCHHHHHHHHHHHH
Q psy5642          79 EMDGIVPLNNVTIVAATNRPDRID-----KALLRPGRLDRLIYVPLPDDLTRAAILKIRL  133 (237)
Q Consensus        79 ~l~~~~~~~~v~vI~ttn~~~~ld-----~al~r~gRf~~~i~~~~P~~~~R~~il~~~l  133 (237)
                      ....    .++.++.+|..|.+++     ++++.  -....|.++.++.+.+.  +..++
T Consensus       248 ~~Rk----~g~~~~l~tQ~~~~l~~~~~~~~i~~--n~~~~i~~~~~~~~~~~--l~~~~  299 (304)
T PF12846_consen  248 EGRK----YGVGLILATQSPSDLPKSPIEDAILA--NCNTKIIFRLEDSDDAE--LAELF  299 (304)
T ss_pred             HHHh----cCCEEEEeeCCHHHHhccchHHHHHH--hCCcEEEecCChHHHHH--HHHHc
Confidence            4443    4678888899999999     78888  78888888888877666  44443

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=92.31  E-value=0.65  Score=39.15  Aligned_cols=59  Identities=15%  Similarity=0.186  Sum_probs=49.0

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCC
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P  120 (237)
                      .-|++|+++|.+..               ...+.||..+++  +..++++|.+|+.++.+.+.+++  |-.. +.++.+
T Consensus        89 ~KV~II~~ae~m~~---------------~AaNaLLK~LEE--Pp~~t~fiLit~~~~~lLpTI~S--RCq~-~~~~~~  147 (261)
T PRK05818         89 KKIYIIYGIEKLNK---------------QSANSLLKLIEE--PPKNTYGIFTTRNENNILNTILS--RCVQ-YVVLSK  147 (261)
T ss_pred             CEEEEeccHhhhCH---------------HHHHHHHHhhcC--CCCCeEEEEEECChHhCchHhhh--heee-eecCCh
Confidence            46999999998833               457999999999  55789999999999999999999  8643 666666

>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=92.18  E-value=1.2  Score=38.35  Aligned_cols=80  Identities=20%  Similarity=0.313  Sum_probs=51.6

Q ss_pred             cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCC---------C-
Q psy5642          40 VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRP---------G-  109 (237)
Q Consensus        40 ~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~---------g-  109 (237)
                      ..|-||+|||+|.+-+.               -+..++..+..+-...++++|.+.+. +.+-.++...         | 
T Consensus       171 ~~~iViiIDdLDR~~~~---------------~i~~~l~~ik~~~~~~~i~~Il~~D~-~~l~~ai~~~~~~~~~~~~~~  234 (325)
T PF07693_consen  171 KKRIVIIIDDLDRCSPE---------------EIVELLEAIKLLLDFPNIIFILAFDP-EILEKAIEKNYGEGFDEIDGR  234 (325)
T ss_pred             CceEEEEEcchhcCCcH---------------HHHHHHHHHHHhcCCCCeEEEEEecH-HHHHHHHHhhcCcccccccHH
Confidence            45789999999998332               13444444444444467777777653 4333333320         0 


Q ss_pred             -----CcccEEEecCCCHHHHHHHHHHHHcC
Q psy5642         110 -----RLDRLIYVPLPDDLTRAAILKIRLAR  135 (237)
Q Consensus       110 -----Rf~~~i~~~~P~~~~R~~il~~~l~~  135 (237)
                           .|+..+.+|.|+..+...++...+..
T Consensus       235 ~yLeKiiq~~~~lP~~~~~~~~~~~~~~~~~  265 (325)
T PF07693_consen  235 EYLEKIIQVPFSLPPPSPSDLERYLNELLES  265 (325)
T ss_pred             HHHHhhcCeEEEeCCCCHHHHHHHHHHHHHH
Confidence                 36788899999999988888877543

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 [].

>KOG1969|consensus

Probab=92.03  E-value=3.8  Score=39.51  Aligned_cols=128  Identities=18%  Similarity=0.185  Sum_probs=75.7

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHHHh--------cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHH
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRARQ--------VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQM   76 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~--------~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~l   76 (237)
                      .++-.+++|++|+=-+      ...+++-...|..        .+|.+|+|||||--.            .....++..+
T Consensus       349 qaGYsVvEINASDeRt------~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa~------------~~~Vdvilsl  410 (877)
T KOG1969|consen  349 QAGYSVVEINASDERT------APMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGAP------------RAAVDVILSL  410 (877)
T ss_pred             hcCceEEEeccccccc------HHHHHHHHHHHHhhccccccCCCcceEEEecccCCc------------HHHHHHHHHH
Confidence            3566788999987653      4445554444443        369999999998531            1112223233


Q ss_pred             HHH----hcCCCC---------CC---CEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-
Q psy5642          77 LTE----MDGIVP---------LN---NVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-  139 (237)
Q Consensus        77 l~~----l~~~~~---------~~---~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-  139 (237)
                      +..    ..+...         ..   ..-||+.+|+  ..-|+|+.-.-|..+|+|..|...--.+=|+....+.... 
T Consensus       411 v~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNd--LYaPaLR~Lr~~A~ii~f~~p~~s~Lv~RL~~IC~rE~mr~  488 (877)
T KOG1969|consen  411 VKATNKQATGKQAKKDKKRKKKRSKLLTRPIICICND--LYAPALRPLRPFAEIIAFVPPSQSRLVERLNEICHRENMRA  488 (877)
T ss_pred             HHhhcchhhcCcccchhhhhhhccccccCCEEEEecC--ccchhhhhcccceEEEEecCCChhHHHHHHHHHHhhhcCCC
Confidence            321    111100         00   1467888885  4458888544699999999998887777777666554443 


Q ss_pred             chhhHHHHHHHCC
Q psy5642         140 EDVCVEELVRLTE  152 (237)
Q Consensus       140 ~~~~~~~la~~t~  152 (237)
                      ....+..|++.|+
T Consensus       489 d~~aL~~L~el~~  501 (877)
T KOG1969|consen  489 DSKALNALCELTQ  501 (877)
T ss_pred             CHHHHHHHHHHhc
Confidence            3344555555544

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=91.83  E-value=0.53  Score=41.14  Aligned_cols=108  Identities=22%  Similarity=0.213  Sum_probs=55.4

Q ss_pred             CceEEEEEeccccccccc-----ChHH-------HHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHH
Q psy5642           6 GLTEVVESIGPELFRKYV-----GESE-------RCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVL   73 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~-----g~~~-------~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~   73 (237)
                      ...||+.|+|..+-....     |...       ..-.-.|..|   ...+|||||+|.+-.               .+.
T Consensus        49 ~~~pfv~vnc~~~~~~~l~~~lfG~~~g~~~ga~~~~~G~~~~a---~gGtL~Ldei~~L~~---------------~~Q  110 (329)
T TIGR02974        49 WQGPLVKLNCAALSENLLDSELFGHEAGAFTGAQKRHQGRFERA---DGGTLFLDELATASL---------------LVQ  110 (329)
T ss_pred             cCCCeEEEeCCCCChHHHHHHHhccccccccCcccccCCchhhC---CCCEEEeCChHhCCH---------------HHH
Confidence            567999999986532110     0000       0000112222   357999999999832               234


Q ss_pred             HHHHHHhcCCC---------CCCCEEEEEEeCCC-------CccchhccCCCCcccEEEecCCCHH----HHHHHHHHHH
Q psy5642          74 AQMLTEMDGIV---------PLNNVTIVAATNRP-------DRIDKALLRPGRLDRLIYVPLPDDL----TRAAILKIRL  133 (237)
Q Consensus        74 ~~ll~~l~~~~---------~~~~v~vI~ttn~~-------~~ld~al~r~gRf~~~i~~~~P~~~----~R~~il~~~l  133 (237)
                      ..|+..|+.-.         ...++-+|++|+..       ..+.+.|..  ||. .+.+..|..-    +...++++++
T Consensus       111 ~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~at~~~l~~~~~~g~fr~dL~~--rl~-~~~i~lPpLReR~eDI~~L~~~fl  187 (329)
T TIGR02974       111 EKLLRVIEYGEFERVGGSQTLQVDVRLVCATNADLPALAAEGRFRADLLD--RLA-FDVITLPPLRERQEDIMLLAEHFA  187 (329)
T ss_pred             HHHHHHHHcCcEEecCCCceeccceEEEEechhhHHHHhhcCchHHHHHH--Hhc-chhcCCCchhhhhhhHHHHHHHHH
Confidence            45555554321         11347888888753       133455555  553 2344445444    4444555555


Q ss_pred             c
Q psy5642         134 A  134 (237)
Q Consensus       134 ~  134 (237)
                      .
T Consensus       188 ~  188 (329)
T TIGR02974       188 I  188 (329)
T ss_pred             H
Confidence            4

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

>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]

Probab=91.71  E-value=2.8  Score=40.02  Aligned_cols=112  Identities=20%  Similarity=0.245  Sum_probs=67.4

Q ss_pred             EEEEEEeCCC-----CccchhccCCCCcccEEEec--CC-CHHHHHHHHHHHHcCC------CCCchhhHHHHHHHCCCC
Q psy5642          89 VTIVAATNRP-----DRIDKALLRPGRLDRLIYVP--LP-DDLTRAAILKIRLARS------PLGEDVCVEELVRLTEGY  154 (237)
Q Consensus        89 v~vI~ttn~~-----~~ld~al~r~gRf~~~i~~~--~P-~~~~R~~il~~~l~~~------~~~~~~~~~~la~~t~g~  154 (237)
                      ..+|+..|.-     ..+++.++.  -|....++.  +| +.+.|..+|..+.+..      +.-....+..|......+
T Consensus       277 ~klI~~Gn~~~l~~l~~~~~~r~~--g~~y~ae~~~~m~~~~~nr~k~~~~~~q~v~~d~~ip~~~~~Av~~li~~a~R~  354 (647)
T COG1067         277 LKLILAGNREDLEDLHEPDRSRIE--GFGYEAEFEDTMPITDANRSKLVQFYVQELARDGNIPHLDKDAVEELIREAARR  354 (647)
T ss_pred             eEEEeeCCHHHHHhhcccCHHHHh--hcceEEEEcCCCCCChHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHh
Confidence            5566665542     244566665  566555555  56 7789999998777532      221333444444333333


Q ss_pred             CcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCC
Q psy5642         155 SGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPR  222 (237)
Q Consensus       155 s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~  222 (237)
                      ++..                  ..-..|+.-|.++++.|..-+..++  ...++.+|+..|++..++.
T Consensus       355 Ag~~------------------~~Ltl~~rdl~~lv~~A~~ia~~~~--~~~I~ae~Ve~a~~~~~~~  402 (647)
T COG1067         355 AGDQ------------------NKLTLRLRDLGNLVREAGDIAVSEG--RKLITAEDVEEALQKRELR  402 (647)
T ss_pred             cccc------------------ceeccCHHHHHHHHHHhhHHHhcCC--cccCcHHHHHHHHHhhhhH
Confidence            3211                  1111222228899998888887765  4579999999999997764

>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=91.69  E-value=1.3  Score=37.25  Aligned_cols=104  Identities=13%  Similarity=0.128  Sum_probs=55.8

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhcc
Q psy5642          27 ERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALL  106 (237)
Q Consensus        27 ~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~  106 (237)
                      ......+.+. -...+++|+||+++...                 ....+...+..  ...+.-||.||+... +-..+.
T Consensus        88 ~~~~~~l~~~-L~~~~~LlVlDdv~~~~-----------------~~~~l~~~~~~--~~~~~kilvTTR~~~-v~~~~~  146 (287)
T PF00931_consen   88 EELQDQLREL-LKDKRCLLVLDDVWDEE-----------------DLEELREPLPS--FSSGSKILVTTRDRS-VAGSLG  146 (287)
T ss_dssp             HHHHHHHHHH-HCCTSEEEEEEEE-SHH-----------------HH-------HC--HHSS-EEEEEESCGG-GGTTHH
T ss_pred             ccccccchhh-hccccceeeeeeecccc-----------------ccccccccccc--ccccccccccccccc-cccccc
Confidence            3334444443 33459999999987642                 12222222211  112456777887642 222222


Q ss_pred             CCCCcccEEEecCCCHHHHHHHHHHHHcCCC----CCchhhHHHHHHHCCCC
Q psy5642         107 RPGRLDRLIYVPLPDDLTRAAILKIRLARSP----LGEDVCVEELVRLTEGY  154 (237)
Q Consensus       107 r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~----~~~~~~~~~la~~t~g~  154 (237)
                      .   -...++++..+.++-.++|........    ........+++..+.|+
T Consensus       147 ~---~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~gl  195 (287)
T PF00931_consen  147 G---TDKVIELEPLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGL  195 (287)
T ss_dssp             S---CEEEEECSS--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-
T ss_pred             c---cccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            1   156899999999999999998876543    11234567888888654

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.

>PRK15115 response regulator GlrR; Provisional

Probab=91.58  E-value=0.41  Score=43.29  Aligned_cols=105  Identities=18%  Similarity=0.292  Sum_probs=57.2

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHH---------------HhcCCeEEEEccccccccccCCCCCCCCCchHH
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRA---------------RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQE   70 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a---------------~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~   70 (237)
                      .+.+|+.++|..+-..      ..-..+|..+               ......+|||||+|.|-..              
T Consensus       184 ~~~~f~~i~c~~~~~~------~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~~--------------  243 (444)
T PRK15115        184 ASKPFIAINCGALPEQ------LLESELFGHARGAFTGAVSNREGLFQAAEGGTLFLDEIGDMPAP--------------  243 (444)
T ss_pred             CCCCeEEEeCCCCCHH------HHHHHhcCCCcCCCCCCccCCCCcEEECCCCEEEEEccccCCHH--------------
Confidence            4578999999876321      1111223211               1123579999999998332              


Q ss_pred             HHHHHHHHHhcCCC-----C----CCCEEEEEEeCCCCccchhccCCCCcc-------cEEEecCCCHHHHHH----HHH
Q psy5642          71 RVLAQMLTEMDGIV-----P----LNNVTIVAATNRPDRIDKALLRPGRLD-------RLIYVPLPDDLTRAA----ILK  130 (237)
Q Consensus        71 ~~~~~ll~~l~~~~-----~----~~~v~vI~ttn~~~~ld~al~r~gRf~-------~~i~~~~P~~~~R~~----il~  130 (237)
                       +...|+..|+.-.     .    ..++.+|+||+.  +++..+.+ |+|.       ..+.+..|...+|.+    +++
T Consensus       244 -~q~~L~~~l~~~~~~~~g~~~~~~~~~rii~~~~~--~l~~~~~~-~~f~~~l~~~l~~~~i~lPpLr~R~eDi~~l~~  319 (444)
T PRK15115        244 -LQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHR--DLPKAMAR-GEFREDLYYRLNVVSLKIPALAERTEDIPLLAN  319 (444)
T ss_pred             -HHHHHHHHHhhCCEEeCCCCceeeeeEEEEEeCCC--CHHHHHHc-CCccHHHHHhhceeeecCCChHhccccHHHHHH
Confidence             2344555554311     0    125788888885  35544443 5662       135566676666643    444


Q ss_pred             HHHc
Q psy5642         131 IRLA  134 (237)
Q Consensus       131 ~~l~  134 (237)
                      .++.
T Consensus       320 ~~l~  323 (444)
T PRK15115        320 HLLR  323 (444)
T ss_pred             HHHH
Confidence            5554

>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=91.39  E-value=2.1  Score=33.51  Aligned_cols=85  Identities=19%  Similarity=0.326  Sum_probs=45.4

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHH---------------HhcCCeEEEEccccccccccCCCCCCCCCchH
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRA---------------RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQ   69 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a---------------~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~   69 (237)
                      ..+.||+.|+|+.+-.      +..-..+|-..               ....-.+||||||+.+-.              
T Consensus        48 r~~~pfi~vnc~~~~~------~~~e~~LFG~~~~~~~~~~~~~~G~l~~A~~GtL~Ld~I~~L~~--------------  107 (168)
T PF00158_consen   48 RKNGPFISVNCAALPE------ELLESELFGHEKGAFTGARSDKKGLLEQANGGTLFLDEIEDLPP--------------  107 (168)
T ss_dssp             TTTS-EEEEETTTS-H------HHHHHHHHEBCSSSSTTTSSEBEHHHHHTTTSEEEEETGGGS-H--------------
T ss_pred             cccCCeEEEehhhhhc------chhhhhhhccccccccccccccCCceeeccceEEeecchhhhHH--------------
Confidence            4678999999987632      22223334211               112347999999999833              


Q ss_pred             HHHHHHHHHHhcC-----CCC----CCCEEEEEEeCCCCccchhccCCCCccc
Q psy5642          70 ERVLAQMLTEMDG-----IVP----LNNVTIVAATNRPDRIDKALLRPGRLDR  113 (237)
Q Consensus        70 ~~~~~~ll~~l~~-----~~~----~~~v~vI~ttn~~~~ld~al~r~gRf~~  113 (237)
                       .+...|+..|+.     ...    .-++-+|+||+.  ++...+.. |+|..
T Consensus       108 -~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~st~~--~l~~~v~~-g~fr~  156 (168)
T PF00158_consen  108 -ELQAKLLRVLEEGKFTRLGSDKPVPVDVRIIASTSK--DLEELVEQ-GRFRE  156 (168)
T ss_dssp             -HHHHHHHHHHHHSEEECCTSSSEEE--EEEEEEESS---HHHHHHT-TSS-H
T ss_pred             -HHHHHHHHHHhhchhccccccccccccceEEeecCc--CHHHHHHc-CCChH
Confidence             233444444442     111    125889999984  45554443 67754

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 ....

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=90.94  E-value=1.2  Score=41.36  Aligned_cols=101  Identities=18%  Similarity=0.284  Sum_probs=51.8

Q ss_pred             CCceEEEEEecccccccc-----cChHH-------HHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHH
Q psy5642           5 GGLTEVVESIGPELFRKY-----VGESE-------RCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERV   72 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~-----~g~~~-------~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~   72 (237)
                      .++.||+.++|+.+-...     +|...       ..-.-+|+.|   ....|||||+|.+-.               .+
T Consensus       253 r~~~pfv~inca~~~~~~~e~elFG~~~~~~~~~~~~~~g~~e~a---~~GtL~LdeI~~L~~---------------~~  314 (520)
T PRK10820        253 RGKKPFLALNCASIPDDVVESELFGHAPGAYPNALEGKKGFFEQA---NGGSVLLDEIGEMSP---------------RM  314 (520)
T ss_pred             CCCCCeEEeccccCCHHHHHHHhcCCCCCCcCCcccCCCChhhhc---CCCEEEEeChhhCCH---------------HH
Confidence            456799999998764211     11000       0001123333   347899999999832               22


Q ss_pred             HHHHHHHhcCC--CC-------CCCEEEEEEeCCC-C------ccchhccCCCCcccEEEecCCCHHHHH
Q psy5642          73 LAQMLTEMDGI--VP-------LNNVTIVAATNRP-D------RIDKALLRPGRLDRLIYVPLPDDLTRA  126 (237)
Q Consensus        73 ~~~ll~~l~~~--~~-------~~~v~vI~ttn~~-~------~ld~al~r~gRf~~~i~~~~P~~~~R~  126 (237)
                      ...|+..++.-  ..       ..++-||+||+.+ .      .+.+.+..  |+. .+.+..|...+|.
T Consensus       315 Q~~Ll~~l~~~~~~~~g~~~~~~~~vRiI~st~~~l~~l~~~g~f~~dL~~--rL~-~~~i~lPpLreR~  381 (520)
T PRK10820        315 QAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGEFREDLYY--RLN-VLTLNLPPLRDRP  381 (520)
T ss_pred             HHHHHHHHhcCCcccCCCCcceeeeeEEEEecCCCHHHHHHcCCccHHHHh--hcC-eeEEeCCCcccCh
Confidence            34455555431  11       1246788887653 2      23334444  443 3555556555544

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

Probab=90.87  E-value=0.59  Score=41.88  Aligned_cols=106  Identities=14%  Similarity=0.137  Sum_probs=57.4

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHh-------c--------CCeEEEEccccccccccCCCCCCCCCchHH
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQ-------V--------SPSVIFFDELDSLAGERGDGGGGGGSNVQE   70 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~-------~--------~P~il~iDeid~l~~~~~~~~~~~~~~~~~   70 (237)
                      ...|||.++|..+......      ..+|-..+.       .        .-.+||+|||..+-..              
T Consensus       129 ~~~PFI~~NCa~~~en~~~------~eLFG~~kGaftGa~~~k~Glfe~A~GGtLfLDEI~~LP~~--------------  188 (403)
T COG1221         129 AEAPFIAFNCAAYSENLQE------AELFGHEKGAFTGAQGGKAGLFEQANGGTLFLDEIHRLPPE--------------  188 (403)
T ss_pred             cCCCEEEEEHHHhCcCHHH------HHHhccccceeecccCCcCchheecCCCEEehhhhhhCCHh--------------
Confidence            5789999999876543211      113332221       1        1359999999988332              


Q ss_pred             HHHHHHHHHhcCC-----C----CCCCEEEEEEeCCCCccchhccC-CC----CcccEEEecCCC--HHHHHHHHHHHHc
Q psy5642          71 RVLAQMLTEMDGI-----V----PLNNVTIVAATNRPDRIDKALLR-PG----RLDRLIYVPLPD--DLTRAAILKIRLA  134 (237)
Q Consensus        71 ~~~~~ll~~l~~~-----~----~~~~v~vI~ttn~~~~ld~al~r-~g----Rf~~~i~~~~P~--~~~R~~il~~~l~  134 (237)
                       ....++..|+.-     -    ....|.+|++|+  ..++.+++. ..    |+-..|.+|+..  .+++..++.++++
T Consensus       189 -~Q~kLl~~le~g~~~rvG~~~~~~~dVRli~AT~--~~l~~~~~~g~dl~~rl~~~~I~LPpLrER~~Di~~L~e~Fl~  265 (403)
T COG1221         189 -GQEKLLRVLEEGEYRRVGGSQPRPVDVRLICATT--EDLEEAVLAGADLTRRLNILTITLPPLRERKEDILLLAEHFLK  265 (403)
T ss_pred             -HHHHHHHHHHcCceEecCCCCCcCCCceeeeccc--cCHHHHHHhhcchhhhhcCceecCCChhhchhhHHHHHHHHHH
Confidence             234455555541     1    122477787777  455555554 11    444455555442  2455555555554

>TIGR00602 rad24 checkpoint protein rad24

Probab=90.86  E-value=3.6  Score=39.32  Aligned_cols=119  Identities=14%  Similarity=0.132  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHHHHh----------cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEe
Q psy5642          26 SERCVRDVFKRARQ----------VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAAT   95 (237)
Q Consensus        26 ~~~~l~~~f~~a~~----------~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~tt   95 (237)
                      ....++.++..|..          ....||+|||++.++...            ...+..++.++.  ...+++.+|+++
T Consensus       170 ~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~r~------------~~~lq~lLr~~~--~e~~~~pLI~I~  235 (637)
T TIGR00602       170 QIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFYRD------------TRALHEILRWKY--VSIGRCPLVFII  235 (637)
T ss_pred             hHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhchhh------------HHHHHHHHHHHh--hcCCCceEEEEe
Confidence            35566666666652          246799999999876431            122334444221  122344445444


Q ss_pred             C-CCC--------c------cchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC--------chhhHHHHHHHCC
Q psy5642          96 N-RPD--------R------IDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG--------EDVCVEELVRLTE  152 (237)
Q Consensus        96 n-~~~--------~------ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~--------~~~~~~~la~~t~  152 (237)
                      + .+.        .      |.++++..-|. .+|.|++.+..+-...|+..+......        ....+..|+.   
T Consensus       236 TE~~~~~~~~~~~~f~~~~lL~~eLls~~rv-~~I~FnPia~t~l~K~L~rIl~~E~~~~~~~~~~p~~~~l~~I~~---  311 (637)
T TIGR00602       236 TESLEGDNNQRRLLFPAETIMNKEILEEPRV-SNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVELLCQ---  311 (637)
T ss_pred             cCCccccccccccccchhcccCHhHhcccce-eEEEeCCCCHHHHHHHHHHHHHhhhhccccccccCCHHHHHHHHH---
Confidence            4 222        1      23667642233 379999999999888888777643211        2235556655   


Q ss_pred             CCCcccccchh
Q psy5642         153 GYSGAEQSLSK  163 (237)
Q Consensus       153 g~s~~Dl~~~~  163 (237)
                       .+.+|++..+
T Consensus       312 -~s~GDiRsAI  321 (637)
T TIGR00602       312 -GCSGDIRSAI  321 (637)
T ss_pred             -hCCChHHHHH
Confidence             4556744443

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

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=90.65  E-value=4.7  Score=38.57  Aligned_cols=127  Identities=16%  Similarity=0.130  Sum_probs=68.2

Q ss_pred             CEEEEEEeCCC--CccchhccCCCCcc---cEEEecC--C-CHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccc
Q psy5642          88 NVTIVAATNRP--DRIDKALLRPGRLD---RLIYVPL--P-DDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQ  159 (237)
Q Consensus        88 ~v~vI~ttn~~--~~ld~al~r~gRf~---~~i~~~~--P-~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl  159 (237)
                      ++.||+++|..  ..+|++++.  ||.   ..++|+.  | +.+.+..+++..-+.....         .....|+..-+
T Consensus       277 dvrvI~a~~~~ll~~~dpdL~~--rfk~~~v~v~f~~~~~d~~e~~~~~~~~iaqe~~~~---------G~l~~f~~eAV  345 (637)
T PRK13765        277 DFIMVAAGNLDALENMHPALRS--RIKGYGYEVYMRDTMEDTPENRRKLVRFVAQEVKRD---------GKIPHFDRDAV  345 (637)
T ss_pred             eeEEEEecCcCHHHhhhHHHHH--HhccCeEEEEcccccCCCHHHHHHHHHHHHHHhhhc---------cCCCCCCHHHH
Confidence            46788888874  578999999  986   4555552  2 3455555555333221100         00112333334


Q ss_pred             cchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCCCHHHHHHH
Q psy5642         160 SLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLY  231 (237)
Q Consensus       160 ~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~~~~~~~~~  231 (237)
                      ..+++.+.+.+..|..   =......|..+++.|...+..++  ...++.++..+|+.. ......+..+.|
T Consensus       346 a~LI~~~~R~ag~r~~---lsl~~~~l~~l~r~a~~~a~~~~--~~~i~~~~v~~a~~~-~~~i~~~~~~~~  411 (637)
T PRK13765        346 EEIIREAKRRAGRKGH---LTLKLRDLGGLVRVAGDIARSEG--AELTTAEHVLEAKKI-ARSIEQQLADRY  411 (637)
T ss_pred             HHHHHHHHHHhCCccc---cccCHHHHHHHHHHHHHHHHhhc--cceecHHHHHHHHHh-hhhhhHHHHHHH
Confidence            4444444443333320   00112238888999888877666  345888888888754 233444444433

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=90.23  E-value=0.77  Score=40.16  Aligned_cols=78  Identities=18%  Similarity=0.259  Sum_probs=47.2

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC----C-------CCCEEEEEEeCCCC-----------
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV----P-------LNNVTIVAATNRPD-----------   99 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~----~-------~~~v~vI~ttn~~~-----------   99 (237)
                      ..|++|||+|.+-.+               ....+...|++..    +       +.+.-|+|++|-..           
T Consensus       122 ~GiccIDe~dk~~~~---------------~~~~l~eaMEqq~isi~kagi~~~l~ar~svlaa~NP~~g~~~~~~~~~~  186 (331)
T PF00493_consen  122 GGICCIDEFDKMKED---------------DRDALHEAMEQQTISIAKAGIVTTLNARCSVLAAANPKFGRYDPNKSLSE  186 (331)
T ss_dssp             TSEEEECTTTT--CH---------------HHHHHHHHHHCSCEEECTSSSEEEEE---EEEEEE--TT--S-TTS-CGC
T ss_pred             Cceeeecccccccch---------------HHHHHHHHHHcCeeccchhhhcccccchhhhHHHHhhhhhhcchhhhhHH
Confidence            479999999987321               2455556665421    1       13578999998766           


Q ss_pred             --ccchhccCCCCcccEEEe-cCCCHHHHHHHHHHHHcCC
Q psy5642         100 --RIDKALLRPGRLDRLIYV-PLPDDLTRAAILKIRLARS  136 (237)
Q Consensus       100 --~ld~al~r~gRf~~~i~~-~~P~~~~R~~il~~~l~~~  136 (237)
                        .+++.|++  |||.++.+ ..|+.+.=..+.++.+..+
T Consensus       187 ni~l~~~LLS--RFDLif~l~D~~d~~~D~~la~~il~~~  224 (331)
T PF00493_consen  187 NINLPPPLLS--RFDLIFLLRDKPDEEEDERLAEHILDSH  224 (331)
T ss_dssp             CT-S-CCCHC--C-SEEECC--TTT-HHHHHHHHHHHTTT
T ss_pred             hcccchhhHh--hcCEEEEeccccccccccccceEEEecc
Confidence              58999999  99987765 5778777777777777654

; 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.

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=89.81  E-value=4  Score=37.89  Aligned_cols=75  Identities=23%  Similarity=0.205  Sum_probs=40.5

Q ss_pred             CceEEEEEeccccccc-----ccChHHH-------HHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHH
Q psy5642           6 GLTEVVESIGPELFRK-----YVGESER-------CVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVL   73 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~-----~~g~~~~-------~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~   73 (237)
                      .+.+|+.|+|..+-..     .+|....       .-.-.|+.|   ....|||||+|.+-.               .+.
T Consensus       237 ~~~p~v~v~c~~~~~~~~e~~lfG~~~g~~~ga~~~~~g~~~~a---~gGtL~ldeI~~L~~---------------~~Q  298 (509)
T PRK05022        237 ADKPLVYLNCAALPESLAESELFGHVKGAFTGAISNRSGKFELA---DGGTLFLDEIGELPL---------------ALQ  298 (509)
T ss_pred             CCCCeEEEEcccCChHHHHHHhcCccccccCCCcccCCcchhhc---CCCEEEecChhhCCH---------------HHH
Confidence            5679999999876421     1110000       000123322   357899999999832               234


Q ss_pred             HHHHHHhcCCC---------CCCCEEEEEEeCCC
Q psy5642          74 AQMLTEMDGIV---------PLNNVTIVAATNRP   98 (237)
Q Consensus        74 ~~ll~~l~~~~---------~~~~v~vI~ttn~~   98 (237)
                      ..|+..++.-.         ...++-+|++|+..
T Consensus       299 ~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~  332 (509)
T PRK05022        299 AKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRD  332 (509)
T ss_pred             HHHHHHHhcCCEeeCCCCcceecceEEEEecCCC
Confidence            44555554321         01247888888753

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

Probab=89.65  E-value=1.5  Score=38.18  Aligned_cols=75  Identities=21%  Similarity=0.297  Sum_probs=50.7

Q ss_pred             ceEEEEEeccccc-ccccChH-HHHHHHHHHHHHh----cCCeEEEEccccccccccCC-CCCCCCCchHHHHHHHHHHH
Q psy5642           7 LTEVVESIGPELF-RKYVGES-ERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGD-GGGGGGSNVQERVLAQMLTE   79 (237)
Q Consensus         7 ~~~~i~v~~s~l~-~~~~g~~-~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~-~~~~~~~~~~~~~~~~ll~~   79 (237)
                      +.||-.-++..|. ..|+|+- +..+.+++..|-.    .+..||||||||.+..+..+ +...+  ....-+...||..
T Consensus       122 nVPFaiADATtLTEAGYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIarkSeN~SITRD--VSGEGVQQALLKi  199 (408)
T COG1219         122 NVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIARKSENPSITRD--VSGEGVQQALLKI  199 (408)
T ss_pred             CCCeeeccccchhhccccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhccCCCCCcccc--cCchHHHHHHHHH
Confidence            5677778887754 5788854 6667777776642    36789999999999977643 22211  1124567778888


Q ss_pred             hcCC
Q psy5642          80 MDGI   83 (237)
Q Consensus        80 l~~~   83 (237)
                      |.+.
T Consensus       200 iEGT  203 (408)
T COG1219         200 IEGT  203 (408)
T ss_pred             HcCc
Confidence            8765

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

Probab=89.53  E-value=1.1  Score=40.85  Aligned_cols=106  Identities=19%  Similarity=0.243  Sum_probs=56.4

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHH---------------HhcCCeEEEEccccccccccCCCCCCCCCchH
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRA---------------RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQ   69 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a---------------~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~   69 (237)
                      ....+|+.++|+.+..      ...-..+|...               .......|||||+|.+-.              
T Consensus       187 ~~~~~~i~i~c~~~~~------~~~~~~lfg~~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l~~--------------  246 (469)
T PRK10923        187 RAKAPFIALNMAAIPK------DLIESELFGHEKGAFTGANTIRQGRFEQADGGTLFLDEIGDMPL--------------  246 (469)
T ss_pred             CCCCCeEeeeCCCCCH------HHHHHHhcCCCCCCCCCCCcCCCCCeeECCCCEEEEeccccCCH--------------
Confidence            3567999999987732      11122232211               112356899999999833              


Q ss_pred             HHHHHHHHHHhcCCC-----C----CCCEEEEEEeCCCC-------ccchhccCCCCcccEEEecCCCHH----HHHHHH
Q psy5642          70 ERVLAQMLTEMDGIV-----P----LNNVTIVAATNRPD-------RIDKALLRPGRLDRLIYVPLPDDL----TRAAIL  129 (237)
Q Consensus        70 ~~~~~~ll~~l~~~~-----~----~~~v~vI~ttn~~~-------~ld~al~r~gRf~~~i~~~~P~~~----~R~~il  129 (237)
                       .+...|+..++.-.     .    ..++-+|+||+..-       .+.+.+..  ||. .+.+..|...    +...++
T Consensus       247 -~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~~~~~L~~--~l~-~~~i~~PpLreR~~Di~~l~  322 (469)
T PRK10923        247 -DVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEGKFREDLFH--RLN-VIRVHLPPLRERREDIPRLA  322 (469)
T ss_pred             -HHHHHHHHHHhcCcEEeCCCCCeEEeeEEEEEeCCCCHHHHHHcCCchHHHHH--Hhc-ceeecCCCcccchhhHHHHH
Confidence             23345555554321     0    12467888887531       34455555  553 2444445443    444456


Q ss_pred             HHHHc
Q psy5642         130 KIRLA  134 (237)
Q Consensus       130 ~~~l~  134 (237)
                      .+++.
T Consensus       323 ~~~l~  327 (469)
T PRK10923        323 RHFLQ  327 (469)
T ss_pred             HHHHH
Confidence            66654

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=89.48  E-value=1.8  Score=37.77  Aligned_cols=108  Identities=20%  Similarity=0.205  Sum_probs=55.8

Q ss_pred             CceEEEEEeccccccc-----ccChHH-------HHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHH
Q psy5642           6 GLTEVVESIGPELFRK-----YVGESE-------RCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVL   73 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~-----~~g~~~-------~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~   73 (237)
                      ...||+.|+|..+-..     ++|...       ..-...|..|   ...+|||||+|.+-.               .+.
T Consensus        56 ~~~pfv~v~c~~~~~~~~~~~lfg~~~~~~~g~~~~~~g~l~~a---~gGtL~l~~i~~L~~---------------~~Q  117 (326)
T PRK11608         56 WQGPFISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFERA---DGGTLFLDELATAPM---------------LVQ  117 (326)
T ss_pred             cCCCeEEEeCCCCCHHHHHHHHccccccccCCcccccCCchhcc---CCCeEEeCChhhCCH---------------HHH
Confidence            4679999999876311     111000       0001122222   357999999999832               234


Q ss_pred             HHHHHHhcCCC--C-------CCCEEEEEEeCCC-------CccchhccCCCCcc-cEEEecCCCH--HHHHHHHHHHH
Q psy5642          74 AQMLTEMDGIV--P-------LNNVTIVAATNRP-------DRIDKALLRPGRLD-RLIYVPLPDD--LTRAAILKIRL  133 (237)
Q Consensus        74 ~~ll~~l~~~~--~-------~~~v~vI~ttn~~-------~~ld~al~r~gRf~-~~i~~~~P~~--~~R~~il~~~l  133 (237)
                      ..|+..++.-.  .       ..++.||+||+..       ..+.+.+..  ||. ..|.+|+...  ++...++.+++
T Consensus       118 ~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~s~~~l~~l~~~g~f~~dL~~--~l~~~~i~lPpLReR~eDI~~L~~~fl  194 (326)
T PRK11608        118 EKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGKFRADLLD--RLAFDVVQLPPLRERQSDIMLMAEHFA  194 (326)
T ss_pred             HHHHHHHhcCcEEeCCCCceeeccEEEEEeCchhHHHHHHcCCchHHHHH--hcCCCEEECCChhhhhhhHHHHHHHHH
Confidence            44555554311  1       1247788888753       245566666  663 3455544421  34445555555

>PF13173 AAA_14: AAA domain

Probab=89.23  E-value=0.62  Score=34.50  Aligned_cols=64  Identities=20%  Similarity=0.221  Sum_probs=34.3

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhcc--CCCCcccEEEec
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALL--RPGRLDRLIYVP  118 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~--r~gRf~~~i~~~  118 (237)
                      .+.+|+|||+..+-            . ....+..+.+   ..   .++-+|.|++....+.....  =+||.. .+++.
T Consensus        61 ~~~~i~iDEiq~~~------------~-~~~~lk~l~d---~~---~~~~ii~tgS~~~~l~~~~~~~l~gr~~-~~~l~  120 (128)
T PF13173_consen   61 GKKYIFIDEIQYLP------------D-WEDALKFLVD---NG---PNIKIILTGSSSSLLSKDIAESLAGRVI-EIELY  120 (128)
T ss_pred             CCcEEEEehhhhhc------------c-HHHHHHHHHH---hc---cCceEEEEccchHHHhhcccccCCCeEE-EEEEC
Confidence            67899999998871            0 1122333333   21   24445555554444422211  135875 57888


Q ss_pred             CCCHHH
Q psy5642         119 LPDDLT  124 (237)
Q Consensus       119 ~P~~~~  124 (237)
                      +.+..+
T Consensus       121 Plsf~E  126 (128)
T PF13173_consen  121 PLSFRE  126 (128)
T ss_pred             CCCHHH
Confidence            877665

>PF14516 AAA_35: AAA-like domain

Probab=88.54  E-value=4  Score=35.64  Aligned_cols=102  Identities=17%  Similarity=0.183  Sum_probs=56.7

Q ss_pred             cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC---CCC--EEEEEEeCCCCccchhc-cCCCCccc
Q psy5642          40 VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP---LNN--VTIVAATNRPDRIDKAL-LRPGRLDR  113 (237)
Q Consensus        40 ~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~---~~~--v~vI~ttn~~~~ld~al-~r~gRf~~  113 (237)
                      ..|-||+|||+|.++...         .....+...+..+-.....   ..+  .+++++|.  ..+.... .+|=-+..
T Consensus       126 ~~~lVL~iDEiD~l~~~~---------~~~~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~--~~~~~~~~~SPFNIg~  194 (331)
T PF14516_consen  126 DKPLVLFIDEIDRLFEYP---------QIADDFFGLLRSWYEQRKNNPIWQKLRLILAGSTE--DYIILDINQSPFNIGQ  194 (331)
T ss_pred             CCCEEEEEechhhhccCc---------chHHHHHHHHHHHHHhcccCcccceEEEEEecCcc--cccccCCCCCCccccc
Confidence            479999999999997642         1223444444444332211   122  33333322  2222222 12212345


Q ss_pred             EEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCC
Q psy5642         114 LIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYS  155 (237)
Q Consensus       114 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s  155 (237)
                      .|+++.-+.++-..+++.+-..  . ....++.+-..|.|.-
T Consensus       195 ~i~L~~Ft~~ev~~L~~~~~~~--~-~~~~~~~l~~~tgGhP  233 (331)
T PF14516_consen  195 PIELPDFTPEEVQELAQRYGLE--F-SQEQLEQLMDWTGGHP  233 (331)
T ss_pred             ceeCCCCCHHHHHHHHHhhhcc--C-CHHHHHHHHHHHCCCH
Confidence            6788877899998888876433  2 2344888888887754

>PRK14700 recombination factor protein RarA; Provisional

Probab=88.14  E-value=2.1  Score=36.80  Aligned_cols=67  Identities=15%  Similarity=0.313  Sum_probs=48.5

Q ss_pred             CCCCEEEEEEeC-CCC-ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC------CCC-chhhHHHHHHHCCCCC
Q psy5642          85 PLNNVTIVAATN-RPD-RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS------PLG-EDVCVEELVRLTEGYS  155 (237)
Q Consensus        85 ~~~~v~vI~ttn-~~~-~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~------~~~-~~~~~~~la~~t~g~s  155 (237)
                      .++.|++||+|. +|. .+.++|++  |. +++.+..++.++-..+++..+...      .+. .+..+..|+.    ++
T Consensus         5 E~G~i~LIGATTENP~f~vn~ALlS--R~-~v~~l~~L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~----~a   77 (300)
T PRK14700          5 ESGKIILIGATTENPTYYLNDALVS--RL-FILRLKRLSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHN----YN   77 (300)
T ss_pred             cCCcEEEEeecCCCccceecHhhhh--hh-heeeecCCCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHH----hc
Confidence            346788888773 354 89999999  88 679999999999999999888631      111 4455555655    45


Q ss_pred             ccc
Q psy5642         156 GAE  158 (237)
Q Consensus       156 ~~D  158 (237)
                      .+|
T Consensus        78 ~GD   80 (300)
T PRK14700         78 EGD   80 (300)
T ss_pred             CCH
Confidence            567

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

Probab=87.49  E-value=1.1  Score=33.72  Aligned_cols=80  Identities=16%  Similarity=0.260  Sum_probs=43.0

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      ..+|+.++|..+-           .++++.+   .+.+|+|+|+|.+-.               .....++..|.... .
T Consensus        49 ~~~~~~~~~~~~~-----------~~~l~~a---~~gtL~l~~i~~L~~---------------~~Q~~L~~~l~~~~-~   98 (138)
T PF14532_consen   49 NGPFIVIDCASLP-----------AELLEQA---KGGTLYLKNIDRLSP---------------EAQRRLLDLLKRQE-R   98 (138)
T ss_dssp             CS-CCCCCHHCTC-----------HHHHHHC---TTSEEEEECGCCS-H---------------HHHHHHHHHHHHCT-T
T ss_pred             CCCeEEechhhCc-----------HHHHHHc---CCCEEEECChHHCCH---------------HHHHHHHHHHHhcC-C
Confidence            4466666666533           3455554   678999999999833               23344555555432 2


Q ss_pred             CCEEEEEEeCC-CCc------cchhccCCCCcc-cEEEec
Q psy5642          87 NNVTIVAATNR-PDR------IDKALLRPGRLD-RLIYVP  118 (237)
Q Consensus        87 ~~v~vI~ttn~-~~~------ld~al~r~gRf~-~~i~~~  118 (237)
                      .++-+|+|++. +..      +++.+..  ||. ..|.+|
T Consensus        99 ~~~RlI~ss~~~l~~l~~~~~~~~~L~~--~l~~~~i~lP  136 (138)
T PF14532_consen   99 SNVRLIASSSQDLEELVEEGRFSPDLYY--RLSQLEIHLP  136 (138)
T ss_dssp             TTSEEEEEECC-CCCHHHHSTHHHHHHH--HCSTCEEEE-
T ss_pred             CCeEEEEEeCCCHHHHhhccchhHHHHH--HhCCCEEeCC
Confidence            34455555543 333      4555555  554 444444

>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=87.05  E-value=0.98  Score=33.94  Aligned_cols=52  Identities=17%  Similarity=0.325  Sum_probs=32.1

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC---------CCCCEEEEEEeCCCC-----ccchhccCC
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV---------PLNNVTIVAATNRPD-----RIDKALLRP  108 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~v~vI~ttn~~~-----~ld~al~r~  108 (237)
                      .|+++||+...-               -++.+.+++.|.+-.         -.++.+||||-|..+     .||++++. 
T Consensus        64 ~ill~DEiNrap---------------pktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~D-  127 (131)
T PF07726_consen   64 NILLADEINRAP---------------PKTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLD-  127 (131)
T ss_dssp             SEEEEETGGGS----------------HHHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT--S------HHHHT-
T ss_pred             ceeeecccccCC---------------HHHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhc-
Confidence            399999985542               356777888775421         124589999999877     78999998 


Q ss_pred             CCc
Q psy5642         109 GRL  111 (237)
Q Consensus       109 gRf  111 (237)
                       ||
T Consensus       128 -RF  129 (131)
T PF07726_consen  128 -RF  129 (131)
T ss_dssp             -TS
T ss_pred             -cc
Confidence             88

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.

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

Probab=86.65  E-value=2.7  Score=38.43  Aligned_cols=98  Identities=18%  Similarity=0.303  Sum_probs=56.5

Q ss_pred             CCceEEEEEecccccccccChHHHHHHH-HHHHHH-------h--------cCCeEEEEccccccccccCCCCCCCCCch
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRD-VFKRAR-------Q--------VSPSVIFFDELDSLAGERGDGGGGGGSNV   68 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~-~f~~a~-------~--------~~P~il~iDeid~l~~~~~~~~~~~~~~~   68 (237)
                      ..+-||+.|+|.-+-       +..+.. +|-..+       .        ..-..||||||..+-.             
T Consensus       190 R~~~PFVavNcaAip-------~~l~ESELFGhekGAFTGA~~~r~G~fE~A~GGTLfLDEI~~mpl-------------  249 (464)
T COG2204         190 RAKGPFIAVNCAAIP-------ENLLESELFGHEKGAFTGAITRRIGRFEQANGGTLFLDEIGEMPL-------------  249 (464)
T ss_pred             ccCCCceeeecccCC-------HHHHHHHhhcccccCcCCcccccCcceeEcCCceEEeeccccCCH-------------
Confidence            456799999997542       222222 333111       1        1246999999988722             


Q ss_pred             HHHHHHHHHHHhcCCC-----CC----CCEEEEEEeCCCCccchhccCCCCcc-------cEEEecCCCHHHHHH
Q psy5642          69 QERVLAQMLTEMDGIV-----PL----NNVTIVAATNRPDRIDKALLRPGRLD-------RLIYVPLPDDLTRAA  127 (237)
Q Consensus        69 ~~~~~~~ll~~l~~~~-----~~----~~v~vI~ttn~~~~ld~al~r~gRf~-------~~i~~~~P~~~~R~~  127 (237)
                        .+...||..|+.-.     .+    -+|-||++||.  ++...+.. |+|-       .++.+..|..-+|.+
T Consensus       250 --~~Q~kLLRvLqe~~~~rvG~~~~i~vdvRiIaaT~~--dL~~~v~~-G~FReDLyyRLnV~~i~iPpLRER~E  319 (464)
T COG2204         250 --ELQVKLLRVLQEREFERVGGNKPIKVDVRIIAATNR--DLEEEVAA-GRFREDLYYRLNVVPLRLPPLRERKE  319 (464)
T ss_pred             --HHHHHHHHHHHcCeeEecCCCcccceeeEEEeecCc--CHHHHHHc-CCcHHHHHhhhccceecCCcccccch
Confidence              34455555554321     11    14889999994  55555554 7774       455677776655544

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=86.25  E-value=2.5  Score=41.81  Aligned_cols=75  Identities=21%  Similarity=0.181  Sum_probs=49.1

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-----------CCCCEEEEEEeCCCC-----------
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-----------PLNNVTIVAATNRPD-----------   99 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vI~ttn~~~-----------   99 (237)
                      ..+++|||+|.+-.               .....|+..|++..           -..+..|||++|-..           
T Consensus       558 gGtL~IDEidkms~---------------~~Q~aLlEaMEqqtIsI~KaGi~~tL~ar~rVIAAaNP~~gryd~~~s~~e  622 (915)
T PTZ00111        558 GGVCCIDELDKCHN---------------ESRLSLYEVMEQQTVTIAKAGIVATLKAETAILASCNPINSRYNKNKAVIE  622 (915)
T ss_pred             CCeEEecchhhCCH---------------HHHHHHHHHHhCCEEEEecCCcceecCCCeEEEEEcCCcccccCcccCccc
Confidence            35889999988722               23344555554321           124688999999742           


Q ss_pred             --ccchhccCCCCcccEE-EecCCCHHHHHHHHHHHH
Q psy5642         100 --RIDKALLRPGRLDRLI-YVPLPDDLTRAAILKIRL  133 (237)
Q Consensus       100 --~ld~al~r~gRf~~~i-~~~~P~~~~R~~il~~~l  133 (237)
                        .+++++++  |||.++ -++.|+.+.=..|-.+.+
T Consensus       623 ni~Lp~~LLS--RFDLIf~l~D~~d~~~D~~lA~hI~  657 (915)
T PTZ00111        623 NINISPSLFT--RFDLIYLVLDHIDQDTDQLISLSIA  657 (915)
T ss_pred             ccCCChHHhh--hhcEEEEecCCCChHHHHHHHHHHH
Confidence              67899999  999765 456777766555555444

>PRK08116 hypothetical protein; Validated

Probab=85.90  E-value=1.2  Score=37.84  Aligned_cols=98  Identities=10%  Similarity=0.144  Sum_probs=48.3

Q ss_pred             ceEEEEEecccccccccC----hHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC
Q psy5642           7 LTEVVESIGPELFRKYVG----ESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG   82 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g----~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~   82 (237)
                      +.+++.++.++++..+..    ........+++...  ...+|+|||+...-.          .....   ..|...++.
T Consensus       142 ~~~v~~~~~~~ll~~i~~~~~~~~~~~~~~~~~~l~--~~dlLviDDlg~e~~----------t~~~~---~~l~~iin~  206 (268)
T PRK08116        142 GVPVIFVNFPQLLNRIKSTYKSSGKEDENEIIRSLV--NADLLILDDLGAERD----------TEWAR---EKVYNIIDS  206 (268)
T ss_pred             CCeEEEEEHHHHHHHHHHHHhccccccHHHHHHHhc--CCCEEEEecccCCCC----------CHHHH---HHHHHHHHH
Confidence            356677777766553321    11111222333222  356999999854211          12222   334444443


Q ss_pred             CCCCCCEEEEEEeCCC-Cc----cchhccCCCCc---ccEEEecCCCH
Q psy5642          83 IVPLNNVTIVAATNRP-DR----IDKALLRPGRL---DRLIYVPLPDD  122 (237)
Q Consensus        83 ~~~~~~v~vI~ttn~~-~~----ld~al~r~gRf---~~~i~~~~P~~  122 (237)
                      ... .+..+|.|||.+ ++    ++..+.+  |+   ...|.+.-|+.
T Consensus       207 r~~-~~~~~IiTsN~~~~eL~~~~~~ri~s--Rl~e~~~~v~~~g~d~  251 (268)
T PRK08116        207 RYR-KGLPTIVTTNLSLEELKNQYGKRIYD--RILEMCTPVENEGKSY  251 (268)
T ss_pred             HHH-CCCCEEEECCCCHHHHHHHHhHHHHH--HHHHcCEEEEeeCcCh
Confidence            222 223467777764 44    3566666  64   34466666664

>PRK07452 DNA polymerase III subunit delta; Validated

Probab=83.56  E-value=28  Score=29.98  Aligned_cols=107  Identities=16%  Similarity=0.159  Sum_probs=62.6

Q ss_pred             HHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCC---ccc
Q psy5642          30 VRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPD---RID  102 (237)
Q Consensus        30 l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~---~ld  102 (237)
                      +..+++.+...    .+-+|++++.+.+-..            .......|...+.+..+ +.++|+.+++.++   .+.
T Consensus        46 ~~~~~~~~~t~pff~~~rlVvv~~~~~~~~~------------~~~~~~~L~~~l~~~~~-~~~li~~~~~~~d~r~k~~  112 (326)
T PRK07452         46 AIQALNEAMTPPFGSGGRLVWLKNSPLCQGC------------SEELLAELERTLPLIPE-NTHLLLTNTKKPDGRLKST  112 (326)
T ss_pred             HHHHHHHhcCCCCCCCceEEEEeCchhhccC------------CHHHHHHHHHHHcCCCC-CcEEEEEeCCCcchHHHHH
Confidence            67777777543    4558888886543211            12445677788887543 3455554444332   233


Q ss_pred             hhccCCCCcccEEEecCC---CHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642         103 KALLRPGRLDRLIYVPLP---DDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P---~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      ..+..   +..+.++..|   +.++...+++..++..+.. ....+..|+..+.
T Consensus       113 k~l~k---~~~~~~~~~~~~~~~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g  163 (326)
T PRK07452        113 KLLQK---LAEEKEFSLIPPWDTEGLKQLVERTAQELGVKLTPEAAELLAEAVG  163 (326)
T ss_pred             HHHHH---ceeEEEecCCCcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhC
Confidence            33443   2335665544   4566778888888777765 5566666777653

>KOG1051|consensus

Probab=83.54  E-value=4  Score=40.36  Aligned_cols=77  Identities=22%  Similarity=0.346  Sum_probs=50.2

Q ss_pred             CCCceEEEEEeccc------cccc---ccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHH
Q psy5642           4 LGGLTEVVESIGPE------LFRK---YVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA   74 (237)
Q Consensus         4 ~~~~~~~i~v~~s~------l~~~---~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~   74 (237)
                      ++++-.+|.++.+.      +.+.   |+|..+-  -.+.+..+...-+||+|||||.--               -.+.+
T Consensus       616 Fgse~~~IriDmse~~evskligsp~gyvG~e~g--g~LteavrrrP~sVVLfdeIEkAh---------------~~v~n  678 (898)
T KOG1051|consen  616 FGSEENFIRLDMSEFQEVSKLIGSPPGYVGKEEG--GQLTEAVKRRPYSVVLFEEIEKAH---------------PDVLN  678 (898)
T ss_pred             cCCccceEEechhhhhhhhhccCCCcccccchhH--HHHHHHHhcCCceEEEEechhhcC---------------HHHHH
Confidence            34556678888873      4333   5554332  356666677677899999998752               24677


Q ss_pred             HHHHHhcCCC---------CCCCEEEEEEeCC
Q psy5642          75 QMLTEMDGIV---------PLNNVTIVAATNR   97 (237)
Q Consensus        75 ~ll~~l~~~~---------~~~~v~vI~ttn~   97 (237)
                      .|++.+|.-.         .-++++||.|+|.
T Consensus       679 ~llq~lD~GrltDs~Gr~Vd~kN~I~IMTsn~  710 (898)
T KOG1051|consen  679 ILLQLLDRGRLTDSHGREVDFKNAIFIMTSNV  710 (898)
T ss_pred             HHHHHHhcCccccCCCcEeeccceEEEEeccc
Confidence            7777776432         1236999999886

>TIGR01128 holA DNA polymerase III, delta subunit

Probab=83.34  E-value=26  Score=29.53  Aligned_cols=95  Identities=14%  Similarity=0.163  Sum_probs=59.5

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc---hhccCCCCcccEEEe
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID---KALLRPGRLDRLIYV  117 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld---~al~r~gRf~~~i~~  117 (237)
                      ..-+++|++++.+...              .....|+..+.+..  +..++|.+++.++.-.   ..+..-+ -...+.+
T Consensus        46 ~~kliii~~~~~~~~~--------------~~~~~L~~~l~~~~--~~~~~i~~~~~~~~~~~~~k~~~~~~-~~~~i~~  108 (302)
T TIGR01128        46 ERRLVELRNPEGKPGA--------------KGLKALEEYLANPP--PDTLLLIEAPKLDKRKKLTKWLKALK-NAQIVEC  108 (302)
T ss_pred             CCeEEEEECCCCCCCH--------------HHHHHHHHHHhcCC--CCEEEEEecCCCCHhHHHHHHHHHhc-CeeEEEe
Confidence            3569999998876321              12566777777743  3444555555333211   1121100 2346889


Q ss_pred             cCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642         118 PLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus       118 ~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      ..|+..+...+++..+...+.. ....+..++..+.
T Consensus       109 ~~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~  144 (302)
T TIGR01128       109 KTPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVE  144 (302)
T ss_pred             cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhC
Confidence            9999999999999999887765 6667777777664

subunit around DNA forming a DNA sliding clamp.

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=82.66  E-value=2.8  Score=37.96  Aligned_cols=68  Identities=24%  Similarity=0.373  Sum_probs=38.7

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-----C----CCCEEEEEEeCCCCccchhccCCCCcc
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-----P----LNNVTIVAATNRPDRIDKALLRPGRLD  112 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----~----~~~v~vI~ttn~~~~ld~al~r~gRf~  112 (237)
                      ..+|||||+|.+-.               .+...|+..++.-.     .    ..++.+|+||+..  +. .+.+.|+|.
T Consensus       238 ~gtl~ld~i~~l~~---------------~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~--l~-~~~~~g~~~  299 (457)
T PRK11361        238 EGTLLLDEIGEMPL---------------VLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRD--LQ-AMVKEGTFR  299 (457)
T ss_pred             CCEEEEechhhCCH---------------HHHHHHHHHHhcCcEEeCCCCceeeeceEEEEeCCCC--HH-HHHHcCCch
Confidence            46999999999833               23445555554321     1    1247889988753  21 222334443


Q ss_pred             c-------EEEecCCCHHHHHH
Q psy5642         113 R-------LIYVPLPDDLTRAA  127 (237)
Q Consensus       113 ~-------~i~~~~P~~~~R~~  127 (237)
                      .       .+.+..|...+|.+
T Consensus       300 ~~l~~~l~~~~i~~ppLreR~~  321 (457)
T PRK11361        300 EDLFYRLNVIHLILPPLRDRRE  321 (457)
T ss_pred             HHHHHHhccceecCCChhhchh
Confidence            3       35667776666644

>PRK04841 transcriptional regulator MalT; Provisional

Probab=82.55  E-value=17  Score=35.81  Aligned_cols=109  Identities=17%  Similarity=0.216  Sum_probs=60.9

Q ss_pred             HHHHHHHHHHHh-cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccch-hc
Q psy5642          28 RCVRDVFKRARQ-VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDK-AL  105 (237)
Q Consensus        28 ~~l~~~f~~a~~-~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~-al  105 (237)
                      ..+..++..... ..|.+|+|||++.+-..           .....+..++..+     ..++.+|.|++..-.++- .+
T Consensus       107 ~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~-----------~~~~~l~~l~~~~-----~~~~~lv~~sR~~~~~~~~~l  170 (903)
T PRK04841        107 SLFAQLFIELADWHQPLYLVIDDYHLITNP-----------EIHEAMRFFLRHQ-----PENLTLVVLSRNLPPLGIANL  170 (903)
T ss_pred             HHHHHHHHHHhcCCCCEEEEEeCcCcCCCh-----------HHHHHHHHHHHhC-----CCCeEEEEEeCCCCCCchHhH
Confidence            344455554443 57999999999987211           1122344444332     234444446654222321 11


Q ss_pred             cCCCCcccEEEec----CCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcc
Q psy5642         106 LRPGRLDRLIYVP----LPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGA  157 (237)
Q Consensus       106 ~r~gRf~~~i~~~----~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~  157 (237)
                      +-   -+..+.+.    .-+.++-.+++...+... + +..++..+...|+|+..+
T Consensus       171 ~~---~~~~~~l~~~~l~f~~~e~~~ll~~~~~~~-~-~~~~~~~l~~~t~Gwp~~  221 (903)
T PRK04841        171 RV---RDQLLEIGSQQLAFDHQEAQQFFDQRLSSP-I-EAAESSRLCDDVEGWATA  221 (903)
T ss_pred             Hh---cCcceecCHHhCCCCHHHHHHHHHhccCCC-C-CHHHHHHHHHHhCChHHH
Confidence            11   12234555    558888888887765432 2 567788899999998755

>KOG1968|consensus

Probab=81.93  E-value=9.8  Score=37.73  Aligned_cols=96  Identities=17%  Similarity=0.213  Sum_probs=64.9

Q ss_pred             EEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHH
Q psy5642          44 VIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDL  123 (237)
Q Consensus        44 il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~  123 (237)
                      ||++||+|.++...            +..+..+...+..    ..+-+|.|+|....-...-..  |-+..++|+.|+..
T Consensus       431 vil~devD~~~~~d------------Rg~v~~l~~l~~k----s~~Piv~~cndr~~p~sr~~~--~~~~~l~f~kP~~~  492 (871)
T KOG1968|consen  431 LILMDEVDGMFGED------------RGGVSKLSSLCKK----SSRPLVCTCNDRNLPKSRALS--RACSDLRFSKPSSE  492 (871)
T ss_pred             EEEEeccccccchh------------hhhHHHHHHHHHh----ccCCeEEEecCCCCccccchh--hhcceeeecCCcHH
Confidence            99999999987621            1223444444442    344578888876665554444  55578999999999


Q ss_pred             HHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccc
Q psy5642         124 TRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSL  161 (237)
Q Consensus       124 ~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~  161 (237)
                      ++..-+..++...... .+..++++...+    ++||+.
T Consensus       493 ~i~~ri~si~~se~~ki~~~~l~~~s~~~----~~DiR~  527 (871)
T KOG1968|consen  493 LIRSRIMSICKSEGIKISDDVLEEISKLS----GGDIRQ  527 (871)
T ss_pred             HHHhhhhhhhcccceecCcHHHHHHHHhc----ccCHHH
Confidence            9888888777655443 567777888776    778444

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=81.92  E-value=2.3  Score=34.85  Aligned_cols=91  Identities=16%  Similarity=0.195  Sum_probs=60.4

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      .+.+.|+.++...+. --.....+.|..+.+.-+.....+|+||-+..++...           ...-+..|++.+..+.
T Consensus        88 ~G~l~~~~~~~~~~~-~~~~~~~~~L~~l~~~~k~~~~dViIIDSls~~~~~~-----------~~~~vl~fm~~~r~l~  155 (235)
T COG2874          88 SGRLLFFPVNLEPVN-WGRRSARKLLDLLLEFIKRWEKDVIIIDSLSAFATYD-----------SEDAVLNFMTFLRKLS  155 (235)
T ss_pred             cceeEEEEecccccc-cChHHHHHHHHHHHhhHHhhcCCEEEEecccHHhhcc-----------cHHHHHHHHHHHHHHH
Confidence            355667776543222 1233567778888887777778899999999887653           1234566777776665


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCc
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRL  111 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf  111 (237)
                      ..+++  |..|-||..++++...  |+
T Consensus       156 d~gKv--IilTvhp~~l~e~~~~--ri  178 (235)
T COG2874         156 DLGKV--IILTVHPSALDEDVLT--RI  178 (235)
T ss_pred             hCCCE--EEEEeChhhcCHHHHH--HH
Confidence            55555  3345568999999887  65

>smart00763 AAA_PrkA PrkA AAA domain

Probab=81.81  E-value=5  Score=35.51  Aligned_cols=75  Identities=23%  Similarity=0.204  Sum_probs=55.5

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC----CC-----CCEEEEEEeCCC-------Cccchhcc
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV----PL-----NNVTIVAATNRP-------DRIDKALL  106 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~----~~-----~~v~vI~ttn~~-------~~ld~al~  106 (237)
                      +|+-|+|+...               ...++..||+.+++-.    ..     -..+||+++|..       ....++++
T Consensus       238 Gi~~f~Ei~K~---------------~~~~l~~LL~~~qE~~v~~~~~~~~~~~d~liia~sNe~e~~~~~~~k~~eaf~  302 (361)
T smart00763      238 GILEFVEMFKA---------------DIKFLHPLLTATQEGNIKGTGGFAMIPIDGLIIAHSNESEWQRFKSNKKNEALL  302 (361)
T ss_pred             ceEEEeehhcC---------------CHHHHHHHhhhhhcceEecCCcccccccceEEEEeCCHHHHhhhhccccchhhh
Confidence            56777766543               1467888888887421    11     126889999987       36789999


Q ss_pred             CCCCcccEEEecCC-CHHHHHHHHHHHHcC
Q psy5642         107 RPGRLDRLIYVPLP-DDLTRAAILKIRLAR  135 (237)
Q Consensus       107 r~gRf~~~i~~~~P-~~~~R~~il~~~l~~  135 (237)
                      +  |+. .+.+++| +..+-.+|.+..+..
T Consensus       303 d--R~~-~i~vpY~l~~~~E~~Iy~k~~~~  329 (361)
T smart00763      303 D--RII-KVKVPYCLRVSEEAQIYEKLLRN  329 (361)
T ss_pred             h--ceE-EEeCCCcCCHHHHHHHHHHHhcc
Confidence            9  998 7999998 778888999988864

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

>KOG0478|consensus

Probab=81.60  E-value=27  Score=33.68  Aligned_cols=47  Identities=21%  Similarity=0.318  Sum_probs=32.2

Q ss_pred             CEEEEEEeCCCC-------------ccchhccCCCCcccEE-EecCCCHHHHHHHHHHHHcCC
Q psy5642          88 NVTIVAATNRPD-------------RIDKALLRPGRLDRLI-YVPLPDDLTRAAILKIRLARS  136 (237)
Q Consensus        88 ~v~vI~ttn~~~-------------~ld~al~r~gRf~~~i-~~~~P~~~~R~~il~~~l~~~  136 (237)
                      +.-|+|++|-..             .|||.|++  |||.++ -+..||+..=+.|-.+....+
T Consensus       569 R~SVLAaANP~~skynp~k~i~eNI~LpptLLS--RFDLIylllD~~DE~~Dr~La~HivsLy  629 (804)
T KOG0478|consen  569 RCSVLAAANPIRSKYNPNKSIIENINLPPTLLS--RFDLIFLLLDKPDERSDRRLADHIVALY  629 (804)
T ss_pred             cceeeeeeccccccCCCCCchhhccCCChhhhh--hhcEEEEEecCcchhHHHHHHHHHHHhc
Confidence            567899998322             78999999  999755 456777764455555544433

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

Probab=81.41  E-value=5.7  Score=28.88  Aligned_cols=53  Identities=13%  Similarity=0.169  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEe
Q psy5642          27 ERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAAT   95 (237)
Q Consensus        27 ~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~tt   95 (237)
                      ......+.+........+|+|||+|.+. +             ..++..+...++.  ..-+++++|+.
T Consensus        73 ~~l~~~~~~~l~~~~~~~lviDe~~~l~-~-------------~~~l~~l~~l~~~--~~~~vvl~G~~  125 (131)
T PF13401_consen   73 DELRSLLIDALDRRRVVLLVIDEADHLF-S-------------DEFLEFLRSLLNE--SNIKVVLVGTP  125 (131)
T ss_dssp             HHHHHHHHHHHHHCTEEEEEEETTHHHH-T-------------HHHHHHHHHHTCS--CBEEEEEEESS
T ss_pred             HHHHHHHHHHHHhcCCeEEEEeChHhcC-C-------------HHHHHHHHHHHhC--CCCeEEEEECh
Confidence            4444444444455445699999999975 1             3456666665552  21235555554

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=81.35  E-value=7.1  Score=37.63  Aligned_cols=107  Identities=20%  Similarity=0.240  Sum_probs=55.7

Q ss_pred             CceEEEEEeccccccc-----ccCh--------HHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHH
Q psy5642           6 GLTEVVESIGPELFRK-----YVGE--------SERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERV   72 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~-----~~g~--------~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~   72 (237)
                      .+-+|+.++|..+...     .+|.        ....+ ..|+.|   ...+|||||+|.+-.               .+
T Consensus       426 ~~~~~v~i~c~~~~~~~~~~~lfg~~~~~~~g~~~~~~-g~le~a---~~GtL~Ldei~~L~~---------------~~  486 (686)
T PRK15429        426 NNRRMVKMNCAAMPAGLLESDLFGHERGAFTGASAQRI-GRFELA---DKSSLFLDEVGDMPL---------------EL  486 (686)
T ss_pred             CCCCeEEEecccCChhHhhhhhcCcccccccccccchh-hHHHhc---CCCeEEEechhhCCH---------------HH
Confidence            5679999999876321     1111        11111 123333   358999999999822               23


Q ss_pred             HHHHHHHhcCCC---------CCCCEEEEEEeCCCCccchhccCCCCccc-------EEEecCCCHHHHHH----HHHHH
Q psy5642          73 LAQMLTEMDGIV---------PLNNVTIVAATNRPDRIDKALLRPGRLDR-------LIYVPLPDDLTRAA----ILKIR  132 (237)
Q Consensus        73 ~~~ll~~l~~~~---------~~~~v~vI~ttn~~~~ld~al~r~gRf~~-------~i~~~~P~~~~R~~----il~~~  132 (237)
                      ...|+..|+.-.         ...++-+|+||+..-  ... ...|+|..       .+.+..|...+|.+    +++.+
T Consensus       487 Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~l--~~~-~~~~~f~~~L~~~l~~~~i~lPpLreR~~Di~~L~~~~  563 (686)
T PRK15429        487 QPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDL--KKM-VADREFRSDLYYRLNVFPIHLPPLRERPEDIPLLVKAF  563 (686)
T ss_pred             HHHHHHHHHhCCEEeCCCCCcccceEEEEEeCCCCH--HHH-HHcCcccHHHHhccCeeEEeCCChhhhHhHHHHHHHHH
Confidence            444555553311         113577888887532  111 11233332       45666666666544    44555


Q ss_pred             Hc
Q psy5642         133 LA  134 (237)
Q Consensus       133 l~  134 (237)
                      +.
T Consensus       564 l~  565 (686)
T PRK15429        564 TF  565 (686)
T ss_pred             HH
Confidence            43

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

Probab=81.15  E-value=4.1  Score=34.59  Aligned_cols=85  Identities=22%  Similarity=0.380  Sum_probs=47.4

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC--------CCCEEEEEEeCCCC---ccchhccCCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP--------LNNVTIVAATNRPD---RIDKALLRPG  109 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~--------~~~v~vI~ttn~~~---~ld~al~r~g  109 (237)
                      +..|+||||+..-..+.-+..      ...+++.++++.= +...        -.++.+||+.+.+.   .+++.+.|  
T Consensus       100 k~lv~fiDDlN~p~~d~ygtq------~~iElLRQ~i~~~-g~yd~~~~~~~~i~~i~~vaa~~p~~Gr~~is~R~~r--  170 (272)
T PF12775_consen  100 KKLVLFIDDLNMPQPDKYGTQ------PPIELLRQLIDYG-GFYDRKKLEWKSIEDIQFVAAMNPTGGRNPISPRFLR--  170 (272)
T ss_dssp             SEEEEEEETTT-S---TTS--------HHHHHHHHHHHCS-EEECTTTTEEEEECSEEEEEEESSTTT--SHHHHHHT--
T ss_pred             cEEEEEecccCCCCCCCCCCc------CHHHHHHHHHHhc-CcccCCCcEEEEEeeeEEEEecCCCCCCCCCChHHhh--
Confidence            356999999876544432211      1123333333321 1111        12588899887533   48888988  


Q ss_pred             CcccEEEecCCCHHHHHHHHHHHHcC
Q psy5642         110 RLDRLIYVPLPDDLTRAAILKIRLAR  135 (237)
Q Consensus       110 Rf~~~i~~~~P~~~~R~~il~~~l~~  135 (237)
                      .|. ++.++.|+.+.-..|+..++..
T Consensus       171 ~f~-i~~~~~p~~~sl~~If~~il~~  195 (272)
T PF12775_consen  171 HFN-ILNIPYPSDESLNTIFSSILQS  195 (272)
T ss_dssp             TEE-EEE----TCCHHHHHHHHHHHH
T ss_pred             heE-EEEecCCChHHHHHHHHHHHhh
Confidence            885 7999999999999998887753

>PRK05574 holA DNA polymerase III subunit delta; Reviewed

Probab=81.13  E-value=35  Score=29.39  Aligned_cols=121  Identities=15%  Similarity=0.244  Sum_probs=70.2

Q ss_pred             HHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCcc----
Q psy5642          30 VRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRI----  101 (237)
Q Consensus        30 l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~l----  101 (237)
                      +..+++.+...    .+-++++++.+.+-...           ....+..+...+ +......++++..++..+.-    
T Consensus        61 ~~~l~~~~~t~~lF~~~klvii~~~~~l~~~~-----------~~~~l~~l~~~l-~~~~~~~~~li~~~~~~~~~~k~~  128 (340)
T PRK05574         61 WDDVLEACQSLPLFSDRKLVELRLPEFLTGAK-----------GEKALKRLEAYL-NPLPHPDLLLIVRLPKLDKAKKKS  128 (340)
T ss_pred             HHHHHHHhhccCccccCeEEEEECCCCCCchh-----------HHHHHHHHHHhc-cCCCCCcEEEEEECCcCCHHHHhh
Confidence            45555555442    35588888887663321           123345556656 43333345556555543321    


Q ss_pred             --chhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhHHhhhh
Q psy5642         102 --DKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKHRAKKI  169 (237)
Q Consensus       102 --d~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~  169 (237)
                        -..+..  + ...+.++.|+..+...+++..+...+.. ....++.|+..+.    .|+..+.....++
T Consensus       129 k~~k~~~~--~-~~~~~~~~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~----~d~~~l~~El~KL  192 (340)
T PRK05574        129 AWFKALKK--K-AVVVEAQPPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVE----GNLLALAQELEKL  192 (340)
T ss_pred             HHHHHHHh--C-ceEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhC----chHHHHHHHHHHH
Confidence              123322  2 3678899999999999999999887765 5566677776654    4644444444443

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=80.88  E-value=2.2  Score=39.88  Aligned_cols=111  Identities=18%  Similarity=0.254  Sum_probs=57.1

Q ss_pred             CCCceEEEEEecccccccc-----cChHHH--------HHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHH
Q psy5642           4 LGGLTEVVESIGPELFRKY-----VGESER--------CVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQE   70 (237)
Q Consensus         4 ~~~~~~~i~v~~s~l~~~~-----~g~~~~--------~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~   70 (237)
                      ...+.||+.|+|..+-...     +|....        .-.-+|+.|   ....|||||++.+-.               
T Consensus       275 ~r~~~pfv~inCaal~e~lleseLFG~~~gaftga~~~~~~Gl~e~A---~gGTLfLdeI~~Lp~---------------  336 (538)
T PRK15424        275 GKKSHPFVAVNCGAIAESLLEAELFGYEEGAFTGSRRGGRAGLFEIA---HGGTLFLDEIGEMPL---------------  336 (538)
T ss_pred             ccCCCCeEEeecccCChhhHHHHhcCCccccccCccccccCCchhcc---CCCEEEEcChHhCCH---------------
Confidence            3467899999998764211     110000        001133333   246999999999832               


Q ss_pred             HHHHHHHHHhcCCC-----C----CCCEEEEEEeCCCCccchhccCCCCccc-------EEEecCCCHHHH----HHHHH
Q psy5642          71 RVLAQMLTEMDGIV-----P----LNNVTIVAATNRPDRIDKALLRPGRLDR-------LIYVPLPDDLTR----AAILK  130 (237)
Q Consensus        71 ~~~~~ll~~l~~~~-----~----~~~v~vI~ttn~~~~ld~al~r~gRf~~-------~i~~~~P~~~~R----~~il~  130 (237)
                      .+...|+..|++-.     .    .-++-+|++|+..  +...+ ..|+|..       .+.+..|..-+|    ..+++
T Consensus       337 ~~Q~kLl~~L~e~~~~r~G~~~~~~~dvRiIaat~~~--L~~~v-~~g~Fr~dL~yrL~~~~I~lPPLReR~eDI~~L~~  413 (538)
T PRK15424        337 PLQTRLLRVLEEKEVTRVGGHQPVPVDVRVISATHCD--LEEDV-RQGRFRRDLFYRLSILRLQLPPLRERVADILPLAE  413 (538)
T ss_pred             HHHHHHHhhhhcCeEEecCCCceeccceEEEEecCCC--HHHHH-hcccchHHHHHHhcCCeecCCChhhchhHHHHHHH
Confidence            23445555554321     1    1236788888753  32222 2345542       345566655554    44555


Q ss_pred             HHHcC
Q psy5642         131 IRLAR  135 (237)
Q Consensus       131 ~~l~~  135 (237)
                      +++..
T Consensus       414 ~fl~~  418 (538)
T PRK15424        414 SFLKQ  418 (538)
T ss_pred             HHHHH
Confidence            66643

>KOG0990|consensus

Probab=80.21  E-value=5.8  Score=34.57  Aligned_cols=89  Identities=15%  Similarity=0.181  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHHh-------cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCc
Q psy5642          28 RCVRDVFKRARQ-------VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDR  100 (237)
Q Consensus        28 ~~l~~~f~~a~~-------~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~  100 (237)
                      +.--..|..++.       ..+..+++||.|+...+               ..+.|-..+..+.  .+.-++-.+|++..
T Consensus       111 r~qi~~fast~~~~~fst~~~fKlvILDEADaMT~~---------------AQnALRRviek~t--~n~rF~ii~n~~~k  173 (360)
T KOG0990|consen  111 RQQIHLFASTQQPTTYSTHAAFKLVILDEADAMTRD---------------AQNALRRVIEKYT--ANTRFATISNPPQK  173 (360)
T ss_pred             HHHHHHHHhhccceeccccCceeEEEecchhHhhHH---------------HHHHHHHHHHHhc--cceEEEEeccChhh
Confidence            333445655553       26789999999987443               1233334445543  34455577899999


Q ss_pred             cchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC
Q psy5642         101 IDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS  136 (237)
Q Consensus       101 ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~  136 (237)
                      +.|++++  ||.. +.+...+..+-...+.+.....
T Consensus       174 i~pa~qs--Rctr-frf~pl~~~~~~~r~shi~e~e  206 (360)
T KOG0990|consen  174 IHPAQQS--RCTR-FRFAPLTMAQQTERQSHIRESE  206 (360)
T ss_pred             cCchhhc--cccc-CCCCCCChhhhhhHHHHHHhcc
Confidence            9999999  9875 6666667666666666666543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	237
3cf0_A	301	Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH		3e-38
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		4e-38
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		4e-38
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		3e-32
2x8a_A	274	Human Nuclear Valosin Containing Protein Like (Nvl)		2e-27
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		5e-26
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		5e-25
4b4t_M	434	Near-Atomic Resolution Structural Model Of The Yeas		6e-25
2r62_A	268	Crystal Structure Of Helicobacter Pylori Atp Depend		4e-24
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		6e-24
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		8e-24
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		8e-24
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		9e-24
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		9e-24
4b4t_H	467	Near-Atomic Resolution Structural Model Of The Yeas		1e-23
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		4e-23
2ce7_A	476	Edta Treated Length = 476		2e-22
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		2e-22
4b4t_I	437	Near-Atomic Resolution Structural Model Of The Yeas		4e-22
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		6e-22
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		6e-22
4eiw_A	508	Whole Cytosolic Region Of Atp-Dependent Metalloprot		7e-22
2dhr_A	499	Whole Cytosolic Region Of Atp-Dependent Metalloprot		8e-22
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		3e-19
3b9p_A	297	Spastin Length = 297		4e-19
2zam_A	444	Crystal Structure Of Mouse Skd1VPS4B APO-Form Lengt		6e-19
1xwi_A	322	Crystal Structure Of Vps4b Length = 322		1e-18
2rko_A	331	Crystal Structure Of The Vps4p-Dimer Length = 331		3e-17
2qp9_X	355	Crystal Structure Of S.Cerevisiae Vps4 Length = 355		3e-17
3vfd_A	389	Human Spastin Aaa Domain Length = 389		5e-17
3eih_A	340	Crystal Structure Of S.Cerevisiae Vps4 In The Prese		7e-17
3eie_A	322	Crystal Structure Of S.Cerevisiae Vps4 In The So4-B		8e-17
3d8b_A	357	Crystal Structure Of Human Fidgetin-Like Protein 1		4e-16

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

Iteration: 1
 Score =  154 bits (390), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 79/155 (50%), Positives = 106/155 (68%), Gaps = 1/155 (0%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           GPEL   + GESE  VR++F +ARQ +P V+FFDELDS+A               +RV+ 
Sbjct: 82  GPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGG-AADRVIN 140
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTEMDG+    NV I+ ATNRPD ID A+LRPGRLD+LIY+PLPD+ +R AILK  L 
Sbjct: 141 QILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLR 200
Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKI 169
           +SP+ +DV +E L ++T G+SGA+ +    RA K+
Sbjct: 201 KSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKL 235

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

Iteration: 1
 Score =  154 bits (389), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 79/155 (50%), Positives = 106/155 (68%), Gaps = 1/155 (0%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           GPEL   + GESE  VR++F +ARQ +P V+FFDELDS+A               +RV+ 
Sbjct: 544 GPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGG-AADRVIN 602
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTEMDG+    NV I+ ATNRPD ID A+LRPGRLD+LIY+PLPD+ +R AILK  L 
Sbjct: 603 QILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLR 662
Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKI 169
           +SP+ +DV +E L ++T G+SGA+ +    RA K+
Sbjct: 663 KSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKL 697

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

Iteration: 1
 Score =  154 bits (389), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 79/155 (50%), Positives = 106/155 (68%), Gaps = 1/155 (0%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           GPEL   + GESE  VR++F +ARQ +P V+FFDELDS+A               +RV+ 
Sbjct: 544 GPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGG-AADRVIN 602
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTEMDG+    NV I+ ATNRPD ID A+LRPGRLD+LIY+PLPD+ +R AILK  L 
Sbjct: 603 QILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLR 662
Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKI 169
           +SP+ +DV +E L ++T G+SGA+ +    RA K+
Sbjct: 663 KSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKL 697

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

Iteration: 1
 Score =  135 bits (339), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 68/145 (46%), Positives = 93/145 (64%), Gaps = 1/145 (0%)
Query: 14  IGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVL 73
           +G EL +K++GE    V+D+FK A++ +PS+IF DE+D++A             VQ R L
Sbjct: 83  VGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQ-RTL 141
Query: 74  AQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
            Q+L EMDG     +V I+ ATNRPD +D A+LRPGR DR+I VP PD+  R  ILKI  
Sbjct: 142 MQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHT 201
Query: 134 ARSPLGEDVCVEELVRLTEGYSGAE 158
            +  L EDV +EE+ ++TEG  GAE
Sbjct: 202 RKMNLAEDVNLEEIAKMTEGCVGAE 226

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

Iteration: 1
 Score =  118 bits (296), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 71/151 (47%), Positives = 91/151 (60%), Gaps = 9/151 (5%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           GPEL   YVGESER VR VF+RA+  +P VIFFDE+D+L            +    RV+ 
Sbjct: 77  GPELLNMYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRE----TGASVRVVN 132
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKI--- 131
           Q+LTEMDG+     V I+AATNRPD ID A+LRPGRLD+ ++V LP    R AILK    
Sbjct: 133 QLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITK 192
Query: 132 RLARSPLGEDVCVEELVR--LTEGYSGAEQS 160
              + PL  DV +E +      + Y+GA+ S
Sbjct: 193 NGTKPPLDADVNLEAIAGDLRCDCYTGADLS 223

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

Iteration: 1
 Score =  114 bits (285), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 55/138 (39%), Positives = 84/138 (60%), Gaps = 1/138 (0%)
Query: 21  KYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLAQMLTEM 80
           KY+GES R +R++F  A++  P +IF DE+D++              +Q R L ++LT+M
Sbjct: 254 KYIGESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQ-RTLMELLTQM 312
Query: 81  DGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGE 140
           DG   L    I+ ATNRPD +D ALLRPGRLDR + +PLP++  R  I KI  A+     
Sbjct: 313 DGFDNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTG 372
Query: 141 DVCVEELVRLTEGYSGAE 158
           +   E  V++++G++GA+
Sbjct: 373 EFDFEAAVKMSDGFNGAD 390

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

Iteration: 1
 Score =  110 bits (276), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 58/144 (40%), Positives = 83/144 (57%), Gaps = 1/144 (0%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           G +    +VG     VRD+F++A++ +P +IF DE+D++               +E+ L 
Sbjct: 78  GSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDE-REQTLN 136
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           QML EMDG      + ++AATNRPD +D ALLRPGR DR + V LPD   R  ILK+ + 
Sbjct: 137 QMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMR 196
Query: 135 RSPLGEDVCVEELVRLTEGYSGAE 158
           R PL  D+    + R T G+SGA+
Sbjct: 197 RVPLAPDIDAAIIARGTPGFSGAD 220

>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Iteration: 1
 Score =  110 bits (275), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 56/144 (38%), Positives = 87/144 (60%), Gaps = 1/144 (0%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
            P+L + Y+GE  + VRD F  A++ +P++IF DELD++              VQ R + 
Sbjct: 248 APQLVQMYIGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQ-RTML 306
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           ++L ++DG    + V ++AATNR D +D ALLR GRLDR I  PLP + +RA IL+I   
Sbjct: 307 ELLNQLDGFSSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSR 366
Query: 135 RSPLGEDVCVEELVRLTEGYSGAE 158
           +    +D+  +EL R T+ ++GA+
Sbjct: 367 KMTTDDDINWQELARSTDEFNGAQ 390

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

Iteration: 1
 Score =  107 bits (268), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 56/145 (38%), Positives = 85/145 (58%), Gaps = 1/145 (0%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           G      +VG     VRD+F+ A++ +PS+IF DE+D++            ++ +E+ L 
Sbjct: 77  GSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLN 136
Query: 75  QMLTEMDGIVPLNN-VTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
           Q+L EMDG    N  V ++AATNRP+ +D AL+RPGR DR + V  PD   R  ILK+ +
Sbjct: 137 QLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHI 196
Query: 134 ARSPLGEDVCVEELVRLTEGYSGAE 158
               L  DV ++E+ +LT G +GA+
Sbjct: 197 KGVKLANDVNLQEVAKLTAGLAGAD 221

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

Iteration: 1
 Score =  107 bits (267), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 58/144 (40%), Positives = 83/144 (57%), Gaps = 1/144 (0%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           G EL +KY+GE  R VR++F  AR+ +PS+IF DE+DS+            S VQ R + 
Sbjct: 215 GAELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQ-RTML 273
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           ++L ++DG     N+ I+ ATNR D +D ALLRPGR+DR I  P P    RA IL+I   
Sbjct: 274 ELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSR 333
Query: 135 RSPLGEDVCVEELVRLTEGYSGAE 158
           +  L   + + ++     G SGA+
Sbjct: 334 KMNLTRGINLRKVAEKMNGCSGAD 357

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  107 bits (266), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 57/144 (39%), Positives = 86/144 (59%), Gaps = 4/144 (2%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           GPE+  K  GESE  +R  F+ A + +P++IF DELD++A             V+ R+++
Sbjct: 271 GPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTH----GEVERRIVS 326
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LT MDG+    +V ++AATNRP+ ID AL R GR DR + + +PD   R  IL+I   
Sbjct: 327 QLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTK 386
Query: 135 RSPLGEDVCVEELVRLTEGYSGAE 158
              L +DV +E++   T G+ GA+
Sbjct: 387 NMKLADDVDLEQVANETHGHVGAD 410

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  107 bits (266), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 57/144 (39%), Positives = 86/144 (59%), Gaps = 4/144 (2%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           GPE+  K  GESE  +R  F+ A + +P++IF DELD++A             V+ R+++
Sbjct: 271 GPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTH----GEVERRIVS 326
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LT MDG+    +V ++AATNRP+ ID AL R GR DR + + +PD   R  IL+I   
Sbjct: 327 QLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTK 386
Query: 135 RSPLGEDVCVEELVRLTEGYSGAE 158
              L +DV +E++   T G+ GA+
Sbjct: 387 NMKLADDVDLEQVANETHGHVGAD 410

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  106 bits (265), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 57/144 (39%), Positives = 86/144 (59%), Gaps = 4/144 (2%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           GPE+  K  GESE  +R  F+ A + +P++IF DELD++A             V+ R+++
Sbjct: 271 GPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTH----GEVERRIVS 326
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LT MDG+    +V ++AATNRP+ ID AL R GR DR + + +PD   R  IL+I   
Sbjct: 327 QLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTK 386
Query: 135 RSPLGEDVCVEELVRLTEGYSGAE 158
              L +DV +E++   T G+ GA+
Sbjct: 387 NMKLADDVDLEQVANETHGHVGAD 410

>pdb|1E32|A Chain A, Structure Of The N-Terminal Domain And The D1 Aaa Domain Of Membrane Fusion Atpase P97 Length = 458

Iteration: 1
 Score =  106 bits (265), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 57/144 (39%), Positives = 86/144 (59%), Gaps = 4/144 (2%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           GPE+  K  GESE  +R  F+ A + +P++IF DELD++A             V+ R+++
Sbjct: 271 GPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTH----GEVERRIVS 326
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LT MDG+    +V ++AATNRP+ ID AL R GR DR + + +PD   R  IL+I   
Sbjct: 327 QLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTK 386
Query: 135 RSPLGEDVCVEELVRLTEGYSGAE 158
              L +DV +E++   T G+ GA+
Sbjct: 387 NMKLADDVDLEQVANETHGHVGAD 410

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

Iteration: 1
 Score =  106 bits (264), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/145 (39%), Positives = 84/145 (57%), Gaps = 1/145 (0%)
Query: 14  IGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVL 73
           IG EL +KYVGE  R VR++F+ AR     +IFFDE+D++            + VQ R +
Sbjct: 275 IGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQ-RTM 333
Query: 74  AQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
            +++T++DG  P  N+ ++ ATNRP+ +D ALLRPGR+DR +   LPD   RA I +I  
Sbjct: 334 LELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHS 393
Query: 134 ARSPLGEDVCVEELVRLTEGYSGAE 158
               +   +  E + RL    +GAE
Sbjct: 394 KSMSVERGIRWELISRLCPNSTGAE 418

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

Iteration: 1
 Score =  104 bits (260), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 61/144 (42%), Positives = 82/144 (56%), Gaps = 2/144 (1%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           G E   KY+GE  R VRDVF+ AR+ +PS+IF DE+DS+A             VQ R+L 
Sbjct: 239 GSEFVHKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQ-RILI 297
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVP-LPDDLTRAAILKIRL 133
           ++LT+MDG     NV ++ ATNR D +D ALLRPGRLDR I  P L D   R  I     
Sbjct: 298 ELLTQMDGFDQSTNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIA 357
Query: 134 ARSPLGEDVCVEELVRLTEGYSGA 157
           ++  L  +  ++ L+   +  SGA
Sbjct: 358 SKMSLAPEADLDSLIIRNDSLSGA 381

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

Iteration: 1
 Score =  102 bits (254), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 56/144 (38%), Positives = 81/144 (56%), Gaps = 1/144 (0%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           G +    +VG     VRD+F +A+  +P ++F DE+D++               +E+ L 
Sbjct: 82  GSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDE-REQTLN 140
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+L EMDG      + ++AATNRPD +D ALLRPGR D+ I V  PD L R  IL+I   
Sbjct: 141 QLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTR 200
Query: 135 RSPLGEDVCVEELVRLTEGYSGAE 158
             PL EDV +E + + T G+ GA+
Sbjct: 201 NKPLAEDVNLEIIAKRTPGFVGAD 224

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

Iteration: 1
 Score =  102 bits (254), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 56/144 (38%), Positives = 81/144 (56%), Gaps = 1/144 (0%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           G +    +VG     VRD+F +A+  +P ++F DE+D++               +E+ L 
Sbjct: 82  GSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDE-REQTLN 140
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+L EMDG      + ++AATNRPD +D ALLRPGR D+ I V  PD L R  IL+I   
Sbjct: 141 QLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTR 200
Query: 135 RSPLGEDVCVEELVRLTEGYSGAE 158
             PL EDV +E + + T G+ GA+
Sbjct: 201 NKPLAEDVNLEIIAKRTPGFVGAD 224

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

Iteration: 1
 Score =  101 bits (251), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 52/145 (35%), Positives = 84/145 (57%), Gaps = 1/145 (0%)
Query: 14  IGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVL 73
           +G EL +KY+G+  R  R +FK A + +PS++F DE+D++              +Q R +
Sbjct: 248 VGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQ-RTM 306
Query: 74  AQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
            ++L ++DG     +V ++ ATN+ + +D AL+RPGR+DR I    PD  T+  IL I  
Sbjct: 307 LELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHT 366
Query: 134 ARSPLGEDVCVEELVRLTEGYSGAE 158
           ++  L EDV +E LV   +  SGA+
Sbjct: 367 SKMNLSEDVNLETLVTTKDDLSGAD 391

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

Iteration: 1
 Score =  100 bits (250), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 55/148 (37%), Positives = 84/148 (56%), Gaps = 1/148 (0%)
Query: 11  VESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQE 70
           + + G +    +VG     VRD+F+ A++ +P ++F DE+D++            ++ +E
Sbjct: 102 ITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGG-NDERE 160
Query: 71  RVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILK 130
           + L Q+L EMDG      + ++AATNRPD +D ALLRPGR DR I +  PD   R  IL+
Sbjct: 161 QTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILR 220
Query: 131 IRLARSPLGEDVCVEELVRLTEGYSGAE 158
           I     PL EDV +  L + T G+ GA+
Sbjct: 221 IHARGKPLAEDVDLALLAKRTPGFVGAD 248

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

Iteration: 1
 Score =  100 bits (249), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 55/148 (37%), Positives = 84/148 (56%), Gaps = 1/148 (0%)
Query: 11  VESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQE 70
           + + G +    +VG     VRD+F+ A++ +P ++F DE+D++            ++ +E
Sbjct: 78  ITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGG-NDERE 136
Query: 71  RVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILK 130
           + L Q+L EMDG      + ++AATNRPD +D ALLRPGR DR I +  PD   R  IL+
Sbjct: 137 QTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILR 196
Query: 131 IRLARSPLGEDVCVEELVRLTEGYSGAE 158
           I     PL EDV +  L + T G+ GA+
Sbjct: 197 IHARGKPLAEDVDLALLAKRTPGFVGAD 224

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

Iteration: 1
 Score =  100 bits (249), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 55/148 (37%), Positives = 84/148 (56%), Gaps = 1/148 (0%)
Query: 11  VESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQE 70
           + + G +    +VG     VRD+F+ A++ +P ++F DE+D++            ++ +E
Sbjct: 102 ITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGG-NDERE 160
Query: 71  RVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILK 130
           + L Q+L EMDG      + ++AATNRPD +D ALLRPGR DR I +  PD   R  IL+
Sbjct: 161 QTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILR 220
Query: 131 IRLARSPLGEDVCVEELVRLTEGYSGAE 158
           I     PL EDV +  L + T G+ GA+
Sbjct: 221 IHARGKPLAEDVDLALLAKRTPGFVGAD 248

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

Iteration: 1
 Score =  100 bits (248), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 55/148 (37%), Positives = 84/148 (56%), Gaps = 1/148 (0%)
Query: 11  VESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQE 70
           + + G +    +VG     VRD+F+ A++ +P ++F DE+D++            ++ +E
Sbjct: 93  ITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGG-NDERE 151
Query: 71  RVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILK 130
           + L Q+L EMDG      + ++AATNRPD +D ALLRPGR DR I +  PD   R  IL+
Sbjct: 152 QTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILR 211
Query: 131 IRLARSPLGEDVCVEELVRLTEGYSGAE 158
           I     PL EDV +  L + T G+ GA+
Sbjct: 212 IHARGKPLAEDVDLALLAKRTPGFVGAD 239

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

Iteration: 1
 Score = 91.7 bits (226), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 50/146 (34%), Positives = 78/146 (53%), Gaps = 2/146 (1%)
Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLA 74
           G E      G     VR +FK AR  +P +++ DE+D++            +  +E+ L 
Sbjct: 72  GAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLN 131
Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+L EMDG+   ++V ++A+TNR D +D AL+RPGRLDR +++ LP    R  I +  L 
Sbjct: 132 QLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLK 191
Query: 135 RSPLGEDVCV--EELVRLTEGYSGAE 158
              L +      + L  LT G+SGA+
Sbjct: 192 SLKLTQSSTFYSQRLAELTPGFSGAD 217

>pdb|3B9P|A Chain A, Spastin Length = 297

Iteration: 1
 Score = 91.3 bits (225), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 72/224 (32%), Positives = 110/224 (49%), Gaps = 33/224 (14%)
Query: 18  LFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLAQML 77
           L  KYVG+ E+ VR +F  AR + PS+IF DE+DSL                 R+  + L
Sbjct: 90  LTSKYVGDGEKLVRALFAVARHMQPSIIFIDEVDSLL----SERSSSEHEASRRLKTEFL 145
Query: 78  TEMDGIVPLN----NVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
            E DG+ P N     + ++AATNRP  +D+A LR  R  + +YV LPD+ TR  +L   L
Sbjct: 146 VEFDGL-PGNPDGDRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLL 202
Query: 134 AR--SPLGEDVCVEELVRLTEGYSGAE-QSLSKHRAKKIRPRRESNPGPPACKPSIVAVC 190
            +  SPL  +  +  L ++T+GYSG++  +L+K  A  + P RE N     C        
Sbjct: 203 QKQGSPLDTE-ALRRLAKITDGYSGSDLTALAKDAA--LEPIRELNVEQVKC-------- 251
Query: 191 DXXXXXXXXXXXXXXYVSHQDFLTALQLVKPRTPPQLIKLYENY 234
                           ++ QDF ++L+ ++    PQ +  YE +
Sbjct: 252 --------LDISAMRAITEQDFHSSLKRIRRSVAPQSLNSYEKW 287

>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form Length = 444

Iteration: 1
 Score = 90.9 bits (224), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 52/147 (35%), Positives = 86/147 (58%), Gaps = 8/147 (5%)
Query: 17  ELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLAQM 76
           +L  K++GESE+ V+++F+ AR+  PS+IF DE+DSL            S    R+  + 
Sbjct: 203 DLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLC----GSRSENESEAARRIKTEF 258
Query: 77  LTEMDGI-VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR 135
           L +M G+ V  + + ++ ATN P  +D A+ R  R ++ IY+PLP+   RAA+ ++ L  
Sbjct: 259 LVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGS 316
Query: 136 SPLG-EDVCVEELVRLTEGYSGAEQSL 161
           +     +   +EL R T+GYSGA+ S+
Sbjct: 317 TQNSLTEADFQELGRKTDGYSGADISI 343

>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b Length = 322

Iteration: 1
 Score = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 53/147 (36%), Positives = 85/147 (57%), Gaps = 8/147 (5%)
Query: 17  ELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLAQM 76
           +L  K++GESE+ V+++F+ AR+  PS+IF DE+DSL            S    R+  + 
Sbjct: 81  DLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLC----GSRSENESEAARRIKTEF 136
Query: 77  LTEMDGI-VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR 135
           L +M G+ V  + + ++ ATN P  +D A+ R  R ++ IY+PLP+   RAA+ K+ L  
Sbjct: 137 LVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGT 194
Query: 136 SPLG-EDVCVEELVRLTEGYSGAEQSL 161
           +     +    EL R T+GYSGA+ S+
Sbjct: 195 TQNSLTEADFRELGRKTDGYSGADISI 221

>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer Length = 331

Iteration: 1
 Score = 85.1 bits (209), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 51/147 (34%), Positives = 82/147 (55%), Gaps = 14/147 (9%)
Query: 17  ELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLAQM 76
           +L  K++GESE+ V+ +F  AR+  PS+IF DE+D+L            S    R+  ++
Sbjct: 95  DLVSKWMGESEKLVKQLFAMARENKPSIIFIDEVDALT----GTRGEGESEASRRIKTEL 150
Query: 77  LTEMDGIV-PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR 135
           L +M+G+      V ++ ATN P ++D A+ R  R +R IY+PLPD   R  + +I +  
Sbjct: 151 LVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGD 208
Query: 136 SPLGEDVCVEELVR----LTEGYSGAE 158
           +P    V  +E  R    +TEGYSG++
Sbjct: 209 TPC---VLTKEDYRTLGAMTEGYSGSD 232

>pdb|2QP9|X Chain X, Crystal Structure Of S.Cerevisiae Vps4 Length = 355

Iteration: 1
 Score = 85.1 bits (209), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 82/147 (55%), Gaps = 14/147 (9%)
Query: 17  ELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLAQM 76
           +L  K++GESE+ V+ +F  AR+  PS+IF D++D+L            S    R+  ++
Sbjct: 119 DLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALT----GTRGEGESEASRRIKTEL 174
Query: 77  LTEMDGIV-PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR 135
           L +M+G+      V ++ ATN P ++D A+ R  R +R IY+PLPD   R  + +I +  
Sbjct: 175 LVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGD 232
Query: 136 SPLGEDVCVEELVR----LTEGYSGAE 158
           +P    V  +E  R    +TEGYSG++
Sbjct: 233 TP---SVLTKEDYRTLGAMTEGYSGSD 256

>pdb|3VFD|A Chain A, Human Spastin Aaa Domain Length = 389

Iteration: 1
 Score = 84.3 bits (207), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 72/224 (32%), Positives = 111/224 (49%), Gaps = 30/224 (13%)
Query: 18  LFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLAQML 77
           L  KYVGE E+ VR +F  AR++ PS+IF D++DSL             +   R+  + L
Sbjct: 184 LTSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSL----LCERREGEHDASRRLKTEFL 239
Query: 78  TEMDGIVPLNN--VTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR 135
            E DG+    +  V ++ ATNRP  +D+A+LR  R  + +YV LP++ TR  +LK  L +
Sbjct: 240 IEFDGVQSAGDDRVLVMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCK 297
Query: 136 --SPLGEDVCVEELVRLTEGYSGAE-QSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDX 192
             SPL +     +L R+T+GYSG++  +L+K  A  + P RE        KP  V     
Sbjct: 298 QGSPLTQKELA-QLARMTDGYSGSDLTALAKDAA--LGPIRE-------LKPEQV----- 342
Query: 193 XXXXXXXXXXXXXYVSHQDFLTALQLVKPRTPPQLIKLYENYIK 236
                         +   DF  +L+ +K    PQ ++ Y  + K
Sbjct: 343 ----KNMSASEMRNIRLSDFTESLKKIKRSVSPQTLEAYIRWNK 382

>pdb|3EIH|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of Atpgammas Length = 340

Iteration: 1
 Score = 84.0 bits (206), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 82/147 (55%), Gaps = 14/147 (9%)
Query: 17  ELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLAQM 76
           +L  K++GESE+ V+ +F  AR+  PS+IF D++D+L            S    R+  ++
Sbjct: 104 DLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALT----GTRGEGESEASRRIKTEL 159
Query: 77  LTEMDGIV-PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR 135
           L +M+G+      V ++ ATN P ++D A+ R  R +R IY+PLPD   R  + +I +  
Sbjct: 160 LVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGD 217
Query: 136 SPLGEDVCVEELVR----LTEGYSGAE 158
           +P    V  +E  R    +TEGYSG++
Sbjct: 218 TPC---VLTKEDYRTLGAMTEGYSGSD 241

>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound State Length = 322

Iteration: 1
 Score = 83.6 bits (205), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 82/147 (55%), Gaps = 14/147 (9%)
Query: 17  ELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLAQM 76
           +L  K++GESE+ V+ +F  AR+  PS+IF D++D+L            S    R+  ++
Sbjct: 86  DLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALT----GTRGEGESEASRRIKTEL 141
Query: 77  LTEMDGIV-PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR 135
           L +M+G+      V ++ ATN P ++D A+ R  R +R IY+PLPD   R  + +I +  
Sbjct: 142 LVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGD 199
Query: 136 SPLGEDVCVEELVR----LTEGYSGAE 158
           +P    V  +E  R    +TEGYSG++
Sbjct: 200 TPC---VLTKEDYRTLGAMTEGYSGSD 223

>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In Complex With Adp Length = 357

Iteration: 1
 Score = 81.3 bits (199), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 111/227 (48%), Gaps = 36/227 (15%)
Query: 18  LFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAXXXXXXXXXXXSNVQERVLAQML 77
           L  K+VGE E+ VR +F  AR   P+VIF DE+DSL                 R+  + L
Sbjct: 153 LTSKWVGEGEKMVRALFAVARCQQPAVIFIDEIDSL----LSQRGDGEHESSRRIKTEFL 208
Query: 78  TEMDGIVPLNN--VTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR 135
            ++DG    +   + +V ATNRP  ID+A  R  RL + +Y+PLP+   R  I+   +++
Sbjct: 209 VQLDGATTSSEDRILVVGATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSK 266
Query: 136 SPLGEDVC-----VEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGP-PACKPSIVAV 189
               E  C     +E++V+ ++ +SGA+ +         +  RE++ GP  + + + +A 
Sbjct: 267 ----EQCCLSEEEIEQIVQQSDAFSGADMT---------QLCREASLGPIRSLQTADIAT 313
Query: 190 CDXXXXXXXXXXXXXXYVSHQDFLTALQLVKPRTPPQLIKLYENYIK 236
                            +++ DF  A + V+P   P+ ++LYEN+ K
Sbjct: 314 ITPDQVRP---------IAYIDFENAFRTVRPSVSPKDLELYENWNK 351

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	237
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	9e-92
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	6e-85
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	2e-82
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	3e-48
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	1e-68
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	4e-61
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	1e-59
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	1e-59
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	3e-58
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	1e-57
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	5e-55
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	4e-53
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	1e-50
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	5e-48
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	1e-47
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	6e-44
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	5e-42
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	6e-42
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	9e-42
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	8e-40
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	2e-39
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	3e-30
2krk_A	86	26S protease regulatory subunit 8; structural geno	3e-17
3kw6_A	78	26S protease regulatory subunit 8; structural geno	6e-15
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	2e-11
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	6e-09
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	4e-08
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-04

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

 Score =  271 bits (694), Expect = 9e-92
 Identities = 90/246 (36%), Positives = 128/246 (52%), Gaps = 51/246 (20%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPEL   + GESE  VR++F +ARQ +P V+FFDELDS+A  RG G  G G    +RV+ 
Sbjct: 82  GPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARG-GNIGDGGGAADRVIN 140

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTEMDG+    NV I+ ATNRPD ID A+LRPGRLD+LIY+PLPD+ +R AILK  L 
Sbjct: 141 QILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLR 200

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
           +SP+ +DV +E L ++T G+SGA+                           +  +C  A 
Sbjct: 201 KSPVAKDVDLEFLAKMTNGFSGAD---------------------------LTEICQRAC 233

Query: 195 LSALENNLEA-----------------------AYVSHQDFLTALQLVKPRTPPQLIKLY 231
             A+  ++E+                         +    F  A++  +       I+ Y
Sbjct: 234 KLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKY 293

Query: 232 ENYIKK 237
           E + + 
Sbjct: 294 EMFAQT 299

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

 Score =  252 bits (647), Expect = 6e-85
 Identities = 84/226 (37%), Positives = 112/226 (49%), Gaps = 45/226 (19%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPEL   YVGESER VR VF+RA+  +P VIFFDE+D+L   R D   G       RV+ 
Sbjct: 77  GPELLNMYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRETG----ASVRVVN 132

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL- 133
           Q+LTEMDG+     V I+AATNRPD ID A+LRPGRLD+ ++V LP    R AILK    
Sbjct: 133 QLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITK 192

Query: 134 --ARSPLGEDVCVEELVR--LTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAV 189
              + PL  DV +E +      + Y+GA+                           + A+
Sbjct: 193 NGTKPPLDADVNLEAIAGDLRCDCYTGAD---------------------------LSAL 225

Query: 190 CDEAALSALENNLEAA---------YVSHQDFLTALQLVKPRTPPQ 226
             EA++ AL   +             VSH+ F  A + V+     +
Sbjct: 226 VREASICALRQEMARQKSGNEKGELKVSHKHFEEAFKKVRSSISKK 271

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

 Score =  211 bits (539), Expect = 1e-68
 Identities = 82/209 (39%), Positives = 119/209 (56%), Gaps = 30/209 (14%)

Query: 14  IGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVL 73
           +G EL +K++GE    V+D+FK A++ +PS+IF DE+D++A +R D   GG   VQ R L
Sbjct: 83  VGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQ-RTL 141

Query: 74  AQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
            Q+L EMDG     +V I+ ATNRPD +D A+LRPGR DR+I VP PD+  R  ILKI  
Sbjct: 142 MQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHT 201

Query: 134 ARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEA 193
            +  L EDV +EE+ ++TEG  GAE                           + A+C EA
Sbjct: 202 RKMNLAEDVNLEEIAKMTEGCVGAE---------------------------LKAICTEA 234

Query: 194 ALSALENNLEAAYVSHQDFLTALQLVKPR 222
            ++A+    +  YV+  DF  A++ +  +
Sbjct: 235 GMNAIRELRD--YVTMDDFRKAVEKIMEK 261

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

 Score =  193 bits (493), Expect = 4e-61
 Identities = 62/239 (25%), Positives = 110/239 (46%), Gaps = 22/239 (9%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
             +L  K++GESE+ V+ +F  AR+  PS+IF D++D+L G RG+G          R+  
Sbjct: 84  SSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEAS----RRIKT 139

Query: 75  QMLTEMDGI-VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
           ++L +M+G+      V ++ ATN P ++D A+ R  R +R IY+PLPD   R  + +I +
Sbjct: 140 ELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINV 197

Query: 134 ARSPLG-EDVCVEELVRLTEGYSGAE--------------QSLSKHRAKKIRPRRESNPG 178
             +P          L  +TEGYSG++              +  S    K +    +    
Sbjct: 198 GDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFKDVSTEDDETRK 257

Query: 179 PPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
              C P      + +      + L+   ++ +DFL A++  +P      +   E + + 
Sbjct: 258 LTPCSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRD 316

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

 Score =  189 bits (482), Expect = 1e-59
 Identities = 64/245 (26%), Positives = 104/245 (42%), Gaps = 28/245 (11%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
             +L  K++GESE+ V+++F+ AR+  PS+IF DE+DSL G R +           R+  
Sbjct: 79  SSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAA----RRIKT 134

Query: 75  QMLTEMDGIVPLN-NVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
           + L +M G+   N  + ++ ATN P  +D A+ R  R ++ IY+PLP+   RAA+ K+ L
Sbjct: 135 EFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHL 192

Query: 134 ARSPLG-EDVCVEELVRLTEGYSGA--------------------EQSLSKHRAKKIRPR 172
             +     +    EL R T+GYSGA                              +  P 
Sbjct: 193 GTTQNSLTEADFRELGRKTDGYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPN 252

Query: 173 RESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYE 232
              +     C P      +   +    + L    VS  D L +L   KP      +   +
Sbjct: 253 HLVDDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMSDMLRSLSNTKPTVNEHDLLKLK 312

Query: 233 NYIKK 237
            + + 
Sbjct: 313 KFTED 317

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

 Score =  190 bits (485), Expect = 1e-59
 Identities = 61/239 (25%), Positives = 110/239 (46%), Gaps = 22/239 (9%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
             +L  K++GESE+ V+ +F  AR+  PS+IF D++D+L G RG+G          R+  
Sbjct: 117 SSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEAS----RRIKT 172

Query: 75  QMLTEMDGI-VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
           ++L +M+G+      V ++ ATN P ++D A+ R  R +R IY+PLPD   R  + +I +
Sbjct: 173 ELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINV 230

Query: 134 ARSP-LGEDVCVEELVRLTEGYSGAE--------------QSLSKHRAKKIRPRRESNPG 178
             +P +        L  +TEGYSG++              +  S    K +    +    
Sbjct: 231 GDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFKDVSTEDDETRK 290

Query: 179 PPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
                P      + +      + L+   ++ +DFL A++  +P      +   E + + 
Sbjct: 291 LTPSSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRD 349

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

 Score =  190 bits (485), Expect = 3e-58
 Identities = 72/222 (32%), Positives = 108/222 (48%), Gaps = 46/222 (20%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPE+  K  GESE  +R  F+ A + +P++IF DELD++A +R    G     V+ R+++
Sbjct: 271 GPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGE----VERRIVS 326

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LT MDG+    +V ++AATNRP+ ID AL R GR DR + + +PD   R  IL+I   
Sbjct: 327 QLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTK 386

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
              L +DV +E++   T G+ GA+                           + A+C EAA
Sbjct: 387 NMKLADDVDLEQVANETHGHVGAD---------------------------LAALCSEAA 419

Query: 195 LSAL---------------ENNLEAAYVSHQDFLTALQLVKP 221
           L A+                  + +  V+  DF  AL    P
Sbjct: 420 LQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNP 461

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

 Score =  187 bits (477), Expect = 1e-57
 Identities = 65/245 (26%), Positives = 106/245 (43%), Gaps = 28/245 (11%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
             +L  K++GESE+ V+++F+ AR+  PS+IF DE+DSL G R +           R+  
Sbjct: 201 SSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAA----RRIKT 256

Query: 75  QMLTEMDGIVPLN-NVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL 133
           + L +M G+   N  + ++ ATN P  +D A+ R  R ++ IY+PLP+   RAA+ ++ L
Sbjct: 257 EFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHL 314

Query: 134 ARSPLG-EDVCVEELVRLTEGYSGA--------------------EQSLSKHRAKKIRPR 172
             +     +   +EL R T+GYSGA                              +  P 
Sbjct: 315 GSTQNSLTEADFQELGRKTDGYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPN 374

Query: 173 RESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYE 232
              N     C P      +   +    + L    VS  D L +L   KP    Q +   +
Sbjct: 375 CIVNDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMWDMLRSLSSTKPTVNEQDLLKLK 434

Query: 233 NYIKK 237
            + + 
Sbjct: 435 KFTED 439

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

 Score =  178 bits (454), Expect = 5e-55
 Identities = 67/236 (28%), Positives = 112/236 (47%), Gaps = 46/236 (19%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
              L  K+VGE E+ VR +F  AR   P+VIF DE+DSL  +RGD    G      R+  
Sbjct: 150 ASSLTSKWVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGD----GEHESSRRIKT 205

Query: 75  QMLTEMDGIV--PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIR 132
           + L ++DG      + + +V ATNRP  ID+A  R  RL + +Y+PLP+   R  I+   
Sbjct: 206 EFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINL 263

Query: 133 LARSP-LGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCD 191
           +++      +  +E++V+ ++ +SGA+                           +  +C 
Sbjct: 264 MSKEQCCLSEEEIEQIVQQSDAFSGAD---------------------------MTQLCR 296

Query: 192 EAALSALENNLEAAY----------VSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           EA+L  + +   A            +++ DF  A + V+P   P+ ++LYEN+ K 
Sbjct: 297 EASLGPIRSLQTADIATITPDQVRPIAYIDFENAFRTVRPSVSPKDLELYENWNKT 352

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

 Score =  172 bits (438), Expect = 4e-53
 Identities = 66/237 (27%), Positives = 106/237 (44%), Gaps = 47/237 (19%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
              L  KYVG+ E+ VR +F  AR + PS+IF DE+DSL  ER             R+  
Sbjct: 87  AASLTSKYVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSS----SEHEASRRLKT 142

Query: 75  QMLTEMDGIVPLNN---VTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKI 131
           + L E DG+    +   + ++AATNRP  +D+A LR  R  + +YV LPD+ TR  +L  
Sbjct: 143 EFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNR 200

Query: 132 RLARSPLGEDVC-VEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVC 190
            L +     D   +  L ++T+GYSG++                           + A+ 
Sbjct: 201 LLQKQGSPLDTEALRRLAKITDGYSGSD---------------------------LTALA 233

Query: 191 DEAALSALENNLEAAY----------VSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
            +AAL  +                  ++ QDF ++L+ ++    PQ +  YE + + 
Sbjct: 234 KDAALEPIRELNVEQVKCLDISAMRAITEQDFHSSLKRIRRSVAPQSLNSYEKWSQD 290

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

 Score =  168 bits (427), Expect = 1e-50
 Identities = 67/236 (28%), Positives = 108/236 (45%), Gaps = 46/236 (19%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
              L  KYVGE E+ VR +F  AR++ PS+IF D++DSL  ER +    G  +   R+  
Sbjct: 181 AASLTSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCERRE----GEHDASRRLKT 236

Query: 75  QMLTEMDGIV--PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIR 132
           + L E DG+     + V ++ ATNRP  +D+A+LR  R  + +YV LP++ TR  +LK  
Sbjct: 237 EFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNL 294

Query: 133 LARSPLG-EDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCD 191
           L +         + +L R+T+GYSG++                           + A+  
Sbjct: 295 LCKQGSPLTQKELAQLARMTDGYSGSD---------------------------LTALAK 327

Query: 192 EAALSALENNLEAAY----------VSHQDFLTALQLVKPRTPPQLIKLYENYIKK 237
           +AAL  +                  +   DF  +L+ +K    PQ ++ Y  + K 
Sbjct: 328 DAALGPIRELKPEQVKNMSASEMRNIRLSDFTESLKKIKRSVSPQTLEAYIRWNKD 383

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

 Score =  159 bits (403), Expect = 5e-48
 Identities = 30/160 (18%), Positives = 60/160 (37%), Gaps = 25/160 (15%)

Query: 15  GPELFRKYVGESERCVRDVFKRA----RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQE 70
             EL     GE  + +R  ++ A    R+ +   +F ++LD+ AG  G         V  
Sbjct: 69  AGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDAGAGRMGGTTQYT---VNN 125

Query: 71  RVLAQMLTE------------MDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVP 118
           +++   L              M        V I+   N    +   L+R GR+++  + P
Sbjct: 126 QMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYWAP 185

Query: 119 LPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAE 158
             +D  R  +           ++V  E++V++ + + G  
Sbjct: 186 TRED--RIGVCTGIF----RTDNVPAEDVVKIVDNFPGQS 219

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

 Score =  157 bits (399), Expect = 1e-47
 Identities = 60/195 (30%), Positives = 95/195 (48%), Gaps = 33/195 (16%)

Query: 23  VGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG 82
           +G +   VR +FK AR  +P +++ DE+D++  +R     G  +  +E+ L Q+L EMDG
Sbjct: 82  LGAAR--VRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDG 139

Query: 83  IVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDV 142
           +   ++V ++A+TNR D +D AL+RPGRLDR +++ LP    R  I +  L    L +  
Sbjct: 140 MGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSS 199

Query: 143 --CVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALEN 200
               + L  LT G+SGA+                           I  +C+EAAL A   
Sbjct: 200 TFYSQRLAELTPGFSGAD---------------------------IANICNEAALHAARE 232

Query: 201 NLEAAYVSHQDFLTA 215
              +  V   +F  A
Sbjct: 233 GHTS--VHTLNFEYA 245

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

 Score =  147 bits (374), Expect = 6e-44
 Identities = 59/137 (43%), Positives = 88/137 (64%), Gaps = 3/137 (2%)

Query: 23  VGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG 82
           +G S   VRD+F+ A++ +PS+IF DE+D++   R  GG   G++ +E+ L Q+L EMDG
Sbjct: 87  LGASR--VRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDG 144

Query: 83  IVPLN-NVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGED 141
               N  V ++AATNRP+ +D AL+RPGR DR + V  PD   R  ILK+ +    L  D
Sbjct: 145 FGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLAND 204

Query: 142 VCVEELVRLTEGYSGAE 158
           V ++E+ +LT G +GA+
Sbjct: 205 VNLQEVAKLTAGLAGAD 221

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

 Score =  142 bits (360), Expect = 5e-42
 Identities = 64/136 (47%), Positives = 89/136 (65%), Gaps = 3/136 (2%)

Query: 23  VGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG 82
           VG S   VRD+F++A++ +P +IF DE+D++  +RG  G GGG + +E+ L QML EMDG
Sbjct: 88  VGASR--VRDMFEQAKKAAPCIIFIDEIDAVGRQRG-AGLGGGHDEREQTLNQMLVEMDG 144

Query: 83  IVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDV 142
                 + ++AATNRPD +D ALLRPGR DR + V LPD   R  ILK+ + R PL  D+
Sbjct: 145 FEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDI 204

Query: 143 CVEELVRLTEGYSGAE 158
               + R T G+SGA+
Sbjct: 205 DAAIIARGTPGFSGAD 220

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

 Score =  142 bits (359), Expect = 6e-42
 Identities = 60/136 (44%), Positives = 87/136 (63%), Gaps = 3/136 (2%)

Query: 23  VGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG 82
           VG +   VRD+F+ A++ +P ++F DE+D++  +RG  G GGG++ +E+ L Q+L EMDG
Sbjct: 92  VGAAR--VRDLFETAKRHAPCIVFIDEIDAVGRKRG-SGVGGGNDEREQTLNQLLVEMDG 148

Query: 83  IVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDV 142
                 + ++AATNRPD +D ALLRPGR DR I +  PD   R  IL+I     PL EDV
Sbjct: 149 FEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDV 208

Query: 143 CVEELVRLTEGYSGAE 158
            +  L + T G+ GA+
Sbjct: 209 DLALLAKRTPGFVGAD 224

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

 Score =  142 bits (360), Expect = 9e-42
 Identities = 60/136 (44%), Positives = 87/136 (63%), Gaps = 3/136 (2%)

Query: 23  VGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG 82
           VG +   VRD+F+ A++ +P ++F DE+D++  +RG  G GGG++ +E+ L Q+L EMDG
Sbjct: 116 VGAAR--VRDLFETAKRHAPCIVFIDEIDAVGRKRG-SGVGGGNDEREQTLNQLLVEMDG 172

Query: 83  IVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDV 142
                 + ++AATNRPD +D ALLRPGR DR I +  PD   R  IL+I     PL EDV
Sbjct: 173 FEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDV 232

Query: 143 CVEELVRLTEGYSGAE 158
            +  L + T G+ GA+
Sbjct: 233 DLALLAKRTPGFVGAD 248

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

 Score =  141 bits (359), Expect = 8e-40
 Identities = 61/136 (44%), Positives = 86/136 (63%), Gaps = 3/136 (2%)

Query: 23  VGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG 82
           VG +   VRD+F +A+  +P ++F DE+D++   RG  G GGG + +E+ L Q+L EMDG
Sbjct: 92  VGAAR--VRDLFAQAKAHAPCIVFIDEIDAVGRHRG-AGLGGGHDEREQTLNQLLVEMDG 148

Query: 83  IVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDV 142
                 + ++AATNRPD +D ALLRPGR D+ I V  PD L R  IL+I     PL EDV
Sbjct: 149 FDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDV 208

Query: 143 CVEELVRLTEGYSGAE 158
            +E + + T G+ GA+
Sbjct: 209 NLEIIAKRTPGFVGAD 224

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

 Score =  141 bits (357), Expect = 2e-39
 Identities = 60/136 (44%), Positives = 87/136 (63%), Gaps = 3/136 (2%)

Query: 23  VGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG 82
           VG +   VRD+F+ A++ +P ++F DE+D++  +RG  G GGG++ +E+ L Q+L EMDG
Sbjct: 107 VGAAR--VRDLFETAKRHAPCIVFIDEIDAVGRKRG-SGVGGGNDEREQTLNQLLVEMDG 163

Query: 83  IVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDV 142
                 + ++AATNRPD +D ALLRPGR DR I +  PD   R  IL+I     PL EDV
Sbjct: 164 FEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDV 223

Query: 143 CVEELVRLTEGYSGAE 158
            +  L + T G+ GA+
Sbjct: 224 DLALLAKRTPGFVGAD 239

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

 Score =  112 bits (281), Expect = 3e-30
 Identities = 23/142 (16%), Positives = 51/142 (35%), Gaps = 11/142 (7%)

Query: 14  IGPELFRKYVGESE-RCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERV 72
             P+    +   ++ + ++ +F  A +   S +  D+++ L      G           V
Sbjct: 96  CSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPR-----FSNLV 150

Query: 73  LAQMLTEMDGIVPLN-NVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKI 131
           L  +L  +    P    + I+  T+R D +   +         I+V  P+  T   +L+ 
Sbjct: 151 LQALLVLLKKAPPQGRKLLIIGTTSRKDVLQ-EMEMLNAFSTTIHV--PNIATGEQLLEA 207

Query: 132 RLARSPLGEDVCVEELVRLTEG 153
            L      +D     + +  +G
Sbjct: 208 -LELLGNFKDKERTTIAQQVKG 228

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens} Length = 86

 Score = 72.9 bits (180), Expect = 3e-17
 Identities = 24/108 (22%), Positives = 39/108 (36%), Gaps = 29/108 (26%)

Query: 115 IYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRE 174
            +   P++  R  ILKI   +  L   + + ++  L  G SGAE                
Sbjct: 6   HHHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAE---------------- 49

Query: 175 SNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPR 222
                      +  VC EA + AL       +V+ +DF  A+  V  +
Sbjct: 50  -----------VKGVCTEAGMYALRER--RVHVTQEDFEMAVAKVMQK 84

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens} Length = 78

 Score = 66.7 bits (164), Expect = 6e-15
 Identities = 25/105 (23%), Positives = 39/105 (37%), Gaps = 29/105 (27%)

Query: 118 PLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNP 177
           P P++  R  ILKI   +  L   + + ++  L  G SGAE                   
Sbjct: 1   PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAE------------------- 41

Query: 178 GPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPR 222
                   +  VC EA + AL       +V+ +DF  A+  V  +
Sbjct: 42  --------VKGVCTEAGMYALRER--RVHVTQEDFEMAVAKVMQK 76

>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B* Length = 83

 Score = 57.3 bits (139), Expect = 2e-11
 Identities = 20/102 (19%), Positives = 36/102 (35%), Gaps = 29/102 (28%)

Query: 121 DDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPP 180
           D   +  I     ++  L E+V +E+ V   +  SGA+                      
Sbjct: 2   DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGAD---------------------- 39

Query: 181 ACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPR 222
                I ++C E+ + A+  N     V  +DF  A + V  +
Sbjct: 40  -----INSICQESGMLAVREN--RYIVLAKDFEKAYKTVIKK 74

>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B Length = 82

 Score = 50.4 bits (121), Expect = 6e-09
 Identities = 18/111 (16%), Positives = 30/111 (27%), Gaps = 30/111 (27%)

Query: 123 LTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPAC 182
           + R  I     ++  L  +  ++ L+   +  SGA                         
Sbjct: 1   MERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAV------------------------ 36

Query: 183 KPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLV-KPRTPPQLIKLYE 232
              I A+  EA L A+  N     +   D   A     K          Y+
Sbjct: 37  ---IAAIMQEAGLRAVRKN--RYVILQSDLEEAYATQVKTDNTVDKFDFYK 82

>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone, chaperone-protein binding complex; HET: DNA; 3.80A {Saccharomyces cerevisiae} PDB: 4a3v_B* Length = 88

 Score = 48.7 bits (117), Expect = 4e-08
 Identities = 19/91 (20%), Positives = 31/91 (34%), Gaps = 29/91 (31%)

Query: 125 RAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKP 184
           RA I +I      +   +  E + RL    +GAE                          
Sbjct: 6   RANIFRIHSKSMSVERGIRWELISRLCPNSTGAE-------------------------- 39

Query: 185 SIVAVCDEAALSALENNLEAAYVSHQDFLTA 215
            + +VC EA + A+    +    + +DFL A
Sbjct: 40  -LRSVCTEAGMFAIRARRK--VATEKDFLKA 67

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A* Length = 456

 Score = 45.0 bits (106), Expect = 1e-05
 Identities = 24/140 (17%), Positives = 44/140 (31%), Gaps = 23/140 (16%)

Query: 4   LGGLTEVVESIGPELFRKYVGESERCVRDVFKRA---RQVSPSVIFFDELDSLAGERGDG 60
           LG        +G E++   + ++E  + + F+RA   R      ++  E+  L     + 
Sbjct: 87  LGSKVPFCPMVGSEVYSTEIKKTEV-LMENFRRAIGLRIKETKEVYEGEVTELTPCETEN 145

Query: 61  GGGGGSNVQERVLAQMLTEMD-----------------GIVPLNNVTIVAATNRPDRIDK 103
             GG       V+  + T                     +   + + I A +    R  +
Sbjct: 146 PMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGR 205

Query: 104 ALLRPGRLDRLI--YVPLPD 121
                   D     YVPLP 
Sbjct: 206 CDTYATEFDLEAEEYVPLPK 225

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 39.8 bits (92), Expect = 6e-04
 Identities = 35/276 (12%), Positives = 73/276 (26%), Gaps = 77/276 (27%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPS--VIFFDELDSLAGERGDGGGGGGSNV---- 68
             ++F KY     +    + +   ++ P+  V+              G  G G       
Sbjct: 122 DNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLID------------GVLGSGKTWVALD 169

Query: 69  ---QERVLAQM------------LTEMDGIVPLNNVTIVAATN---RPDRIDKALLRP-- 108
                +V  +M             +    +  L  +      N   R D      LR   
Sbjct: 170 VCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHS 229

Query: 109 --GRLDRLIYV-PLP------DDLTRAAILK--------------IRLARSPLGEDVCVE 145
               L RL+   P         ++  A                   ++            
Sbjct: 230 IQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHI 289

Query: 146 ELVRLTEGYSGAE-QSLSKHRAKKIRPRRESNPGPPACK--PSIVAVCDEAALSALENNL 202
            L   +   +  E +SL     K +  R +  P        P  +++   A    + + L
Sbjct: 290 SLDHHSMTLTPDEVKSLL---LKYLDCRPQDLP-REVLTTNPRRLSII--AES--IRDGL 341

Query: 203 EA----AYVSHQDFLTALQL-VKPRTPPQLIKLYEN 233
                  +V+     T ++  +    P +  K+++ 
Sbjct: 342 ATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDR 377

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	237
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	100.0
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	100.0
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	100.0
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	100.0
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.98
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.97
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.97
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.97
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.96
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.96
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.94
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.94
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.94
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.94
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.94
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.94
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.93
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.93
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.92
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.91
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.91
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.89
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.89
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.82
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.82
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.55
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	99.52
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	99.52
2krk_A	86	26S protease regulatory subunit 8; structural geno	99.5
3kw6_A	78	26S protease regulatory subunit 8; structural geno	99.49
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.46
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.33
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	99.3
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.29
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.28
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.24
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.23
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.11
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.08
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.05
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.04
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.01
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.96
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.94
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.94
3bos_A	242	Putative DNA replication factor; P-loop containing	98.9
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.9
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.9
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.88
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.88
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.79
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.78
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.76
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.75
3pvs_A	447	Replication-associated recombination protein A; ma	98.74
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.72
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.72
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	98.66
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	98.62
2r44_A	331	Uncharacterized protein; putative ATPase, structur	98.6
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.6
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	98.56
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.55
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.54
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.52
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.51
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.49
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.48
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.46
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	98.39
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.35
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.35
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	98.32
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	98.3
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	98.26
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	98.13
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.12
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	97.99
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.98
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.52
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	97.49
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.45
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.19
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.14
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	97.1
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.05
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	96.61
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	96.48
2fna_A	357	Conserved hypothetical protein; structural genomic	96.41
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	96.39
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	96.38
3co5_A	143	Putative two-component system transcriptional RES	96.19
3f8t_A	506	Predicted ATPase involved in replication control,	95.62
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	95.15
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	95.09
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	91.88
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	91.47
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	89.75
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	89.31
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	88.26
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	85.97
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	85.55
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	82.65
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	80.26

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

Probab=100.00  E-value=2.2e-40  Score=290.93  Aligned_cols=200  Identities=36%  Similarity=0.604  Sum_probs=176.2

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+++|+.|+++++.++|+|+++++++.+|..|+.++||||||||+|.+++.+......+ +...+++++.||++|+++..
T Consensus       206 ~~~~f~~v~~s~l~sk~vGese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~-~~~~~~~l~~lL~~lDg~~~  284 (405)
T 4b4t_J          206 TDCKFIRVSGAELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGG-DSEVQRTMLELLNQLDGFET  284 (405)
T ss_dssp             HTCEEEEEEGGGGSCSSTTHHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSGG-GGHHHHHHHHHHHHHHTTTC
T ss_pred             hCCCceEEEhHHhhccccchHHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCCCC-cHHHHHHHHHHHHhhhccCC
Confidence            47899999999999999999999999999999999999999999999998876554322 34557899999999999988


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      ..+|+||||||+|+.||+|++||||||..|+|++|+.++|.+||+.++++.++..++++..||..|+||||+|       
T Consensus       285 ~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl~~lA~~t~G~SGAD-------  357 (405)
T 4b4t_J          285 SKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGAD-------  357 (405)
T ss_dssp             CCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCCHHHHHHHCCSCCHHH-------
T ss_pred             CCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHCCCCCHHH-------
Confidence            8899999999999999999999999999999999999999999999999998888999999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCCCHHHHHHHHHHh
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYI  235 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~~~~~~~~~~~~~  235 (237)
                                          |.++|++|++.+++++  ...|+.+||..|++.+.|...+..+...+.|+
T Consensus       358 --------------------i~~l~~eA~~~Air~~--~~~vt~~Df~~Al~~v~~~~~~~~~s~~k~~k  405 (405)
T 4b4t_J          358 --------------------VKGVCTEAGMYALRER--RIHVTQEDFELAVGKVMNKNQETAISVAKLFK  405 (405)
T ss_dssp             --------------------HHHHHHHHHHHHHHTT--CSBCCHHHHHHHHHHHHHHHTCC---------
T ss_pred             --------------------HHHHHHHHHHHHHHcC--CCCcCHHHHHHHHHHHhCccccccchhHhhhC
Confidence                                9999999999999886  45799999999999887776666677666664

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

Probab=100.00  E-value=2.8e-39  Score=284.87  Aligned_cols=193  Identities=35%  Similarity=0.582  Sum_probs=176.8

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+++|+.++++++.++|+|+++++++.+|..|+.++||||||||+|.++..|......+ +....++++.||++|++...
T Consensus       240 ~~~~fi~v~~s~l~sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~-~~~~~~~l~~LL~~lDg~~~  318 (437)
T 4b4t_I          240 TSATFLRIVGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGG-EREIQRTMLELLNQLDGFDD  318 (437)
T ss_dssp             HTCEEEEEESGGGCCSSSSHHHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCSCSSCSS-CCHHHHHHHHHHHHHHHCCC
T ss_pred             hCCCEEEEEHHHhhhccCchHHHHHHHHHHHHHhcCCcEEEEehhhhhcccCCCCCCCc-cHHHHHHHHHHHHHhhCcCC
Confidence            46899999999999999999999999999999999999999999999999887655433 34557889999999999988


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      .++|+||||||+|+.||+|++||||||..|+|++|+.++|.+||+.++++.++..++++..||..|+||||+|       
T Consensus       319 ~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dvdl~~LA~~T~GfSGAD-------  391 (437)
T 4b4t_I          319 RGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGAD-------  391 (437)
T ss_dssp             SSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCCCHHHHHHHCCSCCHHH-------
T ss_pred             CCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHH-------
Confidence            8899999999999999999999999999999999999999999999999998888999999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCCCHHHH
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLI  228 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~~~~~~  228 (237)
                                          |.++|++|++.+++++  ...|+.+||..|++.+.|+.+++.+
T Consensus       392 --------------------I~~l~~eA~~~Air~~--~~~It~eDf~~Al~rv~~~~~~e~l  432 (437)
T 4b4t_I          392 --------------------IQAMCTEAGLLALRER--RMQVTAEDFKQAKERVMKNKVEENL  432 (437)
T ss_dssp             --------------------HHHHHHHHHHHHHHTT--CSCBCHHHHHHHHHHHHHHHCCCSS
T ss_pred             --------------------HHHHHHHHHHHHHHcC--CCccCHHHHHHHHHHHhCCCChhhH
Confidence                                9999999999999886  4579999999999988876655544

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

Probab=100.00  E-value=3.6e-38  Score=280.27  Aligned_cols=190  Identities=37%  Similarity=0.608  Sum_probs=175.3

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+++|+.++++++.++|+|+++++++.+|..|+.++||||||||+|.++..|......+ .....++++.||++|+++..
T Consensus       239 ~~~~f~~v~~s~l~~~~vGese~~ir~lF~~A~~~aP~IifiDEiDal~~~R~~~~~~~-~~~~~~~~~~lL~~ldg~~~  317 (434)
T 4b4t_M          239 TNATFLKLAAPQLVQMYIGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKSG-DREVQRTMLELLNQLDGFSS  317 (434)
T ss_dssp             HTCEEEEEEGGGGCSSCSSHHHHHHHHHHHHHHHHCSEEEEEECTHHHHCCCSSGGGGT-THHHHHHHHHHHHHHTTSCS
T ss_pred             hCCCEEEEehhhhhhcccchHHHHHHHHHHHHHhcCCeEEeecchhhhhhccCCCCCCC-chHHHHHHHHHHHHhhccCC
Confidence            46899999999999999999999999999999999999999999999999886654332 23456788999999999988


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      .++|+||||||+|+.||+|++||||||..|+|++|+.++|.+||+.++++.++..++++..||..|+||||+|       
T Consensus       318 ~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~sGAD-------  390 (434)
T 4b4t_M          318 DDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELARSTDEFNGAQ-------  390 (434)
T ss_dssp             SCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCCHHHHHHHCSSCCHHH-------
T ss_pred             CCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHH-------
Confidence            8899999999999999999999999999999999999999999999999988888999999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCCCH
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPP  225 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~~~  225 (237)
                                          |.++|.+|++.+++++  ...|+.+||..|++.++|+.++
T Consensus       391 --------------------i~~l~~eA~~~a~r~~--~~~i~~~Df~~Al~~v~~~~~~  428 (434)
T 4b4t_M          391 --------------------LKAVTVEAGMIALRNG--QSSVKHEDFVEGISEVQARKSK  428 (434)
T ss_dssp             --------------------HHHHHHHHHHHHHHHT--CSSBCHHHHHHHHHSCSSSCCC
T ss_pred             --------------------HHHHHHHHHHHHHHcC--CCCcCHHHHHHHHHHHhCCCCc
Confidence                                9999999999998876  4579999999999999998764

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

Probab=100.00  E-value=5.9e-38  Score=279.16  Aligned_cols=192  Identities=34%  Similarity=0.574  Sum_probs=174.5

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+++|+.++++++.++|+|+++++++.+|..|+.++||||||||+|.++..|...+... +....++++.||++|+++..
T Consensus       239 ~~~~~~~v~~s~l~sk~~Gese~~ir~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~-~~~~~~~l~~lL~~lDg~~~  317 (437)
T 4b4t_L          239 IGANFIFSPASGIVDKYIGESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSA-DREIQRTLMELLTQMDGFDN  317 (437)
T ss_dssp             HTCEEEEEEGGGTCCSSSSHHHHHHHHHHHHHHHSCSEEEEEECCCSSSCCCSSSCCSS-TTHHHHHHHHHHHHHHSSSC
T ss_pred             hCCCEEEEehhhhccccchHHHHHHHHHHHHHHhcCCceeeeecccccccccccCCCCc-chHHHHHHHHHHHHhhcccC
Confidence            46899999999999999999999999999999999999999999999999886655433 34557889999999999988


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      .++|+||||||+|+.||+|++||||||..|+|++|+.++|.+||+.++++.+...++++..+|..|+||||+|       
T Consensus       318 ~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl~~lA~~t~G~sGAD-------  390 (437)
T 4b4t_L          318 LGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGAD-------  390 (437)
T ss_dssp             TTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCCHHHHHHTCCSCCHHH-------
T ss_pred             CCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccCHHHHHHhCCCCCHHH-------
Confidence            8899999999999999999999999999999999999999999999999988888999999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCCCHHH
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQL  227 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~~~~~  227 (237)
                                          |.++|.+|++.+++++  ...|+.+||..|++.+.|+...+.
T Consensus       391 --------------------i~~l~~eA~~~air~~--~~~i~~~d~~~Al~~v~~~~k~e~  430 (437)
T 4b4t_L          391 --------------------IRNCATEAGFFAIRDD--RDHINPDDLMKAVRKVAEVKKLEG  430 (437)
T ss_dssp             --------------------HHHHHHHHHHHHHHTT--CSSBCHHHHHHHHHHHHHTCC---
T ss_pred             --------------------HHHHHHHHHHHHHHcC--CCCCCHHHHHHHHHHHHhccCccc
Confidence                                9999999999999876  456999999999999888755443

>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=100.00  E-value=3e-40  Score=312.15  Aligned_cols=205  Identities=43%  Similarity=0.760  Sum_probs=134.1

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      ..+.+|+.+++++++++|+|+++++++.+|..|+..+||||||||+|.++..|+..... ......+++++||.+|+++.
T Consensus       534 e~~~~f~~v~~~~l~s~~vGese~~vr~lF~~Ar~~~P~IifiDEiDsl~~~R~~~~~~-~~~~~~rv~~~lL~~mdg~~  612 (806)
T 3cf2_A          534 ECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGD-GGGAADRVINQILTEMDGMS  612 (806)
T ss_dssp             TTTCEEEECCHHHHHTTTCSSCHHHHHHHHHHHHTTCSEEEECSCGGGCC---------------CHHHHHHHHHHHSSC
T ss_pred             HhCCceEEeccchhhccccchHHHHHHHHHHHHHHcCCceeechhhhHHhhccCCCCCC-CchHHHHHHHHHHHHHhCCC
Confidence            35789999999999999999999999999999999999999999999999988654321 12345789999999999998


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhH
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      ...+|+||||||+|+.||++++||||||+.|+|++|+.++|.+||+.++++.++..++++..||..|+||||+|      
T Consensus       613 ~~~~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~~~~dl~~la~~t~g~SGad------  686 (806)
T 3cf2_A          613 TKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGAD------  686 (806)
T ss_dssp             SSSSEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--CCC----------------C------
T ss_pred             CCCCEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHhCCCCCHHH------
Confidence            88899999999999999999999999999999999999999999999999998888999999999999999999      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccc-----------------------cCCccHHHHHHHHhhcCC
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLE-----------------------AAYVSHQDFLTALQLVKP  221 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~-----------------------~~~v~~~df~~al~~~~p  221 (237)
                                           |.++|++|++.++++...                       .++|+.+||..|++.++|
T Consensus       687 ---------------------i~~l~~~A~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~df~~al~~~~p  745 (806)
T 3cf2_A          687 ---------------------LTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARR  745 (806)
T ss_dssp             ---------------------HHHHHHHHHHHHHHHHHC-----------------------CCC----CCTTTC-----
T ss_pred             ---------------------HHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccccccccccCccCHHHHHHHHHhCCC
Confidence                                 888888877777654321                       246999999999999999


Q ss_pred             CCCHHHHHHHHHHhhC
Q psy5642         222 RTPPQLIKLYENYIKK  237 (237)
Q Consensus       222 ~~~~~~~~~~~~~~~~  237 (237)
                      +++.++++.|++|.++
T Consensus       746 Svs~~~l~~y~~~~~~  761 (806)
T 3cf2_A          746 SVSDNDIRKYEMFAQT  761 (806)
T ss_dssp             ----------CCCC--
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999999864

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

Probab=100.00  E-value=6.8e-38  Score=278.46  Aligned_cols=199  Identities=37%  Similarity=0.615  Sum_probs=172.1

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+++|+.+++++|.++|+|+++++++.+|..|+.++||||||||+|.++..|...... ......++++.+|++|++...
T Consensus       267 ~~~~fi~vs~s~L~sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~-~~~~~~~~l~~lL~~lDg~~~  345 (467)
T 4b4t_H          267 TDATFIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAG-GDNEVQRTMLELITQLDGFDP  345 (467)
T ss_dssp             HTCEEEEEEGGGGCCCSSSHHHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSSSSCG-GGGHHHHHHHHHHHHHHSSCC
T ss_pred             cCCCeEEEEhHHhhcccCCHHHHHHHHHHHHHHhcCCceEeecccccccccccCcCCC-ccHHHHHHHHHHHHHhhccCC
Confidence            4689999999999999999999999999999999999999999999999988765432 234557889999999999988


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      .++|+||||||+|+.||+|++||||||.+|+|++|+.++|.+||+.++++.++..++++..||..|+||||+|       
T Consensus       346 ~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl~~LA~~T~GfSGAD-------  418 (467)
T 4b4t_H          346 RGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAE-------  418 (467)
T ss_dssp             TTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHHCCSCCHHH-------
T ss_pred             CCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHCCCCCHHH-------
Confidence            8899999999999999999999999999999999999999999999999998888999999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCCC-HHHHHHHHHH
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTP-PQLIKLYENY  234 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~~-~~~~~~~~~~  234 (237)
                                          |.++|++|++.+++++  ...|+.+||..|++.+.+... ......|.+|
T Consensus       419 --------------------I~~l~~eAa~~Air~~--~~~it~~Df~~Al~kV~~g~~k~s~~~~y~~~  466 (467)
T 4b4t_H          419 --------------------LRSVCTEAGMFAIRAR--RKVATEKDFLKAVDKVISGYKKFSSTSRYMQY  466 (467)
T ss_dssp             --------------------HHHHHHHHHHHHHHHT--CSSBCHHHHHHHHHHHHHHHCC----------
T ss_pred             --------------------HHHHHHHHHHHHHHcC--CCccCHHHHHHHHHHHhcCcccchhHHHHHhh
Confidence                                9999999999998876  457999999999987654321 1233445555

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

Probab=100.00  E-value=2.6e-37  Score=274.50  Aligned_cols=192  Identities=38%  Similarity=0.563  Sum_probs=174.5

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+++|+.++++++.++|+|+++++++.+|..|+.++||||||||+|.++..|......+ +....++++.||++|+++..
T Consensus       230 ~~~~~~~v~~~~l~~~~~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~-~~~~~r~l~~lL~~ldg~~~  308 (428)
T 4b4t_K          230 TKAAFIRVNGSEFVHKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGS-DREVQRILIELLTQMDGFDQ  308 (428)
T ss_dssp             HTCEEEEEEGGGTCCSSCSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSCC-CCHHHHHHHHHHHHHHHSCS
T ss_pred             hCCCeEEEecchhhccccchhHHHHHHHHHHHHHcCCCeeechhhhhhhccccCCCCCC-ChHHHHHHHHHHHHhhCCCC
Confidence            46899999999999999999999999999999999999999999999999886654433 34567899999999999988


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEec-CCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVP-LPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~-~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      ..+|+||||||+|+.||+|++||||||..|+|| +|+.++|..||+.++++.++..+.++..+|..|+||||+|      
T Consensus       309 ~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~dl~~lA~~t~G~sgad------  382 (428)
T 4b4t_K          309 STNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAV------  382 (428)
T ss_dssp             SCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTCCHHHHHHHTTTCCHHH------
T ss_pred             CCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHHCCCCCHHH------
Confidence            889999999999999999999999999999996 8999999999999999998888999999999999999999      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhh-cCCCCCHHH
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQL-VKPRTPPQL  227 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~-~~p~~~~~~  227 (237)
                                           |.++|++|++.+++++  ...|+.+||..|+.. ++++.+.+.
T Consensus       383 ---------------------i~~l~~eA~~~a~r~~--~~~i~~~d~~~A~~~~~~~~~~~~~  423 (428)
T 4b4t_K          383 ---------------------IAAIMQEAGLRAVRKN--RYVILQSDLEEAYATQVKTDNTVDK  423 (428)
T ss_dssp             ---------------------HHHHHHHHHHHHHHTT--CSSBCHHHHHHHHHHHSCSCCCSSC
T ss_pred             ---------------------HHHHHHHHHHHHHHCC--CCCCCHHHHHHHHHHhhCccCCccH
Confidence                                 9999999999999887  457999999999975 666655443

>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=100.00  E-value=3.1e-33  Score=264.31  Aligned_cols=189  Identities=38%  Similarity=0.572  Sum_probs=170.6

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      ..+++|+.|+|+++.++|.|+++++++.+|..|+.++||||||||+|.|++.+....    ....++++++|+.+|+++.
T Consensus       261 elg~~~~~v~~~~l~sk~~gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~----~~~~~riv~~LL~~mdg~~  336 (806)
T 3cf2_A          261 ETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTH----GEVERRIVSQLLTLMDGLK  336 (806)
T ss_dssp             TTTCEEEEEEHHHHHSSCTTHHHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTCC----CTTHHHHHHHHHTHHHHCC
T ss_pred             HhCCeEEEEEhHHhhcccchHHHHHHHHHHHHHHHcCCeEEEEehhcccccccCCCC----ChHHHHHHHHHHHHHhccc
Confidence            357899999999999999999999999999999999999999999999999876544    3455789999999999998


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhH
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      .+++|+|||+||+++.||++++|||||+++|+++.|+.++|.+||+.++++.++..++++..+|.+|+||+|+|      
T Consensus       337 ~~~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl~~lA~~T~GfsgaD------  410 (806)
T 3cf2_A          337 QRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGAD------  410 (806)
T ss_dssp             GGGCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTCCHHHHHHHCCSCCHHH------
T ss_pred             ccCCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHhcCCCCHHH------
Confidence            88899999999999999999999999999999999999999999999999988889999999999999999999      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc---------------ccCCccHHHHHHHHhhcCCCCC
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL---------------EAAYVSHQDFLTALQLVKPRTP  224 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~---------------~~~~v~~~df~~al~~~~p~~~  224 (237)
                                           |.++|++|.+.++.+..               ....|+.+||..|++.++|+..
T Consensus       411 ---------------------L~~Lv~eA~~~A~~r~~~~i~~~~~~~~~e~~~~~~v~~~Df~~Al~~~~ps~~  464 (806)
T 3cf2_A          411 ---------------------LAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSAL  464 (806)
T ss_dssp             ---------------------HHHHHHHHHHHHHHHHHHHGGGTCCCCSHHHHHHCEECTTHHHHHHSSSSCCCC
T ss_pred             ---------------------HHHHHHHHHHHHHHhccccccccccccchhhhccceeeHHHHHHHHHhCCCccc
Confidence                                 88888888777765432               1346899999999999998754

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

Probab=99.98  E-value=4.4e-31  Score=227.89  Aligned_cols=198  Identities=31%  Similarity=0.535  Sum_probs=174.4

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC-
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP-   85 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-   85 (237)
                      +.+|+.++++++.++|.|++++.++.+|..|...+|+||||||+|.++..+....    .....++++.++..++++.. 
T Consensus        71 ~~~~~~i~~~~l~~~~~g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~----~~~~~~~~~~ll~~ld~~~~~  146 (322)
T 1xwi_A           71 NSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENE----SEAARRIKTEFLVQMQGVGVD  146 (322)
T ss_dssp             SCEEEEEECCSSCCSSCCSCHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCC----TTHHHHHHHHHHHHHHCSSSC
T ss_pred             CCcEEEEEhHHHHhhhhhHHHHHHHHHHHHHHhcCCcEEEeecHHHhcccccccc----chHHHHHHHHHHHHHhccccc
Confidence            6789999999999999999999999999999999999999999999998776543    34567899999999999764 


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      ..+++||+|||.|+.+|++++|  ||+..++++.|+.++|.+||+.+++..+.. .+.++..||..|+||+|+|      
T Consensus       147 ~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgad------  218 (322)
T 1xwi_A          147 NDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGAD------  218 (322)
T ss_dssp             CTTEEEEEEESCTTTSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHHTCTTCCHHH------
T ss_pred             CCCEEEEEecCCcccCCHHHHh--hcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHH------
Confidence            5689999999999999999999  999999999999999999999999887654 7889999999999999999      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc------------------------------------------
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL------------------------------------------  202 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~------------------------------------------  202 (237)
                                           |.++|++|...++++..                                          
T Consensus       219 ---------------------l~~l~~~A~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  277 (322)
T 1xwi_A          219 ---------------------ISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNHLVDDLLTPCSPGDPGAIEMTWMDV  277 (322)
T ss_dssp             ---------------------HHHHHHHHHTHHHHHHHHCSEEEEEEEECSSCTTSEEEEEEEECCSSSTTEEECCGGGS
T ss_pred             ---------------------HHHHHHHHHHHHHHHHHhhhhhhhhccccccccccccccccccccccccchhhcccccc
Confidence                                 66666666665554311                                          


Q ss_pred             -----ccCCccHHHHHHHHhhcCCCCCHHHHHHHHHHhhC
Q psy5642         203 -----EAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK  237 (237)
Q Consensus       203 -----~~~~v~~~df~~al~~~~p~~~~~~~~~~~~~~~~  237 (237)
                           ...+|+.+||..|++.++|++++++++.|++|.++
T Consensus       278 ~~~~~~~~~v~~~df~~al~~~~ps~~~~~~~~~~~~~~~  317 (322)
T 1xwi_A          278 PGDKLLEPVVSMSDMLRSLSNTKPTVNEHDLLKLKKFTED  317 (322)
T ss_dssp             CGGGBCCCCBCHHHHHHHHHTCCCSCCHHHHHHHHHHHHT
T ss_pred             ccccccCCCcCHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Confidence                 12479999999999999999999999999999864

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

Probab=99.97  E-value=2.1e-31  Score=227.79  Aligned_cols=203  Identities=43%  Similarity=0.765  Sum_probs=172.6

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+|+.++|+++.++|.|++++.++.+|..|....|+||||||+|.+...+....... .....++++.++..|+++...
T Consensus        74 ~~~~i~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~-~~~~~~~~~~lL~~l~~~~~~  152 (301)
T 3cf0_A           74 QANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDG-GGAADRVINQILTEMDGMSTK  152 (301)
T ss_dssp             TCEEEEECHHHHHHHHHTTCTTHHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCS-SCSCCHHHHHHHHHHHSSCTT
T ss_pred             CCCEEEEEhHHHHhhhcCchHHHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCc-chHHHHHHHHHHHHhhcccCC
Confidence            5789999999999999999999999999999999999999999999987765432211 122246788999999988777


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      .+++||+|||.++.+|++++|+|||+..++++.|+.++|.+||+.+++..+...+.++..++..|+||+|+|        
T Consensus       153 ~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~~~~~la~~~~g~sg~d--------  224 (301)
T 3cf0_A          153 KNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGAD--------  224 (301)
T ss_dssp             SSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHTCSSCCHHH--------
T ss_pred             CCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccchHHHHHHHcCCCCHHH--------
Confidence            789999999999999999999999999999999999999999999999887777899999999999999999        


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc-----------------------ccCCccHHHHHHHHhhcCCCC
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL-----------------------EAAYVSHQDFLTALQLVKPRT  223 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~-----------------------~~~~v~~~df~~al~~~~p~~  223 (237)
                                         |.++|++|...+..+..                       ....|+.+||..||+..+|++
T Consensus       225 -------------------l~~l~~~a~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~al~~~~~s~  285 (301)
T 3cf0_A          225 -------------------LTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSV  285 (301)
T ss_dssp             -------------------HHHHHHHHHHHHHHHHHHHHC--------------------CCCBCHHHHHHHHTTCCCSS
T ss_pred             -------------------HHHHHHHHHHHHHHHHHHhhhhhhhhcccccccccccccccCCccCHHHHHHHHHHcCCCC
Confidence                               44444444444332211                       124799999999999999999


Q ss_pred             CHHHHHHHHHHhhC
Q psy5642         224 PPQLIKLYENYIKK  237 (237)
Q Consensus       224 ~~~~~~~~~~~~~~  237 (237)
                      +.+++..|++|.++
T Consensus       286 ~~~~~~~~~~~~~~  299 (301)
T 3cf0_A          286 SDNDIRKYEMFAQT  299 (301)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999999999863

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

Probab=99.97  E-value=1.9e-30  Score=223.82  Aligned_cols=197  Identities=31%  Similarity=0.565  Sum_probs=170.4

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-C
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-P   85 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~   85 (237)
                      +.+|+.++++++.++|.|++++.++.+|..|....|+||||||+|.+...+....    .....++.+.++..+++.. .
T Consensus        76 ~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~----~~~~~~~~~~ll~~l~~~~~~  151 (322)
T 3eie_A           76 NSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGE----SEASRRIKTELLVQMNGVGND  151 (322)
T ss_dssp             TCEEEEEEHHHHHTTTGGGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC----------CCTHHHHHHHHHHHGGGGTS
T ss_pred             CCCEEEEchHHHhhcccchHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCc----chHHHHHHHHHHHHhcccccc
Confidence            5789999999999999999999999999999999999999999999998775433    2334788899999999874 4


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      ..+++||+|||.|+.+|+++++  ||+..++++.|+.++|.+||+.++...+.. .+.++..++..|+||+|+|      
T Consensus       152 ~~~v~vi~atn~~~~ld~al~~--Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~~t~g~sg~d------  223 (322)
T 3eie_A          152 SQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSD------  223 (322)
T ss_dssp             CCCEEEEEEESCGGGSCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHHTTTTCCHHH------
T ss_pred             CCceEEEEecCChhhCCHHHHc--ccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHcCCCCHHH------
Confidence            5679999999999999999999  999999999999999999999999887754 7889999999999999999      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc-----------------------------------------c
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL-----------------------------------------E  203 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~-----------------------------------------~  203 (237)
                                           |.++|++|...++++..                                         .
T Consensus       224 ---------------------i~~l~~~a~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  282 (322)
T 3eie_A          224 ---------------------IAVVVKDALMQPIRKIQSATHFKDVSTEDDETRKLTPCSPGDDGAIEMSWTDIEADELK  282 (322)
T ss_dssp             ---------------------HHHHHHHHTTHHHHHHHHCEEEEECC----CCCCEEECCSSCTTEEEEEGGGSCSSCBC
T ss_pred             ---------------------HHHHHHHHHHHHHHHHhhhhhhhhhcccccccccccccccccccccccccccccccccc
Confidence                                 77777776666654321                                         1


Q ss_pred             cCCccHHHHHHHHhhcCCCCCHHHHHHHHHHhh
Q psy5642         204 AAYVSHQDFLTALQLVKPRTPPQLIKLYENYIK  236 (237)
Q Consensus       204 ~~~v~~~df~~al~~~~p~~~~~~~~~~~~~~~  236 (237)
                      ..+|+.+||..|++.++|+++.+++..|++|.+
T Consensus       283 ~~~it~~df~~al~~~~ps~~~~~~~~~~~~~~  315 (322)
T 3eie_A          283 EPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTR  315 (322)
T ss_dssp             CCCCCHHHHHHHHHHSCCSSCTTHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence            256999999999999999999999999999986

>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=99.97  E-value=5.8e-30  Score=223.64  Aligned_cols=197  Identities=31%  Similarity=0.564  Sum_probs=166.6

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC-
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP-   85 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-   85 (237)
                      +.+|+.++++++.++|.|+.++.++.+|..|....|+||||||+|.+...+....    .....++.+.|+..|++... 
T Consensus       109 ~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~----~~~~~~~~~~ll~~l~~~~~~  184 (355)
T 2qp9_X          109 NSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGE----SEASRRIKTELLVQMNGVGND  184 (355)
T ss_dssp             TCEEEEEEHHHHHSCC---CHHHHHHHHHHHHHTSSEEEEEECGGGGTC----------CTHHHHHHHHHHHHHHHCC--
T ss_pred             CCCEEEeeHHHHhhhhcchHHHHHHHHHHHHHHcCCeEEEEechHhhcccCCCCc----chHHHHHHHHHHHHhhccccc
Confidence            5789999999999999999999999999999999999999999999988765432    34567889999999998754 


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      ..+++||+|||.++.+|++++|  ||+..++++.|+.++|.+||+.++...+.. .+.++..||..|+||+|+|      
T Consensus       185 ~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~~t~G~sg~d------  256 (355)
T 2qp9_X          185 SQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSD------  256 (355)
T ss_dssp             -CCEEEEEEESCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHHHTTTCCHHH------
T ss_pred             CCCeEEEeecCCcccCCHHHHc--ccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHcCCCCHHH------
Confidence            4579999999999999999999  999999999999999999999999887654 6889999999999999999      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc-----------------------------------------c
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL-----------------------------------------E  203 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~-----------------------------------------~  203 (237)
                                           |.++|++|...++.+..                                         .
T Consensus       257 ---------------------l~~l~~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  315 (355)
T 2qp9_X          257 ---------------------IAVVVKDALMQPIRKIQSATHFKDVSTEDDETRKLTPSSPGDDGAIEMSWTDIEADELK  315 (355)
T ss_dssp             ---------------------HHHHHHHHHHHHHHHHHHCSEEEECCC-----CCEEEECTTSSSEEECCGGGSCGGGBC
T ss_pred             ---------------------HHHHHHHHHHHHHHHHHHhhhhhhhccccccccccCcCCccccchhhcccccccccccc
Confidence                                 77777777766665411                                         1


Q ss_pred             cCCccHHHHHHHHhhcCCCCCHHHHHHHHHHhh
Q psy5642         204 AAYVSHQDFLTALQLVKPRTPPQLIKLYENYIK  236 (237)
Q Consensus       204 ~~~v~~~df~~al~~~~p~~~~~~~~~~~~~~~  236 (237)
                      ..+|+.+||..||+.++|+++++++..|++|.+
T Consensus       316 ~~~v~~~df~~Al~~~~ps~~~~~~~~~~~~~~  348 (355)
T 2qp9_X          316 EPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTR  348 (355)
T ss_dssp             CCCBCHHHHHHHHHHSCCSSCHHHHHHHHHHHH
T ss_pred             cCCccHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            246999999999999999999999999999986

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

Probab=99.96  E-value=2e-29  Score=226.34  Aligned_cols=198  Identities=32%  Similarity=0.546  Sum_probs=163.1

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC-
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP-   85 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-   85 (237)
                      +.+|+.++++++.++|.|++++.++.+|..+...+|+||||||+|.+++.+....    .....++.+.|+..|++... 
T Consensus       193 ~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~----~~~~~~~~~~lL~~l~~~~~~  268 (444)
T 2zan_A          193 NSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENE----SEAARRIKTEFLVQMQGVGVD  268 (444)
T ss_dssp             SSEEEEECCC---------CCCTHHHHHHHHHHSCSEEEEESCTTTTCCCSSCCC----CGGGHHHHHHHHTTTTCSSCC
T ss_pred             CCCEEEEeHHHHHhhhcchHHHHHHHHHHHHHHcCCeEEEEechHhhccCCCCcc----ccHHHHHHHHHHHHHhCcccC
Confidence            5789999999999999999999999999999999999999999999988765543    34457889999999998764 


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      ..+++||+|||.|+.+|++++|  ||+..++++.|+.++|..||+.++...+.. .+.++..||..|+||+|+|      
T Consensus       269 ~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgad------  340 (444)
T 2zan_A          269 NDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGAD------  340 (444)
T ss_dssp             CSSCEEEEEESCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHHHTTTCCHHH------
T ss_pred             CCCEEEEecCCCccccCHHHHh--hcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHH------
Confidence            5679999999999999999999  999999999999999999999999877653 6889999999999999999      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhc-------------------------------------------
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENN-------------------------------------------  201 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~-------------------------------------------  201 (237)
                                           |.++|++|.+.++++.                                           
T Consensus       341 ---------------------l~~l~~~a~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  399 (444)
T 2zan_A          341 ---------------------ISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMTWMDV  399 (444)
T ss_dssp             ---------------------HHHHHHHHHTHHHHHHHHCSEEEEECCBCSSCTTSBCSCEEEEECTTSTTEEECCTTTS
T ss_pred             ---------------------HHHHHHHHHHHHHHHHHhhhhhhhhccccccccccccccccccCCCCcccchhcccccC
Confidence                                 5555555555444321                                           


Q ss_pred             ----cccCCccHHHHHHHHhhcCCCCCHHHHHHHHHHhhC
Q psy5642         202 ----LEAAYVSHQDFLTALQLVKPRTPPQLIKLYENYIKK  237 (237)
Q Consensus       202 ----~~~~~v~~~df~~al~~~~p~~~~~~~~~~~~~~~~  237 (237)
                          ....+|+.+||..||+.++|+++.++++.|++|.++
T Consensus       400 ~~~~~~~~~v~~~df~~a~~~~~ps~~~~~~~~~~~~~~~  439 (444)
T 2zan_A          400 PGDKLLEPVVSMWDMLRSLSSTKPTVNEQDLLKLKKFTED  439 (444)
T ss_dssp             CTTCBCCCCEEHHHHHHHHHTCCCSCCHHHHHHHHHHTSS
T ss_pred             chhhccCCccCHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Confidence                112479999999999999999999999999999863

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

Probab=99.96  E-value=4e-29  Score=211.01  Aligned_cols=191  Identities=43%  Similarity=0.663  Sum_probs=156.6

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+++.++++++.++|.|+.++.++.+|+.+....|+++++||+|.++..+.....    ....++++.++.+|++....
T Consensus        69 ~~~~i~i~g~~l~~~~~~~~~~~i~~vf~~a~~~~p~i~~~Deid~~~~~r~~~~~----~~~~~~~~~~l~~Lsgg~~~  144 (274)
T 2x8a_A           69 GLNFISVKGPELLNMYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRET----GASVRVVNQLLTEMDGLEAR  144 (274)
T ss_dssp             TCEEEEEETTTTCSSTTHHHHHHHHHHHHHHHHTCSEEEEEETCTTTCC-------------CTTHHHHHHHHHHTCCST
T ss_pred             CCCEEEEEcHHHHhhhhhHHHHHHHHHHHHHHhcCCCeEeeehhhhhhcccCCCcc----hHHHHHHHHHHHhhhccccc
Confidence            34799999999999999999999999999999889999999999998876543211    11246788999999998777


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcC---CCCCchhhHHHHHHHC--CCCCcccccc
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR---SPLGEDVCVEELVRLT--EGYSGAEQSL  161 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~---~~~~~~~~~~~la~~t--~g~s~~Dl~~  161 (237)
                      ..++++++||+|+.||++++||||||..|++++|+.++|.+||+.+++.   .+...++++..+|..|  +||||+|   
T Consensus       145 ~~~i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~la~~~~~~g~sgad---  221 (274)
T 2x8a_A          145 QQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGAD---  221 (274)
T ss_dssp             TCEEEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHHHTCSGGGSCCHHH---
T ss_pred             CCEEEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHHHHhhccCCcCHHH---
Confidence            7899999999999999999999999999999999999999999999854   3345789999999975  5999999   


Q ss_pred             hhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc---------ccCCccHHHHHHHHhhcCCCCCHHHH
Q psy5642         162 SKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL---------EAAYVSHQDFLTALQLVKPRTPPQLI  228 (237)
Q Consensus       162 ~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~---------~~~~v~~~df~~al~~~~p~~~~~~~  228 (237)
                                              |.++|++|...++++..         ....|+.+||..|++.++|+++++++
T Consensus       222 ------------------------l~~l~~~a~~~a~~~~~~~~~~~~~~~~~~i~~~df~~al~~~~ps~~~~~~  273 (274)
T 2x8a_A          222 ------------------------LSALVREASICALRQEMARQKSGNEKGELKVSHKHFEEAFKKVRSSISKKDQ  273 (274)
T ss_dssp             ------------------------HHHHHHHHHHHHHHHHC-----------CCBCHHHHHHHHTTCCCCC-----
T ss_pred             ------------------------HHHHHHHHHHHHHHHHHhhccccccccCCeecHHHHHHHHHHhcCCCChhhc
Confidence                                    88888888887776422         23479999999999999999988764

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

Probab=99.94  E-value=2.4e-26  Score=206.98  Aligned_cols=185  Identities=38%  Similarity=0.632  Sum_probs=160.8

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+|+.++++++...|.|.+...++.+|..|...+||||||||+|.+...+.... .+......++++.|+..|+++...
T Consensus        74 ~~~f~~is~~~~~~~~~g~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~-~g~~~~~~~~l~~LL~~ld~~~~~  152 (476)
T 2ce7_A           74 NVPFFHISGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGL-GGGHDEREQTLNQLLVEMDGFDSK  152 (476)
T ss_dssp             TCCEEEEEGGGTTTCCTTHHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC----------CHHHHHHHHHHHHHHHSCGG
T ss_pred             CCCeeeCCHHHHHHHHhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhhccccc-CcCcHHHHHHHHHHHHHHhccCCC
Confidence            5789999999999999999999999999999999999999999999988765421 112334467889999999987666


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      .+++||++||.++.+|++++|||||+..|.++.|+..+|.+||+.++++.++..+.++..+|..|+||+|+|        
T Consensus       153 ~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v~l~~la~~t~G~sgad--------  224 (476)
T 2ce7_A          153 EGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGAD--------  224 (476)
T ss_dssp             GTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHH--------
T ss_pred             CCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchhhHHHHHHhcCCCcHHH--------
Confidence            789999999999999999999999999999999999999999999999888778889999999999999999        


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCC
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKP  221 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p  221 (237)
                                         |.++|++|...+..++  ...|+.+||..|+....+
T Consensus       225 -------------------L~~lv~~Aal~A~~~~--~~~I~~~dl~~al~~v~~  258 (476)
T 2ce7_A          225 -------------------LENLVNEAALLAAREG--RDKITMKDFEEAIDRVIA  258 (476)
T ss_dssp             -------------------HHHHHHHHHHHHHHTT--CSSBCHHHHHHHHHHHC-
T ss_pred             -------------------HHHHHHHHHHHHHHcC--CCeecHHHHHHHHHHHhc
Confidence                               9999999998887665  356999999999998765

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

Probab=99.94  E-value=2.3e-26  Score=208.24  Aligned_cols=186  Identities=38%  Similarity=0.592  Sum_probs=166.5

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+|+.++|+.+.+.|.|+....++.+|..|....|++|||||+|.+...+....    .....++.+.|+..|++....
T Consensus       263 ~~~fv~vn~~~l~~~~~g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~----~~~~~~~~~~LL~~ld~~~~~  338 (489)
T 3hu3_A          263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTH----GEVERRIVSQLLTLMDGLKQR  338 (489)
T ss_dssp             SSEEEEEEHHHHHTSCTTHHHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTSCC----CHHHHHHHHHHHHHHHHSCTT
T ss_pred             CCCEEEEEchHhhhhhcchhHHHHHHHHHHHHhcCCcEEEecchhhhcccccccc----chHHHHHHHHHHHHhhccccC
Confidence            6799999999999999999999999999999999999999999999998765432    356678999999999988777


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      .+++||+|||.++.+|++++++|||+..|+++.|+.++|.+||+.+++..++..+.++..++..+.||+++|        
T Consensus       339 ~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~~~l~~la~~t~g~s~~d--------  410 (489)
T 3hu3_A          339 AHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGAD--------  410 (489)
T ss_dssp             SCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCTTCCHHHHHHTCTTCCHHH--------
T ss_pred             CceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcchhhHHHHHHHccCCcHHH--------
Confidence            789999999999999999999999999999999999999999999999888878889999999999999999        


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccc---------------cCCccHHHHHHHHhhcCCCC
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLE---------------AAYVSHQDFLTALQLVKPRT  223 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~---------------~~~v~~~df~~al~~~~p~~  223 (237)
                                         |.++|++|...+..+...               ...|+.+||..|++.++|+.
T Consensus       411 -------------------L~~L~~~A~~~a~r~~~~~i~~~~~~~~~~~~~~~~vt~edf~~Al~~~~ps~  463 (489)
T 3hu3_A          411 -------------------LAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSA  463 (489)
T ss_dssp             -------------------HHHHHHHHHHHHHHTTTTTCCTTCSSCCHHHHHHCCBCHHHHHHHHTSHHHHH
T ss_pred             -------------------HHHHHHHHHHHHHHhccccccccccccchhhcccCcCCHHHHHHHHHhCCchh
Confidence                               888888888888765422               24699999999999877543

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

Probab=99.94  E-value=7.3e-26  Score=197.77  Aligned_cols=197  Identities=34%  Similarity=0.592  Sum_probs=168.0

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC-
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP-   85 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-   85 (237)
                      +.+|+.++|+++.+.|.|+.++.++.+|..+....|+||||||+|.+...+....    .....++.+.++..+++... 
T Consensus       142 ~~~~~~i~~~~l~~~~~g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~----~~~~~~~~~~lL~~l~~~~~~  217 (357)
T 3d8b_A          142 GATFFSISASSLTSKWVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGE----HESSRRIKTEFLVQLDGATTS  217 (357)
T ss_dssp             TCEEEEEEGGGGCCSSTTHHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC----------CHHHHHHHHHHHHHHC----
T ss_pred             CCeEEEEehHHhhccccchHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCc----chHHHHHHHHHHHHHhccccc
Confidence            5789999999999999999999999999999999999999999999988764432    34557888999999998653 


Q ss_pred             -CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchh
Q psy5642          86 -LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSK  163 (237)
Q Consensus        86 -~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~  163 (237)
                       ..+++||+|||.++.+++++++  ||+..++++.|+.++|.++|+.++...... .+.++..++..++||+++|     
T Consensus       218 ~~~~v~vI~atn~~~~l~~~l~~--Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~~t~G~s~~d-----  290 (357)
T 3d8b_A          218 SEDRILVVGATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGAD-----  290 (357)
T ss_dssp             CCCCEEEEEEESCGGGBCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHHHTTTCCHHH-----
T ss_pred             CCCCEEEEEecCChhhCCHHHHh--hCceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHHHcCCCCHHH-----
Confidence             3579999999999999999999  999999999999999999999999776543 6788999999999999999     


Q ss_pred             HHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc----------ccCCccHHHHHHHHhhcCCCCCHHHHHHHHH
Q psy5642         164 HRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL----------EAAYVSHQDFLTALQLVKPRTPPQLIKLYEN  233 (237)
Q Consensus       164 ~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~----------~~~~v~~~df~~al~~~~p~~~~~~~~~~~~  233 (237)
                                            |..+|+.|...++++-.          ...+|+.+||..|++.++|+++.++++.|++
T Consensus       291 ----------------------l~~l~~~a~~~~ir~l~~~~~~~~~~~~~~~i~~~d~~~al~~~~ps~~~~~~~~~~~  348 (357)
T 3d8b_A          291 ----------------------MTQLCREASLGPIRSLQTADIATITPDQVRPIAYIDFENAFRTVRPSVSPKDLELYEN  348 (357)
T ss_dssp             ----------------------HHHHHHHHHTHHHHHCCC----------CCCBCHHHHHHHHHHHGGGCCCCCHHHHHH
T ss_pred             ----------------------HHHHHHHHHHHHHHHhhhhhhccccccccCCcCHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence                                  88888877776665321          2357999999999999999999999999999


Q ss_pred             Hhh
Q psy5642         234 YIK  236 (237)
Q Consensus       234 ~~~  236 (237)
                      |.+
T Consensus       349 ~~~  351 (357)
T 3d8b_A          349 WNK  351 (357)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            986

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

Probab=99.94  E-value=1.3e-25  Score=190.71  Aligned_cols=197  Identities=33%  Similarity=0.594  Sum_probs=166.6

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+|+.++|+.+.+.+.|+++..++.+|..+....|+||||||+|.+...+.....    ....++.+.++..+++....
T Consensus        79 ~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~----~~~~~~~~~ll~~l~~~~~~  154 (297)
T 3b9p_A           79 SATFLNISAASLTSKYVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEH----EASRRLKTEFLVEFDGLPGN  154 (297)
T ss_dssp             TCEEEEEESTTTSSSSCSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC---------CCSHHHHHHHHHHHHHCC--
T ss_pred             CCCeEEeeHHHHhhcccchHHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCcc----hHHHHHHHHHHHHHhccccc
Confidence            57899999999999999999999999999999999999999999999887654321    22356778888888876543


Q ss_pred             ---CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccch
Q psy5642          87 ---NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLS  162 (237)
Q Consensus        87 ---~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~  162 (237)
                         .+++||++||.++.+++++++  ||+..++++.|+.++|..||+.++...+.. .+.++..++..|.||+++|    
T Consensus       155 ~~~~~v~vi~~tn~~~~l~~~l~~--R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~----  228 (297)
T 3b9p_A          155 PDGDRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSD----  228 (297)
T ss_dssp             ----CEEEEEEESCGGGBCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHH----
T ss_pred             CCCCcEEEEeecCChhhCCHHHHh--hCCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHH----
Confidence               469999999999999999999  999999999999999999999999876543 5778999999999999999    


Q ss_pred             hHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc----------ccCCccHHHHHHHHhhcCCCCCHHHHHHHH
Q psy5642         163 KHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL----------EAAYVSHQDFLTALQLVKPRTPPQLIKLYE  232 (237)
Q Consensus       163 ~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~----------~~~~v~~~df~~al~~~~p~~~~~~~~~~~  232 (237)
                                             |.++++.|...++++..          ....|+.+||..|++..+|+++++.++.|+
T Consensus       229 -----------------------l~~l~~~a~~~a~r~~~~~~~~~~~~~~~~~i~~~d~~~a~~~~~~s~~~~~~~~~~  285 (297)
T 3b9p_A          229 -----------------------LTALAKDAALEPIRELNVEQVKCLDISAMRAITEQDFHSSLKRIRRSVAPQSLNSYE  285 (297)
T ss_dssp             -----------------------HHHHHHHHTTHHHHTCC--------CCCCCCCCHHHHHHHTTSCCCSSCHHHHHHHH
T ss_pred             -----------------------HHHHHHHHHHHHHHHHhhhhcccccccccCCcCHHHHHHHHHHcCCCCCHHHHHHHH
Confidence                                   88888877777766531          134799999999999999999999999999


Q ss_pred             HHhh
Q psy5642         233 NYIK  236 (237)
Q Consensus       233 ~~~~  236 (237)
                      +|.+
T Consensus       286 ~~~~  289 (297)
T 3b9p_A          286 KWSQ  289 (297)
T ss_dssp             HHC-
T ss_pred             HHHH
Confidence            9976

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

Probab=99.94  E-value=7.4e-25  Score=182.61  Aligned_cols=185  Identities=40%  Similarity=0.644  Sum_probs=163.0

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+++.++++++.+.+.|++.+.++.+|+.|....|++|+|||+|.+...+..... +......+.++.++..+++....
T Consensus        70 ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~~~~~-~~~~~~~~~~~~ll~~l~~~~~~  148 (257)
T 1lv7_A           70 KVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLG-GGHDEREQTLNQMLVEMDGFEGN  148 (257)
T ss_dssp             TCCEEEECSCSSTTSCCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSC-CTTCHHHHHHHHHHHHHHTCCSS
T ss_pred             CCCEEEEeHHHHHHHhhhhhHHHHHHHHHHHHHcCCeeehhhhhhhhccCCCCCcC-CCchHHHHHHHHHHHHhhCcccC
Confidence            35789999999999999999999999999999989999999999999876644321 12234457889999999988777


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      .+++||+|||.++.+|++++|+|||+..++++.|+.++|.+||+.++++.++..+.++..++..++||+++|        
T Consensus       149 ~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~~~~~la~~~~G~~~~d--------  220 (257)
T 1lv7_A          149 EGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGAD--------  220 (257)
T ss_dssp             SCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHH--------
T ss_pred             CCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCccccHHHHHHHcCCCCHHH--------
Confidence            789999999999999999999999999999999999999999999999888778888999999999999999        


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCC
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKP  221 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p  221 (237)
                                         |.+++..|...+..++  ...|+.+||..|++.+..
T Consensus       221 -------------------l~~l~~~a~~~a~~~~--~~~i~~~~~~~a~~~~~~  254 (257)
T 1lv7_A          221 -------------------LANLVNEAALFAARGN--KRVVSMVEFEKAKDKIMM  254 (257)
T ss_dssp             -------------------HHHHHHHHHHHHHHTT--CSSBCHHHHHHHHHHHTT
T ss_pred             -------------------HHHHHHHHHHHHHHhC--CCcccHHHHHHHHHHHhc
Confidence                               9999999998888765  457999999999987653

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

Probab=99.93  E-value=1.1e-24  Score=192.25  Aligned_cols=198  Identities=34%  Similarity=0.577  Sum_probs=160.6

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+.+|+.++|+.+.+.|.|+.+..++.+|..+....|+||||||+|.++..+....    .....++...|+..+++...
T Consensus       172 ~~~~~~~v~~~~l~~~~~g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~----~~~~~~~~~~ll~~l~~~~~  247 (389)
T 3vfd_A          172 SNATFFNISAASLTSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCERREGE----HDASRRLKTEFLIEFDGVQS  247 (389)
T ss_dssp             TTCEEEEECSCCC-------CHHHHHHHHHHHHHSSSEEEEEETGGGGC------------CTHHHHHHHHHHHHHHHC-
T ss_pred             hcCcEEEeeHHHhhccccchHHHHHHHHHHHHHhcCCeEEEEECchhhcccCCCcc----chHHHHHHHHHHHHhhcccc
Confidence            35799999999999999999999999999999999999999999999987764432    23457888899999887654


Q ss_pred             --CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccch
Q psy5642          86 --LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLS  162 (237)
Q Consensus        86 --~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~  162 (237)
                        ..+++||+|||.++.+++++++  ||+..++++.|+.++|.+||+.++...... .+.++..++..++||+++|    
T Consensus       248 ~~~~~v~vI~atn~~~~l~~~l~~--R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~~~~g~~~~~----  321 (389)
T 3vfd_A          248 AGDDRVLVMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSD----  321 (389)
T ss_dssp             ----CEEEEEEESCGGGCCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHHHTTTCCHHH----
T ss_pred             cCCCCEEEEEecCCchhcCHHHHc--CcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHH----
Confidence              3579999999999999999999  999999999999999999999999876544 6778999999999999999    


Q ss_pred             hHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc----------ccCCccHHHHHHHHhhcCCCCCHHHHHHHH
Q psy5642         163 KHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL----------EAAYVSHQDFLTALQLVKPRTPPQLIKLYE  232 (237)
Q Consensus       163 ~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~----------~~~~v~~~df~~al~~~~p~~~~~~~~~~~  232 (237)
                                             |..++..|...++.+-.          ....|+.+||..+++..+|+.+.+.++.|+
T Consensus       322 -----------------------l~~L~~~a~~~~~rel~~~~~~~~~~~~~~~i~~~d~~~al~~~~~s~~~~~l~~~~  378 (389)
T 3vfd_A          322 -----------------------LTALAKDAALGPIRELKPEQVKNMSASEMRNIRLSDFTESLKKIKRSVSPQTLEAYI  378 (389)
T ss_dssp             -----------------------HHHHHHHHTTHHHHTSCCC---CCSSSCCCCCCHHHHHHHHHHCCCSSCHHHHHHHH
T ss_pred             -----------------------HHHHHHHHHHHHHHhhhhhhhhccchhhcCCcCHHHHHHHHHHcCCCCCHHHHHHHH
Confidence                                   88888888877776521          234799999999999999999999999999


Q ss_pred             HHhh
Q psy5642         233 NYIK  236 (237)
Q Consensus       233 ~~~~  236 (237)
                      +|.+
T Consensus       379 ~~~~  382 (389)
T 3vfd_A          379 RWNK  382 (389)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9975

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

Probab=99.93  E-value=3.4e-24  Score=180.88  Aligned_cols=184  Identities=43%  Similarity=0.747  Sum_probs=164.0

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+++.+.++++.+.+.|+....++.+|..+....|+||||||+|.++..+.+.... ........+..++..+++....
T Consensus        76 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~-~~~~~~~~l~~ll~~~~~~~~~  154 (285)
T 3h4m_A           76 NATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTG-GDREVQRTLMQLLAEMDGFDAR  154 (285)
T ss_dssp             TCEEEEEEGGGGCCCSTTHHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCG-GGGHHHHHHHHHHHHHHTTCSS
T ss_pred             CCCEEEEehHHHHHhccchHHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccCC-ccHHHHHHHHHHHHHhhCCCCC
Confidence            578999999999999999999999999999999999999999999998876554322 2334567788888899887777


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      .+++||+|||.++.+|+++++++||+..++++.|+.++|.+||+.++.......+.++..++..+.||+++|        
T Consensus       155 ~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~l~~~~~g~~~~~--------  226 (285)
T 3h4m_A          155 GDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAE--------  226 (285)
T ss_dssp             SSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHHCTTCCHHH--------
T ss_pred             CCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHcCCCCHHH--------
Confidence            789999999999999999999999999999999999999999999999888778889999999999999999        


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcC
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVK  220 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~  220 (237)
                                         |.+++..|...+..++  ...|+.+||..|++.+.
T Consensus       227 -------------------i~~l~~~a~~~a~~~~--~~~I~~~d~~~al~~~~  259 (285)
T 3h4m_A          227 -------------------LKAICTEAGMNAIREL--RDYVTMDDFRKAVEKIM  259 (285)
T ss_dssp             -------------------HHHHHHHHHHHHHHTT--CSSBCHHHHHHHHHHHH
T ss_pred             -------------------HHHHHHHHHHHHHHhc--cCcCCHHHHHHHHHHHH
Confidence                               9999999999988876  44699999999988654

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

Probab=99.92  E-value=1.1e-24  Score=181.46  Aligned_cols=187  Identities=34%  Similarity=0.542  Sum_probs=143.6

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+++.++++++.+.+.|.+...++.+|..+....|+||+|||+|.+...+...............+..++..+++....
T Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~  143 (262)
T 2qz4_A           64 QVPFLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTT  143 (262)
T ss_dssp             TCCEEEEETTTTSSSSTTHHHHHHHHHHHHHHHTCSEEEEEECC-------------------CHHHHHHHHHHHTCCTT
T ss_pred             CCCEEEechHHHHhhccChhHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCC
Confidence            46899999999999999999999999999999999999999999999877654322111222346778899999987767


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCch--hhHHHHHHHCCCCCcccccchhH
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGED--VCVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~--~~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      .++++|+|||.++.+|++++++|||+..++++.|+.++|.+||+.++...+...+  ..+..++..+.||+++|      
T Consensus       144 ~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~------  217 (262)
T 2qz4_A          144 DHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGAD------  217 (262)
T ss_dssp             CCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHH------
T ss_pred             CCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHH------
Confidence            7899999999999999999999999999999999999999999999987766533  34588999999999999      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCC
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPR  222 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~  222 (237)
                                           |.++++.|...+..++  ...|+.+||..|++.+.|.
T Consensus       218 ---------------------l~~l~~~a~~~a~~~~--~~~i~~~d~~~a~~~~~~~  252 (262)
T 2qz4_A          218 ---------------------IANICNEAALHAAREG--HTSVHTLNFEYAVERVLAG  252 (262)
T ss_dssp             ---------------------HHHHHHHHHTC----------CCBCCHHHHHHHHHHH
T ss_pred             ---------------------HHHHHHHHHHHHHHcC--CCCCCHHHHHHHHHHhccC
Confidence                                 8888888887776654  3468889999999876553

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

Probab=99.91  E-value=2.8e-24  Score=194.64  Aligned_cols=186  Identities=37%  Similarity=0.607  Sum_probs=162.7

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+|+.++++++...+.|...+.++.+|+.+....|+|+||||+|.+...+.... ..........++.++..|++....
T Consensus        89 ~~~~i~i~g~~~~~~~~g~~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~-~~~~~e~~~~l~~LL~~Ldg~~~~  167 (499)
T 2dhr_A           89 RVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGV-GGGNDEREQTLNQLLVEMDGFEKD  167 (499)
T ss_dssp             TCCEEEEEGGGGTSSCTTHHHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSSSST-TTSSHHHHHHHHHHHHHGGGCCSS
T ss_pred             CCCEEEEehhHHHHhhhhhHHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhccCc-CCCcHHHHHHHHHHHHHhcccccC
Confidence            4789999999999999999999999999999888999999999999987664321 112234467889999999988777


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      ..+++|++||.|+.+|++++|||||+..|+|+.|+..+|.+||+.+++..++..+.++..+|..|+||+|+|        
T Consensus       168 ~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~dv~l~~lA~~t~G~~gad--------  239 (499)
T 2dhr_A          168 TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGAD--------  239 (499)
T ss_dssp             CCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCSSTTHHHHTTSCSCCHHH--------
T ss_pred             ccEEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChHHHHHHHHHhcCCCCHHH--------
Confidence            789999999999999999999999999999999999999999999998887778899999999999999999        


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCC
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPR  222 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~  222 (237)
                                         |.+++++|...+..++  ...|+.+||..|+....+.
T Consensus       240 -------------------L~~lv~~Aa~~A~~~~--~~~It~~dl~~al~~v~~~  274 (499)
T 2dhr_A          240 -------------------LENLLNEAALLAAREG--RRKITMKDLEEAADRVMML  274 (499)
T ss_dssp             -------------------HHHHHHHHHHHHTTTC--CSSCCSHHHHHHHHHHTTC
T ss_pred             -------------------HHHHHHHHHHHHHHhC--CCccCHHHHHHHHHHHhcc
Confidence                               9999999988886654  3469999999999987654

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

Probab=99.91  E-value=2.8e-23  Score=172.77  Aligned_cols=180  Identities=38%  Similarity=0.639  Sum_probs=153.2

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCC
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLN   87 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~   87 (237)
                      .+++.+++.++.+.+.+...+.++.+|+.+....|+++++||+|.+...+.... ........+.++.++..|++.....
T Consensus        75 ~~~i~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~i~~~Deid~l~~~~~~~~-~~~~~~~~~~~~~ll~~l~g~~~~~  153 (254)
T 1ixz_A           75 VPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGV-GGGNDEREQTLNQLLVEMDGFEKDT  153 (254)
T ss_dssp             CCEEEEEHHHHHHSCTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC----------CHHHHHHHHHHHHHHHTCCTTC
T ss_pred             CCEEEeeHHHHHHHHhhHHHHHHHHHHHHHHhcCCeEEEehhhhhhhcccCccc-cccchHHHHHHHHHHHHHhCCCCCC
Confidence            678999999999999999999999999999888899999999999986654311 1112344677889999999877767


Q ss_pred             CEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHhh
Q psy5642          88 NVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAK  167 (237)
Q Consensus        88 ~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a~  167 (237)
                      .++++++||.|+.+|++++|++||+..++++.|+.++|.+||+.+++..++..+.++..+|..++||+++|         
T Consensus       154 ~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~d---------  224 (254)
T 1ixz_A          154 AIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGAD---------  224 (254)
T ss_dssp             CEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHH---------
T ss_pred             CEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHH---------
Confidence            79999999999999999999999999999999999999999999998877778889999999999999999         


Q ss_pred             hhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHh
Q psy5642         168 KIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQ  217 (237)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~  217 (237)
                                        |.+++++|...+..++  ...|+.+||.+|++
T Consensus       225 ------------------l~~~~~~a~~~a~~~~--~~~I~~~dl~~a~~  254 (254)
T 1ixz_A          225 ------------------LENLLNEAALLAAREG--RRKITMKDLEEAAS  254 (254)
T ss_dssp             ------------------HHHHHHHHHHHHHHTT--CSSBCHHHHHHHTC
T ss_pred             ------------------HHHHHHHHHHHHHHhc--CCCcCHHHHHHHhC
Confidence                              9999999988887665  34699999998863

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

Probab=99.89  E-value=3.3e-22  Score=168.58  Aligned_cols=180  Identities=38%  Similarity=0.639  Sum_probs=152.8

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCC
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLN   87 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~   87 (237)
                      .+++.+++.++...+.+...+.+..+|+.+....|+++++||+|.+...+.... ..........++.++..+++.....
T Consensus        99 ~~~i~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~i~~iDeid~l~~~~~~~~-~~~~~~~~~~~~~ll~~lsgg~~~~  177 (278)
T 1iy2_A           99 VPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGV-GGGNDEREQTLNQLLVEMDGFEKDT  177 (278)
T ss_dssp             CCEEEEEHHHHHHSTTTHHHHHHHHHHHHHHTSCSEEEEEETHHHHHCC---------CHHHHHHHHHHHHHHTTCCTTC
T ss_pred             CCEEEecHHHHHHHHhhHHHHHHHHHHHHHHhcCCcEEehhhhHhhhccccccc-CCcchHHHHHHHHHHHHHhCCCCCC
Confidence            578999999999999999999999999999988899999999999876554211 1112334677888999999877667


Q ss_pred             CEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHhh
Q psy5642          88 NVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAK  167 (237)
Q Consensus        88 ~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a~  167 (237)
                      .++++++||.|+.+|++++|++||+..++++.|+.++|.+||+.+++...+..+.++..+|..++||+++|         
T Consensus       178 ~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~d---------  248 (278)
T 1iy2_A          178 AIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGAD---------  248 (278)
T ss_dssp             CEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHH---------
T ss_pred             CEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCCcccCHHHHHHHcCCCCHHH---------
Confidence            79999999999999999999999999999999999999999999998877777889999999999999999         


Q ss_pred             hhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHh
Q psy5642         168 KIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQ  217 (237)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~  217 (237)
                                        |.++++.|...+..++  ...|+.+||.+|++
T Consensus       249 ------------------l~~l~~~a~~~a~~~~--~~~I~~~dl~~a~~  278 (278)
T 1iy2_A          249 ------------------LENLLNEAALLAAREG--RRKITMKDLEEAAS  278 (278)
T ss_dssp             ------------------HHHHHHHHHHHHHHTT--CCSBCHHHHHHHTC
T ss_pred             ------------------HHHHHHHHHHHHHHhC--CCCcCHHHHHHHhC
Confidence                              9999998888877654  34699999998863

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

Probab=99.89  E-value=3.4e-25  Score=185.53  Aligned_cols=191  Identities=36%  Similarity=0.557  Sum_probs=154.4

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+|+.++++.+.+.+.|.+...++.+|..+....|+||||||+|.+...+......+.......+++.++..+++....
T Consensus        69 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~  148 (268)
T 2r62_A           69 HVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSE  148 (268)
T ss_dssp             TCCCCCCCSCTTTTSCSSSCSSSSSTTHHHHHHSCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCS
T ss_pred             CCCEEEechHHHHHhhcchHHHHHHHHHHHHHhcCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccC
Confidence            45788999999999999999999999999999999999999999999876533211111111123456777888776543


Q ss_pred             -CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          87 -NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        87 -~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                       .+++||+|||.++.+|++++++|||+..++++.|+.++|.++|+.+++..+...+.++..++..+.||+|+|       
T Consensus       149 ~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~g~~g~d-------  221 (268)
T 2r62_A          149 NAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGAD-------  221 (268)
T ss_dssp             CSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCCSSCCTTTTTSSSCSSCHHH-------
T ss_pred             CCCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCCCccCHHHHHHHcCCCCHHH-------
Confidence             359999999999999999999999999999999999999999999998887777888999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCCCHH
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQ  226 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~~~~  226 (237)
                                          |.++++.|...+..++  ...|+.+||..|++...|+...+
T Consensus       222 --------------------l~~l~~~a~~~a~~~~--~~~i~~~~~~~a~~~~~~~~~~~  260 (268)
T 2r62_A          222 --------------------LANIINEAALLAGRNN--QKEVRQQHLKEAVERGIAGLEKK  260 (268)
T ss_dssp             --------------------HHHHHHHHHHTTSSSC--CCSCCHHHHHTSCTTCCCCCC--
T ss_pred             --------------------HHHHHHHHHHHHHHhc--cCCcCHHHHHHHHHHHhhcchhh
Confidence                                8888888887775443  34699999999999999987554

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

Probab=99.82  E-value=1.8e-20  Score=159.33  Aligned_cols=147  Identities=20%  Similarity=0.321  Sum_probs=111.6

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHH----HhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRA----RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG   82 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a----~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~   82 (237)
                      +.+|+.++++++.+.|+|+++..++.+|..|    +..+|+||||||+|.+++.+.+....  ....+.+.+.|++.|++
T Consensus        61 ~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~~~~~~vl~iDEiD~~~~~~~~~~~~--~~~~~~v~~~Ll~~ld~  138 (293)
T 3t15_A           61 GINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDAGAGRMGGTTQY--TVNNQMVNATLMNIADN  138 (293)
T ss_dssp             TCCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHHTTSSCCCEEEECCC----------------CHHHHHHHHHHHHHC
T ss_pred             CCCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCCCCccc--cchHHHHHHHHHHHhcc
Confidence            5789999999999999999999999999999    56789999999999998855432211  12335677889999874


Q ss_pred             CC-----------CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHC
Q psy5642          83 IV-----------PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLT  151 (237)
Q Consensus        83 ~~-----------~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t  151 (237)
                      ..           ...+++||+|||+++.+|++++|+|||+..|+  .|+.++|.+|++.++..    .+.++..++..+
T Consensus       139 ~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~R~d~~i~--~P~~~~r~~Il~~~~~~----~~~~~~~l~~~~  212 (293)
T 3t15_A          139 PTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYW--APTREDRIGVCTGIFRT----DNVPAEDVVKIV  212 (293)
T ss_dssp             CC-----------CCCCCCEEEECSSCCC--CHHHHHHHEEEEEE--CCCHHHHHHHHHHHHGG----GCCCHHHHHHHH
T ss_pred             ccccccccccccccCCCcEEEEecCCcccCCHHHhCCCCCceeEe--CcCHHHHHHHHHHhccC----CCCCHHHHHHHh
Confidence            43           44579999999999999999999999999887  57999999999988864    356788999999


Q ss_pred             CCCCcccccc
Q psy5642         152 EGYSGAEQSL  161 (237)
Q Consensus       152 ~g~s~~Dl~~  161 (237)
                      +||+++||..
T Consensus       213 ~~~~~~~l~~  222 (293)
T 3t15_A          213 DNFPGQSIDF  222 (293)
T ss_dssp             HHSCSCCHHH
T ss_pred             CCCCcccHHH
Confidence            9999999654

>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=99.55  E-value=9.9e-18  Score=150.70  Aligned_cols=148  Identities=16%  Similarity=0.194  Sum_probs=98.2

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHH---HhcCCeEEEEccccccccccCCCCCCCCCchHH-------------
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRA---RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQE-------------   70 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a---~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~-------------   70 (237)
                      +++|+.++++++.++|.|++++ ++.+|..|   +..+||||||||+|.+++++.....++......             
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~-~~~~f~~a~~~~~~~~~il~iDEid~l~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~  168 (456)
T 2c9o_A           90 KVPFCPMVGSEVYSTEIKKTEV-LMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTK  168 (456)
T ss_dssp             TSCEEEEEGGGGCCSSSCHHHH-HHHHHHHTEEEEEEEEEEEEEEEEEEEEEC--------------CEEEEEEETTEEE
T ss_pred             CceEEEEeHHHHHHHhhhhhHH-HHHHHHHHHhhhhcCCcEEEEechhhcccccCCCCCCCcchHHHHHHHHHhccccch
Confidence            4899999999999999999998 99999999   778999999999999998886543211111111             


Q ss_pred             --HHHHHHHHHhc--CCCCCCCEEEEEEeCCCCccchhccCCCCccc--EEEecCCC--HHHHHHHHHHHHcCCCCCchh
Q psy5642          71 --RVLAQMLTEMD--GIVPLNNVTIVAATNRPDRIDKALLRPGRLDR--LIYVPLPD--DLTRAAILKIRLARSPLGEDV  142 (237)
Q Consensus        71 --~~~~~ll~~l~--~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~--~i~~~~P~--~~~R~~il~~~l~~~~~~~~~  142 (237)
                        ++.+.++..++  +....+.++|++|||.++.+|++++||||||.  .++++.|+  .++|.+|++.+.       ..
T Consensus       169 ~~~~~~~ll~~l~~~~~~~~~~v~i~attn~~~~ld~a~~r~~rfd~~~~~~v~~p~~~~~~R~~il~~~~-------~~  241 (456)
T 2c9o_A          169 QLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVT-------LH  241 (456)
T ss_dssp             EEEECHHHHHHHHHTTCCTTEEEEEETTTCCEEEEEEETTSCCTTSCSSSSEECCCCSCSEEEEEEEEEEE-------HH
T ss_pred             hHhhhHHHHHHHhhccCCCCCEEEEEcCCCCcccCChhhcCCcccCcceeEecCCCchhHHHHHHHHHHHH-------HH
Confidence              22344666665  33333447777999999999999999999998  66777774  578888876544       24


Q ss_pred             hHHHHHHHCCCCCcccccchhH
Q psy5642         143 CVEELVRLTEGYSGAEQSLSKH  164 (237)
Q Consensus       143 ~~~~la~~t~g~s~~Dl~~~~~  164 (237)
                      +++.++..|+|  |+||..++.
T Consensus       242 dl~~~a~~t~g--gadl~~l~~  261 (456)
T 2c9o_A          242 DLDVANARPQG--GQDILSMMG  261 (456)
T ss_dssp             HHHHTC----------------
T ss_pred             HHHHHHHhCCC--hhHHHHHHh
Confidence            78999999999  999777664

>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B*

Probab=99.52  E-value=1.2e-14  Score=100.49  Aligned_cols=82  Identities=27%  Similarity=0.397  Sum_probs=67.7

Q ss_pred             CHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHh
Q psy5642         121 DDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALEN  200 (237)
Q Consensus       121 ~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~  200 (237)
                      |.++|.+||+.++++.++.+++++..||..|+||||+|                           |.++|++|...++.+
T Consensus         2 d~~~R~~Il~~~l~~~~~~~~vdl~~la~~t~G~SGAD---------------------------i~~l~~eA~~~a~~~   54 (83)
T 3aji_B            2 DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGAD---------------------------INSICQESGMLAVRE   54 (83)
T ss_dssp             CHHHHHHHHHHHHTTSCBCTTCCTHHHHTSSCCCCHHH---------------------------HHHHHHHHHHGGGTS
T ss_pred             CHHHHHHHHHHHhCCCCCCcccCHHHHHHHcCCCCHHH---------------------------HHHHHHHHHHHHHHh
Confidence            68899999999999998888999999999999999999                           999999999999887


Q ss_pred             ccccCCccHHHHHHHHhhcCCCCCHHHHHHHH
Q psy5642         201 NLEAAYVSHQDFLTALQLVKPRTPPQLIKLYE  232 (237)
Q Consensus       201 ~~~~~~v~~~df~~al~~~~p~~~~~~~~~~~  232 (237)
                      .  ..+|+.+||..|++.++|+++ +.++.|+
T Consensus        55 ~--~~~i~~~df~~Al~~~~ps~~-~~l~~y~   83 (83)
T 3aji_B           55 N--RYIVLAKDFEKAYKTVIKKDE-QEHEFYK   83 (83)
T ss_dssp             C--CSSBCHHHHHHHHHHHCC-----------
T ss_pred             c--cCCcCHHHHHHHHHHHccCch-HHHHhcC
Confidence            6  467999999999999999998 7666653

>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone, chaperone-protein binding complex; HET: DNA; 3.80A {Saccharomyces cerevisiae} PDB: 4a3v_B*

Probab=99.52  E-value=2.1e-14  Score=100.23  Aligned_cols=85  Identities=27%  Similarity=0.363  Sum_probs=67.5

Q ss_pred             CHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHh
Q psy5642         121 DDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALEN  200 (237)
Q Consensus       121 ~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~  200 (237)
                      |.++|.+||+.++++.++..++++..||..|+||||+|                           |.++|++|++.++++
T Consensus         2 d~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~SGAD---------------------------l~~l~~eAa~~a~r~   54 (88)
T 3vlf_B            2 DLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAE---------------------------LRSVCTEAGMFAIRA   54 (88)
T ss_dssp             CSSHHHHHHHHHHTTSCBCSCCCHHHHHHTCSSCCHHH---------------------------HHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCCCCccCHHHHHHHcCCCcHHH---------------------------HHHHHHHHHHHHHHh
Confidence            56799999999999999888999999999999999999                           999999999999998


Q ss_pred             ccccCCccHHHHHHHHhhcCCCCCH-HHHHHHHHH
Q psy5642         201 NLEAAYVSHQDFLTALQLVKPRTPP-QLIKLYENY  234 (237)
Q Consensus       201 ~~~~~~v~~~df~~al~~~~p~~~~-~~~~~~~~~  234 (237)
                      .  ...|+.+||..|++.+.|...+ .....|.+|
T Consensus        55 ~--~~~i~~~df~~Al~~v~~~~~~~~~~~~y~~w   87 (88)
T 3vlf_B           55 R--RKVATEKDFLKAVDKVISGYKKFSSTSRYMQY   87 (88)
T ss_dssp             S--CSSBCHHHHHHHHHHHTC--------------
T ss_pred             c--cccCCHHHHHHHHHHHhcCcccccchhHHhcc
Confidence            7  4569999999999999998754 447778888

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

Probab=99.50  E-value=1.9e-14  Score=99.98  Aligned_cols=78  Identities=31%  Similarity=0.457  Sum_probs=72.0

Q ss_pred             EecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHH
Q psy5642         116 YVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAAL  195 (237)
Q Consensus       116 ~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~  195 (237)
                      +-.+|+.++|.+||+.++++.++..++++..||..|+||||+|                           |.++|++|++
T Consensus         7 ~~~~Pd~~~R~~IL~~~l~~~~l~~dvdl~~LA~~T~G~SGAD---------------------------L~~l~~eAa~   59 (86)
T 2krk_A            7 HHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAE---------------------------VKGVCTEAGM   59 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHTTTSEECTTCCCHHHHHTCSSCCHHH---------------------------HHHHHHHHHH
T ss_pred             CCCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHH---------------------------HHHHHHHHHH
Confidence            3468999999999999999988888999999999999999999                           9999999999


Q ss_pred             HHHHhccccCCccHHHHHHHHhhcCCC
Q psy5642         196 SALENNLEAAYVSHQDFLTALQLVKPR  222 (237)
Q Consensus       196 ~~~~~~~~~~~v~~~df~~al~~~~p~  222 (237)
                      .++.+.  ...|+.+||..|++.++|.
T Consensus        60 ~alr~~--~~~I~~~df~~Al~~v~p~   84 (86)
T 2krk_A           60 YALRER--RVHVTQEDFEMAVAKVMQK   84 (86)
T ss_dssp             HHHHTT--CSEECHHHHHHHHHHHHCC
T ss_pred             HHHHHc--CCCCCHHHHHHHHHHHccC
Confidence            999887  4679999999999998874

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

Probab=99.49  E-value=4.6e-14  Score=96.31  Aligned_cols=75  Identities=33%  Similarity=0.512  Sum_probs=69.3

Q ss_pred             cCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHH
Q psy5642         118 PLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSA  197 (237)
Q Consensus       118 ~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~  197 (237)
                      |+|+.++|.+||+.++++.++..++++..||..|+||||+|                           |.++|++|.+.+
T Consensus         1 plPd~~~R~~Il~~~l~~~~~~~~~dl~~la~~t~G~SGAD---------------------------i~~l~~eA~~~a   53 (78)
T 3kw6_A            1 PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAE---------------------------VKGVCTEAGMYA   53 (78)
T ss_dssp             CCCCHHHHHHHHHHHHTTSEECTTCCHHHHHHTCTTCCHHH---------------------------HHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCCccCHHHHHHHcCCCCHHH---------------------------HHHHHHHHHHHH
Confidence            68999999999999999988878999999999999999999                           999999999999


Q ss_pred             HHhccccCCccHHHHHHHHhhcCC
Q psy5642         198 LENNLEAAYVSHQDFLTALQLVKP  221 (237)
Q Consensus       198 ~~~~~~~~~v~~~df~~al~~~~p  221 (237)
                      +.++  ...|+.+||..|++.+..
T Consensus        54 ~~~~--~~~i~~~d~~~Al~~v~~   75 (78)
T 3kw6_A           54 LRER--RVHVTQEDFEMAVAKVMQ   75 (78)
T ss_dssp             HHTT--CSEECHHHHHHHHHHHHC
T ss_pred             HHhC--CCCCCHHHHHHHHHHHHh
Confidence            9987  457999999999987654

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

Probab=99.46  E-value=4.5e-13  Score=113.65  Aligned_cols=131  Identities=18%  Similarity=0.218  Sum_probs=104.4

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      ..+++.++++++.+.+.|.....+..+|..+   .++||||||+|.++..+...      .....+.+.|+..++.  ..
T Consensus        99 ~~~~~~~~~~~l~~~~~g~~~~~~~~~~~~~---~~~vl~iDEid~l~~~~~~~------~~~~~~~~~Ll~~l~~--~~  167 (309)
T 3syl_A           99 KGHLVSVTRDDLVGQYIGHTAPKTKEVLKRA---MGGVLFIDEAYYLYRPDNER------DYGQEAIEILLQVMEN--NR  167 (309)
T ss_dssp             SCCEEEECGGGTCCSSTTCHHHHHHHHHHHH---TTSEEEEETGGGSCCCC---------CCTHHHHHHHHHHHHH--CT
T ss_pred             CCcEEEEcHHHhhhhcccccHHHHHHHHHhc---CCCEEEEEChhhhccCCCcc------cccHHHHHHHHHHHhc--CC
Confidence            4589999999999999999999999999887   46899999999998654331      1225678888888886  33


Q ss_pred             CCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHH
Q psy5642          87 NNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRL  150 (237)
Q Consensus        87 ~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~  150 (237)
                      .++++|++||.+.     .+++++++  ||+.+++|+.|+.+++..|++.++...... .+..+..++..
T Consensus       168 ~~~~~i~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~~~~~~~~~il~~~l~~~~~~~~~~~~~~l~~~  235 (309)
T 3syl_A          168 DDLVVILAGYADRMENFFQSNPGFRS--RIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRAY  235 (309)
T ss_dssp             TTCEEEEEECHHHHHHHHHHSTTHHH--HEEEEEEECCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHH
T ss_pred             CCEEEEEeCChHHHHHHHhhCHHHHH--hCCeEEEcCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            5788899998654     35799999  999999999999999999999999866544 44555556554

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

Probab=99.33  E-value=6.5e-12  Score=109.02  Aligned_cols=145  Identities=20%  Similarity=0.219  Sum_probs=109.9

Q ss_pred             HHHHHHHHHHHHhc---------CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEe--
Q psy5642          27 ERCVRDVFKRARQV---------SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAAT--   95 (237)
Q Consensus        27 ~~~l~~~f~~a~~~---------~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~tt--   95 (237)
                      ...++..|..+...         .|+||||||+|.+.               ....+.|+..++...  .+++++++.  
T Consensus       166 ~~~~~~~~~~~~~~~~~~g~~~~~~~vl~IDEi~~l~---------------~~~~~~L~~~le~~~--~~~~ii~t~~~  228 (368)
T 3uk6_A          166 KSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLD---------------IESFSFLNRALESDM--APVLIMATNRG  228 (368)
T ss_dssp             CHHHHHHHHHHHHHHHHHTC---CBCEEEEESGGGSB---------------HHHHHHHHHHTTCTT--CCEEEEEESCS
T ss_pred             HHHHHHHHHHHHHHhhhhccccccCceEEEhhccccC---------------hHHHHHHHHHhhCcC--CCeeeeecccc
Confidence            44555566555431         27899999999883               234667777776632  356666664  


Q ss_pred             ---------CCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhHH
Q psy5642          96 ---------NRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        96 ---------n~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                               |.+..+++++++  ||.. +.|++|+.+++.++++..+...... ++..+..++..+.|.++++       
T Consensus       229 ~~~i~~t~~~~~~~l~~~l~s--R~~~-i~~~~~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~~~G~~r~-------  298 (368)
T 3uk6_A          229 ITRIRGTSYQSPHGIPIDLLD--RLLI-VSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRY-------  298 (368)
T ss_dssp             EEECBTSSCEEETTCCHHHHT--TEEE-EEECCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHHHSCHHH-------
T ss_pred             eeeeeccCCCCcccCCHHHHh--hccE-EEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCCHHH-------
Confidence                     357889999999  9976 8999999999999999888765443 5667888999887667788       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcC
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVK  220 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~  220 (237)
                                          +.+++..+...+..++  ...|+.+++.+|+..+.
T Consensus       299 --------------------~~~ll~~a~~~A~~~~--~~~It~~~v~~a~~~~~  331 (368)
T 3uk6_A          299 --------------------AIQLITAASLVCRKRK--GTEVQVDDIKRVYSLFL  331 (368)
T ss_dssp             --------------------HHHHHHHHHHHHHHTT--CSSBCHHHHHHHHHHSB
T ss_pred             --------------------HHHHHHHHHHHHHHhC--CCCCCHHHHHHHHHHhc
Confidence                                8889999888887665  45799999999998754

>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B

Probab=99.30  E-value=4.3e-13  Score=92.32  Aligned_cols=80  Identities=23%  Similarity=0.316  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc
Q psy5642         123 LTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL  202 (237)
Q Consensus       123 ~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~  202 (237)
                      ++|.+||+.++++.++..++++..||..|+||||+|                           |.++|++|++.++.++ 
T Consensus         1 ~~R~~Il~~~l~~~~~~~~vdl~~lA~~t~G~SGAD---------------------------i~~l~~eAa~~ai~~~-   52 (82)
T 2dzn_B            1 MERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAV---------------------------IAAIMQEAGLRAVRKN-   52 (82)
T ss_dssp             -------------CEECTTCCSTTTTTSSCCCCHHH---------------------------HHHHHHHHHHHHHHTT-
T ss_pred             CHHHHHHHHHHcCCCCCCcCCHHHHHHHcCCCCHHH---------------------------HHHHHHHHHHHHHHhc-
Confidence            479999999999988778899999999999999999                           9999999999999986 


Q ss_pred             ccCCccHHHHHHHHhhc-CCCCCHHHHHHH
Q psy5642         203 EAAYVSHQDFLTALQLV-KPRTPPQLIKLY  231 (237)
Q Consensus       203 ~~~~v~~~df~~al~~~-~p~~~~~~~~~~  231 (237)
                       ...|+.+||..|++.+ .|+.+...++.|
T Consensus        53 -~~~i~~~df~~Al~~v~~~~~~~~~~~~y   81 (82)
T 2dzn_B           53 -RYVILQSDLEEAYATQVKTDNTVDKFDFY   81 (82)
T ss_dssp             -CSEECHHHHHHHHHTTCC-----------
T ss_pred             -cCCcCHHHHHHHHHHHHcCcCChHHHHhh
Confidence             4579999999999998 577777666655

>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=99.29  E-value=2.6e-12  Score=117.78  Aligned_cols=176  Identities=19%  Similarity=0.252  Sum_probs=111.0

Q ss_pred             ceEEEEEecccccc---------cccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHH
Q psy5642           7 LTEVVESIGPELFR---------KYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQML   77 (237)
Q Consensus         7 ~~~~i~v~~s~l~~---------~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll   77 (237)
                      +.++..++++.+..         .|+|.....+...|..+....| ||||||+|.+......           ...+.|+
T Consensus       133 ~~~~~~i~~~~~~~~~~~~g~~~~~ig~~~~~~~~~~~~a~~~~~-vl~lDEid~l~~~~~~-----------~~~~~LL  200 (543)
T 3m6a_A          133 GRKFVRISLGGVRDESEIRGHRRTYVGAMPGRIIQGMKKAGKLNP-VFLLDEIDKMSSDFRG-----------DPSSAML  200 (543)
T ss_dssp             TCEEEEECCCC--------------------CHHHHHHTTCSSSE-EEEEEESSSCC--------------------CCG
T ss_pred             CCCeEEEEecccchhhhhhhHHHHHhccCchHHHHHHHHhhccCC-EEEEhhhhhhhhhhcc-----------CHHHHHH
Confidence            34677787766544         7788888889999998887666 9999999999765421           1345566


Q ss_pred             HHhcCCCC-------------CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHc-----CCCCC
Q psy5642          78 TEMDGIVP-------------LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA-----RSPLG  139 (237)
Q Consensus        78 ~~l~~~~~-------------~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~-----~~~~~  139 (237)
                      ..|+....             ..++++|+|||.++.+|++|++  ||+ +|+|+.|+.+++..|++.++.     .....
T Consensus       201 ~~ld~~~~~~~~~~~~~~~~~~~~v~iI~ttN~~~~l~~aL~~--R~~-vi~~~~~~~~e~~~Il~~~l~~~~~~~~~~~  277 (543)
T 3m6a_A          201 EVLDPEQNSSFSDHYIEETFDLSKVLFIATANNLATIPGPLRD--RME-IINIAGYTEIEKLEIVKDHLLPKQIKEHGLK  277 (543)
T ss_dssp             GGTCTTTTTBCCCSSSCCCCBCSSCEEEEECSSTTTSCHHHHH--HEE-EEECCCCCHHHHHHHHHHTHHHHHHHHTTCC
T ss_pred             HHHhhhhcceeecccCCeeecccceEEEeccCccccCCHHHHh--hcc-eeeeCCCCHHHHHHHHHHHHHHHHHHHcCCC
Confidence            66654321             1468999999999999999999  996 799999999999999998762     22221


Q ss_pred             ------chhhHHHHHHHCCC-CCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHH
Q psy5642         140 ------EDVCVEELVRLTEG-YSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDF  212 (237)
Q Consensus       140 ------~~~~~~~la~~t~g-~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df  212 (237)
                            .+..+..++....+ ...++|+..                       |.++|..+.............|+.+++
T Consensus       278 ~~~i~i~~~~l~~l~~~~~~~~~vR~L~~~-----------------------i~~~~~~aa~~~~~~~~~~~~It~~~l  334 (543)
T 3m6a_A          278 KSNLQLRDQAILDIIRYYTREAGVRSLERQ-----------------------LAAICRKAAKAIVAEERKRITVTEKNL  334 (543)
T ss_dssp             GGGCEECHHHHHHHHHHHCCCSSSHHHHHH-----------------------HHHHHHHHHHHHHTTCCSCCEECTTTT
T ss_pred             cccccCCHHHHHHHHHhCChhhchhHHHHH-----------------------HHHHHHHHHHHHHhcCCcceecCHHHH
Confidence                  34455565553333 223332111                       555666666666655444567999999


Q ss_pred             HHHHhhcC
Q psy5642         213 LTALQLVK  220 (237)
Q Consensus       213 ~~al~~~~  220 (237)
                      ..++...+
T Consensus       335 ~~~Lg~~~  342 (543)
T 3m6a_A          335 QDFIGKRI  342 (543)
T ss_dssp             HHHHCSCC
T ss_pred             HHHhCCcc
Confidence            99987544

>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=99.28  E-value=1.3e-11  Score=103.16  Aligned_cols=139  Identities=16%  Similarity=0.216  Sum_probs=98.9

Q ss_pred             ceEEEEEeccc-ccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           7 LTEVVESIGPE-LFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         7 ~~~~i~v~~s~-l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      +.+|+.+++++ +++...+.....++.+|..+....|++|+|||+|.++..+....     .....++..|...++....
T Consensus        89 ~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~-----~~~~~~l~~L~~~~~~~~~  163 (272)
T 1d2n_A           89 NFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGP-----RFSNLVLQALLVLLKKAPP  163 (272)
T ss_dssp             TCSEEEEECGGGCTTCCHHHHHHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTTT-----BCCHHHHHHHHHHTTCCCS
T ss_pred             CCCEEEEeCHHHhcCCchHHHHHHHHHHHHHHHhcCCcEEEEEChhhhhccCCCCh-----hHHHHHHHHHHHHhcCccC
Confidence            46788888765 33333344457889999999888899999999999986654222     2225667777777776543


Q ss_pred             -CCCEEEEEEeCCCCccch-hccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCC
Q psy5642          86 -LNNVTIVAATNRPDRIDK-ALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYS  155 (237)
Q Consensus        86 -~~~v~vI~ttn~~~~ld~-al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s  155 (237)
                       ..+++||+|||.++.+++ .+++  ||+..|++|.++.  |.+|...+.....+ .+.++..++..+.||+
T Consensus       164 ~~~~~~ii~ttn~~~~l~~~~l~~--rf~~~i~~p~l~~--r~~i~~i~~~~~~~-~~~~~~~l~~~~~g~~  230 (272)
T 1d2n_A          164 QGRKLLIIGTTSRKDVLQEMEMLN--AFSTTIHVPNIAT--GEQLLEALELLGNF-KDKERTTIAQQVKGKK  230 (272)
T ss_dssp             TTCEEEEEEEESCHHHHHHTTCTT--TSSEEEECCCEEE--HHHHHHHHHHHTCS-CHHHHHHHHHHHTTSE
T ss_pred             CCCCEEEEEecCChhhcchhhhhc--ccceEEcCCCccH--HHHHHHHHHhcCCC-CHHHHHHHHHHhcCCC
Confidence             346889999999999998 6777  9998888876654  34444433332233 5778999999999985

>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=99.24  E-value=9.3e-11  Score=99.01  Aligned_cols=182  Identities=16%  Similarity=0.197  Sum_probs=120.4

Q ss_pred             ceEEEEEecccccc-cccCh-HHHHHHHHHHHH-----HhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHH
Q psy5642           7 LTEVVESIGPELFR-KYVGE-SERCVRDVFKRA-----RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTE   79 (237)
Q Consensus         7 ~~~~i~v~~s~l~~-~~~g~-~~~~l~~~f~~a-----~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~   79 (237)
                      +.+++.++|+.+.+ .|+|. ....++.+|..+     ....++||+|||+|.+........   .......+.+.|+..
T Consensus        75 ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~---~~~~~~~~~~~Ll~~  151 (310)
T 1ofh_A           75 NAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSG---ADVSREGVQRDLLPL  151 (310)
T ss_dssp             TCCEEEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCS---SHHHHHHHHHHHHHH
T ss_pred             CCCEEEEcchhcccCCccCccHHHHHHHHHHHhhHHHhhccCCCEEEEEChhhcCccccccc---cchhHHHHHHHHHHH
Confidence            45789999998876 56664 356677777643     122478999999999987653221   122223456778888


Q ss_pred             hcCCC--------CCCCEEEEEE----eCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHH----HH-------cCC
Q psy5642          80 MDGIV--------PLNNVTIVAA----TNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKI----RL-------ARS  136 (237)
Q Consensus        80 l~~~~--------~~~~v~vI~t----tn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~----~l-------~~~  136 (237)
                      +++..        ...++++|++    ++.+..+++++++  ||+..|+|+.|+.+++.+|++.    ++       ...
T Consensus       152 le~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~--R~~~~i~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~  229 (310)
T 1ofh_A          152 VEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEPHASLTEQYKALMATE  229 (310)
T ss_dssp             HHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHHT
T ss_pred             hcCCeEecccccccCCcEEEEEcCCcccCCcccCCHHHHh--hCCceEEcCCcCHHHHHHHHHhhHHHHHHHHHHHHHhc
Confidence            87642        2246788888    5678899999999  9998899999999999999983    21       111


Q ss_pred             CC--C-chhhHHHHHHHCC-------CCCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc----
Q psy5642         137 PL--G-EDVCVEELVRLTE-------GYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL----  202 (237)
Q Consensus       137 ~~--~-~~~~~~~la~~t~-------g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~----  202 (237)
                      ..  . ++..+..++..+.       +..++.                           +.++++.+......+..    
T Consensus       230 ~~~~~~~~~a~~~l~~~~~~~~~~~~~g~~R~---------------------------l~~~l~~~~~~~~~~~~~~~~  282 (310)
T 1ofh_A          230 GVNIAFTTDAVKKIAEAAFRVNEKTENIGARR---------------------------LHTVMERLMDKISFSASDMNG  282 (310)
T ss_dssp             TCEEEECHHHHHHHHHHHHHHHHHSCCCTTHH---------------------------HHHHHHHHSHHHHHHGGGCTT
T ss_pred             CCeeccCHHHHHHHHHHhhhhcccccccCcHH---------------------------HHHHHHHHHHhhhcCCccccC
Confidence            11  1 4455566666552       344555                           66666665544332221    


Q ss_pred             ccCCccHHHHHHHHhhcC
Q psy5642         203 EAAYVSHQDFLTALQLVK  220 (237)
Q Consensus       203 ~~~~v~~~df~~al~~~~  220 (237)
                      ....|+.+++..+++...
T Consensus       283 ~~~~i~~~~v~~~l~~~~  300 (310)
T 1ofh_A          283 QTVNIDAAYVADALGEVV  300 (310)
T ss_dssp             CEEEECHHHHHHHTCSSS
T ss_pred             CEEEEeeHHHHHHHHhhh
Confidence            123599999999998654

>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=99.23  E-value=1.3e-10  Score=110.36  Aligned_cols=180  Identities=19%  Similarity=0.264  Sum_probs=124.5

Q ss_pred             CceEEEEEeccccc--ccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           6 GLTEVVESIGPELF--RKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         6 ~~~~~i~v~~s~l~--~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      .++.++.++++.+.  .+|.|+.+..++.+|..+....++||||||+|.+++.+.....      .    ....+.+..+
T Consensus       241 ~~~~~~~~~~~~l~~~~~~~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~~~------~----~~~~~~L~~~  310 (758)
T 1r6b_X          241 ADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGG------Q----VDAANLIKPL  310 (758)
T ss_dssp             TTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSC------H----HHHHHHHSSC
T ss_pred             cCCEEEEEcHHHHhccccccchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcCCCCcc------h----HHHHHHHHHH
Confidence            46778888888877  5789999999999999999888999999999999876543211      1    1223344444


Q ss_pred             CCCCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC----CCC-chhhHHHHHHHCCC
Q psy5642          84 VPLNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS----PLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~----~~~-~~~~~~~la~~t~g  153 (237)
                      ...+.+.+|++|+.++     .+|+++.+  ||+ .+.|+.|+.++|.+||+.++..+    ... .+..+..++..+.|
T Consensus       311 l~~~~~~~I~at~~~~~~~~~~~d~aL~~--Rf~-~i~v~~p~~~e~~~il~~l~~~~~~~~~v~~~~~al~~~~~~s~~  387 (758)
T 1r6b_X          311 LSSGKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVK  387 (758)
T ss_dssp             SSSCCCEEEEEECHHHHHCCCCCTTSSGG--GEE-EEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHH
T ss_pred             HhCCCeEEEEEeCchHHhhhhhcCHHHHh--Cce-EEEcCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhh
Confidence            4457788999998653     67899999  998 69999999999999999877542    221 45667777777766


Q ss_pred             CCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHh--ccccCCccHHHHHHHHhhcC
Q psy5642         154 YSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALEN--NLEAAYVSHQDFLTALQLVK  220 (237)
Q Consensus       154 ~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~--~~~~~~v~~~df~~al~~~~  220 (237)
                      |.....                      .+..+..++.+|.......  ......|+.+|+..++..+.
T Consensus       388 ~i~~~~----------------------lp~~~i~lld~a~~~~~~~~~~~~~~~v~~~di~~~~~~~~  434 (758)
T 1r6b_X          388 YINDRH----------------------LPDKAIDVIDEAGARARLMPVSKRKKTVNVADIESVVARIA  434 (758)
T ss_dssp             HCTTSC----------------------TTHHHHHHHHHHHHHHHHSSSCCCCCSCCHHHHHHHHHHHS
T ss_pred             hccccc----------------------CchHHHHHHHHHHHHHhcccccccCCccCHHHHHHHHHHhc
Confidence            654430                      0001555555554433321  11235689999999988764

>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=99.11  E-value=1.6e-10  Score=103.31  Aligned_cols=169  Identities=11%  Similarity=0.156  Sum_probs=112.7

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+++++++..+...+.+.........|.......|.||+|||++.+...+             .....++..++.....
T Consensus       160 ~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vL~IDEi~~l~~~~-------------~~q~~l~~~l~~l~~~  226 (440)
T 2z4s_A          160 DLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIGKT-------------GVQTELFHTFNELHDS  226 (440)
T ss_dssp             SSCEEEEEHHHHHHHHHHHHHTTCHHHHHHHHTTTCSEEEEECGGGGSSCH-------------HHHHHHHHHHHHHHTT
T ss_pred             CCeEEEeeHHHHHHHHHHHHHcccHHHHHHHhcCCCCEEEEeCcccccCCh-------------HHHHHHHHHHHHHHHC
Confidence            567888998877654443333222223433333378999999999986531             1123344443333333


Q ss_pred             CCEEEEEEeCCCCc---cchhccCCCCcc--cEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccccc
Q psy5642          87 NNVTIVAATNRPDR---IDKALLRPGRLD--RLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQS  160 (237)
Q Consensus        87 ~~v~vI~ttn~~~~---ld~al~r~gRf~--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~  160 (237)
                      +..+||+|.+.+..   +++.+++  ||.  ..+.++.|+.++|..||+..+...+.. ++..+..++..+.| ++++  
T Consensus       227 ~~~iIitt~~~~~~l~~l~~~L~s--R~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~~e~l~~la~~~~g-n~R~--  301 (440)
T 2z4s_A          227 GKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDD-NLRR--  301 (440)
T ss_dssp             TCEEEEEESSCGGGCSSCCHHHHH--HHHSSBCCBCCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHCCS-CHHH--
T ss_pred             CCeEEEEECCCHHHHHHHHHHHHh--hccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHH--
Confidence            45666666555665   8899999  996  789999999999999999888644332 45557888888754 5566  


Q ss_pred             chhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCC
Q psy5642         161 LSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKP  221 (237)
Q Consensus       161 ~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p  221 (237)
                                               +.+++..+...+...+   ..|+.+++.++++...+
T Consensus       302 -------------------------l~~~L~~~~~~a~~~~---~~It~~~~~~~l~~~~~  334 (440)
T 2z4s_A          302 -------------------------LRGAIIKLLVYKETTG---KEVDLKEAILLLKDFIK  334 (440)
T ss_dssp             -------------------------HHHHHHHHHHHHHHSS---SCCCHHHHHHHTSTTTC
T ss_pred             -------------------------HHHHHHHHHHHHHHhC---CCCCHHHHHHHHHHHhh
Confidence                                     6667776666554443   35999999999988764

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

Probab=99.08  E-value=1.5e-11  Score=109.47  Aligned_cols=110  Identities=15%  Similarity=0.167  Sum_probs=34.9

Q ss_pred             ceEEEEEecccccc-cccCh-HHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           7 LTEVVESIGPELFR-KYVGE-SERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         7 ~~~~i~v~~s~l~~-~~~g~-~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      +++|+.++++.+.+ .|+|+ .++.++.+|..|....    ++||++.+.....       .....++++.|+.+|+++.
T Consensus        75 ~~~~~~v~~~~~~~~g~vG~d~e~~lr~lf~~a~~~~----~~De~d~~~~~~~-------~~~e~rvl~~LL~~~dg~~  143 (444)
T 1g41_A           75 NAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAMKLV----RQQEIAKNRARAE-------DVAEERILDALLPPAKNQW  143 (444)
T ss_dssp             TCCEEEEEGGGGC----CCCCTHHHHHHHHHHHHHHH----HHHHHHSCC------------------------------
T ss_pred             CCCceeecchhhcccceeeccHHHHHHHHHHHHHhcc----hhhhhhhhhccch-------hhHHHHHHHHHHHHhhccc
Confidence            57899999999988 59995 8999999999998754    4888887643221       2334789999999999987


Q ss_pred             CCCCEEEEEE-eCCCCccchhccCCCCcccEEEecCCCHH-HHHHHH
Q psy5642          85 PLNNVTIVAA-TNRPDRIDKALLRPGRLDRLIYVPLPDDL-TRAAIL  129 (237)
Q Consensus        85 ~~~~v~vI~t-tn~~~~ld~al~r~gRf~~~i~~~~P~~~-~R~~il  129 (237)
                      ....+  +++ ||+++.||++|+||||||+.|+++.|+.. .|.+|+
T Consensus       144 ~~~~v--~a~~TN~~~~ld~aL~rggr~D~~i~i~lP~~~~~~~ei~  188 (444)
T 1g41_A          144 GEVEN--HDSHSSTRQAFRKKLREGQLDDKEIEIDVSAGVSMGVEIM  188 (444)
T ss_dssp             -----------------------------------------------
T ss_pred             ccccc--ccccccCHHHHHHHHHcCCCcceEEEEcCCCCccchhhhh
Confidence            65554  455 99999999999999999999999999987 788876

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

Probab=99.05  E-value=1.6e-09  Score=94.15  Aligned_cols=180  Identities=12%  Similarity=0.188  Sum_probs=121.7

Q ss_pred             ceEEEEEeccccccc-ccChH-HHHHHHHHHHH----HhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHh
Q psy5642           7 LTEVVESIGPELFRK-YVGES-ERCVRDVFKRA----RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEM   80 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~-~~g~~-~~~l~~~f~~a----~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l   80 (237)
                      +.+|+.++|+.+... |+|.. ...++.+|..+    ....|+||||||+|.+...+...... .......+.+.|+..|
T Consensus        76 ~~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~~~~~~~~~-~~~~~~~~~~~Ll~~l  154 (363)
T 3hws_A           76 DVPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKSDNPSIT-RDVSGEGVQQALLKLI  154 (363)
T ss_dssp             TCCEEEEEHHHHTTCHHHHHHHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCCCSSCC----CHHHHHHHHHHHHHHH
T ss_pred             CCCEEEechHHhcccccccccHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhcccccccccc-cccchHHHHHHHHHHh
Confidence            578999999998754 88876 77888888877    44468999999999998776543321 1222345889999999


Q ss_pred             cCCC-------------------CCCCEEEEEEeCCC----------Cc-------------------------------
Q psy5642          81 DGIV-------------------PLNNVTIVAATNRP----------DR-------------------------------  100 (237)
Q Consensus        81 ~~~~-------------------~~~~v~vI~ttn~~----------~~-------------------------------  100 (237)
                      ++..                   ...++++|++++..          ..                               
T Consensus       155 eg~~~~~~~~~~~~~~~~~~~~i~tsn~~~i~~g~~~~l~~~i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l  234 (363)
T 3hws_A          155 EGTVAAVPPQGGRKHPQQEFLQVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDL  234 (363)
T ss_dssp             HCC----------------CCCCCTTSSEEEEEECCTTHHHHHHHHHCCCC------------CCSCHHHHHHTCCHHHH
T ss_pred             cCceeeccCccccccCCCceEEEECCCceEEecCCcHHHHHHHHHhhhccccCCccccccccccchhhHHHHHhCCHHHH
Confidence            8421                   22345666666642          11                               


Q ss_pred             ----cchhccCCCCcccEEEecCCCHHHHHHHHHH----HH-------cCCCCC---chhhHHHHHHH--CCCCCccccc
Q psy5642         101 ----IDKALLRPGRLDRLIYVPLPDDLTRAAILKI----RL-------ARSPLG---EDVCVEELVRL--TEGYSGAEQS  160 (237)
Q Consensus       101 ----ld~al~r~gRf~~~i~~~~P~~~~R~~il~~----~l-------~~~~~~---~~~~~~~la~~--t~g~s~~Dl~  160 (237)
                          +.++|+.  ||+.++.+++|+.+++.+|+..    ++       ......   .+..+..|+..  ...+..++  
T Consensus       235 ~~~~~~~~l~~--R~~~~~~~~pl~~~~~~~I~~~~~~~l~~~~~~~~~~~~~~l~~~~~a~~~L~~~~~~~~~gaR~--  310 (363)
T 3hws_A          235 IKFGLIPEFIG--RLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARG--  310 (363)
T ss_dssp             HHHTCCHHHHT--TCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTTTT--
T ss_pred             HHcCCCHHHhc--ccCeeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHHHHHhhcCCccCchH--
Confidence                6788888  9999999999999999999986    22       111221   45556667653  34556677  


Q ss_pred             chhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccc-----cCCccHHHHHHHH
Q psy5642         161 LSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLE-----AAYVSHQDFLTAL  216 (237)
Q Consensus       161 ~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~-----~~~v~~~df~~al  216 (237)
                                               |.++++.+....+.+...     ...|+.+++.+.+
T Consensus       311 -------------------------L~~~ie~~~~~~l~~~~~~~~~~~~~I~~~~v~~~~  346 (363)
T 3hws_A          311 -------------------------LRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQS  346 (363)
T ss_dssp             -------------------------HHHHHHHHHHHHHHSTTTCCCSEEEECHHHHTTCCS
T ss_pred             -------------------------HHHHHHHHHHHHHHhcccccCCceeEEcHHHHhCcC
Confidence                                     777777777776654322     3357777776544

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

Probab=99.04  E-value=4.3e-09  Score=91.14  Aligned_cols=134  Identities=17%  Similarity=0.149  Sum_probs=91.6

Q ss_pred             ceEEEEEecccccccc----------------cCh-HHHHHHHHHHHHHhc-CCeEEEEccccccccccCCCCCCCCCch
Q psy5642           7 LTEVVESIGPELFRKY----------------VGE-SERCVRDVFKRARQV-SPSVIFFDELDSLAGERGDGGGGGGSNV   68 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~----------------~g~-~~~~l~~~f~~a~~~-~P~il~iDeid~l~~~~~~~~~~~~~~~   68 (237)
                      +.+++.++|....+.+                .|. ....+..++...... .|++|+|||+|.+...+          .
T Consensus        78 ~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~----------~  147 (387)
T 2v1u_A           78 LVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRP----------G  147 (387)
T ss_dssp             CEEEEEEETTTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHST----------T
T ss_pred             CeEEEEEECCcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccC----------C
Confidence            6889999987644321                122 233455566555443 48899999999986532          0


Q ss_pred             HHHHHHHHHHHhcCCCCCCCEEEEEEeCCC---CccchhccCCCCccc-EEEecCCCHHHHHHHHHHHHcC--CCC-Cch
Q psy5642          69 QERVLAQMLTEMDGIVPLNNVTIVAATNRP---DRIDKALLRPGRLDR-LIYVPLPDDLTRAAILKIRLAR--SPL-GED  141 (237)
Q Consensus        69 ~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~---~~ld~al~r~gRf~~-~i~~~~P~~~~R~~il~~~l~~--~~~-~~~  141 (237)
                      ....+..++..+.......++.+|++||.+   +.+++.+.+  ||.. .++|++|+.+++.++++..+..  .+. -.+
T Consensus       148 ~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~~~~~l~~~l~~--r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~  225 (387)
T 2v1u_A          148 GQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKS--SLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDP  225 (387)
T ss_dssp             HHHHHHHHHHGGGCC-----CEEEEECSCSTTSSSSCHHHHT--TTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCS
T ss_pred             CChHHHhHhhchhhcCCCceEEEEEEECCCchHhhhCHHHHh--cCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCH
Confidence            145677777777654324678999999988   789999999  9975 8999999999999999988753  111 145


Q ss_pred             hhHHHHHHHCC
Q psy5642         142 VCVEELVRLTE  152 (237)
Q Consensus       142 ~~~~~la~~t~  152 (237)
                      ..+..++..+.
T Consensus       226 ~~~~~l~~~~~  236 (387)
T 2v1u_A          226 DVVPLCAALAA  236 (387)
T ss_dssp             SHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            55677777765

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

Probab=99.01  E-value=8.3e-09  Score=88.44  Aligned_cols=126  Identities=15%  Similarity=0.206  Sum_probs=91.1

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC--
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV--   84 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--   84 (237)
                      +.+|+.++|+.+.      ....+..++..  ...+++|||||+|.+..               .....|+..++...  
T Consensus        80 ~~~~~~~~~~~~~------~~~~~~~~~~~--~~~~~vl~lDEi~~l~~---------------~~~~~Ll~~l~~~~~~  136 (338)
T 3pfi_A           80 SANIKTTAAPMIE------KSGDLAAILTN--LSEGDILFIDEIHRLSP---------------AIEEVLYPAMEDYRLD  136 (338)
T ss_dssp             TCCEEEEEGGGCC------SHHHHHHHHHT--CCTTCEEEEETGGGCCH---------------HHHHHHHHHHHTSCC-
T ss_pred             CCCeEEecchhcc------chhHHHHHHHh--ccCCCEEEEechhhcCH---------------HHHHHHHHHHHhccch
Confidence            4578888887653      23344444433  24689999999999842               23455666665432  


Q ss_pred             --------------CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHH
Q psy5642          85 --------------PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVR  149 (237)
Q Consensus        85 --------------~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~  149 (237)
                                    ...++.+|++||....+++++++  ||+..++|+.|+.+++..+++.++...... .+..+..++.
T Consensus       137 ~~~~~~~~~~~~~~~~~~~~~i~atn~~~~l~~~L~~--R~~~~i~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~l~~  214 (338)
T 3pfi_A          137 IIIGSGPAAQTIKIDLPKFTLIGATTRAGMLSNPLRD--RFGMQFRLEFYKDSELALILQKAALKLNKTCEEKAALEIAK  214 (338)
T ss_dssp             --------CCCCCCCCCCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHH
T ss_pred             hhcccCccccceecCCCCeEEEEeCCCccccCHHHHh--hcCEEeeCCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence                          01248999999999999999999  999999999999999999999988766543 5566777887


Q ss_pred             HCCCCCccc
Q psy5642         150 LTEGYSGAE  158 (237)
Q Consensus       150 ~t~g~s~~D  158 (237)
                      .+.|. +++
T Consensus       215 ~~~G~-~r~  222 (338)
T 3pfi_A          215 RSRST-PRI  222 (338)
T ss_dssp             TTTTC-HHH
T ss_pred             HHCcC-HHH
Confidence            55543 345

>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=98.96  E-value=6.9e-10  Score=106.72  Aligned_cols=138  Identities=22%  Similarity=0.292  Sum_probs=88.5

Q ss_pred             CceEEEEEeccccc--ccccChHHHHHHHHHHHHHhc-CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC
Q psy5642           6 GLTEVVESIGPELF--RKYVGESERCVRDVFKRARQV-SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG   82 (237)
Q Consensus         6 ~~~~~i~v~~s~l~--~~~~g~~~~~l~~~f~~a~~~-~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~   82 (237)
                      .+.+++.++++.+.  .+|.|+.+..++.+|..+... .|+||||||+|.+.+.+...+.       ..+.+.+...+..
T Consensus       225 ~~~~~~~l~~~~l~~g~~~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~g~-------~~~~~~L~~~l~~  297 (854)
T 1qvr_A          225 KGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGA-------VDAGNMLKPALAR  297 (854)
T ss_dssp             TTCEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC--------------------------HHHHHT
T ss_pred             cCCeEEEeehHHhhccCccchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCccch-------HHHHHHHHHHHhC
Confidence            37899999999987  688999999999999999875 7999999999999866543321       1223334444433


Q ss_pred             CCCCCCEEEEEEeCCCC----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC----CCC-chhhHHHHHHHCCC
Q psy5642          83 IVPLNNVTIVAATNRPD----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS----PLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        83 ~~~~~~v~vI~ttn~~~----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~----~~~-~~~~~~~la~~t~g  153 (237)
                          +.+.+|++|+.++    .+|+++++  ||+. |.|+.|+.+++.+||+.++..+    ... .+..+..++..+.|
T Consensus       298 ----~~i~~I~at~~~~~~~~~~d~aL~r--Rf~~-i~l~~p~~~e~~~iL~~~~~~~~~~~~~~i~~~al~~~~~ls~r  370 (854)
T 1qvr_A          298 ----GELRLIGATTLDEYREIEKDPALER--RFQP-VYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHR  370 (854)
T ss_dssp             ----TCCCEEEEECHHHHHHHTTCTTTCS--CCCC-EEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHH
T ss_pred             ----CCeEEEEecCchHHhhhccCHHHHh--CCce-EEeCCCCHHHHHHHHHhhhhhhhhhcCCCCCHHHHHHHHHHHhh
Confidence                5678999998775    47999999  9986 9999999999999999777533    222 56667778887766


Q ss_pred             CCcc
Q psy5642         154 YSGA  157 (237)
Q Consensus       154 ~s~~  157 (237)
                      |...
T Consensus       371 ~i~~  374 (854)
T 1qvr_A          371 YITE  374 (854)
T ss_dssp             HCCS
T ss_pred             hccc
Confidence            6543

>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=98.94  E-value=9.2e-09  Score=87.43  Aligned_cols=139  Identities=17%  Similarity=0.192  Sum_probs=95.6

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC--
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV--   84 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--   84 (237)
                      +.+++.++|+.+..      ...+...|..+ ...+++|||||+|.+...               ....++..++...  
T Consensus        63 ~~~~~~~~~~~~~~------~~~l~~~l~~~-~~~~~~l~lDEi~~l~~~---------------~~~~L~~~l~~~~~~  120 (324)
T 1hqc_A           63 GVNLRVTSGPAIEK------PGDLAAILANS-LEEGDILFIDEIHRLSRQ---------------AEEHLYPAMEDFVMD  120 (324)
T ss_dssp             TCCEEEECTTTCCS------HHHHHHHHTTT-CCTTCEEEETTTTSCCHH---------------HHHHHHHHHHHSEEE
T ss_pred             CCCEEEEeccccCC------hHHHHHHHHHh-ccCCCEEEEECCcccccc---------------hHHHHHHHHHhhhhH
Confidence            35677788876532      23333333321 136889999999987421               2334444444321  


Q ss_pred             --------------CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHH
Q psy5642          85 --------------PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVR  149 (237)
Q Consensus        85 --------------~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~  149 (237)
                                    ...++.+|++||.+..+++++.+  ||+..+.++.|+.+++..+++.++...... .+..+..++.
T Consensus       121 ~v~~~~~~~~~~~~~~~~~~~i~~t~~~~~~~~~l~~--R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~  198 (324)
T 1hqc_A          121 IVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGR  198 (324)
T ss_dssp             ECCSSSSSCCCEEEECCCCEEEEEESCCSSCSCSTTT--TCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHH
T ss_pred             HhccccccccccccCCCCEEEEEeCCCcccCCHHHHh--cccEEEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence                          01257899999999999999999  999899999999999999999988765544 5667888999


Q ss_pred             HCCCCCcccccchhHHhhhhc
Q psy5642         150 LTEGYSGAEQSLSKHRAKKIR  170 (237)
Q Consensus       150 ~t~g~s~~Dl~~~~~~a~~~~  170 (237)
                      .+.|+ ++++..+++++...+
T Consensus       199 ~~~G~-~r~l~~~l~~~~~~a  218 (324)
T 1hqc_A          199 RSRGT-MRVAKRLFRRVRDFA  218 (324)
T ss_dssp             HSCSC-HHHHHHHHHHHTTTS
T ss_pred             HccCC-HHHHHHHHHHHHHHH
Confidence            88765 466555555554433

>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=98.94  E-value=1.5e-08  Score=80.45  Aligned_cols=150  Identities=15%  Similarity=0.133  Sum_probs=100.5

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHH------hcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHh
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRAR------QVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEM   80 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~------~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l   80 (237)
                      ..+++.++++...+      ...+...+....      ...|.+|+|||+|.+...               ....++..+
T Consensus        68 ~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~---------------~~~~l~~~l  126 (226)
T 2chg_A           68 RDNFIEMNASDERG------IDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTAD---------------AQAALRRTM  126 (226)
T ss_dssp             GGGEEEEETTCTTC------HHHHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCHH---------------HHHHHHHHH
T ss_pred             ccceEEeccccccC------hHHHHHHHHHHhcccCCCccCceEEEEeChhhcCHH---------------HHHHHHHHH
Confidence            45677787765433      222333333222      246899999999998432               234455555


Q ss_pred             cCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccc
Q psy5642          81 DGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQ  159 (237)
Q Consensus        81 ~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl  159 (237)
                      +..  ..++.+|++||.+..+++++.+  ||. .++++.|+.++..++++.++...+.. .+..+..++..+.| .++. 
T Consensus       127 ~~~--~~~~~~i~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g-~~r~-  199 (226)
T 2chg_A          127 EMY--SKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGG-DFRK-  199 (226)
T ss_dssp             HHT--TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTT-CHHH-
T ss_pred             Hhc--CCCCeEEEEeCChhhcCHHHHH--hCc-eeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHH-
Confidence            542  3467889999999999999999  998 89999999999999999888644433 45567777776644 2222 


Q ss_pred             cchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHh
Q psy5642         160 SLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQ  217 (237)
Q Consensus       160 ~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~  217 (237)
                                                +.++++.+...+       ..|+.+|+.+++.
T Consensus       200 --------------------------l~~~l~~~~~~~-------~~I~~~~v~~~~~  224 (226)
T 2chg_A          200 --------------------------AINALQGAAAIG-------EVVDADTIYQITA  224 (226)
T ss_dssp             --------------------------HHHHHHHHHHTC-------SCBCHHHHHHHHH
T ss_pred             --------------------------HHHHHHHHHhcC-------ceecHHHHHHHhc
Confidence                                      444444443322       3699999998876

>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=98.90  E-value=5.1e-09  Score=84.71  Aligned_cols=154  Identities=14%  Similarity=0.045  Sum_probs=98.4

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCC
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLN   87 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~   87 (237)
                      .+++.++++++...+..        ++..  ...|.+|+|||+|.+....             .....++..++.....+
T Consensus        81 ~~~~~~~~~~~~~~~~~--------~~~~--~~~~~vliiDe~~~~~~~~-------------~~~~~l~~~l~~~~~~~  137 (242)
T 3bos_A           81 RRSFYIPLGIHASISTA--------LLEG--LEQFDLICIDDVDAVAGHP-------------LWEEAIFDLYNRVAEQK  137 (242)
T ss_dssp             CCEEEEEGGGGGGSCGG--------GGTT--GGGSSEEEEETGGGGTTCH-------------HHHHHHHHHHHHHHHHC
T ss_pred             CeEEEEEHHHHHHHHHH--------HHHh--ccCCCEEEEeccccccCCH-------------HHHHHHHHHHHHHHHcC
Confidence            45667777766554321        1111  1357899999999984421             11223333333322223


Q ss_pred             CE-EEEEEeCCCC---ccchhccCCCCcc--cEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccccc
Q psy5642          88 NV-TIVAATNRPD---RIDKALLRPGRLD--RLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQS  160 (237)
Q Consensus        88 ~v-~vI~ttn~~~---~ld~al~r~gRf~--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~  160 (237)
                      .+ +|++++..+.   .+++.+.+  ||.  ..++++.|+.+++.+++..++...+.. .+..+..++..+.| ..++  
T Consensus       138 ~~~ii~~~~~~~~~~~~~~~~l~~--r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g-~~r~--  212 (242)
T 3bos_A          138 RGSLIVSASASPMEAGFVLPDLVS--RMHWGLTYQLQPMMDDEKLAALQRRAAMRGLQLPEDVGRFLLNRMAR-DLRT--  212 (242)
T ss_dssp             SCEEEEEESSCTTTTTCCCHHHHH--HHHHSEEEECCCCCGGGHHHHHHHHHHHTTCCCCHHHHHHHHHHTTT-CHHH--
T ss_pred             CCeEEEEcCCCHHHHHHhhhhhhh--HhhcCceEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccC-CHHH--
Confidence            44 5555554454   45688888  886  889999999999999999988755443 55667778887754 4445  


Q ss_pred             chhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHh
Q psy5642         161 LSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQ  217 (237)
Q Consensus       161 ~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~  217 (237)
                                               +.++++.+...+..++   ..|+.+++.++++
T Consensus       213 -------------------------l~~~l~~~~~~a~~~~---~~It~~~v~~~l~  241 (242)
T 3bos_A          213 -------------------------LFDVLDRLDKASMVHQ---RKLTIPFVKEMLR  241 (242)
T ss_dssp             -------------------------HHHHHHHHHHHHHHHT---CCCCHHHHHHHHT
T ss_pred             -------------------------HHHHHHHHHHHHHHhC---CCCcHHHHHHHhh
Confidence                                     6677776666654333   4599999998875

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

Probab=98.90  E-value=5.7e-09  Score=93.87  Aligned_cols=123  Identities=24%  Similarity=0.265  Sum_probs=86.8

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+.+|+.++++   ++|.|+.+..++.+|..+....|+|||||      .   .          ....+.|+..|    .
T Consensus       235 ~~~~~~~l~~~---~~~~g~~e~~~~~~~~~~~~~~~~iLfiD------~---~----------~~a~~~L~~~L----~  288 (468)
T 3pxg_A          235 RDKRVMTLDMG---TKYRGEFEDRLKKVMDEIRQAGNIILFID------A---A----------IDASNILKPSL----A  288 (468)
T ss_dssp             SSCCEECC-------------CTTHHHHHHHHHTCCCCEEEEC------C---------------------CCCT----T
T ss_pred             cCCeEEEeeCC---ccccchHHHHHHHHHHHHHhcCCeEEEEe------C---c----------hhHHHHHHHhh----c
Confidence            46788899888   88899999999999999999899999999      0   0          01123333333    3


Q ss_pred             CCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC----CCC-chhhHHHHHHHCCCCC
Q psy5642          86 LNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS----PLG-EDVCVEELVRLTEGYS  155 (237)
Q Consensus        86 ~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~----~~~-~~~~~~~la~~t~g~s  155 (237)
                      .+.+.+|++||.++     .+|+++++  ||. .|.|+.|+.+++..||+.++..+    ... .+..+..++..+.+|.
T Consensus       289 ~g~v~vI~at~~~e~~~~~~~~~al~~--Rf~-~i~v~~p~~e~~~~iL~~~~~~~~~~~~~~i~~~al~~l~~~s~~~~  365 (468)
T 3pxg_A          289 RGELQCIGATTLDEYRKYIEKDAALER--RFQ-PIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYI  365 (468)
T ss_dssp             SSSCEEEEECCTTTTHHHHTTCSHHHH--SEE-EEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSS
T ss_pred             CCCEEEEecCCHHHHHHHhhcCHHHHH--hCc-cceeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHh
Confidence            46799999999987     79999999  998 59999999999999999888763    222 5677888888888777


Q ss_pred             cc
Q psy5642         156 GA  157 (237)
Q Consensus       156 ~~  157 (237)
                      +.
T Consensus       366 ~~  367 (468)
T 3pxg_A          366 SD  367 (468)
T ss_dssp             CC
T ss_pred             cc
Confidence            65

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=98.90  E-value=4.4e-09  Score=89.79  Aligned_cols=133  Identities=20%  Similarity=0.318  Sum_probs=89.8

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +.+++++++.++...+.+.........|..... .|++|+|||++.+..++             .....++..++.....
T Consensus        65 ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~vL~iDEi~~l~~~~-------------~~~~~l~~~l~~~~~~  130 (324)
T 1l8q_A           65 GYRVIYSSADDFAQAMVEHLKKGTINEFRNMYK-SVDLLLLDDVQFLSGKE-------------RTQIEFFHIFNTLYLL  130 (324)
T ss_dssp             TCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHHH-TCSEEEEECGGGGTTCH-------------HHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEEHHHHHHHHHHHHHcCcHHHHHHHhc-CCCEEEEcCcccccCCh-------------HHHHHHHHHHHHHHHC
Confidence            567889999887666555444333334444333 48999999999986431             1122233333322223


Q ss_pred             CCEEEEEEeCCCC---ccchhccCCCCcc--cEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          87 NNVTIVAATNRPD---RIDKALLRPGRLD--RLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        87 ~~v~vI~ttn~~~---~ld~al~r~gRf~--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      +..+|+++++.+.   .+++++++  ||.  ..+++++ +.++|..+|+..+...+.. ++..+..++..+ | ..++
T Consensus       131 ~~~iii~~~~~~~~l~~l~~~L~s--R~~~~~~i~l~~-~~~e~~~il~~~~~~~~~~l~~~~l~~l~~~~-g-~~r~  203 (324)
T 1l8q_A          131 EKQIILASDRHPQKLDGVSDRLVS--RFEGGILVEIEL-DNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-K-NVRE  203 (324)
T ss_dssp             TCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEECCC-CHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-S-SHHH
T ss_pred             CCeEEEEecCChHHHHHhhhHhhh--cccCceEEEeCC-CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhC-C-CHHH
Confidence            4567777777766   68999999  996  6789999 9999999999988755443 566688888888 3 4455

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

Probab=98.88  E-value=9.8e-10  Score=85.50  Aligned_cols=110  Identities=25%  Similarity=0.308  Sum_probs=80.0

Q ss_pred             CceEEEEEeccccc--ccccChHHHHHHHHHHHHHh-cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC
Q psy5642           6 GLTEVVESIGPELF--RKYVGESERCVRDVFKRARQ-VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG   82 (237)
Q Consensus         6 ~~~~~i~v~~s~l~--~~~~g~~~~~l~~~f~~a~~-~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~   82 (237)
                      .+.+++.++++.+.  ..+.|.....++.++..+.. ..|+||+|||+|.+...+.......       +...+...++.
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~~-------~~~~l~~~~~~  149 (195)
T 1jbk_A           77 KGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMD-------AGNMLKPALAR  149 (195)
T ss_dssp             TTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCC-------CHHHHHHHHHT
T ss_pred             cCCcEEEeeHHHHhccCCccccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhccCcccchHH-------HHHHHHHhhcc
Confidence            46788999998876  56677888889999987754 4688999999999976543322111       12222333332


Q ss_pred             CCCCCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHH
Q psy5642          83 IVPLNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAIL  129 (237)
Q Consensus        83 ~~~~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il  129 (237)
                          .++.+|++||.+.     .+++++++  ||+ .++++.|+.++|.+||
T Consensus       150 ----~~~~~i~~~~~~~~~~~~~~~~~l~~--r~~-~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          150 ----GELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             ----TSCCEEEEECHHHHHHHTTTCHHHHT--TEE-EEECCCCCHHHHHTTC
T ss_pred             ----CCeEEEEeCCHHHHHHHHhcCHHHHH--Hhc-eeecCCCCHHHHHHHh
Confidence                4678899998876     78999999  998 6999999999999876

>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=98.88  E-value=1.4e-08  Score=81.58  Aligned_cols=137  Identities=21%  Similarity=0.244  Sum_probs=102.0

Q ss_pred             HHHHHHHHHHHH----hcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRAR----QVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~----~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.++..+.    ...|.+|+|||+|.+..               .....++..++..  ..++.+|++|+.+..++
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~---------------~~~~~l~~~l~~~--~~~~~~i~~t~~~~~~~  170 (250)
T 1njg_A          108 VEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSR---------------HSFNALLKTLEEP--PEHVKFLLATTDPQKLP  170 (250)
T ss_dssp             HHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCH---------------HHHHHHHHHHHSC--CTTEEEEEEESCGGGSC
T ss_pred             HHHHHHHHHHhhhchhcCCceEEEEECcccccH---------------HHHHHHHHHHhcC--CCceEEEEEeCChHhCC
Confidence            455666666553    23589999999998722               3456677777663  35788999999999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhHHhhhhccccCCCCCCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPA  181 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~  181 (237)
                      +.+++  |+ ..++++.|+.++..++++.++...... .+..+..++..+.| .++.                       
T Consensus       171 ~~l~~--r~-~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G-~~~~-----------------------  223 (250)
T 1njg_A          171 VTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEG-SLRD-----------------------  223 (250)
T ss_dssp             HHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHTT-CHHH-----------------------
T ss_pred             HHHHH--Hh-hhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCC-CHHH-----------------------
Confidence            99998  86 579999999999999999988654433 55668889999877 6777                       


Q ss_pred             CchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHh
Q psy5642         182 CKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQ  217 (237)
Q Consensus       182 ~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~  217 (237)
                          +.++++.+....      ...|+.+++.+++.
T Consensus       224 ----~~~~~~~~~~~~------~~~i~~~~v~~~~~  249 (250)
T 1njg_A          224 ----ALSLTDQAIASG------DGQVSTQAVSAMLG  249 (250)
T ss_dssp             ----HHHHHHHHHTTT------TSSBCHHHHHHHSC
T ss_pred             ----HHHHHHHHHhcc------CceecHHHHHHHhC
Confidence                777776664221      23699999988764

>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=98.79  E-value=2.3e-07  Score=80.39  Aligned_cols=179  Identities=11%  Similarity=0.070  Sum_probs=112.4

Q ss_pred             ceEEEEEeccccccc----------------ccC-hHHHHHHHHHHHHHh-cCCeEEEEccccccccccCCCCCCCCCch
Q psy5642           7 LTEVVESIGPELFRK----------------YVG-ESERCVRDVFKRARQ-VSPSVIFFDELDSLAGERGDGGGGGGSNV   68 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~----------------~~g-~~~~~l~~~f~~a~~-~~P~il~iDeid~l~~~~~~~~~~~~~~~   68 (237)
                      +.+++.++|+...+.                ..+ .....+..+...... ..|.+|+|||+|.+  +            
T Consensus        73 ~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l--~------------  138 (389)
T 1fnn_A           73 TARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL--A------------  138 (389)
T ss_dssp             CCEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGS--C------------
T ss_pred             CeeEEEEeCccCCCHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECcccc--c------------
Confidence            467888887664421                011 122333333333333 35899999999998  1            


Q ss_pred             HHHHHHHHHHHhcCCCC--CCCEEEEEEeCCC---CccchhccCCCCccc-EEEecCCCHHHHHHHHHHHHcC---CCCC
Q psy5642          69 QERVLAQMLTEMDGIVP--LNNVTIVAATNRP---DRIDKALLRPGRLDR-LIYVPLPDDLTRAAILKIRLAR---SPLG  139 (237)
Q Consensus        69 ~~~~~~~ll~~l~~~~~--~~~v~vI~ttn~~---~~ld~al~r~gRf~~-~i~~~~P~~~~R~~il~~~l~~---~~~~  139 (237)
                       ......|+..+.....  ..++.+|++||.+   +.+++.+.+  ||.. .+.|++++.++..++++..+..   ...-
T Consensus       139 -~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~--r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~  215 (389)
T 1fnn_A          139 -PDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSY  215 (389)
T ss_dssp             -HHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSS
T ss_pred             -hHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhh--cCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCC
Confidence             2456677777765432  1478899999988   678888888  8875 8999999999999999987753   1222


Q ss_pred             chhhHHHHHHHCCCCC-----cccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHH
Q psy5642         140 EDVCVEELVRLTEGYS-----GAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLT  214 (237)
Q Consensus       140 ~~~~~~~la~~t~g~s-----~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~  214 (237)
                      .+..+..++..+.+.+     ++++..                        +.++++.+...+..++  ...++.+++..
T Consensus       216 ~~~~~~~l~~~~~~~~~~~~~~G~~r~------------------------~~~~l~~a~~~a~~~~--~~~i~~~~v~~  269 (389)
T 1fnn_A          216 SEDILQMIADITGAQTPLDTNRGDARL------------------------AIDILYRSAYAAQQNG--RKHIAPEDVRK  269 (389)
T ss_dssp             CHHHHHHHHHHHSBSSTTCTTSCCHHH------------------------HHHHHHHHHHHHHHTT--CSSCCHHHHHH
T ss_pred             CHHHHHHHHHHHhhcccCCCCCCcHHH------------------------HHHHHHHHHHHHHHhC--CCCcCHHHHHH
Confidence            5677888888885442     234211                        4455555554444333  23466667766


Q ss_pred             HHhhcCCCCCHHHH
Q psy5642         215 ALQLVKPRTPPQLI  228 (237)
Q Consensus       215 al~~~~p~~~~~~~  228 (237)
                      ++....+....+.+
T Consensus       270 ~~~~~~~~~~~~~l  283 (389)
T 1fnn_A          270 SSKEVLFGISEEVL  283 (389)
T ss_dssp             HHHHHSCCCCHHHH
T ss_pred             HHHHHhhhhHHHHH
Confidence            66665554444333

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.78  E-value=1.2e-08  Score=87.09  Aligned_cols=111  Identities=12%  Similarity=0.077  Sum_probs=85.1

Q ss_pred             ceEEEEEecccccccc----------------cChHHHHHHHHHHHH--HhcCCeEEEEccccccccccCCCCCCCCCch
Q psy5642           7 LTEVVESIGPELFRKY----------------VGESERCVRDVFKRA--RQVSPSVIFFDELDSLAGERGDGGGGGGSNV   68 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~----------------~g~~~~~l~~~f~~a--~~~~P~il~iDeid~l~~~~~~~~~~~~~~~   68 (237)
                      ...+++|+|..+.+.+                .+++...++.+|...  ....|+||+|||+|.+. .            
T Consensus        80 ~~~~v~INc~~~~t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~-~------------  146 (318)
T 3te6_A           80 IFDYIHIDALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLL-S------------  146 (318)
T ss_dssp             CEEEEEEETTCCC--HHHHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSC-C------------
T ss_pred             ceEEEEEeccccCCHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhh-c------------
Confidence            5789999998765431                345678899999875  34578999999999997 1            


Q ss_pred             HHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCc----cchhccCCCCcc-cEEEecCCCHHHHHHHHHHHHcC
Q psy5642          69 QERVLAQMLTEMDGIVPLNNVTIVAATNRPDR----IDKALLRPGRLD-RLIYVPLPDDLTRAAILKIRLAR  135 (237)
Q Consensus        69 ~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~----ld~al~r~gRf~-~~i~~~~P~~~~R~~il~~~l~~  135 (237)
                       +.++..++.+...  ...+++||+++|..+.    +++++++  ||. ..|.|++++.+|..+|++..+..
T Consensus       147 -q~~L~~l~~~~~~--~~s~~~vI~i~n~~d~~~~~L~~~v~S--R~~~~~i~F~pYt~~el~~Il~~Rl~~  213 (318)
T 3te6_A          147 -EKILQYFEKWISS--KNSKLSIICVGGHNVTIREQINIMPSL--KAHFTEIKLNKVDKNELQQMIITRLKS  213 (318)
T ss_dssp             -THHHHHHHHHHHC--SSCCEEEEEECCSSCCCHHHHHTCHHH--HTTEEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             -chHHHHHHhcccc--cCCcEEEEEEecCcccchhhcchhhhc--cCCceEEEeCCCCHHHHHHHHHHHHHh
Confidence             2466777776543  4468999999999764    5666777  887 68999999999999999988764

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

Probab=98.76  E-value=5.5e-08  Score=92.32  Aligned_cols=121  Identities=24%  Similarity=0.259  Sum_probs=82.8

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+++++.+++   .++|.|+.+..++.+|..+....|+|||||      .   .          ....+.|+..|+    
T Consensus       235 ~~~~~~~~~~---g~~~~G~~e~~l~~~~~~~~~~~~~iLfiD------~---~----------~~~~~~L~~~l~----  288 (758)
T 3pxi_A          235 RDKRVMTLDM---GTKYRGEFEDRLKKVMDEIRQAGNIILFID------A---A----------IDASNILKPSLA----  288 (758)
T ss_dssp             SSCCEECC-------------CTTHHHHHHHHHTCCCCEEEEC------C---------------------CCCTT----
T ss_pred             cCCeEEEecc---cccccchHHHHHHHHHHHHHhcCCEEEEEc------C---c----------hhHHHHHHHHHh----
Confidence            4677888887   677899999999999999999999999999      0   0          012233333333    


Q ss_pred             CCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCC----CC-chhhHHHHHHHCCCCC
Q psy5642          86 LNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSP----LG-EDVCVEELVRLTEGYS  155 (237)
Q Consensus        86 ~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~----~~-~~~~~~~la~~t~g~s  155 (237)
                      .+.+.+|++||..+     .+|++++|  ||. .|.|+.|+.+++.+||+.++..+.    .. .+..+..++..+.+|.
T Consensus       289 ~~~v~~I~at~~~~~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il~~~~~~~~~~~~~~i~~~al~~~~~~s~~~i  365 (758)
T 3pxi_A          289 RGELQCIGATTLDEYRKYIEKDAALER--RFQ-PIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYI  365 (758)
T ss_dssp             SSSCEEEEECCTTTTHHHHTTCSHHHH--SEE-EEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSS
T ss_pred             cCCEEEEeCCChHHHHHHhhccHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccc
Confidence            46799999999988     79999999  995 699999999999999998876632    22 4566777777665554

>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=98.75  E-value=1.1e-07  Score=82.48  Aligned_cols=132  Identities=17%  Similarity=0.192  Sum_probs=88.3

Q ss_pred             ceEEEEEeccccc-cc-----------------ccCh-HHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCc
Q psy5642           7 LTEVVESIGPELF-RK-----------------YVGE-SERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSN   67 (237)
Q Consensus         7 ~~~~i~v~~s~l~-~~-----------------~~g~-~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~   67 (237)
                      +.+++.++|.... +.                 ..|. ....+..++..+....+ +|+|||+|.+.....         
T Consensus        81 ~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~-vlilDEi~~l~~~~~---------  150 (384)
T 2qby_B           81 DVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRA-IIYLDEVDTLVKRRG---------  150 (384)
T ss_dssp             TCEEEEEEHHHHCSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCE-EEEEETTHHHHHSTT---------
T ss_pred             CceEEEEECccCCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCC-EEEEECHHHhccCCC---------
Confidence            6788999887643 11                 1121 13445555555554444 999999999865320         


Q ss_pred             hHHHH-HHHHHHHhcCCCCCCCEEEEEEeCCC---CccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcC-C--CCCc
Q psy5642          68 VQERV-LAQMLTEMDGIVPLNNVTIVAATNRP---DRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR-S--PLGE  140 (237)
Q Consensus        68 ~~~~~-~~~ll~~l~~~~~~~~v~vI~ttn~~---~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~-~--~~~~  140 (237)
                        ... +..++...      .++.+|+|||.+   +.+++.+++  ||...++|++|+.++..++++..+.. .  ..-.
T Consensus       151 --~~~~l~~l~~~~------~~~~iI~~t~~~~~~~~l~~~l~s--r~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~  220 (384)
T 2qby_B          151 --GDIVLYQLLRSD------ANISVIMISNDINVRDYMEPRVLS--SLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYD  220 (384)
T ss_dssp             --SHHHHHHHHTSS------SCEEEEEECSSTTTTTTSCHHHHH--TCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCC
T ss_pred             --CceeHHHHhcCC------cceEEEEEECCCchHhhhCHHHHh--cCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcC
Confidence              122 33333332      678999999987   789999999  99889999999999999999988753 1  1124


Q ss_pred             hhhHHHHHHHCCCCCcccc
Q psy5642         141 DVCVEELVRLTEGYSGAEQ  159 (237)
Q Consensus       141 ~~~~~~la~~t~g~s~~Dl  159 (237)
                      +..+..++..+.+ .++|+
T Consensus       221 ~~~~~~i~~~~~~-~~G~~  238 (384)
T 2qby_B          221 DEILSYIAAISAK-EHGDA  238 (384)
T ss_dssp             SHHHHHHHHHHHT-TCCCH
T ss_pred             HHHHHHHHHHHHh-ccCCH
Confidence            5567778887753 33553

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

Probab=98.74  E-value=5.7e-08  Score=86.85  Aligned_cols=159  Identities=16%  Similarity=0.188  Sum_probs=103.6

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG   82 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~   82 (237)
                      +.+|+.+++...       +.+.++.+|..+..    ..++||||||+|.+...               ....|+..++.
T Consensus        75 ~~~f~~l~a~~~-------~~~~ir~~~~~a~~~~~~~~~~iLfIDEI~~l~~~---------------~q~~LL~~le~  132 (447)
T 3pvs_A           75 NADVERISAVTS-------GVKEIREAIERARQNRNAGRRTILFVDEVHRFNKS---------------QQDAFLPHIED  132 (447)
T ss_dssp             TCEEEEEETTTC-------CHHHHHHHHHHHHHHHHTTCCEEEEEETTTCC---------------------CCHHHHHT
T ss_pred             CCCeEEEEeccC-------CHHHHHHHHHHHHHhhhcCCCcEEEEeChhhhCHH---------------HHHHHHHHHhc
Confidence            457777776532       34567777777664    36899999999998432               13446666665


Q ss_pred             CCCCCCEEEEEEe--CCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCC-------CC-chhhHHHHHHHCC
Q psy5642          83 IVPLNNVTIVAAT--NRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSP-------LG-EDVCVEELVRLTE  152 (237)
Q Consensus        83 ~~~~~~v~vI~tt--n~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~-------~~-~~~~~~~la~~t~  152 (237)
                          +.+++|++|  |....+++++++  ||. ++.|+.|+.+++..+++..+....       .. ++..+..++..+.
T Consensus       133 ----~~v~lI~att~n~~~~l~~aL~s--R~~-v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~  205 (447)
T 3pvs_A          133 ----GTITFIGATTENPSFELNSALLS--RAR-VYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVN  205 (447)
T ss_dssp             ----TSCEEEEEESSCGGGSSCHHHHT--TEE-EEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHC
T ss_pred             ----CceEEEecCCCCcccccCHHHhC--cee-EEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCC
Confidence                456666666  334589999999  997 688999999999999999887521       11 4556777777754


Q ss_pred             CCCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCC
Q psy5642         153 GYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPR  222 (237)
Q Consensus       153 g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~  222 (237)
                      | ..++                           +.++++.+...+.........|+.+++.+++....+.
T Consensus       206 G-d~R~---------------------------lln~Le~a~~~a~~~~~~~~~It~e~v~~~l~~~~~~  247 (447)
T 3pvs_A          206 G-DARR---------------------------ALNTLEMMADMAEVDDSGKRVLKPELLTEIAGERSAR  247 (447)
T ss_dssp             S-CHHH---------------------------HHHHHHHHHHHSCBCTTSCEECCHHHHHHHHTCCCCC
T ss_pred             C-CHHH---------------------------HHHHHHHHHHhcccccCCCCccCHHHHHHHHhhhhhc
Confidence            3 2223                           5555665554432111122468889998888876554

>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=98.72  E-value=2.2e-07  Score=80.24  Aligned_cols=112  Identities=19%  Similarity=0.237  Sum_probs=77.4

Q ss_pred             HHHHHHHHHHHHhcC-CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCC---Cccc
Q psy5642          27 ERCVRDVFKRARQVS-PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRP---DRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~~-P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~---~~ld  102 (237)
                      ...+..++....... |++|+|||++.+.....           ...+..++..++.. ...++.+|++|+.+   ..++
T Consensus       113 ~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~-----------~~~l~~l~~~~~~~-~~~~~~~I~~~~~~~~~~~~~  180 (386)
T 2qby_A          113 AELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYN-----------DDILYKLSRINSEV-NKSKISFIGITNDVKFVDLLD  180 (386)
T ss_dssp             HHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSC-----------STHHHHHHHHHHSC-CC--EEEEEEESCGGGGGGCT
T ss_pred             HHHHHHHHHHHhccCCeEEEEEcChhhhhccCc-----------CHHHHHHhhchhhc-CCCeEEEEEEECCCChHhhhC
Confidence            344556666555544 99999999999865421           12466777777654 34578899999987   4678


Q ss_pred             hhccCCCCcc-cEEEecCCCHHHHHHHHHHHHcCC---CCCchhhHHHHHHHCC
Q psy5642         103 KALLRPGRLD-RLIYVPLPDDLTRAAILKIRLARS---PLGEDVCVEELVRLTE  152 (237)
Q Consensus       103 ~al~r~gRf~-~~i~~~~P~~~~R~~il~~~l~~~---~~~~~~~~~~la~~t~  152 (237)
                      +.+.+  ||. ..+++++|+.++..++++..+...   ..-.+..+..++..+.
T Consensus       181 ~~~~~--r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~  232 (386)
T 2qby_A          181 PRVKS--SLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAA  232 (386)
T ss_dssp             THHHH--TTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHH
T ss_pred             HHHhc--cCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHH
Confidence            88888  886 489999999999999999876521   1114555666776665

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

Probab=98.72  E-value=7e-08  Score=91.62  Aligned_cols=132  Identities=13%  Similarity=0.193  Sum_probs=91.7

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-   84 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-   84 (237)
                      .+.+|+.++|+.+...+....    ..++.......++||||||+|.+.               ..+.+.|+..|+.-. 
T Consensus       548 ~~~~~i~i~~s~~~~~~~~~~----~~l~~~~~~~~~~vl~lDEi~~~~---------------~~~~~~Ll~~le~g~~  608 (758)
T 3pxi_A          548 DEESMIRIDMSEYMEKHSTSG----GQLTEKVRRKPYSVVLLDAIEKAH---------------PDVFNILLQVLEDGRL  608 (758)
T ss_dssp             CTTCEEEEEGGGGCSSCCCC-------CHHHHHHCSSSEEEEECGGGSC---------------HHHHHHHHHHHHHSBC
T ss_pred             CCcceEEEechhccccccccc----chhhHHHHhCCCeEEEEeCccccC---------------HHHHHHHHHHhccCeE
Confidence            467899999999998887762    223334445567899999998772               245677777776521 


Q ss_pred             --------CCCCEEEEEEeCCCCc------------cchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC-------C
Q psy5642          85 --------PLNNVTIVAATNRPDR------------IDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS-------P  137 (237)
Q Consensus        85 --------~~~~v~vI~ttn~~~~------------ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~-------~  137 (237)
                              ...++++|+|||.+..            ++|+++.  ||+.+|.|++|+.+++..|++.++...       .
T Consensus       609 ~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~~~~~f~p~l~~--Rl~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~  686 (758)
T 3pxi_A          609 TDSKGRTVDFRNTILIMTSNVGASEKDKVMGELKRAFRPEFIN--RIDEIIVFHSLEKKHLTEIVSLMSDQLTKRLKEQD  686 (758)
T ss_dssp             C-----CCBCTTCEEEEEESSSTTCCHHHHHHHHHHSCHHHHT--TSSEEEECC--CHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             EcCCCCEeccCCeEEEEeCCCChhhHHHHHHHHHhhCCHHHHh--hCCeEEecCCCCHHHHHHHHHHHHHHHHHHHHhCC
Confidence                    1235899999997654            7899998  999999999999999999999877542       1


Q ss_pred             CC---chhhHHHHHHHC--CCCCccc
Q psy5642         138 LG---EDVCVEELVRLT--EGYSGAE  158 (237)
Q Consensus       138 ~~---~~~~~~~la~~t--~g~s~~D  158 (237)
                      ..   ++..+..|+...  ..+..++
T Consensus       687 ~~~~~~~~a~~~l~~~~~~~~~~~R~  712 (758)
T 3pxi_A          687 LSIELTDAAKAKVAEEGVDLEYGARP  712 (758)
T ss_dssp             CEEEECHHHHHHHHGGGCCTTTTTTT
T ss_pred             CeEEECHHHHHHHHHhCCCCCCCChH
Confidence            11   455666676642  3455666

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

Probab=98.66  E-value=1.7e-07  Score=79.05  Aligned_cols=133  Identities=18%  Similarity=0.234  Sum_probs=88.7

Q ss_pred             ceEEEEEecccccccc-----c-------ChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHH
Q psy5642           7 LTEVVESIGPELFRKY-----V-------GESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA   74 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~-----~-------g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~   74 (237)
                      ..+++.++|+.+....     +       |....  ..+........+++|||||+|.+..               .+.+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~--~~~~~~~~~~~~~vl~lDEi~~l~~---------------~~~~  137 (311)
T 4fcw_A           75 EEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEG--GQLTEAVRRRPYSVILFDAIEKAHP---------------DVFN  137 (311)
T ss_dssp             GGGEEEEEGGGCCSTTHHHHHHCCCTTSTTTTTC--CHHHHHHHHCSSEEEEEETGGGSCH---------------HHHH
T ss_pred             CcceEEeecccccccccHHHhcCCCCcccccccc--chHHHHHHhCCCeEEEEeChhhcCH---------------HHHH
Confidence            4568888888765431     1       11100  1222333344458999999998722               3456


Q ss_pred             HHHHHhcCCC---------CCCCEEEEEEeCC--------------------------CCccchhccCCCCcccEEEecC
Q psy5642          75 QMLTEMDGIV---------PLNNVTIVAATNR--------------------------PDRIDKALLRPGRLDRLIYVPL  119 (237)
Q Consensus        75 ~ll~~l~~~~---------~~~~v~vI~ttn~--------------------------~~~ld~al~r~gRf~~~i~~~~  119 (237)
                      .|+..|+...         .-.++++|+|||.                          ...+++++++  ||+..+.+++
T Consensus       138 ~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~--R~~~~~~~~p  215 (311)
T 4fcw_A          138 ILLQMLDDGRLTDSHGRTVDFRNTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRP  215 (311)
T ss_dssp             HHHHHHHHSEEECTTSCEEECTTEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHT--TCSEEEECCC
T ss_pred             HHHHHHhcCEEEcCCCCEEECCCcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHh--cCCeEEEeCC
Confidence            6666665421         1136789999998                          4578899998  9999999999


Q ss_pred             CCHHHHHHHHHHHHcCC---------CCC-chhhHHHHHHHCC--CCCccc
Q psy5642         120 PDDLTRAAILKIRLARS---------PLG-EDVCVEELVRLTE--GYSGAE  158 (237)
Q Consensus       120 P~~~~R~~il~~~l~~~---------~~~-~~~~~~~la~~t~--g~s~~D  158 (237)
                      |+.+++..|++.++...         ... .+..+..|+...-  .+..++
T Consensus       216 ~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~gn~R~  266 (311)
T 4fcw_A          216 LTKEQIRQIVEIQMSYLRARLAEKRISLELTEAAKDFLAERGYDPVFGARP  266 (311)
T ss_dssp             CCHHHHHHHHHHHTHHHHHHHHTTTCEEEECHHHHHHHHHHSCBTTTBTTT
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhCCcEEEeCHHHHHHHHHhCCCccCCchh
Confidence            99999999999877542         111 4566777777654  566777

>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=98.62  E-value=2.5e-07  Score=80.55  Aligned_cols=181  Identities=16%  Similarity=0.191  Sum_probs=104.6

Q ss_pred             ceEEEEEeccccc-ccccChH-HHHHHHHHHHHH----hcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHh
Q psy5642           7 LTEVVESIGPELF-RKYVGES-ERCVRDVFKRAR----QVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEM   80 (237)
Q Consensus         7 ~~~~i~v~~s~l~-~~~~g~~-~~~l~~~f~~a~----~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l   80 (237)
                      +.+|+.++|+.+. ..|.|.. ...+..+|..+.    ...++||||||+|.+...+...... .......+.+.|+..|
T Consensus        97 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~~-~~~~~~~~~~~Ll~~l  175 (376)
T 1um8_A           97 DIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSIT-RDVSGEGVQQALLKIV  175 (376)
T ss_dssp             TCCEEEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC---------------CHHHHHHHHHHH
T ss_pred             CCCEEEecchhhhhcCcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHhhhcCCCcee-cccchHHHHHHHHHHh
Confidence            4689999998876 4566654 556777776543    3368999999999998764332111 0111134678888888


Q ss_pred             cCCC-------------------CCCCEEEEEEeCCC-----------------------------------------Cc
Q psy5642          81 DGIV-------------------PLNNVTIVAATNRP-----------------------------------------DR  100 (237)
Q Consensus        81 ~~~~-------------------~~~~v~vI~ttn~~-----------------------------------------~~  100 (237)
                      ++..                   ...++++|+|+|..                                         ..
T Consensus       176 e~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~R~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~  255 (376)
T 1um8_A          176 EGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYG  255 (376)
T ss_dssp             HCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTT
T ss_pred             hccceecccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHHHhcccccCCCchhhhccchhHHHhhcCHHHHhhcC
Confidence            7531                   12456788887720                                         12


Q ss_pred             cchhccCCCCcccEEEecCCCHHHHHHHHHH----HHc-------CCC--CC-chhhHHHHHHHCC--CCCcccccchhH
Q psy5642         101 IDKALLRPGRLDRLIYVPLPDDLTRAAILKI----RLA-------RSP--LG-EDVCVEELVRLTE--GYSGAEQSLSKH  164 (237)
Q Consensus       101 ld~al~r~gRf~~~i~~~~P~~~~R~~il~~----~l~-------~~~--~~-~~~~~~~la~~t~--g~s~~Dl~~~~~  164 (237)
                      +.++++.  ||+.++.|+.++.++...|+..    ++.       ...  +. ++..+..|+..+-  +...+.      
T Consensus       256 ~~p~l~~--R~~~~i~~~~l~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~------  327 (376)
T 1um8_A          256 LIPELIG--RLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKTGARG------  327 (376)
T ss_dssp             CCHHHHT--TCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTGGG------
T ss_pred             CChHHhc--CCCceeeccCCCHHHHHHHHhhhHHHHHHHHHHHHhhcCceEEECHHHHHHHHHHhcccccCcHH------
Confidence            4567777  8888899999999999988862    211       111  11 3455566665532  244555      


Q ss_pred             HhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc----ccCCccHHHHHHHHh
Q psy5642         165 RAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL----EAAYVSHQDFLTALQ  217 (237)
Q Consensus       165 ~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~----~~~~v~~~df~~al~  217 (237)
                                           +.++++.+....+.+..    ....|+.+++..+++
T Consensus       328 ---------------------L~~~le~~~~~~~~~~~~~~~~~~~i~~~~v~~~~~  363 (376)
T 1um8_A          328 ---------------------LRAIIEDFCLDIMFDLPKLKGSEVRITKDCVLKQAE  363 (376)
T ss_dssp             ---------------------HHHHHHHHHHHHHHTGGGGTTSEEEECHHHHTTSSC
T ss_pred             ---------------------HHHHHHHHHHHHHhhccCCCCCEEEEeHHHhcCCCC
Confidence                                 77777777766655432    234688888876544

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

Probab=98.60  E-value=4.8e-07  Score=77.24  Aligned_cols=77  Identities=17%  Similarity=0.185  Sum_probs=58.3

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC---------CCCCCEEEEEEeCCCC-----ccchhccCC
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI---------VPLNNVTIVAATNRPD-----RIDKALLRP  108 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---------~~~~~v~vI~ttn~~~-----~ld~al~r~  108 (237)
                      +||||||+|.+..               ...+.|+..|+..         ....++++|+|+|..+     .+++++++ 
T Consensus       111 ~vl~iDEi~~~~~---------------~~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~~~~~~~~l~~~l~~-  174 (331)
T 2r44_A          111 NFILADEVNRSPA---------------KVQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPVEQEGTYPLPEAQVD-  174 (331)
T ss_dssp             SEEEEETGGGSCH---------------HHHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTTCCSCCCCCCHHHHT-
T ss_pred             cEEEEEccccCCH---------------HHHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCCcccCcccCCHHHHh-
Confidence            7999999998622               3345555555532         1233678888888443     38999999 


Q ss_pred             CCcccEEEecCCCHHHHHHHHHHHHcCC
Q psy5642         109 GRLDRLIYVPLPDDLTRAAILKIRLARS  136 (237)
Q Consensus       109 gRf~~~i~~~~P~~~~R~~il~~~l~~~  136 (237)
                       ||+..+++++|+.++|.+||+..+...
T Consensus       175 -Rf~~~i~i~~p~~~~~~~il~~~~~~~  201 (331)
T 2r44_A          175 -RFMMKIHLTYLDKESELEVMRRVSNMN  201 (331)
T ss_dssp             -TSSEEEECCCCCHHHHHHHHHHHHCTT
T ss_pred             -heeEEEEcCCCCHHHHHHHHHhccccC
Confidence             999889999999999999999988653

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

Probab=98.60  E-value=2e-07  Score=88.35  Aligned_cols=140  Identities=16%  Similarity=0.156  Sum_probs=95.4

Q ss_pred             ceEEEEEeccccccc------------ccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHH
Q psy5642           7 LTEVVESIGPELFRK------------YVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA   74 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~------------~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~   74 (237)
                      +.+|+.++|+.+..+            |+|..+.  ..+........++||||||+|.+.               ..+.+
T Consensus       513 ~~~~~~i~~s~~~~~~~~~~l~g~~~g~~g~~~~--~~l~~~~~~~~~~vl~lDEi~~~~---------------~~~~~  575 (758)
T 1r6b_X          513 GIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQG--GLLTDAVIKHPHAVLLLDEIEKAH---------------PDVFN  575 (758)
T ss_dssp             TCEEEEEEGGGCSSSSCCSSSCCCCSCSHHHHHT--THHHHHHHHCSSEEEEEETGGGSC---------------HHHHH
T ss_pred             cCCEEEEechhhcchhhHhhhcCCCCCCcCcccc--chHHHHHHhCCCcEEEEeCccccC---------------HHHHH
Confidence            368899999887653            4443222  123344445567999999999762               24677


Q ss_pred             HHHHHhcCCC---------CCCCEEEEEEeCCCC-------------------------ccchhccCCCCcccEEEecCC
Q psy5642          75 QMLTEMDGIV---------PLNNVTIVAATNRPD-------------------------RIDKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus        75 ~ll~~l~~~~---------~~~~v~vI~ttn~~~-------------------------~ld~al~r~gRf~~~i~~~~P  120 (237)
                      .|++.|+.-.         .-.++++|+|||...                         .+++++++  ||+.+|.|++|
T Consensus       576 ~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~l  653 (758)
T 1r6b_X          576 ILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHL  653 (758)
T ss_dssp             HHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHT--TCSEEEECCCC
T ss_pred             HHHHHhcCcEEEcCCCCEEecCCeEEEEecCcchhhhhhcccCccccchHHHHHHHHHHhcCHHHHh--hCCcceeeCCC
Confidence            7788777421         014688999999754                         67899999  99999999999


Q ss_pred             CHHHHHHHHHHHHcCC-------C--CC-chhhHHHHHHHC--CCCCcccccchhHH
Q psy5642         121 DDLTRAAILKIRLARS-------P--LG-EDVCVEELVRLT--EGYSGAEQSLSKHR  165 (237)
Q Consensus       121 ~~~~R~~il~~~l~~~-------~--~~-~~~~~~~la~~t--~g~s~~Dl~~~~~~  165 (237)
                      +.+++..|++.++...       .  +. .+..+..|+...  .+|..++|..++++
T Consensus       654 ~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~g~R~l~~~i~~  710 (758)
T 1r6b_X          654 STDVIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAEKGYDRAMGARPMARVIQD  710 (758)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHTTEEEEECHHHHHHHHHHHCBTTTBTTTHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCcEEEeCHHHHHHHHHhCCCcCCCchHHHHHHHH
Confidence            9999999999887632       1  11 455566677644  45667774443333

>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=98.56  E-value=6.3e-07  Score=76.71  Aligned_cols=76  Identities=20%  Similarity=0.309  Sum_probs=56.4

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC----CCC-------CCCEEEEEEeCCCC-ccchhccCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG----IVP-------LNNVTIVAATNRPD-RIDKALLRP  108 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~----~~~-------~~~v~vI~ttn~~~-~ld~al~r~  108 (237)
                      .+++|||||+|.+..               ...+.|+..++.    +..       ..++++|+|||..+ .+++++++ 
T Consensus       144 ~~~vl~iDEi~~l~~---------------~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~-  207 (350)
T 1g8p_A          144 NRGYLYIDECNLLED---------------HIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD-  207 (350)
T ss_dssp             TTEEEEETTGGGSCH---------------HHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT-
T ss_pred             CCCEEEEeChhhCCH---------------HHHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCCCCCCCCHHHHh-
Confidence            378999999998733               234455555443    111       12689999999744 89999999 


Q ss_pred             CCcccEEEecCC-CHHHHHHHHHHHH
Q psy5642         109 GRLDRLIYVPLP-DDLTRAAILKIRL  133 (237)
Q Consensus       109 gRf~~~i~~~~P-~~~~R~~il~~~l  133 (237)
                       ||+..++++.| +.++|.+|++..+
T Consensus       208 -R~~~~~~l~~~~~~~~~~~il~~~~  232 (350)
T 1g8p_A          208 -RFGLSVEVLSPRDVETRVEVIRRRD  232 (350)
T ss_dssp             -TCSEEEECCCCCSHHHHHHHHHHHH
T ss_pred             -hcceEEEcCCCCcHHHHHHHHHHHH
Confidence             99988999999 6788889987743

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

Probab=98.55  E-value=4.9e-08  Score=75.60  Aligned_cols=103  Identities=23%  Similarity=0.349  Sum_probs=75.1

Q ss_pred             CceEEEEEeccccc--ccccChHHHHHHHHHHHHHhc-CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC
Q psy5642           6 GLTEVVESIGPELF--RKYVGESERCVRDVFKRARQV-SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG   82 (237)
Q Consensus         6 ~~~~~i~v~~s~l~--~~~~g~~~~~l~~~f~~a~~~-~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~   82 (237)
                      .+.+++.++++.+.  ..+.+.....++.++..+... .|.+|+|||+|.+...+.....  ..    .+.+.+...++.
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~--~~----~~~~~l~~~~~~  150 (187)
T 2p65_A           77 KGRKLVSLDLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGAVAEG--AL----DAGNILKPMLAR  150 (187)
T ss_dssp             TTCEEEEECHHHHHHHCCSHHHHHHHHHHHHHHHHHTTTSEEEEETTGGGGSSSSSSCTT--SC----CTHHHHHHHHHT
T ss_pred             cCCeEEEEeHHHhhcCCCchhHHHHHHHHHHHHHHhcCCceEEEEeCHHHhccccccccc--ch----HHHHHHHHHHhc
Confidence            46788899888776  446677788899999888775 7899999999999865442111  01    123333344433


Q ss_pred             CCCCCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCC
Q psy5642          83 IVPLNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPD  121 (237)
Q Consensus        83 ~~~~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~  121 (237)
                          .++++|++||.+.     .+++++++  ||+. ++++.|+
T Consensus       151 ----~~~~ii~~~~~~~~~~~~~~~~~l~~--R~~~-i~i~~p~  187 (187)
T 2p65_A          151 ----GELRCIGATTVSEYRQFIEKDKALER--RFQQ-ILVEQPS  187 (187)
T ss_dssp             ----TCSCEEEEECHHHHHHHTTTCHHHHH--HEEE-EECCSCC
T ss_pred             ----CCeeEEEecCHHHHHHHHhccHHHHH--hcCc-ccCCCCC
Confidence                5678999999865     68999999  9995 9999986

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

Probab=98.54  E-value=7.7e-07  Score=75.67  Aligned_cols=121  Identities=21%  Similarity=0.223  Sum_probs=83.0

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhc-----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQV-----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~-----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      +.+++++++++..       ...++..+..+...     .+.||+|||+|.+..              ....+.|+..++
T Consensus        73 ~~~~~~i~~~~~~-------~~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~--------------~~~~~~L~~~le  131 (324)
T 3u61_B           73 NADMMFVNGSDCK-------IDFVRGPLTNFASAASFDGRQKVIVIDEFDRSGL--------------AESQRHLRSFME  131 (324)
T ss_dssp             TEEEEEEETTTCC-------HHHHHTHHHHHHHBCCCSSCEEEEEEESCCCGGG--------------HHHHHHHHHHHH
T ss_pred             CCCEEEEcccccC-------HHHHHHHHHHHHhhcccCCCCeEEEEECCcccCc--------------HHHHHHHHHHHH
Confidence            4688899987632       44555555544333     578999999999851              122345555555


Q ss_pred             CCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHc-------CCCCC-ch-hhHHHHHHHCC
Q psy5642          82 GIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA-------RSPLG-ED-VCVEELVRLTE  152 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~-------~~~~~-~~-~~~~~la~~t~  152 (237)
                      ..  ..++.+|+|||.+..+++++++  ||. .++|+.|+.++|.+|++.++.       ..... ++ ..+..++..+.
T Consensus       132 ~~--~~~~~iI~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~  206 (324)
T 3u61_B          132 AY--SSNCSIIITANNIDGIIKPLQS--RCR-VITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNF  206 (324)
T ss_dssp             HH--GGGCEEEEEESSGGGSCTTHHH--HSE-EEECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCBSCHHHHHHHHHHTC
T ss_pred             hC--CCCcEEEEEeCCccccCHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHhCC
Confidence            42  2467889999999999999999  996 699999999998777665432       22222 34 66777777654


Q ss_pred             C
Q psy5642         153 G  153 (237)
Q Consensus       153 g  153 (237)
                      |
T Consensus       207 g  207 (324)
T 3u61_B          207 P  207 (324)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=98.52  E-value=1.3e-06  Score=74.76  Aligned_cols=93  Identities=16%  Similarity=0.214  Sum_probs=72.0

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P  120 (237)
                      .+.||+|||+|.+...               ..+.|+..++...  .+..+|.+||++..+++++++  |+. .+.+++|
T Consensus       133 ~~~vliiDE~~~l~~~---------------~~~~Ll~~le~~~--~~~~~il~~~~~~~l~~~l~s--R~~-~i~~~~~  192 (353)
T 1sxj_D          133 PYKIIILDEADSMTAD---------------AQSALRRTMETYS--GVTRFCLICNYVTRIIDPLAS--QCS-KFRFKAL  192 (353)
T ss_dssp             SCEEEEETTGGGSCHH---------------HHHHHHHHHHHTT--TTEEEEEEESCGGGSCHHHHH--HSE-EEECCCC
T ss_pred             CceEEEEECCCccCHH---------------HHHHHHHHHHhcC--CCceEEEEeCchhhCcchhhc--cCc-eEEeCCC
Confidence            4569999999998432               2355666666532  356677788999999999999  997 7999999


Q ss_pred             CHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         121 DDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       121 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +.++...+++..+...+.. ++..+..++..+.|
T Consensus       193 ~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G  226 (353)
T 1sxj_D          193 DASNAIDRLRFISEQENVKCDDGVLERILDISAG  226 (353)
T ss_dssp             CHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSS
T ss_pred             CHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Confidence            9999999999988665443 56678888888765

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.51  E-value=2.7e-07  Score=83.90  Aligned_cols=128  Identities=16%  Similarity=0.164  Sum_probs=79.0

Q ss_pred             ceEEEEEecccccccccChHHH-------HHHHHHHHH-----HhcCCeEEEEccccccccccCCCCCCCCCchHHHHHH
Q psy5642           7 LTEVVESIGPELFRKYVGESER-------CVRDVFKRA-----RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA   74 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~-------~l~~~f~~a-----~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~   74 (237)
                      +.++++++|+++.+.+..+...       .+..+|..+     ....++||+|||+|.+....            ...+.
T Consensus       102 ~~~~i~in~s~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~------------~~~l~  169 (516)
T 1sxj_A          102 GYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGD------------RGGVG  169 (516)
T ss_dssp             TCEEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTS------------TTHHH
T ss_pred             CCCEEEEeCCCcchHHHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccchhh------------HHHHH
Confidence            5789999999876643221110       022333333     22468999999999996532            11245


Q ss_pred             HHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642          75 QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus        75 ~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      .++..++.  ...++++|+++.....+++ ++   |+...+.|+.|+.+++.++|...+...+.. .+..+..++..+.
T Consensus       170 ~L~~~l~~--~~~~iIli~~~~~~~~l~~-l~---~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~~~l~~la~~s~  242 (516)
T 1sxj_A          170 QLAQFCRK--TSTPLILICNERNLPKMRP-FD---RVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTR  242 (516)
T ss_dssp             HHHHHHHH--CSSCEEEEESCTTSSTTGG-GT---TTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTT
T ss_pred             HHHHHHHh--cCCCEEEEEcCCCCccchh-hH---hceEEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            55555554  2234555555444445544 43   455689999999999999998876543332 4556888888764

>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=98.49  E-value=5.8e-07  Score=75.73  Aligned_cols=125  Identities=14%  Similarity=0.145  Sum_probs=85.1

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHH--hcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRAR--QVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~--~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      +.+++.+++++..+.  ......+........  ...+.+|+|||+|.+..               ...+.|+..++.. 
T Consensus        68 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~---------------~~~~~L~~~le~~-  129 (319)
T 2chq_A           68 RDNFIEMNASDERGI--DVVRHKIKEFARTAPIGGAPFKIIFLDEADALTA---------------DAQAALRRTMEMY-  129 (319)
T ss_dssp             HHHCEEEETTSTTCT--TTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCH---------------HHHHTTGGGTSSS-
T ss_pred             cCCeEEEeCccccCh--HHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCH---------------HHHHHHHHHHHhc-
Confidence            345777888765331  112222222221111  13478999999999833               2345566666652 


Q ss_pred             CCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642          85 PLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        85 ~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                       ..++.+|++||.+..+++++++  |+. .+.+++|+.+++..++...+...+.. ++..+..++..+.|
T Consensus       130 -~~~~~~i~~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G  195 (319)
T 2chq_A          130 -SKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGG  195 (319)
T ss_dssp             -SSSEEEEEEESCGGGSCHHHHT--TCE-EEECCCCCHHHHHHHHHHHHHTTCCCBCHHHHHHHHHTTTT
T ss_pred             -CCCCeEEEEeCChhhcchHHHh--hCe-EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence             3578899999999999999999  986 79999999999999999988766554 55667777765543

>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=98.48  E-value=1.3e-06  Score=73.61  Aligned_cols=120  Identities=17%  Similarity=0.144  Sum_probs=86.1

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHH-------hcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHh
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRAR-------QVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEM   80 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~-------~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l   80 (237)
                      .+++.+++++..+      ...++.++....       ...+.+|+|||+|.+...               ..+.|+..+
T Consensus        73 ~~~~~~~~~~~~~------~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~~---------------~~~~L~~~l  131 (323)
T 1sxj_B           73 DGVLELNASDDRG------IDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAG---------------AQQALRRTM  131 (323)
T ss_dssp             HHEEEECTTSCCS------HHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHH---------------HHHTTHHHH
T ss_pred             CCEEEecCccccC------hHHHHHHHHHHHhccccCCCCCceEEEEECcccCCHH---------------HHHHHHHHH
Confidence            4577777765322      445566666554       224889999999998431               234556666


Q ss_pred             cCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642          81 DGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        81 ~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +.  ...++.+|++|+.+..+++.+++  |+. .+.++.|+.++..++++..+...+.. ++..+..++..+.|
T Consensus       132 e~--~~~~~~~il~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G  200 (323)
T 1sxj_B          132 EL--YSNSTRFAFACNQSNKIIEPLQS--QCA-ILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEG  200 (323)
T ss_dssp             HH--TTTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTT
T ss_pred             hc--cCCCceEEEEeCChhhchhHHHh--hce-EEeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            55  23567888899999999999999  886 79999999999999999887654433 45667778887755

>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=98.46  E-value=7.9e-07  Score=76.70  Aligned_cols=109  Identities=20%  Similarity=0.240  Sum_probs=82.3

Q ss_pred             HHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchh
Q psy5642          29 CVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKA  104 (237)
Q Consensus        29 ~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~a  104 (237)
                      .++.+++.+..    ..+.||+|||+|.+..               ...+.|+..++..  ..++++|++|+.+..+++.
T Consensus       103 ~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~---------------~~~~~Ll~~le~~--~~~~~~Il~~~~~~~l~~~  165 (373)
T 1jr3_A          103 DTRDLLDNVQYAPARGRFKVYLIDEVHMLSR---------------HSFNALLKTLEEP--PEHVKFLLATTDPQKLPVT  165 (373)
T ss_dssp             CHHHHHHHTTSCCSSSSSEEEEEECGGGSCH---------------HHHHHHHHHHHSC--CSSEEEEEEESCGGGSCHH
T ss_pred             HHHHHHHHHhhccccCCeEEEEEECcchhcH---------------HHHHHHHHHHhcC--CCceEEEEEeCChHhCcHH
Confidence            35566666553    2478999999998832               2356777777763  3578899999999999999


Q ss_pred             ccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642         105 LLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus       105 l~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      +++  |+ ..+.++.|+.++...+++..+...+.. .+..+..++..+.| .+++
T Consensus       166 l~s--r~-~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~a~~~l~~~~~G-~~r~  216 (373)
T 1jr3_A          166 ILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEG-SLRD  216 (373)
T ss_dssp             HHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHSSS-CHHH
T ss_pred             HHh--he-eEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHCCC-CHHH
Confidence            998  87 679999999999999999888655443 45567788888866 4445

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

Probab=98.39  E-value=1.3e-06  Score=78.12  Aligned_cols=129  Identities=21%  Similarity=0.246  Sum_probs=95.2

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEE---------eC---CCCccchhccCCC
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAA---------TN---RPDRIDKALLRPG  109 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~t---------tn---~~~~ld~al~r~g  109 (237)
                      |.|++|||+|.+.               ....+.|+..|+...  .++++++|         ++   .+..+++.+++  
T Consensus       296 ~~VliIDEa~~l~---------------~~a~~aLlk~lEe~~--~~~~il~tn~~~~~i~~~~~~~~~~~l~~~i~s--  356 (456)
T 2c9o_A          296 PGVLFVDEVHMLD---------------IECFTYLHRALESSI--APIVIFASNRGNCVIRGTEDITSPHGIPLDLLD--  356 (456)
T ss_dssp             ECEEEEESGGGCB---------------HHHHHHHHHHTTSTT--CCEEEEEECCSEEECBTTSSCEEETTCCHHHHT--
T ss_pred             ceEEEEechhhcC---------------HHHHHHHHHHhhccC--CCEEEEecCCccccccccccccccccCChhHHh--
Confidence            5699999999982               346788888888743  34655566         33   27889999999  


Q ss_pred             CcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHC-CCCCcccccchhHHhhhhccccCCCCCCCCCchhHH
Q psy5642         110 RLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLT-EGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIV  187 (237)
Q Consensus       110 Rf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t-~g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~  187 (237)
                      ||.. +.+++|+.++..++|+..+...... .+..+..++..+ .| +++.                           ..
T Consensus       357 R~~~-~~~~~~~~~e~~~iL~~~~~~~~~~~~~~~~~~i~~~a~~g-~~r~---------------------------a~  407 (456)
T 2c9o_A          357 RVMI-IRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKT-TLRY---------------------------SV  407 (456)
T ss_dssp             TEEE-EECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHS-CHHH---------------------------HH
T ss_pred             hcce-eeCCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHccCC-CHHH---------------------------HH
Confidence            9987 6999999999999999877533332 455566677766 44 5555                           56


Q ss_pred             HHHHHHHHHHHHhccccCCccHHHHHHHHhhcC
Q psy5642         188 AVCDEAALSALENNLEAAYVSHQDFLTALQLVK  220 (237)
Q Consensus       188 ~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~  220 (237)
                      .+++.|...+..++  ...|+.+|+..|+..+-
T Consensus       408 ~ll~~a~~~A~~~~--~~~v~~~~v~~~~~~~~  438 (456)
T 2c9o_A          408 QLLTPANLLAKING--KDSIEKEHVEEISELFY  438 (456)
T ss_dssp             HTHHHHHHHHHHTT--CSSBCHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHhhcC--CCccCHHHHHHHHHHhc
Confidence            66777766666555  34699999999988764

>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=98.35  E-value=3.5e-06  Score=71.14  Aligned_cols=93  Identities=20%  Similarity=0.262  Sum_probs=72.9

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P  120 (237)
                      .+.+|+|||+|.+..               ...+.|+..++..  ..++.+|++||.+..+++++++  |+. .+.+++|
T Consensus       110 ~~~vliiDe~~~l~~---------------~~~~~L~~~le~~--~~~~~~i~~~~~~~~l~~~l~s--r~~-~~~~~~l  169 (327)
T 1iqp_A          110 SFKIIFLDEADALTQ---------------DAQQALRRTMEMF--SSNVRFILSCNYSSKIIEPIQS--RCA-IFRFRPL  169 (327)
T ss_dssp             SCEEEEEETGGGSCH---------------HHHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHH--TEE-EEECCCC
T ss_pred             CCeEEEEeCCCcCCH---------------HHHHHHHHHHHhc--CCCCeEEEEeCCccccCHHHHh--hCc-EEEecCC
Confidence            478999999999832               2345566666652  3467888899999999999999  987 7999999


Q ss_pred             CHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         121 DDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       121 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +.++...+++..+...+.. ++..+..++..+.|
T Consensus       170 ~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g  203 (327)
T 1iqp_A          170 RDEDIAKRLRYIAENEGLELTEEGLQAILYIAEG  203 (327)
T ss_dssp             CHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHCCC
Confidence            9999999999988766543 55667778887754

>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=98.35  E-value=1.9e-06  Score=82.84  Aligned_cols=134  Identities=21%  Similarity=0.258  Sum_probs=90.0

Q ss_pred             CceEEEEEeccccccc------------ccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHH
Q psy5642           6 GLTEVVESIGPELFRK------------YVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVL   73 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~------------~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~   73 (237)
                      .+.+|+.++|+.+...            |+|...  ...+........+++|||||+|.+-               ..+.
T Consensus       615 ~~~~~i~i~~~~~~~~~~~s~l~g~~~~~~G~~~--~g~l~~~~~~~~~~vl~lDEi~~l~---------------~~~~  677 (854)
T 1qvr_A          615 TEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEE--GGQLTEAVRRRPYSVILFDEIEKAH---------------PDVF  677 (854)
T ss_dssp             SGGGEEEECTTTCCSSGGGGGC----------------CHHHHHHHCSSEEEEESSGGGSC---------------HHHH
T ss_pred             CCCcEEEEechhccchhHHHHHcCCCCCCcCccc--cchHHHHHHhCCCeEEEEecccccC---------------HHHH
Confidence            3578999999877654            223222  1223334444556899999998762               3567


Q ss_pred             HHHHHHhcCCC---------CCCCEEEEEEeCCC--------------------------CccchhccCCCCcccEEEec
Q psy5642          74 AQMLTEMDGIV---------PLNNVTIVAATNRP--------------------------DRIDKALLRPGRLDRLIYVP  118 (237)
Q Consensus        74 ~~ll~~l~~~~---------~~~~v~vI~ttn~~--------------------------~~ld~al~r~gRf~~~i~~~  118 (237)
                      +.|+..|+.-.         .-.+++||+|||..                          ..+.|+|+.  ||+.++.+.
T Consensus       678 ~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~--Rl~~~i~~~  755 (854)
T 1qvr_A          678 NILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFR  755 (854)
T ss_dssp             HHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCC
T ss_pred             HHHHHHhccCceECCCCCEeccCCeEEEEecCcChHHHhhhcccccchHHHHHHHHHHHHhhCCHHHHH--hcCeEEeCC
Confidence            88888887532         11368899999972                          245677777  999999999


Q ss_pred             CCCHHHHHHHHHHHHcCC---------CCC-chhhHHHHHHHCC--CCCccc
Q psy5642         119 LPDDLTRAAILKIRLARS---------PLG-EDVCVEELVRLTE--GYSGAE  158 (237)
Q Consensus       119 ~P~~~~R~~il~~~l~~~---------~~~-~~~~~~~la~~t~--g~s~~D  158 (237)
                      +|+.++...|++.++...         .+. ++..+..|+..+-  .+..++
T Consensus       756 pl~~edi~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~L~~~~~~~~gn~R~  807 (854)
T 1qvr_A          756 PLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDFLAERGYDPVFGARP  807 (854)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHHHHCBTTTBTST
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHhCCceEEECHHHHHHHHHcCCCCCCChHH
Confidence            999999999999887521         111 4566777777654  567788

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

Probab=98.32  E-value=4e-06  Score=77.48  Aligned_cols=160  Identities=15%  Similarity=0.152  Sum_probs=98.8

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC-----------CCCCEEEEEEeCCCC-----------
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV-----------PLNNVTIVAATNRPD-----------   99 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vI~ttn~~~-----------   99 (237)
                      .+||||||+|.+..               ...+.|+..|++-.           ...++.||||||.+.           
T Consensus       392 ~gil~IDEid~l~~---------------~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaatNp~~G~~~~~~~~~~  456 (595)
T 3f9v_A          392 GGIAVIDEIDKMRD---------------EDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPKFGRYISERPVSD  456 (595)
T ss_dssp             SSEECCTTTTCCCS---------------HHHHHHHHHHHSSSEEEESSSSEEEECCCCEEEEEECCTTCCSCTTSCSCT
T ss_pred             CCcEEeehhhhCCH---------------hHhhhhHHHHhCCEEEEecCCcEEEecCceEEEEEcCCcCCccCcccCchh
Confidence            58999999998732               23456666665422           123588999999887           


Q ss_pred             --ccchhccCCCCcc-cEEEecCCCHHHHHHHHHHHHcCCCCC------chhhHHHHH---HH--CCCCCcccccchhHH
Q psy5642         100 --RIDKALLRPGRLD-RLIYVPLPDDLTRAAILKIRLARSPLG------EDVCVEELV---RL--TEGYSGAEQSLSKHR  165 (237)
Q Consensus       100 --~ld~al~r~gRf~-~~i~~~~P~~~~R~~il~~~l~~~~~~------~~~~~~~la---~~--t~g~s~~Dl~~~~~~  165 (237)
                        .+++++++  ||| ..+..+.|+.+ ...|.+..+......      +..++..+.   ..  ...++......+...
T Consensus       457 ni~l~~aLl~--RFDl~~~~~~~~~~e-~~~i~~~il~~~~~~~~~~~l~~~~l~~~i~~ar~~~~p~ls~ea~~~l~~~  533 (595)
T 3f9v_A          457 NINLPPTILS--RFDLIFILKDQPGEQ-DRELANYILDVHSGKSTKNIIDIDTLRKYIAYARKYVTPKITSEAKNLITDF  533 (595)
T ss_dssp             TTCSCSSSGG--GCSCCEEECCTTHHH-HHHHHHHHHTTTCCCSSSSTTCCTTTHHHHHHHHHHHCCCCCCCTHHHHHHH
T ss_pred             ccCCCHHHHh--hCeEEEEeCCCCCHH-HHHHHHHHHHHhhccccccCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Confidence              89999999  998 45566778888 888888888654321      122222222   11  123444334444444


Q ss_pred             hhhhccccCCCC--CCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCC
Q psy5642         166 AKKIRPRRESNP--GPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKP  221 (237)
Q Consensus       166 a~~~~~~~~~~~--~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p  221 (237)
                      ...++.....+.  ....+...+.++++.|...+..+.  ...|+.+|+..|++.++.
T Consensus       534 y~~lR~~~~~~~~~~~~~s~R~l~~lirla~a~A~l~~--~~~V~~~dv~~Ai~l~~~  589 (595)
T 3f9v_A          534 FVEMRKKSSETPDSPILITPRQLEALIRISEAYAKMAL--KAEVTREDAERAINIMRL  589 (595)
T ss_dssp             HTTSSCSCCBCSSSCBCSSTTTTTHHHHHHHHHHHTTS--SCCSSHHHHHHHHHHHHH
T ss_pred             HHHHHHhhccCCCccccccHHHHHHHHHHHHHHHHHhC--cCCCCHHHHHHHHHHHHH
Confidence            333222221111  234445557788887777776655  346999999999876543

>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=98.30  E-value=1.2e-05  Score=68.86  Aligned_cols=68  Identities=19%  Similarity=0.203  Sum_probs=56.1

Q ss_pred             CEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642          88 NVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus        88 ~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      .+.++++|+.+..+++.+++  ||...+.+++|+.++..++++......... .+..+..+|.++.|. +++
T Consensus       150 ~~~li~at~~~~~Ls~~l~s--R~~l~~~Ld~~~~~~l~~iL~~~~~~~~~~~~~~~~~~ia~~~~G~-~R~  218 (334)
T 1in4_A          150 PFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGT-PRI  218 (334)
T ss_dssp             CCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTC-HHH
T ss_pred             CeEEEEecCCcccCCHHHHH--hcCceeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhcCCC-hHH
Confidence            46778899999999999999  999889999999999999999887654443 456678889888764 355

>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=98.26  E-value=2.5e-05  Score=69.48  Aligned_cols=172  Identities=17%  Similarity=0.220  Sum_probs=104.1

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC--------CCCCEEEEEEe---
Q psy5642          27 ERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV--------PLNNVTIVAAT---   95 (237)
Q Consensus        27 ~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--------~~~~v~vI~tt---   95 (237)
                      ....+.+...|..+  .||++||+|.++...++.   +.+....-+...||..|++..        ..++|++|+|.   
T Consensus       238 ~~~~~~ai~~ae~~--~il~~DEidki~~~~~~~---~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~  312 (444)
T 1g41_A          238 EELKQKAIDAVEQN--GIVFIDEIDKICKKGEYS---GADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQ  312 (444)
T ss_dssp             HHHHHHHHHHHHHH--CEEEEETGGGGSCCSSCS---SSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCS
T ss_pred             HHHHHHHHHHhccC--CeeeHHHHHHHhhccCCC---CCCchHHHHHHHHHHHhcccccccccceecCCcEEEEeccccc
Confidence            34455555555332  699999999998764321   112222346678999998732        34679999997   


Q ss_pred             -CCCCccchhccCCCCcccEEEecCCCHHHHHHHHH---H--------HHcCCCCC---chhhHHHHHHH-------CCC
Q psy5642          96 -NRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILK---I--------RLARSPLG---EDVCVEELVRL-------TEG  153 (237)
Q Consensus        96 -n~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~---~--------~l~~~~~~---~~~~~~~la~~-------t~g  153 (237)
                       +.|.++-|.|+.  ||..+|.|+..+.++..+|+.   .        .+...+..   ++..+..++..       |+.
T Consensus       313 ~~~~~dlipel~~--R~~i~i~l~~lt~~e~~~Il~~~~~~l~~q~~~~~~~~~~~l~~~~~al~~i~~~a~~~~~~t~~  390 (444)
T 1g41_A          313 VARPSDLIPELQG--RLPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTEN  390 (444)
T ss_dssp             SCCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHHHHHSCC
T ss_pred             cCChhhcchHHhc--ccceeeeCCCCCHHHHHHHHHHHHHhHHHHHHHHhcccCceEEECHHHHHHHHHHHHHhccCCcc
Confidence             355666688998  999999999999999999993   1        22212221   45566666653       444


Q ss_pred             CCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcCCCCCHHHHHHH
Q psy5642         154 YSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLY  231 (237)
Q Consensus       154 ~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~p~~~~~~~~~~  231 (237)
                      ...+-|+.+                       |..+++++.............|+.+++...+.   |....+++.+|
T Consensus       391 ~GaR~L~~~-----------------------ie~~~~~~~~~~~~~~~~~~~i~~~~v~~~l~---~~~~~~dl~~~  442 (444)
T 1g41_A          391 IGARRLHTV-----------------------MERLMDKISFSASDMNGQTVNIDAAYVADALG---EVVENEDLSRF  442 (444)
T ss_dssp             CGGGHHHHH-----------------------HHHHHHHHHHHGGGCTTCEEEECHHHHHHHHT---TTTTCHHHHHH
T ss_pred             CCchHHHHH-----------------------HHHHHHHHHhhccccCCCeEEEeHHHHHHhcC---ccccCCChhcc
Confidence            444442221                       33333333333332222345689998887664   44455555544

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

Probab=98.13  E-value=5.9e-06  Score=74.74  Aligned_cols=76  Identities=20%  Similarity=0.254  Sum_probs=52.5

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC--------CCCCEEEEEEeCCCCc---cchhccCCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV--------PLNNVTIVAATNRPDR---IDKALLRPG  109 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--------~~~~v~vI~ttn~~~~---ld~al~r~g  109 (237)
                      .|+||||||++.+.               ..+.+.|+..|+.-.        ..+..++|++||.+..   ..+++++  
T Consensus       109 ~~~IL~IDEI~r~~---------------~~~q~~LL~~lee~~v~i~G~~~~~~~~~iI~ATN~lpe~~~~~~aLld--  171 (500)
T 3nbx_X          109 EAEIVFLDEIWKAG---------------PAILNTLLTAINERQFRNGAHVEKIPMRLLVAASNELPEADSSLEALYD--  171 (500)
T ss_dssp             GCSEEEEESGGGCC---------------HHHHHHHHHHHHSSEEECSSSEEECCCCEEEEEESSCCCTTCTTHHHHT--
T ss_pred             cceeeeHHhHhhhc---------------HHHHHHHHHHHHHHhccCCCCcCCcchhhhhhccccCCCccccHHHHHH--
Confidence            47899999997541               345677777775321        1122346777775322   3459999  


Q ss_pred             CcccEEEecCCCH-HHHHHHHHHHH
Q psy5642         110 RLDRLIYVPLPDD-LTRAAILKIRL  133 (237)
Q Consensus       110 Rf~~~i~~~~P~~-~~R~~il~~~l  133 (237)
                      ||...+++++|+. +++..|++...
T Consensus       172 RF~~~i~v~~p~~~ee~~~IL~~~~  196 (500)
T 3nbx_X          172 RMLIRLWLDKVQDKANFRSMLTSQQ  196 (500)
T ss_dssp             TCCEEEECCSCCCHHHHHHHHTCCC
T ss_pred             HHHHHHHHHHhhhhhhHHHHHhccc
Confidence            9999999999987 78889988654

>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=98.12  E-value=1.8e-05  Score=67.74  Aligned_cols=104  Identities=19%  Similarity=0.313  Sum_probs=80.8

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++.+++.+...    .+.|++|||+|.+..               ...+.|+..|++  ...++++|.+|+.++.++
T Consensus        90 i~~ir~l~~~~~~~~~~~~~kvviIdead~l~~---------------~a~naLLk~lEe--p~~~~~~Il~t~~~~~l~  152 (334)
T 1a5t_A           90 VDAVREVTEKLNEHARLGGAKVVWVTDAALLTD---------------AAANALLKTLEE--PPAETWFFLATREPERLL  152 (334)
T ss_dssp             HHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCH---------------HHHHHHHHHHTS--CCTTEEEEEEESCGGGSC
T ss_pred             HHHHHHHHHHHhhccccCCcEEEEECchhhcCH---------------HHHHHHHHHhcC--CCCCeEEEEEeCChHhCc
Confidence            45677888777642    367999999999832               235778888887  445788999999999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGY  154 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~  154 (237)
                      +.+++  |+. .+.|+.|+.++..++++...   .. .+..+..++..+.|-
T Consensus       153 ~ti~S--Rc~-~~~~~~~~~~~~~~~L~~~~---~~-~~~~~~~l~~~s~G~  197 (334)
T 1a5t_A          153 ATLRS--RCR-LHYLAPPPEQYAVTWLSREV---TM-SQDALLAALRLSAGS  197 (334)
T ss_dssp             HHHHT--TSE-EEECCCCCHHHHHHHHHHHC---CC-CHHHHHHHHHHTTTC
T ss_pred             HHHhh--cce-eeeCCCCCHHHHHHHHHHhc---CC-CHHHHHHHHHHcCCC
Confidence            99999  885 69999999999999998775   22 455667777777653

>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=97.99  E-value=7.1e-05  Score=65.10  Aligned_cols=102  Identities=13%  Similarity=0.098  Sum_probs=69.2

Q ss_pred             cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC-C--CCEEEEEEeCCCC---ccc---hhccCCCC
Q psy5642          40 VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP-L--NNVTIVAATNRPD---RID---KALLRPGR  110 (237)
Q Consensus        40 ~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-~--~~v~vI~ttn~~~---~ld---~al~r~gR  110 (237)
                      ..|.+|+|||+|.+......      +   ...+..++..+..... .  .++.+|++|+.++   .++   +.+.+  +
T Consensus       137 ~~~~llvlDe~~~l~~~~~~------~---~~~l~~l~~~~~~~~~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~--~  205 (412)
T 1w5s_A          137 NHYLLVILDEFQSMLSSPRI------A---AEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVES--Q  205 (412)
T ss_dssp             TCEEEEEEESTHHHHSCTTS------C---HHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--T
T ss_pred             CCeEEEEEeCHHHHhhccCc------c---hHHHHHHHHHHHhcccCCCCceEEEEEEeccccHHHHHhhhcchhhh--h
Confidence            46899999999998643110      0   2345555555554321 2  5788999988765   344   66777  7


Q ss_pred             cccEEEecCCCHHHHHHHHHHHHcCC---CCCchhhHHHHHHHCC
Q psy5642         111 LDRLIYVPLPDDLTRAAILKIRLARS---PLGEDVCVEELVRLTE  152 (237)
Q Consensus       111 f~~~i~~~~P~~~~R~~il~~~l~~~---~~~~~~~~~~la~~t~  152 (237)
                      |...+.+++++.++..+++...+...   ....+..+..++..+.
T Consensus       206 ~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~  250 (412)
T 1w5s_A          206 IGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYG  250 (412)
T ss_dssp             CSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHC
T ss_pred             cCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHH
Confidence            76669999999999999998766421   1124566777888887

>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=97.98  E-value=1.7e-05  Score=67.99  Aligned_cols=93  Identities=17%  Similarity=0.265  Sum_probs=72.5

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P  120 (237)
                      .|.||+|||++.+..               ...+.++..|+...  .+..+|.+|+.+..+.+.+++  |+ ..+.|++|
T Consensus       134 ~~~vlilDE~~~L~~---------------~~~~~L~~~le~~~--~~~~~Il~t~~~~~l~~~l~s--R~-~~~~~~~~  193 (354)
T 1sxj_E          134 RYKCVIINEANSLTK---------------DAQAALRRTMEKYS--KNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAP  193 (354)
T ss_dssp             CCEEEEEECTTSSCH---------------HHHHHHHHHHHHST--TTEEEEEEESCSCSSCHHHHT--TS-EEEECCCC
T ss_pred             CCeEEEEeCccccCH---------------HHHHHHHHHHHhhc--CCCEEEEEeCCHHHHHHHHHh--hc-eEEecCCc
Confidence            577999999998521               23455666666542  357888999999999999999  98 67999999


Q ss_pred             CHHHHHHHHHHHHcCCCCC-c-hhhHHHHHHHCCC
Q psy5642         121 DDLTRAAILKIRLARSPLG-E-DVCVEELVRLTEG  153 (237)
Q Consensus       121 ~~~~R~~il~~~l~~~~~~-~-~~~~~~la~~t~g  153 (237)
                      +.++...+++..+...+.. + +..+..++..+.|
T Consensus       194 ~~~~~~~~l~~~~~~~~~~~~~~~~l~~i~~~~~G  228 (354)
T 1sxj_E          194 SDSEISTILSDVVTNERIQLETKDILKRIAQASNG  228 (354)
T ss_dssp             CHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCC
Confidence            9999999999888655443 4 5677888888755

>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=97.52  E-value=0.00022  Score=60.42  Aligned_cols=99  Identities=12%  Similarity=0.122  Sum_probs=75.7

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI   83 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   83 (237)
                      ..+++++++.-     ..+...++.+.+.+...    ...|++|||+|.+..               ...+.|+..|++ 
T Consensus        50 ~d~~~l~~~~~-----~~~id~ir~li~~~~~~p~~~~~kvviIdead~lt~---------------~a~naLLk~LEe-  108 (305)
T 2gno_A           50 SDVLEIDPEGE-----NIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQ---------------QAANAFLKALEE-  108 (305)
T ss_dssp             TTEEEECCSSS-----CBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCH---------------HHHHHTHHHHHS-
T ss_pred             CCEEEEcCCcC-----CCCHHHHHHHHHHHhhccccCCceEEEeccHHHhCH---------------HHHHHHHHHHhC-
Confidence            35666666421     12355678888888643    235999999999832               236789999987 


Q ss_pred             CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHH
Q psy5642          84 VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRL  133 (237)
Q Consensus        84 ~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l  133 (237)
                       ...++++|.+|++++.+.+++++  |   .+.|++|+.++...+++..+
T Consensus       109 -p~~~t~fIl~t~~~~kl~~tI~S--R---~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A          109 -PPEYAVIVLNTRRWHYLLPTIKS--R---VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             -CCTTEEEEEEESCGGGSCHHHHT--T---SEEEECCCCHHHHHHHHHHH
T ss_pred             -CCCCeEEEEEECChHhChHHHHc--e---eEeCCCCCHHHHHHHHHHHh
Confidence             44578888888999999999999  8   89999999999999998876

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=97.49  E-value=0.0004  Score=64.18  Aligned_cols=132  Identities=24%  Similarity=0.353  Sum_probs=82.1

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC----------------C---CCCEEEEEEeCCC--C
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV----------------P---LNNVTIVAATNRP--D   99 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~----------------~---~~~v~vI~ttn~~--~   99 (237)
                      .+.+|||||++.+-+               .+...|+..|+.-.                .   ..++.||++||..  +
T Consensus       201 ~~gvL~LDEi~~l~~---------------~~q~~Ll~~Le~~~~~~~g~~~~~~~~~l~~~~~p~~~~vI~atn~~~~~  265 (604)
T 3k1j_A          201 HKGVLFIDEIATLSL---------------KMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNLDTVD  265 (604)
T ss_dssp             TTSEEEETTGGGSCH---------------HHHHHHHHHHHHSEECCBCSCTTSGGGGCBCSCEECCCEEEEEECHHHHH
T ss_pred             CCCEEEEechhhCCH---------------HHHHHHHHHHHcCcEEecccccccccccCCCCccceeEEEEEecCHHHHh
Confidence            567999999999721               23344555444110                1   1257899999976  6


Q ss_pred             ccchhccCCCCcc---cEEEecC--C-CHHHHHHHHHHHHcC------CCCCchhhHHHHHHHC---CCC------Cccc
Q psy5642         100 RIDKALLRPGRLD---RLIYVPL--P-DDLTRAAILKIRLAR------SPLGEDVCVEELVRLT---EGY------SGAE  158 (237)
Q Consensus       100 ~ld~al~r~gRf~---~~i~~~~--P-~~~~R~~il~~~l~~------~~~~~~~~~~~la~~t---~g~------s~~D  158 (237)
                      .++++|++  ||+   ..+.++.  + ..+....+++.+...      ...-.+..+..|....   .|-      +.++
T Consensus       266 ~l~~~l~~--R~~v~~i~i~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ls~eAl~~Li~~~~r~~g~r~~l~~~~R~  343 (604)
T 3k1j_A          266 KMHPALRS--RIRGYGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEIVREAQKRAGRKGHLTLRLRD  343 (604)
T ss_dssp             HSCHHHHH--HHHHHSEEEECCSEEECCHHHHHHHHHHHHHHHHHHCSSCCBBHHHHHHHHHHHHHTTCSTTEEECCHHH
T ss_pred             hcCHHHHH--HhhccceEeeccccccCCHHHHHHHHHHHHHHHhhccCcccCCHHHHHHHHHHHhhhhccccccccCHHH
Confidence            89999999  997   4555543  2 345566666543321      1111445555555543   331      2334


Q ss_pred             ccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhh
Q psy5642         159 QSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQL  218 (237)
Q Consensus       159 l~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~  218 (237)
                                                 +.++++.|...+..++  ...|+.+|+.+|++.
T Consensus       344 ---------------------------l~~llr~A~~~A~~~~--~~~I~~edv~~A~~~  374 (604)
T 3k1j_A          344 ---------------------------LGGIVRAAGDIAVKKG--KKYVEREDVIEAVKM  374 (604)
T ss_dssp             ---------------------------HHHHHHHHHHHHHHTT--CSSBCHHHHHHHHHH
T ss_pred             ---------------------------HHHHHHHHHHHHHhcC--cccccHHHHHHHHHh
Confidence                                       8888888877665554  446999999999965

>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=97.45  E-value=0.00045  Score=58.94  Aligned_cols=93  Identities=15%  Similarity=0.182  Sum_probs=68.8

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P  120 (237)
                      .+.|++|||+|.+..               ...+.|+..++..  .....+|++||.+..+.+++++  |+. .+.++.+
T Consensus       110 ~~~viiiDe~~~l~~---------------~~~~~L~~~le~~--~~~~~~il~~n~~~~i~~~i~s--R~~-~~~~~~l  169 (340)
T 1sxj_C          110 GFKLIILDEADAMTN---------------AAQNALRRVIERY--TKNTRFCVLANYAHKLTPALLS--QCT-RFRFQPL  169 (340)
T ss_dssp             SCEEEEETTGGGSCH---------------HHHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCC
T ss_pred             CceEEEEeCCCCCCH---------------HHHHHHHHHHhcC--CCCeEEEEEecCccccchhHHh--hce-eEeccCC
Confidence            368999999998832               1245566666653  2456778889999999999999  986 6899999


Q ss_pred             CHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         121 DDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       121 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +.++..+++...+...... .+..+..++..+.|
T Consensus       170 ~~~~~~~~l~~~~~~~~~~i~~~~~~~i~~~s~G  203 (340)
T 1sxj_C          170 PQEAIERRIANVLVHEKLKLSPNAEKALIELSNG  203 (340)
T ss_dssp             CHHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            9999999999888544433 44556667765543

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=97.19  E-value=0.00035  Score=71.11  Aligned_cols=77  Identities=17%  Similarity=0.212  Sum_probs=61.8

Q ss_pred             ccccCh----HHHHHHHHHHHHHhcCCeEEEEccccccccccCC---CCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEE
Q psy5642          20 RKYVGE----SERCVRDVFKRARQVSPSVIFFDELDSLAGERGD---GGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIV   92 (237)
Q Consensus        20 ~~~~g~----~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~---~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI   92 (237)
                      ++|+++    +++.++.+|..|+...||+|++|++|+|++.+..   ..+.. .....|+++++|..|++.....+|+||
T Consensus      1135 ~~~~~~~~~~~e~~l~~~~~~ar~~~~~~i~~d~~~al~~~~~~~g~~~~~~-~~~~~r~~~q~l~~~~~~~~~~~v~v~ 1213 (1706)
T 3cmw_A         1135 DNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSH-MGLAARMMSQAMRKLAGNLKQSNTLLI 1213 (1706)
T ss_dssp             GGCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCGGGCCCHHHHHSCTTCCC-TTHHHHHHHHHHHHHHHHHHHTTCEEE
T ss_pred             HHHhhccccchHHHHHHHHHHHHhcCCeEEEeCchHhcCccccccccccccc-ccHHHHHHHHHHHHHHhhhccCCeEEE
Confidence            788888    9999999999999999999999999999998532   22211 256678999999999997776788888


Q ss_pred             EEeCCC
Q psy5642          93 AATNRP   98 (237)
Q Consensus        93 ~ttn~~   98 (237)
                       +||+.
T Consensus      1214 -~~n~~ 1218 (1706)
T 3cmw_A         1214 -FINQI 1218 (1706)
T ss_dssp             -EEECE
T ss_pred             -Eeccc
Confidence             55654

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.14  E-value=0.00031  Score=59.29  Aligned_cols=107  Identities=19%  Similarity=0.246  Sum_probs=60.3

Q ss_pred             CceEEEEEecccccccc-------------cChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHH
Q psy5642           6 GLTEVVESIGPELFRKY-------------VGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERV   72 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~-------------~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~   72 (237)
                      .+.+|+.++|+.+....             .|... .....|..|.   +++|||||+|.+..               .+
T Consensus        52 ~~~~~v~v~~~~~~~~l~~~~lfg~~~g~~tg~~~-~~~g~~~~a~---~g~L~LDEi~~l~~---------------~~  112 (304)
T 1ojl_A           52 SDRPLVTLNCAALNESLLESELFGHEKGAFTGADK-RREGRFVEAD---GGTLFLDEIGDISP---------------LM  112 (304)
T ss_dssp             SSSCCCEEECSSCCHHHHHHHHTCCCSSCCC---C-CCCCHHHHHT---TSEEEEESCTTCCH---------------HH
T ss_pred             cCCCeEEEeCCCCChHHHHHHhcCccccccCchhh-hhcCHHHhcC---CCEEEEeccccCCH---------------HH
Confidence            45789999998764311             11111 1223344443   57999999999832               23


Q ss_pred             HHHHHHHhcCCC---------CCCCEEEEEEeCCC-------CccchhccCCCCcccEEEecCCCHH----HHHHHHHHH
Q psy5642          73 LAQMLTEMDGIV---------PLNNVTIVAATNRP-------DRIDKALLRPGRLDRLIYVPLPDDL----TRAAILKIR  132 (237)
Q Consensus        73 ~~~ll~~l~~~~---------~~~~v~vI~ttn~~-------~~ld~al~r~gRf~~~i~~~~P~~~----~R~~il~~~  132 (237)
                      ...|+..++...         ...++.||++||.+       ..+++.+..  ||. .+.+..|...    +...+++.+
T Consensus       113 q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~l~~~v~~g~fr~~L~~--Rl~-~~~i~lPpL~eR~edi~~l~~~~  189 (304)
T 1ojl_A          113 QVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYY--RLN-VVAIEMPSLRQRREDIPLLADHF  189 (304)
T ss_dssp             HHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSCHHHHHHHTSSCHHHHH--HHS-SEEEECCCSGGGGGGHHHHHHHH
T ss_pred             HHHHHHHHhcCEeeecCCcccccCCeEEEEecCccHHHHHHhCCcHHHHHh--hcC-eeEEeccCHHHhHhhHHHHHHHH
Confidence            455666665432         12358899999975       134555665  664 4555555544    444466655


Q ss_pred             Hc
Q psy5642         133 LA  134 (237)
Q Consensus       133 l~  134 (237)
                      +.
T Consensus       190 l~  191 (304)
T 1ojl_A          190 LR  191 (304)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

>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=97.10  E-value=0.0011  Score=70.27  Aligned_cols=113  Identities=19%  Similarity=0.262  Sum_probs=73.9

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHH---------------hcCCeEEEEccccccccccCCCCCCCCCchHHH
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRAR---------------QVSPSVIFFDELDSLAGERGDGGGGGGSNVQER   71 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~---------------~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~   71 (237)
                      +..++.++++...+      ...+...+...-               ...++||||||++....++.+.      ....+
T Consensus      1293 ~~~~~~infsa~ts------~~~~~~~i~~~~~~~~~~~g~~~~P~~~gk~~VlFiDEinmp~~d~yg~------q~~le 1360 (2695)
T 4akg_A         1293 LYDVVGINFSKDTT------TEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDEINLPKLDKYGS------QNVVL 1360 (2695)
T ss_dssp             SCEEEEEECCTTCC------HHHHHHHHHHHBCCEEETTTEEEEEBSSSSCEEEEEETTTCSCCCSSSC------CHHHH
T ss_pred             CCceEEEEeecCCC------HHHHHHHHHHHhhhccccCCccccCCCCCceEEEEecccccccccccCc------hhHHH
Confidence            45677777766543      234445554321               1234799999998744433221      12234


Q ss_pred             HHHHHHHHhcCCCC---C-----CCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcC
Q psy5642          72 VLAQMLTEMDGIVP---L-----NNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR  135 (237)
Q Consensus        72 ~~~~ll~~l~~~~~---~-----~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~  135 (237)
                      ++.++++. .+...   .     .++.+||++|.|.     .|+++++|  || ..++++.|+.+++..|+..+++.
T Consensus      1361 lLRq~le~-gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllR--rf-~vi~i~~P~~~~l~~I~~~il~~ 1433 (2695)
T 4akg_A         1361 FLRQLMEK-QGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTR--HA-AILYLGYPSGKSLSQIYEIYYKA 1433 (2695)
T ss_dssp             HHHHHHHT-SSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHT--TE-EEEECCCCTTTHHHHHHHHHHHH
T ss_pred             HHHHHHhc-CCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhh--ee-eEEEeCCCCHHHHHHHHHHHHHH
Confidence            44554432 11111   1     2589999999994     89999999  99 78999999999999999987753

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=97.05  E-value=0.0035  Score=51.27  Aligned_cols=75  Identities=24%  Similarity=0.179  Sum_probs=45.4

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC---------CCCCEEEEEEeCCC-------Cccchh
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV---------PLNNVTIVAATNRP-------DRIDKA  104 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~v~vI~ttn~~-------~~ld~a  104 (237)
                      .+++|||||+|.+..               .+...|+..++.-.         ...++.+|+|||.+       ..+++.
T Consensus       100 ~~~~l~lDEi~~l~~---------------~~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~~~~~~~~~~~~~~~  164 (265)
T 2bjv_A          100 DGGTLFLDELATAPM---------------MVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRAD  164 (265)
T ss_dssp             TTSEEEEESGGGSCH---------------HHHHHHHHHHHHCEECCCCC--CEECCCEEEEEESSCHHHHHHHTSSCHH
T ss_pred             CCcEEEEechHhcCH---------------HHHHHHHHHHHhCCeecCCCcccccCCeEEEEecCcCHHHHHHcCCccHH
Confidence            467999999998833               23344555554310         12357889999874       246788


Q ss_pred             ccCCCCcccEEEecCCCHH----HHHHHHHHHH
Q psy5642         105 LLRPGRLDRLIYVPLPDDL----TRAAILKIRL  133 (237)
Q Consensus       105 l~r~gRf~~~i~~~~P~~~----~R~~il~~~l  133 (237)
                      +.+  ||.. +.+..|...    +...+++.++
T Consensus       165 L~~--Rl~~-~~i~lp~L~~R~~di~~l~~~~l  194 (265)
T 2bjv_A          165 LLD--ALAF-DVVQLPPLRERESDIMLMAEYFA  194 (265)
T ss_dssp             HHH--HHCS-EEEECCCGGGCHHHHHHHHHHHH
T ss_pred             HHH--hhcC-cEEeCCChhhhhHHHHHHHHHHH
Confidence            888  8863 444444443    4444555444

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=96.61  E-value=0.04  Score=46.14  Aligned_cols=107  Identities=23%  Similarity=0.315  Sum_probs=65.2

Q ss_pred             HHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccch---------hccC
Q psy5642          37 ARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDK---------ALLR  107 (237)
Q Consensus        37 a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~---------al~r  107 (237)
                      +....|.+|+|||++.+...... .    +   ..+...+...++..   .++.+|.|++....+..         .+. 
T Consensus       124 ~~~~~~~vlvlDe~~~~~~~~~~-~----~---~~~~~~L~~~~~~~---~~~~~il~g~~~~~l~~~l~~~~~~~~l~-  191 (350)
T 2qen_A          124 GEELGEFIVAFDEAQYLRFYGSR-G----G---KELLALFAYAYDSL---PNLKIILTGSEVGLLHDFLKITDYESPLY-  191 (350)
T ss_dssp             HHHHSCEEEEEETGGGGGGBTTT-T----T---HHHHHHHHHHHHHC---TTEEEEEEESSHHHHHHHHCTTCTTSTTT-
T ss_pred             HhccCCEEEEEeCHHHHhccCcc-c----h---hhHHHHHHHHHHhc---CCeEEEEECCcHHHHHHHHhhcCCCCccc-
Confidence            33335999999999998641100 0    1   12233333333332   36666666654321221         222 


Q ss_pred             CCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCc
Q psy5642         108 PGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSG  156 (237)
Q Consensus       108 ~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~  156 (237)
                       ||+...+.+++.+.++-.+++...+...+.. ....+..+...|.|+..
T Consensus       192 -~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~~~~~~~~i~~~tgG~P~  240 (350)
T 2qen_A          192 -GRIAGEVLVKPFDKDTSVEFLKRGFREVNLDVPENEIEEAVELLDGIPG  240 (350)
T ss_dssp             -TCCCEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHTTCHH
T ss_pred             -cCccceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHH
Confidence             3666789999999999999999877654432 45677888889988764

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=96.48  E-value=0.0029  Score=50.04  Aligned_cols=73  Identities=15%  Similarity=0.160  Sum_probs=52.0

Q ss_pred             cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecC
Q psy5642          40 VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPL  119 (237)
Q Consensus        40 ~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~  119 (237)
                      ..++||+|||++.+.+.+.....   .       ..++..+... ....+-+|.+|+.++.|+.++++  |++..++++.
T Consensus        86 ~~~~vliIDEAq~l~~~~~~~~e---~-------~rll~~l~~~-r~~~~~iil~tq~~~~l~~~lr~--ri~~~~~l~~  152 (199)
T 2r2a_A           86 NIGSIVIVDEAQDVWPARSAGSK---I-------PENVQWLNTH-RHQGIDIFVLTQGPKLLDQNLRT--LVRKHYHIAS  152 (199)
T ss_dssp             GTTCEEEETTGGGTSBCCCTTCC---C-------CHHHHGGGGT-TTTTCEEEEEESCGGGBCHHHHT--TEEEEEEEEE
T ss_pred             cCceEEEEEChhhhccCccccch---h-------HHHHHHHHhc-CcCCeEEEEECCCHHHHhHHHHH--HhheEEEEcC
Confidence            35789999999999876532211   0       1255555543 23456778888889999999999  9999999998


Q ss_pred             CCHHHH
Q psy5642         120 PDDLTR  125 (237)
Q Consensus       120 P~~~~R  125 (237)
                      |....+
T Consensus       153 ~~~~~~  158 (199)
T 2r2a_A          153 NKMGMR  158 (199)
T ss_dssp             CSSCCE
T ss_pred             cccCcc
Confidence            755443

>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=96.41  E-value=0.042  Score=46.13  Aligned_cols=111  Identities=15%  Similarity=0.180  Sum_probs=66.2

Q ss_pred             HHHHHHHHHhc--CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccch----
Q psy5642          30 VRDVFKRARQV--SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDK----  103 (237)
Q Consensus        30 l~~~f~~a~~~--~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~----  103 (237)
                      +..++......  .|.+|+|||++.+......       .. ...+..+...   .   .++.+|.|++....+..    
T Consensus       124 ~~~l~~~l~~~~~~~~vlvlDe~~~~~~~~~~-------~~-~~~l~~~~~~---~---~~~~~i~~g~~~~~l~~~l~~  189 (357)
T 2fna_A          124 FANLLESFEQASKDNVIIVLDEAQELVKLRGV-------NL-LPALAYAYDN---L---KRIKFIMSGSEMGLLYDYLRV  189 (357)
T ss_dssp             HHHHHHHHHHTCSSCEEEEEETGGGGGGCTTC-------CC-HHHHHHHHHH---C---TTEEEEEEESSHHHHHHHTTT
T ss_pred             HHHHHHHHHhcCCCCeEEEEECHHHhhccCch-------hH-HHHHHHHHHc---C---CCeEEEEEcCchHHHHHHHhc
Confidence            44555555443  4999999999998652100       11 1223333322   1   35667777765322221    


Q ss_pred             -----hccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcc
Q psy5642         104 -----ALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGA  157 (237)
Q Consensus       104 -----al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~  157 (237)
                           .+.  ||+...+.++..+.++..+++...+...+...+ +...+...|.|+...
T Consensus       190 ~~~~~~l~--~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~-~~~~i~~~t~G~P~~  245 (357)
T 2fna_A          190 EDPESPLF--GRAFSTVELKPFSREEAIEFLRRGFQEADIDFK-DYEVVYEKIGGIPGW  245 (357)
T ss_dssp             TCTTSTTT--TCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCC-CHHHHHHHHCSCHHH
T ss_pred             cCCCCccc--cCccceeecCCCCHHHHHHHHHHHHHHcCCCCC-cHHHHHHHhCCCHHH
Confidence                 122  366678999999999999999987653222222 237888899887643

>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=96.39  E-value=0.048  Score=46.21  Aligned_cols=106  Identities=15%  Similarity=0.145  Sum_probs=70.8

Q ss_pred             HHHHHHHHHHHh----cCCeEEEEccccc-cccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCC----
Q psy5642          28 RCVRDVFKRARQ----VSPSVIFFDELDS-LAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRP----   98 (237)
Q Consensus        28 ~~l~~~f~~a~~----~~P~il~iDeid~-l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~----   98 (237)
                      ..++.+++.+..    ...-|++|||+|. +..               ...+.|+..+++..  ..+++|.+|+.+    
T Consensus        59 ~~~~~l~~~~~~~plf~~~kvvii~~~~~kl~~---------------~~~~aLl~~le~p~--~~~~~il~~~~~~~~~  121 (343)
T 1jr3_D           59 TDWNAIFSLCQAMSLFASRQTLLLLLPENGPNA---------------AINEQLLTLTGLLH--DDLLLIVRGNKLSKAQ  121 (343)
T ss_dssp             CCHHHHHHHHHHHHHCCSCEEEEEECCSSCCCT---------------THHHHHHHHHTTCB--TTEEEEEEESCCCTTT
T ss_pred             CCHHHHHHHhcCcCCccCCeEEEEECCCCCCCh---------------HHHHHHHHHHhcCC--CCeEEEEEcCCCChhh
Confidence            345666666553    2466999999887 521               13566788888743  344444444442    


Q ss_pred             --CccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642          99 --DRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        99 --~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                        ..+.+++.+  |. ..+.+..|+..+....++..+...+.. ....+..++..+.|
T Consensus       122 ~~~k~~~~i~s--r~-~~~~~~~l~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g  176 (343)
T 1jr3_D          122 ENAAWFTALAN--RS-VQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEG  176 (343)
T ss_dssp             TTSHHHHHHTT--TC-EEEEECCCCTTHHHHHHHHHHHHTTCEECHHHHHHHHHSSTT
T ss_pred             HhhHHHHHHHh--Cc-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhch
Confidence              467788887  65 479999999999999999988776654 45566667765543

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=96.38  E-value=0.0018  Score=48.20  Aligned_cols=66  Identities=8%  Similarity=0.022  Sum_probs=43.4

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+.+|+ ++|+.+.+.      ......|..+   .+++|||||+|.+..               .....++..|..  .
T Consensus        51 ~~~~~v-~~~~~~~~~------~~~~~~~~~a---~~g~l~ldei~~l~~---------------~~q~~Ll~~l~~--~  103 (145)
T 3n70_A           51 AQGEFV-YRELTPDNA------PQLNDFIALA---QGGTLVLSHPEHLTR---------------EQQYHLVQLQSQ--E  103 (145)
T ss_dssp             TTSCCE-EEECCTTTS------SCHHHHHHHH---TTSCEEEECGGGSCH---------------HHHHHHHHHHHS--S
T ss_pred             cCCCEE-EECCCCCcc------hhhhcHHHHc---CCcEEEEcChHHCCH---------------HHHHHHHHHHhh--c
Confidence            466888 999887654      3344556555   357999999998832               234456666644  2


Q ss_pred             CCCEEEEEEeCCC
Q psy5642          86 LNNVTIVAATNRP   98 (237)
Q Consensus        86 ~~~v~vI~ttn~~   98 (237)
                      ..++.+|+|||.+
T Consensus       104 ~~~~~~I~~t~~~  116 (145)
T 3n70_A          104 HRPFRLIGIGDTS  116 (145)
T ss_dssp             SCSSCEEEEESSC
T ss_pred             CCCEEEEEECCcC
Confidence            3456788888864

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=96.19  E-value=0.0035  Score=46.50  Aligned_cols=83  Identities=10%  Similarity=0.193  Sum_probs=50.4

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNN   88 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~   88 (237)
                      +|+.++|+.+...+       ...+|..+.   +++|||||+|.+...               ....++..++... ..+
T Consensus        53 ~~~~~~~~~~~~~~-------~~~~~~~a~---~~~l~lDei~~l~~~---------------~q~~Ll~~l~~~~-~~~  106 (143)
T 3co5_A           53 PWVSPARVEYLIDM-------PMELLQKAE---GGVLYVGDIAQYSRN---------------IQTGITFIIGKAE-RCR  106 (143)
T ss_dssp             CEECCSSTTHHHHC-------HHHHHHHTT---TSEEEEEECTTCCHH---------------HHHHHHHHHHHHT-TTT
T ss_pred             CeEEechhhCChHh-------hhhHHHhCC---CCeEEEeChHHCCHH---------------HHHHHHHHHHhCC-CCC
Confidence            78999998876543       455666554   589999999998332               2333444444321 345


Q ss_pred             EEEEEEeCCC-Cc----cchhccCCCCcc-cEEEecC
Q psy5642          89 VTIVAATNRP-DR----IDKALLRPGRLD-RLIYVPL  119 (237)
Q Consensus        89 v~vI~ttn~~-~~----ld~al~r~gRf~-~~i~~~~  119 (237)
                      +.+|+|||.+ ..    +++.+..  ||. ..|++|+
T Consensus       107 ~~iI~~tn~~~~~~~~~~~~~L~~--rl~~~~i~lPp  141 (143)
T 3co5_A          107 VRVIASCSYAAGSDGISCEEKLAG--LFSESVVRIPP  141 (143)
T ss_dssp             CEEEEEEEECTTTC--CHHHHHHH--HSSSEEEEECC
T ss_pred             EEEEEecCCCHHHHHhCccHHHHH--HhcCcEEeCCC
Confidence            7788888754 33    4444554  543 3455554

>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=95.62  E-value=0.11  Score=46.43  Aligned_cols=153  Identities=16%  Similarity=0.128  Sum_probs=75.5

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC-------CCCCCEEEEEEeCCCC-----------ccchh
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI-------VPLNNVTIVAATNRPD-----------RIDKA  104 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-------~~~~~v~vI~ttn~~~-----------~ld~a  104 (237)
                      .++|+||++.+-               ..+...|+..|++-       .-..++.||||+|...           .|+++
T Consensus       302 Gvl~lDEIn~~~---------------~~~qsaLlEaMEe~~VtI~G~~lparf~VIAA~NP~~~yd~~~s~~~~~Lp~a  366 (506)
T 3f8t_A          302 GILAVDHLEGAP---------------EPHRWALMEAMDKGTVTVDGIALNARCAVLAAINPGEQWPSDPPIARIDLDQD  366 (506)
T ss_dssp             SEEEEECCTTCC---------------HHHHHHHHHHHHHSEEEETTEEEECCCEEEEEECCCC--CCSCGGGGCCSCHH
T ss_pred             CeeehHhhhhCC---------------HHHHHHHHHHHhCCcEEECCEEcCCCeEEEEEeCcccccCCCCCccccCCChH
Confidence            699999998862               23456666666531       1124689999999765           88999


Q ss_pred             ccCCCCcccEE-EecCCCHHHHHHHHHHHHcCCCCCchhhHHH---HHH-H-CCC-CCcccccchhHHhhhhccccC---
Q psy5642         105 LLRPGRLDRLI-YVPLPDDLTRAAILKIRLARSPLGEDVCVEE---LVR-L-TEG-YSGAEQSLSKHRAKKIRPRRE---  174 (237)
Q Consensus       105 l~r~gRf~~~i-~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~---la~-~-t~g-~s~~Dl~~~~~~a~~~~~~~~---  174 (237)
                      +++  |||..+ .+++|+.+.-.+-      ..+.-+...+..   .|. . ..- .+..-...+++.....+....   
T Consensus       367 lLD--RFDLi~i~~d~pd~e~d~e~------~~~~ls~e~L~~yi~~ar~~~~~p~ls~ea~~yI~~~y~~tR~~~~~~~  438 (506)
T 3f8t_A          367 FLS--HFDLIAFLGVDPRPGEPEEQ------DTEVPSYTLLRRYLLYAIREHPAPELTEEARKRLEHWYETRREEVEERL  438 (506)
T ss_dssp             HHT--TCSEEEETTC--------------------CCHHHHHHHHHHHHHHCSCCEECHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             Hhh--heeeEEEecCCCChhHhhcc------cCCCCCHHHHHHHHHHHHhcCCCceeCHHHHHHHHHHHHHHhcCccccc
Confidence            999  998644 4566765542110      000001111111   111 0 001 111111111111111110000   


Q ss_pred             --CCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhcC
Q psy5642         175 --SNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLVK  220 (237)
Q Consensus       175 --~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~~  220 (237)
                        .......++..+..+++-|...|..+.  ...|+.+|+..|++-++
T Consensus       439 ~~~~~~~giSpR~leaLiRlA~A~A~L~g--R~~V~~eDV~~Ai~L~~  484 (506)
T 3f8t_A          439 GMGLPTLPVTRRQLESVERLAKAHARMRL--SDDVEPEDVDIAAELVD  484 (506)
T ss_dssp             HTTCCCCCCCHHHHHHHHHHHHHHHHHTT--CSEECHHHHHHHHHHHH
T ss_pred             ccccccccccHHHHHHHHHHHHHHHHHcC--cCCCCHHHHHHHHHHHH
Confidence              001233444457788887777777766  44689999999987654

>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=95.15  E-value=0.033  Score=48.42  Aligned_cols=107  Identities=22%  Similarity=0.271  Sum_probs=55.0

Q ss_pred             CceEEEEEecccccccc-------------cChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHH
Q psy5642           6 GLTEVVESIGPELFRKY-------------VGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERV   72 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~-------------~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~   72 (237)
                      ...+|+.++|+.+-...             .|... .-...|..|.   .++|||||++.+-.               .+
T Consensus       187 ~~~~fv~v~~~~~~~~~~~~elfg~~~g~~tga~~-~~~g~~~~a~---~gtlfldei~~l~~---------------~~  247 (387)
T 1ny5_A          187 SKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVS-SKEGFFELAD---GGTLFLDEIGELSL---------------EA  247 (387)
T ss_dssp             TTSCEEEEETTTSCHHHHHHHHHCBCTTSSTTCCS-CBCCHHHHTT---TSEEEEESGGGCCH---------------HH
T ss_pred             CCCCeEEEecCCCCHHHHHHHhcCCCCCCCCCccc-ccCCceeeCC---CcEEEEcChhhCCH---------------HH
Confidence            45789999998753210             00000 0112334433   37999999999832               23


Q ss_pred             HHHHHHHhcCC-----CC----CCCEEEEEEeCCCCccchhccCCCCccc-------EEEecCCCH----HHHHHHHHHH
Q psy5642          73 LAQMLTEMDGI-----VP----LNNVTIVAATNRPDRIDKALLRPGRLDR-------LIYVPLPDD----LTRAAILKIR  132 (237)
Q Consensus        73 ~~~ll~~l~~~-----~~----~~~v~vI~ttn~~~~ld~al~r~gRf~~-------~i~~~~P~~----~~R~~il~~~  132 (237)
                      ...|+..|+.-     ..    ..++.+|++||.  .+...+ ..|+|..       .+.+..|..    ++...++.++
T Consensus       248 q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~--~l~~~~-~~g~fr~dl~~rl~~~~i~lPpLreR~~Di~~l~~~~  324 (387)
T 1ny5_A          248 QAKLLRVIESGKFYRLGGRKEIEVNVRILAATNR--NIKELV-KEGKFREDLYYRLGVIEIEIPPLRERKEDIIPLANHF  324 (387)
T ss_dssp             HHHHHHHHHHSEECCBTCCSBEECCCEEEEEESS--CHHHHH-HTTSSCHHHHHHHTTEEEECCCGGGCHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCcEEeCCCCceeeccEEEEEeCCC--CHHHHH-HcCCccHHHHHhhcCCeecCCcchhccccHHHHHHHH
Confidence            44455554421     11    124778999985  222222 2355531       244555554    4445555555


Q ss_pred             Hc
Q psy5642         133 LA  134 (237)
Q Consensus       133 l~  134 (237)
                      +.
T Consensus       325 l~  326 (387)
T 1ny5_A          325 LK  326 (387)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=95.09  E-value=0.015  Score=49.46  Aligned_cols=93  Identities=20%  Similarity=0.296  Sum_probs=51.4

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      .+.|+.+...+..+.+..+.+..+..+++......  +|+||+++.+..........+..   .+.+..++..|.++...
T Consensus       150 ~VlyIs~~~eE~v~~~~~~le~~l~~i~~~l~~~~--LLVIDsI~aL~~~~~~~s~~G~v---~~~lrqlL~~L~~~~k~  224 (331)
T 2vhj_A          150 KDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHR--VIVIDSLKNVIGAAGGNTTSGGI---SRGAFDLLSDIGAMAAS  224 (331)
T ss_dssp             TSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCS--EEEEECCTTTC-----------C---CHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEecchhhhhhhhcCHHHHHHHHHHHHhhCC--EEEEecccccccccccccccchH---HHHHHHHHHHHHHHHhh
Confidence            34555553334444455667778888888777654  99999999986544321111111   12344444444443333


Q ss_pred             CCEEEEEEeCCCCccchhc
Q psy5642          87 NNVTIVAATNRPDRIDKAL  105 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al  105 (237)
                      .++.+|+++| +...++++
T Consensus       225 ~gvtVIlttn-p~s~deal  242 (331)
T 2vhj_A          225 RGCVVIASLN-PTSNDDKI  242 (331)
T ss_dssp             HTCEEEEECC-CSSCSSSH
T ss_pred             CCCEEEEEeC-CcccchhH
Confidence            4677888888 56666654

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=91.88  E-value=0.09  Score=39.16  Aligned_cols=77  Identities=9%  Similarity=0.175  Sum_probs=42.9

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCC
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNN   88 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~   88 (237)
                      ..+++++.++...               +....|.+|+|||++.+....            +..+-.+++.+..   .+.
T Consensus        66 ~~~~~~~~~~~~~---------------~~~~~~~lLilDE~~~~~~~~------------~~~l~~li~~~~~---~g~  115 (149)
T 2kjq_A           66 NAAYIDAASMPLT---------------DAAFEAEYLAVDQVEKLGNEE------------QALLFSIFNRFRN---SGK  115 (149)
T ss_dssp             CEEEEETTTSCCC---------------GGGGGCSEEEEESTTCCCSHH------------HHHHHHHHHHHHH---HTC
T ss_pred             cEEEEcHHHhhHH---------------HHHhCCCEEEEeCccccChHH------------HHHHHHHHHHHHH---cCC
Confidence            3566677666543               112368899999998753221            2334444444332   223


Q ss_pred             E-EEEEEeC-CCCccc--hhccCCCCcccEEEec
Q psy5642          89 V-TIVAATN-RPDRID--KALLRPGRLDRLIYVP  118 (237)
Q Consensus        89 v-~vI~ttn-~~~~ld--~al~r~gRf~~~i~~~  118 (237)
                      . ++| ||+ .|..+.  +.+++  ||..-+.+.
T Consensus       116 ~~iii-ts~~~p~~l~~~~~L~S--Rl~~g~~~~  146 (149)
T 2kjq_A          116 GFLLL-GSEYTPQQLVIREDLRT--RMAYCLVYE  146 (149)
T ss_dssp             CEEEE-EESSCTTTSSCCHHHHH--HGGGSEECC
T ss_pred             cEEEE-ECCCCHHHccccHHHHH--HHhcCeeEE
Confidence            3 444 555 565454  78888  886555443

>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=91.47  E-value=0.74  Score=49.37  Aligned_cols=108  Identities=13%  Similarity=0.072  Sum_probs=70.2

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC---
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI---   83 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---   83 (237)
                      +.+++.++|++-++      ...+..+|..+... .+.++|||++.+-..-        -+.....+..+...+...   
T Consensus       670 g~~~v~~nc~e~ld------~~~lg~~~~g~~~~-Gaw~~~DE~nr~~~ev--------Ls~l~~~l~~i~~al~~~~~~  734 (2695)
T 4akg_A          670 GRVVVVFNCDDSFD------YQVLSRLLVGITQI-GAWGCFDEFNRLDEKV--------LSAVSANIQQIQNGLQVGKSH  734 (2695)
T ss_dssp             TCCCEEEETTSSCC------HHHHHHHHHHHHHH-TCEEEEETTTSSCHHH--------HHHHHHHHHHHHHHHHHTCSE
T ss_pred             CCcEEEEECCCCCC------hhHhhHHHHHHHhc-CCEeeehhhhhcChHH--------HHHHHHHHHHHHHHHHcCCcE
Confidence            45678888987665      46678888877764 5899999998763210        001111111222222111   


Q ss_pred             --------CCCCCEEEEEEeC----CCCccchhccCCCCcccEEEecCCCHHHHHHHHHHH
Q psy5642          84 --------VPLNNVTIVAATN----RPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIR  132 (237)
Q Consensus        84 --------~~~~~v~vI~ttn----~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~  132 (237)
                              .-..+..|++|.|    ....+|+++++  ||- .|.+..|+.+...+|+...
T Consensus       735 i~~~g~~i~l~~~~~vfiT~NPgy~g~~eLP~~Lk~--~Fr-~v~m~~Pd~~~i~ei~l~s  792 (2695)
T 4akg_A          735 ITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKK--SFR-EFSMKSPQSGTIAEMILQI  792 (2695)
T ss_dssp             EECSSSEEECCTTCEEEEEECCCSSSSCCCCHHHHT--TEE-EEECCCCCHHHHHHHHHHH
T ss_pred             EeeCCcEEecCCCceEEEEeCCCccCcccccHHHHh--heE-EEEeeCCCHHHHHHHHHHh
Confidence                    1123467888888    45689999999  995 6999999999888886543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=89.75  E-value=0.24  Score=51.60  Aligned_cols=71  Identities=18%  Similarity=0.284  Sum_probs=50.0

Q ss_pred             hHHHHHHHHHHHHHhcCCeEEEEcccccccccc---CCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeC
Q psy5642          25 ESERCVRDVFKRARQVSPSVIFFDELDSLAGER---GDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATN   96 (237)
Q Consensus        25 ~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~---~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn   96 (237)
                      ..++.++.++..++..+|++|+||+++.+.+..   +...++. .....++++.++..|.+.....+++||.|--
T Consensus      1489 ~~E~~l~~~~~lvr~~~~~lVVIDsi~al~p~~~~~g~~~~~~-~~~~~R~lsqlL~~L~~~~~~~~v~VI~tNq 1562 (2050)
T 3cmu_A         1489 TGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSH-MGLAARMMSQAMRKLAGNLKQSNTLLIFINQ 1562 (2050)
T ss_dssp             SHHHHHHHHHHHHHHTCCSEEEESCGGGCCCHHHHHSCTTCCC-TTHHHHHHHHHHHHHHHHHHTTTCEEEEEEC
T ss_pred             hHHHHHHHHHHHHhcCCCCEEEEcChhHhcccccccccccccc-cchHHHHHHHHHHHHHHHHHhCCcEEEEEcc
Confidence            457888889999999999999999999988743   1111111 1124678888888887766666776666643

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=89.31  E-value=0.65  Score=50.43  Aligned_cols=83  Identities=19%  Similarity=0.237  Sum_probs=54.4

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC-------CCCEEEEEEeCCC-----CccchhccCCCC
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP-------LNNVTIVAATNRP-----DRIDKALLRPGR  110 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-------~~~v~vI~ttn~~-----~~ld~al~r~gR  110 (237)
                      .|+||||++--..+.-+.      .....++..+++.=.-+..       -.++.+|||.|.|     ..|+++++|  |
T Consensus      1376 ~VlFiDDiNmp~~D~yGt------Q~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp~~gGr~~l~~Rf~r--~ 1447 (3245)
T 3vkg_A         1376 LVVFCDEINLPSTDKYGT------QRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLR--H 1447 (3245)
T ss_dssp             EEEEETTTTCCCCCTTSC------CHHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECCTTSTTCCCCCHHHHT--T
T ss_pred             EEEEecccCCCCcccccc------ccHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCCCCCCCccCCHHHHh--h
Confidence            599999998533222111      1123444444443110111       1358899999987     469999999  9


Q ss_pred             cccEEEecCCCHHHHHHHHHHHHc
Q psy5642         111 LDRLIYVPLPDDLTRAAILKIRLA  134 (237)
Q Consensus       111 f~~~i~~~~P~~~~R~~il~~~l~  134 (237)
                      |.. ++++.|+.++-..|+..++.
T Consensus      1448 F~v-i~i~~ps~esL~~If~til~ 1470 (3245)
T 3vkg_A         1448 API-LLVDFPSTSSLTQIYGTFNR 1470 (3245)
T ss_dssp             CCE-EECCCCCHHHHHHHHHHHHH
T ss_pred             ceE-EEeCCCCHHHHHHHHHHHHH
Confidence            964 99999999999999876543

>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=88.26  E-value=5.7  Score=33.92  Aligned_cols=125  Identities=12%  Similarity=0.034  Sum_probs=72.3

Q ss_pred             eEEEEEecccccccccChH----HHHHHHHHHHHHh--cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           8 TEVVESIGPELFRKYVGES----ERCVRDVFKRARQ--VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~----~~~l~~~f~~a~~--~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      .+++.++-+.|.+....-.    -..+..+|..+..  ..|.++++||++.++....        ......+..++....
T Consensus       223 ~~~vv~dl~~l~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~~~i~iDEa~~~~~~~~--------~~~~~~l~~~~~~~R  294 (392)
T 4ag6_A          223 SDFIVFDVHDLQNAEDQVKRAQYFNVLSFAWNILERDRRERTVLVVDEAWMLVDPQT--------PQAIAFLRDTSKRIR  294 (392)
T ss_dssp             SSEEEEECGGGTTSCHHHHHHHHHHHHHHHHHHHHHSCCTTCEEEETTGGGGCCTTC--------THHHHHHHHHHHHGG
T ss_pred             CCEEEEEchhhhcCCHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEecHHHHhCcCc--------hHHHHHHHHHHHHhh
Confidence            4677777777764210000    1234445555554  3589999999999986321        122334444444444


Q ss_pred             CCCCCCCEEEEEEeCCCCccch--------hccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCC
Q psy5642          82 GIVPLNNVTIVAATNRPDRIDK--------ALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTE  152 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn~~~~ld~--------al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~  152 (237)
                      .    .++.++.+|-++.++..        +++.  ..+..|.++.+. .++..+ ...+.   + ++...+.|.....
T Consensus       295 k----~g~~~~~~tQ~~~d~~~~~~~~~~~~il~--n~~~~i~l~~~~-~~~~~~-~~~~~---l-s~~e~~~l~~~~~  361 (392)
T 4ag6_A          295 K----YNGSLIVISQNVIDFLAPEVQRYGQALLD--NPTYKLLLAQGE-KDLEAI-TTLMN---L-SEAEHDLLVNAKR  361 (392)
T ss_dssp             G----GTCEEEEEESCGGGGGSTTTHHHHHHHHH--SCSEEEECSCCH-HHHHHH-HHHTT---C-CHHHHHHHHTCCT
T ss_pred             h----hCeEEEEEcCCHHHhhChhhHHHHHHHHH--hhhhhheeCCCh-hhHHHH-HHHhC---C-CHHHHHhccCCCC
Confidence            3    35677888888888864        5666  667788888764 444444 33333   3 3455555555443

>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=85.97  E-value=0.82  Score=39.20  Aligned_cols=75  Identities=21%  Similarity=0.373  Sum_probs=42.4

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC-----CCC----CCEEEEEEeCCCCccchhccCCCCcc
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI-----VPL----NNVTIVAATNRPDRIDKALLRPGRLD  112 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-----~~~----~~v~vI~ttn~~~~ld~al~r~gRf~  112 (237)
                      ..+||||||+.+-.               .+...|+..|+.-     -..    -++-+|++||.  ++...+. .|+|.
T Consensus       223 ~gtlfldei~~l~~---------------~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~--~l~~~v~-~g~fr  284 (368)
T 3dzd_A          223 QGTLFLDEVGELDQ---------------RVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNK--NLEEEIK-KGNFR  284 (368)
T ss_dssp             TSEEEEETGGGSCH---------------HHHHHHHHHHHHSEECCBTCCCBEECCCEEEEEESS--CHHHHHH-TTSSC
T ss_pred             CCeEEecChhhCCH---------------HHHHHHHHHHHhCCcccCCCCcceeeeeEEEEecCC--CHHHHHH-cCCcc
Confidence            36899999999822               2345555555421     111    14678888884  3333333 35664


Q ss_pred             c---------EEEecCCCH--HHHHHHHHHHHc
Q psy5642         113 R---------LIYVPLPDD--LTRAAILKIRLA  134 (237)
Q Consensus       113 ~---------~i~~~~P~~--~~R~~il~~~l~  134 (237)
                      .         .|++|+...  ++...++.+++.
T Consensus       285 ~dL~~rl~~~~i~lPpLreR~~Di~~l~~~~l~  317 (368)
T 3dzd_A          285 EDLYYRLSVFQIYLPPLRERGKDVILLAEYFLK  317 (368)
T ss_dssp             HHHHHHHTSEEEECCCGGGSTTHHHHHHHHHHH
T ss_pred             HHHHHHhCCeEEeCCChhhchhhHHHHHHHHHH
Confidence            3         455555544  556666666664

>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=85.55  E-value=5.9  Score=29.97  Aligned_cols=67  Identities=21%  Similarity=0.205  Sum_probs=37.9

Q ss_pred             HhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEe--CCCCccchhccCCCCcc-cE
Q psy5642          38 RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAAT--NRPDRIDKALLRPGRLD-RL  114 (237)
Q Consensus        38 ~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~tt--n~~~~ld~al~r~gRf~-~~  114 (237)
                      ....|.+|++||++-...-         +   ......+...+..    .+..+|.++  ++...+-..+.+  |-+ .+
T Consensus        96 l~~~p~llilDEigp~~~l---------d---~~~~~~l~~~l~~----~~~~~i~~~H~~h~~~~~~~i~~--r~~~~i  157 (178)
T 1ye8_A           96 KKDRRKVIIIDEIGKMELF---------S---KKFRDLVRQIMHD----PNVNVVATIPIRDVHPLVKEIRR--LPGAVL  157 (178)
T ss_dssp             HHCTTCEEEECCCSTTGGG---------C---HHHHHHHHHHHTC----TTSEEEEECCSSCCSHHHHHHHT--CTTCEE
T ss_pred             cccCCCEEEEeCCCCcccC---------C---HHHHHHHHHHHhc----CCCeEEEEEccCCCchHHHHHHh--cCCcEE
Confidence            5678999999997633221         1   2334555566655    233355555  344445455666  543 45


Q ss_pred             EEecCCCH
Q psy5642         115 IYVPLPDD  122 (237)
Q Consensus       115 i~~~~P~~  122 (237)
                      +++...+.
T Consensus       158 ~~~~~~~r  165 (178)
T 1ye8_A          158 IELTPENR  165 (178)
T ss_dssp             EECCTTTT
T ss_pred             EEecCcCH
Confidence            67766654

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=82.65  E-value=0.35  Score=41.84  Aligned_cols=69  Identities=16%  Similarity=0.338  Sum_probs=45.5

Q ss_pred             cCCeEEEEcccccccc-ccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEec
Q psy5642          40 VSPSVIFFDELDSLAG-ERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVP  118 (237)
Q Consensus        40 ~~P~il~iDeid~l~~-~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~  118 (237)
                      .+..++++||++.+.. .+.-...   ...  .....+.+.+++     .+.|+++||+++.+ +++.+|||++..++..
T Consensus       215 ~q~~~~l~dd~~~~~~~~r~l~~~---~~~--~~~~~l~~~ldG-----~v~v~~~tn~~~~l-~alf~pg~ld~~~~~l  283 (377)
T 1svm_A          215 IDQFLVVFEDVKGTGGESRDLPSG---QGI--NNLDNLRDYLDG-----SVKVNLEKKHLNKR-TQIFPPGIVTMNEYSV  283 (377)
T ss_dssp             TTCSCEEETTCCCSTTTTTTCCCC---SHH--HHHHTTHHHHHC-----SSCEEECCSSSCCE-EECCCCEEEEECSCCC
T ss_pred             cchhHHHHHHHHHHHHHHhhcccc---Ccc--hHHHHHHHHhcC-----CCeEeeccCchhhH-HHhhcCcccChhHHhh
Confidence            4567889999998875 2221110   110  122445555655     34678899999999 7899999998877665


Q ss_pred             C
Q psy5642         119 L  119 (237)
Q Consensus       119 ~  119 (237)
                      +
T Consensus       284 ~  284 (377)
T 1svm_A          284 P  284 (377)
T ss_dssp             C
T ss_pred             c
Confidence            5

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=80.26  E-value=2.3  Score=38.80  Aligned_cols=74  Identities=18%  Similarity=0.319  Sum_probs=53.2

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCC--ccchhccCCCCcccEEEecCC
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPD--RIDKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~--~ld~al~r~gRf~~~i~~~~P  120 (237)
                      .+|+|||+..++....           ..+ ...+..|-..-..-+|.+|.+|.+|+  .|+..++.  -|...|-+...
T Consensus       345 ivvVIDE~~~L~~~~~-----------~~~-~~~L~~Iar~GRa~GIhLIlaTQRPs~d~I~~~Ira--n~~~RI~lrv~  410 (574)
T 2iut_A          345 IVVVVDEFADMMMIVG-----------KKV-EELIARIAQKARAAGIHLILATQRPSVDVITGLIKA--NIPTRIAFQVS  410 (574)
T ss_dssp             EEEEESCCTTHHHHTC-----------HHH-HHHHHHHHHHCTTTTEEEEEEESCCCTTTSCHHHHH--TCCEEEEECCS
T ss_pred             EEEEEeCHHHHhhhhh-----------HHH-HHHHHHHHHHHhhCCeEEEEEecCcccccccHHHHh--hhccEEEEEcC
Confidence            5999999998875321           112 22233222222335799999999988  89999998  89889999999


Q ss_pred             CHHHHHHHHH
Q psy5642         121 DDLTRAAILK  130 (237)
Q Consensus       121 ~~~~R~~il~  130 (237)
                      +..+...+|-
T Consensus       411 s~~Dsr~ILd  420 (574)
T 2iut_A          411 SKIDSRTILD  420 (574)
T ss_dssp             CHHHHHHHHS
T ss_pred             CHHHHHHhcC
Confidence            9988888873

---

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	237
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	3e-62
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	6e-62
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	3e-42
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	3e-34
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	2e-24
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	2e-16
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	6e-15
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	1e-14
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	7e-07

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]} Length = 247

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

 Score =  193 bits (491), Expect = 3e-62
 Identities = 68/201 (33%), Positives = 102/201 (50%), Gaps = 30/201 (14%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           G +    +VG     VRD+F+ A++ +P ++F DE+D++  +RG G GGG ++ +E+ L 
Sbjct: 75  GSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGG-NDEREQTLN 133

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+L EMDG      + ++AATNRPD +D ALLRPGR DR I +  PD   R  IL+I   
Sbjct: 134 QLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHAR 193

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
             PL EDV +  L + T G+ GA+                           +  + +EAA
Sbjct: 194 GKPLAEDVDLALLAKRTPGFVGAD---------------------------LENLLNEAA 226

Query: 195 LSALENNLEAAYVSHQDFLTA 215
           L A         ++ +D   A
Sbjct: 227 LLAAREGRRK--ITMKDLEEA 245

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]} Length = 256

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

 Score =  192 bits (489), Expect = 6e-62
 Identities = 74/205 (36%), Positives = 106/205 (51%), Gaps = 30/205 (14%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           G +    +VG     VRD+F++A++ +P +IF DE+D++  +RG G GGG  + +E+ L 
Sbjct: 78  GSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGG-HDEREQTLN 136

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           QML EMDG      + ++AATNRPD +D ALLRPGR DR + V LPD   R  ILK+ + 
Sbjct: 137 QMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMR 196

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
           R PL  D+    + R T G+SGA+                           +  + +EAA
Sbjct: 197 RVPLAPDIDAAIIARGTPGFSGAD---------------------------LANLVNEAA 229

Query: 195 LSALENNLEAAYVSHQDFLTALQLV 219
           L A   N     VS  +F  A   +
Sbjct: 230 LFAARGNKRV--VSMVEFEKAKDKI 252

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 265

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  142 bits (358), Expect = 3e-42
 Identities = 86/200 (43%), Positives = 119/200 (59%), Gaps = 28/200 (14%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPEL   + GESE  VR++F +ARQ +P V+FFDELDS+A  RG   G GG    +RV+ 
Sbjct: 74  GPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGG-AADRVIN 132

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LTEMDG+    NV I+ ATNRPD ID A+LRPGRLD+LIY+PLPD+ +R AILK  L 
Sbjct: 133 QILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLR 192

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
           +SP+ +DV +E L ++T G+SGA+                           +  +C  A 
Sbjct: 193 KSPVAKDVDLEFLAKMTNGFSGAD---------------------------LTEICQRAC 225

Query: 195 LSALENNLEAAYVSHQDFLT 214
             A+  ++E+     ++  T
Sbjct: 226 KLAIRESIESEIRRERERQT 245

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]} Length = 321

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

 Score =  122 bits (308), Expect = 3e-34
 Identities = 23/124 (18%), Positives = 41/124 (33%), Gaps = 8/124 (6%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
             E    Y  +    V D+ +   Q    VI  D L ++ G  G     GG     R   
Sbjct: 158 FGEPLSGYNTDFNVFVDDIARAMLQ--HRVIVIDSLKNVIGAAGGNTTSGGI---SRGAF 212

Query: 75  QMLTEMDGIVPLNNVTIVAATNR---PDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKI 131
            +L+++  +       ++A+ N     D+I + +    R +    V   D      +L  
Sbjct: 213 DLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTR 272

Query: 132 RLAR 135
               
Sbjct: 273 TGEG 276

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 258

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 95.9 bits (237), Expect = 2e-24
 Identities = 71/218 (32%), Positives = 107/218 (49%), Gaps = 46/218 (21%)

Query: 15  GPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLA 74
           GPE+  K  GESE  +R  F+ A + +P++IF DELD++A +R    G     V+ R+++
Sbjct: 71  GPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGE----VERRIVS 126

Query: 75  QMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLA 134
           Q+LT MDG+    +V ++AATNRP+ ID AL R GR DR + + +PD   R  IL+I   
Sbjct: 127 QLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTK 186

Query: 135 RSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAA 194
              L +DV +E++   T G+ GA+                           + A+C EAA
Sbjct: 187 NMKLADDVDLEQVANETHGHVGAD---------------------------LAALCSEAA 219

Query: 195 LSALENNLEAAY---------------VSHQDFLTALQ 217
           L A+   ++                  V+  DF  AL 
Sbjct: 220 LQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALS 257

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]} Length = 273

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

 Score = 74.2 bits (181), Expect = 2e-16
 Identities = 24/225 (10%), Positives = 53/225 (23%), Gaps = 41/225 (18%)

Query: 17  ELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQER-VLAQ 75
           +    +    +   +DV K     S  +                  G G         A 
Sbjct: 70  QQHPNFDELVKLYEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTDVPIQTAT 129

Query: 76  ML------TEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAIL 129
           ML      T+M  +      + +    R + +        R        +        + 
Sbjct: 130 MLQAKGYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVKNLPTNLE 189

Query: 130 KIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAV 189
              L ++ L  D+ +       + YS  E                             ++
Sbjct: 190 T--LHKTGLFSDIRL-YNREGVKLYSSLE---------------------------TPSI 219

Query: 190 CDEAALSALENNLEAAYVSHQDFLTALQLVKPRTPPQLIKLYENY 234
             +  L    N      VS ++    L+ ++ +      +    +
Sbjct: 220 SPKETLEKELNR----KVSGKEIQPTLERIEQKMVLNKHQETPEF 260

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]} Length = 362

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

 Score = 70.9 bits (173), Expect = 6e-15
 Identities = 21/158 (13%), Positives = 39/158 (24%), Gaps = 24/158 (15%)

Query: 9   EVVESIGPELFRKY-VGESERCVRDVFKRARQVS------PSVIFFDELDSLAGERGDGG 61
           + +    P     + +G +      VF+  +         PS    + LD+L     DG 
Sbjct: 181 KALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYL-DGS 239

Query: 62  GGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPD 121
                  +       +              +   N             R  + I     D
Sbjct: 240 VKVNLEKKHLNKRTQIFPP----------GIVTMN---EYSVPKTLQARFVKQIDFRPKD 286

Query: 122 DLTRAA-ILKIRLARSPLGEDVCVEELVRLTEGYSGAE 158
            L       +  L +  +     +  L+ L      AE
Sbjct: 287 YLKHCLERSEFLLEKRIIQSG--IALLLMLIWYRPVAE 322

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]} Length = 246

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

 Score = 68.4 bits (166), Expect = 1e-14
 Identities = 22/144 (15%), Positives = 50/144 (34%), Gaps = 11/144 (7%)

Query: 15  GPELFRKYVGESE-RCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVL 73
            P+    +   ++ + ++ +F  A +   S +  D+++ L      G           VL
Sbjct: 73  SPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIG-----PRFSNLVL 127

Query: 74  AQMLTEMDGIVPLNNVTI-VAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIR 132
             +L  +    P     + +  T+R D + +  +        I+VP     T   +L+  
Sbjct: 128 QALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEML-NAFSTTIHVPNIA--TGEQLLEA- 183

Query: 133 LARSPLGEDVCVEELVRLTEGYSG 156
           L      +D     + +  +G   
Sbjct: 184 LELLGNFKDKERTTIAQQVKGKKV 207

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 309

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]

 Score = 46.8 bits (110), Expect = 7e-07
 Identities = 24/132 (18%), Positives = 44/132 (33%), Gaps = 22/132 (16%)

Query: 21  KYVGESERCVRDVFKRARQV-----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQ 75
               E +  +RD+   A           ++F DE+D +  +    G        E V   
Sbjct: 90  YVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGADVSR---EGVQRD 146

Query: 76  MLTEMDG--------IVPLNNVTIVAA----TNRPDRIDKALLRPGRLDRLIYVPLPDDL 123
           +L  ++G        +V  +++  +A+      RP  +   L   GRL   + +      
Sbjct: 147 LLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQ--GRLPIRVELTALSAA 204

Query: 124 TRAAILKIRLAR 135
               IL    A 
Sbjct: 205 DFERILTEPHAS 216

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	237
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	100.0
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	100.0
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.98
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.79
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.73
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.27
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.04
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.89
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.71
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.64
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.59
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.58
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.54
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.48
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.46
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.29
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.28
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	98.27
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.07
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.05
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.97
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	97.94
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.9
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.85
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.42
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	97.17
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	97.01
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.99
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	94.32
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.49
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	92.22
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.14
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	84.65
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	82.95

>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=100.00  E-value=9.6e-37  Score=253.00  Aligned_cols=183  Identities=40%  Similarity=0.658  Sum_probs=168.5

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCC
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPL   86 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~   86 (237)
                      +++++.++++++.++|+|+++++++.+|+.|+.++||||||||+|.++.+++...... .....++++.|+.+|+++..+
T Consensus        70 ~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~-~~~~~~~~~~ll~~~d~~~~~  148 (256)
T d1lv7a_          70 KVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGG-HDEREQTLNQMLVEMDGFEGN  148 (256)
T ss_dssp             TCCEEEECSCSSTTSCCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCT-TCHHHHHHHHHHHHHHTCCSS
T ss_pred             CCCEEEEEhHHhhhcchhHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCC-cHHHHHHHHHHHHHhhCCCCC
Confidence            6899999999999999999999999999999999999999999999998876554433 345578899999999998888


Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      ++|+||||||+|+.||++++||||||+.|+|++|+.++|.+||+.++++.++..+.++..+|..|+||+++|        
T Consensus       149 ~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~ad--------  220 (256)
T d1lv7a_         149 EGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGAD--------  220 (256)
T ss_dssp             SCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHH--------
T ss_pred             CCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCcccCHHHHHHhCCCCCHHH--------
Confidence            889999999999999999999999999999999999999999999999998888999999999999999999        


Q ss_pred             hhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhc
Q psy5642         167 KKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLV  219 (237)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~  219 (237)
                                         |.+++++|...+.+++  ...++.+||..|++.+
T Consensus       221 -------------------i~~l~~~A~~~a~~~~--~~~i~~~d~~~Al~rv  252 (256)
T d1lv7a_         221 -------------------LANLVNEAALFAARGN--KRVVSMVEFEKAKDKI  252 (256)
T ss_dssp             -------------------HHHHHHHHHHHHHHTT--CSSBCHHHHHHHHHHH
T ss_pred             -------------------HHHHHHHHHHHHHHcC--CCccCHHHHHHHHHHH
Confidence                               9999999999888776  4569999999999864

>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=100.00  E-value=2.3e-36  Score=249.66  Aligned_cols=181  Identities=38%  Similarity=0.632  Sum_probs=161.2

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+++++.+++++|.++|+|+++++++++|+.|+.++||||||||+|.++.+++...... +....++++.|+.+|+++..
T Consensus        66 ~~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~-~~~~~~~~~~ll~~~d~~~~  144 (247)
T d1ixza_          66 ARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGG-NDEREQTLNQLLVEMDGFEK  144 (247)
T ss_dssp             TTCCEEEEEHHHHHHSCTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC----------CHHHHHHHHHHHHHHHTCCT
T ss_pred             cCCCEEEEEhHHhhhccccHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCC-cHHHHHHHHHHHHHhhCCCC
Confidence            36899999999999999999999999999999999999999999999998876654432 34567899999999999988


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      +.+|+||||||+|+.||++++|||||+++|+|++|+.++|.+||+.++.+.+...+.++..+|+.|+||+++|       
T Consensus       145 ~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~d-------  217 (247)
T d1ixza_         145 DTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGAD-------  217 (247)
T ss_dssp             TCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHH-------
T ss_pred             CCCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCccccCHHHHHHHCCCCCHHH-------
Confidence            8899999999999999999999999999999999999999999999999888888999999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHH
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTAL  216 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al  216 (237)
                                          |.++|++|...+++++  ...|+.+||..|+
T Consensus       218 --------------------i~~lv~~A~l~a~~~~--~~~i~~~d~~~A~  246 (247)
T d1ixza_         218 --------------------LENLLNEAALLAAREG--RRKITMKDLEEAA  246 (247)
T ss_dssp             --------------------HHHHHHHHHHHHHHTT--CSSBCHHHHHHHT
T ss_pred             --------------------HHHHHHHHHHHHHHcC--CCCcCHHHHHHhh
Confidence                                9999999999888876  4579999999986

>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=100.00  E-value=5.4e-35  Score=243.01  Aligned_cols=182  Identities=38%  Similarity=0.586  Sum_probs=162.8

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .+.+|+.++++++.+.|+|+++++++.+|..|..++||||||||+|.++.++....    ++...++++.++..++....
T Consensus        62 ~~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~----~~~~~~~~~~~~~~~~~~~~  137 (258)
T d1e32a2          62 TGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTH----GEVERRIVSQLLTLMDGLKQ  137 (258)
T ss_dssp             TTCEEEEECHHHHTTSCTTHHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCC----CTTHHHHHHHHHHHHHTCCC
T ss_pred             hCCeEEEEEchhhcccccccHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCC----CchHHHHHHHhccccccccc
Confidence            57899999999999999999999999999999999999999999999998876543    23346788999999999888


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      ..+|+||||||+|+.+|++++||||||++|+|++|+.++|.+||+.++++.++..+.++..||++|+||||+|       
T Consensus       138 ~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~ad-------  210 (258)
T d1e32a2         138 RAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGAD-------  210 (258)
T ss_dssp             SSCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTCCHHHHHHHCTTCCHHH-------
T ss_pred             cCCccEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccccccchhhhhhcccCCCHHH-------
Confidence            8899999999999999999999999999999999999999999999999888888899999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhcc---------------ccCCccHHHHHHHHhh
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNL---------------EAAYVSHQDFLTALQL  218 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~---------------~~~~v~~~df~~al~~  218 (237)
                                          |.++|++|...++++..               ...+|+++||..||++
T Consensus       211 --------------------l~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~it~~Df~~AL~~  258 (258)
T d1e32a2         211 --------------------LAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQ  258 (258)
T ss_dssp             --------------------HHHHHHHHHHHHHHHHHHHHCCCSSCCBHHHHHHCCBCHHHHHHHHTC
T ss_pred             --------------------HHHHHHHHHHHHHHhhccccchhhhhhhhhhhccCccCHHHHHHHhCc
Confidence                                77788777777665431               2357999999999864

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.98  E-value=6.6e-33  Score=231.12  Aligned_cols=168  Identities=49%  Similarity=0.850  Sum_probs=141.7

Q ss_pred             CceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      .++||+.++++++.+.|.|+++..++.+|..|+.++||||+|||+|.++.+++....+. .....++++.++.+|+++..
T Consensus        65 ~~~~~~~~~~~~l~~~~~~~~~~~l~~~f~~A~~~~p~il~ideid~l~~~~~~~~~~~-~~~~~~~~~~ll~~l~~~~~  143 (265)
T d1r7ra3          65 CQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDG-GGAADRVINQILTEMDGMST  143 (265)
T ss_dssp             TTCEEEEECHHHHHTSCTTTHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTT-HHHHHHHHHHHHHTCC----
T ss_pred             hCCcEEEEEHHHhhhccccchHHHHHHHHHHHHhcCCcceeHHhhhhccccCCCcCCCC-cHHHHHHHHHHHHHhhCcCC
Confidence            47899999999999999999999999999999999999999999999998775543322 23346788999999999888


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHH
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      +.+++||||||+|+.||++++|+|||+++|+|++|+.++|.+||+.++++.....+.++..+|.+|+|||++|       
T Consensus       144 ~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~g~s~~d-------  216 (265)
T d1r7ra3         144 KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGAD-------  216 (265)
T ss_dssp             --CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC----CCCCHHHHHHHCSSCCHH-------
T ss_pred             CCCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCchhhhhHHHHHhcCCCCCHHH-------
Confidence            7889999999999999999999999999999999999999999999999888778899999999999999999       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhc
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENN  201 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~  201 (237)
                                          |.++|++|...++++.
T Consensus       217 --------------------i~~lv~~A~~~A~~~~  232 (265)
T d1r7ra3         217 --------------------LTEICQRACKLAIRES  232 (265)
T ss_dssp             --------------------HHHHHHHHHHHHHHHC
T ss_pred             --------------------HHHHHHHHHHHHHHHH
Confidence                                7777777776666554

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=99.79  E-value=3.1e-22  Score=169.06  Aligned_cols=127  Identities=20%  Similarity=0.218  Sum_probs=102.2

Q ss_pred             CCceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      +++.+|+.+++++++++|+|+++++++.+|+.|+.  ||||||||||.+.+.+..+..++.   ..++++++|..||++.
T Consensus       148 ~~~~~~~~~~~~~~~~~~~G~~e~~~~~~f~~a~~--~~ilf~DEid~~~~~r~~~~~~~~---~~r~v~~lL~e~dg~~  222 (321)
T d1w44a_         148 GGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQ--HRVIVIDSLKNVIGAAGGNTTSGG---ISRGAFDLLSDIGAMA  222 (321)
T ss_dssp             HTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHH--CSEEEEECCTTTC--------------CCHHHHHHHHHHHHHH
T ss_pred             cCCCCeEEEEhhHhhhcccchHHHHHHHHHHHHhh--ccEEEeehhhhhccccccCCCCCc---chhhhhhhhhhccccc
Confidence            35678999999999999999999999999999985  899999999999998866544322   2579999999999988


Q ss_pred             CCCCEEEEEEeCC---CCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC
Q psy5642          85 PLNNVTIVAATNR---PDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS  136 (237)
Q Consensus        85 ~~~~v~vI~ttn~---~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~  136 (237)
                      ...+|+||||||.   +..+++++.|||||+..+++++|+.+.|.+||+.+....
T Consensus       223 ~~~~v~viaatN~~~~~~~i~~~~~r~~Rf~~~v~v~~pd~~~r~~il~~~~~~~  277 (321)
T d1w44a_         223 ASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGL  277 (321)
T ss_dssp             HHHTCEEEEECCCCCCCHHHHHHHHHHHHHSCSEEEEECSSTTEEEEEEECBTTC
T ss_pred             cCCCeEEEEeCCCcccccchhhhhhccCcccceeecCCCChHHHHHHHHHhccCc
Confidence            7778999999994   234566678999999999999999999999987666544

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=99.73  E-value=9.9e-18  Score=137.07  Aligned_cols=143  Identities=15%  Similarity=0.179  Sum_probs=109.4

Q ss_pred             CceEEEEEecccccccccChH-HHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC
Q psy5642           6 GLTEVVESIGPELFRKYVGES-ERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV   84 (237)
Q Consensus         6 ~~~~~i~v~~s~l~~~~~g~~-~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~   84 (237)
                      .+.+|+.+++++++.++.+.. .+.++.+|+.|+..+||||||||+|.++..+....     ...+++++.++..+++..
T Consensus        64 ~~~~~~~i~~~~~~~g~~~~~~~~~i~~if~~A~~~~p~il~iDEid~l~~~~~~~~-----~~~~~~~~~ll~~l~~~~  138 (246)
T d1d2na_          64 SNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGP-----RFSNLVLQALLVLLKKAP  138 (246)
T ss_dssp             HTCSEEEEECGGGCTTCCHHHHHHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTTT-----BCCHHHHHHHHHHTTCCC
T ss_pred             ccccccccccccccccccccchhhhhhhhhhhhhhcccceeehhhhhhHhhhccccc-----chhHHHHHHHHHHhcCCC
Confidence            367999999998888777766 47899999999999999999999999987654422     222678889999999876


Q ss_pred             CCC-CEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCcc
Q psy5642          85 PLN-NVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGA  157 (237)
Q Consensus        85 ~~~-~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~  157 (237)
                      ..+ +|+||||||+++.+|++.++ +||+..|++|  +..+|.++++.+... ....+.++..++..+.|.+..
T Consensus       139 ~~~~~v~vi~tTn~~~~ld~~~~~-~rF~~~i~~P--~~~~r~~il~~l~~~-~~~~~~~~~~i~~~~~g~~~~  208 (246)
T d1d2na_         139 PQGRKLLIIGTTSRKDVLQEMEML-NAFSTTIHVP--NIATGEQLLEALELL-GNFKDKERTTIAQQVKGKKVW  208 (246)
T ss_dssp             STTCEEEEEEEESCHHHHHHTTCT-TTSSEEEECC--CEEEHHHHHHHHHHH-TCSCHHHHHHHHHHHTTSEEE
T ss_pred             ccccceeeeeccCChhhccchhhc-CccceEEecC--CchhHHHHHHHHHhc-cCCChHHHHHHHHHcCCCccc
Confidence            543 69999999999999976443 4999999884  444555666544332 223577888899998886644

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=99.27  E-value=3.3e-12  Score=107.12  Aligned_cols=121  Identities=17%  Similarity=0.237  Sum_probs=97.2

Q ss_pred             ceEEEEEeccccc--ccccChHHHHHHHHHHHHHhc-----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHH
Q psy5642           7 LTEVVESIGPELF--RKYVGESERCVRDVFKRARQV-----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTE   79 (237)
Q Consensus         7 ~~~~i~v~~s~l~--~~~~g~~~~~l~~~f~~a~~~-----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~   79 (237)
                      +.+|+.++++.+.  +.|.|++++.++.+|..|...     +||||||||+|.+++.+.....   ......+++.||+.
T Consensus        74 ~~~~~~i~~s~~~~~~~~~~~~~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~~~~~~~~---~~~~~gv~~~LL~~  150 (309)
T d1ofha_          74 NAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGA---DVSREGVQRDLLPL  150 (309)
T ss_dssp             TCCEEEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSS---HHHHHHHHHHHHHH
T ss_pred             ccchhcccccccccceeEeeeccccccccchhhhcccccccCCceEEehhhhhhhhhccCccc---chhhhHHHHHhhHH
Confidence            4689999999997  568999999999999998653     6899999999999876654431   12234578889999


Q ss_pred             hcCCC--------CCCCEEEEEE----eCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHH
Q psy5642          80 MDGIV--------PLNNVTIVAA----TNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIR  132 (237)
Q Consensus        80 l~~~~--------~~~~v~vI~t----tn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~  132 (237)
                      +++..        ..+++++|++    ++.++.++|+++.  ||+.++.++.|+..++.+|+..+
T Consensus       151 ~dg~~~~~~~~~i~~s~ilfi~~ga~~~~~~~~~~p~l~~--R~~~~i~~~~~~~~~~~~Il~~~  213 (309)
T d1ofha_         151 VEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEP  213 (309)
T ss_dssp             HHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSS
T ss_pred             hcCCEEecCCeEEEccceeEEeccchhhcCcccchhhhhh--hhheeeeccCCCHHHHHHHHHHH
Confidence            99743        1235677777    5788899999997  99999999999999999998643

>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=99.04  E-value=7.3e-10  Score=90.45  Aligned_cols=180  Identities=19%  Similarity=0.247  Sum_probs=123.0

Q ss_pred             CCceEEEEEecccccc--cccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcC
Q psy5642           5 GGLTEVVESIGPELFR--KYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDG   82 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~--~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~   82 (237)
                      ..+.+++.++.+.|..  +|.|+-+..++.+++.+....+.||||||++.|+......+.          ...+.+.|..
T Consensus        72 l~~~~i~~l~~~~liag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~----------~~d~a~~Lkp  141 (268)
T d1r6bx2          72 MADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGG----------QVDAANLIKP  141 (268)
T ss_dssp             GTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSC----------HHHHHHHHSS
T ss_pred             cccceeEEeeechHhccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCc----------cccHHHHhhH
Confidence            3567899999999986  889999999999999999988899999999999876544331          1234444555


Q ss_pred             CCCCCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC----CCC-chhhHHHHHHHCC
Q psy5642          83 IVPLNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS----PLG-EDVCVEELVRLTE  152 (237)
Q Consensus        83 ~~~~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~----~~~-~~~~~~~la~~t~  152 (237)
                      +-.++.+-+||+|...+     +-|++|.|  ||. .|.+..|+.++-..||+.+...+    .+. .+..+..+...+.
T Consensus       142 ~L~rg~i~vIgatT~eey~~~~e~d~al~r--rF~-~I~V~Eps~e~t~~IL~~~~~~~e~~h~v~~~~~al~~~v~ls~  218 (268)
T d1r6bx2         142 LLSSGKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAV  218 (268)
T ss_dssp             CSSSCCCEEEEEECHHHHHCCCCCTTSSGG--GEE-EEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHH
T ss_pred             HHhCCCCeEEEeCCHHHHHHHHhhcHHHHh--hhc-ccccCCCCHHHHHHHHHHhhHHHhccCCEEeChHHHHHHHHHHH
Confidence            55568899999987533     56899999  997 59999999999999998655332    222 5666666666666


Q ss_pred             CCCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhc--cccCCccHHHHHHHHhhc
Q psy5642         153 GYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENN--LEAAYVSHQDFLTALQLV  219 (237)
Q Consensus       153 g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~--~~~~~v~~~df~~al~~~  219 (237)
                      .|-+.-  .+-+.                    -..+..+|........  .....++.+|+...+..+
T Consensus       219 ryi~~~--~~PdK--------------------AIdllDea~a~~~~~~~~~~~~~i~~~di~~~i~~~  265 (268)
T d1r6bx2         219 KYINDR--HLPDK--------------------AIDVIDEAGARARLMPVSKRKKTVNVADIESVVARI  265 (268)
T ss_dssp             HHCTTS--CTTHH--------------------HHHHHHHHHHHHHHSSSCCCCCSCCHHHHHHHHHHH
T ss_pred             hhccCC--CCCcH--------------------HHHHHHHHHHHHHhhccccCcccCCHHHHHHHHHHH
Confidence            555533  11111                    3335555544433222  224468888887766654

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=98.89  E-value=2.8e-08  Score=78.97  Aligned_cols=158  Identities=15%  Similarity=0.228  Sum_probs=106.2

Q ss_pred             ceEEEEEecccccccccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCC---
Q psy5642           7 LTEVVESIGPELFRKYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGI---   83 (237)
Q Consensus         7 ~~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---   83 (237)
                      +++++.++++.+..      ...+..++...  ...++++|||+|.+....               ...++..+...   
T Consensus        60 ~~~~~~~~~~~~~~------~~~~~~~~~~~--~~~~~~~ide~~~~~~~~---------------~~~l~~~~~~~~~~  116 (238)
T d1in4a2          60 QTNIHVTSGPVLVK------QGDMAAILTSL--ERGDVLFIDEIHRLNKAV---------------EELLYSAIEDFQID  116 (238)
T ss_dssp             TCCEEEEETTTCCS------HHHHHHHHHHC--CTTCEEEEETGGGCCHHH---------------HHHHHHHHHTSCCC
T ss_pred             CCCcccccCccccc------HHHHHHHHHhh--ccCCchHHHHHHHhhhHH---------------Hhhcccceeeeeee
Confidence            34566677766543      34455555443  356899999999984321               11122222111   


Q ss_pred             -------------CCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHH
Q psy5642          84 -------------VPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVR  149 (237)
Q Consensus        84 -------------~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~  149 (237)
                                   ....++++|++||++..+++++++  ||+..+.++.|+..++..+++......+.. .+..+..++.
T Consensus       117 ~~~~~~~~~~~~~~~~~~~~~I~at~~~~~~~~~~~~--r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~  194 (238)
T d1in4a2         117 IMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAK  194 (238)
T ss_dssp             C---------------CCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHH
T ss_pred             eeecCcccccccccCCCCeEEEEecCCCcccccccee--eeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHH
Confidence                         012468999999999999999999  999999999999999999999988776665 5556888887


Q ss_pred             HCCCCCcccccchhHHhhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhc
Q psy5642         150 LTEGYSGAEQSLSKHRAKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLV  219 (237)
Q Consensus       150 ~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~  219 (237)
                      .+.| +++.                           ..++++.+...+...+  ...|+.++..+|++..
T Consensus       195 ~s~g-d~R~---------------------------ai~~l~~~~~~~~~~~--~~~it~~~~~~al~~l  234 (238)
T d1in4a2         195 RSRG-TPRI---------------------------AIRLTKRVRDMLTVVK--ADRINTDIVLKTMEVL  234 (238)
T ss_dssp             TSTT-CHHH---------------------------HHHHHHHHHHHHHHHT--CSSBCHHHHHHHHHHH
T ss_pred             hCCC-CHHH---------------------------HHHHHHHHHHHHHHhc--CCccCHHHHHHHHHhh
Confidence            7755 3444                           4455555544443333  2358889998888753

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.71  E-value=4.5e-09  Score=81.48  Aligned_cols=111  Identities=24%  Similarity=0.293  Sum_probs=82.1

Q ss_pred             CCceEEEEEeccccc--ccccChHHHHHHHHHHHHHhcC-CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           5 GGLTEVVESIGPELF--RKYVGESERCVRDVFKRARQVS-PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~--~~~~g~~~~~l~~~f~~a~~~~-P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      ..+.+++.++.+.|.  .+|.|+-+..++.+++.+.... +.||||||++.++......+..+       +.+.|...|.
T Consensus        76 L~~~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d-------~~~~Lkp~L~  148 (195)
T d1jbka_          76 LKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMD-------AGNMLKPALA  148 (195)
T ss_dssp             GTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCC-------CHHHHHHHHH
T ss_pred             HcCceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCccc-------HHHHHHHHHh
Confidence            456789999999998  6677899999999999987654 78999999999987654432211       2344444454


Q ss_pred             CCCCCCCEEEEEEeCCCC-----ccchhccCCCCcccEEEecCCCHHHHHHHH
Q psy5642          82 GIVPLNNVTIVAATNRPD-----RIDKALLRPGRLDRLIYVPLPDDLTRAAIL  129 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn~~~-----~ld~al~r~gRf~~~i~~~~P~~~~R~~il  129 (237)
                      .    +.+.+||+|...+     +-|++|.|  ||. .|.+..|+.++-..||
T Consensus       149 r----g~l~~IgatT~eey~~~~e~d~aL~r--rF~-~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         149 R----GELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             T----TSCCEEEEECHHHHHHHTTTCHHHHT--TEE-EEECCCCCHHHHHTTC
T ss_pred             C----CCceEEecCCHHHHHHHHHcCHHHHh--cCC-EeecCCCCHHHHHHHh
Confidence            3    6788898887533     55999999  997 5999999999877665

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.64  E-value=1.2e-08  Score=87.42  Aligned_cols=140  Identities=21%  Similarity=0.275  Sum_probs=86.2

Q ss_pred             CCceEEEEEecccccc--cccChHHHHHHHHHHHHHhcC-CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           5 GGLTEVVESIGPELFR--KYVGESERCVRDVFKRARQVS-PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~--~~~g~~~~~l~~~f~~a~~~~-P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      ..+.+++.++...|..  +|.|+-+..+..++..+.... +.||||||++.+++.....+..       .+.+.|...|.
T Consensus        76 l~~~~i~~ld~~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~-------d~a~~Lkp~L~  148 (387)
T d1qvra2          76 LKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAV-------DAGNMLKPALA  148 (387)
T ss_dssp             STTCEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC--------------------------HHHHH
T ss_pred             HcCceEEEeeHhhhhcccCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcc-------cHHHHHHHHHh
Confidence            3567899999999985  778999999999999998764 7899999999998765433221       22344444454


Q ss_pred             CCCCCCCEEEEEEeCCCC----ccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCC----CCC-chhhHHHHHHHCC
Q psy5642          82 GIVPLNNVTIVAATNRPD----RIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARS----PLG-EDVCVEELVRLTE  152 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn~~~----~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~----~~~-~~~~~~~la~~t~  152 (237)
                      .    +.+-+||+|...+    .-|++|.|  ||.. |.|..|+.++-..||+.....+    .+. .+..+...+..+.
T Consensus       149 r----g~~~~I~~tT~~ey~~~e~d~al~r--rF~~-v~v~ep~~~~~~~il~~~~~~~e~~h~v~~~~~ai~~~v~ls~  221 (387)
T d1qvra2         149 R----GELRLIGATTLDEYREIEKDPALER--RFQP-VYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSH  221 (387)
T ss_dssp             T----TCCCEEEEECHHHHHHHTTCTTTCS--CCCC-EEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHH
T ss_pred             C----CCcceeeecCHHHHHHhcccHHHHH--hccc-ccCCCCcHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHhcc
Confidence            4    6788899987432    34899999  9975 9999999999999999766543    332 5666777777665


Q ss_pred             CCCccc
Q psy5642         153 GYSGAE  158 (237)
Q Consensus       153 g~s~~D  158 (237)
                      .|-+.-
T Consensus       222 ryi~~r  227 (387)
T d1qvra2         222 RYITER  227 (387)
T ss_dssp             HHCCSS
T ss_pred             cccccc
Confidence            555443

>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=98.59  E-value=4e-07  Score=72.48  Aligned_cols=118  Identities=19%  Similarity=0.255  Sum_probs=86.5

Q ss_pred             EEEEecccccccccChHHHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCC
Q psy5642          10 VVESIGPELFRKYVGESERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVP   85 (237)
Q Consensus        10 ~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~   85 (237)
                      +++++.++..      +...++.+++.+...    ...|++|||+|.+..               ...+.|+..|+.  .
T Consensus        86 ~~~~~~~~~~------~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~~---------------~~q~~Llk~lE~--~  142 (239)
T d1njfa_          86 LIEIDAASRT------KVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSR---------------HSFNALLKTLEE--P  142 (239)
T ss_dssp             EEEEETTCSS------SHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCH---------------HHHHHHHHHHHS--C
T ss_pred             EEEecchhcC------CHHHHHHHHHHHHhccccCCCEEEEEECcccCCH---------------HHHHHHHHHHhc--C
Confidence            5566654322      134466666666432    245999999999832               235678888886  3


Q ss_pred             CCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642          86 LNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        86 ~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      .++..+|++||+++.+.+++++  |+ ..+.++.|+.++-..++.......+.. .+..++.++..+.|
T Consensus       143 ~~~~~~il~tn~~~~i~~~i~S--Rc-~~i~~~~~~~~~i~~~l~~i~~~e~~~~~~~~l~~i~~~s~G  208 (239)
T d1njfa_         143 PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEG  208 (239)
T ss_dssp             CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHTTT
T ss_pred             CCCeEEEEEcCCccccChhHhh--hh-cccccccCcHHHhhhHHHHHHhhhccCCCHHHHHHHHHHcCC
Confidence            4678899999999999999999  98 479999999999999888877654443 56778888887754

>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=98.58  E-value=3.7e-07  Score=73.34  Aligned_cols=161  Identities=11%  Similarity=0.034  Sum_probs=108.2

Q ss_pred             ChHHHHHHHHHHHHH--hcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCcc
Q psy5642          24 GESERCVRDVFKRAR--QVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRI  101 (237)
Q Consensus        24 g~~~~~l~~~f~~a~--~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~l  101 (237)
                      +.....+...+....  ...+.++++|++|.+.......      ......+..+.+.+.......+..+|+.++.++..
T Consensus       113 ~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~------~~~~~~l~~l~~~l~~~~~~~~~~~i~i~~~~~~~  186 (287)
T d1w5sa2         113 GAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIA------AEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRAL  186 (287)
T ss_dssp             TCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSC------HHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHH
T ss_pred             cchHHHHHHHHHHHHHhccCccccceeEEEEeccccccc------hhHHHHHHHHHHhcchhhcccceeEEeecccHHHH
Confidence            334444444444433  3356789999999997654322      12223344455666666666677788887776643


Q ss_pred             ------chhccCCCCcccEEEecCCCHHHHHHHHHHHHcC--CCC-CchhhHHHHHHHCCCCCc--ccccchhHHhhhhc
Q psy5642         102 ------DKALLRPGRLDRLIYVPLPDDLTRAAILKIRLAR--SPL-GEDVCVEELVRLTEGYSG--AEQSLSKHRAKKIR  170 (237)
Q Consensus       102 ------d~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~--~~~-~~~~~~~~la~~t~g~s~--~Dl~~~~~~a~~~~  170 (237)
                            ++.+.+  ||...++++.++.++..+|++..+..  ... -.+..++.+|+.+.+|.+  +|+..         
T Consensus       187 ~~~~~~~~~~~~--r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~~~~~~~~~gd~R~---------  255 (287)
T d1w5sa2         187 SYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARR---------  255 (287)
T ss_dssp             HHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCHHH---------
T ss_pred             HHHHhhccchhc--ccceeeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHHHhccccCCCCHHH---------
Confidence                  367777  99999999999999999999987753  121 146678889988876543  44211         


Q ss_pred             cccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhh
Q psy5642         171 PRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQL  218 (237)
Q Consensus       171 ~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~  218 (237)
                                     ..++++.|...+..++  ...|+.+++.+|+.+
T Consensus       256 ---------------ai~~l~~a~~~A~~~~--~~~It~~~V~~A~~e  286 (287)
T d1w5sa2         256 ---------------AIVALKMACEMAEAMG--RDSLSEDLVRKAVSE  286 (287)
T ss_dssp             ---------------HHHHHHHHHHHHHHTT--CSSCCHHHHHHHHHH
T ss_pred             ---------------HHHHHHHHHHHHHHcC--CCCCCHHHHHHHHhc
Confidence                           4567777887776666  457999999999875

>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=98.54  E-value=1.6e-07  Score=74.12  Aligned_cols=120  Identities=18%  Similarity=0.212  Sum_probs=88.1

Q ss_pred             eEEEEEecccccccccChHHHHHHHHHHHHH------hcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           8 TEVVESIGPELFRKYVGESERCVRDVFKRAR------QVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         8 ~~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~------~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      ..++++++++..+.      ..++..+....      ...+.||++||+|.+...               ....|+..+.
T Consensus        76 ~~~~e~n~s~~~~~------~~~~~~~~~~~~~~~~~~~~~~iilide~d~~~~~---------------~~~~ll~~l~  134 (231)
T d1iqpa2          76 HNFLELNASDERGI------NVIREKVKEFARTKPIGGASFKIIFLDEADALTQD---------------AQQALRRTME  134 (231)
T ss_dssp             HHEEEEETTCHHHH------HTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCHH---------------HHHHHHHHHH
T ss_pred             CCeeEEecCcccch------hHHHHHHHHHHhhhhccCCCceEEeehhhhhcchh---------------HHHHHhhhcc
Confidence            46777887765432      22222222222      235789999999987443               2344666665


Q ss_pred             CCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642          82 GIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      .  ...++.+|++||++..+++++++  |+. .+.++.|+..+...+++..+...++. .+..+..++..+.|
T Consensus       135 ~--~~~~~~~i~~~n~~~~i~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~~~~e~i~i~~~~l~~I~~~~~g  202 (231)
T d1iqpa2         135 M--FSSNVRFILSCNYSSKIIEPIQS--RCA-IFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEG  202 (231)
T ss_dssp             H--TTTTEEEEEEESCGGGSCHHHHH--TEE-EEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTT
T ss_pred             c--CCcceEEEeccCChhhchHhHhC--ccc-cccccccchhhHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Confidence            5  33578899999999999999999  985 69999999999999999999887765 67778899988765

>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=98.48  E-value=2.3e-06  Score=67.56  Aligned_cols=101  Identities=17%  Similarity=0.096  Sum_probs=74.8

Q ss_pred             CCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCcccccchhHH
Q psy5642          87 NNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAEQSLSKHR  165 (237)
Q Consensus        87 ~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~Dl~~~~~~  165 (237)
                      .++++|++|+++..+++..++  |+...+.+..|+.+++..++...+...... ....+..++..+.| ..+.       
T Consensus       134 ~~~~~i~~~~~~~~~~~~~l~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~~~~~l~~ia~~s~g-d~R~-------  203 (239)
T d1ixsb2         134 PRFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRG-TMRV-------  203 (239)
T ss_dssp             CCCEEEEEESCCSSCSCGGGG--GCSEEEECCCCCHHHHHHHHHHHHGGGCCCBCHHHHHHHHHHTTS-SHHH-------
T ss_pred             CCEEEEeeccCcccccchhhc--ccceeeEeeccChhhhhHHHHHHHHHhCCccchHHHHHHHHHcCC-CHHH-------
Confidence            468899999999999999999  899999999999999999999888776655 45678888998887 3333       


Q ss_pred             hhhhccccCCCCCCCCCchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhc
Q psy5642         166 AKKIRPRRESNPGPPACKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLV  219 (237)
Q Consensus       166 a~~~~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~  219 (237)
                                          ..++++.+...+...  ....||.++..++|..+
T Consensus       204 --------------------a~~~l~~~~~~a~~~--~~~~It~~~~~~~l~~l  235 (239)
T d1ixsb2         204 --------------------AKRLFRRVRDFAQVA--GEEVITRERALEALAAL  235 (239)
T ss_dssp             --------------------HHHHHHHHHHHHTTS--CCSCBCHHHHHHHHHHH
T ss_pred             --------------------HHHHHHHHHHHHHHh--CCCCcCHHHHHHHHhhh
Confidence                                334444433322222  24568999998888643

>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=98.46  E-value=7.7e-08  Score=75.81  Aligned_cols=92  Identities=15%  Similarity=0.185  Sum_probs=74.3

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCC
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPD  121 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~  121 (237)
                      ..+|+|||+|.+...               ..+.|+..|+..  ..+.+++.+||.+..+++++++  |+. .+.|+.|+
T Consensus       100 ~kiiiiDe~d~~~~~---------------~~~~Ll~~le~~--~~~~~~~~~~~~~~~i~~~i~s--r~~-~i~~~~~~  159 (227)
T d1sxjc2         100 FKLIILDEADAMTNA---------------AQNALRRVIERY--TKNTRFCVLANYAHKLTPALLS--QCT-RFRFQPLP  159 (227)
T ss_dssp             CEEEEETTGGGSCHH---------------HHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCC
T ss_pred             eEEEEEeccccchhh---------------HHHHHHHHhhhc--ccceeeccccCcHHHhHHHHHH--HHh-hhcccccc
Confidence            459999999987432               345666777653  3578899999999999999999  884 68999999


Q ss_pred             HHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         122 DLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       122 ~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      ..+...++...+...+.. ++..++.+++.+.|
T Consensus       160 ~~~i~~~l~~I~~~e~i~i~~~~l~~i~~~s~G  192 (227)
T d1sxjc2         160 QEAIERRIANVLVHEKLKLSPNAEKALIELSNG  192 (227)
T ss_dssp             HHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTT
T ss_pred             ccccccccccccccccccCCHHHHHHHHHHcCC
Confidence            999999999988776655 67778889998865

>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=98.29  E-value=3e-06  Score=66.54  Aligned_cols=91  Identities=16%  Similarity=0.213  Sum_probs=71.0

Q ss_pred             eEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCH
Q psy5642          43 SVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDD  122 (237)
Q Consensus        43 ~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~  122 (237)
                      .+|+|||+|.+...               ..+.++..+..  ......+|.+++..+.+.+++++  || ..|.|++|+.
T Consensus       110 ~viiiDe~d~l~~~---------------~~~~l~~~~~~--~~~~~~~i~~~~~~~~~~~~l~s--r~-~~i~f~~~~~  169 (237)
T d1sxjd2         110 KIIILDEADSMTAD---------------AQSALRRTMET--YSGVTRFCLICNYVTRIIDPLAS--QC-SKFRFKALDA  169 (237)
T ss_dssp             EEEEETTGGGSCHH---------------HHHHHHHHHHH--TTTTEEEEEEESCGGGSCHHHHH--HS-EEEECCCCCH
T ss_pred             eEEEEecccccCHH---------------HHHHHhhcccc--ccccccccccccccccccccccc--hh-hhhccccccc
Confidence            49999999988442               23344444444  23466788889999999999999  98 5799999999


Q ss_pred             HHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         123 LTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       123 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      .+...+|+..+.+..+. .+..+..+|..+.|
T Consensus       170 ~~~~~~L~~i~~~e~i~i~~~~l~~ia~~s~g  201 (237)
T d1sxjd2         170 SNAIDRLRFISEQENVKCDDGVLERILDISAG  201 (237)
T ss_dssp             HHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSS
T ss_pred             cccchhhhhhhhhhcCcCCHHHHHHHHHHcCC
Confidence            99999999998876654 67778899998754

>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=98.28  E-value=8e-07  Score=70.61  Aligned_cols=92  Identities=16%  Similarity=0.243  Sum_probs=71.2

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCC
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPD  121 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~  121 (237)
                      ..+++|||+|.+..               ...+.++..++.  ...++.+|++||+++.+++++++  || ..|+|++|+
T Consensus       132 ~~iiiide~d~l~~---------------~~~~~l~~~~e~--~~~~~~~Il~tn~~~~i~~~l~s--R~-~~i~~~~~~  191 (252)
T d1sxje2         132 YKCVIINEANSLTK---------------DAQAALRRTMEK--YSKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPS  191 (252)
T ss_dssp             CEEEEEECTTSSCH---------------HHHHHHHHHHHH--STTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCC
T ss_pred             ceEEEecccccccc---------------ccchhhhccccc--ccccccceeeeccccchhhhhhc--ch-heeeecccc
Confidence            45999999998732               234556666665  33568889999999999999999  99 479999999


Q ss_pred             HHHHHHHHHHHHcCCCC--CchhhHHHHHHHCCC
Q psy5642         122 DLTRAAILKIRLARSPL--GEDVCVEELVRLTEG  153 (237)
Q Consensus       122 ~~~R~~il~~~l~~~~~--~~~~~~~~la~~t~g  153 (237)
                      .++..+++...+.....  ..+..++.++..+.|
T Consensus       192 ~~~~~~~l~~i~~~e~~~~~~~~~l~~i~~~s~G  225 (252)
T d1sxje2         192 DSEISTILSDVVTNERIQLETKDILKRIAQASNG  225 (252)
T ss_dssp             HHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTT
T ss_pred             hhhHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCC
Confidence            99999999988765433  345667888887765

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=98.27  E-value=4.5e-07  Score=76.78  Aligned_cols=72  Identities=15%  Similarity=0.012  Sum_probs=54.8

Q ss_pred             EEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHH-HHHHHHHcCCCCCchhhHHHHHHHCCCCCcccccchhHHh
Q psy5642          90 TIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRA-AILKIRLARSPLGEDVCVEELVRLTEGYSGAEQSLSKHRA  166 (237)
Q Consensus        90 ~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~-~il~~~l~~~~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a  166 (237)
                      .+|+|||+   ++.++.+|+||+..+++..|+...|. +++..++++..+.  .+.+.++..+.|++++|+..+++.+
T Consensus       258 p~i~ttN~---~~~~~~r~~Rf~~~i~~~~~~~~~~~~~~l~~i~~~~~l~--~~~~~L~~li~~~s~~D~~~~i~~~  330 (362)
T d1svma_         258 PGIVTMNE---YSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQ--SGIALLLMLIWYRPVAEFAQSIQSR  330 (362)
T ss_dssp             CEEEEECS---CCCCHHHHTTEEEEEECCCCHHHHHHHHTCTHHHHTTCTT--CHHHHHHHHHHHSCGGGSCGGGHHH
T ss_pred             Cceeeccc---ccccccccccCceEEeecCCCcHHHHHHHHHHHhcccCCC--CCHHHHHHHccCCCHHHHHHHHHHH
Confidence            37889995   46677788999999999999877764 5666777766653  4566788889999999966655543

>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=98.07  E-value=5.6e-06  Score=64.29  Aligned_cols=103  Identities=20%  Similarity=0.336  Sum_probs=78.4

Q ss_pred             HHHHHHHHHHHHh----cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQ----VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~----~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      ...++++.+.+..    ...-|++|||+|.+..               ...+.|+..|+.  ...++++|.+|++++.|.
T Consensus        90 ~~~ir~l~~~~~~~~~~~~~kviIide~d~l~~---------------~a~n~Llk~lEe--p~~~~~fIl~t~~~~~ll  152 (207)
T d1a5ta2          90 VDAVREVTEKLNEHARLGGAKVVWVTDAALLTD---------------AAANALLKTLEE--PPAETWFFLATREPERLL  152 (207)
T ss_dssp             HHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCH---------------HHHHHHHHHHTS--CCTTEEEEEEESCGGGSC
T ss_pred             cchhhHHhhhhhhccccCccceEEechhhhhhh---------------hhhHHHHHHHHh--hcccceeeeeecChhhhh
Confidence            4456666665543    2456999999999843               346889999998  446899999999999999


Q ss_pred             hhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCC
Q psy5642         103 KALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEG  153 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g  153 (237)
                      +.|++  |+ ..|.|+.|+.++...+|+..+.   . .+..+..++..+.|
T Consensus       153 ~tI~S--Rc-~~i~~~~~~~~~~~~~L~~~~~---~-~~~~~~~i~~~s~G  196 (207)
T d1a5ta2         153 ATLRS--RC-RLHYLAPPPEQYAVTWLSREVT---M-SQDALLAALRLSAG  196 (207)
T ss_dssp             HHHHT--TS-EEEECCCCCHHHHHHHHHHHCC---C-CHHHHHHHHHHTTT
T ss_pred             hhhcc--ee-EEEecCCCCHHHHHHHHHHcCC---C-CHHHHHHHHHHcCC
Confidence            99999  98 6899999999998888865432   2 45667777776653

>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=98.05  E-value=1.9e-05  Score=62.36  Aligned_cols=95  Identities=17%  Similarity=0.214  Sum_probs=64.8

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCC
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLP  120 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P  120 (237)
                      .+.++++||+|.+....            +.....++.....  ....++++++++....+++ ++   |+...|+|++|
T Consensus       123 ~~~vi~ide~~~~~~~~------------~~~~~~~~~~~~~--~~~~ii~i~~~~~~~~~~~-l~---~~~~~i~f~~~  184 (253)
T d1sxja2         123 KHFVIIMDEVDGMSGGD------------RGGVGQLAQFCRK--TSTPLILICNERNLPKMRP-FD---RVCLDIQFRRP  184 (253)
T ss_dssp             TSEEEEECSGGGCCTTS------------TTHHHHHHHHHHH--CSSCEEEEESCTTSSTTGG-GT---TTSEEEECCCC
T ss_pred             cceEEEeeeccccccch------------hhhhHHHhhhhcc--ccccccccccccccccccc-cc---ceeeeeecccc
Confidence            46799999999986542            1123444444433  2235666666666666654 44   55678999999


Q ss_pred             CHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCC
Q psy5642         121 DDLTRAAILKIRLARSPLG-EDVCVEELVRLTEG  153 (237)
Q Consensus       121 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  153 (237)
                      +.+++..+++..+...++. .+..+..++..+.|
T Consensus       185 ~~~~i~~~l~~i~~~e~i~i~~~~l~~i~~~s~G  218 (253)
T d1sxja2         185 DANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRG  218 (253)
T ss_dssp             CHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTT
T ss_pred             chhHHHHHHHHHHHHhCCCCCHHHHHHHHHhCCC
Confidence            9999999999988654433 55678999998754

>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=97.97  E-value=9.8e-06  Score=63.23  Aligned_cols=100  Identities=22%  Similarity=0.377  Sum_probs=70.4

Q ss_pred             CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc---hhccCCCCcc--cEE
Q psy5642          41 SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID---KALLRPGRLD--RLI  115 (237)
Q Consensus        41 ~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld---~al~r~gRf~--~~i  115 (237)
                      ...+|+|||+|.+..+.          ..+..+-.+++.   ....++-+||++...|..++   +.+++  ||.  .++
T Consensus        97 ~~dll~iDDi~~i~~~~----------~~~~~lf~lin~---~~~~~~~iiits~~~p~~l~~~~~dL~S--RL~~g~~~  161 (213)
T d1l8qa2          97 SVDLLLLDDVQFLSGKE----------RTQIEFFHIFNT---LYLLEKQIILASDRHPQKLDGVSDRLVS--RFEGGILV  161 (213)
T ss_dssp             TCSEEEEECGGGGTTCH----------HHHHHHHHHHHH---HHHTTCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEE
T ss_pred             hccchhhhhhhhhcCch----------HHHHHHHHHHHH---HhhccceEEEecCCcchhccccchHHHH--HhhCceEE
Confidence            45799999999996542          112233334443   33345667777778887664   77888  885  566


Q ss_pred             EecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCCCCCccc
Q psy5642         116 YVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus       116 ~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~D  158 (237)
                      .++ |+.+.|.++++.+....++. ++..+.-|++++.  +.+|
T Consensus       162 ~i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~yl~~~~~--~~R~  202 (213)
T d1l8qa2         162 EIE-LDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTK--NVRE  202 (213)
T ss_dssp             ECC-CCHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHCS--SHHH
T ss_pred             EEC-CCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcC--cHHH
Confidence            776 67789999999988777766 7778888888874  4677

>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=97.94  E-value=3.9e-05  Score=60.63  Aligned_cols=154  Identities=12%  Similarity=0.063  Sum_probs=95.5

Q ss_pred             HHHHHHHHHh-cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCC---ccchhc
Q psy5642          30 VRDVFKRARQ-VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPD---RIDKAL  105 (237)
Q Consensus        30 l~~~f~~a~~-~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~---~ld~al  105 (237)
                      +..+...... ..+.++++|++|.+....            ......++..+... ...++.+|++++...   .+++.+
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~d~~~~~~------------~~~~~~~~~~~~~~-~~~~~~~i~~~~~~~~~~~~~~~~  178 (276)
T d1fnna2         112 LALLVEHLRERDLYMFLVLDDAFNLAPDI------------LSTFIRLGQEADKL-GAFRIALVIVGHNDAVLNNLDPST  178 (276)
T ss_dssp             HHHHHHHHHHTTCCEEEEEETGGGSCHHH------------HHHHHHHTTCHHHH-SSCCEEEEEEESSTHHHHTSCHHH
T ss_pred             HHHHHHHHhhcccccccchhHHHHhhhhh------------hhhHHHHHhccccc-cccceEEeecCCchhhhhhcchhh
Confidence            3334444433 357788899998874321            11122222222111 234678888888744   567778


Q ss_pred             cCCCCcc-cEEEecCCCHHHHHHHHHHHHcCC---CCCchhhHHHHHHHCCCCCcccccchhHHhhhhccccCCCCCCCC
Q psy5642         106 LRPGRLD-RLIYVPLPDDLTRAAILKIRLARS---PLGEDVCVEELVRLTEGYSGAEQSLSKHRAKKIRPRRESNPGPPA  181 (237)
Q Consensus       106 ~r~gRf~-~~i~~~~P~~~~R~~il~~~l~~~---~~~~~~~~~~la~~t~g~s~~Dl~~~~~~a~~~~~~~~~~~~~~~  181 (237)
                      .+  |+. ..|.|+.|+.+++.+|++..+...   ....+..++.++..+.++.......=                   
T Consensus       179 ~~--r~~~~~i~~~~~~~~e~~~il~~r~~~~~~~~~~~~~~l~~ia~~~~~~~~~~~~~G-------------------  237 (276)
T d1fnna2         179 RG--IMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRG-------------------  237 (276)
T ss_dssp             HH--HHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSC-------------------
T ss_pred             hh--hhcchhccccchhHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhhhhhhhhhcCC-------------------
Confidence            77  653 568999999999999999877531   12256677788887754433321000                   


Q ss_pred             CchhHHHHHHHHHHHHHHhccccCCccHHHHHHHHhhc
Q psy5642         182 CKPSIVAVCDEAALSALENNLEAAYVSHQDFLTALQLV  219 (237)
Q Consensus       182 ~~~~i~~~~~~a~~~~~~~~~~~~~v~~~df~~al~~~  219 (237)
                      ....+.++++.|...+..++  ...|+.+|+.+|+++.
T Consensus       238 ~~R~a~~ll~~a~~~A~~~~--~~~I~~edv~~A~~~~  273 (276)
T d1fnna2         238 DARLAIDILYRSAYAAQQNG--RKHIAPEDVRKSSKEV  273 (276)
T ss_dssp             CHHHHHHHHHHHHHHHHHTT--CSSCCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHcC--CCCcCHHHHHHHHHHH
Confidence            00015677888888777776  4579999999998764

>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=97.90  E-value=4.7e-05  Score=59.18  Aligned_cols=118  Identities=17%  Similarity=0.136  Sum_probs=83.1

Q ss_pred             EEEEEecccccccccChHHHHHHHHHHHHHh-------cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhc
Q psy5642           9 EVVESIGPELFRKYVGESERCVRDVFKRARQ-------VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMD   81 (237)
Q Consensus         9 ~~i~v~~s~l~~~~~g~~~~~l~~~f~~a~~-------~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~   81 (237)
                      .++++++++..+      ...++..+.....       ..+.+++|||+|.+...               ..+.++..++
T Consensus        68 ~~~~~n~~~~~~------~~~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~~~~---------------~~~~ll~~~e  126 (224)
T d1sxjb2          68 GVLELNASDDRG------IDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAG---------------AQQALRRTME  126 (224)
T ss_dssp             HEEEECTTSCCS------HHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHH---------------HHHTTHHHHH
T ss_pred             ccccccccccCC------ceehhhHHHHHHHhhccCCCcceEEEEEecccccchh---------------HHHHHhhhcc
Confidence            456666665443      2333333333322       13559999999998443               2344555555


Q ss_pred             CCCCCCCEEEEEEeCCCCccchhccCCCCcccEEEecCCCHHHHHHHHHHHHcCCCCC-chhhHHHHHHHCC
Q psy5642          82 GIVPLNNVTIVAATNRPDRIDKALLRPGRLDRLIYVPLPDDLTRAAILKIRLARSPLG-EDVCVEELVRLTE  152 (237)
Q Consensus        82 ~~~~~~~v~vI~ttn~~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  152 (237)
                      .  ......++.+|+..+.+.+++++  |+. .|.|+.|+.++...+|...+...+.. .+..+..++..+.
T Consensus       127 ~--~~~~~~~i~~~~~~~~i~~~l~s--r~~-~i~~~~~~~~~i~~~l~~i~~~e~~~i~~~~l~~I~~~s~  193 (224)
T d1sxjb2         127 L--YSNSTRFAFACNQSNKIIEPLQS--QCA-ILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAE  193 (224)
T ss_dssp             H--TTTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHT
T ss_pred             c--cccceeeeeccCchhhhhhHHHH--HHH-HhhhcccchhhhHHHHHHHHHhcccCCCHHHHHHHHHHcC
Confidence            5  33567889999999999999999  985 69999999999999999988765554 5666788888764

>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=97.85  E-value=2.7e-05  Score=64.27  Aligned_cols=136  Identities=20%  Similarity=0.270  Sum_probs=88.5

Q ss_pred             CCceEEEEEecccccc------------cccChHHHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHH
Q psy5642           5 GGLTEVVESIGPELFR------------KYVGESERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERV   72 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~------------~~~g~~~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~   72 (237)
                      +.+.+++.++++++..            .|+|..+.  ..+.+..+.+..+||+|||+|...+               .+
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~L~g~~~gyvG~~~~--~~l~~~~~~~p~~Vvl~DEieK~~~---------------~v  141 (315)
T d1qvra3          79 DTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEG--GQLTEAVRRRPYSVILFDEIEKAHP---------------DV  141 (315)
T ss_dssp             SSGGGEEEECTTTCCSSGGGGGC----------------CHHHHHHHCSSEEEEESSGGGSCH---------------HH
T ss_pred             CCCcceEEEeccccccchhhhhhcCCCCCCcCcccC--ChHHHHHHhCCCcEEEEehHhhcCH---------------HH
Confidence            3466889999887764            24442221  2234445566669999999999632               35


Q ss_pred             HHHHHHHhcCC---------CCCCCEEEEEEeCC--------------------------CCccchhccCCCCcccEEEe
Q psy5642          73 LAQMLTEMDGI---------VPLNNVTIVAATNR--------------------------PDRIDKALLRPGRLDRLIYV  117 (237)
Q Consensus        73 ~~~ll~~l~~~---------~~~~~v~vI~ttn~--------------------------~~~ld~al~r~gRf~~~i~~  117 (237)
                      .+.|+..++.-         ...++.++|+|||-                          ...+.|.++.  |||.++.|
T Consensus       142 ~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~tsnlG~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~Ii~F  219 (315)
T d1qvra3         142 FNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVF  219 (315)
T ss_dssp             HHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBC
T ss_pred             HHHHHHHhccCceeCCCCcEecCcceEEEEecccChHHHhhhcccccchhhhhHHHHHHHHhhcCHHHHh--cCCeeeec
Confidence            66677776542         11246999999995                          2458899999  99999999


Q ss_pred             cCCCHHHHHHHHHHHHcC-------CCCC---chhhHHHHHHH--CCCCCcccc
Q psy5642         118 PLPDDLTRAAILKIRLAR-------SPLG---EDVCVEELVRL--TEGYSGAEQ  159 (237)
Q Consensus       118 ~~P~~~~R~~il~~~l~~-------~~~~---~~~~~~~la~~--t~g~s~~Dl  159 (237)
                      .+.+.++..+|+...+..       ....   .+..++.|+.+  ...|.++.|
T Consensus       220 ~~L~~~~~~~I~~~~l~~l~~rl~~~~i~l~i~~~~~~~L~~~~y~~~~GAR~L  273 (315)
T d1qvra3         220 RPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDFLAERGYDPVFGARPL  273 (315)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHHHHCBTTTBTSTH
T ss_pred             cchhhhhhHHHHHHHHHHHHHHHHhccccccccHHHHHHHHHhCCCCCCCcchH
Confidence            999999999998755432       2221   45566778775  355666773

>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=97.42  E-value=0.00039  Score=57.03  Aligned_cols=134  Identities=15%  Similarity=0.147  Sum_probs=86.6

Q ss_pred             eEEEEEeccccccc-----ccCh----HHHHH-HHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHH
Q psy5642           8 TEVVESIGPELFRK-----YVGE----SERCV-RDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQML   77 (237)
Q Consensus         8 ~~~i~v~~s~l~~~-----~~g~----~~~~l-~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll   77 (237)
                      .+|+.++++.+...     ..|.    ....- ..+.........+|++|||+|...               ..+.+.|+
T Consensus        78 ~~~i~~d~s~~~~~~~~~~l~g~~~gy~g~~~~~~l~~~~~~~~~~vvl~DeieKa~---------------~~V~~~lL  142 (315)
T d1r6bx3          78 IELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAH---------------PDVFNILL  142 (315)
T ss_dssp             CEEEEEEGGGCSSSSCCSSSCCCCSCSHHHHHTTHHHHHHHHCSSEEEEEETGGGSC---------------HHHHHHHH
T ss_pred             CCeeEeccccccchhhhhhhcccCCCccccccCChhhHHHHhCccchhhhccccccc---------------chHhhhhH
Confidence            57899998877532     2221    12221 123344556677899999999862               23567777


Q ss_pred             HHhcCC---------CCCCCEEEEEEeCCCC-------------------------ccchhccCCCCcccEEEecCCCHH
Q psy5642          78 TEMDGI---------VPLNNVTIVAATNRPD-------------------------RIDKALLRPGRLDRLIYVPLPDDL  123 (237)
Q Consensus        78 ~~l~~~---------~~~~~v~vI~ttn~~~-------------------------~ld~al~r~gRf~~~i~~~~P~~~  123 (237)
                      +.++.-         ..-.+.++|.|+|--.                         .+.|.++.  |||.++.|.+.+.+
T Consensus       143 qild~G~ltd~~Gr~vdf~n~iiI~Tsnig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~ii~f~~l~~~  220 (315)
T d1r6bx3         143 QVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTD  220 (315)
T ss_dssp             HHHHHSEEEETTTEEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHT--TCSEEEECCCCCHH
T ss_pred             HhhccceecCCCCCccCccceEEEeccchhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHHHh--hhhhhhcccchhhh
Confidence            777421         1234688999999532                         36788888  99999999999999


Q ss_pred             HHHHHHHHHHcCC-------CCC---chhhHHHHHHH--CCCCCccc
Q psy5642         124 TRAAILKIRLARS-------PLG---EDVCVEELVRL--TEGYSGAE  158 (237)
Q Consensus       124 ~R~~il~~~l~~~-------~~~---~~~~~~~la~~--t~g~s~~D  158 (237)
                      +...|+..++...       ...   .+..+..++..  ...|.++.
T Consensus       221 ~~~~I~~~~l~~~~~~l~~~~i~l~~~~~a~~~l~~~~yd~~~GaR~  267 (315)
T d1r6bx3         221 VIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAEKGYDRAMGARP  267 (315)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTEEEEECHHHHHHHHHHHCBTTTBTTT
T ss_pred             HHHHHHHHHHHHHHHHHHhcCcchhhHHHHHHHHHHhCCCCCCChhh
Confidence            9998887666422       111   45556666654  34555566

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=97.17  E-value=0.0025  Score=53.10  Aligned_cols=149  Identities=17%  Similarity=0.226  Sum_probs=86.7

Q ss_pred             ceEEEEEecccccc-cccC-hHHHHHHHHHHHH----HhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHh
Q psy5642           7 LTEVVESIGPELFR-KYVG-ESERCVRDVFKRA----RQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEM   80 (237)
Q Consensus         7 ~~~~i~v~~s~l~~-~~~g-~~~~~l~~~f~~a----~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l   80 (237)
                      +.+|+.++++.+.. .|+| +.+..++++...+    .....+|+++||+|...+........ .......+.+.||+.+
T Consensus        93 ~~~~ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~v~~~~~~iv~lDEieK~~~~s~~~~~~-~d~a~~~V~~~lLqil  171 (364)
T d1um8a_          93 DIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSIT-RDVSGEGVQQALLKIV  171 (364)
T ss_dssp             TCCEEEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC---------------CHHHHHHHHHHH
T ss_pred             ccceeehhhhhcccchhhHhhhccchhhhhhhchhHHHHhhcccchhhhhhhhcccccccccc-ccccchHHHHhhhhhh
Confidence            56899999987654 3444 3466777777654    33467899999999987654322111 1112245778888888


Q ss_pred             cCCC-----------CCCCEEEEEEeCC-------------------------------------------------CCc
Q psy5642          81 DGIV-----------PLNNVTIVAATNR-------------------------------------------------PDR  100 (237)
Q Consensus        81 ~~~~-----------~~~~v~vI~ttn~-------------------------------------------------~~~  100 (237)
                      ++-.           ...+.++|.|+|-                                                 +..
T Consensus       172 d~~~~~~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  251 (364)
T d1um8a_         172 EGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYG  251 (364)
T ss_dssp             HCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTT
T ss_pred             cCceeccCCCCCCcCCcceeEEEeehhhhhhhcccchhhhhhhhhhcccccccccccccchhhhhhhhccccHHHHhhhh
Confidence            8421           1123556666664                                                 123


Q ss_pred             cchhccCCCCcccEEEecCCCHHHHHHHHHH-----------HHcCCCCC---chhhHHHHHHHC--CCCCccc
Q psy5642         101 IDKALLRPGRLDRLIYVPLPDDLTRAAILKI-----------RLARSPLG---EDVCVEELVRLT--EGYSGAE  158 (237)
Q Consensus       101 ld~al~r~gRf~~~i~~~~P~~~~R~~il~~-----------~l~~~~~~---~~~~~~~la~~t--~g~s~~D  158 (237)
                      +.|.++.  ||+.++.|...+.++-.+|+..           ++...++.   .+..+..||.+.  .+|..+-
T Consensus       252 f~PEf~g--Ri~~iv~f~~L~~~~l~~Il~~~~~~l~kq~~~~l~~~gi~L~~td~a~~~la~~g~d~~~GAR~  323 (364)
T d1um8a_         252 LIPELIG--RLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKTGARG  323 (364)
T ss_dssp             CCHHHHT--TCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTGGG
T ss_pred             hHHHHHH--HhcchhhHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHhccCCCCCchH
Confidence            6677887  9999999999999999999852           23333333   566677777654  4555555

>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=97.01  E-value=0.0067  Score=49.41  Aligned_cols=73  Identities=19%  Similarity=0.279  Sum_probs=54.9

Q ss_pred             CeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC----C-------CCCEEEEEEeCC-CCccchhccCCC
Q psy5642          42 PSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV----P-------LNNVTIVAATNR-PDRIDKALLRPG  109 (237)
Q Consensus        42 P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~----~-------~~~v~vI~ttn~-~~~ld~al~r~g  109 (237)
                      ..|+||||+..+-               ..+.+.|++-|++-.    .       ..++++|+|+|- +..+++++++  
T Consensus       128 ~gvl~iDEi~~~~---------------~~~~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~~l~~~llD--  190 (333)
T d1g8pa_         128 RGYLYIDECNLLE---------------DHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--  190 (333)
T ss_dssp             TEEEEETTGGGSC---------------HHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--
T ss_pred             ccEeecccHHHHH---------------HHHHHHHhhhhcCCeEEecccCceecCCCCEEEEEecCccccccccchhh--
Confidence            4799999998772               356788888886321    0       125788999887 4579999999  


Q ss_pred             CcccEEEecCC-CHHHHHHHHHH
Q psy5642         110 RLDRLIYVPLP-DDLTRAAILKI  131 (237)
Q Consensus       110 Rf~~~i~~~~P-~~~~R~~il~~  131 (237)
                      ||+..+.++.| +...|.++...
T Consensus       191 Rf~~~i~v~~~~~~~~~~~~~~~  213 (333)
T d1g8pa_         191 RFGLSVEVLSPRDVETRVEVIRR  213 (333)
T ss_dssp             TCSEEEECCCCCSHHHHHHHHHH
T ss_pred             hhcceeeccCcchhhHHHHHHHh
Confidence            99999999987 56777766654

>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=96.99  E-value=0.00039  Score=53.18  Aligned_cols=76  Identities=13%  Similarity=0.200  Sum_probs=60.0

Q ss_pred             HHHHHHHHHHHHhc----CCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccc
Q psy5642          27 ERCVRDVFKRARQV----SPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRID  102 (237)
Q Consensus        27 ~~~l~~~f~~a~~~----~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld  102 (237)
                      -..+|++.+.+...    ..-|++|||+|.+..               ...+.||..|++  ...+.++|.+|++++.+.
T Consensus        61 Id~IR~i~~~~~~~~~~~~~KviIId~ad~l~~---------------~aqNaLLK~LEE--Pp~~t~fiLit~~~~~ll  123 (198)
T d2gnoa2          61 IDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQ---------------QAANAFLKALEE--PPEYAVIVLNTRRWHYLL  123 (198)
T ss_dssp             HHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCH---------------HHHHHTHHHHHS--CCTTEEEEEEESCGGGSC
T ss_pred             HHHHHHHHHHHhhCcccCCCEEEEEeCccccch---------------hhhhHHHHHHhC--CCCCceeeeccCChhhCH
Confidence            56677777777643    234999999999833               357889999998  446888999999999999


Q ss_pred             hhccCCCCcccEEEecCCCH
Q psy5642         103 KALLRPGRLDRLIYVPLPDD  122 (237)
Q Consensus       103 ~al~r~gRf~~~i~~~~P~~  122 (237)
                      +.+++  |. ..+.++.|..
T Consensus       124 ~TI~S--RC-~~i~~~~p~~  140 (198)
T d2gnoa2         124 PTIKS--RV-FRVVVNVPKE  140 (198)
T ss_dssp             HHHHT--TS-EEEECCCCHH
T ss_pred             HHHhc--ce-EEEeCCCchH
Confidence            99999  97 4688888754

>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=94.32  E-value=0.11  Score=40.26  Aligned_cols=40  Identities=20%  Similarity=0.241  Sum_probs=25.4

Q ss_pred             CCceEEEEEecccccccccChHHHHHHH------------------HHHHHHhcCCeEEEEcccccc
Q psy5642           5 GGLTEVVESIGPELFRKYVGESERCVRD------------------VFKRARQVSPSVIFFDELDSL   53 (237)
Q Consensus         5 ~~~~~~i~v~~s~l~~~~~g~~~~~l~~------------------~f~~a~~~~P~il~iDeid~l   53 (237)
                      ....+++.++|+.+...      .....                  +|+.|   ...+|||||+|.+
T Consensus        49 ~~~~~~~~~~~~~~~~~------~~~~~lfg~~~~~~~~~~~~~~g~l~~a---~gGtL~l~~i~~L  106 (247)
T d1ny5a2          49 RSKEPFVALNVASIPRD------IFEAELFGYEKGAFTGAVSSKEGFFELA---DGGTLFLDEIGEL  106 (247)
T ss_dssp             TTTSCEEEEETTTSCHH------HHHHHHHCBCTTSSTTCCSCBCCHHHHT---TTSEEEEESGGGC
T ss_pred             Ccccccccchhhhhhhc------ccHHHhcCcccCCcCCcccccCCHHHcc---CCCEEEEeChHhC
Confidence            45678889999766432      12222                  23333   2368999999998

>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=93.49  E-value=1.2  Score=37.10  Aligned_cols=95  Identities=18%  Similarity=0.265  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCC--------CCCCEEEEEEeCC---
Q psy5642          29 CVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIV--------PLNNVTIVAATNR---   97 (237)
Q Consensus        29 ~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--------~~~~v~vI~ttn~---   97 (237)
                      .....+..+..  +.++++||+|.........+   .+.....+...++..+.+..        ..+.+++|++...   
T Consensus       239 i~~~ai~~v~~--~~~~~~dei~k~~~~~~~~g---~d~~~eg~~~~ll~~~e~~~v~~~~~~~~~~~~l~i~~~~~~~~  313 (443)
T d1g41a_         239 LKQKAIDAVEQ--NGIVFIDEIDKICKKGEYSG---ADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVA  313 (443)
T ss_dssp             HHHHHHHHHHH--HCEEEEETGGGGSCCSSCSS---SHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSC
T ss_pred             HHHHHHHHHhc--cCccccchhhhhhhcccCCC---CCcccchhhhhhhhhccccccccccccccccchhhccccchhhc
Confidence            33444444444  47999999999987755433   22333455666777665532        2345777777644   


Q ss_pred             -CCccchhccCCCCcccEEEecCCCHHHHHHHHH
Q psy5642          98 -PDRIDKALLRPGRLDRLIYVPLPDDLTRAAILK  130 (237)
Q Consensus        98 -~~~ld~al~r~gRf~~~i~~~~P~~~~R~~il~  130 (237)
                       +..|=|.|..  ||..++.+...+.++-..||.
T Consensus       314 ~~~gliPEliG--RlPi~v~L~~L~~~dL~rILt  345 (443)
T d1g41a_         314 RPSDLIPELQG--RLPIRVELTALSAADFERILT  345 (443)
T ss_dssp             CGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHH
T ss_pred             ccccchhhhcc--ceEEEEEccCccHHHHHHHHH
Confidence             3456677886  999999999999999888883

>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=92.22  E-value=0.5  Score=35.67  Aligned_cols=115  Identities=14%  Similarity=0.107  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHHh--cCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCCccchhc
Q psy5642          28 RCVRDVFKRARQ--VSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPDRIDKAL  105 (237)
Q Consensus        28 ~~l~~~f~~a~~--~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~~ld~al  105 (237)
                      ..+..+++....  ..+.++++||++.+.......           +...+...++.   ..++..+.+......+...+
T Consensus       121 ~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~~~~~-----------~~~~l~~~~~~---~~~~~~i~~~~~~~~~~~~~  186 (283)
T d2fnaa2         121 LSFANLLESFEQASKDNVIIVLDEAQELVKLRGVN-----------LLPALAYAYDN---LKRIKFIMSGSEMGLLYDYL  186 (283)
T ss_dssp             CCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCC-----------CHHHHHHHHHH---CTTEEEEEEESSHHHHHHHT
T ss_pred             hHHHHHHHHHHhhcccccccccchhhhhcccchHH-----------HHHHHHHHHHh---hhhhhhhhccccchHHHHHH
Confidence            334445554433  468899999999986543211           12222222222   13444555444322111111


Q ss_pred             c-------CCCCcccEEEecCCCHHHHHHHHHHHHcCCCCCchhhHHHHHHHCCCCCccc
Q psy5642         106 L-------RPGRLDRLIYVPLPDDLTRAAILKIRLARSPLGEDVCVEELVRLTEGYSGAE  158 (237)
Q Consensus       106 ~-------r~gRf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~D  158 (237)
                      .       -.||+...++++..+.++..++++..+...... ..++..+.+.+.|. |.-
T Consensus       187 ~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~-~~~~~~i~~~~~G~-P~~  244 (283)
T d2fnaa2         187 RVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADID-FKDYEVVYEKIGGI-PGW  244 (283)
T ss_dssp             TTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCC-CCCHHHHHHHHCSC-HHH
T ss_pred             HhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCCC-HHHHHHHHHHhCCC-HHH
Confidence            1       123666789999999999999999877654443 33467888888886 445

>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=82.95  E-value=3.2  Score=28.83  Aligned_cols=78  Identities=19%  Similarity=0.208  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHHhcCCeEEEEccccccccccCCCCCCCCCchHHHHHHHHHHHhcCCCCCCCEEEEEEeCCCC--ccchh
Q psy5642          27 ERCVRDVFKRARQVSPSVIFFDELDSLAGERGDGGGGGGSNVQERVLAQMLTEMDGIVPLNNVTIVAATNRPD--RIDKA  104 (237)
Q Consensus        27 ~~~l~~~f~~a~~~~P~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vI~ttn~~~--~ld~a  104 (237)
                      ....+..+..+....|.+|++||+......            .......+...+..    .+..+|+++....  .+-..
T Consensus        85 ~~~~~~~l~~~~~~~~~vlllDE~~~~~~~------------~~~~~~~l~~~l~~----~~~~il~~~h~~~~~~~~~~  148 (178)
T d1ye8a1          85 IPILERAYREAKKDRRKVIIIDEIGKMELF------------SKKFRDLVRQIMHD----PNVNVVATIPIRDVHPLVKE  148 (178)
T ss_dssp             HHHHHHHHHHHHHCTTCEEEECCCSTTGGG------------CHHHHHHHHHHHTC----TTSEEEEECCSSCCSHHHHH
T ss_pred             hhhHHHHHHHHHhcCCCceeecCCCccchh------------hHHHHHHHHHHhcc----CCCEEEEEEccHHHHHhhce
Confidence            445666777788889999999997543221            13445555555654    3445666666543  22223


Q ss_pred             ccCCCCc-ccEEEecCCCH
Q psy5642         105 LLRPGRL-DRLIYVPLPDD  122 (237)
Q Consensus       105 l~r~gRf-~~~i~~~~P~~  122 (237)
                      +.+  +- -..+++...+.
T Consensus       149 i~~--~~~~~i~~v~~~nr  165 (178)
T d1ye8a1         149 IRR--LPGAVLIELTPENR  165 (178)
T ss_dssp             HHT--CTTCEEEECCTTTT
T ss_pred             EEE--EeCCEEEEECCccH
Confidence            333  32 24556655543