Psyllid ID: psy4285

---

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-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530---
Protein Sequence
IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEAPPDPQ
Secondary Structure (PSIPRED)
ccccccccEEEEEccccccccHHHHccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHccccHHHHHHHHHHHHHHccccccccEEEEEEccccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHccccccccccEEEEEcccccccHHHHHHHHHHccccHHHHHHHHHHHcccHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHcHHHHHHHHHHHccccccEEEEcccccccHHHHHHHHHHHHccccccccEEEEEccccccHHHHHHHHHHHHHcccccccccccEEEEcccccccHHHHHHHHHHHHHHccccEEEEEccccccccHHHHHcccEEEEccccHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHccccHHcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cccHcHccEEEEEEcHHHHHcHHHHHcccEEEcccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHccHHHHHHHHHHHHHHHccccccHHHHHHHcccccHHHHHHHHHHHHccHHHHHHHcccHHHHHHHHHHcccHHHcccccccccHHHHHHHHHHHHHHHHHHEEEEccccccccHHHHHHHHHHHccccccccccEEEEEccHHHHHHHHHHHHHHHHHHHHcccEEEEEEccccHHHHHHHHHHHHHHccccccHHHHHHHHccccHHHHHHHHHHHHccHHHHHHHHHHHHHHccccEEEEEccccccHHHHHHHHHHHHHcHHHHHHHEEEEcccccccHHHHHHHHHHHHccccccccccEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHEEEEEHHHHHHcHHHHHcccEEEcccccHHHHHHHHHHccccccHHHHHHHHHcccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHccHHHHHHHccccHHHHHHHHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
IEKFTTNVRFCIICNYlskitpaiqsrctrfrfgpldssliMSRLDYVIEQekvnvtpdgkkAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEkyrpstldeLVSHQdiistieipeSMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLElnasddrgigIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRrklpvtpdgkkaiidlsdgDMRKVLNILQSAATAhadevnedtvynsvgyptkTEITNILRWLLNESMDLCYKINRfidenelphllfygppgtgkttTILACARKLYTKAQFNAMVLELnasddrgigIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNylskippaiqsrctrfrfgpldsslimsrldyddisfFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSardkleappdpq
Flexible Loop (DISEMBL)
iekfttnvrFCIICNylskitpaiqsRCTRFRFGPLDSSLIMSRLDYVIEqekvnvtpdgkKAIIDLSDGDMRKVLNILQSAatahadevneDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLElnasddrgigIVRDQIFQFastktmhksSYKLIILDEADAMTNDAQNalrrklpvtpdgKKAIidlsdgdmRKVLNILQSAatahadevnedtvynsvgyptkTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELnasddrgiGIVRDQIFQFastktmhksSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYlskippaiqSRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSArdkleappdpq
Low Complexity Region (SEG)
IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNiiiwyikiqeikiekGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEAPPDPQ
Disordered region (IsUnstruct)
***FTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADA********************KAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAF**************
Disordered Region (DISOPRED)
*EKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM*KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDK*E******
Disordered Region (DISEMBL)
IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEAPPDPQ
Disordered Region (DISPRO)
*EKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEA*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEAPPDPQ
Positional Conservation
no confident homologs detected

---

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	533	2.2.26 [Sep-21-2011]
P40937	340	Replication factor C subu	yes	N/A	0.313	0.491	0.623	5e-60
Q9D0F6	339	Replication factor C subu	yes	N/A	0.228	0.359	0.693	9e-60
O14003	342	Replication factor C subu	yes	N/A	0.435	0.678	0.449	1e-59
P34429	368	Probable replication fact	yes	N/A	0.272	0.394	0.642	9e-55
O74111	338	Replication factor C subu	N/A	N/A	0.270	0.426	0.627	2e-50
P38629	340	Replication factor C subu	yes	N/A	0.281	0.441	0.594	4e-50
Q54ST4	347	Probable replication fact	yes	N/A	0.258	0.397	0.659	1e-47
A3MS28	326	Replication factor C smal	yes	N/A	0.268	0.438	0.520	4e-39
A1RSA2	329	Replication factor C smal	yes	N/A	0.272	0.440	0.506	1e-38
Q8ZYK4	329	Replication factor C smal	yes	N/A	0.272	0.440	0.506	1e-38

>sp|P40937|RFC5_HUMAN Replication factor C subunit 5 OS=Homo sapiens GN=RFC5 PE=1 SV=1

 Score =  232 bits (592), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 111/178 (62%), Positives = 135/178 (75%), Gaps = 11/178 (6%)

Query: 274 PTKTEITNILRWL-------LNE---SMDLCYKINRFIDENELPHLLFYGPPGTGKTTTI 323
           P  T+I N L W+       LN+     D+   I +FI+E+ LPHLL YGPPGTGKT+TI
Sbjct: 12  PAATKIRN-LPWVEKYRPQTLNDLISHQDILSTIQKFINEDRLPHLLLYGPPGTGKTSTI 70

Query: 324 LACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAM 383
           LACA++LY   +F +MVLELNASDDRGI I+R  I  FAST+T+ K  +KL+ILDEADAM
Sbjct: 71  LACAKQLYKDKEFGSMVLELNASDDRGIDIIRGPILSFASTRTIFKKGFKLVILDEADAM 130

Query: 384 TNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
           T DAQNALRR+IEKFT N RFC+ICNYLSKI PA+QSRCTRFRFGPL   L++ RL++
Sbjct: 131 TQDAQNALRRVIEKFTENTRFCLICNYLSKIIPALQSRCTRFRFGPLTPELMVPRLEH 188

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

>sp|Q9D0F6|RFC5_MOUSE Replication factor C subunit 5 OS=Mus musculus GN=Rfc5 PE=2 SV=1

 Score =  231 bits (590), Expect = 9e-60,   Method: Compositional matrix adjust.
 Identities = 104/150 (69%), Positives = 123/150 (82%)

Query: 292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
           D+   I +FI E+ LPHLL YGPPGTGKT+TILACA++LY   +F +MVLELNASDDRGI
Sbjct: 38  DILSTIQKFISEDRLPHLLLYGPPGTGKTSTILACAKQLYKDKEFGSMVLELNASDDRGI 97

Query: 352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
            IVR  I  FAST+T+ K  +KL+ILDEADAMT DAQNALRR+IEKFT N RFC+ICNYL
Sbjct: 98  DIVRGPILSFASTRTIFKKGFKLVILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYL 157

Query: 412 SKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
           SKI PA+QSRCTRFRFGPL   L++ RL++
Sbjct: 158 SKIIPALQSRCTRFRFGPLTPELMVPRLEH 187

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

Mus musculus (taxid: 10090)

>sp|O14003|RFC3_SCHPO Replication factor C subunit 3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rfc3 PE=1 SV=2

 Score =  231 bits (589), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 133/296 (44%), Positives = 174/296 (58%), Gaps = 64/296 (21%)

Query: 292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
           D+   + +FI  N +PH+LFYGPPGTGKT+TILACARK+Y    +   ++ELNASDDRGI
Sbjct: 42  DIISTLEKFISSNRVPHMLFYGPPGTGKTSTILACARKIYG-PNYRNQLMELNASDDRGI 100

Query: 352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
             VR+QI  FAST+ +  S++K+IILDEADAMT  AQNALRR+IEK+T NVRFCIICNY+
Sbjct: 101 DAVREQIKNFASTRQIFASTFKMIILDEADAMTLAAQNALRRVIEKYTKNVRFCIICNYI 160

Query: 412 SKIPPAIQSRCTRFRFGPL----------------------DSSLIMSRLD--------- 440
           +KI PAIQSRCTRFRF PL                      D+ + + RL          
Sbjct: 161 NKISPAIQSRCTRFRFQPLPPKEIEKTVDHVIQSEHCNIDPDAKMAVLRLSKGDMRKALN 220

Query: 441 --------YD-----------------DISFF-------NIIIWYIKIQEIKIEKGLALT 468
                   YD                 DI +F         +I +  I  IK +KGLAL 
Sbjct: 221 ILQACHAAYDHIDVSAIYNCVGHPHPSDIDYFLKSIMNDEFVIAFNTISSIKQQKGLALQ 280

Query: 469 DILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD 524
           DILT I   +  LEI  +  + ++ +++ IE+R++ G SEKIQLSA+IA+  +  D
Sbjct: 281 DILTCIFEALDELEIKPNAKIFILDQLATIEHRMSFGCSEKIQLSAMIASIKTGVD 336

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins PCNA and activator 1. Subunit 3 binds ATP. Also involved in replication and DNA damage checkpoint controls, probably functioning as a checkpoint sensor.

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

>sp|P34429|RFC5_CAEEL Probable replication factor C subunit 5 OS=Caenorhabditis elegans GN=F44B9.8 PE=3 SV=3

 Score =  215 bits (547), Expect = 9e-55,   Method: Compositional matrix adjust.
 Identities = 99/154 (64%), Positives = 119/154 (77%), Gaps = 9/154 (5%)

Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD 356
           + +FI+   LPHLLFYGPPGTGKTTT+LA AR++Y+  +  +MVLELNASD+RGI +VR+
Sbjct: 53  LTKFIENRTLPHLLFYGPPGTGKTTTVLAAARQMYSPTKMASMVLELNASDERGIDVVRN 112

Query: 357 QIFQFASTKTMHKSS---------YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCII 407
            I  FA TK +   S         +KL+ILDEADAMT DAQNALRR+IEK+T NVRFCII
Sbjct: 113 TIVNFAQTKGLQAFSTSSNTGTVPFKLVILDEADAMTKDAQNALRRVIEKYTDNVRFCII 172

Query: 408 CNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
           CNYL+ I PAIQSRCTRFRF PLD  LI+ RL+Y
Sbjct: 173 CNYLASIVPAIQSRCTRFRFAPLDQKLIVPRLEY 206

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

Caenorhabditis elegans (taxid: 6239)

>sp|O74111|RFC3_BLAAD Replication factor C subunit 3 OS=Blastobotrys adeninivorans GN=RFC3 PE=3 SV=1

 Score =  201 bits (510), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 91/145 (62%), Positives = 114/145 (78%), Gaps = 1/145 (0%)

Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD 356
           I +F++E +LPHLLF+GPPGTGKTTTI+A AR++Y K  +  M+LELNASD+RGI +VRD
Sbjct: 41  IKKFVEEGKLPHLLFHGPPGTGKTTTIIAVARQIYGK-NYRNMILELNASDERGIDVVRD 99

Query: 357 QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPP 416
           QI  FAST+ +  S +KL+ILDEADAMTN AQNALRRIIEK++ + RFCI+ NY  K+ P
Sbjct: 100 QIKTFASTRQIFSSGFKLVILDEADAMTNAAQNALRRIIEKYSAHTRFCILANYTHKLNP 159

Query: 417 AIQSRCTRFRFGPLDSSLIMSRLDY 441
           A+ SRCTRFRF PL    I  RL +
Sbjct: 160 ALLSRCTRFRFSPLKEDAIKHRLAH 184

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. Subunit 3 binds ATP.

Blastobotrys adeninivorans (taxid: 409370)

>sp|P38629|RFC3_YEAST Replication factor C subunit 3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RFC3 PE=1 SV=1

 Score =  199 bits (506), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 94/158 (59%), Positives = 118/158 (74%), Gaps = 8/158 (5%)

Query: 289 ESMDLCYKIN-------RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVL 341
           E++D  Y  N       +F+DE +LPHLLFYGPPGTGKT+TI+A AR++Y K  ++ MVL
Sbjct: 22  ETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGK-NYSNMVL 80

Query: 342 ELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTN 401
           ELNASDDRGI +VR+QI  FAST+ +    +KLIILDEADAMTN AQNALRR+IE++T N
Sbjct: 81  ELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKN 140

Query: 402 VRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
            RFC++ NY  K+ PA+ SRCTRFRF PL    I  R+
Sbjct: 141 TRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRI 178

Component of ATP-dependent clamp loader (RFC and RFC-like) complexes for DNA clamps, such as the POL30/PCNA homotrimer and the checkpoint clamp DDC1:MEC3:RAD17 complex. During a clamp loading circle, the RFC:clamp complex binds to DNA and the recognition of the double-stranded/single-stranded junction stimulates ATP hydrolysis by RFC. The complex presumably provides bipartite ATP sites in which one subunit supplies a catalytic site for hydrolysis of ATP bound to the neighboring subunit. Dissociation of RFC from the clamp leaves the clamp encircling DNA. Component of the replication factor C (RFC or activator 1) complex which loads POL30/PCNA and acts during elongation of primed DNA templates by DNA polymerase delta and epsilon. RFC has an essential but redundant activity in sister chromatid cohesion establishment. Component of the RFC-like complex CTF18-RFC which is required for efficient establishment of chromosome cohesion during S-phase and may load or unload POL30/PCNA. Component of the RFC-like RAD24-RFC complex which loads the checkpoint clamp DDC1:MEC3:RAD17 complex and is involved in DNA repair pathways. Component of the RFC-like ELG1-RFC complex which appears to have a role in DNA replication, replication fork re-start, recombination and repair. RFC3 supplies a catalytic site to the ATP site of RFC4.

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

>sp|Q54ST4|RFC5_DICDI Probable replication factor C subunit 5 OS=Dictyostelium discoideum GN=rfc5 PE=3 SV=1

 Score =  191 bits (485), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 93/141 (65%), Positives = 109/141 (77%), Gaps = 3/141 (2%)

Query: 292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
           D+   I + ID N LPHLLFYGPPGTGKT+TI A ARKLY    ++ MVLELNASDDRGI
Sbjct: 43  DITQTITKLIDNNTLPHLLFYGPPGTGKTSTIQAIARKLYGD-NYSRMVLELNASDDRGI 101

Query: 352 GIVRDQIFQFASTKTMHKSS--YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN 409
            +VR+QI  FAS+     ++  YKLIILDEAD+MTN AQ ALRR+IEK+T   RFCI+CN
Sbjct: 102 DVVREQIKTFASSMFFFNTTVPYKLIILDEADSMTNIAQTALRRVIEKYTKTTRFCIVCN 161

Query: 410 YLSKIPPAIQSRCTRFRFGPL 430
           Y+ KI PA+QSRCTRFRF PL
Sbjct: 162 YVIKIIPALQSRCTRFRFSPL 182

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

Dictyostelium discoideum (taxid: 44689)

>sp|A3MS28|RFCS_PYRCJ Replication factor C small subunit OS=Pyrobaculum calidifontis (strain JCM 11548 / VA1) GN=rfcS PE=3 SV=1

 Score =  162 bits (411), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 75/144 (52%), Positives = 101/144 (70%), Gaps = 1/144 (0%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
           ++  F+    LPHLLFYGPPGTGKTT  L  AR+LY +  +    LELNASD+RGIG++R
Sbjct: 27  RLREFVKAGNLPHLLFYGPPGTGKTTMALVLARELYGE-YWRENTLELNASDERGIGVIR 85

Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
           +++ +FA T  + K+ +KL+ILDEAD MT+DAQ ALRRI+E +  N RF ++ NY+S+I 
Sbjct: 86  ERVKEFARTAPVGKAPFKLVILDEADNMTSDAQQALRRIMEIYAQNTRFILLANYVSRII 145

Query: 416 PAIQSRCTRFRFGPLDSSLIMSRL 439
             I SRC  FRF P+   L+  RL
Sbjct: 146 DPIISRCAVFRFSPMPRHLMAERL 169

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

Pyrobaculum calidifontis (strain JCM 11548 / VA1) (taxid: 410359)

>sp|A1RSA2|RFCS1_PYRIL Replication factor C small subunit 1 OS=Pyrobaculum islandicum (strain DSM 4184 / JCM 9189) GN=rfcS1 PE=3 SV=1

 Score =  161 bits (408), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 74/146 (50%), Positives = 101/146 (69%), Gaps = 1/146 (0%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
           ++  F+    +PHLLFYGPPGTGKTT  L  AR+LY +  +    LELNASD+RGI ++R
Sbjct: 27  RLREFVKSGNMPHLLFYGPPGTGKTTMALVLARELYGE-YWRENTLELNASDERGINVIR 85

Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
           +++ +FA T  + K+ +KL+ILDEAD MT+DAQ ALRRI+E +  N RF ++ NY+S+I 
Sbjct: 86  ERVKEFARTAPVGKAPFKLVILDEADNMTSDAQQALRRIMEIYAQNTRFILLANYVSRII 145

Query: 416 PAIQSRCTRFRFGPLDSSLIMSRLDY 441
             I SRC  FRF P+   L+  RL Y
Sbjct: 146 DPIISRCAVFRFSPMPRHLMAERLKY 171

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

Pyrobaculum islandicum (strain DSM 4184 / JCM 9189) (taxid: 384616)

>sp|Q8ZYK4|RFCS1_PYRAE Replication factor C small subunit 1 OS=Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827) GN=rfcS1 PE=3 SV=1

 Score =  161 bits (407), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 74/146 (50%), Positives = 102/146 (69%), Gaps = 1/146 (0%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
           ++  F+    +PHLLFYGPPGTGKTT  L  AR+LY +  +    LELNASD+RGI ++R
Sbjct: 27  RLREFVKAGNMPHLLFYGPPGTGKTTMALVLARELYGE-YWRENTLELNASDERGINVIR 85

Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
           +++ +FA T  + K+ +KL+ILDEAD MT+DAQ ALRRI+E +  N RF ++ NY+S+I 
Sbjct: 86  ERVKEFARTAPVGKAPFKLVILDEADNMTSDAQQALRRIMEIYAQNTRFILLANYVSRII 145

Query: 416 PAIQSRCTRFRFGPLDSSLIMSRLDY 441
             I SRC  FRF P+  SL+  RL +
Sbjct: 146 DPIISRCAVFRFSPMPRSLMAERLKF 171

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

Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827) (taxid: 178306)

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	533
147902441	335	MGC80325 protein [Xenopus laevis] gi|491	0.444	0.707	0.53	4e-79
157123250	330	replication factor c / DNA polymerase ii	0.431	0.696	0.540	1e-78
321458433	330	hypothetical protein DAPPUDRAFT_202808 [	0.435	0.703	0.522	1e-78
260791339	329	hypothetical protein BRAFLDRAFT_125553 [	0.437	0.708	0.513	1e-77
48097300	328	PREDICTED: replication factor C subunit	0.427	0.695	0.532	5e-77
383849950	329	PREDICTED: replication factor C subunit	0.437	0.708	0.510	5e-76
158292645	327	AGAP005144-PA [Anopheles gambiae str. PE	0.425	0.694	0.542	7e-76
114050971	334	replication factor C (activator 1) 5 [Bo	0.442	0.706	0.51	2e-75
312372786	335	hypothetical protein AND_19724 [Anophele	0.425	0.677	0.529	8e-75
380015701	330	PREDICTED: replication factor C subunit	0.427	0.690	0.527	1e-74

>gi|147902441|ref|NP_001085526.1| MGC80325 protein [Xenopus laevis] gi|49117945|gb|AAH72889.1| MGC80325 protein [Xenopus laevis]

 Score =  301 bits (772), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 159/300 (53%), Positives = 193/300 (64%), Gaps = 63/300 (21%)

Query: 292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
           D+   I RFI E++LPHLLFYGPPGTGKT+TILACA++LY   +FN+MVLELNASDDRGI
Sbjct: 34  DILSTIQRFISEDKLPHLLFYGPPGTGKTSTILACAKQLYKDREFNSMVLELNASDDRGI 93

Query: 352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
            IVR  +  FAST+T+ K  +KL+ILDEADAMT DAQNALRR+IEKFT N RFC+ICNYL
Sbjct: 94  DIVRGPVLSFASTRTIFKKGFKLVILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYL 153

Query: 412 SKIPPAIQSRCTRFRFGPLDSSLIMSRL------DYDDIS-------------------- 445
           SKI PA+QSRCTRFRFGPL S +++ RL      ++ DIS                    
Sbjct: 154 SKIIPALQSRCTRFRFGPLSSEMMIPRLEHVVKEEHVDISPDGMKALVTLSNGDMRRSLN 213

Query: 446 ----------------------------FFNIIIW---------YIKIQEIKIEKGLALT 468
                                         NI+ W         Y  I E+K  KGLAL 
Sbjct: 214 ILQSTNMAYSKVTEDTVYTCTGHPLRSDIANILDWMLNKDFTSAYKNIMELKTLKGLALH 273

Query: 469 DILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEA 528
           DILTEI L VHR++ P  + + L++KM+DIEYRLA+GTSEKIQLS++IAAF  ARD + A
Sbjct: 274 DILTEIHLYVHRVDFPALVRIHLLVKMADIEYRLASGTSEKIQLSSMIAAFQVARDMVAA 333

Source: Xenopus laevis

Species: Xenopus laevis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|157123250|ref|XP_001660080.1| replication factor c / DNA polymerase iii gamma-tau subunit [Aedes aegypti] gi|108874432|gb|EAT38657.1| AAEL009465-PA [Aedes aegypti]

 Score =  300 bits (768), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 159/294 (54%), Positives = 187/294 (63%), Gaps = 64/294 (21%)

Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD 356
           IN+FI E +LPHLLFYGPPGTGKT+TILACAR+LY    FN MVLELNASDDRGI IVR+
Sbjct: 33  INKFIQEEQLPHLLFYGPPGTGKTSTILACARQLYKPQSFNQMVLELNASDDRGINIVRN 92

Query: 357 QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPP 416
           QI  FAST+T+    YKLIILDEADAMTNDAQNALRRIIEK+T NVRFCIICNYLSKI P
Sbjct: 93  QILNFASTRTIFSGGYKLIILDEADAMTNDAQNALRRIIEKYTDNVRFCIICNYLSKIIP 152

Query: 417 AIQSRCTRFRFGPLDSSLIMSRLDY----------DD----------------------- 443
           A+QSRCTRFRF PL    I+ RL++          DD                       
Sbjct: 153 ALQSRCTRFRFAPLSPDQILPRLEHVIDAEGIKVSDDGKKALMTLAGGDMRKVLNVLQST 212

Query: 444 ---------------------ISFFNIIIWYI----------KIQEIKIEKGLALTDILT 472
                                I   NI+ W +          KIQE+K  KGLAL DILT
Sbjct: 213 WMAYKDVTEDNVYTCVGHPLKIDITNIVNWLLNVESFKETFEKIQELKTNKGLALEDILT 272

Query: 473 EISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKL 526
           EI L VHR+E+P  ++  L++KM+ +E RLAAG  EK Q+++LIAAF  ARD++
Sbjct: 273 EIHLYVHRMELPPRVMSQLLIKMAAVEERLAAGCVEKPQMASLIAAFQIARDQV 326

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321458433|gb|EFX69502.1| hypothetical protein DAPPUDRAFT_202808 [Daphnia pulex]

 Score =  300 bits (768), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 154/295 (52%), Positives = 195/295 (66%), Gaps = 63/295 (21%)

Query: 292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
           D+   I +FI+EN LPHLLFYGPPGTGKT+TILACA++LYT  QFN+MVLELNASDDRGI
Sbjct: 26  DIISTIRKFINENRLPHLLFYGPPGTGKTSTILACAKELYTPQQFNSMVLELNASDDRGI 85

Query: 352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
            +VR+QI  FAST+++ KS +KLIILDEADAMTNDAQNALRR+IEKFT NVRFC+ICNY+
Sbjct: 86  NVVRNQIMSFASTRSIFKSGFKLIILDEADAMTNDAQNALRRVIEKFTENVRFCLICNYM 145

Query: 412 SKIPPAIQSRCTRFRFGPLDSSLIMSR--------------------------------- 438
           SKI PAIQSRCTRFRFGPL S  I+ R                                 
Sbjct: 146 SKIIPAIQSRCTRFRFGPLKSDQILPRMNYVIEEEKIKVTEDGRQALLSLAHGDMRRVIN 205

Query: 439 ------LDYDDIS---------------FFNIIIW---------YIKIQEIKIEKGLALT 468
                 + +D+++                 N++ W         Y KI++++  KGLAL 
Sbjct: 206 ILQSTSMAFDEVNEDHVYTCVGHPLKSDIANVVSWMLNEDLTSAYSKIRDLQTFKGLALQ 265

Query: 469 DILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSAR 523
           DILTE  L VH++E P ++ V L+ KM+D+EYRL+AG SEK+QL +L+AAF+S +
Sbjct: 266 DILTETHLYVHKIEFPPNVRVFLLEKMADVEYRLSAGCSEKLQLGSLLAAFDSIK 320

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|260791339|ref|XP_002590697.1| hypothetical protein BRAFLDRAFT_125553 [Branchiostoma floridae] gi|229275893|gb|EEN46708.1| hypothetical protein BRAFLDRAFT_125553 [Branchiostoma floridae]

 Score =  296 bits (759), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 152/296 (51%), Positives = 190/296 (64%), Gaps = 63/296 (21%)

Query: 292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
           D+   I RF+DE+ LPHLLFYGPPGTGKT+TILACAR+LY   +FN+MVLELNASDDRGI
Sbjct: 29  DIISTIQRFLDEDRLPHLLFYGPPGTGKTSTILACARRLYADREFNSMVLELNASDDRGI 88

Query: 352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
           GIVR  + QFAST+T+ K  +KL+ILDEADAMT DAQNALRR++EKFT N RFC+ICNYL
Sbjct: 89  GIVRGPVLQFASTRTIFKRGFKLVILDEADAMTGDAQNALRRVMEKFTENTRFCLICNYL 148

Query: 412 SKIPPAIQSRCTRFRFGPLDSSLIMSRL-------------------------------- 439
           SKI PAIQSRCTRFRFGPL    ++ RL                                
Sbjct: 149 SKIIPAIQSRCTRFRFGPLGVDQMLPRLEHVIQEEKVDVTDDGKKAILQLANGDMRRVLN 208

Query: 440 ------------DYDDISFF----------NIIIW---------YIKIQEIKIEKGLALT 468
                       D D++             NI+ W         Y  I ++K+ KGLAL 
Sbjct: 209 ILQSTSMAHDVVDEDNVYLVTGQPLRSDIANIVNWMLNENFTTAYNNIFQLKVLKGLALQ 268

Query: 469 DILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD 524
           DILTE+ L VHR++ P ++ + L+ KM+D+EYRL+AGT+EK+QLS++IAAF   R+
Sbjct: 269 DILTEVHLFVHRIDFPMAVKMVLLQKMADVEYRLSAGTNEKLQLSSVIAAFQVVRN 324

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Phylum: Chordata

Superkingdom: Eukaryota

>gi|48097300|ref|XP_393747.1| PREDICTED: replication factor C subunit 5-like [Apis mellifera]

 Score =  295 bits (754), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 155/291 (53%), Positives = 191/291 (65%), Gaps = 63/291 (21%)

Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD 356
           IN+FIDEN LPHLLFYGPPGTGKT+TILACARKLYT AQFN+MVLE+NASDDRGI IVR 
Sbjct: 35  INKFIDENLLPHLLFYGPPGTGKTSTILACARKLYTSAQFNSMVLEMNASDDRGINIVRG 94

Query: 357 QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPP 416
           QI  FAST TM+KS +KLIILDEADAMTNDAQNALRRIIEK+T NVRFCIICNYLSKI P
Sbjct: 95  QILSFASTGTMYKSGFKLIILDEADAMTNDAQNALRRIIEKYTDNVRFCIICNYLSKIIP 154

Query: 417 AIQSRC-----------------------------------------------------T 423
           A+QSRC                                                     T
Sbjct: 155 ALQSRCTKFRFGPLSIDQILPRLDTIIKEENLNVTEDGKQALITLSGGDMRKVLNVLQST 214

Query: 424 RFRFGPLDSSLIMSRLDYD-DISFFNIIIW---------YIKIQEIKIEKGLALTDILTE 473
              FG +    + S + +   I   NI+ W         Y KIQ+IK++KGLAL DILTE
Sbjct: 215 WLAFGAVTEENVYSCVGHPLPIDIKNIVNWLFNESYELCYCKIQDIKLKKGLALQDILTE 274

Query: 474 ISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD 524
           + L ++++E P+S+L+DL++K+++IE R++ G SE +QL+AL++AF +ARD
Sbjct: 275 LHLFINKIEFPDSILIDLIIKLAEIEKRVSIGCSEAVQLNALVSAFQNARD 325

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383849950|ref|XP_003700596.1| PREDICTED: replication factor C subunit 5-like [Megachile rotundata]

 Score =  291 bits (746), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 151/296 (51%), Positives = 194/296 (65%), Gaps = 63/296 (21%)

Query: 292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
           D+   IN+FI+E++LPHLLFYGPPGTGKT+TILACARKLYT  QFN+MVLE+NASDDRGI
Sbjct: 30  DIIKTINKFINEDQLPHLLFYGPPGTGKTSTILACARKLYTAGQFNSMVLEMNASDDRGI 89

Query: 352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
           GIVR QI  FAST T++KS +KLIILDEADAMTNDAQNALRRIIEK+T NVRFCIICNYL
Sbjct: 90  GIVRGQILNFASTGTLYKSGFKLIILDEADAMTNDAQNALRRIIEKYTDNVRFCIICNYL 149

Query: 412 SKIPPAIQSRC------------------------------------------------- 422
           SKI PA+QSRC                                                 
Sbjct: 150 SKIIPALQSRCTKFRFGPLSSDQILPRLETIIKEENLNVSEDGKEALIALSGGDMRKVLN 209

Query: 423 ----TRFRFGPLDSSLIMSRLDYD-DISFFNIIIW---------YIKIQEIKIEKGLALT 468
               T   FG +    + + + +   I   NI+ W         Y KIQ+IK++KGLAL 
Sbjct: 210 VLQSTWLAFGTVTEETVYTCVGHPLPIDIKNIVNWLLNESYELCYCKIQDIKLKKGLALQ 269

Query: 469 DILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD 524
           DILT++ L V+++E P+S+L++L++K+++IE R+A G SE +QL+AL++AF +AR+
Sbjct: 270 DILTQLHLFVNKIEFPDSILIELIIKLAEIEKRVAIGCSEPVQLNALVSAFQNARN 325

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158292645|ref|XP_314028.3| AGAP005144-PA [Anopheles gambiae str. PEST] gi|157017089|gb|EAA09454.3| AGAP005144-PA [Anopheles gambiae str. PEST]

 Score =  291 bits (745), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 158/291 (54%), Positives = 185/291 (63%), Gaps = 64/291 (21%)

Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD 356
           IN+FI E +LPHLLFYGPPGTGKT+TILACAR+LY    F +MVLELNASDDRGI IVR 
Sbjct: 33  INKFIKEEQLPHLLFYGPPGTGKTSTILACARQLYKPQSFGSMVLELNASDDRGINIVRG 92

Query: 357 QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPP 416
           QI  FAST+T+ K  YKLIILDEADAMTNDAQNALRRIIEK+T NVRFCIICNYLSKI P
Sbjct: 93  QILDFASTRTIFKGGYKLIILDEADAMTNDAQNALRRIIEKYTENVRFCIICNYLSKIIP 152

Query: 417 AIQSRCTRFRFGPLDSSLIMSRLDY----------DD----------------------- 443
           AIQSRCTRFRF PL    I+ RL++          DD                       
Sbjct: 153 AIQSRCTRFRFAPLSPDQILPRLEHVVEAEGIDVTDDGKKALMTLAGGDMRKVLNVLQST 212

Query: 444 ---------ISFFN------------IIIW----------YIKIQEIKIEKGLALTDILT 472
                    ++ +N            II W          Y KIQ++K +KGLAL DILT
Sbjct: 213 WMAYKKVTEVNVYNCVGHPLKEDINNIIFWLLNEESFKACYEKIQQLKTQKGLALEDILT 272

Query: 473 EISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSAR 523
           EI L+V+RLEIP  +   L++ ++ IE RLA G  EK Q++ALIAAF+  R
Sbjct: 273 EIHLVVNRLEIPPRVSSQLLINLASIEERLADGCVEKPQITALIAAFSKVR 323

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|114050971|ref|NP_001040148.1| replication factor C (activator 1) 5 [Bombyx mori] gi|87248211|gb|ABD36158.1| replication factor C (activator 1) 5 [Bombyx mori]

 Score =  290 bits (741), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 153/300 (51%), Positives = 197/300 (65%), Gaps = 64/300 (21%)

Query: 292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
           D+   IN+F+ EN+LPHLLFYGPPGTGKT+TILACA+++YT  QF++MVLELNASDDRGI
Sbjct: 29  DIIKTINQFMKENQLPHLLFYGPPGTGKTSTILACAKQMYTPQQFSSMVLELNASDDRGI 88

Query: 352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
           GIVR QI  FAST+T+ K+  KLIILDEADAMTNDAQNALRRIIEK+T NVRFCIICNYL
Sbjct: 89  GIVRGQILSFASTRTIFKAGPKLIILDEADAMTNDAQNALRRIIEKYTENVRFCIICNYL 148

Query: 412 SKIPPAIQSRCTRFRF-------------------------GPLDSSLIMSRLD------ 440
            KI PA+QSRCTRFRF                         G + + L +S  D      
Sbjct: 149 GKIIPALQSRCTRFRFAPLKQDQIVPRLQEIVTTEGVKMSEGGMKALLTLSGGDMRKVLN 208

Query: 441 --------YDDISFFN---------------IIIWYIK----------IQEIKIEKGLAL 467
                   Y D++  N               I+ W +           IQ++KI KGLAL
Sbjct: 209 TLQSTWLAYRDVTEDNVYTCVGHPLRADIDSILNWLLNENDFSACFKSIQDLKIAKGLAL 268

Query: 468 TDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLE 527
           +DIL E+  ++ R+++P  +LV L++KMSD E RLA+G+SE+++L+ALIA+F  ARD+++
Sbjct: 269 SDILAEVHTIIQRVKLPPEVLVSLLIKMSDAEARLASGSSERVELAALIASFQIARDQVK 328

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312372786|gb|EFR20672.1| hypothetical protein AND_19724 [Anopheles darlingi]

 Score =  287 bits (735), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 154/291 (52%), Positives = 184/291 (63%), Gaps = 64/291 (21%)

Query: 298 NRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQ 357
           N+FI E +LPHLLFYGPPGTGKT+TILACAR+LY    F +MVLELNASDDRGI IVR Q
Sbjct: 42  NKFIKEEQLPHLLFYGPPGTGKTSTILACARQLYKPQSFGSMVLELNASDDRGINIVRGQ 101

Query: 358 IFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPA 417
           I  FAST+T+ K  YKLIILDEADAMTNDAQNALRRIIEK+T NVRFCIICNYLSKI PA
Sbjct: 102 ILDFASTRTIFKGGYKLIILDEADAMTNDAQNALRRIIEKYTENVRFCIICNYLSKIIPA 161

Query: 418 IQSRCTRFRFGPLDSSLIMSRLDY------------------------------------ 441
           IQSRCTRFRF PL    I+ RL++                                    
Sbjct: 162 IQSRCTRFRFAPLGVEQILPRLEHVIEAEGIEATEDGKKALITLAGGDMRKVLNVLQSTW 221

Query: 442 ------DDISFFN------------IIIW----------YIKIQEIKIEKGLALTDILTE 473
                  +I+ +N            II W          Y KIQ++K +KGLAL DILTE
Sbjct: 222 MAYKSVTEINVYNCVGHPLKEDINDIIFWLLNEESFKTCYEKIQQLKTQKGLALEDILTE 281

Query: 474 ISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD 524
           I L+++RLEIP  +   L++ ++ IE RLA G  EK Q++ALI+AF+  R+
Sbjct: 282 IHLVINRLEIPPRVSSQLLITLASIEERLADGCVEKPQIAALISAFSKVRE 332

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380015701|ref|XP_003691836.1| PREDICTED: replication factor C subunit 5-like [Apis florea]

 Score =  286 bits (733), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 154/292 (52%), Positives = 190/292 (65%), Gaps = 64/292 (21%)

Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD 356
           IN+FIDEN LPHLLFYGPPGTGKT+TILACARKLYT AQFN+MVLE+NASDDRGI IVR 
Sbjct: 36  INKFIDENLLPHLLFYGPPGTGKTSTILACARKLYTPAQFNSMVLEMNASDDRGINIVRG 95

Query: 357 QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPP 416
           QI  FAST TM++S +KLIILDEADAMTNDAQNALRRIIEK+T NVRFCIICNYLSKI P
Sbjct: 96  QILSFASTGTMYRSGFKLIILDEADAMTNDAQNALRRIIEKYTDNVRFCIICNYLSKIIP 155

Query: 417 AIQSRC-----------------------------------------------------T 423
           A+QSRC                                                     T
Sbjct: 156 ALQSRCTKFRFGPLSIDQILPRLDTIIKEENLNVTEDGKQALITLSGGDMRKVLNVLQST 215

Query: 424 RFRFGPLDSSLIMSRLDYD-DISFFNIIIW---------YIKIQEIKIEKGLALTDILTE 473
              FG +    + S + +   I   NI+ W         Y KIQ+IK++KGLAL DILTE
Sbjct: 216 WLAFGAVTEENVYSCVGHPLPIDIKNIVNWLFNESYELCYCKIQDIKLKKGLALQDILTE 275

Query: 474 ISLLVHRL-EIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD 524
           + L + ++ E P+S+L+DL++K+++IE R++ G SE +QL+AL++AF +ARD
Sbjct: 276 LHLFIIKVFEFPDSILIDLIIKLAEIEKRVSIGCSEAVQLNALVSAFQNARD 327

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

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	533
ZFIN|ZDB-GENE-040907-1	334	rfc5 "replication factor C (ac	0.281	0.449	0.7	2.9e-74
UNIPROTKB|P40937	340	RFC5 "Replication factor C sub	0.313	0.491	0.623	5.3e-73
MGI|MGI:1919401	339	Rfc5 "replication factor C (ac	0.281	0.442	0.693	6.7e-73
UNIPROTKB|F1RKG3	354	RFC5 "Uncharacterized protein"	0.281	0.423	0.693	1.1e-72
UNIPROTKB|E2RCF4	339	RFC5 "Uncharacterized protein"	0.281	0.442	0.693	1.4e-72
RGD|1309280	339	Rfc5 "replication factor C (ac	0.281	0.442	0.693	1.4e-72
FB|FBgn0032244	332	RfC3 "Replication factor C sub	0.270	0.433	0.756	3.3e-69
UNIPROTKB|J9NUF8	316	RFC5 "Uncharacterized protein"	0.281	0.474	0.693	5.4e-59
UNIPROTKB|Q32PI3	316	RFC5 "Uncharacterized protein"	0.281	0.474	0.693	1.1e-58
WB|WBGene00018409	368	F44B9.8 [Caenorhabditis elegan	0.272	0.394	0.642	9.9e-58

ZFIN|ZDB-GENE-040907-1 rfc5 "replication factor C (activator 1) 5" [Danio rerio (taxid:7955)]

 Score = 565 (203.9 bits), Expect = 2.9e-74, Sum P(2) = 2.9e-74
 Identities = 105/150 (70%), Positives = 125/150 (83%)

Query:   292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
             D+   I +FI E+ LPHLLFYGPPGTGKT+TILACAR+LY   +FN+MVLELNASDDRGI
Sbjct:    33 DILSTIQKFISEDRLPHLLFYGPPGTGKTSTILACARQLYKDKEFNSMVLELNASDDRGI 92

Query:   352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
              +VR  I  FAST+T+ K  +KL+ILDEADAMT DAQNALRR+IEKFT N RFC+ICNYL
Sbjct:    93 DVVRGPILSFASTRTIFKKGFKLVILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYL 152

Query:   412 SKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
             SKI PA+QSRCTRFRFGPL  + ++ RL++
Sbjct:   153 SKIIPALQSRCTRFRFGPLSQNQMIPRLEH 182

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0060041 "retina development in camera-type eye" evidence=IMP

UNIPROTKB|P40937 RFC5 "Replication factor C subunit 5" [Homo sapiens (taxid:9606)]

 Score = 557 (201.1 bits), Expect = 5.3e-73, Sum P(2) = 5.3e-73
 Identities = 111/178 (62%), Positives = 136/178 (76%)

Query:   274 PTKTEITNILRWL-------LNESM---DLCYKINRFIDENELPHLLFYGPPGTGKTTTI 323
             P  T+I N L W+       LN+ +   D+   I +FI+E+ LPHLL YGPPGTGKT+TI
Sbjct:    12 PAATKIRN-LPWVEKYRPQTLNDLISHQDILSTIQKFINEDRLPHLLLYGPPGTGKTSTI 70

Query:   324 LACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAM 383
             LACA++LY   +F +MVLELNASDDRGI I+R  I  FAST+T+ K  +KL+ILDEADAM
Sbjct:    71 LACAKQLYKDKEFGSMVLELNASDDRGIDIIRGPILSFASTRTIFKKGFKLVILDEADAM 130

Query:   384 TNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
             T DAQNALRR+IEKFT N RFC+ICNYLSKI PA+QSRCTRFRFGPL   L++ RL++
Sbjct:   131 TQDAQNALRRVIEKFTENTRFCLICNYLSKIIPALQSRCTRFRFGPLTPELMVPRLEH 188

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0019899 "enzyme binding" evidence=NAS

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

GO:0005515 "protein binding" evidence=IPI

GO:0006281 "DNA repair" evidence=NAS;TAS

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

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

GO:0000723 "telomere maintenance" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

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

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

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

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

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

GO:0000075 "cell cycle checkpoint" evidence=TAS

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

GO:0000278 "mitotic cell cycle" evidence=TAS

MGI|MGI:1919401 Rfc5 "replication factor C (activator 1) 5" [Mus musculus (taxid:10090)]

 Score = 554 (200.1 bits), Expect = 6.7e-73, Sum P(2) = 6.7e-73
 Identities = 104/150 (69%), Positives = 123/150 (82%)

Query:   292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
             D+   I +FI E+ LPHLL YGPPGTGKT+TILACA++LY   +F +MVLELNASDDRGI
Sbjct:    38 DILSTIQKFISEDRLPHLLLYGPPGTGKTSTILACAKQLYKDKEFGSMVLELNASDDRGI 97

Query:   352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
              IVR  I  FAST+T+ K  +KL+ILDEADAMT DAQNALRR+IEKFT N RFC+ICNYL
Sbjct:    98 DIVRGPILSFASTRTIFKKGFKLVILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYL 157

Query:   412 SKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
             SKI PA+QSRCTRFRFGPL   L++ RL++
Sbjct:   158 SKIIPALQSRCTRFRFGPLTPELMVPRLEH 187

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0006260 "DNA replication" evidence=IEA

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

UNIPROTKB|F1RKG3 RFC5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 554 (200.1 bits), Expect = 1.1e-72, Sum P(2) = 1.1e-72
 Identities = 104/150 (69%), Positives = 123/150 (82%)

Query:   292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
             D+   I +FI E+ LPHLL YGPPGTGKT+TILACA++LY   +F +MVLELNASDDRGI
Sbjct:    53 DILSTIQKFISEDRLPHLLLYGPPGTGKTSTILACAKQLYKDKEFGSMVLELNASDDRGI 112

Query:   352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
              IVR  I  FAST+T+ K  +KL+ILDEADAMT DAQNALRR+IEKFT N RFC+ICNYL
Sbjct:   113 DIVRGPILSFASTRTIFKKGFKLVILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYL 172

Query:   412 SKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
             SKI PA+QSRCTRFRFGPL   L++ RL++
Sbjct:   173 SKIIPALQSRCTRFRFGPLTPELMVPRLEH 202

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

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RCF4 RFC5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 554 (200.1 bits), Expect = 1.4e-72, Sum P(2) = 1.4e-72
 Identities = 104/150 (69%), Positives = 123/150 (82%)

Query:   292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
             D+   I +FI E+ LPHLL YGPPGTGKT+TILACA++LY   +F +MVLELNASDDRGI
Sbjct:    38 DILSTIQKFISEDRLPHLLLYGPPGTGKTSTILACAKQLYKDKEFGSMVLELNASDDRGI 97

Query:   352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
              IVR  I  FAST+T+ K  +KL+ILDEADAMT DAQNALRR+IEKFT N RFC+ICNYL
Sbjct:    98 DIVRGPILSFASTRTIFKKGFKLVILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYL 157

Query:   412 SKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
             SKI PA+QSRCTRFRFGPL   L++ RL++
Sbjct:   158 SKIIPALQSRCTRFRFGPLTPELMVPRLEH 187

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

RGD|1309280 Rfc5 "replication factor C (activator 1) 5" [Rattus norvegicus (taxid:10116)]

 Score = 553 (199.7 bits), Expect = 1.4e-72, Sum P(2) = 1.4e-72
 Identities = 104/150 (69%), Positives = 123/150 (82%)

Query:   292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
             D+   I +FI E+ LPHLL YGPPGTGKT+TILACA++LY   +F +MVLELNASDDRGI
Sbjct:    38 DILSTIQKFISEDRLPHLLLYGPPGTGKTSTILACAKQLYKDKEFGSMVLELNASDDRGI 97

Query:   352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
              IVR  I  FAST+T+ K  +KL+ILDEADAMT DAQNALRR+IEKFT N RFC+ICNYL
Sbjct:    98 DIVRGPILSFASTRTIFKRGFKLVILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYL 157

Query:   412 SKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
             SKI PA+QSRCTRFRFGPL   L++ RL++
Sbjct:   158 SKIIPALQSRCTRFRFGPLTPELMVPRLEH 187

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

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

GO:0006260 "DNA replication" evidence=IEA

GO:0008150 "biological_process" evidence=ND

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

FB|FBgn0032244 RfC3 "Replication factor C subunit 3" [Drosophila melanogaster (taxid:7227)]

 Score = 571 (206.1 bits), Expect = 3.3e-69, Sum P(2) = 3.3e-69
 Identities = 109/144 (75%), Positives = 123/144 (85%)

Query:   297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD 356
             I RFI   +LPHLLFYGPPGTGKT+TILACAR+LY+  QF +MVLELNASDDRGIGIVR 
Sbjct:    35 ITRFISRKQLPHLLFYGPPGTGKTSTILACARQLYSPQQFKSMVLELNASDDRGIGIVRG 94

Query:   357 QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPP 416
             QI  FAST+T+   ++KLIILDEADAMTNDAQNALRRIIEK+T NVRFC+ICNYLSKI P
Sbjct:    95 QILNFASTRTIFCDTFKLIILDEADAMTNDAQNALRRIIEKYTDNVRFCVICNYLSKIIP 154

Query:   417 AIQSRCTRFRFGPLDSSLIMSRLD 440
             A+QSRCTRFRF PL    +M RL+
Sbjct:   155 ALQSRCTRFRFAPLSQDQMMPRLE 178

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

GO:0006260 "DNA replication" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

GO:0005524 "ATP binding" evidence=IEA

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

GO:0005875 "microtubule associated complex" evidence=IDA

GO:0022008 "neurogenesis" evidence=IMP

GO:0046331 "lateral inhibition" evidence=IMP

UNIPROTKB|J9NUF8 RFC5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 554 (200.1 bits), Expect = 5.4e-59, Sum P(2) = 5.4e-59
 Identities = 104/150 (69%), Positives = 123/150 (82%)

Query:   292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
             D+   I +FI E+ LPHLL YGPPGTGKT+TILACA++LY   +F +MVLELNASDDRGI
Sbjct:    38 DILSTIQKFISEDRLPHLLLYGPPGTGKTSTILACAKQLYKDKEFGSMVLELNASDDRGI 97

Query:   352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
              IVR  I  FAST+T+ K  +KL+ILDEADAMT DAQNALRR+IEKFT N RFC+ICNYL
Sbjct:    98 DIVRGPILSFASTRTIFKKGFKLVILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYL 157

Query:   412 SKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
             SKI PA+QSRCTRFRFGPL   L++ RL++
Sbjct:   158 SKIIPALQSRCTRFRFGPLTPELMVPRLEH 187

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q32PI3 RFC5 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 554 (200.1 bits), Expect = 1.1e-58, Sum P(2) = 1.1e-58
 Identities = 104/150 (69%), Positives = 123/150 (82%)

Query:   292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
             D+   I +FI E+ LPHLL YGPPGTGKT+TILACA++LY   +F +MVLELNASDDRGI
Sbjct:    38 DILSTIQKFISEDRLPHLLLYGPPGTGKTSTILACAKQLYKDKEFGSMVLELNASDDRGI 97

Query:   352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
              IVR  I  FAST+T+ K  +KL+ILDEADAMT DAQNALRR+IEKFT N RFC+ICNYL
Sbjct:    98 DIVRGPILSFASTRTIFKKGFKLVILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYL 157

Query:   412 SKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
             SKI PA+QSRCTRFRFGPL   L++ RL++
Sbjct:   158 SKIIPALQSRCTRFRFGPLTPELMVPRLEH 187

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

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

WB|WBGene00018409 F44B9.8 [Caenorhabditis elegans (taxid:6239)]

 Score = 507 (183.5 bits), Expect = 9.9e-58, Sum P(2) = 9.9e-58
 Identities = 99/154 (64%), Positives = 119/154 (77%)

Query:   297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD 356
             + +FI+   LPHLLFYGPPGTGKTTT+LA AR++Y+  +  +MVLELNASD+RGI +VR+
Sbjct:    53 LTKFIENRTLPHLLFYGPPGTGKTTTVLAAARQMYSPTKMASMVLELNASDERGIDVVRN 112

Query:   357 QIFQFASTKTMHKSS---------YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCII 407
              I  FA TK +   S         +KL+ILDEADAMT DAQNALRR+IEK+T NVRFCII
Sbjct:   113 TIVNFAQTKGLQAFSTSSNTGTVPFKLVILDEADAMTKDAQNALRRVIEKYTDNVRFCII 172

Query:   408 CNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
             CNYL+ I PAIQSRCTRFRF PLD  LI+ RL+Y
Sbjct:   173 CNYLASIVPAIQSRCTRFRFAPLDQKLIVPRLEY 206

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0009378 "four-way junction helicase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0009360 "DNA polymerase III complex" evidence=IEA

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

---

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)
A3MS28	RFCS_PYRCJ	No assigned EC number	0.5208	0.2682	0.4386	yes	N/A
P40937	RFC5_HUMAN	No assigned EC number	0.6235	0.3133	0.4911	yes	N/A
A1RSA2	RFCS1_PYRIL	No assigned EC number	0.5068	0.2720	0.4407	yes	N/A
Q5UZE5	RFCS_HALMA	No assigned EC number	0.5333	0.2495	0.4092	yes	N/A
Q0W037	RFCS_UNCMA	No assigned EC number	0.5072	0.2570	0.4254	yes	N/A
A4WGV2	RFCS1_PYRAR	No assigned EC number	0.5068	0.2720	0.4407	yes	N/A
P38629	RFC3_YEAST	No assigned EC number	0.5949	0.2814	0.4411	yes	N/A
Q8ZYK4	RFCS1_PYRAE	No assigned EC number	0.5068	0.2720	0.4407	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	533
PRK00440	319	PRK00440, rfc, replication factor C small subunit;	2e-59
PLN03025	319	PLN03025, PLN03025, replication factor C subunit;	3e-41
PRK00440	319	PRK00440, rfc, replication factor C small subunit;	3e-40
PRK00440	319	PRK00440, rfc, replication factor C small subunit;	2e-34
PRK04132	846	PRK04132, PRK04132, replication factor C small sub	7e-34
PHA02544	316	PHA02544, 44, clamp loader, small subunit; Provisi	5e-30
PRK04132	846	PRK04132, PRK04132, replication factor C small sub	1e-29
PRK12402	337	PRK12402, PRK12402, replication factor C small sub	2e-28
PLN03025	319	PLN03025, PLN03025, replication factor C subunit;	5e-25
PRK12402	337	PRK12402, PRK12402, replication factor C small sub	3e-20
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	4e-20
PLN03025	319	PLN03025, PLN03025, replication factor C subunit;	1e-19
TIGR00678	188	TIGR00678, holB, DNA polymerase III, delta' subuni	3e-18
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	5e-16
PRK04132	846	PRK04132, PRK04132, replication factor C small sub	2e-14
COG2812	515	COG2812, DnaX, DNA polymerase III, gamma/tau subun	4e-14
pfam13177	161	pfam13177, DNA_pol3_delta2, DNA polymerase III, de	6e-14
TIGR02397	355	TIGR02397, dnaX_nterm, DNA polymerase III, subunit	2e-13
PRK14953	486	PRK14953, PRK14953, DNA polymerase III subunits ga	4e-13
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-13
pfam08542	89	pfam08542, Rep_fac_C, Replication factor C C-termi	6e-13
PRK14962	472	PRK14962, PRK14962, DNA polymerase III subunits ga	1e-12
PRK05896	605	PRK05896, PRK05896, DNA polymerase III subunits ga	6e-11
PHA02544	316	PHA02544, 44, clamp loader, small subunit; Provisi	1e-10
PRK14963	504	PRK14963, PRK14963, DNA polymerase III subunits ga	2e-10
COG0470	230	COG0470, HolB, ATPase involved in DNA replication	3e-10
TIGR02397	355	TIGR02397, dnaX_nterm, DNA polymerase III, subunit	4e-10
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	7e-10
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	1e-09
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	2e-09
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	3e-09
PHA02544	316	PHA02544, 44, clamp loader, small subunit; Provisi	6e-09
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	6e-09
COG2256	436	COG2256, MGS1, ATPase related to the helicase subu	6e-09
PRK14953	486	PRK14953, PRK14953, DNA polymerase III subunits ga	7e-09
COG2256	436	COG2256, MGS1, ATPase related to the helicase subu	7e-09
PRK06305	451	PRK06305, PRK06305, DNA polymerase III subunits ga	8e-09
smart00382	148	smart00382, AAA, ATPases associated with a variety	9e-09
pfam08542	89	pfam08542, Rep_fac_C, Replication factor C C-termi	1e-08
PRK00440	319	PRK00440, rfc, replication factor C small subunit;	3e-08
PRK05896	605	PRK05896, PRK05896, DNA polymerase III subunits ga	3e-08
COG2812	515	COG2812, DnaX, DNA polymerase III, gamma/tau subun	4e-08
PRK14970	367	PRK14970, PRK14970, DNA polymerase III subunits ga	4e-08
PRK06090	319	PRK06090, PRK06090, DNA polymerase III subunit del	4e-08
PRK12402	337	PRK12402, PRK12402, replication factor C small sub	1e-07
PRK07399	314	PRK07399, PRK07399, DNA polymerase III subunit del	1e-07
PRK14956	484	PRK14956, PRK14956, DNA polymerase III subunits ga	1e-07
PRK05707	328	PRK05707, PRK05707, DNA polymerase III subunit del	2e-07
PRK06647	563	PRK06647, PRK06647, DNA polymerase III subunits ga	2e-07
PRK05563	559	PRK05563, PRK05563, DNA polymerase III subunits ga	3e-07
PRK14964	491	PRK14964, PRK14964, DNA polymerase III subunits ga	4e-07
PRK05564	313	PRK05564, PRK05564, DNA polymerase III subunit del	5e-07
PRK14959	624	PRK14959, PRK14959, DNA polymerase III subunits ga	5e-07
pfam13401	124	pfam13401, AAA_22, AAA domain	5e-07
PRK05563	559	PRK05563, PRK05563, DNA polymerase III subunits ga	8e-07
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	1e-06
PRK07133	725	PRK07133, PRK07133, DNA polymerase III subunits ga	1e-06
PRK04132	846	PRK04132, PRK04132, replication factor C small sub	2e-06
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	2e-06
PRK08058	329	PRK08058, PRK08058, DNA polymerase III subunit del	2e-06
PRK14961	363	PRK14961, PRK14961, DNA polymerase III subunits ga	3e-06
PRK07471	365	PRK07471, PRK07471, DNA polymerase III subunit del	3e-06
PRK08451	535	PRK08451, PRK08451, DNA polymerase III subunits ga	4e-06
PRK14969	527	PRK14969, PRK14969, DNA polymerase III subunits ga	5e-06
PRK09112	351	PRK09112, PRK09112, DNA polymerase III subunit del	7e-06
PRK14962	472	PRK14962, PRK14962, DNA polymerase III subunits ga	2e-05
PRK14952	584	PRK14952, PRK14952, DNA polymerase III subunits ga	2e-05
PRK08691	709	PRK08691, PRK08691, DNA polymerase III subunits ga	2e-05
PRK13341	725	PRK13341, PRK13341, recombination factor protein R	2e-05
PRK12402	337	PRK12402, PRK12402, replication factor C small sub	4e-05
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	4e-05
PRK14969	527	PRK14969, PRK14969, DNA polymerase III subunits ga	5e-05
PRK07133	725	PRK07133, PRK07133, DNA polymerase III subunits ga	8e-05
PRK06964	342	PRK06964, PRK06964, DNA polymerase III subunit del	9e-05
COG0470	230	COG0470, HolB, ATPase involved in DNA replication	1e-04
PRK14955	397	PRK14955, PRK14955, DNA polymerase III subunits ga	1e-04
PRK14964	491	PRK14964, PRK14964, DNA polymerase III subunits ga	2e-04
PRK14961	363	PRK14961, PRK14961, DNA polymerase III subunits ga	2e-04
PRK06645	507	PRK06645, PRK06645, DNA polymerase III subunits ga	2e-04
PRK08699	325	PRK08699, PRK08699, DNA polymerase III subunit del	2e-04
PRK14954	620	PRK14954, PRK14954, DNA polymerase III subunits ga	3e-04
PRK05917	290	PRK05917, PRK05917, DNA polymerase III subunit del	3e-04
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	4e-04
PRK14955	397	PRK14955, PRK14955, DNA polymerase III subunits ga	4e-04
PRK13341	725	PRK13341, PRK13341, recombination factor protein R	5e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	5e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	5e-04
PRK14963	504	PRK14963, PRK14963, DNA polymerase III subunits ga	7e-04
PRK00080	328	PRK00080, ruvB, Holliday junction DNA helicase Ruv	8e-04
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	9e-04
PRK08769	319	PRK08769, PRK08769, DNA polymerase III subunit del	0.001
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	0.001
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	0.001
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	0.002
PRK07132	299	PRK07132, PRK07132, DNA polymerase III subunit del	0.002
COG1474	366	COG1474, CDC6, Cdc6-related protein, AAA superfami	0.002
pfam13173	127	pfam13173, AAA_14, AAA domain	0.002
TIGR00678	188	TIGR00678, holB, DNA polymerase III, delta' subuni	0.003
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	0.003
TIGR02902	531	TIGR02902, spore_lonB, ATP-dependent protease LonB	0.003
PRK06581	263	PRK06581, PRK06581, DNA polymerase III subunit del	0.004

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

 Score =  198 bits (507), Expect = 2e-59
 Identities = 75/144 (52%), Positives = 98/144 (68%), Gaps = 3/144 (2%)

Query: 299 RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKA-QFNAMVLELNASDDRGIGIVRDQ 357
            ++ E  +PHLLF GPPGTGKTT  LA AR+LY +  + N   LELNASD+RGI ++R++
Sbjct: 31  SYVKEKNMPHLLFAGPPGTGKTTAALALARELYGEDWREN--FLELNASDERGIDVIRNK 88

Query: 358 IFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPA 417
           I +FA T  +  + +K+I LDEAD +T+DAQ ALRR +E ++ N RF + CNY SKI   
Sbjct: 89  IKEFARTAPVGGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDP 148

Query: 418 IQSRCTRFRFGPLDSSLIMSRLDY 441
           IQSRC  FRF PL    +  RL Y
Sbjct: 149 IQSRCAVFRFSPLKKEAVAERLRY 172

Length = 319

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

 Score =  150 bits (380), Expect = 3e-41
 Identities = 70/135 (51%), Positives = 89/135 (65%), Gaps = 2/135 (1%)

Query: 306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTK 365
           +P+L+  GPPGTGKTT+ILA A +L       A VLELNASDDRGI +VR++I  FA  K
Sbjct: 34  MPNLILSGPPGTGKTTSILALAHELLGPNYKEA-VLELNASDDRGIDVVRNKIKMFAQKK 92

Query: 366 -TMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTR 424
            T+    +K++ILDEAD+MT+ AQ ALRR +E ++   RF + CN  SKI   IQSRC  
Sbjct: 93  VTLPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAI 152

Query: 425 FRFGPLDSSLIMSRL 439
            RF  L    I+ RL
Sbjct: 153 VRFSRLSDQEILGRL 167

Length = 319

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

 Score =  147 bits (374), Expect = 3e-40
 Identities = 67/188 (35%), Positives = 100/188 (53%), Gaps = 28/188 (14%)

Query: 2   EKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGK 61
           E ++ N RF + CNY SKI   IQSRC  FRF PL    +  RL Y+ E E + +T D  
Sbjct: 127 EMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIEITDDAL 186

Query: 62  KAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLL-VSRVEKYRP------------ 108
           +AI  +S+GDMRK +N LQ+AA     EV E+ ++ +   +R E+ R             
Sbjct: 187 EAIYYVSEGDMRKAINALQAAAAT-GKEVTEEAVYKITGTARPEEIREMIELALNGDFTE 245

Query: 109 --STLDEL-----VSHQDIISTI-------EIPESMLVDLVLKMSDIEYRLAAGTSEKIQ 154
               L +L     +S +DII  I       +IPE + V+L+  + + ++R+  G +E+IQ
Sbjct: 246 AREKLRDLMIDYGLSGEDIIKQIHREVWSLDIPEELKVELIDAIGEADFRITEGANERIQ 305

Query: 155 LSALIAAF 162
           L AL+A  
Sbjct: 306 LEALLAKL 313

Length = 319

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

 Score =  131 bits (333), Expect = 2e-34
 Identities = 78/251 (31%), Positives = 110/251 (43%), Gaps = 83/251 (33%)

Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAG------TSEKIQLS 156
           VEKYRP TLDE+V  ++I+         L   V K  ++ + L AG      T+      
Sbjct: 8   VEKYRPRTLDEIVGQEEIVER-------LKSYV-KEKNMPHLLFAGPPGTGKTT------ 53

Query: 157 ALIAAFNSARD------KLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDE 210
              AA   AR+      +   LELNASD+RGI ++R++I +FA T  +  + +K+I LDE
Sbjct: 54  ---AALALARELYGEDWRENFLELNASDERGIDVIRNKIKEFARTAPVGGAPFKIIFLDE 110

Query: 211 ADAMTNDAQNALRR---------------------------------------------- 224
           AD +T+DAQ ALRR                                              
Sbjct: 111 ADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERL 170

Query: 225 -------KLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKT 277
                   + +T D  +AI  +S+GDMRK +N LQ+AA     EV E+ VY   G     
Sbjct: 171 RYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAAT-GKEVTEEAVYKITGTARPE 229

Query: 278 EITNILRWLLN 288
           EI  ++   LN
Sbjct: 230 EIREMIELALN 240

Length = 319

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

 Score =  136 bits (344), Expect = 7e-34
 Identities = 65/122 (53%), Positives = 85/122 (69%), Gaps = 1/122 (0%)

Query: 320 TTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDE 379
           TT  LA AR+L+ +  +    LELNASD+RGI ++R+++ +FA TK +  +S+K+I LDE
Sbjct: 580 TTAALALARELFGE-NWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDE 638

Query: 380 ADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
           ADA+T DAQ ALRR +E F++NVRF + CNY SKI   IQSRC  FRF PL    I  RL
Sbjct: 639 ADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRL 698

Query: 440 DY 441
            Y
Sbjct: 699 RY 700

Length = 846

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

 Score =  119 bits (300), Expect = 5e-30
 Identities = 47/131 (35%), Positives = 69/131 (52%), Gaps = 10/131 (7%)

Query: 300 FIDENELPHLLFYGP-PGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI 358
            + +  +P++L + P PGTGKTT   A         +  A VL +N SD R I  VR+++
Sbjct: 36  IVKKGRIPNMLLHSPSPGTGKTTVAKALC------NEVGAEVLFVNGSDCR-IDFVRNRL 88

Query: 359 FQFASTKTMHKSSYKLIILDEAD-AMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPA 417
            +FAST ++     K+II+DE D     DAQ  LR  +E ++ N  F I  N  + I   
Sbjct: 89  TRFASTVSL-TGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEP 147

Query: 418 IQSRCTRFRFG 428
           ++SRC    FG
Sbjct: 148 LRSRCRVIDFG 158

Length = 316

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

 Score =  123 bits (310), Expect = 1e-29
 Identities = 69/190 (36%), Positives = 99/190 (52%), Gaps = 30/190 (15%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           +E F++NVRF + CNY SKI   IQSRC  FRF PL    I  RL Y+ E E + +T +G
Sbjct: 654 MEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEG 713

Query: 61  KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRV----------------- 103
            +AI+ +++GDMR+ +NILQ+AA    D+   D    L+ SR                  
Sbjct: 714 LQAILYIAEGDMRRAINILQAAAA--LDDKITDENVFLVASRARPEDIREMMLLALKGNF 771

Query: 104 ----EKYRPSTLDELVSHQDI-------ISTIEIPESMLVDLVLKMSDIEYRLAAGTSEK 152
               EK R   L + +S +D+       +  + I E   V+L  K+ +  +RL  G +E 
Sbjct: 772 LKAREKLREILLKQGLSGEDVLVQMHREVFNLPIDEPKKVELADKIGEYNFRLVEGANEM 831

Query: 153 IQLSALIAAF 162
           IQL AL+A F
Sbjct: 832 IQLEALLAQF 841

Length = 846

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

 Score =  115 bits (290), Expect = 2e-28
 Identities = 59/166 (35%), Positives = 79/166 (47%), Gaps = 26/166 (15%)

Query: 299 RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD--DRG-IGIVR 355
           R +D   LPHLL  GPPG+GKT  + A AR+LY    +     E N +D  D+G   +V 
Sbjct: 29  RAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGD-PWENNFTEFNVADFFDQGKKYLVE 87

Query: 356 DQIF-QFASTKTMHKSS---------------------YKLIILDEADAMTNDAQNALRR 393
           D  F  F  T    +SS                     YK I+LD A+A+  DAQ ALRR
Sbjct: 88  DPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRR 147

Query: 394 IIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
           I+E+++   RF I     SK+ P I+SRC    F       ++  L
Sbjct: 148 IMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVL 193

Length = 337

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

 Score =  105 bits (263), Expect = 5e-25
 Identities = 77/248 (31%), Positives = 110/248 (44%), Gaps = 62/248 (25%)

Query: 103 VEKYRPSTLDELVSHQDIISTIE-IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAA 161
           VEKYRP+ LD++V ++D +S ++ I           M ++      GT +   + AL   
Sbjct: 4   VEKYRPTKLDDIVGNEDAVSRLQVIARDG------NMPNLILSGPPGTGKTTSILALAHE 57

Query: 162 FNSARDKLEVLELNASDDRGIGIVRDQIFQFASTK-TMHKSSYKLIILDEADAMTNDAQN 220
                 K  VLELNASDDRGI +VR++I  FA  K T+    +K++ILDEAD+MT+ AQ 
Sbjct: 58  LLGPNYKEAVLELNASDDRGIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTSGAQQ 117

Query: 221 ALRR-----------------------------------------------------KLP 227
           ALRR                                                     K+P
Sbjct: 118 ALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVP 177

Query: 228 VTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLL 287
             P+G +AII  +DGDMR+ LN LQ+  +     VN++ V+     P    + NI+R  L
Sbjct: 178 YVPEGLEAIIFTADGDMRQALNNLQATHSGFG-FVNQENVFKVCDQPHPLHVKNIVRNCL 236

Query: 288 NESMDLCY 295
               D   
Sbjct: 237 KGKFDDAC 244

Length = 319

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

 Score = 91.6 bits (228), Expect = 3e-20
 Identities = 46/191 (24%), Positives = 77/191 (40%), Gaps = 34/191 (17%)

Query: 2   EKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGK 61
           E+++   RF I     SK+ P I+SRC    F       ++  L+ + E E V+   DG 
Sbjct: 150 EQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDYDDDGL 209

Query: 62  KAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVS---HQ 118
           + I   + GD+RK +  LQ+AA   A E+  +  +  L   V       ++ L+      
Sbjct: 210 ELIAYYAGGDLRKAILTLQTAAL-AAGEITMEAAYEAL-GDVG--TDEVIESLLDAAEAG 265

Query: 119 DIISTIEIPESMLVD---------------------------LVLKMSDIEYRLAAGTSE 151
           D     +  + +L+D                           L    +D + RL  G ++
Sbjct: 266 DFTDARKTLDDLLIDEGLSGGEVLEELLRVARSRYRGDNLARLHRLAADADARLTDGAND 325

Query: 152 KIQLSALIAAF 162
           +IQL AL+A  
Sbjct: 326 RIQLEALLAEL 336

Length = 337

>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 = 86.8 bits (215), Expect = 4e-20
 Identities = 42/146 (28%), Positives = 62/146 (42%), Gaps = 15/146 (10%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
            +   ++     +LL YGPPGTGKTT   A A +L+      A  L LNASD     +V 
Sbjct: 9   ALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP---GAPFLYLNASDLLEGLVVA 65

Query: 356 DQI---FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTT------NVRFCI 406
           +           +   K+   ++ +DE D+++  AQNAL R++E          NVR   
Sbjct: 66  ELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIG 125

Query: 407 ICNY--LSKIPPAIQSRC-TRFRFGP 429
             N   L  +  A+  R   R     
Sbjct: 126 ATNRPLLGDLDRALYDRLDIRIVIPL 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|178596 PLN03025, PLN03025, replication factor C subunit; Provisional

 Score = 89.4 bits (222), Expect = 1e-19
 Identities = 58/194 (29%), Positives = 90/194 (46%), Gaps = 27/194 (13%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           +E ++   RF + CN  SKI   IQSRC   RF  L    I+ RL  V+E EKV   P+G
Sbjct: 123 MEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVPYVPEG 182

Query: 61  KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFT--------LLVSRVEKYRPSTLD 112
            +AII  +DGDMR+ LN LQ+  +     VN++ +F          + + V        D
Sbjct: 183 LEAIIFTADGDMRQALNNLQATHSGFG-FVNQENVFKVCDQPHPLHVKNIVRNCLKGKFD 241

Query: 113 ELV-----------SHQDIISTI-------EIPESMLVDLVLKMSDIEYRLAAGTSEKIQ 154
           +             S  DII+T+       ++PE + ++ + ++     R+  G    +Q
Sbjct: 242 DACDGLKQLYDLGYSPTDIITTLFRVVKNYDMPEFLKLEYLREIGFAHMRICDGVGSLLQ 301

Query: 155 LSALIAAFNSARDK 168
           LS L+A     R+ 
Sbjct: 302 LSGLLAKLCLVRET 315

Length = 319

>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit

 Score = 82.3 bits (204), Expect = 3e-18
 Identities = 41/160 (25%), Positives = 65/160 (40%), Gaps = 24/160 (15%)

Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNA--------------------M 339
           +++  L H  LF GP G GK    LA A+ L  +                          
Sbjct: 8   LEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLH 67

Query: 340 VLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT 399
            LE        +  VR+ + +F S      S  +++I+++A+ M   A NAL + +E+  
Sbjct: 68  RLEPEG-QSIKVDQVRE-LVEFLSRTPQE-SGRRVVIIEDAERMNEAAANALLKTLEEPP 124

Query: 400 TNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
            N  F +I     K+ P I+SRC    F PL    ++  L
Sbjct: 125 PNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQWL 164

This model describes the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tighly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classisified as delta'. The noise cutoff is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits. 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 188

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

 Score = 74.6 bits (184), Expect = 5e-16
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 33/143 (23%)

Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGI------VRDQIFQFA 362
           LL YGPPGTGKTT   A A++L       A  +E++ S+     +      +R ++F+ A
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKEL------GAPFIEISGSELVSKYVGESEKRLR-ELFEAA 53

Query: 363 STKTMHKSSYKLIILDEADAM-----------TNDAQNALRRIIEKFTTN---VRFCIIC 408
                 K +  +I +DE DA+           +    N L   ++ FT++   V      
Sbjct: 54  K-----KLAPCVIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAAT 108

Query: 409 NYLSKIPPAI-QSRCTRFRFGPL 430
           N   K+ PA+ + R  R    PL
Sbjct: 109 NRPDKLDPALLRGRFDRIIEFPL 131

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

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

 Score = 76.0 bits (187), Expect = 2e-14
 Identities = 32/55 (58%), Positives = 45/55 (81%)

Query: 172 LELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKL 226
           LELNASD+RGI ++R+++ +FA TK +  +S+K+I LDEADA+T DAQ ALRR +
Sbjct: 600 LELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTM 654

Length = 846

>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

 Score = 74.4 bits (183), Expect = 4e-14
 Identities = 47/162 (29%), Positives = 72/162 (44%), Gaps = 25/162 (15%)

Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----------------CARKLYTKAQFNAMVL 341
           ++   + H  LF GP G GKTT   ILA                C             V+
Sbjct: 32  LENGRIAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISCKEINEGSLIDVI 91

Query: 342 ELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT 399
           E++A+ + G+  +R+ I    +A ++      YK+ I+DE   ++  A NAL + +E+  
Sbjct: 92  EIDAASNTGVDDIREIIEKVNYAPSE----GRYKVYIIDEVHMLSKQAFNALLKTLEEPP 147

Query: 400 TNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
           ++V+F +      KIP  I SRC RF F  LD   I   L  
Sbjct: 148 SHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAA 189

Length = 515

>gnl|CDD|221959 pfam13177, DNA_pol3_delta2, DNA polymerase III, delta subunit

 Score = 69.2 bits (170), Expect = 6e-14
 Identities = 41/151 (27%), Positives = 69/151 (45%), Gaps = 22/151 (14%)

Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNA----------MVLELN----- 344
           I +N+L H  LF GP G GK    L  A+ L+ +   +            +   N     
Sbjct: 13  IKKNKLSHAYLFSGPDGVGKLELALEFAKALFCENPQDDEPCGECKSCKRIENGNHPDVI 72

Query: 345 --ASDDRGIGI--VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTT 400
               + + I I  +R+ + +  S K   +   K+ I+++A+ MT  A NAL + +E+   
Sbjct: 73  IIEPEGKSIKIDQIRE-LIEEFSKKPF-EGKKKVYIIEDAEKMTESAANALLKTLEEPPE 130

Query: 401 NVRFCIICNYLSKIPPAIQSRCTRFRFGPLD 431
           N  F ++ +  +K+ P I+SRC    F PL 
Sbjct: 131 NTYFILLTSNPNKLLPTIRSRCQVINFKPLS 161

DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalyzed reaction. The delta subunit is also known as HolA. Length = 161

>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau

 Score = 71.1 bits (175), Expect = 2e-13
 Identities = 46/163 (28%), Positives = 72/163 (44%), Gaps = 27/163 (16%)

Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----------------CARKLYTKAQFNAMVL 341
           I    + H  LF GP GTGKT+   I A                C       +  +  V+
Sbjct: 30  IKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDVI 89

Query: 342 ELNASDDRGIGIVR---DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF 398
           E++A+ + G+  +R   D + ++A +       YK+ I+DE   ++  A NAL + +E+ 
Sbjct: 90  EIDAASNNGVDDIREILDNV-KYAPSSGK----YKVYIIDEVHMLSKSAFNALLKTLEEP 144

Query: 399 TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
             +V F +      KIP  I SRC RF F  +    I+ RL  
Sbjct: 145 PEHVVFILATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKK 187

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 355

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

 Score = 71.0 bits (174), Expect = 4e-13
 Identities = 47/151 (31%), Positives = 66/151 (43%), Gaps = 22/151 (14%)

Query: 310 LFYGPPGTGKTTTILACARKL-------------------YTKAQFNAMVLELNASDDRG 350
           +F GP GTGKTT     A+ L                     K  F  ++ E++A+ +RG
Sbjct: 42  IFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFPDLI-EIDAASNRG 100

Query: 351 IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY 410
           I  +R  +    S   + K  YK+ I+DEA  +T +A NAL + +E+      F +    
Sbjct: 101 IDDIR-ALRDAVSYTPI-KGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTE 158

Query: 411 LSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
             KIPP I SRC RF F       I   L  
Sbjct: 159 YDKIPPTILSRCQRFIFSKPTKEQIKEYLKR 189

Length = 486

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

 Score = 70.7 bits (174), Expect = 5e-13
 Identities = 32/93 (34%), Positives = 48/93 (51%), Gaps = 10/93 (10%)

Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH 368
           LL YGPPG GKT+   A A        +   V+ELNASD R   ++     + A++ ++ 
Sbjct: 42  LLLYGPPGVGKTSLAHALAN------DYGWEVIELNASDQRTADVIERVAGEAATSGSLF 95

Query: 369 KSSYKLIILDEADAM--TNDA--QNALRRIIEK 397
            +  KLI+LDE D +    D     A+  +I+K
Sbjct: 96  GARRKLILLDEVDGIHGNEDRGGARAILELIKK 128

Length = 482

>gnl|CDD|203973 pfam08542, Rep_fac_C, Replication factor C C-terminal domain

 Score = 64.1 bits (157), Expect = 6e-13
 Identities = 25/67 (37%), Positives = 47/67 (70%), Gaps = 1/67 (1%)

Query: 453 YIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQL 512
              + E+ +E G++  DIL ++  ++ RL+IP+S+ ++++ ++++IE+RL+ G  E IQL
Sbjct: 24  RETLYELLVE-GISAEDILKQLHEVLIRLDIPDSLKLEIIKELAEIEHRLSDGAKEIIQL 82

Query: 513 SALIAAF 519
            ALIA F
Sbjct: 83  EALIAKF 89

This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A. Length = 89

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

 Score = 69.8 bits (171), Expect = 1e-12
 Identities = 50/158 (31%), Positives = 77/158 (48%), Gaps = 21/158 (13%)

Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLY-TKAQF----------------NAM-VL 341
           + +N + H  +F GP GTGKTT     A+ L     +                   M V+
Sbjct: 30  LKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVI 89

Query: 342 ELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTN 401
           EL+A+ +RGI  +R +I      + M +  YK+ I+DE   +T +A NAL + +E+  ++
Sbjct: 90  ELDAASNRGIDEIR-KIRDAVGYRPM-EGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSH 147

Query: 402 VRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
           V F +    L K+PP I SRC    F  +   LI+ RL
Sbjct: 148 VVFVLATTNLEKVPPTIISRCQVIEFRNISDELIIKRL 185

Length = 472

>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau; Validated

 Score = 64.5 bits (157), Expect = 6e-11
 Identities = 53/185 (28%), Positives = 80/185 (43%), Gaps = 38/185 (20%)

Query: 301 IDENELPH-LLFYGPPGTGKTT--TILACARKLYTKAQFNAM----------------VL 341
           I  N+L H  +F GP G GKT+   I A A         +                  ++
Sbjct: 32  ILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSVCESINTNQSVDIV 91

Query: 342 ELNASDDRGIGIVR---DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF 398
           EL+A+ + G+  +R   D I    +T       YK+ I+DEA  ++  A NAL + +E+ 
Sbjct: 92  ELDAASNNGVDEIRNIIDNINYLPTT-----FKYKVYIIDEAHMLSTSAWNALLKTLEEP 146

Query: 399 TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQE 458
             +V F        KIP  I SRC R+ F  L++S +   L        +I     K ++
Sbjct: 147 PKHVVFIFATTEFQKIPLTIISRCQRYNFKKLNNSELQELLK-------SI----AKKEK 195

Query: 459 IKIEK 463
           IKIE 
Sbjct: 196 IKIED 200

Length = 605

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

 Score = 62.3 bits (152), Expect = 1e-10
 Identities = 42/129 (32%), Positives = 63/129 (48%), Gaps = 26/129 (20%)

Query: 103 VEKYRPSTLDELV-------SHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQL 155
            +KYRPST+DE +       + + I+    IP +ML+          +  + GT +    
Sbjct: 12  EQKYRPSTIDECILPAADKETFKSIVKKGRIP-NMLL----------HSPSPGTGKTTVA 60

Query: 156 SALIAAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD-AM 214
            AL     +     EVL +N SD R I  VR+++ +FAST ++     K+II+DE D   
Sbjct: 61  KALCNEVGA-----EVLFVNGSDCR-IDFVRNRLTRFASTVSL-TGGGKVIIIDEFDRLG 113

Query: 215 TNDAQNALR 223
             DAQ  LR
Sbjct: 114 LADAQRHLR 122

Length = 316

>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau; Provisional

 Score = 62.9 bits (153), Expect = 2e-10
 Identities = 47/149 (31%), Positives = 67/149 (44%), Gaps = 23/149 (15%)

Query: 310 LFYGPPGTGKTTT--ILA---------------CARKLYTKAQFNAMVLELNASDDRGIG 352
           LF GP G GKTTT  ++A               C   L  +   +  VLE++A+ +  + 
Sbjct: 40  LFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVLEIDAASNNSVE 99

Query: 353 IVRD--QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY 410
            VRD  +    A  +       K+ ILDEA  M+  A NAL + +E+   +V F +    
Sbjct: 100 DVRDLREKVLLAPLR----GGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTE 155

Query: 411 LSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
             K+PP I SR   FRF  L    I  +L
Sbjct: 156 PEKMPPTILSRTQHFRFRRLTEEEIAGKL 184

Length = 504

>gnl|CDD|223546 COG0470, HolB, ATPase involved in DNA replication [DNA replication, recombination, and repair]

 Score = 60.0 bits (145), Expect = 3e-10
 Identities = 50/200 (25%), Positives = 76/200 (38%), Gaps = 42/200 (21%)

Query: 4   FTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKA 63
              N RF +I N  SKI P I+SRC R RF P       SRL+ +   E       G + 
Sbjct: 41  PPKNTRFILITNDPSKILPTIRSRCQRIRFKPP------SRLEAIAWLED-----QGLEE 89

Query: 64  IIDLSDGDMRKVLNILQSAATAHADEVNE---------------------DTIFTLLVSR 102
           I  +++GD RK +N LQ+ A     E +                             +  
Sbjct: 90  IAAVAEGDARKAINPLQALAALEIGEESIYEALLLALPESLAQLAALELLKLAENKFLEA 149

Query: 103 VEKYRPSTLDELVSHQDIISTIE----------IPESMLVDLVLKMSDIEYRLAAGTSEK 152
           +EK     L E +  +D++  ++          I E    +L+  ++    RL  G    
Sbjct: 150 LEKLWLLLLLEGLLGEDLLDQLQRELLKLDKALIQEEKAAELLDALAQARRRLLDGLLAL 209

Query: 153 IQLSALIAAFNSARDKLEVL 172
           IQL  L+A     +  LE +
Sbjct: 210 IQLENLLAELLLLQLLLEGV 229

Length = 230

>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau

 Score = 61.4 bits (150), Expect = 4e-10
 Identities = 40/166 (24%), Positives = 73/166 (43%), Gaps = 8/166 (4%)

Query: 19  KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
           KI   I SRC RF F  +    I+ RL  ++++E + +  +  + I   +DG +R  L++
Sbjct: 159 KIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSL 218

Query: 79  LQSAATAHADEVNEDTIFTLL--VSRVEKYRPSTLDELVSHQDIISTIEIPESML---VD 133
           L    +     +  + +  LL  V   +      L E + ++D    ++I + +L   VD
Sbjct: 219 LDQLISFGNGNITYEDVNELLGLVDDEKLIE---LLEAILNKDTAEALKILDEILESGVD 275

Query: 134 LVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDD 179
               + D+   L      K   S L+A   S ++ L+ L L  S +
Sbjct: 276 PEKFLEDLIEILRDLLLIKKTPSNLLAVLESEQEFLKELALKLSLE 321

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 355

>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional

 Score = 61.3 bits (149), Expect = 7e-10
 Identities = 46/160 (28%), Positives = 75/160 (46%), Gaps = 21/160 (13%)

Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----CARKLYTK-----------AQFNAM-VL 341
           ID   + H  LF G  G GKT+T  ILA    C + L  +            +  ++ V 
Sbjct: 32  IDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPCVEITEGRSVDVF 91

Query: 342 ELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTN 401
           E++ + + G+  +R+   +        +S YK+ I+DE   ++ +A NAL + +E+   +
Sbjct: 92  EIDGASNTGVDDIRE--LRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPH 149

Query: 402 VRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
           V+F        K+P  I SRC RF F  +    I+ RL Y
Sbjct: 150 VKFIFATTEPHKVPITILSRCQRFDFRRIPLQKIVDRLRY 189

Length = 576

>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed

 Score = 59.7 bits (146), Expect = 1e-09
 Identities = 40/153 (26%), Positives = 61/153 (39%), Gaps = 27/153 (17%)

Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD 356
           + R I+   L  ++ +GPPGTGKTT     A    T A F      L+A    G+  +R 
Sbjct: 27  LRRMIEAGRLSSMILWGPPGTGKTTLARIIAG--ATDAPF----EALSAVTS-GVKDLR- 78

Query: 357 QIFQFASTKTMHKSSYK-LIILDEADAMTNDAQNALRRIIEKF-------TT-NVRFCII 407
           ++ + A  +    +  + ++ +DE        Q+AL   +E         TT N  F + 
Sbjct: 79  EVIEEA--RQRRSAGRRTILFIDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVN 136

Query: 408 CNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLD 440
                   PA+ SR   F   PL    I   L 
Sbjct: 137 --------PALLSRAQVFELKPLSEEDIEQLLK 161

Length = 413

>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed

 Score = 58.9 bits (144), Expect = 2e-09
 Identities = 31/106 (29%), Positives = 49/106 (46%), Gaps = 8/106 (7%)

Query: 20  ITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEK---VNVTPDGKKAIIDLSDGDMRKVL 76
           + PA+ SR   F   PL    I   L   +E ++   V +  +   A+  L++GD R+ L
Sbjct: 135 VNPALLSRAQVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRAL 194

Query: 77  NILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIIS 122
           N+L+ AA    D +  + +   L  R  +Y     DE   H D+IS
Sbjct: 195 NLLELAALGV-DSITLELLEEALQKRAARYD-KDGDE---HYDLIS 235

Length = 413

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 59.1 bits (143), Expect = 3e-09
 Identities = 46/149 (30%), Positives = 69/149 (46%), Gaps = 26/149 (17%)

Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILACARKLYTK----------------AQFNAM-V 340
           I E  + H  LF GP G GKT+T  ILA A    T                 A+ +A+ V
Sbjct: 32  IAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCEMCRAIAEGSAVDV 91

Query: 341 LELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF 398
           +E++A+    +   R+ I   QF        + YK+ I+DE   ++  A NAL + +E+ 
Sbjct: 92  IEMDAASHTSVDDAREIIERVQFRPAL----ARYKVYIIDEVHMLSTAAFNALLKTLEEP 147

Query: 399 TTNVRFCIICNYLSKIPPAIQSRCTRFRF 427
             +  F +    + K+P  I SRC RF F
Sbjct: 148 PPHAIFILATTEVHKVPATILSRCQRFDF 176

Length = 585

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

 Score = 57.3 bits (139), Expect = 6e-09
 Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 7/91 (7%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDS-------SLIMSRLDYVIEQEK 53
           +E ++ N  F I  N  + I   ++SRC    FG             ++ R   ++E E 
Sbjct: 125 MEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQMIVRCKGILEAEG 184

Query: 54  VNVTPDGKKAIIDLSDGDMRKVLNILQSAAT 84
           V V      A++  +  D R+ +N LQ  A+
Sbjct: 185 VEVDMKVLAALVKKNFPDFRRTINELQRYAS 215

Length = 316

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

 Score = 58.0 bits (141), Expect = 6e-09
 Identities = 51/250 (20%), Positives = 81/250 (32%), Gaps = 87/250 (34%)

Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALI--- 159
           VEKYRP TL ++V ++     +                IE     G  +K    AL+   
Sbjct: 5   VEKYRPKTLSDVVGNEKAKEQLR-------------EWIE-SWLKGKPKK----ALLLYG 46

Query: 160 --------AAFNSARD-KLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDE 210
                    A   A D   EV+ELNASD R   ++     + A++ ++  +  KLI+LDE
Sbjct: 47  PPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGARRKLILLDE 106

Query: 211 ADAM---------------------------------------------------TNDAQ 219
            D +                                                   T    
Sbjct: 107 VDGIHGNEDRGGARAILELIKKAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIV 166

Query: 220 NALRR-----KLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYP 274
             L+R      +    +  K I + S GD+R  +N LQ+ A     ++  + V       
Sbjct: 167 PVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAEG-YGKLTLEDVKTLGRRD 225

Query: 275 TKTEITNILR 284
            +  I + L 
Sbjct: 226 REESIFDALD 235

Length = 482

>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

 Score = 57.6 bits (140), Expect = 6e-09
 Identities = 28/112 (25%), Positives = 50/112 (44%), Gaps = 13/112 (11%)

Query: 20  ITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEK-------VNVTPDGKKAIIDLSDGDM 72
           + PA+ SR   F   PL S  I   L   +  E+       + +  +    ++ LS+GD 
Sbjct: 147 LNPALLSRARVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDA 206

Query: 73  RKVLNILQSAATAH--ADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIIS 122
           R+ LN+L+ AA +    + +  + +  +L  R  ++     D    H D+IS
Sbjct: 207 RRALNLLELAALSAEPDEVLILELLEEILQRRSARFDKDG-DA---HYDLIS 254

Length = 436

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

 Score = 57.9 bits (140), Expect = 7e-09
 Identities = 23/83 (27%), Positives = 33/83 (39%)

Query: 17  LSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVL 76
             KI P I SRC RF F       I   L  +  +EK+         +   S+G MR   
Sbjct: 159 YDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQASEGGMRDAA 218

Query: 77  NILQSAATAHADEVNEDTIFTLL 99
           ++L  A+T    +V    +   L
Sbjct: 219 SLLDQASTYGEGKVTIKVVEEFL 241

Length = 486

>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

 Score = 57.6 bits (140), Expect = 7e-09
 Identities = 41/153 (26%), Positives = 59/153 (38%), Gaps = 27/153 (17%)

Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD 356
           + R ++   L  ++ +GPPGTGKTT  LA      T A F      L+A    G+  +R+
Sbjct: 39  LRRAVEAGHLHSMILWGPPGTGKTT--LARLIAGTTNAAF----EALSAVTS-GVKDLRE 91

Query: 357 QIFQFASTKTMHKSSYKLII-LDEADAMTNDAQNALRRIIEK--------FTTNVRFCII 407
                   +       + I+ LDE        Q+AL   +E          T N  F   
Sbjct: 92  ---IIEEARKNRLLGRRTILFLDEIHRFNKAQQDALLPHVENGTIILIGATTENPSF--- 145

Query: 408 CNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLD 440
                ++ PA+ SR   F   PL S  I   L 
Sbjct: 146 -----ELNPALLSRARVFELKPLSSEDIKKLLK 173

Length = 436

>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau; Validated

 Score = 57.5 bits (139), Expect = 8e-09
 Identities = 44/151 (29%), Positives = 66/151 (43%), Gaps = 25/151 (16%)

Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAM-------------------VLELNASDDRG 350
           LF G  GTGKTT     A+ L  +                         VLE++ +  RG
Sbjct: 43  LFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTSLDVLEIDGASHRG 102

Query: 351 IGIVRDQIFQFASTK--TMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIIC 408
           I    + I Q   T   T  KS YK+ I+DE   +T +A N+L + +E+   +V+F +  
Sbjct: 103 I----EDIRQINETVLFTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLAT 158

Query: 409 NYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
             + KIP  I SRC +     +    I+ +L
Sbjct: 159 TEIHKIPGTILSRCQKMHLKRIPEETIIDKL 189

Length = 451

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

 Score = 53.9 bits (129), Expect = 9e-09
 Identities = 31/142 (21%), Positives = 51/142 (35%), Gaps = 25/142 (17%)

Query: 308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT- 366
            +L  GPPG+GKTT   A AR+L         V+ ++  D     + +  +      K  
Sbjct: 4   VILIVGPPGSGKTTLARALARELGPP---GGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60

Query: 367 -------------MHKSSYKLIILDEADAMTNDAQNALRR--------IIEKFTTNVRFC 405
                          K    ++ILDE  ++ +  Q AL          ++ K   N+   
Sbjct: 61  GSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVI 120

Query: 406 IICNYLSKIPPAIQSRCTRFRF 427
           +  N    + PA+  R    R 
Sbjct: 121 LTTNDEKDLGPALLRRRFDRRI 142

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

>gnl|CDD|203973 pfam08542, Rep_fac_C, Replication factor C C-terminal domain

 Score = 52.1 bits (126), Expect = 1e-08
 Identities = 23/65 (35%), Positives = 40/65 (61%), Gaps = 11/65 (16%)

Query: 109 STLDELVSH----QDIISTI-------EIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSA 157
            TL EL+      +DI+  +       +IP+S+ ++++ ++++IE+RL+ G  E IQL A
Sbjct: 25  ETLYELLVEGISAEDILKQLHEVLIRLDIPDSLKLEIIKELAEIEHRLSDGAKEIIQLEA 84

Query: 158 LIAAF 162
           LIA F
Sbjct: 85  LIAKF 89

This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A. Length = 89

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

 Score = 55.3 bits (134), Expect = 3e-08
 Identities = 23/65 (35%), Positives = 43/65 (66%)

Query: 455 KIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSA 514
           K++++ I+ GL+  DI+ +I   V  L+IPE + V+L+  + + ++R+  G +E+IQL A
Sbjct: 249 KLRDLMIDYGLSGEDIIKQIHREVWSLDIPEELKVELIDAIGEADFRITEGANERIQLEA 308

Query: 515 LIAAF 519
           L+A  
Sbjct: 309 LLAKL 313

Length = 319

>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau; Validated

 Score = 56.0 bits (135), Expect = 3e-08
 Identities = 33/109 (30%), Positives = 52/109 (47%), Gaps = 5/109 (4%)

Query: 19  KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
           KI   I SRC R+ F  L++S +   L  + ++EK+ +  +    I DL+DG +R  L+I
Sbjct: 161 KIPLTIISRCQRYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKIADLADGSLRDGLSI 220

Query: 79  LQSAATAHADEVNEDTIFTL--LVSRVEKYRPSTLDELVSHQDIISTIE 125
           L   +T    E++ + I     LV   +K     L EL+   DI     
Sbjct: 221 LDQLSTFKNSEIDIEDINKTFGLVDNNKKI---NLIELIQKNDIEELRN 266

Length = 605

>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

 Score = 55.5 bits (134), Expect = 4e-08
 Identities = 26/95 (27%), Positives = 47/95 (49%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           +E+  ++V+F +      KI   I SRC RF F  LD   I   L  ++++E +N+  D 
Sbjct: 143 LEEPPSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAAILDKEGINIEEDA 202

Query: 61  KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTI 95
              I   ++G +R  L++L  A      E+  +++
Sbjct: 203 LSLIARAAEGSLRDALSLLDQAIAFGEGEITLESV 237

Length = 515

>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau; Provisional

 Score = 55.3 bits (133), Expect = 4e-08
 Identities = 44/134 (32%), Positives = 64/134 (47%), Gaps = 9/134 (6%)

Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKL----YTKAQ--FNAMVLELNASDDRGIGI 353
           I+ N L   LLF GP G GKTT     ARK+    Y      F+  + EL+A+ +  +  
Sbjct: 33  IENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDD 92

Query: 354 VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSK 413
           +R+ I Q        K  YK+ I+DE   +++ A NA  + +E+   +  F +      K
Sbjct: 93  IRNLIDQVRIPPQTGK--YKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHK 150

Query: 414 IPPAIQSRCTRFRF 427
           I P I SRC  F F
Sbjct: 151 IIPTILSRCQIFDF 164

Length = 367

>gnl|CDD|180394 PRK06090, PRK06090, DNA polymerase III subunit delta'; Validated

 Score = 54.4 bits (131), Expect = 4e-08
 Identities = 28/94 (29%), Positives = 47/94 (50%), Gaps = 6/94 (6%)

Query: 350 GIGIVRDQIFQFASTKTMHKSS----YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFC 405
           G  I  +QI Q    +   +SS    Y+L +++ ADAM   A NAL + +E+   N  F 
Sbjct: 85  GKSITVEQIRQ--CNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFL 142

Query: 406 IICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
           ++ +   ++ P I SRC ++   P  ++  M  L
Sbjct: 143 LVTHNQKRLLPTIVSRCQQWVVTPPSTAQAMQWL 176

Length = 319

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

 Score = 53.1 bits (128), Expect = 1e-07
 Identities = 55/261 (21%), Positives = 91/261 (34%), Gaps = 89/261 (34%)

Query: 104 EKYRPSTLDELVSHQDIISTIE--IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAA 161
           EKYRP+ L++++   +++  +   +    L  L+++          G+ +   + AL   
Sbjct: 7   EKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGP-------PGSGKTAAVRALARE 59

Query: 162 FNSARDKLEVLELNASD--DRG-IGIVRDQIF-QFASTKTMHKSS--------------- 202
                 +    E N +D  D+G   +V D  F  F  T    +SS               
Sbjct: 60  LYGDPWENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASY 119

Query: 203 ------YKLIILDEADAMTNDAQNALRR-------------------------------- 224
                 YK I+LD A+A+  DAQ ALRR                                
Sbjct: 120 RPLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPL 179

Query: 225 ---------------------KLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVN 263
                                 +    DG + I   + GD+RK +  LQ+AA   A E+ 
Sbjct: 180 FFRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL-AAGEIT 238

Query: 264 EDTVYNSVG-YPTKTEITNIL 283
            +  Y ++G   T   I ++L
Sbjct: 239 MEAAYEALGDVGTDEVIESLL 259

Length = 337

>gnl|CDD|236011 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated

 Score = 53.0 bits (128), Expect = 1e-07
 Identities = 36/177 (20%), Positives = 62/177 (35%), Gaps = 37/177 (20%)

Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAMVLE-----------------------LNAS 346
           LF GP G G+    L     L ++   +  +                         + AS
Sbjct: 30  LFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQHQGKLITAS 89

Query: 347 D-------DRGIGIVR-DQI---FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRII 395
           +        +    +R +QI    +F S   +  +  K++++++A+ M   A NAL + +
Sbjct: 90  EAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLE-APRKVVVIEDAETMNEAAANALLKTL 148

Query: 396 EKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL-DYDDISFFNIII 451
           E+   N    +I      + P I SRC    F  L    +   L    D    NI  
Sbjct: 149 EE-PGNGTLILIAPSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEILNINF 204

Length = 314

>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau; Provisional

 Score = 53.8 bits (129), Expect = 1e-07
 Identities = 40/138 (28%), Positives = 64/138 (46%), Gaps = 24/138 (17%)

Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFN------------------AMVLELNASDDRGI 351
           +F+GP G GKTT     A++L  +                      + VLE++A+ +RGI
Sbjct: 44  IFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTSCLEITKGISSDVLEIDAASNRGI 103

Query: 352 GIVRD--QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN 409
             +R+     +FA         YK+ I+DE   +T+ + NAL + +E+   ++ F +   
Sbjct: 104 ENIRELRDNVKFAPMG----GKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATT 159

Query: 410 YLSKIPPAIQSRCTRFRF 427
              KIP  I SRC  F F
Sbjct: 160 EFHKIPETILSRCQDFIF 177

Length = 484

>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated

 Score = 52.8 bits (127), Expect = 2e-07
 Identities = 40/151 (26%), Positives = 67/151 (44%), Gaps = 27/151 (17%)

Query: 306 LPH-LLFYGPPGTGKTTTILACARKLYTKAQ--------------FNA------MVLELN 344
            PH  L +GP G GK       A  L  +A                 A       VLE  
Sbjct: 21  HPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPE 80

Query: 345 ASDDRGIGIVRDQIFQFAS--TKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNV 402
            +D + I +  DQ+ +  S   +T      K+++++ A+AM  +A NAL + +E+ + + 
Sbjct: 81  EAD-KTIKV--DQVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDT 137

Query: 403 RFCIICNYLSKIPPAIQSRCTRFRFGPLDSS 433
              +I +  S++ P I+SRC +    PL S+
Sbjct: 138 VLLLISHQPSRLLPTIKSRCQQQAC-PLPSN 167

Length = 328

>gnl|CDD|235845 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau; Validated

 Score = 53.2 bits (128), Expect = 2e-07
 Identities = 45/162 (27%), Positives = 74/162 (45%), Gaps = 29/162 (17%)

Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VL 341
           I+ N++ +  +F GP G GKT++  A AR L        M                  V+
Sbjct: 32  IESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSSCKSIDNDNSLDVI 91

Query: 342 ELNASDDRGIGIVR---DQI-FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEK 397
           E++ + +  +  VR   ++I F  AS++      Y++ I+DE   ++N A NAL + IE+
Sbjct: 92  EIDGASNTSVQDVRQIKEEIMFPPASSR------YRVYIIDEVHMLSNSAFNALLKTIEE 145

Query: 398 FTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
               + F      + K+P  I+SRC  F F  L    I + L
Sbjct: 146 PPPYIVFIFATTEVHKLPATIKSRCQHFNFRLLSLEKIYNML 187

Length = 563

>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau; Validated

 Score = 52.6 bits (127), Expect = 3e-07
 Identities = 23/75 (30%), Positives = 38/75 (50%)

Query: 19  KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
           KI   I SRC RF F  +    I+ RL Y++++E +    +  + I   ++G MR  L+I
Sbjct: 161 KIPATILSRCQRFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAAEGGMRDALSI 220

Query: 79  LQSAATAHADEVNED 93
           L  A +    +V  +
Sbjct: 221 LDQAISFGDGKVTYE 235

Length = 559

>gnl|CDD|237870 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau; Provisional

 Score = 52.1 bits (125), Expect = 4e-07
 Identities = 39/155 (25%), Positives = 71/155 (45%), Gaps = 21/155 (13%)

Query: 304 NELPH-LLFYGPPGTGKTTT--ILA----------------CARKLYTKAQFNAMVLELN 344
           N++P  +L  G  G GKTT   I++                C   +  K   +  V+E++
Sbjct: 32  NKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEID 91

Query: 345 ASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRF 404
           A+ +  +  ++  +    S      S +K+ I+DE   ++N A NAL + +E+   +V+F
Sbjct: 92  AASNTSVDDIK--VILENSCYLPISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKF 149

Query: 405 CIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
            +    + KIP  I SRC RF    + +  ++  L
Sbjct: 150 ILATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHL 184

Length = 491

>gnl|CDD|180132 PRK05564, PRK05564, DNA polymerase III subunit delta'; Validated

 Score = 51.2 bits (123), Expect = 5e-07
 Identities = 43/156 (27%), Positives = 71/156 (45%), Gaps = 9/156 (5%)

Query: 297 INRFIDENELPHL-LFYGPPGTGKTTTILACARKLYTKAQFNAMV--LELNASDDRGIGI 353
           I   I +N   H  +  G  G GK+      A K+  K+Q    V  +E    + + IG+
Sbjct: 16  IKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGV 75

Query: 354 --VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
             +R+ I +    K  ++   K+II+  ++ MT  AQNA  + IE+    V   ++C  L
Sbjct: 76  DDIRNIIEEV--NKKPYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENL 133

Query: 412 SKIPPAIQSRCTRFRFGPLDSSLIMSRLD--YDDIS 445
            +I   I+SRC  ++   L    I   +   Y+DI 
Sbjct: 134 EQILDTIKSRCQIYKLNRLSKEEIEKFISYKYNDIK 169

Length = 313

>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau; Provisional

 Score = 52.0 bits (124), Expect = 5e-07
 Identities = 46/155 (29%), Positives = 67/155 (43%), Gaps = 25/155 (16%)

Query: 297 INRFIDENEL-PHLLFYGPPGTGKTTT--ILA----CA--------------RKLYTKAQ 335
           ++R   EN + P  LF G  G GKTT   I A    C               RK+     
Sbjct: 28  LSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQCRKVTQGMH 87

Query: 336 FNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRII 395
            +  V+E++ + +RGI   +    + A      +  YK+ I+DEA  +T +A NAL + +
Sbjct: 88  VD--VVEIDGASNRGIDDAKR--LKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTL 143

Query: 396 EKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPL 430
           E+    V F +      K P  I SRC  F F  L
Sbjct: 144 EEPPARVTFVLATTEPHKFPVTIVSRCQHFTFTRL 178

Length = 624

>gnl|CDD|222104 pfam13401, AAA_22, AAA domain

 Score = 48.4 bits (116), Expect = 5e-07
 Identities = 21/115 (18%), Positives = 39/115 (33%), Gaps = 20/115 (17%)

Query: 308 HLLFYGPPGTGKTT-------------TILACARKLYTKAQFNAMVL-ELNASDDRG-IG 352
             +  G  G+GKTT              +   A  L T       +L  L      G   
Sbjct: 6   IGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTTA 65

Query: 353 IVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCII 407
            + + I      +        L+I+DEA  ++ +A   LR + +     ++  ++
Sbjct: 66  ELLEAILDALKRRGR-----PLLIIDEAQHLSLEALEELRDLYDLSEKGIQVILV 115

Length = 124

>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau; Validated

 Score = 51.4 bits (124), Expect = 8e-07
 Identities = 47/159 (29%), Positives = 72/159 (45%), Gaps = 38/159 (23%)

Query: 310 LFYGPPGTGKTTT--ILACARKLYTKA----------------------QFNAM-VLELN 344
           LF GP GTGKT+   I A       KA                        + M V+E++
Sbjct: 42  LFSGPRGTGKTSAAKIFA-------KAVNCLNPPDGEPCNECEICKAITNGSLMDVIEID 94

Query: 345 ASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNV 402
           A+ + G+  +RD     ++A ++    + YK+ I+DE   ++  A NAL + +E+   +V
Sbjct: 95  AASNNGVDEIRDIRDKVKYAPSE----AKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHV 150

Query: 403 RFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
            F +      KIP  I SRC RF F  +    I+ RL Y
Sbjct: 151 IFILATTEPHKIPATILSRCQRFDFKRISVEDIVERLKY 189

Length = 559

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 51.0 bits (122), Expect = 1e-06
 Identities = 23/72 (31%), Positives = 35/72 (48%)

Query: 19  KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
           K+   I SRC RF F     + + + L  +   E +N+ P   +AI   + G MR   N+
Sbjct: 162 KVPATILSRCQRFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDAENL 221

Query: 79  LQSAATAHADEV 90
           LQ  AT +  E+
Sbjct: 222 LQQLATTYGGEI 233

Length = 585

>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau; Validated

 Score = 51.0 bits (122), Expect = 1e-06
 Identities = 51/174 (29%), Positives = 84/174 (48%), Gaps = 22/174 (12%)

Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILACARKLYTKAQF-------------NAMVLELN 344
           I  N++ H  LF GP GTGKT+   I A A     K                +  ++E++
Sbjct: 34  IKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNSLDIIEMD 93

Query: 345 ASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRF 404
           A+ + G+  +R+ I    +  T  +S YK+ I+DE   ++  A NAL + +E+   +V F
Sbjct: 94  AASNNGVDEIRELIENVKNLPT--QSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIF 151

Query: 405 CIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY----DDISFFNIIIWYI 454
            +    + KIP  I SR  RF F  +    I+SRL++    ++IS+    +  I
Sbjct: 152 ILATTEVHKIPLTILSRVQRFNFRRISEDEIVSRLEFILEKENISYEKNALKLI 205

Length = 725

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

 Score = 50.2 bits (120), Expect = 2e-06
 Identities = 25/65 (38%), Positives = 40/65 (61%)

Query: 455 KIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSA 514
           K++EI +++GL+  D+L ++   V  L I E   V+L  K+ +  +RL  G +E IQL A
Sbjct: 777 KLREILLKQGLSGEDVLVQMHREVFNLPIDEPKKVELADKIGEYNFRLVEGANEMIQLEA 836

Query: 515 LIAAF 519
           L+A F
Sbjct: 837 LLAQF 841

Length = 846

>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional

 Score = 50.1 bits (120), Expect = 2e-06
 Identities = 25/81 (30%), Positives = 38/81 (46%)

Query: 19  KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
           K+   I SRC RF F  +    I+ RL Y+ +QE ++++      +    DG MR  L+ 
Sbjct: 161 KVPITILSRCQRFDFRRIPLQKIVDRLRYIADQEGISISDAALALVARKGDGSMRDSLST 220

Query: 79  LQSAATAHADEVNEDTIFTLL 99
           L        D V +D +  LL
Sbjct: 221 LDQVLAFCGDAVGDDDVAELL 241

Length = 576

>gnl|CDD|181214 PRK08058, PRK08058, DNA polymerase III subunit delta'; Validated

 Score = 49.5 bits (119), Expect = 2e-06
 Identities = 47/163 (28%), Positives = 72/163 (44%), Gaps = 18/163 (11%)

Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAM----------VLELNASDDR 349
           I +N L H  LF G  GTGK  T L  A+ L+   +              +   N  D  
Sbjct: 22  IAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVH 81

Query: 350 -----GIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNV 402
                G  I +DQI   +   +K+  +S+ K+ I++ AD MT  A N+L + +E+ +   
Sbjct: 82  LVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGT 141

Query: 403 RFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDIS 445
              ++     +I P I SRC    F PL    ++ RL  + IS
Sbjct: 142 TAILLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQEEGIS 184

Length = 329

>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau; Provisional

 Score = 49.4 bits (118), Expect = 3e-06
 Identities = 35/145 (24%), Positives = 66/145 (45%), Gaps = 11/145 (7%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           +E+   +++F +    + KI   I SRC +F+   +    I + L Y++ +E ++     
Sbjct: 143 LEEPPQHIKFILATTDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKESIDTDEYA 202

Query: 61  KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDI 120
            K I   + G MR  LN+L+ A       +N   +  +L    EK      D L+  +D 
Sbjct: 203 LKLIAYHAHGSMRDALNLLEHAINLGKGNINIKNVTDMLGLLNEKQSFLLTDALLK-KDS 261

Query: 121 ---------ISTIEIP-ESMLVDLV 135
                    IS+I I  E++L++++
Sbjct: 262 KKTMLLLNKISSIGIEWENILIEML 286

Length = 363

>gnl|CDD|236022 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated

 Score = 49.3 bits (118), Expect = 3e-06
 Identities = 19/55 (34%), Positives = 33/55 (60%)

Query: 376 ILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPL 430
           I+D AD M  +A NAL +++E+      F ++ +  +++ P I+SRC + R  PL
Sbjct: 146 IVDTADEMNANAANALLKVLEEPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPL 200

Length = 365

>gnl|CDD|236267 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau; Validated

 Score = 49.3 bits (118), Expect = 4e-06
 Identities = 48/161 (29%), Positives = 79/161 (49%), Gaps = 27/161 (16%)

Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VL 341
           +D N L H  LF G  G+GKT++    AR L  +   ++                   ++
Sbjct: 30  LDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDII 89

Query: 342 ELNASDDRGIGIVRDQIFQFASTKTMHKSS---YKLIILDEADAMTNDAQNALRRIIEKF 398
           E++A+ +RGI  +R+ I Q     T +K S   +K+ I+DE   +T +A NAL + +E+ 
Sbjct: 90  EMDAASNRGIDDIRELIEQ-----TKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEP 144

Query: 399 TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
            + V+F +      K+P  I SR   FRF  +  + I+S L
Sbjct: 145 PSYVKFILATTDPLKLPATILSRTQHFRFKQIPQNSIISHL 185

Length = 535

>gnl|CDD|237873 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau; Provisional

 Score = 49.0 bits (117), Expect = 5e-06
 Identities = 42/160 (26%), Positives = 75/160 (46%), Gaps = 25/160 (15%)

Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----CARKLYTK--AQFNAMV----------L 341
           +++  L H  LF G  G GKTT   ILA    C   +        +A +          +
Sbjct: 32  LEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLI 91

Query: 342 ELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT 399
           E++A+ +  +  +R+ +   Q+A T+      +K+ I+DE   ++  A NA+ + +E+  
Sbjct: 92  EVDAASNTQVDAMRELLDNAQYAPTR----GRFKVYIIDEVHMLSKSAFNAMLKTLEEPP 147

Query: 400 TNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
            +V+F +      KIP  + SRC +F    +   LI+S L
Sbjct: 148 EHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPPLIVSHL 187

Length = 527

>gnl|CDD|169667 PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated

 Score = 48.1 bits (115), Expect = 7e-06
 Identities = 20/68 (29%), Positives = 38/68 (55%)

Query: 364 TKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCT 423
           ++T    +++++I+D AD M  +A NA+ + +E+      F +I +   ++ P I+SRC 
Sbjct: 134 SQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPARALFILISHSSGRLLPTIRSRCQ 193

Query: 424 RFRFGPLD 431
                PLD
Sbjct: 194 PISLKPLD 201

Length = 351

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

 Score = 46.7 bits (111), Expect = 2e-05
 Identities = 24/95 (25%), Positives = 43/95 (45%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           +E+  ++V F +    L K+ P I SRC    F  +   LI+ RL  V E E + +  + 
Sbjct: 141 LEEPPSHVVFVLATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGIEIDREA 200

Query: 61  KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTI 95
              I   + G +R  L +L+        ++  +T+
Sbjct: 201 LSFIAKRASGGLRDALTMLEQVWKFSEGKITLETV 235

Length = 472

>gnl|CDD|237866 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.2 bits (112), Expect = 2e-05
 Identities = 44/151 (29%), Positives = 70/151 (46%), Gaps = 29/151 (19%)

Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----CAR--------------KLYTKAQFNAM 339
           +D   + H  LF GP G GKT++  ILA    CA+               L      +  
Sbjct: 29  LDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPNGPGSID 88

Query: 340 VLELNASDDRGIG---IVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIE 396
           V+EL+A+   G+     +RD+ F +A  +    S Y++ I+DEA  +T    NAL +I+E
Sbjct: 89  VVELDAASHGGVDDTRELRDRAF-YAPAQ----SRYRIFIVDEAHMVTTAGFNALLKIVE 143

Query: 397 KFTTNVRFCIICNYLSKIPPAIQSRCTRFRF 427
           +   ++ F        K+ P I+SR   + F
Sbjct: 144 EPPEHLIFIFATTEPEKVLPTIRSRTHHYPF 174

Length = 584

>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau; Validated

 Score = 47.0 bits (111), Expect = 2e-05
 Identities = 40/144 (27%), Positives = 66/144 (45%), Gaps = 21/144 (14%)

Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTK--------------AQFNAM----VL 341
           +DE  L H  L  G  G GKTT     A+ L  +               Q +A     +L
Sbjct: 32  LDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLL 91

Query: 342 ELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTN 401
           E++A+ + GI  +R+ +       T  K  YK+ I+DE   ++  A NA+ + +E+   +
Sbjct: 92  EIDAASNTGIDNIREVLENAQYAPTAGK--YKVYIIDEVHMLSKSAFNAMLKTLEEPPEH 149

Query: 402 VRFCIICNYLSKIPPAIQSRCTRF 425
           V+F +      K+P  + SRC +F
Sbjct: 150 VKFILATTDPHKVPVTVLSRCLQF 173

Length = 709

>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed

 Score = 47.0 bits (112), Expect = 2e-05
 Identities = 38/148 (25%), Positives = 60/148 (40%), Gaps = 36/148 (24%)

Query: 299 RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAM------VLELNASDDRGIG 352
           R I  + +  L+ YGPPG GKTT  LA     +T+A F+++      V +L A  DR   
Sbjct: 45  RAIKADRVGSLILYGPPGVGKTT--LARIIANHTRAHFSSLNAVLAGVKDLRAEVDRA-- 100

Query: 353 IVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEK--------FTTNVRF 404
             ++++ +    +T       ++ +DE        Q+AL   +E          T N  F
Sbjct: 101 --KERLERHGK-RT-------ILFIDEVHRFNKAQQDALLPWVENGTITLIGATTENPYF 150

Query: 405 CIICNYLSKIPPAIQSRCTRFRFGPLDS 432
            +          A+ SR   FR   L  
Sbjct: 151 EVN--------KALVSRSRLFRLKSLSD 170

Length = 725

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

 Score = 45.4 bits (108), Expect = 4e-05
 Identities = 17/64 (26%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 456 IQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSAL 515
           + ++ I++GL+  ++L E+  +       ++ L  L    +D + RL  G +++IQL AL
Sbjct: 274 LDDLLIDEGLSGGEVLEELLRVARSRYRGDN-LARLHRLAADADARLTDGANDRIQLEAL 332

Query: 516 IAAF 519
           +A  
Sbjct: 333 LAEL 336

Length = 337

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 46.0 bits (109), Expect = 4e-05
 Identities = 44/166 (26%), Positives = 76/166 (45%), Gaps = 30/166 (18%)

Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA------------------CAR-KLYTKAQFNA 338
           +++  L H  LF G  G GKTT   ILA                  C + +  T+     
Sbjct: 32  LEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGR 91

Query: 339 MV--LELNASDDRGIGIVRDQIFQFASTKTMHKSS--YKLIILDEADAMTNDAQNALRRI 394
            V  +E++A+ +RG+    D++ Q         ++  +K+ ++DE   +TN A NA+ + 
Sbjct: 92  FVDYIEMDAASNRGV----DEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKT 147

Query: 395 IEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLD 440
           +E+   +V+F +      KIP  + SRC +F    +    I+S LD
Sbjct: 148 LEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPGHIVSHLD 193

Length = 700

>gnl|CDD|237873 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.5 bits (108), Expect = 5e-05
 Identities = 30/112 (26%), Positives = 55/112 (49%), Gaps = 1/112 (0%)

Query: 19  KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
           KI   + SRC +F    +   LI+S L +++EQE +       + +   + G MR  L++
Sbjct: 161 KIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAAAGSMRDALSL 220

Query: 79  LQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESM 130
           L  A       VNE  +  +L +  + Y  + L+ L++ QD  + + I ++M
Sbjct: 221 LDQAIAYGGGTVNESEVRAMLGAIDQDYLFALLEALLA-QDGAALLAIADAM 271

Length = 527

>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau; Validated

 Score = 45.2 bits (107), Expect = 8e-05
 Identities = 23/80 (28%), Positives = 41/80 (51%)

Query: 19  KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
           KI   I SR  RF F  +    I+SRL++++E+E ++   +  K I  LS G +R  L+I
Sbjct: 160 KIPLTILSRVQRFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLSSGSLRDALSI 219

Query: 79  LQSAATAHADEVNEDTIFTL 98
            +  +    +++    +  L
Sbjct: 220 AEQVSIFGNNKITLKNVEEL 239

Length = 725

>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated

 Score = 44.4 bits (105), Expect = 9e-05
 Identities = 39/170 (22%), Positives = 63/170 (37%), Gaps = 53/170 (31%)

Query: 306 LPH-LLFYGPPGTGKTTTILACARKLYTK------------------AQFN--------- 337
           LPH LL +G  G GK       A+ L  +                  AQ N         
Sbjct: 20  LPHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRP 79

Query: 338 -AMVLELNAS---------DDRG---------IGIVRDQI---FQFASTKTMHKSSYKLI 375
            A+  E   +         D+ G         I I  +Q+     F    T H+   +++
Sbjct: 80  EALAAEAPGAADEAKEADADEGGKKTKAPSKEIKI--EQVRALLDFCGVGT-HRGGARVV 136

Query: 376 ILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRF 425
           +L  A+A+   A NAL + +E+      F ++   + ++ P I SRC +F
Sbjct: 137 VLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQF 186

Length = 342

>gnl|CDD|223546 COG0470, HolB, ATPase involved in DNA replication [DNA replication, recombination, and repair]

 Score = 43.1 bits (101), Expect = 1e-04
 Identities = 17/34 (50%), Positives = 19/34 (55%)

Query: 398 FTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLD 431
              N RF +I N  SKI P I+SRC R RF P  
Sbjct: 41  PPKNTRFILITNDPSKILPTIRSRCQRIRFKPPS 74

Length = 230

>gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau; Provisional

 Score = 44.1 bits (104), Expect = 1e-04
 Identities = 24/79 (30%), Positives = 34/79 (43%)

Query: 17  LSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVL 76
           L KI   I SRC RF F  +    I  +L  + E E ++V  D  + I   + G MR   
Sbjct: 167 LHKIPATIASRCQRFNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDAQ 226

Query: 77  NILQSAATAHADEVNEDTI 95
           +IL        +   E +I
Sbjct: 227 SILDQVIAFSVESEGEGSI 245

Length = 397

>gnl|CDD|237870 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau; Provisional

 Score = 43.6 bits (103), Expect = 2e-04
 Identities = 25/92 (27%), Positives = 46/92 (50%)

Query: 8   VRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL 67
           V+F +    + KI   I SRC RF    + +  ++  L  + ++E +    +  K I + 
Sbjct: 147 VKFILATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLIAEN 206

Query: 68  SDGDMRKVLNILQSAATAHADEVNEDTIFTLL 99
           S G MR  L +L+ AA    ++++E ++  LL
Sbjct: 207 SSGSMRNALFLLEQAAIYSNNKISEKSVRDLL 238

Length = 491

>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau; Provisional

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 21/73 (28%), Positives = 40/73 (54%)

Query: 369 KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFG 428
           KS +K+ ++DE   ++  + NAL + +E+   +++F +    + KIP  I SRC +F+  
Sbjct: 117 KSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFKLK 176

Query: 429 PLDSSLIMSRLDY 441
            +    I + L Y
Sbjct: 177 IISEEKIFNFLKY 189

Length = 363

>gnl|CDD|180643 PRK06645, PRK06645, DNA polymerase III subunits gamma and tau; Validated

 Score = 44.1 bits (104), Expect = 2e-04
 Identities = 28/102 (27%), Positives = 52/102 (50%), Gaps = 2/102 (1%)

Query: 340 VLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT 399
           ++E++A+    +  +R +I + A  K + +  +K+ I+DE   ++  A NAL + +E+  
Sbjct: 99  IIEIDAASKTSVDDIR-RIIESAEYKPL-QGKHKIFIIDEVHMLSKGAFNALLKTLEEPP 156

Query: 400 TNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
            ++ F      + KIP  I SRC R+    L    I   L+Y
Sbjct: 157 PHIIFIFATTEVQKIPATIISRCQRYDLRRLSFEEIFKLLEY 198

Length = 507

>gnl|CDD|181538 PRK08699, PRK08699, DNA polymerase III subunit delta'; Validated

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 351 IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY 410
           I  VR+ I       T  +   ++I++  A++M   A N+L +++E+    V F ++ + 
Sbjct: 95  IDAVRE-IIDNVYL-TSVRGGLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHA 152

Query: 411 LSKIPPAIQSRCTRFRFGPLDSS 433
             K+ P I+SRC +         
Sbjct: 153 ADKVLPTIKSRCRKMVLPAPSHE 175

Length = 325

>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau; Provisional

 Score = 43.0 bits (101), Expect = 3e-04
 Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 2/66 (3%)

Query: 368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF 427
            K  Y++ I+DE   ++  A NA  + +E+   +  F      L KIP  I SRC RF F
Sbjct: 124 QKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNF 183

Query: 428 G--PLD 431
              PLD
Sbjct: 184 KRIPLD 189

Length = 620

>gnl|CDD|102059 PRK05917, PRK05917, DNA polymerase III subunit delta'; Validated

 Score = 42.5 bits (100), Expect = 3e-04
 Identities = 28/104 (26%), Positives = 50/104 (48%), Gaps = 6/104 (5%)

Query: 368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF 427
           ++S YK+ I+ EAD MT DA +A  +++E    +    +      ++PP I+SR      
Sbjct: 92  YESPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTIRSRSLSIHI 151

Query: 428 GPLDSSLIMSRLDYDDISF-FNIIIWYIKIQEI-KIEKGLALTD 469
              + +L+      +DI++          + E+ +I KG A TD
Sbjct: 152 PMEEKTLV----SKEDIAYLIGYAQGKESVTEVGQIVKGSADTD 191

Length = 290

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.6 bits (100), Expect = 4e-04
 Identities = 27/112 (24%), Positives = 52/112 (46%), Gaps = 1/112 (0%)

Query: 19  KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
           KI   + SRC +F    +    I+S LD ++ +E +    +  + +   + G MR  L++
Sbjct: 166 KIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALRLLAQAAQGSMRDALSL 225

Query: 79  LQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESM 130
              A    A  V+E+ +  +L +  + Y    LD L + +D  + + I + M
Sbjct: 226 TDQAIAYSAGNVSEEAVRGMLGAIDQSYLVRLLDALAA-EDGAALLAIADEM 276

Length = 700

>gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.6 bits (100), Expect = 4e-04
 Identities = 21/60 (35%), Positives = 30/60 (50%)

Query: 368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF 427
            K  Y++ I+DE   ++  A NA  + +E+   +  F      L KIP  I SRC RF F
Sbjct: 124 QKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNF 183

Length = 397

>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed

 Score = 42.3 bits (100), Expect = 5e-04
 Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 7/70 (10%)

Query: 20  ITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQE-------KVNVTPDGKKAIIDLSDGDM 72
           +  A+ SR   FR   L    +   L   ++ +       KV++ P+ +K ++D+++GD 
Sbjct: 152 VNKALVSRSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDA 211

Query: 73  RKVLNILQSA 82
           R +LN L+ A
Sbjct: 212 RSLLNALELA 221

Length = 725

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.5 bits (100), Expect = 5e-04
 Identities = 22/60 (36%), Positives = 31/60 (51%)

Query: 19  KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
           KI P I SRC  F F  +  + I++ L YV  +E +   P+    I   +DG MR  L+I
Sbjct: 163 KILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSI 222

Length = 614

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.5 bits (100), Expect = 5e-04
 Identities = 46/167 (27%), Positives = 70/167 (41%), Gaps = 34/167 (20%)

Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLY-------------------------TKA 334
           I  N+L H  LF GP G GKTT    CAR                             + 
Sbjct: 33  IATNKLAHAYLFCGPRGVGKTT----CARIFAKTINCQNLTADGEACNECESCVAFNEQR 88

Query: 335 QFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRI 394
            +N  + EL+A+ +  +  +R+ I Q      + K  YK+ I+DE   ++  A NA  + 
Sbjct: 89  SYN--IHELDAASNNSVDDIRNLIEQVRIPPQIGK--YKIYIIDEVHMLSQAAFNAFLKT 144

Query: 395 IEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
           +E+  +   F +      KI P I SRC  F F  +  + I++ L Y
Sbjct: 145 LEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQY 191

Length = 614

>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.7 bits (98), Expect = 7e-04
 Identities = 19/55 (34%), Positives = 27/55 (49%)

Query: 19  KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMR 73
           K+ P I SR   FRF  L    I  +L  ++E E     P+  + +  L+DG MR
Sbjct: 158 KMPPTILSRTQHFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMR 212

Length = 504

>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed

 Score = 41.3 bits (98), Expect = 8e-04
 Identities = 14/22 (63%), Positives = 16/22 (72%), Gaps = 2/22 (9%)

Query: 306 LPHLLFYGPPGTGKTT--TILA 325
           L H+L YGPPG GKTT   I+A
Sbjct: 51  LDHVLLYGPPGLGKTTLANIIA 72

Length = 328

>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed

 Score = 41.6 bits (99), Expect = 9e-04
 Identities = 12/54 (22%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 219 QNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVG 272
           ++  R  + +  +   A+  L++GD R+ LN+L+ AA    D +  + +  ++ 
Sbjct: 165 EDKERGLVELDDEALDALARLANGDARRALNLLELAALGV-DSITLELLEEALQ 217

Length = 413

>gnl|CDD|181551 PRK08769, PRK08769, DNA polymerase III subunit delta'; Validated

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 42/159 (26%), Positives = 67/159 (42%), Gaps = 25/159 (15%)

Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAMV--------------LEL-- 343
           +D   L H LL  GP G GK    LA A  +       A                L+L  
Sbjct: 20  LDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVS 79

Query: 344 ---NASDDR-GIGIVRDQIFQFAS--TKTMHKSSYKLIILDEADAMTNDAQNALRRIIEK 397
              N + D+    IV +Q+ + +     T      +++I+D ADA+   A NAL + +E+
Sbjct: 80  FIPNRTGDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEE 139

Query: 398 FTTNVRFCIICNYLSKIPPAIQSRCTR--FRFGPLDSSL 434
            +      +I    +++P  I+SRC R  F+  P   +L
Sbjct: 140 PSPGRYLWLISAQPARLPATIRSRCQRLEFKLPPAHEAL 178

Length = 319

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 41.4 bits (97), Expect = 0.001
 Identities = 27/109 (24%), Positives = 51/109 (46%)

Query: 8   VRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL 67
           V+F +      KI   + SRC +F    + +  I+S L+ ++ +E++   P   + +   
Sbjct: 150 VKFILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERILGEERIAFEPQALRLLARA 209

Query: 68  SDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVS 116
           + G MR  L++   A    A+EV E  +  +L +  + Y    LD L +
Sbjct: 210 AQGSMRDALSLTDQAIAYSANEVTETAVSGMLGALDQTYMVRLLDALAA 258

Length = 830

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

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 42/141 (29%), Positives = 62/141 (43%), Gaps = 32/141 (22%)

Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIG--IVRDQIFQFASTKT 366
           +L YGPPGTGKT    A A   +T A F  +V         G G  +VRD +F+ A    
Sbjct: 182 VLLYGPPGTGKTMLAKAVAH--HTTATFIRVVGSEFVQKYLGEGPRMVRD-VFRLA---- 234

Query: 367 MHKSSYKLIILDEADAMTN---DAQNALRRIIEKF-------------TTNVRFCIICNY 410
             +++  +I +DE D++     DAQ    R +++              TTNV+  +  N 
Sbjct: 235 -RENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNR 293

Query: 411 LSKIPPAIQSRCTRFRFGPLD 431
              + PA+       R G LD
Sbjct: 294 ADTLDPAL------LRPGRLD 308

Length = 398

>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 = 38.7 bits (90), Expect = 0.002
 Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 3/65 (4%)

Query: 163 NSARDKLEVLELNASDDRGIGIVRDQI---FQFASTKTMHKSSYKLIILDEADAMTNDAQ 219
              R     L LNASD     +V +           +   K+   ++ +DE D+++  AQ
Sbjct: 42  ELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQ 101

Query: 220 NALRR 224
           NAL R
Sbjct: 102 NALLR 106

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|180855 PRK07132, PRK07132, DNA polymerase III subunit delta'; Validated

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 9/94 (9%)

Query: 365 KTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTR 424
            +  +S  K++I+   +  +N   NAL + IE+   +  F +    ++K+ P I SRC  
Sbjct: 84  SSFVQSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQV 143

Query: 425 FRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQE 458
           F              D   I    +     K   
Sbjct: 144 FNV---------KEPDQQKILAKLLSKNKEKEYN 168

Length = 299

>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

 Score = 40.4 bits (95), Expect = 0.002
 Identities = 28/126 (22%), Positives = 47/126 (37%), Gaps = 19/126 (15%)

Query: 300 FIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG--------- 350
            +      +++ YGP GTGKT T+     +L   +  N  V+ +N  + R          
Sbjct: 36  ALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSA-NVEVVYINCLELRTPYQVLSKIL 94

Query: 351 --------IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTN- 401
                    G    +I +        K    ++ILDE DA+ +     L  ++     N 
Sbjct: 95  NKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGENK 154

Query: 402 VRFCII 407
           V+  II
Sbjct: 155 VKVSII 160

Length = 366

>gnl|CDD|221955 pfam13173, AAA_14, AAA domain

 Score = 37.9 bits (89), Expect = 0.002
 Identities = 22/98 (22%), Positives = 45/98 (45%), Gaps = 9/98 (9%)

Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH 368
           ++  GP   GKTT +L   ++L ++      +L +N  D R + +    + +      + 
Sbjct: 5   IVITGPRQVGKTTLLLQFLKELLSEN-----ILYINLDDPRFLRLALLDLLEEF--LKLL 57

Query: 369 KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCI 406
               K + LDE   +  D ++AL+R+ +    N+R  +
Sbjct: 58  LPGKKYLFLDEIQKV-PDWEDALKRLYDDG-RNLRIIL 93

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Length = 127

>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit

 Score = 38.4 bits (90), Expect = 0.003
 Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 182 IGI--VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNAL 222
           I +  VR+ + +F S      S  +++I+++A+ M   A NAL
Sbjct: 76  IKVDQVRE-LVEFLSRTPQE-SGRRVVIIEDAERMNEAAANAL 116

This model describes the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tighly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classisified as delta'. The noise cutoff is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits. 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 188

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

 Score = 39.9 bits (94), Expect = 0.003
 Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 18/79 (22%)

Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD--DRGIG----IVRDQIFQFAS 363
           L YGPPGTGKT    A A       Q +A  + +  S+   + IG    +VR+ +F+ A 
Sbjct: 189 LLYGPPGTGKTLLAKAVA------NQTDATFIRVVGSELVQKYIGEGARLVRE-LFELAR 241

Query: 364 TKTMHKSSYKLIILDEADA 382
                  S  +I +DE DA
Sbjct: 242 ---EKAPS--IIFIDEIDA 255

Length = 406

>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB

 Score = 39.8 bits (93), Expect = 0.003
 Identities = 27/72 (37%), Positives = 36/72 (50%), Gaps = 21/72 (29%)

Query: 308 HLLFYGPPGTGKTTTILACAR------KLYTKAQFN--AMVLELNAS----DDRGI---- 351
           H++ YGPPG GKT    A AR      K    + F   A  +E++A+    D+RGI    
Sbjct: 88  HVIIYGPPGVGKT----AAARLVLEEAKKNPASPFKEGAAFVEIDATTARFDERGIADPL 143

Query: 352 -GIVRDQIFQFA 362
            G V D I+Q A
Sbjct: 144 IGSVHDPIYQGA 155

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 [Protein fate, Degradation of proteins, peptides, and glycopeptides, Cellular processes, Sporulation and germination]. Length = 531

>gnl|CDD|235833 PRK06581, PRK06581, DNA polymerase III subunit delta'; Validated

 Score = 38.7 bits (90), Expect = 0.004
 Identities = 23/77 (29%), Positives = 39/77 (50%)

Query: 346 SDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFC 405
           S+ + I I + +  Q   +KT   S YK+ I+  A+ M  +A N+  +I+E    N    
Sbjct: 64  SNAKNISIEQIRKLQDFLSKTSAISGYKVAIIYSAELMNLNAANSCLKILEDAPKNSYIF 123

Query: 406 IICNYLSKIPPAIQSRC 422
           +I +  + I   I+SRC
Sbjct: 124 LITSRAASIISTIRSRC 140

Length = 263

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	533
KOG0991|consensus	333		100.0
PLN03025	319	replication factor C subunit; Provisional	99.97
KOG0989|consensus	346		99.97
KOG2035|consensus	351		99.96
KOG0991|consensus	333		99.94
KOG0990|consensus	360		99.94
PRK04132	846	replication factor C small subunit; Provisional	99.93
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	99.92
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.91
KOG2035|consensus	351		99.91
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.91
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.91
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.9
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.9
KOG0733|consensus	802		99.9
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.89
KOG0730|consensus	693		99.89
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.89
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.88
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.88
PRK12402	337	replication factor C small subunit 2; Reviewed	99.88
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.88
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.88
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.88
PHA02544	316	44 clamp loader, small subunit; Provisional	99.87
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.87
PRK07993	334	DNA polymerase III subunit delta'; Validated	99.87
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.87
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.87
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.87
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.87
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	99.87
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.87
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.86
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.86
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	99.86
KOG0989|consensus	346		99.86
PRK06964	342	DNA polymerase III subunit delta'; Validated	99.86
PRK05707	328	DNA polymerase III subunit delta'; Validated	99.86
PRK06871	325	DNA polymerase III subunit delta'; Validated	99.85
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.85
PRK08769	319	DNA polymerase III subunit delta'; Validated	99.85
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.85
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.85
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.85
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.85
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.84
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.84
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.84
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.84
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.84
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.84
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.83
PRK04132	846	replication factor C small subunit; Provisional	99.83
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.83
PRK06090	319	DNA polymerase III subunit delta'; Validated	99.83
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.83
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.83
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	99.82
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.82
PRK05917	290	DNA polymerase III subunit delta'; Validated	99.82
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.82
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.81
PLN03025	319	replication factor C subunit; Provisional	99.81
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.8
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.8
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.8
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.8
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.8
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.8
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.79
KOG2028|consensus	554		99.79
PRK08699	325	DNA polymerase III subunit delta'; Validated	99.78
KOG0990|consensus	360		99.77
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.77
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.76
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.75
PRK07276	290	DNA polymerase III subunit delta'; Validated	99.75
PRK04195	482	replication factor C large subunit; Provisional	99.75
KOG0735|consensus	952		99.75
KOG0736|consensus	953		99.74
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.72
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.72
CHL00095	821	clpC Clp protease ATP binding subunit	99.71
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.7
PRK07132	299	DNA polymerase III subunit delta'; Validated	99.7
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.7
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.7
KOG0733|consensus	802		99.69
PRK13342	413	recombination factor protein RarA; Reviewed	99.69
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	99.69
PRK05818	261	DNA polymerase III subunit delta'; Validated	99.69
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.69
PRK13341	725	recombination factor protein RarA/unknown domain f	99.68
CHL00195	489	ycf46 Ycf46; Provisional	99.67
KOG0738|consensus	491		99.67
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.67
KOG0734|consensus	752		99.66
KOG0727|consensus	408		99.63
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.62
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.62
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.62
KOG0739|consensus	439		99.62
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.61
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.61
PRK14700	300	recombination factor protein RarA; Provisional	99.61
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.6
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.6
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.6
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.6
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.6
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.59
CHL00181	287	cbbX CbbX; Provisional	99.58
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.58
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.58
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.57
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.57
KOG0728|consensus	404		99.57
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.57
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.57
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.57
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.56
PF00004	132	AAA: ATPase family associated with various cellula	99.56
PRK10865	857	protein disaggregation chaperone; Provisional	99.56
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.55
KOG0652|consensus	424		99.54
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.54
KOG0729|consensus	435		99.54
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.54
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.54
PRK06581	263	DNA polymerase III subunit delta'; Validated	99.53
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.53
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.52
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.52
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.52
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.51
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.51
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.51
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.51
CHL00176	638	ftsH cell division protein; Validated	99.51
KOG0731|consensus	774		99.51
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.5
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	99.49
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.49
CHL00206	2281	ycf2 Ycf2; Provisional	99.48
PRK08084	235	DNA replication initiation factor; Provisional	99.48
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.48
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.48
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.48
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.47
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.47
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.47
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.46
KOG0726|consensus	440		99.46
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.45
KOG0737|consensus	386		99.45
PRK06893	229	DNA replication initiation factor; Validated	99.45
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.45
KOG0744|consensus	423		99.44
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.44
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.44
KOG0742|consensus	630		99.43
KOG0743|consensus	457		99.43
KOG1969|consensus	877		99.43
PRK12402	337	replication factor C small subunit 2; Reviewed	99.42
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.41
PRK13531	498	regulatory ATPase RavA; Provisional	99.41
PRK08485	206	DNA polymerase III subunit delta'; Validated	99.41
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.41
PRK08727	233	hypothetical protein; Validated	99.4
KOG2004|consensus	906		99.4
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.4
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	99.4
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.4
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.39
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	99.38
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.38
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.38
PHA02244	383	ATPase-like protein	99.37
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.37
PRK07993	334	DNA polymerase III subunit delta'; Validated	99.37
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.37
COG2204	464	AtoC Response regulator containing CheY-like recei	99.36
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.36
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.35
KOG1969|consensus	877		99.35
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.34
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.33
PRK06526	254	transposase; Provisional	99.33
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.33
KOG0651|consensus	388		99.32
PRK08181	269	transposase; Validated	99.32
KOG0740|consensus	428		99.32
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.31
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.31
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.3
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.3
PRK05642	234	DNA replication initiation factor; Validated	99.3
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.3
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	99.3
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.29
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.29
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.29
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.28
KOG0730|consensus	693		99.27
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.27
COG1221	403	PspF Transcriptional regulators containing an AAA-	99.27
PF07726	131	AAA_3: ATPase family associated with various cellu	99.27
PRK06090	319	DNA polymerase III subunit delta'; Validated	99.27
PRK08769	319	DNA polymerase III subunit delta'; Validated	99.27
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.27
KOG0741|consensus	744		99.27
COG0714	329	MoxR-like ATPases [General function prediction onl	99.27
PRK06871	325	DNA polymerase III subunit delta'; Validated	99.26
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	99.26
PRK11608	326	pspF phage shock protein operon transcriptional ac	99.26
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.26
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.25
PRK09183	259	transposase/IS protein; Provisional	99.24
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	99.24
PRK10865	857	protein disaggregation chaperone; Provisional	99.23
PHA02544	316	44 clamp loader, small subunit; Provisional	99.23
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	99.22
PRK05707	328	DNA polymerase III subunit delta'; Validated	99.22
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.21
PRK15424	538	propionate catabolism operon regulatory protein Pr	99.21
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.21
PRK05022	509	anaerobic nitric oxide reductase transcription reg	99.2
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	99.2
PRK12422	445	chromosomal replication initiation protein; Provis	99.2
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.19
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.19
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	99.19
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.19
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.18
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	99.18
COG0593	408	DnaA ATPase involved in DNA replication initiation	99.17
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.16
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	99.16
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.16
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.16
PRK05818	261	DNA polymerase III subunit delta'; Validated	99.15
PRK06620	214	hypothetical protein; Validated	99.14
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.14
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	99.14
CHL00095	821	clpC Clp protease ATP binding subunit	99.14
PRK09087	226	hypothetical protein; Validated	99.13
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.13
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	99.13
PRK06964	342	DNA polymerase III subunit delta'; Validated	99.12
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.11
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.1
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	99.1
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.1
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	99.1
PRK07276	290	DNA polymerase III subunit delta'; Validated	99.09
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.08
PRK07132	299	DNA polymerase III subunit delta'; Validated	99.07
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	99.07
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	99.07
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.05
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	99.05
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.03
PRK12377	248	putative replication protein; Provisional	99.03
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.03
KOG0741|consensus	744		99.03
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.03
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.03
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	99.02
KOG0732|consensus	1080		98.99
KOG0735|consensus	952		98.98
smart00350	509	MCM minichromosome maintenance proteins.	98.96
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	98.95
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	98.95
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	98.95
PRK06921	266	hypothetical protein; Provisional	98.95
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	98.95
PRK08116	268	hypothetical protein; Validated	98.95
PRK05917	290	DNA polymerase III subunit delta'; Validated	98.95
PRK04195	482	replication factor C large subunit; Provisional	98.95
PRK13342	413	recombination factor protein RarA; Reviewed	98.93
KOG2028|consensus	554		98.92
PRK08485	206	DNA polymerase III subunit delta'; Validated	98.92
PRK15115	444	response regulator GlrR; Provisional	98.91
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.9
KOG1051|consensus	898		98.9
KOG1942|consensus	456		98.9
PRK07952	244	DNA replication protein DnaC; Validated	98.89
KOG1514|consensus	767		98.89
PF13173	128	AAA_14: AAA domain	98.88
PRK06835	329	DNA replication protein DnaC; Validated	98.88
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	98.87
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	98.87
smart00382	148	AAA ATPases associated with a variety of cellular	98.86
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	98.85
PRK06581	263	DNA polymerase III subunit delta'; Validated	98.85
PRK13341	725	recombination factor protein RarA/unknown domain f	98.83
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	98.83
KOG2227|consensus	529		98.82
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	98.82
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.8
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	98.8
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	98.76
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	98.73
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	98.71
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	98.7
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	98.69
PRK10365	441	transcriptional regulatory protein ZraR; Provision	98.68
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.66
PRK13765	637	ATP-dependent protease Lon; Provisional	98.65
KOG0745|consensus	564		98.65
PRK08084	235	DNA replication initiation factor; Provisional	98.63
PRK08939	306	primosomal protein DnaI; Reviewed	98.63
PRK09862	506	putative ATP-dependent protease; Provisional	98.61
KOG2680|consensus	454		98.6
PF08542	89	Rep_fac_C: Replication factor C C-terminal domain;	98.59
PRK10875	615	recD exonuclease V subunit alpha; Provisional	98.58
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.58
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	98.57
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	98.56
KOG2170|consensus	344		98.55
KOG0736|consensus	953		98.54
PF05729	166	NACHT: NACHT domain	98.52
PRK08727	233	hypothetical protein; Validated	98.52
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.5
KOG0480|consensus	764		98.49
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.49
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	98.49
KOG0478|consensus	804		98.48
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	98.48
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	98.45
COG0606	490	Predicted ATPase with chaperone activity [Posttran	98.44
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.44
TIGR01128	302	holA DNA polymerase III, delta subunit. subunit ar	98.43
PRK10536	262	hypothetical protein; Provisional	98.42
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.42
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	98.41
PRK06620	214	hypothetical protein; Validated	98.39
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	98.39
PHA00729	226	NTP-binding motif containing protein	98.38
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	98.37
KOG1968|consensus	871		98.35
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	98.33
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	98.33
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	98.33
PRK08699	325	DNA polymerase III subunit delta'; Validated	98.32
CHL00195	489	ycf46 Ycf46; Provisional	98.3
PHA02774	613	E1; Provisional	98.29
PRK06893	229	DNA replication initiation factor; Validated	98.28
PRK09087	226	hypothetical protein; Validated	98.27
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	98.25
COG1241	682	MCM2 Predicted ATPase involved in replication cont	98.25
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	98.24
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	98.24
PHA02624	647	large T antigen; Provisional	98.24
KOG1970|consensus	634		98.23
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.21
PRK05642	234	DNA replication initiation factor; Validated	98.18
COG4650	531	RtcR Sigma54-dependent transcription regulator con	98.17
PRK04296	190	thymidine kinase; Provisional	98.14
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	98.12
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	98.07
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.06
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.02
PRK13889	988	conjugal transfer relaxase TraA; Provisional	98.02
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	97.97
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	97.96
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.96
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.95
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	97.94
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	97.93
KOG2228|consensus	408		97.91
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	97.89
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.87
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	97.84
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.84
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	97.83
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.83
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	97.81
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.81
KOG0477|consensus	854		97.8
CHL00181	287	cbbX CbbX; Provisional	97.8
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.8
COG4619	223	ABC-type uncharacterized transport system, ATPase	97.79
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	97.77
PRK05629	318	hypothetical protein; Validated	97.76
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.76
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	97.76
PRK12422	445	chromosomal replication initiation protein; Provis	97.73
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.72
KOG1968|consensus	871		97.7
PRK07452	326	DNA polymerase III subunit delta; Validated	97.69
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.67
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.66
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	97.66
PRK05574	340	holA DNA polymerase III subunit delta; Reviewed	97.66
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.65
PRK14532	188	adenylate kinase; Provisional	97.63
PRK07914	320	hypothetical protein; Reviewed	97.62
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	97.6
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.6
PRK14528	186	adenylate kinase; Provisional	97.59
KOG0482|consensus	721		97.59
KOG0481|consensus	729		97.58
COG4178	604	ABC-type uncharacterized transport system, permeas	97.57
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.56
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	97.56
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	97.55
PRK06851	367	hypothetical protein; Provisional	97.55
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.55
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.54
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	97.53
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	97.52
PRK04841	903	transcriptional regulator MalT; Provisional	97.51
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.49
KOG3347|consensus	176		97.49
PF14516	331	AAA_35: AAA-like domain	97.48
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	97.47
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	97.46
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	97.46
PRK06585	343	holA DNA polymerase III subunit delta; Reviewed	97.45
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.43
TIGR01613	304	primase_Cterm phage/plasmid primase, P4 family, C-	97.43
PF06144	172	DNA_pol3_delta: DNA polymerase III, delta subunit;	97.41
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.39
PF13245	76	AAA_19: Part of AAA domain	97.37
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.37
PRK12608	380	transcription termination factor Rho; Provisional	97.35
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	97.35
PRK13695	174	putative NTPase; Provisional	97.34
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	97.34
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.33
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	97.33
COG1485	367	Predicted ATPase [General function prediction only	97.33
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.32
PRK14974	336	cell division protein FtsY; Provisional	97.3
PRK08487	328	DNA polymerase III subunit delta; Validated	97.29
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	97.28
PRK06067	234	flagellar accessory protein FlaH; Validated	97.28
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	97.27
PF00519	432	PPV_E1_C: Papillomavirus helicase; InterPro: IPR00	97.27
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	97.26
COG1119	257	ModF ABC-type molybdenum transport system, ATPase	97.25
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	97.25
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.25
PRK00279	215	adk adenylate kinase; Reviewed	97.25
cd01128	249	rho_factor Transcription termination factor rho is	97.25
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.25
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	97.23
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.22
PRK08118	167	topology modulation protein; Reviewed	97.22
PTZ00202	550	tuzin; Provisional	97.22
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	97.2
cd03216	163	ABC_Carb_Monos_I This family represents the domain	97.19
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	97.19
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	97.18
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.18
smart00487	201	DEXDc DEAD-like helicases superfamily.	97.18
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.17
PLN02674	244	adenylate kinase	97.16
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	97.16
cd03246	173	ABCC_Protease_Secretion This family represents the	97.13
PRK14700	300	recombination factor protein RarA; Provisional	97.12
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.12
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	97.1
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.08
PRK03839	180	putative kinase; Provisional	97.06
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	97.06
PRK00625	173	shikimate kinase; Provisional	97.06
PF13479	213	AAA_24: AAA domain	97.06
PRK00131	175	aroK shikimate kinase; Reviewed	97.05
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	97.05
PRK11823	446	DNA repair protein RadA; Provisional	97.05
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	97.04
PRK13947	171	shikimate kinase; Provisional	97.04
PRK13808	333	adenylate kinase; Provisional	97.04
PRK09376	416	rho transcription termination factor Rho; Provisio	97.03
PLN03210	1153	Resistant to P. syringae 6; Provisional	97.03
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	97.02
PRK05907	311	hypothetical protein; Provisional	97.02
PRK14527	191	adenylate kinase; Provisional	97.01
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.99
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	96.99
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	96.99
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	96.99
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.98
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.98
PRK04328	249	hypothetical protein; Provisional	96.97
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	96.96
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.96
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	96.95
KOG1808|consensus	1856		96.95
KOG2543|consensus	438		96.95
KOG0479|consensus	818		96.94
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	96.93
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.93
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	96.93
TIGR00767	415	rho transcription termination factor Rho. Members	96.92
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	96.91
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.9

>KOG0991|consensus

Probab=100.00  E-value=1.5e-34  Score=254.59  Aligned_cols=238  Identities=35%  Similarity=0.558  Sum_probs=215.5

Q ss_pred             hhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhccc
Q psy4285         287 LNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT  366 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  366 (533)
                      ..|+++.++.+.-+...+..||++|.|||||||||.+.++|++++++. +...++++|+++.++.+++|+.++.|++.+.
T Consensus        29 IVGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~-~ke~vLELNASdeRGIDvVRn~IK~FAQ~kv  107 (333)
T KOG0991|consen   29 IVGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDS-YKEAVLELNASDERGIDVVRNKIKMFAQKKV  107 (333)
T ss_pred             hhCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChh-hhhHhhhccCccccccHHHHHHHHHHHHhhc
Confidence            368899999999999999999999999999999999999999998875 4678999999999999999999999998776


Q ss_pred             CC-CCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC---
Q psy4285         367 MH-KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD---  442 (533)
Q Consensus       367 ~~-~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~---  442 (533)
                      .. +++.+++|+||+|+|+..+|.+|.+.||-++..++|.++||...++.+++.|||..++|..+++.++..+|..+   
T Consensus       108 ~lp~grhKIiILDEADSMT~gAQQAlRRtMEiyS~ttRFalaCN~s~KIiEPIQSRCAiLRysklsd~qiL~Rl~~v~k~  187 (333)
T KOG0991|consen  108 TLPPGRHKIIILDEADSMTAGAQQALRRTMEIYSNTTRFALACNQSEKIIEPIQSRCAILRYSKLSDQQILKRLLEVAKA  187 (333)
T ss_pred             cCCCCceeEEEeeccchhhhHHHHHHHHHHHHHcccchhhhhhcchhhhhhhHHhhhHhhhhcccCHHHHHHHHHHHHHH
Confidence            55 36789999999999999999999999999999999999999999999999999999999999999999999887   


Q ss_pred             ---------------------------------------------------HHHHHHHHHH---------HHHHHHHHHh
Q psy4285         443 ---------------------------------------------------DISFFNIIIW---------YIKIQEIKIE  462 (533)
Q Consensus       443 ---------------------------------------------------~~~~~~ll~~---------~~~l~~l~~~  462 (533)
                                                                         |.-+.+++..         ++.+..+ ..
T Consensus       188 Ekv~yt~dgLeaiifta~GDMRQalNnLQst~~g~g~Vn~enVfKv~d~PhP~~v~~ml~~~~~~~~~~A~~il~~l-w~  266 (333)
T KOG0991|consen  188 EKVNYTDDGLEAIIFTAQGDMRQALNNLQSTVNGFGLVNQENVFKVCDEPHPLLVKKMLQACLKRNIDEALKILAEL-WK  266 (333)
T ss_pred             hCCCCCcchHHHhhhhccchHHHHHHHHHHHhccccccchhhhhhccCCCChHHHHHHHHHHHhccHHHHHHHHHHH-HH
Confidence                                                               3444444433         5666665 56


Q ss_pred             cCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhHh
Q psy4285         463 KGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKL  526 (533)
Q Consensus       463 ~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~~~~  526 (533)
                      .|||+.||+..++++++..+.++..+.++++.++..++|+..|+.+.+++..+++++..+-++=
T Consensus       267 lgysp~Dii~~~FRv~K~~~~~E~~rlE~ikeig~thmrI~eGv~s~LQl~glla~l~~~~~k~  330 (333)
T KOG0991|consen  267 LGYSPEDIITTLFRVVKNMDVAESLRLEFIKEIGLTHMRILEGVNSLLQLSGLLAKLCKVGEKA  330 (333)
T ss_pred             cCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhHHhHHHhhHhHHHHHHHHHHHHHHhcccc
Confidence            7999999999999999999999999999999999999999999999999999999998776543

>PLN03025 replication factor C subunit; Provisional

Probab=99.97  E-value=1.3e-29  Score=250.88  Aligned_cols=239  Identities=37%  Similarity=0.566  Sum_probs=203.8

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM  367 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (533)
                      .|++++...|+.++..+..||++|+|||||||||+|+++|+++++.. +...++++++++.++.+.+++.++.+......
T Consensus        16 ~g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~~~-~~~~~~eln~sd~~~~~~vr~~i~~~~~~~~~   94 (319)
T PLN03025         16 VGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGPN-YKEAVLELNASDDRGIDVVRNKIKMFAQKKVT   94 (319)
T ss_pred             cCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhccc-CccceeeecccccccHHHHHHHHHHHHhcccc
Confidence            46778888888888888889999999999999999999999997764 34568889999888888899888877654322


Q ss_pred             C-CCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC----
Q psy4285         368 H-KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD----  442 (533)
Q Consensus       368 ~-~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~----  442 (533)
                      . .+.++++||||+|.|+..++++|++.+|.++.+++||++||....+.++|+|||..+.|.+++++++..++..+    
T Consensus        95 ~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~f~~l~~~~l~~~L~~i~~~e  174 (319)
T PLN03025         95 LPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAE  174 (319)
T ss_pred             CCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhcccCCCCCHHHHHHHHHHHHHHc
Confidence            1 24589999999999999999999999999888999999999999999999999999999999999999999876    


Q ss_pred             --------------------------------------------------HHHHHHHHHH---------HHHHHHHHHhc
Q psy4285         443 --------------------------------------------------DISFFNIIIW---------YIKIQEIKIEK  463 (533)
Q Consensus       443 --------------------------------------------------~~~~~~ll~~---------~~~l~~l~~~~  463 (533)
                                                                        +..+..+++.         +..+.++ ...
T Consensus       175 gi~i~~~~l~~i~~~~~gDlR~aln~Lq~~~~~~~~i~~~~v~~~~~~~~~~~i~~~i~~~~~~~~~~a~~~l~~l-l~~  253 (319)
T PLN03025        175 KVPYVPEGLEAIIFTADGDMRQALNNLQATHSGFGFVNQENVFKVCDQPHPLHVKNIVRNCLKGKFDDACDGLKQL-YDL  253 (319)
T ss_pred             CCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCCHHHHHHHHHHHHcCCHHHHHHHHHHH-HHc
Confidence                                                              1122222222         3445555 456


Q ss_pred             CCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhHhcC
Q psy4285         464 GLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEA  528 (533)
Q Consensus       464 ~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~~~~~~  528 (533)
                      |+++.+|+..+++.+...++++..+.+++.+++++++|+..|+++.+||++|+++++.+.+.-.|
T Consensus       254 g~~~~~Il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~a~~~~~~~~~~~~~~  318 (319)
T PLN03025        254 GYSPTDIITTLFRVVKNYDMPEFLKLEYLREIGFAHMRICDGVGSLLQLSGLLAKLCLVRETAKA  318 (319)
T ss_pred             CCCHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHhcc
Confidence            99999999999999988888999999999999999999999999999999999999999876544

>KOG0989|consensus

Probab=99.97  E-value=4.9e-30  Score=236.09  Aligned_cols=236  Identities=37%  Similarity=0.629  Sum_probs=201.8

Q ss_pred             hhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhccc
Q psy4285         287 LNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT  366 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  366 (533)
                      ..+|+.++..|...+.++..||+|||||||||||++|+++|++++|+..+...+.++|+++.+|...+++.++.|++...
T Consensus        38 ~~gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Kik~fakl~~  117 (346)
T KOG0989|consen   38 LAGQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVREKIKNFAKLTV  117 (346)
T ss_pred             hcchHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchhhhhcCHHHHhh
Confidence            35788889999888888888999999999999999999999999997766777889999999999999999988876433


Q ss_pred             CC-------CCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         367 MH-------KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       367 ~~-------~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ..       ...++|+|+||+|.|+.++|++|++.||.++.+++||++||+.+++++++.|||.+++|.++.++.+.++|
T Consensus       118 ~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~KfrFk~L~d~~iv~rL  197 (346)
T KOG0989|consen  118 LLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKKLKDEDIVDRL  197 (346)
T ss_pred             ccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHhcCCCcchHHHHHHH
Confidence            22       23469999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcC-------------------------------------------------------HHHHHHHHHH---------HHH
Q psy4285         440 DYD-------------------------------------------------------DISFFNIIIW---------YIK  455 (533)
Q Consensus       440 ~~~-------------------------------------------------------~~~~~~ll~~---------~~~  455 (533)
                      +.|                                                       .+.+.++++.         ...
T Consensus       198 ~~Ia~~E~v~~d~~al~~I~~~S~GdLR~Ait~Lqsls~~gk~It~~~~~e~~~GvVp~~~l~~lle~a~S~d~~~~v~~  277 (346)
T KOG0989|consen  198 EKIASKEGVDIDDDALKLIAKISDGDLRRAITTLQSLSLLGKRITTSLVNEELAGVVPDEKLLDLLELALSADTPNTVKR  277 (346)
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHhhccCcccchHHHHHHHhccCCHHHHHHHHHHHHccChHHHHHH
Confidence            998                                                       1112223322         223


Q ss_pred             HHHHHHhcCCCHHHHHHHHHHHHHhc-CCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHH
Q psy4285         456 IQEIKIEKGLALTDILTEISLLVHRL-EIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSAR  523 (533)
Q Consensus       456 l~~l~~~~~~~~~di~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~  523 (533)
                      +.++ ...|+++..+++++..++... ...+..+..+-..+...+.++..|.+..++|-.|..+.+.++
T Consensus       278 ~Rei-~~sg~~~~~lmsQLa~vi~~~~g~~d~~k~~~~~kl~~~~~~~~dg~~l~~~L~~L~~~~~ql~  345 (346)
T KOG0989|consen  278 VREI-MRSGYSPLQLMSQLAEVIMDIIGLSDEQKAQISLKLFTRDKRLEDGEDLELALKDLLEAEKQLR  345 (346)
T ss_pred             HHHH-HHhccCHHHHHHHHHHHHHhccccchHHHHHHHHHHHhccchhhcchhHHHHHHHHHHHHHHHh
Confidence            3333 456999999999999999887 677888888888888999999999999999999998887764

>KOG2035|consensus

Probab=99.96  E-value=3.6e-28  Score=219.95  Aligned_cols=240  Identities=26%  Similarity=0.431  Sum_probs=201.3

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc-----------------------cCcceEEec
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ-----------------------FNAMVLELN  344 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~-----------------------~~~~~~~~~  344 (533)
                      .++++....+......+..||+++|||+|+||.|.+.++.+++++.+.                       .....++++
T Consensus        16 ~~~~e~~~~Lksl~~~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEistvsS~yHlEit   95 (351)
T KOG2035|consen   16 IYHEELANLLKSLSSTGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEISTVSSNYHLEIT   95 (351)
T ss_pred             ccHHHHHHHHHHhcccCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEEecccceEEeC
Confidence            445666667777777788899999999999999999999999998653                       112356777


Q ss_pred             CCCCCchh--HHHHHHHHHHhcccCC---CCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhh
Q psy4285         345 ASDDRGIG--IVRDQIFQFASTKTMH---KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQ  419 (533)
Q Consensus       345 ~~~~~~~~--~~~~~~~~~~~~~~~~---~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~  419 (533)
                      +++....+  .+.++++..+++.+..   ....+|++|-|+|.++.++|.+|.++||+|..++++|++||..+++.++++
T Consensus        96 PSDaG~~DRvViQellKevAQt~qie~~~qr~fKvvvi~ead~LT~dAQ~aLRRTMEkYs~~~RlIl~cns~SriIepIr  175 (351)
T KOG2035|consen   96 PSDAGNYDRVVIQELLKEVAQTQQIETQGQRPFKVVVINEADELTRDAQHALRRTMEKYSSNCRLILVCNSTSRIIEPIR  175 (351)
T ss_pred             hhhcCcccHHHHHHHHHHHHhhcchhhccccceEEEEEechHhhhHHHHHHHHHHHHHHhcCceEEEEecCcccchhHHh
Confidence            88765544  6788888888776543   346899999999999999999999999999999999999999999999999


Q ss_pred             ccceeeeecCCCHHHHHHHhhcC-------------------------------------------------HHHHHH--
Q psy4285         420 SRCTRFRFGPLDSSLIMSRLDYD-------------------------------------------------DISFFN--  448 (533)
Q Consensus       420 sR~~~i~~~~~~~~~~~~~l~~~-------------------------------------------------~~~~~~--  448 (533)
                      |||..++.+.|+++++..++..+                                                 +.|+.-  
T Consensus       176 SRCl~iRvpaps~eeI~~vl~~v~~kE~l~lp~~~l~rIa~kS~~nLRrAllmlE~~~~~n~~~~a~~~~i~~~dWe~~i  255 (351)
T KOG2035|consen  176 SRCLFIRVPAPSDEEITSVLSKVLKKEGLQLPKELLKRIAEKSNRNLRRALLMLEAVRVNNEPFTANSQVIPKPDWEIYI  255 (351)
T ss_pred             hheeEEeCCCCCHHHHHHHHHHHHHHhcccCcHHHHHHHHHHhcccHHHHHHHHHHHHhccccccccCCCCCCccHHHHH
Confidence            99999999999999999999887                                                 111111  


Q ss_pred             ---------------HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCChHHHHH
Q psy4285         449 ---------------IIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLS  513 (533)
Q Consensus       449 ---------------ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~  513 (533)
                                     +++.++.++++ ..++++|.-|+.++...+.. ..+...+.+++++++++++|+..|.+..+||+
T Consensus       256 ~e~a~~i~~eQs~~~L~~vR~~LYeL-L~~CIPP~~Ilk~Ll~~Ll~-~~d~~~k~~~~~~Aa~yEhRl~lG~KaIfHLE  333 (351)
T KOG2035|consen  256 QEIARVILKEQSPAKLLEVRGRLYEL-LSHCIPPNTILKELLEELLL-KCDTQLKLEVIQHAAKYEHRLRLGQKAIFHLE  333 (351)
T ss_pred             HHHHHHHHhccCHHHHHHHHHHHHHH-HhccCChHHHHHHHHHHHHh-cCCchhHHHHHHHHHHHHHHHhhcchhhhhHH
Confidence                           12227777777 67899999999999988766 55788999999999999999999999999999


Q ss_pred             HHHHHHHHHHhHhcCC
Q psy4285         514 ALIAAFNSARDKLEAP  529 (533)
Q Consensus       514 ~~~~~~~~~~~~~~~~  529 (533)
                      +|+|++|.+-..+.-.
T Consensus       334 aFVA~fM~iy~~~~~~  349 (351)
T KOG2035|consen  334 AFVAKFMCIYKKFLSS  349 (351)
T ss_pred             HHHHHHHHHHHHHhcc
Confidence            9999999998877544

>KOG0991|consensus

Probab=99.94  E-value=1e-26  Score=205.33  Aligned_cols=201  Identities=35%  Similarity=0.471  Sum_probs=168.2

Q ss_pred             hhccccchhHHHHHhchHHHHhhcCCChhhHHHHHhhccCccccccCCCChhhHHHHHHHHHhcccccceeeeecCCccc
Q psy4285         101 SRVEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDR  180 (533)
Q Consensus       101 ~~~ek~~~~~l~~lls~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~  180 (533)
                      +|++||+|..+.++++|++.+..+....    . -....+....||||+|||+.+.+++..+.+...+..|+|+||||+|
T Consensus        16 ~wVeKYrP~~l~dIVGNe~tv~rl~via----~-~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeR   90 (333)
T KOG0991|consen   16 PWVEKYRPSVLQDIVGNEDTVERLSVIA----K-EGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDER   90 (333)
T ss_pred             hHHHhhCchHHHHhhCCHHHHHHHHHHH----H-cCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCcccc
Confidence            5999999999999999999887653210    0 1234567788999999999999999999988889999999999999


Q ss_pred             chhhhHHHHhhhhhcccc-cCCCceEEEEcCccccCHHHHHHHHc-----------------------------------
Q psy4285         181 GIGIVRDQIFQFASTKTM-HKSSYKLIILDEADAMTNDAQNALRR-----------------------------------  224 (533)
Q Consensus       181 g~~~~~d~i~~~a~~~~l-~~~~~~~iilDE~d~l~~~a~~~LRr-----------------------------------  224 (533)
                      |++++|.+|+.||+++.. ++++.|++||||+|+|+..||++|||                                   
T Consensus        91 GIDvVRn~IK~FAQ~kv~lp~grhKIiILDEADSMT~gAQQAlRRtMEiyS~ttRFalaCN~s~KIiEPIQSRCAiLRys  170 (333)
T KOG0991|consen   91 GIDVVRNKIKMFAQKKVTLPPGRHKIIILDEADSMTAGAQQALRRTMEIYSNTTRFALACNQSEKIIEPIQSRCAILRYS  170 (333)
T ss_pred             ccHHHHHHHHHHHHhhccCCCCceeEEEeeccchhhhHHHHHHHHHHHHHcccchhhhhhcchhhhhhhHHhhhHhhhhc
Confidence            999999999999998854 56677899999999999999999998                                   


Q ss_pred             ------------------cCCCChhHHHHHHHhccCchHHhhcHHHHHHhhcCCCCCccccccccCCCCHHHHHHHHHHH
Q psy4285         225 ------------------KLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWL  286 (533)
Q Consensus       225 ------------------~~~~~~~~l~~l~~~s~~di~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  286 (533)
                                        .+++++++|++++..++||+|+++|.||+....+ .-++.+++|+..+.|++.-+...+...
T Consensus       171 klsd~qiL~Rl~~v~k~Ekv~yt~dgLeaiifta~GDMRQalNnLQst~~g~-g~Vn~enVfKv~d~PhP~~v~~ml~~~  249 (333)
T KOG0991|consen  171 KLSDQQILKRLLEVAKAEKVNYTDDGLEAIIFTAQGDMRQALNNLQSTVNGF-GLVNQENVFKVCDEPHPLLVKKMLQAC  249 (333)
T ss_pred             ccCHHHHHHHHHHHHHHhCCCCCcchHHHhhhhccchHHHHHHHHHHHhccc-cccchhhhhhccCCCChHHHHHHHHHH
Confidence                              2589999999999999999999999999987764 456778899999999999999888766


Q ss_pred             hhh-chhhhhhhcccccccCCC
Q psy4285         287 LNE-SMDLCYKINRFIDENELP  307 (533)
Q Consensus       287 ~~~-~~~~~~~l~~~~~~~~~~  307 (533)
                      ... -++..+.+..+.+.+..|
T Consensus       250 ~~~~~~~A~~il~~lw~lgysp  271 (333)
T KOG0991|consen  250 LKRNIDEALKILAELWKLGYSP  271 (333)
T ss_pred             HhccHHHHHHHHHHHHHcCCCH
Confidence            543 245555566665555443

>KOG0990|consensus

Probab=99.94  E-value=9.1e-26  Score=209.07  Aligned_cols=239  Identities=46%  Similarity=0.628  Sum_probs=210.5

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhccc-
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT-  366 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  366 (533)
                      .++++.+..+.++...++.||+|+|||||||||+...+.|+.++++.++...+.++++++.++.+.+++.++.|+.+.. 
T Consensus        44 ~~~~ei~st~~~~~~~~~lPh~L~YgPPGtGktsti~a~a~~ly~~~~~~~m~lelnaSd~rgid~vr~qi~~fast~~~  123 (360)
T KOG0990|consen   44 IKQEPIWSTENRYSGMPGLPHLLFYGPPGTGKTSTILANARDFYSPHPTTSMLLELNASDDRGIDPVRQQIHLFASTQQP  123 (360)
T ss_pred             hcCCchhhHHHHhccCCCCCcccccCCCCCCCCCchhhhhhhhcCCCCchhHHHHhhccCccCCcchHHHHHHHHhhccc
Confidence            4678888888899999999999999999999999999999999997767778999999999999999999888877653 


Q ss_pred             -CCCC--CcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC-
Q psy4285         367 -MHKS--SYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD-  442 (533)
Q Consensus       367 -~~~~--~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~-  442 (533)
                       .+..  .++++|+||+|.|+.++||+|.+.++++..+++|++++|++..+.|+++|||..++|.|++..+...++.++ 
T Consensus       124 ~~fst~~~fKlvILDEADaMT~~AQnALRRviek~t~n~rF~ii~n~~~ki~pa~qsRctrfrf~pl~~~~~~~r~shi~  203 (360)
T KOG0990|consen  124 TTYSTHAAFKLVILDEADAMTRDAQNALRRVIEKYTANTRFATISNPPQKIHPAQQSRCTRFRFAPLTMAQQTERQSHIR  203 (360)
T ss_pred             eeccccCceeEEEecchhHhhHHHHHHHHHHHHHhccceEEEEeccChhhcCchhhcccccCCCCCCChhhhhhHHHHHH
Confidence             2333  789999999999999999999999999999999999999999999999999999999999999988888887 


Q ss_pred             ----------------------------------------------------------HHHHHHHHHH---------HHH
Q psy4285         443 ----------------------------------------------------------DISFFNIIIW---------YIK  455 (533)
Q Consensus       443 ----------------------------------------------------------~~~~~~ll~~---------~~~  455 (533)
                                                                                |.++++++++         +..
T Consensus       204 e~e~~~~~~~~~~a~~r~s~gDmr~a~n~Lqs~~~~~~~~~e~~~~~~~vy~c~g~p~~~dI~~I~~~il~~~~~~~~~~  283 (360)
T KOG0990|consen  204 ESEQKETNPEGYSALGRLSVGDMRVALNYLQSILKKVMERKELNNPNDLVYQCKGAPQPSDIRQIIEKRMNGEDIELMLD  283 (360)
T ss_pred             hcchhhcCHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCCCCCCCCchhhHHHhcCCCChhHHHHHHHHHhcCchHHHHhh
Confidence                                                                      5577777776         334


Q ss_pred             HHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhHh
Q psy4285         456 IQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKL  526 (533)
Q Consensus       456 l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~~~~  526 (533)
                      +..+....|+.-.|++.++...+.....+..++..++..++.+++++..|-++..++.++++.|..-+..+
T Consensus       284 is~lk~~~gla~~d~i~~l~~~~~~~~~~~~~~~~I~~~l~~Ie~~ls~g~~~~~ql~aii~~~~~~~~~~  354 (360)
T KOG0990|consen  284 DSELKKPKGLARQDRRAELEQRFAIVISKTPVEGHILYQLADIEERLSKGCMQKEQLKAIIKNFAAELKAL  354 (360)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHHHHHhcchHHHHHHHHhHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHH
Confidence            44444556788888999999888888888899999999999999999999999999999999998776544

>PRK04132 replication factor C small subunit; Provisional

Probab=99.93  E-value=3.5e-24  Score=229.63  Aligned_cols=213  Identities=43%  Similarity=0.656  Sum_probs=184.5

Q ss_pred             eeEeC--CCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHH
Q psy4285         309 LLFYG--PPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTND  386 (533)
Q Consensus       309 ~ll~G--ppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~  386 (533)
                      -+..|  |++.||||+|+++|+.+++.. ++..++++|+++.++.+.+++.++.+.+..+....+++|+||||+|+|+.+
T Consensus       567 ~~~~G~lPh~lGKTT~A~ala~~l~g~~-~~~~~lElNASd~rgid~IR~iIk~~a~~~~~~~~~~KVvIIDEaD~Lt~~  645 (846)
T PRK04132        567 NFIGGNLPTVLHNTTAALALARELFGEN-WRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQD  645 (846)
T ss_pred             hhhcCCCCCcccHHHHHHHHHHhhhccc-ccCeEEEEeCCCcccHHHHHHHHHHHHhcCCcCCCCCEEEEEECcccCCHH
Confidence            46778  999999999999999997753 567899999999999999999999887665543235789999999999999


Q ss_pred             HHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC------------------------
Q psy4285         387 AQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD------------------------  442 (533)
Q Consensus       387 ~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~------------------------  442 (533)
                      +|++|+++||+|+.+++||++||.+..+.++|+|||..+.|.+++.+++..+|.++                        
T Consensus       646 AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi~i~~e~L~~Ia~~s~GDl  725 (846)
T PRK04132        646 AQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDM  725 (846)
T ss_pred             HHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCH
Confidence            99999999999999999999999999999999999999999999999999888754                        


Q ss_pred             ------------------------------HHHHHHHHHH---------HHHHHHHHHhcCCCHHHHHHHHHHHHHhcCC
Q psy4285         443 ------------------------------DISFFNIIIW---------YIKIQEIKIEKGLALTDILTEISLLVHRLEI  483 (533)
Q Consensus       443 ------------------------------~~~~~~ll~~---------~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~  483 (533)
                                                    +.++.+++..         +..+.++....|+++.+++..++..+...++
T Consensus       726 R~AIn~Lq~~~~~~~~It~~~V~~~~~~~~~~~I~~il~~~l~~~~~~ar~~l~ell~~~G~~~~~iL~~l~~~l~~~~i  805 (846)
T PRK04132        726 RRAINILQAAAALDDKITDENVFLVASRARPEDIREMMLLALKGNFLKAREKLREILLKQGLSGEDVLVQMHREVFNLPI  805 (846)
T ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHhCCCCHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCC
Confidence                                          2233333332         3345555456899999999999999988788


Q ss_pred             ChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHH
Q psy4285         484 PESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSA  522 (533)
Q Consensus       484 ~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~  522 (533)
                      ++..+..++..+++++.++..|+++.+||++|+++++.+
T Consensus       806 ~~~~k~~ll~~lae~e~rl~~G~n~~iqL~a~la~~~~~  844 (846)
T PRK04132        806 DEPKKVELADKIGEYNFRLVEGANEMIQLEALLAQFTLM  844 (846)
T ss_pred             CHHHHHHHHHHHHHHhHHHHCCCCHHHHHHHHHHHHHhh
Confidence            899999999999999999999999999999999999754

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=99.92  E-value=7.1e-23  Score=210.47  Aligned_cols=234  Identities=24%  Similarity=0.323  Sum_probs=182.1

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc------------------cCcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ------------------FNAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~------------------~~~~~~~~~~~~  347 (533)
                      ..||+.+...|..++..++.+| +||+||||+|||++|+++++.+.|...                  ....++++++++
T Consensus        16 iiGqe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv~eldaas   95 (535)
T PRK08451         16 LIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDIIEMDAAS   95 (535)
T ss_pred             ccCcHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeEEEecccc
Confidence            4678889999999999999999 599999999999999999999987542                  123467777776


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.+++.+......+  ..++++|+||||+|+|+.+++++|++.||+++++++||++|+.+..+.++|+|||..+.|
T Consensus        96 ~~gId~IRelie~~~~~P--~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~ttd~~kL~~tI~SRc~~~~F  173 (535)
T PRK08451         96 NRGIDDIRELIEQTKYKP--SMARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKLPATILSRTQHFRF  173 (535)
T ss_pred             ccCHHHHHHHHHHHhhCc--ccCCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEEECChhhCchHHHhhceeEEc
Confidence            677888888876543222  135789999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHhhcC---------HH----------------------------------------------HHHHHHHH
Q psy4285         428 GPLDSSLIMSRLDYD---------DI----------------------------------------------SFFNIIIW  452 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~---------~~----------------------------------------------~~~~ll~~  452 (533)
                      .+++.+++..++.++         ++                                              .+.++++.
T Consensus       174 ~~Ls~~ei~~~L~~Il~~EGi~i~~~Al~~Ia~~s~GdlR~alnlLdqai~~~~~~It~~~V~~~lg~~~~~~I~~li~a  253 (535)
T PRK08451        174 KQIPQNSIISHLKTILEKEGVSYEPEALEILARSGNGSLRDTLTLLDQAIIYCKNAITESKVADMLGLLDPSKLEDFFQA  253 (535)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCCHHHHHHHHHH
Confidence            999999999999865         11                                              11111111


Q ss_pred             -----H-HHHHHHHHhcCCCHHHHHHHHHHHHHhc------CCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHH
Q psy4285         453 -----Y-IKIQEIKIEKGLALTDILTEISLLVHRL------EIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFN  520 (533)
Q Consensus       453 -----~-~~l~~l~~~~~~~~~di~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~  520 (533)
                           . ..+..+....|++..+++..+...++..      ........+++..+.++...+..|.++.++++.++.++.
T Consensus       254 i~~~d~~~a~~~l~~L~g~~~~~~l~~l~~~l~~~~~~~~~~~~l~~l~r~~riL~~~k~~l~~g~~~~i~l~~~~~~~~  333 (535)
T PRK08451        254 ILNQDKEKLFELLKELEDYEAEMVLDEMMLFLKEKFLSKDSEFSILLYERFFRILSSAKSLLKEGADDGFVLLLMLFKMK  333 (535)
T ss_pred             HHhcCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhcccccccHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence                 0 1111111224677777777777776632      123344566778899999999999999999999999888


Q ss_pred             HH
Q psy4285         521 SA  522 (533)
Q Consensus       521 ~~  522 (533)
                      ..
T Consensus       334 ~~  335 (535)
T PRK08451        334 EA  335 (535)
T ss_pred             Hh
Confidence            73

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.91  E-value=1.1e-22  Score=211.75  Aligned_cols=154  Identities=25%  Similarity=0.392  Sum_probs=134.2

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~  347 (533)
                      +.||+++++.|..++..++.+| +||+||+||||||+++.+++.+.|....                  ...++++++.+
T Consensus        18 VIGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~G~h~DviEIDAas   97 (830)
T PRK07003         18 LVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRFVDYVEMDAAS   97 (830)
T ss_pred             HcCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHHHHHHhcCCCceEEEecccc
Confidence            3589999999999999999888 6999999999999999999999875311                  12467888877


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      .++.+.+++++........  .++++|+||||+|+|+...+|+|+++||+++.+++||++||...+++++|+|||..+.|
T Consensus        98 ~rgVDdIReLIe~a~~~P~--~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KIp~TIrSRCq~f~F  175 (830)
T PRK07003         98 NRGVDEMAALLERAVYAPV--DARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVLSRCLQFNL  175 (830)
T ss_pred             cccHHHHHHHHHHHHhccc--cCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhccchhhhheEEEec
Confidence            7888888888776543322  35789999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+++.+++.++|.++
T Consensus       176 k~Ls~eeIv~~L~~I  190 (830)
T PRK07003        176 KQMPAGHIVSHLERI  190 (830)
T ss_pred             CCcCHHHHHHHHHHH
Confidence            999999999998876

>KOG2035|consensus

Probab=99.91  E-value=1.9e-24  Score=195.90  Aligned_cols=166  Identities=25%  Similarity=0.408  Sum_probs=133.1

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|++++|+|++||+.++|++||||||..+|++.|+++|+...|.+++++|++.++++.+..|++.|+||+|+|+-+||
T Consensus       151 MEkYs~~~RlIl~cns~SriIepIrSRCl~iRvpaps~eeI~~vl~~v~~kE~l~lp~~~l~rIa~kS~~nLRrAllmlE  230 (351)
T KOG2035|consen  151 MEKYSSNCRLILVCNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQLPKELLKRIAEKSNRNLRRALLMLE  230 (351)
T ss_pred             HHHHhcCceEEEEecCcccchhHHhhheeEEeCCCCCHHHHHHHHHHHHHHhcccCcHHHHHHHHHHhcccHHHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhccccc------------h-------hHHHHHhchH---HH-Hh----hc--CCChhhH
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRVEKYR------------P-------STLDELVSHQ---DI-IS----TI--EIPESML  131 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~ek~~------------~-------~~l~~lls~~---~~-l~----~l--~~~~~~~  131 (533)
                      .+...+. ..+.+. ..+..+.|+.|.            |       ..+|++++++   .+ ++    .+  +.+...+
T Consensus       231 ~~~~~n~-~~~a~~-~~i~~~dWe~~i~e~a~~i~~eQs~~~L~~vR~~LYeLL~~CIPP~~Ilk~Ll~~Ll~~~d~~~k  308 (351)
T KOG2035|consen  231 AVRVNNE-PFTANS-QVIPKPDWEIYIQEIARVILKEQSPAKLLEVRGRLYELLSHCIPPNTILKELLEELLLKCDTQLK  308 (351)
T ss_pred             HHHhccc-cccccC-CCCCCccHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHhcCCchhH
Confidence            9988533 333321 112223333332            2       3466666554   22 11    11  3444556


Q ss_pred             HHHHhhccCccccccCCCChhhHHHHHHHHHhccccc
Q psy4285         132 VDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDK  168 (533)
Q Consensus       132 ~~~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~~~~~  168 (533)
                      ..++...+.+++|+.-|.+.++|+++|++.||+.+.+
T Consensus       309 ~~~~~~Aa~yEhRl~lG~KaIfHLEaFVA~fM~iy~~  345 (351)
T KOG2035|consen  309 LEVIQHAAKYEHRLRLGQKAIFHLEAFVAKFMCIYKK  345 (351)
T ss_pred             HHHHHHHHHHHHHHhhcchhhhhHHHHHHHHHHHHHH
Confidence            7778888999999999999999999999999987653

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.91  E-value=8.9e-23  Score=205.40  Aligned_cols=154  Identities=26%  Similarity=0.405  Sum_probs=132.2

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc------------------cCcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ------------------FNAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~------------------~~~~~~~~~~~~  347 (533)
                      +.||+.+...|..++..++.+| +||+|||||||||+|+.+|+.+.|...                  ....++++++..
T Consensus        20 vVGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~dviEIdaas   99 (484)
T PRK14956         20 VIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTSCLEITKGISSDVLEIDAAS   99 (484)
T ss_pred             HhChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCCcHHHHHHccCCccceeechhh
Confidence            3588889999999999999888 799999999999999999999987531                  112466777766


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.+++.........  ..++++|+||||+|+|+.+++++|++.||+++.++.||++|+.+..++++|+|||..+.|
T Consensus       100 ~~gVd~IReL~e~l~~~p--~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~TI~SRCq~~~f  177 (484)
T PRK14956        100 NRGIENIRELRDNVKFAP--MGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRCQDFIF  177 (484)
T ss_pred             cccHHHHHHHHHHHHhhh--hcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHHHHhhhheeee
Confidence            677888887766544322  135789999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+++.+++.+++.++
T Consensus       178 ~~ls~~~i~~~L~~i  192 (484)
T PRK14956        178 KKVPLSVLQDYSEKL  192 (484)
T ss_pred             cCCCHHHHHHHHHHH
Confidence            999999999999887

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.91  E-value=3.8e-22  Score=198.92  Aligned_cols=234  Identities=42%  Similarity=0.713  Sum_probs=191.7

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM  367 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (533)
                      .+++++...+..+++.+..++++|+||||||||++++++++.+.+.. +...++.++.++..+...+++.+..+....+.
T Consensus        20 ~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~-~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~   98 (319)
T PRK00440         20 VGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGED-WRENFLELNASDERGIDVIRNKIKEFARTAPV   98 (319)
T ss_pred             cCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCc-cccceEEeccccccchHHHHHHHHHHHhcCCC
Confidence            36777888888888888888899999999999999999999987654 24456777777766666666666666655544


Q ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC-----
Q psy4285         368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD-----  442 (533)
Q Consensus       368 ~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~-----  442 (533)
                      .....++++|||+|.++.+.++.|++.++.++.++.+|+++|....+.+++.+||..+.|.+++++++..++.++     
T Consensus        99 ~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~l~~~ei~~~l~~~~~~~~  178 (319)
T PRK00440         99 GGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEG  178 (319)
T ss_pred             CCCCceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhheeeeCCCCHHHHHHHHHHHHHHcC
Confidence            334678999999999999999999999999888999999999999999999999999999999999999988865     


Q ss_pred             -------------------------------------------------HHHHHHHHHH---------HHHHHHHHHhcC
Q psy4285         443 -------------------------------------------------DISFFNIIIW---------YIKIQEIKIEKG  464 (533)
Q Consensus       443 -------------------------------------------------~~~~~~ll~~---------~~~l~~l~~~~~  464 (533)
                                                                       +.++.++++.         ...+..+....|
T Consensus       179 ~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~~~~it~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~a~~~l~~ll~~~g  258 (319)
T PRK00440        179 IEITDDALEAIYYVSEGDMRKAINALQAAAATGKEVTEEAVYKITGTARPEEIREMIELALNGDFTEAREKLRDLMIDYG  258 (319)
T ss_pred             CCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcC
Confidence                                                             1222222221         444455444579


Q ss_pred             CCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHH
Q psy4285         465 LALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSA  522 (533)
Q Consensus       465 ~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~  522 (533)
                      +++.+++..+...+....++.....+++..+.++++++..|.++.++++.|+++++.+
T Consensus       259 ~~~~~i~~~l~~~~~~~~~~~~~l~~~~~~~~~~d~~~k~g~~~~~~le~~i~~~~~~  316 (319)
T PRK00440        259 LSGEDIIKQIHREVWSLDIPEELKVELIDAIGEADFRITEGANERIQLEALLAKLALL  316 (319)
T ss_pred             CCHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHh
Confidence            9999999998877666678888889999999999999999999999999999999875

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.90  E-value=1.3e-22  Score=208.67  Aligned_cols=154  Identities=26%  Similarity=0.392  Sum_probs=134.7

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc-----------------------cCcceEE
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ-----------------------FNAMVLE  342 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~-----------------------~~~~~~~  342 (533)
                      +.||+++.+.|..++..++.+| +||+||+||||||+|+.+++.+.|...                       ....+++
T Consensus        18 VIGQe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG~hpDviE   97 (700)
T PRK12323         18 LVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGRFVDYIE   97 (700)
T ss_pred             HcCcHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHHcCCCCcceE
Confidence            4689999999999999999999 699999999999999999999998320                       0124677


Q ss_pred             ecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccc
Q psy4285         343 LNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRC  422 (533)
Q Consensus       343 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~  422 (533)
                      +++.+..+.+.+++++........  .++++|+||||+|+|+...+|+|+++||+++.++.||++||.+.+++++|+|||
T Consensus        98 IdAas~~gVDdIReLie~~~~~P~--~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kLlpTIrSRC  175 (700)
T PRK12323         98 MDAASNRGVDEMAQLLDKAVYAPT--AGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRC  175 (700)
T ss_pred             ecccccCCHHHHHHHHHHHHhchh--cCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhhhhHHHHHH
Confidence            888777888899998876544332  367899999999999999999999999999999999999999999999999999


Q ss_pred             eeeeecCCCHHHHHHHhhcC
Q psy4285         423 TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       423 ~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..+.|.+++.+++.++|.++
T Consensus       176 q~f~f~~ls~eei~~~L~~I  195 (700)
T PRK12323        176 LQFNLKQMPPGHIVSHLDAI  195 (700)
T ss_pred             HhcccCCCChHHHHHHHHHH
Confidence            99999999999999998865

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.90  E-value=3.3e-22  Score=212.16  Aligned_cols=233  Identities=17%  Similarity=0.242  Sum_probs=175.2

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~  347 (533)
                      +.||+.++..|+.++..++.+| +||+|||||||||+|+.+|+.+.|....                  ...++++++.+
T Consensus        18 IIGQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~DviEidAas   97 (944)
T PRK14949         18 MVGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDLIEVDAAS   97 (944)
T ss_pred             hcCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceEEEecccc
Confidence            3589999999999999999999 5999999999999999999999885311                  12245666665


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.+|+++..+....  ..++++|+||||+|+|+.+++++|+++||+++.+++||++|+.+.++.++|+|||..+.|
T Consensus        98 ~~kVDdIReLie~v~~~P--~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~~kLl~TIlSRCq~f~f  175 (944)
T PRK14949         98 RTKVDDTRELLDNVQYRP--SRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPVTVLSRCLQFNL  175 (944)
T ss_pred             ccCHHHHHHHHHHHHhhh--hcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCchhchHHHHHhheEEeC
Confidence            567788888876654332  236789999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHhhcC-----------------------HHHHHHHH--------------------------------HH
Q psy4285         428 GPLDSSLIMSRLDYD-----------------------DISFFNII--------------------------------IW  452 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~-----------------------~~~~~~ll--------------------------------~~  452 (533)
                      .+++.+++..+|.++                       +.++..++                                +.
T Consensus       176 kpLs~eEI~~~L~~il~~EgI~~edeAL~lIA~~S~Gd~R~ALnLLdQala~~~~~It~~~V~~llG~iD~~~V~~llks  255 (944)
T PRK14949        176 KSLTQDEIGTQLNHILTQEQLPFEAEALTLLAKAANGSMRDALSLTDQAIAFGGGQVMLTQVQTMLGSIDEQHVIALLKA  255 (944)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCcccHHHHHHHhCCCCHHHHHHHHHH
Confidence            999999999999884                       12111111                                11


Q ss_pred             ---------HHHHHHHHHhcCCCHHHHHHHHHHHHHhc---CC---------------------ChhHHHHHHHHHHHHH
Q psy4285         453 ---------YIKIQEIKIEKGLALTDILTEISLLVHRL---EI---------------------PESMLVDLVLKMSDIE  499 (533)
Q Consensus       453 ---------~~~l~~l~~~~~~~~~di~~~~~~~~~~~---~~---------------------~~~~~~~~~~~~~~~~  499 (533)
                               ...+..+ ...|..+.+++..+...++..   ..                     +.+....+++.+....
T Consensus       256 I~~~D~~aaL~~l~~L-l~~G~D~~~ILr~Ll~~lRDill~k~~~~~~~l~i~~e~i~~~a~~~s~~~L~~~ie~l~~a~  334 (944)
T PRK14949        256 LTDADIGVLMQTCAQV-LAFGADAQEVLRSLLELLHQITLTQFAPAAAQQSLYSEQIRAFAEQLSPEQVQLYYQILLTGR  334 (944)
T ss_pred             HHcCCHHHHHHHHHHH-HHcCCCHHHHHHHHHHHHHHHHHHHhccchhhccchHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence                     2222222 345788888877777665432   11                     1111223455666777


Q ss_pred             HHHhCCCChHHHHHHHHHHHHHH
Q psy4285         500 YRLAAGTSEKIQLSALIAAFNSA  522 (533)
Q Consensus       500 ~~l~~g~~~~~~l~~~~~~~~~~  522 (533)
                      .+|....+.++.++-++.++...
T Consensus       335 ~~L~~n~n~rl~lE~~LLrl~~~  357 (944)
T PRK14949        335 KDLPHAPDPKSGLEMALLRAVAF  357 (944)
T ss_pred             HHHhhCCChHHHHHHHHHHHHHc
Confidence            78888888888888887777643

>KOG0733|consensus

Probab=99.90  E-value=3.7e-22  Score=198.77  Aligned_cols=151  Identities=23%  Similarity=0.223  Sum_probs=109.7

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      ..+|++||||||||.+|+++|++.      +..|+.+.+++..      +...+|..+...   .   ...++|+|+||+
T Consensus       546 sGvLL~GPPGCGKTLlAKAVANEa------g~NFisVKGPELlNkYVGESErAVR~vFqRA---R---~saPCVIFFDEi  613 (802)
T KOG0733|consen  546 SGVLLCGPPGCGKTLLAKAVANEA------GANFISVKGPELLNKYVGESERAVRQVFQRA---R---ASAPCVIFFDEI  613 (802)
T ss_pred             CceEEeCCCCccHHHHHHHHhhhc------cCceEeecCHHHHHHHhhhHHHHHHHHHHHh---h---cCCCeEEEecch
Confidence            349999999999999999999998      8889999887643      333444443222   1   246899999999


Q ss_pred             CCCCH-----------HHHHHHHHHHHh--cCCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC--
Q psy4285         381 DAMTN-----------DAQNALRRIIEK--FTTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD--  442 (533)
Q Consensus       381 d~l~~-----------~~~~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~--  442 (533)
                      |.|.+           ...|.|+.-|+.  ...++.+|.+||+|+.+||++++  |++ .+++..|+.++..++|+.+  
T Consensus       614 DaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tk  693 (802)
T KOG0733|consen  614 DALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEERVAILKTITK  693 (802)
T ss_pred             hhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHHHHHHHHHhc
Confidence            99954           345667777763  34678899999999999999999  996 5555677888888888776  


Q ss_pred             --------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHH
Q psy4285         443 --------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISL  476 (533)
Q Consensus       443 --------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~  476 (533)
                              .-++.++..       .....||++.|+.--+.+
T Consensus       694 n~k~pl~~dVdl~eia~-------~~~c~gftGADLaaLvre  728 (802)
T KOG0733|consen  694 NTKPPLSSDVDLDEIAR-------NTKCEGFTGADLAALVRE  728 (802)
T ss_pred             cCCCCCCcccCHHHHhh-------cccccCCchhhHHHHHHH
Confidence                    223444444       112348999887654443

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.89  E-value=1e-21  Score=205.97  Aligned_cols=154  Identities=23%  Similarity=0.361  Sum_probs=132.3

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~  347 (533)
                      +.||+.+...|...+..++.+| +||+||+|+||||+|+.+|+.+.|....                  ...++++++.+
T Consensus        18 ivGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~~C~~i~~g~~~D~ieidaas   97 (647)
T PRK07994         18 VVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGECDNCREIEQGRFVDLIEIDAAS   97 (647)
T ss_pred             hcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCCHHHHHHHcCCCCCceeecccc
Confidence            3589999999999999999999 6999999999999999999999885321                  11356677765


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.+++++..+.....  .++++|+||||+|+|+...+|+|+++||+++.+++||++|+.+..+.++|+|||..+.|
T Consensus        98 ~~~VddiR~li~~~~~~p~--~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~TI~SRC~~~~f  175 (647)
T PRK07994         98 RTKVEDTRELLDNVQYAPA--RGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHL  175 (647)
T ss_pred             cCCHHHHHHHHHHHHhhhh--cCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccchHHHhhheEeeC
Confidence            5677888888766543322  36789999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+++.+++..+|.++
T Consensus       176 ~~Ls~~ei~~~L~~i  190 (647)
T PRK07994        176 KALDVEQIRQQLEHI  190 (647)
T ss_pred             CCCCHHHHHHHHHHH
Confidence            999999999998764

>KOG0730|consensus

Probab=99.89  E-value=1.3e-22  Score=204.94  Aligned_cols=307  Identities=20%  Similarity=0.225  Sum_probs=198.2

Q ss_pred             CccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhhhH-HH--HhhhhhcccccCCCceEEEEcCccccCH
Q psy4285         140 DIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVR-DQ--IFQFASTKTMHKSSYKLIILDEADAMTN  216 (533)
Q Consensus       140 ~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~~~-d~--i~~~a~~~~l~~~~~~~iilDE~d~l~~  216 (533)
                      ....+++||+||+..+.+++.+..     ..+..+|++.+.+.--+. +.  -+.|+......  .|.++++||+|.++.
T Consensus       220 g~Ll~gppg~Gkt~l~~aVa~e~~-----a~~~~i~~peli~k~~gEte~~LR~~f~~a~k~~--~psii~IdEld~l~p  292 (693)
T KOG0730|consen  220 GLLLYGPPGTGKTFLVRAVANEYG-----AFLFLINGPELISKFPGETESNLRKAFAEALKFQ--VPSIIFIDELDALCP  292 (693)
T ss_pred             CccccCCCCCChHHHHHHHHHHhC-----ceeEecccHHHHHhcccchHHHHHHHHHHHhccC--CCeeEeHHhHhhhCC
Confidence            355788999999999999998887     578888888776665555 33  33444444322  277999999998873


Q ss_pred             -----HH-----HH-----------------------------HHHc--------------------------cCCCC-h
Q psy4285         217 -----DA-----QN-----------------------------ALRR--------------------------KLPVT-P  230 (533)
Q Consensus       217 -----~a-----~~-----------------------------~LRr--------------------------~~~~~-~  230 (533)
                           +.     ..                             .+||                          .|+.. .
T Consensus       293 ~r~~~~~~e~Rv~sqlltL~dg~~~~~~vivl~atnrp~sld~alRRgRfd~ev~IgiP~~~~RldIl~~l~k~~~~~~~  372 (693)
T KOG0730|consen  293 KREGADDVESRVVSQLLTLLDGLKPDAKVIVLAATNRPDSLDPALRRGRFDREVEIGIPGSDGRLDILRVLTKKMNLLSD  372 (693)
T ss_pred             cccccchHHHHHHHHHHHHHhhCcCcCcEEEEEecCCccccChhhhcCCCcceeeecCCCchhHHHHHHHHHHhcCCcch
Confidence                 01     00                             4563                          13444 3


Q ss_pred             hHHHHHHHhccCchHHhhcHHHHHHhhcCCCC-----------------------CccccccccCCCC--HHHHHHHHHH
Q psy4285         231 DGKKAIIDLSDGDMRKVLNILQSAATAHADEV-----------------------NEDTVYNSVGYPT--KTEITNILRW  285 (533)
Q Consensus       231 ~~l~~l~~~s~~di~~~L~~L~~~~~~~~~~~-----------------------~~~~~~~~~~~~~--~~~~~~~l~~  285 (533)
                      ..+..++..+.|.+-..+..|...+.......                       .+..-|.+.|...  +..+...+.|
T Consensus       373 ~~l~~iA~~thGyvGaDL~~l~~ea~~~~~r~~~~~~~~A~~~i~psa~Re~~ve~p~v~W~dIGGlE~lK~elq~~V~~  452 (693)
T KOG0730|consen  373 VDLEDIAVSTHGYVGADLAALCREASLQATRRTLEIFQEALMGIRPSALREILVEMPNVSWDDIGGLEELKRELQQAVEW  452 (693)
T ss_pred             hhHHHHHHHccchhHHHHHHHHHHHHHHHhhhhHHHHHHHHhcCCchhhhheeccCCCCChhhccCHHHHHHHHHHHHhh
Confidence            56778888888888777777666554321111                       1111234444321  1122222223


Q ss_pred             HhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC------CCchhHHHHHHH
Q psy4285         286 LLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD------DRGIGIVRDQIF  359 (533)
Q Consensus       286 ~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~  359 (533)
                      .....    +.+.++- -..+..+|||||||||||++|+++|++.      +..++.+.+++      +.++..+++.+.
T Consensus       453 p~~~p----e~F~r~G-i~ppkGVLlyGPPGC~KT~lAkalAne~------~~nFlsvkgpEL~sk~vGeSEr~ir~iF~  521 (693)
T KOG0730|consen  453 PLKHP----EKFARFG-ISPPKGVLLYGPPGCGKTLLAKALANEA------GMNFLSVKGPELFSKYVGESERAIREVFR  521 (693)
T ss_pred             hhhch----HHHHHhc-CCCCceEEEECCCCcchHHHHHHHhhhh------cCCeeeccCHHHHHHhcCchHHHHHHHHH
Confidence            22211    1111111 0122349999999999999999999998      67788887765      345566766655


Q ss_pred             HHHhcccCCCCCcEEEEEeCCCCCCHHH-----------HHHHHHHHHh--cCCCcEEEEEeCCCCCCChhhhc--ccee
Q psy4285         360 QFASTKTMHKSSYKLIILDEADAMTNDA-----------QNALRRIIEK--FTTNVRFCIICNYLSKIPPAIQS--RCTR  424 (533)
Q Consensus       360 ~~~~~~~~~~~~~~vliiDE~d~l~~~~-----------~~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~s--R~~~  424 (533)
                      ...+      ..++|+|+||+|.+..+.           .+.|++-|+.  ..+++.+|.+||+++.+|++++|  |++.
T Consensus       522 kAR~------~aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~ViAATNRpd~ID~ALlRPGRlD~  595 (693)
T KOG0730|consen  522 KARQ------VAPCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVLVIAATNRPDMIDPALLRPGRLDR  595 (693)
T ss_pred             HHhh------cCCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCcEEEEeccCChhhcCHHHcCCcccce
Confidence            4433      345899999999986543           3556666653  34689999999999999999999  9964


Q ss_pred             -eeecCCCHHHHHHHhhcC-------HH-HHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Q psy4285         425 -FRFGPLDSSLIMSRLDYD-------DI-SFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVH  479 (533)
Q Consensus       425 -i~~~~~~~~~~~~~l~~~-------~~-~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~  479 (533)
                       +.+++|+.+...++++..       +. ++.++.+         .+.|||+.|+..-+.++.+
T Consensus       596 iiyVplPD~~aR~~Ilk~~~kkmp~~~~vdl~~La~---------~T~g~SGAel~~lCq~A~~  650 (693)
T KOG0730|consen  596 IIYVPLPDLEARLEILKQCAKKMPFSEDVDLEELAQ---------ATEGYSGAEIVAVCQEAAL  650 (693)
T ss_pred             eEeecCccHHHHHHHHHHHHhcCCCCccccHHHHHH---------HhccCChHHHHHHHHHHHH
Confidence             555556655566666554       22 5566666         8899999999888777653

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.89  E-value=4.2e-21  Score=198.51  Aligned_cols=219  Identities=26%  Similarity=0.312  Sum_probs=175.2

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc-----------------cCcceEEecCCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ-----------------FNAMVLELNASDD  348 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~-----------------~~~~~~~~~~~~~  348 (533)
                      +.||+.+...|..++..++.+| +||+|||||||||+|+++|+.+.|...                 ....++++++++.
T Consensus        16 vvGq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~el~~~~~   95 (504)
T PRK14963         16 VVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVLEIDAASN   95 (504)
T ss_pred             hcChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCceEEeccccc
Confidence            3688889999999999999999 499999999999999999999987431                 2234777887766


Q ss_pred             CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeec
Q psy4285         349 RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFG  428 (533)
Q Consensus       349 ~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~  428 (533)
                      .+.+.+++....... .+. .+.++|+||||+|.++...+++|++.+++++.++.+|++++.+..+.+++.|||..+.|.
T Consensus        96 ~~vd~iR~l~~~~~~-~p~-~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SRc~~~~f~  173 (504)
T PRK14963         96 NSVEDVRDLREKVLL-APL-RGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQHFRFR  173 (504)
T ss_pred             CCHHHHHHHHHHHhh-ccc-cCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcceEEEEec
Confidence            777788876544433 222 357899999999999999999999999999899999999999999999999999999999


Q ss_pred             CCCHHHHHHHhhcC------------------------------------------------------HHHHHHHHHH--
Q psy4285         429 PLDSSLIMSRLDYD------------------------------------------------------DISFFNIIIW--  452 (533)
Q Consensus       429 ~~~~~~~~~~l~~~------------------------------------------------------~~~~~~ll~~--  452 (533)
                      +++.+++.+++.++                                                      +.++.++++.  
T Consensus       174 ~ls~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~GdlR~aln~Lekl~~~~~~It~~~V~~~l~~~~~~~if~Li~al~  253 (504)
T PRK14963        174 RLTEEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDAESLLERLLALGTPVTRKQVEEALGLPPQERLRGIAAALA  253 (504)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCcHHHHHHHHHHHH
Confidence            99999999999875                                                      1122222222  


Q ss_pred             -------HHHHHHHHHhcCCCHHHHHHHHHHHHH-------------hcCCChhHHHHHHHHHHHHHHHHhCCCCh
Q psy4285         453 -------YIKIQEIKIEKGLALTDILTEISLLVH-------------RLEIPESMLVDLVLKMSDIEYRLAAGTSE  508 (533)
Q Consensus       453 -------~~~l~~l~~~~~~~~~di~~~~~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~l~~g~~~  508 (533)
                             ...+.++ ...|.++.+++..+.+.++             ..++++......++.+++.++++..|++.
T Consensus       254 ~~d~~~Al~~l~~L-l~~G~~~~~Il~~L~~~~r~ll~~k~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~  328 (504)
T PRK14963        254 QGDAAEALSGAAQL-YRDGFAARTLVEGLLEAFRAALYAELGLGGGPRLEGAEPRLLAAMTALDEQMERFARRSDA  328 (504)
T ss_pred             cCCHHHHHHHHHHH-HHcCCCHHHHHHHHHHHHHHHHHHHhccCcccccccCcHHHHHHHHHHHHHHHHHHhccch
Confidence                   3344444 4468999999999888877             34556777888999999999999999863

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.88  E-value=4.8e-21  Score=200.02  Aligned_cols=153  Identities=25%  Similarity=0.338  Sum_probs=132.3

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc--------------------cCcceEEecCC
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ--------------------FNAMVLELNAS  346 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~--------------------~~~~~~~~~~~  346 (533)
                      .||+.+.+.|..++..++.+| +||+||+||||||+|+.+|+.+.|...                    ....+++++++
T Consensus        16 vGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~~~~~~~dvieidaa   95 (584)
T PRK14952         16 VGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPNGPGSIDVVELDAA   95 (584)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccHHHHHhhcccCCCceEEEeccc
Confidence            589999999999999999999 699999999999999999999987431                    12346677777


Q ss_pred             CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeee
Q psy4285         347 DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFR  426 (533)
Q Consensus       347 ~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~  426 (533)
                      ...+.+.++++........  ..+.++|+||||+|+|+..++|+|++.||+++.++.||++|+.+.++.++|+|||..+.
T Consensus        96 s~~gvd~iRel~~~~~~~P--~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll~TI~SRc~~~~  173 (584)
T PRK14952         96 SHGGVDDTRELRDRAFYAP--AQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRSRTHHYP  173 (584)
T ss_pred             cccCHHHHHHHHHHHHhhh--hcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhHHHHHHhceEEE
Confidence            6678888888765543322  13678999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCHHHHHHHhhcC
Q psy4285         427 FGPLDSSLIMSRLDYD  442 (533)
Q Consensus       427 ~~~~~~~~~~~~l~~~  442 (533)
                      |.+++.+++.++|.++
T Consensus       174 F~~l~~~~i~~~L~~i  189 (584)
T PRK14952        174 FRLLPPRTMRALIARI  189 (584)
T ss_pred             eeCCCHHHHHHHHHHH
Confidence            9999999999999775

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

Probab=99.88  E-value=2.5e-22  Score=192.33  Aligned_cols=214  Identities=24%  Similarity=0.272  Sum_probs=160.5

Q ss_pred             hhchhhh---hhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhc
Q psy4285         288 NESMDLC---YKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAST  364 (533)
Q Consensus       288 ~~~~~~~---~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  364 (533)
                      .||++++   .-+.++++.+..++++|||||||||||+|+.||...      +..|..+++.. .+.+.+++.+....+.
T Consensus        27 vGQ~HLlg~~~~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~------~~~f~~~sAv~-~gvkdlr~i~e~a~~~   99 (436)
T COG2256          27 VGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTT------NAAFEALSAVT-SGVKDLREIIEEARKN   99 (436)
T ss_pred             cChHhhhCCCchHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhh------CCceEEecccc-ccHHHHHHHHHHHHHH
Confidence            4566555   357788899999999999999999999999999987      77888998877 5777788877766444


Q ss_pred             ccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEe--CCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         365 KTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIIC--NYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       365 ~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~--n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..  .+...||||||+++++...|..|+..+|.  ..+.+|.+|  |+...+.++|+|||.++.|.|++.+++...+.+.
T Consensus       100 ~~--~gr~tiLflDEIHRfnK~QQD~lLp~vE~--G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra  175 (436)
T COG2256         100 RL--LGRRTILFLDEIHRFNKAQQDALLPHVEN--GTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRA  175 (436)
T ss_pred             Hh--cCCceEEEEehhhhcChhhhhhhhhhhcC--CeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHHHHHHHHH
Confidence            33  24678999999999999999999999985  335666655  7777999999999999999999999999999983


Q ss_pred             ---------------------------HHHHHHHHHH---------------HHHHHHHH-------HhcCCCHHHHHHH
Q psy4285         443 ---------------------------DISFFNIIIW---------------YIKIQEIK-------IEKGLALTDILTE  473 (533)
Q Consensus       443 ---------------------------~~~~~~ll~~---------------~~~l~~l~-------~~~~~~~~di~~~  473 (533)
                                                 .+|.+..++.               .+.+.++.       ...|-.++|+++.
T Consensus       176 ~~~~~rgl~~~~~~i~~~a~~~l~~~s~GD~R~aLN~LE~~~~~~~~~~~~~~~~l~~~l~~~~~~~Dk~gD~hYdliSA  255 (436)
T COG2256         176 LLDEERGLGGQIIVLDEEALDYLVRLSNGDARRALNLLELAALSAEPDEVLILELLEEILQRRSARFDKDGDAHYDLISA  255 (436)
T ss_pred             HhhhhcCCCcccccCCHHHHHHHHHhcCchHHHHHHHHHHHHHhcCCCcccCHHHHHHHHhhhhhccCCCcchHHHHHHH
Confidence                                       2334433333               11222211       2345677899999


Q ss_pred             HHHHHHhcCCChhHHHHHHHHH-------HHHHHHHhCCCChHHHHHH
Q psy4285         474 ISLLVHRLEIPESMLVDLVLKM-------SDIEYRLAAGTSEKIQLSA  514 (533)
Q Consensus       474 ~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~l~~g~~~~~~l~~  514 (533)
                      +++.++.++.  +...+++.++       .++.+||..-+++.+++++
T Consensus       256 ~hKSvRGSD~--dAALyylARmi~~GeDp~yiARRlv~~AsEDIGlAd  301 (436)
T COG2256         256 LHKSVRGSDP--DAALYYLARMIEAGEDPLYIARRLVRIASEDIGLAD  301 (436)
T ss_pred             HHHhhccCCc--CHHHHHHHHHHhcCCCHHHHHHHHHHHHHhhccCCC
Confidence            9999998772  2333444333       2678888888888877543

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.88  E-value=7.3e-21  Score=191.14  Aligned_cols=229  Identities=31%  Similarity=0.480  Sum_probs=176.2

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------------------
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------------------  349 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------------------  349 (533)
                      .|++.+...+..++..+..||++|+||||||||++|+++++.+.+.. ....+..+++++..                  
T Consensus        18 ~g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~~~-~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~   96 (337)
T PRK12402         18 LGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDP-WENNFTEFNVADFFDQGKKYLVEDPRFAHFLG   96 (337)
T ss_pred             cCCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcCcc-cccceEEechhhhhhcchhhhhcCcchhhhhh
Confidence            36788888888888888888999999999999999999999987653 12334555554311                  


Q ss_pred             --------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhcc
Q psy4285         350 --------GIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSR  421 (533)
Q Consensus       350 --------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR  421 (533)
                              ..+.+++.++.+....+. ....++|||||++.++.+.++.|++.++.++.++++|++++.+..+.+++++|
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~~~~~~~L~sr  175 (337)
T PRK12402         97 TDKRIRSSKIDNFKHVLKEYASYRPL-SADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSR  175 (337)
T ss_pred             hhhhhccchHHHHHHHHHHHHhcCCC-CCCCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCChhhCchhhcCC
Confidence                    112233333344333322 24568999999999999999999999998888899999998888899999999


Q ss_pred             ceeeeecCCCHHHHHHHhhcC------------------------------------------HHH-------------H
Q psy4285         422 CTRFRFGPLDSSLIMSRLDYD------------------------------------------DIS-------------F  446 (533)
Q Consensus       422 ~~~i~~~~~~~~~~~~~l~~~------------------------------------------~~~-------------~  446 (533)
                      |..+.|.+++.+++..++.++                                          .++             +
T Consensus       176 ~~~v~~~~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~~~~~It~~~v~~~~~~~~~~~~i  255 (337)
T PRK12402        176 CLPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAGEITMEAAYEALGDVGTDEVI  255 (337)
T ss_pred             ceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCCCHHHH
Confidence            999999999999999998875                                          111             2


Q ss_pred             HHHHHH---------HHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHH
Q psy4285         447 FNIIIW---------YIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIA  517 (533)
Q Consensus       447 ~~ll~~---------~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~  517 (533)
                      .++++.         ...+..+....|+++.++...+...+... ++.....+++..+.++++++..|.++.++++.|++
T Consensus       256 ~~l~~ai~~~~~~~a~~~l~~l~~~~g~~~~~i~~~l~~~~~~~-~~~~~l~~~~~~l~~~d~~lk~g~~~~~~le~~i~  334 (337)
T PRK12402        256 ESLLDAAEAGDFTDARKTLDDLLIDEGLSGGEVLEELLRVARSR-YRGDNLARLHRLAADADARLTDGANDRIQLEALLA  334 (337)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH-CCHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            222221         33344443457999999999988776554 78888889999999999999999999999999998


Q ss_pred             HH
Q psy4285         518 AF  519 (533)
Q Consensus       518 ~~  519 (533)
                      ++
T Consensus       335 ~~  336 (337)
T PRK12402        335 EL  336 (337)
T ss_pred             hh
Confidence            75

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.88  E-value=2.3e-21  Score=200.98  Aligned_cols=154  Identities=23%  Similarity=0.343  Sum_probs=134.5

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~  347 (533)
                      ..||+.++..|..++..++.+| +||+|||||||||+|+.+|+.+.|....                  ...+++++++.
T Consensus        18 ivGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~eidaas   97 (509)
T PRK14958         18 VIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLFEVDAAS   97 (509)
T ss_pred             hcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEEEEcccc
Confidence            3589999999999999999999 7999999999999999999999885421                  12377888877


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.+++.+........  .++++|+||||+|+|+.+++++|+++||++++++.||++|+.+.+++++++|||..+.|
T Consensus        98 ~~~v~~iR~l~~~~~~~p~--~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIlattd~~kl~~tI~SRc~~~~f  175 (509)
T PRK14958         98 RTKVEDTRELLDNIPYAPT--KGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRCLQFHL  175 (509)
T ss_pred             cCCHHHHHHHHHHHhhccc--cCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEEECChHhchHHHHHHhhhhhc
Confidence            7888889988776544332  35789999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+++.+++.+++.++
T Consensus       176 ~~l~~~~i~~~l~~i  190 (509)
T PRK14958        176 AQLPPLQIAAHCQHL  190 (509)
T ss_pred             CCCCHHHHHHHHHHH
Confidence            999999999887776

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.88  E-value=6.4e-21  Score=200.43  Aligned_cols=154  Identities=29%  Similarity=0.449  Sum_probs=132.9

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc------------------cCcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ------------------FNAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~------------------~~~~~~~~~~~~  347 (533)
                      +.||+.+...|..++..++.+| +||+||+|||||++|+.+|+.+.|...                  ....+++++++.
T Consensus        18 viGq~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C~~C~~i~~g~~~dv~eidaas   97 (559)
T PRK05563         18 VVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNECEICKAITNGSLMDVIEIDAAS   97 (559)
T ss_pred             ccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccHHHHHHhcCCCCCeEEeeccc
Confidence            3588999999999999998889 799999999999999999999987542                  123567777777


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.+++........+.  .+.++|+||||+|+|+..++++|++++|+++.++.||++|+.+..++++++|||..+.|
T Consensus        98 ~~~vd~ir~i~~~v~~~p~--~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~tI~SRc~~~~f  175 (559)
T PRK05563         98 NNGVDEIRDIRDKVKYAPS--EAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPATILSRCQRFDF  175 (559)
T ss_pred             cCCHHHHHHHHHHHhhCcc--cCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcHHHHhHheEEec
Confidence            7788888887766443322  36789999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+++.+++..++..+
T Consensus       176 ~~~~~~ei~~~L~~i  190 (559)
T PRK05563        176 KRISVEDIVERLKYI  190 (559)
T ss_pred             CCCCHHHHHHHHHHH
Confidence            999999999999764

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.88  E-value=7.2e-21  Score=196.41  Aligned_cols=154  Identities=23%  Similarity=0.350  Sum_probs=132.8

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc------------------cCcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ------------------FNAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~------------------~~~~~~~~~~~~  347 (533)
                      +.||+.+.+.|..++..++.+| +||+|||||||||+|+++|+.+.|...                  ....++++++++
T Consensus        17 VIGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDviEIDAAs   96 (702)
T PRK14960         17 LVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLIEIDAAS   96 (702)
T ss_pred             hcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCceEEecccc
Confidence            3588999999999999999888 699999999999999999999987431                  122467788877


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.+++.+........  .++++|+||||+|+|+...+++|++.||+++.++.||++|+.+..++++++|||..+.|
T Consensus        97 ~~~VddIReli~~~~y~P~--~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~~kIp~TIlSRCq~feF  174 (702)
T PRK14960         97 RTKVEDTRELLDNVPYAPT--QGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVISRCLQFTL  174 (702)
T ss_pred             cCCHHHHHHHHHHHhhhhh--cCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECChHhhhHHHHHhhheeec
Confidence            6788888888766543322  35789999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+++.+++.+++.++
T Consensus       175 kpLs~eEI~k~L~~I  189 (702)
T PRK14960        175 RPLAVDEITKHLGAI  189 (702)
T ss_pred             cCCCHHHHHHHHHHH
Confidence            999999999999876

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.87  E-value=1.7e-20  Score=186.56  Aligned_cols=228  Identities=22%  Similarity=0.304  Sum_probs=167.1

Q ss_pred             hhchhhhhhhcccccccCCCce-eEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhccc
Q psy4285         288 NESMDLCYKINRFIDENELPHL-LFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT  366 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~-ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  366 (533)
                      .++++....+..++..+..+|+ +++||||+|||++++++++.+      +..+..+++++.. .+.+++.+..+....+
T Consensus        24 ~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~------~~~~~~i~~~~~~-~~~i~~~l~~~~~~~~   96 (316)
T PHA02544         24 ILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV------GAEVLFVNGSDCR-IDFVRNRLTRFASTVS   96 (316)
T ss_pred             cCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHh------CccceEeccCccc-HHHHHHHHHHHHHhhc
Confidence            5778888888888888888885 559999999999999999987      4466778877733 5556665555554432


Q ss_pred             CCCCCcEEEEEeCCCCC-CHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC---
Q psy4285         367 MHKSSYKLIILDEADAM-TNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD---  442 (533)
Q Consensus       367 ~~~~~~~vliiDE~d~l-~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~---  442 (533)
                      . .+.++++||||+|.+ ..+.++.|...+++++.++++|++||....++++++|||..+.|..|+.++..+++...   
T Consensus        97 ~-~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~~~l~sR~~~i~~~~p~~~~~~~il~~~~~~  175 (316)
T PHA02544         97 L-TGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQMIVR  175 (316)
T ss_pred             c-cCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhchHHHHhhceEEEeCCCCHHHHHHHHHHHHHH
Confidence            2 246789999999999 66778888888999989999999999999999999999999999888888765443221   


Q ss_pred             -------------HHHHHHHHH----------------------------------------H-----HHHHHHHHHhcC
Q psy4285         443 -------------DISFFNIII----------------------------------------W-----YIKIQEIKIEKG  464 (533)
Q Consensus       443 -------------~~~~~~ll~----------------------------------------~-----~~~l~~l~~~~~  464 (533)
                                   ++.+..+++                                        +     ...+......-+
T Consensus       176 ~~~~~~~~~~~i~~~al~~l~~~~~~d~r~~l~~l~~~~~~~~i~~~~l~~~~~~~~~~l~~~l~~~d~~~~~~~~~~~~  255 (316)
T PHA02544        176 CKGILEAEGVEVDMKVLAALVKKNFPDFRRTINELQRYASTGKIDAGILSEVTNSDIDDVVEALKAKDFKAVRALAPNYA  255 (316)
T ss_pred             HHHHHHhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHccCCCCHHHHHHhhHHHHHHHHHHHHcCCHHHHHHHHHHhc
Confidence                         111111111                                        1     111111112224


Q ss_pred             CCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHh
Q psy4285         465 LALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD  524 (533)
Q Consensus       465 ~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~~  524 (533)
                      .++.+++..+.+.+.. ..+.....++.+.++..+.++..|.++.+++++|++++|.-|+
T Consensus       256 ~~~~~~l~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~le~~l~~~~~~~~  314 (316)
T PHA02544        256 NDYASFVGKLYDELYP-QVTPPSIIRLIEIIGENNQYHGFAADQEIHLLYLLTQLMLECE  314 (316)
T ss_pred             cCHHHHHHHHHHHHHH-hCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcc
Confidence            5555666666555544 3456677788999999999999999999999999999997653

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.87  E-value=7.7e-21  Score=200.82  Aligned_cols=154  Identities=29%  Similarity=0.467  Sum_probs=132.3

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~  347 (533)
                      +.||+++...|..++..++.+| +||+||+|+|||++|+.+++.+.|....                  ...++++++..
T Consensus        18 iiGq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~~c~~i~~g~~~d~~eid~~s   97 (576)
T PRK14965         18 LTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPCVEITEGRSVDVFEIDGAS   97 (576)
T ss_pred             ccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccHHHHHHhcCCCCCeeeeeccC
Confidence            3588899999999999999888 6999999999999999999999885421                  22366777776


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.++++........  ..+.++|+||||+|+|+..++|+|+++||+++.++.||++|+.+.++.++|+|||..+.|
T Consensus        98 ~~~v~~ir~l~~~~~~~p--~~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~tI~SRc~~~~f  175 (576)
T PRK14965         98 NTGVDDIRELRENVKYLP--SRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITILSRCQRFDF  175 (576)
T ss_pred             ccCHHHHHHHHHHHHhcc--ccCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHHHHHhhhhhhc
Confidence            677888888766554332  236789999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+++.+++..++..+
T Consensus       176 ~~l~~~~i~~~L~~i  190 (576)
T PRK14965        176 RRIPLQKIVDRLRYI  190 (576)
T ss_pred             CCCCHHHHHHHHHHH
Confidence            999999999998864

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=99.87  E-value=1.1e-20  Score=185.87  Aligned_cols=152  Identities=20%  Similarity=0.263  Sum_probs=128.9

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc------------------cCcceEEecCC--
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ------------------FNAMVLELNAS--  346 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~------------------~~~~~~~~~~~--  346 (533)
                      .|+....+.+...+.+++.+| +||+||+|+||+++|.++|+.+.|...                  ....+..+.+.  
T Consensus         5 PWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~   84 (334)
T PRK07993          5 PWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTPEKG   84 (334)
T ss_pred             CCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccc
Confidence            466777888888889999999 789999999999999999999998532                  11223444332  


Q ss_pred             -CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceee
Q psy4285         347 -DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRF  425 (533)
Q Consensus       347 -~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i  425 (533)
                       ...+.+.+|+..+.+.....  .++++|+|||++|+|+.+++|+|+|+|||||.++.||++|+.++.++|+|+|||..+
T Consensus        85 ~~~I~idqiR~l~~~~~~~~~--~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRCq~~  162 (334)
T PRK07993         85 KSSLGVDAVREVTEKLYEHAR--LGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRCRLH  162 (334)
T ss_pred             cccCCHHHHHHHHHHHhhccc--cCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhccccc
Confidence             23678899998777665543  478999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCHHHHHHHhhc
Q psy4285         426 RFGPLDSSLIMSRLDY  441 (533)
Q Consensus       426 ~~~~~~~~~~~~~l~~  441 (533)
                      .|.+++.+++...|.+
T Consensus       163 ~~~~~~~~~~~~~L~~  178 (334)
T PRK07993        163 YLAPPPEQYALTWLSR  178 (334)
T ss_pred             cCCCCCHHHHHHHHHH
Confidence            9999999999998854

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

Probab=99.87  E-value=3.6e-21  Score=195.28  Aligned_cols=153  Identities=29%  Similarity=0.443  Sum_probs=136.9

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc-c-----------------CcceEEecCCCC
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ-F-----------------NAMVLELNASDD  348 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~-~-----------------~~~~~~~~~~~~  348 (533)
                      .||+.+...|...+..++..| .+|+||.||||||+||.+|+.+.|... .                 ...++++++...
T Consensus        19 vGQe~v~~~L~nal~~~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C~~Ck~I~~g~~~DviEiDaASn   98 (515)
T COG2812          19 VGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISCKEINEGSLIDVIEIDAASN   98 (515)
T ss_pred             cccHHHHHHHHHHHHhCcchhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCCcchhhhhhHhhhcCCcccchhhhhhhc
Confidence            689999999999999999999 899999999999999999999998752 1                 133566677777


Q ss_pred             CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeec
Q psy4285         349 RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFG  428 (533)
Q Consensus       349 ~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~  428 (533)
                      .+.+.+|++.......+.  .++++|+||||++|++..+.|+||+++||||.++.||++|..+.+++++++|||+.+.|.
T Consensus        99 ~gVddiR~i~e~v~y~P~--~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip~TIlSRcq~f~fk  176 (515)
T COG2812          99 TGVDDIREIIEKVNYAPS--EGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTILSRCQRFDFK  176 (515)
T ss_pred             cChHHHHHHHHHhccCCc--cccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCchhhhhcccccccc
Confidence            789999998776544433  478999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHhhcC
Q psy4285         429 PLDSSLIMSRLDYD  442 (533)
Q Consensus       429 ~~~~~~~~~~l~~~  442 (533)
                      .++.+++...|..+
T Consensus       177 ri~~~~I~~~L~~i  190 (515)
T COG2812         177 RLDLEEIAKHLAAI  190 (515)
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999999998

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.87  E-value=2.9e-20  Score=186.98  Aligned_cols=153  Identities=23%  Similarity=0.372  Sum_probs=126.9

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccccC------------------cceEEecCCCC
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFN------------------AMVLELNASDD  348 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~~------------------~~~~~~~~~~~  348 (533)
                      .||+.+.+.+..++..++.+| ++|+||||+||||+|+++|+.+.|.....                  ..+.+++++..
T Consensus        19 iGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~~c~~~~~~~~~d~~~~~~~~~   98 (363)
T PRK14961         19 IGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCIICKEIEKGLCLDLIEIDAASR   98 (363)
T ss_pred             cChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceEEeccccc
Confidence            588999999999999888888 69999999999999999999998743211                  13455555544


Q ss_pred             CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeec
Q psy4285         349 RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFG  428 (533)
Q Consensus       349 ~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~  428 (533)
                      .+.+.+++.+......+  ..+.++|+||||+|+++..++++|++.+|+++.++.||++|+....+.++++|||..+.|.
T Consensus        99 ~~v~~ir~i~~~~~~~p--~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l~~tI~SRc~~~~~~  176 (363)
T PRK14961         99 TKVEEMREILDNIYYSP--SKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFKLK  176 (363)
T ss_pred             CCHHHHHHHHHHHhcCc--ccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhhhHHHHhhceEEeCC
Confidence            56667777665543322  1356789999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHhhcC
Q psy4285         429 PLDSSLIMSRLDYD  442 (533)
Q Consensus       429 ~~~~~~~~~~l~~~  442 (533)
                      +++.+++.+++.++
T Consensus       177 ~l~~~el~~~L~~~  190 (363)
T PRK14961        177 IISEEKIFNFLKYI  190 (363)
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999998874

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.87  E-value=2.2e-20  Score=191.57  Aligned_cols=237  Identities=23%  Similarity=0.328  Sum_probs=177.4

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc-------------------cCcceEEecCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ-------------------FNAMVLELNAS  346 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~-------------------~~~~~~~~~~~  346 (533)
                      ..||+.++..+..++..++.+| +||+||||+|||++|+++|+.+.|...                   ....++.+++.
T Consensus        19 iiGq~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~~~~d~~~i~g~   98 (451)
T PRK06305         19 ILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTSLDVLEIDGA   98 (451)
T ss_pred             hcCcHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcCCCCceEEeecc
Confidence            3578888889999999888888 899999999999999999999987521                   11245666665


Q ss_pred             CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeee
Q psy4285         347 DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFR  426 (533)
Q Consensus       347 ~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~  426 (533)
                      ...+.+.++...........  .+.++|+||||+|.++...++.|++.+|+++.++.+|++||....+.++|+|||..+.
T Consensus        99 ~~~gid~ir~i~~~l~~~~~--~~~~kvvIIdead~lt~~~~n~LLk~lEep~~~~~~Il~t~~~~kl~~tI~sRc~~v~  176 (451)
T PRK06305         99 SHRGIEDIRQINETVLFTPS--KSRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPGTILSRCQKMH  176 (451)
T ss_pred             ccCCHHHHHHHHHHHHhhhh--cCCCEEEEEecHHhhCHHHHHHHHHHhhcCCCCceEEEEeCChHhcchHHHHhceEEe
Confidence            55667777766544332221  3578999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCHHHHHHHhhcC---------HHHHHHHHHH---------------------------------------------
Q psy4285         427 FGPLDSSLIMSRLDYD---------DISFFNIIIW---------------------------------------------  452 (533)
Q Consensus       427 ~~~~~~~~~~~~l~~~---------~~~~~~ll~~---------------------------------------------  452 (533)
                      |.+++++++.+++..+         ++.+..++..                                             
T Consensus       177 f~~l~~~el~~~L~~~~~~eg~~i~~~al~~L~~~s~gdlr~a~~~Lekl~~~~~~~It~~~V~~l~~~~~~~~vf~L~~  256 (451)
T PRK06305        177 LKRIPEETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDAESLYDYVVGLFPKSLDPDSVAKALGLLSQDSLYTLDE  256 (451)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCcCHHHHHHHHCCCCHHHHHHHHH
Confidence            9999999999988864         1111111111                                             


Q ss_pred             ----------HHHHHHHHHhcCCCHHHHHHHHHHHHHh--------------cCCChhHHHHHHHHHHHHHHHHhCCCCh
Q psy4285         453 ----------YIKIQEIKIEKGLALTDILTEISLLVHR--------------LEIPESMLVDLVLKMSDIEYRLAAGTSE  508 (533)
Q Consensus       453 ----------~~~l~~l~~~~~~~~~di~~~~~~~~~~--------------~~~~~~~~~~~~~~~~~~~~~l~~g~~~  508 (533)
                                ...+..+ ...|..+..++..+...++.              ..++.+...+++..+.++++++..|.+.
T Consensus       257 ai~~~d~~~al~~l~~L-~~~g~~~~~iL~~L~~~fR~ll~vk~~~~~~~~a~~~s~~~L~~ii~~l~e~d~~lk~~~~~  335 (451)
T PRK06305        257 AITTQNYAQALEPVTDA-MNSGVAPAHFLHDLTLFFRNILLKQYNKQLSSVATKYSSEQLLEIIDFLGESAKHIQLTIFE  335 (451)
T ss_pred             HHHcCCHHHHHHHHHHH-HHcCcCHHHHHHHHHHHHHHHHHHhhhhHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhCCCh
Confidence                      1111122 23455665554444322222              1456666678889999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhHh
Q psy4285         509 KIQLSALIAAFNSARDKL  526 (533)
Q Consensus       509 ~~~l~~~~~~~~~~~~~~  526 (533)
                      .+.++.|+.++..+..++
T Consensus       336 k~~lE~lll~l~~~~~~~  353 (451)
T PRK06305        336 KTFLETVIIHLIRIYQRP  353 (451)
T ss_pred             HHHHHHHHHHHHHHhcCC
Confidence            999999999998876543

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.87  E-value=2.1e-20  Score=194.98  Aligned_cols=154  Identities=25%  Similarity=0.386  Sum_probs=131.5

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~  347 (533)
                      +.||+.++..|..++..++.+| +||+||+|||||++|+.+++.+.|....                  ...+++++++.
T Consensus        18 IIGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~DvlEidaAs   97 (709)
T PRK08691         18 LVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLLEIDAAS   97 (709)
T ss_pred             HcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccceEEEeccc
Confidence            3688999999999999999888 7999999999999999999999876321                  11346677777


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.+++.+...... +. .++++|+||||+|+|+...+++|++.||+++.++.||++|+.+.++.++++|||..+.|
T Consensus        98 ~~gVd~IRelle~a~~~-P~-~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaTtd~~kL~~TIrSRC~~f~f  175 (709)
T PRK08691         98 NTGIDNIREVLENAQYA-PT-AGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVTVLSRCLQFVL  175 (709)
T ss_pred             cCCHHHHHHHHHHHHhh-hh-hCCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEEEEEeCCccccchHHHHHHhhhhc
Confidence            77888888887653322 21 25679999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+++.+++.++|.++
T Consensus       176 ~~Ls~eeI~~~L~~I  190 (709)
T PRK08691        176 RNMTAQQVADHLAHV  190 (709)
T ss_pred             CCCCHHHHHHHHHHH
Confidence            999999999999876

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=99.87  E-value=2.1e-20  Score=196.88  Aligned_cols=154  Identities=30%  Similarity=0.484  Sum_probs=130.3

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc---------------CcceEEecCCCCCc
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF---------------NAMVLELNASDDRG  350 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~---------------~~~~~~~~~~~~~~  350 (533)
                      ..||+.+...|..++..++.+| +||+||+|+|||++|+++|+.+.|....               ...++++++....+
T Consensus        20 IiGQe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~~Dvieidaasn~~   99 (725)
T PRK07133         20 IVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNSLDIIEMDAASNNG   99 (725)
T ss_pred             hcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHhhcCCCcEEEEeccccCC
Confidence            3588999999999999999899 6999999999999999999999885321               12245555554466


Q ss_pred             hhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCC
Q psy4285         351 IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPL  430 (533)
Q Consensus       351 ~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~  430 (533)
                      .+.+++++......+.  .++++|+||||+|+|+..++++|++.||+++..+.||++|+.+..++++|+|||..+.|.++
T Consensus       100 vd~IReLie~~~~~P~--~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl~TI~SRcq~ieF~~L  177 (725)
T PRK07133        100 VDEIRELIENVKNLPT--QSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPLTILSRVQRFNFRRI  177 (725)
T ss_pred             HHHHHHHHHHHHhchh--cCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhhHHHHhhceeEEccCC
Confidence            7778887766544332  36789999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHhhcC
Q psy4285         431 DSSLIMSRLDYD  442 (533)
Q Consensus       431 ~~~~~~~~l~~~  442 (533)
                      +.+++.++|..+
T Consensus       178 ~~eeI~~~L~~i  189 (725)
T PRK07133        178 SEDEIVSRLEFI  189 (725)
T ss_pred             CHHHHHHHHHHH
Confidence            999999999764

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.87  E-value=2.3e-20  Score=190.45  Aligned_cols=153  Identities=24%  Similarity=0.340  Sum_probs=135.4

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc------------------cCcceEEecCCCC
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ------------------FNAMVLELNASDD  348 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~------------------~~~~~~~~~~~~~  348 (533)
                      .||+.+.+.|..++..++.+| +||+||||+||||+|+.+|+.+.|..+                  ....++++++++.
T Consensus        16 iGQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~eidaas~   95 (491)
T PRK14964         16 VGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEIDAASN   95 (491)
T ss_pred             cCcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEEecccC
Confidence            588999999999999999887 999999999999999999999877532                  2345788898888


Q ss_pred             CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeec
Q psy4285         349 RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFG  428 (533)
Q Consensus       349 ~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~  428 (533)
                      .+.+.+++.+......+  ..+.++|+||||+|+++.+++++|++.||++++++.||++|+...++.++++|||..+.|.
T Consensus        96 ~~vddIR~Iie~~~~~P--~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlatte~~Kl~~tI~SRc~~~~f~  173 (491)
T PRK14964         96 TSVDDIKVILENSCYLP--ISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQ  173 (491)
T ss_pred             CCHHHHHHHHHHHHhcc--ccCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEeCChHHHHHHHHHhheeeecc
Confidence            88999999877654433  2367899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHhhcC
Q psy4285         429 PLDSSLIMSRLDYD  442 (533)
Q Consensus       429 ~~~~~~~~~~l~~~  442 (533)
                      +++.+++.+++.++
T Consensus       174 ~l~~~el~~~L~~i  187 (491)
T PRK14964        174 KIPTDKLVEHLVDI  187 (491)
T ss_pred             cccHHHHHHHHHHH
Confidence            99999999999986

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.86  E-value=2.5e-20  Score=201.87  Aligned_cols=154  Identities=25%  Similarity=0.331  Sum_probs=132.0

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc--------------------cCcceEEecC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ--------------------FNAMVLELNA  345 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~--------------------~~~~~~~~~~  345 (533)
                      +.||+.+.+.|..++..++.+| +||+||+|||||++|+.|++.++|...                    ....++++++
T Consensus        17 iiGqe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~~~~dv~eida   96 (824)
T PRK07764         17 VIGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGPGSLDVTEIDA   96 (824)
T ss_pred             hcCcHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCCCCCcEEEecc
Confidence            3578999999999999999999 799999999999999999999988432                    1234667777


Q ss_pred             CCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceee
Q psy4285         346 SDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRF  425 (533)
Q Consensus       346 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i  425 (533)
                      ....+.+.++++........  ..++++|+||||+|+|+...+|+|+++||+++.+++||++|+..+++.++|+|||..+
T Consensus        97 as~~~Vd~iR~l~~~~~~~p--~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kLl~TIrSRc~~v  174 (824)
T PRK07764         97 ASHGGVDDARELRERAFFAP--AESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPDKVIGTIRSRTHHY  174 (824)
T ss_pred             cccCCHHHHHHHHHHHHhch--hcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhheeEE
Confidence            66677888888655433222  2367899999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCHHHHHHHhhcC
Q psy4285         426 RFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       426 ~~~~~~~~~~~~~l~~~  442 (533)
                      .|.+++.+++.++|.++
T Consensus       175 ~F~~l~~~~l~~~L~~i  191 (824)
T PRK07764        175 PFRLVPPEVMRGYLERI  191 (824)
T ss_pred             EeeCCCHHHHHHHHHHH
Confidence            99999999999998875

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.86  E-value=2.2e-20  Score=195.63  Aligned_cols=153  Identities=24%  Similarity=0.392  Sum_probs=133.2

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc-----------------------cCcceEEe
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ-----------------------FNAMVLEL  343 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~-----------------------~~~~~~~~  343 (533)
                      .||+.++..|..++..++.+| +||+||+||||||+|+.+|+.+.|...                       ....++++
T Consensus        19 iGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C~~i~~g~h~D~~el   98 (618)
T PRK14951         19 VGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVCQACRDIDSGRFVDYTEL   98 (618)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCccHHHHHHHcCCCCceeec
Confidence            478999999999999999999 699999999999999999999988421                       11246777


Q ss_pred             cCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccce
Q psy4285         344 NASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCT  423 (533)
Q Consensus       344 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~  423 (533)
                      ++.+..+.+.+++.+........  .++++|+||||+|+|+...+|+|++.||+++.++.||++|+.+.+++++++|||.
T Consensus        99 daas~~~Vd~iReli~~~~~~p~--~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~kil~TIlSRc~  176 (618)
T PRK14951         99 DAASNRGVDEVQQLLEQAVYKPV--QGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPVTVLSRCL  176 (618)
T ss_pred             CcccccCHHHHHHHHHHHHhCcc--cCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhhhHHHHHhce
Confidence            77777788889988876543332  3678999999999999999999999999999999999999999999999999999


Q ss_pred             eeeecCCCHHHHHHHhhcC
Q psy4285         424 RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 ~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.|.+++.+++.++|.++
T Consensus       177 ~~~f~~Ls~eei~~~L~~i  195 (618)
T PRK14951        177 QFNLRPMAPETVLEHLTQV  195 (618)
T ss_pred             eeecCCCCHHHHHHHHHHH
Confidence            9999999999999999875

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

Probab=99.86  E-value=3e-21  Score=170.95  Aligned_cols=141  Identities=37%  Similarity=0.568  Sum_probs=109.9

Q ss_pred             hchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc-----------------CcceEEecCCCC--
Q psy4285         289 ESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF-----------------NAMVLELNASDD--  348 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~-----------------~~~~~~~~~~~~--  348 (533)
                      ||+.+.+.|...+..++.|| +||+||+|+||+++|+++++.++|....                 ...+..+.....  
T Consensus         1 gq~~~~~~L~~~~~~~~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~   80 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGRLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKK   80 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSS
T ss_pred             CcHHHHHHHHHHHHcCCcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccc
Confidence            67788888999999999999 7999999999999999999999986643                 234555555543  


Q ss_pred             -CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         349 -RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       349 -~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                       .+.+.+++....+.....  .++++|+||||+|.|+.+++|+|+++||+|+.+++||++|+.++.+.|+++|||..+.|
T Consensus        81 ~i~i~~ir~i~~~~~~~~~--~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~~il~TI~SRc~~i~~  158 (162)
T PF13177_consen   81 SIKIDQIREIIEFLSLSPS--EGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPSKILPTIRSRCQVIRF  158 (162)
T ss_dssp             SBSHHHHHHHHHHCTSS-T--TSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GGGS-HHHHTTSEEEEE
T ss_pred             hhhHHHHHHHHHHHHHHHh--cCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChHHChHHHHhhceEEec
Confidence             467888877666544332  36799999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q psy4285         428 GPLD  431 (533)
Q Consensus       428 ~~~~  431 (533)
                      .+++
T Consensus       159 ~~ls  162 (162)
T PF13177_consen  159 RPLS  162 (162)
T ss_dssp             ----
T ss_pred             CCCC
Confidence            8864

...

>KOG0989|consensus

Probab=99.86  E-value=2.8e-21  Score=178.45  Aligned_cols=162  Identities=30%  Similarity=0.508  Sum_probs=126.1

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||.++.+|||||+||+.++|+++|.|||+.|+|+++.++++.++|+.||.+||+++++++++.|+..|+||+|+|+++||
T Consensus       153 mE~~s~~trFiLIcnylsrii~pi~SRC~KfrFk~L~d~~iv~rL~~Ia~~E~v~~d~~al~~I~~~S~GdLR~Ait~Lq  232 (346)
T KOG0989|consen  153 MEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKKLKDEDIVDRLEKIASKEGVDIDDDALKLIAKISDGDLRRAITTLQ  232 (346)
T ss_pred             HhccccceEEEEEcCChhhCChHHHhhHHHhcCCCcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhh-h-------------------hccccchhHHHH------HhchH-HHHhh-cCCChhhHH
Q psy4285          81 SAATAHADEVNEDTIFTLLV-S-------------------RVEKYRPSTLDE------LVSHQ-DIIST-IEIPESMLV  132 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~-~-------------------~~ek~~~~~l~~------lls~~-~~l~~-l~~~~~~~~  132 (533)
                      +++. .++.|+...+.+.++ .                   ..+++...-+..      ++++. +++.. ++..+..+.
T Consensus       233 sls~-~gk~It~~~~~e~~~GvVp~~~l~~lle~a~S~d~~~~v~~~Rei~~sg~~~~~lmsQLa~vi~~~~g~~d~~k~  311 (346)
T KOG0989|consen  233 SLSL-LGKRITTSLVNEELAGVVPDEKLLDLLELALSADTPNTVKRVREIMRSGYSPLQLMSQLAEVIMDIIGLSDEQKA  311 (346)
T ss_pred             Hhhc-cCcccchHHHHHHHhccCCHHHHHHHHHHHHccChHHHHHHHHHHHHhccCHHHHHHHHHHHHHhccccchHHHH
Confidence            9998 556677554333222 1                   111111111111      11211 22222 256667777


Q ss_pred             HHHhhccCccccccCCCChhhHHHHHHHHHh
Q psy4285         133 DLVLKMSDIEYRLAAGTSEKIQLSALIAAFN  163 (533)
Q Consensus       133 ~~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~  163 (533)
                      .+..++...+.+...|++.+.++..+.....
T Consensus       312 ~~~~kl~~~~~~~~dg~~l~~~L~~L~~~~~  342 (346)
T KOG0989|consen  312 QISLKLFTRDKRLEDGEDLELALKDLLEAEK  342 (346)
T ss_pred             HHHHHHHhccchhhcchhHHHHHHHHHHHHH
Confidence            7778888899999999999999887776543

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=99.86  E-value=7.9e-20  Score=179.08  Aligned_cols=150  Identities=21%  Similarity=0.294  Sum_probs=118.5

Q ss_pred             hchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc--C-----------------cceEEecCC--
Q psy4285         289 ESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF--N-----------------AMVLELNAS--  346 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~--~-----------------~~~~~~~~~--  346 (533)
                      |+......+...  .++.+| +||+||+|+||+++|+.+|+.+.|....  +                 ..+..+.+.  
T Consensus         5 W~~~~~~~l~~~--~~rl~ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~~~~~~~~Cg~C~~C~~~~~~~HPD~~~i~p~~~   82 (342)
T PRK06964          5 WQTDDWNRLQAL--RARLPHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRPEAL   82 (342)
T ss_pred             ccHHHHHHHHHh--cCCcceEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccc
Confidence            444455555554  457777 8999999999999999999999986421  0                 112223211  


Q ss_pred             ---------------------------CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcC
Q psy4285         347 ---------------------------DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT  399 (533)
Q Consensus       347 ---------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~  399 (533)
                                                 ...+.+.+++.........  ..++.+|+|||++|+|+.+++|+|+++||||+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~k~~~~~~~I~idqiR~l~~~~~~~~--~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp  160 (342)
T PRK06964         83 AAEAPGAADEAKEADADEGGKKTKAPSKEIKIEQVRALLDFCGVGT--HRGGARVVVLYPAEALNVAAANALLKTLEEPP  160 (342)
T ss_pred             cccccccccccccchhhcccccccccccccCHHHHHHHHHHhccCC--ccCCceEEEEechhhcCHHHHHHHHHHhcCCC
Confidence                                       1245678888766544332  24688999999999999999999999999999


Q ss_pred             CCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         400 TNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       400 ~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +++.||++|+.++.++|+|+|||..+.|.+++.+++.++|...
T Consensus       161 ~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~~  203 (342)
T PRK06964        161 PGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAAQ  203 (342)
T ss_pred             cCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHHc
Confidence            9999999999999999999999999999999999999999864

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=99.86  E-value=1.1e-19  Score=178.57  Aligned_cols=139  Identities=23%  Similarity=0.320  Sum_probs=116.4

Q ss_pred             ccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCC---CCCchhHHHHHH
Q psy4285         301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNAS---DDRGIGIVRDQI  358 (533)
Q Consensus       301 ~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~---~~~~~~~~~~~~  358 (533)
                      +..++.+| +||+||+|+|||++|+.+|+.+.|....                  ...+..+.+.   ...+.+.+|+..
T Consensus        16 ~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~~~i~id~iR~l~   95 (328)
T PRK05707         16 AGRGRHPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEADKTIKVDQVRELV   95 (328)
T ss_pred             HHCCCcceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCCCCCCCHHHHHHHH
Confidence            34477788 8999999999999999999999985321                  1133444332   345788999987


Q ss_pred             HHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHH
Q psy4285         359 FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSR  438 (533)
Q Consensus       359 ~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~  438 (533)
                      ..+...+.  .++.+|+|||++|+|+.+++|+|+++||||+.++.||++|+.+..++|+|+|||..+.|.+++.+++.++
T Consensus        96 ~~~~~~~~--~~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~  173 (328)
T PRK05707         96 SFVVQTAQ--LGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQW  173 (328)
T ss_pred             HHHhhccc--cCCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHHHHH
Confidence            76655443  4688999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             hhc
Q psy4285         439 LDY  441 (533)
Q Consensus       439 l~~  441 (533)
                      |..
T Consensus       174 L~~  176 (328)
T PRK05707        174 LQQ  176 (328)
T ss_pred             HHH
Confidence            875

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=99.85  E-value=8.8e-20  Score=177.50  Aligned_cols=153  Identities=22%  Similarity=0.274  Sum_probs=128.2

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCC--
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNAS--  346 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~--  346 (533)
                      .|+......+...+.+++.+| +||+||+|+||+++|+.+|+.+.|....                  ...+..+.+.  
T Consensus         5 PW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~   84 (325)
T PRK06871          5 PWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPIDN   84 (325)
T ss_pred             cchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccccC
Confidence            455666777888888899999 7899999999999999999999985421                  1224444332  


Q ss_pred             CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeee
Q psy4285         347 DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFR  426 (533)
Q Consensus       347 ~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~  426 (533)
                      ...+.+.+|+..+.....+.  .++.+|+|||++|+|+..++|+|+++|||||+++.||++|+.++.++|+++|||..+.
T Consensus        85 ~~I~id~iR~l~~~~~~~~~--~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~  162 (325)
T PRK06871         85 KDIGVDQVREINEKVSQHAQ--QGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWL  162 (325)
T ss_pred             CCCCHHHHHHHHHHHhhccc--cCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceEEe
Confidence            33578889988776654443  4688999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCHHHHHHHhhcC
Q psy4285         427 FGPLDSSLIMSRLDYD  442 (533)
Q Consensus       427 ~~~~~~~~~~~~l~~~  442 (533)
                      |.+++.+++.++|...
T Consensus       163 ~~~~~~~~~~~~L~~~  178 (325)
T PRK06871        163 IHPPEEQQALDWLQAQ  178 (325)
T ss_pred             CCCCCHHHHHHHHHHH
Confidence            9999999999888764

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=99.85  E-value=4.6e-20  Score=180.20  Aligned_cols=153  Identities=21%  Similarity=0.290  Sum_probs=124.0

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------CcceEEecCC-------
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------NAMVLELNAS-------  346 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------~~~~~~~~~~-------  346 (533)
                      ..||+.+...+...+..++.+| +||+||+|+||+++|.++|+.++|....            ...+..+.+.       
T Consensus         6 iiGq~~~~~~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~~~~~g~~   85 (314)
T PRK07399          6 LIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQHQGKL   85 (314)
T ss_pred             hCCHHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEeccccccccc
Confidence            4688999999999999999877 8999999999999999999999886411            1112222211       


Q ss_pred             ----------------CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         347 ----------------DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       347 ----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                                      .....+.+++....+ ...+. .++++|+|||++|.|+..++|+|+++||+|+ ++.||++|+.
T Consensus        86 ~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l-~~~p~-~~~~kVvII~~ae~m~~~aaNaLLK~LEEPp-~~~fILi~~~  162 (314)
T PRK07399         86 ITASEAEEAGLKRKAPPQIRLEQIREIKRFL-SRPPL-EAPRKVVVIEDAETMNEAAANALLKTLEEPG-NGTLILIAPS  162 (314)
T ss_pred             cchhhhhhccccccccccCcHHHHHHHHHHH-ccCcc-cCCceEEEEEchhhcCHHHHHHHHHHHhCCC-CCeEEEEECC
Confidence                            012244666654443 33332 4689999999999999999999999999998 8899999999


Q ss_pred             CCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         411 LSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       411 ~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ++.+.|+|+|||..+.|.+++++++.++|.+.
T Consensus       163 ~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~  194 (314)
T PRK07399        163 PESLLPTIVSRCQIIPFYRLSDEQLEQVLKRL  194 (314)
T ss_pred             hHhCcHHHHhhceEEecCCCCHHHHHHHHHHh
Confidence            99999999999999999999999999999876

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=99.85  E-value=1.4e-19  Score=175.88  Aligned_cols=154  Identities=24%  Similarity=0.286  Sum_probs=126.7

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc---------------CcceEEe--cCCC-
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF---------------NAMVLEL--NASD-  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~---------------~~~~~~~--~~~~-  347 (533)
                      ..|+......+...+..++.|| +||+||+|+||+++|.++|+.++|....               ...+..+  .+.. 
T Consensus         6 yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~   85 (319)
T PRK08769          6 SPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRT   85 (319)
T ss_pred             cccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCcc
Confidence            3466777888888889999999 8999999999999999999999986421               1123333  2211 


Q ss_pred             ------CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhcc
Q psy4285         348 ------DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSR  421 (533)
Q Consensus       348 ------~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR  421 (533)
                            ..+.+.+++..........  .++.+|+|||++|.|+.+++|+|+++||||+.++.||++|+.++.+.|+|+||
T Consensus        86 ~~k~~~~I~idqIR~l~~~~~~~p~--~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIrSR  163 (319)
T PRK08769         86 GDKLRTEIVIEQVREISQKLALTPQ--YGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSR  163 (319)
T ss_pred             cccccccccHHHHHHHHHHHhhCcc--cCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHHhh
Confidence                  1346778877665544433  36789999999999999999999999999999999999999999999999999


Q ss_pred             ceeeeecCCCHHHHHHHhhcC
Q psy4285         422 CTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       422 ~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      |..+.|.+|+.+++..+|...
T Consensus       164 Cq~i~~~~~~~~~~~~~L~~~  184 (319)
T PRK08769        164 CQRLEFKLPPAHEALAWLLAQ  184 (319)
T ss_pred             heEeeCCCcCHHHHHHHHHHc
Confidence            999999999999999999765

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.85  E-value=9.8e-20  Score=180.27  Aligned_cols=155  Identities=26%  Similarity=0.355  Sum_probs=128.0

Q ss_pred             HhhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCC
Q psy4285         286 LLNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNAS  346 (533)
Q Consensus       286 ~~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~  346 (533)
                      +..+|+.+.+.+...+..++.+| +||+||+|+|||++|+.+++.+.|....                  ...+..+...
T Consensus         7 i~~~q~~~~~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~i~~~   86 (329)
T PRK08058          7 LTALQPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHLVAPD   86 (329)
T ss_pred             HHhhHHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEeccc
Confidence            34458899999999999999999 6999999999999999999999886411                  1122233221


Q ss_pred             -CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceee
Q psy4285         347 -DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRF  425 (533)
Q Consensus       347 -~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i  425 (533)
                       ...+.+.+++....+...+  ..++++|+||||+|.|+.+++|+|++.||+||+++.||++|+.+.++.|+|+|||..+
T Consensus        87 ~~~i~id~ir~l~~~~~~~~--~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TIrSRc~~i  164 (329)
T PRK08058         87 GQSIKKDQIRYLKEEFSKSG--VESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTILSRCQVV  164 (329)
T ss_pred             cccCCHHHHHHHHHHHhhCC--cccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHHHhhceee
Confidence             2245667888776665443  2467899999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCHHHHHHHhhcC
Q psy4285         426 RFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       426 ~~~~~~~~~~~~~l~~~  442 (533)
                      .|.+++.+++.+++...
T Consensus       165 ~~~~~~~~~~~~~L~~~  181 (329)
T PRK08058        165 EFRPLPPESLIQRLQEE  181 (329)
T ss_pred             eCCCCCHHHHHHHHHHc
Confidence            99999999999888764

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.85  E-value=1.8e-19  Score=186.49  Aligned_cols=154  Identities=22%  Similarity=0.340  Sum_probs=130.3

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~  347 (533)
                      ..||+.+...|..++..++.+| +||+||||+||||+|+.+|+.+.|....                  ...++++++..
T Consensus        18 iiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlieidaas   97 (546)
T PRK14957         18 VAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEIDAAS   97 (546)
T ss_pred             hcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEeeccc
Confidence            3588888889999999988888 7899999999999999999999874321                  12455666655


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.+++.+..+....  ..++++|+||||+|+|+..++++|++.||+++.++.||++|+....+.++++|||..+.|
T Consensus        98 ~~gvd~ir~ii~~~~~~p--~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~Ttd~~kil~tI~SRc~~~~f  175 (546)
T PRK14957         98 RTGVEETKEILDNIQYMP--SQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIPVTILSRCIQLHL  175 (546)
T ss_pred             ccCHHHHHHHHHHHHhhh--hcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEEECChhhhhhhHHHheeeEEe
Confidence            567777888776654332  236789999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+++.+++..++.++
T Consensus       176 ~~Ls~~eI~~~L~~i  190 (546)
T PRK14957        176 KHISQADIKDQLKII  190 (546)
T ss_pred             CCCCHHHHHHHHHHH
Confidence            999999999888874

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.85  E-value=1.2e-19  Score=182.00  Aligned_cols=153  Identities=20%  Similarity=0.318  Sum_probs=124.1

Q ss_pred             hhhchhhhhhhcccccccC---------CCc-eeEeCCCCCChHHHHHHHHHHHcccccc-----------------Ccc
Q psy4285         287 LNESMDLCYKINRFIDENE---------LPH-LLFYGPPGTGKTTTILACARKLYTKAQF-----------------NAM  339 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~---------~~~-~ll~GppGtGKT~la~~la~~l~~~~~~-----------------~~~  339 (533)
                      +.||+.+...|+.++..++         .+| +||+||||+|||++|+++|+.+.|....                 ...
T Consensus         7 IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~hpD   86 (394)
T PRK07940          7 LVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGTHPD   86 (394)
T ss_pred             ccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCC
Confidence            3578888888888887765         677 8999999999999999999999886310                 111


Q ss_pred             eEEecCC-CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhh
Q psy4285         340 VLELNAS-DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAI  418 (533)
Q Consensus       340 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l  418 (533)
                      +..+.+. ...+.+.+++.+......+.  .++++|+||||+|.|+...+|+|+++||+++.++.||++|+.+..++|+|
T Consensus        87 ~~~i~~~~~~i~i~~iR~l~~~~~~~p~--~~~~kViiIDead~m~~~aanaLLk~LEep~~~~~fIL~a~~~~~llpTI  164 (394)
T PRK07940         87 VRVVAPEGLSIGVDEVRELVTIAARRPS--TGRWRIVVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPSPEDVLPTI  164 (394)
T ss_pred             EEEeccccccCCHHHHHHHHHHHHhCcc--cCCcEEEEEechhhcCHHHHHHHHHHhhcCCCCCeEEEEECChHHChHHH
Confidence            2223221 23456778887766544332  36789999999999999999999999999999999999999999999999


Q ss_pred             hccceeeeecCCCHHHHHHHhhc
Q psy4285         419 QSRCTRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       419 ~sR~~~i~~~~~~~~~~~~~l~~  441 (533)
                      +|||..+.|.+|+.+++.++|.+
T Consensus       165 rSRc~~i~f~~~~~~~i~~~L~~  187 (394)
T PRK07940        165 RSRCRHVALRTPSVEAVAEVLVR  187 (394)
T ss_pred             HhhCeEEECCCCCHHHHHHHHHH
Confidence            99999999999999999999863

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.85  E-value=1.7e-19  Score=186.62  Aligned_cols=153  Identities=29%  Similarity=0.390  Sum_probs=131.1

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCCC
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASDD  348 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~~  348 (533)
                      .||+.+...+..++..++.+| +||+||||+|||++|+.+|+.+.|..+.                  ...+++++++..
T Consensus        19 IGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C~sCr~i~~~~h~DiieIdaas~   98 (605)
T PRK05896         19 IGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSVCESINTNQSVDIVELDAASN   98 (605)
T ss_pred             cCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHHcCCCCceEEeccccc
Confidence            488888999999998888888 8999999999999999999999875421                  124566776666


Q ss_pred             CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeec
Q psy4285         349 RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFG  428 (533)
Q Consensus       349 ~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~  428 (533)
                      .+.+.+++.+..+...+.  .++++|+||||+|+|+..++++|++.||+++.++.+|++|+.+..+.++++|||..+.|.
T Consensus        99 igVd~IReIi~~~~~~P~--~~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~TI~SRcq~ieF~  176 (605)
T PRK05896         99 NGVDEIRNIIDNINYLPT--TFKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTIISRCQRYNFK  176 (605)
T ss_pred             cCHHHHHHHHHHHHhchh--hCCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhHHHHhhhhhcccC
Confidence            778888887766554332  356899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHhhcC
Q psy4285         429 PLDSSLIMSRLDYD  442 (533)
Q Consensus       429 ~~~~~~~~~~l~~~  442 (533)
                      +++.+++..++..+
T Consensus       177 ~Ls~~eL~~~L~~i  190 (605)
T PRK05896        177 KLNNSELQELLKSI  190 (605)
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999999874

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.84  E-value=2.9e-19  Score=183.41  Aligned_cols=154  Identities=32%  Similarity=0.479  Sum_probs=128.9

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc------------------cCcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ------------------FNAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~------------------~~~~~~~~~~~~  347 (533)
                      ..||+++...|..++..++.+| +||+|||||||||+|+++|+.+.|...                  ....++.++++.
T Consensus        16 ivGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~el~aa~   95 (472)
T PRK14962         16 VVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVIELDAAS   95 (472)
T ss_pred             ccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccEEEeCcc
Confidence            3577888888888899888888 799999999999999999999977431                  112467788876


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.+++.... ....+. .+..+|+||||+|+++.+.++.|++.+++++.++.+|++|+.+..+.++++|||..+.|
T Consensus        96 ~~gid~iR~i~~~-~~~~p~-~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Ilattn~~kl~~~L~SR~~vv~f  173 (472)
T PRK14962         96 NRGIDEIRKIRDA-VGYRPM-EGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPPTIISRCQVIEF  173 (472)
T ss_pred             cCCHHHHHHHHHH-HhhChh-cCCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEEEEEeCChHhhhHHHhcCcEEEEE
Confidence            6778888765443 333322 35788999999999999999999999999999999999998888999999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+++.+++..++..+
T Consensus       174 ~~l~~~el~~~L~~i  188 (472)
T PRK14962        174 RNISDELIIKRLQEV  188 (472)
T ss_pred             CCccHHHHHHHHHHH
Confidence            999999999998886

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.84  E-value=3e-19  Score=187.74  Aligned_cols=154  Identities=25%  Similarity=0.410  Sum_probs=132.8

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc-----------------------CcceEE
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF-----------------------NAMVLE  342 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~-----------------------~~~~~~  342 (533)
                      +.||+.+++.|..++..++.+| +||+||+|+|||++|+.+|+.+.|....                       ...+++
T Consensus        26 liGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~c~~C~~i~~g~h~Dv~e  105 (598)
T PRK09111         26 LIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGVGEHCQAIMEGRHVDVLE  105 (598)
T ss_pred             hcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCcccHHHHHHhcCCCCceEE
Confidence            3588999999999999999888 9999999999999999999999875311                       123566


Q ss_pred             ecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccc
Q psy4285         343 LNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRC  422 (533)
Q Consensus       343 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~  422 (533)
                      +++....+.+.+++.+...... +. .+.++|+||||+|+|+...+++|++.||+++.++.||++|+...++.++++|||
T Consensus       106 ~~a~s~~gvd~IReIie~~~~~-P~-~a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kll~tI~SRc  183 (598)
T PRK09111        106 MDAASHTGVDDIREIIESVRYR-PV-SARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKVPVTVLSRC  183 (598)
T ss_pred             ecccccCCHHHHHHHHHHHHhc-hh-cCCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhhhHHHHhhe
Confidence            6666667888899887654333 32 367899999999999999999999999999999999999999999999999999


Q ss_pred             eeeeecCCCHHHHHHHhhcC
Q psy4285         423 TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       423 ~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..+.|.+++.+++..++.++
T Consensus       184 q~~~f~~l~~~el~~~L~~i  203 (598)
T PRK09111        184 QRFDLRRIEADVLAAHLSRI  203 (598)
T ss_pred             eEEEecCCCHHHHHHHHHHH
Confidence            99999999999999999886

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.84  E-value=3.2e-19  Score=186.79  Aligned_cols=154  Identities=27%  Similarity=0.388  Sum_probs=128.3

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~  347 (533)
                      ..||+.+...|..++..++.+| +||+||||+|||++|+++|+.+.|..+.                  ...++.+++..
T Consensus        18 iiGqe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C~~C~~i~~~~~~dv~~idgas   97 (563)
T PRK06647         18 LEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSSCKSIDNDNSLDVIEIDGAS   97 (563)
T ss_pred             ccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccchHHHHHHcCCCCCeEEecCcc
Confidence            3588999999999999999998 8999999999999999999999875311                  12345566554


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.+++........ + ..++++|+||||+|+|+..++++|++.+|+++.++.||++|+.+..+.++|+|||..+.|
T Consensus        98 ~~~vddIr~l~e~~~~~-p-~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~~tI~SRc~~~~f  175 (563)
T PRK06647         98 NTSVQDVRQIKEEIMFP-P-ASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIKSRCQHFNF  175 (563)
T ss_pred             cCCHHHHHHHHHHHHhc-h-hcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhHHHHHHhceEEEe
Confidence            45667777665443322 2 236789999999999999999999999999999999999999889999999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+++.+++.+++.++
T Consensus       176 ~~l~~~el~~~L~~i  190 (563)
T PRK06647        176 RLLSLEKIYNMLKKV  190 (563)
T ss_pred             cCCCHHHHHHHHHHH
Confidence            999999999888765

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.84  E-value=4.9e-19  Score=182.28  Aligned_cols=154  Identities=25%  Similarity=0.342  Sum_probs=132.0

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc----------------------cCcceEEe
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ----------------------FNAMVLEL  343 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~----------------------~~~~~~~~  343 (533)
                      ..||+.++..|...+..++.+| +||+|||||||||+|+.+|+.+.|...                      ....++++
T Consensus        23 liGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C~~i~~~~h~Dv~ei  102 (507)
T PRK06645         23 LQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNCISFNNHNHPDIIEI  102 (507)
T ss_pred             hcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHHHHHhcCCCCcEEEe
Confidence            3688888999988888888776 899999999999999999999987531                      11346777


Q ss_pred             cCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccce
Q psy4285         344 NASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCT  423 (533)
Q Consensus       344 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~  423 (533)
                      ++.+..+.+.+++.+...... + ..+.++|+||||+|+++...+++|++.+|+++.++.||++|+...+++++++|||.
T Consensus       103 daas~~~vd~Ir~iie~a~~~-P-~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI~~tI~SRc~  180 (507)
T PRK06645        103 DAASKTSVDDIRRIIESAEYK-P-LQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIISRCQ  180 (507)
T ss_pred             eccCCCCHHHHHHHHHHHHhc-c-ccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHhhHHHHhcce
Confidence            777667888898887665433 3 23678999999999999999999999999999999999999999999999999999


Q ss_pred             eeeecCCCHHHHHHHhhcC
Q psy4285         424 RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 ~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.|.+++.+++.+++.++
T Consensus       181 ~~ef~~ls~~el~~~L~~i  199 (507)
T PRK06645        181 RYDLRRLSFEEIFKLLEYI  199 (507)
T ss_pred             EEEccCCCHHHHHHHHHHH
Confidence            9999999999999999876

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.84  E-value=3.1e-19  Score=186.46  Aligned_cols=153  Identities=24%  Similarity=0.391  Sum_probs=130.2

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCCC
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASDD  348 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~~  348 (533)
                      .||+.++..|..++..++.+| +||+||||+||||+|+.+|+.+.|....                  ...+++++++..
T Consensus        19 vGq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~ei~~~~~   98 (527)
T PRK14969         19 VGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLIEVDAASN   98 (527)
T ss_pred             cCcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceeEeecccc
Confidence            588999999999999999999 6999999999999999999999885321                  113556666655


Q ss_pred             CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeec
Q psy4285         349 RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFG  428 (533)
Q Consensus       349 ~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~  428 (533)
                      .+.+.+++.+...... + ..++++|+||||+|+|+.+++|+|++.||+++.++.||++|+.+..+.++++|||..+.|.
T Consensus        99 ~~vd~ir~l~~~~~~~-p-~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t~d~~kil~tI~SRc~~~~f~  176 (527)
T PRK14969         99 TQVDAMRELLDNAQYA-P-TRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLK  176 (527)
T ss_pred             CCHHHHHHHHHHHhhC-c-ccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEeCChhhCchhHHHHHHHHhcC
Confidence            6778888877654332 2 2367899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHhhcC
Q psy4285         429 PLDSSLIMSRLDYD  442 (533)
Q Consensus       429 ~~~~~~~~~~l~~~  442 (533)
                      +++.+++.+++.++
T Consensus       177 ~l~~~~i~~~L~~i  190 (527)
T PRK14969        177 QMPPPLIVSHLQHI  190 (527)
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999888765

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.84  E-value=5.8e-19  Score=186.96  Aligned_cols=154  Identities=28%  Similarity=0.414  Sum_probs=131.2

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc-------------------cCcceEEecCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ-------------------FNAMVLELNAS  346 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~-------------------~~~~~~~~~~~  346 (533)
                      +.||+.+...|..++..++.+| +||+||+|+|||++|+.+|+.+.|...                   ....+..+++.
T Consensus        19 viGq~~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n~~~ld~~   98 (614)
T PRK14971         19 VVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYNIHELDAA   98 (614)
T ss_pred             hcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCceEEeccc
Confidence            3588899999999999999999 799999999999999999999986421                   12345667776


Q ss_pred             CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeee
Q psy4285         347 DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFR  426 (533)
Q Consensus       347 ~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~  426 (533)
                      +..+.+.++..+...... + ..++++|+||||+|+|+.+++++|++.||+++.++.||++|+...++.++|+|||..+.
T Consensus        99 ~~~~vd~Ir~li~~~~~~-P-~~~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~tifIL~tt~~~kIl~tI~SRc~iv~  176 (614)
T PRK14971         99 SNNSVDDIRNLIEQVRIP-P-QIGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFD  176 (614)
T ss_pred             ccCCHHHHHHHHHHHhhC-c-ccCCcEEEEEECcccCCHHHHHHHHHHHhCCCCCeEEEEEeCCchhchHHHHhhhheee
Confidence            656677888877655333 2 23678999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCHHHHHHHhhcC
Q psy4285         427 FGPLDSSLIMSRLDYD  442 (533)
Q Consensus       427 ~~~~~~~~~~~~l~~~  442 (533)
                      |.+++.+++..++..+
T Consensus       177 f~~ls~~ei~~~L~~i  192 (614)
T PRK14971        177 FNRIQVADIVNHLQYV  192 (614)
T ss_pred             cCCCCHHHHHHHHHHH
Confidence            9999999999999764

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.83  E-value=6.3e-19  Score=186.61  Aligned_cols=154  Identities=25%  Similarity=0.384  Sum_probs=128.4

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc--------------------CcceEEecC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF--------------------NAMVLELNA  345 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~--------------------~~~~~~~~~  345 (533)
                      ..|++.+...|..++..++.+| +||+||||+|||++|+++|+.+.|....                    ...++++++
T Consensus        18 liGq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg~C~~C~~i~~g~h~D~~ei~~   97 (620)
T PRK14948         18 LVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCGKCELCRAIAAGNALDVIEIDA   97 (620)
T ss_pred             ccChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCcccHHHHHHhcCCCccEEEEec
Confidence            4578888888988888887655 8999999999999999999999884311                    123556666


Q ss_pred             CCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceee
Q psy4285         346 SDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRF  425 (533)
Q Consensus       346 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i  425 (533)
                      ....+.+.+++.+...... + ..+.++|+||||+|+|+.+++++|++.||+++..+.||++|+.+..+.++|+|||..+
T Consensus        98 ~~~~~vd~IReii~~a~~~-p-~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~llpTIrSRc~~~  175 (620)
T PRK14948         98 ASNTGVDNIRELIERAQFA-P-VQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTIISRCQRF  175 (620)
T ss_pred             cccCCHHHHHHHHHHHhhC-h-hcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhhhHHHHhheeEE
Confidence            6557778888887654332 2 2357899999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCHHHHHHHhhcC
Q psy4285         426 RFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       426 ~~~~~~~~~~~~~l~~~  442 (533)
                      .|.+++.+++..++.++
T Consensus       176 ~f~~l~~~ei~~~L~~i  192 (620)
T PRK14948        176 DFRRIPLEAMVQHLSEI  192 (620)
T ss_pred             EecCCCHHHHHHHHHHH
Confidence            99999999999888753

>PRK04132 replication factor C small subunit; Provisional

Probab=99.83  E-value=3.7e-20  Score=198.87  Aligned_cols=163  Identities=39%  Similarity=0.686  Sum_probs=133.3

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+||++++||++||++++|+|||+|||++|+|++++.+++.++|+++|++|++.++++++..|+..|+||+|+|+|+||
T Consensus       654 lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi~i~~e~L~~Ia~~s~GDlR~AIn~Lq  733 (846)
T PRK04132        654 MEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQ  733 (846)
T ss_pred             hhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhcc-------------ccc--hhHHHHHh-----chHHHHhh-------cCCChhhHHH
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRVE-------------KYR--PSTLDELV-----SHQDIIST-------IEIPESMLVD  133 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~e-------------k~~--~~~l~~ll-----s~~~~l~~-------l~~~~~~~~~  133 (533)
                      .++.. ...|+.+.+..+.+....             ++.  ...+++++     +..+++.+       ..+++..+..
T Consensus       734 ~~~~~-~~~It~~~V~~~~~~~~~~~I~~il~~~l~~~~~~ar~~l~ell~~~G~~~~~iL~~l~~~l~~~~i~~~~k~~  812 (846)
T PRK04132        734 AAAAL-DDKITDENVFLVASRARPEDIREMMLLALKGNFLKAREKLREILLKQGLSGEDVLVQMHREVFNLPIDEPKKVE  812 (846)
T ss_pred             HHHHh-cCCCCHHHHHHHhCCCCHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCHHHHHH
Confidence            98764 346888776543321100             000  11244443     12233332       2467778888


Q ss_pred             HHhhccCccccccCCCChhhHHHHHHHHHhc
Q psy4285         134 LVLKMSDIEYRLAAGTSEKIQLSALIAAFNS  164 (533)
Q Consensus       134 ~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~  164 (533)
                      ++..++++++++..|+++.+|+++|++.++.
T Consensus       813 ll~~lae~e~rl~~G~n~~iqL~a~la~~~~  843 (846)
T PRK04132        813 LADKIGEYNFRLVEGANEMIQLEALLAQFTL  843 (846)
T ss_pred             HHHHHHHHhHHHHCCCCHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999864

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

Probab=99.83  E-value=4e-19  Score=177.63  Aligned_cols=138  Identities=45%  Similarity=0.685  Sum_probs=114.6

Q ss_pred             ccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc------------------cCcceEEecCCCCCchhHHHHHHHHHHh
Q psy4285         303 ENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ------------------FNAMVLELNASDDRGIGIVRDQIFQFAS  363 (533)
Q Consensus       303 ~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~  363 (533)
                      .++.+| +||+||||+|||++|.++|+.++|...                  ....++++++++.+..+...+.++.+..
T Consensus        20 ~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~i~~~~vr~~~~   99 (325)
T COG0470          20 SGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKIDIIVEQVRELAE   99 (325)
T ss_pred             cCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecccccCCCcchHHHHHHHHH
Confidence            557888 999999999999999999999987652                  2357899999998775544444444443


Q ss_pred             cccCC--CCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhh
Q psy4285         364 TKTMH--KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       364 ~~~~~--~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~  440 (533)
                      .....  .++.+|+||||+|.|+.+++++|++++|+++.+++||++||.+..+.++|+|||..+.|.+++.........
T Consensus       100 ~~~~~~~~~~~kviiidead~mt~~A~nallk~lEep~~~~~~il~~n~~~~il~tI~SRc~~i~f~~~~~~~~i~~~e  178 (325)
T COG0470         100 FLSESPLEGGYKVVIIDEADKLTEDAANALLKTLEEPPKNTRFILITNDPSKILPTIRSRCQRIRFKPPSRLEAIAWLE  178 (325)
T ss_pred             HhccCCCCCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCeEEEEEcCChhhccchhhhcceeeecCCchHHHHHHHhh
Confidence            32222  367899999999999999999999999999999999999999999999999999999999977666666655

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=99.83  E-value=1.2e-18  Score=169.09  Aligned_cols=153  Identities=20%  Similarity=0.293  Sum_probs=127.3

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc-----------------CcceEEecCC---
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF-----------------NAMVLELNAS---  346 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~-----------------~~~~~~~~~~---  346 (533)
                      .|+......+...+..++.+| +||+||.|+||+++|+.+|+.+.|....                 ...+..+.+.   
T Consensus         6 PWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~   85 (319)
T PRK06090          6 PWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPEKEG   85 (319)
T ss_pred             ccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecCcCC
Confidence            456677778888888899999 8999999999999999999999986421                 1234444432   


Q ss_pred             CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeee
Q psy4285         347 DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFR  426 (533)
Q Consensus       347 ~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~  426 (533)
                      ...+.+.+|+..........  .++++|+|||++|+|+..++|+|++++||||+++.||++|+.++.+.|+|+|||..+.
T Consensus        86 ~~I~vdqiR~l~~~~~~~~~--~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~SRCq~~~  163 (319)
T PRK06090         86 KSITVEQIRQCNRLAQESSQ--LNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWV  163 (319)
T ss_pred             CcCCHHHHHHHHHHHhhCcc--cCCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcceeEe
Confidence            23567788877655443332  4678999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCHHHHHHHhhcC
Q psy4285         427 FGPLDSSLIMSRLDYD  442 (533)
Q Consensus       427 ~~~~~~~~~~~~l~~~  442 (533)
                      |.+|+++++.++|...
T Consensus       164 ~~~~~~~~~~~~L~~~  179 (319)
T PRK06090        164 VTPPSTAQAMQWLKGQ  179 (319)
T ss_pred             CCCCCHHHHHHHHHHc
Confidence            9999999999998765

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.83  E-value=6.1e-19  Score=179.35  Aligned_cols=154  Identities=23%  Similarity=0.341  Sum_probs=128.1

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc--------------------------Ccc
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF--------------------------NAM  339 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~--------------------------~~~  339 (533)
                      ..||+.+...|..++.+++.+| +||+||||+||||+|+++|+.+.|....                          ...
T Consensus        18 iiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~~~~~~~~~n   97 (397)
T PRK14955         18 ITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCRDFDAGTSLN   97 (397)
T ss_pred             ccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHHHHhcCCCCC
Confidence            3578888889999999999999 8999999999999999999999884211                          112


Q ss_pred             eEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhh
Q psy4285         340 VLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQ  419 (533)
Q Consensus       340 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~  419 (533)
                      +..+++.+..+.+.+++........+  ..+.++|+||||+|.++...++.|++.+|++++.+.||++++....+.++++
T Consensus        98 ~~~~~~~~~~~id~Ir~l~~~~~~~p--~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~kl~~tl~  175 (397)
T PRK14955         98 ISEFDAASNNSVDDIRLLRENVRYGP--QKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIA  175 (397)
T ss_pred             eEeecccccCCHHHHHHHHHHHhhch--hcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHHhHHHHH
Confidence            44555555556777877665553332  2367899999999999999999999999999999999999988889999999


Q ss_pred             ccceeeeecCCCHHHHHHHhhcC
Q psy4285         420 SRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       420 sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +||..+.|.+++.+++.+++..+
T Consensus       176 sR~~~v~f~~l~~~ei~~~l~~~  198 (397)
T PRK14955        176 SRCQRFNFKRIPLEEIQQQLQGI  198 (397)
T ss_pred             HHHHHhhcCCCCHHHHHHHHHHH
Confidence            99999999999999999888874

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.83  E-value=1.3e-18  Score=172.07  Aligned_cols=153  Identities=25%  Similarity=0.378  Sum_probs=127.7

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc--CcceEEecCC--CCCchhHHHHHHHHH
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF--NAMVLELNAS--DDRGIGIVRDQIFQF  361 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~--~~~~~~~~~~--~~~~~~~~~~~~~~~  361 (533)
                      ..||+.+.+.+...+..++.+| ++|+||+|+|||++|+.+++.+.|....  ...+..+...  ...+.+.+++....+
T Consensus         6 i~g~~~~~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~ir~~~~~~   85 (313)
T PRK05564          6 IIGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDDIRNIIEEV   85 (313)
T ss_pred             ccCcHHHHHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHHHHHHHHHH
Confidence            3478888888999999999999 6999999999999999999999886421  2234444442  234566788877655


Q ss_pred             HhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhc
Q psy4285         362 ASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       362 ~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~  441 (533)
                      ...+  ..++++|+|||++|.|+.+++|+|++.+|++|+++.||++|+.++.+.|+++|||..+.|.+++++++..++.+
T Consensus        86 ~~~p--~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~l~~  163 (313)
T PRK05564         86 NKKP--YEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEIEKFISY  163 (313)
T ss_pred             hcCc--ccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhceeeeCCCcCHHHHHHHHHH
Confidence            4333  24689999999999999999999999999999999999999999999999999999999999999999988864

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.82  E-value=1.9e-18  Score=178.31  Aligned_cols=154  Identities=29%  Similarity=0.396  Sum_probs=128.5

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~  347 (533)
                      ..||+.+...+..++..++.+| +||+||||+|||++|+.+|+.+.|....                  ...+++++++.
T Consensus        18 iiGq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~~~d~~eidaas   97 (486)
T PRK14953         18 VIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFPDLIEIDAAS   97 (486)
T ss_pred             ccChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCCCCcEEEEeCcc
Confidence            3588999999999999988888 6899999999999999999999863211                  12355566666


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.++....... ..+. .+.++|+||||+|+++..++++|++.+++++.++.+|++|+....++++++|||..+.|
T Consensus        98 ~~gvd~ir~I~~~~~-~~P~-~~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v~Il~tt~~~kl~~tI~SRc~~i~f  175 (486)
T PRK14953         98 NRGIDDIRALRDAVS-YTPI-KGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILSRCQRFIF  175 (486)
T ss_pred             CCCHHHHHHHHHHHH-hCcc-cCCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEECCHHHHHHHHHHhceEEEc
Confidence            577777777654433 3332 36789999999999999999999999999999999999999888999999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+++.+++..++.++
T Consensus       176 ~~ls~~el~~~L~~i  190 (486)
T PRK14953        176 SKPTKEQIKEYLKRI  190 (486)
T ss_pred             CCCCHHHHHHHHHHH
Confidence            999999999988885

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.82  E-value=1.3e-18  Score=180.88  Aligned_cols=153  Identities=27%  Similarity=0.389  Sum_probs=128.2

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc------------------cCcceEEecCCCC
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ------------------FNAMVLELNASDD  348 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~------------------~~~~~~~~~~~~~  348 (533)
                      .||+.+...|..++..++.+| +||+||||||||++|+.+|+.+.|...                  ....++++++...
T Consensus        19 iGQe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C~sC~~i~~g~hpDv~eId~a~~   98 (624)
T PRK14959         19 AGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQCRKVTQGMHVDVVEIDGASN   98 (624)
T ss_pred             cCCHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCcccHHHHHHhcCCCCceEEEecccc
Confidence            478888999999999887666 889999999999999999999988521                  1223667777666


Q ss_pred             CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeec
Q psy4285         349 RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFG  428 (533)
Q Consensus       349 ~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~  428 (533)
                      .+.+.++.+...+....  ..+.++|+||||+|+|+...+++|++.||+++.++.||++|+.+..+.++|+|||..+.|.
T Consensus        99 ~~Id~iR~L~~~~~~~p--~~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll~TI~SRcq~i~F~  176 (624)
T PRK14959         99 RGIDDAKRLKEAIGYAP--MEGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIVSRCQHFTFT  176 (624)
T ss_pred             cCHHHHHHHHHHHHhhh--hcCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhhHHHHhhhhccccC
Confidence            67777877554443222  2357899999999999999999999999999899999999999999999999999999999


Q ss_pred             CCCHHHHHHHhhcC
Q psy4285         429 PLDSSLIMSRLDYD  442 (533)
Q Consensus       429 ~~~~~~~~~~l~~~  442 (533)
                      +++.+++.++|..+
T Consensus       177 pLs~~eL~~~L~~i  190 (624)
T PRK14959        177 RLSEAGLEAHLTKV  190 (624)
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999999864

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=99.82  E-value=3.5e-18  Score=162.42  Aligned_cols=224  Identities=17%  Similarity=0.182  Sum_probs=151.8

Q ss_pred             hhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc----------cCcceEEecCCC---CCchhHHHHHH
Q psy4285         293 LCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ----------FNAMVLELNASD---DRGIGIVRDQI  358 (533)
Q Consensus       293 ~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~----------~~~~~~~~~~~~---~~~~~~~~~~~  358 (533)
                      ..+.+...++.++.+| +||+||+|+||+++|.++|+.++|...          ....+..+.+..   ..+.+.+++..
T Consensus         5 ~~~~L~~~i~~~rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~~~~I~idqiR~l~   84 (290)
T PRK05917          5 AWEALIQRVRDQKVPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGKGRLHSIETPRAIK   84 (290)
T ss_pred             HHHHHHHHHHcCCcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCCCCcCcHHHHHHHH
Confidence            4556777888889999 789999999999999999999998531          122333343221   24678888877


Q ss_pred             HHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCC-----HH
Q psy4285         359 FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLD-----SS  433 (533)
Q Consensus       359 ~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~-----~~  433 (533)
                      +.+...+  ..++++|+|||++|+|+.+++|+|+++|||||+++.||++|+.++.++|+++|||..+.|.++.     ++
T Consensus        85 ~~~~~~p--~e~~~kv~ii~~ad~mt~~AaNaLLK~LEEPp~~~~fiL~~~~~~~ll~TI~SRcq~~~~~~~~~~~i~~~  162 (290)
T PRK05917         85 KQIWIHP--YESPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTIRSRSLSIHIPMEEKTLVSKE  162 (290)
T ss_pred             HHHhhCc--cCCCceEEEEechhhcCHHHHHHHHHHhhcCCCCeEEEEEeCChhhCcHHHHhcceEEEccchhccCCCHH
Confidence            7665443  2478999999999999999999999999999999999999999999999999999999998754     23


Q ss_pred             HHHHHhhcC--HHHHHH----------------------HHHH-HHHHHHHH-HhcCCC-----HHHHHHHHHHHHHhcC
Q psy4285         434 LIMSRLDYD--DISFFN----------------------IIIW-YIKIQEIK-IEKGLA-----LTDILTEISLLVHRLE  482 (533)
Q Consensus       434 ~~~~~l~~~--~~~~~~----------------------ll~~-~~~l~~l~-~~~~~~-----~~di~~~~~~~~~~~~  482 (533)
                      +....+...  ..++.+                      +++. ...+.++. ...|..     ..|....+.    ...
T Consensus       163 ~~~~l~~~~~g~~~~~~~~~~l~~~~~~~~~~~re~~~~~L~~ll~~~RD~l~~~~~~~~~~l~~~d~~~~l~----~~~  238 (290)
T PRK05917        163 DIAYLIGYAQGKESVTEVGQIVKGSADTDKQVLRDKTKAMLEVLLQLFRDRFLLALKVPASALAYPDLLKEIL----TLP  238 (290)
T ss_pred             HHHHHHHHhCCChhHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCchhhhccHHHHHHHH----hcc
Confidence            332222111  011111                      1111 00011100 111111     112221111    111


Q ss_pred             CChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHh
Q psy4285         483 IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD  524 (533)
Q Consensus       483 ~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~~  524 (533)
                        ......+++.+.+..+++..+++..+.++.++-++..+..
T Consensus       239 --~~~l~~~i~~i~~a~~~l~~N~N~~l~le~l~l~l~~~~~  278 (290)
T PRK05917        239 --VLPLEKVLSIIERAVQALDNSSSAPSCLEWVALQLWSLKN  278 (290)
T ss_pred             --cccHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Confidence              1113356888889999999999999999999888877654

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.82  E-value=2.2e-18  Score=181.40  Aligned_cols=154  Identities=24%  Similarity=0.375  Sum_probs=129.1

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc--------------------------Ccc
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF--------------------------NAM  339 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~--------------------------~~~  339 (533)
                      ..||+.+...|+.++..++.+| +||+|||||||||+|+.+|+.+.|....                          ...
T Consensus        18 ivGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC~~~~~g~~~n   97 (620)
T PRK14954         18 ITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESCRDFDAGTSLN   97 (620)
T ss_pred             hcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHHHHHhccCCCC
Confidence            3588999999999999999999 8999999999999999999999884311                          113


Q ss_pred             eEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhh
Q psy4285         340 VLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQ  419 (533)
Q Consensus       340 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~  419 (533)
                      +..+++....+.+.+++....+...+  ..+.++|+||||+|.|+...+++|++.||+++..+.||++|+...++.++|+
T Consensus        98 ~~~~d~~s~~~vd~Ir~l~e~~~~~P--~~~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~kLl~TI~  175 (620)
T PRK14954         98 ISEFDAASNNSVDDIRQLRENVRYGP--QKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIA  175 (620)
T ss_pred             eEEecccccCCHHHHHHHHHHHHhhh--hcCCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHH
Confidence            44555545556778887766554322  2367899999999999999999999999999999999999998899999999


Q ss_pred             ccceeeeecCCCHHHHHHHhhcC
Q psy4285         420 SRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       420 sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      |||..+.|.+++.+++..++.++
T Consensus       176 SRc~~vef~~l~~~ei~~~L~~i  198 (620)
T PRK14954        176 SRCQRFNFKRIPLDEIQSQLQMI  198 (620)
T ss_pred             hhceEEecCCCCHHHHHHHHHHH
Confidence            99999999999999999888863

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

Probab=99.81  E-value=3.9e-19  Score=167.79  Aligned_cols=189  Identities=22%  Similarity=0.339  Sum_probs=130.0

Q ss_pred             CccccccccCCCCHH--HHHHHHHHHhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcce
Q psy4285         263 NEDTVYNSVGYPTKT--EITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV  340 (533)
Q Consensus       263 ~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~  340 (533)
                      .++..|.++|...++  .+.+.+. ++.-+.+....+.    -..+..+|||||||||||.+|+|+|++.      +..|
T Consensus       145 ~PdvtY~dIGGL~~Qi~EirE~VE-LPL~~PElF~~~G----I~PPKGVLLYGPPGTGKTLLAkAVA~~T------~AtF  213 (406)
T COG1222         145 KPDVTYEDIGGLDEQIQEIREVVE-LPLKNPELFEELG----IDPPKGVLLYGPPGTGKTLLAKAVANQT------DATF  213 (406)
T ss_pred             CCCCChhhccCHHHHHHHHHHHhc-ccccCHHHHHHcC----CCCCCceEeeCCCCCcHHHHHHHHHhcc------CceE
Confidence            456678888775432  2333322 2222333332221    1122349999999999999999999986      7889


Q ss_pred             EEecCCC------CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH-----------HHHHHHHHHHHh-----c
Q psy4285         341 LELNASD------DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN-----------DAQNALRRIIEK-----F  398 (533)
Q Consensus       341 ~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~Ll~~le~-----~  398 (533)
                      +.+.+|+      +.+...+|+.+.-. ..     ..++|+||||+|.+..           +.|..++++|.+     +
T Consensus       214 IrvvgSElVqKYiGEGaRlVRelF~lA-re-----kaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~  287 (406)
T COG1222         214 IRVVGSELVQKYIGEGARLVRELFELA-RE-----KAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDP  287 (406)
T ss_pred             EEeccHHHHHHHhccchHHHHHHHHHH-hh-----cCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCC
Confidence            9999886      34556666654432 22     4678999999999843           567777777654     4


Q ss_pred             CCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC--------HHHHHHHHHHHHHHHHHHHhcCCCH
Q psy4285         399 TTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD--------DISFFNIIIWYIKIQEIKIEKGLAL  467 (533)
Q Consensus       399 ~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~--------~~~~~~ll~~~~~l~~l~~~~~~~~  467 (533)
                      ..++++|++||+++.|||+|++  ||+ .+.|+.|+.+...+++.-.        .-++..+..         .+.|+|+
T Consensus       288 ~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~---------~~~g~sG  358 (406)
T COG1222         288 RGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLAR---------LTEGFSG  358 (406)
T ss_pred             CCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHH---------hcCCCch
Confidence            6789999999999999999999  995 8888888877777777655        223444444         6778888


Q ss_pred             HHHHHHHHHH
Q psy4285         468 TDILTEISLL  477 (533)
Q Consensus       468 ~di~~~~~~~  477 (533)
                      .|+-.-+.++
T Consensus       359 AdlkaictEA  368 (406)
T COG1222         359 ADLKAICTEA  368 (406)
T ss_pred             HHHHHHHHHH
Confidence            8876665543

>PLN03025 replication factor C subunit; Provisional

Probab=99.81  E-value=2.7e-19  Score=177.19  Aligned_cols=164  Identities=34%  Similarity=0.496  Sum_probs=133.5

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+++++|||+||+.++++|+|+|||++++|++++++++..+|+++++++|+.+++++++.++..++||+|+|+|.||
T Consensus       123 lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~f~~l~~~~l~~~L~~i~~~egi~i~~~~l~~i~~~~~gDlR~aln~Lq  202 (319)
T PLN03025        123 MEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVPYVPEGLEAIIFTADGDMRQALNNLQ  202 (319)
T ss_pred             HhcccCCceEEEEeCCccccchhHHHhhhcccCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhccccc---------------hhHHHHHhc----hHHHH-------hhcCCChhhHHHH
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRVEKYR---------------PSTLDELVS----HQDII-------STIEIPESMLVDL  134 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~ek~~---------------~~~l~~lls----~~~~l-------~~l~~~~~~~~~~  134 (533)
                      .++. ..+.|+.+.+.++.+...+...               ...+++++.    ..+++       ...++++..+..+
T Consensus       203 ~~~~-~~~~i~~~~v~~~~~~~~~~~i~~~i~~~~~~~~~~a~~~l~~ll~~g~~~~~Il~~l~~~~~~~~~~~~~~~~~  281 (319)
T PLN03025        203 ATHS-GFGFVNQENVFKVCDQPHPLHVKNIVRNCLKGKFDDACDGLKQLYDLGYSPTDIITTLFRVVKNYDMPEFLKLEY  281 (319)
T ss_pred             HHHh-cCCCCCHHHHHHHcCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCHHHHHHH
Confidence            7765 3446888777654332111110               012444432    22232       2335677788889


Q ss_pred             HhhccCccccccCCCChhhHHHHHHHHHhcc
Q psy4285         135 VLKMSDIEYRLAAGTSEKIQLSALIAAFNSA  165 (533)
Q Consensus       135 ~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~~  165 (533)
                      +..++++++|+..|+++.+|+++|++.++..
T Consensus       282 ~~~~~~~~~~~~~g~~~~~~l~a~~~~~~~~  312 (319)
T PLN03025        282 LREIGFAHMRICDGVGSLLQLSGLLAKLCLV  312 (319)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999754

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.80  E-value=6.4e-18  Score=170.98  Aligned_cols=154  Identities=28%  Similarity=0.429  Sum_probs=127.1

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASD  347 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~  347 (533)
                      ..|++.....+..++..++.+| +||+||||+|||++|+++++.+.|....                  ...++.+++..
T Consensus        16 iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~~~~~~~~   95 (355)
T TIGR02397        16 VIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDVIEIDAAS   95 (355)
T ss_pred             ccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEeeccc
Confidence            3578888888888888888888 7999999999999999999999875311                  12356666665


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.+++.+..... .+ ..++++|+||||+|.++...++.|++.+++++.++.+|++|+.+..+.+++++||..+.|
T Consensus        96 ~~~~~~~~~l~~~~~~-~p-~~~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~  173 (355)
T TIGR02397        96 NNGVDDIREILDNVKY-AP-SSGKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKIPATILSRCQRFDF  173 (355)
T ss_pred             cCCHHHHHHHHHHHhc-Cc-ccCCceEEEEeChhhcCHHHHHHHHHHHhCCccceeEEEEeCCHHHHHHHHHhheeEEEc
Confidence            5566667776655432 22 236788999999999999999999999999999999999999998899999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+++++++.+++..+
T Consensus       174 ~~~~~~~l~~~l~~~  188 (355)
T TIGR02397       174 KRIPLEDIVERLKKI  188 (355)
T ss_pred             CCCCHHHHHHHHHHH
Confidence            999999999999864

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.

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.80  E-value=4.7e-18  Score=168.33  Aligned_cols=154  Identities=24%  Similarity=0.383  Sum_probs=127.0

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc-----c-------------------CcceE
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ-----F-------------------NAMVL  341 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~-----~-------------------~~~~~  341 (533)
                      +.||+++...+..++..++.+| +||+||+|+|||++|+.+|+.+.|...     .                   ...+.
T Consensus        25 l~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~~~~~c~~c~~i~~~~hPdl~  104 (351)
T PRK09112         25 LFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLADPDPASPVWRQIAQGAHPNLL  104 (351)
T ss_pred             ccCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCCCCCCCHHHHHHHcCCCCCEE
Confidence            4689999999999999999999 899999999999999999999988310     0                   01122


Q ss_pred             EecCC---------CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         342 ELNAS---------DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       342 ~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      .+..+         ...+.+.+++....+.....  .++++|+||||+|.|+..++|+|++.+|+++.++.||++|+.+.
T Consensus       105 ~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~--~g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~~~fiLit~~~~  182 (351)
T PRK09112        105 HITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSG--DGNWRIVIIDPADDMNRNAANAILKTLEEPPARALFILISHSSG  182 (351)
T ss_pred             EeecccccccccccccCCHHHHHHHHHHhhhccc--cCCceEEEEEchhhcCHHHHHHHHHHHhcCCCCceEEEEECChh
Confidence            23211         12345677776655544432  36789999999999999999999999999999999999999999


Q ss_pred             CCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         413 KIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       413 ~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.|+++|||..+.|.+++.+++.++|.+.
T Consensus       183 ~llptIrSRc~~i~l~pl~~~~~~~~L~~~  212 (351)
T PRK09112        183 RLLPTIRSRCQPISLKPLDDDELKKALSHL  212 (351)
T ss_pred             hccHHHHhhccEEEecCCCHHHHHHHHHHh
Confidence            999999999999999999999999999874

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.80  E-value=7.6e-18  Score=179.11  Aligned_cols=154  Identities=26%  Similarity=0.387  Sum_probs=128.0

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc-------------------CcceEEecCC
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF-------------------NAMVLELNAS  346 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~-------------------~~~~~~~~~~  346 (533)
                      +.||+.+...|..++..++.+| +||+||||+|||++|+.+++.+.|....                   ...+++++++
T Consensus        18 iiGq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~~c~~c~~i~~~~~~d~~~i~~~   97 (585)
T PRK14950         18 LVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCEMCRAIAEGSAVDVIEMDAA   97 (585)
T ss_pred             hcCCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccCHHHHHHhcCCCCeEEEEecc
Confidence            3588889999999888888888 6999999999999999999999874310                   1235566665


Q ss_pred             CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeee
Q psy4285         347 DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFR  426 (533)
Q Consensus       347 ~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~  426 (533)
                      ...+.+.+++.+..... .+. .+.++|+||||+|+|+.+.++.|++.+|+++.++.||++++....+.++++|||..+.
T Consensus        98 ~~~~vd~ir~ii~~~~~-~p~-~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll~tI~SR~~~i~  175 (585)
T PRK14950         98 SHTSVDDAREIIERVQF-RPA-LARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILSRCQRFD  175 (585)
T ss_pred             ccCCHHHHHHHHHHHhh-Ccc-cCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhhHHHHhccceee
Confidence            55677778877654432 222 3578999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCHHHHHHHhhcC
Q psy4285         427 FGPLDSSLIMSRLDYD  442 (533)
Q Consensus       427 ~~~~~~~~~~~~l~~~  442 (533)
                      |.+++..++..++..+
T Consensus       176 f~~l~~~el~~~L~~~  191 (585)
T PRK14950        176 FHRHSVADMAAHLRKI  191 (585)
T ss_pred             CCCCCHHHHHHHHHHH
Confidence            9999999999888765

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.80  E-value=3.2e-18  Score=187.74  Aligned_cols=149  Identities=21%  Similarity=0.261  Sum_probs=107.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      ++|||||||||||++|+++|+++      +..++.+++++.      .+...++..+.....      ..++||||||+|
T Consensus       489 giLL~GppGtGKT~lakalA~e~------~~~fi~v~~~~l~~~~vGese~~i~~~f~~A~~------~~p~iifiDEid  556 (733)
T TIGR01243       489 GVLLFGPPGTGKTLLAKAVATES------GANFIAVRGPEILSKWVGESEKAIREIFRKARQ------AAPAIIFFDEID  556 (733)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhc------CCCEEEEehHHHhhcccCcHHHHHHHHHHHHHh------cCCEEEEEEChh
Confidence            48999999999999999999997      567777776542      223344444333221      356899999999


Q ss_pred             CCCH------------HHHHHHHHHHHh--cCCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC--
Q psy4285         382 AMTN------------DAQNALRRIIEK--FTTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD--  442 (533)
Q Consensus       382 ~l~~------------~~~~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~--  442 (533)
                      .+.+            ...+.|+..|+.  ...++.+|++||.++.+|+++++  ||+ .+.+++|+.++..+++...  
T Consensus       557 ~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~  636 (733)
T TIGR01243       557 AIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTR  636 (733)
T ss_pred             hhhccCCCCCCccHHHHHHHHHHHHhhcccCCCCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhc
Confidence            8742            234567777763  35678899999999999999997  995 7777888888888777543  


Q ss_pred             ------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 ------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 ------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                            ..++..+.+         .+.|+++.|+..-+.++
T Consensus       637 ~~~~~~~~~l~~la~---------~t~g~sgadi~~~~~~A  668 (733)
T TIGR01243       637 SMPLAEDVDLEELAE---------MTEGYTGADIEAVCREA  668 (733)
T ss_pred             CCCCCccCCHHHHHH---------HcCCCCHHHHHHHHHHH
Confidence                  123444444         67899999987655444

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.

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

Probab=99.80  E-value=7.7e-19  Score=158.15  Aligned_cols=141  Identities=18%  Similarity=0.219  Sum_probs=96.8

Q ss_pred             hhchhhhhhhccccc-----ccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHH
Q psy4285         288 NESMDLCYKINRFID-----ENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFA  362 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~-----~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (533)
                      .||+++...+.-+++     ....+|++||||||+||||+|+.+|+++      +..+..++++.......+...+..+ 
T Consensus        27 iGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~------~~~~~~~sg~~i~k~~dl~~il~~l-   99 (233)
T PF05496_consen   27 IGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANEL------GVNFKITSGPAIEKAGDLAAILTNL-   99 (233)
T ss_dssp             -S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHC------T--EEEEECCC--SCHHHHHHHHT--
T ss_pred             cCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhcc------CCCeEeccchhhhhHHHHHHHHHhc-
Confidence            456666655544332     2346789999999999999999999998      6677777776655555555444332 


Q ss_pred             hcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcC------------------CCcEEEEEeCCCCCCChhhhcccee
Q psy4285         363 STKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT------------------TNVRFCIICNYLSKIPPAIQSRCTR  424 (533)
Q Consensus       363 ~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~------------------~~~~~I~~~n~~~~l~~~l~sR~~~  424 (533)
                             ...+||||||+++++...++.|+..||.+.                  +...+|.+|+....+.+++++||..
T Consensus       100 -------~~~~ILFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FTligATTr~g~ls~pLrdRFgi  172 (233)
T PF05496_consen  100 -------KEGDILFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFTLIGATTRAGLLSSPLRDRFGI  172 (233)
T ss_dssp             --------TT-EEEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----EEEEEESSGCCTSHCCCTTSSE
T ss_pred             -------CCCcEEEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCCCceEeeeeccccccchhHHhhcce
Confidence                   246799999999999999999999999641                  3366888889999999999999975


Q ss_pred             -eeecCCCHHHHHHHhhcC
Q psy4285         425 -FRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       425 -i~~~~~~~~~~~~~l~~~  442 (533)
                       .++..|+.+++.+++.+.
T Consensus       173 ~~~l~~Y~~~el~~Iv~r~  191 (233)
T PF05496_consen  173 VLRLEFYSEEELAKIVKRS  191 (233)
T ss_dssp             EEE----THHHHHHHHHHC
T ss_pred             ecchhcCCHHHHHHHHHHH
Confidence             579999999999999876

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.

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

Probab=99.80  E-value=2.1e-19  Score=161.80  Aligned_cols=151  Identities=26%  Similarity=0.313  Sum_probs=118.5

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch------hHHHHHHHHHHhcccCCCCCcEEEEEeC
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI------GIVRDQIFQFASTKTMHKSSYKLIILDE  379 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~vliiDE  379 (533)
                      +.++|||||||||||++|+++|++.      ..+++.++++...+.      ..++++.....      +..++|+||||
T Consensus       151 PknVLFyGppGTGKTm~Akalane~------kvp~l~vkat~liGehVGdgar~Ihely~rA~------~~aPcivFiDE  218 (368)
T COG1223         151 PKNVLFYGPPGTGKTMMAKALANEA------KVPLLLVKATELIGEHVGDGARRIHELYERAR------KAAPCIVFIDE  218 (368)
T ss_pred             cceeEEECCCCccHHHHHHHHhccc------CCceEEechHHHHHHHhhhHHHHHHHHHHHHH------hcCCeEEEehh
Confidence            4579999999999999999999987      788898988775443      34444433222      24689999999


Q ss_pred             CCCCCH------------HHHHHHHHHHHh--cCCCcEEEEEeCCCCCCChhhhccc-eeeeecCCCHHHHHHHhhcC--
Q psy4285         380 ADAMTN------------DAQNALRRIIEK--FTTNVRFCIICNYLSKIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD--  442 (533)
Q Consensus       380 ~d~l~~------------~~~~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~--  442 (533)
                      +|.+..            +..|+|+.-|+.  ...++..|++||++..||++++||| ..+.|.-|++++...+++..  
T Consensus       219 ~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGVvtIaaTN~p~~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y~k  298 (368)
T COG1223         219 LDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAATNRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYYAK  298 (368)
T ss_pred             hhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCceEEEeecCChhhcCHHHHhhhhheeeeeCCChHHHHHHHHHHHH
Confidence            999854            346888888874  2456889999999999999999999 59999999999999999886  


Q ss_pred             ------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 ------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 ------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                            ..+++.+..         .+.|+|++||...+++.
T Consensus       299 ~~Plpv~~~~~~~~~---------~t~g~SgRdikekvlK~  330 (368)
T COG1223         299 KFPLPVDADLRYLAA---------KTKGMSGRDIKEKVLKT  330 (368)
T ss_pred             hCCCccccCHHHHHH---------HhCCCCchhHHHHHHHH
Confidence                  223444444         78899999998777653

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.79  E-value=3.2e-18  Score=170.49  Aligned_cols=154  Identities=26%  Similarity=0.379  Sum_probs=127.5

Q ss_pred             hhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccccC----------------------------
Q psy4285         287 LNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFN----------------------------  337 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~~----------------------------  337 (533)
                      +.||+.+...|.+.+..++.+| +||+||+|+||+++|.++|+.++|....+                            
T Consensus        21 iiGq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~~~~c~~c~~i~~~~H  100 (365)
T PRK07471         21 LFGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDHPVARRIAAGAH  100 (365)
T ss_pred             ccChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccCCCCChHHHHHHccCC
Confidence            3589999999999999999999 89999999999999999999998854210                            


Q ss_pred             cceEEecC--C-------CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEe
Q psy4285         338 AMVLELNA--S-------DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIIC  408 (533)
Q Consensus       338 ~~~~~~~~--~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~  408 (533)
                      ..+..+..  .       .....+.+++....+....  ..++++|+||||+|.++...+|+|++++|+++.++.||++|
T Consensus       101 PDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~--~~~~~kVviIDead~m~~~aanaLLK~LEepp~~~~~IL~t  178 (365)
T PRK07471        101 GGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTA--AEGGWRVVIVDTADEMNANAANALLKVLEEPPARSLFLLVS  178 (365)
T ss_pred             CCeEEEecccccccccccccccHHHHHHHHHHhCcCc--ccCCCEEEEEechHhcCHHHHHHHHHHHhcCCCCeEEEEEE
Confidence            11223322  1       1234667777765554332  24678999999999999999999999999999999999999


Q ss_pred             CCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         409 NYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       409 n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +.++.+.++++|||..+.|.+++.+++.++|.+.
T Consensus       179 ~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~  212 (365)
T PRK07471        179 HAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAA  212 (365)
T ss_pred             CCchhchHHhhccceEEECCCCCHHHHHHHHHHh
Confidence            9999999999999999999999999999999875

>KOG2028|consensus

Probab=99.79  E-value=3.9e-19  Score=167.24  Aligned_cols=210  Identities=20%  Similarity=0.255  Sum_probs=151.2

Q ss_pred             hhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEE
Q psy4285         296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLI  375 (533)
Q Consensus       296 ~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl  375 (533)
                      .|+.++++++.|.++||||||||||++|+.++.....+   ...++++++... +...+|..++....... +..+..||
T Consensus       152 llrs~ieq~~ipSmIlWGppG~GKTtlArlia~tsk~~---SyrfvelSAt~a-~t~dvR~ife~aq~~~~-l~krkTil  226 (554)
T KOG2028|consen  152 LLRSLIEQNRIPSMILWGPPGTGKTTLARLIASTSKKH---SYRFVELSATNA-KTNDVRDIFEQAQNEKS-LTKRKTIL  226 (554)
T ss_pred             HHHHHHHcCCCCceEEecCCCCchHHHHHHHHhhcCCC---ceEEEEEecccc-chHHHHHHHHHHHHHHh-hhcceeEE
Confidence            46778899999999999999999999999999876333   356788887763 44556666554333222 23567899


Q ss_pred             EEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEe--CCCCCCChhhhccceeeeecCCCHHHHHHHhhcC-----------
Q psy4285         376 ILDEADAMTNDAQNALRRIIEKFTTNVRFCIIC--NYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD-----------  442 (533)
Q Consensus       376 iiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~--n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~-----------  442 (533)
                      ||||+++++...|..|+-.+|..  .+.+|.+|  |....+..+|.|||.++.+.+++.+.+..+|.+-           
T Consensus       227 FiDEiHRFNksQQD~fLP~VE~G--~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~v~~iL~raia~l~dser~~  304 (554)
T KOG2028|consen  227 FIDEIHRFNKSQQDTFLPHVENG--DITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRAIASLGDSERPT  304 (554)
T ss_pred             EeHHhhhhhhhhhhcccceeccC--ceEEEecccCCCccchhHHHHhccceeEeccCCHHHHHHHHHHHHHhhccccccC
Confidence            99999999999999999999753  36666655  6777999999999999999999999999999883           


Q ss_pred             ----------------------HHHHHHHHHHHHHH---------------------HH-------HHHhcCCCHHHHHH
Q psy4285         443 ----------------------DISFFNIIIWYIKI---------------------QE-------IKIEKGLALTDILT  472 (533)
Q Consensus       443 ----------------------~~~~~~ll~~~~~l---------------------~~-------l~~~~~~~~~di~~  472 (533)
                                            .+|.+..++..+..                     .+       +....|-.+++.++
T Consensus       305 ~~l~n~s~~ve~siidyla~lsdGDaR~aLN~Lems~~m~~tr~g~~~~~~lSidDvke~lq~s~~~YDr~Ge~HYntIS  384 (554)
T KOG2028|consen  305 DPLPNSSMFVEDSIIDYLAYLSDGDARAALNALEMSLSMFCTRSGQSSRVLLSIDDVKEGLQRSHILYDRAGEEHYNTIS  384 (554)
T ss_pred             CCCCCcchhhhHHHHHHHHHhcCchHHHHHHHHHHHHHHHHhhcCCcccceecHHHHHHHHhhccceecccchhHHHHHH
Confidence                                  12222222211100                     00       11223556677788


Q ss_pred             HHHHHHHhcCCChhHHHHHHHHHH-------HHHHHHhCCCChHHHHHH
Q psy4285         473 EISLLVHRLEIPESMLVDLVLKMS-------DIEYRLAAGTSEKIQLSA  514 (533)
Q Consensus       473 ~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~l~~g~~~~~~l~~  514 (533)
                      .+++.++..+  .+...+++.++.       ++.+||.+=+++.++|.+
T Consensus       385 A~HKSmRG~D--~nAslY~LaRMLegGEdPLYVARRlvR~ASEDIGlaD  431 (554)
T KOG2028|consen  385 ALHKSMRGSD--QNASLYWLARMLEGGEDPLYVARRLVRFASEDIGLAD  431 (554)
T ss_pred             HHHHhhcCCc--cchHHHHHHHHHccCCCcHHHHHHHHHHhhcccCcCC
Confidence            8888887755  345556666665       789999999998887653

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=99.78  E-value=3.7e-17  Score=160.47  Aligned_cols=150  Identities=22%  Similarity=0.311  Sum_probs=118.8

Q ss_pred             hchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc-------------------CcceEEecCCC-
Q psy4285         289 ESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF-------------------NAMVLELNASD-  347 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~-------------------~~~~~~~~~~~-  347 (533)
                      |+......+...  .++.+| +||+||+|+|||++|+.+|+.+.|..+.                   ...+..+.+.. 
T Consensus         5 W~~~~w~~l~~~--~~r~~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~   82 (325)
T PRK08699          5 WHQEQWRQIAEH--WERRPNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSD   82 (325)
T ss_pred             ccHHHHHHHHHh--cCCcceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecccc
Confidence            344444444444  357778 8999999999999999999999885421                   13355555421 


Q ss_pred             ---------CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhh
Q psy4285         348 ---------DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAI  418 (533)
Q Consensus       348 ---------~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l  418 (533)
                               ..+.+.+|+........+.  .++.+|+++|+++.|+...+++|++++|+++.++.||++|+.+..+.+++
T Consensus        83 ~~~~g~~~~~I~id~iR~l~~~~~~~p~--~~~~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti  160 (325)
T PRK08699         83 EPENGRKLLQIKIDAVREIIDNVYLTSV--RGGLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTI  160 (325)
T ss_pred             cccccccCCCcCHHHHHHHHHHHhhCcc--cCCceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHH
Confidence                     2467788887655543332  36789999999999999999999999999988899999999999999999


Q ss_pred             hccceeeeecCCCHHHHHHHhhcC
Q psy4285         419 QSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       419 ~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +|||..+.|.+++.+++..+|.+.
T Consensus       161 ~SRc~~~~~~~~~~~~~~~~L~~~  184 (325)
T PRK08699        161 KSRCRKMVLPAPSHEEALAYLRER  184 (325)
T ss_pred             HHHhhhhcCCCCCHHHHHHHHHhc
Confidence            999999999999999999888753

>KOG0990|consensus

Probab=99.77  E-value=6.9e-19  Score=163.63  Aligned_cols=185  Identities=41%  Similarity=0.504  Sum_probs=155.2

Q ss_pred             hhhhccccchhHHHHHhchHHHHhhcCCChhhHHHHHhhccCccccccCCCChhhHHHHHHHHHhcccc-cceeeeecCC
Q psy4285          99 LVSRVEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD-KLEVLELNAS  177 (533)
Q Consensus        99 ~~~~~ek~~~~~l~~lls~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~~~~-~~~~~e~nas  177 (533)
                      -.+|+++|+|..+.+++++.+++.++.-     ......+.|..++++||+|++..+.+.+..+.+.+. +..++|+|+|
T Consensus        28 ~~pwvekyrP~~l~dv~~~~ei~st~~~-----~~~~~~lPh~L~YgPPGtGktsti~a~a~~ly~~~~~~~m~lelnaS  102 (360)
T KOG0990|consen   28 PQPWVEKYRPPFLGIVIKQEPIWSTENR-----YSGMPGLPHLLFYGPPGTGKTSTILANARDFYSPHPTTSMLLELNAS  102 (360)
T ss_pred             CCCCccCCCCchhhhHhcCCchhhHHHH-----hccCCCCCcccccCCCCCCCCCchhhhhhhhcCCCCchhHHHHhhcc
Confidence            3589999999999999999999876531     112234458889999999999999999999998654 7889999999


Q ss_pred             cccchhhhHHHHhhhhhccc--ccCC--CceEEEEcCccccCHHHHHHHHc-----------------------------
Q psy4285         178 DDRGIGIVRDQIFQFASTKT--MHKS--SYKLIILDEADAMTNDAQNALRR-----------------------------  224 (533)
Q Consensus       178 d~~g~~~~~d~i~~~a~~~~--l~~~--~~~~iilDE~d~l~~~a~~~LRr-----------------------------  224 (533)
                      |.||++..+.++..||..++  +++.  .+|++||||+|.|+.+||.+|||                             
T Consensus       103 d~rgid~vr~qi~~fast~~~~~fst~~~fKlvILDEADaMT~~AQnALRRviek~t~n~rF~ii~n~~~ki~pa~qsRc  182 (360)
T KOG0990|consen  103 DDRGIDPVRQQIHLFASTQQPTTYSTHAAFKLVILDEADAMTRDAQNALRRVIEKYTANTRFATISNPPQKIHPAQQSRC  182 (360)
T ss_pred             CccCCcchHHHHHHHHhhccceeccccCceeEEEecchhHhhHHHHHHHHHHHHHhccceEEEEeccChhhcCchhhccc
Confidence            99999999999989998884  4565  78899999999999999999998                             


Q ss_pred             ------------------------cCCCChhHHHHHHHhccCchHHhhcHHHHHHhhcCCCCCccc-----cccccCCCC
Q psy4285         225 ------------------------KLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDT-----VYNSVGYPT  275 (533)
Q Consensus       225 ------------------------~~~~~~~~l~~l~~~s~~di~~~L~~L~~~~~~~~~~~~~~~-----~~~~~~~~~  275 (533)
                                              ..+.++++..++...+.||++.+++.|+...... .++.+..     +|...|++.
T Consensus       183 trfrf~pl~~~~~~~r~shi~e~e~~~~~~~~~~a~~r~s~gDmr~a~n~Lqs~~~~~-~~~~e~~~~~~~vy~c~g~p~  261 (360)
T KOG0990|consen  183 TRFRFAPLTMAQQTERQSHIRESEQKETNPEGYSALGRLSVGDMRVALNYLQSILKKV-MERKELNNPNDLVYQCKGAPQ  261 (360)
T ss_pred             ccCCCCCCChhhhhhHHHHHHhcchhhcCHHHHHHHHHHhHHHHHHHHHHHHHHHHHh-CCCCCCCCchhhHHHhcCCCC
Confidence                                    1367788889999999999999999999988764 3334444     899999999


Q ss_pred             HHHHHHHHHHHhhh
Q psy4285         276 KTEITNILRWLLNE  289 (533)
Q Consensus       276 ~~~~~~~l~~~~~~  289 (533)
                      +.++..++.|+..+
T Consensus       262 ~~dI~~I~~~il~~  275 (360)
T KOG0990|consen  262 PSDIRQIIEKRMNG  275 (360)
T ss_pred             hhHHHHHHHHHhcC
Confidence            99999999887654

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.77  E-value=9.9e-17  Score=162.53  Aligned_cols=153  Identities=29%  Similarity=0.407  Sum_probs=125.3

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc------cCcceEEecCCCCCchhHHHHHHHH
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ------FNAMVLELNASDDRGIGIVRDQIFQ  360 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~  360 (533)
                      .||+.+...+...++.+..+| ++||||||+|||++|+++++.+.+...      +...++++++....+.+.+++.+..
T Consensus        20 ig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~l~~~   99 (367)
T PRK14970         20 VGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDDIRNLIDQ   99 (367)
T ss_pred             CCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCHHHHHHHHHH
Confidence            578888888888888887775 899999999999999999999977421      1233455665555556777776665


Q ss_pred             HHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhh
Q psy4285         361 FASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       361 ~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~  440 (533)
                      ....+  ..++++++||||+|.++...++.|++.+++++..+.+|++|+....+.+++.|||..+.|.+++++++..++.
T Consensus       100 ~~~~p--~~~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~sr~~~v~~~~~~~~~l~~~l~  177 (367)
T PRK14970        100 VRIPP--QTGKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEHLA  177 (367)
T ss_pred             Hhhcc--ccCCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHHhcceeEecCCccHHHHHHHHH
Confidence            43222  2356789999999999999999999999998888999999999999999999999999999999999998888


Q ss_pred             cC
Q psy4285         441 YD  442 (533)
Q Consensus       441 ~~  442 (533)
                      .+
T Consensus       178 ~~  179 (367)
T PRK14970        178 GI  179 (367)
T ss_pred             HH
Confidence            64

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.76  E-value=6.7e-18  Score=154.46  Aligned_cols=145  Identities=28%  Similarity=0.453  Sum_probs=114.3

Q ss_pred             hhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCC-CCCchhHHH
Q psy4285         296 KINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNAS-DDRGIGIVR  355 (533)
Q Consensus       296 ~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~-~~~~~~~~~  355 (533)
                      .+.+.+..++.+| +||+||||+|||++|+.+++.+.|....                  ...+..+... ...+.+.++
T Consensus         3 ~l~~~i~~~~~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i~   82 (188)
T TIGR00678         3 QLKRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQVR   82 (188)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHHH
Confidence            3556667777777 8999999999999999999999875210                  0112222221 124556777


Q ss_pred             HHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHH
Q psy4285         356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLI  435 (533)
Q Consensus       356 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~  435 (533)
                      ..+..+....  ..+.++|+||||+|.++.+.++.|++.||++++++.+|++++.+..+.++++|||..+.|.+++.+++
T Consensus        83 ~i~~~~~~~~--~~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~~~~~~~~~~~~~~  160 (188)
T TIGR00678        83 ELVEFLSRTP--QESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEAL  160 (188)
T ss_pred             HHHHHHccCc--ccCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhcEEeeCCCCCHHHH
Confidence            6665544333  23678999999999999999999999999999999999999988999999999999999999999999


Q ss_pred             HHHhhcC
Q psy4285         436 MSRLDYD  442 (533)
Q Consensus       436 ~~~l~~~  442 (533)
                      .+++.+.
T Consensus       161 ~~~l~~~  167 (188)
T TIGR00678       161 LQWLIRQ  167 (188)
T ss_pred             HHHHHHc
Confidence            9888775

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.

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

Probab=99.75  E-value=1.4e-16  Score=174.23  Aligned_cols=291  Identities=19%  Similarity=0.253  Sum_probs=178.3

Q ss_pred             cCccccccCCCChhhHHHHHHHHHhccc-----ccceeeeecCCccc-ch---hhhHHHHhhhhhcccccCCCceEEEEc
Q psy4285         139 SDIEYRLAAGTSEKIQLSALIAAFNSAR-----DKLEVLELNASDDR-GI---GIVRDQIFQFASTKTMHKSSYKLIILD  209 (533)
Q Consensus       139 ~~~~~~~~~G~~~~~~l~~~~~~~~~~~-----~~~~~~e~nasd~~-g~---~~~~d~i~~~a~~~~l~~~~~~~iilD  209 (533)
                      ..+...|+||+|||.-+++++..+....     .+..++.+|.+..- |.   +-.+.+++..-....  ...+.++|+|
T Consensus       204 ~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~~~~~l~a~~~~~g~~e~~l~~i~~~~~--~~~~~ILfiD  281 (731)
T TIGR02639       204 NNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLLAGTKYRGDFEERLKAVVSEIE--KEPNAILFID  281 (731)
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEecHHHHhhhccccchHHHHHHHHHHHHh--ccCCeEEEEe
Confidence            5677889999999999999998874321     14677888754432 11   111133322222110  1234599999


Q ss_pred             CccccCH---------HHHHHH-------------------------------Hc-------------------------
Q psy4285         210 EADAMTN---------DAQNAL-------------------------------RR-------------------------  224 (533)
Q Consensus       210 E~d~l~~---------~a~~~L-------------------------------Rr-------------------------  224 (533)
                      |++.+..         ++++.|                               ||                         
T Consensus       282 Eih~l~~~g~~~~~~~~~~~~L~~~l~~g~i~~IgaTt~~e~~~~~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~~~~  361 (731)
T TIGR02639       282 EIHTIVGAGATSGGSMDASNLLKPALSSGKLRCIGSTTYEEYKNHFEKDRALSRRFQKIDVGEPSIEETVKILKGLKEKY  361 (731)
T ss_pred             cHHHHhccCCCCCccHHHHHHHHHHHhCCCeEEEEecCHHHHHHHhhhhHHHHHhCceEEeCCCCHHHHHHHHHHHHHHH
Confidence            9987752         223322                               22                         


Q ss_pred             ----cCCCChhHHHHHHHhccCch------HHhhcHHHHHHhhcC--------CCCCccc----cccccCCCCHH-----
Q psy4285         225 ----KLPVTPDGKKAIIDLSDGDM------RKVLNILQSAATAHA--------DEVNEDT----VYNSVGYPTKT-----  277 (533)
Q Consensus       225 ----~~~~~~~~l~~l~~~s~~di------~~~L~~L~~~~~~~~--------~~~~~~~----~~~~~~~~~~~-----  277 (533)
                          .+.++++++..++..+...+      ..+++.+.......+        ..++.+.    +-...+.|...     
T Consensus       362 e~~~~v~i~~~al~~~~~ls~ryi~~r~~P~kai~lld~a~a~~~~~~~~~~~~~v~~~~i~~~i~~~tgiP~~~~~~~~  441 (731)
T TIGR02639       362 EEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAGASFRLRPKAKKKANVSVKDIENVVAKMAHIPVKTVSVDD  441 (731)
T ss_pred             HhccCcccCHHHHHHHHHhhhcccccccCCHHHHHHHHHhhhhhhcCcccccccccCHHHHHHHHHHHhCCChhhhhhHH
Confidence                13577888888888776544      334544443332111        0122221    23344555321     


Q ss_pred             -----HHHHHHHHHhhhchhhhhhhccccccc--------CC-CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEe
Q psy4285         278 -----EITNILRWLLNESMDLCYKINRFIDEN--------EL-PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLEL  343 (533)
Q Consensus       278 -----~~~~~l~~~~~~~~~~~~~l~~~~~~~--------~~-~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~  343 (533)
                           .+...+.....||+++++.+...+...        ++ .+++|+||||||||++|+++|+.+      +..++.+
T Consensus       442 ~~~l~~l~~~l~~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l------~~~~~~~  515 (731)
T TIGR02639       442 REKLKNLEKNLKAKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEAL------GVHLERF  515 (731)
T ss_pred             HHHHHHHHHHHhcceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHh------cCCeEEE
Confidence                 122233344578888887776665532        12 238999999999999999999988      3345555


Q ss_pred             cCCCCCchhHHHHH---------------HHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc----------
Q psy4285         344 NASDDRGIGIVRDQ---------------IFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF----------  398 (533)
Q Consensus       344 ~~~~~~~~~~~~~~---------------~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~----------  398 (533)
                      +.++......+...               +.....     ..+++|++|||+|++.++.++.|++++++.          
T Consensus       516 d~se~~~~~~~~~lig~~~gyvg~~~~~~l~~~~~-----~~p~~VvllDEieka~~~~~~~Ll~~ld~g~~~d~~g~~v  590 (731)
T TIGR02639       516 DMSEYMEKHTVSRLIGAPPGYVGFEQGGLLTEAVR-----KHPHCVLLLDEIEKAHPDIYNILLQVMDYATLTDNNGRKA  590 (731)
T ss_pred             eCchhhhcccHHHHhcCCCCCcccchhhHHHHHHH-----hCCCeEEEEechhhcCHHHHHHHHHhhccCeeecCCCccc
Confidence            54442221111111               111111     135689999999999999999999999864          


Q ss_pred             -CCCcEEEEEeCCCC-------------------------CCChhhhccce-eeeecCCCHHHHHHHhhcC
Q psy4285         399 -TTNVRFCIICNYLS-------------------------KIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       399 -~~~~~~I~~~n~~~-------------------------~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                       -.++.||+|||...                         .+.|.++.|+. .+.|.|++.+++.+++...
T Consensus       591 d~~~~iii~Tsn~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef~~Rid~Vi~F~pLs~e~l~~Iv~~~  661 (731)
T TIGR02639       591 DFRNVILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRNRLDAIIHFNPLSEEVLEKIVQKF  661 (731)
T ss_pred             CCCCCEEEECCCcchhhhhhccCCcchhhhHHHHHHHHHhhcChHHHhcCCeEEEcCCCCHHHHHHHHHHH
Confidence             24677999997531                         25788899994 8999999999999888765

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=99.75  E-value=1.3e-16  Score=152.48  Aligned_cols=150  Identities=19%  Similarity=0.341  Sum_probs=123.2

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCC-C
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNAS-D  347 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~-~  347 (533)
                      ..|+.+...+...+..++.+| +||+||  +||+++|+.+|+.+.|....                  ...+..+.+. .
T Consensus         5 ~~q~~~~~~L~~~~~~~rl~hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~~~Cg~C~~C~~i~~~~HPD~~~i~p~~~   82 (290)
T PRK07276          5 QKQPKVFQRFQTILEQDRLNHAYLFSGD--FASFEMALFLAQSLFCEQKEGVLPCGHCRSCRLIEQGEFSDVTVIEPQGQ   82 (290)
T ss_pred             HHHHHHHHHHHHHHHcCCcceeeeeeCC--ccHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCeeeecCCCC
Confidence            456778888999999999999 799996  68999999999999986421                  1223333332 2


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeee
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF  427 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~  427 (533)
                      ..+.+.+|+..+.+...+.  .++++|+|||++|+|+..++|+|++++|||++++.||++|+.++.+.|+|+|||..+.|
T Consensus        83 ~I~idqIR~l~~~~~~~p~--~~~~kV~II~~ad~m~~~AaNaLLKtLEEPp~~t~~iL~t~~~~~lLpTI~SRcq~i~f  160 (290)
T PRK07276         83 VIKTDTIRELVKNFSQSGY--EGKQQVFIIKDADKMHVNAANSLLKVIEEPQSEIYIFLLTNDENKVLPTIKSRTQIFHF  160 (290)
T ss_pred             cCCHHHHHHHHHHHhhCcc--cCCcEEEEeehhhhcCHHHHHHHHHHhcCCCCCeEEEEEECChhhCchHHHHcceeeeC
Confidence            2467889988777765543  46789999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHhhcC
Q psy4285         428 GPLDSSLIMSRLDYD  442 (533)
Q Consensus       428 ~~~~~~~~~~~l~~~  442 (533)
                      .+ +.+++.+++...
T Consensus       161 ~~-~~~~~~~~L~~~  174 (290)
T PRK07276        161 PK-NEAYLIQLLEQK  174 (290)
T ss_pred             CC-cHHHHHHHHHHc
Confidence            76 788888887654

>PRK04195 replication factor C large subunit; Provisional

Probab=99.75  E-value=9.9e-17  Score=167.54  Aligned_cols=146  Identities=26%  Similarity=0.380  Sum_probs=116.7

Q ss_pred             hchhhhhhhcccccc---cC-CCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhc
Q psy4285         289 ESMDLCYKINRFIDE---NE-LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAST  364 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~---~~-~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  364 (533)
                      +++.....+..|+..   +. .++++|+|||||||||+|+++|+.+      +..++++++++.+....++..+......
T Consensus        18 g~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el------~~~~ielnasd~r~~~~i~~~i~~~~~~   91 (482)
T PRK04195         18 GNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDY------GWEVIELNASDQRTADVIERVAGEAATS   91 (482)
T ss_pred             CCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHc------CCCEEEEcccccccHHHHHHHHHHhhcc
Confidence            455555555555543   22 3459999999999999999999998      6678999999888777777777666554


Q ss_pred             ccCCCCCcEEEEEeCCCCCCH----HHHHHHHHHHHhcCCCcEEEEEeCCCCCCCh-hhhccceeeeecCCCHHHHHHHh
Q psy4285         365 KTMHKSSYKLIILDEADAMTN----DAQNALRRIIEKFTTNVRFCIICNYLSKIPP-AIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       365 ~~~~~~~~~vliiDE~d~l~~----~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~-~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ........++|||||+|.+..    ...++|+++++.  .+..+|++||.+..+.+ ++++||..+.|.+++.+++..++
T Consensus        92 ~sl~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~--~~~~iIli~n~~~~~~~k~Lrsr~~~I~f~~~~~~~i~~~L  169 (482)
T PRK04195         92 GSLFGARRKLILLDEVDGIHGNEDRGGARAILELIKK--AKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVL  169 (482)
T ss_pred             CcccCCCCeEEEEecCcccccccchhHHHHHHHHHHc--CCCCEEEeccCccccchhhHhccceEEEecCCCHHHHHHHH
Confidence            443323678999999999976    567889999984  44678999999888887 89999999999999999999999


Q ss_pred             hcC
Q psy4285         440 DYD  442 (533)
Q Consensus       440 ~~~  442 (533)
                      ..+
T Consensus       170 ~~i  172 (482)
T PRK04195        170 KRI  172 (482)
T ss_pred             HHH
Confidence            886

>KOG0735|consensus

Probab=99.75  E-value=1.1e-16  Score=162.56  Aligned_cols=148  Identities=20%  Similarity=0.243  Sum_probs=109.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      ++|+|||||||||.+|.++|...      +..++.+.+++.      .++..+|..+....      ..+++|||+||+|
T Consensus       703 giLLyGppGcGKT~la~a~a~~~------~~~fisvKGPElL~KyIGaSEq~vR~lF~rA~------~a~PCiLFFDEfd  770 (952)
T KOG0735|consen  703 GILLYGPPGCGKTLLASAIASNS------NLRFISVKGPELLSKYIGASEQNVRDLFERAQ------SAKPCILFFDEFD  770 (952)
T ss_pred             ceEEECCCCCcHHHHHHHHHhhC------CeeEEEecCHHHHHHHhcccHHHHHHHHHHhh------ccCCeEEEecccc
Confidence            49999999999999999999987      778888888763      34455666544432      2578999999999


Q ss_pred             CCCH-----------HHHHHHHHHHH--hcCCCcEEEEEeCCCCCCChhhhc--cceeeee-cCCCHHHHHHHhhcC---
Q psy4285         382 AMTN-----------DAQNALRRIIE--KFTTNVRFCIICNYLSKIPPAIQS--RCTRFRF-GPLDSSLIMSRLDYD---  442 (533)
Q Consensus       382 ~l~~-----------~~~~~Ll~~le--~~~~~~~~I~~~n~~~~l~~~l~s--R~~~i~~-~~~~~~~~~~~l~~~---  442 (533)
                      .+.+           ...|.|+..|+  |.-.++.++.+|.+++.+||+|++  |++...+ +.|++.+..+++..+   
T Consensus       771 SiAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s  850 (952)
T KOG0735|consen  771 SIAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGVYILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSNS  850 (952)
T ss_pred             ccCcccCCCCCCchHHHHHHHHHhhccccccceEEEEEecCCccccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhhc
Confidence            9965           45688888887  345678889999999999999999  8876555 456666666666655   


Q ss_pred             -----HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHH
Q psy4285         443 -----DISFFNIIIWYIKIQEIKIEKGLALTDILTEISL  476 (533)
Q Consensus       443 -----~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~  476 (533)
                           ..++.-       +..  .+.|+++.|+-.-+.+
T Consensus       851 ~~~~~~vdl~~-------~a~--~T~g~tgADlq~ll~~  880 (952)
T KOG0735|consen  851 LLKDTDVDLEC-------LAQ--KTDGFTGADLQSLLYN  880 (952)
T ss_pred             cCCccccchHH-------Hhh--hcCCCchhhHHHHHHH
Confidence                 122222       222  6789999998655544

>KOG0736|consensus

Probab=99.74  E-value=3.1e-16  Score=160.76  Aligned_cols=113  Identities=22%  Similarity=0.294  Sum_probs=87.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+|||||||||||.+|+|+|.++      .-.|+.+.+++.      .++..+|+.+.+..      .+.++|||+||+|
T Consensus       707 GILLYGPPGTGKTLlAKAVATEc------sL~FlSVKGPELLNMYVGqSE~NVR~VFerAR------~A~PCVIFFDELD  774 (953)
T KOG0736|consen  707 GILLYGPPGTGKTLLAKAVATEC------SLNFLSVKGPELLNMYVGQSEENVREVFERAR------SAAPCVIFFDELD  774 (953)
T ss_pred             eeEEECCCCCchHHHHHHHHhhc------eeeEEeecCHHHHHHHhcchHHHHHHHHHHhh------ccCCeEEEecccc
Confidence            49999999999999999999998      677888887763      34556666544432      2578999999999


Q ss_pred             CCCHH-------------HHHHHHHHHHh----cCCCcEEEEEeCCCCCCChhhhc--cceeeeecCCCH
Q psy4285         382 AMTND-------------AQNALRRIIEK----FTTNVRFCIICNYLSKIPPAIQS--RCTRFRFGPLDS  432 (533)
Q Consensus       382 ~l~~~-------------~~~~Ll~~le~----~~~~~~~I~~~n~~~~l~~~l~s--R~~~i~~~~~~~  432 (533)
                      .+.+.             ..+.|+.-|+.    ....+.+|.+||+|+-+||+|++  ||+++.+-.+++
T Consensus       775 SlAP~RG~sGDSGGVMDRVVSQLLAELDgls~~~s~~VFViGATNRPDLLDpALLRPGRFDKLvyvG~~~  844 (953)
T KOG0736|consen  775 SLAPNRGRSGDSGGVMDRVVSQLLAELDGLSDSSSQDVFVIGATNRPDLLDPALLRPGRFDKLVYVGPNE  844 (953)
T ss_pred             ccCccCCCCCCccccHHHHHHHHHHHhhcccCCCCCceEEEecCCCccccChhhcCCCccceeEEecCCc
Confidence            99763             34556666664    34568889999999999999999  998777655543

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.72  E-value=2.3e-16  Score=173.42  Aligned_cols=154  Identities=23%  Similarity=0.303  Sum_probs=107.7

Q ss_pred             HHHHHHhhhchhhhhhhcccccc-------cCCC--ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch
Q psy4285         281 NILRWLLNESMDLCYKINRFIDE-------NELP--HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI  351 (533)
Q Consensus       281 ~~l~~~~~~~~~~~~~l~~~~~~-------~~~~--~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~  351 (533)
                      ..+...+.||+..+..+...+..       ...|  .++|+||||||||.+|+++|+.+++.   ...++.++.++....
T Consensus       562 ~~L~~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~---~~~~~~~dmse~~~~  638 (852)
T TIGR03345       562 DRLAERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGG---EQNLITINMSEFQEA  638 (852)
T ss_pred             HHhcCeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhCC---CcceEEEeHHHhhhh
Confidence            33444457777776666554432       2223  38999999999999999999998654   235555554432211


Q ss_pred             hHHHH---------------HHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcC-----------CCcEEE
Q psy4285         352 GIVRD---------------QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT-----------TNVRFC  405 (533)
Q Consensus       352 ~~~~~---------------~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~-----------~~~~~I  405 (533)
                      ..+..               .+.....     ..+++||+|||++++.++.++.|++++++..           .++.||
T Consensus       639 ~~~~~l~g~~~gyvg~~~~g~L~~~v~-----~~p~svvllDEieka~~~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI  713 (852)
T TIGR03345       639 HTVSRLKGSPPGYVGYGEGGVLTEAVR-----RKPYSVVLLDEVEKAHPDVLELFYQVFDKGVMEDGEGREIDFKNTVIL  713 (852)
T ss_pred             hhhccccCCCCCcccccccchHHHHHH-----hCCCcEEEEechhhcCHHHHHHHHHHhhcceeecCCCcEEeccccEEE
Confidence            11111               1111111     1356899999999999999999999999764           778999


Q ss_pred             EEeCCCC-----------------------------CCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         406 IICNYLS-----------------------------KIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       406 ~~~n~~~-----------------------------~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +|||...                             .+.|++++|+..+.|.|++.+++.+++...
T Consensus       714 ~TSNlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEflnRi~iI~F~pLs~e~l~~Iv~~~  779 (852)
T TIGR03345       714 LTSNAGSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLGRMTVIPYLPLDDDVLAAIVRLK  779 (852)
T ss_pred             EeCCCchHHHHHhccCcccCcchHHHHHHHHHHHHHhccHHHhcceeEEEeCCCCHHHHHHHHHHH
Confidence            9998411                             267889999999999999999999888765

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.

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

Probab=99.72  E-value=1.9e-16  Score=145.22  Aligned_cols=141  Identities=16%  Similarity=0.220  Sum_probs=111.5

Q ss_pred             hhchhhhhhhcccccc-----cCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHH
Q psy4285         288 NESMDLCYKINRFIDE-----NELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFA  362 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~-----~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (533)
                      .||+++.+++.-+++.     ....|+||+||||.||||+|..+|+++      +..+...+++-......+...+... 
T Consensus        29 iGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Em------gvn~k~tsGp~leK~gDlaaiLt~L-  101 (332)
T COG2255          29 IGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANEL------GVNLKITSGPALEKPGDLAAILTNL-  101 (332)
T ss_pred             cChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHh------cCCeEecccccccChhhHHHHHhcC-
Confidence            4666666666544432     234689999999999999999999999      6666666666655555555544332 


Q ss_pred             hcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcC------------------CCcEEEEEeCCCCCCChhhhccc-e
Q psy4285         363 STKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT------------------TNVRFCIICNYLSKIPPAIQSRC-T  423 (533)
Q Consensus       363 ~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~------------------~~~~~I~~~n~~~~l~~~l~sR~-~  423 (533)
                             ...+||||||++++++...+.|+.+||.+.                  +...+|.+|.+...+..+|++|| .
T Consensus       102 -------e~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTLIGATTr~G~lt~PLrdRFGi  174 (332)
T COG2255         102 -------EEGDVLFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTLIGATTRAGMLTNPLRDRFGI  174 (332)
T ss_pred             -------CcCCeEEEehhhhcChhHHHHhhhhhhheeEEEEEccCCccceEeccCCCeeEeeeccccccccchhHHhcCC
Confidence                   467899999999999999999999999641                  33568888899999999999999 5


Q ss_pred             eeeecCCCHHHHHHHhhcC
Q psy4285         424 RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 ~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..++..|+++++..++.+-
T Consensus       175 ~~rlefY~~~eL~~Iv~r~  193 (332)
T COG2255         175 IQRLEFYTVEELEEIVKRS  193 (332)
T ss_pred             eeeeecCCHHHHHHHHHHH
Confidence            8889999999999999886

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.71  E-value=4.9e-16  Score=171.85  Aligned_cols=153  Identities=21%  Similarity=0.269  Sum_probs=107.9

Q ss_pred             HHHHHhhhchhhhhhhccccccc-------CCC--ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchh
Q psy4285         282 ILRWLLNESMDLCYKINRFIDEN-------ELP--HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIG  352 (533)
Q Consensus       282 ~l~~~~~~~~~~~~~l~~~~~~~-------~~~--~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~  352 (533)
                      .+...+.||++++..+...+...       ..|  .++|+||||||||++|+++|+.+++..   ..++.++.++.....
T Consensus       506 ~L~~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~---~~~~~~d~s~~~~~~  582 (821)
T CHL00095        506 TLHKRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGSE---DAMIRLDMSEYMEKH  582 (821)
T ss_pred             HhcCcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCc---cceEEEEchhccccc
Confidence            33445578888888776665422       112  379999999999999999999997752   355566554432211


Q ss_pred             HHHHH---------------HHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEE
Q psy4285         353 IVRDQ---------------IFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF-----------TTNVRFCI  406 (533)
Q Consensus       353 ~~~~~---------------~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~  406 (533)
                      .+...               +.....     ..+++|++|||+|++.++.++.|++++|++           ..++.||+
T Consensus       583 ~~~~l~g~~~gyvg~~~~~~l~~~~~-----~~p~~VvllDeieka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~  657 (821)
T CHL00095        583 TVSKLIGSPPGYVGYNEGGQLTEAVR-----KKPYTVVLFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIM  657 (821)
T ss_pred             cHHHhcCCCCcccCcCccchHHHHHH-----hCCCeEEEECChhhCCHHHHHHHHHHhccCceecCCCcEEecCceEEEE
Confidence            11111               111111     135689999999999999999999999974           36788999


Q ss_pred             EeCCCCC-------------------------------------CChhhhccc-eeeeecCCCHHHHHHHhhcC
Q psy4285         407 ICNYLSK-------------------------------------IPPAIQSRC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       407 ~~n~~~~-------------------------------------l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      |||....                                     +.|.+++|+ ..+.|.|++.+++.+++...
T Consensus       658 Tsn~g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~peflnRid~ii~F~pL~~~~l~~Iv~~~  731 (821)
T CHL00095        658 TSNLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLNRLDEIIVFRQLTKNDVWEIAEIM  731 (821)
T ss_pred             eCCcchHHHHhhccccCCcccccccccccHHHHHHHHHHHHHHhcCHHHhccCCeEEEeCCCCHHHHHHHHHHH
Confidence            9874311                                     346788898 68999999999998888665

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.70  E-value=4.3e-17  Score=170.30  Aligned_cols=102  Identities=24%  Similarity=0.433  Sum_probs=94.4

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||||+.+++|||+||++++|++||+|||+.|+|++++.++|.++|++|+.+|++.++++.+..|++.++||+|+|+|+|+
T Consensus       143 LEEPP~~v~FILaTtd~~KIp~TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI~id~eAL~lIA~~A~GsmRdALsLLd  222 (830)
T PRK07003        143 LEEPPPHVKFILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERILGEERIAFEPQALRLLARAAQGSMRDALSLTD  222 (830)
T ss_pred             HHhcCCCeEEEEEECChhhccchhhhheEEEecCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHhCCCCcchhhHHhhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVSR  102 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~  102 (533)
                      ++.....+.|+.+.|..+++..
T Consensus       223 QAia~~~~~It~~~V~~~LG~~  244 (830)
T PRK07003        223 QAIAYSANEVTETAVSGMLGAL  244 (830)
T ss_pred             HHHHhccCCcCHHHHHHHhCCC
Confidence            8776555679998887766643

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=99.70  E-value=4.5e-15  Score=143.35  Aligned_cols=149  Identities=19%  Similarity=0.240  Sum_probs=118.4

Q ss_pred             hhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccc-----cCc--ceEEecC-CCCCchhHHHHHHHHHHh
Q psy4285         293 LCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQ-----FNA--MVLELNA-SDDRGIGIVRDQIFQFAS  363 (533)
Q Consensus       293 ~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~-----~~~--~~~~~~~-~~~~~~~~~~~~~~~~~~  363 (533)
                      +...+...++.++.+| .||+|+.|.||+++++.+++.+.|...     -.+  .+..++. ....+.+.+++....+..
T Consensus         4 ~~~~l~~~i~~~~l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~i~vd~Ir~l~~~~~~   83 (299)
T PRK07132          4 WIKFLDNSATQNKISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKDLSKSEFLSAINKLYF   83 (299)
T ss_pred             HHHHHHHHHHhCCCCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCcCCHHHHHHHHHHhcc
Confidence            3456667778888888 689999999999999999999988431     011  2333431 122456677776665533


Q ss_pred             cccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         364 TKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       364 ~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+. ..++++|+|||++++++..++|+|++.||+||+++.+|++|+.+..+.|+++|||..+.|.+++++++..+|...
T Consensus        84 ~~~-~~~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~f~~l~~~~l~~~l~~~  161 (299)
T PRK07132         84 SSF-VQSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPDQQKILAKLLSK  161 (299)
T ss_pred             CCc-ccCCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEEECCCCCHHHHHHHHHHc
Confidence            321 125889999999999999999999999999999999999999999999999999999999999999999888763

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.70  E-value=6.7e-17  Score=163.15  Aligned_cols=101  Identities=21%  Similarity=0.313  Sum_probs=94.0

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||.+++|||+|+.+++|+|||+|||+.|+|++++.+++.++|+++|.++++.++++++..|++.|+||+|+|+++||
T Consensus       145 LEEPp~~viFILaTte~~kI~~TI~SRCq~~~f~~ls~~~i~~~L~~i~~~Egi~~e~eAL~~Ia~~S~Gd~RdAL~lLe  224 (484)
T PRK14956        145 LEEPPAHIVFILATTEFHKIPETILSRCQDFIFKKVPLSVLQDYSEKLCKIENVQYDQEGLFWIAKKGDGSVRDMLSFME  224 (484)
T ss_pred             hhcCCCceEEEeecCChhhccHHHHhhhheeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCChHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVS  101 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~  101 (533)
                      .+.......|+.+.|.++++.
T Consensus       225 q~i~~~~~~it~~~V~~~lg~  245 (484)
T PRK14956        225 QAIVFTDSKLTGVKIRKMIGY  245 (484)
T ss_pred             HHHHhCCCCcCHHHHHHHhCC
Confidence            877655557999988776653

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

Probab=99.70  E-value=9.2e-16  Score=165.46  Aligned_cols=209  Identities=21%  Similarity=0.274  Sum_probs=132.1

Q ss_pred             CCCChhHHHHHHHhccCch------HHhhcHHHHHHhhcC--------CCCCccc----cccccCCCCHH----------
Q psy4285         226 LPVTPDGKKAIIDLSDGDM------RKVLNILQSAATAHA--------DEVNEDT----VYNSVGYPTKT----------  277 (533)
Q Consensus       226 ~~~~~~~l~~l~~~s~~di------~~~L~~L~~~~~~~~--------~~~~~~~----~~~~~~~~~~~----------  277 (533)
                      +.++++++...++++...+      ..+++.|...+...+        ..++.+.    +-...|.|...          
T Consensus       371 v~i~~~al~~a~~ls~ryi~~r~lPdKaidlldea~a~~~~~~~~~~~~~v~~~~i~~v~~~~tgip~~~~~~~~~~~l~  450 (758)
T PRK11034        371 VRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPVSKRKKTVNVADIESVVARIARIPEKSVSQSDRDTLK  450 (758)
T ss_pred             CCcCHHHHHHHHHHhhccccCccChHHHHHHHHHHHHhhccCcccccccccChhhHHHHHHHHhCCChhhhhhhHHHHHH
Confidence            4667778877777665444      244555544432111        1112111    33445555321          


Q ss_pred             HHHHHHHHHhhhchhhhhhhccccccc--------CC-CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC
Q psy4285         278 EITNILRWLLNESMDLCYKINRFIDEN--------EL-PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD  348 (533)
Q Consensus       278 ~~~~~l~~~~~~~~~~~~~l~~~~~~~--------~~-~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~  348 (533)
                      .+...+...+.||+++++.+...+...        ++ .+++|+||||||||++|+++|+.+      +..++.+++++.
T Consensus       451 ~l~~~L~~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l------~~~~i~id~se~  524 (758)
T PRK11034        451 NLGDRLKMLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL------GIELLRFDMSEY  524 (758)
T ss_pred             HHHHHhcceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHh------CCCcEEeechhh
Confidence            122223334578888888777666521        11 248999999999999999999998      445666666554


Q ss_pred             CchhHHHHHHHH------------HHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcC-----------CCcEEE
Q psy4285         349 RGIGIVRDQIFQ------------FASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT-----------TNVRFC  405 (533)
Q Consensus       349 ~~~~~~~~~~~~------------~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~-----------~~~~~I  405 (533)
                      .....+...++.            +...  ....+++|++|||+|++.++.++.|+++|++..           .++.||
T Consensus       525 ~~~~~~~~LiG~~~gyvg~~~~g~L~~~--v~~~p~sVlllDEieka~~~v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI  602 (758)
T PRK11034        525 MERHTVSRLIGAPPGYVGFDQGGLLTDA--VIKHPHAVLLLDEIEKAHPDVFNLLLQVMDNGTLTDNNGRKADFRNVVLV  602 (758)
T ss_pred             cccccHHHHcCCCCCcccccccchHHHH--HHhCCCcEEEeccHhhhhHHHHHHHHHHHhcCeeecCCCceecCCCcEEE
Confidence            322222222110            0000  001356899999999999999999999998641           467799


Q ss_pred             EEeCCC-------------------------CCCChhhhccce-eeeecCCCHHHHHHHhhcC
Q psy4285         406 IICNYL-------------------------SKIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       406 ~~~n~~-------------------------~~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                      +|||.-                         ..+.|.++.|++ .+.|.|++.+++..++...
T Consensus       603 ~TsN~g~~~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~Rid~ii~f~~L~~~~l~~I~~~~  665 (758)
T PRK11034        603 MTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKF  665 (758)
T ss_pred             EeCCcCHHHHhhcccCcccchhhHHHHHHHHHhcCHHHHccCCEEEEcCCCCHHHHHHHHHHH
Confidence            999832                         136789999995 8999999999998887654

>KOG0733|consensus

Probab=99.69  E-value=1.8e-16  Score=158.68  Aligned_cols=147  Identities=22%  Similarity=0.291  Sum_probs=113.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC------CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD------DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+|||||||||||.+|+++|.++      +.+++.+++++      +.+.+.+++.+....+      ..++|+||||+|
T Consensus       225 GvLlHGPPGCGKT~lA~AiAgel------~vPf~~isApeivSGvSGESEkkiRelF~~A~~------~aPcivFiDeID  292 (802)
T KOG0733|consen  225 GVLLHGPPGCGKTSLANAIAGEL------GVPFLSISAPEIVSGVSGESEKKIRELFDQAKS------NAPCIVFIDEID  292 (802)
T ss_pred             ceeeeCCCCccHHHHHHHHhhhc------CCceEeecchhhhcccCcccHHHHHHHHHHHhc------cCCeEEEeeccc
Confidence            39999999999999999999998      88889888765      3456677777665443      357999999999


Q ss_pred             CCCHHH-----------HHHHHHHHHhc------CCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhc
Q psy4285         382 AMTNDA-----------QNALRRIIEKF------TTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       382 ~l~~~~-----------~~~Ll~~le~~------~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~  441 (533)
                      .+++..           ...|+..|++.      ...+.+|.+||+|+.+||+|++  || ..|.+.-|+..+..++|..
T Consensus       293 AI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~  372 (802)
T KOG0733|consen  293 AITPKREEAQREMERRIVAQLLTSMDELSNEKTKGDPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETAREEILRI  372 (802)
T ss_pred             ccccchhhHHHHHHHHHHHHHHHhhhcccccccCCCCeEEEecCCCCcccCHHHhccccccceeeecCCchHHHHHHHHH
Confidence            998643           24477777753      2457899999999999999998  89 4899999999998888887


Q ss_pred             C--------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285         442 D--------DISFFNIIIWYIKIQEIKIEKGLALTDILTEIS  475 (533)
Q Consensus       442 ~--------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~  475 (533)
                      +        +-+..++..         .+.||.+.|+..-+.
T Consensus       373 ~~~~lrl~g~~d~~qlA~---------lTPGfVGADL~AL~~  405 (802)
T KOG0733|consen  373 ICRGLRLSGDFDFKQLAK---------LTPGFVGADLMALCR  405 (802)
T ss_pred             HHhhCCCCCCcCHHHHHh---------cCCCccchhHHHHHH
Confidence            6        223344444         677888887654433

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.69  E-value=2.8e-15  Score=153.66  Aligned_cols=144  Identities=25%  Similarity=0.338  Sum_probs=111.5

Q ss_pred             hhchhhhhh---hcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhc
Q psy4285         288 NESMDLCYK---INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAST  364 (533)
Q Consensus       288 ~~~~~~~~~---l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  364 (533)
                      .|+++.+..   +..++..+..++++|+|||||||||+|+.+++.+      +..+..+++.. .+.+.+++.+......
T Consensus        15 vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~------~~~~~~l~a~~-~~~~~ir~ii~~~~~~   87 (413)
T PRK13342         15 VGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGAT------DAPFEALSAVT-SGVKDLREVIEEARQR   87 (413)
T ss_pred             cCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHh------CCCEEEEeccc-ccHHHHHHHHHHHHHh
Confidence            456666555   7777888887889999999999999999999987      55677777765 3455566665554332


Q ss_pred             ccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEe--CCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         365 KTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIIC--NYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       365 ~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~--n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..  .+...+|||||+|+++...++.|+..+++.  .+.+|.+|  |....++++++|||..+.|.+++.+++..++.+.
T Consensus        88 ~~--~g~~~vL~IDEi~~l~~~~q~~LL~~le~~--~iilI~att~n~~~~l~~aL~SR~~~~~~~~ls~e~i~~lL~~~  163 (413)
T PRK13342         88 RS--AGRRTILFIDEIHRFNKAQQDALLPHVEDG--TITLIGATTENPSFEVNPALLSRAQVFELKPLSEEDIEQLLKRA  163 (413)
T ss_pred             hh--cCCceEEEEechhhhCHHHHHHHHHHhhcC--cEEEEEeCCCChhhhccHHHhccceeeEeCCCCHHHHHHHHHHH
Confidence            21  246789999999999999999999999863  35555554  4455899999999999999999999998888763

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=99.69  E-value=2.2e-16  Score=162.71  Aligned_cols=163  Identities=19%  Similarity=0.296  Sum_probs=124.8

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+||++++|||+|+.+++|+|||+|||+.|+|++++.+++..||.+++.++|+.++++++..+++.++||+|+|++.|+
T Consensus       141 LEEpp~~t~FIL~ttd~~kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi~i~~~Al~~Ia~~s~GdlR~alnlLd  220 (535)
T PRK08451        141 LEEPPSYVKFILATTDPLKLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGVSYEPEALEILARSGNGSLRDTLTLLD  220 (535)
T ss_pred             HhhcCCceEEEEEECChhhCchHHHhhceeEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhccccc-----------hhH----HHHHhc--hHHHHh----hcC---------CChhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRVEKYR-----------PST----LDELVS--HQDIIS----TIE---------IPESM  130 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~ek~~-----------~~~----l~~lls--~~~~l~----~l~---------~~~~~  130 (533)
                      .+.....+.||.+.+.++++.......           ...    +.++.+  ...++.    .++         .....
T Consensus       221 qai~~~~~~It~~~V~~~lg~~~~~~I~~li~ai~~~d~~~a~~~l~~L~g~~~~~~l~~l~~~l~~~~~~~~~~~~l~~  300 (535)
T PRK08451        221 QAIIYCKNAITESKVADMLGLLDPSKLEDFFQAILNQDKEKLFELLKELEDYEAEMVLDEMMLFLKEKFLSKDSEFSILL  300 (535)
T ss_pred             HHHHhcCCCCCHHHHHHHhCCCCHHHHHHHHHHHHhcCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhcccccccHHH
Confidence            887755557888887766553221111           111    111110  001111    010         11122


Q ss_pred             HHHHHhhccCccccccCCCChhhHHHHHHHHHh
Q psy4285         131 LVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFN  163 (533)
Q Consensus       131 ~~~~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~  163 (533)
                      +.+.+..++.+...+..|.++.+++++++.++.
T Consensus       301 l~r~~riL~~~k~~l~~g~~~~i~l~~~~~~~~  333 (535)
T PRK08451        301 YERFFRILSSAKSLLKEGADDGFVLLLMLFKMK  333 (535)
T ss_pred             HHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            345556677888899999999999999998876

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=99.69  E-value=9.5e-16  Score=142.47  Aligned_cols=125  Identities=14%  Similarity=0.119  Sum_probs=100.9

Q ss_pred             CCCc-eeEeCCCCCChHHHHHHHHHHHccccccC----------------cceEEecC-CCCCchhHHHHHHHHHHhccc
Q psy4285         305 ELPH-LLFYGPPGTGKTTTILACARKLYTKAQFN----------------AMVLELNA-SDDRGIGIVRDQIFQFASTKT  366 (533)
Q Consensus       305 ~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~~----------------~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  366 (533)
                      ..|| +||+||+|+||..+|.++|+.+.|....+                ..+..+.+ ....+.+.+++..+.+.... 
T Consensus         5 ~~~HA~Lf~G~~G~G~~~lA~~~A~~llC~~~~~~Cg~C~sC~~i~~~~HPDl~~i~p~~~~I~id~ir~l~~~l~~~s-   83 (261)
T PRK05818          5 NKTHPLLLIERKGSFLKPFLYEYLTSIVCTKANGFCKTCESCLKILNGKYNDFYLIFDQKNPIKKEDALSIINKLNRPS-   83 (261)
T ss_pred             CCCcceeeeCCCCCcHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHhcCCCCCEEEecCCcccCCHHHHHHHHHHHccCc-
Confidence            3456 89999999999999999999998864211                12222222 22356778888877765332 


Q ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCC
Q psy4285         367 MHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPL  430 (533)
Q Consensus       367 ~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~  430 (533)
                      ...++++|+|||++|+|+.+++|+|++++||||+++.||++|+.++.++|+++|||..+.|+++
T Consensus        84 ~e~~~~KV~II~~ae~m~~~AaNaLLK~LEEPp~~t~fiLit~~~~~lLpTI~SRCq~~~~~~~  147 (261)
T PRK05818         84 VESNGKKIYIIYGIEKLNKQSANSLLKLIEEPPKNTYGIFTTRNENNILNTILSRCVQYVVLSK  147 (261)
T ss_pred             hhcCCCEEEEeccHhhhCHHHHHHHHHhhcCCCCCeEEEEEECChHhCchHhhhheeeeecCCh
Confidence            1124689999999999999999999999999999999999999999999999999999999887

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

Probab=99.69  E-value=1.2e-16  Score=162.50  Aligned_cols=108  Identities=25%  Similarity=0.385  Sum_probs=100.1

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      +||||.+++|||+|+.+++|.+||+||||.|.|++++.++|...|..|+.+|++.++++++..+++.++|++|.++++|+
T Consensus       143 LEEPP~hV~FIlATTe~~Kip~TIlSRcq~f~fkri~~~~I~~~L~~i~~~E~I~~e~~aL~~ia~~a~Gs~RDalslLD  222 (515)
T COG2812         143 LEEPPSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAAILDKEGINIEEDALSLIARAAEGSLRDALSLLD  222 (515)
T ss_pred             cccCccCeEEEEecCCcCcCchhhhhccccccccCCCHHHHHHHHHHHHHhcCCccCHHHHHHHHHHcCCChhhHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhccccch
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRVEKYRP  108 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~ek~~~  108 (533)
                      ++....++.||.+.+.+++|.....+..
T Consensus       223 q~i~~~~~~It~~~v~~~lG~~~~~~~~  250 (515)
T COG2812         223 QAIAFGEGEITLESVRDMLGLTDIEKLL  250 (515)
T ss_pred             HHHHccCCcccHHHHHHHhCCCCHHHHH
Confidence            9988766779999998888765444333

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

Probab=99.68  E-value=5.4e-16  Score=166.45  Aligned_cols=145  Identities=23%  Similarity=0.283  Sum_probs=106.7

Q ss_pred             hhchhhh---hhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhc
Q psy4285         288 NESMDLC---YKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAST  364 (533)
Q Consensus       288 ~~~~~~~---~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  364 (533)
                      .|+++.+   ..+.+++..+..++++|+|||||||||+|+++++.+      ...++.+++.. .+...+++.+......
T Consensus        31 vGQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~------~~~f~~lna~~-~~i~dir~~i~~a~~~  103 (725)
T PRK13341         31 VGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHT------RAHFSSLNAVL-AGVKDLRAEVDRAKER  103 (725)
T ss_pred             cCcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHh------cCcceeehhhh-hhhHHHHHHHHHHHHH
Confidence            3566655   356777788888899999999999999999999986      44556666654 3334444444433221


Q ss_pred             ccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEe--CCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         365 KTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIIC--NYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       365 ~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~--n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ... .....+|||||+|+++...+++|+..+++.  .+.+|.+|  |....++++++|||..+.|.+++.+++..++.+.
T Consensus       104 l~~-~~~~~IL~IDEIh~Ln~~qQdaLL~~lE~g--~IiLI~aTTenp~~~l~~aL~SR~~v~~l~pLs~edi~~IL~~~  180 (725)
T PRK13341        104 LER-HGKRTILFIDEVHRFNKAQQDALLPWVENG--TITLIGATTENPYFEVNKALVSRSRLFRLKSLSDEDLHQLLKRA  180 (725)
T ss_pred             hhh-cCCceEEEEeChhhCCHHHHHHHHHHhcCc--eEEEEEecCCChHhhhhhHhhccccceecCCCCHHHHHHHHHHH
Confidence            111 135679999999999999999999999752  34445444  4445789999999999999999999988888664

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.67  E-value=2.7e-15  Score=154.28  Aligned_cols=151  Identities=17%  Similarity=0.132  Sum_probs=110.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+||+||||||||++|+++|+++      +.+++.++.+..      .+...+++.+.....      ..++||+|||+|
T Consensus       261 GILL~GPpGTGKTllAkaiA~e~------~~~~~~l~~~~l~~~~vGese~~l~~~f~~A~~------~~P~IL~IDEID  328 (489)
T CHL00195        261 GLLLVGIQGTGKSLTAKAIANDW------QLPLLRLDVGKLFGGIVGESESRMRQMIRIAEA------LSPCILWIDEID  328 (489)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHh------CCCEEEEEhHHhcccccChHHHHHHHHHHHHHh------cCCcEEEehhhh
Confidence            49999999999999999999998      667777776432      233445554433221      356899999999


Q ss_pred             CCCHH------------HHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC----
Q psy4285         382 AMTND------------AQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD----  442 (533)
Q Consensus       382 ~l~~~------------~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~----  442 (533)
                      .+...            ..+.|+..|++....+.+|+|||.++.+|+++++  ||+ .+.++.|+.++..+++...    
T Consensus       329 ~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~  408 (489)
T CHL00195        329 KAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKF  408 (489)
T ss_pred             hhhccccCCCCchHHHHHHHHHHHHHhcCCCceEEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhc
Confidence            87431            2345677777766778899999999999999987  895 6777888888888887755    


Q ss_pred             -H-----HHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Q psy4285         443 -D-----ISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVH  479 (533)
Q Consensus       443 -~-----~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~  479 (533)
                       |     .++..+.+         .+.||++.||...+.++..
T Consensus       409 ~~~~~~~~dl~~La~---------~T~GfSGAdI~~lv~eA~~  442 (489)
T CHL00195        409 RPKSWKKYDIKKLSK---------LSNKFSGAEIEQSIIEAMY  442 (489)
T ss_pred             CCCcccccCHHHHHh---------hcCCCCHHHHHHHHHHHHH
Confidence             1     11222222         6789999999887776654

>KOG0738|consensus

Probab=99.67  E-value=2.8e-16  Score=149.55  Aligned_cols=149  Identities=22%  Similarity=0.255  Sum_probs=106.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+|++||||||||.+|+++|.++      +..|+.++.++..      +++.+|- +...+...     .+.+|||||||
T Consensus       247 gvLm~GPPGTGKTlLAKAvATEc------~tTFFNVSsstltSKwRGeSEKlvRl-LFemARfy-----APStIFiDEID  314 (491)
T KOG0738|consen  247 GVLMVGPPGTGKTLLAKAVATEC------GTTFFNVSSSTLTSKWRGESEKLVRL-LFEMARFY-----APSTIFIDEID  314 (491)
T ss_pred             eeeeeCCCCCcHHHHHHHHHHhh------cCeEEEechhhhhhhhccchHHHHHH-HHHHHHHh-----CCceeehhhHH
Confidence            49999999999999999999998      7788888877642      2333433 33333321     45799999999


Q ss_pred             CCCH------------HHHHHHHHHHHhc------CCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC-
Q psy4285         382 AMTN------------DAQNALRRIIEKF------TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD-  442 (533)
Q Consensus       382 ~l~~------------~~~~~Ll~~le~~------~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~-  442 (533)
                      .+..            ...+.||-.|+.-      ...+.++.+||.|..||+++++||.+-.+-|+|+.+.+.-|.++ 
T Consensus       315 slcs~RG~s~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN~PWdiDEAlrRRlEKRIyIPLP~~~~R~~Li~~~  394 (491)
T KOG0738|consen  315 SLCSQRGGSSEHEASRRVKSELLVQMDGVQGTLENSKVVMVLAATNFPWDIDEALRRRLEKRIYIPLPDAEARSALIKIL  394 (491)
T ss_pred             HHHhcCCCccchhHHHHHHHHHHHHhhccccccccceeEEEEeccCCCcchHHHHHHHHhhheeeeCCCHHHHHHHHHHh
Confidence            9843            2356788888732      22356666789999999999999976666666666666666555 


Q ss_pred             --------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 --------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 --------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                              |-.+..+.+         ..+|||+.||...+.++
T Consensus       395 l~~~~~~~~~~~~~lae---------~~eGySGaDI~nvCreA  428 (491)
T KOG0738|consen  395 LRSVELDDPVNLEDLAE---------RSEGYSGADITNVCREA  428 (491)
T ss_pred             hccccCCCCccHHHHHH---------HhcCCChHHHHHHHHHH
Confidence                    333444444         67899999998777654

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.67  E-value=1.8e-16  Score=163.67  Aligned_cols=102  Identities=23%  Similarity=0.386  Sum_probs=93.9

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||||+++++|||+||++++|++||+|||+.|+|++++.+++.++|++++.++++.++++++..|++.++||+|+|+++++
T Consensus       148 LEEPP~~v~FILaTtep~kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~Egi~~d~eAL~~IA~~A~Gs~RdALsLLd  227 (700)
T PRK12323        148 LEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALRLLAQAAQGSMRDALSLTD  227 (700)
T ss_pred             hccCCCCceEEEEeCChHhhhhHHHHHHHhcccCCCChHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHhCCCCcchhhHHhhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVSR  102 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~  102 (533)
                      .+.......|+.+.|.++++..
T Consensus       228 Qaia~~~~~It~~~V~~~LG~~  249 (700)
T PRK12323        228 QAIAYSAGNVSEEAVRGMLGAI  249 (700)
T ss_pred             HHHHhccCCcCHHHHHHHhCCC
Confidence            8765555578888887776643

>KOG0734|consensus

Probab=99.66  E-value=5e-16  Score=153.09  Aligned_cols=179  Identities=20%  Similarity=0.201  Sum_probs=123.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+||+||||||||.+||++|-+.      +.+|+...+++.      .+...+|+++.....      ..++||||||+|
T Consensus       339 GVLLvGPPGTGKTlLARAvAGEA------~VPFF~~sGSEFdEm~VGvGArRVRdLF~aAk~------~APcIIFIDEiD  406 (752)
T KOG0734|consen  339 GVLLVGPPGTGKTLLARAVAGEA------GVPFFYASGSEFDEMFVGVGARRVRDLFAAAKA------RAPCIIFIDEID  406 (752)
T ss_pred             ceEEeCCCCCchhHHHHHhhccc------CCCeEeccccchhhhhhcccHHHHHHHHHHHHh------cCCeEEEEechh
Confidence            39999999999999999999887      888898888863      466778877655432      357999999999


Q ss_pred             CCCHH-----------HHHHHHHHHHhc--CCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC---
Q psy4285         382 AMTND-----------AQNALRRIIEKF--TTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD---  442 (533)
Q Consensus       382 ~l~~~-----------~~~~Ll~~le~~--~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~---  442 (533)
                      .+...           ..|.|+--|+.+  ...+.+|.+||.++.||++|.+  ||+ .+..+.|+..-..++|...   
T Consensus       407 avG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe~LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~k  486 (752)
T KOG0734|consen  407 AVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPEALDKALTRPGRFDRHVTVPLPDVRGRTEILKLYLSK  486 (752)
T ss_pred             hhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChhhhhHHhcCCCccceeEecCCCCcccHHHHHHHHHhc
Confidence            98531           224444445533  4568888899999999999999  995 7777778877777777665   


Q ss_pred             -----HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCCh
Q psy4285         443 -----DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSE  508 (533)
Q Consensus       443 -----~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~  508 (533)
                           .-|..-+..         .+.|+++.|+.+-+..+..+...++.... -+..+.....|+-.|+..
T Consensus       487 i~~~~~VD~~iiAR---------GT~GFsGAdLaNlVNqAAlkAa~dga~~V-tM~~LE~akDrIlMG~ER  547 (752)
T KOG0734|consen  487 IPLDEDVDPKIIAR---------GTPGFSGADLANLVNQAALKAAVDGAEMV-TMKHLEFAKDRILMGPER  547 (752)
T ss_pred             CCcccCCCHhHhcc---------CCCCCchHHHHHHHHHHHHHHHhcCcccc-cHHHHhhhhhheeecccc
Confidence                 112222222         77899999988777665444333332221 123444455566666543

>KOG0727|consensus

Probab=99.63  E-value=4.7e-15  Score=133.29  Aligned_cols=164  Identities=28%  Similarity=0.379  Sum_probs=110.6

Q ss_pred             CCccccccccCCCC--HHHHHHHHHHHhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcc
Q psy4285         262 VNEDTVYNSVGYPT--KTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAM  339 (533)
Q Consensus       262 ~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~  339 (533)
                      ..++..|.+.|...  .+.+.+... +...+.++.+++.    -..+..+|+|||||||||.+++++|+.-      ...
T Consensus       148 ekpdvsy~diggld~qkqeireave-lplt~~~ly~qig----idpprgvllygppg~gktml~kava~~t------~a~  216 (408)
T KOG0727|consen  148 EKPDVSYADIGGLDVQKQEIREAVE-LPLTHADLYKQIG----IDPPRGVLLYGPPGTGKTMLAKAVANHT------TAA  216 (408)
T ss_pred             CCCCccccccccchhhHHHHHHHHh-ccchHHHHHHHhC----CCCCcceEEeCCCCCcHHHHHHHHhhcc------chh
Confidence            35566788888754  334444432 2222333333332    2223349999999999999999999875      678


Q ss_pred             eEEecCCC------CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH-----------HHHHHHHHHHHh-----
Q psy4285         340 VLELNASD------DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN-----------DAQNALRRIIEK-----  397 (533)
Q Consensus       340 ~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~Ll~~le~-----  397 (533)
                      ++.+.+++      +.+...++..++- +.     ++.+.++||||+|.+..           +.|..|+.++..     
T Consensus       217 firvvgsefvqkylgegprmvrdvfrl-ak-----enapsiifideidaiatkrfdaqtgadrevqril~ellnqmdgfd  290 (408)
T KOG0727|consen  217 FIRVVGSEFVQKYLGEGPRMVRDVFRL-AK-----ENAPSIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDGFD  290 (408)
T ss_pred             eeeeccHHHHHHHhccCcHHHHHHHHH-Hh-----ccCCcEEEeehhhhHhhhhccccccccHHHHHHHHHHHHhccCcC
Confidence            88888876      2344445544332 22     24678999999998843           456666666653     


Q ss_pred             cCCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhcC
Q psy4285         398 FTTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       398 ~~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ...|+.+|++||+.+.+||++++  |+ .++.|+-|+..+-+-+...+
T Consensus       291 q~~nvkvimatnradtldpallrpgrldrkiefplpdrrqkrlvf~ti  338 (408)
T KOG0727|consen  291 QTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFSTI  338 (408)
T ss_pred             cccceEEEEecCcccccCHhhcCCccccccccCCCCchhhhhhhHHhh
Confidence            35789999999999999999998  77 48899877766655554444

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.62  E-value=4.8e-15  Score=146.58  Aligned_cols=141  Identities=17%  Similarity=0.255  Sum_probs=102.8

Q ss_pred             hhchhhhhhhccccc-----ccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHH
Q psy4285         288 NESMDLCYKINRFID-----ENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFA  362 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~-----~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (533)
                      .|+++..+.+..++.     .+..++++|+||||||||++|+++|+.+      +..+....++.......+...+... 
T Consensus         7 iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~------~~~~~~~~~~~~~~~~~l~~~l~~~-   79 (305)
T TIGR00635         7 IGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEM------GVNLKITSGPALEKPGDLAAILTNL-   79 (305)
T ss_pred             cCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHh------CCCEEEeccchhcCchhHHHHHHhc-
Confidence            456666666666554     2345579999999999999999999988      3333333333222222333322221 


Q ss_pred             hcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcC------------------CCcEEEEEeCCCCCCChhhhccc-e
Q psy4285         363 STKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT------------------TNVRFCIICNYLSKIPPAIQSRC-T  423 (533)
Q Consensus       363 ~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~------------------~~~~~I~~~n~~~~l~~~l~sR~-~  423 (533)
                             ..+.+|||||++.++...++.|+.++++..                  +...+|.+||.+..++++++||| .
T Consensus        80 -------~~~~vl~iDEi~~l~~~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li~~t~~~~~l~~~l~sR~~~  152 (305)
T TIGR00635        80 -------EEGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPLRDRFGI  152 (305)
T ss_pred             -------ccCCEEEEehHhhhCHHHHHHhhHHHhhhheeeeeccCccccceeecCCCeEEEEecCCccccCHHHHhhcce
Confidence                   245799999999999999999998887432                  23678888899999999999999 4


Q ss_pred             eeeecCCCHHHHHHHhhcC
Q psy4285         424 RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 ~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.|.+++.+++.+++.+.
T Consensus       153 ~~~l~~l~~~e~~~il~~~  171 (305)
T TIGR00635       153 ILRLEFYTVEELAEIVSRS  171 (305)
T ss_pred             EEEeCCCCHHHHHHHHHHH
Confidence            6799999999999999876

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.

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.62  E-value=2.1e-15  Score=158.71  Aligned_cols=101  Identities=24%  Similarity=0.437  Sum_probs=93.7

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+.+++|++||+|||+.|+|++++.+++.++|++++.++++.++++++..|+..|+||+|+|+++++
T Consensus       143 LEEPp~~v~FIL~Tt~~~kLl~TI~SRC~~~~f~~Ls~~ei~~~L~~il~~e~i~~e~~aL~~Ia~~s~Gs~R~Al~lld  222 (647)
T PRK07994        143 LEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRQQLEHILQAEQIPFEPRALQLLARAADGSMRDALSLTD  222 (647)
T ss_pred             HHcCCCCeEEEEecCCccccchHHHhhheEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVS  101 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~  101 (533)
                      .+....+..|+.+.+.++++.
T Consensus       223 qaia~~~~~it~~~v~~~lg~  243 (647)
T PRK07994        223 QAIASGNGQVTTDDVSAMLGT  243 (647)
T ss_pred             HHHHhcCCCcCHHHHHHHHcc
Confidence            887655557888888776654

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.62  E-value=2.1e-14  Score=143.02  Aligned_cols=141  Identities=16%  Similarity=0.220  Sum_probs=102.1

Q ss_pred             hhchhhhhhhccccc-----ccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHH
Q psy4285         288 NESMDLCYKINRFID-----ENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFA  362 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~-----~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (533)
                      .|+++....+..++.     ....++++|+||||||||++|+++|+.+      +..+...+++.......+...+... 
T Consensus        28 vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l------~~~~~~~~~~~~~~~~~l~~~l~~l-  100 (328)
T PRK00080         28 IGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEM------GVNIRITSGPALEKPGDLAAILTNL-  100 (328)
T ss_pred             cCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHh------CCCeEEEecccccChHHHHHHHHhc-
Confidence            355555555544433     2234579999999999999999999998      3334444443322333333332221 


Q ss_pred             hcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcC------------------CCcEEEEEeCCCCCCChhhhccc-e
Q psy4285         363 STKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT------------------TNVRFCIICNYLSKIPPAIQSRC-T  423 (533)
Q Consensus       363 ~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~------------------~~~~~I~~~n~~~~l~~~l~sR~-~  423 (533)
                             ..+++|||||+|.++...++.|+.+++++.                  +...+|++||....++++++||| .
T Consensus       101 -------~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~~~~~l~~~~~~~~~~~~l~~~~li~at~~~~~l~~~L~sRf~~  173 (328)
T PRK00080        101 -------EEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRAGLLTSPLRDRFGI  173 (328)
T ss_pred             -------ccCCEEEEecHhhcchHHHHHHHHHHHhcceeeeeccCccccceeecCCCceEEeecCCcccCCHHHHHhcCe
Confidence                   346799999999999888888888887542                  23678889999999999999999 5


Q ss_pred             eeeecCCCHHHHHHHhhcC
Q psy4285         424 RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 ~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.|.+++.+++.+++.+.
T Consensus       174 ~~~l~~~~~~e~~~il~~~  192 (328)
T PRK00080        174 VQRLEFYTVEELEKIVKRS  192 (328)
T ss_pred             eeecCCCCHHHHHHHHHHH
Confidence            7899999999999999876

>KOG0739|consensus

Probab=99.62  E-value=1.3e-15  Score=140.01  Aligned_cols=144  Identities=22%  Similarity=0.273  Sum_probs=108.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+||||||||||+.+|+++|.+.      +..++.++.++..      +.+.+++++.. +.     +..+.|+||||+|
T Consensus       168 giLLyGPPGTGKSYLAKAVATEA------nSTFFSvSSSDLvSKWmGESEkLVknLFem-AR-----e~kPSIIFiDEiD  235 (439)
T KOG0739|consen  168 GILLYGPPGTGKSYLAKAVATEA------NSTFFSVSSSDLVSKWMGESEKLVKNLFEM-AR-----ENKPSIIFIDEID  235 (439)
T ss_pred             eEEEeCCCCCcHHHHHHHHHhhc------CCceEEeehHHHHHHHhccHHHHHHHHHHH-HH-----hcCCcEEEeehhh
Confidence            39999999999999999999987      6788888887742      33344443322 21     2467899999999


Q ss_pred             CCCHH-----------HHHHHHHHHHh---cCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC-----
Q psy4285         382 AMTND-----------AQNALRRIIEK---FTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD-----  442 (533)
Q Consensus       382 ~l~~~-----------~~~~Ll~~le~---~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~-----  442 (533)
                      .+...           ....|+-.|..   -...+.++.+||-+..||.+|++||..-.+-|+++...+..+.++     
T Consensus       236 slcg~r~enEseasRRIKTEfLVQMqGVG~d~~gvLVLgATNiPw~LDsAIRRRFekRIYIPLPe~~AR~~MF~lhlG~t  315 (439)
T KOG0739|consen  236 SLCGSRSENESEASRRIKTEFLVQMQGVGNDNDGVLVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARARMFKLHLGDT  315 (439)
T ss_pred             hhccCCCCCchHHHHHHHHHHHHhhhccccCCCceEEEecCCCchhHHHHHHHHhhcceeccCCcHHHhhhhheeccCCC
Confidence            88531           12234444442   245677888899999999999999988888899999999998887     


Q ss_pred             -----HHHHHHHHHHHHHHHHHHHhcCCCHHHHHH
Q psy4285         443 -----DISFFNIIIWYIKIQEIKIEKGLALTDILT  472 (533)
Q Consensus       443 -----~~~~~~ll~~~~~l~~l~~~~~~~~~di~~  472 (533)
                           ..+++++..         .+.|||+.||.-
T Consensus       316 p~~LT~~d~~eL~~---------kTeGySGsDisi  341 (439)
T KOG0739|consen  316 PHVLTEQDFKELAR---------KTEGYSGSDISI  341 (439)
T ss_pred             ccccchhhHHHHHh---------hcCCCCcCceEE
Confidence                 566777666         788999988643

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.61  E-value=1.2e-14  Score=139.96  Aligned_cols=133  Identities=18%  Similarity=0.235  Sum_probs=92.0

Q ss_pred             CCCceeEeCCCCCChHHHHHHHHHHHccccc-cCcceEEecCCCCCchh--HHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         305 ELPHLLFYGPPGTGKTTTILACARKLYTKAQ-FNAMVLELNASDDRGIG--IVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       305 ~~~~~ll~GppGtGKT~la~~la~~l~~~~~-~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      ..+|++|+||||||||++|+++|+.+..... ....++.+++++..+..  .....+......     ...+||||||+|
T Consensus        41 ~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~~l~~~~~g~~~~~~~~~~~~-----a~~~VL~IDE~~  115 (261)
T TIGR02881        41 QVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERADLVGEYIGHTAQKTREVIKK-----ALGGVLFIDEAY  115 (261)
T ss_pred             CcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecHHHhhhhhccchHHHHHHHHHh-----ccCCEEEEechh
Confidence            3457999999999999999999998743221 12345555554432211  001111111111     234699999999


Q ss_pred             CCC--------HHHHHHHHHHHHhcCCCcEEEEEeCCCC-----CCChhhhccc-eeeeecCCCHHHHHHHhhcC
Q psy4285         382 AMT--------NDAQNALRRIIEKFTTNVRFCIICNYLS-----KIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       382 ~l~--------~~~~~~Ll~~le~~~~~~~~I~~~n~~~-----~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.        .+.++.|++.+++...++.+|++++...     .++|+++||| ..+.|++++.+++.+++.+.
T Consensus       116 ~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~vila~~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el~~Il~~~  190 (261)
T TIGR02881       116 SLARGGEKDFGKEAIDTLVKGMEDNRNEFVLILAGYSDEMDYFLSLNPGLRSRFPISIDFPDYTVEELMEIAERM  190 (261)
T ss_pred             hhccCCccchHHHHHHHHHHHHhccCCCEEEEecCCcchhHHHHhcChHHHhccceEEEECCCCHHHHHHHHHHH
Confidence            975        3567889999998777777777764332     4789999999 57999999999999888766

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.61  E-value=9.9e-14  Score=154.05  Aligned_cols=153  Identities=20%  Similarity=0.272  Sum_probs=104.5

Q ss_pred             HHhhhchhhhhhhccccccc--------CC-CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHH
Q psy4285         285 WLLNESMDLCYKINRFIDEN--------EL-PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR  355 (533)
Q Consensus       285 ~~~~~~~~~~~~l~~~~~~~--------~~-~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~  355 (533)
                      ..+.||+.++..+...+...        ++ ..++|+||||||||++|+++++.+++.   ...++.++.+.........
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~---~~~~i~~d~s~~~~~~~~~  641 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDD---EDAMVRIDMSEYMEKHSVA  641 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCC---CCcEEEEechhhcccchHH
Confidence            34566776666665555432        12 238999999999999999999998765   3456666665432222111


Q ss_pred             HHHH------------HHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCCC
Q psy4285         356 DQIF------------QFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYLS  412 (533)
Q Consensus       356 ~~~~------------~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~~  412 (533)
                      ..++            .+....  ...++.||+|||+++++++.++.|+++|++.           -.++.||+|||...
T Consensus       642 ~l~g~~~g~~g~~~~g~l~~~v--~~~p~~vlllDeieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~g~  719 (852)
T TIGR03346       642 RLIGAPPGYVGYEEGGQLTEAV--RRKPYSVVLFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGS  719 (852)
T ss_pred             HhcCCCCCccCcccccHHHHHH--HcCCCcEEEEeccccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCcch
Confidence            1110            000000  0134679999999999999999999999875           25677999998722


Q ss_pred             -------------------------CCChhhhccc-eeeeecCCCHHHHHHHhhcC
Q psy4285         413 -------------------------KIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       413 -------------------------~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                                               .+.|.+..|+ ..+.|.|++.+++.+++...
T Consensus       720 ~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel~~Rid~IivF~PL~~e~l~~I~~l~  775 (852)
T TIGR03346       720 QFIQELAGGDDYEEMREAVMEVLRAHFRPEFLNRIDEIVVFHPLGREQIARIVEIQ  775 (852)
T ss_pred             HhHhhhcccccHHHHHHHHHHHHHhhcCHHHhcCcCeEEecCCcCHHHHHHHHHHH
Confidence                                     2457788888 58899999999988887665

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.

>PRK14700 recombination factor protein RarA; Provisional

Probab=99.61  E-value=4.1e-15  Score=139.87  Aligned_cols=114  Identities=18%  Similarity=0.195  Sum_probs=96.0

Q ss_pred             CCceEEEEEc--CCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhc------CCCCCHHHHHHHHHhcCCCHHHHH
Q psy4285           5 TTNVRFCIIC--NYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQE------KVNVTPDGKKAIIDLSDGDMRKVL   76 (533)
Q Consensus         5 ~~~~~~il~~--~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~------~~~~~~~~~~~~~~~~~g~~r~a~   76 (533)
                      .+.+.+|-+|  ||++.|+|+|+|||++|.|++++.+++...|++++..+      ++.+++++++.|+..|+||.|+|+
T Consensus         6 ~G~i~LIGATTENP~f~vn~ALlSR~~v~~l~~L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~~a~GDaR~aL   85 (300)
T PRK14700          6 SGKIILIGATTENPTYYLNDALVSRLFILRLKRLSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHNYNEGDCRKIL   85 (300)
T ss_pred             CCcEEEEeecCCCccceecHhhhhhhheeeecCCCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHHhcCCHHHHHH
Confidence            4667777777  99999999999999999999999999999999998742      367999999999999999999999


Q ss_pred             HHHHHHHHhC-C-C--CcchhhHHhhhhhhccccchh--HHHHHhchH
Q psy4285          77 NILQSAATAH-A-D--EVNEDTIFTLLVSRVEKYRPS--TLDELVSHQ  118 (533)
Q Consensus        77 ~~l~~~~~~~-~-~--~i~~~~i~~~~~~~~ek~~~~--~l~~lls~~  118 (533)
                      |.||.++... . .  .||.+.+.+.++.....|+.+  .||+++|-.
T Consensus        86 N~LE~a~~~~~~~~~~~it~~~~~~~~~~~~~~yDk~gd~HYd~iSAf  133 (300)
T PRK14700         86 NLLERMFLISTRGDEIYLNKELFDQAVGETSRDFHREGKEFYEQLSAF  133 (300)
T ss_pred             HHHHHHHhhccccCCCccCHHHHHHHHhHHHhcccCCcchhHHHHHHH
Confidence            9999976522 1 1  289999988888777777754  799998643

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.60  E-value=1.2e-14  Score=147.39  Aligned_cols=150  Identities=24%  Similarity=0.327  Sum_probs=105.3

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .+++|+||||||||++|+++|+.+      +..++.+++++..      +...++..+....      ...++||||||+
T Consensus       166 ~gvLL~GppGtGKT~lAkaia~~~------~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~------~~~p~IlfiDEi  233 (389)
T PRK03992        166 KGVLLYGPPGTGKTLLAKAVAHET------NATFIRVVGSELVQKFIGEGARLVRELFELAR------EKAPSIIFIDEI  233 (389)
T ss_pred             CceEEECCCCCChHHHHHHHHHHh------CCCEEEeehHHHhHhhccchHHHHHHHHHHHH------hcCCeEEEEech
Confidence            459999999999999999999987      5566777665431      2223333322211      134679999999


Q ss_pred             CCCC-----------HHHHHHHHHHHHh-----cCCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhc
Q psy4285         381 DAMT-----------NDAQNALRRIIEK-----FTTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       381 d~l~-----------~~~~~~Ll~~le~-----~~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~  441 (533)
                      |.+.           .+.+..+.+++.+     ...++.+|++||.++.+++++++  || ..+.|++|+.++..+++..
T Consensus       234 D~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~  313 (389)
T PRK03992        234 DAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKI  313 (389)
T ss_pred             hhhhcccccCCCCccHHHHHHHHHHHHhccccCCCCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHH
Confidence            9983           3344555555543     13478899999999999999997  88 4799999999999998886


Q ss_pred             C------H--HHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         442 D------D--ISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       442 ~------~--~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                      .      +  .++..+..         .+.|+++.|+..-+.++
T Consensus       314 ~~~~~~~~~~~~~~~la~---------~t~g~sgadl~~l~~eA  348 (389)
T PRK03992        314 HTRKMNLADDVDLEELAE---------LTEGASGADLKAICTEA  348 (389)
T ss_pred             HhccCCCCCcCCHHHHHH---------HcCCCCHHHHHHHHHHH
Confidence            5      1  12333333         66789988877655444

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

Probab=99.60  E-value=6.2e-15  Score=141.98  Aligned_cols=126  Identities=15%  Similarity=0.153  Sum_probs=94.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADA  382 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~  382 (533)
                      ++||||||||||.+|+++|+++      +..++.+++++.      .+...+++.+........ ....++||||||+|.
T Consensus       151 llL~GPPGcGKTllAraiA~el------g~~~i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~-~~~aPcVLFIDEIDA  223 (413)
T PLN00020        151 LGIWGGKGQGKSFQCELVFKKM------GIEPIVMSAGELESENAGEPGKLIRQRYREAADIIK-KKGKMSCLFINDLDA  223 (413)
T ss_pred             EEeeCCCCCCHHHHHHHHHHHc------CCCeEEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhh-ccCCCeEEEEehhhh
Confidence            8999999999999999999998      777888887653      345667776655443210 124689999999998


Q ss_pred             CCHH-----------H-HHHHHHHHHh--------------cCCCcEEEEEeCCCCCCChhhhc--cceeeeecCCCHHH
Q psy4285         383 MTND-----------A-QNALRRIIEK--------------FTTNVRFCIICNYLSKIPPAIQS--RCTRFRFGPLDSSL  434 (533)
Q Consensus       383 l~~~-----------~-~~~Ll~~le~--------------~~~~~~~I~~~n~~~~l~~~l~s--R~~~i~~~~~~~~~  434 (533)
                      +.+.           . ...|+..++.              ....+.+|.|||+++.|+|+|++  ||+... ..|+.++
T Consensus       224 ~~g~r~~~~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd~LDpALlRpGRfDk~i-~lPd~e~  302 (413)
T PLN00020        224 GAGRFGTTQYTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFSTLYAPLIRDGRMEKFY-WAPTRED  302 (413)
T ss_pred             cCCCCCCCCcchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCCCcccCCHhHcCCCCCCcee-CCCCHHH
Confidence            8542           1 1346666553              24568899999999999999999  998754 4788888


Q ss_pred             HHHHhhcC
Q psy4285         435 IMSRLDYD  442 (533)
Q Consensus       435 ~~~~l~~~  442 (533)
                      ..+++..+
T Consensus       303 R~eIL~~~  310 (413)
T PLN00020        303 RIGVVHGI  310 (413)
T ss_pred             HHHHHHHH
Confidence            88888765

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

Probab=99.60  E-value=5.4e-14  Score=148.58  Aligned_cols=157  Identities=22%  Similarity=0.296  Sum_probs=117.2

Q ss_pred             HHHHhhhchhhhhhhccccccc-------CCC--ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhH
Q psy4285         283 LRWLLNESMDLCYKINRFIDEN-------ELP--HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGI  353 (533)
Q Consensus       283 l~~~~~~~~~~~~~l~~~~~~~-------~~~--~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~  353 (533)
                      +...+.||++++..+...+...       +.|  .++|.||+|+|||.+|+++|..+++.   ...++.++.|+......
T Consensus       489 L~~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~---e~aliR~DMSEy~EkHs  565 (786)
T COG0542         489 LKKRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGD---EQALIRIDMSEYMEKHS  565 (786)
T ss_pred             HhcceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCC---CccceeechHHHHHHHH
Confidence            3345578888887776665532       223  38999999999999999999999776   46788888888766666


Q ss_pred             HHHHHHHHHhccc----------CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCCC
Q psy4285         354 VRDQIFQFASTKT----------MHKSSYKLIILDEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYLS  412 (533)
Q Consensus       354 ~~~~~~~~~~~~~----------~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~~  412 (533)
                      +..+++.-...-.          ....+++|+++||+++..++..+.|+++|+..           -.|+.+|+|||.-.
T Consensus       566 VSrLIGaPPGYVGyeeGG~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVlDdGrLTD~~Gr~VdFrNtiIImTSN~Gs  645 (786)
T COG0542         566 VSRLIGAPPGYVGYEEGGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNAGS  645 (786)
T ss_pred             HHHHhCCCCCCceeccccchhHhhhcCCCeEEEechhhhcCHHHHHHHHHHhcCCeeecCCCCEEecceeEEEEecccch
Confidence            6655443111100          01246899999999999999999999999864           26788999997321


Q ss_pred             ----------------------------CCChhhhccce-eeeecCCCHHHHHHHhhcC
Q psy4285         413 ----------------------------KIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       413 ----------------------------~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                                                  .+.|.++.|++ .+.|.+++.+.+.+++...
T Consensus       646 ~~i~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFLNRid~II~F~~L~~~~l~~Iv~~~  704 (786)
T COG0542         646 EEILRDADGDDFADKEALKEAVMEELKKHFRPEFLNRIDEIIPFNPLSKEVLERIVDLQ  704 (786)
T ss_pred             HHHHhhccccccchhhhHHHHHHHHHHhhCCHHHHhhcccEEeccCCCHHHHHHHHHHH
Confidence                                        25677888886 9999999999888887766

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.60  E-value=5.2e-15  Score=153.54  Aligned_cols=111  Identities=20%  Similarity=0.334  Sum_probs=99.6

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+||++++|||+|+.++++++||+|||++++|++++.+++.++|.++++++++.++++++..++..++||+|+|+|+|+
T Consensus       143 LEepp~~v~fIL~Ttd~~kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~egi~~e~~Al~~Ia~~s~GdlR~alnlLe  222 (546)
T PRK14957        143 LEEPPEYVKFILATTDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENINSDEQSLEYIAYHAKGSLRDALSLLD  222 (546)
T ss_pred             HhcCCCCceEEEEECChhhhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhccccchhHHHHHh
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELV  115 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~ek~~~~~l~~ll  115 (533)
                      .+....++.|+.+.+.++++.    +..+.+++++
T Consensus       223 k~i~~~~~~It~~~V~~~l~~----~~~~~v~~ll  253 (546)
T PRK14957        223 QAISFCGGELKQAQIKQMLGI----IDSEEVYSII  253 (546)
T ss_pred             HHHHhccCCCCHHHHHHHHcc----CCHHHHHHHH
Confidence            987765667999888877664    2344555554

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.60  E-value=4.7e-15  Score=158.18  Aligned_cols=100  Identities=21%  Similarity=0.355  Sum_probs=91.1

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+++.+|++||+|||++|+|++++.+++..+|++++.++++.++++++..|++.++||+|+|+++++
T Consensus       143 LEEPP~~vrFILaTTe~~kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il~~EgI~~edeAL~lIA~~S~Gd~R~ALnLLd  222 (944)
T PRK14949        143 LEEPPEHVKFLLATTDPQKLPVTVLSRCLQFNLKSLTQDEIGTQLNHILTQEQLPFEAEALTLLAKAANGSMRDALSLTD  222 (944)
T ss_pred             HhccCCCeEEEEECCCchhchHHHHHhheEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHhCCCCcchhhHHhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLV  100 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~  100 (533)
                      .+.....+.++.+.+.++++
T Consensus       223 Qala~~~~~It~~~V~~llG  242 (944)
T PRK14949        223 QAIAFGGGQVMLTQVQTMLG  242 (944)
T ss_pred             HHHHhcCCcccHHHHHHHhC
Confidence            87765555677776655443

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.59  E-value=4e-15  Score=154.67  Aligned_cols=105  Identities=18%  Similarity=0.294  Sum_probs=96.3

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+.++++++||+|||++|+|++++.+++..+|+++++++|+.++++++..+++.++||+|.|+++|+
T Consensus       143 LEepp~~~~fIlattd~~kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi~~~~~al~~ia~~s~GslR~al~lLd  222 (509)
T PRK14958        143 LEEPPSHVKFILATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEENVEFENAALDLLARAANGSVRDALSLLD  222 (509)
T ss_pred             HhccCCCeEEEEEECChHhchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhccc
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRVEK  105 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~ek  105 (533)
                      .+.....+.|+.+.|.++++...+.
T Consensus       223 q~ia~~~~~It~~~V~~~lg~~~~~  247 (509)
T PRK14958        223 QSIAYGNGKVLIADVKTMLGTIEPL  247 (509)
T ss_pred             HHHhcCCCCcCHHHHHHHHCCCCHH
Confidence            8776555679999998877654433

>CHL00181 cbbX CbbX; Provisional

Probab=99.58  E-value=3.4e-14  Score=137.51  Aligned_cols=132  Identities=21%  Similarity=0.249  Sum_probs=91.4

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHHcccccc-CcceEEecCCCCCchhH--HHHHHHHHHhcccCCCCCcEEEEEeCCCC
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKLYTKAQF-NAMVLELNASDDRGIGI--VRDQIFQFASTKTMHKSSYKLIILDEADA  382 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l~~~~~~-~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~vliiDE~d~  382 (533)
                      ..|++|+||||||||++|+++++.+...+.. ...++.++.++..+...  ...........     ..++||||||++.
T Consensus        59 ~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~~~l~~~~~g~~~~~~~~~l~~-----a~ggVLfIDE~~~  133 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDDLVGQYIGHTAPKTKEVLKK-----AMGGVLFIDEAYY  133 (287)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecHHHHHHHHhccchHHHHHHHHH-----ccCCEEEEEccch
Confidence            3469999999999999999999987543221 22366666443211000  00001111111     2346999999998


Q ss_pred             C---------CHHHHHHHHHHHHhcCCCcEEEEEeCCCC-----CCChhhhccce-eeeecCCCHHHHHHHhhcC
Q psy4285         383 M---------TNDAQNALRRIIEKFTTNVRFCIICNYLS-----KIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       383 l---------~~~~~~~Ll~~le~~~~~~~~I~~~n~~~-----~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                      +         ..+.++.|++.|+....++++|++++...     ..+|+++|||. .+.|++++.+++.+++...
T Consensus       134 l~~~~~~~~~~~e~~~~L~~~me~~~~~~~vI~ag~~~~~~~~~~~np~L~sR~~~~i~F~~~t~~el~~I~~~~  208 (287)
T CHL00181        134 LYKPDNERDYGSEAIEILLQVMENQRDDLVVIFAGYKDRMDKFYESNPGLSSRIANHVDFPDYTPEELLQIAKIM  208 (287)
T ss_pred             hccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhcCHHHHHhCCceEEcCCcCHHHHHHHHHHH
Confidence            7         45678899999998877888888875322     35699999995 8999999999999888776

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

Probab=99.58  E-value=2.7e-14  Score=143.94  Aligned_cols=151  Identities=24%  Similarity=0.319  Sum_probs=102.8

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .+++|+||||||||++|+++|+.+      +..++.+.++..      .+...+++.+....      ...+.||||||+
T Consensus       180 kgvLL~GppGTGKT~LAkalA~~l------~~~fi~i~~s~l~~k~~ge~~~~lr~lf~~A~------~~~P~ILfIDEI  247 (398)
T PTZ00454        180 RGVLLYGPPGTGKTMLAKAVAHHT------TATFIRVVGSEFVQKYLGEGPRMVRDVFRLAR------ENAPSIIFIDEV  247 (398)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhc------CCCEEEEehHHHHHHhcchhHHHHHHHHHHHH------hcCCeEEEEECH
Confidence            359999999999999999999987      455666654331      12223333332221      135689999999


Q ss_pred             CCCCH-----------HHHHHH---HHHHHh--cCCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhc
Q psy4285         381 DAMTN-----------DAQNAL---RRIIEK--FTTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       381 d~l~~-----------~~~~~L---l~~le~--~~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~  441 (533)
                      |.+..           ..+..+   +..++.  ...++.+|++||.++.+||++++  || ..+.|++|+.++...++..
T Consensus       248 D~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~  327 (398)
T PTZ00454        248 DSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQT  327 (398)
T ss_pred             hhhccccccccCCccHHHHHHHHHHHHHhhccCCCCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHH
Confidence            98732           223334   444443  23568899999999999999987  88 4789999999988887775


Q ss_pred             C--------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q psy4285         442 D--------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLV  478 (533)
Q Consensus       442 ~--------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~  478 (533)
                      .        ..++.+++.         .+.|+++.|+..-+.++.
T Consensus       328 ~~~~~~l~~dvd~~~la~---------~t~g~sgaDI~~l~~eA~  363 (398)
T PTZ00454        328 ITSKMNLSEEVDLEDFVS---------RPEKISAADIAAICQEAG  363 (398)
T ss_pred             HHhcCCCCcccCHHHHHH---------HcCCCCHHHHHHHHHHHH
Confidence            5        112333333         677999998776655543

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.58  E-value=8.3e-15  Score=153.44  Aligned_cols=102  Identities=22%  Similarity=0.275  Sum_probs=94.5

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+.+++|++||+|||++|+|++++.+++.+||.++++++++.++++++..+++.++||+|.|+|+|+
T Consensus       142 LEEpp~~~~fIL~tte~~kll~TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi~i~~~al~~Ia~~s~GdlR~aln~Ld  221 (584)
T PRK14952        142 VEEPPEHLIFIFATTEPEKVLPTIRSRTHHYPFRLLPPRTMRALIARICEQEGVVVDDAVYPLVIRAGGGSPRDTLSVLD  221 (584)
T ss_pred             HhcCCCCeEEEEEeCChHhhHHHHHHhceEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhC-CCCcchhhHHhhhhhh
Q psy4285          81 SAATAH-ADEVNEDTIFTLLVSR  102 (533)
Q Consensus        81 ~~~~~~-~~~i~~~~i~~~~~~~  102 (533)
                      .+.... .+.||.+.+.++++..
T Consensus       222 ql~~~~~~~~It~~~v~~llg~~  244 (584)
T PRK14952        222 QLLAGAADTHVTYQRALGLLGAT  244 (584)
T ss_pred             HHHhccCCCCcCHHHHHHHHCCC
Confidence            987754 4569999887776653

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.57  E-value=1.2e-14  Score=152.71  Aligned_cols=112  Identities=20%  Similarity=0.349  Sum_probs=99.5

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+.++++++||+|||++|+|++++.+++.++|++++.++|+.++++++..|++.++||+|.++++++
T Consensus       148 LEEPP~~~~fIL~Ttd~~kil~TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi~ie~~AL~~La~~s~GslR~al~lLd  227 (618)
T PRK14951        148 LEEPPEYLKFVLATTDPQKVPVTVLSRCLQFNLRPMAPETVLEHLTQVLAAENVPAEPQALRLLARAARGSMRDALSLTD  227 (618)
T ss_pred             cccCCCCeEEEEEECCchhhhHHHHHhceeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhccccchhHHH
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRVEKYRPSTLD  112 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~ek~~~~~l~  112 (533)
                      .+.......|+.+.|.++++...+.+...-++
T Consensus       228 q~ia~~~~~It~~~V~~~Lg~~~~~~i~~Lld  259 (618)
T PRK14951        228 QAIAFGSGQLQEAAVRQMLGSVDRSHVFRLID  259 (618)
T ss_pred             HHHHhcCCCcCHHHHHHHHcCCCHHHHHHHHH
Confidence            77665556799999988887655443333333

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.57  E-value=4.9e-14  Score=135.34  Aligned_cols=156  Identities=19%  Similarity=0.189  Sum_probs=105.3

Q ss_pred             hhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhH-H--------HHHHHHHHh-
Q psy4285         294 CYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGI-V--------RDQIFQFAS-  363 (533)
Q Consensus       294 ~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~-~--------~~~~~~~~~-  363 (533)
                      .+.+..++..+.  +++|+||||||||++|+++|+.+      +.+++.+++........ +        ......+.. 
T Consensus        11 ~~~~l~~l~~g~--~vLL~G~~GtGKT~lA~~la~~l------g~~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~~~~   82 (262)
T TIGR02640        11 TSRALRYLKSGY--PVHLRGPAGTGKTTLAMHVARKR------DRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHN   82 (262)
T ss_pred             HHHHHHHHhcCC--eEEEEcCCCCCHHHHHHHHHHHh------CCCEEEEeCCccCCHHHHhhhhcccchhhHHHHHHHH
Confidence            344445555544  79999999999999999999876      55666665543221111 0        000011100 


Q ss_pred             ---c----------ccCC--CCCcEEEEEeCCCCCCHHHHHHHHHHHHhc----------------CCCcEEEEEeCCCC
Q psy4285         364 ---T----------KTMH--KSSYKLIILDEADAMTNDAQNALRRIIEKF----------------TTNVRFCIICNYLS  412 (533)
Q Consensus       364 ---~----------~~~~--~~~~~vliiDE~d~l~~~~~~~Ll~~le~~----------------~~~~~~I~~~n~~~  412 (533)
                         .          .+..  ...+.+|++||+++++++.++.|+.+|++.                +++.++|+|+|...
T Consensus        83 ~~~~~~~~~~~~~~g~l~~A~~~g~~lllDEi~r~~~~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~  162 (262)
T TIGR02640        83 VVKLEDIVRQNWVDNRLTLAVREGFTLVYDEFTRSKPETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVE  162 (262)
T ss_pred             hhhhhcccceeecCchHHHHHHcCCEEEEcchhhCCHHHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCcc
Confidence               0          0000  023469999999999999999999999753                13678999999753


Q ss_pred             -----CCChhhhccceeeeecCCCHHHHHHHhhcC----HHHHHHHHHHHHHHH
Q psy4285         413 -----KIPPAIQSRCTRFRFGPLDSSLIMSRLDYD----DISFFNIIIWYIKIQ  457 (533)
Q Consensus       413 -----~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~----~~~~~~ll~~~~~l~  457 (533)
                           .+++++++||..+.+..|+.++..+++...    +..+..+++....+.
T Consensus       163 ~~g~~~l~~aL~~R~~~i~i~~P~~~~e~~Il~~~~~~~~~~~~~iv~~~~~~R  216 (262)
T TIGR02640       163 YAGVHETQDALLDRLITIFMDYPDIDTETAILRAKTDVAEDSAATIVRLVREFR  216 (262)
T ss_pred             ccceecccHHHHhhcEEEECCCCCHHHHHHHHHHhhCCCHHHHHHHHHHHHHHH
Confidence                 578999999999999999999999999875    444455555444444

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).

>KOG0728|consensus

Probab=99.57  E-value=2.2e-14  Score=128.85  Aligned_cols=162  Identities=23%  Similarity=0.410  Sum_probs=111.3

Q ss_pred             ccccccccCCCCH--HHHHHHHHHHhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceE
Q psy4285         264 EDTVYNSVGYPTK--TEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVL  341 (533)
Q Consensus       264 ~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~  341 (533)
                      ++..|...|....  +.+.+.+ .+...+.++.+.+.-    ..+..+++|||||||||.+|+++|+..      ...++
T Consensus       142 PDStYeMiGgLd~QIkeIkEVI-eLPvKHPELF~aLGI----aQPKGvlLygppgtGktLlaraVahht------~c~fi  210 (404)
T KOG0728|consen  142 PDSTYEMIGGLDKQIKEIKEVI-ELPVKHPELFEALGI----AQPKGVLLYGPPGTGKTLLARAVAHHT------DCTFI  210 (404)
T ss_pred             CccHHHHhccHHHHHHHHHHHH-hccccCHHHHHhcCC----CCCcceEEecCCCCchhHHHHHHHhhc------ceEEE
Confidence            4446666666432  2334333 233344555444432    233459999999999999999999876      45678


Q ss_pred             EecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH-----------HHHHHHHHHHHh-----cC
Q psy4285         342 ELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN-----------DAQNALRRIIEK-----FT  399 (533)
Q Consensus       342 ~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~Ll~~le~-----~~  399 (533)
                      .+++++.      .+...+++++-...      +..+.++|+||+|.+..           +.|..++.++.+     ..
T Consensus       211 rvsgselvqk~igegsrmvrelfvmar------ehapsiifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfeat  284 (404)
T KOG0728|consen  211 RVSGSELVQKYIGEGSRMVRELFVMAR------EHAPSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEAT  284 (404)
T ss_pred             EechHHHHHHHhhhhHHHHHHHHHHHH------hcCCceEeeecccccccccccCCCCccHHHHHHHHHHHHhccccccc
Confidence            8887752      33444555432221      23578999999999843           456666666543     36


Q ss_pred             CCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhcC
Q psy4285         400 TNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       400 ~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .++.+|++||+.+-+||++++  |. ..+.|+||+++...++|+-.
T Consensus       285 knikvimatnridild~allrpgridrkiefp~p~e~ar~~ilkih  330 (404)
T KOG0728|consen  285 KNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKIH  330 (404)
T ss_pred             cceEEEEeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHHh
Confidence            789999999999999999998  77 58999999999888887654

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.57  E-value=2.8e-14  Score=149.75  Aligned_cols=150  Identities=25%  Similarity=0.264  Sum_probs=104.8

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .++||+||||||||++|+++|.++      +.+++.+++++.      .+...++..+.....      ..++||||||+
T Consensus        89 ~giLL~GppGtGKT~la~alA~~~------~~~~~~i~~~~~~~~~~g~~~~~l~~~f~~a~~------~~p~Il~iDEi  156 (495)
T TIGR01241        89 KGVLLVGPPGTGKTLLAKAVAGEA------GVPFFSISGSDFVEMFVGVGASRVRDLFEQAKK------NAPCIIFIDEI  156 (495)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHc------CCCeeeccHHHHHHHHhcccHHHHHHHHHHHHh------cCCCEEEEech
Confidence            359999999999999999999987      566777766542      223344444433221      34679999999


Q ss_pred             CCCCHH--------------HHHHHHHHHHhc--CCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhc
Q psy4285         381 DAMTND--------------AQNALRRIIEKF--TTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       381 d~l~~~--------------~~~~Ll~~le~~--~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~  441 (533)
                      |.+...              ..+.|+..|+..  ..++.+|++||.++.+||++++  || ..+.++.|+.++..+++..
T Consensus       157 d~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~  236 (495)
T TIGR01241       157 DAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKV  236 (495)
T ss_pred             hhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHH
Confidence            998532              234566666543  3457889999999999999998  78 4788889998888888776


Q ss_pred             C--------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         442 D--------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       442 ~--------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                      .        ..++..+.+         .+.|+++.|+..-+.++
T Consensus       237 ~l~~~~~~~~~~l~~la~---------~t~G~sgadl~~l~~eA  271 (495)
T TIGR01241       237 HAKNKKLAPDVDLKAVAR---------RTPGFSGADLANLLNEA  271 (495)
T ss_pred             HHhcCCCCcchhHHHHHH---------hCCCCCHHHHHHHHHHH
Confidence            5        112222222         56788888877666554

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.

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.57  E-value=9.7e-15  Score=151.41  Aligned_cols=102  Identities=22%  Similarity=0.352  Sum_probs=95.0

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+||++++|||+|+.+.++++||+|||++|+|++++.+++.++|+++++++++.++++++..|++.++||+|.|+|+|+
T Consensus       142 LEEPP~~v~FILaTtd~~kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~kEgI~id~eAL~~IA~~S~GdLRdALnLLD  221 (702)
T PRK14960        142 LEEPPEHVKFLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQIAADQDAIWQIAESAQGSLRDALSLTD  221 (702)
T ss_pred             HhcCCCCcEEEEEECChHhhhHHHHHhhheeeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHhCCCCcchhhHHhhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVSR  102 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~  102 (533)
                      .+.....+.|+.+.|.++++..
T Consensus       222 QaIayg~g~IT~edV~~lLG~~  243 (702)
T PRK14960        222 QAIAYGQGAVHHQDVKEMLGLI  243 (702)
T ss_pred             HHHHhcCCCcCHHHHHHHhccC
Confidence            8766555679999998877743

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.57  E-value=9.5e-14  Score=134.58  Aligned_cols=126  Identities=20%  Similarity=0.260  Sum_probs=90.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcccccc-CcceEEecCCCCCc------hhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQF-NAMVLELNASDDRG------IGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~-~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      |++|+||||||||++|+++++.+...+.. ...++.+++++..+      ....++.+..         ...++|||||+
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~~~l~~~~~g~~~~~~~~~~~~---------a~~gvL~iDEi  130 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEILKR---------AMGGVLFIDEA  130 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecHHHHhHhhcccchHHHHHHHHH---------ccCcEEEEech
Confidence            69999999999999999999988543321 22466666543211      1111221111         23479999999


Q ss_pred             CCC---------CHHHHHHHHHHHHhcCCCcEEEEEeCCC--C---CCChhhhccc-eeeeecCCCHHHHHHHhhcC
Q psy4285         381 DAM---------TNDAQNALRRIIEKFTTNVRFCIICNYL--S---KIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       381 d~l---------~~~~~~~Ll~~le~~~~~~~~I~~~n~~--~---~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +.+         ..+.++.|++.|+....++++|++++..  .   .++|+++||| ..+.|++++.+++..++.+.
T Consensus       131 ~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~l~~edl~~I~~~~  207 (284)
T TIGR02880       131 YYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMDSFFESNPGFSSRVAHHVDFPDYSEAELLVIAGLM  207 (284)
T ss_pred             hhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHHHHHHHHHH
Confidence            987         3456789999999887788888887543  1   4589999999 58999999988888877665

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.

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.56  E-value=1.2e-14  Score=148.75  Aligned_cols=103  Identities=25%  Similarity=0.400  Sum_probs=96.4

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+...++.+||+|||+.+.|++++.+++.++|.++++++++.+++++++.|++.++||+|.|++.|+
T Consensus       140 LEePp~~v~fIlatte~~Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~Egi~i~~eAL~lIa~~s~GslR~alslLd  219 (491)
T PRK14964        140 LEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNALFLLE  219 (491)
T ss_pred             HhCCCCCeEEEEEeCChHHHHHHHHHhheeeecccccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhc
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRV  103 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~  103 (533)
                      .+....++.||.+.|.++++...
T Consensus       220 qli~y~~~~It~e~V~~llg~~~  242 (491)
T PRK14964        220 QAAIYSNNKISEKSVRDLLGCVD  242 (491)
T ss_pred             HHHHhcCCCCCHHHHHHHHccCC
Confidence            98876666799999988776543

>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=99.56  E-value=2e-14  Score=123.48  Aligned_cols=106  Identities=29%  Similarity=0.366  Sum_probs=81.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCCC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEADA  382 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~  382 (533)
                      ++|+||||||||++|+.+|+.+      +..++.+++++..      ....+...+......     ..+.|++|||+|.
T Consensus         1 ill~G~~G~GKT~l~~~la~~l------~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~-----~~~~vl~iDe~d~   69 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL------GFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKS-----AKPCVLFIDEIDK   69 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT------TSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHT-----STSEEEEEETGGG
T ss_pred             CEEECcCCCCeeHHHHHHHhhc------cccccccccccccccccccccccccccccccccc-----ccceeeeeccchh
Confidence            6899999999999999999998      6778888876543      122333333332211     1368999999999


Q ss_pred             CCHHH-----------HHHHHHHHHhcCC---CcEEEEEeCCCCCCChhhh-ccceee
Q psy4285         383 MTNDA-----------QNALRRIIEKFTT---NVRFCIICNYLSKIPPAIQ-SRCTRF  425 (533)
Q Consensus       383 l~~~~-----------~~~Ll~~le~~~~---~~~~I~~~n~~~~l~~~l~-sR~~~i  425 (533)
                      +....           .+.|+..++....   ++.+|++||..+.++++++ +||...
T Consensus        70 l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~~i~~~l~~~rf~~~  127 (132)
T PF00004_consen   70 LFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPDKIDPALLRSRFDRR  127 (132)
T ss_dssp             TSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGGGSCHHHHSTTSEEE
T ss_pred             cccccccccccccccccceeeecccccccccccceeEEeeCChhhCCHhHHhCCCcEE
Confidence            98765           6788888887554   5899999999999999999 999643

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 ....

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.56  E-value=3.5e-13  Score=149.00  Aligned_cols=152  Identities=20%  Similarity=0.263  Sum_probs=102.5

Q ss_pred             Hhhhchhhhhhhccccccc-------CC--CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHH
Q psy4285         286 LLNESMDLCYKINRFIDEN-------EL--PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD  356 (533)
Q Consensus       286 ~~~~~~~~~~~l~~~~~~~-------~~--~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  356 (533)
                      .+.||+.++..+...+...       ..  ..++|+||||||||++|+++++.+++.   +..++.++.++.........
T Consensus       569 ~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~---~~~~i~id~se~~~~~~~~~  645 (857)
T PRK10865        569 RVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMFDS---DDAMVRIDMSEFMEKHSVSR  645 (857)
T ss_pred             eEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHhhcC---CCcEEEEEhHHhhhhhhHHH
Confidence            3467777766665555432       11  248999999999999999999988654   33566666554322211111


Q ss_pred             HHH------------HHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC--
Q psy4285         357 QIF------------QFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL--  411 (533)
Q Consensus       357 ~~~------------~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~--  411 (533)
                      .++            .+....  ...+++||+|||++++.++.++.|++++++.           -.++.||+|||..  
T Consensus       646 LiG~~pgy~g~~~~g~l~~~v--~~~p~~vLllDEieka~~~v~~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TSN~g~~  723 (857)
T PRK10865        646 LVGAPPGYVGYEEGGYLTEAV--RRRPYSVILLDEVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSD  723 (857)
T ss_pred             HhCCCCcccccchhHHHHHHH--HhCCCCeEEEeehhhCCHHHHHHHHHHHhhCceecCCceEEeecccEEEEeCCcchH
Confidence            110            000000  0134579999999999999999999999864           2456699999863  


Q ss_pred             -----------------------CCCChhhhccc-eeeeecCCCHHHHHHHhhcC
Q psy4285         412 -----------------------SKIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       412 -----------------------~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                                             ..+.|++++|+ ..+.|.|++.+++..++...
T Consensus       724 ~~~~~~~~~~~~~~~~~~~~~~~~~f~PELlnRld~iivF~PL~~edl~~Iv~~~  778 (857)
T PRK10865        724 LIQERFGELDYAHMKELVLGVVSHNFRPEFINRIDEVVVFHPLGEQHIASIAQIQ  778 (857)
T ss_pred             HHHHhccccchHHHHHHHHHHHcccccHHHHHhCCeeEecCCCCHHHHHHHHHHH
Confidence                                   13567899999 68999999988877666554

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.55  E-value=1.4e-14  Score=151.71  Aligned_cols=103  Identities=20%  Similarity=0.361  Sum_probs=94.9

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+++++|||+|+.+.++++||+|||+.|+|++++.+++..+|.+++.++++.++++++..|++.++||+|.|+++|+
T Consensus       143 LEEPp~~v~fILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A~GslRdAlnLLD  222 (709)
T PRK08691        143 LEEPPEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIAYEPPALQLLGRAAAGSMRDALSLLD  222 (709)
T ss_pred             HHhCCCCcEEEEEeCCccccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhc
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRV  103 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~  103 (533)
                      .+.......|+.+.|..+++...
T Consensus       223 qaia~g~g~It~e~V~~lLG~~d  245 (709)
T PRK08691        223 QAIALGSGKVAENDVRQMIGAVD  245 (709)
T ss_pred             HHHHhcCCCcCHHHHHHHHcccC
Confidence            87765555799988877766543

>KOG0652|consensus

Probab=99.54  E-value=1.5e-13  Score=124.20  Aligned_cols=121  Identities=29%  Similarity=0.475  Sum_probs=85.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC------CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD------DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+|+|||||||||.+|++.|..-      ...|+.+.++.      +.+.+.++..+.-   ..   +..+.++||||+|
T Consensus       207 GvLmYGPPGTGKTlmARAcAaqT------~aTFLKLAgPQLVQMfIGdGAkLVRDAFaL---AK---EkaP~IIFIDElD  274 (424)
T KOG0652|consen  207 GVLMYGPPGTGKTLMARACAAQT------NATFLKLAGPQLVQMFIGDGAKLVRDAFAL---AK---EKAPTIIFIDELD  274 (424)
T ss_pred             ceEeeCCCCCcHHHHHHHHHHhc------cchHHHhcchHHHhhhhcchHHHHHHHHHH---hh---ccCCeEEEEechh
Confidence            49999999999999999999765      44555554443      2345555554321   11   2467899999999


Q ss_pred             CCCH-----------HHHHHHHHHHHh-----cCCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhh
Q psy4285         382 AMTN-----------DAQNALRRIIEK-----FTTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       382 ~l~~-----------~~~~~Ll~~le~-----~~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~  440 (533)
                      .+..           +.|..++.++.+     +...+.+|.+||+.+-+||+|++  |+ .++.|+.|+++....++.
T Consensus       275 AIGtKRfDSek~GDREVQRTMLELLNQLDGFss~~~vKviAATNRvDiLDPALlRSGRLDRKIEfP~Pne~aRarIlQ  352 (424)
T KOG0652|consen  275 AIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSDDRVKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARILQ  352 (424)
T ss_pred             hhccccccccccccHHHHHHHHHHHHhhcCCCCccceEEEeecccccccCHHHhhcccccccccCCCCChHHHHHHHH
Confidence            8843           455555555543     34568899999999999999998  77 488887777665554443

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.54  E-value=1.5e-14  Score=153.11  Aligned_cols=102  Identities=27%  Similarity=0.438  Sum_probs=95.3

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+||.+++|++||+|||++|+|++++.+++..+|..+++++|+.++++++..+++.++||+|.|++.|+
T Consensus       143 LEepp~~~~fIl~t~~~~kl~~tI~SRc~~~~f~~l~~~~i~~~L~~i~~~egi~i~~~al~~la~~a~G~lr~al~~Ld  222 (576)
T PRK14965        143 LEEPPPHVKFIFATTEPHKVPITILSRCQRFDFRRIPLQKIVDRLRYIADQEGISISDAALALVARKGDGSMRDSLSTLD  222 (576)
T ss_pred             HHcCCCCeEEEEEeCChhhhhHHHHHhhhhhhcCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVSR  102 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~  102 (533)
                      .+....++.|+.+.+.++++..
T Consensus       223 qliay~g~~It~edV~~llG~~  244 (576)
T PRK14965        223 QVLAFCGDAVGDDDVAELLGVV  244 (576)
T ss_pred             HHHHhccCCCCHHHHHHHhCCC
Confidence            9877666679999887776643

>KOG0729|consensus

Probab=99.54  E-value=1.2e-13  Score=125.21  Aligned_cols=120  Identities=28%  Similarity=0.425  Sum_probs=89.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+++|||||||||.+|+++|+.-      +.+++.+-+++.      .+...+++++. .+.+     .+.+++|+||+|
T Consensus       213 gvllygppgtgktl~aravanrt------dacfirvigselvqkyvgegarmvrelf~-mart-----kkaciiffdeid  280 (435)
T KOG0729|consen  213 GVLLYGPPGTGKTLCARAVANRT------DACFIRVIGSELVQKYVGEGARMVRELFE-MART-----KKACIIFFDEID  280 (435)
T ss_pred             ceEEeCCCCCchhHHHHHHhccc------CceEEeehhHHHHHHHhhhhHHHHHHHHH-Hhcc-----cceEEEEeeccc
Confidence            49999999999999999999875      788898887763      34444555433 2222     357899999999


Q ss_pred             CCCH-----------HHHHHHHHHHHh-----cCCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHh
Q psy4285         382 AMTN-----------DAQNALRRIIEK-----FTTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       382 ~l~~-----------~~~~~Ll~~le~-----~~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l  439 (533)
                      .+..           +.|..++.++.+     +..|+.++++||+++.+||+|++  |+ .++.|.-|+-+-...++
T Consensus       281 aiggarfddg~ggdnevqrtmleli~qldgfdprgnikvlmatnrpdtldpallrpgrldrkvef~lpdlegrt~i~  357 (435)
T KOG0729|consen  281 AIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIKVLMATNRPDTLDPALLRPGRLDRKVEFGLPDLEGRTHIF  357 (435)
T ss_pred             cccCccccCCCCCcHHHHHHHHHHHHhccCCCCCCCeEEEeecCCCCCcCHhhcCCcccccceeccCCcccccceeE
Confidence            8843           556667766653     46789999999999999999998  77 47777766654444433

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

Probab=99.54  E-value=1.4e-13  Score=144.94  Aligned_cols=159  Identities=19%  Similarity=0.191  Sum_probs=113.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+||+||||||||++|+++|.++      +..++.+..++..      ....+++.+....      ...++||||||+|
T Consensus       278 giLl~GpPGtGKT~lAkava~~~------~~~fi~v~~~~l~sk~vGesek~ir~~F~~A~------~~~p~iiFiDEiD  345 (494)
T COG0464         278 GVLLYGPPGTGKTLLAKAVALES------RSRFISVKGSELLSKWVGESEKNIRELFEKAR------KLAPSIIFIDEID  345 (494)
T ss_pred             eeEEECCCCCCHHHHHHHHHhhC------CCeEEEeeCHHHhccccchHHHHHHHHHHHHH------cCCCcEEEEEchh
Confidence            59999999999999999999977      7788888776533      2344555444332      2457899999999


Q ss_pred             CCCH-----------HHHHHHHHHHH--hcCCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcCHHH
Q psy4285         382 AMTN-----------DAQNALRRIIE--KFTTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYDDIS  445 (533)
Q Consensus       382 ~l~~-----------~~~~~Ll~~le--~~~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~~~~  445 (533)
                      .+..           ...+.|+..++  +...++.+|.+||.++.+|+++++  ||+ .+.+++|+.++..+++.....+
T Consensus       346 s~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~  425 (494)
T COG0464         346 SLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRD  425 (494)
T ss_pred             hhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCCCHHHHHHHHHHHhcc
Confidence            9843           34566777775  445678899999999999999999  995 7777888888888887776211


Q ss_pred             HHH-HHHH--HHHHHHHHHhcCCCHHHHHHHHHHHHHh
Q psy4285         446 FFN-IIIW--YIKIQEIKIEKGLALTDILTEISLLVHR  480 (533)
Q Consensus       446 ~~~-ll~~--~~~l~~l~~~~~~~~~di~~~~~~~~~~  480 (533)
                      ... +...  ...+..  .+.|++..|+...+.++...
T Consensus       426 ~~~~~~~~~~~~~l~~--~t~~~sgadi~~i~~ea~~~  461 (494)
T COG0464         426 KKPPLAEDVDLEELAE--ITEGYSGADIAALVREAALE  461 (494)
T ss_pred             cCCcchhhhhHHHHHH--HhcCCCHHHHHHHHHHHHHH
Confidence            100 1111  112222  57799999998888776654

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.54  E-value=2.5e-13  Score=139.53  Aligned_cols=134  Identities=21%  Similarity=0.227  Sum_probs=91.5

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEE
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLII  376 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vli  376 (533)
                      .++|||||||||||++|+++|+.+.....    ....++.+..++..      ....++..+.......  ....+.|+|
T Consensus       217 ~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl~v~~~eLl~kyvGete~~ir~iF~~Ar~~a--~~g~p~IIf  294 (512)
T TIGR03689       217 KGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKA--SDGRPVIVF  294 (512)
T ss_pred             cceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEEeccchhhcccccchHHHHHHHHHHHHHHHh--hcCCCceEE
Confidence            35999999999999999999999843310    12233444433321      1223333332222111  113578999


Q ss_pred             EeCCCCCCHH------------HHHHHHHHHHhc--CCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHh
Q psy4285         377 LDEADAMTND------------AQNALRRIIEKF--TTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRL  439 (533)
Q Consensus       377 iDE~d~l~~~------------~~~~Ll~~le~~--~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l  439 (533)
                      |||+|.+...            ..+.|+..|+..  ..++.+|++||.++.+||+++|  ||+ .+.|++|+.++..+++
T Consensus       295 IDEiD~L~~~R~~~~s~d~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il  374 (512)
T TIGR03689       295 FDEMDSIFRTRGSGVSSDVETTVVPQLLSELDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIF  374 (512)
T ss_pred             EehhhhhhcccCCCccchHHHHHHHHHHHHhcccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHH
Confidence            9999988431            134666777643  2568899999999999999998  995 7999999999999999


Q ss_pred             hcC
Q psy4285         440 DYD  442 (533)
Q Consensus       440 ~~~  442 (533)
                      ...
T Consensus       375 ~~~  377 (512)
T TIGR03689       375 SKY  377 (512)
T ss_pred             HHH
Confidence            776

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.

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=99.53  E-value=1.8e-12  Score=117.77  Aligned_cols=145  Identities=18%  Similarity=0.133  Sum_probs=117.8

Q ss_pred             hhcccccccCCCc-eeEeCCCC-CChHHHHHHHHHHHccccc---cCcceEEecCC-------CCCchhHHHHHHHHHHh
Q psy4285         296 KINRFIDENELPH-LLFYGPPG-TGKTTTILACARKLYTKAQ---FNAMVLELNAS-------DDRGIGIVRDQIFQFAS  363 (533)
Q Consensus       296 ~l~~~~~~~~~~~-~ll~GppG-tGKT~la~~la~~l~~~~~---~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~  363 (533)
                      .+...++.++..| .||.|..+ +||..++..+++.+.|...   ....+..+.+.       ...+.+.+|+..+.+..
T Consensus         4 ~L~~~iq~~kLshAYLfeG~n~~~~~~~~~~f~~~~l~~~~i~~~~HPD~~~I~pe~~~~~~~~~I~IdqIReL~~~l~~   83 (263)
T PRK06581          4 RLEFNLKHNKLYNSWLIEAENIEQALKDLEKFIYIKLFKNSIPLENNPDYHFIARETSATSNAKNISIEQIRKLQDFLSK   83 (263)
T ss_pred             HHHHHHHcCcchheeeEeCCChhhHHHHHHHHHHHHHhccCcccCCCCCEEEEeccccccccCCcccHHHHHHHHHHHhh
Confidence            4555667777778 89999998 9999999999999877521   12334444432       23567889987776654


Q ss_pred             cccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         364 TKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       364 ~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.  .++.+|++||++|.|+.+++|+|++++||||.++.||++|+.+..++|+++|||..+.|..+......+.....
T Consensus        84 ~p~--~g~~KViII~~ae~mt~~AANALLKtLEEPP~~t~fILit~~~~~LLpTIrSRCq~i~~~~p~~~~~~e~~~~~  160 (263)
T PRK06581         84 TSA--ISGYKVAIIYSAELMNLNAANSCLKILEDAPKNSYIFLITSRAASIISTIRSRCFKINVRSSILHAYNELYSQF  160 (263)
T ss_pred             Ccc--cCCcEEEEEechHHhCHHHHHHHHHhhcCCCCCeEEEEEeCChhhCchhHhhceEEEeCCCCCHHHHHHHHHHh
Confidence            432  46899999999999999999999999999999999999999999999999999999999999987777766665

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.53  E-value=1.1e-13  Score=147.11  Aligned_cols=98  Identities=24%  Similarity=0.445  Sum_probs=89.7

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+||++++|||+|+..++|+|||+|||++++|++++.+++..||.+++.++|+.++++++..|+..++||+|+|++.|+
T Consensus       145 LEepp~~tifIL~tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~Le  224 (614)
T PRK14971        145 LEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFD  224 (614)
T ss_pred             HhCCCCCeEEEEEeCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhh
Q psy4285          81 SAATAHADEVNEDTIFTL   98 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~   98 (533)
                      .++...+..|+.+.+.+.
T Consensus       225 kl~~y~~~~It~~~V~~~  242 (614)
T PRK14971        225 QVVSFTGGNITYKSVIEN  242 (614)
T ss_pred             HHHHhccCCccHHHHHHH
Confidence            976655545777665443

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

Probab=99.52  E-value=7.6e-14  Score=141.46  Aligned_cols=148  Identities=23%  Similarity=0.367  Sum_probs=101.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      +++|+||||||||++|+++|+.+      ...++.+.+++..      +...++..+....      ...+.|+||||+|
T Consensus       219 gVLL~GPPGTGKT~LAraIA~el------~~~fi~V~~seL~~k~~Ge~~~~vr~lF~~A~------~~~P~ILfIDEID  286 (438)
T PTZ00361        219 GVILYGPPGTGKTLLAKAVANET------SATFLRVVGSELIQKYLGDGPKLVRELFRVAE------ENAPSIVFIDEID  286 (438)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhh------CCCEEEEecchhhhhhcchHHHHHHHHHHHHH------hCCCcEEeHHHHH
Confidence            59999999999999999999987      4556666665432      2223333332221      1356799999998


Q ss_pred             CCCH-----------HHHHHHHHHH---Hh--cCCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhcC
Q psy4285         382 AMTN-----------DAQNALRRII---EK--FTTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       382 ~l~~-----------~~~~~Ll~~l---e~--~~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+..           +.+..++.++   +.  ...++.+|++||.++.+++++++  || ..+.|++|+.++..+++...
T Consensus       287 ~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~  366 (438)
T PTZ00361        287 AIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIH  366 (438)
T ss_pred             HHhccCCCCCCcccHHHHHHHHHHHHHHhhhcccCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHH
Confidence            8742           2334444444   32  24578999999999999999986  88 48999999999999988865


Q ss_pred             --------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHH
Q psy4285         443 --------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISL  476 (533)
Q Consensus       443 --------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~  476 (533)
                              ..++..++.         .+.|+++.|+..-+..
T Consensus       367 ~~k~~l~~dvdl~~la~---------~t~g~sgAdI~~i~~e  399 (438)
T PTZ00361        367 TSKMTLAEDVDLEEFIM---------AKDELSGADIKAICTE  399 (438)
T ss_pred             HhcCCCCcCcCHHHHHH---------hcCCCCHHHHHHHHHH
Confidence                    112333333         6678888886654433

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.52  E-value=3.3e-14  Score=148.84  Aligned_cols=102  Identities=25%  Similarity=0.419  Sum_probs=94.8

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+.+.++++||+|||+.|+|++++.+++.++|.++++++++.++++++..+++.++||+|+|+++++
T Consensus       143 LEepp~~~~fIL~t~d~~kil~tI~SRc~~~~f~~l~~~~i~~~L~~il~~egi~~~~~al~~la~~s~Gslr~al~lld  222 (527)
T PRK14969        143 LEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAAAGSMRDALSLLD  222 (527)
T ss_pred             HhCCCCCEEEEEEeCChhhCchhHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVSR  102 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~  102 (533)
                      .+.......|+.+.+.++++..
T Consensus       223 qai~~~~~~I~~~~v~~~~~~~  244 (527)
T PRK14969        223 QAIAYGGGTVNESEVRAMLGAI  244 (527)
T ss_pred             HHHHhcCCCcCHHHHHHHHCCC
Confidence            8877666679999887766543

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.52  E-value=6.2e-14  Score=141.15  Aligned_cols=102  Identities=24%  Similarity=0.395  Sum_probs=94.1

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+||++++|||+|+.+.++.+||+|||+.++|++++.+++.++|.++++++++.+++++++.++..++||+|+|++.|+
T Consensus       143 lEe~~~~~~fIl~t~~~~~l~~tI~SRc~~~~~~~l~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s~G~~R~al~~l~  222 (363)
T PRK14961        143 LEEPPQHIKFILATTDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLE  222 (363)
T ss_pred             HhcCCCCeEEEEEcCChHhhhHHHHhhceEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVSR  102 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~  102 (533)
                      .+.......|+.+.|.++++..
T Consensus       223 ~~~~~~~~~It~~~v~~~l~~~  244 (363)
T PRK14961        223 HAINLGKGNINIKNVTDMLGLL  244 (363)
T ss_pred             HHHHhcCCCCCHHHHHHHHCCC
Confidence            9877655679998887766543

>TIGR00763 lon ATP-dependent protease La

Probab=99.51  E-value=1.3e-13  Score=151.78  Aligned_cols=148  Identities=21%  Similarity=0.258  Sum_probs=101.0

Q ss_pred             HHHHHhhhchhhhhhhcccccc------cCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc-----
Q psy4285         282 ILRWLLNESMDLCYKINRFIDE------NELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG-----  350 (533)
Q Consensus       282 ~l~~~~~~~~~~~~~l~~~~~~------~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~-----  350 (533)
                      .+.....|++.+.+.+..++..      ...++++|+||||||||++|+++|+.+      +..++.++......     
T Consensus       317 ~l~~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l------~~~~~~i~~~~~~~~~~i~  390 (775)
T TIGR00763       317 ILDEDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKAL------NRKFVRFSLGGVRDEAEIR  390 (775)
T ss_pred             HhhhhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHh------cCCeEEEeCCCcccHHHHc
Confidence            3333344556555555544321      133469999999999999999999998      44455554332111     


Q ss_pred             ----------hhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHH----HHHHHHHHHHhc---------------CCC
Q psy4285         351 ----------IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTND----AQNALRRIIEKF---------------TTN  401 (533)
Q Consensus       351 ----------~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~----~~~~Ll~~le~~---------------~~~  401 (533)
                                .+.+.+.+.   ...    ....|++|||+|++...    ..++|++.|+..               .++
T Consensus       391 g~~~~~~g~~~g~i~~~l~---~~~----~~~~villDEidk~~~~~~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~  463 (775)
T TIGR00763       391 GHRRTYVGAMPGRIIQGLK---KAK----TKNPLFLLDEIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSK  463 (775)
T ss_pred             CCCCceeCCCCchHHHHHH---HhC----cCCCEEEEechhhcCCccCCCHHHHHHHhcCHHhcCccccccCCceeccCC
Confidence                      111222211   111    23349999999999763    347899888631               146


Q ss_pred             cEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         402 VRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       402 ~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +.||+|||..+.+++++++||..+.|.+|+.++...++...
T Consensus       464 v~~I~TtN~~~~i~~~L~~R~~vi~~~~~~~~e~~~I~~~~  504 (775)
T TIGR00763       464 VIFIATANSIDTIPRPLLDRMEVIELSGYTEEEKLEIAKKY  504 (775)
T ss_pred             EEEEEecCCchhCCHHHhCCeeEEecCCCCHHHHHHHHHHH
Confidence            78999999999999999999999999999999988887654

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.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.51  E-value=1.6e-13  Score=141.18  Aligned_cols=165  Identities=15%  Similarity=0.236  Sum_probs=122.0

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+++++||++||...++++||+|||++++|++++++++.+||.++++++|+.+++++++.++..++||+|+|++.|+
T Consensus       145 lEep~~~~~~Il~t~~~~kl~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~~i~~~al~~L~~~s~gdlr~a~~~Le  224 (451)
T PRK06305        145 LEEPPQHVKFFLATTEIHKIPGTILSRCQKMHLKRIPEETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDAESLYD  224 (451)
T ss_pred             hhcCCCCceEEEEeCChHhcchHHHHhceEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhc--------cccc---hh----HHHHHh--------------chHHHHhh--------
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRV--------EKYR---PS----TLDELV--------------SHQDIIST--------  123 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~--------ek~~---~~----~l~~ll--------------s~~~~l~~--------  123 (533)
                      .+....+..|+.+.|.++++...        +.+.   ..    .+.+++              .+...+..        
T Consensus       225 kl~~~~~~~It~~~V~~l~~~~~~~~vf~L~~ai~~~d~~~al~~l~~L~~~g~~~~~iL~~L~~~fR~ll~vk~~~~~~  304 (451)
T PRK06305        225 YVVGLFPKSLDPDSVAKALGLLSQDSLYTLDEAITTQNYAQALEPVTDAMNSGVAPAHFLHDLTLFFRNILLKQYNKQLS  304 (451)
T ss_pred             HHHHhccCCcCHHHHHHHHCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHHHhhhhHHH
Confidence            98764445588777654433211        0000   00    011111              11111100        


Q ss_pred             ---cCCChhhHHHHHhhccCccccccCCCChhhHHHHHHHHHhcc
Q psy4285         124 ---IEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSA  165 (533)
Q Consensus       124 ---l~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~~  165 (533)
                         -.+.......++..+.+.+..+..|.+..+.++.++.++...
T Consensus       305 ~~a~~~s~~~L~~ii~~l~e~d~~lk~~~~~k~~lE~lll~l~~~  349 (451)
T PRK06305        305 SVATKYSSEQLLEIIDFLGESAKHIQLTIFEKTFLETVIIHLIRI  349 (451)
T ss_pred             HHHHhCCHHHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHH
Confidence               123334445566677778888888888888888888877643

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

Probab=99.51  E-value=9.1e-14  Score=142.76  Aligned_cols=126  Identities=23%  Similarity=0.329  Sum_probs=98.1

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH------------HHHHhcccCCCCCcEE
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI------------FQFASTKTMHKSSYKL  374 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~v  374 (533)
                      |-++|+||||+|||++++.||+.+      +..|++++-...+....+|.--            +.....    .....|
T Consensus       351 pILcLVGPPGVGKTSLgkSIA~al------~RkfvR~sLGGvrDEAEIRGHRRTYIGamPGrIiQ~mkka----~~~NPv  420 (782)
T COG0466         351 PILCLVGPPGVGKTSLGKSIAKAL------GRKFVRISLGGVRDEAEIRGHRRTYIGAMPGKIIQGMKKA----GVKNPV  420 (782)
T ss_pred             cEEEEECCCCCCchhHHHHHHHHh------CCCEEEEecCccccHHHhccccccccccCChHHHHHHHHh----CCcCCe
Confidence            558999999999999999999999      7778887765444433333221            111111    134569


Q ss_pred             EEEeCCCCCCH----HHHHHHHHHHHhc---------------CCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHH
Q psy4285         375 IILDEADAMTN----DAQNALRRIIEKF---------------TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLI  435 (533)
Q Consensus       375 liiDE~d~l~~----~~~~~Ll~~le~~---------------~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~  435 (533)
                      +++||+|+|+.    +-.++||..|+-.               -+++.||+|+|..+.++.+|++|...+.+..|++++-
T Consensus       421 ~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTANsl~tIP~PLlDRMEiI~lsgYt~~EK  500 (782)
T COG0466         421 FLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATANSLDTIPAPLLDRMEVIRLSGYTEDEK  500 (782)
T ss_pred             EEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccchhheEEEeecCccccCChHHhcceeeeeecCCChHHH
Confidence            99999999975    4568999998621               2568899999999999999999999999999999999


Q ss_pred             HHHhhcC
Q psy4285         436 MSRLDYD  442 (533)
Q Consensus       436 ~~~l~~~  442 (533)
                      .++..+.
T Consensus       501 l~IAk~~  507 (782)
T COG0466         501 LEIAKRH  507 (782)
T ss_pred             HHHHHHh
Confidence            9888876

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.51  E-value=7.3e-14  Score=147.29  Aligned_cols=103  Identities=26%  Similarity=0.425  Sum_probs=95.1

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+||.+++|||+|+.+++++|||+|||+.+.|++++.+++.+||+++++++|+.++++++..++..++||+|.|++.|+
T Consensus       143 LEepp~~~ifIlatt~~~ki~~tI~SRc~~~~f~~~~~~ei~~~L~~i~~~egi~i~~~al~~ia~~s~G~~R~al~~Ld  222 (559)
T PRK05563        143 LEEPPAHVIFILATTEPHKIPATILSRCQRFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAAEGGMRDALSILD  222 (559)
T ss_pred             hcCCCCCeEEEEEeCChhhCcHHHHhHheEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhc
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRV  103 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~  103 (533)
                      .+.......|+.+.|.++++...
T Consensus       223 q~~~~~~~~It~~~V~~vlg~~~  245 (559)
T PRK05563        223 QAISFGDGKVTYEDALEVTGSVS  245 (559)
T ss_pred             HHHHhccCCCCHHHHHHHhCCCC
Confidence            88765556799998887766543

>CHL00176 ftsH cell division protein; Validated

Probab=99.51  E-value=5e-13  Score=142.00  Aligned_cols=157  Identities=21%  Similarity=0.230  Sum_probs=104.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .++||+||||||||++|+++|.++      +.+++.+++++..      +...++..+....      ...++||||||+
T Consensus       217 ~gVLL~GPpGTGKT~LAralA~e~------~~p~i~is~s~f~~~~~g~~~~~vr~lF~~A~------~~~P~ILfIDEI  284 (638)
T CHL00176        217 KGVLLVGPPGTGKTLLAKAIAGEA------EVPFFSISGSEFVEMFVGVGAARVRDLFKKAK------ENSPCIVFIDEI  284 (638)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh------CCCeeeccHHHHHHHhhhhhHHHHHHHHHHHh------cCCCcEEEEecc
Confidence            359999999999999999999987      5667777665432      2223333333321      135689999999


Q ss_pred             CCCCH-----------HHH---HHHHHHHHhc--CCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhc
Q psy4285         381 DAMTN-----------DAQ---NALRRIIEKF--TTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       381 d~l~~-----------~~~---~~Ll~~le~~--~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~  441 (533)
                      |.+..           +.+   +.|+..++..  ..++.+|++||.++.+++++++  || ..+.+..|+.++..+++..
T Consensus       285 D~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~  364 (638)
T CHL00176        285 DAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKV  364 (638)
T ss_pred             hhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHH
Confidence            98842           223   3344444432  3567899999999999999997  67 5899999999999998877


Q ss_pred             CHHHHHHHHHH--HHHHHHHHHhcCCCHHHHHHHHHHHH
Q psy4285         442 DDISFFNIIIW--YIKIQEIKIEKGLALTDILTEISLLV  478 (533)
Q Consensus       442 ~~~~~~~ll~~--~~~l~~l~~~~~~~~~di~~~~~~~~  478 (533)
                      .-.. ..+...  ...+..  .+.|+++.|+..-+.++.
T Consensus       365 ~l~~-~~~~~d~~l~~lA~--~t~G~sgaDL~~lvneAa  400 (638)
T CHL00176        365 HARN-KKLSPDVSLELIAR--RTPGFSGADLANLLNEAA  400 (638)
T ss_pred             HHhh-cccchhHHHHHHHh--cCCCCCHHHHHHHHHHHH
Confidence            6110 000000  111111  567888888877666553

>KOG0731|consensus

Probab=99.51  E-value=1.9e-13  Score=143.35  Aligned_cols=154  Identities=23%  Similarity=0.237  Sum_probs=108.4

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADA  382 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~  382 (533)
                      +||+||||||||.+|+|+|.+.      +.+|+.+++++.      .+...+++++....      ...+++++|||+|.
T Consensus       347 vLL~GPPGTGKTLLAKAiAGEA------gVPF~svSGSEFvE~~~g~~asrvr~lf~~ar------~~aP~iifideida  414 (774)
T KOG0731|consen  347 VLLVGPPGTGKTLLAKAIAGEA------GVPFFSVSGSEFVEMFVGVGASRVRDLFPLAR------KNAPSIIFIDEIDA  414 (774)
T ss_pred             eEEECCCCCcHHHHHHHHhccc------CCceeeechHHHHHHhcccchHHHHHHHHHhh------ccCCeEEEeccccc
Confidence            9999999999999999999988      889999999873      23455565543322      24678999999998


Q ss_pred             CCHH------------HH---HHHHHHHHh--cCCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC
Q psy4285         383 MTND------------AQ---NALRRIIEK--FTTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       383 l~~~------------~~---~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                      +...            ..   |.|+--||.  ...++.++.+||+++.+|+++++  ||+ .+.+..|+.....+++.-.
T Consensus       415 ~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h  494 (774)
T KOG0731|consen  415 VGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVH  494 (774)
T ss_pred             ccccccccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHH
Confidence            7532            22   334444443  34568888899999999999999  995 7777778777777776655


Q ss_pred             --HHHH-HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 --DISF-FNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 --~~~~-~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                        +-.+ .+..+ +..+..  .+.|+++.|+.+-+.++
T Consensus       495 ~~~~~~~~e~~d-l~~~a~--~t~gf~gadl~n~~nea  529 (774)
T KOG0731|consen  495 LRKKKLDDEDVD-LSKLAS--LTPGFSGADLANLCNEA  529 (774)
T ss_pred             hhccCCCcchhh-HHHHHh--cCCCCcHHHHHhhhhHH
Confidence              0000 11111 111222  78899999998866654

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.50  E-value=5.2e-13  Score=140.37  Aligned_cols=155  Identities=21%  Similarity=0.291  Sum_probs=106.0

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHcccc--cc--CcceEEecCCCCCc-hhHHH-HHHHH-
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKA--QF--NAMVLELNASDDRG-IGIVR-DQIFQ-  360 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~--~~--~~~~~~~~~~~~~~-~~~~~-~~~~~-  360 (533)
                      .|++..+..+...+......|++|+||||||||++|+++++......  .+  ...++.+++..... ...+. ..++. 
T Consensus        68 iGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~fi~id~~~~~~~~~~~~~~li~~~  147 (531)
T TIGR02902        68 IGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAFVEIDATTARFDERGIADPLIGSV  147 (531)
T ss_pred             eCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCCEEEEccccccCCccccchhhcCCc
Confidence            45566666666555555566899999999999999999987653221  11  35678887654211 00010 01000 


Q ss_pred             ---HHh--------------cccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc-------------------------
Q psy4285         361 ---FAS--------------TKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF-------------------------  398 (533)
Q Consensus       361 ---~~~--------------~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~-------------------------  398 (533)
                         ...              ......+..++|||||++.|+...|+.|++.|++.                         
T Consensus       148 ~~p~~~~~~~~g~~g~~~~~~G~l~~a~gG~L~IdEI~~L~~~~q~~LL~~Le~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (531)
T TIGR02902       148 HDPIYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGELHPVQMNKLLKVLEDRKVFLDSAYYNSENPNIPSHIHDIFQ  227 (531)
T ss_pred             ccchhccccccccCCcccccCchhhccCCcEEEEechhhCCHHHHHHHHHHHHhCeeeeccccccccCcccccchhhhcc
Confidence               000              00001245689999999999999999999999752                         


Q ss_pred             ---CCCcEEEEEe-CCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         399 ---TTNVRFCIIC-NYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       399 ---~~~~~~I~~~-n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                         +.++++|++| +.+..++|+++|||..+.|.+++.+++..++.+.
T Consensus       228 ~~~~~d~rlI~ATt~~p~~L~paLrsR~~~I~f~pL~~eei~~Il~~~  275 (531)
T TIGR02902       228 NGLPADFRLIGATTRNPEEIPPALRSRCVEIFFRPLLDEEIKEIAKNA  275 (531)
T ss_pred             cCcccceEEEEEecCCcccCChHHhhhhheeeCCCCCHHHHHHHHHHH
Confidence               2235666655 6788999999999999999999999998888876

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.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=99.49  E-value=1.3e-13  Score=146.10  Aligned_cols=101  Identities=26%  Similarity=0.422  Sum_probs=92.8

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+.+++|+|||+|||++++|++++.+++.++|..++.++++.++++++..++..++||+|.|+++++
T Consensus       142 LEEPP~~tifILaTte~~KLl~TI~SRcq~ieF~~L~~eeI~~~L~~il~kegI~id~eAl~~LA~lS~GslR~AlslLe  221 (725)
T PRK07133        142 LEEPPKHVIFILATTEVHKIPLTILSRVQRFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLSSGSLRDALSIAE  221 (725)
T ss_pred             hhcCCCceEEEEEcCChhhhhHHHHhhceeEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVS  101 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~  101 (533)
                      .+.......|+.+.+.++++.
T Consensus       222 kl~~y~~~~It~e~V~ellg~  242 (725)
T PRK07133        222 QVSIFGNNKITLKNVEELFGL  242 (725)
T ss_pred             HHHHhccCCCCHHHHHHHHcC
Confidence            987655556888887765543

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.49  E-value=1.2e-13  Score=150.26  Aligned_cols=102  Identities=21%  Similarity=0.318  Sum_probs=93.7

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||||+.+++|||+|+...+|++||+|||++|+|++++.+++.+||+++++++++.++++.+..+++.++||+|.+++.||
T Consensus       144 LEEpP~~~~fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~EGv~id~eal~lLa~~sgGdlR~Al~eLE  223 (824)
T PRK07764        144 VEEPPEHLKFIFATTEPDKVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQEGVPVEPGVLPLVIRAGGGSVRDSLSVLD  223 (824)
T ss_pred             HhCCCCCeEEEEEeCChhhhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhC-CCCcchhhHHhhhhhh
Q psy4285          81 SAATAH-ADEVNEDTIFTLLVSR  102 (533)
Q Consensus        81 ~~~~~~-~~~i~~~~i~~~~~~~  102 (533)
                      .+.... .+.||.+.+.++++..
T Consensus       224 KLia~~~~~~IT~e~V~allg~~  246 (824)
T PRK07764        224 QLLAGAGPEGVTYERAVALLGVT  246 (824)
T ss_pred             HHHhhcCCCCCCHHHHHHHhcCC
Confidence            987643 3469998887776643

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.48  E-value=2.4e-13  Score=152.72  Aligned_cols=150  Identities=14%  Similarity=0.066  Sum_probs=102.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc-------------------------------------
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG-------------------------------------  350 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~-------------------------------------  350 (533)
                      .+|++||||||||.+|+++|.+.      +.+++.+++++...                                     
T Consensus      1632 GILLiGPPGTGKTlLAKALA~es------~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~~~~e~~e~~ 1705 (2281)
T CHL00206       1632 GILVIGSIGTGRSYLVKYLATNS------YVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDLDTELLTMM 1705 (2281)
T ss_pred             ceEEECCCCCCHHHHHHHHHHhc------CCceEEEEHHHHhhcccccccccccccccccccccccccccccchhhhhhc
Confidence            49999999999999999999997      45555554432210                                     


Q ss_pred             ----------hh--HHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHH-----HHHHHHHHHhc-----CCCcEEEEEe
Q psy4285         351 ----------IG--IVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDA-----QNALRRIIEKF-----TTNVRFCIIC  408 (533)
Q Consensus       351 ----------~~--~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~-----~~~Ll~~le~~-----~~~~~~I~~~  408 (533)
                                .+  .++..+..   ..   ...++||+|||+|.+....     .+.|+..|+..     ..++.||++|
T Consensus      1706 n~~~~~m~~~e~~~rIr~lFel---AR---k~SPCIIFIDEIDaL~~~ds~~ltL~qLLneLDg~~~~~s~~~VIVIAAT 1779 (2281)
T CHL00206       1706 NALTMDMMPKIDRFYITLQFEL---AK---AMSPCIIWIPNIHDLNVNESNYLSLGLLVNSLSRDCERCSTRNILVIAST 1779 (2281)
T ss_pred             chhhhhhhhhhhHHHHHHHHHH---HH---HCCCeEEEEEchhhcCCCccceehHHHHHHHhccccccCCCCCEEEEEeC
Confidence                      00  02222211   11   1468999999999997532     45666777632     3467899999


Q ss_pred             CCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhc------C-----HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHH
Q psy4285         409 NYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDY------D-----DISFFNIIIWYIKIQEIKIEKGLALTDILTEI  474 (533)
Q Consensus       409 n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~------~-----~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~  474 (533)
                      |.++.+||||++  ||+ .+.++.|+..+..+++..      .     +.++..+..         .+.|++++|+..-+
T Consensus      1780 NRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA~---------~T~GfSGADLanLv 1850 (2281)
T CHL00206       1780 HIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGS---------ITMGSNARDLVALT 1850 (2281)
T ss_pred             CCcccCCHhHcCCCCCCeEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHHHHHH---------hCCCCCHHHHHHHH
Confidence            999999999999  995 677777776666655431      1     122333333         78899999998877


Q ss_pred             HHHH
Q psy4285         475 SLLV  478 (533)
Q Consensus       475 ~~~~  478 (533)
                      .+++
T Consensus      1851 NEAa 1854 (2281)
T CHL00206       1851 NEAL 1854 (2281)
T ss_pred             HHHH
Confidence            7665

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.48  E-value=2.1e-13  Score=128.72  Aligned_cols=141  Identities=13%  Similarity=0.199  Sum_probs=94.4

Q ss_pred             hchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCC
Q psy4285         289 ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH  368 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  368 (533)
                      .+......+..+......++++|+|||||||||+++++++.+...   +..+..++.....  ....+..+.+       
T Consensus        28 ~n~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~---~~~v~y~~~~~~~--~~~~~~~~~~-------   95 (235)
T PRK08084         28 DNDSLLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAELSQR---GRAVGYVPLDKRA--WFVPEVLEGM-------   95 (235)
T ss_pred             ccHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEEHHHHh--hhhHHHHHHh-------
Confidence            455566666666555555679999999999999999999987533   2233333332211  0111222222       


Q ss_pred             CCCcEEEEEeCCCCCCH--HHHHHHHHHHHhcC--CCcEEEEEeCCCC----CCChhhhccc---eeeeecCCCHHHHHH
Q psy4285         369 KSSYKLIILDEADAMTN--DAQNALRRIIEKFT--TNVRFCIICNYLS----KIPPAIQSRC---TRFRFGPLDSSLIMS  437 (533)
Q Consensus       369 ~~~~~vliiDE~d~l~~--~~~~~Ll~~le~~~--~~~~~I~~~n~~~----~l~~~l~sR~---~~i~~~~~~~~~~~~  437 (533)
                       ...++|+|||++.+..  ..+..|+.+++...  .+..+|+||+.+.    .+.|.|+|||   ..+.+.+|+.++...
T Consensus        96 -~~~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~~~~~~~~~~  174 (235)
T PRK08084         96 -EQLSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEKLQ  174 (235)
T ss_pred             -hhCCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHHHhCCceeeecCCCHHHHHH
Confidence             1236999999999863  44566666665432  3357888887553    3689999999   799999999999998


Q ss_pred             HhhcC
Q psy4285         438 RLDYD  442 (533)
Q Consensus       438 ~l~~~  442 (533)
                      ++.+.
T Consensus       175 ~l~~~  179 (235)
T PRK08084        175 ALQLR  179 (235)
T ss_pred             HHHHH
Confidence            88763

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.48  E-value=2.3e-13  Score=137.54  Aligned_cols=149  Identities=25%  Similarity=0.334  Sum_probs=99.6

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .+++|+||||||||++|+++++.+      +..++.+.+++..      +...++..+....      ...+.||||||+
T Consensus       157 ~gvLL~GppGtGKT~lakaia~~l------~~~~~~v~~~~l~~~~~g~~~~~i~~~f~~a~------~~~p~il~iDEi  224 (364)
T TIGR01242       157 KGVLLYGPPGTGKTLLAKAVAHET------NATFIRVVGSELVRKYIGEGARLVREIFELAK------EKAPSIIFIDEI  224 (364)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhC------CCCEEecchHHHHHHhhhHHHHHHHHHHHHHH------hcCCcEEEhhhh
Confidence            359999999999999999999987      4455555543211      1112222222111      134679999999


Q ss_pred             CCCC-----------HHHHHHHHHHHHh---c--CCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhc
Q psy4285         381 DAMT-----------NDAQNALRRIIEK---F--TTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       381 d~l~-----------~~~~~~Ll~~le~---~--~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~  441 (533)
                      |.+.           ...+..+.+++.+   .  ..++.+|+|||.++.+++++++  || ..+.|+.|+.++..+++..
T Consensus       225 D~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~  304 (364)
T TIGR01242       225 DAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKI  304 (364)
T ss_pred             hhhccccccCCCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHH
Confidence            9883           2334455555532   2  3578899999999999999987  77 4788999999999988876


Q ss_pred             C------H--HHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHH
Q psy4285         442 D------D--ISFFNIIIWYIKIQEIKIEKGLALTDILTEISL  476 (533)
Q Consensus       442 ~------~--~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~  476 (533)
                      .      +  .++..+..         .+.|+++.|+..-+..
T Consensus       305 ~~~~~~l~~~~~~~~la~---------~t~g~sg~dl~~l~~~  338 (364)
T TIGR01242       305 HTRKMKLAEDVDLEAIAK---------MTEGASGADLKAICTE  338 (364)
T ss_pred             HHhcCCCCccCCHHHHHH---------HcCCCCHHHHHHHHHH
Confidence            5      1  12222222         5678888887655443

Many proteins may score above the trusted cutoff because an internal

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.48  E-value=1.6e-13  Score=141.77  Aligned_cols=104  Identities=25%  Similarity=0.375  Sum_probs=94.8

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+||++++||++|+...+|.+||+|||+.|+|++++.+++.++|+++++++++.++++++..|+..++||+|.|++.|+
T Consensus       152 LEepp~~~vfI~aTte~~kI~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~GslR~al~~Ld  231 (507)
T PRK06645        152 LEEPPPHIIFIFATTEVQKIPATIISRCQRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSILD  231 (507)
T ss_pred             HhhcCCCEEEEEEeCChHHhhHHHHhcceEEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCC---CCcchhhHHhhhhhhcc
Q psy4285          81 SAATAHA---DEVNEDTIFTLLVSRVE  104 (533)
Q Consensus        81 ~~~~~~~---~~i~~~~i~~~~~~~~e  104 (533)
                      .+.....   ..||.+.|.++++...+
T Consensus       232 kai~~~~~~~~~It~~~V~~llg~~~~  258 (507)
T PRK06645        232 QAASMSAKSDNIISPQVINQMLGLVDS  258 (507)
T ss_pred             HHHHhhccCCCCcCHHHHHHHHCCCCH
Confidence            9865432   25999999887765444

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.48  E-value=1.7e-13  Score=144.59  Aligned_cols=102  Identities=23%  Similarity=0.409  Sum_probs=94.4

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+...++++||+|||++|.|++++.+++..||.+++.++++.++++++..|++.++||+|.+++.|+
T Consensus       156 LEePp~~~~fIl~tte~~kll~tI~SRcq~~~f~~l~~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~Gdlr~al~~Ld  235 (598)
T PRK09111        156 LEEPPPHVKFIFATTEIRKVPVTVLSRCQRFDLRRIEADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLLD  235 (598)
T ss_pred             HHhCCCCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHhCCCCcchhhHHhhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVSR  102 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~  102 (533)
                      .+.......||.+.|.++++..
T Consensus       236 kli~~g~g~It~e~V~~llg~~  257 (598)
T PRK09111        236 QAIAHGAGEVTAEAVRDMLGLA  257 (598)
T ss_pred             HHHhhcCCCcCHHHHHHHhCCC
Confidence            8766555579999998776643

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.47  E-value=1.2e-13  Score=143.42  Aligned_cols=100  Identities=28%  Similarity=0.444  Sum_probs=92.4

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+||++++|||+|+.+++++|||+|||++++|++++.+++..||.+++.++++.++++++..++..++||+|.|++.|+
T Consensus       143 LEEPp~~tvfIL~Tt~~~KLl~TI~SRcq~ieF~~Ls~~eL~~~L~~il~kegi~Is~eal~~La~lS~GdlR~AlnlLe  222 (605)
T PRK05896        143 LEEPPKHVVFIFATTEFQKIPLTIISRCQRYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKIADLADGSLRDGLSILD  222 (605)
T ss_pred             HHhCCCcEEEEEECCChHhhhHHHHhhhhhcccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLV  100 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~  100 (533)
                      .+....+..|+.+.|.++++
T Consensus       223 kL~~y~~~~It~e~V~ellg  242 (605)
T PRK05896        223 QLSTFKNSEIDIEDINKTFG  242 (605)
T ss_pred             HHHhhcCCCCCHHHHHHHhc
Confidence            98776555588888776543

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.47  E-value=7.5e-13  Score=131.93  Aligned_cols=164  Identities=38%  Similarity=0.671  Sum_probs=130.6

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      +|+++.+++||++||...+++++++|||.+++|++++.+++..++++++.++++.+++++++.++..++||+|+|++.|+
T Consensus       126 le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~  205 (319)
T PRK00440        126 MEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQ  205 (319)
T ss_pred             HhcCCCCCeEEEEeCCccccchhHHHHhheeeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            57889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhccc--------c---ch----hHHHHHhc-----hHHHHhhc-------CCChhhHHH
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRVEK--------Y---RP----STLDELVS-----HQDIISTI-------EIPESMLVD  133 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~ek--------~---~~----~~l~~lls-----~~~~l~~l-------~~~~~~~~~  133 (533)
                      .++.. +..||.+.|..++....+.        .   ..    ..+++++.     ..+++..+       +.......+
T Consensus       206 ~~~~~-~~~it~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~a~~~l~~ll~~~g~~~~~i~~~l~~~~~~~~~~~~~l~~  284 (319)
T PRK00440        206 AAAAT-GKEVTEEAVYKITGTARPEEIREMIELALNGDFTEAREKLRDLMIDYGLSGEDIIKQIHREVWSLDIPEELKVE  284 (319)
T ss_pred             HHHHc-CCCCCHHHHHHHhCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCHHHHHH
Confidence            98774 4568888876544321110        0   00    12444431     22333222       355556677


Q ss_pred             HHhhccCccccccCCCChhhHHHHHHHHHhcc
Q psy4285         134 LVLKMSDIEYRLAAGTSEKIQLSALIAAFNSA  165 (533)
Q Consensus       134 ~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~~  165 (533)
                      ++..++++++++..|.++..+++.|+.+++..
T Consensus       285 ~~~~~~~~d~~~k~g~~~~~~le~~i~~~~~~  316 (319)
T PRK00440        285 LIDAIGEADFRITEGANERIQLEALLAKLALL  316 (319)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHh
Confidence            88888999999999999999999999998643

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

Probab=99.47  E-value=3.1e-13  Score=130.36  Aligned_cols=113  Identities=23%  Similarity=0.314  Sum_probs=93.1

Q ss_pred             CceEEEEEc--CCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhc--CCC-----CCHHHHHHHHHhcCCCHHHHH
Q psy4285           6 TNVRFCIIC--NYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQE--KVN-----VTPDGKKAIIDLSDGDMRKVL   76 (533)
Q Consensus         6 ~~~~~il~~--~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~--~~~-----~~~~~~~~~~~~~~g~~r~a~   76 (533)
                      +.+.||-+|  ||+|.++|+|+|||++|.|+|++.++|.+.|.+++..+  ++.     +++++++.++..++||.|+|+
T Consensus       131 G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~GD~R~aL  210 (436)
T COG2256         131 GTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRAL  210 (436)
T ss_pred             CeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCchHHHHH
Confidence            455566655  99999999999999999999999999999999966532  333     789999999999999999999


Q ss_pred             HHHHHHHHhCCC--CcchhhHHhhhhhhccccch--hHHHHHhchH
Q psy4285          77 NILQSAATAHAD--EVNEDTIFTLLVSRVEKYRP--STLDELVSHQ  118 (533)
Q Consensus        77 ~~l~~~~~~~~~--~i~~~~i~~~~~~~~ek~~~--~~l~~lls~~  118 (533)
                      |.||.++.....  .++.+.+.++++.....|+.  +.||+++|-.
T Consensus       211 N~LE~~~~~~~~~~~~~~~~l~~~l~~~~~~~Dk~gD~hYdliSA~  256 (436)
T COG2256         211 NLLELAALSAEPDEVLILELLEEILQRRSARFDKDGDAHYDLISAL  256 (436)
T ss_pred             HHHHHHHHhcCCCcccCHHHHHHHHhhhhhccCCCcchHHHHHHHH
Confidence            999999886543  35578888888877766665  4799998743

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.46  E-value=3e-13  Score=140.41  Aligned_cols=102  Identities=25%  Similarity=0.352  Sum_probs=94.3

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+.+++||++|+.+.++.++|+|||++|+|++++.+++.+||+++++++|+.++++++..|++.++||+|+|+|.||
T Consensus       140 LEep~~~t~~Il~t~~~~kl~~~I~SRc~~~~f~~ls~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~GdlR~aln~Le  219 (504)
T PRK14963        140 LEEPPEHVIFILATTEPEKMPPTILSRTQHFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDAESLLE  219 (504)
T ss_pred             HHhCCCCEEEEEEcCChhhCChHHhcceEEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhc
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRV  103 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~  103 (533)
                      .+... +..||.+.|.++++...
T Consensus       220 kl~~~-~~~It~~~V~~~l~~~~  241 (504)
T PRK14963        220 RLLAL-GTPVTRKQVEEALGLPP  241 (504)
T ss_pred             HHHhc-CCCCCHHHHHHHHCCCc
Confidence            98764 45799999887766544

>KOG0726|consensus

Probab=99.46  E-value=5.8e-13  Score=122.35  Aligned_cols=122  Identities=23%  Similarity=0.376  Sum_probs=89.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC------CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD------DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+++||+||||||.+|+++|+.-      ...|+++.+++      +.+...+|++++-...      ..+.++||||+|
T Consensus       221 GVIlyG~PGTGKTLLAKAVANqT------SATFlRvvGseLiQkylGdGpklvRqlF~vA~e------~apSIvFiDEId  288 (440)
T KOG0726|consen  221 GVILYGEPGTGKTLLAKAVANQT------SATFLRVVGSELIQKYLGDGPKLVRELFRVAEE------HAPSIVFIDEID  288 (440)
T ss_pred             eeEEeCCCCCchhHHHHHHhccc------chhhhhhhhHHHHHHHhccchHHHHHHHHHHHh------cCCceEEeehhh
Confidence            49999999999999999999875      56677777665      2355566665543322      356899999999


Q ss_pred             CCCH-----------HHHHHHHHHHHh-----cCCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC
Q psy4285         382 AMTN-----------DAQNALRRIIEK-----FTTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       382 ~l~~-----------~~~~~Ll~~le~-----~~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+..           +.|..++.++++     ....+.+|++||..+.+||+|.+  |.+ .+.|+.|+.. .+..+..+
T Consensus       289 AiGtKRyds~SggerEiQrtmLELLNQldGFdsrgDvKvimATnrie~LDPaLiRPGrIDrKIef~~pDe~-TkkkIf~I  367 (440)
T KOG0726|consen  289 AIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK-TKKKIFQI  367 (440)
T ss_pred             hhccccccCCCccHHHHHHHHHHHHHhccCccccCCeEEEEecccccccCHhhcCCCccccccccCCCchh-hhceeEEE
Confidence            9853           446666666653     24679999999999999999998  774 6777666544 44445444

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.45  E-value=2.8e-13  Score=141.45  Aligned_cols=100  Identities=22%  Similarity=0.328  Sum_probs=92.4

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+++++|||+||.++++++||+|||++|+|++++.+++..+|+++++++++.+++++++.|+..++||+|+|+++|+
T Consensus       143 LEEP~~~~ifILaTt~~~kll~TI~SRcq~i~F~pLs~~eL~~~L~~il~~egi~id~eal~lIA~~s~GdlR~Al~lLe  222 (624)
T PRK14959        143 LEEPPARVTFVLATTEPHKFPVTIVSRCQHFTFTRLSEAGLEAHLTKVLGREGVDYDPAAVRLIARRAAGSVRDSMSLLG  222 (624)
T ss_pred             hhccCCCEEEEEecCChhhhhHHHHhhhhccccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLV  100 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~  100 (533)
                      .+.......|+.+.|.++++
T Consensus       223 qll~~g~~~It~d~V~~~lg  242 (624)
T PRK14959        223 QVLALGESRLTIDGARGVLG  242 (624)
T ss_pred             HHHHhcCCCcCHHHHHHHhC
Confidence            87654555799888877654

>KOG0737|consensus

Probab=99.45  E-value=4.7e-13  Score=127.74  Aligned_cols=159  Identities=22%  Similarity=0.234  Sum_probs=102.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchh--HHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIG--IVRDQIFQFASTKTMHKSSYKLIILDEADAMTN  385 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~  385 (533)
                      ++|++||||||||.+|+++|++.      +..++.+..+...+..  .-....+.....+.  .-.+.++||||+|.+..
T Consensus       129 GiLL~GPpG~GKTmlAKA~Akea------ga~fInv~~s~lt~KWfgE~eKlv~AvFslAs--Kl~P~iIFIDEvds~L~  200 (386)
T KOG0737|consen  129 GILLYGPPGTGKTMLAKAIAKEA------GANFINVSVSNLTSKWFGEAQKLVKAVFSLAS--KLQPSIIFIDEVDSFLG  200 (386)
T ss_pred             cceecCCCCchHHHHHHHHHHHc------CCCcceeeccccchhhHHHHHHHHHHHHhhhh--hcCcceeehhhHHHHHh
Confidence            59999999999999999999998      6777777777654421  11111221111111  23578999999998864


Q ss_pred             HHH---H--------HHHHHHH----hcCCCcEEEEEeCCCCCCChhhhccc-eeeeecCCCHHHHHHHhhcC--HHHHH
Q psy4285         386 DAQ---N--------ALRRIIE----KFTTNVRFCIICNYLSKIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD--DISFF  447 (533)
Q Consensus       386 ~~~---~--------~Ll~~le----~~~~~~~~I~~~n~~~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~--~~~~~  447 (533)
                      ..+   +        .|...=+    .....+.+..+||+|..+|+++.||+ ..+++.-|+..+..++|.-+  ++.+.
T Consensus       201 ~R~s~dHEa~a~mK~eFM~~WDGl~s~~~~rVlVlgATNRP~DlDeAiiRR~p~rf~V~lP~~~qR~kILkviLk~e~~e  280 (386)
T KOG0737|consen  201 QRRSTDHEATAMMKNEFMALWDGLSSKDSERVLVLGATNRPFDLDEAIIRRLPRRFHVGLPDAEQRRKILKVILKKEKLE  280 (386)
T ss_pred             hcccchHHHHHHHHHHHHHHhccccCCCCceEEEEeCCCCCccHHHHHHHhCcceeeeCCCchhhHHHHHHHHhcccccC
Confidence            221   1        1111111    12334667778899999999999998 57888888888888888776  22221


Q ss_pred             HHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         448 NIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       448 ~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                      .=++ +..+..  .+.|||+.|+..-+..+
T Consensus       281 ~~vD-~~~iA~--~t~GySGSDLkelC~~A  307 (386)
T KOG0737|consen  281 DDVD-LDEIAQ--MTEGYSGSDLKELCRLA  307 (386)
T ss_pred             cccC-HHHHHH--hcCCCcHHHHHHHHHHH
Confidence            1111 222222  78899999987665544

>PRK06893 DNA replication initiation factor; Validated

Probab=99.45  E-value=6.5e-13  Score=125.01  Aligned_cols=124  Identities=16%  Similarity=0.241  Sum_probs=82.1

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCC-
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMT-  384 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~-  384 (533)
                      .|.++|+|||||||||+++++++++.... ....++.++..+...    .+.+..+        ...++|+|||++.+. 
T Consensus        39 ~~~l~l~G~~G~GKThL~~ai~~~~~~~~-~~~~y~~~~~~~~~~----~~~~~~~--------~~~dlLilDDi~~~~~  105 (229)
T PRK06893         39 QPFFYIWGGKSSGKSHLLKAVSNHYLLNQ-RTAIYIPLSKSQYFS----PAVLENL--------EQQDLVCLDDLQAVIG  105 (229)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcC-CCeEEeeHHHhhhhh----HHHHhhc--------ccCCEEEEeChhhhcC
Confidence            34589999999999999999999875442 122333332221111    1111111        245799999999985 


Q ss_pred             -HHHHHHHHHHHHhcCC-C-cEEEEEeCCC-C---CCChhhhccce---eeeecCCCHHHHHHHhhcC
Q psy4285         385 -NDAQNALRRIIEKFTT-N-VRFCIICNYL-S---KIPPAIQSRCT---RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       385 -~~~~~~Ll~~le~~~~-~-~~~I~~~n~~-~---~l~~~l~sR~~---~i~~~~~~~~~~~~~l~~~  442 (533)
                       ...+..|+.+++.... + ..+|+++|.. .   ..++.++||+.   .+.+.+|++++...++.+.
T Consensus       106 ~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~  173 (229)
T PRK06893        106 NEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRN  173 (229)
T ss_pred             ChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHH
Confidence             3345578887765432 2 3446666653 2   24589999985   8889999999999888765

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.45  E-value=2.3e-12  Score=135.78  Aligned_cols=149  Identities=20%  Similarity=0.270  Sum_probs=96.7

Q ss_pred             hhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccc---cc-CcceEEecCCCCCchhHH-HHH----------
Q psy4285         294 CYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKA---QF-NAMVLELNASDDRGIGIV-RDQ----------  357 (533)
Q Consensus       294 ~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~---~~-~~~~~~~~~~~~~~~~~~-~~~----------  357 (533)
                      ...|..++......+ ++++|+||||||++++.+.+++....   .. ...++++++........+ ..+          
T Consensus       768 asfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIYqvI~qqL~g~~P~  847 (1164)
T PTZ00112        768 HGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAYQVLYKQLFNKKPP  847 (1164)
T ss_pred             HHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHHHHHHHHHcCCCCC
Confidence            344445554444344 46999999999999999998874321   11 245677887553332211 111          


Q ss_pred             --------HHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh---cCCCcEEEEEeCC---CCCCChhhhccce
Q psy4285         358 --------IFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEK---FTTNVRFCIICNY---LSKIPPAIQSRCT  423 (533)
Q Consensus       358 --------~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~---~~~~~~~I~~~n~---~~~l~~~l~sR~~  423 (533)
                              +..+............||||||+|.+....+..|+.+++.   ....+.+|+++|.   +..++|.++|||.
T Consensus       848 ~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLIGISNdlDLperLdPRLRSRLg  927 (1164)
T PTZ00112        848 NALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLIAISNTMDLPERLIPRCRSRLA  927 (1164)
T ss_pred             ccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEEEecCchhcchhhhhhhhhccc
Confidence                    1111111000012356999999999987667777777653   2345667778875   4578899999984


Q ss_pred             --eeeecCCCHHHHHHHhhcC
Q psy4285         424 --RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 --~i~~~~~~~~~~~~~l~~~  442 (533)
                        .+.|.||+.+++.++|...
T Consensus       928 ~eeIvF~PYTaEQL~dILk~R  948 (1164)
T PTZ00112        928 FGRLVFSPYKGDEIEKIIKER  948 (1164)
T ss_pred             cccccCCCCCHHHHHHHHHHH
Confidence              5999999999999999876

>KOG0744|consensus

Probab=99.44  E-value=1.3e-12  Score=121.86  Aligned_cols=130  Identities=25%  Similarity=0.383  Sum_probs=92.4

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcccc---ccCcceEEecCCCC---------CchhHHHHHHHHHHhcccCCCCCcEEEE
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKA---QFNAMVLELNASDD---------RGIGIVRDQIFQFASTKTMHKSSYKLII  376 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~---~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~vli  376 (533)
                      +|++||||||||++++++|+.+.-..   .+....+++|+...         +-...+.+.+......    ++..-.++
T Consensus       180 iLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d----~~~lVfvL  255 (423)
T KOG0744|consen  180 ILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVED----RGNLVFVL  255 (423)
T ss_pred             EEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhC----CCcEEEEE
Confidence            89999999999999999999984321   12334677776432         1122233333333333    24556889


Q ss_pred             EeCCCCCCH---------------HHHHHHHHHHHh--cCCCcEEEEEeCCCCCCChhhhccce-eeeecCCCHHHHHHH
Q psy4285         377 LDEADAMTN---------------DAQNALRRIIEK--FTTNVRFCIICNYLSKIPPAIQSRCT-RFRFGPLDSSLIMSR  438 (533)
Q Consensus       377 iDE~d~l~~---------------~~~~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~sR~~-~i~~~~~~~~~~~~~  438 (533)
                      |||++.+..               ...|+++..|++  ..+|+.+..|+|..+.+|.++.+|.+ +..+.+|+.+.+.++
T Consensus       256 IDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDrlK~~~NvliL~TSNl~~siD~AfVDRADi~~yVG~Pt~~ai~~I  335 (423)
T KOG0744|consen  256 IDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDRLKRYPNVLILATSNLTDSIDVAFVDRADIVFYVGPPTAEAIYEI  335 (423)
T ss_pred             eHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHhccCCCEEEEeccchHHHHHHHhhhHhhheeecCCccHHHHHHH
Confidence            999998853               246889999985  45778888888999999999999997 555677777777777


Q ss_pred             hhcC
Q psy4285         439 LDYD  442 (533)
Q Consensus       439 l~~~  442 (533)
                      ++..
T Consensus       336 lksc  339 (423)
T KOG0744|consen  336 LKSC  339 (423)
T ss_pred             HHHH
Confidence            7654

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.44  E-value=4.7e-13  Score=137.78  Aligned_cols=102  Identities=25%  Similarity=0.408  Sum_probs=93.5

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+++++||++|+++.++.++|+|||+++.|++++.+++..+|++++..+++.++++++..|++.++||+|.|+|.|+
T Consensus       141 LE~p~~~vv~Ilattn~~kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi~i~~eal~~Ia~~s~GdlR~aln~Le  220 (472)
T PRK14962        141 LEEPPSHVVFVLATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLE  220 (472)
T ss_pred             HHhCCCcEEEEEEeCChHhhhHHHhcCcEEEEECCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVSR  102 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~  102 (533)
                      .++......||.+.+.++++..
T Consensus       221 ~l~~~~~~~It~e~V~~~l~~~  242 (472)
T PRK14962        221 QVWKFSEGKITLETVHEALGLI  242 (472)
T ss_pred             HHHHhcCCCCCHHHHHHHHcCC
Confidence            9876544569999887766543

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.44  E-value=5.2e-13  Score=140.26  Aligned_cols=101  Identities=20%  Similarity=0.300  Sum_probs=93.7

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+||.+++|||+|+.+.++++||+|||++++|++++.+++.++|++++.++++.++++++..|++.++||+|.|++.|+
T Consensus       143 LEepp~~~vfI~~tte~~kL~~tI~SRc~~~~f~~l~~~el~~~L~~i~~~egi~id~eAl~lLa~~s~GdlR~alslLd  222 (563)
T PRK06647        143 IEEPPPYIVFIFATTEVHKLPATIKSRCQHFNFRLLSLEKIYNMLKKVCLEDQIKYEDEALKWIAYKSTGSVRDAYTLFD  222 (563)
T ss_pred             hccCCCCEEEEEecCChHHhHHHHHHhceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVS  101 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~  101 (533)
                      .+....+..|+.+.+.++++.
T Consensus       223 klis~~~~~It~e~V~~llg~  243 (563)
T PRK06647        223 QVVSFSDSDITLEQIRSKMGL  243 (563)
T ss_pred             HHHhhcCCCCCHHHHHHHhCC
Confidence            887655567898888776654

>KOG0742|consensus

Probab=99.43  E-value=1.5e-12  Score=124.90  Aligned_cols=160  Identities=21%  Similarity=0.257  Sum_probs=105.0

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC--c---hhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR--G---IGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~--~---~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .|++||||||||||..|+.+|+..      +..+-.+.+.+..  +   ...+++++......     .++-+|||||+|
T Consensus       385 RNilfyGPPGTGKTm~ArelAr~S------GlDYA~mTGGDVAPlG~qaVTkiH~lFDWakkS-----~rGLllFIDEAD  453 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMFARELARHS------GLDYAIMTGGDVAPLGAQAVTKIHKLFDWAKKS-----RRGLLLFIDEAD  453 (630)
T ss_pred             hheeeeCCCCCCchHHHHHHHhhc------CCceehhcCCCccccchHHHHHHHHHHHHHhhc-----ccceEEEehhhH
Confidence            469999999999999999999876      4444445554432  2   23344443332222     356799999998


Q ss_pred             CCC---------HHHHHHHHHHH---HhcCCCcEEEEEeCCCCCCChhhhccce-eeeecCCCHHHHHHHhhcC------
Q psy4285         382 AMT---------NDAQNALRRII---EKFTTNVRFCIICNYLSKIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD------  442 (533)
Q Consensus       382 ~l~---------~~~~~~Ll~~l---e~~~~~~~~I~~~n~~~~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~------  442 (533)
                      .+.         .....+|.-+|   -+.+..+.++++||++..+|.++-+|++ .+.|+-|..++...+|...      
T Consensus       454 AFLceRnktymSEaqRsaLNAlLfRTGdqSrdivLvlAtNrpgdlDsAV~DRide~veFpLPGeEERfkll~lYlnkyi~  533 (630)
T KOG0742|consen  454 AFLCERNKTYMSEAQRSALNALLFRTGDQSRDIVLVLATNRPGDLDSAVNDRIDEVVEFPLPGEEERFKLLNLYLNKYIL  533 (630)
T ss_pred             HHHHHhchhhhcHHHHHHHHHHHHHhcccccceEEEeccCCccchhHHHHhhhhheeecCCCChHHHHHHHHHHHHHHhc
Confidence            763         22223333332   3456778899999999999999999995 7888777777777666554      


Q ss_pred             -------HHHHHHHHHH------------HHHHHH-HHHhcCCCHHHHHHHHHHH
Q psy4285         443 -------DISFFNIIIW------------YIKIQE-IKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 -------~~~~~~ll~~------------~~~l~~-l~~~~~~~~~di~~~~~~~  477 (533)
                             |..+..+++.            -..+.+ ...+.|+|+++|..-+...
T Consensus       534 ~~~~~~~~~~~~~lfkk~sQ~i~l~~~~t~~~~~EaAkkTeGfSGREiakLva~v  588 (630)
T KOG0742|consen  534 KPATSGKPGKWSHLFKKESQRIKLAGFDTGRKCSEAAKKTEGFSGREIAKLVASV  588 (630)
T ss_pred             CcCCCCCCchhhHHHhhhhheeeeccchHHHHHHHHHHhccCCcHHHHHHHHHHH
Confidence                   4445555543            112222 2266788888887666543

>KOG0743|consensus

Probab=99.43  E-value=3.9e-12  Score=124.94  Aligned_cols=149  Identities=17%  Similarity=0.236  Sum_probs=105.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH---
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN---  385 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~---  385 (533)
                      .|||||||||||+++-|+|+.+      +..++.++-++......++.++...        .+..||+|.+||.-..   
T Consensus       238 YLLYGPPGTGKSS~IaAmAn~L------~ydIydLeLt~v~~n~dLr~LL~~t--------~~kSIivIEDIDcs~~l~~  303 (457)
T KOG0743|consen  238 YLLYGPPGTGKSSFIAAMANYL------NYDIYDLELTEVKLDSDLRHLLLAT--------PNKSILLIEDIDCSFDLRE  303 (457)
T ss_pred             ceeeCCCCCCHHHHHHHHHhhc------CCceEEeeeccccCcHHHHHHHHhC--------CCCcEEEEeeccccccccc
Confidence            7999999999999999999998      7888888887766666677765432        4568999999997621   


Q ss_pred             ---------------HHHHHHHHHHHhcCC----CcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC-
Q psy4285         386 ---------------DAQNALRRIIEKFTT----NVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD-  442 (533)
Q Consensus       386 ---------------~~~~~Ll~~le~~~~----~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~-  442 (533)
                                     -..+.||..++..-+    ...+|+|||..++|||||+|  |.+ ++.+..=+.++......+. 
T Consensus       304 ~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL  383 (457)
T KOG0743|consen  304 RRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYL  383 (457)
T ss_pred             ccccccccccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhc
Confidence                           123568888885433    34789999999999999999  664 7777777777777666665 


Q ss_pred             --HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285         443 --DISFFNIIIWYIKIQEIKIEKGLALTDILTEIS  475 (533)
Q Consensus       443 --~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~  475 (533)
                        ++ --.++...+   .+......+|+|+...+.
T Consensus       384 ~~~~-~h~L~~eie---~l~~~~~~tPA~V~e~lm  414 (457)
T KOG0743|consen  384 GIEE-DHRLFDEIE---RLIEETEVTPAQVAEELM  414 (457)
T ss_pred             CCCC-CcchhHHHH---HHhhcCccCHHHHHHHHh
Confidence              11 111122111   122444667777766653

>KOG1969|consensus

Probab=99.43  E-value=2.5e-12  Score=131.96  Aligned_cols=128  Identities=27%  Similarity=0.373  Sum_probs=105.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCC--CCcEEEEEeCCCCCCHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHK--SSYKLIILDEADAMTND  386 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~vliiDE~d~l~~~  386 (533)
                      +||+||||.||||+|+.+|++.      |+.++++|+++.+....+++.+....+......  ..+..|||||||--...
T Consensus       329 lLL~GppGlGKTTLAHViAkqa------GYsVvEINASDeRt~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa~~~  402 (877)
T KOG1969|consen  329 LLLCGPPGLGKTTLAHVIAKQA------GYSVVEINASDERTAPMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGAPRA  402 (877)
T ss_pred             EEeecCCCCChhHHHHHHHHhc------CceEEEecccccccHHHHHHHHHHHHhhccccccCCCcceEEEecccCCcHH
Confidence            7999999999999999999998      999999999999999999998887766554442  57889999999999988


Q ss_pred             HHHHHHHHHHh------cCC---------------CcEEEEEeCCCC-CCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         387 AQNALRRIIEK------FTT---------------NVRFCIICNYLS-KIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       387 ~~~~Ll~~le~------~~~---------------~~~~I~~~n~~~-~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +.+.++.+++.      ++.               .-.||++||... .-..+|+--+..+.|.+|+...+.++|..|
T Consensus       403 ~Vdvilslv~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNdLYaPaLR~Lr~~A~ii~f~~p~~s~Lv~RL~~I  480 (877)
T KOG1969|consen  403 AVDVILSLVKATNKQATGKQAKKDKKRKKKRSKLLTRPIICICNDLYAPALRPLRPFAEIIAFVPPSQSRLVERLNEI  480 (877)
T ss_pred             HHHHHHHHHHhhcchhhcCcccchhhhhhhccccccCCEEEEecCccchhhhhcccceEEEEecCCChhHHHHHHHHH
Confidence            89999998862      111               134899999765 223344445689999999999999999998

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.42  E-value=2.3e-12  Score=129.51  Aligned_cols=161  Identities=29%  Similarity=0.448  Sum_probs=125.9

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+++++++||++|+.+.+++++|+|||..++|.+++.+++..+|++++.++++.+++++++.++..++||+|++++.|+
T Consensus       149 le~~~~~~~~Il~~~~~~~~~~~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~  228 (337)
T PRK12402        149 MEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQ  228 (337)
T ss_pred             HHhccCCCeEEEEeCChhhCchhhcCCceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            46788899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhh-hcc-cc----------ch----hHHHHHh-----chHHHHhhc------CCChhhHHH
Q psy4285          81 SAATAHADEVNEDTIFTLLVS-RVE-KY----------RP----STLDELV-----SHQDIISTI------EIPESMLVD  133 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~-~~e-k~----------~~----~~l~~ll-----s~~~~l~~l------~~~~~~~~~  133 (533)
                      .++. ....||.+.+.++++. ..+ ..          +.    ..+++++     +...+...+      +.....+.+
T Consensus       229 ~~~~-~~~~It~~~v~~~~~~~~~~~~i~~l~~ai~~~~~~~a~~~l~~l~~~~g~~~~~i~~~l~~~~~~~~~~~~l~~  307 (337)
T PRK12402        229 TAAL-AAGEITMEAAYEALGDVGTDEVIESLLDAAEAGDFTDARKTLDDLLIDEGLSGGEVLEELLRVARSRYRGDNLAR  307 (337)
T ss_pred             HHHH-cCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHCCHHHHHH
Confidence            8774 3346888887665442 111 10          01    1233332     112222221      244455567


Q ss_pred             HHhhccCccccccCCCChhhHHHHHHHHH
Q psy4285         134 LVLKMSDIEYRLAAGTSEKIQLSALIAAF  162 (533)
Q Consensus       134 ~~~~~~~~~~~~~~G~~~~~~l~~~~~~~  162 (533)
                      .+..++++++.+..|..+.+++++|+.++
T Consensus       308 ~~~~l~~~d~~lk~g~~~~~~le~~i~~~  336 (337)
T PRK12402        308 LHRLAADADARLTDGANDRIQLEALLAEL  336 (337)
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence            78888999999999999999999999875

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.41  E-value=9.6e-13  Score=139.01  Aligned_cols=100  Identities=25%  Similarity=0.375  Sum_probs=91.4

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+||++++|||+|+..++|++||+|||++++|++++.+++..||.+++.++++.+++++++.++..++||+|.|++.|+
T Consensus       151 LEePp~~tv~IL~t~~~~kLl~TI~SRc~~vef~~l~~~ei~~~L~~i~~~egi~I~~eal~~La~~s~Gdlr~al~eLe  230 (620)
T PRK14954        151 LEEPPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLDEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDAQSILD  230 (620)
T ss_pred             HhCCCCCeEEEEEeCChhhhhHHHHhhceEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhC-----CCCcchhhHHhhhh
Q psy4285          81 SAATAH-----ADEVNEDTIFTLLV  100 (533)
Q Consensus        81 ~~~~~~-----~~~i~~~~i~~~~~  100 (533)
                      .+....     ...|+.+.|.+++.
T Consensus       231 KL~~y~~~~~~~~~It~~~V~~lv~  255 (620)
T PRK14954        231 QVIAFSVGSEAEKVIAYQGVAELLN  255 (620)
T ss_pred             HHHHhccccccCCccCHHHHHHHHc
Confidence            887654     34588877766554

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.41  E-value=6.7e-12  Score=126.67  Aligned_cols=206  Identities=14%  Similarity=0.105  Sum_probs=115.3

Q ss_pred             HHHHHHHhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEe-cCCCCCchhHHHHH-
Q psy4285         280 TNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLEL-NASDDRGIGIVRDQ-  357 (533)
Q Consensus       280 ~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~-  357 (533)
                      ...+.....|++++++.+...+..+.  |++|+||||||||++|+++++.+.....+......+ .+++..+...+... 
T Consensus        15 ~~~l~~~i~gre~vI~lll~aalag~--hVLL~GpPGTGKT~LAraLa~~~~~~~~F~~~~~~fttp~DLfG~l~i~~~~   92 (498)
T PRK13531         15 SSALEKGLYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFGPLSIQALK   92 (498)
T ss_pred             HHHHhhhccCcHHHHHHHHHHHccCC--CEEEECCCChhHHHHHHHHHHHhcccCcceeeeeeecCcHHhcCcHHHhhhh
Confidence            33344456788888887777766555  899999999999999999999864321111111111 12222221111111 


Q ss_pred             -HHHHHh-cccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcC---------CCcEE-EEEeCCCC---CCChhhhccc
Q psy4285         358 -IFQFAS-TKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT---------TNVRF-CIICNYLS---KIPPAIQSRC  422 (533)
Q Consensus       358 -~~~~~~-~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~---------~~~~~-I~~~n~~~---~l~~~l~sR~  422 (533)
                       .+.|.. ..... ....++|+||+..+++..+++|+..|++..         -..++ +++||...   ...+++..||
T Consensus        93 ~~g~f~r~~~G~L-~~A~lLfLDEI~rasp~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN~LPE~g~~leAL~DRF  171 (498)
T PRK13531         93 DEGRYQRLTSGYL-PEAEIVFLDEIWKAGPAILNTLLTAINERRFRNGAHEEKIPMRLLVTASNELPEADSSLEALYDRM  171 (498)
T ss_pred             hcCchhhhcCCcc-ccccEEeecccccCCHHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECCCCcccCCchHHhHhhE
Confidence             111211 11101 134599999999999999999999997532         22344 55555332   2345999999


Q ss_pred             e-eeeecCCCH-HHHHHHhhcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHH
Q psy4285         423 T-RFRFGPLDS-SLIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDI  498 (533)
Q Consensus       423 ~-~i~~~~~~~-~~~~~~l~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~  498 (533)
                      . .+.++++++ ++..++|.........-..         ....++..++ ..+.+.+....+++.+..++......+
T Consensus       172 liri~vp~l~~~~~e~~lL~~~~~~~~~~~~---------~~~vis~eel-~~lq~~v~~V~v~d~v~eyI~~L~~~l  239 (498)
T PRK13531        172 LIRLWLDKVQDKANFRSMLTSQQDENDNPVP---------ASLQITDEEY-QQWQKEIGKITLPDHVFELIFQLRQQL  239 (498)
T ss_pred             EEEEECCCCCchHHHHHHHHcccccccCCCc---------ccCCCCHHHH-HHHHHHhcceeCCHHHHHHHHHHHHHH
Confidence            4 677777764 4456666542000000000         0113455554 345555666666666666655555443

>PRK08485 DNA polymerase III subunit delta'; Validated

Probab=99.41  E-value=2.3e-13  Score=120.15  Aligned_cols=83  Identities=20%  Similarity=0.216  Sum_probs=76.7

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhcccee-------------EEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHh
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTR-------------FRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL   67 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~-------------~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   67 (533)
                      +||||++++|||+|+.+++++|||+|||++             +.|++++.+++.++|++ .+++++...+++++.|+..
T Consensus        78 LEEPp~~~~fiL~t~~~~~llpTI~SRc~~~~~~~~~~~~~l~l~l~~l~~~~i~~~L~~-~~ke~~~~~~ea~~lIa~l  156 (206)
T PRK08485         78 LEEPPKNICFIIVAKSKNLLLPTIRSRLIIEKRKQKKPVKPLDLDLKKLDLKDIYEFLKE-LEKENKLSKEELKELIESL  156 (206)
T ss_pred             hcCCCCCeEEEEEeCChHhCchHHHhhheeccccccccccccccccCCCCHHHHHHHHHH-HHHcccccHHHHHHHHHHH
Confidence            699999999999999999999999999997             78999999999999998 6788887788889999999


Q ss_pred             cCCCHHHHHHHHHHHHH
Q psy4285          68 SDGDMRKVLNILQSAAT   84 (533)
Q Consensus        68 ~~g~~r~a~~~l~~~~~   84 (533)
                      +.|++|.++.+.+....
T Consensus       157 a~~s~r~~l~l~~q~l~  173 (206)
T PRK08485        157 LKECVKYKIPLNEEELE  173 (206)
T ss_pred             HHHHHHHHcCccHHHHH
Confidence            99999999988887654

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.41  E-value=1.6e-12  Score=122.84  Aligned_cols=141  Identities=16%  Similarity=0.266  Sum_probs=95.8

Q ss_pred             hchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCC
Q psy4285         289 ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH  368 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  368 (533)
                      ++......+++++......+++|+||||||||++|+++++.+...   +..++.+++.+....  ..+.+..+       
T Consensus        21 ~~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~~~---~~~~~~i~~~~~~~~--~~~~~~~~-------   88 (226)
T TIGR03420        21 GNAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEER---GKSAIYLPLAELAQA--DPEVLEGL-------   88 (226)
T ss_pred             CcHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHHhc---CCcEEEEeHHHHHHh--HHHHHhhc-------
Confidence            455666777776655555579999999999999999999987533   334555555432211  11111111       


Q ss_pred             CCCcEEEEEeCCCCCCHHH--HHHHHHHHHhc-CCCcEEEEEeCCCC-C--C-Chhhhccc---eeeeecCCCHHHHHHH
Q psy4285         369 KSSYKLIILDEADAMTNDA--QNALRRIIEKF-TTNVRFCIICNYLS-K--I-PPAIQSRC---TRFRFGPLDSSLIMSR  438 (533)
Q Consensus       369 ~~~~~vliiDE~d~l~~~~--~~~Ll~~le~~-~~~~~~I~~~n~~~-~--l-~~~l~sR~---~~i~~~~~~~~~~~~~  438 (533)
                       ...++|+|||++.+....  ++.|+.+++.. ..+..+|++++... .  . .+.+.+|+   ..+.+++++.++...+
T Consensus        89 -~~~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~~~i~l~~l~~~e~~~~  167 (226)
T TIGR03420        89 -EQADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWGLVFQLPPLSDEEKIAA  167 (226)
T ss_pred             -ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcCeeEecCCCCHHHHHHH
Confidence             234699999999998643  78888887652 23357888887543 2  2 37888887   4789999999998888


Q ss_pred             hhcC
Q psy4285         439 LDYD  442 (533)
Q Consensus       439 l~~~  442 (533)
                      +.+.
T Consensus       168 l~~~  171 (226)
T TIGR03420       168 LQSR  171 (226)
T ss_pred             HHHH
Confidence            8754

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.

>PRK08727 hypothetical protein; Validated

Probab=99.40  E-value=4.7e-12  Score=119.41  Aligned_cols=122  Identities=22%  Similarity=0.306  Sum_probs=86.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCC--H
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMT--N  385 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~--~  385 (533)
                      .++|+||+||||||++.++++++...   +..+..++..+..  ..+...+..+        ...++|+|||++.+.  .
T Consensus        43 ~l~l~G~~G~GKThL~~a~~~~~~~~---~~~~~y~~~~~~~--~~~~~~~~~l--------~~~dlLiIDDi~~l~~~~  109 (233)
T PRK08727         43 WLYLSGPAGTGKTHLALALCAAAEQA---GRSSAYLPLQAAA--GRLRDALEAL--------EGRSLVALDGLESIAGQR  109 (233)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEEeHHHhh--hhHHHHHHHH--------hcCCEEEEeCcccccCCh
Confidence            49999999999999999999987443   3333444432211  1122222222        245699999999986  3


Q ss_pred             HHHHHHHHHHHhcC-CCcEEEEEeCCCC----CCChhhhcc---ceeeeecCCCHHHHHHHhhcC
Q psy4285         386 DAQNALRRIIEKFT-TNVRFCIICNYLS----KIPPAIQSR---CTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       386 ~~~~~Ll~~le~~~-~~~~~I~~~n~~~----~l~~~l~sR---~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..+..++.+++... .+..+|+|+|.+.    .+++.++||   +..+.|.+|+.+++.+++.+.
T Consensus       110 ~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~SRl~~~~~~~l~~~~~e~~~~iL~~~  174 (233)
T PRK08727        110 EDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSRLAQCIRIGLPVLDDVARAAVLRER  174 (233)
T ss_pred             HHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHHHHhcCceEEecCCCHHHHHHHHHHH
Confidence            45667888877532 3456888887543    357999999   578999999999999999974

>KOG2004|consensus

Probab=99.40  E-value=1.5e-12  Score=133.26  Aligned_cols=140  Identities=24%  Similarity=0.342  Sum_probs=100.1

Q ss_pred             chhhhhhhcccccccC------CCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchh-----------
Q psy4285         290 SMDLCYKINRFIDENE------LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIG-----------  352 (533)
Q Consensus       290 ~~~~~~~l~~~~~~~~------~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~-----------  352 (533)
                      -+++.+++.+++.-+.      .+-++|+||||+|||++++.||+.+      ++.|++++-.......           
T Consensus       416 m~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~AL------nRkFfRfSvGG~tDvAeIkGHRRTYVG  489 (906)
T KOG2004|consen  416 MEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARAL------NRKFFRFSVGGMTDVAEIKGHRRTYVG  489 (906)
T ss_pred             hHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHh------CCceEEEeccccccHHhhcccceeeec
Confidence            3445555555544332      2338999999999999999999999      5566665543222211           


Q ss_pred             ----HHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH----HHHHHHHHHHHhc---------------CCCcEEEEEeC
Q psy4285         353 ----IVRDQIFQFASTKTMHKSSYKLIILDEADAMTN----DAQNALRRIIEKF---------------TTNVRFCIICN  409 (533)
Q Consensus       353 ----~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~----~~~~~Ll~~le~~---------------~~~~~~I~~~n  409 (533)
                          .+-+.++..       .....+++|||+|++..    +-..+|+.+|+-.               -+.+.||+|.|
T Consensus       490 AMPGkiIq~LK~v-------~t~NPliLiDEvDKlG~g~qGDPasALLElLDPEQNanFlDHYLdVp~DLSkVLFicTAN  562 (906)
T KOG2004|consen  490 AMPGKIIQCLKKV-------KTENPLILIDEVDKLGSGHQGDPASALLELLDPEQNANFLDHYLDVPVDLSKVLFICTAN  562 (906)
T ss_pred             cCChHHHHHHHhh-------CCCCceEEeehhhhhCCCCCCChHHHHHHhcChhhccchhhhccccccchhheEEEEecc
Confidence                122222221       13456999999999964    4568899988621               14588999999


Q ss_pred             CCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         410 YLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       410 ~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..+.++++|++|...|.+..|..++-.++.++.
T Consensus       563 ~idtIP~pLlDRMEvIelsGYv~eEKv~IA~~y  595 (906)
T KOG2004|consen  563 VIDTIPPPLLDRMEVIELSGYVAEEKVKIAERY  595 (906)
T ss_pred             ccccCChhhhhhhheeeccCccHHHHHHHHHHh
Confidence            999999999999999999999999988887776

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

Probab=99.40  E-value=1.1e-12  Score=143.13  Aligned_cols=126  Identities=24%  Similarity=0.343  Sum_probs=92.1

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHH------------HHHHHhcccCCCCCcE
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQ------------IFQFASTKTMHKSSYK  373 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~  373 (533)
                      .+.++|+||||+|||++++.+++.+      +..+..++.........+...            ...+...    .....
T Consensus       349 g~~i~l~GppG~GKTtl~~~ia~~l------~~~~~~i~~~~~~d~~~i~g~~~~~~g~~~G~~~~~l~~~----~~~~~  418 (784)
T PRK10787        349 GPILCLVGPPGVGKTSLGQSIAKAT------GRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQKMAKV----GVKNP  418 (784)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHh------CCCEEEEEcCCCCCHHHhccchhccCCCCCcHHHHHHHhc----CCCCC
Confidence            3458999999999999999999987      455555554433222222111            1111111    12345


Q ss_pred             EEEEeCCCCCCHHH----HHHHHHHHHhc---------------CCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHH
Q psy4285         374 LIILDEADAMTNDA----QNALRRIIEKF---------------TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSL  434 (533)
Q Consensus       374 vliiDE~d~l~~~~----~~~Ll~~le~~---------------~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~  434 (533)
                      |++|||+|+++.+.    +++|+.+++..               -+++.||+|+|.. .++++|++||..+.|.+++.++
T Consensus       419 villDEidk~~~~~~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~-~i~~aLl~R~~ii~~~~~t~ee  497 (784)
T PRK10787        419 LFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSM-NIPAPLLDRMEVIRLSGYTEDE  497 (784)
T ss_pred             EEEEEChhhcccccCCCHHHHHHHHhccccEEEEecccccccccCCceEEEEcCCCC-CCCHHHhcceeeeecCCCCHHH
Confidence            99999999998764    58999999741               1678888888877 5999999999999999999999


Q ss_pred             HHHHhhcC
Q psy4285         435 IMSRLDYD  442 (533)
Q Consensus       435 ~~~~l~~~  442 (533)
                      ..++..+.
T Consensus       498 k~~Ia~~~  505 (784)
T PRK10787        498 KLNIAKRH  505 (784)
T ss_pred             HHHHHHHh
Confidence            99888776

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.40  E-value=1.3e-12  Score=135.15  Aligned_cols=102  Identities=25%  Similarity=0.346  Sum_probs=94.3

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+||++++|||+|+.++++.+||+|||+.++|++++.+++..||.++++++|+.++++++..++..++||+|.|++.|+
T Consensus       143 LEepp~~~v~Il~tt~~~kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi~id~~al~~La~~s~G~lr~al~~Ld  222 (486)
T PRK14953        143 LEEPPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQASEGGMRDAASLLD  222 (486)
T ss_pred             HhcCCCCeEEEEEECCHHHHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVSR  102 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~  102 (533)
                      .+....+..||.+.|.++++..
T Consensus       223 kl~~~~~~~It~~~V~~~lg~~  244 (486)
T PRK14953        223 QASTYGEGKVTIKVVEEFLGIV  244 (486)
T ss_pred             HHHHhcCCCcCHHHHHHHhCCC
Confidence            9876666679999887766543

>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=99.40  E-value=2.8e-12  Score=112.01  Aligned_cols=133  Identities=31%  Similarity=0.335  Sum_probs=87.6

Q ss_pred             hhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHH---HHHhcccCCC
Q psy4285         293 LCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIF---QFASTKTMHK  369 (533)
Q Consensus       293 ~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~  369 (533)
                      ....+...+......+++++||||||||++++.+++.+...   +..++.++...............   ..........
T Consensus         6 ~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~---~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (151)
T cd00009           6 AIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP---GAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEK   82 (151)
T ss_pred             HHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhcC---CCCeEEEehhhhhhhhHHHHHhhhhhHhHHHHhhcc
Confidence            34444444444344579999999999999999999987522   34556666554333222221111   0000001112


Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhc------CCCcEEEEEeCCCC--CCChhhhccc-eeeeec
Q psy4285         370 SSYKLIILDEADAMTNDAQNALRRIIEKF------TTNVRFCIICNYLS--KIPPAIQSRC-TRFRFG  428 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~~Ll~~le~~------~~~~~~I~~~n~~~--~l~~~l~sR~-~~i~~~  428 (533)
                      ....++++||++.+.......+++.++..      ..++.+|+++|...  .+++.+.+|| ..+.++
T Consensus        83 ~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~r~~~~i~~~  150 (151)
T cd00009          83 AKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIP  150 (151)
T ss_pred             CCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHhhhccEeecC
Confidence            45789999999999888888888888765      36788999998777  7889999999 455443

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.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.39  E-value=1.4e-11  Score=125.25  Aligned_cols=143  Identities=20%  Similarity=0.292  Sum_probs=91.7

Q ss_pred             ccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc---cCcceEEecCCCCCch-hHHHHHHHHHH------------
Q psy4285         299 RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ---FNAMVLELNASDDRGI-GIVRDQIFQFA------------  362 (533)
Q Consensus       299 ~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~---~~~~~~~~~~~~~~~~-~~~~~~~~~~~------------  362 (533)
                      ..+..+..++++++||||||||++++.+++.+.....   ....++.+++....+. ..+......+.            
T Consensus        33 ~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~  112 (365)
T TIGR02928        33 PILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLRGSGEEVPTTGLS  112 (365)
T ss_pred             HHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHHHHHHHHhhcCCCCCCCCCC
Confidence            3333444557999999999999999999998743210   1134566676543332 22222222221            


Q ss_pred             ---------hcccCCCCCcEEEEEeCCCCCCHH---HHHHHHHH--HHhcC-CCcEEEEEeCCCC---CCChhhhccc--
Q psy4285         363 ---------STKTMHKSSYKLIILDEADAMTND---AQNALRRI--IEKFT-TNVRFCIICNYLS---KIPPAIQSRC--  422 (533)
Q Consensus       363 ---------~~~~~~~~~~~vliiDE~d~l~~~---~~~~Ll~~--le~~~-~~~~~I~~~n~~~---~l~~~l~sR~--  422 (533)
                               .... ....+.||+|||+|.+...   ....|+++  ..+.+ .++.+|+++|.+.   .+++.+.+||  
T Consensus       113 ~~~~~~~l~~~l~-~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~~~~~l~~~~~s~~~~  191 (365)
T TIGR02928       113 TSEVFRRLYKELN-ERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGISNDLKFRENLDPRVKSSLCE  191 (365)
T ss_pred             HHHHHHHHHHHHH-hcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEECCcchHhhcCHHHhccCCc
Confidence                     0000 0134679999999999532   23344444  22222 5678899998775   5888999998  


Q ss_pred             eeeeecCCCHHHHHHHhhcC
Q psy4285         423 TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       423 ~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..+.|.|++.+++.+++...
T Consensus       192 ~~i~f~p~~~~e~~~il~~r  211 (365)
T TIGR02928       192 EEIIFPPYDAEELRDILENR  211 (365)
T ss_pred             ceeeeCCCCHHHHHHHHHHH
Confidence            47999999999999999765

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.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=99.38  E-value=6.8e-12  Score=124.10  Aligned_cols=168  Identities=16%  Similarity=0.152  Sum_probs=112.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH-HH----HHhc----c-cCCCCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI-FQ----FAST----K-TMHKSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~----~~~~----~-~~~~~~~~vlii  377 (533)
                      +++|+|++||||+++|+++.......   ..+++.+++..... ..+...+ +.    |...    . ....+..++|||
T Consensus        24 pVLI~GE~GtGK~~lAr~iH~~s~r~---~~pfv~vnc~~~~~-~~l~~~lfG~~~g~~~ga~~~~~G~~~~a~gGtL~L   99 (329)
T TIGR02974        24 PVLIIGERGTGKELIAARLHYLSKRW---QGPLVKLNCAALSE-NLLDSELFGHEAGAFTGAQKRHQGRFERADGGTLFL   99 (329)
T ss_pred             CEEEECCCCChHHHHHHHHHHhcCcc---CCCeEEEeCCCCCh-HHHHHHHhccccccccCcccccCCchhhCCCCEEEe
Confidence            59999999999999999998765332   56888899876432 2222221 10    0000    0 011345789999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         378 DEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ||++.|+.+.|..|++.+++.           +.++++|++|+..       ..+.+.|..|+..+.+.-|+       |
T Consensus       100 dei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~at~~~l~~~~~~g~fr~dL~~rl~~~~i~lPp-------L  172 (329)
T TIGR02974       100 DELATASLLVQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNADLPALAAEGRFRADLLDRLAFDVITLPP-------L  172 (329)
T ss_pred             CChHhCCHHHHHHHHHHHHcCcEEecCCCceeccceEEEEechhhHHHHhhcCchHHHHHHHhcchhcCCCc-------h
Confidence            999999999999999999853           2457999999753       35678888899766666666       4


Q ss_pred             hcCHHHHHHHHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHhcCCChhHH
Q psy4285         440 DYDDISFFNIIIWYIKIQEIKIEKGLAL-TDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       440 ~~~~~~~~~ll~~~~~l~~l~~~~~~~~-~di~~~~~~~~~~~~~~~~~~  488 (533)
                      +..++|+..+++.+-.  .+....|... ..+-......+..+.||++++
T Consensus       173 ReR~eDI~~L~~~fl~--~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvr  220 (329)
T TIGR02974       173 RERQEDIMLLAEHFAI--RMARELGLPLFPGFTPQAREQLLEYHWPGNVR  220 (329)
T ss_pred             hhhhhhHHHHHHHHHH--HHHHHhCCCCCCCcCHHHHHHHHhCCCCchHH
Confidence            4444455555543211  1112234443 356677888899999999987

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

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.38  E-value=1.9e-12  Score=137.63  Aligned_cols=100  Identities=21%  Similarity=0.436  Sum_probs=91.6

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+.+++|||+|+.+.+++|||+|||+.++|++++.+++..+|.+++.++++.++++++..+++.++||+|+|+++|+
T Consensus       145 LEePp~~tvfIL~t~~~~~llpTIrSRc~~~~f~~l~~~ei~~~L~~ia~kegi~is~~al~~La~~s~G~lr~A~~lLe  224 (620)
T PRK14948        145 LEEPPPRVVFVLATTDPQRVLPTIISRCQRFDFRRIPLEAMVQHLSEIAEKESIEIEPEALTLVAQRSQGGLRDAESLLD  224 (620)
T ss_pred             HhcCCcCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVS  101 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~  101 (533)
                      ..+... ..|+.+.|.++++.
T Consensus       225 klsL~~-~~It~e~V~~lvg~  244 (620)
T PRK14948        225 QLSLLP-GPITPEAVWDLLGA  244 (620)
T ss_pred             HHHhcc-CCCCHHHHHHHhcC
Confidence            987643 46888887765543

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.38  E-value=3.7e-12  Score=137.06  Aligned_cols=152  Identities=25%  Similarity=0.255  Sum_probs=107.1

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .+++|+||||||||+++++++.++      +.+++.+++++.      .+...++..+....      ...++|+||||+
T Consensus       186 ~gill~G~~G~GKt~~~~~~a~~~------~~~f~~is~~~~~~~~~g~~~~~~~~~f~~a~------~~~P~IifIDEi  253 (644)
T PRK10733        186 KGVLMVGPPGTGKTLLAKAIAGEA------KVPFFTISGSDFVEMFVGVGASRVRDMFEQAK------KAAPCIIFIDEI  253 (644)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHc------CCCEEEEehHHhHHhhhcccHHHHHHHHHHHH------hcCCcEEEehhH
Confidence            359999999999999999999987      566777776542      23334444443321      135689999999


Q ss_pred             CCCCHH--------------HHHHHHHHHHhc--CCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhc
Q psy4285         381 DAMTND--------------AQNALRRIIEKF--TTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       381 d~l~~~--------------~~~~Ll~~le~~--~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~  441 (533)
                      |.+...              ..+.|+..|+..  ...+.+|++||.++.+|+++++  || ..+.++.|+.++..+++..
T Consensus       254 D~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~  333 (644)
T PRK10733        254 DAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKV  333 (644)
T ss_pred             hhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCHHHHHHHHHH
Confidence            998431              234555556643  3457888899999999999997  89 5888888998888888776


Q ss_pred             C--------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Q psy4285         442 D--------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVH  479 (533)
Q Consensus       442 ~--------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~  479 (533)
                      .        ..++..+.+         .+.|+++.|+..-+.++..
T Consensus       334 ~~~~~~l~~~~d~~~la~---------~t~G~sgadl~~l~~eAa~  370 (644)
T PRK10733        334 HMRRVPLAPDIDAAIIAR---------GTPGFSGADLANLVNEAAL  370 (644)
T ss_pred             HhhcCCCCCcCCHHHHHh---------hCCCCCHHHHHHHHHHHHH
Confidence            5        111222222         6778999988777766543

>PHA02244 ATPase-like protein

Probab=99.37  E-value=1.3e-11  Score=120.30  Aligned_cols=122  Identities=24%  Similarity=0.258  Sum_probs=86.2

Q ss_pred             hcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC----Cc----hhHHHHHHHHHHhcccCC
Q psy4285         297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD----RG----IGIVRDQIFQFASTKTMH  368 (533)
Q Consensus       297 l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~----~~----~~~~~~~~~~~~~~~~~~  368 (533)
                      +.+++..+.  +++|+||||||||++|+++|+.+      +.+++.++....    .+    .....  -..+...    
T Consensus       112 i~r~l~~~~--PVLL~GppGtGKTtLA~aLA~~l------g~pfv~In~l~d~~~L~G~i~~~g~~~--dgpLl~A----  177 (383)
T PHA02244        112 IAKIVNANI--PVFLKGGAGSGKNHIAEQIAEAL------DLDFYFMNAIMDEFELKGFIDANGKFH--ETPFYEA----  177 (383)
T ss_pred             HHHHHhcCC--CEEEECCCCCCHHHHHHHHHHHh------CCCEEEEecChHHHhhccccccccccc--chHHHHH----
Confidence            334555443  69999999999999999999987      555665553210    00    00000  0001100    


Q ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHHHHh-----------cCCCcEEEEEeCCC-----------CCCChhhhccceeee
Q psy4285         369 KSSYKLIILDEADAMTNDAQNALRRIIEK-----------FTTNVRFCIICNYL-----------SKIPPAIQSRCTRFR  426 (533)
Q Consensus       369 ~~~~~vliiDE~d~l~~~~~~~Ll~~le~-----------~~~~~~~I~~~n~~-----------~~l~~~l~sR~~~i~  426 (533)
                      ...+.+|+|||++.+.++.+..|...++.           .+++.++|+|+|..           ..+.+++++||..+.
T Consensus       178 ~~~GgvLiLDEId~a~p~vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~~~~G~~~~y~G~k~L~~AllDRFv~I~  257 (383)
T PHA02244        178 FKKGGLFFIDEIDASIPEALIIINSAIANKFFDFADERVTAHEDFRVISAGNTLGKGADHIYVARNKIDGATLDRFAPIE  257 (383)
T ss_pred             hhcCCEEEEeCcCcCCHHHHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCCCccCcccccCCCcccCHHHHhhcEEee
Confidence            13467999999999999999999999963           24688999999973           468999999999999


Q ss_pred             ecCCCH
Q psy4285         427 FGPLDS  432 (533)
Q Consensus       427 ~~~~~~  432 (533)
                      |..|++
T Consensus       258 ~dyp~~  263 (383)
T PHA02244        258 FDYDEK  263 (383)
T ss_pred             CCCCcH
Confidence            988873

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

Probab=99.37  E-value=1.6e-12  Score=134.12  Aligned_cols=149  Identities=24%  Similarity=0.255  Sum_probs=109.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC------CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD------DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      +++++||||||||.+|+++|.+.      +.+++.+++++      +.+...+|.+..+..+.      .++++||||+|
T Consensus       185 GvlLvGpPGTGKTLLAkAvAgEA------~VPFf~iSGS~FVemfVGvGAsRVRdLF~qAkk~------aP~IIFIDEiD  252 (596)
T COG0465         185 GVLLVGPPGTGKTLLAKAVAGEA------GVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKN------APCIIFIDEID  252 (596)
T ss_pred             ceeEecCCCCCcHHHHHHHhccc------CCCceeccchhhhhhhcCCCcHHHHHHHHHhhcc------CCCeEEEehhh
Confidence            49999999999999999999887      78888888876      34677888876665433      45899999999


Q ss_pred             CCCHH--------------HHHHHHHHHHhcC--CCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC
Q psy4285         382 AMTND--------------AQNALRRIIEKFT--TNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       382 ~l~~~--------------~~~~Ll~~le~~~--~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+...              ..|.|+--||.+.  ..+.++.+||+++-+||+|++  ||+ .+.+..|+-....+++.-.
T Consensus       253 AvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~~~gviviaaTNRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH  332 (596)
T COG0465         253 AVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVH  332 (596)
T ss_pred             hcccccCCCCCCCchHHHHHHHHHHhhhccCCCCCceEEEecCCCcccchHhhcCCCCcceeeecCCcchhhHHHHHHHH
Confidence            98542              2355555566554  457788889999999999998  885 6677777767777777732


Q ss_pred             ------H--HHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 ------D--ISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 ------~--~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                            .  -++..+..         .+.|++..|+.+.+.+.
T Consensus       333 ~~~~~l~~~Vdl~~iAr---------~tpGfsGAdL~nl~NEA  366 (596)
T COG0465         333 AKNKPLAEDVDLKKIAR---------GTPGFSGADLANLLNEA  366 (596)
T ss_pred             hhcCCCCCcCCHHHHhh---------hCCCcccchHhhhHHHH
Confidence                  1  12222222         67788888887777544

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=99.37  E-value=9e-13  Score=130.08  Aligned_cols=76  Identities=24%  Similarity=0.409  Sum_probs=68.5

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++|+|||+|+.+++++|||+||||.++|++++.+++.+||.+     ...++++....+++.++|++.+|+.+++
T Consensus       132 LEEPp~~t~fiL~t~~~~~lLpTIrSRCq~~~~~~~~~~~~~~~L~~-----~~~~~~~~a~~~~~la~G~~~~Al~l~~  206 (334)
T PRK07993        132 LEEPPENTWFFLACREPARLLATLRSRCRLHYLAPPPEQYALTWLSR-----EVTMSQDALLAALRLSAGAPGAALALLQ  206 (334)
T ss_pred             hcCCCCCeEEEEEECChhhChHHHHhccccccCCCCCHHHHHHHHHH-----ccCCCHHHHHHHHHHcCCCHHHHHHHhc
Confidence            79999999999999999999999999999999999999999999962     2346677778899999999999998875


Q ss_pred             H
Q psy4285          81 S   81 (533)
Q Consensus        81 ~   81 (533)
                      .
T Consensus       207 ~  207 (334)
T PRK07993        207 P  207 (334)
T ss_pred             C
Confidence            3

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.37  E-value=6.6e-12  Score=118.50  Aligned_cols=136  Identities=13%  Similarity=0.223  Sum_probs=91.1

Q ss_pred             hchhhhhhhccccccc-CCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC
Q psy4285         289 ESMDLCYKINRFIDEN-ELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM  367 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~-~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (533)
                      ++......+..+.... ...+++|+||||||||++|+++++.+...   +..+..+++.....      .. .+      
T Consensus        24 ~~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~---~~~~~~i~~~~~~~------~~-~~------   87 (227)
T PRK08903         24 ENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASYG---GRNARYLDAASPLL------AF-DF------   87 (227)
T ss_pred             CcHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHHHhC---CCcEEEEehHHhHH------HH-hh------
Confidence            3444555555554422 22359999999999999999999987443   34555555543211      11 01      


Q ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCC--cEEEEEeCCCC---CCChhhhccc---eeeeecCCCHHHHHHHh
Q psy4285         368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTN--VRFCIICNYLS---KIPPAIQSRC---TRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       368 ~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~--~~~I~~~n~~~---~l~~~l~sR~---~~i~~~~~~~~~~~~~l  439 (533)
                       ....++|+|||+|.++.+.+..|+.+++....+  ..++++++...   .+.+.+.||+   ..+.++|+++++...++
T Consensus        88 -~~~~~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~~~~~~~~l  166 (227)
T PRK08903         88 -DPEAELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLSDADKIAAL  166 (227)
T ss_pred             -cccCCEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCCHHHHHHHH
Confidence             134679999999999998899999998753322  34566665432   4668888887   68999999988766555


Q ss_pred             hc
Q psy4285         440 DY  441 (533)
Q Consensus       440 ~~  441 (533)
                      .+
T Consensus       167 ~~  168 (227)
T PRK08903        167 KA  168 (227)
T ss_pred             HH
Confidence            43

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

Probab=99.36  E-value=1.2e-11  Score=124.60  Aligned_cols=182  Identities=15%  Similarity=0.151  Sum_probs=128.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHH-HHHH----HHhc----c-cCCCCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD-QIFQ----FAST----K-TMHKSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~----~~~~----~-~~~~~~~~vlii  377 (533)
                      +++++|++||||..+|++|.+..-..   +.+|+.+|+.... ...+.. +++.    |...    . .+..+..+.||+
T Consensus       166 ~VLI~GESGtGKElvAr~IH~~S~R~---~~PFVavNcaAip-~~l~ESELFGhekGAFTGA~~~r~G~fE~A~GGTLfL  241 (464)
T COG2204         166 SVLITGESGTGKELVARAIHQASPRA---KGPFIAVNCAAIP-ENLLESELFGHEKGAFTGAITRRIGRFEQANGGTLFL  241 (464)
T ss_pred             CEEEECCCCCcHHHHHHHHHhhCccc---CCCceeeecccCC-HHHHHHHhhcccccCcCCcccccCcceeEcCCceEEe
Confidence            59999999999999999999875333   5689999987643 222222 2211    1000    0 111356889999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         378 DEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      |||..|+.+.|..|++.|++.           +-+++||.+||..       ..+-+.|..|+.++.+.-|+       |
T Consensus       242 DEI~~mpl~~Q~kLLRvLqe~~~~rvG~~~~i~vdvRiIaaT~~dL~~~v~~G~FReDLyyRLnV~~i~iPp-------L  314 (464)
T COG2204         242 DEIGEMPLELQVKLLRVLQEREFERVGGNKPIKVDVRIIAATNRDLEEEVAAGRFREDLYYRLNVVPLRLPP-------L  314 (464)
T ss_pred             eccccCCHHHHHHHHHHHHcCeeEecCCCcccceeeEEEeecCcCHHHHHHcCCcHHHHHhhhccceecCCc-------c
Confidence            999999999999999999863           3568899999864       35788899999998888888       4


Q ss_pred             hcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCC
Q psy4285         440 DYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTS  507 (533)
Q Consensus       440 ~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~  507 (533)
                      +..++|+--+++.+-.  ++....|..+..+.......+..++||++++     .+..+..|...+..
T Consensus       315 RER~EDIp~L~~hfl~--~~~~~~~~~~~~~s~~a~~~L~~y~WPGNVR-----EL~N~ver~~il~~  375 (464)
T COG2204         315 RERKEDIPLLAEHFLK--RFAAELGRPPKGFSPEALAALLAYDWPGNVR-----ELENVVERAVILSE  375 (464)
T ss_pred             cccchhHHHHHHHHHH--HHHHHcCCCCCCCCHHHHHHHHhCCCChHHH-----HHHHHHHHHHhcCC
Confidence            4555555555553222  3335567777888888999999999999998     44444444444443

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.36  E-value=6e-11  Score=121.83  Aligned_cols=144  Identities=24%  Similarity=0.318  Sum_probs=93.8

Q ss_pred             hcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchh-HHHHHHHHHH-------------
Q psy4285         297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIG-IVRDQIFQFA-------------  362 (533)
Q Consensus       297 l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~-------------  362 (533)
                      +...+.....++++++||||||||++++.+++.+.... ....++.+++....+.. .+......+.             
T Consensus        46 l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~-~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~  124 (394)
T PRK00411         46 LRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIA-VKVVYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDE  124 (394)
T ss_pred             HHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhc-CCcEEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHH
Confidence            33444444556799999999999999999999874332 13455666664432211 1111111111             


Q ss_pred             ------hcccCCCCCcEEEEEeCCCCCC----HHHHHHHHHHHHhcCC-CcEEEEEeCCCC---CCChhhhccc--eeee
Q psy4285         363 ------STKTMHKSSYKLIILDEADAMT----NDAQNALRRIIEKFTT-NVRFCIICNYLS---KIPPAIQSRC--TRFR  426 (533)
Q Consensus       363 ------~~~~~~~~~~~vliiDE~d~l~----~~~~~~Ll~~le~~~~-~~~~I~~~n~~~---~l~~~l~sR~--~~i~  426 (533)
                            .... ....+.||+|||+|.+.    .+....|+++++..+. ++.+|+++|...   .+++.+.+|+  ..+.
T Consensus       125 ~~~~~~~~l~-~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~v~vI~i~~~~~~~~~l~~~~~s~~~~~~i~  203 (394)
T PRK00411        125 LFDKIAEYLD-ERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEEYPGARIGVIGISSDLTFLYILDPRVKSVFRPEEIY  203 (394)
T ss_pred             HHHHHHHHHH-hcCCEEEEEECCHhHhhccCCchHHHHHHHhhhccCCCeEEEEEEECCcchhhhcCHHHHhcCCcceee
Confidence                  0000 01345799999999986    3455666666655433 577899988664   5788888887  5789


Q ss_pred             ecCCCHHHHHHHhhcC
Q psy4285         427 FGPLDSSLIMSRLDYD  442 (533)
Q Consensus       427 ~~~~~~~~~~~~l~~~  442 (533)
                      |.|++.+++.+++...
T Consensus       204 f~py~~~e~~~il~~r  219 (394)
T PRK00411        204 FPPYTADEIFDILKDR  219 (394)
T ss_pred             cCCCCHHHHHHHHHHH
Confidence            9999999999998865

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

Probab=99.35  E-value=6.3e-12  Score=127.08  Aligned_cols=119  Identities=23%  Similarity=0.305  Sum_probs=79.9

Q ss_pred             CCCHHHHHHHHHHHhhhchhhhhhhcccccc-------c---------CCCceeEeCCCCCChHHHHHHHHHHHcccccc
Q psy4285         273 YPTKTEITNILRWLLNESMDLCYKINRFIDE-------N---------ELPHLLFYGPPGTGKTTTILACARKLYTKAQF  336 (533)
Q Consensus       273 ~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~-------~---------~~~~~ll~GppGtGKT~la~~la~~l~~~~~~  336 (533)
                      .+.+..+...+.....||+.+.+.+...+..       .         ...++||+||||||||++|+++|+.+      
T Consensus        59 ~~~p~~i~~~L~~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l------  132 (412)
T PRK05342         59 LPTPKEIKAHLDQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARIL------  132 (412)
T ss_pred             CCCHHHHHHHHhhHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHh------
Confidence            6788999999888888998887766443311       0         12469999999999999999999987      


Q ss_pred             CcceEEecCCCCCchh----HHHHHHHHHHhcc--cCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHH
Q psy4285         337 NAMVLELNASDDRGIG----IVRDQIFQFASTK--TMHKSSYKLIILDEADAMTN--------------DAQNALRRIIE  396 (533)
Q Consensus       337 ~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~--~~~~~~~~vliiDE~d~l~~--------------~~~~~Ll~~le  396 (533)
                      +.+++.++++......    .....+.......  ......++||||||+|+++.              ..|++|+++||
T Consensus       133 ~~pf~~id~~~l~~~gyvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~~~~~~~~~~d~s~~~vQ~~LL~~Le  212 (412)
T PRK05342        133 DVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILE  212 (412)
T ss_pred             CCCceecchhhcccCCcccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhccccCCCCcCCCcccHHHHHHHHHHHh
Confidence            5566666655432111    1122222111110  00124568999999999975              37899999998


Q ss_pred             h
Q psy4285         397 K  397 (533)
Q Consensus       397 ~  397 (533)
                      .
T Consensus       213 g  213 (412)
T PRK05342        213 G  213 (412)
T ss_pred             c
Confidence            4

>KOG1969|consensus

Probab=99.35  E-value=5.9e-12  Score=129.25  Aligned_cols=154  Identities=19%  Similarity=0.253  Sum_probs=114.7

Q ss_pred             hhccccchhHHHHHhchHHHH-hhcCCChhhHHHHHh-------------------hc---------cCccccccCCCCh
Q psy4285         101 SRVEKYRPSTLDELVSHQDII-STIEIPESMLVDLVL-------------------KM---------SDIEYRLAAGTSE  151 (533)
Q Consensus       101 ~~~ek~~~~~l~~lls~~~~l-~~l~~~~~~~~~~~~-------------------~~---------~~~~~~~~~G~~~  151 (533)
                      .|+++|+|+.+-+|+|...+- .-+.|...|-+..+.                   ..         .....+|+||.||
T Consensus       260 LWVdky~Pk~FtdLLsDe~tNR~~L~WLK~WD~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~GppGlGK  339 (877)
T KOG1969|consen  260 LWVDKYRPKKFTDLLSDEKTNRRMLGWLKQWDPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPPGLGK  339 (877)
T ss_pred             eeecccChhHHHHHhcchhHHHHHHHHHHhhcHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCCCCCh
Confidence            699999999999999977552 222222222221111                   00         1234788999998


Q ss_pred             hhHHHHHHHHHhcccccceeeeecCCcccchhhhHHHHhhhhhcccccC--CCceEEEEcCccccCHHHHHHHH------
Q psy4285         152 KIQLSALIAAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHK--SSYKLIILDEADAMTNDAQNALR------  223 (533)
Q Consensus       152 ~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~~~d~i~~~a~~~~l~~--~~~~~iilDE~d~l~~~a~~~LR------  223 (533)
                      |+.+.-.+.+.+     |.|+|+||||+|....++.+|.+..++.+..+  .+|.++|+||+|+-...+..+++      
T Consensus       340 TTLAHViAkqaG-----YsVvEINASDeRt~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa~~~~Vdvilslv~a~  414 (877)
T KOG1969|consen  340 TTLAHVIAKQAG-----YSVVEINASDERTAPMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGAPRAAVDVILSLVKAT  414 (877)
T ss_pred             hHHHHHHHHhcC-----ceEEEecccccccHHHHHHHHHHHHhhccccccCCCcceEEEecccCCcHHHHHHHHHHHHhh
Confidence            776544444444     99999999999999999999988888888875  67779999999887644444221      


Q ss_pred             ---------------------------------------------------------------------ccCCCChhHHH
Q psy4285         224 ---------------------------------------------------------------------RKLPVTPDGKK  234 (533)
Q Consensus       224 ---------------------------------------------------------------------r~~~~~~~~l~  234 (533)
                                                                                           +.|.++..+|.
T Consensus       415 ~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNdLYaPaLR~Lr~~A~ii~f~~p~~s~Lv~RL~~IC~rE~mr~d~~aL~  494 (877)
T KOG1969|consen  415 NKQATGKQAKKDKKRKKKRSKLLTRPIICICNDLYAPALRPLRPFAEIIAFVPPSQSRLVERLNEICHRENMRADSKALN  494 (877)
T ss_pred             cchhhcCcccchhhhhhhccccccCCEEEEecCccchhhhhcccceEEEEecCCChhHHHHHHHHHHhhhcCCCCHHHHH
Confidence                                                                                 14789999999


Q ss_pred             HHHHhccCchHHhhcHHHHHHhhcC
Q psy4285         235 AIIDLSDGDMRKVLNILQSAATAHA  259 (533)
Q Consensus       235 ~l~~~s~~di~~~L~~L~~~~~~~~  259 (533)
                      +|++++.+|+|.+||.||.......
T Consensus       495 ~L~el~~~DIRsCINtLQfLa~~~~  519 (877)
T KOG1969|consen  495 ALCELTQNDIRSCINTLQFLASNVD  519 (877)
T ss_pred             HHHHHhcchHHHHHHHHHHHHHhcc
Confidence            9999999999999999999887643

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

Probab=99.34  E-value=6.3e-12  Score=125.27  Aligned_cols=150  Identities=21%  Similarity=0.283  Sum_probs=102.9

Q ss_pred             hhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHH-HHHHHHHhcccC---
Q psy4285         292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR-DQIFQFASTKTM---  367 (533)
Q Consensus       292 ~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~---  367 (533)
                      .+...+..++..+.+.|+++|||||||||++++.+++++..... ...+.++|+....+...+- .....+...+..   
T Consensus        28 ~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~-~~~~~yINc~~~~t~~~i~~~i~~~~~~~p~~g~~  106 (366)
T COG1474          28 QLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSA-NVEVVYINCLELRTPYQVLSKILNKLGKVPLTGDS  106 (366)
T ss_pred             HHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhc-cCceEEEeeeeCCCHHHHHHHHHHHcCCCCCCCCc
Confidence            33445667777777778999999999999999999999865531 2226777776554433222 222211110000   


Q ss_pred             -------------CCCCcEEEEEeCCCCCCHHHHHHH---HHHHHhcCCCcEEEEEeCCC---CCCChhhhccc--eeee
Q psy4285         368 -------------HKSSYKLIILDEADAMTNDAQNAL---RRIIEKFTTNVRFCIICNYL---SKIPPAIQSRC--TRFR  426 (533)
Q Consensus       368 -------------~~~~~~vliiDE~d~l~~~~~~~L---l~~le~~~~~~~~I~~~n~~---~~l~~~l~sR~--~~i~  426 (533)
                                   .....-|+++||+|.|....+..|   +++-+....++.+|+++|..   ..++|.+.|++  ..+.
T Consensus       107 ~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~~~LY~L~r~~~~~~~~v~vi~i~n~~~~~~~ld~rv~s~l~~~~I~  186 (366)
T COG1474         107 SLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPRVKSSLGPSEIV  186 (366)
T ss_pred             hHHHHHHHHHHHHhcCCeEEEEEcchhhhccccchHHHHHHhhccccceeEEEEEEeccHHHHHHhhhhhhhccCcceee
Confidence                         024567999999999976644444   44444444446677777765   37899999988  4788


Q ss_pred             ecCCCHHHHHHHhhcC
Q psy4285         427 FGPLDSSLIMSRLDYD  442 (533)
Q Consensus       427 ~~~~~~~~~~~~l~~~  442 (533)
                      |+|++.+|+.++|...
T Consensus       187 F~pY~a~el~~Il~~R  202 (366)
T COG1474         187 FPPYTAEELYDILRER  202 (366)
T ss_pred             eCCCCHHHHHHHHHHH
Confidence            9999999999999988

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

Probab=99.33  E-value=4.8e-12  Score=138.75  Aligned_cols=151  Identities=18%  Similarity=0.162  Sum_probs=104.1

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCCC----chhHHHHHHH
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDDR----GIGIVRDQIF  359 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~~----~~~~~~~~~~  359 (533)
                      .|+++.+..+...+.....+|++|+||||||||++++++|+.+.....    .+..++.++.+...    ..+...+.++
T Consensus       185 igr~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~~~~~l~a~~~~~g~~e~~l~  264 (731)
T TIGR02639       185 IGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLLAGTKYRGDFEERLK  264 (731)
T ss_pred             cCcHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEecHHHHhhhccccchHHHHHH
Confidence            455555555666666667778999999999999999999998744321    13455666543221    1112222333


Q ss_pred             HHHhcccCCCCCcEEEEEeCCCCCC---------HHHHHHHHHHHHhcCCCcEEEEEeCCC-----CCCChhhhccceee
Q psy4285         360 QFASTKTMHKSSYKLIILDEADAMT---------NDAQNALRRIIEKFTTNVRFCIICNYL-----SKIPPAIQSRCTRF  425 (533)
Q Consensus       360 ~~~~~~~~~~~~~~vliiDE~d~l~---------~~~~~~Ll~~le~~~~~~~~I~~~n~~-----~~l~~~l~sR~~~i  425 (533)
                      .......  ...+.||||||+|.+.         .+.++.|...++.  ..+.+|.+||..     ...++++.|||..+
T Consensus       265 ~i~~~~~--~~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l~~--g~i~~IgaTt~~e~~~~~~~d~al~rRf~~i  340 (731)
T TIGR02639       265 AVVSEIE--KEPNAILFIDEIHTIVGAGATSGGSMDASNLLKPALSS--GKLRCIGSTTYEEYKNHFEKDRALSRRFQKI  340 (731)
T ss_pred             HHHHHHh--ccCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHHhC--CCeEEEEecCHHHHHHHhhhhHHHHHhCceE
Confidence            3222111  1245799999999885         2456777777764  458889998853     35799999999999


Q ss_pred             eecCCCHHHHHHHhhcC
Q psy4285         426 RFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       426 ~~~~~~~~~~~~~l~~~  442 (533)
                      .+.+|+.++...+|...
T Consensus       341 ~v~~p~~~~~~~il~~~  357 (731)
T TIGR02639       341 DVGEPSIEETVKILKGL  357 (731)
T ss_pred             EeCCCCHHHHHHHHHHH
Confidence            99999999999999965

>PRK06526 transposase; Provisional

Probab=99.33  E-value=7.8e-13  Score=125.46  Aligned_cols=160  Identities=16%  Similarity=0.241  Sum_probs=101.4

Q ss_pred             ccCchHHhhcHHHHHHhhcCCCCCccccccccCCCCHHHHHHHHHHHhhh-chhhhhhh--cccccccCCCceeEeCCCC
Q psy4285         240 SDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNE-SMDLCYKI--NRFIDENELPHLLFYGPPG  316 (533)
Q Consensus       240 s~~di~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~l--~~~~~~~~~~~~ll~GppG  316 (533)
                      ......+.+..|...+...++....+...+..++|....+.++-.....+ .......+  ..|+..+  .+++|+||||
T Consensus        31 ~~~~~~e~l~~ll~~E~~~R~~~~~~~~lk~a~~p~~~~le~fd~~~~~~~~~~~~~~l~~~~fi~~~--~nlll~Gp~G  108 (254)
T PRK06526         31 ESWSHEEFLAACLQREVAARESHGGEGRIRAARFPARKSLEEFDFDHQRSLKRDTIAHLGTLDFVTGK--ENVVFLGPPG  108 (254)
T ss_pred             cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCChhhccCccCCCcchHHHHHHhcCchhhcC--ceEEEEeCCC
Confidence            44567788888888888777666667788888898877777653221111 12222222  2455433  4799999999


Q ss_pred             CChHHHHHHHHHHHccccccCcceEEecCCCCCc-------hhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCC--HHH
Q psy4285         317 TGKTTTILACARKLYTKAQFNAMVLELNASDDRG-------IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMT--NDA  387 (533)
Q Consensus       317 tGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~--~~~  387 (533)
                      ||||++|.+++.++...   +..+...+..+...       .+.....+..+        .++++|||||++...  .+.
T Consensus       109 tGKThLa~al~~~a~~~---g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l--------~~~dlLIIDD~g~~~~~~~~  177 (254)
T PRK06526        109 TGKTHLAIGLGIRACQA---GHRVLFATAAQWVARLAAAHHAGRLQAELVKL--------GRYPLLIVDEVGYIPFEPEA  177 (254)
T ss_pred             CchHHHHHHHHHHHHHC---CCchhhhhHHHHHHHHHHHHhcCcHHHHHHHh--------ccCCEEEEcccccCCCCHHH
Confidence            99999999999987443   22222222211100       00111111111        346899999999874  667


Q ss_pred             HHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         388 QNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       388 ~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      ++.|+++++....+..+|+|||.+.
T Consensus       178 ~~~L~~li~~r~~~~s~IitSn~~~  202 (254)
T PRK06526        178 ANLFFQLVSSRYERASLIVTSNKPF  202 (254)
T ss_pred             HHHHHHHHHHHHhcCCEEEEcCCCH
Confidence            7889999987555567999999764

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.33  E-value=1.6e-11  Score=135.12  Aligned_cols=147  Identities=21%  Similarity=0.296  Sum_probs=102.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      +++|+||||||||++++++|+++      +..++.+++++..      ....++..+....      ...+.+|+|||+|
T Consensus       214 giLL~GppGtGKT~laraia~~~------~~~~i~i~~~~i~~~~~g~~~~~l~~lf~~a~------~~~p~il~iDEid  281 (733)
T TIGR01243       214 GVLLYGPPGTGKTLLAKAVANEA------GAYFISINGPEIMSKYYGESEERLREIFKEAE------ENAPSIIFIDEID  281 (733)
T ss_pred             eEEEECCCCCChHHHHHHHHHHh------CCeEEEEecHHHhcccccHHHHHHHHHHHHHH------hcCCcEEEeehhh
Confidence            59999999999999999999987      5566777664321      1223333333221      1346799999999


Q ss_pred             CCCH-----------HHHHHHHHHHHhcC--CCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhcC---
Q psy4285         382 AMTN-----------DAQNALRRIIEKFT--TNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDYD---  442 (533)
Q Consensus       382 ~l~~-----------~~~~~Ll~~le~~~--~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~---  442 (533)
                      .+..           ..++.|++.|+...  ..+.+|.+||.++.+++++++  || ..+.+..|+.++..+++...   
T Consensus       282 ~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~  361 (733)
T TIGR01243       282 AIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRN  361 (733)
T ss_pred             hhcccccCCcchHHHHHHHHHHHHhhccccCCCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcC
Confidence            8743           34667888887543  346677789999999999987  78 47888889988888888744   


Q ss_pred             -----HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285         443 -----DISFFNIIIWYIKIQEIKIEKGLALTDILTEIS  475 (533)
Q Consensus       443 -----~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~  475 (533)
                           ..++..+.+         .+.|++..|+..-..
T Consensus       362 ~~l~~d~~l~~la~---------~t~G~~gadl~~l~~  390 (733)
T TIGR01243       362 MPLAEDVDLDKLAE---------VTHGFVGADLAALAK  390 (733)
T ss_pred             CCCccccCHHHHHH---------hCCCCCHHHHHHHHH
Confidence                 112233333         567888887755433

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.

>KOG0651|consensus

Probab=99.32  E-value=1.4e-11  Score=114.60  Aligned_cols=123  Identities=26%  Similarity=0.303  Sum_probs=85.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+++|||||||||.+|++++..+      +..++.+.++..      .+...+|+........      .++++|+||+|
T Consensus       168 g~ll~GppGtGKTlla~~Vaa~m------g~nfl~v~ss~lv~kyiGEsaRlIRemf~yA~~~------~pciifmdeiD  235 (388)
T KOG0651|consen  168 GLLLYGPPGTGKTLLARAVAATM------GVNFLKVVSSALVDKYIGESARLIRDMFRYAREV------IPCIIFMDEID  235 (388)
T ss_pred             eeEEeCCCCCchhHHHHHHHHhc------CCceEEeeHhhhhhhhcccHHHHHHHHHHHHhhh------CceEEeehhhh
Confidence            38999999999999999999988      666666665542      2344555554433322      35899999999


Q ss_pred             CCCH-----------HHHHHHHHHHHh-----cCCCcEEEEEeCCCCCCChhhhc--cceeeeecCCCHHHHHHHhhcC
Q psy4285         382 AMTN-----------DAQNALRRIIEK-----FTTNVRFCIICNYLSKIPPAIQS--RCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       382 ~l~~-----------~~~~~Ll~~le~-----~~~~~~~I~~~n~~~~l~~~l~s--R~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ....           ..+..|.+++++     .-..+.+|++||+++.|+|+|++  |++...-.|++.++-+-.+.++
T Consensus       236 AigGRr~se~Ts~dreiqrTLMeLlnqmdgfd~l~rVk~ImatNrpdtLdpaLlRpGRldrk~~iPlpne~~r~~I~Ki  314 (388)
T KOG0651|consen  236 AIGGRRFSEGTSSDREIQRTLMELLNQMDGFDTLHRVKTIMATNRPDTLDPALLRPGRLDRKVEIPLPNEQARLGILKI  314 (388)
T ss_pred             hhccEEeccccchhHHHHHHHHHHHHhhccchhcccccEEEecCCccccchhhcCCccccceeccCCcchhhceeeEee
Confidence            8743           345555555543     13568899999999999999998  8865544555555555445454

>PRK08181 transposase; Validated

Probab=99.32  E-value=1.6e-12  Score=123.87  Aligned_cols=160  Identities=16%  Similarity=0.167  Sum_probs=101.4

Q ss_pred             ccCchHHhhcHHHHHHhhcCCCCCccccccccCCCCHHHHHHHHHHHhh----hchhhhhhhcccccccCCCceeEeCCC
Q psy4285         240 SDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLN----ESMDLCYKINRFIDENELPHLLFYGPP  315 (533)
Q Consensus       240 s~~di~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~----~~~~~~~~l~~~~~~~~~~~~ll~Gpp  315 (533)
                      ....+.+.+..|...+...++....+...+..++|....+.++......    .+......+..|+..+  .+++|+|||
T Consensus        38 ~~~~~~e~L~~ll~~E~~~R~~~~~~r~lk~A~~p~~~tle~fd~~~~~~~~~~~~~~L~~~~~~~~~~--~nlll~Gp~  115 (269)
T PRK08181         38 EGWPAARFLAAIAEHELAERARRRIERHLAEAHLPPGKTLDSFDFEAVPMVSKAQVMAIAAGDSWLAKG--ANLLLFGPP  115 (269)
T ss_pred             cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHhhCCccCCCCCCHHHHHHHHHHHHHHhcC--ceEEEEecC
Confidence            3456778888888877776665555667788888876666665322111    1111222333566544  379999999


Q ss_pred             CCChHHHHHHHHHHHccccccCcceEEecCCCCCch-------hHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCC--HH
Q psy4285         316 GTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI-------GIVRDQIFQFASTKTMHKSSYKLIILDEADAMT--ND  386 (533)
Q Consensus       316 GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~--~~  386 (533)
                      |||||+++.++++++...   +..++.++..+....       ....+.++.+        ...++|||||++...  ..
T Consensus       116 GtGKTHLa~Aia~~a~~~---g~~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l--------~~~dLLIIDDlg~~~~~~~  184 (269)
T PRK08181        116 GGGKSHLAAAIGLALIEN---GWRVLFTRTTDLVQKLQVARRELQLESAIAKL--------DKFDLLILDDLAYVTKDQA  184 (269)
T ss_pred             CCcHHHHHHHHHHHHHHc---CCceeeeeHHHHHHHHHHHHhCCcHHHHHHHH--------hcCCEEEEeccccccCCHH
Confidence            999999999999987543   334444443221100       0111111111        356799999999874  45


Q ss_pred             HHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         387 AQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       387 ~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      .+..|+++++....+..+|+|||.+.
T Consensus       185 ~~~~Lf~lin~R~~~~s~IiTSN~~~  210 (269)
T PRK08181        185 ETSVLFELISARYERRSILITANQPF  210 (269)
T ss_pred             HHHHHHHHHHHHHhCCCEEEEcCCCH
Confidence            56789999987666678999998764

>KOG0740|consensus

Probab=99.32  E-value=7.7e-12  Score=123.93  Aligned_cols=152  Identities=21%  Similarity=0.166  Sum_probs=103.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+|+.||||+|||.+++++|.+.      +..+..++++...      +...++.+++- ++.     ..+.|+||||+|
T Consensus       188 glLLfGPpgtGKtmL~~aiAsE~------~atff~iSassLtsK~~Ge~eK~vralf~v-Ar~-----~qPsvifidEid  255 (428)
T KOG0740|consen  188 GLLLFGPPGTGKTMLAKAIATES------GATFFNISASSLTSKYVGESEKLVRALFKV-ARS-----LQPSVIFIDEID  255 (428)
T ss_pred             hhheecCCCCchHHHHHHHHhhh------cceEeeccHHHhhhhccChHHHHHHHHHHH-HHh-----cCCeEEEechhH
Confidence            48999999999999999999998      7778888876532      23344443332 222     356899999999


Q ss_pred             CCCHHH------------HHHHHHHHH---hcCCCcEEEEEeCCCCCCChhhhccceeee-ecCCCHHHHHHHhhcC---
Q psy4285         382 AMTNDA------------QNALRRIIE---KFTTNVRFCIICNYLSKIPPAIQSRCTRFR-FGPLDSSLIMSRLDYD---  442 (533)
Q Consensus       382 ~l~~~~------------~~~Ll~~le---~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~-~~~~~~~~~~~~l~~~---  442 (533)
                      ++....            ...|++..-   .+.+++.+|.+||.+..+|+++++||.... ++.|+.+....++.+.   
T Consensus       256 slls~Rs~~e~e~srr~ktefLiq~~~~~s~~~drvlvigaTN~P~e~Dea~~Rrf~kr~yiplPd~etr~~~~~~ll~~  335 (428)
T KOG0740|consen  256 SLLSKRSDNEHESSRRLKTEFLLQFDGKNSAPDDRVLVIGATNRPWELDEAARRRFVKRLYIPLPDYETRSLLWKQLLKE  335 (428)
T ss_pred             HHHhhcCCcccccchhhhhHHHhhhccccCCCCCeEEEEecCCCchHHHHHHHHHhhceeeecCCCHHHHHHHHHHHHHh
Confidence            985321            122333321   234678899999999999999999996544 4555555555555554   


Q ss_pred             ------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHh
Q psy4285         443 ------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHR  480 (533)
Q Consensus       443 ------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~  480 (533)
                            ..++..+++         .++||+..|+..-+-++...
T Consensus       336 ~~~~l~~~d~~~l~~---------~Tegysgsdi~~l~kea~~~  370 (428)
T KOG0740|consen  336 QPNGLSDLDISLLAK---------VTEGYSGSDITALCKEAAMG  370 (428)
T ss_pred             CCCCccHHHHHHHHH---------HhcCcccccHHHHHHHhhcC
Confidence                  233444433         78899999988877666543

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=99.31  E-value=4.3e-12  Score=124.31  Aligned_cols=78  Identities=19%  Similarity=0.264  Sum_probs=68.2

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||||| +++|||+|+.+++++|||+|||++++|++++++++.++|.+.+..++.+   .....++..++||+++|++.++
T Consensus       148 LEEPp-~~~fILi~~~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~~~~---~~~~~l~~~a~Gs~~~al~~l~  223 (314)
T PRK07399        148 LEEPG-NGTLILIAPSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEILN---INFPELLALAQGSPGAAIANIE  223 (314)
T ss_pred             HhCCC-CCeEEEEECChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhccccch---hHHHHHHHHcCCCHHHHHHHHH
Confidence            69999 8999999999999999999999999999999999999999876444332   2256889999999999999987


Q ss_pred             HH
Q psy4285          81 SA   82 (533)
Q Consensus        81 ~~   82 (533)
                      ..
T Consensus       224 ~~  225 (314)
T PRK07399        224 QL  225 (314)
T ss_pred             HH
Confidence            64

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.31  E-value=3e-11  Score=116.72  Aligned_cols=128  Identities=21%  Similarity=0.238  Sum_probs=90.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHH--HHHH--HHHHhcccC--CCCCcEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIV--RDQI--FQFASTKTM--HKSSYKLI  375 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~--~~~~--~~~~~~~~~--~~~~~~vl  375 (533)
                      +++|.||||||||++++.+|+.+      +.+++.++....      .+...+  ++..  ..|.. .+.  ....+.++
T Consensus        66 ~ilL~G~pGtGKTtla~~lA~~l------~~~~~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f~~-GpL~~A~~~g~il  138 (327)
T TIGR01650        66 RVMVQGYHGTGKSTHIEQIAARL------NWPCVRVNLDSHVSRIDLVGKDAIVLKDGKQITEFRD-GILPWALQHNVAL  138 (327)
T ss_pred             cEEEEeCCCChHHHHHHHHHHHH------CCCeEEEEecCCCChhhcCCCceeeccCCcceeEEec-CcchhHHhCCeEE
Confidence            69999999999999999999998      555555554332      221111  0000  00000 000  01245689


Q ss_pred             EEeCCCCCCHHHHHHHHHHHHh--------------cCCCcEEEEEeCCCC------------CCChhhhccce-eeeec
Q psy4285         376 ILDEADAMTNDAQNALRRIIEK--------------FTTNVRFCIICNYLS------------KIPPAIQSRCT-RFRFG  428 (533)
Q Consensus       376 iiDE~d~l~~~~~~~Ll~~le~--------------~~~~~~~I~~~n~~~------------~l~~~l~sR~~-~i~~~  428 (533)
                      ++||+|...++.++.|..+||.              +.+..++|+|+|...            .++++.++||. .+.+.
T Consensus       139 llDEin~a~p~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~Gd~~G~y~Gt~~l~~A~lDRF~i~~~~~  218 (327)
T TIGR01650       139 CFDEYDAGRPDVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLGDTTGLYHGTQQINQAQMDRWSIVTTLN  218 (327)
T ss_pred             EechhhccCHHHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcCCCCcceeeeecCCHHHHhheeeEeeCC
Confidence            9999999999999999999983              234678899999743            57899999996 56899


Q ss_pred             CCCHHHHHHHhhcC
Q psy4285         429 PLDSSLIMSRLDYD  442 (533)
Q Consensus       429 ~~~~~~~~~~l~~~  442 (533)
                      +|+.++..+++...
T Consensus       219 Yp~~e~E~~Il~~~  232 (327)
T TIGR01650       219 YLEHDNEAAIVLAK  232 (327)
T ss_pred             CCCHHHHHHHHHhh
Confidence            99999999998765

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.30  E-value=6.6e-12  Score=127.98  Aligned_cols=102  Identities=26%  Similarity=0.358  Sum_probs=91.8

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|++.++||++|+...++++||+|||++++|++++.+++.+|+.++++++++.+++++++.++..++||+|.|++.|+
T Consensus       151 LEep~~~t~~Il~t~~~~kl~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~~i~~~al~~l~~~s~g~lr~a~~~L~  230 (397)
T PRK14955        151 LEEPPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDAQSILD  230 (397)
T ss_pred             HhcCCCCeEEEEEeCChHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhC-----CCCcchhhHHhhhhhh
Q psy4285          81 SAATAH-----ADEVNEDTIFTLLVSR  102 (533)
Q Consensus        81 ~~~~~~-----~~~i~~~~i~~~~~~~  102 (533)
                      .+....     ...|+.+.|.++++..
T Consensus       231 kl~~~~~~~~~~~~It~~~v~~~v~~~  257 (397)
T PRK14955        231 QVIAFSVESEGEGSIRYDKVAELLNYI  257 (397)
T ss_pred             HHHHhccccCCCCccCHHHHHHHHCCC
Confidence            876542     2358888877665443

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.30  E-value=5.7e-11  Score=131.17  Aligned_cols=148  Identities=16%  Similarity=0.167  Sum_probs=101.3

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCC----Cch----hHHH
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDD----RGI----GIVR  355 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~----~~~----~~~~  355 (533)
                      .|+++.+..+...+.++..+|++|+||||||||++|+.+|+.+.....    .+..++.++.+..    ...    ..++
T Consensus       190 iGr~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l~ag~~~~ge~e~~lk  269 (852)
T TIGR03345       190 LGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQAGASVKGEFENRLK  269 (852)
T ss_pred             cCCHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEeehhhhhcccccchHHHHHHH
Confidence            344555555555555667778999999999999999999998743211    1233444433221    111    2344


Q ss_pred             HHHHHHHhcccCCCCCcEEEEEeCCCCCCH--------HHHHHHHHHHHhcCCCcEEEEEeCCC-----CCCChhhhccc
Q psy4285         356 DQIFQFASTKTMHKSSYKLIILDEADAMTN--------DAQNALRRIIEKFTTNVRFCIICNYL-----SKIPPAIQSRC  422 (533)
Q Consensus       356 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------~~~~~Ll~~le~~~~~~~~I~~~n~~-----~~l~~~l~sR~  422 (533)
                      ..+......     ..+.||||||++.+..        +..+.|...++.  ...++|.+|+..     ..++++|.|||
T Consensus       270 ~ii~e~~~~-----~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~~--G~l~~IgaTT~~e~~~~~~~d~AL~rRf  342 (852)
T TIGR03345       270 SVIDEVKAS-----PQPIILFIDEAHTLIGAGGQAGQGDAANLLKPALAR--GELRTIAATTWAEYKKYFEKDPALTRRF  342 (852)
T ss_pred             HHHHHHHhc-----CCCeEEEEeChHHhccCCCccccccHHHHhhHHhhC--CCeEEEEecCHHHHhhhhhccHHHHHhC
Confidence            444433221     3567999999999953        234567777764  458899998753     35899999999


Q ss_pred             eeeeecCCCHHHHHHHhhcC
Q psy4285         423 TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       423 ~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..+.+.+|+.++...+|..+
T Consensus       343 ~~i~v~eps~~~~~~iL~~~  362 (852)
T TIGR03345       343 QVVKVEEPDEETAIRMLRGL  362 (852)
T ss_pred             eEEEeCCCCHHHHHHHHHHH
Confidence            99999999999999997655

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.

>PRK05642 DNA replication initiation factor; Validated

Probab=99.30  E-value=2.8e-11  Score=114.18  Aligned_cols=122  Identities=16%  Similarity=0.283  Sum_probs=84.7

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCC--
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMT--  384 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~--  384 (533)
                      ++++|+||+|+||||+++++++++...   +..++.++..+....  .....+.+        ...++|+|||++.+.  
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~---~~~v~y~~~~~~~~~--~~~~~~~~--------~~~d~LiiDDi~~~~~~  112 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQR---GEPAVYLPLAELLDR--GPELLDNL--------EQYELVCLDDLDVIAGK  112 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhC---CCcEEEeeHHHHHhh--hHHHHHhh--------hhCCEEEEechhhhcCC
Confidence            358999999999999999999887433   334455554332111  11111111        234699999999885  


Q ss_pred             HHHHHHHHHHHHhcC-CCcEEEEEeCCCC----CCChhhhccc---eeeeecCCCHHHHHHHhhc
Q psy4285         385 NDAQNALRRIIEKFT-TNVRFCIICNYLS----KIPPAIQSRC---TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       385 ~~~~~~Ll~~le~~~-~~~~~I~~~n~~~----~l~~~l~sR~---~~i~~~~~~~~~~~~~l~~  441 (533)
                      +..+..|+.+++... .+..+|++++...    ...|.++|||   ..+.+.+|+.++...++..
T Consensus       113 ~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~  177 (234)
T PRK05642        113 ADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQL  177 (234)
T ss_pred             hHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHH
Confidence            344677888887643 3567788876432    3479999999   6888999999999888873

>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=99.30  E-value=3.4e-12  Score=110.65  Aligned_cols=109  Identities=27%  Similarity=0.342  Sum_probs=73.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHH----HHHhcccCC-C--CCcEEEEEeCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIF----QFASTKTMH-K--SSYKLIILDEA  380 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~-~--~~~~vliiDE~  380 (533)
                      +++|+||||||||++|+.+|+.+      +..+..+..+.......+.....    .+....... .  ..+.+++|||+
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~------~~~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~~~~~il~lDEi   74 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALL------GRPVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAMRKGGILVLDEI   74 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH------TCEEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTHHEEEEEEESSC
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh------hcceEEEEeccccccccceeeeeecccccccccccccccccceeEEEECCc
Confidence            48999999999999999999998      55666666554333322211100    000000000 0  24789999999


Q ss_pred             CCCCHHHHHHHHHHHHhc-------------CC------CcEEEEEeCCCC----CCChhhhccc
Q psy4285         381 DAMTNDAQNALRRIIEKF-------------TT------NVRFCIICNYLS----KIPPAIQSRC  422 (533)
Q Consensus       381 d~l~~~~~~~Ll~~le~~-------------~~------~~~~I~~~n~~~----~l~~~l~sR~  422 (533)
                      +...++.++.|+.++++.             +.      +.++|+|+|...    .++++++|||
T Consensus        75 n~a~~~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~l~~al~~Rf  139 (139)
T PF07728_consen   75 NRAPPEVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKELSPALLDRF  139 (139)
T ss_dssp             GG--HHHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTTTCHHHHTT-
T ss_pred             ccCCHHHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCcCCHHHHhhC
Confidence            999999999999999752             12      389999999888    8999999997

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.

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

Probab=99.30  E-value=3.7e-11  Score=120.38  Aligned_cols=148  Identities=16%  Similarity=0.209  Sum_probs=90.7

Q ss_pred             hhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHcccccc-CcceEEecC------------CCCCchhHHHHHHH
Q psy4285         293 LCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQF-NAMVLELNA------------SDDRGIGIVRDQIF  359 (533)
Q Consensus       293 ~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~-~~~~~~~~~------------~~~~~~~~~~~~~~  359 (533)
                      ..+.+...+..+  .+++|+||||||||++|+.+|..+.+.... ....+.+..            +...+.......+.
T Consensus       183 ~le~l~~~L~~~--~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~~vgy~~~~G~f~  260 (459)
T PRK11331        183 TIETILKRLTIK--KNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIFY  260 (459)
T ss_pred             HHHHHHHHHhcC--CCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCCCCCeEecCchHH
Confidence            334444444433  379999999999999999999988543211 111111111            01111111111122


Q ss_pred             HHHhcccCCCCCcEEEEEeCCCCCCHHH-HHHHHHHHHh----------------------cCCCcEEEEEeCCCC----
Q psy4285         360 QFASTKTMHKSSYKLIILDEADAMTNDA-QNALRRIIEK----------------------FTTNVRFCIICNYLS----  412 (533)
Q Consensus       360 ~~~~~~~~~~~~~~vliiDE~d~l~~~~-~~~Ll~~le~----------------------~~~~~~~I~~~n~~~----  412 (533)
                      .+.......+..+.+|||||+++...+. ...++.+||.                      .|.++.+|.|+|..+    
T Consensus       261 ~~~~~A~~~p~~~~vliIDEINRani~kiFGel~~lLE~~~rg~~~~v~l~y~e~d~e~f~iP~Nl~IIgTMNt~Drs~~  340 (459)
T PRK11331        261 NFCQQAKEQPEKKYVFIIDEINRANLSKVFGEVMMLMEHDKRGENWSVPLTYSENDEERFYVPENVYIIGLMNTADRSLA  340 (459)
T ss_pred             HHHHHHHhcccCCcEEEEehhhccCHHHhhhhhhhhccccccccccceeeeccccccccccCCCCeEEEEecCccccchh
Confidence            2222111112357899999999998654 6677777662                      256788999999877    


Q ss_pred             CCChhhhccceeeeecC-CCHHHHHHHhhcC
Q psy4285         413 KIPPAIQSRCTRFRFGP-LDSSLIMSRLDYD  442 (533)
Q Consensus       413 ~l~~~l~sR~~~i~~~~-~~~~~~~~~l~~~  442 (533)
                      .+|.++++||..+.+.| ++...+.+.+...
T Consensus       341 ~lD~AlrRRF~fi~i~p~~~~~~~~~~l~~~  371 (459)
T PRK11331        341 VVDYALRRRFSFIDIEPGFDTPQFRNFLLNK  371 (459)
T ss_pred             hccHHHHhhhheEEecCCCChHHHHHHHHhc
Confidence            68999999999888877 4555666665543

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.29  E-value=2.9e-11  Score=129.18  Aligned_cols=154  Identities=21%  Similarity=0.239  Sum_probs=100.1

Q ss_pred             hchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCCCc-hhHHHH-------
Q psy4285         289 ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDDRG-IGIVRD-------  356 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~~~-~~~~~~-------  356 (533)
                      |++..+..+...+.....++++|+|||||||||+|+.+++.......    ....++.+++..... ...+..       
T Consensus       158 Gqs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~~llg~~~  237 (615)
T TIGR02903       158 GQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTNPLLGSVH  237 (615)
T ss_pred             eCcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHhHHhcCCcc
Confidence            45555555555555555667999999999999999999876632211    134577777654321 001100       


Q ss_pred             ------HHHHHHhc-------ccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcC------------------------
Q psy4285         357 ------QIFQFAST-------KTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT------------------------  399 (533)
Q Consensus       357 ------~~~~~~~~-------~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~------------------------  399 (533)
                            ..+.+...       ........++|||||++.|+...++.|++.+++..                        
T Consensus       238 ~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~ik~~~~  317 (615)
T TIGR02903       238 DPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLEDKRVEFSSSYYDPDDPNVPKYIKKLFE  317 (615)
T ss_pred             HHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCHHHHHHHHHHHhhCeEEeecceeccCCcccchhhhhhcc
Confidence                  00000100       00012346799999999999999999999997531                        


Q ss_pred             ----CCcEEEEE-eCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         400 ----TNVRFCII-CNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       400 ----~~~~~I~~-~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                          ..+++|.+ ++.+..++++++|||..+.|.+++.+++..++.+.
T Consensus       318 ~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~Il~~~  365 (615)
T TIGR02903       318 EGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIALIVLNA  365 (615)
T ss_pred             cCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHHHHHHH
Confidence                11233333 45677899999999999999999998888877764

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.

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.29  E-value=1.2e-11  Score=125.14  Aligned_cols=102  Identities=24%  Similarity=0.392  Sum_probs=93.1

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      +|+||++++||++|+++.+++++|+|||+.+.|++++.+++.+|+.++++++++.++++++..++..++||+|.|++.++
T Consensus       141 le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g~~~~a~~~le  220 (355)
T TIGR02397       141 LEEPPEHVVFILATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLLD  220 (355)
T ss_pred             HhCCccceeEEEEeCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCChHHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVSR  102 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~  102 (533)
                      .+.......|+.+.|.+++...
T Consensus       221 kl~~~~~~~it~~~v~~~~~~~  242 (355)
T TIGR02397       221 QLISFGNGNITYEDVNELLGLV  242 (355)
T ss_pred             HHHhhcCCCCCHHHHHHHhCCC
Confidence            9877555568998887655443

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.

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

Probab=99.29  E-value=2.3e-11  Score=122.23  Aligned_cols=131  Identities=24%  Similarity=0.266  Sum_probs=84.9

Q ss_pred             CCCHHHHHHHHHHHhhhchhhhhhhccccc-----------cc-------CCCceeEeCCCCCChHHHHHHHHHHHcccc
Q psy4285         273 YPTKTEITNILRWLLNESMDLCYKINRFID-----------EN-------ELPHLLFYGPPGTGKTTTILACARKLYTKA  334 (533)
Q Consensus       273 ~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~-----------~~-------~~~~~ll~GppGtGKT~la~~la~~l~~~~  334 (533)
                      .+.+..+...+.....||+++.+.+...+.           ..       ...+++|+||||||||++|+++|+.+    
T Consensus        65 ~~~p~~i~~~L~~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l----  140 (413)
T TIGR00382        65 LPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARIL----  140 (413)
T ss_pred             CCCHHHHHHHhcceecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhc----
Confidence            677888888888888888888776644331           11       12469999999999999999999887    


Q ss_pred             ccCcceEEecCCCCC-----chhHHHHHHHHHHhccc--CCCCCcEEEEEeCCCCCCH--------------HHHHHHHH
Q psy4285         335 QFNAMVLELNASDDR-----GIGIVRDQIFQFASTKT--MHKSSYKLIILDEADAMTN--------------DAQNALRR  393 (533)
Q Consensus       335 ~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~--~~~~~~~vliiDE~d~l~~--------------~~~~~Ll~  393 (533)
                        +.++..++++...     +.+ ....+........  .....+.+|+|||+|.+..              ..|++|++
T Consensus       141 --~~pf~~~da~~L~~~gyvG~d-~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~~~~~~s~~~dvsg~~vq~~LL~  217 (413)
T TIGR00382       141 --NVPFAIADATTLTEAGYVGED-VENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLK  217 (413)
T ss_pred             --CCCeEEechhhcccccccccc-HHHHHHHHHHhCcccHHhcccceEEecccchhchhhccccccccccchhHHHHHHH
Confidence              4445545443321     111 1222222111110  0123457999999999976              58999999


Q ss_pred             HHHhc-------------CCCcEEEEEeCC
Q psy4285         394 IIEKF-------------TTNVRFCIICNY  410 (533)
Q Consensus       394 ~le~~-------------~~~~~~I~~~n~  410 (533)
                      +||..             ..+..+|.|+|.
T Consensus       218 iLeG~~~~v~~~~gr~~~~~~~i~i~TsNi  247 (413)
T TIGR00382       218 IIEGTVANVPPQGGRKHPYQEFIQIDTSNI  247 (413)
T ss_pred             HhhccceecccCCCccccCCCeEEEEcCCc
Confidence            99632             134557777775

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.

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.28  E-value=2.2e-11  Score=123.57  Aligned_cols=100  Identities=23%  Similarity=0.341  Sum_probs=91.6

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+.+++||++|+...++.|+|+|||++++|++++++++..|+.+++.++|+.+++++++.++..++||+|++++.|+
T Consensus       132 le~~~~~~~~Il~~~~~~kl~~~l~sr~~~v~~~~~~~~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~gdlr~~~~~le  211 (367)
T PRK14970        132 LEEPPAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFD  211 (367)
T ss_pred             HhCCCCceEEEEEeCCcccCCHHHHhcceeEecCCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHHH
Confidence            58899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLV  100 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~  100 (533)
                      .+.......|+.+.+.++++
T Consensus       212 kl~~y~~~~it~~~v~~~~~  231 (367)
T PRK14970        212 RVVTFCGKNITRQAVTENLN  231 (367)
T ss_pred             HHHHhcCCCCCHHHHHHHhC
Confidence            98875444588888766544

>KOG0730|consensus

Probab=99.27  E-value=4.6e-11  Score=122.00  Aligned_cols=151  Identities=23%  Similarity=0.313  Sum_probs=111.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC------CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD------DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      ..+|+|||||||||.+++++|++.      +..++.++++.      +.+...+|..+.......     .+.+++|||+
T Consensus       219 rg~Ll~gppg~Gkt~l~~aVa~e~------~a~~~~i~~peli~k~~gEte~~LR~~f~~a~k~~-----~psii~IdEl  287 (693)
T KOG0730|consen  219 RGLLLYGPPGTGKTFLVRAVANEY------GAFLFLINGPELISKFPGETESNLRKAFAEALKFQ-----VPSIIFIDEL  287 (693)
T ss_pred             CCccccCCCCCChHHHHHHHHHHh------CceeEecccHHHHHhcccchHHHHHHHHHHHhccC-----CCeeEeHHhH
Confidence            459999999999999999999997      66677777764      233445555544433322     2789999999


Q ss_pred             CCCCH----------HHHHHHHHHHHhcC--CCcEEEEEeCCCCCCChhhhc-cce-eeeecCCCHHHHHHHhhcC----
Q psy4285         381 DAMTN----------DAQNALRRIIEKFT--TNVRFCIICNYLSKIPPAIQS-RCT-RFRFGPLDSSLIMSRLDYD----  442 (533)
Q Consensus       381 d~l~~----------~~~~~Ll~~le~~~--~~~~~I~~~n~~~~l~~~l~s-R~~-~i~~~~~~~~~~~~~l~~~----  442 (533)
                      |.+.+          .....|+.+++...  .++.++.++|++..+++++++ ||+ .+.+.-|+..+..++++..    
T Consensus       288 d~l~p~r~~~~~~e~Rv~sqlltL~dg~~~~~~vivl~atnrp~sld~alRRgRfd~ev~IgiP~~~~RldIl~~l~k~~  367 (693)
T KOG0730|consen  288 DALCPKREGADDVESRVVSQLLTLLDGLKPDAKVIVLAATNRPDSLDPALRRGRFDREVEIGIPGSDGRLDILRVLTKKM  367 (693)
T ss_pred             hhhCCcccccchHHHHHHHHHHHHHhhCcCcCcEEEEEecCCccccChhhhcCCCcceeeecCCCchhHHHHHHHHHHhc
Confidence            99974          23566888888644  678888899999999999997 994 7888888888888888876    


Q ss_pred             ----HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 ----DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 ----~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                          ..++..+..         .++||.+.|+...+...
T Consensus       368 ~~~~~~~l~~iA~---------~thGyvGaDL~~l~~ea  397 (693)
T KOG0730|consen  368 NLLSDVDLEDIAV---------STHGYVGADLAALCREA  397 (693)
T ss_pred             CCcchhhHHHHHH---------HccchhHHHHHHHHHHH
Confidence                134444444         66778777776655544

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.27  E-value=8.5e-12  Score=123.89  Aligned_cols=80  Identities=24%  Similarity=0.402  Sum_probs=72.9

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+.+++++|||+|||+.++|++++.+++.++|++.+...+  ++++.+..+++.|+|++|+|+++++
T Consensus       165 LEEpp~~~~fiLit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~~~--~~~~~~~~i~~~s~G~pr~Al~ll~  242 (351)
T PRK09112        165 LEEPPARALFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSSQG--SDGEITEALLQRSKGSVRKALLLLN  242 (351)
T ss_pred             HhcCCCCceEEEEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcccC--CCHHHHHHHHHHcCCCHHHHHHHHh
Confidence            69999999999999999999999999999999999999999999998654443  6688899999999999999999987


Q ss_pred             HH
Q psy4285          81 SA   82 (533)
Q Consensus        81 ~~   82 (533)
                      .-
T Consensus       243 ~~  244 (351)
T PRK09112        243 YG  244 (351)
T ss_pred             cC
Confidence            53

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

Probab=99.27  E-value=2.9e-11  Score=119.57  Aligned_cols=179  Identities=15%  Similarity=0.141  Sum_probs=119.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHH----HHh----cccC-CCCCcEEEEEe
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQ----FAS----TKTM-HKSSYKLIILD  378 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~----~~~~-~~~~~~vliiD  378 (533)
                      +++++|++||||+.+|+.|.......  ...+++.+|++.........++++.    |..    .... ..+..+.||+|
T Consensus       103 ~vLi~GetGtGKel~A~~iH~~s~r~--~~~PFI~~NCa~~~en~~~~eLFG~~kGaftGa~~~k~Glfe~A~GGtLfLD  180 (403)
T COG1221         103 PVLIIGETGTGKELFARLIHALSARR--AEAPFIAFNCAAYSENLQEAELFGHEKGAFTGAQGGKAGLFEQANGGTLFLD  180 (403)
T ss_pred             cEEEecCCCccHHHHHHHHHHhhhcc--cCCCEEEEEHHHhCcCHHHHHHhccccceeecccCCcCchheecCCCEEehh
Confidence            59999999999999999999443221  3678999999876554444333221    111    0111 13568899999


Q ss_pred             CCCCCCHHHHHHHHHHHHh-----------cCCCcEEEEEeCC--CCCCCh--hhhccceeeeecCCCHHHHHHHhhcCH
Q psy4285         379 EADAMTNDAQNALRRIIEK-----------FTTNVRFCIICNY--LSKIPP--AIQSRCTRFRFGPLDSSLIMSRLDYDD  443 (533)
Q Consensus       379 E~d~l~~~~~~~Ll~~le~-----------~~~~~~~I~~~n~--~~~l~~--~l~sR~~~i~~~~~~~~~~~~~l~~~~  443 (533)
                      |++.|+++.|..|++.||+           .+.++++|++|+.  .+.+..  ++.+|+....+.-|+       |+..+
T Consensus       181 EI~~LP~~~Q~kLl~~le~g~~~rvG~~~~~~~dVRli~AT~~~l~~~~~~g~dl~~rl~~~~I~LPp-------LrER~  253 (403)
T COG1221         181 EIHRLPPEGQEKLLRVLEEGEYRRVGGSQPRPVDVRLICATTEDLEEAVLAGADLTRRLNILTITLPP-------LRERK  253 (403)
T ss_pred             hhhhCCHhHHHHHHHHHHcCceEecCCCCCcCCCceeeeccccCHHHHHHhhcchhhhhcCceecCCC-------hhhch
Confidence            9999999999999999997           3577999999863  345555  788877655555555       33334


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHH
Q psy4285         444 ISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDI  498 (533)
Q Consensus       444 ~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~  498 (533)
                      .|+..+++.+-....  ...+.+.........+.+..+.||++++ ++-+.+..+
T Consensus       254 ~Di~~L~e~Fl~~~~--~~l~~~~~~~~~~a~~~L~~y~~pGNir-ELkN~Ve~~  305 (403)
T COG1221         254 EDILLLAEHFLKSEA--RRLGLPLSVDSPEALRALLAYDWPGNIR-ELKNLVERA  305 (403)
T ss_pred             hhHHHHHHHHHHHHH--HHcCCCCCCCCHHHHHHHHhCCCCCcHH-HHHHHHHHH
Confidence            455555554333333  3345554444467778888999999987 444444433

>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=99.27  E-value=4.8e-12  Score=104.04  Aligned_cols=108  Identities=23%  Similarity=0.208  Sum_probs=60.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHH------HHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQ------IFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      |+|+.|+||+|||++|+++|+.+      +..+.++......-...+...      .+.+.-...  +--..++++||+.
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~------~~~f~RIq~tpdllPsDi~G~~v~~~~~~~f~~~~G--Pif~~ill~DEiN   72 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSL------GLSFKRIQFTPDLLPSDILGFPVYDQETGEFEFRPG--PIFTNILLADEIN   72 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHT------T--EEEEE--TT--HHHHHEEEEEETTTTEEEEEE---TT-SSEEEEETGG
T ss_pred             CEeeECCCccHHHHHHHHHHHHc------CCceeEEEecCCCCcccceeeeeeccCCCeeEeecC--hhhhceeeecccc
Confidence            68999999999999999999998      444444443211111111100      000100110  1124699999999


Q ss_pred             CCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCCC-----CCChhhhccce
Q psy4285         382 AMTNDAQNALRRIIEKF-----------TTNVRFCIICNYLS-----KIPPAIQSRCT  423 (533)
Q Consensus       382 ~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~~-----~l~~~l~sR~~  423 (533)
                      +.++..|++|+++|+|.           +....+|.|.|..+     .+++++++||.
T Consensus        73 rappktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~DRF~  130 (131)
T PF07726_consen   73 RAPPKTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLDRFM  130 (131)
T ss_dssp             GS-HHHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT--S------HHHHTTSS
T ss_pred             cCCHHHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhcccc
Confidence            99999999999999874           34456666778665     68999999984

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.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=99.27  E-value=8.3e-12  Score=121.55  Aligned_cols=72  Identities=21%  Similarity=0.371  Sum_probs=63.9

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      +||||++|+|||+|+.+++++|||+|||+.++|++|+.+++.+||..    .+++  .  ...+++.++|++.+|+.+++
T Consensus       132 LEEPp~~t~fiL~t~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~L~~----~~~~--~--~~~~l~l~~G~p~~A~~~~~  203 (319)
T PRK06090        132 LEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWVVTPPSTAQAMQWLKG----QGIT--V--PAYALKLNMGSPLKTLAMMK  203 (319)
T ss_pred             hcCCCCCeEEEEEECChhhChHHHHhcceeEeCCCCCHHHHHHHHHH----cCCc--h--HHHHHHHcCCCHHHHHHHhC
Confidence            69999999999999999999999999999999999999999999973    4443  2  34678999999999998864

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=99.27  E-value=8.6e-12  Score=121.62  Aligned_cols=75  Identities=17%  Similarity=0.267  Sum_probs=66.5

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+.+++|+|||||||+.++|++|+.+++.+||.+    .+  +++.....++..++|++.+|+.+++
T Consensus       137 LEEPp~~~~fiL~~~~~~~lLpTIrSRCq~i~~~~~~~~~~~~~L~~----~~--~~~~~a~~~~~l~~G~p~~A~~~~~  210 (319)
T PRK08769        137 LEEPSPGRYLWLISAQPARLPATIRSRCQRLEFKLPPAHEALAWLLA----QG--VSERAAQEALDAARGHPGLAAQWLR  210 (319)
T ss_pred             hhCCCCCCeEEEEECChhhCchHHHhhheEeeCCCcCHHHHHHHHHH----cC--CChHHHHHHHHHcCCCHHHHHHHhc
Confidence            69999999999999999999999999999999999999999999973    33  4456566789999999999988774


Q ss_pred             H
Q psy4285          81 S   81 (533)
Q Consensus        81 ~   81 (533)
                      .
T Consensus       211 ~  211 (319)
T PRK08769        211 E  211 (319)
T ss_pred             C
Confidence            3

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.27  E-value=7.1e-11  Score=116.00  Aligned_cols=156  Identities=13%  Similarity=0.109  Sum_probs=91.9

Q ss_pred             hhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc-------cC--------------------cc
Q psy4285         287 LNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ-------FN--------------------AM  339 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~-------~~--------------------~~  339 (533)
                      ..|+++....+.-.+-....+|+||+|+||||||++|+++++.+-+...       ..                    .+
T Consensus        10 i~Gq~~~~~~l~~~~~~~~~~~vLl~G~pG~gKT~lar~la~llP~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~p   89 (334)
T PRK13407         10 IVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSARPEDCPEWAHVSSTTMIERPTP   89 (334)
T ss_pred             hCCHHHHHHHHHHHHhccCCCcEEEEcCCCCCHHHHHHHHHHHCCCcchhcccccccCcccCCcccccccCCcccccCCc
Confidence            3466776665553332123458999999999999999999998732110       00                    00


Q ss_pred             eEEecC--CC--CCchhHHHHHH--HHHHhccc-CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc-------------C
Q psy4285         340 VLELNA--SD--DRGIGIVRDQI--FQFASTKT-MHKSSYKLIILDEADAMTNDAQNALRRIIEKF-------------T  399 (533)
Q Consensus       340 ~~~~~~--~~--~~~~~~~~~~~--~~~~~~~~-~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~-------------~  399 (533)
                      +..+..  ++  ..|.-.+...+  +.+..... ...+..++|++||++.+++..++.|++.|++.             +
T Consensus        90 ~~~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~l~~A~~GiL~lDEInrl~~~~q~~Lle~mee~~v~v~r~G~~~~~p  169 (334)
T PRK13407         90 VVDLPLGVTEDRVVGALDIERALTRGEKAFEPGLLARANRGYLYIDEVNLLEDHIVDLLLDVAQSGENVVEREGLSIRHP  169 (334)
T ss_pred             cccCCCCCCcceeecchhhhhhhhcCCeeecCCceEEcCCCeEEecChHhCCHHHHHHHHHHHHcCCeEEEECCeEEecC
Confidence            000000  00  11111111111  00100111 11234579999999999999999999999864             2


Q ss_pred             CCcEEEEEeCCCC-CCChhhhccce-eeeecCCCH-HHHHHHhhcC
Q psy4285         400 TNVRFCIICNYLS-KIPPAIQSRCT-RFRFGPLDS-SLIMSRLDYD  442 (533)
Q Consensus       400 ~~~~~I~~~n~~~-~l~~~l~sR~~-~i~~~~~~~-~~~~~~l~~~  442 (533)
                      ....++.++|..+ .+.+++.+||. .+.+.++++ ++..+++.+.
T Consensus       170 ~rfiviAt~NP~e~~l~~aLldRF~~~v~v~~~~~~~e~~~il~~~  215 (334)
T PRK13407        170 ARFVLVGSGNPEEGELRPQLLDRFGLSVEVRSPRDVETRVEVIRRR  215 (334)
T ss_pred             CCEEEEecCCcccCCCCHHHHhhcceEEEcCCCCcHHHHHHHHHHh
Confidence            3345555567544 68999999994 677777766 5656666553

>KOG0741|consensus

Probab=99.27  E-value=6.1e-12  Score=124.48  Aligned_cols=149  Identities=21%  Similarity=0.289  Sum_probs=102.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC------CCchhHHHHHHHHHHhccc--CCCCCcEEEEEeCC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD------DRGIGIVRDQIFQFASTKT--MHKSSYKLIILDEA  380 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~--~~~~~~~vliiDE~  380 (533)
                      +|||||||||||.+||.|.+.+....     -.-+|+++      +.++..+|+++........  ...++-.|+|+||+
T Consensus       259 iLLyGPPGTGKTLiARqIGkMLNAre-----PKIVNGPeIL~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEi  333 (744)
T KOG0741|consen  259 ILLYGPPGTGKTLIARQIGKMLNARE-----PKIVNGPEILNKYVGESEENVRKLFADAEEEQRRLGANSGLHIIIFDEI  333 (744)
T ss_pred             EEEECCCCCChhHHHHHHHHHhcCCC-----CcccCcHHHHHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEEEehhh
Confidence            89999999999999999999985442     12344443      3456677777655433211  11356789999999


Q ss_pred             CCCCH-------------HHHHHHHHHHH--hcCCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC
Q psy4285         381 DAMTN-------------DAQNALRRIIE--KFTTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       381 d~l~~-------------~~~~~Ll~~le--~~~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                      |.+..             ...|.|+.-|+  +.-.|+.+|..||+.+.+|++|++  |+. .+.+.-|++.-..+++.-.
T Consensus       334 DAICKqRGS~~g~TGVhD~VVNQLLsKmDGVeqLNNILVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gRlQIl~IH  413 (744)
T KOG0741|consen  334 DAICKQRGSMAGSTGVHDTVVNQLLSKMDGVEQLNNILVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGRLQILKIH  413 (744)
T ss_pred             HHHHHhcCCCCCCCCccHHHHHHHHHhcccHHhhhcEEEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCceEEEEhh
Confidence            98743             34677777776  345788999999999999999999  884 6666666666555555433


Q ss_pred             ------------HHHHHHHHHHHHHHHHHHHhcCCCHHHHH
Q psy4285         443 ------------DISFFNIIIWYIKIQEIKIEKGLALTDIL  471 (533)
Q Consensus       443 ------------~~~~~~ll~~~~~l~~l~~~~~~~~~di~  471 (533)
                                  .-++.++..         .+..+|+.++.
T Consensus       414 T~rMre~~~l~~dVdl~elA~---------lTKNfSGAEle  445 (744)
T KOG0741|consen  414 TKRMRENNKLSADVDLKELAA---------LTKNFSGAELE  445 (744)
T ss_pred             hhhhhhcCCCCCCcCHHHHHH---------HhcCCchhHHH
Confidence                        234444444         56677776653

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

Probab=99.27  E-value=7.7e-10  Score=110.27  Aligned_cols=145  Identities=21%  Similarity=0.184  Sum_probs=93.3

Q ss_pred             chhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHH---HH
Q psy4285         290 SMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQI---FQ  360 (533)
Q Consensus       290 ~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~---~~  360 (533)
                      .++........+..++  |++|.||||||||++|+.+|+.+      +..+..+.+....      +...+....   +.
T Consensus        29 ~~~~~~~~l~a~~~~~--~vll~G~PG~gKT~la~~lA~~l------~~~~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~  100 (329)
T COG0714          29 DEEVIELALLALLAGG--HVLLEGPPGVGKTLLARALARAL------GLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGE  100 (329)
T ss_pred             cHHHHHHHHHHHHcCC--CEEEECCCCccHHHHHHHHHHHh------CCCeEEEecCCCCCHHHhcCchhHhhhhccCCe
Confidence            3333333333333343  79999999999999999999998      5566666654332      222222221   11


Q ss_pred             HHhc-ccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc------------CCCcEEEEEeC-----CCCCCChhhhccc
Q psy4285         361 FAST-KTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF------------TTNVRFCIICN-----YLSKIPPAIQSRC  422 (533)
Q Consensus       361 ~~~~-~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~------------~~~~~~I~~~n-----~~~~l~~~l~sR~  422 (533)
                      +... .+...+-..++++|||++..+..+++|+..|++.            +....+|.|+|     ....+++++++||
T Consensus       101 ~~~~~gpl~~~~~~ill~DEInra~p~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~g~~~l~eA~ldRf  180 (329)
T COG0714         101 FRFVPGPLFAAVRVILLLDEINRAPPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEGTYPLPEALLDRF  180 (329)
T ss_pred             EEEecCCcccccceEEEEeccccCCHHHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccCCCcCCCHHHHhhE
Confidence            1101 1111111149999999999999999999999872            23455666668     4557899999999


Q ss_pred             -eeeeecCC-CHHHHHHHhhcC
Q psy4285         423 -TRFRFGPL-DSSLIMSRLDYD  442 (533)
Q Consensus       423 -~~i~~~~~-~~~~~~~~l~~~  442 (533)
                       ..+.+.+| +..+...++.+.
T Consensus       181 ~~~~~v~yp~~~~e~~~i~~~~  202 (329)
T COG0714         181 LLRIYVDYPDSEEEERIILARV  202 (329)
T ss_pred             EEEEecCCCCchHHHHHHHHhC
Confidence             78888888 444444444444

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=99.26  E-value=9.8e-12  Score=121.37  Aligned_cols=76  Identities=17%  Similarity=0.264  Sum_probs=66.3

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+.+++++|||+|||+.++|++++.+++.+||....     ..++.....++..++|++.+|+.+++
T Consensus       131 LEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~~~~~~~~~~~~~L~~~~-----~~~~~~~~~~~~l~~g~p~~A~~~~~  205 (325)
T PRK06871        131 LEEPRPNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQQALDWLQAQS-----SAEISEILTALRINYGRPLLALTFLE  205 (325)
T ss_pred             hcCCCCCeEEEEEECChHhCchHHHhhceEEeCCCCCHHHHHHHHHHHh-----ccChHHHHHHHHHcCCCHHHHHHHhh
Confidence            7999999999999999999999999999999999999999999998543     22344566788999999999988765


Q ss_pred             H
Q psy4285          81 S   81 (533)
Q Consensus        81 ~   81 (533)
                      .
T Consensus       206 ~  206 (325)
T PRK06871        206 Q  206 (325)
T ss_pred             C
Confidence            4

>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=99.26  E-value=9.5e-12  Score=110.84  Aligned_cols=101  Identities=24%  Similarity=0.315  Sum_probs=72.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHc-cccccCcceEEecCCCCCc----hhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLY-TKAQFNAMVLELNASDDRG----IGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~-~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+++|.||+|||||.+|+++++.++ +.   ..+++.++++....    ...+...+........  .....||++||+|
T Consensus         4 ~~~ll~GpsGvGKT~la~~la~~l~~~~---~~~~~~~d~s~~~~~~~~~~~~~~l~~~~~~~v~--~~~~gVVllDEid   78 (171)
T PF07724_consen    4 SNFLLAGPSGVGKTELAKALAELLFVGS---ERPLIRIDMSEYSEGDDVESSVSKLLGSPPGYVG--AEEGGVVLLDEID   78 (171)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHT-SS---CCEEEEEEGGGHCSHHHCSCHCHHHHHHTTCHHH--HHHHTEEEEETGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhccCC---ccchHHHhhhcccccchHHhhhhhhhhcccceee--ccchhhhhhHHHh
Confidence            3589999999999999999999996 33   45778888776655    3333333222110000  0123499999999


Q ss_pred             CCCH-----------HHHHHHHHHHHhc-----------CCCcEEEEEeCCCC
Q psy4285         382 AMTN-----------DAQNALRRIIEKF-----------TTNVRFCIICNYLS  412 (533)
Q Consensus       382 ~l~~-----------~~~~~Ll~~le~~-----------~~~~~~I~~~n~~~  412 (533)
                      +..+           ..++.|++++|+.           -.++.||+|||.-.
T Consensus        79 Ka~~~~~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~~  131 (171)
T PF07724_consen   79 KAHPSNSGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFGA  131 (171)
T ss_dssp             GCSHTTTTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSST
T ss_pred             hccccccccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEeccccc
Confidence            9999           9999999999863           36788999998654

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 ....

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=99.26  E-value=1.1e-10  Score=115.62  Aligned_cols=168  Identities=17%  Similarity=0.147  Sum_probs=109.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHh----------cccCCCCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAS----------TKTMHKSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~vlii  377 (533)
                      +++|+|++||||+++|+++.......   ..+++.+++..... ..+...+.....          ......+..++|+|
T Consensus        31 pVlI~GE~GtGK~~lA~~iH~~s~r~---~~pfv~v~c~~~~~-~~~~~~lfg~~~~~~~g~~~~~~g~l~~a~gGtL~l  106 (326)
T PRK11608         31 PVLIIGERGTGKELIASRLHYLSSRW---QGPFISLNCAALNE-NLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFL  106 (326)
T ss_pred             CEEEECCCCCcHHHHHHHHHHhCCcc---CCCeEEEeCCCCCH-HHHHHHHccccccccCCcccccCCchhccCCCeEEe
Confidence            69999999999999999998654222   46788888887432 222222211000          00011345689999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhcC-----------CCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         378 DEADAMTNDAQNALRRIIEKFT-----------TNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~~-----------~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ||++.|+...|..|++.+++..           .++++|++|+..       ..+.+.|..|+....+.-|+       |
T Consensus       107 ~~i~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~s~~~l~~l~~~g~f~~dL~~~l~~~~i~lPp-------L  179 (326)
T PRK11608        107 DELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGKFRADLLDRLAFDVVQLPP-------L  179 (326)
T ss_pred             CChhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCchhHHHHHHcCCchHHHHHhcCCCEEECCC-------h
Confidence            9999999999999999997532           257899988753       35778888898766666666       4


Q ss_pred             hcCHHHHHHHHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHhcCCChhHH
Q psy4285         440 DYDDISFFNIIIWYIKIQEIKIEKGLAL-TDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       440 ~~~~~~~~~ll~~~~~l~~l~~~~~~~~-~di~~~~~~~~~~~~~~~~~~  488 (533)
                      +..++|+..+++.+-.  .+....+.+. ..+-......+..+.||++++
T Consensus       180 ReR~eDI~~L~~~fl~--~~~~~~~~~~~~~~s~~al~~L~~y~WPGNvr  227 (326)
T PRK11608        180 RERQSDIMLMAEHFAI--QMCRELGLPLFPGFTERARETLLNYRWPGNIR  227 (326)
T ss_pred             hhhhhhHHHHHHHHHH--HHHHHhCCCCCCCCCHHHHHHHHhCCCCcHHH
Confidence            4444455555543211  1112223321 235567788889999999987

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.26  E-value=2.4e-11  Score=129.67  Aligned_cols=101  Identities=27%  Similarity=0.396  Sum_probs=93.3

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+.+++|||+|+..++++++|+|||+.+.|++++..++..++.+++.++++.++++++..++..++||+|.|++.|+
T Consensus       144 LEepp~~tv~Il~t~~~~kll~tI~SR~~~i~f~~l~~~el~~~L~~~a~~egl~i~~eal~~La~~s~Gdlr~al~~Le  223 (585)
T PRK14950        144 LEEPPPHAIFILATTEVHKVPATILSRCQRFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDAENLLQ  223 (585)
T ss_pred             HhcCCCCeEEEEEeCChhhhhHHHHhccceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVS  101 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~  101 (533)
                      .+....+..|+.+.|.++++.
T Consensus       224 kL~~y~~~~It~e~V~~ll~~  244 (585)
T PRK14950        224 QLATTYGGEISLSQVQSLLGI  244 (585)
T ss_pred             HHHHhcCCCCCHHHHHHHhcC
Confidence            987755567999888766554

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

Probab=99.25  E-value=5.9e-11  Score=110.63  Aligned_cols=130  Identities=23%  Similarity=0.330  Sum_probs=83.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc--hhHHHH-HHHHHHhcccCCCCCcEEEEEeCCCCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG--IGIVRD-QIFQFASTKTMHKSSYKLIILDEADAMT  384 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~--~~~~~~-~~~~~~~~~~~~~~~~~vliiDE~d~l~  384 (533)
                      .+++|||+|+||||+..++++++.... .+..++.+++.+...  ...++. ....+...    -...++|+||+++.+.
T Consensus        36 ~l~l~G~~G~GKTHLL~Ai~~~~~~~~-~~~~v~y~~~~~f~~~~~~~~~~~~~~~~~~~----~~~~DlL~iDDi~~l~  110 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHLLQAIANEAQKQH-PGKRVVYLSAEEFIREFADALRDGEIEEFKDR----LRSADLLIIDDIQFLA  110 (219)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHHC-TTS-EEEEEHHHHHHHHHHHHHTTSHHHHHHH----HCTSSEEEEETGGGGT
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHhcc-ccccceeecHHHHHHHHHHHHHcccchhhhhh----hhcCCEEEEecchhhc
Confidence            389999999999999999999886532 144556665433110  000000 01111111    0356899999999997


Q ss_pred             HH--HHHHHHHHHHhc-CCCcEEEEEeCCC----CCCChhhhccc---eeeeecCCCHHHHHHHhhcC
Q psy4285         385 ND--AQNALRRIIEKF-TTNVRFCIICNYL----SKIPPAIQSRC---TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       385 ~~--~~~~Ll~~le~~-~~~~~~I~~~n~~----~~l~~~l~sR~---~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..  .+..|+.+++.. ..+..+|++++.+    ..+++.++||+   ..+.+.+|+.+..+.++.+.
T Consensus       111 ~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~~  178 (219)
T PF00308_consen  111 GKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDEDRRRILQKK  178 (219)
T ss_dssp             THHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHHHHHHHHHH
Confidence            64  478888888753 2456788888543    24788999998   48999999999999998876

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.

>PRK09183 transposase/IS protein; Provisional

Probab=99.24  E-value=7.5e-12  Score=119.57  Aligned_cols=165  Identities=15%  Similarity=0.143  Sum_probs=103.2

Q ss_pred             ccCchHHhhcHHHHHHhhcCCCCCccccccccCCCCHHHHHHHHHHHhhh-chhhhhhhcc--cccccCCCceeEeCCCC
Q psy4285         240 SDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNE-SMDLCYKINR--FIDENELPHLLFYGPPG  316 (533)
Q Consensus       240 s~~di~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~l~~--~~~~~~~~~~ll~GppG  316 (533)
                      ......+.+..|...+...++....+...+..++|...++.++......+ ....+..+..  ++..+  .+++|+||||
T Consensus        35 ~~~~~~e~l~~ll~~E~~~R~~~~~~~~~k~a~~p~~~~l~~fd~~~~~~~~~~~i~~L~~~~~i~~~--~~v~l~Gp~G  112 (259)
T PRK09183         35 QEWSYMDFLEHLLHEEKLARHQRKQAMYTRMAAFPAVKTFEEYDFTFATGAPQKQLQSLRSLSFIERN--ENIVLLGPSG  112 (259)
T ss_pred             cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhcccccCCCCCHHHHHHHhcCCchhcC--CeEEEEeCCC
Confidence            44567888888888888777666667788888999887777764332222 2334444432  34433  3799999999


Q ss_pred             CChHHHHHHHHHHHccccccCcceEEecCCCCCch-hH--HHHHHHHHHhcccCCCCCcEEEEEeCCCCC--CHHHHHHH
Q psy4285         317 TGKTTTILACARKLYTKAQFNAMVLELNASDDRGI-GI--VRDQIFQFASTKTMHKSSYKLIILDEADAM--TNDAQNAL  391 (533)
Q Consensus       317 tGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~-~~--~~~~~~~~~~~~~~~~~~~~vliiDE~d~l--~~~~~~~L  391 (533)
                      |||||++.+++..+...   +..+..++..+.... ..  ....+.......   ....+++||||++..  +.+.++.|
T Consensus       113 tGKThLa~al~~~a~~~---G~~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~---~~~~dlLiiDdlg~~~~~~~~~~~l  186 (259)
T PRK09183        113 VGKTHLAIALGYEAVRA---GIKVRFTTAADLLLQLSTAQRQGRYKTTLQRG---VMAPRLLIIDEIGYLPFSQEEANLF  186 (259)
T ss_pred             CCHHHHHHHHHHHHHHc---CCeEEEEeHHHHHHHHHHHHHCCcHHHHHHHH---hcCCCEEEEcccccCCCChHHHHHH
Confidence            99999999998875332   334444443221100 00  000010111000   134579999999985  45666789


Q ss_pred             HHHHHhcCCCcEEEEEeCCCC
Q psy4285         392 RRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       392 l~~le~~~~~~~~I~~~n~~~  412 (533)
                      +++++....+..+|+|||.+.
T Consensus       187 f~li~~r~~~~s~iiTsn~~~  207 (259)
T PRK09183        187 FQVIAKRYEKGSMILTSNLPF  207 (259)
T ss_pred             HHHHHHHHhcCcEEEecCCCH
Confidence            999987655567899998764

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=99.24  E-value=1.1e-10  Score=117.34  Aligned_cols=168  Identities=16%  Similarity=0.172  Sum_probs=116.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHH-----HHhcc-----cC-CCCCcEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQ-----FASTK-----TM-HKSSYKLII  376 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~-----~~-~~~~~~vli  376 (533)
                      .+|+.|.+||||..+|++|.+..-..   ..+|+.+||... ....+...+..     |....     .. ..+..+.||
T Consensus       270 tVLi~GESGTGKElfA~~IH~~S~R~---~~PFIaiNCaAi-Pe~LlESELFGye~GAFTGA~~~GK~GlfE~A~gGTLF  345 (560)
T COG3829         270 TVLILGESGTGKELFARAIHNLSPRA---NGPFIAINCAAI-PETLLESELFGYEKGAFTGASKGGKPGLFELANGGTLF  345 (560)
T ss_pred             cEEEecCCCccHHHHHHHHHhcCccc---CCCeEEEecccC-CHHHHHHHHhCcCCccccccccCCCCcceeeccCCeEE
Confidence            59999999999999999999865433   568999998763 22222222211     11110     11 124578999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHH
Q psy4285         377 LDEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSR  438 (533)
Q Consensus       377 iDE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~  438 (533)
                      +|||..|+...|..|++.|++.           +.++++|.+||..       ..+-+.|.-|+.++.+.-||   ++++
T Consensus       346 LDEIgempl~LQaKLLRVLQEkei~rvG~t~~~~vDVRIIAATN~nL~~~i~~G~FReDLYYRLNV~~i~iPP---LReR  422 (560)
T COG3829         346 LDEIGEMPLPLQAKLLRVLQEKEIERVGGTKPIPVDVRIIAATNRNLEKMIAEGTFREDLYYRLNVIPITIPP---LRER  422 (560)
T ss_pred             ehhhccCCHHHHHHHHHHHhhceEEecCCCCceeeEEEEEeccCcCHHHHHhcCcchhhheeeeceeeecCCC---cccC
Confidence            9999999999999999999863           4679999999864       25667777888888888777   3344


Q ss_pred             hhcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHH
Q psy4285         439 LDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       439 l~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~  488 (533)
                      -..+|.-+..+++      ......+-....+.......+..+.||+++|
T Consensus       423 ~eDI~~L~~~Fl~------k~s~~~~~~v~~ls~~a~~~L~~y~WPGNVR  466 (560)
T COG3829         423 KEDIPLLAEYFLD------KFSRRYGRNVKGLSPDALALLLRYDWPGNVR  466 (560)
T ss_pred             cchHHHHHHHHHH------HHHHHcCCCcccCCHHHHHHHHhCCCCchHH
Confidence            4444444444444      2223345555556666778889999999998

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.23  E-value=1.2e-10  Score=129.15  Aligned_cols=148  Identities=14%  Similarity=0.145  Sum_probs=103.0

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCCC----c----hhHHH
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDDR----G----IGIVR  355 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~~----~----~~~~~  355 (533)
                      .|++..+.++...+.+...++++|+||||||||++|+.+|+.+.....    .+..++.++.....    .    ...++
T Consensus       181 igr~~ei~~~i~iL~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~l~ag~~~~g~~e~~lk  260 (857)
T PRK10865        181 IGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLK  260 (857)
T ss_pred             CCCHHHHHHHHHHHhcCCcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEehhhhhhccchhhhhHHHHH
Confidence            345555555555566666678999999999999999999998743211    13455555433211    1    12344


Q ss_pred             HHHHHHHhcccCCCCCcEEEEEeCCCCCCH--------HHHHHHHHHHHhcCCCcEEEEEeCCCC-----CCChhhhccc
Q psy4285         356 DQIFQFASTKTMHKSSYKLIILDEADAMTN--------DAQNALRRIIEKFTTNVRFCIICNYLS-----KIPPAIQSRC  422 (533)
Q Consensus       356 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------~~~~~Ll~~le~~~~~~~~I~~~n~~~-----~l~~~l~sR~  422 (533)
                      ..+......     ..+.||||||+|.+..        +.++.|...++.  ...++|.+|+..+     .+++++.|||
T Consensus       261 ~~~~~~~~~-----~~~~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l~~--g~l~~IgaTt~~e~r~~~~~d~al~rRf  333 (857)
T PRK10865        261 GVLNDLAKQ-----EGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR--GELHCVGATTLDEYRQYIEKDAALERRF  333 (857)
T ss_pred             HHHHHHHHc-----CCCeEEEEecHHHhccCCCCccchhHHHHhcchhhc--CCCeEEEcCCCHHHHHHhhhcHHHHhhC
Confidence            444333221     3567999999999963        356777777764  4688999987765     5899999999


Q ss_pred             eeeeecCCCHHHHHHHhhcC
Q psy4285         423 TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       423 ~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..+.+..|+.++...+++.+
T Consensus       334 ~~i~v~eP~~~~~~~iL~~l  353 (857)
T PRK10865        334 QKVFVAEPSVEDTIAILRGL  353 (857)
T ss_pred             CEEEeCCCCHHHHHHHHHHH
Confidence            99999999999999888766

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.23  E-value=1.6e-10  Score=114.86  Aligned_cols=162  Identities=17%  Similarity=0.276  Sum_probs=117.2

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHH-------HHHHhhcCCCCCHHHHHHHHHhcCCCHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRL-------DYVIEQEKVNVTPDGKKAIIDLSDGDMR   73 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l-------~~~~~~~~~~~~~~~~~~~~~~~~g~~r   73 (533)
                      ||+|+++++||++||.++++.|+|+|||..+.|++|+.++...++       ..++.++++.++++++..++..+.||.|
T Consensus       125 le~~~~~~~~Ilt~n~~~~l~~~l~sR~~~i~~~~p~~~~~~~il~~~~~~~~~~~~~~~~~i~~~al~~l~~~~~~d~r  204 (316)
T PHA02544        125 MEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQMIVRCKGILEAEGVEVDMKVLAALVKKNFPDFR  204 (316)
T ss_pred             HHhcCCCceEEEEcCChhhchHHHHhhceEEEeCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhcCCCHH
Confidence            588999999999999999999999999999999999998876543       4456678999999999999999999999


Q ss_pred             HHHHHHHHHHHhCCCCcchhhHHhhh-------hhhccccchhHHHHH-----hchHHHHhhc------CCChhhHHHHH
Q psy4285          74 KVLNILQSAATAHADEVNEDTIFTLL-------VSRVEKYRPSTLDEL-----VSHQDIISTI------EIPESMLVDLV  135 (533)
Q Consensus        74 ~a~~~l~~~~~~~~~~i~~~~i~~~~-------~~~~ek~~~~~l~~l-----ls~~~~l~~l------~~~~~~~~~~~  135 (533)
                      ++++.++.++.  ...++.+.+..+.       ..|............     .+..+++..+      .+....+....
T Consensus       205 ~~l~~l~~~~~--~~~i~~~~l~~~~~~~~~~l~~~l~~~d~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  282 (316)
T PHA02544        205 RTINELQRYAS--TGKIDAGILSEVTNSDIDDVVEALKAKDFKAVRALAPNYANDYASFVGKLYDELYPQVTPPSIIRLI  282 (316)
T ss_pred             HHHHHHHHHHc--cCCCCHHHHHHhhHHHHHHHHHHHHcCCHHHHHHHHHHhccCHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            99999998764  2356654432211       111111121111111     1111222221      23444556677


Q ss_pred             hhccCccccccCCCChhhHHHHHHHHHhc
Q psy4285         136 LKMSDIEYRLAAGTSEKIQLSALIAAFNS  164 (533)
Q Consensus       136 ~~~~~~~~~~~~G~~~~~~l~~~~~~~~~  164 (533)
                      ..++..+.++..|.++..++++++..+|+
T Consensus       283 ~~l~~~~~~~~~~~~~~l~le~~l~~~~~  311 (316)
T PHA02544        283 EIIGENNQYHGFAADQEIHLLYLLTQLML  311 (316)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            77888999999999999999999999985

>TIGR01817 nifA Nif-specific regulatory protein

Probab=99.22  E-value=1.8e-10  Score=122.55  Aligned_cols=167  Identities=15%  Similarity=0.142  Sum_probs=109.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH-HH----HHh----ccc-CCCCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI-FQ----FAS----TKT-MHKSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~----~~~----~~~-~~~~~~~vlii  377 (533)
                      +++|+|++||||+++|++++......   +.+++.+++..... ..+...+ +.    +..    ... ...+..++|||
T Consensus       221 pvli~Ge~GtGK~~lA~~ih~~s~r~---~~pfv~i~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~l  296 (534)
T TIGR01817       221 TVLLRGESGTGKELIAKAIHYLSPRA---KRPFVKVNCAALSE-TLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFL  296 (534)
T ss_pred             CEEEECCCCccHHHHHHHHHHhCCCC---CCCeEEeecCCCCH-HHHHHHHcCCCCCccCCCCcCCCCcccccCCCeEEE
Confidence            59999999999999999999875332   56888999876532 2222211 10    000    000 11345689999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhcC-----------CCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         378 DEADAMTNDAQNALRRIIEKFT-----------TNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~~-----------~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ||++.++.+.|..|++.+++..           .++++|++|+..       ..+.+.|..|+..+.+.-|+       |
T Consensus       297 dei~~L~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~s~~~l~~~~~~~~f~~~L~~rl~~~~i~lPp-------L  369 (534)
T TIGR01817       297 DEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLYYRINVVPIFLPP-------L  369 (534)
T ss_pred             echhhCCHHHHHHHHHHHhcCcEEECCCCceEeecEEEEEeCCCCHHHHHHcCCCCHHHHHHhcCCeeeCCC-------c
Confidence            9999999999999999998632           247899998753       35677888888766665555       3


Q ss_pred             hcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHH
Q psy4285         440 DYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       440 ~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~  488 (533)
                      +..++|+..+++.+-  .++....+.. ..+-......+..+.||++++
T Consensus       370 reR~eDi~~L~~~~l--~~~~~~~~~~-~~~s~~a~~~L~~~~WPGNvr  415 (534)
T TIGR01817       370 RERREDIPLLAEAFL--EKFNRENGRP-LTITPSAIRVLMSCKWPGNVR  415 (534)
T ss_pred             ccccccHHHHHHHHH--HHHHHHcCCC-CCCCHHHHHHHHhCCCCChHH
Confidence            333444444444321  1121222333 345667888899999999987

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.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=99.22  E-value=2.3e-11  Score=119.77  Aligned_cols=76  Identities=16%  Similarity=0.281  Sum_probs=66.9

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+.++.++|||+|||+.++|++++.+++.+||.+..    -..+++....++..++|++.+|+.+++
T Consensus       130 LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~L~~~~----~~~~~~~~~~~l~la~Gsp~~A~~l~~  205 (328)
T PRK05707        130 LEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQWLQQAL----PESDERERIELLTLAGGSPLRALQLHE  205 (328)
T ss_pred             HhCCCCCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHHHHHHHHhc----ccCChHHHHHHHHHcCCCHHHHHHHHC
Confidence            6999999999999999999999999999999999999999999997532    123466677889999999999998764

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.21  E-value=4.4e-10  Score=110.56  Aligned_cols=155  Identities=12%  Similarity=0.095  Sum_probs=97.1

Q ss_pred             hhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCc-ceEEecC--------------------
Q psy4285         287 LNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNA-MVLELNA--------------------  345 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~-~~~~~~~--------------------  345 (533)
                      ..||++....|.-.+.+....+++|+|++|||||++|+++++.+.+...... ++. ..+                    
T Consensus        19 ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~ar~~~~~l~~~~~~~~~pf~-~~p~~p~~~~~~~~~~~~~~~~~   97 (350)
T CHL00081         19 IVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTTIRALVDLLPEIEVVKDDPFN-SHPSDPELMSDEVREAIQNGETI   97 (350)
T ss_pred             HhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHHHHHHHHHHhhcCccCCCCCC-CCCCChhhhchhhhhhhcccccc
Confidence            4577777777777666666677999999999999999999988743221100 010 000                    


Q ss_pred             ------------CCCCchhH------HHHHHHHHH---hcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc------
Q psy4285         346 ------------SDDRGIGI------VRDQIFQFA---STKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF------  398 (533)
Q Consensus       346 ------------~~~~~~~~------~~~~~~~~~---~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~------  398 (533)
                                  +.+...+.      +...+..-.   .......+..++|++||++.+++..|+.|++.|++.      
T Consensus        98 ~~~~~~~~~~~lp~~~ted~l~G~iD~~~al~~g~~~~~~GlL~~A~~GiL~lDEInrL~~~~Q~~LLeam~e~~~~ier  177 (350)
T CHL00081         98 ETEKIKIPMVDLPLGATEDRVCGTIDIEKALTEGVKAFEPGLLAKANRGILYVDEVNLLDDHLVDILLDSAASGWNTVER  177 (350)
T ss_pred             cceeccccceecCCCCchhhccCcccHHHHhhcCcccccCCeeeecCCCEEEecChHhCCHHHHHHHHHHHHhCCeEEee
Confidence                        00001111      111110000   001111345789999999999999999999999762      


Q ss_pred             -------CCCcEEEEEeCCCC-CCChhhhccce-eeeecCCC-HHHHHHHhhcC
Q psy4285         399 -------TTNVRFCIICNYLS-KIPPAIQSRCT-RFRFGPLD-SSLIMSRLDYD  442 (533)
Q Consensus       399 -------~~~~~~I~~~n~~~-~l~~~l~sR~~-~i~~~~~~-~~~~~~~l~~~  442 (533)
                             +..+.+|.+.|..+ .+.+++.+||. .+.+.+++ .++..+++.+.
T Consensus       178 ~G~s~~~p~rfiviaT~np~eg~l~~~LldRf~l~i~l~~~~~~~~e~~il~~~  231 (350)
T CHL00081        178 EGISIRHPARFVLVGSGNPEEGELRPQLLDRFGMHAEIRTVKDPELRVKIVEQR  231 (350)
T ss_pred             CCeeeecCCCEEEEeccCcccCCCCHHHHHHhCceeecCCCCChHHHHHHHHhh
Confidence                   22334444446544 69999999994 77888777 47777777664

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=99.21  E-value=3.7e-10  Score=117.75  Aligned_cols=181  Identities=17%  Similarity=0.204  Sum_probs=114.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc-----ccccCcceEEecCCCCCchhHHHHHHHH-----HHhc-----cc-CCCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT-----KAQFNAMVLELNASDDRGIGIVRDQIFQ-----FAST-----KT-MHKSS  371 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~-----~~-~~~~~  371 (533)
                      +++|+|++||||+++|+++.+.+..     ......+++.+++..... ..+...+..     |...     .+ ...+.
T Consensus       244 pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~inCaal~e-~lleseLFG~~~gaftga~~~~~~Gl~e~A~  322 (538)
T PRK15424        244 AVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIAE-SLLEAELFGYEEGAFTGSRRGGRAGLFEIAH  322 (538)
T ss_pred             cEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEeecccCCh-hhHHHHhcCCccccccCccccccCCchhccC
Confidence            5999999999999999999987220     111256889999887532 222222111     1000     01 11245


Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCCC-------CCChhhhccceeeeecCCCHH
Q psy4285         372 YKLIILDEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYLS-------KIPPAIQSRCTRFRFGPLDSS  433 (533)
Q Consensus       372 ~~vliiDE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~~-------~l~~~l~sR~~~i~~~~~~~~  433 (533)
                      .+.|||||++.|+...|..|++.+++.           +.++++|++||..-       .+.+.+..|+..+.+.-||  
T Consensus       323 gGTLfLdeI~~Lp~~~Q~kLl~~L~e~~~~r~G~~~~~~~dvRiIaat~~~L~~~v~~g~Fr~dL~yrL~~~~I~lPP--  400 (538)
T PRK15424        323 GGTLFLDEIGEMPLPLQTRLLRVLEEKEVTRVGGHQPVPVDVRVISATHCDLEEDVRQGRFRRDLFYRLSILRLQLPP--  400 (538)
T ss_pred             CCEEEEcChHhCCHHHHHHHHhhhhcCeEEecCCCceeccceEEEEecCCCHHHHHhcccchHHHHHHhcCCeecCCC--
Confidence            689999999999999999999999863           23568999987542       3556777788777777777  


Q ss_pred             HHHHHhhcCHHHHHHHHHHHHHHHHHHHhcCCCHHH--HHHHHHHHHHhcCCChhHHHHHHHHHHH
Q psy4285         434 LIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTD--ILTEISLLVHRLEIPESMLVDLVLKMSD  497 (533)
Q Consensus       434 ~~~~~l~~~~~~~~~ll~~~~~l~~l~~~~~~~~~d--i~~~~~~~~~~~~~~~~~~~~~~~~~~~  497 (533)
                           |+..++|+..++..+-.-..-.....+++.-  +.......+..++||++++ ++-+.+..
T Consensus       401 -----LReR~eDI~~L~~~fl~~~~~~~~~~~~~~a~~~~~~a~~~L~~y~WPGNvR-EL~nvier  460 (538)
T PRK15424        401 -----LRERVADILPLAESFLKQSLAALSAPFSAALRQGLQQCETLLLHYDWPGNVR-ELRNLMER  460 (538)
T ss_pred             -----hhhchhHHHHHHHHHHHHHHHHcCCCCCHHHHHhhHHHHHHHHhCCCCchHH-HHHHHHHH
Confidence                 4444555555555421111000112344432  4456667889999999987 44444443

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

Probab=99.21  E-value=5e-11  Score=129.10  Aligned_cols=145  Identities=14%  Similarity=0.176  Sum_probs=95.0

Q ss_pred             chhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCC------Cc--hhHHHHH
Q psy4285         290 SMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDD------RG--IGIVRDQ  357 (533)
Q Consensus       290 ~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~------~~--~~~~~~~  357 (533)
                      .+..+..+.+.+.....++++|+||||||||++|+.++..+.....    .+..++.++....      .+  ...++..
T Consensus       191 R~~ei~~~i~iL~r~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l~~~~llaG~~~~Ge~e~rl~~l  270 (758)
T PRK11034        191 REKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKAL  270 (758)
T ss_pred             CCHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEeccHHHHhcccchhhhHHHHHHHH
Confidence            3334444444455555667999999999999999999987633210    1223333332211      11  1223333


Q ss_pred             HHHHHhcccCCCCCcEEEEEeCCCCCC---------HHHHHHHHHHHHhcCCCcEEEEEeCCCC-----CCChhhhccce
Q psy4285         358 IFQFASTKTMHKSSYKLIILDEADAMT---------NDAQNALRRIIEKFTTNVRFCIICNYLS-----KIPPAIQSRCT  423 (533)
Q Consensus       358 ~~~~~~~~~~~~~~~~vliiDE~d~l~---------~~~~~~Ll~~le~~~~~~~~I~~~n~~~-----~l~~~l~sR~~  423 (533)
                      +..+..      ..+.+|||||+|.+.         .+..+.|...+..  ...++|.+|+..+     ..|+++.|||.
T Consensus       271 ~~~l~~------~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~~--g~i~vIgATt~~E~~~~~~~D~AL~rRFq  342 (758)
T PRK11034        271 LKQLEQ------DTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSS--GKIRVIGSTTYQEFSNIFEKDRALARRFQ  342 (758)
T ss_pred             HHHHHh------cCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHhC--CCeEEEecCChHHHHHHhhccHHHHhhCc
Confidence            332221      245699999999872         2334455556653  4588888888653     57999999999


Q ss_pred             eeeecCCCHHHHHHHhhcC
Q psy4285         424 RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 ~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.+.+|+.++...+|..+
T Consensus       343 ~I~v~ePs~~~~~~IL~~~  361 (758)
T PRK11034        343 KIDITEPSIEETVQIINGL  361 (758)
T ss_pred             EEEeCCCCHHHHHHHHHHH
Confidence            9999999999999999965

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=99.20  E-value=3.3e-10  Score=119.40  Aligned_cols=168  Identities=14%  Similarity=0.167  Sum_probs=113.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHH-HHHH----HHhc----c-cCCCCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD-QIFQ----FAST----K-TMHKSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~----~~~~----~-~~~~~~~~vlii  377 (533)
                      +++|+|++||||+++|+++.......   +.+++.+++..... ..+.. +++.    |...    . ....+..++|||
T Consensus       212 pVlI~Ge~GtGK~~~A~~ih~~s~r~---~~p~v~v~c~~~~~-~~~e~~lfG~~~g~~~ga~~~~~g~~~~a~gGtL~l  287 (509)
T PRK05022        212 NVLILGETGVGKELVARAIHAASPRA---DKPLVYLNCAALPE-SLAESELFGHVKGAFTGAISNRSGKFELADGGTLFL  287 (509)
T ss_pred             cEEEECCCCccHHHHHHHHHHhCCcC---CCCeEEEEcccCCh-HHHHHHhcCccccccCCCcccCCcchhhcCCCEEEe
Confidence            59999999999999999999875332   56888888876532 22221 1110    0000    0 011245689999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhcC-----------CCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         378 DEADAMTNDAQNALRRIIEKFT-----------TNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~~-----------~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ||++.|+.+.|..|++.+++..           .++++|++||..       ..+.+.|..|+..+.+.-|+       |
T Consensus       288 deI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~l~~~~~~~~f~~dL~~rl~~~~i~lPp-------L  360 (509)
T PRK05022        288 DEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRDLREEVRAGRFRADLYHRLSVFPLSVPP-------L  360 (509)
T ss_pred             cChhhCCHHHHHHHHHHHhcCCEeeCCCCcceecceEEEEecCCCHHHHHHcCCccHHHHhcccccEeeCCC-------c
Confidence            9999999999999999997532           367999999754       35778888888777776666       4


Q ss_pred             hcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHH
Q psy4285         440 DYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       440 ~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~  488 (533)
                      +..++|+..+++.+-.  +.....|.....+.......+..+.||++++
T Consensus       361 reR~eDI~~L~~~fl~--~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvr  407 (509)
T PRK05022        361 RERGDDVLLLAGYFLE--QNRARLGLRSLRLSPAAQAALLAYDWPGNVR  407 (509)
T ss_pred             hhchhhHHHHHHHHHH--HHHHHcCCCCCCCCHHHHHHHHhCCCCCcHH
Confidence            4444455444443211  1212334344456677888899999999987

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=99.20  E-value=6.5e-10  Score=116.14  Aligned_cols=171  Identities=16%  Similarity=0.194  Sum_probs=109.3

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHH-----HHh-----cccC-CCCCcEEE
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQ-----FAS-----TKTM-HKSSYKLI  375 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~-----~~~~-~~~~~~vl  375 (533)
                      .+++|+|++||||+++|+++.+.....   ..+++.+++..... ..+...+..     |..     ..+. ..+..+.|
T Consensus       236 ~pVLI~GE~GTGKe~lA~~IH~~S~r~---~~pfv~inC~~l~e-~lleseLFG~~~gaftga~~~~~~Gl~e~A~gGTL  311 (526)
T TIGR02329       236 ATVLILGESGTGKELVAQAIHQLSGRR---DFPFVAINCGAIAE-SLLEAELFGYEEGAFTGARRGGRTGLIEAAHRGTL  311 (526)
T ss_pred             CcEEEECCCCcCHHHHHHHHHHhcCcC---CCCEEEeccccCCh-hHHHHHhcCCcccccccccccccccchhhcCCceE
Confidence            369999999999999999998764322   56889999876532 222221111     000     0111 12456899


Q ss_pred             EEeCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCCC-------CCChhhhccceeeeecCCCHHHHHH
Q psy4285         376 ILDEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYLS-------KIPPAIQSRCTRFRFGPLDSSLIMS  437 (533)
Q Consensus       376 iiDE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~~-------~l~~~l~sR~~~i~~~~~~~~~~~~  437 (533)
                      ||||++.|+.+.|..|++.+++.           +.++++|++|+...       .+.+.|..|+..+.+.-||      
T Consensus       312 fLdeI~~Lp~~~Q~~Ll~~L~~~~~~r~g~~~~~~~dvRiIaat~~~l~~~v~~g~fr~dL~~rL~~~~I~lPP------  385 (526)
T TIGR02329       312 FLDEIGEMPLPLQTRLLRVLEEREVVRVGGTEPVPVDVRVVAATHCALTTAVQQGRFRRDLFYRLSILRIALPP------  385 (526)
T ss_pred             EecChHhCCHHHHHHHHHHHhcCcEEecCCCceeeecceEEeccCCCHHHHhhhcchhHHHHHhcCCcEEeCCC------
Confidence            99999999999999999999863           23468999987542       4556677788766776666      


Q ss_pred             HhhcCHHHHHHHHHHHHHHHHHHHhcCCCHHHH--HHHHHHHHHhcCCChhHH
Q psy4285         438 RLDYDDISFFNIIIWYIKIQEIKIEKGLALTDI--LTEISLLVHRLEIPESML  488 (533)
Q Consensus       438 ~l~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di--~~~~~~~~~~~~~~~~~~  488 (533)
                       |+..++|+..++..+-.-..-....++++..+  +..+.+.+..+.||++++
T Consensus       386 -LReR~eDI~~L~~~fl~~~~~~~~~~~~~~a~~~~~~~~~~L~~y~WPGNvr  437 (526)
T TIGR02329       386 -LRERPGDILPLAAEYLVQAAAALRLPDSEAAAQVLAGVADPLQRYPWPGNVR  437 (526)
T ss_pred             -chhchhHHHHHHHHHHHHHHHHcCCCCCHHHHHHhHHHHHHHHhCCCCchHH
Confidence             44444454444443211111001124555432  345667799999999987

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

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.20  E-value=1e-10  Score=119.97  Aligned_cols=128  Identities=16%  Similarity=0.278  Sum_probs=88.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc--hhHHHH-HHHHHHhcccCCCCCcEEEEEeCCCCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG--IGIVRD-QIFQFASTKTMHKSSYKLIILDEADAMT  384 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~--~~~~~~-~~~~~~~~~~~~~~~~~vliiDE~d~l~  384 (533)
                      +++||||||+||||+++++++.+...   +..++.++..+...  ...++. ....+...    ....++|+|||++.+.
T Consensus       143 pl~L~G~~G~GKTHLl~Ai~~~l~~~---~~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~----~~~~dvLiIDDiq~l~  215 (445)
T PRK12422        143 PIYLFGPEGSGKTHLMQAAVHALRES---GGKILYVRSELFTEHLVSAIRSGEMQRFRQF----YRNVDALFIEDIEVFS  215 (445)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHc---CCCEEEeeHHHHHHHHHHHHhcchHHHHHHH----cccCCEEEEcchhhhc
Confidence            48999999999999999999998543   34455555432110  000110 01111111    1356799999999985


Q ss_pred             H--HHHHHHHHHHHhc-CCCcEEEEEeCCC----CCCChhhhccc---eeeeecCCCHHHHHHHhhcC
Q psy4285         385 N--DAQNALRRIIEKF-TTNVRFCIICNYL----SKIPPAIQSRC---TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       385 ~--~~~~~Ll~~le~~-~~~~~~I~~~n~~----~~l~~~l~sR~---~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .  ..+..|+.+++.. ..+..+|++||.+    ..++++++|||   ..+.+.+|+.++...+|.+.
T Consensus       216 ~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k  283 (445)
T PRK12422        216 GKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERK  283 (445)
T ss_pred             CChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHH
Confidence            4  4577787777642 2456788888764    35789999999   58999999999999999875

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.19  E-value=6.3e-11  Score=121.89  Aligned_cols=132  Identities=13%  Similarity=0.193  Sum_probs=85.8

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch--hHHH-HHHHHHHhcccCCCCCcEEEEEeCCCCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI--GIVR-DQIFQFASTKTMHKSSYKLIILDEADAM  383 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~--~~~~-~~~~~~~~~~~~~~~~~~vliiDE~d~l  383 (533)
                      .+++||||||+||||+++++++++.... .+..++.+++.+....  ..++ +....+....   ....++|+|||++.+
T Consensus       131 n~l~lyG~~G~GKTHLl~ai~~~l~~~~-~~~~v~yi~~~~f~~~~~~~~~~~~~~~f~~~~---~~~~dvLlIDDi~~l  206 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQSIGNYVVQNE-PDLRVMYITSEKFLNDLVDSMKEGKLNEFREKY---RKKVDVLLIDDVQFL  206 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHHHHHhC-CCCeEEEEEHHHHHHHHHHHHhcccHHHHHHHH---HhcCCEEEEechhhh
Confidence            3499999999999999999999875432 1344555554331100  0000 0011111110   124679999999987


Q ss_pred             CH--HHHHHHHHHHHhcC-CCcEEEEEeCCCC----CCChhhhccce---eeeecCCCHHHHHHHhhcC
Q psy4285         384 TN--DAQNALRRIIEKFT-TNVRFCIICNYLS----KIPPAIQSRCT---RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       384 ~~--~~~~~Ll~~le~~~-~~~~~I~~~n~~~----~l~~~l~sR~~---~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..  ..+..|+.+++... .+..+|++|+...    .+.+.++|||.   .+.+.+|+.+....++.+.
T Consensus       207 ~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~  275 (440)
T PRK14088        207 IGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIARKM  275 (440)
T ss_pred             cCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHHHH
Confidence            43  34567777776532 3356777776432    46788999995   8899999999999999876

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.19  E-value=7.9e-11  Score=122.70  Aligned_cols=129  Identities=14%  Similarity=0.192  Sum_probs=88.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch--hHHHH-HHHHHHhcccCCCCCcEEEEEeCCCCCCH
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI--GIVRD-QIFQFASTKTMHKSSYKLIILDEADAMTN  385 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~-~~~~~~~~~~~~~~~~~vliiDE~d~l~~  385 (533)
                      ++|||++|+|||||++++++.+.... .+..+++++..+....  ..++. ....|....    ...++|+|||++.+..
T Consensus       317 L~LyG~sGsGKTHLL~AIa~~a~~~~-~g~~V~Yitaeef~~el~~al~~~~~~~f~~~y----~~~DLLlIDDIq~l~g  391 (617)
T PRK14086        317 LFIYGESGLGKTHLLHAIGHYARRLY-PGTRVRYVSSEEFTNEFINSIRDGKGDSFRRRY----REMDILLVDDIQFLED  391 (617)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHhC-CCCeEEEeeHHHHHHHHHHHHHhccHHHHHHHh----hcCCEEEEehhccccC
Confidence            89999999999999999999874321 1345555555432110  00110 111121111    2468999999999854


Q ss_pred             --HHHHHHHHHHHhcCC-CcEEEEEeCCCC----CCChhhhccc---eeeeecCCCHHHHHHHhhcC
Q psy4285         386 --DAQNALRRIIEKFTT-NVRFCIICNYLS----KIPPAIQSRC---TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       386 --~~~~~Ll~~le~~~~-~~~~I~~~n~~~----~l~~~l~sR~---~~i~~~~~~~~~~~~~l~~~  442 (533)
                        ..+..|+.+++.... +..+|++||...    .+++.|+|||   ..+.+.+|+.+....+|...
T Consensus       392 ke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~kk  458 (617)
T PRK14086        392 KESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAILRKK  458 (617)
T ss_pred             CHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHHHH
Confidence              346788888876433 466888888653    5789999999   47899999999999999876

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=99.19  E-value=3.6e-10  Score=119.11  Aligned_cols=168  Identities=18%  Similarity=0.263  Sum_probs=112.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHh---------cccCC-CCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAS---------TKTMH-KSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~-~~~~~vlii  377 (533)
                      +++|+|++||||+++|+++.......   ..+++.++++.... ..+...+.....         ....+ .+..++|+|
T Consensus       229 pvlI~GE~GtGK~~lA~aiH~~s~r~---~~pfv~inca~~~~-~~~e~elFG~~~~~~~~~~~~~~g~~e~a~~GtL~L  304 (520)
T PRK10820        229 PLLITGDTGTGKDLLAYACHLRSPRG---KKPFLALNCASIPD-DVVESELFGHAPGAYPNALEGKKGFFEQANGGSVLL  304 (520)
T ss_pred             CEEEECCCCccHHHHHHHHHHhCCCC---CCCeEEeccccCCH-HHHHHHhcCCCCCCcCCcccCCCChhhhcCCCEEEE
Confidence            59999999999999999987654322   46788888877432 222221111000         00111 245689999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         378 DEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ||++.|+...|..|++.+++.           +.++++|++|+..       ..+.+.|..|+..+.+.-|+       |
T Consensus       305 deI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~vRiI~st~~~l~~l~~~g~f~~dL~~rL~~~~i~lPp-------L  377 (520)
T PRK10820        305 DEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGEFREDLYYRLNVLTLNLPP-------L  377 (520)
T ss_pred             eChhhCCHHHHHHHHHHHhcCCcccCCCCcceeeeeEEEEecCCCHHHHHHcCCccHHHHhhcCeeEEeCCC-------c
Confidence            999999999999999999763           2356899988654       24677888998767776666       4


Q ss_pred             hcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHH
Q psy4285         440 DYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       440 ~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~  488 (533)
                      +..++|+..+++.+-.  .+....|.+...+-......+..+.||++++
T Consensus       378 reR~~Di~~L~~~fl~--~~~~~~g~~~~~ls~~a~~~L~~y~WPGNvr  424 (520)
T PRK10820        378 RDRPQDIMPLTELFVA--RFADEQGVPRPKLAADLNTVLTRYGWPGNVR  424 (520)
T ss_pred             ccChhHHHHHHHHHHH--HHHHHcCCCCCCcCHHHHHHHhcCCCCCHHH
Confidence            4555555555553211  2223345444456677888899999999987

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.19  E-value=8.7e-10  Score=108.60  Aligned_cols=155  Identities=13%  Similarity=0.134  Sum_probs=92.6

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHc-------cccc---cCc-------------------
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLY-------TKAQ---FNA-------------------  338 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~-------~~~~---~~~-------------------  338 (533)
                      .||+++...+.-.+-.....++++.|+||+||||++++++..+-       ++..   ...                   
T Consensus         7 vgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~   86 (337)
T TIGR02030         7 VGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAVRALAALLPEIKAVAGCPFNSSPSDPEMMCEEVRIRVDSQEPLSI   86 (337)
T ss_pred             ccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHHHHHHHhhcccccccCCCCCCCCCCccccChHHhhhhhccccccc
Confidence            46777766654444444456899999999999999999998761       1110   000                   


Q ss_pred             -----ceEEecC--C--CCCchhHHHHHHHH--HHhccc-CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc--------
Q psy4285         339 -----MVLELNA--S--DDRGIGIVRDQIFQ--FASTKT-MHKSSYKLIILDEADAMTNDAQNALRRIIEKF--------  398 (533)
Q Consensus       339 -----~~~~~~~--~--~~~~~~~~~~~~~~--~~~~~~-~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~--------  398 (533)
                           ++..+..  +  ...+.-.+...+..  +..... ...+..++|++||++.+++..|+.|++.|++.        
T Consensus        87 ~~~~~~~~~lP~~~t~d~l~G~~d~~~~l~~g~~~~~~GlL~~A~~GvL~lDEi~~L~~~~Q~~Ll~~l~~g~~~v~r~G  166 (337)
T TIGR02030        87 IKKPVPVVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLARANRGILYIDEVNLLEDHLVDVLLDVAASGWNVVEREG  166 (337)
T ss_pred             ccCCCCcCCCCCCCcccceecchhHhhHhhcCCEEeecCcceeccCCEEEecChHhCCHHHHHHHHHHHHhCCeEEEECC
Confidence                 0011000  0  01111112221110  100111 11245689999999999999999999999763        


Q ss_pred             -----CCCcEEEEEeCCCC-CCChhhhccce-eeeecCCCH-HHHHHHhhcC
Q psy4285         399 -----TTNVRFCIICNYLS-KIPPAIQSRCT-RFRFGPLDS-SLIMSRLDYD  442 (533)
Q Consensus       399 -----~~~~~~I~~~n~~~-~l~~~l~sR~~-~i~~~~~~~-~~~~~~l~~~  442 (533)
                           +..+.+|.++|..+ .+.+++.+||. .+.+.++.+ ++..+++.+.
T Consensus       167 ~~~~~~~r~iviat~np~eg~l~~~LldRf~l~i~l~~p~~~eer~eIL~~~  218 (337)
T TIGR02030       167 ISIRHPARFVLVGSGNPEEGELRPQLLDRFGLHAEIRTVRDVELRVEIVERR  218 (337)
T ss_pred             EEEEcCCCEEEEeccccccCCCCHHHHhhcceEEECCCCCCHHHHHHHHHhh
Confidence                 22344455556544 68999999995 667777765 5666666653

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.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.18  E-value=1.2e-10  Score=121.11  Aligned_cols=130  Identities=17%  Similarity=0.255  Sum_probs=87.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch--hHHHH-HHHHHHhcccCCCCCcEEEEEeCCCCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI--GIVRD-QIFQFASTKTMHKSSYKLIILDEADAMT  384 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~-~~~~~~~~~~~~~~~~~vliiDE~d~l~  384 (533)
                      .++|||||||||||+++++++++.... .+..++.+++.+....  ..++. ....+....    ...++|+|||++.+.
T Consensus       150 ~l~l~G~~G~GKThL~~ai~~~~~~~~-~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~----~~~dlLiiDDi~~l~  224 (450)
T PRK00149        150 PLFIYGGVGLGKTHLLHAIGNYILEKN-PNAKVVYVTSEKFTNDFVNALRNNTMEEFKEKY----RSVDVLLIDDIQFLA  224 (450)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHhC-CCCeEEEEEHHHHHHHHHHHHHcCcHHHHHHHH----hcCCEEEEehhhhhc
Confidence            489999999999999999999985432 1344556655432110  00100 001111110    246799999999985


Q ss_pred             H--HHHHHHHHHHHhcC-CCcEEEEEeCCCC----CCChhhhccc---eeeeecCCCHHHHHHHhhcC
Q psy4285         385 N--DAQNALRRIIEKFT-TNVRFCIICNYLS----KIPPAIQSRC---TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       385 ~--~~~~~Ll~~le~~~-~~~~~I~~~n~~~----~l~~~l~sR~---~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .  ..+..|+.+++... .+..+|+++|.+.    .+++.++|||   ..+.+.+|+.++..+++...
T Consensus       225 ~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~il~~~  292 (450)
T PRK00149        225 GKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIAILKKK  292 (450)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHHHHHHH
Confidence            4  35667777776432 3345777777543    3778999999   47999999999999999887

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=99.18  E-value=3.3e-10  Score=123.98  Aligned_cols=168  Identities=18%  Similarity=0.211  Sum_probs=109.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHH-HHH----HHh-----cccCCCCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQ-IFQ----FAS-----TKTMHKSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~----~~~-----~~~~~~~~~~vlii  377 (533)
                      +++|+|++|||||++|+++.......   +.+++.+++..... ..+... ++.    +..     ......+..++|||
T Consensus       401 pVLI~GE~GTGK~~lA~~ih~~s~r~---~~~~v~i~c~~~~~-~~~~~~lfg~~~~~~~g~~~~~~g~le~a~~GtL~L  476 (686)
T PRK15429        401 TVLILGETGTGKELIARAIHNLSGRN---NRRMVKMNCAAMPA-GLLESDLFGHERGAFTGASAQRIGRFELADKSSLFL  476 (686)
T ss_pred             CEEEECCCCcCHHHHHHHHHHhcCCC---CCCeEEEecccCCh-hHhhhhhcCcccccccccccchhhHHHhcCCCeEEE
Confidence            69999999999999999998865322   56788888765422 111111 110    000     00001234679999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         378 DEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ||++.++.+.|..|++.+++.           +.++++|++|+..       ..+.+.+..|+..+.+.-||       |
T Consensus       477 dei~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~l~~~~~~~~f~~~L~~~l~~~~i~lPp-------L  549 (686)
T PRK15429        477 DEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLKKMVADREFRSDLYYRLNVFPIHLPP-------L  549 (686)
T ss_pred             echhhCCHHHHHHHHHHHHhCCEEeCCCCCcccceEEEEEeCCCCHHHHHHcCcccHHHHhccCeeEEeCCC-------h
Confidence            999999999999999999763           2467899999754       24566677788777777677       4


Q ss_pred             hcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHH
Q psy4285         440 DYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       440 ~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~  488 (533)
                      +..++|+..+++.+-  .++....|.....+-....+.+..+.||++++
T Consensus       550 reR~~Di~~L~~~~l--~~~~~~~~~~~~~~s~~al~~L~~y~WPGNvr  596 (686)
T PRK15429        550 RERPEDIPLLVKAFT--FKIARRMGRNIDSIPAETLRTLSNMEWPGNVR  596 (686)
T ss_pred             hhhHhHHHHHHHHHH--HHHHHHcCCCCCCcCHHHHHHHHhCCCCCcHH
Confidence            444455555555321  11112234444445567788899999999987

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

Probab=99.17  E-value=1.4e-10  Score=115.17  Aligned_cols=130  Identities=18%  Similarity=0.272  Sum_probs=89.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch--hHHH-HHHHHHHhcccCCCCCcEEEEEeCCCCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI--GIVR-DQIFQFASTKTMHKSSYKLIILDEADAM  383 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~--~~~~-~~~~~~~~~~~~~~~~~~vliiDE~d~l  383 (533)
                      +.++||||+|.|||||++++++...... ....++.+.+.+....  ..++ +.+..|...    . ..++++||+++.+
T Consensus       114 nplfi~G~~GlGKTHLl~Aign~~~~~~-~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~----y-~~dlllIDDiq~l  187 (408)
T COG0593         114 NPLFIYGGVGLGKTHLLQAIGNEALANG-PNARVVYLTSEDFTNDFVKALRDNEMEKFKEK----Y-SLDLLLIDDIQFL  187 (408)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHhhC-CCceEEeccHHHHHHHHHHHHHhhhHHHHHHh----h-ccCeeeechHhHh
Confidence            3499999999999999999999986553 2344555555442111  1111 112222211    1 4579999999998


Q ss_pred             CH--HHHHHHHHHHHhcC-CCcEEEEEeCCCC----CCChhhhccc---eeeeecCCCHHHHHHHhhcC
Q psy4285         384 TN--DAQNALRRIIEKFT-TNVRFCIICNYLS----KIPPAIQSRC---TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       384 ~~--~~~~~Ll~~le~~~-~~~~~I~~~n~~~----~l~~~l~sR~---~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..  ..+..|+.+++... .+..+|+|++.+.    .+.|.|+|||   ..+.+.||+.+....+|...
T Consensus       188 ~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r~aiL~kk  256 (408)
T COG0593         188 AGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAILRKK  256 (408)
T ss_pred             cCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHHHHHHHHHH
Confidence            65  44778887776533 3347888886554    4679999998   48999999999999999985

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

Probab=99.16  E-value=3.9e-10  Score=103.61  Aligned_cols=141  Identities=17%  Similarity=0.240  Sum_probs=99.4

Q ss_pred             hhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCC
Q psy4285         291 MDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKS  370 (533)
Q Consensus       291 ~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  370 (533)
                      +.+.+....++......|+|++|++|||||++++++..++...   +..++++...+......+-+.+.   ..     .
T Consensus        37 ~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~---GLRlIev~k~~L~~l~~l~~~l~---~~-----~  105 (249)
T PF05673_consen   37 EALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQ---GLRLIEVSKEDLGDLPELLDLLR---DR-----P  105 (249)
T ss_pred             HHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhc---CceEEEECHHHhccHHHHHHHHh---cC-----C
Confidence            4455666777777666679999999999999999999988554   46677877766555444443333   22     2


Q ss_pred             CcEEEEEeCCCCCCHHHHHH-HHHHHH----hcCCCcEEEEEeCCCCCCCh-----------------------hhhccc
Q psy4285         371 SYKLIILDEADAMTNDAQNA-LRRIIE----KFTTNVRFCIICNYLSKIPP-----------------------AIQSRC  422 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~-Ll~~le----~~~~~~~~I~~~n~~~~l~~-----------------------~l~sR~  422 (533)
                      ..-|||+|+...=..+.... |..+||    ..|.|+.+..|+|+..-+.+                       +|.+||
T Consensus       106 ~kFIlf~DDLsFe~~d~~yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E~~~d~~~~~~~eih~~d~~eEklSLsDRF  185 (249)
T PF05673_consen  106 YKFILFCDDLSFEEGDTEYKALKSVLEGGLEARPDNVLIYATSNRRHLVPESFSDREDIQDDEIHPSDTIEEKLSLSDRF  185 (249)
T ss_pred             CCEEEEecCCCCCCCcHHHHHHHHHhcCccccCCCcEEEEEecchhhccchhhhhccCCCccccCcchHHHHHHhHHHhC
Confidence            35699999987544444444 444444    56899999999986432211                       556688


Q ss_pred             -eeeeecCCCHHHHHHHhhcC
Q psy4285         423 -TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       423 -~~i~~~~~~~~~~~~~l~~~  442 (533)
                       ..+.|.+++.++..+++.+.
T Consensus       186 GL~l~F~~~~q~~YL~IV~~~  206 (249)
T PF05673_consen  186 GLWLSFYPPDQEEYLAIVRHY  206 (249)
T ss_pred             CcEEEecCCCHHHHHHHHHHH
Confidence             58999999999999888876

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=99.16  E-value=5e-10  Score=121.78  Aligned_cols=175  Identities=11%  Similarity=0.090  Sum_probs=113.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhc-----c-cCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAST-----K-TMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~-~~~~~~~~vliiDE~d  381 (533)
                      +++|+|++||||+++|+++.+.....   ..+++.+++........-.++++.....     . ....+..++|||||++
T Consensus       350 pvli~Ge~GtGK~~~A~~ih~~s~r~---~~pfv~vnc~~~~~~~~~~elfg~~~~~~~~~~~g~~~~a~~GtL~ldei~  426 (638)
T PRK11388        350 PVLLCGEEGVGKALLAQAIHNESERA---AGPYIAVNCQLYPDEALAEEFLGSDRTDSENGRLSKFELAHGGTLFLEKVE  426 (638)
T ss_pred             CEEEECCCCcCHHHHHHHHHHhCCcc---CCCeEEEECCCCChHHHHHHhcCCCCcCccCCCCCceeECCCCEEEEcChh
Confidence            59999999999999999999875332   4688889887653322222222211000     0 0112457899999999


Q ss_pred             CCCHHHHHHHHHHHHhcC-----------CCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHhhcCH
Q psy4285         382 AMTNDAQNALRRIIEKFT-----------TNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDD  443 (533)
Q Consensus       382 ~l~~~~~~~Ll~~le~~~-----------~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~~  443 (533)
                      .|+.+.|..|++.+++..           .++++|++|+..       ..+.+.|..|+..+.+.-|+       |+..+
T Consensus       427 ~l~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~t~~~l~~~~~~~~f~~dL~~~l~~~~i~lPp-------LreR~  499 (638)
T PRK11388        427 YLSPELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNRFSRQLYYALHAFEITIPP-------LRMRR  499 (638)
T ss_pred             hCCHHHHHHHHHHHhcCcEEeCCCCceEEeeEEEEEeccCCHHHHHhcCCChHHHhhhhceeEEeCCC-------hhhhh
Confidence            999999999999998532           257899998753       35667777888777776666       33444


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHH
Q psy4285         444 ISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMS  496 (533)
Q Consensus       444 ~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~  496 (533)
                      +|+..+++.+-.  .+....+... .+.......+..+.||++++ ++.+.+.
T Consensus       500 ~Di~~L~~~~l~--~~~~~~~~~~-~~s~~a~~~L~~y~WPGNvr-eL~~~l~  548 (638)
T PRK11388        500 EDIPALVNNKLR--SLEKRFSTRL-KIDDDALARLVSYRWPGNDF-ELRSVIE  548 (638)
T ss_pred             hHHHHHHHHHHH--HHHHHhCCCC-CcCHHHHHHHHcCCCCChHH-HHHHHHH
Confidence            555555553211  1111223222 35677888899999999986 4444333

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.16  E-value=1.6e-10  Score=128.60  Aligned_cols=148  Identities=15%  Similarity=0.162  Sum_probs=101.0

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCC------Cc--hhHHH
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDD------RG--IGIVR  355 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~------~~--~~~~~  355 (533)
                      .|+++.+..+...+.+...++++|+||||||||++++.+++.+.....    .+..++.++....      .+  ...++
T Consensus       176 igr~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l~~~~l~a~~~~~g~~e~~l~  255 (852)
T TIGR03346       176 IGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEERLK  255 (852)
T ss_pred             CCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEeeHHHHhhcchhhhhHHHHHH
Confidence            445555566666666666678999999999999999999998743211    1344555543221      11  12333


Q ss_pred             HHHHHHHhcccCCCCCcEEEEEeCCCCCCH--------HHHHHHHHHHHhcCCCcEEEEEeCCC-----CCCChhhhccc
Q psy4285         356 DQIFQFASTKTMHKSSYKLIILDEADAMTN--------DAQNALRRIIEKFTTNVRFCIICNYL-----SKIPPAIQSRC  422 (533)
Q Consensus       356 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------~~~~~Ll~~le~~~~~~~~I~~~n~~-----~~l~~~l~sR~  422 (533)
                      ..+......     ..+.||||||++.+..        +..+.|...++.  ....+|.+|+..     ..+++++.|||
T Consensus       256 ~~l~~~~~~-----~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l~~--g~i~~IgaTt~~e~r~~~~~d~al~rRf  328 (852)
T TIGR03346       256 AVLNEVTKS-----EGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALAR--GELHCIGATTLDEYRKYIEKDAALERRF  328 (852)
T ss_pred             HHHHHHHhc-----CCCeEEEeccHHHhhcCCCCcchhHHHHHhchhhhc--CceEEEEeCcHHHHHHHhhcCHHHHhcC
Confidence            333333211     2468999999998852        345666666653  458888888765     35799999999


Q ss_pred             eeeeecCCCHHHHHHHhhcC
Q psy4285         423 TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       423 ~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..+.+..|+.++...+|..+
T Consensus       329 ~~i~v~~p~~~~~~~iL~~~  348 (852)
T TIGR03346       329 QPVFVDEPTVEDTISILRGL  348 (852)
T ss_pred             CEEEeCCCCHHHHHHHHHHH
Confidence            99999999999999988865

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.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.16  E-value=3.5e-10  Score=116.54  Aligned_cols=130  Identities=15%  Similarity=0.263  Sum_probs=89.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch--hHHH---HHHHHHHhcccCCCCCcEEEEEeCCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI--GIVR---DQIFQFASTKTMHKSSYKLIILDEADA  382 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~--~~~~---~~~~~~~~~~~~~~~~~~vliiDE~d~  382 (533)
                      .++|||++|+||||+++++++.+.... .+..++.+++.+....  ..+.   +.+..+....    ...++|+|||++.
T Consensus       143 pl~i~G~~G~GKTHLl~Ai~~~l~~~~-~~~~v~yv~~~~f~~~~~~~l~~~~~~~~~~~~~~----~~~dvLiIDDiq~  217 (450)
T PRK14087        143 PLFIYGESGMGKTHLLKAAKNYIESNF-SDLKVSYMSGDEFARKAVDILQKTHKEIEQFKNEI----CQNDVLIIDDVQF  217 (450)
T ss_pred             ceEEECCCCCcHHHHHHHHHHHHHHhC-CCCeEEEEEHHHHHHHHHHHHHHhhhHHHHHHHHh----ccCCEEEEecccc
Confidence            489999999999999999999875321 1345555655432110  0111   1111121111    3467999999999


Q ss_pred             CC--HHHHHHHHHHHHhc-CCCcEEEEEeCCCC----CCChhhhccce---eeeecCCCHHHHHHHhhcC
Q psy4285         383 MT--NDAQNALRRIIEKF-TTNVRFCIICNYLS----KIPPAIQSRCT---RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       383 l~--~~~~~~Ll~~le~~-~~~~~~I~~~n~~~----~l~~~l~sR~~---~i~~~~~~~~~~~~~l~~~  442 (533)
                      +.  ...++.|+.+++.. ..+..+|+++|.+.    .+++.|+|||.   .+.+.+|+.++...+|.+.
T Consensus       218 l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~~  287 (450)
T PRK14087        218 LSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKKE  287 (450)
T ss_pred             ccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHHHH
Confidence            86  56678888888753 23346888887653    46889999984   8899999999999999765

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=99.15  E-value=1.1e-10  Score=108.88  Aligned_cols=73  Identities=19%  Similarity=0.197  Sum_probs=61.8

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCC----------CHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCC
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPL----------DSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDG   70 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~----------~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g   70 (533)
                      +||||++++|||+|+.+++|+|||+||||.+.|+++          ++.++...|..   ..  .+++    .++..++|
T Consensus       112 LEEPp~~t~fiLit~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~~~~~~~i~~~L~~---~~--~~d~----~i~~~a~g  182 (261)
T PRK05818        112 IEEPPKNTYGIFTTRNENNILNTILSRCVQYVVLSKEKKVPFKVESNDRYFQYILLS---FY--SVDE----QLQAYNNG  182 (261)
T ss_pred             hcCCCCCeEEEEEECChHhCchHhhhheeeeecCChhhhcccccccChHHHHHHHHH---cc--CccH----HHHHHcCC
Confidence            699999999999999999999999999999999998          66666666642   22  2333    78889999


Q ss_pred             CHHHHHHHHHHH
Q psy4285          71 DMRKVLNILQSA   82 (533)
Q Consensus        71 ~~r~a~~~l~~~   82 (533)
                      |..+|+.+++.+
T Consensus       183 ~~~~a~~l~~~l  194 (261)
T PRK05818        183 SFSKLKNIIETL  194 (261)
T ss_pred             CHHHHHHHHHHH
Confidence            999999999965

>PRK06620 hypothetical protein; Validated

Probab=99.14  E-value=6.1e-10  Score=103.27  Aligned_cols=108  Identities=19%  Similarity=0.228  Sum_probs=68.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTND  386 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~  386 (533)
                      +.++||||||+||||+++++++..      +..+  +.....     ..    .+.       ...++|+|||++.+...
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~------~~~~--~~~~~~-----~~----~~~-------~~~d~lliDdi~~~~~~  100 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLS------NAYI--IKDIFF-----NE----EIL-------EKYNAFIIEDIENWQEP  100 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhcc------CCEE--cchhhh-----ch----hHH-------hcCCEEEEeccccchHH
Confidence            349999999999999999988764      2211  111100     00    111       13469999999976432


Q ss_pred             HHHHHHHHHHhc-CCCcEEEEEeCCCC---CCChhhhccce---eeeecCCCHHHHHHHhhcC
Q psy4285         387 AQNALRRIIEKF-TTNVRFCIICNYLS---KIPPAIQSRCT---RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       387 ~~~~Ll~~le~~-~~~~~~I~~~n~~~---~l~~~l~sR~~---~i~~~~~~~~~~~~~l~~~  442 (533)
                         .|+.+++.. ..+..++++++.+.   .+ |+++||+.   .+.+.+|+.+++..++.+.
T Consensus       101 ---~lf~l~N~~~e~g~~ilits~~~p~~l~l-~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~  159 (214)
T PRK06620        101 ---ALLHIFNIINEKQKYLLLTSSDKSRNFTL-PDLSSRIKSVLSILLNSPDDELIKILIFKH  159 (214)
T ss_pred             ---HHHHHHHHHHhcCCEEEEEcCCCccccch-HHHHHHHhCCceEeeCCCCHHHHHHHHHHH
Confidence               344443321 12345666664332   35 89999996   8999999999887777654

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.14  E-value=1.6e-10  Score=118.61  Aligned_cols=129  Identities=17%  Similarity=0.271  Sum_probs=87.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHH----HHHHHHhcccCCCCCcEEEEEeCCCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD----QIFQFASTKTMHKSSYKLIILDEADAM  383 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~vliiDE~d~l  383 (533)
                      .++||||||+|||++++++++++.... .+..++.+++.+... .....    ....+....    ...++|+|||++.+
T Consensus       138 ~l~l~G~~G~GKThL~~ai~~~l~~~~-~~~~v~yi~~~~~~~-~~~~~~~~~~~~~~~~~~----~~~dlLiiDDi~~l  211 (405)
T TIGR00362       138 PLFIYGGVGLGKTHLLHAIGNEILENN-PNAKVVYVSSEKFTN-DFVNALRNNKMEEFKEKY----RSVDLLLIDDIQFL  211 (405)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHHHHhC-CCCcEEEEEHHHHHH-HHHHHHHcCCHHHHHHHH----HhCCEEEEehhhhh
Confidence            489999999999999999999985432 134556665543211 00000    011111110    23579999999998


Q ss_pred             CH--HHHHHHHHHHHhc-CCCcEEEEEeCCCC----CCChhhhccce---eeeecCCCHHHHHHHhhcC
Q psy4285         384 TN--DAQNALRRIIEKF-TTNVRFCIICNYLS----KIPPAIQSRCT---RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       384 ~~--~~~~~Ll~~le~~-~~~~~~I~~~n~~~----~l~~~l~sR~~---~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..  ..+..|+.+++.. ..+..+|+++|...    .+++.++|||.   .+.+.+|+.++...++...
T Consensus       212 ~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~~  280 (405)
T TIGR00362       212 AGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQKK  280 (405)
T ss_pred             cCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHHHH
Confidence            54  3567788877653 23456888887532    47789999994   6999999999999999887

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).

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=99.14  E-value=5.5e-10  Score=110.90  Aligned_cols=177  Identities=16%  Similarity=0.149  Sum_probs=121.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHH----H----HhcccCC-CCCcEEEEEe
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQ----F----ASTKTMH-KSSYKLIILD  378 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~----~~~~~~~-~~~~~vliiD  378 (533)
                      .+|+.|.+||||..+|++|.+.....   ..+++.+|++..-..-.-.++++.    |    ......+ -+.++.||+|
T Consensus       248 tVLi~GETGtGKElvAraIH~~S~R~---~kPfV~~NCAAlPesLlESELFGHeKGAFTGA~~~r~GrFElAdGGTLFLD  324 (550)
T COG3604         248 TVLIRGETGTGKELVARAIHQLSPRR---DKPFVKLNCAALPESLLESELFGHEKGAFTGAINTRRGRFELADGGTLFLD  324 (550)
T ss_pred             eEEEecCCCccHHHHHHHHHhhCccc---CCCceeeeccccchHHHHHHHhcccccccccchhccCcceeecCCCeEech
Confidence            49999999999999999999865443   678899998764221111111111    1    1111111 2467899999


Q ss_pred             CCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHhh
Q psy4285         379 EADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       379 E~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l~  440 (533)
                      ||.-|+...|..|++.+.+.           .-++++|++||.-       .++-..|..|..++.+.-||       |+
T Consensus       325 EIGelPL~lQaKLLRvLQegEieRvG~~r~ikVDVRiIAATNRDL~~~V~~G~FRaDLYyRLsV~Pl~lPP-------LR  397 (550)
T COG3604         325 EIGELPLALQAKLLRVLQEGEIERVGGDRTIKVDVRVIAATNRDLEEMVRDGEFRADLYYRLSVFPLELPP-------LR  397 (550)
T ss_pred             hhccCCHHHHHHHHHHHhhcceeecCCCceeEEEEEEEeccchhHHHHHHcCcchhhhhhcccccccCCCC-------cc
Confidence            99999999999999999863           3468999999964       35666777788888887777       55


Q ss_pred             cCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHH
Q psy4285         441 YDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSD  497 (533)
Q Consensus       441 ~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~  497 (533)
                      +.++|+--+...  -+.++....|...-.+-.+..+.+..+.||++++ ++-+.+..
T Consensus       398 ER~~DIplLA~~--Fle~~~~~~gr~~l~ls~~Al~~L~~y~wPGNVR-ELen~veR  451 (550)
T COG3604         398 ERPEDIPLLAGY--FLEKFRRRLGRAILSLSAEALELLSSYEWPGNVR-ELENVVER  451 (550)
T ss_pred             cCCccHHHHHHH--HHHHHHHhcCCcccccCHHHHHHHHcCCCCCcHH-HHHHHHHH
Confidence            555554444432  1123335557766677778889999999999998 44444443

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.14  E-value=1.1e-09  Score=121.78  Aligned_cols=146  Identities=15%  Similarity=0.206  Sum_probs=102.1

Q ss_pred             hchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCC------Cc--hhHHHH
Q psy4285         289 ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDD------RG--IGIVRD  356 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~------~~--~~~~~~  356 (533)
                      |.+..++.+...+.....+|++|+||||||||++|+.+|..+.....    .+..++.++.+..      ++  ...++.
T Consensus       183 gr~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l~~~~l~ag~~~~ge~e~rl~~  262 (821)
T CHL00095        183 GREKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEFEERLKR  262 (821)
T ss_pred             CcHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeHHHHhccCCCccHHHHHHHH
Confidence            44555556666666667778999999999999999999998743211    2345666665321      22  123334


Q ss_pred             HHHHHHhcccCCCCCcEEEEEeCCCCCCH--------HHHHHHHHHHHhcCCCcEEEEEeCCCC-----CCChhhhccce
Q psy4285         357 QIFQFASTKTMHKSSYKLIILDEADAMTN--------DAQNALRRIIEKFTTNVRFCIICNYLS-----KIPPAIQSRCT  423 (533)
Q Consensus       357 ~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------~~~~~Ll~~le~~~~~~~~I~~~n~~~-----~l~~~l~sR~~  423 (533)
                      .+.....      .++.||||||+|.+..        +..+.|...+..  ..+++|.+|+...     ..++++.+||.
T Consensus       263 i~~~~~~------~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~r--g~l~~IgaTt~~ey~~~ie~D~aL~rRf~  334 (821)
T CHL00095        263 IFDEIQE------NNNIILVIDEVHTLIGAGAAEGAIDAANILKPALAR--GELQCIGATTLDEYRKHIEKDPALERRFQ  334 (821)
T ss_pred             HHHHHHh------cCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHhC--CCcEEEEeCCHHHHHHHHhcCHHHHhcce
Confidence            4333321      2457999999997743        345666666764  4588899887653     57999999999


Q ss_pred             eeeecCCCHHHHHHHhhcC
Q psy4285         424 RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 ~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.+..|+.++...+++.+
T Consensus       335 ~I~v~ep~~~e~~aILr~l  353 (821)
T CHL00095        335 PVYVGEPSVEETIEILFGL  353 (821)
T ss_pred             EEecCCCCHHHHHHHHHHH
Confidence            9999999999988888766

>PRK09087 hypothetical protein; Validated

Probab=99.13  E-value=4.7e-10  Score=104.92  Aligned_cols=126  Identities=17%  Similarity=0.244  Sum_probs=83.1

Q ss_pred             hhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCc
Q psy4285         293 LCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSY  372 (533)
Q Consensus       293 ~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  372 (533)
                      +...+..+... ..+.++|+||+|+||||+++++++..      +..+  ++... ...+.+.    ..         ..
T Consensus        32 a~~~l~~~~~~-~~~~l~l~G~~GsGKThLl~~~~~~~------~~~~--i~~~~-~~~~~~~----~~---------~~   88 (226)
T PRK09087         32 AVSLVDHWPNW-PSPVVVLAGPVGSGKTHLASIWREKS------DALL--IHPNE-IGSDAAN----AA---------AE   88 (226)
T ss_pred             HHHHHHhcccC-CCCeEEEECCCCCCHHHHHHHHHHhc------CCEE--ecHHH-cchHHHH----hh---------hc
Confidence            44444443322 22449999999999999999998764      2222  22211 1111111    00         12


Q ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHhcC-CCcEEEEEeCCCC----CCChhhhccc---eeeeecCCCHHHHHHHhhcC
Q psy4285         373 KLIILDEADAMTNDAQNALRRIIEKFT-TNVRFCIICNYLS----KIPPAIQSRC---TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       373 ~vliiDE~d~l~~~~~~~Ll~~le~~~-~~~~~I~~~n~~~----~l~~~l~sR~---~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ++|+|||++.+.. .+.+|+.+++... .+..+|++++.+.    ...+.++|||   ..+.+.+|+.++...++.+.
T Consensus        89 ~~l~iDDi~~~~~-~~~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~~~  165 (226)
T PRK09087         89 GPVLIEDIDAGGF-DETGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKL  165 (226)
T ss_pred             CeEEEECCCCCCC-CHHHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHHHH
Confidence            4899999998743 3566888776533 3567888886433    3579999999   79999999999999998876

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.13  E-value=9.5e-11  Score=118.05  Aligned_cols=76  Identities=14%  Similarity=0.282  Sum_probs=68.4

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++||++|++++.++|||+|||++++|++|+.+++.++|.+   +.  .++++.+..++..|+|++++|+.+++
T Consensus       141 LEep~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~---~~--~~~~~~a~~la~~s~G~~~~A~~l~~  215 (394)
T PRK07940        141 VEEPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVR---RD--GVDPETARRAARASQGHIGRARRLAT  215 (394)
T ss_pred             hhcCCCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHH---hc--CCCHHHHHHHHHHcCCCHHHHHHHhc
Confidence            69999999999999999999999999999999999999999999972   22  35688888999999999999998875


Q ss_pred             H
Q psy4285          81 S   81 (533)
Q Consensus        81 ~   81 (533)
                      .
T Consensus       216 ~  216 (394)
T PRK07940        216 D  216 (394)
T ss_pred             C
Confidence            3

>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=99.13  E-value=8.5e-11  Score=104.41  Aligned_cols=117  Identities=18%  Similarity=0.173  Sum_probs=76.1

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHh----c-----ccCCCCCcEEEEE
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAS----T-----KTMHKSSYKLIIL  377 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~-----~~~~~~~~~vlii  377 (533)
                      .+++++|++||||+.+|++|.+.....   ..+++.++++.......-.++++....    .     .....+..++|+|
T Consensus        23 ~pVlI~GE~GtGK~~lA~~IH~~s~r~---~~pfi~vnc~~~~~~~~e~~LFG~~~~~~~~~~~~~~G~l~~A~~GtL~L   99 (168)
T PF00158_consen   23 LPVLITGETGTGKELLARAIHNNSPRK---NGPFISVNCAALPEELLESELFGHEKGAFTGARSDKKGLLEQANGGTLFL   99 (168)
T ss_dssp             S-EEEECSTTSSHHHHHHHHHHCSTTT---TS-EEEEETTTS-HHHHHHHHHEBCSSSSTTTSSEBEHHHHHTTTSEEEE
T ss_pred             CCEEEEcCCCCcHHHHHHHHHHhhhcc---cCCeEEEehhhhhcchhhhhhhccccccccccccccCCceeeccceEEee
Confidence            469999999999999999999854322   568999999875333222222211000    0     0001246789999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeee
Q psy4285         378 DEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFR  426 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~  426 (533)
                      ||++.|+...|..|++.|++.           +.++++|++|+..       ..+.+.|..|+..+.
T Consensus       100 d~I~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~st~~~l~~~v~~g~fr~dLy~rL~~~~  166 (168)
T PF00158_consen  100 DEIEDLPPELQAKLLRVLEEGKFTRLGSDKPVPVDVRIIASTSKDLEELVEQGRFREDLYYRLNVFT  166 (168)
T ss_dssp             ETGGGS-HHHHHHHHHHHHHSEEECCTSSSEEE--EEEEEEESS-HHHHHHTTSS-HHHHHHHTTEE
T ss_pred             cchhhhHHHHHHHHHHHHhhchhccccccccccccceEEeecCcCHHHHHHcCCChHHHHHHhceEe
Confidence            999999999999999999853           3479999999854       356666666665443

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 ....

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=99.12  E-value=1.1e-10  Score=114.95  Aligned_cols=72  Identities=18%  Similarity=0.315  Sum_probs=62.9

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++|+|||+|+.+++++|||+|||+.++|++|+.+++.+||..    .+  +++  .+.++..++|++.+|+.+++
T Consensus       156 LEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~----~~--~~~--~~~~l~~~~Gsp~~Al~~~~  227 (342)
T PRK06964        156 LEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAA----QG--VAD--ADALLAEAGGAPLAALALAS  227 (342)
T ss_pred             hcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHH----cC--CCh--HHHHHHHcCCCHHHHHHHHC
Confidence            69999999999999999999999999999999999999999999974    23  333  23467889999999998873

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.11  E-value=1.6e-10  Score=114.45  Aligned_cols=76  Identities=28%  Similarity=0.472  Sum_probs=67.9

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++|+|||+|+.+++++|||+|||++++|++++.+++..||++...    .++++.+..++.+++|++.+|...+.
T Consensus       117 LEepp~~t~~il~~~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~l~~~~~----~~~~~~~~~l~~~~~g~~~~a~~~~~  192 (313)
T PRK05564        117 IEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEIEKFISYKYN----DIKEEEKKSAIAFSDGIPGKVEKFIE  192 (313)
T ss_pred             hcCCCCCeEEEEEeCChHhCcHHHHhhceeeeCCCcCHHHHHHHHHHHhc----CCCHHHHHHHHHHcCCCHHHHHHHhc
Confidence            69999999999999999999999999999999999999999999975431    45678888999999999999987654

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.10  E-value=1.2e-09  Score=108.20  Aligned_cols=72  Identities=24%  Similarity=0.286  Sum_probs=57.9

Q ss_pred             CcEEEEEeCCCCCCH------------HHHHHHHHHHHhc----------CCCcEEEEEeC----CCCCCChhhhccc-e
Q psy4285         371 SYKLIILDEADAMTN------------DAQNALRRIIEKF----------TTNVRFCIICN----YLSKIPPAIQSRC-T  423 (533)
Q Consensus       371 ~~~vliiDE~d~l~~------------~~~~~Ll~~le~~----------~~~~~~I~~~n----~~~~l~~~l~sR~-~  423 (533)
                      ..+|+||||+|++..            ..|++||+++|..          ..++.||+.+-    .++.+.|.+..|| .
T Consensus       247 ~~GIVfiDEiDKIa~~~~~~~~DvS~eGVQ~~LLkilEGt~v~~k~~~v~T~~ILFI~~GAF~~~kp~DlIPEl~GR~Pi  326 (441)
T TIGR00390       247 QSGIIFIDEIDKIAKKGESSGADVSREGVQRDLLPIVEGSTVNTKYGMVKTDHILFIAAGAFQLAKPSDLIPELQGRFPI  326 (441)
T ss_pred             cCCEEEEEchhhhcccCCCCCCCCCccchhccccccccCceeeecceeEECCceeEEecCCcCCCChhhccHHHhCccce
Confidence            467999999999853            3688999999852          24566776663    4567999999999 5


Q ss_pred             eeeecCCCHHHHHHHhhcC
Q psy4285         424 RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 ~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.+.+++.+++..+|..-
T Consensus       327 ~v~L~~L~~edL~rILteP  345 (441)
T TIGR00390       327 RVELQALTTDDFERILTEP  345 (441)
T ss_pred             EEECCCCCHHHHHHHhcCC
Confidence            8899999999999999776

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.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=99.10  E-value=2.1e-09  Score=117.03  Aligned_cols=99  Identities=20%  Similarity=0.231  Sum_probs=65.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHH-------HHHHHhccc--------CCCCCc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQ-------IFQFASTKT--------MHKSSY  372 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~--------~~~~~~  372 (533)
                      .++++|+|||||||+++++.+.+....  +...+.+.+++++....+.+.       +..+.....        ......
T Consensus       340 ~~iitGgpGTGKTt~l~~i~~~~~~~~--~~~~v~l~ApTg~AA~~L~e~~g~~a~Tih~lL~~~~~~~~~~~~~~~~~~  417 (720)
T TIGR01448       340 VVILTGGPGTGKTTITRAIIELAEELG--GLLPVGLAAPTGRAAKRLGEVTGLTASTIHRLLGYGPDTFRHNHLEDPIDC  417 (720)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcC--CCceEEEEeCchHHHHHHHHhcCCccccHHHHhhccCCccchhhhhccccC
Confidence            589999999999999999988764321  112344455554444444332       111111100        001357


Q ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         373 KLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       373 ~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      ++|||||++|++......|++.+   +.++++|++++..
T Consensus       418 ~llIvDEaSMvd~~~~~~Ll~~~---~~~~rlilvGD~~  453 (720)
T TIGR01448       418 DLLIVDESSMMDTWLALSLLAAL---PDHARLLLVGDTD  453 (720)
T ss_pred             CEEEEeccccCCHHHHHHHHHhC---CCCCEEEEECccc
Confidence            89999999999999888888876   5678999999643

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

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

Probab=99.10  E-value=1.2e-09  Score=108.44  Aligned_cols=72  Identities=21%  Similarity=0.289  Sum_probs=57.4

Q ss_pred             CcEEEEEeCCCCCCH------------HHHHHHHHHHHhc----------CCCcEEEEEe----CCCCCCChhhhccc-e
Q psy4285         371 SYKLIILDEADAMTN------------DAQNALRRIIEKF----------TTNVRFCIIC----NYLSKIPPAIQSRC-T  423 (533)
Q Consensus       371 ~~~vliiDE~d~l~~------------~~~~~Ll~~le~~----------~~~~~~I~~~----n~~~~l~~~l~sR~-~  423 (533)
                      ..+|+||||+|++..            ..|.+||+++|..          ..++.||+.+    ..++.+.|.+..|| .
T Consensus       249 ~~GIVfiDEiDKIa~~~~~~~~DvS~eGVQ~~LLki~EG~~v~~k~~~i~T~~ILFI~~GAF~~~kp~DlIPEl~GR~Pi  328 (443)
T PRK05201        249 QNGIVFIDEIDKIAARGGSSGPDVSREGVQRDLLPLVEGSTVSTKYGMVKTDHILFIASGAFHVSKPSDLIPELQGRFPI  328 (443)
T ss_pred             cCCEEEEEcchhhcccCCCCCCCCCccchhcccccccccceeeecceeEECCceeEEecCCcCCCChhhccHHHhCccce
Confidence            467999999999853            3688999999852          2456666665    34567899999999 5


Q ss_pred             eeeecCCCHHHHHHHhhcC
Q psy4285         424 RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 ~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.+.+++.+++..+|..-
T Consensus       329 ~v~L~~L~~~dL~~ILteP  347 (443)
T PRK05201        329 RVELDALTEEDFVRILTEP  347 (443)
T ss_pred             EEECCCCCHHHHHHHhcCC
Confidence            8889999999999999875

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

Probab=99.10  E-value=1e-08  Score=96.13  Aligned_cols=125  Identities=22%  Similarity=0.268  Sum_probs=86.5

Q ss_pred             cccccCCCCHHHHHHHHHHHhhhchhhhhhhccccccc---------------CCCceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         267 VYNSVGYPTKTEITNILRWLLNESMDLCYKINRFIDEN---------------ELPHLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       267 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~---------------~~~~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .......|.+..+..+++....||+...+.|.-++.++               ...|+|+.||+|+|||.+|+.+|+.+ 
T Consensus        43 ~~~~~~lPtP~eik~~Ld~YVIGQe~AKKvLsVAVYNHYKRl~~~~~~~dvEL~KSNILLiGPTGsGKTlLAqTLAk~L-  121 (408)
T COG1219          43 EKELSELPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQTLAKIL-  121 (408)
T ss_pred             chhhccCCChHHHHHHhhhheecchhhhceeeeeehhHHHHHhccCCCCceeeeeccEEEECCCCCcHHHHHHHHHHHh-
Confidence            34455779999999999988888887766553332211               12569999999999999999999998 


Q ss_pred             cccccCcceEEecCCCCCchh----HHHHHHHHHHhcccC--CCCCcEEEEEeCCCCCCH--------------HHHHHH
Q psy4285         332 TKAQFNAMVLELNASDDRGIG----IVRDQIFQFASTKTM--HKSSYKLIILDEADAMTN--------------DAQNAL  391 (533)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~--~~~~~~vliiDE~d~l~~--------------~~~~~L  391 (533)
                           +.+|--.++.+.....    .+.+.+..+.+....  ..+..++++|||+|++..              ..|.+|
T Consensus       122 -----nVPFaiADATtLTEAGYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIarkSeN~SITRDVSGEGVQQAL  196 (408)
T COG1219         122 -----NVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQAL  196 (408)
T ss_pred             -----CCCeeeccccchhhccccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhccCCCCCcccccCchHHHHHH
Confidence                 6666666665544332    233333333332211  124578999999999853              468999


Q ss_pred             HHHHHh
Q psy4285         392 RRIIEK  397 (533)
Q Consensus       392 l~~le~  397 (533)
                      ++++|.
T Consensus       197 LKiiEG  202 (408)
T COG1219         197 LKIIEG  202 (408)
T ss_pred             HHHHcC
Confidence            999984

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=99.09  E-value=2.1e-10  Score=109.99  Aligned_cols=72  Identities=19%  Similarity=0.325  Sum_probs=59.0

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      +||||++++|||+|++++.|+|||+|||+.++|++ +++++.++|.    ++++.  .+....++.. .|++.+|+.+++
T Consensus       128 LEEPp~~t~~iL~t~~~~~lLpTI~SRcq~i~f~~-~~~~~~~~L~----~~g~~--~~~a~~la~~-~~s~~~A~~l~~  199 (290)
T PRK07276        128 IEEPQSEIYIFLLTNDENKVLPTIKSRTQIFHFPK-NEAYLIQLLE----QKGLL--KTQAELLAKL-AQSTSEAEKLAQ  199 (290)
T ss_pred             hcCCCCCeEEEEEECChhhCchHHHHcceeeeCCC-cHHHHHHHHH----HcCCC--hHHHHHHHHH-CCCHHHHHHHhC
Confidence            69999999999999999999999999999999977 7888888886    45543  4444445555 468999998874

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.08  E-value=2.2e-10  Score=113.69  Aligned_cols=74  Identities=20%  Similarity=0.385  Sum_probs=63.6

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+|+.+++|+|||+|||++++|++++.+++.++|+    +++  ++++....++.. .|++++|+.+++
T Consensus       134 LEEPp~~~~~Il~t~~~~~ll~TIrSRc~~i~~~~~~~~~~~~~L~----~~g--i~~~~~~~l~~~-~g~~~~A~~l~~  206 (329)
T PRK08058        134 LEEPSGGTTAILLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQ----EEG--ISESLATLLAGL-TNSVEEALALSE  206 (329)
T ss_pred             hcCCCCCceEEEEeCChHhCcHHHHhhceeeeCCCCCHHHHHHHHH----HcC--CChHHHHHHHHH-cCCHHHHHHHhc
Confidence            7999999999999999999999999999999999999999999996    355  445555566666 489999998876


Q ss_pred             H
Q psy4285          81 S   81 (533)
Q Consensus        81 ~   81 (533)
                      .
T Consensus       207 ~  207 (329)
T PRK08058        207 D  207 (329)
T ss_pred             C
Confidence            4

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=99.07  E-value=3.1e-10  Score=109.89  Aligned_cols=73  Identities=18%  Similarity=0.264  Sum_probs=63.6

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++|+|||+|+.+.+++|||+|||++++|++++++++.++|..    .+  ++++....++..++| +.+|+.+++
T Consensus       114 LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~f~~l~~~~l~~~l~~----~~--~~~~~a~~~a~~~~~-~~~a~~~~~  186 (299)
T PRK07132        114 IEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPDQQKILAKLLS----KN--KEKEYNWFYAYIFSN-FEQAEKYIN  186 (299)
T ss_pred             hhCCCCCeEEEEEeCChHhChHHHHhCeEEEECCCCCHHHHHHHHHH----cC--CChhHHHHHHHHcCC-HHHHHHHHh
Confidence            69999999999999999999999999999999999999999999973    23  566667777777774 999998854

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

Probab=99.07  E-value=6e-10  Score=107.64  Aligned_cols=70  Identities=19%  Similarity=0.191  Sum_probs=53.6

Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC------------CCCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         372 YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY------------LSKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       372 ~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~------------~~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ++||||||+++|+-+....|.+++|.. -...+|++||+            +.-++..+++||..+...|++.+++++++
T Consensus       279 pGVLFIDEvHmLDiEcFsfLnralEs~-~sPiiIlATNRg~~~irGt~~~sphGiP~DlLDRllII~t~py~~~ei~~Il  357 (398)
T PF06068_consen  279 PGVLFIDEVHMLDIECFSFLNRALESE-LSPIIILATNRGITKIRGTDIISPHGIPLDLLDRLLIIRTKPYSEEEIKQIL  357 (398)
T ss_dssp             E-EEEEESGGGSBHHHHHHHHHHHTST-T--EEEEEES-SEEE-BTTS-EEETT--HHHHTTEEEEEE----HHHHHHHH
T ss_pred             cceEEecchhhccHHHHHHHHHHhcCC-CCcEEEEecCceeeeccCccCcCCCCCCcchHhhcEEEECCCCCHHHHHHHH
Confidence            789999999999999999999999864 34678888884            34688899999999999999999999998


Q ss_pred             hcC
Q psy4285         440 DYD  442 (533)
Q Consensus       440 ~~~  442 (533)
                      .-.
T Consensus       358 ~iR  360 (398)
T PF06068_consen  358 KIR  360 (398)
T ss_dssp             HHH
T ss_pred             Hhh
Confidence            776

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.

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

Probab=99.07  E-value=8.4e-11  Score=105.68  Aligned_cols=100  Identities=31%  Similarity=0.401  Sum_probs=62.2

Q ss_pred             ccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC-------CchhHHHHHHHHHHhcccCCCCC
Q psy4285         299 RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD-------RGIGIVRDQIFQFASTKTMHKSS  371 (533)
Q Consensus       299 ~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~  371 (533)
                      .|++.+  .+++|+||||||||++|.++++++...   +..+..++.++.       .......+.++.+.        .
T Consensus        42 ~~~~~~--~~l~l~G~~G~GKThLa~ai~~~~~~~---g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l~--------~  108 (178)
T PF01695_consen   42 EFIENG--ENLILYGPPGTGKTHLAVAIANEAIRK---GYSVLFITASDLLDELKQSRSDGSYEELLKRLK--------R  108 (178)
T ss_dssp             -S-SC----EEEEEESTTSSHHHHHHHHHHHHHHT---T--EEEEEHHHHHHHHHCCHCCTTHCHHHHHHH--------T
T ss_pred             CCcccC--eEEEEEhhHhHHHHHHHHHHHHHhccC---CcceeEeecCceeccccccccccchhhhcCccc--------c
Confidence            344433  379999999999999999999988653   334444433211       01111222233332        4


Q ss_pred             cEEEEEeCCCCC--CHHHHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         372 YKLIILDEADAM--TNDAQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       372 ~~vliiDE~d~l--~~~~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      .++|||||+...  +.+..+.|+++++....+...|+|||..
T Consensus       109 ~dlLilDDlG~~~~~~~~~~~l~~ii~~R~~~~~tIiTSN~~  150 (178)
T PF01695_consen  109 VDLLILDDLGYEPLSEWEAELLFEIIDERYERKPTIITSNLS  150 (178)
T ss_dssp             SSCEEEETCTSS---HHHHHCTHHHHHHHHHT-EEEEEESS-
T ss_pred             ccEecccccceeeecccccccchhhhhHhhcccCeEeeCCCc
Confidence            579999999876  4566777999998765566789999865

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

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.05  E-value=3.9e-10  Score=112.74  Aligned_cols=77  Identities=21%  Similarity=0.460  Sum_probs=68.0

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      +||||++++||++|+.++.++|||+|||+.++|++++.+++.++|.+.    ....+++.+..++..|+||+++|+++++
T Consensus       165 LEepp~~~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~----~~~~~~~~~~~l~~~s~Gsp~~Al~ll~  240 (365)
T PRK07471        165 LEEPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAA----GPDLPDDPRAALAALAEGSVGRALRLAG  240 (365)
T ss_pred             HhcCCCCeEEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHh----cccCCHHHHHHHHHHcCCCHHHHHHHhc
Confidence            599999999999999999999999999999999999999999999853    2334455567899999999999999986


Q ss_pred             H
Q psy4285          81 S   81 (533)
Q Consensus        81 ~   81 (533)
                      .
T Consensus       241 ~  241 (365)
T PRK07471        241 G  241 (365)
T ss_pred             c
Confidence            4

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

Probab=99.05  E-value=2.3e-09  Score=101.85  Aligned_cols=70  Identities=16%  Similarity=0.150  Sum_probs=62.1

Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC------------CCCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         372 YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY------------LSKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       372 ~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~------------~~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      +.||||||+++|+-+....|.+.||..- ...+|++||+            |.-++..+++|...+.-.|++.+++++++
T Consensus       292 pGVLFIDEvHmLDIE~FsFlnrAlEse~-aPIii~AtNRG~~kiRGTd~~sPhGIP~DlLDRllII~t~py~~~EireIi  370 (450)
T COG1224         292 PGVLFIDEVHMLDIECFSFLNRALESEL-APIIILATNRGMTKIRGTDIESPHGIPLDLLDRLLIISTRPYSREEIREII  370 (450)
T ss_pred             cceEEEechhhhhHHHHHHHHHHhhccc-CcEEEEEcCCceeeecccCCcCCCCCCHhhhhheeEEecCCCCHHHHHHHH
Confidence            7899999999999999999999998643 3567888874            45789999999999999999999999999


Q ss_pred             hcC
Q psy4285         440 DYD  442 (533)
Q Consensus       440 ~~~  442 (533)
                      ...
T Consensus       371 ~iR  373 (450)
T COG1224         371 RIR  373 (450)
T ss_pred             HHh
Confidence            887

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.03  E-value=4e-09  Score=110.17  Aligned_cols=168  Identities=15%  Similarity=0.160  Sum_probs=111.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHH-----h----cc-cCCCCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFA-----S----TK-TMHKSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~----~~-~~~~~~~~vlii  377 (533)
                      +++++|++||||+++|+++.......   ..+++.+++..... ..+...+....     .    .. ....+.+++|+|
T Consensus       164 ~vli~Ge~GtGK~~lA~~ih~~s~~~---~~~~v~v~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l  239 (445)
T TIGR02915       164 TVLLLGESGTGKEVLARALHQLSDRK---DKRFVAINCAAIPE-NLLESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFL  239 (445)
T ss_pred             CEEEECCCCcCHHHHHHHHHHhCCcC---CCCeEEEECCCCCh-HHHHHHhcCCCCCCcCCCccCCCCceeECCCCEEEE
Confidence            58999999999999999998765322   45678888876432 22222211100     0    00 011245789999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         378 DEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ||++.|+...|..|++.+++.           +.++++|++|+..       ..+.+.|..|+..+.+.-|+       |
T Consensus       240 ~~i~~l~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~~~~~L~~~l~~~~i~lPp-------L  312 (445)
T TIGR02915       240 DEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIAEGTFREDLFYRIAEISITIPP-------L  312 (445)
T ss_pred             echhhCCHHHHHHHHHHHhhCeEEeCCCCceeeeceEEEEecCCCHHHHHHcCCccHHHHHHhccceecCCC-------c
Confidence            999999999999999999853           1367899999765       35677788888777776666       4


Q ss_pred             hcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHH
Q psy4285         440 DYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       440 ~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~  488 (533)
                      +..++|+..+++.+  +.++....+.....+.......+..+.||++++
T Consensus       313 r~R~~Di~~l~~~~--l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNvr  359 (445)
T TIGR02915       313 RSRDGDAVLLANAF--LERFARELKRKTKGFTDDALRALEAHAWPGNVR  359 (445)
T ss_pred             hhchhhHHHHHHHH--HHHHHHHhCCCCCCCCHHHHHHHHhCCCCChHH
Confidence            44445555555432  112212224343446677888899999999987

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).

>PRK12377 putative replication protein; Provisional

Probab=99.03  E-value=3.4e-10  Score=106.63  Aligned_cols=107  Identities=23%  Similarity=0.341  Sum_probs=70.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH------HHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI------FQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .+++|+||||||||++|.++++.+...   +..+..++.++...  .++...      ..+...    -...++|||||+
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l~~~---g~~v~~i~~~~l~~--~l~~~~~~~~~~~~~l~~----l~~~dLLiIDDl  172 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRLLAK---GRSVIVVTVPDVMS--RLHESYDNGQSGEKFLQE----LCKVDLLVLDEI  172 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc---CCCeEEEEHHHHHH--HHHHHHhccchHHHHHHH----hcCCCEEEEcCC
Confidence            469999999999999999999998643   33444444332111  111100      001000    135789999999


Q ss_pred             C--CCCHHHHHHHHHHHHhcCC-CcEEEEEeCCCC-----CCChhhhccc
Q psy4285         381 D--AMTNDAQNALRRIIEKFTT-NVRFCIICNYLS-----KIPPAIQSRC  422 (533)
Q Consensus       381 d--~l~~~~~~~Ll~~le~~~~-~~~~I~~~n~~~-----~l~~~l~sR~  422 (533)
                      +  ..+.+.+..|+.+++.... ...+|+|||...     .+.+.+.||+
T Consensus       173 g~~~~s~~~~~~l~~ii~~R~~~~~ptiitSNl~~~~l~~~~~~ri~dRl  222 (248)
T PRK12377        173 GIQRETKNEQVVLNQIIDRRTASMRSVGMLTNLNHEAMSTLLGERVMDRM  222 (248)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHhcCCCEEEEcCCCHHHHHHHhhHHHHHHH
Confidence            4  4577888999999997654 467899999653     3566777776

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.03  E-value=3.5e-10  Score=103.40  Aligned_cols=69  Identities=23%  Similarity=0.418  Sum_probs=64.3

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKV   75 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a   75 (533)
                      ||+||+++.|||+|+.+.++.++|+|||+++.|++++.+++.+||.+.    +  +++++++.++..++||+|+|
T Consensus       120 le~~~~~~~~il~~~~~~~l~~~i~sr~~~~~~~~~~~~~~~~~l~~~----g--i~~~~~~~i~~~~~g~~r~~  188 (188)
T TIGR00678       120 LEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQWLIRQ----G--ISEEAAELLLALAGGSPGAA  188 (188)
T ss_pred             hcCCCCCeEEEEEECChHhChHHHHhhcEEeeCCCCCHHHHHHHHHHc----C--CCHHHHHHHHHHcCCCcccC
Confidence            699999999999999999999999999999999999999999999853    4  67899999999999999986

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.

>KOG0741|consensus

Probab=99.03  E-value=1.1e-08  Score=101.74  Aligned_cols=123  Identities=16%  Similarity=0.214  Sum_probs=70.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC-CCCchh------HHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS-DDRGIG------IVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~-~~~~~~------~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .+||.||||+|||++|-.+|...      .-+++.+..+ +..+..      .+.+.+...      +.+.-.++++|++
T Consensus       540 SvLl~Gp~~sGKTaLAA~iA~~S------~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DA------YkS~lsiivvDdi  607 (744)
T KOG0741|consen  540 SVLLEGPPGSGKTALAAKIALSS------DFPFVKIISPEDMIGLSESAKCAHIKKIFEDA------YKSPLSIIVVDDI  607 (744)
T ss_pred             EEEEecCCCCChHHHHHHHHhhc------CCCeEEEeChHHccCccHHHHHHHHHHHHHHh------hcCcceEEEEcch
Confidence            38999999999999999999865      5566555443 222221      222222222      2345679999999


Q ss_pred             CCCC------HHHHHHHHHH----HHhc-CCC-cEEEEEeCCCCCCC--hhhhccc-eeeeecCCCH-HHHHHHhhcC
Q psy4285         381 DAMT------NDAQNALRRI----IEKF-TTN-VRFCIICNYLSKIP--PAIQSRC-TRFRFGPLDS-SLIMSRLDYD  442 (533)
Q Consensus       381 d~l~------~~~~~~Ll~~----le~~-~~~-~~~I~~~n~~~~l~--~~l~sR~-~~i~~~~~~~-~~~~~~l~~~  442 (533)
                      +++-      +...|.++++    +.+. |.+ -.+|++|.....+.  -.+.+-| ..+..+.++. +++.+++...
T Consensus       608 ErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpnl~~~~~~~~vl~~~  685 (744)
T KOG0741|consen  608 ERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPNLTTGEQLLEVLEEL  685 (744)
T ss_pred             hhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCccCchHHHHHHHHHc
Confidence            8873      3444555544    4443 332 33455443322111  1222333 3667777666 6777777766

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

Probab=99.03  E-value=3.2e-09  Score=111.67  Aligned_cols=168  Identities=18%  Similarity=0.187  Sum_probs=112.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH-HHHH----h-----cccCCCCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI-FQFA----S-----TKTMHKSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~----~-----~~~~~~~~~~vlii  377 (533)
                      .++++|++|||||++|++++......   ..+++.+++..... ..+...+ +...    .     ......+..+.|||
T Consensus       163 ~vli~Ge~GtGK~~lA~~ih~~s~~~---~~~~i~i~c~~~~~-~~~~~~lfg~~~g~~~~~~~~~~g~~~~a~~Gtl~l  238 (469)
T PRK10923        163 SVLINGESGTGKELVAHALHRHSPRA---KAPFIALNMAAIPK-DLIESELFGHEKGAFTGANTIRQGRFEQADGGTLFL  238 (469)
T ss_pred             eEEEEeCCCCcHHHHHHHHHhcCCCC---CCCeEeeeCCCCCH-HHHHHHhcCCCCCCCCCCCcCCCCCeeECCCCEEEE
Confidence            49999999999999999998865332   56788888876522 2222221 1100    0     00011234679999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhcC-----------CCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         378 DEADAMTNDAQNALRRIIEKFT-----------TNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~~-----------~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ||++.++.+.|..|++.+++..           .++++|++|+..       ..+.+.|..|+..+.+.-|+       |
T Consensus       239 ~~i~~l~~~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~~~~~L~~~l~~~~i~~Pp-------L  311 (469)
T PRK10923        239 DEIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEGKFREDLFHRLNVIRVHLPP-------L  311 (469)
T ss_pred             eccccCCHHHHHHHHHHHhcCcEEeCCCCCeEEeeEEEEEeCCCCHHHHHHcCCchHHHHHHhcceeecCCC-------c
Confidence            9999999999999999998631           346899998753       35778888998777776666       5


Q ss_pred             hcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHH
Q psy4285         440 DYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       440 ~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~  488 (533)
                      +..++|+..+++.+-.  +.....|.....+.......+..+.||++++
T Consensus       312 reR~~Di~~l~~~~l~--~~~~~~~~~~~~~~~~a~~~L~~~~wpgNv~  358 (469)
T PRK10923        312 RERREDIPRLARHFLQ--VAARELGVEAKLLHPETEAALTRLAWPGNVR  358 (469)
T ss_pred             ccchhhHHHHHHHHHH--HHHHHcCCCCCCcCHHHHHHHHhCCCCChHH
Confidence            5555566666554221  1212234333345567788889999999987

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

Probab=99.03  E-value=1.3e-10  Score=116.21  Aligned_cols=74  Identities=39%  Similarity=0.583  Sum_probs=64.4

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+.+++|||+||.+++|+|||+|||+.++|++++..      +.++..+     ++.+..++..+.||+|+++|.++
T Consensus       133 lEep~~~~~~il~~n~~~~il~tI~SRc~~i~f~~~~~~------~~i~~~e-----~~~l~~i~~~~~gd~r~~i~~lq  201 (325)
T COG0470         133 LEEPPKNTRFILITNDPSKILPTIRSRCQRIRFKPPSRL------EAIAWLE-----DQGLEEIAAVAEGDARKAINPLQ  201 (325)
T ss_pred             hccCCCCeEEEEEcCChhhccchhhhcceeeecCCchHH------HHHHHhh-----ccchhHHHHHHHHHHHcCCCHHH
Confidence            799999999999999999999999999999999995544      4444344     46688999999999999999999


Q ss_pred             HHHHh
Q psy4285          81 SAATA   85 (533)
Q Consensus        81 ~~~~~   85 (533)
                      .++..
T Consensus       202 ~~~~~  206 (325)
T COG0470         202 ALAAL  206 (325)
T ss_pred             HHHHh
Confidence            99875

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=99.02  E-value=2e-08  Score=108.22  Aligned_cols=155  Identities=12%  Similarity=0.057  Sum_probs=95.4

Q ss_pred             hhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHc-----------cccc------------------cC
Q psy4285         287 LNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLY-----------TKAQ------------------FN  337 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~-----------~~~~------------------~~  337 (533)
                      +.||+.+...+.-........++||.|+||||||++|+++++.+-           |...                  ..
T Consensus         6 ivGq~~~~~al~~~av~~~~g~vli~G~~GtgKs~lar~l~~~lp~~~~~~~~~~~c~p~~~~~~~~~~~~~~~~~~~~~   85 (633)
T TIGR02442         6 IVGQEDLKLALLLNAVDPRIGGVLIRGEKGTAKSTAARGLAALLPPIDVVAGCPFSCDPDDPEEWCEECRRKYRPSEQRP   85 (633)
T ss_pred             hcChHHHHHHHHHHhhCCCCCeEEEEcCCCCcHHHHHHHHHHhCCCceeccCCcCCCCCCCccccChhhhhcccccccCC
Confidence            356777776666665555556799999999999999999998871           1110                  01


Q ss_pred             cceEEecCCC----CCchhHHHHHHHH--HHhccc-CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc------------
Q psy4285         338 AMVLELNASD----DRGIGIVRDQIFQ--FASTKT-MHKSSYKLIILDEADAMTNDAQNALRRIIEKF------------  398 (533)
Q Consensus       338 ~~~~~~~~~~----~~~~~~~~~~~~~--~~~~~~-~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~------------  398 (533)
                      .+++.+....    ..+...+...+..  ...... ...+..++|+|||++.++...++.|++.|++.            
T Consensus        86 ~pfv~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~L~~A~~GiL~lDEi~~l~~~~q~~Ll~~le~g~~~v~r~g~~~~  165 (633)
T TIGR02442        86 VPFVNLPLGATEDRVVGSLDIERALREGEKAFQPGLLAEAHRGILYIDEVNLLDDHLVDVLLDAAAMGVNRVEREGLSVS  165 (633)
T ss_pred             CCeeeCCCCCcHHHcCCcccHHHHhhcCCeeecCcceeecCCCeEEeChhhhCCHHHHHHHHHHHhcCCEEEEECCceee
Confidence            2333332221    0111111211110  000011 11245679999999999999999999999854            


Q ss_pred             -CCCcEEEEEeCCCC-CCChhhhccce-eeeecCCC-HHHHHHHhhc
Q psy4285         399 -TTNVRFCIICNYLS-KIPPAIQSRCT-RFRFGPLD-SSLIMSRLDY  441 (533)
Q Consensus       399 -~~~~~~I~~~n~~~-~l~~~l~sR~~-~i~~~~~~-~~~~~~~l~~  441 (533)
                       +.++.+|.++|..+ .+.++|.+||. .+.+.++. .++..+++.+
T Consensus       166 ~~~~~~lIat~np~eg~l~~~L~dR~~l~i~v~~~~~~~~~~~il~~  212 (633)
T TIGR02442       166 HPARFVLIGTMNPEEGDLRPQLLDRFGLCVDVAAPRDPEERVEIIRR  212 (633)
T ss_pred             ecCCeEEEEecCCCCCCCCHHHHhhcceEEEccCCCchHHHHHHHHH
Confidence             24577888888643 68899999995 45555554 3444444443

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.

>KOG0732|consensus

Probab=98.99  E-value=5.3e-09  Score=113.45  Aligned_cols=151  Identities=23%  Similarity=0.290  Sum_probs=93.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC------CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD------DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+||+||||||||..|+++|..+..... ...++.-.+++      +....+.+-+...+..      ..+.|+++||||
T Consensus       301 gvL~~GppGTGkTl~araLa~~~s~~~~-kisffmrkgaD~lskwvgEaERqlrllFeeA~k------~qPSIIffdeId  373 (1080)
T KOG0732|consen  301 GVLFHGPPGTGKTLMARALAAACSRGNR-KISFFMRKGADCLSKWVGEAERQLRLLFEEAQK------TQPSIIFFDEID  373 (1080)
T ss_pred             ceeecCCCCCchhHHHHhhhhhhccccc-ccchhhhcCchhhccccCcHHHHHHHHHHHHhc------cCceEEeccccc
Confidence            3999999999999999999998744321 11122222222      1223344433333332      246799999999


Q ss_pred             CCCH-----------HHHHHHHHHHHhcC--CCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC---
Q psy4285         382 AMTN-----------DAQNALRRIIEKFT--TNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD---  442 (533)
Q Consensus       382 ~l~~-----------~~~~~Ll~~le~~~--~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~---  442 (533)
                      -+.+           .....|+.+|+..+  ..+++|.+||+++.++|++++  ||. .+.|+-|+.+...+++.-.   
T Consensus       374 GlapvrSskqEqih~SIvSTLLaLmdGldsRgqVvvigATnRpda~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrk  453 (1080)
T KOG0732|consen  374 GLAPVRSSKQEQIHASIVSTLLALMDGLDSRGQVVVIGATNRPDAIDPALRRPGRFDREFYFPLPDVDARAKILDIHTRK  453 (1080)
T ss_pred             cccccccchHHHhhhhHHHHHHHhccCCCCCCceEEEcccCCccccchhhcCCcccceeEeeeCCchHHHHHHHHHhccC
Confidence            7754           22355777777543  456777888999999999988  785 5666666666666665544   


Q ss_pred             --HHHHHHHHHHHHHHHHHHHhcCCCHHHH
Q psy4285         443 --DISFFNIIIWYIKIQEIKIEKGLALTDI  470 (533)
Q Consensus       443 --~~~~~~ll~~~~~l~~l~~~~~~~~~di  470 (533)
                        |.-...++.+   +..  .+.||.++|+
T Consensus       454 w~~~i~~~l~~~---la~--~t~gy~gaDl  478 (1080)
T KOG0732|consen  454 WEPPISRELLLW---LAE--ETSGYGGADL  478 (1080)
T ss_pred             CCCCCCHHHHHH---HHH--hccccchHHH
Confidence              2222222221   111  5567888774

>KOG0735|consensus

Probab=98.98  E-value=9e-09  Score=105.86  Aligned_cols=168  Identities=16%  Similarity=0.127  Sum_probs=107.2

Q ss_pred             CCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc--hhHHHHHHHHHHhcccCCCCCcEEEEEeCCCC
Q psy4285         305 ELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG--IGIVRDQIFQFASTKTMHKSSYKLIILDEADA  382 (533)
Q Consensus       305 ~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~  382 (533)
                      +.++++++||+|+|||.+++++++++....  ...+..+++++..+  .+.++..+........  .-.+.|+++|++|.
T Consensus       430 ~~~~Ill~G~~GsGKT~L~kal~~~~~k~~--~~hv~~v~Cs~l~~~~~e~iQk~l~~vfse~~--~~~PSiIvLDdld~  505 (952)
T KOG0735|consen  430 RHGNILLNGPKGSGKTNLVKALFDYYSKDL--IAHVEIVSCSTLDGSSLEKIQKFLNNVFSEAL--WYAPSIIVLDDLDC  505 (952)
T ss_pred             ccccEEEeCCCCCCHhHHHHHHHHHhcccc--ceEEEEEechhccchhHHHHHHHHHHHHHHHH--hhCCcEEEEcchhh
Confidence            345799999999999999999999987543  34455556655443  3344444443322221  13578999999999


Q ss_pred             CCH-------------HHHHH-HHHHHHh---cCCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhcC
Q psy4285         383 MTN-------------DAQNA-LRRIIEK---FTTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       383 l~~-------------~~~~~-Ll~~le~---~~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +..             ..... |.+.+..   ....+.+|++++....+.|.|.|  +| .++.+++|...+..++|..+
T Consensus       506 l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~R~~IL~~~  585 (952)
T KOG0735|consen  506 LASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAVTRRKEILTTI  585 (952)
T ss_pred             hhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCCcchhHHHHHHHHH
Confidence            854             11122 3344433   34446788889999999999988  45 47889999999999999887


Q ss_pred             -HHHH-HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q psy4285         443 -DISF-FNIIIWYIKIQEIKIEKGLALTDILTEISLLV  478 (533)
Q Consensus       443 -~~~~-~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~  478 (533)
                       .... ....+....+..  .+.||.+.|+..-.-+++
T Consensus       586 ~s~~~~~~~~~dLd~ls~--~TEGy~~~DL~ifVeRai  621 (952)
T KOG0735|consen  586 FSKNLSDITMDDLDFLSV--KTEGYLATDLVIFVERAI  621 (952)
T ss_pred             HHhhhhhhhhHHHHHHHH--hcCCccchhHHHHHHHHH
Confidence             1111 111111222222  778999998765444433

>smart00350 MCM minichromosome maintenance proteins

Probab=98.96  E-value=1.9e-09  Score=113.34  Aligned_cols=131  Identities=18%  Similarity=0.232  Sum_probs=83.2

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc--hhHHHHH-HHHHH-hcccCCCCCcEEEEEeCCCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG--IGIVRDQ-IFQFA-STKTMHKSSYKLIILDEADA  382 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~--~~~~~~~-~~~~~-~~~~~~~~~~~vliiDE~d~  382 (533)
                      .|+||+|+||||||++|+++++.....     .+.....++..+  ...++.. .+.+. .......+..++++|||++.
T Consensus       237 ~~vLL~G~pGtGKs~lar~l~~~~~r~-----~~~~~~~~~~~~l~~~~~~~~~~g~~~~~~G~l~~A~~Gil~iDEi~~  311 (509)
T smart00350      237 INILLLGDPGTAKSQLLKYVEKTAPRA-----VYTTGKGSSAVGLTAAVTRDPETREFTLEGGALVLADNGVCCIDEFDK  311 (509)
T ss_pred             ceEEEeCCCChhHHHHHHHHHHHcCcc-----eEcCCCCCCcCCccccceEccCcceEEecCccEEecCCCEEEEechhh
Confidence            379999999999999999999875211     111100011000  0111110 00000 00011124568999999999


Q ss_pred             CCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC-------------CCChhhhcccee--eeecCCCHHH
Q psy4285         383 MTNDAQNALRRIIEKF-------------TTNVRFCIICNYLS-------------KIPPAIQSRCTR--FRFGPLDSSL  434 (533)
Q Consensus       383 l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~-------------~l~~~l~sR~~~--i~~~~~~~~~  434 (533)
                      ++...+.+|++.|++.             +..+++|+++|...             .++++++|||+.  +...+++.+.
T Consensus       312 l~~~~q~~L~e~me~~~i~i~k~G~~~~l~~~~~viAa~NP~~g~y~~~~~~~~n~~l~~~lLsRFdLi~~~~d~~~~~~  391 (509)
T smart00350      312 MDDSDRTAIHEAMEQQTISIAKAGITTTLNARCSVLAAANPIGGRYDPKLTPEENIDLPAPILSRFDLLFVVLDEVDEER  391 (509)
T ss_pred             CCHHHHHHHHHHHhcCEEEEEeCCEEEEecCCcEEEEEeCCCCcccCCCcChhhccCCChHHhCceeeEEEecCCCChHH
Confidence            9999999999999863             35688999998652             589999999953  3445666666


Q ss_pred             HHHHhhcC
Q psy4285         435 IMSRLDYD  442 (533)
Q Consensus       435 ~~~~l~~~  442 (533)
                      -..++.++
T Consensus       392 d~~i~~~i  399 (509)
T smart00350      392 DRELAKHV  399 (509)
T ss_pred             HHHHHHHH
Confidence            66666554

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=98.95  E-value=1.2e-08  Score=106.87  Aligned_cols=168  Identities=15%  Similarity=0.143  Sum_probs=108.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH-HHH----Hh-----cccCCCCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI-FQF----AS-----TKTMHKSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~----~~-----~~~~~~~~~~vlii  377 (533)
                      +++++|++||||+++|+++.......   +.+++.+++..... ..+...+ +..    ..     ......+..++|||
T Consensus       168 ~vli~Ge~GtGK~~lA~~ih~~s~~~---~~~~~~i~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l  243 (457)
T PRK11361        168 SVLISGESGTGKELIARAIHYNSRRA---KGPFIKVNCAALPE-SLLESELFGHEKGAFTGAQTLRQGLFERANEGTLLL  243 (457)
T ss_pred             EEEEEcCCCccHHHHHHHHHHhCCCC---CCCeEEEECCCCCH-HHHHHHhcCCCCCCCCCCCCCCCCceEECCCCEEEE
Confidence            59999999999999999998765322   45788888776432 2222211 100    00     00011245679999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         378 DEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ||++.++...|..|++.+++.           +.++++|++||..       ..+.+.+..|+..+.+.-|+       |
T Consensus       244 d~i~~l~~~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~l~~~~~~g~~~~~l~~~l~~~~i~~pp-------L  316 (457)
T PRK11361        244 DEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFREDLFYRLNVIHLILPP-------L  316 (457)
T ss_pred             echhhCCHHHHHHHHHHHhcCcEEeCCCCceeeeceEEEEeCCCCHHHHHHcCCchHHHHHHhccceecCCC-------h
Confidence            999999999999999999753           1357899999754       25667777888766666666       3


Q ss_pred             hcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHH
Q psy4285         440 DYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       440 ~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~  488 (533)
                      +..++|+..++..+  +.++....+.....+.......+..+.||++++
T Consensus       317 reR~~di~~l~~~~--l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNv~  363 (457)
T PRK11361        317 RDRREDISLLANHF--LQKFSSENQRDIIDIDPMAMSLLTAWSWPGNIR  363 (457)
T ss_pred             hhchhhHHHHHHHH--HHHHHHHcCCCCCCcCHHHHHHHHcCCCCCcHH
Confidence            33444554444432  112212223333345567778889999999987

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

Probab=98.95  E-value=5.5e-10  Score=100.60  Aligned_cols=119  Identities=20%  Similarity=0.210  Sum_probs=65.3

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEe------cC----------CCCCc-
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLEL------NA----------SDDRG-  350 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~------~~----------~~~~~-  350 (533)
                      .||+.....+.-+...+  .|++++||||||||++|+.+...+-.-.  .....++      ..          .-.+. 
T Consensus         6 ~GQe~aKrAL~iAAaG~--h~lLl~GppGtGKTmlA~~l~~lLP~l~--~~e~le~~~i~s~~~~~~~~~~~~~~Pfr~p   81 (206)
T PF01078_consen    6 VGQEEAKRALEIAAAGG--HHLLLIGPPGTGKTMLARRLPSLLPPLT--EEEALEVSKIYSVAGLGPDEGLIRQRPFRAP   81 (206)
T ss_dssp             SSTHHHHHHHHHHHHCC----EEEES-CCCTHHHHHHHHHHCS--CC--EECCESS--S-TT---S---EEEE---EEEE
T ss_pred             cCcHHHHHHHHHHHcCC--CCeEEECCCCCCHHHHHHHHHHhCCCCc--hHHHhhhccccccccCCCCCceecCCCcccC
Confidence            46777777766555543  4799999999999999999997541110  0000000      00          00000 


Q ss_pred             --hhHHHHHHHHHHhcc--cCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh-------------cCCCcEEEEEeCC
Q psy4285         351 --IGIVRDQIFQFASTK--TMHKSSYKLIILDEADAMTNDAQNALRRIIEK-------------FTTNVRFCIICNY  410 (533)
Q Consensus       351 --~~~~~~~~~~~~~~~--~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~-------------~~~~~~~I~~~n~  410 (533)
                        .-....+++.-....  ....+..+|||+||+..+.....+.|++.+++             +|.+..+|.++|.
T Consensus        82 hhs~s~~~liGgg~~~~PGeislAh~GVLflDE~~ef~~~vld~Lr~ple~g~v~i~R~~~~~~~Pa~f~lv~a~NP  158 (206)
T PF01078_consen   82 HHSASEAALIGGGRPPRPGEISLAHRGVLFLDELNEFDRSVLDALRQPLEDGEVTISRAGGSVTYPARFLLVAAMNP  158 (206)
T ss_dssp             -TT--HHHHHEEGGGEEE-CGGGGTTSEEEECETTTS-HHHHHHHHHHHHHSBEEEEETTEEEEEB--EEEEEEE-S
T ss_pred             CCCcCHHHHhCCCcCCCcCHHHHhcCCEEEechhhhcCHHHHHHHHHHHHCCeEEEEECCceEEEecccEEEEEecc
Confidence              001111111110000  00125678999999999999999999999986             3667778888764

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

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=98.95  E-value=4e-08  Score=104.73  Aligned_cols=134  Identities=16%  Similarity=0.178  Sum_probs=85.8

Q ss_pred             CCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC--CC--CchhHHHHHHH--HHHhcc-cCCCCCcEEEEE
Q psy4285         305 ELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS--DD--RGIGIVRDQIF--QFASTK-TMHKSSYKLIIL  377 (533)
Q Consensus       305 ~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~--~~--~~~~~~~~~~~--~~~~~~-~~~~~~~~vlii  377 (533)
                      ...|++|.|+||||||++|+++++.+...    .+++.+...  ..  .+.-.+...+.  .+.... ........+|++
T Consensus        15 ~~g~vLl~G~~GtgKs~lar~l~~~~~~~----~pfv~i~~~~t~d~L~G~idl~~~~~~g~~~~~~G~L~~A~~GvL~l   90 (589)
T TIGR02031        15 SLGGVAIRARAGTGKTALARALAEILPPI----MPFVELPLGVTEDRLIGGIDVEESLAGGQRVTQPGLLDEAPRGVLYV   90 (589)
T ss_pred             CcceEEEEcCCCcHHHHHHHHHHHhCCcC----CCeEecCcccchhhcccchhhhhhhhcCcccCCCCCeeeCCCCcEec
Confidence            36689999999999999999999976321    235544421  10  11101111110  000011 111245679999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC---CCChhhhccce-eeeecC-CCHHHHHHHh
Q psy4285         378 DEADAMTNDAQNALRRIIEKF-------------TTNVRFCIICNYLS---KIPPAIQSRCT-RFRFGP-LDSSLIMSRL  439 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~---~l~~~l~sR~~-~i~~~~-~~~~~~~~~l  439 (533)
                      ||++.+++..++.|+..|++.             +..+++|.++|...   .+.+++.+||. .+...+ ++.++..+++
T Consensus        91 DEi~rl~~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~LldRf~l~v~~~~~~~~~er~eil  170 (589)
T TIGR02031        91 DMANLLDDGLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLDRLALHVSLEDVASQDLRVEIV  170 (589)
T ss_pred             cchhhCCHHHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHHhccCeeecCCCCCHHHHHHHH
Confidence            999999999999999999864             24678888888765   79999999995 344444 3444445555


Q ss_pred             hcC
Q psy4285         440 DYD  442 (533)
Q Consensus       440 ~~~  442 (533)
                      .+.
T Consensus       171 ~~~  173 (589)
T TIGR02031       171 RRE  173 (589)
T ss_pred             HHH
Confidence            543

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.

>PRK06921 hypothetical protein; Provisional

Probab=98.95  E-value=1.6e-09  Score=103.89  Aligned_cols=111  Identities=19%  Similarity=0.227  Sum_probs=69.0

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCC----
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADA----  382 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~----  382 (533)
                      .+++|+||||||||+++.++++++....  +..++.+...+..  ..+......+...... -...++|||||++.    
T Consensus       118 ~~l~l~G~~G~GKThLa~aia~~l~~~~--g~~v~y~~~~~l~--~~l~~~~~~~~~~~~~-~~~~dlLiIDDl~~~~~g  192 (266)
T PRK06921        118 NSIALLGQPGSGKTHLLTAAANELMRKK--GVPVLYFPFVEGF--GDLKDDFDLLEAKLNR-MKKVEVLFIDDLFKPVNG  192 (266)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHhhhc--CceEEEEEHHHHH--HHHHHHHHHHHHHHHH-hcCCCEEEEeccccccCC
Confidence            4699999999999999999999985442  2344444433211  1111111111100000 13568999999943    


Q ss_pred             ---CCHHHHHHHHHHHHhcC-CCcEEEEEeCCCC----CCChhhhccc
Q psy4285         383 ---MTNDAQNALRRIIEKFT-TNVRFCIICNYLS----KIPPAIQSRC  422 (533)
Q Consensus       383 ---l~~~~~~~Ll~~le~~~-~~~~~I~~~n~~~----~l~~~l~sR~  422 (533)
                         .+.+.+..|+.+++... .+..+|+|||.+.    .+++.+.||+
T Consensus       193 ~e~~t~~~~~~lf~iin~R~~~~k~tIitsn~~~~el~~~~~~l~sRi  240 (266)
T PRK06921        193 KPRATEWQIEQMYSVLNYRYLNHKPILISSELTIDELLDIDEALGSRI  240 (266)
T ss_pred             CccCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHhhhhhHHHHHH
Confidence               56667778999998654 3466888998653    3456777764

>TIGR00602 rad24 checkpoint protein rad24

Probab=98.95  E-value=4.1e-09  Score=111.56  Aligned_cols=154  Identities=18%  Similarity=0.264  Sum_probs=84.3

Q ss_pred             hhchhhhhhhcccccccCCC----c-eeEeCCCCCChHHHHHHHHHHHccccc-cCcceEEecCCC--------------
Q psy4285         288 NESMDLCYKINRFIDENELP----H-LLFYGPPGTGKTTTILACARKLYTKAQ-FNAMVLELNASD--------------  347 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~----~-~ll~GppGtGKT~la~~la~~l~~~~~-~~~~~~~~~~~~--------------  347 (533)
                      .+|++.+..+..++.....+    . ++|+|||||||||+++.+++.+..... +..++......+              
T Consensus        87 ~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~~~~~Ew~npv~~~~~~~~~~~~~s~~~~~~~  166 (637)
T TIGR00602        87 AVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELGIQVQEWSNPTLPDFQKNDHKVTLSLESCFSN  166 (637)
T ss_pred             cCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhhhHHHHHhhhhhhcccccccccchhhhhcccc
Confidence            34555555555555543222    2 899999999999999999998733210 000000000000              


Q ss_pred             -CCchhHHHHHHHHHHhcccC----CCCCcEEEEEeCCCCCCHH---HHHHHHH-HHHhcCCCcEEEEEeCC-CC-----
Q psy4285         348 -DRGIGIVRDQIFQFASTKTM----HKSSYKLIILDEADAMTND---AQNALRR-IIEKFTTNVRFCIICNY-LS-----  412 (533)
Q Consensus       348 -~~~~~~~~~~~~~~~~~~~~----~~~~~~vliiDE~d~l~~~---~~~~Ll~-~le~~~~~~~~I~~~n~-~~-----  412 (533)
                       ......+...+.........    ......||+|||++.+...   .+..+++ ...+ ...+.+|++++. +.     
T Consensus       167 ~~s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~r~~~~lq~lLr~~~~e-~~~~pLI~I~TE~~~~~~~~  245 (637)
T TIGR00602       167 FQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFYRDTRALHEILRWKYVS-IGRCPLVFIITESLEGDNNQ  245 (637)
T ss_pred             ccchHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhchhhHHHHHHHHHHHhhc-CCCceEEEEecCCccccccc
Confidence             01122233333222111000    1245789999999776543   3333433 2222 234456665542 11     


Q ss_pred             -----C----CChhhhc--cceeeeecCCCHHHHHHHhhcC
Q psy4285         413 -----K----IPPAIQS--RCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       413 -----~----l~~~l~s--R~~~i~~~~~~~~~~~~~l~~~  442 (533)
                           .    +.+++++  |+..+.|.|++..++.+.|.++
T Consensus       246 ~~~~f~~~~lL~~eLls~~rv~~I~FnPia~t~l~K~L~rI  286 (637)
T TIGR00602       246 RRLLFPAETIMNKEILEEPRVSNISFNPIAPTIMKKFLNRI  286 (637)
T ss_pred             cccccchhcccCHhHhcccceeEEEeCCCCHHHHHHHHHHH
Confidence                 1    3378887  6678999999999988888887

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

>PRK08116 hypothetical protein; Validated

Probab=98.95  E-value=1.7e-09  Score=103.88  Aligned_cols=115  Identities=23%  Similarity=0.247  Sum_probs=76.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH--------HHHHhcccCCCCCcEEEEEeC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI--------FQFASTKTMHKSSYKLIILDE  379 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~vliiDE  379 (533)
                      .++|+|+||||||++|.++++.+...   +..++.++.++...  .+....        ..+...    -...++|||||
T Consensus       116 gl~l~G~~GtGKThLa~aia~~l~~~---~~~v~~~~~~~ll~--~i~~~~~~~~~~~~~~~~~~----l~~~dlLviDD  186 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACIANELIEK---GVPVIFVNFPQLLN--RIKSTYKSSGKEDENEIIRS----LVNADLLILDD  186 (268)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEEHHHHHH--HHHHHHhccccccHHHHHHH----hcCCCEEEEec
Confidence            49999999999999999999998654   34455555433110  111000        001100    13457999999


Q ss_pred             C--CCCCHHHHHHHHHHHHhc-CCCcEEEEEeCCCC-----CCChhhhcc----ceeeeecCCC
Q psy4285         380 A--DAMTNDAQNALRRIIEKF-TTNVRFCIICNYLS-----KIPPAIQSR----CTRFRFGPLD  431 (533)
Q Consensus       380 ~--d~l~~~~~~~Ll~~le~~-~~~~~~I~~~n~~~-----~l~~~l~sR----~~~i~~~~~~  431 (533)
                      +  +..+.+.+..|+.+++.. ..+..+|+|||...     .+++.+.||    |..+.+..++
T Consensus       187 lg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~~~eL~~~~~~ri~sRl~e~~~~v~~~g~d  250 (268)
T PRK08116        187 LGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLSLEELKNQYGKRIYDRILEMCTPVENEGKS  250 (268)
T ss_pred             ccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHhHHHHHHHHHcCEEEEeeCcC
Confidence            9  556888899999999864 34567999998764     256788888    4566666655

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=98.95  E-value=1.3e-09  Score=104.15  Aligned_cols=58  Identities=14%  Similarity=0.202  Sum_probs=51.6

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMR   73 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r   73 (533)
                      |||||++++|||+|+++++++|||+|||+.++|+++.             +  ..++++....++..++|++.
T Consensus       119 LEEPp~~~~fiL~~~~~~~ll~TI~SRcq~~~~~~~~-------------~--~~i~~~~~~~l~~~~~g~~~  176 (290)
T PRK05917        119 LEDPPQHGVIILTSAKPQRLPPTIRSRSLSIHIPMEE-------------K--TLVSKEDIAYLIGYAQGKES  176 (290)
T ss_pred             hhcCCCCeEEEEEeCChhhCcHHHHhcceEEEccchh-------------c--cCCCHHHHHHHHHHhCCChh
Confidence            6999999999999999999999999999999999861             1  24678888889999999995

>PRK04195 replication factor C large subunit; Provisional

Probab=98.95  E-value=5.5e-09  Score=109.48  Aligned_cols=93  Identities=20%  Similarity=0.282  Sum_probs=82.8

Q ss_pred             CceEEEEEcCCCCcCch-hhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHH
Q psy4285           6 TNVRFCIICNYLSKITP-AIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAAT   84 (533)
Q Consensus         6 ~~~~~il~~~~~~~i~~-~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~~~   84 (533)
                      .+..+|++||.+..+.+ +|+|||+.++|++|+.+++..+|++++.++++.+++++++.|+..++||+|.|+|.|+.++.
T Consensus       129 ~~~~iIli~n~~~~~~~k~Lrsr~~~I~f~~~~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~~s~GDlR~ain~Lq~~a~  208 (482)
T PRK04195        129 AKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAE  208 (482)
T ss_pred             CCCCEEEeccCccccchhhHhccceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence            34668999999998888 99999999999999999999999999999999999999999999999999999999999654


Q ss_pred             hCCCCcchhhHHhhh
Q psy4285          85 AHADEVNEDTIFTLL   99 (533)
Q Consensus        85 ~~~~~i~~~~i~~~~   99 (533)
                       ....++.+.+..+.
T Consensus       209 -~~~~it~~~v~~~~  222 (482)
T PRK04195        209 -GYGKLTLEDVKTLG  222 (482)
T ss_pred             -CCCCCcHHHHHHhh
Confidence             44568888876544

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.93  E-value=7.1e-09  Score=106.56  Aligned_cols=110  Identities=25%  Similarity=0.378  Sum_probs=89.0

Q ss_pred             CceEEEEEc--CCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhc--CC-CCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           6 TNVRFCIIC--NYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQE--KV-NVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         6 ~~~~~il~~--~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~--~~-~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      +.+.||.+|  |+.+.++++|+|||++++|++++.+++..+|++++...  ++ .+++++++.+++.++||+|+++|.|+
T Consensus       119 ~~iilI~att~n~~~~l~~aL~SR~~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~Le  198 (413)
T PRK13342        119 GTITLIGATTENPSFEVNPALLSRAQVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLLE  198 (413)
T ss_pred             CcEEEEEeCCCChhhhccHHHhccceeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHHH
Confidence            445566554  56779999999999999999999999999999987653  44 78899999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhccccch--hHHHHHhc
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRVEKYRP--STLDELVS  116 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~ek~~~--~~l~~lls  116 (533)
                      .++.. ...|+.+.+.++++.....|..  ..++++++
T Consensus       199 ~~~~~-~~~It~~~v~~~~~~~~~~~d~~~~~~~~~is  235 (413)
T PRK13342        199 LAALG-VDSITLELLEEALQKRAARYDKDGDEHYDLIS  235 (413)
T ss_pred             HHHHc-cCCCCHHHHHHHHhhhhhccCCCccHHHHHHH
Confidence            98875 5569999988877765444544  35666654

>KOG2028|consensus

Probab=98.92  E-value=5e-09  Score=99.75  Aligned_cols=112  Identities=21%  Similarity=0.189  Sum_probs=89.1

Q ss_pred             CceEEEEEc--CCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHh------h-----c--CCCCCHHHHHHHHHhcCC
Q psy4285           6 TNVRFCIIC--NYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIE------Q-----E--KVNVTPDGKKAIIDLSDG   70 (533)
Q Consensus         6 ~~~~~il~~--~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~------~-----~--~~~~~~~~~~~~~~~~~g   70 (533)
                      +.+.||-+|  ||+|+++.+|.|||.+|.+++++.+++..+|.+...      +     .  .+.+++..++.++..|.|
T Consensus       249 G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyla~lsdG  328 (554)
T KOG2028|consen  249 GDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDG  328 (554)
T ss_pred             CceEEEecccCCCccchhHHHHhccceeEeccCCHHHHHHHHHHHHHhhccccccCCCCCCcchhhhHHHHHHHHHhcCc
Confidence            445566655  899999999999999999999999999999999643      1     1  134678889999999999


Q ss_pred             CHHHHHHHHHHHHHh----CC----CCcchhhHHhhhhhhccccchh--HHHHHhch
Q psy4285          71 DMRKVLNILQSAATA----HA----DEVNEDTIFTLLVSRVEKYRPS--TLDELVSH  117 (533)
Q Consensus        71 ~~r~a~~~l~~~~~~----~~----~~i~~~~i~~~~~~~~ek~~~~--~l~~lls~  117 (533)
                      |.|.|+|.||.....    .+    ..++.+++++.++....-|++.  .||+.+|-
T Consensus       329 DaR~aLN~Lems~~m~~tr~g~~~~~~lSidDvke~lq~s~~~YDr~Ge~HYntISA  385 (554)
T KOG2028|consen  329 DARAALNALEMSLSMFCTRSGQSSRVLLSIDDVKEGLQRSHILYDRAGEEHYNTISA  385 (554)
T ss_pred             hHHHHHHHHHHHHHHHHhhcCCcccceecHHHHHHHHhhccceecccchhHHHHHHH
Confidence            999999999988332    11    1388888988888777777764  68888763

>PRK08485 DNA polymerase III subunit delta'; Validated

Probab=98.92  E-value=3.4e-08  Score=87.65  Aligned_cols=92  Identities=27%  Similarity=0.272  Sum_probs=75.3

Q ss_pred             CCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhcccee
Q psy4285         345 ASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTR  424 (533)
Q Consensus       345 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~  424 (533)
                      ..+..+.+.+|+.+.......    ...+ +||+++|+|+.+++|+|++++||||.++.||++|+.+..++|+++|||..
T Consensus        33 ~~~~i~Vd~iReii~~~~~~~----~~~k-~iI~~a~~l~~~A~NaLLK~LEEPp~~~~fiL~t~~~~~llpTI~SRc~~  107 (206)
T PRK08485         33 IKEEFKIEDAKEVIAEAYIAE----SEEK-IIVIAAPSYGIEAQNALLKILEEPPKNICFIIVAKSKNLLLPTIRSRLII  107 (206)
T ss_pred             CCCCCCHHHHHHHHHHHhhCC----CCcE-EEEEchHhhCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCchHHHhhhee
Confidence            444578889999877755443    2233 46889999999999999999999999999999999999999999999975


Q ss_pred             -------------eeecCCCHHHHHHHhhc
Q psy4285         425 -------------FRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       425 -------------i~~~~~~~~~~~~~l~~  441 (533)
                                   +.+.+++.+++.+.+.+
T Consensus       108 ~~~~~~~~~~~l~l~l~~l~~~~i~~~L~~  137 (206)
T PRK08485        108 EKRKQKKPVKPLDLDLKKLDLKDIYEFLKE  137 (206)
T ss_pred             ccccccccccccccccCCCCHHHHHHHHHH
Confidence                         66777877777776654

>PRK15115 response regulator GlrR; Provisional

Probab=98.91  E-value=1.9e-08  Score=104.98  Aligned_cols=169  Identities=14%  Similarity=0.116  Sum_probs=107.6

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHh---------cc-cCCCCCcEEEE
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAS---------TK-TMHKSSYKLII  376 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~-~~~~~~~~vli  376 (533)
                      ++++++|++|||||++|+++.+.....   +.+++.+++..... ..+...+.....         .. .......++||
T Consensus       158 ~~vli~Ge~GtGk~~lA~~ih~~s~r~---~~~f~~i~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~  233 (444)
T PRK15115        158 VSVLINGQSGTGKEILAQAIHNASPRA---SKPFIAINCGALPE-QLLESELFGHARGAFTGAVSNREGLFQAAEGGTLF  233 (444)
T ss_pred             CeEEEEcCCcchHHHHHHHHHHhcCCC---CCCeEEEeCCCCCH-HHHHHHhcCCCcCCCCCCccCCCCcEEECCCCEEE
Confidence            358999999999999999998865322   46788888876422 222222111000         00 01124467999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhcC-----------CCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHH
Q psy4285         377 LDEADAMTNDAQNALRRIIEKFT-----------TNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSR  438 (533)
Q Consensus       377 iDE~d~l~~~~~~~Ll~~le~~~-----------~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~  438 (533)
                      |||++.|+...|..|++.+++..           .++++|++|+..       ..+.+.+..|+..+.+.-|+   ++++
T Consensus       234 l~~i~~l~~~~q~~L~~~l~~~~~~~~g~~~~~~~~~rii~~~~~~l~~~~~~~~f~~~l~~~l~~~~i~lPp---Lr~R  310 (444)
T PRK15115        234 LDEIGDMPAPLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHRDLPKAMARGEFREDLYYRLNVVSLKIPA---LAER  310 (444)
T ss_pred             EEccccCCHHHHHHHHHHHhhCCEEeCCCCceeeeeEEEEEeCCCCHHHHHHcCCccHHHHHhhceeeecCCC---hHhc
Confidence            99999999999999999998632           257899988753       24566677777767776666   3333


Q ss_pred             hhcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHH
Q psy4285         439 LDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       439 l~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~  488 (533)
                      -..+|.-+..++..      +....+.....+-......+..+.||++++
T Consensus       311 ~eDi~~l~~~~l~~------~~~~~~~~~~~~~~~a~~~L~~~~WpgNvr  354 (444)
T PRK15115        311 TEDIPLLANHLLRQ------AAERHKPFVRAFSTDAMKRLMTASWPGNVR  354 (444)
T ss_pred             cccHHHHHHHHHHH------HHHHhCCCCCCcCHHHHHHHHhCCCCChHH
Confidence            33333333333332      112223222335566778889999999987

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

Probab=98.90  E-value=9.1e-10  Score=104.66  Aligned_cols=98  Identities=23%  Similarity=0.319  Sum_probs=65.4

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHH------HHhcccCCCCCcEEEEEeC
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQ------FASTKTMHKSSYKLIILDE  379 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~vliiDE  379 (533)
                      ..+++|+||||||||++|-++++++. ..  +..+..++.++..  ..+......      +...    -...++|||||
T Consensus       105 ~~nl~l~G~~G~GKThLa~Ai~~~l~-~~--g~sv~f~~~~el~--~~Lk~~~~~~~~~~~l~~~----l~~~dlLIiDD  175 (254)
T COG1484         105 GENLVLLGPPGVGKTHLAIAIGNELL-KA--GISVLFITAPDLL--SKLKAAFDEGRLEEKLLRE----LKKVDLLIIDD  175 (254)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHH-Hc--CCeEEEEEHHHHH--HHHHHHHhcCchHHHHHHH----hhcCCEEEEec
Confidence            34799999999999999999999997 33  4555555554421  111111100      0110    13578999999


Q ss_pred             CCCC--CHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         380 ADAM--TNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       380 ~d~l--~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      +.+.  +.+..+.+++++.........++|+|.+.
T Consensus       176 lG~~~~~~~~~~~~~q~I~~r~~~~~~~~tsN~~~  210 (254)
T COG1484         176 IGYEPFSQEEADLLFQLISRRYESRSLIITSNLSF  210 (254)
T ss_pred             ccCccCCHHHHHHHHHHHHHHHhhccceeecCCCh
Confidence            9985  56677888888876555555599998765

>KOG1051|consensus

Probab=98.90  E-value=7.5e-08  Score=104.01  Aligned_cols=119  Identities=21%  Similarity=0.287  Sum_probs=84.7

Q ss_pred             HHHHhhhchhhhhhhcccccccC-----C-Cc--eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------
Q psy4285         283 LRWLLNESMDLCYKINRFIDENE-----L-PH--LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------  348 (533)
Q Consensus       283 l~~~~~~~~~~~~~l~~~~~~~~-----~-~~--~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------  348 (533)
                      +.....||++++..+..++...+     . |.  ++|.||.|+|||-+|+++|..+++.   ...++.++.++.      
T Consensus       560 L~~~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgs---e~~~IriDmse~~evskl  636 (898)
T KOG1051|consen  560 LHERVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYVFGS---EENFIRLDMSEFQEVSKL  636 (898)
T ss_pred             HHhhccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHHHcCC---ccceEEechhhhhhhhhc
Confidence            33456889888877766654322     1 22  8999999999999999999999776   456677766541      


Q ss_pred             -------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCC
Q psy4285         349 -------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNY  410 (533)
Q Consensus       349 -------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~  410 (533)
                             .+......+.... .     ..++.|++|||||...+..++.|++++|++           -.|+.||+|+|.
T Consensus       637 igsp~gyvG~e~gg~Lteav-r-----rrP~sVVLfdeIEkAh~~v~n~llq~lD~GrltDs~Gr~Vd~kN~I~IMTsn~  710 (898)
T KOG1051|consen  637 IGSPPGYVGKEEGGQLTEAV-K-----RRPYSVVLFEEIEKAHPDVLNILLQLLDRGRLTDSHGREVDFKNAIFIMTSNV  710 (898)
T ss_pred             cCCCcccccchhHHHHHHHH-h-----cCCceEEEEechhhcCHHHHHHHHHHHhcCccccCCCcEeeccceEEEEeccc
Confidence                   1121221111111 1     246789999999999999999999999974           367899999864

>KOG1942|consensus

Probab=98.90  E-value=1.5e-08  Score=93.72  Aligned_cols=71  Identities=18%  Similarity=0.206  Sum_probs=62.5

Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC-------------CCCCChhhhccceeeeecCCCHHHHHH
Q psy4285         371 SYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY-------------LSKIPPAIQSRCTRFRFGPLDSSLIMS  437 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~-------------~~~l~~~l~sR~~~i~~~~~~~~~~~~  437 (533)
                      -++||||||+++++-+....|.+.+|.+ -...+|+++|+             |..+++.+++|+..++-.+++++++++
T Consensus       296 vPGVLFIDEVhMLDiEcFTyL~kalES~-iaPivifAsNrG~~~irGt~d~~sPhGip~dllDRl~Iirt~~y~~~e~r~  374 (456)
T KOG1942|consen  296 VPGVLFIDEVHMLDIECFTYLHKALESP-IAPIVIFASNRGMCTIRGTEDILSPHGIPPDLLDRLLIIRTLPYDEEEIRQ  374 (456)
T ss_pred             cCcceEeeehhhhhhHHHHHHHHHhcCC-CCceEEEecCCcceeecCCcCCCCCCCCCHHHhhheeEEeeccCCHHHHHH
Confidence            3789999999999999999999999875 34678888874             456899999999999999999999999


Q ss_pred             HhhcC
Q psy4285         438 RLDYD  442 (533)
Q Consensus       438 ~l~~~  442 (533)
                      ++...
T Consensus       375 Ii~~R  379 (456)
T KOG1942|consen  375 IIKIR  379 (456)
T ss_pred             HHHHH
Confidence            99887

>PRK07952 DNA replication protein DnaC; Validated

Probab=98.89  E-value=2.9e-09  Score=100.12  Aligned_cols=113  Identities=19%  Similarity=0.250  Sum_probs=72.8

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch---------hHHHHHHHHHHhcccCCCCCcEEEEE
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI---------GIVRDQIFQFASTKTMHKSSYKLIIL  377 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~vlii  377 (533)
                      .+++|+|+||||||+++.++++.+...   +..+..++.++....         ......+..+        ...++|||
T Consensus       100 ~~~~l~G~~GtGKThLa~aia~~l~~~---g~~v~~it~~~l~~~l~~~~~~~~~~~~~~l~~l--------~~~dlLvI  168 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAAICNELLLR---GKSVLIITVADIMSAMKDTFSNSETSEEQLLNDL--------SNVDLLVI  168 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEHHHHHHHHHHHHhhccccHHHHHHHh--------ccCCEEEE
Confidence            369999999999999999999998554   334444443321100         0001111111        35789999


Q ss_pred             eCCCCCC--HHHHHHHHHHHHhcC-CCcEEEEEeCCCC-----CCChhhhccce-----eeeecCC
Q psy4285         378 DEADAMT--NDAQNALRRIIEKFT-TNVRFCIICNYLS-----KIPPAIQSRCT-----RFRFGPL  430 (533)
Q Consensus       378 DE~d~l~--~~~~~~Ll~~le~~~-~~~~~I~~~n~~~-----~l~~~l~sR~~-----~i~~~~~  430 (533)
                      ||++...  ......|+.+++... ....+|+|||...     .+.+.+.||+.     .+.|...
T Consensus       169 DDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl~~~~l~~~~g~ri~sRl~~~~~~~i~f~~~  234 (244)
T PRK07952        169 DEIGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNSNMEEMTKLLGERVMDRMRLGNSLWVIFNWD  234 (244)
T ss_pred             eCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCCCHHHHHHHhChHHHHHHHHCCceEEEeeCC
Confidence            9998764  445667888998654 4678999999754     35667777762     4555543

>KOG1514|consensus

Probab=98.89  E-value=9.1e-08  Score=98.88  Aligned_cols=150  Identities=21%  Similarity=0.275  Sum_probs=100.7

Q ss_pred             hhhhhhcccccc-cCCCceeEeCCCCCChHHHHHHHHHHHcccc----ccCcceEEecCCCCCchhHHHHHHH-------
Q psy4285         292 DLCYKINRFIDE-NELPHLLFYGPPGTGKTTTILACARKLYTKA----QFNAMVLELNASDDRGIGIVRDQIF-------  359 (533)
Q Consensus       292 ~~~~~l~~~~~~-~~~~~~ll~GppGtGKT~la~~la~~l~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~-------  359 (533)
                      ++...+..++.. +....+.++|-||||||.+++.+.+.+....    .....++++|+....+...+-+.+-       
T Consensus       407 ~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~Y~~I~~~lsg~~  486 (767)
T KOG1514|consen  407 EIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREIYEKIWEALSGER  486 (767)
T ss_pred             HHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHHHHHHHHhcccCc
Confidence            344455555555 2222489999999999999999999875221    1234678888876555433332221       


Q ss_pred             -----------HHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc---CCCcEEEEEeCCCC----CCChhhhcc
Q psy4285         360 -----------QFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF---TTNVRFCIICNYLS----KIPPAIQSR  421 (533)
Q Consensus       360 -----------~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~---~~~~~~I~~~n~~~----~l~~~l~sR  421 (533)
                                 .... .+.......|++|||.|.|-...|..|+.+++.+   .....+|.++|..+    .+...+.||
T Consensus       487 ~~~~~al~~L~~~f~-~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~IaNTmdlPEr~l~nrvsSR  565 (767)
T KOG1514|consen  487 VTWDAALEALNFRFT-VPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIAIANTMDLPERLLMNRVSSR  565 (767)
T ss_pred             ccHHHHHHHHHHhhc-cCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEEecccccCHHHHhccchhhh
Confidence                       1111 1112356789999999999887788888888754   34566666777554    234466677


Q ss_pred             c--eeeeecCCCHHHHHHHhhcC
Q psy4285         422 C--TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       422 ~--~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .  ..+.|.|++.+|+.+++...
T Consensus       566 lg~tRi~F~pYth~qLq~Ii~~R  588 (767)
T KOG1514|consen  566 LGLTRICFQPYTHEQLQEIISAR  588 (767)
T ss_pred             ccceeeecCCCCHHHHHHHHHHh
Confidence            6  69999999999999988776

>PF13173 AAA_14: AAA domain

Probab=98.88  E-value=1.5e-08  Score=86.33  Aligned_cols=119  Identities=24%  Similarity=0.358  Sum_probs=79.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHH-HHHHHHHhcccCCCCCcEEEEEeCCCCCCHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR-DQIFQFASTKTMHKSSYKLIILDEADAMTND  386 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~  386 (533)
                      .++++||+|+||||+++.+++.+. .   ...++.++..+........ +....+....   ..+..++||||++.+. +
T Consensus         4 ~~~l~G~R~vGKTtll~~~~~~~~-~---~~~~~yi~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~i~iDEiq~~~-~   75 (128)
T PF13173_consen    4 IIILTGPRGVGKTTLLKQLAKDLL-P---PENILYINFDDPRDRRLADPDLLEYFLELI---KPGKKYIFIDEIQYLP-D   75 (128)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhc-c---cccceeeccCCHHHHHHhhhhhHHHHHHhh---ccCCcEEEEehhhhhc-c
Confidence            479999999999999999999874 1   3455666655533221110 0112222211   1256799999999996 4


Q ss_pred             HHHHHHHHHHhcCCCcEEEEEeCCCC----CCChhhhccceeeeecCCCHHHH
Q psy4285         387 AQNALRRIIEKFTTNVRFCIICNYLS----KIPPAIQSRCTRFRFGPLDSSLI  435 (533)
Q Consensus       387 ~~~~Ll~~le~~~~~~~~I~~~n~~~----~l~~~l~sR~~~i~~~~~~~~~~  435 (533)
                      ....+....+.. .+..+|+|+....    ...+.+..|...+.+.|++-.|.
T Consensus        76 ~~~~lk~l~d~~-~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   76 WEDALKFLVDNG-PNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             HHHHHHHHHHhc-cCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            556666666654 5688999886554    34567777889999999987654

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.88  E-value=3.9e-09  Score=103.83  Aligned_cols=118  Identities=25%  Similarity=0.284  Sum_probs=75.8

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH-H---HHHhcccCCCCCcEEEEEeCCCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI-F---QFASTKTMHKSSYKLIILDEADA  382 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~---~~~~~~~~~~~~~~vliiDE~d~  382 (533)
                      .+++|+||||||||+++.++|+++...   +..++.++..+...  .+.... .   ....... .-...++|||||++.
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~---g~~V~y~t~~~l~~--~l~~~~~~~~~~~~~~~~-~l~~~DLLIIDDlG~  257 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDR---GKSVIYRTADELIE--ILREIRFNNDKELEEVYD-LLINCDLLIIDDLGT  257 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHC---CCeEEEEEHHHHHH--HHHHHHhccchhHHHHHH-HhccCCEEEEeccCC
Confidence            469999999999999999999998654   44555555543211  111100 0   0000000 013568999999965


Q ss_pred             C--CHHHHHHHHHHHHhcC-CCcEEEEEeCCCC-----CCChhhhccc----eeeeecCC
Q psy4285         383 M--TNDAQNALRRIIEKFT-TNVRFCIICNYLS-----KIPPAIQSRC----TRFRFGPL  430 (533)
Q Consensus       383 l--~~~~~~~Ll~~le~~~-~~~~~I~~~n~~~-----~l~~~l~sR~----~~i~~~~~  430 (533)
                      .  +...++.|+.++++.. .+..+|+|||...     .+++.+.||+    ..+.|...
T Consensus       258 e~~t~~~~~~Lf~iin~R~~~~k~tIiTSNl~~~el~~~~~eri~SRL~~~~~~i~~~G~  317 (329)
T PRK06835        258 EKITEFSKSELFNLINKRLLRQKKMIISTNLSLEELLKTYSERISSRLLGNFTLLKFYGE  317 (329)
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHhHHHHHHHHcCCEEEEecCc
Confidence            4  6777889999998754 3467899998653     3567888886    34555443

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=98.87  E-value=2.6e-08  Score=104.66  Aligned_cols=168  Identities=18%  Similarity=0.181  Sum_probs=108.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH-HH----HHhc-----ccCCCCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI-FQ----FAST-----KTMHKSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~----~~~~-----~~~~~~~~~vlii  377 (533)
                      .+++.|.+||||+++|+++.+.....   ..+++.+++.... ...+...+ +.    +...     .....+..++|+|
T Consensus       159 ~vli~Ge~GtGK~~~A~~ih~~~~~~---~~~~~~~~c~~~~-~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l  234 (463)
T TIGR01818       159 TVLINGESGTGKELVARALHRHSPRA---NGPFIALNMAAIP-KDLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFL  234 (463)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhCCCC---CCCeEEEeCCCCC-HHHHHHHhcCCCCCCCCCcccCCCCcEEECCCCeEEE
Confidence            48999999999999999998865322   4678888877642 22222222 10    0000     0011234678999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhcC-----------CCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         378 DEADAMTNDAQNALRRIIEKFT-----------TNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~~-----------~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ||++.++.+.|..|++.+++..           .++++|++|+..       ..+.+.|..|+..+.+.-|+       |
T Consensus       235 ~ei~~l~~~~q~~ll~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~f~~~L~~rl~~~~i~lPp-------L  307 (463)
T TIGR01818       235 DEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFREDLFHRLNVIRIHLPP-------L  307 (463)
T ss_pred             EchhhCCHHHHHHHHHHHhcCcEEECCCCceeeeeeEEEEeCCCCHHHHHHcCCcHHHHHHHhCcceecCCC-------c
Confidence            9999999999999999998532           257899998754       25667888888655555555       4


Q ss_pred             hcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHH
Q psy4285         440 DYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       440 ~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~  488 (533)
                      +..++|+..+++.+-.  .+....+.....+-......+..++||++++
T Consensus       308 r~R~~Di~~l~~~~l~--~~~~~~~~~~~~~~~~a~~~L~~~~wpgNvr  354 (463)
T TIGR01818       308 RERREDIPRLARHFLA--LAARELDVEPKLLDPEALERLKQLRWPGNVR  354 (463)
T ss_pred             ccchhhHHHHHHHHHH--HHHHHhCCCCCCcCHHHHHHHHhCCCCChHH
Confidence            4445555555553211  1112223333345567788889999999887

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.

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

Probab=98.87  E-value=3.1e-08  Score=89.50  Aligned_cols=141  Identities=17%  Similarity=0.221  Sum_probs=98.9

Q ss_pred             hhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCC
Q psy4285         291 MDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKS  370 (533)
Q Consensus       291 ~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  370 (533)
                      +...+....+++.....|+|++|..|||||++++++..++...   +...++++..+......+-+.++..        .
T Consensus        70 ~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~~---glrLVEV~k~dl~~Lp~l~~~Lr~~--------~  138 (287)
T COG2607          70 EALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYADE---GLRLVEVDKEDLATLPDLVELLRAR--------P  138 (287)
T ss_pred             HHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHHhc---CCeEEEEcHHHHhhHHHHHHHHhcC--------C
Confidence            3445556677776666679999999999999999999998655   4558888877765554444443321        2


Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHH-HHH----hcCCCcEEEEEeCCCCCCCh----------------------hhhccc-
Q psy4285         371 SYKLIILDEADAMTNDAQNALRR-IIE----KFTTNVRFCIICNYLSKIPP----------------------AIQSRC-  422 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~-~le----~~~~~~~~I~~~n~~~~l~~----------------------~l~sR~-  422 (533)
                      ..-|||+|+.+.=..+.....++ +||    ..|.|+.|..|+|+...+++                      ++..|| 
T Consensus       139 ~kFIlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNRRHLl~e~~~dn~~~~~eih~~eaveEKlSlSDRFG  218 (287)
T COG2607         139 EKFILFCDDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSNRRHLLPEDMKDNEGSTGEIHPSEAVEEKLSLSDRFG  218 (287)
T ss_pred             ceEEEEecCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecCCcccccHhhhhCCCcccccChhHHHHHhhchhhhcc
Confidence            45699999987766555555444 443    56889999999987653332                      344577 


Q ss_pred             eeeeecCCCHHHHHHHhhcC
Q psy4285         423 TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       423 ~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..+.|.|.+.++...++.+.
T Consensus       219 LwL~F~~~~Q~~YL~~V~~~  238 (287)
T COG2607         219 LWLSFYPCDQDEYLKIVDHY  238 (287)
T ss_pred             eeecccCCCHHHHHHHHHHH
Confidence            47888888888888777766

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.86  E-value=3.1e-08  Score=85.53  Aligned_cols=107  Identities=27%  Similarity=0.306  Sum_probs=64.8

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc--------------------hhHHHHHHHHHHhccc
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG--------------------IGIVRDQIFQFASTKT  366 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~~~  366 (533)
                      .+++|+||||||||++++.++..+....   ..++.++......                    ....+.... ....  
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~--   76 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPG---GGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALA-LARK--   76 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCC---CCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHH-HHHh--
Confidence            3689999999999999999999885432   2345555443211                    112221111 1111  


Q ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHH--------HHHhcCCCcEEEEEeCC-CCCCChhhhccc
Q psy4285         367 MHKSSYKLIILDEADAMTNDAQNALRR--------IIEKFTTNVRFCIICNY-LSKIPPAIQSRC  422 (533)
Q Consensus       367 ~~~~~~~vliiDE~d~l~~~~~~~Ll~--------~le~~~~~~~~I~~~n~-~~~l~~~l~sR~  422 (533)
                         ..+.++++||++.+..........        .......+..+|+++|. .......+..|+
T Consensus        77 ---~~~~viiiDei~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~  138 (148)
T smart00382       77 ---LKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRRRF  138 (148)
T ss_pred             ---cCCCEEEEECCcccCCHHHHHHHHhhhhhHHHHHHHhcCCCEEEEEeCCCccCchhhhhhcc
Confidence               125899999999998766555433        22334567888888886 333444444454

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.

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

Probab=98.85  E-value=4.6e-09  Score=90.73  Aligned_cols=101  Identities=21%  Similarity=0.278  Sum_probs=68.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDA  387 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~  387 (533)
                      +++|+|+|||||+++|++++......   ...++..++....     .+.+..         .....|+|+|+|.++.+.
T Consensus        23 pvli~GE~GtGK~~~A~~lh~~~~~~---~~~~~~~~~~~~~-----~~~l~~---------a~~gtL~l~~i~~L~~~~   85 (138)
T PF14532_consen   23 PVLITGEPGTGKSLLARALHRYSGRA---NGPFIVIDCASLP-----AELLEQ---------AKGGTLYLKNIDRLSPEA   85 (138)
T ss_dssp             -EEEECCTTSSHHHHHHCCHHTTTTC---CS-CCCCCHHCTC-----HHHHHH---------CTTSEEEEECGCCS-HHH
T ss_pred             cEEEEcCCCCCHHHHHHHHHhhcCcc---CCCeEEechhhCc-----HHHHHH---------cCCCEEEECChHHCCHHH
Confidence            59999999999999999998754221   2233333333221     222221         245699999999999999


Q ss_pred             HHHHHHHHHhc-CCCcEEEEEeCCCC-------CCChhhhccceee
Q psy4285         388 QNALRRIIEKF-TTNVRFCIICNYLS-------KIPPAIQSRCTRF  425 (533)
Q Consensus       388 ~~~Ll~~le~~-~~~~~~I~~~n~~~-------~l~~~l~sR~~~i  425 (533)
                      |..|+..++.. ..++++|+++...-       .+++.|..|+..+
T Consensus        86 Q~~L~~~l~~~~~~~~RlI~ss~~~l~~l~~~~~~~~~L~~~l~~~  131 (138)
T PF14532_consen   86 QRRLLDLLKRQERSNVRLIASSSQDLEELVEEGRFSPDLYYRLSQL  131 (138)
T ss_dssp             HHHHHHHHHHCTTTTSEEEEEECC-CCCHHHHSTHHHHHHHHCSTC
T ss_pred             HHHHHHHHHhcCCCCeEEEEEeCCCHHHHhhccchhHHHHHHhCCC
Confidence            99999999864 57789999986442       4567777777433

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=98.85  E-value=7.9e-09  Score=94.23  Aligned_cols=81  Identities=15%  Similarity=0.139  Sum_probs=64.6

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      +||||++++|||+|+.+..++|||||||+.++|+.+...+..++........   .+...++-|.+...-|....+.+.+
T Consensus       113 LEEPP~~t~fILit~~~~~LLpTIrSRCq~i~~~~p~~~~~~e~~~~~~~p~---~~~~~l~~i~~~~~~d~~~w~~~~~  189 (263)
T PRK06581        113 LEDAPKNSYIFLITSRAASIISTIRSRCFKINVRSSILHAYNELYSQFIQPI---ADNKTLDFINRFTTKDRELWLDFID  189 (263)
T ss_pred             hcCCCCCeEEEEEeCChhhCchhHhhceEEEeCCCCCHHHHHHHHHHhcccc---cccHHHHHHHHHhhhhHHHHHHHHH
Confidence            6999999999999999999999999999999999999988887765433221   2344577777777777777777777


Q ss_pred             HHHH
Q psy4285          81 SAAT   84 (533)
Q Consensus        81 ~~~~   84 (533)
                      .+-.
T Consensus       190 ~~~~  193 (263)
T PRK06581        190 NLLL  193 (263)
T ss_pred             HHHH
Confidence            6643

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

Probab=98.83  E-value=1.3e-08  Score=110.12  Aligned_cols=111  Identities=21%  Similarity=0.327  Sum_probs=84.1

Q ss_pred             CceEEEEEc--CCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHh-------hcCCCCCHHHHHHHHHhcCCCHHHHH
Q psy4285           6 TNVRFCIIC--NYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIE-------QEKVNVTPDGKKAIIDLSDGDMRKVL   76 (533)
Q Consensus         6 ~~~~~il~~--~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~-------~~~~~~~~~~~~~~~~~~~g~~r~a~   76 (533)
                      +.+++|.+|  |+++.++++|+|||++|+|++++.+++..+|++++.       .+++.+++++++.|++.++||+|+++
T Consensus       136 g~IiLI~aTTenp~~~l~~aL~SR~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD~R~ll  215 (725)
T PRK13341        136 GTITLIGATTENPYFEVNKALVSRSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDARSLL  215 (725)
T ss_pred             ceEEEEEecCCChHhhhhhHhhccccceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCCHHHHH
Confidence            344555544  667889999999999999999999999999999987       56788999999999999999999999


Q ss_pred             HHHHHHHHhCC----C--CcchhhHHhhhhhhccccch--hHHHHHhc
Q psy4285          77 NILQSAATAHA----D--EVNEDTIFTLLVSRVEKYRP--STLDELVS  116 (533)
Q Consensus        77 ~~l~~~~~~~~----~--~i~~~~i~~~~~~~~ek~~~--~~l~~lls  116 (533)
                      |.|+.++....    .  .||.+.+.+.++.....|+.  ..+|+.+|
T Consensus       216 n~Le~a~~~~~~~~~~~i~It~~~~~e~l~~~~~~ydk~gd~hyd~Is  263 (725)
T PRK13341        216 NALELAVESTPPDEDGLIDITLAIAEESIQQRAVLYDKEGDAHFDTIS  263 (725)
T ss_pred             HHHHHHHHhcccCCCCceeccHHHHHHHHHHhhhhcccCCCCCHHHHH
Confidence            99999865321    1  16666666655543333332  24555543

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=98.83  E-value=2.4e-08  Score=95.00  Aligned_cols=170  Identities=18%  Similarity=0.192  Sum_probs=117.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHh---cccC-CCCCcEEEEEeCCCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAS---TKTM-HKSSYKLIILDEADAM  383 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~~~vliiDE~d~l  383 (533)
                      .+++.|.+||||-.+|++........   ..+++.+|+...-....-.++++....   .... ..+..+.+++||+..|
T Consensus       229 PLLI~GeTGTGKdLlAkaCH~~S~R~---~~pFlalNCA~lPe~~aEsElFG~apg~~gk~GffE~AngGTVlLDeIgEm  305 (511)
T COG3283         229 PLLITGETGTGKDLLAKACHLASPRH---SKPFLALNCASLPEDAAESELFGHAPGDEGKKGFFEQANGGTVLLDEIGEM  305 (511)
T ss_pred             CeEEecCCCchHHHHHHHHhhcCccc---CCCeeEeecCCCchhHhHHHHhcCCCCCCCccchhhhccCCeEEeehhhhc
Confidence            48999999999999999887654333   578899998764333332333222110   0111 1245789999999999


Q ss_pred             CHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHhhcCHHH
Q psy4285         384 TNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDIS  445 (533)
Q Consensus       384 ~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~  445 (533)
                      ++..|..|++.+...           .-++++|++|...       .++-+.+.-|+.++.+.-|+       |+..+.|
T Consensus       306 Sp~lQaKLLRFL~DGtFRRVGee~Ev~vdVRVIcatq~nL~~lv~~g~fReDLfyRLNVLtl~~Pp-------LRer~~d  378 (511)
T COG3283         306 SPRLQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQVNLVELVQKGKFREDLFYRLNVLTLNLPP-------LRERPQD  378 (511)
T ss_pred             CHHHHHHHHHHhcCCceeecCCcceEEEEEEEEecccccHHHHHhcCchHHHHHHHhheeeecCCc-------cccCccc
Confidence            999999999999642           4568999998543       35667777888888888887       4444445


Q ss_pred             HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHH
Q psy4285         446 FFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLV  489 (533)
Q Consensus       446 ~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~  489 (533)
                      +..+.+.+  +.+.....|.+...+...+...+..+.||++++.
T Consensus       379 i~pL~e~F--v~q~s~elg~p~pkl~~~~~~~L~~y~WpGNVRq  420 (511)
T COG3283         379 IMPLAELF--VQQFSDELGVPRPKLAADLLTVLTRYAWPGNVRQ  420 (511)
T ss_pred             chHHHHHH--HHHHHHHhCCCCCccCHHHHHHHHHcCCCccHHH
Confidence            44444431  2233345577777777888888999999999873

>KOG2227|consensus

Probab=98.82  E-value=6.9e-08  Score=95.36  Aligned_cols=228  Identities=17%  Similarity=0.188  Sum_probs=133.5

Q ss_pred             cccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHH-HHHHHHH---------------
Q psy4285         298 NRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIV-RDQIFQF---------------  361 (533)
Q Consensus       298 ~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~---------------  361 (533)
                      ...+.....+.+.+.|-||||||.+...+...+.+.. .....+.+|+........+ ......+               
T Consensus       167 ~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~-~~~~~v~inc~sl~~~~aiF~kI~~~~~q~~~s~~~~~~~~~  245 (529)
T KOG2227|consen  167 SLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSS-KSPVTVYINCTSLTEASAIFKKIFSSLLQDLVSPGTGMQHLE  245 (529)
T ss_pred             HhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhc-ccceeEEEeeccccchHHHHHHHHHHHHHHhcCCchhHHHHH
Confidence            3344444555699999999999999988877765443 1224467777653332222 1111111               


Q ss_pred             --HhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh---cCCCcEEEEEeCCCC---CCChhhhccc----eeeeecC
Q psy4285         362 --ASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEK---FTTNVRFCIICNYLS---KIPPAIQSRC----TRFRFGP  429 (533)
Q Consensus       362 --~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~---~~~~~~~I~~~n~~~---~l~~~l~sR~----~~i~~~~  429 (533)
                        ...... ....-++++||+|.+....+..|+.+.+.   +...+.+|.+.|..+   ++.|.|..|+    ..+.|+|
T Consensus       246 ~~~~h~~q-~k~~~llVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~P  324 (529)
T KOG2227|consen  246 KFEKHTKQ-SKFMLLLVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFPP  324 (529)
T ss_pred             HHHHHHhc-ccceEEEEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeecC
Confidence              111110 12366999999999988777777777664   234445555557554   6778888866    5899999


Q ss_pred             CCHHHHHHHhhcC------------------------HHHHHHHHHHHHHHHHHHHh-------c----CCCHHHH----
Q psy4285         430 LDSSLIMSRLDYD------------------------DISFFNIIIWYIKIQEIKIE-------K----GLALTDI----  470 (533)
Q Consensus       430 ~~~~~~~~~l~~~------------------------~~~~~~ll~~~~~l~~l~~~-------~----~~~~~di----  470 (533)
                      |+.+++.+++...                        .+|++..++......++...       .    |-++..-    
T Consensus       325 YTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~SGDlRkaLdv~R~aiEI~E~e~r~~~~~~l~~~~~p~~~~~v~  404 (529)
T KOG2227|consen  325 YTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAPSGDLRKALDVCRRAIEIAEIEKRKILDDPLSPGTSPEKKKKVG  404 (529)
T ss_pred             CCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCcccccccc
Confidence            9999999999887                        46666666652222221111       0    1111111    


Q ss_pred             HHHHHHHHHhcCCChhHHHHH-----HHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhHhc
Q psy4285         471 LTEISLLVHRLEIPESMLVDL-----VLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLE  527 (533)
Q Consensus       471 ~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~~~~~  527 (533)
                      +.++..++.+..-.+..+...     -+.+-..-..+.+|.+..+.++.+.-+-..+|....
T Consensus       405 ~~~va~viSk~~~s~~~~s~~slplqqkiilctl~~l~r~~kkd~s~~eL~e~Y~k~C~~~~  466 (529)
T KOG2227|consen  405 VEHVAAVISKVDGSPSARSRESLPLQQKIILCTLVLLIRGNKKDVSIAELYEAYLKACQKRE  466 (529)
T ss_pred             hHHHHHHhhhhccChhhhhhhhcCcccchhHHHHHHHHhcccccccHHHHHHHHHHHHHhcc
Confidence            444444444443333322221     123334455666777777788887777777776544

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=98.82  E-value=7.5e-08  Score=102.82  Aligned_cols=54  Identities=19%  Similarity=0.236  Sum_probs=45.2

Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhc---------------------CCCcEEEEEeCCC--CCCChhhhccce
Q psy4285         370 SSYKLIILDEADAMTNDAQNALRRIIEKF---------------------TTNVRFCIICNYL--SKIPPAIQSRCT  423 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~~Ll~~le~~---------------------~~~~~~I~~~n~~--~~l~~~l~sR~~  423 (533)
                      +..++|+|||++.|+...|..|++.|++.                     +.++++|+++|..  ..++|++++||.
T Consensus       216 AngGtL~Ldei~~L~~~~q~~Ll~~L~~~~i~~~g~~e~~~~~~~~~~~ip~dvrvIa~~~~~~l~~l~~~l~~rf~  292 (608)
T TIGR00764       216 AHKGVLYIDEIKTMPLEVQQYLLTALQDKKFPITGQSENSSGAMVRTEPVPCDFILVASGNLDDLEGMHPALRSRIR  292 (608)
T ss_pred             CCCCEEEEEChHhCCHHHHHHHHHHHHhCcEEecCccccccccccCCCCCccceEEEEECCHHHHhhcCHHHHHHhc
Confidence            44689999999999999999999999742                     2357889999864  579999999997

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

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

Probab=98.80  E-value=1.3e-07  Score=91.83  Aligned_cols=131  Identities=19%  Similarity=0.260  Sum_probs=74.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC-----------------Cch--hHHHHHHHHHHhcccCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD-----------------RGI--GIVRDQIFQFASTKTMH  368 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~-----------------~~~--~~~~~~~~~~~~~~~~~  368 (533)
                      .++++||+|+||||+++.+++.+....   .....+..+..                 .+.  ......+..+..... .
T Consensus        45 ~~~l~G~~G~GKTtl~~~l~~~l~~~~---~~~~~~~~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~~~-~  120 (269)
T TIGR03015        45 FILITGEVGAGKTTLIRNLLKRLDQER---VVAAKLVNTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLIEQF-A  120 (269)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCCC---eEEeeeeCCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHH-h
Confidence            489999999999999999998874321   11111111000                 000  001111111111100 1


Q ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHHHHhc---CCCcEEEEEeCCC------CCCChhhhccc-eeeeecCCCHHHHHHH
Q psy4285         369 KSSYKLIILDEADAMTNDAQNALRRIIEKF---TTNVRFCIICNYL------SKIPPAIQSRC-TRFRFGPLDSSLIMSR  438 (533)
Q Consensus       369 ~~~~~vliiDE~d~l~~~~~~~Ll~~le~~---~~~~~~I~~~n~~------~~l~~~l~sR~-~~i~~~~~~~~~~~~~  438 (533)
                      .+...+++|||++.++.+..+.|..+.+..   ...+.+++++...      ..-...+.+|+ ..+.+.+++.+++.+.
T Consensus       121 ~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~r~~~~~~l~~l~~~e~~~~  200 (269)
T TIGR03015       121 AGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPEFRETLQSPQLQQLRQRIIASCHLGPLDREETREY  200 (269)
T ss_pred             CCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHHHHHHHcCchhHHHHhheeeeeeCCCCCHHHHHHH
Confidence            235679999999999988777665544321   2234556666432      11133577775 5788999999988887


Q ss_pred             hhcC
Q psy4285         439 LDYD  442 (533)
Q Consensus       439 l~~~  442 (533)
                      +.+.
T Consensus       201 l~~~  204 (269)
T TIGR03015       201 IEHR  204 (269)
T ss_pred             HHHH
Confidence            7654

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.

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=98.80  E-value=3e-07  Score=90.51  Aligned_cols=157  Identities=13%  Similarity=0.045  Sum_probs=95.3

Q ss_pred             HhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHcccccc---------Ccc-----------------
Q psy4285         286 LLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQF---------NAM-----------------  339 (533)
Q Consensus       286 ~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~---------~~~-----------------  339 (533)
                      ...|++.....|.--.-......+|+.|+.||||||++|+++..|-.-...         ..+                 
T Consensus        18 aivGqd~lk~aL~l~av~P~iggvLI~G~kGtaKSt~~Rala~LLp~~~~V~gc~f~cdP~~P~~~c~~c~~k~~e~~~~   97 (423)
T COG1239          18 AIVGQDPLKLALGLNAVDPQIGGALIAGEKGTAKSTLARALADLLPEIEVVIGCPFNCDPDDPEEMCDECRAKGDELEWL   97 (423)
T ss_pred             hhcCchHHHHHHhhhhcccccceeEEecCCCccHHHHHHHHHHhCCccceecCCCCCCCCCChhhhhHHHHhhccccccc
Confidence            345666655544333344455569999999999999999999876211000         000                 


Q ss_pred             ------eEEecCCCCCchh------HHHHHHHHH---HhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc------
Q psy4285         340 ------VLELNASDDRGIG------IVRDQIFQF---ASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF------  398 (533)
Q Consensus       340 ------~~~~~~~~~~~~~------~~~~~~~~~---~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~------  398 (533)
                            +-.++.+.+...+      .+...++.-   .+......++.+|++|||+..++...++.|+..+++.      
T Consensus        98 ~~~~r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~AnRGIlYvDEvnlL~d~lvd~LLd~aaeG~n~ver  177 (423)
T COG1239          98 PREKRKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARANRGILYVDEVNLLDDHLVDALLDVAAEGVNDVER  177 (423)
T ss_pred             cccceecceecCCCccchhhhccccCHHHHHhcCccccCCcchhhccCCEEEEeccccccHHHHHHHHHHHHhCCceeee
Confidence                  0011111111111      111111110   0001111356889999999999999999999999863      


Q ss_pred             -------CCCcEEEEEeCCCC-CCChhhhccc-eeeeecC-CCHHHHHHHhhcC
Q psy4285         399 -------TTNVRFCIICNYLS-KIPPAIQSRC-TRFRFGP-LDSSLIMSRLDYD  442 (533)
Q Consensus       399 -------~~~~~~I~~~n~~~-~l~~~l~sR~-~~i~~~~-~~~~~~~~~l~~~  442 (533)
                             +.++.+|.|+|... .|-|.|++|| ..+...+ .+.++..+++.+.
T Consensus       178 eGisi~hpa~fvligTmNPEeGeLrpqLlDRfg~~v~~~~~~~~~~rv~Ii~r~  231 (423)
T COG1239         178 EGISIRHPARFLLIGTMNPEEGELRPQLLDRFGLEVDTHYPLDLEERVEIIRRR  231 (423)
T ss_pred             CceeeccCccEEEEeecCccccccchhhHhhhcceeeccCCCCHHHHHHHHHHH
Confidence                   56677888888765 7999999999 3555544 4555556666555

>TIGR00368 Mg chelatase-related protein

Probab=98.76  E-value=3.3e-08  Score=102.63  Aligned_cols=147  Identities=17%  Similarity=0.134  Sum_probs=90.8

Q ss_pred             hhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC-C---------Cchh----
Q psy4285         287 LNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD-D---------RGIG----  352 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~-~---------~~~~----  352 (533)
                      ..|+....+.+...+..+  .+++|.||||||||++++.++..+-...  +.-.++..... .         ....    
T Consensus       194 v~Gq~~~~~al~~aa~~g--~~vlliG~pGsGKTtlar~l~~llp~~~--~~~~le~~~i~s~~g~~~~~~~~~~~Pf~~  269 (499)
T TIGR00368       194 IKGQQHAKRALEIAAAGG--HNLLLFGPPGSGKTMLASRLQGILPPLT--NEEAIETARIWSLVGKLIDRKQIKQRPFRS  269 (499)
T ss_pred             hcCcHHHHhhhhhhccCC--CEEEEEecCCCCHHHHHHHHhcccCCCC--CcEEEeccccccchhhhccccccccCCccc
Confidence            356666666666655544  3699999999999999999987542111  11111111100 0         0000    


Q ss_pred             -----HHHHHHHHH--HhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCC-
Q psy4285         353 -----IVRDQIFQF--ASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF-------------TTNVRFCIICNYL-  411 (533)
Q Consensus       353 -----~~~~~~~~~--~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~-  411 (533)
                           .....++.-  .+......+...+|||||++.++...++.|++.||..             +.++++|+++|.- 
T Consensus       270 p~~s~s~~~~~ggg~~~~pG~i~lA~~GvLfLDEi~e~~~~~~~~L~~~LE~~~v~i~r~g~~~~~pa~frlIaa~Npcp  349 (499)
T TIGR00368       270 PHHSASKPALVGGGPIPLPGEISLAHNGVLFLDELPEFKRSVLDALREPIEDGSISISRASAKIFYPARFQLVAAMNPCP  349 (499)
T ss_pred             cccccchhhhhCCccccchhhhhccCCCeEecCChhhCCHHHHHHHHHHHHcCcEEEEecCcceeccCCeEEEEecCCcc
Confidence                 000000000  0000001245689999999999999999999999853             3578899999852 


Q ss_pred             ----------------------CCCChhhhccce-eeeecCCCHHHHHH
Q psy4285         412 ----------------------SKIPPAIQSRCT-RFRFGPLDSSLIMS  437 (533)
Q Consensus       412 ----------------------~~l~~~l~sR~~-~i~~~~~~~~~~~~  437 (533)
                                            .++..+|++||+ .+.+.+++.+++.+
T Consensus       350 cg~~~~~~~~c~c~~~~~~~y~~~is~pllDR~dl~~~~~~~~~~~l~~  398 (499)
T TIGR00368       350 CGHYGGKNTHCRCSPQQISRYWNKLSGPFLDRIDLSVEVPLLPPEKLLS  398 (499)
T ss_pred             cCcCCCCcccccCCHHHHHHHhhhccHhHHhhCCEEEEEcCCCHHHHhc
Confidence                                  158899999996 67778787766543

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=98.73  E-value=1.5e-07  Score=100.45  Aligned_cols=147  Identities=14%  Similarity=0.181  Sum_probs=102.7

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCC------CCCc--hhHHH
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNAS------DDRG--IGIVR  355 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~------~~~~--~~~~~  355 (533)
                      .|.++-+.+..+.+.+....|-++.|+||+|||.++..+|..+.....    .+..++.++.+      ..++  ...++
T Consensus       173 IGRd~EI~r~iqIL~RR~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sLD~g~LvAGakyRGeFEeRlk  252 (786)
T COG0542         173 IGRDEEIRRTIQILSRRTKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEERLK  252 (786)
T ss_pred             cChHHHHHHHHHHHhccCCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEecHHHHhccccccCcHHHHHH
Confidence            344444455555666666677899999999999999999999865432    13344555432      2222  33444


Q ss_pred             HHHHHHHhcccCCCCCcEEEEEeCCCCCC---------HHHHHHHHHHHHhcCCCcEEEEEeCC-----CCCCChhhhcc
Q psy4285         356 DQIFQFASTKTMHKSSYKLIILDEADAMT---------NDAQNALRRIIEKFTTNVRFCIICNY-----LSKIPPAIQSR  421 (533)
Q Consensus       356 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~---------~~~~~~Ll~~le~~~~~~~~I~~~n~-----~~~l~~~l~sR  421 (533)
                      ..++....      .++-||||||++.+-         .++.|.|...|..  ...++|.+|..     .-.-|++|-+|
T Consensus       253 ~vl~ev~~------~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaLAR--GeL~~IGATT~~EYRk~iEKD~AL~RR  324 (786)
T COG0542         253 AVLKEVEK------SKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALAR--GELRCIGATTLDEYRKYIEKDAALERR  324 (786)
T ss_pred             HHHHHHhc------CCCeEEEEechhhhcCCCcccccccchhhhhHHHHhc--CCeEEEEeccHHHHHHHhhhchHHHhc
Confidence            44444332      236799999999882         3466777777764  44788888853     33579999999


Q ss_pred             ceeeeecCCCHHHHHHHhhcC
Q psy4285         422 CTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       422 ~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      |+.+....|+.++...+|+-+
T Consensus       325 FQ~V~V~EPs~e~ti~ILrGl  345 (786)
T COG0542         325 FQKVLVDEPSVEDTIAILRGL  345 (786)
T ss_pred             CceeeCCCCCHHHHHHHHHHH
Confidence            999999999999999999988

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

Probab=98.71  E-value=2.5e-07  Score=86.46  Aligned_cols=121  Identities=24%  Similarity=0.278  Sum_probs=85.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQ  388 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~  388 (533)
                      -.++||+|||||++++.+|+.+      +..++.+++++......+.+.+...++.       +.-+++||+++++.+..
T Consensus        35 ~~~~GpagtGKtetik~La~~l------G~~~~vfnc~~~~~~~~l~ril~G~~~~-------GaW~cfdefnrl~~~vL  101 (231)
T PF12774_consen   35 GALSGPAGTGKTETIKDLARAL------GRFVVVFNCSEQMDYQSLSRILKGLAQS-------GAWLCFDEFNRLSEEVL  101 (231)
T ss_dssp             EEEESSTTSSHHHHHHHHHHCT------T--EEEEETTSSS-HHHHHHHHHHHHHH-------T-EEEEETCCCSSHHHH
T ss_pred             CCCcCCCCCCchhHHHHHHHHh------CCeEEEecccccccHHHHHHHHHHHhhc-------CchhhhhhhhhhhHHHH
Confidence            4689999999999999999998      8899999999988888888888777654       34899999999998776


Q ss_pred             HHHHHHHHh-------c-------------CCCcEEEEEeCC----CCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         389 NALRRIIEK-------F-------------TTNVRFCIICNY----LSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       389 ~~Ll~~le~-------~-------------~~~~~~I~~~n~----~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..+-+.+..       .             .+++.+.+|.|.    ...+++.+++-|..+.+..|+-..+.+++...
T Consensus       102 S~i~~~i~~i~~al~~~~~~~~~~g~~i~l~~~~~iFiT~np~y~gr~~LP~nLk~lFRpvam~~PD~~~I~ei~L~s  179 (231)
T PF12774_consen  102 SVISQQIQSIQDALRAKQKSFTLEGQEIKLNPNCGIFITMNPGYAGRSELPENLKALFRPVAMMVPDLSLIAEILLLS  179 (231)
T ss_dssp             HHHHHHHHHHHHHHHCTSSEEEETTCEEE--TT-EEEEEE-B-CCCC--S-HHHCTTEEEEE--S--HHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHhhcccccccccCCCEEEEccceeEEEeeccccCCcccCCHhHHHHhheeEEeCCCHHHHHHHHHHH
Confidence            655444321       1             245667777773    34789999999999999999977777666544

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=98.70  E-value=3.3e-08  Score=106.91  Aligned_cols=129  Identities=14%  Similarity=0.137  Sum_probs=79.0

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccc-cCcceEEecCCCCCchhHHHHH-HHHHHhcc-cCCCCCcEEEEEeCCCCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQ-FNAMVLELNASDDRGIGIVRDQ-IFQFASTK-TMHKSSYKLIILDEADAM  383 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~-~~~~~~~~vliiDE~d~l  383 (533)
                      .|+||.|+||||||.+|+++++....... .+..+..+.....   ...... .+.+.... ....+..++++|||++.|
T Consensus       493 ihVLLvGDPGTGKSqLAr~Ih~lspR~~ytsG~~~s~vgLTa~---~~~~d~~tG~~~le~GaLvlAdgGtL~IDEidkm  569 (915)
T PTZ00111        493 INVLLCGDPGTAKSQLLHYTHLLSPRSIYTSGKSSSSVGLTAS---IKFNESDNGRAMIQPGAVVLANGGVCCIDELDKC  569 (915)
T ss_pred             ceEEEeCCCCccHHHHHHHHHHhCCccccCCCCCCccccccch---hhhcccccCcccccCCcEEEcCCCeEEecchhhC
Confidence            37999999999999999999985421110 0112222111110   000000 00110000 111245689999999999


Q ss_pred             CHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC-------------CCChhhhccceee--eecCCCHHHH
Q psy4285         384 TNDAQNALRRIIEKF-------------TTNVRFCIICNYLS-------------KIPPAIQSRCTRF--RFGPLDSSLI  435 (533)
Q Consensus       384 ~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~-------------~l~~~l~sR~~~i--~~~~~~~~~~  435 (533)
                      +...+.+|+++||+.             +..+++|+++|+..             .++++|+|||+.+  ..+.++.+.-
T Consensus       570 s~~~Q~aLlEaMEqqtIsI~KaGi~~tL~ar~rVIAAaNP~~gryd~~~s~~eni~Lp~~LLSRFDLIf~l~D~~d~~~D  649 (915)
T PTZ00111        570 HNESRLSLYEVMEQQTVTIAKAGIVATLKAETAILASCNPINSRYNKNKAVIENINISPSLFTRFDLIYLVLDHIDQDTD  649 (915)
T ss_pred             CHHHHHHHHHHHhCCEEEEecCCcceecCCCeEEEEEcCCcccccCcccCcccccCCChHHhhhhcEEEEecCCCChHHH
Confidence            999999999999864             25788999998742             5889999999644  3345554443


Q ss_pred             HHH
Q psy4285         436 MSR  438 (533)
Q Consensus       436 ~~~  438 (533)
                      ..+
T Consensus       650 ~~l  652 (915)
T PTZ00111        650 QLI  652 (915)
T ss_pred             HHH
Confidence            333

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

Probab=98.69  E-value=2.4e-07  Score=87.70  Aligned_cols=72  Identities=21%  Similarity=0.272  Sum_probs=55.6

Q ss_pred             CcEEEEEeCCCCCCH------------HHHHHHHHHHHhc----------CCCcEEEEEe----CCCCCCChhhhccc-e
Q psy4285         371 SYKLIILDEADAMTN------------DAQNALRRIIEKF----------TTNVRFCIIC----NYLSKIPPAIQSRC-T  423 (533)
Q Consensus       371 ~~~vliiDE~d~l~~------------~~~~~Ll~~le~~----------~~~~~~I~~~----n~~~~l~~~l~sR~-~  423 (533)
                      ..+++||||+|++..            ..|.-|+-++|..          ..++.||.++    ..|+.|.|.|..|| -
T Consensus       250 ~~GIvFIDEIDKIa~~~~~g~~dvSREGVQRDlLPlvEGstV~TKyG~VkTdHILFIasGAFh~sKPSDLiPELQGRfPI  329 (444)
T COG1220         250 QNGIVFIDEIDKIAKRGGSGGPDVSREGVQRDLLPLVEGSTVSTKYGPVKTDHILFIASGAFHVAKPSDLIPELQGRFPI  329 (444)
T ss_pred             hcCeEEEehhhHHHhcCCCCCCCcchhhhcccccccccCceeeccccccccceEEEEecCceecCChhhcChhhcCCCce
Confidence            357999999999843            2356688887731          2445566665    56789999999999 5


Q ss_pred             eeeecCCCHHHHHHHhhcC
Q psy4285         424 RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 ~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.+.+++.++...+|..-
T Consensus       330 RVEL~~Lt~~Df~rILtep  348 (444)
T COG1220         330 RVELDALTKEDFERILTEP  348 (444)
T ss_pred             EEEcccCCHHHHHHHHcCc
Confidence            8999999999999888776

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=98.68  E-value=2.8e-07  Score=96.27  Aligned_cols=175  Identities=15%  Similarity=0.149  Sum_probs=108.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHh----------cccCCCCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAS----------TKTMHKSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~vlii  377 (533)
                      .++++|.+||||+++|+++.......   ..+++.+++.... ...+...+.....          ......+.+++|||
T Consensus       164 ~vli~ge~g~gk~~~a~~ih~~s~~~---~~~~i~~~c~~~~-~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l  239 (441)
T PRK10365        164 TVLIHGDSGTGKELVARAIHASSARS---EKPLVTLNCAALN-ESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFL  239 (441)
T ss_pred             eEEEEecCCCCHHHHHHHHHHcCCCC---CCCeeeeeCCCCC-HHHHHHHhcCCCCCCcCCCCcCCCCceeECCCCEEEE
Confidence            48999999999999999998765322   4678888887643 2333332211000          00011245789999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhcC-----------CCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         378 DEADAMTNDAQNALRRIIEKFT-----------TNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~~-----------~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ||++.|+...|..|++.+++..           .++++|++|+..       ..+.+.+..|+..+.+.-|+       |
T Consensus       240 dei~~l~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~~~~~~~~~~~~~~l~~~l~~~~i~~pp-------L  312 (441)
T PRK10365        240 DEIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVAIEVPS-------L  312 (441)
T ss_pred             eccccCCHHHHHHHHHHHccCcEEeCCCCceeeeceEEEEeCCCCHHHHHHcCCchHHHHHHhccceecCCC-------h
Confidence            9999999999999999998632           256788888654       24566677777767776666       3


Q ss_pred             hcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHH
Q psy4285         440 DYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMS  496 (533)
Q Consensus       440 ~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~  496 (533)
                      +..++|+..+++.+-  .++....+.....+.......+..+.||++++ ++.+.+.
T Consensus       313 reR~~Di~~l~~~~l--~~~~~~~~~~~~~~~~~a~~~L~~~~wpgN~r-eL~~~~~  366 (441)
T PRK10365        313 RQRREDIPLLAGHFL--QRFAERNRKAVKGFTPQAMDLLIHYDWPGNIR-ELENAVE  366 (441)
T ss_pred             hhcchhHHHHHHHHH--HHHHHHhCCCCCCcCHHHHHHHHhCCCCCHHH-HHHHHHH
Confidence            333344444444321  11111222222234456777788899999987 3333333

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

Probab=98.66  E-value=7.5e-07  Score=84.86  Aligned_cols=156  Identities=16%  Similarity=0.233  Sum_probs=89.7

Q ss_pred             ccCCCCHHHHHHHHHHHhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc---cCcceEEecCC
Q psy4285         270 SVGYPTKTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ---FNAMVLELNAS  346 (533)
Q Consensus       270 ~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~---~~~~~~~~~~~  346 (533)
                      +++|+.-..+-+.+..+.           ..-...+.|+++++|++|.|||++++.+.+.--....   ...+++.+..+
T Consensus        36 WIgY~~A~~~L~~L~~Ll-----------~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P  104 (302)
T PF05621_consen   36 WIGYPRAKEALDRLEELL-----------EYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMP  104 (302)
T ss_pred             eecCHHHHHHHHHHHHHH-----------hCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecC
Confidence            456665555555444433           2334567889999999999999999999976422111   12345555544


Q ss_pred             CCCchhHHHHH-HHHHHhcc---------------cCCCCCcEEEEEeCCCCCC---HHHHHHHHHHHHhc--CCCcEEE
Q psy4285         347 DDRGIGIVRDQ-IFQFASTK---------------TMHKSSYKLIILDEADAMT---NDAQNALRRIIEKF--TTNVRFC  405 (533)
Q Consensus       347 ~~~~~~~~~~~-~~~~~~~~---------------~~~~~~~~vliiDE~d~l~---~~~~~~Ll~~le~~--~~~~~~I  405 (533)
                      ..-+...+... +..+....               ....-+.++|||||++.+.   ...|..++.++...  .-.+.+|
T Consensus       105 ~~p~~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV  184 (302)
T PF05621_consen  105 PEPDERRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIV  184 (302)
T ss_pred             CCCChHHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeE
Confidence            32222221111 11110000               0001356899999999862   34455555555432  2235566


Q ss_pred             EEeCC----CCCCChhhhccceeeeecCCCHHHHH
Q psy4285         406 IICNY----LSKIPPAIQSRCTRFRFGPLDSSLIM  436 (533)
Q Consensus       406 ~~~n~----~~~l~~~l~sR~~~i~~~~~~~~~~~  436 (533)
                      +++..    .-.-|+.+.+||..+.++++..++-.
T Consensus       185 ~vGt~~A~~al~~D~QLa~RF~~~~Lp~W~~d~ef  219 (302)
T PF05621_consen  185 GVGTREAYRALRTDPQLASRFEPFELPRWELDEEF  219 (302)
T ss_pred             EeccHHHHHHhccCHHHHhccCCccCCCCCCCcHH
Confidence            66632    23568999999999988887755433

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

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=98.65  E-value=4.7e-07  Score=96.39  Aligned_cols=46  Identities=24%  Similarity=0.313  Sum_probs=38.3

Q ss_pred             HhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         286 LLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       286 ~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      -..+|++....+...+..+.  +++|+||||||||++++++++.+.+.
T Consensus        32 ~vigq~~a~~~L~~~~~~~~--~~l~~G~~G~GKttla~~l~~~l~~~   77 (637)
T PRK13765         32 QVIGQEHAVEVIKKAAKQRR--HVMMIGSPGTGKSMLAKAMAELLPKE   77 (637)
T ss_pred             HcCChHHHHHHHHHHHHhCC--eEEEECCCCCcHHHHHHHHHHHcChH
Confidence            35678888888888777664  89999999999999999999887544

>KOG0745|consensus

Probab=98.65  E-value=9.8e-08  Score=93.14  Aligned_cols=85  Identities=27%  Similarity=0.390  Sum_probs=60.0

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchh----HHHHHHHHHHhcccC--CCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIG----IVRDQIFQFASTKTM--HKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~--~~~~~~vliiDE~  380 (533)
                      .|+|+.||+|+|||.+|+.+|+.+      +.++.-.++.+.....    .+...+..+......  ..+...|+||||+
T Consensus       227 SNvLllGPtGsGKTllaqTLAr~l------dVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGIVflDEv  300 (564)
T KOG0745|consen  227 SNVLLLGPTGSGKTLLAQTLARVL------DVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEV  300 (564)
T ss_pred             ccEEEECCCCCchhHHHHHHHHHh------CCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCeEEEehh
Confidence            579999999999999999999998      7777777776644322    222223332222111  1245689999999


Q ss_pred             CCCCH--------------HHHHHHHHHHHh
Q psy4285         381 DAMTN--------------DAQNALRRIIEK  397 (533)
Q Consensus       381 d~l~~--------------~~~~~Ll~~le~  397 (533)
                      |++..              ..|.+||+++|.
T Consensus       301 DKi~~~~~~i~~~RDVsGEGVQQaLLKllEG  331 (564)
T KOG0745|consen  301 DKITKKAESIHTSRDVSGEGVQQALLKLLEG  331 (564)
T ss_pred             hhhcccCccccccccccchhHHHHHHHHhcc
Confidence            99962              468999999983

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.63  E-value=2.5e-07  Score=87.42  Aligned_cols=94  Identities=16%  Similarity=0.217  Sum_probs=79.0

Q ss_pred             CceEEEEEcC-CCCc---Cchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHH
Q psy4285           6 TNVRFCIICN-YLSK---ITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI   78 (533)
Q Consensus         6 ~~~~~il~~~-~~~~---i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~   78 (533)
                      +++.+|++++ ++..   ++|.|+|||   .++.+++|++++..++|++.+...++.++++.++.|++.+.||+|.+++.
T Consensus       130 g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~~~~~~~~~~~l~~~a~~~~~~l~~~v~~~L~~~~~~d~r~l~~~  209 (235)
T PRK08084        130 GRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEKLQALQLRARLRGFELPEDVGRFLLKRLDREMRTLFMT  209 (235)
T ss_pred             CCCeEEEeCCCChHHcCcccHHHHHHHhCCceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhhcCCHHHHHHH
Confidence            4556777775 4444   689999999   99999999999999999997888899999999999999999999999999


Q ss_pred             HHHHHHh---CCCCcchhhHHhhh
Q psy4285          79 LQSAATA---HADEVNEDTIFTLL   99 (533)
Q Consensus        79 l~~~~~~---~~~~i~~~~i~~~~   99 (533)
                      |+.+...   ...+||.+.+++++
T Consensus       210 l~~l~~~~l~~~~~it~~~~k~~l  233 (235)
T PRK08084        210 LDQLDRASITAQRKLTIPFVKEIL  233 (235)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHH
Confidence            9997422   34568888876654

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.63  E-value=1.2e-07  Score=92.54  Aligned_cols=95  Identities=21%  Similarity=0.250  Sum_probs=60.1

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC-------chhHHHHHHHHHHhcccCCCCCcEEEEEeC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR-------GIGIVRDQIFQFASTKTMHKSSYKLIILDE  379 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE  379 (533)
                      .+++|+||||||||+++.++|+++...   +..+..+..++..       ......+.+..+        ...++|||||
T Consensus       157 ~gl~L~G~~G~GKThLa~Aia~~l~~~---g~~v~~~~~~~l~~~lk~~~~~~~~~~~l~~l--------~~~dlLiIDD  225 (306)
T PRK08939        157 KGLYLYGDFGVGKSYLLAAIANELAKK---GVSSTLLHFPEFIRELKNSISDGSVKEKIDAV--------KEAPVLMLDD  225 (306)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc---CCCEEEEEHHHHHHHHHHHHhcCcHHHHHHHh--------cCCCEEEEec
Confidence            469999999999999999999998643   3333333322210       000111112211        3568999999


Q ss_pred             CCC--CCHHHHHHHHH-HHHhc-CCCcEEEEEeCCCC
Q psy4285         380 ADA--MTNDAQNALRR-IIEKF-TTNVRFCIICNYLS  412 (533)
Q Consensus       380 ~d~--l~~~~~~~Ll~-~le~~-~~~~~~I~~~n~~~  412 (533)
                      ++.  ++.+....++. +++.. ......|+|||.+.
T Consensus       226 iG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl~~  262 (306)
T PRK08939        226 IGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNFDF  262 (306)
T ss_pred             CCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCCCH
Confidence            975  45666655554 55644 46788999999764

>PRK09862 putative ATP-dependent protease; Provisional

Probab=98.61  E-value=1.2e-07  Score=97.97  Aligned_cols=144  Identities=17%  Similarity=0.157  Sum_probs=87.0

Q ss_pred             hchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEec------CCC----------CCch-
Q psy4285         289 ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELN------ASD----------DRGI-  351 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~------~~~----------~~~~-  351 (533)
                      |+..+.+.+.-.+..+  .++++.||||+|||++++.++..+-...  +.-.++..      +..          .+.. 
T Consensus       195 Gq~~~~~al~laa~~G--~~llliG~~GsGKTtLak~L~gllpp~~--g~e~le~~~i~s~~g~~~~~~~~~~rPfr~ph  270 (506)
T PRK09862        195 GQEQGKRGLEITAAGG--HNLLLIGPPGTGKTMLASRINGLLPDLS--NEEALESAAILSLVNAESVQKQWRQRPFRSPH  270 (506)
T ss_pred             CcHHHHhhhheeccCC--cEEEEECCCCCcHHHHHHHHhccCCCCC--CcEEEecchhhhhhccccccCCcCCCCccCCC
Confidence            4444555554444433  3699999999999999999987652111  11111111      000          0000 


Q ss_pred             --hHHHHHHHHH--HhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC--
Q psy4285         352 --GIVRDQIFQF--ASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF-------------TTNVRFCIICNYLS--  412 (533)
Q Consensus       352 --~~~~~~~~~~--~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~--  412 (533)
                        -....+++.-  ........+...+||+||++.+....++.|++.||+.             +.++++|.++|...  
T Consensus       271 ~~~s~~~l~GGg~~~~pG~l~~A~gGvLfLDEi~e~~~~~~~~L~~~LE~g~v~I~r~g~~~~~pa~f~lIAa~NP~pcG  350 (506)
T PRK09862        271 HSASLTAMVGGGAIPGPGEISLAHNGVLFLDELPEFERRTLDALREPIESGQIHLSRTRAKITYPARFQLVAAMNPSPTG  350 (506)
T ss_pred             ccchHHHHhCCCceehhhHhhhccCCEEecCCchhCCHHHHHHHHHHHHcCcEEEecCCcceeccCCEEEEEeecCccce
Confidence              0011111100  0000001245789999999999999999999999752             45688999998652  


Q ss_pred             -------------------CCChhhhccce-eeeecCCCHHHHH
Q psy4285         413 -------------------KIPPAIQSRCT-RFRFGPLDSSLIM  436 (533)
Q Consensus       413 -------------------~l~~~l~sR~~-~i~~~~~~~~~~~  436 (533)
                                         ++..++++||+ .+.+.+++.+++.
T Consensus       351 ~~~~~~c~c~~~~~~~Y~~~ls~plLDRfdL~v~v~~~~~~~l~  394 (506)
T PRK09862        351 HYQGNHNRCTPEQTLRYLNRLSGPFLDRFDLSLEIPLPPPGILS  394 (506)
T ss_pred             ecCCCCCCcCHHHHHHHHhhCCHhHHhhccEEEEeCCCCHHHHh
Confidence                               47889999996 5777777766443

>KOG2680|consensus

Probab=98.60  E-value=1.8e-06  Score=80.45  Aligned_cols=70  Identities=17%  Similarity=0.154  Sum_probs=59.6

Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC------------CCCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         372 YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY------------LSKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       372 ~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~------------~~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ++||||||+++++-+....|.+.+|.-- ...+|++||+            +..++-.+++|...+.-.|++.+++.++|
T Consensus       289 pGVLFIDEvHMLDIEcFsFlNrAlE~d~-~PiiimaTNrgit~iRGTn~~SphGiP~D~lDR~lII~t~py~~~d~~~IL  367 (454)
T KOG2680|consen  289 PGVLFIDEVHMLDIECFSFLNRALENDM-APIIIMATNRGITRIRGTNYRSPHGIPIDLLDRMLIISTQPYTEEDIKKIL  367 (454)
T ss_pred             cceEEEeeehhhhhHHHHHHHHHhhhcc-CcEEEEEcCCceEEeecCCCCCCCCCcHHHhhhhheeecccCcHHHHHHHH
Confidence            7899999999999999999999998633 2456666653            44688899999999999999999999999


Q ss_pred             hcC
Q psy4285         440 DYD  442 (533)
Q Consensus       440 ~~~  442 (533)
                      ...
T Consensus       368 ~iR  370 (454)
T KOG2680|consen  368 RIR  370 (454)
T ss_pred             Hhh
Confidence            887

>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []

Probab=98.59  E-value=8.1e-07  Score=70.21  Aligned_cols=86  Identities=31%  Similarity=0.464  Sum_probs=65.0

Q ss_pred             CCHHHHHHHhhcC-HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCCh
Q psy4285         430 LDSSLIMSRLDYD-DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSE  508 (533)
Q Consensus       430 ~~~~~~~~~l~~~-~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~  508 (533)
                      |+++.+.+++... ..   .+-+.+..+.++... |+++.+++..+++.+...++++..+.+++..++++++||..|+++
T Consensus         3 p~~~~i~~i~~~~~~~---~~~~~~~~~~~l~~~-G~s~~~Il~~l~~~l~~~~~~~~~k~~i~~~la~~e~rl~~G~~e   78 (89)
T PF08542_consen    3 PPPEVIEEILESCLNG---DFKEARKKLYELLVE-GYSASDILKQLHEVLVESDIPDSQKAEILKILAEIEYRLSDGASE   78 (89)
T ss_dssp             --HHHHHHHHHHHHHT---CHHHHHHHHHHHHHT-T--HHHHHHHHHHHHHTSTSSHHHHHHHHHHHHHHHHHHHTTC-H
T ss_pred             CCHHHHHHHHHHHHhC---CHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHhHHHHCCCCH
Confidence            4455555555554 11   122225566677555 999999999999999998999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q psy4285         509 KIQLSALIAAF  519 (533)
Q Consensus       509 ~~~l~~~~~~~  519 (533)
                      .+|+++|++++
T Consensus        79 ~lQl~alva~~   89 (89)
T PF08542_consen   79 ILQLEALVAAF   89 (89)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHhhC
Confidence            99999999985

PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=98.58  E-value=1.6e-07  Score=99.82  Aligned_cols=100  Identities=18%  Similarity=0.231  Sum_probs=68.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHH------------------------HHh
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQ------------------------FAS  363 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------------~~~  363 (533)
                      ..+++|+|||||||+++.+...+..........+.+.+++++....+.+.+..                        +..
T Consensus       169 ~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~~~~~~~~~~~~a~TiHrlLg  248 (615)
T PRK10875        169 ISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEEASTLHRLLG  248 (615)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhccccchhhhhcCCCchHHHHHHhC
Confidence            48999999999999999998876432111223456666666655555543321                        111


Q ss_pred             cccC---------CCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         364 TKTM---------HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       364 ~~~~---------~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ..+.         .+...+++||||++|++......|++.+   ++++++|++++.
T Consensus       249 ~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd~~lm~~ll~al---~~~~rlIlvGD~  301 (615)
T PRK10875        249 AQPGSQRLRYHAGNPLHLDVLVVDEASMVDLPMMARLIDAL---PPHARVIFLGDR  301 (615)
T ss_pred             cCCCccchhhccccCCCCCeEEEChHhcccHHHHHHHHHhc---ccCCEEEEecch
Confidence            1100         1123589999999999999999999988   678999999964

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

Probab=98.58  E-value=1.3e-07  Score=80.83  Aligned_cols=101  Identities=25%  Similarity=0.434  Sum_probs=58.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcccccc--CcceEEecCCCCCchh-HHHHHHHHHHhcccC---------------CC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQF--NAMVLELNASDDRGIG-IVRDQIFQFASTKTM---------------HK  369 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~--~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~---------------~~  369 (533)
                      +++++||||+|||++++.+++.+......  ...++.++.+...... ........+......               ..
T Consensus         6 ~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l~~   85 (131)
T PF13401_consen    6 ILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDALDR   85 (131)
T ss_dssp             -EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHHHH
T ss_pred             ccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHHHh
Confidence            58999999999999999999987431100  2233344332222211 111111111111000               01


Q ss_pred             CCcEEEEEeCCCCC-CHHHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAM-TNDAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l-~~~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ....+|+|||+|.+ .....+.|..+++  ..++.+|++++.
T Consensus        86 ~~~~~lviDe~~~l~~~~~l~~l~~l~~--~~~~~vvl~G~~  125 (131)
T PF13401_consen   86 RRVVLLVIDEADHLFSDEFLEFLRSLLN--ESNIKVVLVGTP  125 (131)
T ss_dssp             CTEEEEEEETTHHHHTHHHHHHHHHHTC--SCBEEEEEEESS
T ss_pred             cCCeEEEEeChHhcCCHHHHHHHHHHHh--CCCCeEEEEECh
Confidence            12369999999999 8777777877776  567889998875

>smart00763 AAA_PrkA PrkA AAA domain

Probab=98.57  E-value=7.5e-07  Score=87.45  Aligned_cols=62  Identities=10%  Similarity=-0.068  Sum_probs=49.5

Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCC
Q psy4285         370 SSYKLIILDEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLD  431 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~  431 (533)
                      ++.+++-|+|+.+...+.++.|+.++++.           +-+..||+++|..       .+..+++++||..+.++.+.
T Consensus       235 aNrGi~~f~Ei~K~~~~~l~~LL~~~qE~~v~~~~~~~~~~~d~liia~sNe~e~~~~~~~k~~eaf~dR~~~i~vpY~l  314 (361)
T smart00763      235 ANRGILEFVEMFKADIKFLHPLLTATQEGNIKGTGGFAMIPIDGLIIAHSNESEWQRFKSNKKNEALLDRIIKVKVPYCL  314 (361)
T ss_pred             ccCceEEEeehhcCCHHHHHHHhhhhhcceEecCCcccccccceEEEEeCCHHHHhhhhccccchhhhhceEEEeCCCcC
Confidence            45689999999999999999999999863           1234567777766       36789999999988887654

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

>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=98.56  E-value=4.2e-07  Score=87.42  Aligned_cols=138  Identities=17%  Similarity=0.225  Sum_probs=80.1

Q ss_pred             cccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhccc-----CCCCCcEE
Q psy4285         300 FIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT-----MHKSSYKL  374 (533)
Q Consensus       300 ~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~v  374 (533)
                      ++..++  +++|+||+|||||++++.+.+.+...   ......++.+.......+.+.+........     ...++..|
T Consensus        29 l~~~~~--pvLl~G~~GtGKT~li~~~l~~l~~~---~~~~~~~~~s~~Tts~~~q~~ie~~l~k~~~~~~gP~~~k~lv  103 (272)
T PF12775_consen   29 LLSNGR--PVLLVGPSGTGKTSLIQNFLSSLDSD---KYLVITINFSAQTTSNQLQKIIESKLEKRRGRVYGPPGGKKLV  103 (272)
T ss_dssp             HHHCTE--EEEEESSTTSSHHHHHHHHHHCSTTC---CEEEEEEES-TTHHHHHHHHCCCTTECECTTEEEEEESSSEEE
T ss_pred             HHHcCC--cEEEECCCCCchhHHHHhhhccCCcc---ccceeEeeccCCCCHHHHHHHHhhcEEcCCCCCCCCCCCcEEE
Confidence            344443  69999999999999999887654221   222334444443333333333221111100     01245679


Q ss_pred             EEEeCCCCCCHH------HHHHHHHHHHhc------------CCCcEEEEEeCCCC---CCChhhhccceeeeecCCCHH
Q psy4285         375 IILDEADAMTND------AQNALRRIIEKF------------TTNVRFCIICNYLS---KIPPAIQSRCTRFRFGPLDSS  433 (533)
Q Consensus       375 liiDE~d~l~~~------~~~~Ll~~le~~------------~~~~~~I~~~n~~~---~l~~~l~sR~~~i~~~~~~~~  433 (533)
                      ++|||+.+-..+      ..+.|.++++..            -.++.+|.+++...   .+++.+.|.|..+.+.+|+.+
T Consensus       104 ~fiDDlN~p~~d~ygtq~~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~~Gr~~is~R~~r~f~i~~~~~p~~~  183 (272)
T PF12775_consen  104 LFIDDLNMPQPDKYGTQPPIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPTGGRNPISPRFLRHFNILNIPYPSDE  183 (272)
T ss_dssp             EEEETTT-S---TTS--HHHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESSTTT--SHHHHHHTTEEEEE----TCC
T ss_pred             EEecccCCCCCCCCCCcCHHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCCCCCCCCChHHhhheEEEEecCCChH
Confidence            999999876543      345566667631            14577888887543   477888888899999999999


Q ss_pred             HHHHHhhcC
Q psy4285         434 LIMSRLDYD  442 (533)
Q Consensus       434 ~~~~~l~~~  442 (533)
                      .+..+...+
T Consensus       184 sl~~If~~i  192 (272)
T PF12775_consen  184 SLNTIFSSI  192 (272)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888777665

>KOG2170|consensus

Probab=98.55  E-value=2.7e-07  Score=86.29  Aligned_cols=134  Identities=17%  Similarity=0.194  Sum_probs=86.1

Q ss_pred             HHHHHHHHhhhc----hhhhhhhcccccccCCCc---eeEeCCCCCChHHHHHHHHHHHccccccCcce----EEecCCC
Q psy4285         279 ITNILRWLLNES----MDLCYKINRFIDENELPH---LLFYGPPGTGKTTTILACARKLYTKAQFNAMV----LELNASD  347 (533)
Q Consensus       279 ~~~~l~~~~~~~----~~~~~~l~~~~~~~~~~~---~ll~GppGtGKT~la~~la~~l~~~~~~~~~~----~~~~~~~  347 (533)
                      +...+...+.||    +.++..++.++.+..+..   +-|+|+|||||..+++.||+.++..+.....+    -....+.
T Consensus        76 Le~dL~~~lfGQHla~~~Vv~alk~~~~n~~p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~  155 (344)
T KOG2170|consen   76 LEKDLARALFGQHLAKQLVVNALKSHWANPNPRKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPH  155 (344)
T ss_pred             HHHHHHHHhhchHHHHHHHHHHHHHHhcCCCCCCCeEEEecCCCCCchhHHHHHHHHHHHhccccchhHHHhhhhccCCC
Confidence            333444444555    445566677776665322   56999999999999999999987654222211    1223344


Q ss_pred             CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcC-------CCcEEEEEeCCCCC
Q psy4285         348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT-------TNVRFCIICNYLSK  413 (533)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~-------~~~~~I~~~n~~~~  413 (533)
                      ....+..+..++........ .-...++|+||+|+|.+...+.|--.++.++       .+..||+.+|.-..
T Consensus       156 ~~~ie~Yk~eL~~~v~~~v~-~C~rslFIFDE~DKmp~gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg~  227 (344)
T KOG2170|consen  156 ASKIEDYKEELKNRVRGTVQ-ACQRSLFIFDEVDKLPPGLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGGS  227 (344)
T ss_pred             hHHHHHHHHHHHHHHHHHHH-hcCCceEEechhhhcCHhHHHHHhhhhccccccccccccceEEEEEcCCcch
Confidence            44555555544443222111 1346799999999999999999998888542       45778999987653

>KOG0736|consensus

Probab=98.54  E-value=5.1e-07  Score=94.17  Aligned_cols=127  Identities=21%  Similarity=0.342  Sum_probs=87.5

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc--hhHHHHHHH-HHHhcccCCCCCcEEEEEeCCCCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG--IGIVRDQIF-QFASTKTMHKSSYKLIILDEADAM  383 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~-~~~~~~~~~~~~~~vliiDE~d~l  383 (533)
                      +.+|++|+||||||++++++|.++      +..++++++.+...  .+.....+. .|.....   ..+.||++-.+|-+
T Consensus       432 ~~vLLhG~~g~GK~t~V~~vas~l------g~h~~evdc~el~~~s~~~~etkl~~~f~~a~~---~~pavifl~~~dvl  502 (953)
T KOG0736|consen  432 PSVLLHGPPGSGKTTVVRAVASEL------GLHLLEVDCYELVAESASHTETKLQAIFSRARR---CSPAVLFLRNLDVL  502 (953)
T ss_pred             eEEEEeCCCCCChHHHHHHHHHHh------CCceEeccHHHHhhcccchhHHHHHHHHHHHhh---cCceEEEEecccee
Confidence            348999999999999999999998      77777777654321  111111111 2222221   35678888888776


Q ss_pred             CH--------HHHHHHHHHHH--h---cCCCcEEEEEeCCCCCCChhhhccc-eeeeecCCCHHHHHHHhhcC
Q psy4285         384 TN--------DAQNALRRIIE--K---FTTNVRFCIICNYLSKIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       384 ~~--------~~~~~Ll~~le--~---~~~~~~~I~~~n~~~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..        ..+..+...+.  .   ....+.+|.+++..+.+++.+++-| ..+.++.++++|..++|+..
T Consensus       503 ~id~dgged~rl~~~i~~~ls~e~~~~~~~~~ivv~t~~s~~~lp~~i~~~f~~ei~~~~lse~qRl~iLq~y  575 (953)
T KOG0736|consen  503 GIDQDGGEDARLLKVIRHLLSNEDFKFSCPPVIVVATTSSIEDLPADIQSLFLHEIEVPALSEEQRLEILQWY  575 (953)
T ss_pred             eecCCCchhHHHHHHHHHHHhcccccCCCCceEEEEeccccccCCHHHHHhhhhhccCCCCCHHHHHHHHHHH
Confidence            42        12233333333  1   2345778888999999999999977 68999999999999998877

>PF05729 NACHT: NACHT domain

Probab=98.52  E-value=8.4e-07  Score=79.01  Aligned_cols=131  Identities=21%  Similarity=0.307  Sum_probs=76.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccC---cceEEecCCCCCch---hHHHHHHHHHHhcc----------cCCCCCc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFN---AMVLELNASDDRGI---GIVRDQIFQFASTK----------TMHKSSY  372 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~---~~~~~~~~~~~~~~---~~~~~~~~~~~~~~----------~~~~~~~  372 (533)
                      ++++|+||+|||++++.++..+.......   ..++.....+....   ..+.+.+.......          .......
T Consensus         3 l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~   82 (166)
T PF05729_consen    3 LWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEELLQELLEKNKR   82 (166)
T ss_pred             EEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHHHHHHHHHcCCc
Confidence            78999999999999999998886544222   12222322221111   12222221110000          0002456


Q ss_pred             EEEEEeCCCCCCHHHH--------HHHHHHHHh-cCCCcEEEEEeCCCCCCChhhhccc---eeeeecCCCHHHHHHHhh
Q psy4285         373 KLIILDEADAMTNDAQ--------NALRRIIEK-FTTNVRFCIICNYLSKIPPAIQSRC---TRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       373 ~vliiDE~d~l~~~~~--------~~Ll~~le~-~~~~~~~I~~~n~~~~l~~~l~sR~---~~i~~~~~~~~~~~~~l~  440 (533)
                      -+++||.+|.+.....        ..|..++.. .+.+++++++|.....  +.+.+++   ..+.+.+++++++...+.
T Consensus        83 ~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~--~~~~~~~~~~~~~~l~~~~~~~~~~~~~  160 (166)
T PF05729_consen   83 VLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAF--PDLRRRLKQAQILELEPFSEEDIKQYLR  160 (166)
T ss_pred             eEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChH--HHHHHhcCCCcEEEECCCCHHHHHHHHH
Confidence            7899999999876332        234455554 3567889888865432  1133333   578899999999888876


Q ss_pred             c
Q psy4285         441 Y  441 (533)
Q Consensus       441 ~  441 (533)
                      +
T Consensus       161 ~  161 (166)
T PF05729_consen  161 K  161 (166)
T ss_pred             H
Confidence            5

>PRK08727 hypothetical protein; Validated

Probab=98.52  E-value=7.2e-07  Score=84.19  Aligned_cols=94  Identities=13%  Similarity=0.210  Sum_probs=77.7

Q ss_pred             ceEEEEEcC-CCCc---Cchhhhcc---ceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Q psy4285           7 NVRFCIICN-YLSK---ITPAIQSR---CTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNIL   79 (533)
Q Consensus         7 ~~~~il~~~-~~~~---i~~~i~SR---c~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l   79 (533)
                      +..+|+++| ++..   ++|.|+||   |+++.|++|+.+++.++|++.+...++.++++++..|+..++||+|.++++|
T Consensus       126 ~~~vI~ts~~~p~~l~~~~~dL~SRl~~~~~~~l~~~~~e~~~~iL~~~a~~~~l~l~~e~~~~La~~~~rd~r~~l~~L  205 (233)
T PRK08727        126 GITLLYTARQMPDGLALVLPDLRSRLAQCIRIGLPVLDDVARAAVLRERAQRRGLALDEAAIDWLLTHGERELAGLVALL  205 (233)
T ss_pred             CCeEEEECCCChhhhhhhhHHHHHHHhcCceEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHH
Confidence            344677675 4443   47999999   9999999999999999999989888999999999999999999999999999


Q ss_pred             HHHHH---hCCCCcchhhHHhhhh
Q psy4285          80 QSAAT---AHADEVNEDTIFTLLV  100 (533)
Q Consensus        80 ~~~~~---~~~~~i~~~~i~~~~~  100 (533)
                      +.+..   .....||.+.++++++
T Consensus       206 ~~l~~~~~~~~~~it~~~~~~~l~  229 (233)
T PRK08727        206 DRLDRESLAAKRRVTVPFLRRVLE  229 (233)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHh
Confidence            98752   2334588877766543

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

Probab=98.50  E-value=1.9e-07  Score=88.31  Aligned_cols=145  Identities=18%  Similarity=0.268  Sum_probs=80.4

Q ss_pred             chhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch------------------
Q psy4285         290 SMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI------------------  351 (533)
Q Consensus       290 ~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~------------------  351 (533)
                      .+...+.+.+++..+...+++++||+|+|||++++.+.+.+....   ...+.+........                  
T Consensus         4 R~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~~~~~~~---~~~~y~~~~~~~~~~~~~~~~~~~~~~~~l~~   80 (234)
T PF01637_consen    4 REKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFINELKEKG---YKVVYIDFLEESNESSLRSFIEETSLADELSE   80 (234)
T ss_dssp             -HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHHHCT--E---ECCCHHCCTTBSHHHHHHHHHHHHHHHCHCHH
T ss_pred             HHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHHHhhhcC---CcEEEEecccchhhhHHHHHHHHHHHHHHHHH
Confidence            344455666677766556799999999999999999999873221   11111111111111                  


Q ss_pred             -----------------------hHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCC------HHHHHHHHHHHHh--cCC
Q psy4285         352 -----------------------GIVRDQIFQFASTKTMHKSSYKLIILDEADAMT------NDAQNALRRIIEK--FTT  400 (533)
Q Consensus       352 -----------------------~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~------~~~~~~Ll~~le~--~~~  400 (533)
                                             ..+...+..+...     ....+|+|||++.+.      ......|.+.++.  ...
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~-----~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  155 (234)
T PF01637_consen   81 ALGISIPSITLEKISKDLSEDSFSALERLLEKLKKK-----GKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQ  155 (234)
T ss_dssp             HHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHC-----HCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----T
T ss_pred             HHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhc-----CCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccccC
Confidence                                   1111111111111     223899999999998      4555667777765  245


Q ss_pred             CcEEEEEeCCC------CCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         401 NVRFCIICNYL------SKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       401 ~~~~I~~~n~~------~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +..+|+++...      ..-..++..|+..+.+.+++.++..+.+...
T Consensus       156 ~~~~v~~~S~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~e~~~~~~~~  203 (234)
T PF01637_consen  156 NVSIVITGSSDSLMEEFLDDKSPLFGRFSHIELKPLSKEEAREFLKEL  203 (234)
T ss_dssp             TEEEEEEESSHHHHHHTT-TTSTTTT---EEEE----HHHHHHHHHHH
T ss_pred             CceEEEECCchHHHHHhhcccCccccccceEEEeeCCHHHHHHHHHHH
Confidence            56666666432      1234567788888999999999999888874

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

>KOG0480|consensus

Probab=98.49  E-value=1.9e-06  Score=88.10  Aligned_cols=125  Identities=18%  Similarity=0.201  Sum_probs=78.1

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecC--CCCC--chhHHHHH-HHHHHhcccC-CCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNA--SDDR--GIGIVRDQ-IFQFASTKTM-HKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~--~~~~--~~~~~~~~-~~~~~~~~~~-~~~~~~vliiDE~  380 (533)
                      .|+++.|.||||||-+.++.+..+      ... ++.++  ++..  ....++.- -+.|.-.... .-+..+|..|||+
T Consensus       379 inv~iVGDPgt~KSQfLk~v~~fs------PR~-vYtsGkaSSaAGLTaaVvkD~esgdf~iEAGALmLADnGICCIDEF  451 (764)
T KOG0480|consen  379 INVCIVGDPGTGKSQFLKAVCAFS------PRS-VYTSGKASSAAGLTAAVVKDEESGDFTIEAGALMLADNGICCIDEF  451 (764)
T ss_pred             ceEEEeCCCCccHHHHHHHHhccC------Ccc-eEecCcccccccceEEEEecCCCCceeeecCcEEEccCceEEechh
Confidence            579999999999999999988754      111 22222  1111  11111110 1112111111 1246789999999


Q ss_pred             CCCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC-------------CCChhhhccceeeee--cCCCH
Q psy4285         381 DAMTNDAQNALRRIIEKF-------------TTNVRFCIICNYLS-------------KIPPAIQSRCTRFRF--GPLDS  432 (533)
Q Consensus       381 d~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~-------------~l~~~l~sR~~~i~~--~~~~~  432 (533)
                      |+|+...+.+++++||+.             +..+.++.++|+..             ++.++|+|||+.+++  +.+++
T Consensus       452 DKMd~~dqvAihEAMEQQtISIaKAGv~aTLnARtSIlAAANPv~GhYdR~ktl~eNi~msApimSRFDL~FiLlD~~nE  531 (764)
T KOG0480|consen  452 DKMDVKDQVAIHEAMEQQTISIAKAGVVATLNARTSILAAANPVGGHYDRKKTLRENINMSAPIMSRFDLFFILLDDCNE  531 (764)
T ss_pred             cccChHhHHHHHHHHHhheehheecceEEeecchhhhhhhcCCcCCccccccchhhhcCCCchhhhhhcEEEEEecCCch
Confidence            999999999999999964             45566777777542             589999999975444  44554


Q ss_pred             HHHHHH
Q psy4285         433 SLIMSR  438 (533)
Q Consensus       433 ~~~~~~  438 (533)
                      ..-..+
T Consensus       532 ~~D~~i  537 (764)
T KOG0480|consen  532 VVDYAI  537 (764)
T ss_pred             HHHHHH
Confidence            433333

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

Probab=98.49  E-value=3.2e-07  Score=84.11  Aligned_cols=99  Identities=23%  Similarity=0.325  Sum_probs=61.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH-------HHHHhcccCC-------CCCcE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI-------FQFASTKTMH-------KSSYK  373 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~-------~~~~~  373 (533)
                      ..++.||||||||++++.+.+.+...   +..++.+ +++......+++..       ..+.......       ....+
T Consensus        20 ~~~l~G~aGtGKT~~l~~~~~~~~~~---g~~v~~~-apT~~Aa~~L~~~~~~~a~Ti~~~l~~~~~~~~~~~~~~~~~~   95 (196)
T PF13604_consen   20 VSVLQGPAGTGKTTLLKALAEALEAA---GKRVIGL-APTNKAAKELREKTGIEAQTIHSFLYRIPNGDDEGRPELPKKD   95 (196)
T ss_dssp             EEEEEESTTSTHHHHHHHHHHHHHHT---T--EEEE-ESSHHHHHHHHHHHTS-EEEHHHHTTEECCEECCSSCC-TSTS
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHhC---CCeEEEE-CCcHHHHHHHHHhhCcchhhHHHHHhcCCcccccccccCCccc
Confidence            37889999999999999998877443   3344443 33334444444332       1121111110       13468


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         374 LIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       374 vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      ++||||+++++......|++.+..  .+.++|++++...
T Consensus        96 vliVDEasmv~~~~~~~ll~~~~~--~~~klilvGD~~Q  132 (196)
T PF13604_consen   96 VLIVDEASMVDSRQLARLLRLAKK--SGAKLILVGDPNQ  132 (196)
T ss_dssp             EEEESSGGG-BHHHHHHHHHHS-T---T-EEEEEE-TTS
T ss_pred             EEEEecccccCHHHHHHHHHHHHh--cCCEEEEECCcch
Confidence            999999999999988888888864  4689999997543

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=98.49  E-value=6e-07  Score=94.84  Aligned_cols=94  Identities=22%  Similarity=0.299  Sum_probs=77.9

Q ss_pred             CCCceEEEEEc-CCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285           4 FTTNVRFCIIC-NYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSA   82 (533)
Q Consensus         4 ~~~~~~~il~~-~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~   82 (533)
                      .|.++++|.+| +++..+.|+++|||..++|++++.+++..++++.+++.++.+++++++.+..++. |.|.+.|+++.+
T Consensus       230 ~~~d~rlI~ATt~~p~~L~paLrsR~~~I~f~pL~~eei~~Il~~~a~k~~i~is~~al~~I~~y~~-n~Rel~nll~~A  308 (531)
T TIGR02902       230 LPADFRLIGATTRNPEEIPPALRSRCVEIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYAS-NGREAVNIVQLA  308 (531)
T ss_pred             cccceEEEEEecCCcccCChHHhhhhheeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhh-hHHHHHHHHHHH
Confidence            35567777765 5788999999999999999999999999999999999999999999998888775 999999999998


Q ss_pred             HHhCC----CCcchhhHHhh
Q psy4285          83 ATAHA----DEVNEDTIFTL   98 (533)
Q Consensus        83 ~~~~~----~~i~~~~i~~~   98 (533)
                      +....    ..|+.+++.+.
T Consensus       309 a~~A~~~~~~~It~~dI~~v  328 (531)
T TIGR02902       309 AGIALGEGRKRILAEDIEWV  328 (531)
T ss_pred             HHHHhhCCCcEEcHHHHHHH
Confidence            65321    23666666544

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.

>KOG0478|consensus

Probab=98.48  E-value=1.4e-06  Score=89.68  Aligned_cols=128  Identities=21%  Similarity=0.301  Sum_probs=79.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecC--CCCCc--hhHHHH-HHHHHHh-cccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNA--SDDRG--IGIVRD-QIFQFAS-TKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~--~~~~~--~~~~~~-~~~~~~~-~~~~~~~~~~vliiDE~d  381 (533)
                      |+||+|.||||||.+.+.+++.+-..       .+.++  +..-+  ....+. ..+++.. .....-+..++..|||+|
T Consensus       464 NILL~GDPGtsKSqlLqyv~~l~pRg-------~yTSGkGsSavGLTayVtrd~dtkqlVLesGALVLSD~GiCCIDEFD  536 (804)
T KOG0478|consen  464 NILLVGDPGTSKSQLLQYCHRLLPRG-------VYTSGKGSSAVGLTAYVTKDPDTRQLVLESGALVLSDNGICCIDEFD  536 (804)
T ss_pred             eEEEecCCCcCHHHHHHHHHHhCCcc-------eeecCCccchhcceeeEEecCccceeeeecCcEEEcCCceEEchhhh
Confidence            69999999999999999999875221       11111  00000  000000 0001100 111112467899999999


Q ss_pred             CCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC-------------CCChhhhcccee--eeecCCCHH
Q psy4285         382 AMTNDAQNALRRIIEKF-------------TTNVRFCIICNYLS-------------KIPPAIQSRCTR--FRFGPLDSS  433 (533)
Q Consensus       382 ~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~-------------~l~~~l~sR~~~--i~~~~~~~~  433 (533)
                      +|+.+.++.|++.||..             +..+.++.++|...             .++|+|+|||+.  +.+.++++.
T Consensus       537 KM~dStrSvLhEvMEQQTvSIAKAGII~sLNAR~SVLAaANP~~skynp~k~i~eNI~LpptLLSRFDLIylllD~~DE~  616 (804)
T KOG0478|consen  537 KMSDSTRSVLHEVMEQQTLSIAKAGIIASLNARCSVLAAANPIRSKYNPNKSIIENINLPPTLLSRFDLIFLLLDKPDER  616 (804)
T ss_pred             hhhHHHHHHHHHHHHHhhhhHhhcceeeeccccceeeeeeccccccCCCCCchhhccCCChhhhhhhcEEEEEecCcchh
Confidence            99999999999999863             46677888888432             489999999974  445666655


Q ss_pred             HHHHHhhcC
Q psy4285         434 LIMSRLDYD  442 (533)
Q Consensus       434 ~~~~~l~~~  442 (533)
                      .=+.+-.|+
T Consensus       617 ~Dr~La~Hi  625 (804)
T KOG0478|consen  617 SDRRLADHI  625 (804)
T ss_pred             HHHHHHHHH
Confidence            444444444

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=98.48  E-value=4.2e-07  Score=96.54  Aligned_cols=100  Identities=19%  Similarity=0.282  Sum_probs=67.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcccccc-CcceEEecCCCCCchhHHHHHHHHH------------------------H
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQF-NAMVLELNASDDRGIGIVRDQIFQF------------------------A  362 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~------------------------~  362 (533)
                      ..+++|+|||||||++..+...+...... +..-+.+.+++++....+.+.+...                        .
T Consensus       162 ~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~~~~~l~~~~~~~~~~~~~a~TiHrlL  241 (586)
T TIGR01447       162 FSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKAVKNLAAAEALIAALPSEAVTIHRLL  241 (586)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHhhhcccccchhhhhccccccchhhhhh
Confidence            48999999999999999998776432210 1123556666666555555443321                        0


Q ss_pred             hccc---------CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         363 STKT---------MHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       363 ~~~~---------~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...+         ......++|||||++|++......|++.+   +.++++|++++.
T Consensus       242 g~~~~~~~~~~~~~~~l~~dvlIiDEaSMvd~~l~~~ll~al---~~~~rlIlvGD~  295 (586)
T TIGR01447       242 GIKPDTKRFRHHERNPLPLDVLVVDEASMVDLPLMAKLLKAL---PPNTKLILLGDK  295 (586)
T ss_pred             cccCCcchhhhcccCCCcccEEEEcccccCCHHHHHHHHHhc---CCCCEEEEECCh
Confidence            0000         01234689999999999999888888887   578999999964

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=98.45  E-value=5.3e-06  Score=82.66  Aligned_cols=97  Identities=14%  Similarity=0.220  Sum_probs=57.1

Q ss_pred             ccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEe
Q psy4285         299 RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILD  378 (533)
Q Consensus       299 ~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiD  378 (533)
                      .+++.+.  |+++.||||||||+++.+++....+..  + .  ..     .....+.+.    .......-..+++|+||
T Consensus       204 ~fve~~~--Nli~lGp~GTGKThla~~l~~~~a~~s--G-~--f~-----T~a~Lf~~L----~~~~lg~v~~~DlLI~D  267 (449)
T TIGR02688       204 PLVEPNY--NLIELGPKGTGKSYIYNNLSPYVILIS--G-G--TI-----TVAKLFYNI----STRQIGLVGRWDVVAFD  267 (449)
T ss_pred             HHHhcCC--cEEEECCCCCCHHHHHHHHhHHHHHHc--C-C--cC-----cHHHHHHHH----HHHHHhhhccCCEEEEE
Confidence            3455444  899999999999999999987732222  1 0  00     111111111    11110012467899999


Q ss_pred             CCCCCCHH----HHHHHHHHHHhc---------CCCcEEEEEeCCC
Q psy4285         379 EADAMTND----AQNALRRIIEKF---------TTNVRFCIICNYL  411 (533)
Q Consensus       379 E~d~l~~~----~~~~Ll~~le~~---------~~~~~~I~~~n~~  411 (533)
                      |+..+...    ..+.|...|+..         ..+..+++.+|-.
T Consensus       268 Evgylp~~~~~~~v~imK~yMesg~fsRG~~~~~a~as~vfvGNi~  313 (449)
T TIGR02688       268 EVATLKFAKPKELIGILKNYMESGSFTRGDETKSSDASFVFLGNVP  313 (449)
T ss_pred             cCCCCcCCchHHHHHHHHHHHHhCceeccceeeeeeeEEEEEcccC
Confidence            99997543    345555556532         3467788888754

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

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

Probab=98.44  E-value=1e-07  Score=95.16  Aligned_cols=146  Identities=15%  Similarity=0.144  Sum_probs=81.4

Q ss_pred             hhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----------------cC-cceEEecCCCC-
Q psy4285         287 LNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----------------FN-AMVLELNASDD-  348 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----------------~~-~~~~~~~~~~~-  348 (533)
                      ..||+...+.+.-....+.  |++++||||||||.+|+.+...+-.-..                .. ..++...+-.. 
T Consensus       181 V~GQ~~AKrAleiAAAGgH--nLl~~GpPGtGKTmla~Rl~~lLPpls~~E~lE~s~I~s~~g~~~~~~~~~~~rPFr~P  258 (490)
T COG0606         181 VKGQEQAKRALEIAAAGGH--NLLLVGPPGTGKTMLASRLPGLLPPLSIPEALEVSAIHSLAGDLHEGCPLKIHRPFRAP  258 (490)
T ss_pred             hcCcHHHHHHHHHHHhcCC--cEEEecCCCCchHHhhhhhcccCCCCChHHHHHHHHHhhhcccccccCccceeCCccCC
Confidence            4678888877776666553  7999999999999999988755410000                00 00010000000 


Q ss_pred             CchhHHHHHHHHHHhcc--cCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh-------------cCCCcEEEEEeCCC--
Q psy4285         349 RGIGIVRDQIFQFASTK--TMHKSSYKLIILDEADAMTNDAQNALRRIIEK-------------FTTNVRFCIICNYL--  411 (533)
Q Consensus       349 ~~~~~~~~~~~~~~~~~--~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~-------------~~~~~~~I~~~n~~--  411 (533)
                      ........+++......  ....+..+|||+||+-.......++|.+-||.             ++.+..+|+++|..  
T Consensus       259 HHsaS~~aLvGGG~~p~PGeIsLAH~GVLFLDElpef~~~iLe~LR~PLE~g~i~IsRa~~~v~ypa~Fqlv~AmNpcpc  338 (490)
T COG0606         259 HHSASLAALVGGGGVPRPGEISLAHNGVLFLDELPEFKRSILEALREPLENGKIIISRAGSKVTYPARFQLVAAMNPCPC  338 (490)
T ss_pred             CccchHHHHhCCCCCCCCCceeeecCCEEEeeccchhhHHHHHHHhCccccCcEEEEEcCCeeEEeeeeEEhhhcCCCCc
Confidence            00011111221111000  00124678999999999888888888888874             34455566666632  


Q ss_pred             ---------------------CCCChhhhccce-eeeecCCCHHH
Q psy4285         412 ---------------------SKIPPAIQSRCT-RFRFGPLDSSL  434 (533)
Q Consensus       412 ---------------------~~l~~~l~sR~~-~i~~~~~~~~~  434 (533)
                                           .++..++++|++ .+....++..+
T Consensus       339 G~~~~~~~~C~c~~~~~~~Y~~klSgp~lDRiDl~vev~~~~~~e  383 (490)
T COG0606         339 GNLGAPLRRCPCSPRQIKRYLNKLSGPFLDRIDLMVEVPRLSAGE  383 (490)
T ss_pred             cCCCCCCCCcCCCHHHHHHHHHHhhHHHHhhhhheecccCCCHHH
Confidence                                 235667777774 45555554333

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.44  E-value=1.6e-06  Score=85.75  Aligned_cols=95  Identities=14%  Similarity=0.122  Sum_probs=81.3

Q ss_pred             ceEEEEEcCCCCcCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHh
Q psy4285           7 NVRFCIICNYLSKITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATA   85 (533)
Q Consensus         7 ~~~~il~~~~~~~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~~~~   85 (533)
                      .+.+|.+||.+..+.++++||| ..++|.+++.+++.+.+++.+...++.++++++..|++.++|++|.++++++.+...
T Consensus       129 ~~~li~~t~~~~~l~~~l~sR~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~  208 (305)
T TIGR00635       129 PFTLVGATTRAGMLTSPLRDRFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDF  208 (305)
T ss_pred             CeEEEEecCCccccCHHHHhhcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHH
Confidence            3778999999999999999999 568999999999999999999988999999999999999999999999999886432


Q ss_pred             ----CCCCcchhhHHhhhhh
Q psy4285          86 ----HADEVNEDTIFTLLVS  101 (533)
Q Consensus        86 ----~~~~i~~~~i~~~~~~  101 (533)
                          ....|+.+.+...+..
T Consensus       209 a~~~~~~~it~~~v~~~l~~  228 (305)
T TIGR00635       209 AQVRGQKIINRDIALKALEM  228 (305)
T ss_pred             HHHcCCCCcCHHHHHHHHHH
Confidence                2345787777654443

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.

>TIGR01128 holA DNA polymerase III, delta subunit

Probab=98.43  E-value=2e-06  Score=84.99  Aligned_cols=102  Identities=10%  Similarity=0.144  Sum_probs=86.7

Q ss_pred             CCCCCCceEEEEEcCCCCc------CchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSK------ITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRK   74 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~------i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~   74 (533)
                      +++||+++.+|++++...+      .+.++ ++|.++.|++++..++..|+...+.++|+.+++++++.++..++||++.
T Consensus        71 l~~~~~~~~~i~~~~~~~~~~~~~k~~~~~-~~~~~i~~~~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~  149 (302)
T TIGR01128        71 LANPPPDTLLLIEAPKLDKRKKLTKWLKAL-KNAQIVECKTPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLA  149 (302)
T ss_pred             HhcCCCCEEEEEecCCCCHhHHHHHHHHHh-cCeeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHH
Confidence            4678899999999875543      44555 6999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhC-CCCcchhhHHhhhhhhc
Q psy4285          75 VLNILQSAATAH-ADEVNEDTIFTLLVSRV  103 (533)
Q Consensus        75 a~~~l~~~~~~~-~~~i~~~~i~~~~~~~~  103 (533)
                      +.|.++.++... +..||.+.|.+++....
T Consensus       150 l~~el~KL~~~~~~~~It~e~I~~~~~~~~  179 (302)
T TIGR01128       150 IAQELEKLALYAPDGKITLEDVEEAVSDSA  179 (302)
T ss_pred             HHHHHHHHHhhCCCCCCCHHHHHHHHhhhh
Confidence            999999988753 34699998877665443

subunit around DNA forming a DNA sliding clamp.

>PRK10536 hypothetical protein; Provisional

Probab=98.42  E-value=3.4e-07  Score=85.53  Aligned_cols=38  Identities=21%  Similarity=0.250  Sum_probs=31.6

Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         371 SYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      ..+++|+||+++++......++.-+   ..++++|++++..
T Consensus       176 ~~~~vIvDEaqn~~~~~~k~~ltR~---g~~sk~v~~GD~~  213 (262)
T PRK10536        176 ENAVVILDEAQNVTAAQMKMFLTRL---GENVTVIVNGDIT  213 (262)
T ss_pred             cCCEEEEechhcCCHHHHHHHHhhc---CCCCEEEEeCChh
Confidence            4689999999999998777777766   6789999999643

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.42  E-value=1.5e-06  Score=86.70  Aligned_cols=92  Identities=12%  Similarity=0.065  Sum_probs=80.7

Q ss_pred             eEEEEEcCCCCcCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHh-
Q psy4285           8 VRFCIICNYLSKITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATA-   85 (533)
Q Consensus         8 ~~~il~~~~~~~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~~~~-   85 (533)
                      +.+|.+||+...+.++|+||| ..++|.+++.+++.++|++.+...++.++++++..|+..|+|++|.|.++|+.+... 
T Consensus       151 ~~li~at~~~~~l~~~L~sRf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a  230 (328)
T PRK00080        151 FTLIGATTRAGLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFA  230 (328)
T ss_pred             ceEEeecCCcccCCHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHH
Confidence            678999999999999999998 679999999999999999999999999999999999999999999999999986432 


Q ss_pred             ---CCCCcchhhHHhhh
Q psy4285          86 ---HADEVNEDTIFTLL   99 (533)
Q Consensus        86 ---~~~~i~~~~i~~~~   99 (533)
                         ....|+.+.+...+
T Consensus       231 ~~~~~~~I~~~~v~~~l  247 (328)
T PRK00080        231 QVKGDGVITKEIADKAL  247 (328)
T ss_pred             HHcCCCCCCHHHHHHHH
Confidence               23458877776544

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=98.41  E-value=1.4e-06  Score=90.85  Aligned_cols=129  Identities=22%  Similarity=0.322  Sum_probs=73.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC-----------Cc----hhHHHHH---HHHH-HhcccC-
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD-----------RG----IGIVRDQ---IFQF-ASTKTM-  367 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~-----------~~----~~~~~~~---~~~~-~~~~~~-  367 (533)
                      .++|+|||||||||+++.+|+++      +..+.+...+..           .+    .+.....   +..| ...... 
T Consensus        47 iLlLtGP~G~GKtttv~~La~el------g~~v~Ew~np~~~~~~~~~~~d~~s~~~~~~~f~sq~~~F~~f~l~~s~y~  120 (519)
T PF03215_consen   47 ILLLTGPSGCGKTTTVKVLAKEL------GFEVQEWINPVSFRESDNQEDDFESDFNKFDEFLSQSDKFSEFLLRASKYS  120 (519)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh------CCeeEEecCCCCccccccccccccccccccccccchhhhhccccccccccc
Confidence            37999999999999999999998      333333221110           00    0000011   1112 000000 


Q ss_pred             --------CCCCcEEEEEeCCCCCCHHHHHHHHHHHH----hcCC-CcEEEEE-eC------CCC--------CCChhhh
Q psy4285         368 --------HKSSYKLIILDEADAMTNDAQNALRRIIE----KFTT-NVRFCII-CN------YLS--------KIPPAIQ  419 (533)
Q Consensus       368 --------~~~~~~vliiDE~d~l~~~~~~~Ll~~le----~~~~-~~~~I~~-~n------~~~--------~l~~~l~  419 (533)
                              .....+||+|||+-.+.......|...|.    .... .+.||++ ++      ...        -+.+.++
T Consensus       121 ~l~~~g~~~~~~~kvILVEDlPN~~~~~~~~f~~~L~~~l~~~~~~PlV~iiSe~~~~~~~~~~~~~~~t~~~L~~~~il  200 (519)
T PF03215_consen  121 SLSMSGSNSSSNKKVILVEDLPNVFHRDTSRFREALRQYLRSSRCLPLVFIISETESLSGDNSYRSNSFTAERLFPKEIL  200 (519)
T ss_pred             cccccCCCcCCCceEEEeeccccccchhHHHHHHHHHHHHHcCCCCCEEEEEecccccCCCCcccccchhhhhccCHHHH
Confidence                    11357899999997764433344444444    3222 3344444 01      111        2456676


Q ss_pred             c--cceeeeecCCCHHHHHHHhhcC
Q psy4285         420 S--RCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       420 s--R~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .  ++..|.|.|..+.-+.+.|.++
T Consensus       201 ~~~~i~~I~FNpIa~T~mkKaL~rI  225 (519)
T PF03215_consen  201 NHPGITRIKFNPIAPTFMKKALKRI  225 (519)
T ss_pred             hCCCceEEEecCCCHHHHHHHHHHH
Confidence            6  4579999999999999999888

>PRK06620 hypothetical protein; Validated

Probab=98.39  E-value=2.9e-06  Score=78.79  Aligned_cols=78  Identities=13%  Similarity=0.136  Sum_probs=67.9

Q ss_pred             chhhhccce---eEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHh---CCCCcchhh
Q psy4285          21 TPAIQSRCT---RFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATA---HADEVNEDT   94 (533)
Q Consensus        21 ~~~i~SRc~---~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~~~~---~~~~i~~~~   94 (533)
                      +|.|+||+.   ++.+++|+++++..++++.+...++.+++++++.|+..++||+|.+++.|+.+...   ....||.+.
T Consensus       129 l~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~~~l~l~~ev~~~L~~~~~~d~r~l~~~l~~l~~~~~~~~~~it~~~  208 (214)
T PRK06620        129 LPDLSSRIKSVLSILLNSPDDELIKILIFKHFSISSVTISRQIIDFLLVNLPREYSKIIEILENINYFALISKRKITISL  208 (214)
T ss_pred             hHHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHcCCCCCHHH
Confidence            499999998   99999999999999999999888999999999999999999999999999997432   233588777


Q ss_pred             HHhh
Q psy4285          95 IFTL   98 (533)
Q Consensus        95 i~~~   98 (533)
                      ++++
T Consensus       209 ~~~~  212 (214)
T PRK06620        209 VKEV  212 (214)
T ss_pred             HHHH
Confidence            6654

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=98.39  E-value=1.1e-06  Score=74.81  Aligned_cols=25  Identities=48%  Similarity=0.723  Sum_probs=22.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      +.++|+||+||||++..++..+...
T Consensus         8 i~ITG~PGvGKtTl~~ki~e~L~~~   32 (179)
T COG1618           8 IFITGRPGVGKTTLVLKIAEKLREK   32 (179)
T ss_pred             EEEeCCCCccHHHHHHHHHHHHHhc
Confidence            8999999999999999999887544

>PHA00729 NTP-binding motif containing protein

Probab=98.38  E-value=5.7e-06  Score=76.14  Aligned_cols=114  Identities=20%  Similarity=0.233  Sum_probs=66.1

Q ss_pred             CCCceeEeCCCCCChHHHHHHHHHHHcccc-c---------cCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEE
Q psy4285         305 ELPHLLFYGPPGTGKTTTILACARKLYTKA-Q---------FNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKL  374 (533)
Q Consensus       305 ~~~~~ll~GppGtGKT~la~~la~~l~~~~-~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v  374 (533)
                      ...+++++|+|||||||+|.++++.+.... .         .+.....+      ....+.+.+......    ....++
T Consensus        16 ~f~nIlItG~pGvGKT~LA~aLa~~l~~~l~~l~~~~~~~d~~~~~~fi------d~~~Ll~~L~~a~~~----~~~~dl   85 (226)
T PHA00729         16 GFVSAVIFGKQGSGKTTYALKVARDVFWKLNNLSTKDDAWQYVQNSYFF------ELPDALEKIQDAIDN----DYRIPL   85 (226)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHHHHhhcccccchhhHHhcCCcEEEE------EHHHHHHHHHHHHhc----CCCCCE
Confidence            344799999999999999999999873110 0         00111111      122222222222111    123468


Q ss_pred             EEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         375 IILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       375 liiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      |||||+..-...   ..  +-.   ..    +  .....+.++++||+..+.|.+++++++.++++..
T Consensus        86 LIIDd~G~~~~~---~~--wh~---~~----~--~~yf~L~~aLrSR~~l~il~~ls~edL~~~Lr~R  139 (226)
T PHA00729         86 IIFDDAGIWLSK---YV--WYE---DY----M--KTFYKIYALIRTRVSAVIFTTPSPEDLAFYLREK  139 (226)
T ss_pred             EEEeCCchhhcc---cc--hhh---hc----c--chHHHHHHHHHhhCcEEEEecCCHHHHHHHHHhC
Confidence            999997542111   00  000   00    0  1122467788899999999999999999999986

>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=98.37  E-value=1.2e-06  Score=85.95  Aligned_cols=131  Identities=18%  Similarity=0.233  Sum_probs=70.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCc-ceEEecCCCCCchhHHHHHHHHHHhcccC-----------------CC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNA-MVLELNASDDRGIGIVRDQIFQFASTKTM-----------------HK  369 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~  369 (533)
                      .+.++|++|+|||++|..+++.......++. .++.+.... ............+......                 ..
T Consensus        21 ~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~   99 (287)
T PF00931_consen   21 VVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNP-SLEQLLEQILRQLGEPDSSISDPKDIEELQDQLRELLK   99 (287)
T ss_dssp             EEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-S-CCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHHHC
T ss_pred             EEEEEcCCcCCcceeeeeccccccccccccccccccccccc-ccccccccccccccccccccccccccccccccchhhhc
Confidence            4899999999999999999987432222221 222222211 1122223322222221000                 02


Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         370 SSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ....+||+|+++...  ....+...+.....++++|+||.... +..........+.+.+++.++..+.+.+.
T Consensus       100 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~kilvTTR~~~-v~~~~~~~~~~~~l~~L~~~ea~~L~~~~  169 (287)
T PF00931_consen  100 DKRCLLVLDDVWDEE--DLEELREPLPSFSSGSKILVTTRDRS-VAGSLGGTDKVIELEPLSEEEALELFKKR  169 (287)
T ss_dssp             CTSEEEEEEEE-SHH--HH-------HCHHSS-EEEEEESCGG-GGTTHHSCEEEEECSS--HHHHHHHHHHH
T ss_pred             cccceeeeeeecccc--cccccccccccccccccccccccccc-ccccccccccccccccccccccccccccc
Confidence            447899999988654  23334444433445789999987643 22222223678999999999998888876

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.

>KOG1968|consensus

Probab=98.35  E-value=2.6e-06  Score=93.08  Aligned_cols=126  Identities=31%  Similarity=0.427  Sum_probs=94.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCC------------CCCcEEEE
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH------------KSSYKLII  376 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~vli  376 (533)
                      ++++||||+|||+.+...++.+      +..+++.|+++.++...+.+.+..+.......            .....||+
T Consensus       360 ~l~~G~pGigKT~~~h~~~k~~------g~~v~E~Nas~~RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vil  433 (871)
T KOG1968|consen  360 LLLSGPPGIGKTTAAHKAAKEL------GFKVVEKNASDVRSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLIL  433 (871)
T ss_pred             HHhcCCCCCCchhhHhhhhhhc------ccceeecCccccccccHHHhhhhccccccchhhhhcccccccccccceeEEE
Confidence            5899999999999999999998      78899999998887666666554432211110            12244999


Q ss_pred             EeCCCCCCHHH---HHHHHHHHHhcCCCcEEEEEeCCCCCCCh-hhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         377 LDEADAMTNDA---QNALRRIIEKFTTNVRFCIICNYLSKIPP-AIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       377 iDE~d~l~~~~---~~~Ll~~le~~~~~~~~I~~~n~~~~l~~-~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +||+|-+..+.   ...+-.++.  .....+|++||....-.. ++.+-|..++|..|+.+++..++..+
T Consensus       434 ~devD~~~~~dRg~v~~l~~l~~--ks~~Piv~~cndr~~p~sr~~~~~~~~l~f~kP~~~~i~~ri~si  501 (871)
T KOG1968|consen  434 MDEVDGMFGEDRGGVSKLSSLCK--KSSRPLVCTCNDRNLPKSRALSRACSDLRFSKPSSELIRSRIMSI  501 (871)
T ss_pred             EeccccccchhhhhHHHHHHHHH--hccCCeEEEecCCCCccccchhhhcceeeecCCcHHHHHhhhhhh
Confidence            99999998733   344555565  345779999998775444 56566799999999999999999998

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=98.33  E-value=7.1e-07  Score=79.29  Aligned_cols=63  Identities=17%  Similarity=0.244  Sum_probs=37.5

Q ss_pred             CcEEEEEeCCCCC---CHHHHHHHHHHHHhcCCCcEEEEEeCC--CCCCChhhhccc--eeeeecCCCHHHHH
Q psy4285         371 SYKLIILDEADAM---TNDAQNALRRIIEKFTTNVRFCIICNY--LSKIPPAIQSRC--TRFRFGPLDSSLIM  436 (533)
Q Consensus       371 ~~~vliiDE~d~l---~~~~~~~Ll~~le~~~~~~~~I~~~n~--~~~l~~~l~sR~--~~i~~~~~~~~~~~  436 (533)
                      ..++++|||+..|   .+...+++.++|+   ++..+|.|-..  ...+.+.+.+|.  ..+.+.+-+.+.+.
T Consensus        95 ~~~liviDEIG~mEl~~~~F~~~v~~~l~---s~~~vi~vv~~~~~~~~l~~i~~~~~~~i~~vt~~NRd~l~  164 (168)
T PF03266_consen   95 SSDLIVIDEIGKMELKSPGFREAVEKLLD---SNKPVIGVVHKRSDNPFLEEIKRRPDVKIFEVTEENRDALP  164 (168)
T ss_dssp             CCHEEEE---STTCCC-CHHHHHHHHHHC---TTSEEEEE--SS--SCCHHHHHTTTTSEEEE--TTTCCCHH
T ss_pred             CCCEEEEeccchhhhcCHHHHHHHHHHHc---CCCcEEEEEecCCCcHHHHHHHhCCCcEEEEeChhHHhhHh
Confidence            5679999999888   4567888899996   34456666543  346788888884  56666655544443

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=98.33  E-value=2.5e-05  Score=82.83  Aligned_cols=129  Identities=11%  Similarity=0.059  Sum_probs=83.1

Q ss_pred             CCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEec--CCC--CCchhHHHHHHHHHHh--ccc-CCCCCcEEEEE
Q psy4285         305 ELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELN--ASD--DRGIGIVRDQIFQFAS--TKT-MHKSSYKLIIL  377 (533)
Q Consensus       305 ~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~--~~~--~~~~~~~~~~~~~~~~--~~~-~~~~~~~vlii  377 (533)
                      ....+++.|++|||||+++++++..+-..    .++..+-  .++  ..+...+...+..-..  .+. ...+...|||+
T Consensus        24 ~~gGv~i~g~~G~~ks~~~r~l~~llp~~----~p~r~~p~~~t~~~L~Gg~Dl~~~l~~g~~~~~pGlla~Ah~GvL~l   99 (584)
T PRK13406         24 GLGGVVLRARAGPVRDRWLAALRALLPAG----TPLRRLPPGIADDRLLGGLDLAATLRAGRPVAQRGLLAEADGGVLVL   99 (584)
T ss_pred             ccceEEEEcCCCcHHHHHHHHHHHhcCCC----CCcccCCCCCcHHHccCCchHHhHhhcCCcCCCCCceeeccCCEEEe
Confidence            44569999999999999999999876221    2333222  221  1222223322221111  001 11345789999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCC---CCCCChhhhccc-eeeeecCCCHHHHHH
Q psy4285         378 DEADAMTNDAQNALRRIIEKF-------------TTNVRFCIICNY---LSKIPPAIQSRC-TRFRFGPLDSSLIMS  437 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~---~~~l~~~l~sR~-~~i~~~~~~~~~~~~  437 (533)
                      ||+..+.+..++.|++.|++.             |....+|.+-|.   ...+.+++++|| ..+.+.+++..+.++
T Consensus       100 De~n~~~~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~~~L~~~lLDRf~l~v~v~~~~~~~~~~  176 (584)
T PRK13406        100 AMAERLEPGTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEEDERAPAALADRLAFHLDLDGLALRDARE  176 (584)
T ss_pred             cCcccCCHHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcccCCCHHhHhheEEEEEcCCCChHHhcc
Confidence            999999999999999999863             344445554222   245899999999 478888888776643

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=98.33  E-value=5.8e-06  Score=76.07  Aligned_cols=172  Identities=15%  Similarity=0.165  Sum_probs=103.7

Q ss_pred             cccccCCCCHHHHHHHHHHHhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC
Q psy4285         267 VYNSVGYPTKTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS  346 (533)
Q Consensus       267 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~  346 (533)
                      +|...+.|...+....+......+.+.+..+...+..++ .-+.++|+-|+|||.+.|++...+...   ....+.+...
T Consensus        13 ~~g~~~~pf~~~~~~~~~~~~a~h~e~l~~l~~~i~d~q-g~~~vtGevGsGKTv~~Ral~~s~~~d---~~~~v~i~~~   88 (269)
T COG3267          13 HFGFSRLPFSWDIQPGLDYWAADHNEALLMLHAAIADGQ-GILAVTGEVGSGKTVLRRALLASLNED---QVAVVVIDKP   88 (269)
T ss_pred             HhhhccCCCccchhhhhhhhhhhhhHHHHHHHHHHhcCC-ceEEEEecCCCchhHHHHHHHHhcCCC---ceEEEEecCc
Confidence            344444554444444444444556667777777766554 237899999999999999777666433   2334455544


Q ss_pred             CCCchhHHHHHHHHHHh------------------cccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHH---hcCCCcEEE
Q psy4285         347 DDRGIGIVRDQIFQFAS------------------TKTMHKSSYKLIILDEADAMTNDAQNALRRIIE---KFTTNVRFC  405 (533)
Q Consensus       347 ~~~~~~~~~~~~~~~~~------------------~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le---~~~~~~~~I  405 (533)
                      ...........+..+..                  ........+.++++||++.+..+....|..+.+   ++.+...++
T Consensus        89 ~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~~~g~r~v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~iv  168 (269)
T COG3267          89 TLSDATLLEAIVADLESQPKVNVNAVLEQIDRELAALVKKGKRPVVLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIV  168 (269)
T ss_pred             chhHHHHHHHHHHHhccCccchhHHHHHHHHHHHHHHHHhCCCCeEEeehhHhhhChhHHHHHHHHHhhcccccCceeee
Confidence            43222222221111111                  000001234799999999999988888766654   344556677


Q ss_pred             EEeCCCC------CCChhhhcccee-eeecCCCHHHHHHHhhcC
Q psy4285         406 IICNYLS------KIPPAIQSRCTR-FRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       406 ~~~n~~~------~l~~~l~sR~~~-i~~~~~~~~~~~~~l~~~  442 (533)
                      +++...-      .....+..||.. +..+|++.++...++.+.
T Consensus       169 L~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~~~~~t~~yl~~~  212 (269)
T COG3267         169 LIGQPKLRPRLRLPVLRELEQRIDIRIELPPLTEAETGLYLRHR  212 (269)
T ss_pred             ecCCcccchhhchHHHHhhhheEEEEEecCCcChHHHHHHHHHH
Confidence            7774321      112344458876 999999999888888776

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=98.32  E-value=5.2e-07  Score=89.00  Aligned_cols=65  Identities=18%  Similarity=0.309  Sum_probs=52.9

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMR   73 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r   73 (533)
                      ||||+.++.||++|+.++.++|||+|||++++|++++.+++.+||.+    .++.  +. . .....++|.+.
T Consensus       137 LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~~~L~~----~~~~--~~-~-~~l~~~~g~p~  201 (325)
T PRK08699        137 LEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLRE----RGVA--EP-E-ERLAFHSGAPL  201 (325)
T ss_pred             HHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHHHHHHh----cCCC--cH-H-HHHHHhCCChh
Confidence            68999999999999999999999999999999999999999999973    3432  22 1 22345778763

>CHL00195 ycf46 Ycf46; Provisional

Probab=98.30  E-value=1e-05  Score=83.96  Aligned_cols=189  Identities=13%  Similarity=0.183  Sum_probs=118.5

Q ss_pred             CCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCC-HHHHHHHHHHHHHhCCCCcchhhH
Q psy4285          17 LSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGD-MRKVLNILQSAATAHADEVNEDTI   95 (533)
Q Consensus        17 ~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~-~r~a~~~l~~~~~~~~~~i~~~~i   95 (533)
                      .-.+.+-|..=+.++.|+-|+.+++.+.|+.++...++.++++.++.+++.+.|- .-++.+.+..+.. ....++.+.+
T Consensus       123 ~~~~p~el~~~~~~~~~~lP~~~ei~~~l~~~~~~~~~~~~~~~~~~l~~~~~gls~~~~~~~~~~~~~-~~~~~~~~~~  201 (489)
T CHL00195        123 ELNIPKELKDLITVLEFPLPTESEIKKELTRLIKSLNIKIDSELLENLTRACQGLSLERIRRVLSKIIA-TYKTIDENSI  201 (489)
T ss_pred             CCCCCHHHHhceeEEeecCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHHHHH-HcCCCChhhH
Confidence            4567777887788999999999999999998887778888999999999998774 4555555554433 3334666654


Q ss_pred             Hhhhh-------h-hccccch--hHHHHHhchHHHHhhcCCChhhHHHH-----HhhccCccccccCCCChhhHHHHHHH
Q psy4285          96 FTLLV-------S-RVEKYRP--STLDELVSHQDIISTIEIPESMLVDL-----VLKMSDIEYRLAAGTSEKIQLSALIA  160 (533)
Q Consensus        96 ~~~~~-------~-~~ek~~~--~~l~~lls~~~~l~~l~~~~~~~~~~-----~~~~~~~~~~~~~G~~~~~~l~~~~~  160 (533)
                      ..++.       . -...|.+  ..+.++-+...++..+.-........     +.....+...|+||||||..+.+++.
T Consensus       202 ~~i~~~k~q~~~~~~~le~~~~~~~~~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~  281 (489)
T CHL00195        202 PLILEEKKQIISQTEILEFYSVNEKISDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIAN  281 (489)
T ss_pred             HHHHHHHHHHHhhhccccccCCCCCHHHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHH
Confidence            32221       1 1112222  24566655544433322000000000     11123366889999999999999999


Q ss_pred             HHhcccccceeeeecCCcccchhhhH-----HHHhhhhhcccccCCCceEEEEcCccccCH
Q psy4285         161 AFNSARDKLEVLELNASDDRGIGIVR-----DQIFQFASTKTMHKSSYKLIILDEADAMTN  216 (533)
Q Consensus       161 ~~~~~~~~~~~~e~nasd~~g~~~~~-----d~i~~~a~~~~l~~~~~~~iilDE~d~l~~  216 (533)
                      .+.     ..++.+++++..+..++.     .++...|.     ...|.++++||+|.+..
T Consensus       282 e~~-----~~~~~l~~~~l~~~~vGese~~l~~~f~~A~-----~~~P~IL~IDEID~~~~  332 (489)
T CHL00195        282 DWQ-----LPLLRLDVGKLFGGIVGESESRMRQMIRIAE-----ALSPCILWIDEIDKAFS  332 (489)
T ss_pred             HhC-----CCEEEEEhHHhcccccChHHHHHHHHHHHHH-----hcCCcEEEehhhhhhhc
Confidence            887     678888877765544333     22222222     22466999999998753

>PHA02774 E1; Provisional

Probab=98.29  E-value=5.4e-06  Score=85.55  Aligned_cols=118  Identities=22%  Similarity=0.276  Sum_probs=72.4

Q ss_pred             hhhhhcccccccCC-CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCC
Q psy4285         293 LCYKINRFIDENEL-PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSS  371 (533)
Q Consensus       293 ~~~~l~~~~~~~~~-~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  371 (533)
                      ....++.+++.... ..++|+||||||||++|.++++.+.     +..+..+|....            |.-. +  -..
T Consensus       420 fl~~lk~~l~~~PKknciv~~GPP~TGKS~fa~sL~~~L~-----G~vi~fvN~~s~------------FwLq-p--l~d  479 (613)
T PHA02774        420 FLTALKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFLK-----GKVISFVNSKSH------------FWLQ-P--LAD  479 (613)
T ss_pred             HHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhC-----CCEEEEEECccc------------cccc-h--hcc
Confidence            44556666654322 2499999999999999999999873     222333443211            1100 1  135


Q ss_pred             cEEEEEeCCCCC-CHHHHHHHHHHHHhcC-------------CCcEEEEEeCCCCCCC---hhhhccceeeeecCC
Q psy4285         372 YKLIILDEADAM-TNDAQNALRRIIEKFT-------------TNVRFCIICNYLSKIP---PAIQSRCTRFRFGPL  430 (533)
Q Consensus       372 ~~vliiDE~d~l-~~~~~~~Ll~~le~~~-------------~~~~~I~~~n~~~~l~---~~l~sR~~~i~~~~~  430 (533)
                      .+++++||+-.- .......|..+|+..+             ....+|+|||....-+   ..|.||...+.|..+
T Consensus       480 ~ki~vlDD~t~~~w~y~d~~Lrn~LdG~~v~lD~Khk~~~q~k~pPlIITSN~d~~~~~~~~yL~sRi~~f~F~n~  555 (613)
T PHA02774        480 AKIALLDDATHPCWDYIDTYLRNALDGNPVSIDCKHKAPVQIKCPPLLITSNIDVKAEDRYKYLHSRITVFEFPNP  555 (613)
T ss_pred             CCEEEEecCcchHHHHHHHHHHHHcCCCcceeeecccCcccccCCCEEEecCCCcccchhhHHhhhhEEEEECCCC
Confidence            679999999322 1233446777776431             2256899999654444   366779888888543

>PRK06893 DNA replication initiation factor; Validated

Probab=98.28  E-value=6.1e-06  Score=77.74  Aligned_cols=93  Identities=15%  Similarity=0.186  Sum_probs=75.7

Q ss_pred             ceEEEEEcCC-CCc---Cchhhhccce---eEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Q psy4285           7 NVRFCIICNY-LSK---ITPAIQSRCT---RFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNIL   79 (533)
Q Consensus         7 ~~~~il~~~~-~~~---i~~~i~SRc~---~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l   79 (533)
                      ++.+++++|. +..   .+|.|+|||.   ++++++|++++..++|++.+...++.++++++..|++.++||+|.+++.|
T Consensus       125 ~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a~~~~l~l~~~v~~~L~~~~~~d~r~l~~~l  204 (229)
T PRK06893        125 KTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRNAYQRGIELSDEVANFLLKRLDRDMHTLFDAL  204 (229)
T ss_pred             CcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHH
Confidence            3445666654 332   4599999996   99999999999999999999888999999999999999999999999999


Q ss_pred             HHHHHh---CCCCcchhhHHhhh
Q psy4285          80 QSAATA---HADEVNEDTIFTLL   99 (533)
Q Consensus        80 ~~~~~~---~~~~i~~~~i~~~~   99 (533)
                      +.+...   ....||...+++++
T Consensus       205 ~~l~~~~~~~~~~it~~~v~~~L  227 (229)
T PRK06893        205 DLLDKASLQAQRKLTIPFVKEIL  227 (229)
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHh
Confidence            987432   23358888776654

>PRK09087 hypothetical protein; Validated

Probab=98.27  E-value=4.9e-06  Score=77.94  Aligned_cols=94  Identities=13%  Similarity=0.169  Sum_probs=76.6

Q ss_pred             ceEEEEEcCC-C---CcCchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Q psy4285           7 NVRFCIICNY-L---SKITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNIL   79 (533)
Q Consensus         7 ~~~~il~~~~-~---~~i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l   79 (533)
                      +..++++++. +   ...+|.|+|||   .++++++|+.+++.++|++.++..++.++++.++.|++.+.||+|.++..+
T Consensus       117 g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~~~~~~~~~~l~~ev~~~La~~~~r~~~~l~~~l  196 (226)
T PRK09087        117 GTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKLFADRQLYVDPHVVYYLVSRMERSLFAAQTIV  196 (226)
T ss_pred             CCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhhhHHHHHHHH
Confidence            3456666652 2   23489999999   999999999999999999999999999999999999999999999999866


Q ss_pred             HHH---HHhCCCCcchhhHHhhhh
Q psy4285          80 QSA---ATAHADEVNEDTIFTLLV  100 (533)
Q Consensus        80 ~~~---~~~~~~~i~~~~i~~~~~  100 (533)
                      +.+   +.....+||...+++++.
T Consensus       197 ~~L~~~~~~~~~~it~~~~~~~l~  220 (226)
T PRK09087        197 DRLDRLALERKSRITRALAAEVLN  220 (226)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHH
Confidence            665   333345688888776654

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=98.25  E-value=4.1e-06  Score=86.51  Aligned_cols=172  Identities=14%  Similarity=0.086  Sum_probs=109.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHH----HH----h--cccCCCCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQ----FA----S--TKTMHKSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~----~--~~~~~~~~~~vlii  377 (533)
                      ++++.|.|||||-.+++++.+... .   ..+++.+|+......-.-.++++.    |.    +  ......+..+.+|+
T Consensus       338 pvll~GEtGtGKe~laraiH~~s~-~---~gpfvAvNCaAip~~liesELFGy~~GafTga~~kG~~g~~~~A~gGtlFl  413 (606)
T COG3284         338 PVLLQGETGTGKEVLARAIHQNSE-A---AGPFVAVNCAAIPEALIESELFGYVAGAFTGARRKGYKGKLEQADGGTLFL  413 (606)
T ss_pred             CeEecCCcchhHHHHHHHHHhccc-c---cCCeEEEEeccchHHhhhHHHhccCccccccchhccccccceecCCCccHH
Confidence            489999999999999999998764 2   457788887654322222222211    11    0  01111355789999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhc----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHhh
Q psy4285         378 DEADAMTNDAQNALRRIIEKF----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l~  440 (533)
                      |||..|+-..|..|++.|++.          +-++++|.+|+..       ..+-+.|..|+..+.+.-|+-.+..   .
T Consensus       414 deIgd~p~~~Qs~LLrVl~e~~v~p~g~~~~~vdirvi~ath~dl~~lv~~g~fredLyyrL~~~~i~lP~lr~R~---d  490 (606)
T COG3284         414 DEIGDMPLALQSRLLRVLQEGVVTPLGGTRIKVDIRVIAATHRDLAQLVEQGRFREDLYYRLNAFVITLPPLRERS---D  490 (606)
T ss_pred             HHhhhchHHHHHHHHHHHhhCceeccCCcceeEEEEEEeccCcCHHHHHHcCCchHHHHHHhcCeeeccCchhccc---c
Confidence            999999999999999999874          3457788888654       3567778888876666666522211   1


Q ss_pred             cCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHH
Q psy4285         441 YDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDI  498 (533)
Q Consensus       441 ~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~  498 (533)
                      + ...+.+++.          .++-.+-++-..+...+..+.||++++ ++.+.+...
T Consensus       491 ~-~~~l~~~~~----------~~~~~~~~l~~~~~~~l~~~~WPGNir-el~~v~~~~  536 (606)
T COG3284         491 R-IPLLDRILK----------RENDWRLQLDDDALARLLAYRWPGNIR-ELDNVIERL  536 (606)
T ss_pred             c-HHHHHHHHH----------HccCCCccCCHHHHHHHHhCCCCCcHH-HHHHHHHHH
Confidence            1 122233332          222244456667777888899999987 444444443

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=98.25  E-value=4.8e-07  Score=95.69  Aligned_cols=127  Identities=19%  Similarity=0.218  Sum_probs=79.8

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEec--CCCCCc--hhHHHHHH-HHHHhc-ccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELN--ASDDRG--IGIVRDQI-FQFAST-KTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~--~~~~~~--~~~~~~~~-~~~~~~-~~~~~~~~~vliiDE~  380 (533)
                      -|+|+.|.||||||.+.+.+++.+      .. .+..+  ++.+.+  ....+... +.+... .....+.++|+.|||+
T Consensus       320 InILLvGDPgtaKSqlLk~v~~~a------Pr-~vytsgkgss~~GLTAav~rd~~tge~~LeaGALVlAD~Gv~cIDEf  392 (682)
T COG1241         320 IHILLVGDPGTAKSQLLKYVAKLA------PR-GVYTSGKGSSAAGLTAAVVRDKVTGEWVLEAGALVLADGGVCCIDEF  392 (682)
T ss_pred             eeEEEcCCCchhHHHHHHHHHhhC------Cc-eEEEccccccccCceeEEEEccCCCeEEEeCCEEEEecCCEEEEEec
Confidence            379999999999999999999875      11 12222  222111  11111111 111111 1111256789999999


Q ss_pred             CCCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC-------------CCChhhhccceeeeec--CCCH
Q psy4285         381 DAMTNDAQNALRRIIEKF-------------TTNVRFCIICNYLS-------------KIPPAIQSRCTRFRFG--PLDS  432 (533)
Q Consensus       381 d~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~-------------~l~~~l~sR~~~i~~~--~~~~  432 (533)
                      |+|+.+...++...||+.             +..+.+++++|+..             .++++|+|||+.+++-  .+++
T Consensus       393 dKm~~~dr~aihEaMEQQtIsIaKAGI~atLnARcsvLAAaNP~~Gryd~~~~~~enI~l~~~lLSRFDLifvl~D~~d~  472 (682)
T COG1241         393 DKMNEEDRVAIHEAMEQQTISIAKAGITATLNARCSVLAAANPKFGRYDPKKTVAENINLPAPLLSRFDLIFVLKDDPDE  472 (682)
T ss_pred             cCCChHHHHHHHHHHHhcEeeecccceeeecchhhhhhhhhCCCCCcCCCCCCHHHhcCCChhHHhhCCeeEEecCCCCc
Confidence            999999999999999964             34566777777653             4889999999866553  3444


Q ss_pred             HHHHHHhh
Q psy4285         433 SLIMSRLD  440 (533)
Q Consensus       433 ~~~~~~l~  440 (533)
                      +.-..+-.
T Consensus       473 ~~D~~ia~  480 (682)
T COG1241         473 EKDEEIAE  480 (682)
T ss_pred             cchHHHHH
Confidence            33333333

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=98.24  E-value=1.6e-07  Score=93.17  Aligned_cols=118  Identities=22%  Similarity=0.315  Sum_probs=63.8

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC--CCCc--hhHHHHH-HHHHH-hcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS--DDRG--IGIVRDQ-IFQFA-STKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~--~~~~--~~~~~~~-~~~~~-~~~~~~~~~~~vliiDE~  380 (533)
                      -|+||.|.||||||.+.+.+++..      . ..+..++.  ...+  ....+.. .+.+. .......+..+|++|||+
T Consensus        58 ihiLlvGdpg~gKS~ll~~~~~~~------p-r~v~~~g~~~s~~gLta~~~~d~~~~~~~leaGalvlad~GiccIDe~  130 (331)
T PF00493_consen   58 IHILLVGDPGTGKSQLLKYVAKLA------P-RSVYTSGKGSSAAGLTASVSRDPVTGEWVLEAGALVLADGGICCIDEF  130 (331)
T ss_dssp             --EEEECSCHHCHHHHHHCCCCT-------S-SEEEEECCGSTCCCCCEEECCCGGTSSECEEE-HHHHCTTSEEEECTT
T ss_pred             cceeeccchhhhHHHHHHHHHhhC------C-ceEEECCCCcccCCccceeccccccceeEEeCCchhcccCceeeeccc
Confidence            479999999999999999776543      1 11111111  1000  0000000 00000 000001245689999999


Q ss_pred             CCCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC-------------CCChhhhccceeeee--cCCC
Q psy4285         381 DAMTNDAQNALRRIIEKF-------------TTNVRFCIICNYLS-------------KIPPAIQSRCTRFRF--GPLD  431 (533)
Q Consensus       381 d~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~-------------~l~~~l~sR~~~i~~--~~~~  431 (533)
                      |++..+....|++.||..             +.++.++.++|+..             .++++|.|||+.+.+  .+++
T Consensus       131 dk~~~~~~~~l~eaMEqq~isi~kagi~~~l~ar~svlaa~NP~~g~~~~~~~~~~ni~l~~~LLSRFDLif~l~D~~d  209 (331)
T PF00493_consen  131 DKMKEDDRDALHEAMEQQTISIAKAGIVTTLNARCSVLAAANPKFGRYDPNKSLSENINLPPPLLSRFDLIFLLRDKPD  209 (331)
T ss_dssp             TT--CHHHHHHHHHHHCSCEEECTSSSEEEEE---EEEEEE--TT--S-TTS-CGCCT-S-CCCHCC-SEEECC--TTT
T ss_pred             ccccchHHHHHHHHHHcCeeccchhhhcccccchhhhHHHHhhhhhhcchhhhhHHhcccchhhHhhcCEEEEeccccc
Confidence            999999999999999963             45678999998654             478899999985543  4454

; 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.

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=98.24  E-value=2.2e-06  Score=70.22  Aligned_cols=73  Identities=26%  Similarity=0.436  Sum_probs=46.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccc--cCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQ--FNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTND  386 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~  386 (533)
                      +.|+||||+|||++|+.+++.+.....  ....++..+..+            .+...    -.+..++++||+......
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~~~~~~~~~vy~~~~~~------------~~w~g----Y~~q~vvi~DD~~~~~~~   64 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKHIGEPTKDSVYTRNPGD------------KFWDG----YQGQPVVIIDDFGQDNDG   64 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHhccCCCCcEEeCCCcc------------chhhc----cCCCcEEEEeecCccccc
Confidence            579999999999999999998864321  112233222221            11111    124579999999888643


Q ss_pred             ----HHHHHHHHHHh
Q psy4285         387 ----AQNALRRIIEK  397 (533)
Q Consensus       387 ----~~~~Ll~~le~  397 (533)
                          ....++++++.
T Consensus        65 ~~~~~~~~l~~l~s~   79 (107)
T PF00910_consen   65 YNYSDESELIRLISS   79 (107)
T ss_pred             cchHHHHHHHHHHhc
Confidence                45667777653

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>PHA02624 large T antigen; Provisional

Probab=98.24  E-value=2.8e-05  Score=80.73  Aligned_cols=128  Identities=18%  Similarity=0.256  Sum_probs=76.0

Q ss_pred             hhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCC
Q psy4285         293 LCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSS  371 (533)
Q Consensus       293 ~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  371 (533)
                      ....++.++..-...+ ++|+||||||||+++.++++.+      +..++.++.++.+..         |.-...   ..
T Consensus       417 ~~~~lk~~l~giPKk~~il~~GPpnTGKTtf~~sLl~~L------~G~vlsVNsPt~ks~---------FwL~pl---~D  478 (647)
T PHA02624        417 IYDILKLIVENVPKRRYWLFKGPVNSGKTTLAAALLDLC------GGKSLNVNCPPDKLN---------FELGCA---ID  478 (647)
T ss_pred             HHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHc------CCeEEEeeCCcchhH---------HHhhhh---hh
Confidence            3344455544332223 8999999999999999999988      334555776553322         111111   24


Q ss_pred             cEEEEEeCCC-------------CCCHHHHHHHHHHHHhc-C-------------CCcEEEEEeCCCCCCChhhhccce-
Q psy4285         372 YKLIILDEAD-------------AMTNDAQNALRRIIEKF-T-------------TNVRFCIICNYLSKIPPAIQSRCT-  423 (533)
Q Consensus       372 ~~vliiDE~d-------------~l~~~~~~~Ll~~le~~-~-------------~~~~~I~~~n~~~~l~~~l~sR~~-  423 (533)
                      ..+.++|++-             .++  -...|+..|+.. +             .-...|+|||.. .++.++.-||. 
T Consensus       479 ~~~~l~dD~t~~~~~~~~Lp~G~~~d--Nl~~lRn~LDG~V~v~ld~KH~n~~q~~~PPlliT~Ney-~iP~T~~~Rf~~  555 (647)
T PHA02624        479 QFMVVFEDVKGQPADNKDLPSGQGMN--NLDNLRDYLDGSVPVNLEKKHLNKRSQIFPPGIVTMNEY-LIPQTVKARFAK  555 (647)
T ss_pred             ceEEEeeeccccccccccCCcccccc--hhhHHHhhcCCCCccccchhccCchhccCCCeEEeecCc-ccchhHHHHHHH
Confidence            5799999983             222  113455555532 1             113367777765 48899999994 


Q ss_pred             eeeecCCCHHHHHHHhhcCH
Q psy4285         424 RFRFGPLDSSLIMSRLDYDD  443 (533)
Q Consensus       424 ~i~~~~~~~~~~~~~l~~~~  443 (533)
                      .+.|.+-  .-+..-|..-|
T Consensus       556 ~~~F~~k--~~l~~sL~~~~  573 (647)
T PHA02624        556 VLDFKPK--PYLKKSLKKNE  573 (647)
T ss_pred             hcccccc--HHHHHHHhcCH
Confidence            6666543  33455555553

>KOG1970|consensus

Probab=98.23  E-value=6.6e-06  Score=83.15  Aligned_cols=128  Identities=20%  Similarity=0.279  Sum_probs=71.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC-------------CCCchhHHHH--HHHHHHh----------
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS-------------DDRGIGIVRD--QIFQFAS----------  363 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~-------------~~~~~~~~~~--~~~~~~~----------  363 (533)
                      +|++||+||||||+++.+++++      +..+.+...+             ...+......  .++.|..          
T Consensus       113 LLltGPsGcGKSTtvkvLskel------g~~~~Ew~Npi~~~~~~~~h~~t~~~~~~~~s~L~~fesFler~~kyg~l~~  186 (634)
T KOG1970|consen  113 LLLTGPSGCGKSTTVKVLSKEL------GYQLIEWSNPINLKEPENLHNETSFLMFPYQSQLAVFESFLLRATKYGSLQM  186 (634)
T ss_pred             EEEeCCCCCCchhHHHHHHHhh------CceeeeecCCccccccccccccchhcccchhhHHHHHHHHHHHHHhhchhhh
Confidence            7999999999999999999998      4444444311             1111011111  0111111          


Q ss_pred             cccCCCCCcEEEEEeCCCCCCHH-H---HHHHHHHHHhcCCCcEEEEEeCCCC--------CCChhh--hccceeeeecC
Q psy4285         364 TKTMHKSSYKLIILDEADAMTND-A---QNALRRIIEKFTTNVRFCIICNYLS--------KIPPAI--QSRCTRFRFGP  429 (533)
Q Consensus       364 ~~~~~~~~~~vliiDE~d~l~~~-~---~~~Ll~~le~~~~~~~~I~~~n~~~--------~l~~~l--~sR~~~i~~~~  429 (533)
                      ........+++|+|||+-..... .   +..+++.+-..+....|+++|+...        .....+  .-|...+.|.|
T Consensus       187 ~g~~~~~~~~liLveDLPn~~~~d~~~~f~evL~~y~s~g~~PlIf~iTd~~~~g~nnq~rlf~~d~q~~~ri~~IsFNP  266 (634)
T KOG1970|consen  187 SGDDLRTDKKLILVEDLPNQFYRDDSETFREVLRLYVSIGRCPLIFIITDSLSNGNNNQDRLFPKDIQEEPRISNISFNP  266 (634)
T ss_pred             cccccccCceEEEeeccchhhhhhhHHHHHHHHHHHHhcCCCcEEEEEeccccCCCcchhhhchhhhhhccCcceEeecC
Confidence            01111245679999998655432 2   2333333333333334555553221        122222  23667999999


Q ss_pred             CCHHHHHHHhhcC
Q psy4285         430 LDSSLIMSRLDYD  442 (533)
Q Consensus       430 ~~~~~~~~~l~~~  442 (533)
                      ..+.-+.+.|.++
T Consensus       267 Ia~T~MKK~L~ri  279 (634)
T KOG1970|consen  267 IAPTIMKKFLKRI  279 (634)
T ss_pred             CcHHHHHHHHHHH
Confidence            9999999999988

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.21  E-value=4.5e-06  Score=80.41  Aligned_cols=86  Identities=15%  Similarity=0.234  Sum_probs=72.6

Q ss_pred             CCCCCCceEEEEEcCC-----CCcCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHh-------
Q psy4285           1 IEKFTTNVRFCIICNY-----LSKITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL-------   67 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~-----~~~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-------   67 (533)
                      ||+++.++++|+++++     ...+.|+++||| ..+.|++++.+++.+++++.+...+..++++++..+...       
T Consensus       137 ~e~~~~~~~vila~~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~a~~~l~~~~~~~~~~  216 (261)
T TIGR02881       137 MEDNRNEFVLILAGYSDEMDYFLSLNPGLRSRFPISIDFPDYTVEELMEIAERMVKEREYKLTEEAKWKLREHLYKVDQL  216 (261)
T ss_pred             HhccCCCEEEEecCCcchhHHHHhcChHHHhccceEEEECCCCHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHHHHHhc
Confidence            5778888888888744     345889999999 679999999999999999999988888999988887543       


Q ss_pred             ---cCCCHHHHHHHHHHHHHhC
Q psy4285          68 ---SDGDMRKVLNILQSAATAH   86 (533)
Q Consensus        68 ---~~g~~r~a~~~l~~~~~~~   86 (533)
                         +.||.|.+.|+++.+...+
T Consensus       217 ~~~~~gn~R~~~n~~e~a~~~~  238 (261)
T TIGR02881       217 SSREFSNARYVRNIIEKAIRRQ  238 (261)
T ss_pred             cCCCCchHHHHHHHHHHHHHHH
Confidence               3699999999999986643

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.

>PRK05642 DNA replication initiation factor; Validated

Probab=98.18  E-value=1.3e-05  Score=75.66  Aligned_cols=93  Identities=14%  Similarity=0.175  Sum_probs=75.5

Q ss_pred             ceEEEEEcC-CC---CcCchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Q psy4285           7 NVRFCIICN-YL---SKITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNIL   79 (533)
Q Consensus         7 ~~~~il~~~-~~---~~i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l   79 (533)
                      +..++++++ ++   ...+|.|+|||   .++.+++|+.++...+|++.+...++.+++++++.|++.++||+|.+++.|
T Consensus       130 g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~ka~~~~~~l~~ev~~~L~~~~~~d~r~l~~~l  209 (234)
T PRK05642        130 GRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQLRASRRGLHLTDEVGHFILTRGTRSMSALFDLL  209 (234)
T ss_pred             CCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Confidence            455667664 22   23479999999   999999999999999999667777899999999999999999999999999


Q ss_pred             HHHHHh---CCCCcchhhHHhhh
Q psy4285          80 QSAATA---HADEVNEDTIFTLL   99 (533)
Q Consensus        80 ~~~~~~---~~~~i~~~~i~~~~   99 (533)
                      +.+...   ...+||...+++++
T Consensus       210 ~~l~~~~l~~~~~it~~~~~~~L  232 (234)
T PRK05642        210 ERLDQASLQAQRKLTIPFLKETL  232 (234)
T ss_pred             HHHHHHHHHcCCcCCHHHHHHHh
Confidence            988532   23468888776654

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.17  E-value=4.4e-06  Score=77.75  Aligned_cols=90  Identities=22%  Similarity=0.312  Sum_probs=69.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhc---------ccCCCCCcEEEEEe
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAST---------KTMHKSSYKLIILD  378 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~vliiD  378 (533)
                      .+++.||+|.||+.+|+.+-..-....++...++++|+.+.++...+..+++.....         .....+..+++|+|
T Consensus       210 p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghvkgaftga~~~r~gllrsadggmlfld  289 (531)
T COG4650         210 PILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHVKGAFTGARESREGLLRSADGGMLFLD  289 (531)
T ss_pred             CeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecCchHHHHHHhhhccccccchhhhhhhhccCCCceEehH
Confidence            489999999999999999976544444567789999999988877776665442111         00012457899999


Q ss_pred             CCCCCCHHHHHHHHHHHHh
Q psy4285         379 EADAMTNDAQNALRRIIEK  397 (533)
Q Consensus       379 E~d~l~~~~~~~Ll~~le~  397 (533)
                      |+..+..+.|..|++.+|+
T Consensus       290 eigelgadeqamllkaiee  308 (531)
T COG4650         290 EIGELGADEQAMLLKAIEE  308 (531)
T ss_pred             hhhhcCccHHHHHHHHHHh
Confidence            9999999999999999986

>PRK04296 thymidine kinase; Provisional

Probab=98.14  E-value=2.3e-05  Score=71.47  Aligned_cols=93  Identities=17%  Similarity=0.253  Sum_probs=55.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC-C---C-------Cc-------hhHHHHHHHHHHhcccCCCC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS-D---D-------RG-------IGIVRDQIFQFASTKTMHKS  370 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~-~---~-------~~-------~~~~~~~~~~~~~~~~~~~~  370 (533)
                      .+++||||+||||++..++..+....   ..++.+.+. +   .       .+       .....+....+..    ...
T Consensus         5 ~litG~~GsGKTT~~l~~~~~~~~~g---~~v~i~k~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~----~~~   77 (190)
T PRK04296          5 EFIYGAMNSGKSTELLQRAYNYEERG---MKVLVFKPAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE----EGE   77 (190)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHcC---CeEEEEeccccccccCCcEecCCCCcccceEeCChHHHHHHHHh----hCC
Confidence            58999999999999999998875442   222222221 0   0       00       0111222222211    124


Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         371 SYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ..++|+|||++.++.+....+.+.+.  +.+..+|+++-.
T Consensus        78 ~~dvviIDEaq~l~~~~v~~l~~~l~--~~g~~vi~tgl~  115 (190)
T PRK04296         78 KIDCVLIDEAQFLDKEQVVQLAEVLD--DLGIPVICYGLD  115 (190)
T ss_pred             CCCEEEEEccccCCHHHHHHHHHHHH--HcCCeEEEEecC
Confidence            67899999999997775555666654  356778888744

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=98.12  E-value=7.7e-06  Score=89.86  Aligned_cols=96  Identities=16%  Similarity=0.208  Sum_probs=62.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHH-----------HHHHHHHHhcccCCCCCcEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIV-----------RDQIFQFASTKTMHKSSYKLII  376 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~vli  376 (533)
                      .++++|+|||||||+++++...+...   +..+. +.+++++....+           ...+..+..... .....++||
T Consensus       370 ~~il~G~aGTGKTtll~~i~~~~~~~---g~~V~-~~ApTg~Aa~~L~~~~g~~a~Ti~~~~~~~~~~~~-~~~~~~llI  444 (744)
T TIGR02768       370 IAVVVGRAGTGKSTMLKAAREAWEAA---GYRVI-GAALSGKAAEGLQAESGIESRTLASLEYAWANGRD-LLSDKDVLV  444 (744)
T ss_pred             EEEEEecCCCCHHHHHHHHHHHHHhC---CCeEE-EEeCcHHHHHHHHhccCCceeeHHHHHhhhccCcc-cCCCCcEEE
Confidence            47999999999999999998766332   33333 333333333322           222222211111 124678999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         377 LDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       377 iDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      |||+.+++......|++...+  .+.++|++++.
T Consensus       445 vDEasMv~~~~~~~Ll~~~~~--~~~kliLVGD~  476 (744)
T TIGR02768       445 IDEAGMVGSRQMARVLKEAEE--AGAKVVLVGDP  476 (744)
T ss_pred             EECcccCCHHHHHHHHHHHHh--cCCEEEEECCh
Confidence            999999999888888876543  46889999853

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>TIGR00602 rad24 checkpoint protein rad24

Probab=98.07  E-value=1.3e-05  Score=85.38  Aligned_cols=66  Identities=20%  Similarity=0.378  Sum_probs=56.8

Q ss_pred             Cchhhhc--cceeEEeCCCCHHHHHHHHHHHHhhcCCC------C-CHHHHHHHHHhcCCCHHHHHHHHHHHHHh
Q psy4285          20 ITPAIQS--RCTRFRFGPLDSSLIMSRLDYVIEQEKVN------V-TPDGKKAIIDLSDGDMRKVLNILQSAATA   85 (533)
Q Consensus        20 i~~~i~S--Rc~~~~~~~~~~~~~~~~l~~~~~~~~~~------~-~~~~~~~~~~~~~g~~r~a~~~l~~~~~~   85 (533)
                      +.|.|+|  ||.+|.|+|++...|.+.|.+|+++|+..      + +++++..|+..++||+|.|||.||.++..
T Consensus       256 L~~eLls~~rv~~I~FnPia~t~l~K~L~rIl~~E~~~~~~~~~~p~~~~l~~I~~~s~GDiRsAIn~LQf~~~~  330 (637)
T TIGR00602       256 MNKEILEEPRVSNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVELLCQGCSGDIRSAINSLQFSSSK  330 (637)
T ss_pred             cCHhHhcccceeEEEeCCCCHHHHHHHHHHHHHhhhhccccccccCCHHHHHHHHHhCCChHHHHHHHHHHHHhc
Confidence            5589998  66789999999999999999999877432      2 35789999999999999999999998763

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

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.06  E-value=2.4e-05  Score=84.04  Aligned_cols=93  Identities=19%  Similarity=0.236  Sum_probs=73.7

Q ss_pred             CCceEEEEEcCC---CCcCchhhhcccee--EEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHH---hcCCCHHHHH
Q psy4285           5 TTNVRFCIICNY---LSKITPAIQSRCTR--FRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIID---LSDGDMRKVL   76 (533)
Q Consensus         5 ~~~~~~il~~~~---~~~i~~~i~SRc~~--~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~---~~~g~~r~a~   76 (533)
                      ...+.+|.++|+   +..+.|.++|||..  +.|+|++.+++.++|+..++.....+++++++.+++   ..+||+|+||
T Consensus       900 ~SKLiLIGISNdlDLperLdPRLRSRLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIArkVAq~SGDARKAL  979 (1164)
T PTZ00112        900 NSKLVLIAISNTMDLPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCARKVANVSGDIRKAL  979 (1164)
T ss_pred             CCeEEEEEecCchhcchhhhhhhhhccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhhcCCHHHHHH
Confidence            456778888875   56889999999965  899999999999999988765434588999999988   7789999999


Q ss_pred             HHHHHHHHhCC-CCcchhhHHh
Q psy4285          77 NILQSAATAHA-DEVNEDTIFT   97 (533)
Q Consensus        77 ~~l~~~~~~~~-~~i~~~~i~~   97 (533)
                      .+|..+..... ..|+.+.|.+
T Consensus       980 DILRrAgEikegskVT~eHVrk 1001 (1164)
T PTZ00112        980 QICRKAFENKRGQKIVPRDITE 1001 (1164)
T ss_pred             HHHHHHHhhcCCCccCHHHHHH
Confidence            99999876422 2355555543

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.02  E-value=5.6e-05  Score=71.25  Aligned_cols=93  Identities=10%  Similarity=0.156  Sum_probs=76.3

Q ss_pred             eEEEEEcCCC---CcCchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q psy4285           8 VRFCIICNYL---SKITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQS   81 (533)
Q Consensus         8 ~~~il~~~~~---~~i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~   81 (533)
                      .+++++++..   ..+.+.++|||   ..++++||++++....|.+.+...++.+++++++.++..+.||+|.+.+.++.
T Consensus       123 ~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~~~~~~~~l~~~~~~~~v~l~~~al~~L~~~~~gn~~~l~~~l~~  202 (227)
T PRK08903        123 GALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLSDADKIAALKAAAAERGLQLADEVPDYLLTHFRRDMPSLMALLDA  202 (227)
T ss_pred             cEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHHHH
Confidence            3466666532   24678899995   89999999999999999999888999999999999999999999999999988


Q ss_pred             HHH---hCCCCcchhhHHhhhh
Q psy4285          82 AAT---AHADEVNEDTIFTLLV  100 (533)
Q Consensus        82 ~~~---~~~~~i~~~~i~~~~~  100 (533)
                      +..   .....||...++++++
T Consensus       203 l~~~~~~~~~~i~~~~~~~~l~  224 (227)
T PRK08903        203 LDRYSLEQKRPVTLPLLREMLA  224 (227)
T ss_pred             HHHHHHHhCCCCCHHHHHHHHh
Confidence            743   2345699888877654

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=98.02  E-value=1.3e-05  Score=89.39  Aligned_cols=96  Identities=11%  Similarity=0.108  Sum_probs=61.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC-----------chhHHHHHHHHHHhcccCCCCCcEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR-----------GIGIVRDQIFQFASTKTMHKSSYKLII  376 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~vli  376 (533)
                      .++++|+|||||||+.+++...+...   +..++-+ +++++           ....+...+..+..... .....++||
T Consensus       364 v~vv~G~AGTGKTT~l~~~~~~~e~~---G~~V~~~-ApTGkAA~~L~e~tGi~a~TI~sll~~~~~~~~-~l~~~~vlI  438 (988)
T PRK13889        364 LGVVVGYAGTGKSAMLGVAREAWEAA---GYEVRGA-ALSGIAAENLEGGSGIASRTIASLEHGWGQGRD-LLTSRDVLV  438 (988)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEe-cCcHHHHHHHhhccCcchhhHHHHHhhhccccc-ccccCcEEE
Confidence            47899999999999998877655322   2333333 33222           22333333222211111 124568999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         377 LDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       377 iDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      |||++|++......|++..+.  .+.++|++++.
T Consensus       439 VDEASMv~~~~m~~LL~~a~~--~garvVLVGD~  470 (988)
T PRK13889        439 IDEAGMVGTRQLERVLSHAAD--AGAKVVLVGDP  470 (988)
T ss_pred             EECcccCCHHHHHHHHHhhhh--CCCEEEEECCH
Confidence            999999999988888887653  56899999853

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.97  E-value=0.00011  Score=82.51  Aligned_cols=129  Identities=20%  Similarity=0.269  Sum_probs=91.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch------hHHHHHHHHHHhc-ccCC--CCCcEEEEEe
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI------GIVRDQIFQFAST-KTMH--KSSYKLIILD  378 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~-~~~~--~~~~~vliiD  378 (533)
                      .+++.|.||+|||+++.++|+..      +...+++|-++....      +..-+.-+.|... .+..  ...+.-+++|
T Consensus      1545 pilLEGsPGVGKTSlItaLAr~t------G~kliRINLSeQTdL~DLfGsd~Pve~~Gef~w~dapfL~amr~G~WVlLD 1618 (4600)
T COG5271        1545 PILLEGSPGVGKTSLITALARKT------GKKLIRINLSEQTDLCDLFGSDLPVEEGGEFRWMDAPFLHAMRDGGWVLLD 1618 (4600)
T ss_pred             ceeecCCCCccHHHHHHHHHHHh------cCceEEeeccccchHHHHhCCCCCcccCceeEecccHHHHHhhcCCEEEee
Confidence            59999999999999999999987      777777776653211      1000000000000 0000  1245689999


Q ss_pred             CCCCCCHHHHHHHHHHHHhc--------------CCCcEEEEEeCCCC------CCChhhhccceeeeecCCCHHHHHHH
Q psy4285         379 EADAMTNDAQNALRRIIEKF--------------TTNVRFCIICNYLS------KIPPAIQSRCTRFRFGPLDSSLIMSR  438 (533)
Q Consensus       379 E~d~l~~~~~~~Ll~~le~~--------------~~~~~~I~~~n~~~------~l~~~l~sR~~~i~~~~~~~~~~~~~  438 (533)
                      |+.-.+.+..+.|...++.+              .++.++..+-|+..      .++..+..||.++.+..++.+++..+
T Consensus      1619 EiNLaSQSVlEGLNacLDhR~eayIPEld~~f~~HpnfrVFAaqNPq~qggGRKgLPkSF~nRFsvV~~d~lt~dDi~~I 1698 (4600)
T COG5271        1619 EINLASQSVLEGLNACLDHRREAYIPELDKTFDVHPNFRVFAAQNPQDQGGGRKGLPKSFLNRFSVVKMDGLTTDDITHI 1698 (4600)
T ss_pred             hhhhhHHHHHHHHHHHHhhccccccccccceeeccCCeeeeeecCchhcCCCcccCCHHHhhhhheEEecccccchHHHH
Confidence            99999888888888887742              35666666666543      58999999999999999999999999


Q ss_pred             hhcC
Q psy4285         439 LDYD  442 (533)
Q Consensus       439 l~~~  442 (533)
                      ..+.
T Consensus      1699 a~~~ 1702 (4600)
T COG5271        1699 ANKM 1702 (4600)
T ss_pred             HHhh
Confidence            9887

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=97.96  E-value=3.9e-05  Score=66.89  Aligned_cols=109  Identities=17%  Similarity=0.196  Sum_probs=64.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEE-ecCCC---------------------C-----Cc-hhH---HHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLE-LNASD---------------------D-----RG-IGI---VRD  356 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~-~~~~~---------------------~-----~~-~~~---~~~  356 (533)
                      .+.+|+++|+||||+|-.+|-...+.+. ...++. +.+..                     .     .. ...   .++
T Consensus         4 ~i~vy~g~G~Gkt~~a~g~~~ra~~~g~-~v~~vQFlKg~~~~gE~~~l~~l~~v~~~~~g~~~~~~~~~~~~~~~~a~~   82 (159)
T cd00561           4 LIQVYTGNGKGKTTAALGLALRALGHGY-RVGVVQFLKGGWKYGELKALERLPNIEIHRMGRGFFWTTENDEEDIAAAAE   82 (159)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCC-eEEEEEEeCCCCccCHHHHHHhCCCcEEEECCCCCccCCCChHHHHHHHHH
Confidence            3778889999999999999988765531 112211 22210                     0     00 011   111


Q ss_pred             HHHHHHhcccCCCCCcEEEEEeCCCCCCH---HHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccc
Q psy4285         357 QIFQFASTKTMHKSSYKLIILDEADAMTN---DAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRC  422 (533)
Q Consensus       357 ~~~~~~~~~~~~~~~~~vliiDE~d~l~~---~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~  422 (533)
                      ... ++.... ....+++||+||+...-.   -..+.++++++..|.++-+|+|+....   +.|..+.
T Consensus        83 ~~~-~a~~~~-~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p---~~l~e~A  146 (159)
T cd00561          83 GWA-FAKEAI-ASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAP---KELIEAA  146 (159)
T ss_pred             HHH-HHHHHH-hcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCC---HHHHHhC
Confidence            111 111111 135789999999976522   124578889999999999999997643   4454444

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.96  E-value=1.5e-05  Score=80.49  Aligned_cols=116  Identities=17%  Similarity=0.188  Sum_probs=63.0

Q ss_pred             hhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchh------HHHHHHHHHHh--
Q psy4285         292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIG------IVRDQIFQFAS--  363 (533)
Q Consensus       292 ~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~--  363 (533)
                      .+.+.+...+......+++++||.|||||++.+++...+...   + ..+.+.++++..+.      .++..++--..  
T Consensus         8 ~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~~~---~-~~~~~~a~tg~AA~~i~~G~T~hs~f~i~~~~~   83 (364)
T PF05970_consen    8 RVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYLRSR---G-KKVLVTAPTGIAAFNIPGGRTIHSFFGIPINNN   83 (364)
T ss_pred             HHHHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHhccc---c-ceEEEecchHHHHHhccCCcchHHhcCcccccc
Confidence            333333333333344468999999999999999999877332   1 12223333322211      11211110000  


Q ss_pred             -----------cccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHH---------hcCCCcEEEEEeCCC
Q psy4285         364 -----------TKTMHKSSYKLIILDEADAMTNDAQNALRRIIE---------KFTTNVRFCIICNYL  411 (533)
Q Consensus       364 -----------~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le---------~~~~~~~~I~~~n~~  411 (533)
                                 .....-...++|||||+.+++......+-+.|.         .+-.+..+|+.++..
T Consensus        84 ~~~~~~~~~~~~~~~~l~~~~~lIiDEism~~~~~l~~i~~~lr~i~~~~~~~~pFGG~~vil~GDf~  151 (364)
T PF05970_consen   84 EKSQCKISKNSRLRERLRKADVLIIDEISMVSADMLDAIDRRLRDIRKSKDSDKPFGGKQVILFGDFL  151 (364)
T ss_pred             ccccccccccchhhhhhhhheeeecccccchhHHHHHHHHHhhhhhhcccchhhhcCcceEEeehhhh
Confidence                       000001245799999999999887766554443         233456778877543

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.95  E-value=8.6e-05  Score=65.69  Aligned_cols=23  Identities=43%  Similarity=0.739  Sum_probs=21.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      ++++||||+|||+++..++..+.
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~   24 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIA   24 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHH
Confidence            68999999999999999998874

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

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=97.94  E-value=5.1e-06  Score=82.98  Aligned_cols=117  Identities=19%  Similarity=0.212  Sum_probs=66.4

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEe--------cCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEE
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLEL--------NASDDRGIGIVRDQIFQFASTKTMHKSSYKLIIL  377 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlii  377 (533)
                      +.++.||||+|+|||.+.-.+...+-........+-..        .... ...+.+......+.       ....+|++
T Consensus        62 ~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~Fm~~vh~~l~~~~-~~~~~l~~va~~l~-------~~~~lLcf  133 (362)
T PF03969_consen   62 PKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHEFMLDVHSRLHQLR-GQDDPLPQVADELA-------KESRLLCF  133 (362)
T ss_pred             CceEEEECCCCCchhHHHHHHHHhCCccccccccccHHHHHHHHHHHHHh-CCCccHHHHHHHHH-------hcCCEEEE
Confidence            34599999999999999999988763321100000000        0000 01111222222221       34569999


Q ss_pred             eCCCCCCHHHHHHHHHHHHh-cCCCcEEEEEeCCCCC--------------CChhhhccceeeeecCC
Q psy4285         378 DEADAMTNDAQNALRRIIEK-FTTNVRFCIICNYLSK--------------IPPAIQSRCTRFRFGPL  430 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~-~~~~~~~I~~~n~~~~--------------l~~~l~sR~~~i~~~~~  430 (533)
                      ||++--+....-.|-++++. ...++.+|+|||.+..              ..+.|.++|.++.+...
T Consensus       134 DEF~V~DiaDAmil~rLf~~l~~~gvvlVaTSN~~P~~Ly~~gl~r~~Flp~I~~l~~~~~vv~ld~~  201 (362)
T PF03969_consen  134 DEFQVTDIADAMILKRLFEALFKRGVVLVATSNRPPEDLYKNGLQRERFLPFIDLLKRRCDVVELDGG  201 (362)
T ss_pred             eeeeccchhHHHHHHHHHHHHHHCCCEEEecCCCChHHHcCCcccHHHHHHHHHHHHhceEEEEecCC
Confidence            99987765444333333332 2466889999986531              23466778888887665

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.93  E-value=8.8e-05  Score=83.34  Aligned_cols=135  Identities=21%  Similarity=0.271  Sum_probs=99.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC---C--------CCCcEEEEE
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM---H--------KSSYKLIIL  377 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~--------~~~~~vlii  377 (533)
                      +|+-||+.+|||+++..+|+..      ++.++++|..+...   ..+.++.+......   +        -.++.-+++
T Consensus       891 ~LiQGpTSSGKTSMI~yla~~t------ghkfVRINNHEHTd---lqeYiGTyvTdd~G~lsFkEGvLVeAlR~GyWIVL  961 (4600)
T COG5271         891 LLIQGPTSSGKTSMILYLARET------GHKFVRINNHEHTD---LQEYIGTYVTDDDGSLSFKEGVLVEALRRGYWIVL  961 (4600)
T ss_pred             EEEecCCCCCcchHHHHHHHHh------CccEEEecCcccch---HHHHhhceeecCCCceeeehhHHHHHHhcCcEEEe
Confidence            8999999999999999999987      78888888654322   22222222211100   0        123568999


Q ss_pred             eCCCCCCHHHHHHHHHHHHh--------------cCCCcEEEEEeCCCC------CCChhhhccceeeeecCCCHHHHHH
Q psy4285         378 DEADAMTNDAQNALRRIIEK--------------FTTNVRFCIICNYLS------KIPPAIQSRCTRFRFGPLDSSLIMS  437 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~--------------~~~~~~~I~~~n~~~------~l~~~l~sR~~~i~~~~~~~~~~~~  437 (533)
                      ||..-...+..++|.++++.              |.++.++..|-|+|.      .+..+++.||..++|...+++++..
T Consensus       962 DELNLApTDVLEaLNRLLDDNRelfIPETqevV~PHp~F~lFATQNppg~YgGRK~LSrAFRNRFlE~hFddipedEle~ 1041 (4600)
T COG5271         962 DELNLAPTDVLEALNRLLDDNRELFIPETQEVVVPHPNFRLFATQNPPGGYGGRKGLSRAFRNRFLEMHFDDIPEDELEE 1041 (4600)
T ss_pred             eccccCcHHHHHHHHHhhccccceecCCcceeeccCCCeeEEeecCCCccccchHHHHHHHHhhhHhhhcccCcHHHHHH
Confidence            99999999999999999974              345566666667654      4788999999999999999999999


Q ss_pred             HhhcC----HHHHHHHHHH
Q psy4285         438 RLDYD----DISFFNIIIW  452 (533)
Q Consensus       438 ~l~~~----~~~~~~ll~~  452 (533)
                      +|...    |.-...+.+.
T Consensus      1042 ILh~rc~iapSyakKiVeV 1060 (4600)
T COG5271        1042 ILHGRCEIAPSYAKKIVEV 1060 (4600)
T ss_pred             HHhccCccCHHHHHHHHHH
Confidence            99987    5555555554

>KOG2228|consensus

Probab=97.91  E-value=0.00017  Score=69.02  Aligned_cols=147  Identities=18%  Similarity=0.174  Sum_probs=80.3

Q ss_pred             hhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHH------------
Q psy4285         295 YKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFA------------  362 (533)
Q Consensus       295 ~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------  362 (533)
                      ..+++-+..|....+++.||.|+|||.+........ ...+-....+.+|+.-....-.++++..++.            
T Consensus        38 ~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~-q~~~E~~l~v~Lng~~~~dk~al~~I~rql~~e~~~~~k~~gs  116 (408)
T KOG2228|consen   38 ELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDI-QENGENFLLVRLNGELQTDKIALKGITRQLALELNRIVKSFGS  116 (408)
T ss_pred             HHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhH-HhcCCeEEEEEECccchhhHHHHHHHHHHHHHHHhhhheeecc
Confidence            334444445555569999999999999887665541 1111123455666543221111221111110            


Q ss_pred             ------------hcccCCCCCcEEEEEeCCCCCCH-HHHHHHHHHHHh---cCCCcEEEEEeCCC---CCCChhhhccce
Q psy4285         363 ------------STKTMHKSSYKLIILDEADAMTN-DAQNALRRIIEK---FTTNVRFCIICNYL---SKIPPAIQSRCT  423 (533)
Q Consensus       363 ------------~~~~~~~~~~~vliiDE~d~l~~-~~~~~Ll~~le~---~~~~~~~I~~~n~~---~~l~~~l~sR~~  423 (533)
                                  .......+.+-+.|+||+|-..+ ..|--|+..+|-   ....+.+|..|...   +.+...++|||.
T Consensus       117 fte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrld~lE~LEKRVKSRFs  196 (408)
T KOG2228|consen  117 FTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRLDILELLEKRVKSRFS  196 (408)
T ss_pred             cchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeeccccHHHHHHHHHHhhcc
Confidence                        00111123456777789997754 455555666552   23335566655444   356789999993


Q ss_pred             ---eeeecCCCHHHHHHHhhcC
Q psy4285         424 ---RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 ---~i~~~~~~~~~~~~~l~~~  442 (533)
                         ...+++.+-++..++.+..
T Consensus       197 hr~I~m~~~~~l~~yv~l~r~l  218 (408)
T KOG2228|consen  197 HRVIFMLPSLPLGDYVDLYRKL  218 (408)
T ss_pred             cceeeccCCCChHHHHHHHHHH
Confidence               3344556667777777665

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

Probab=97.89  E-value=6.9e-05  Score=61.95  Aligned_cols=60  Identities=25%  Similarity=0.215  Sum_probs=42.3

Q ss_pred             CHHHHHHHHHHHhhhchhh----hhhhcccccccCC--Cc-eeEeCCCCCChHHHHHHHHHHHcccc
Q psy4285         275 TKTEITNILRWLLNESMDL----CYKINRFIDENEL--PH-LLFYGPPGTGKTTTILACARKLYTKA  334 (533)
Q Consensus       275 ~~~~~~~~l~~~~~~~~~~----~~~l~~~~~~~~~--~~-~ll~GppGtGKT~la~~la~~l~~~~  334 (533)
                      ....++..+...+.||.-+    ...+..++....+  |- +-|+|+||||||.+++.||+.++..+
T Consensus        15 ~~~~L~~~L~~~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~ly~~G   81 (127)
T PF06309_consen   15 NITGLEKDLQRNLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHLYKSG   81 (127)
T ss_pred             CHHHHHHHHHHHccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHHHhcc
Confidence            3455666666666777544    4455566655432  22 56999999999999999999998764

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

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.87  E-value=9.1e-05  Score=79.73  Aligned_cols=76  Identities=24%  Similarity=0.268  Sum_probs=64.6

Q ss_pred             eEEEEEc-CCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHH
Q psy4285           8 VRFCIIC-NYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAAT   84 (533)
Q Consensus         8 ~~~il~~-~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~~~   84 (533)
                      +++|.+| +++..+.|+|+|||..+.|++++.+++..++++.+.+.++.+++++++.|+.++. +.|+|+|.|+.+..
T Consensus       324 ~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~-~gRraln~L~~~~~  400 (615)
T TIGR02903       324 FVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIALIVLNAAEKINVHLAAGVEELIARYTI-EGRKAVNILADVYG  400 (615)
T ss_pred             EEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCC-cHHHHHHHHHHHHH
Confidence            3444434 5677899999999999999999999999999999988888899998888888764 88999999988753

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.

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.84  E-value=0.00012  Score=65.07  Aligned_cols=27  Identities=37%  Similarity=0.599  Sum_probs=23.7

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      |-++|+|+||+||||+|+.+|+.+...
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L~~~   28 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKELRQE   28 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHHHHh
Confidence            458999999999999999999998543

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=97.84  E-value=2e-05  Score=71.83  Aligned_cols=102  Identities=19%  Similarity=0.312  Sum_probs=48.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC-CCc---------------hhHHHHHHHH---------HH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD-DRG---------------IGIVRDQIFQ---------FA  362 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~-~~~---------------~~~~~~~~~~---------~~  362 (533)
                      .+++.||+|||||.+|.+.|..+...+.+..-++.-+... +..               ...+...+..         ..
T Consensus        21 ~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~p~~d~l~~~~~~~~~~~~~  100 (205)
T PF02562_consen   21 LVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLRPIYDALEELFGKEKLEELI  100 (205)
T ss_dssp             EEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHHHHHHTTTS-TTCHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHHHHHHHHHHHHhChHhHHHHh
Confidence            5899999999999999999987765543332222211110 000               0011111111         00


Q ss_pred             hcc------cCC----CCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         363 STK------TMH----KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       363 ~~~------~~~----~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      ...      ..+    .-...++|+||+..+++.....++.   +...++++|++++...
T Consensus       101 ~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~ilT---R~g~~skii~~GD~~Q  157 (205)
T PF02562_consen  101 QNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKMILT---RIGEGSKIIITGDPSQ  157 (205)
T ss_dssp             HTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHT---TB-TT-EEEEEE----
T ss_pred             hcCeEEEEehhhhcCccccceEEEEecccCCCHHHHHHHHc---ccCCCcEEEEecCcee
Confidence            000      000    1236899999999999876555544   4467899999997543

; GO: 0005524 ATP binding; PDB: 3B85_A.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=97.83  E-value=0.00014  Score=68.44  Aligned_cols=92  Identities=14%  Similarity=0.247  Sum_probs=74.5

Q ss_pred             eEEEEEcCCCC-c--Cc-hhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           8 VRFCIICNYLS-K--IT-PAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         8 ~~~il~~~~~~-~--i~-~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ..+|++++... .  +. +.++||+   ..+++++++++++...+++.+.+.++.+++++++.|+..+.||+|.+.+.++
T Consensus       124 ~~iIits~~~~~~~~~~~~~L~~r~~~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~l~~L~~~~~gn~r~L~~~l~  203 (226)
T TIGR03420       124 GRLLIAGRAAPAQLPLRLPDLRTRLAWGLVFQLPPLSDEEKIAALQSRAARRGLQLPDEVADYLLRHGSRDMGSLMALLD  203 (226)
T ss_pred             CeEEEECCCChHHCCcccHHHHHHHhcCeeEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHHH
Confidence            46778777433 2  23 8899997   5899999999999999999888888999999999999999999999999988


Q ss_pred             HHHH---hCCCCcchhhHHhhh
Q psy4285          81 SAAT---AHADEVNEDTIFTLL   99 (533)
Q Consensus        81 ~~~~---~~~~~i~~~~i~~~~   99 (533)
                      .+..   ..+..||.+.+.+++
T Consensus       204 ~~~~~~~~~~~~i~~~~~~~~~  225 (226)
T TIGR03420       204 ALDRASLAAKRKITIPFVKEVL  225 (226)
T ss_pred             HHHHHHHHhCCCCCHHHHHHHh
Confidence            8753   334468888776543

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.

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.83  E-value=8.1e-05  Score=83.60  Aligned_cols=96  Identities=14%  Similarity=0.201  Sum_probs=62.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHH-------HHHH----HhcccCCCCCcEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQ-------IFQF----ASTKTMHKSSYKLII  376 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~----~~~~~~~~~~~~vli  376 (533)
                      ..++.|++||||||+.+++...+...   +..++-+ +++++....+.+.       +..+    ..... .-....|||
T Consensus       399 ~~~v~G~AGTGKTt~l~~~~~~~e~~---G~~V~g~-ApTgkAA~~L~e~~Gi~a~TIas~ll~~~~~~~-~l~~~~vlV  473 (1102)
T PRK13826        399 IAAVVGRAGAGKTTMMKAAREAWEAA---GYRVVGG-ALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRD-QLDNKTVFV  473 (1102)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEE-cCcHHHHHHHHHhhCCCeeeHHHHHhhhccCcc-CCCCCcEEE
Confidence            47999999999999999998765332   3344433 3333333333221       1111    11111 113468999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         377 LDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       377 iDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      |||++|++......|++..+.  .++++|++++.
T Consensus       474 IDEAsMv~~~~m~~Ll~~~~~--~garvVLVGD~  505 (1102)
T PRK13826        474 LDEAGMVASRQMALFVEAVTR--AGAKLVLVGDP  505 (1102)
T ss_pred             EECcccCCHHHHHHHHHHHHh--cCCEEEEECCH
Confidence            999999999999999988864  46899999854

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=97.81  E-value=7.6e-05  Score=66.82  Aligned_cols=103  Identities=16%  Similarity=0.173  Sum_probs=60.8

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEE-ecCC---------------------CC---C--c----hhHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLE-LNAS---------------------DD---R--G----IGIVR  355 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~-~~~~---------------------~~---~--~----~~~~~  355 (533)
                      .++++||++|.||||.|..++....+.+. ...++. +.+.                     ..   .  .    ....+
T Consensus        23 g~v~v~~g~GkGKtt~a~g~a~ra~g~G~-~V~ivQFlKg~~~~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~~~~  101 (191)
T PRK05986         23 GLLIVHTGNGKGKSTAAFGMALRAVGHGK-KVGVVQFIKGAWSTGERNLLEFGGGVEFHVMGTGFTWETQDRERDIAAAR  101 (191)
T ss_pred             CeEEEECCCCCChHHHHHHHHHHHHHCCC-eEEEEEEecCCCccCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHHHHH
Confidence            35999999999999999999988765531 111111 1110                     00   0  0    01111


Q ss_pred             HHHHHHHhcccCCCCCcEEEEEeCCCCCCH---HHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         356 DQIFQFASTKTMHKSSYKLIILDEADAMTN---DAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       356 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~---~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      +........  .....+++||+||+-....   =....++++|+..|.++-+|+|+....
T Consensus       102 ~~~~~a~~~--l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p  159 (191)
T PRK05986        102 EGWEEAKRM--LADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAP  159 (191)
T ss_pred             HHHHHHHHH--HhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCC
Confidence            111111111  1135789999999855422   113567888888899999999997543

>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=97.81  E-value=3.7e-05  Score=70.19  Aligned_cols=78  Identities=10%  Similarity=0.098  Sum_probs=64.8

Q ss_pred             ceEEEEEcCCCCcCchhhhccceeE-EeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHH
Q psy4285           7 NVRFCIICNYLSKITPAIQSRCTRF-RFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAAT   84 (533)
Q Consensus         7 ~~~~il~~~~~~~i~~~i~SRc~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~~~   84 (533)
                      ...+|-+|+....+.+|+++|+-++ ++...+.+++.+++.+.+...++++++++...|++.|.|.+|-|.++|..+..
T Consensus       149 ~FTligATTr~g~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~i~~~~~~~Ia~rsrGtPRiAnrll~rvrD  227 (233)
T PF05496_consen  149 PFTLIGATTRAGLLSSPLRDRFGIVLRLEFYSEEELAKIVKRSARILNIEIDEDAAEEIARRSRGTPRIANRLLRRVRD  227 (233)
T ss_dssp             --EEEEEESSGCCTSHCCCTTSSEEEE----THHHHHHHHHHCCHCTT-EE-HHHHHHHHHCTTTSHHHHHHHHHHHCC
T ss_pred             CceEeeeeccccccchhHHhhcceecchhcCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHhcCCChHHHHHHHHHHHH
Confidence            4568889999999999999999764 89999999999999999989999999999999999999999999999988743

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.

>KOG0477|consensus

Probab=97.80  E-value=1.1e-05  Score=82.29  Aligned_cols=123  Identities=15%  Similarity=0.247  Sum_probs=73.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEec-CCCC--Cchh-----HHHHHHHHHHhcccCCCCCcEEEEEeC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELN-ASDD--RGIG-----IVRDQIFQFASTKTMHKSSYKLIILDE  379 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~-~~~~--~~~~-----~~~~~~~~~~~~~~~~~~~~~vliiDE  379 (533)
                      |+||.|.||||||-..+.+++..      ...++... ++..  ....     ..+++.-.  .... .-+..+|.+|||
T Consensus       484 nvLL~GDPGTaKSQFLKY~eK~s------~RAV~tTGqGASavGLTa~v~KdPvtrEWTLE--aGAL-VLADkGvClIDE  554 (854)
T KOG0477|consen  484 NVLLLGDPGTAKSQFLKYAEKTS------PRAVFTTGQGASAVGLTAYVRKDPVTREWTLE--AGAL-VLADKGVCLIDE  554 (854)
T ss_pred             eEEEecCCCccHHHHHHHHHhcC------cceeEeccCCccccceeEEEeeCCccceeeec--cCeE-EEccCceEEeeh
Confidence            59999999999999999998864      22222111 0000  0000     11111100  0000 124578999999


Q ss_pred             CCCCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC-------------CCChhhhccceeeee-----c
Q psy4285         380 ADAMTNDAQNALRRIIEKF-------------TTNVRFCIICNYLS-------------KIPPAIQSRCTRFRF-----G  428 (533)
Q Consensus       380 ~d~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~-------------~l~~~l~sR~~~i~~-----~  428 (533)
                      +|+|+......+..+||+.             ...+.+|+++|...             .+.++++|||+.+..     .
T Consensus       555 FDKMndqDRtSIHEAMEQQSISISKAGIVtsLqArctvIAAanPigGRY~~s~tFaqNV~ltePIlSRFDiLcVvkD~vd  634 (854)
T KOG0477|consen  555 FDKMNDQDRTSIHEAMEQQSISISKAGIVTSLQARCTVIAAANPIGGRYNPSLTFAQNVDLTEPILSRFDILCVVKDTVD  634 (854)
T ss_pred             hhhhcccccchHHHHHHhcchhhhhhhHHHHHHhhhhhheecCCCCCccCCccchhhccccccchhhhcceeeeeecccC
Confidence            9999887666777777653             35678899988621             578899999964433     3


Q ss_pred             CCCHHHHHHHh
Q psy4285         429 PLDSSLIMSRL  439 (533)
Q Consensus       429 ~~~~~~~~~~l  439 (533)
                      |..++.+.+.+
T Consensus       635 ~~~De~lA~fV  645 (854)
T KOG0477|consen  635 PVQDEKLAKFV  645 (854)
T ss_pred             chhHHHHHHHH
Confidence            44444444444

>CHL00181 cbbX CbbX; Provisional

Probab=97.80  E-value=3.9e-05  Score=74.59  Aligned_cols=87  Identities=20%  Similarity=0.286  Sum_probs=71.5

Q ss_pred             CCCCCCceEEEEEcCCC-----CcCchhhhccce-eEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHh-------
Q psy4285           1 IEKFTTNVRFCIICNYL-----SKITPAIQSRCT-RFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL-------   67 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~-----~~i~~~i~SRc~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-------   67 (533)
                      ||++..++++|+++++.     ..++|+++|||. .+.|++++.+++.+++.+.+++.+..+++++...+...       
T Consensus       155 me~~~~~~~vI~ag~~~~~~~~~~~np~L~sR~~~~i~F~~~t~~el~~I~~~~l~~~~~~l~~~~~~~L~~~i~~~~~~  234 (287)
T CHL00181        155 MENQRDDLVVIFAGYKDRMDKFYESNPGLSSRIANHVDFPDYTPEELLQIAKIMLEEQQYQLTPEAEKALLDYIKKRMEQ  234 (287)
T ss_pred             HhcCCCCEEEEEeCCcHHHHHHHhcCHHHHHhCCceEEcCCcCHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHhCCC
Confidence            57778889988888632     345799999985 79999999999999999999988888888877666554       


Q ss_pred             -cCCCHHHHHHHHHHHHHhCC
Q psy4285          68 -SDGDMRKVLNILQSAATAHA   87 (533)
Q Consensus        68 -~~g~~r~a~~~l~~~~~~~~   87 (533)
                       .-||.|.+.|+++.+...+.
T Consensus       235 ~~~GNaR~vrn~ve~~~~~~~  255 (287)
T CHL00181        235 PLFANARSVRNALDRARMRQA  255 (287)
T ss_pred             CCCccHHHHHHHHHHHHHHHH
Confidence             23999999999999877543

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

Probab=97.80  E-value=3.9e-05  Score=69.64  Aligned_cols=32  Identities=28%  Similarity=0.439  Sum_probs=21.2

Q ss_pred             cccCCCceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         302 DENELPHLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       302 ~~~~~~~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ..+..++++++|++|+|||++.+.+...+...
T Consensus        20 ~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen   20 QSGSPRNLLLTGESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             SS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred             HcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            33444569999999999999999998887544

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.79  E-value=0.00019  Score=61.75  Aligned_cols=23  Identities=30%  Similarity=0.531  Sum_probs=21.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.++||+|||||++.+.+|...
T Consensus        31 ~iaitGPSG~GKStllk~va~Li   53 (223)
T COG4619          31 FIAITGPSGCGKSTLLKIVASLI   53 (223)
T ss_pred             eEEEeCCCCccHHHHHHHHHhcc
Confidence            58999999999999999999764

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=97.77  E-value=0.00022  Score=68.29  Aligned_cols=138  Identities=16%  Similarity=0.234  Sum_probs=86.0

Q ss_pred             hcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEE
Q psy4285         297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLII  376 (533)
Q Consensus       297 l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vli  376 (533)
                      +.+.+... .+|+++.|.+|+||+++++..+...      +..++.+..+..-+....++.++........ .+.+.+++
T Consensus        23 i~RvL~~~-~Gh~LLvG~~GsGr~sl~rLaa~i~------~~~~~~i~~~~~y~~~~f~~dLk~~~~~ag~-~~~~~vfl   94 (268)
T PF12780_consen   23 ISRVLSQP-RGHALLVGVGGSGRQSLARLAAFIC------GYEVFQIEITKGYSIKDFKEDLKKALQKAGI-KGKPTVFL   94 (268)
T ss_dssp             HHHHHCST-TEEEEEECTTTSCHHHHHHHHHHHT------TEEEE-TTTSTTTHHHHHHHHHHHHHHHHHC-S-S-EEEE
T ss_pred             HHHHHcCC-CCCeEEecCCCccHHHHHHHHHHHh------ccceEEEEeeCCcCHHHHHHHHHHHHHHHhc-cCCCeEEE
Confidence            34444432 3579999999999999999777654      5566777666655566666666665443332 35677888


Q ss_pred             EeCCCCCCHHHHHH---------------------HHHH---------------------HHhcCCCcEEEEEeCCCCC-
Q psy4285         377 LDEADAMTNDAQNA---------------------LRRI---------------------IEKFTTNVRFCIICNYLSK-  413 (533)
Q Consensus       377 iDE~d~l~~~~~~~---------------------Ll~~---------------------le~~~~~~~~I~~~n~~~~-  413 (533)
                      ++|.+-......+.                     +...                     +++-..+.++|++-++... 
T Consensus        95 l~d~qi~~~~fLe~in~LL~sGeip~LF~~eE~~~i~~~l~~~~~~~~~~~~~~~~~~~F~~rvr~nLHivl~~sp~~~~  174 (268)
T PF12780_consen   95 LTDSQIVDESFLEDINSLLSSGEIPNLFTKEELDNIISSLREEAKAEGISDSRESLYEFFIERVRKNLHIVLCMSPVGPN  174 (268)
T ss_dssp             EECCCSSSCHHHHHHHHHHHCSS-TTTS-TCHHHHHHHHHHHHHHHCT--SSHHHHHHHHHHHHCCCEEEEEEESTTTTC
T ss_pred             ecCcccchHhHHHHHHHHHhCCCCCCCccHHHHHHHHHHhHHHHHHcCCCCchHHHHHHHHHHHHhheeEEEEECCCCch
Confidence            88876553321111                     1111                     1122577888888765542 


Q ss_pred             ------CChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         414 ------IPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       414 ------l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                            .-|+|.++|....|.++|.+.+..+-.+.
T Consensus       175 ~r~~~~~fPaL~~~ctIdW~~~W~~eaL~~Va~~~  209 (268)
T PF12780_consen  175 FRDRCRSFPALVNCCTIDWFDPWPEEALLSVANKF  209 (268)
T ss_dssp             CCHHHHHHCCHHHHSEEEEEES--HHHHHHHHHHH
T ss_pred             HHHHHHhCcchhcccEEEeCCcCCHHHHHHHHHHH
Confidence                  34788888999999999999888776654

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PRK05629 hypothetical protein; Validated

Probab=97.76  E-value=0.0002  Score=71.06  Aligned_cols=102  Identities=12%  Similarity=0.144  Sum_probs=86.1

Q ss_pred             CCCCCceEEEEEcCCCC---cCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHH
Q psy4285           2 EKFTTNVRFCIICNYLS---KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI   78 (533)
Q Consensus         2 E~~~~~~~~il~~~~~~---~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~   78 (533)
                      ++|++.+.+||++....   ++..+++..+.++.|.++...++..|+.+.+.+.|+++++++++.++..+++|+..+.+-
T Consensus        89 ~~~~~~~~Lil~~~~~~~~kk~~K~l~k~~~~ve~~~~~~~~l~~wi~~~~~~~g~~i~~~A~~~L~~~~g~dl~~l~~E  168 (318)
T PRK05629         89 VDPSPGIYLIIMHSGGGRTKSMVPKLEKIAVVHEAAKLKPRERPGWVTQEFKNHGVRPTPDVVHALLEGVGSDLRELASA  168 (318)
T ss_pred             hCCCCCeEEEEEcCCcchhhHHHHHHHhcceEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHH
Confidence            56778888888885332   344578888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhCCCCcchhhHHhhhhhhc
Q psy4285          79 LQSAATAHADEVNEDTIFTLLVSRV  103 (533)
Q Consensus        79 l~~~~~~~~~~i~~~~i~~~~~~~~  103 (533)
                      ++.++...++.||.+.|.+++....
T Consensus       169 leKL~~~~~~~It~e~V~~~v~~~~  193 (318)
T PRK05629        169 ISQLVEDTQGNVTVEKVRAYYVGVA  193 (318)
T ss_pred             HHHHHhcCCCCcCHHHHHHHhCCCc
Confidence            9988765456799999977666544

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=97.76  E-value=0.0014  Score=61.25  Aligned_cols=131  Identities=18%  Similarity=0.238  Sum_probs=77.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC---------------chhH-------HHHHHHHHHhcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR---------------GIGI-------VRDQIFQFASTK  365 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~---------------~~~~-------~~~~~~~~~~~~  365 (533)
                      .+++.|++|+|||+++..+...+...  +. .++.+......               ..+.       ..+.+.......
T Consensus        15 r~viIG~sGSGKT~li~~lL~~~~~~--f~-~I~l~t~~~n~~~~~~i~p~~i~~~~~~e~le~~l~~~k~~I~k~~~k~   91 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTLIKSLLYYLRHK--FD-HIFLITPEYNNEYYKYIWPDHIFKVFDKEELEYILIRQKEKIEKYIKKS   91 (241)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhhccc--CC-EEEEEecCCchhhhhhcchhhccccccHHHHHHHHHHHHHHHHHHhhhh
Confidence            48999999999999999998765332  11 11111111100               0011       111122222211


Q ss_pred             cC-CCCCcEEEEEeCCCCCCHHHHHHHHHHHH-hcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         366 TM-HKSSYKLIILDEADAMTNDAQNALRRIIE-KFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       366 ~~-~~~~~~vliiDE~d~l~~~~~~~Ll~~le-~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .. ......++|+|++..- .-....+...+. .+.-++.+|+.+.....+++.+++-...+.+...+..++..++...
T Consensus        92 ~~~k~~~~~LiIlDD~~~~-~~k~~~l~~~~~~gRH~~is~i~l~Q~~~~lp~~iR~n~~y~i~~~~s~~dl~~i~~~~  169 (241)
T PF04665_consen   92 PQKKNNPRFLIILDDLGDK-KLKSKILRQFFNNGRHYNISIIFLSQSYFHLPPNIRSNIDYFIIFNNSKRDLENIYRNM  169 (241)
T ss_pred             cccCCCCCeEEEEeCCCCc-hhhhHHHHHHHhcccccceEEEEEeeecccCCHHHhhcceEEEEecCcHHHHHHHHHhc
Confidence            11 1245789999998641 112233444443 3456788999999999999999887765555567877777776665

This is thought to be an ATPase involved in viral DNA packaging [].

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=97.76  E-value=0.00026  Score=62.48  Aligned_cols=106  Identities=14%  Similarity=0.174  Sum_probs=62.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceE-EecCCCCCch-----------------------------hHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVL-ELNASDDRGI-----------------------------GIVRDQ  357 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~-~~~~~~~~~~-----------------------------~~~~~~  357 (533)
                      -+.+++++|.||||.|..+|-...+.+. ...++ .+.+....+.                             ...++.
T Consensus         7 li~v~~g~GkGKtt~a~g~a~ra~~~g~-~v~ivQFlKg~~~~GE~~~l~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~   85 (173)
T TIGR00708         7 IIIVHTGNGKGKTTAAFGMALRALGHGK-KVGVIQFIKGAWPNGERAAFEPHGVEFQVMGTGFTWETQNREADTAIAKAA   85 (173)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHHCCC-eEEEEEEecCCcccChHHHHHhcCcEEEECCCCCeecCCCcHHHHHHHHHH
Confidence            4788999999999999999988765531 11111 1111100000                             111111


Q ss_pred             HHHHHhcccCCCCCcEEEEEeCCCC------CCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccc
Q psy4285         358 IFQFASTKTMHKSSYKLIILDEADA------MTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRC  422 (533)
Q Consensus       358 ~~~~~~~~~~~~~~~~vliiDE~d~------l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~  422 (533)
                      .......  .....+++||+||+..      ++.   +.++++|+..|.++-+|+|+...   ++.|....
T Consensus        86 ~~~a~~~--l~~~~~DlvVLDEi~~A~~~gli~~---~~v~~lL~~rp~~~evVlTGR~~---p~~l~e~A  148 (173)
T TIGR00708        86 WQHAKEM--LADPELDLVLLDELTYALKYGYLDV---EEVVEALQERPGHQHVIITGRGC---PQDLLELA  148 (173)
T ss_pred             HHHHHHH--HhcCCCCEEEehhhHHHHHCCCcCH---HHHHHHHHhCCCCCEEEEECCCC---CHHHHHhC
Confidence            1111111  1135789999999863      333   36778888889999999999755   34444443

Alternate name: corrinoid adenosyltransferase.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.73  E-value=0.00018  Score=74.24  Aligned_cols=95  Identities=17%  Similarity=0.173  Sum_probs=79.3

Q ss_pred             ceEEEEEcCCC----CcCchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Q psy4285           7 NVRFCIICNYL----SKITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNIL   79 (533)
Q Consensus         7 ~~~~il~~~~~----~~i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l   79 (533)
                      +..+|++|+.+    ..+.+.|+|||   .++.+.+|+.++...+|++.++..++.++++.++.|+....||+|..++.|
T Consensus       235 ~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k~~~~~~~l~~evl~~la~~~~~dir~L~g~l  314 (445)
T PRK12422        235 GKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERKAEALSIRIEETALDFLIEALSSNVKSLLHAL  314 (445)
T ss_pred             CCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Confidence            34577777653    45779999999   799999999999999999999999999999999999999999999999999


Q ss_pred             HHHH---Hh---CCCCcchhhHHhhhhh
Q psy4285          80 QSAA---TA---HADEVNEDTIFTLLVS  101 (533)
Q Consensus        80 ~~~~---~~---~~~~i~~~~i~~~~~~  101 (533)
                      +.++   ..   .+..||.+.+.+++..
T Consensus       315 ~~l~~~~a~~~~~~~~i~~~~~~~~l~~  342 (445)
T PRK12422        315 TLLAKRVAYKKLSHQLLYVDDIKALLHD  342 (445)
T ss_pred             HHHHHHHHHHHhhCCCCCHHHHHHHHHH
Confidence            9884   21   2345888887766653

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

Probab=97.72  E-value=0.00046  Score=70.42  Aligned_cols=131  Identities=20%  Similarity=0.224  Sum_probs=82.0

Q ss_pred             hhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch-hHHHHHHHHHHhcccCCCCCcE
Q psy4285         295 YKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI-GIVRDQIFQFASTKTMHKSSYK  373 (533)
Q Consensus       295 ~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  373 (533)
                      ..+.+.+..... .++++||.+|||||+++.+.+.+..      ..+.++..+.... ....+....+.....   .+..
T Consensus        27 ~~l~~~~~~~~~-i~~i~GpR~~GKTtll~~l~~~~~~------~~iy~~~~d~~~~~~~l~d~~~~~~~~~~---~~~~   96 (398)
T COG1373          27 PRLIKKLDLRPF-IILILGPRQVGKTTLLKLLIKGLLE------EIIYINFDDLRLDRIELLDLLRAYIELKE---REKS   96 (398)
T ss_pred             HHHHhhcccCCc-EEEEECCccccHHHHHHHHHhhCCc------ceEEEEecchhcchhhHHHHHHHHHHhhc---cCCc
Confidence            334444443322 5799999999999999887776522      1444444433221 122333333333222   1457


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC----CCChhhhccceeeeecCCCHHHHHHH
Q psy4285         374 LIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS----KIPPAIQSRCTRFRFGPLDSSLIMSR  438 (533)
Q Consensus       374 vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~----~l~~~l~sR~~~i~~~~~~~~~~~~~  438 (533)
                      .+|+||++.+..+ ..++..+.+..+.  .+++++....    ...+.+..|...+.+.|++-.+....
T Consensus        97 yifLDEIq~v~~W-~~~lk~l~d~~~~--~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Efl~~  162 (398)
T COG1373          97 YIFLDEIQNVPDW-ERALKYLYDRGNL--DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREFLKL  162 (398)
T ss_pred             eEEEecccCchhH-HHHHHHHHccccc--eEEEECCchhhhccchhhhcCCCceeEEECCCCHHHHHhh
Confidence            9999999999775 4466666665443  6676665443    45567777888999999998888654

>KOG1968|consensus

Probab=97.70  E-value=6.8e-05  Score=82.25  Aligned_cols=153  Identities=20%  Similarity=0.231  Sum_probs=108.4

Q ss_pred             hhhccccchhHHHHHhchHHHHhhc-CCChhhH--------HHHHhhccC--ccccccCCCChhhHHHHHHHHHhccccc
Q psy4285         100 VSRVEKYRPSTLDELVSHQDIISTI-EIPESML--------VDLVLKMSD--IEYRLAAGTSEKIQLSALIAAFNSARDK  168 (533)
Q Consensus       100 ~~~~ek~~~~~l~~lls~~~~l~~l-~~~~~~~--------~~~~~~~~~--~~~~~~~G~~~~~~l~~~~~~~~~~~~~  168 (533)
                      ..|.++|.|....++..+......+ +|.+.|+        .........  ....|+||.|+|+.+...+..+.     
T Consensus       308 ~~~~~k~~p~~~k~~~~~~~~~~~~~~~l~~~k~~~~~sy~~~~~~ss~~~~~l~~G~pGigKT~~~h~~~k~~g-----  382 (871)
T KOG1968|consen  308 AGWTEKYQPTSSKALEGNASSSKKASKWLAKSKDKEKSSYKENEPDSSKKKALLLSGPPGIGKTTAAHKAAKELG-----  382 (871)
T ss_pred             cccccccccccHHhhhcccchhhhhhhHHHhhhccccccccccCcchhhHHHHHhcCCCCCCchhhHhhhhhhcc-----
Confidence            4688999998877776655443222 2322221        000000111  35678999999998877777776     


Q ss_pred             ceeeeecCCcccchhhhHHHHhhhhhcccccCCC------------ceEEEEcCccccCHHHHH-------HHH------
Q psy4285         169 LEVLELNASDDRGIGIVRDQIFQFASTKTMHKSS------------YKLIILDEADAMTNDAQN-------ALR------  223 (533)
Q Consensus       169 ~~~~e~nasd~~g~~~~~d~i~~~a~~~~l~~~~------------~~~iilDE~d~l~~~a~~-------~LR------  223 (533)
                      +.++|.|++|.|+.....++++.+.....+.+..            ..++++||+|.|......       +.+      
T Consensus       383 ~~v~E~Nas~~RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vil~devD~~~~~dRg~v~~l~~l~~ks~~Pi  462 (871)
T KOG1968|consen  383 FKVVEKNASDVRSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLILMDEVDGMFGEDRGGVSKLSSLCKKSSRPL  462 (871)
T ss_pred             cceeecCccccccccHHHhhhhccccccchhhhhcccccccccccceeEEEEeccccccchhhhhHHHHHHHHHhccCCe
Confidence            8999999999999998889998888877775433            118899999999762222       111      


Q ss_pred             ------------------------------------------ccCCCChhHHHHHHHhccCchHHhhcHHHHHHhh
Q psy4285         224 ------------------------------------------RKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATA  257 (533)
Q Consensus       224 ------------------------------------------r~~~~~~~~l~~l~~~s~~di~~~L~~L~~~~~~  257 (533)
                                                                ..+.++++.++.+...+.+|+|+.++.|+.....
T Consensus       463 v~~cndr~~p~sr~~~~~~~~l~f~kP~~~~i~~ri~si~~se~~ki~~~~l~~~s~~~~~DiR~~i~~lq~~~~~  538 (871)
T KOG1968|consen  463 VCTCNDRNLPKSRALSRACSDLRFSKPSSELIRSRIMSICKSEGIKISDDVLEEISKLSGGDIRQIIMQLQFWSLS  538 (871)
T ss_pred             EEEecCCCCccccchhhhcceeeecCCcHHHHHhhhhhhhcccceecCcHHHHHHHHhcccCHHHHHHHHhhhhcc
Confidence                                                      0357889999999999999999999999987443

>PRK07452 DNA polymerase III subunit delta; Validated

Probab=97.69  E-value=0.00027  Score=70.60  Aligned_cols=101  Identities=15%  Similarity=0.221  Sum_probs=84.2

Q ss_pred             CCCCCCceEEEEEcCCC----CcCchhhhccceeEEeCCC---CHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHH
Q psy4285           1 IEKFTTNVRFCIICNYL----SKITPAIQSRCTRFRFGPL---DSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMR   73 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~----~~i~~~i~SRc~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r   73 (533)
                      +|+||+++++|+++...    .+...++...|.+..|.++   +.+++..|++..+.+.|+.+++++++.++...+||++
T Consensus        88 l~~~~~~~~li~~~~~~~d~r~k~~k~l~k~~~~~~~~~~~~~~~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~  167 (326)
T PRK07452         88 LPLIPENTHLLLTNTKKPDGRLKSTKLLQKLAEEKEFSLIPPWDTEGLKQLVERTAQELGVKLTPEAAELLAEAVGNDSR  167 (326)
T ss_pred             HcCCCCCcEEEEEeCCCcchHHHHHHHHHHceeEEEecCCCcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHH
Confidence            47888999999975432    3466778889999998776   4577999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhC---CCCcchhhHHhhhhh
Q psy4285          74 KVLNILQSAATAH---ADEVNEDTIFTLLVS  101 (533)
Q Consensus        74 ~a~~~l~~~~~~~---~~~i~~~~i~~~~~~  101 (533)
                      .+.|-++.++...   +..||.+.|..++..
T Consensus       168 ~l~~EleKL~ly~~~~~~~It~~~V~~~v~~  198 (326)
T PRK07452        168 RLYNELEKLALYAENSTKPISAEEVKALVSN  198 (326)
T ss_pred             HHHHHHHHHHHhccCCCCccCHHHHHHHhcc
Confidence            9999999998752   346999999876653

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.67  E-value=0.00021  Score=74.49  Aligned_cols=93  Identities=12%  Similarity=0.145  Sum_probs=75.3

Q ss_pred             EEEEEcCC-CCc---Cchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q psy4285           9 RFCIICNY-LSK---ITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQS   81 (533)
Q Consensus         9 ~~il~~~~-~~~---i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~   81 (533)
                      .+++++|. +..   +.|.|+||+   .++.|.+|+.++...+|++.+...++.++++.++.|+..+.||+|.++..|+.
T Consensus       246 ~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~R~l~~~l~~  325 (450)
T PRK00149        246 QIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIAILKKKAEEEGIDLPDEVLEFIAKNITSNVRELEGALNR  325 (450)
T ss_pred             cEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHcCcCCCHHHHHHHHHH
Confidence            35666654 333   668999999   68999999999999999999988899999999999999999999997777766


Q ss_pred             HHH---hCCCCcchhhHHhhhhh
Q psy4285          82 AAT---AHADEVNEDTIFTLLVS  101 (533)
Q Consensus        82 ~~~---~~~~~i~~~~i~~~~~~  101 (533)
                      +..   ..+..||.+.+.+++..
T Consensus       326 l~~~~~~~~~~it~~~~~~~l~~  348 (450)
T PRK00149        326 LIAYASLTGKPITLELAKEALKD  348 (450)
T ss_pred             HHHHHHhhCCCCCHHHHHHHHHH
Confidence            643   23456888888776654

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.66  E-value=6.1e-05  Score=73.24  Aligned_cols=87  Identities=13%  Similarity=0.229  Sum_probs=73.4

Q ss_pred             CCCCCCceEEEEEcCC-----CCcCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHh-------
Q psy4285           1 IEKFTTNVRFCIICNY-----LSKITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL-------   67 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~-----~~~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-------   67 (533)
                      ||+...++++|+++++     +..++|+++||| ..+.|++++.+|+.+++.+.+++.+..+++++...+..+       
T Consensus       154 le~~~~~~~vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~l~~edl~~I~~~~l~~~~~~l~~~a~~~L~~~l~~~~~~  233 (284)
T TIGR02880       154 MENQRDDLVVILAGYKDRMDSFFESNPGFSSRVAHHVDFPDYSEAELLVIAGLMLKEQQYRFSAEAEEAFADYIALRRTQ  233 (284)
T ss_pred             HhcCCCCEEEEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHHHHHHHHHHHHHhccccCHHHHHHHHHHHHHhCCC
Confidence            4667788888888754     235689999999 679999999999999999999888888999988888776       


Q ss_pred             -cCCCHHHHHHHHHHHHHhCC
Q psy4285          68 -SDGDMRKVLNILQSAATAHA   87 (533)
Q Consensus        68 -~~g~~r~a~~~l~~~~~~~~   87 (533)
                       .-||.|.+.|+++.+...+.
T Consensus       234 ~~~GN~R~lrn~ve~~~~~~~  254 (284)
T TIGR02880       234 PHFANARSIRNAIDRARLRQA  254 (284)
T ss_pred             CCCChHHHHHHHHHHHHHHHH
Confidence             24999999999999987654

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.

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=97.66  E-value=0.00016  Score=65.93  Aligned_cols=99  Identities=19%  Similarity=0.261  Sum_probs=67.4

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQ  388 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~  388 (533)
                      ++|.|+.|+||||..+.|+...+..     .   +...  ...+....+.            +.-++.+||++.+.....
T Consensus        55 lvl~G~QG~GKStf~~~L~~~~~~d-----~---~~~~--~~kd~~~~l~------------~~~iveldEl~~~~k~~~  112 (198)
T PF05272_consen   55 LVLVGKQGIGKSTFFRKLGPEYFSD-----S---INDF--DDKDFLEQLQ------------GKWIVELDELDGLSKKDV  112 (198)
T ss_pred             eeEecCCcccHHHHHHHHhHHhccC-----c---cccC--CCcHHHHHHH------------HhHheeHHHHhhcchhhH
Confidence            7999999999999999997664222     1   1111  1122222221            224899999999997777


Q ss_pred             HHHHHHHHh---------------cCCCcEEEEEeCCCCCC-ChhhhccceeeeecC
Q psy4285         389 NALRRIIEK---------------FTTNVRFCIICNYLSKI-PPAIQSRCTRFRFGP  429 (533)
Q Consensus       389 ~~Ll~~le~---------------~~~~~~~I~~~n~~~~l-~~~l~sR~~~i~~~~  429 (533)
                      +.|-..+..               .+..+.||.|||...-| |++=-|||..+.+..
T Consensus       113 ~~lK~~iT~~~~~~R~pY~~~~~~~~R~~~figTtN~~~~L~D~TGnRRf~~v~v~~  169 (198)
T PF05272_consen  113 EALKSFITRRTDTYRPPYGRDPEEFPRRAVFIGTTNDDDFLKDPTGNRRFWPVEVSK  169 (198)
T ss_pred             HHHHHHhcccceeeecCCcCcceeeceeEEEEeccCCcceeeCCCCCeEEEEEEEcC
Confidence            777777642               24567789999987744 566678998777776

>PRK05574 holA DNA polymerase III subunit delta; Reviewed

Probab=97.66  E-value=0.00056  Score=68.73  Aligned_cols=97  Identities=8%  Similarity=0.135  Sum_probs=80.6

Q ss_pred             ceEEEEEcCCCC---cC---chhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           7 NVRFCIICNYLS---KI---TPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         7 ~~~~il~~~~~~---~i---~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ++.|++.++...   ++   ..++.++|.++.|++++..++..|++..+.+.|+.+++++++.++..++||++.+.+-++
T Consensus       111 ~~~li~~~~~~~~~~k~~k~~k~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~  190 (340)
T PRK05574        111 DLLLIVRLPKLDKAKKKSAWFKALKKKAVVVEAQPPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELE  190 (340)
T ss_pred             cEEEEEECCcCCHHHHhhHHHHHHHhCceEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHH
Confidence            455666654322   33   678999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhC-CCCcchhhHHhhhhhhc
Q psy4285          81 SAATAH-ADEVNEDTIFTLLVSRV  103 (533)
Q Consensus        81 ~~~~~~-~~~i~~~~i~~~~~~~~  103 (533)
                      .++... +..||.+.|.+++....
T Consensus       191 KL~l~~~~~~It~~~I~~~i~~~~  214 (340)
T PRK05574        191 KLALLYPDGKITLEDVEEAVPDSA  214 (340)
T ss_pred             HHHhhcCCCCCCHHHHHHHHhhhh
Confidence            998754 33499999877665543

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=97.65  E-value=0.00015  Score=73.06  Aligned_cols=22  Identities=45%  Similarity=0.652  Sum_probs=21.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++.|.||||||.+|..+++.+
T Consensus         4 ~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    4 ILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             EEEEecCCcCHHHHHHHHHHHh
Confidence            7899999999999999999998

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK14532 adenylate kinase; Provisional

Probab=97.63  E-value=0.00097  Score=60.76  Aligned_cols=23  Identities=30%  Similarity=0.634  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++.||||+||||+++.+|+.+
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~   24 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEER   24 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            47999999999999999999886

>PRK07914 hypothetical protein; Reviewed

Probab=97.62  E-value=0.00062  Score=67.66  Aligned_cols=103  Identities=8%  Similarity=0.114  Sum_probs=84.3

Q ss_pred             CCCCCCceEEEEEcCCCC---cCchhhhcc-ceeEEeCCC-CHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLS---KITPAIQSR-CTRFRFGPL-DSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKV   75 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~---~i~~~i~SR-c~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a   75 (533)
                      ++.||+.+.+||+++...   ++..+|+.. |.++.|.++ +..++..|+++.+.+.|+.+++++++.++...+||+..+
T Consensus        88 l~~~~~~t~lil~~~~~~~~kk~~K~L~k~g~~~v~~~~~~~~~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l  167 (320)
T PRK07914         88 AADLPPGTVLVVVHSGGGRAKALANQLRKLGAEVHPCARITKAAERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLREL  167 (320)
T ss_pred             HhCCCCCeEEEEEecCCcchhHHHHHHHHCCCEEEecCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHH
Confidence            367888888888864322   234477766 679999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCCCcchhhHHhhhhhhc
Q psy4285          76 LNILQSAATAHADEVNEDTIFTLLVSRV  103 (533)
Q Consensus        76 ~~~l~~~~~~~~~~i~~~~i~~~~~~~~  103 (533)
                      -+-++.++...++.||.+.|.+++....
T Consensus       168 ~~EleKL~~~~~~~It~e~V~~~v~~~~  195 (320)
T PRK07914        168 ASACSQLVADTGGAVDAAAVRRYHSGKA  195 (320)
T ss_pred             HHHHHHHhcCCCCCcCHHHHHHHcCCCe
Confidence            9999988754455799999877665443

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=97.60  E-value=0.00023  Score=83.58  Aligned_cols=100  Identities=19%  Similarity=0.164  Sum_probs=62.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccc-cCcceEEecCCCCCc----------hhHHHHHHHHHHh---cccCCCCCcE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQ-FNAMVLELNASDDRG----------IGIVRDQIFQFAS---TKTMHKSSYK  373 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~-~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~---~~~~~~~~~~  373 (533)
                      .+++.|.|||||||+.+.+...+..... .+..++-+ +++++.          ...+...+.....   .........+
T Consensus       986 ~~~I~G~AGTGKTT~l~~v~~~~~~l~~~~~~~V~gl-APTgrAAk~L~e~Gi~A~TI~s~L~~~~~~~~~~~~~~~~~~ 1064 (1747)
T PRK13709        986 FTVVQGYAGVGKTTQFRAVMSAVNTLPESERPRVVGL-GPTHRAVGEMRSAGVDAQTLASFLHDTQLQQRSGETPDFSNT 1064 (1747)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHhhcccCceEEEE-CCcHHHHHHHHhcCcchhhHHHHhcccccccccccCCCCCCc
Confidence            4899999999999999999887531100 02223322 333332          2233333321100   0000113468


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         374 LIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       374 vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ++||||++|++......|++.++.  .+.++|++++.
T Consensus      1065 llIVDEaSMv~~~~m~~Ll~~~~~--~garvVLVGD~ 1099 (1747)
T PRK13709       1065 LFLLDESSMVGNTDMARAYALIAA--GGGRAVSSGDT 1099 (1747)
T ss_pred             EEEEEccccccHHHHHHHHHhhhc--CCCEEEEecch
Confidence            999999999999999999998863  35899999853

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=97.60  E-value=0.00042  Score=63.02  Aligned_cols=24  Identities=42%  Similarity=0.447  Sum_probs=21.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      ++++||||||||+++..++.....
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~   25 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLA   25 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHH
Confidence            689999999999999999887643

A related protein is found in archaea.

>PRK14528 adenylate kinase; Provisional

Probab=97.59  E-value=0.00084  Score=60.99  Aligned_cols=23  Identities=39%  Similarity=0.814  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++.||||+||||+++.+++.+
T Consensus         3 ~i~i~G~pGsGKtt~a~~la~~~   25 (186)
T PRK14528          3 NIIFMGPPGAGKGTQAKILCERL   25 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999876

>KOG0482|consensus

Probab=97.59  E-value=0.00036  Score=70.04  Aligned_cols=110  Identities=18%  Similarity=0.254  Sum_probs=67.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEE-ecCCCCCc--hhHHHHHHHH-H--HhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLE-LNASDDRG--IGIVRDQIFQ-F--ASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~-~~~~~~~~--~~~~~~~~~~-~--~~~~~~~~~~~~vliiDE~d  381 (533)
                      |+++.|.||+.||-+.+.+.+..-.      ..+. -.++.+-+  ..+++.-+-. .  ..... .-+..+|..|||+|
T Consensus       377 NicLmGDPGVAKSQLLkyi~rlapR------gvYTTGrGSSGVGLTAAVmkDpvTgEM~LEGGAL-VLAD~GICCIDEfD  449 (721)
T KOG0482|consen  377 NICLMGDPGVAKSQLLKYISRLAPR------GVYTTGRGSSGVGLTAAVMKDPVTGEMVLEGGAL-VLADGGICCIDEFD  449 (721)
T ss_pred             eEEecCCCchhHHHHHHHHHhcCcc------cceecCCCCCccccchhhhcCCCCCeeEeccceE-EEccCceEeehhhh
Confidence            5999999999999999999885411      1111 11222111  1122211100 0  00000 01457899999999


Q ss_pred             CCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC-------------CCChhhhcccee
Q psy4285         382 AMTNDAQNALRRIIEKF-------------TTNVRFCIICNYLS-------------KIPPAIQSRCTR  424 (533)
Q Consensus       382 ~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~-------------~l~~~l~sR~~~  424 (533)
                      +|.....-++.+.||+.             ...+.++.+.|...             .|+++|+|||+.
T Consensus       450 KM~e~DRtAIHEVMEQQTISIaKAGI~TtLNAR~sILaAANPayGRYnprrs~e~NI~LPaALLSRFDl  518 (721)
T KOG0482|consen  450 KMDESDRTAIHEVMEQQTISIAKAGINTTLNARTSILAAANPAYGRYNPRRSPEQNINLPAALLSRFDL  518 (721)
T ss_pred             hhhhhhhHHHHHHHHhhhhhhhhhccccchhhhHHhhhhcCccccccCcccChhHhcCCcHHHHHhhhh
Confidence            99998888999999863             23355666666431             589999999963

>KOG0481|consensus

Probab=97.58  E-value=8.3e-05  Score=74.50  Aligned_cols=121  Identities=19%  Similarity=0.233  Sum_probs=74.0

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecC--CC--CCchhHHHHHHH-HHHhcc-cCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNA--SD--DRGIGIVRDQIF-QFASTK-TMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~--~~--~~~~~~~~~~~~-~~~~~~-~~~~~~~~vliiDE~  380 (533)
                      -|+|+.|.|||.|+-+.+.+-+..       .--++.++  +.  +....+++.-.. .|.... ...-+.++|+.|||+
T Consensus       365 INVLLLGDPgtAKSQlLKFvEkvs-------PIaVYTSGKGSSAAGLTASV~RD~~tReFylEGGAMVLADgGVvCIDEF  437 (729)
T KOG0481|consen  365 INVLLLGDPGTAKSQLLKFVEKVS-------PIAVYTSGKGSSAAGLTASVIRDPSTREFYLEGGAMVLADGGVVCIDEF  437 (729)
T ss_pred             eeEEEecCCchhHHHHHHHHHhcC-------ceEEEecCCCcccccceeeEEecCCcceEEEecceEEEecCCEEEeehh
Confidence            359999999999999999876542       11122221  11  111222222111 111100 001245789999999


Q ss_pred             CCCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC-------------CCChhhhccceeeeecCCCHHH
Q psy4285         381 DAMTNDAQNALRRIIEKF-------------TTNVRFCIICNYLS-------------KIPPAIQSRCTRFRFGPLDSSL  434 (533)
Q Consensus       381 d~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~-------------~l~~~l~sR~~~i~~~~~~~~~  434 (533)
                      |+|..+..-++.+.||+.             ...+.++.+.|...             .+-++++|||+.+++..-...+
T Consensus       438 DKMre~DRVAIHEAMEQQTISIAKAGITT~LNSRtSVLAAANpvfGRyDd~Kt~~dNIDf~~TILSRFDmIFIVKD~h~~  517 (729)
T KOG0481|consen  438 DKMREDDRVAIHEAMEQQTISIAKAGITTTLNSRTSVLAAANPVFGRYDDTKTGEDNIDFMPTILSRFDMIFIVKDEHDE  517 (729)
T ss_pred             hccCchhhhHHHHHHHhhhHHHhhhcceeeecchhhhhhhcCCccccccccCCcccccchhhhHhhhccEEEEEeccCcc
Confidence            999999888999999863             34566777777542             2568999999877775443333

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=97.57  E-value=0.00029  Score=73.82  Aligned_cols=43  Identities=16%  Similarity=0.288  Sum_probs=36.2

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      .+++++|+||+ +.++++.+..+++++++.-+++.+|-++.++.
T Consensus       532 ~kP~~v~LDEATsALDe~~e~~l~q~l~~~lp~~tvISV~Hr~t  575 (604)
T COG4178         532 HKPKWVFLDEATSALDEETEDRLYQLLKEELPDATVISVGHRPT  575 (604)
T ss_pred             cCCCEEEEecchhccChHHHHHHHHHHHhhCCCCEEEEeccchh
Confidence            46899999998 67889999999999988656788999987654

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.56  E-value=0.00097  Score=66.66  Aligned_cols=24  Identities=38%  Similarity=0.515  Sum_probs=21.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++|.||+|+||||++..++..+.
T Consensus       139 ii~lvGptGvGKTTtiakLA~~~~  162 (374)
T PRK14722        139 VFALMGPTGVGKTTTTAKLAARCV  162 (374)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            589999999999999999998763

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=97.56  E-value=0.00029  Score=81.81  Aligned_cols=100  Identities=18%  Similarity=0.170  Sum_probs=60.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc-cccCcceEEecCCCCCch----------hHHHHHHHHHH---hcccCCCCCcE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK-AQFNAMVLELNASDDRGI----------GIVRDQIFQFA---STKTMHKSSYK  373 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~-~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~---~~~~~~~~~~~  373 (533)
                      .+++.|+|||||||+.+.+...+..- ...+..++-+ +++++..          ..+...+....   ...........
T Consensus       854 ~~~IqG~AGTGKTT~l~~i~~~~~~l~e~~g~~V~gl-APTgkAa~~L~e~Gi~A~TIasfL~~~~~~~~~~~~~~~~~~  932 (1623)
T PRK14712        854 FTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGL-GPTHRAVGEMRSAGVDAQTLASFLHDTQLQQRSGETPDFSNT  932 (1623)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHHhhccCceEEEE-echHHHHHHHHHhCchHhhHHHHhccccchhhcccCCCCCCc
Confidence            48999999999999998887654210 0002223322 3333222          22333222110   00000012468


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         374 LIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       374 vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ++||||++|++......|++.++.  .+.++|++++.
T Consensus       933 llIVDEASMV~~~~m~~ll~~~~~--~garvVLVGD~  967 (1623)
T PRK14712        933 LFLLDESSMVGNTDMARAYALIAA--GGGRAVASGDT  967 (1623)
T ss_pred             EEEEEccccccHHHHHHHHHhhhh--CCCEEEEEcch
Confidence            999999999999999999998863  45899999964

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=97.55  E-value=0.0011  Score=57.76  Aligned_cols=140  Identities=19%  Similarity=0.203  Sum_probs=73.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDA  387 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~  387 (533)
                      .++++|.|||||||+++.++ .+      +..++.++.           ..+....... .....+=+++|+        
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~-~l------g~~~i~l~e-----------l~~e~~~~~~-~de~r~s~~vD~--------   54 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR-EL------GYKVIELNE-----------LAKENGLYTE-YDELRKSVIVDV--------   54 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH-Hh------CCceeeHHH-----------HHHhcCCeec-cCCccceEEeeH--------
Confidence            47899999999999999999 55      555554431           1111000000 011223444443        


Q ss_pred             HHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC---HHHHHH-----HHHH--HHHHH
Q psy4285         388 QNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD---DISFFN-----IIIW--YIKIQ  457 (533)
Q Consensus       388 ~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~---~~~~~~-----ll~~--~~~l~  457 (533)
                       ..+...+++.-.....|+-+.....++     -|..+..-.-+++.+.++|+..   ++.+.+     +++.  .+...
T Consensus        55 -d~~~~~le~~~~~~~~Ivd~H~~hl~~-----~~dlVvVLR~~p~~L~~RLk~RGy~~eKI~ENveAEi~~vi~~EA~E  128 (180)
T COG1936          55 -DKLRKRLEELLREGSGIVDSHLSHLLP-----DCDLVVVLRADPEVLYERLKGRGYSEEKILENVEAEILDVILIEAVE  128 (180)
T ss_pred             -HHHHHHHHHHhccCCeEeechhhhcCC-----CCCEEEEEcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence             344444443212223444444333222     4566666677788888888887   222222     2221  11111


Q ss_pred             HH-----HHhcCCCHHHHHHHHHHHHHh
Q psy4285         458 EI-----KIEKGLALTDILTEISLLVHR  480 (533)
Q Consensus       458 ~l-----~~~~~~~~~di~~~~~~~~~~  480 (533)
                      ..     ..+.+.++.++...+.+.+..
T Consensus       129 ~~~~v~evdtt~~s~ee~~~~i~~ii~~  156 (180)
T COG1936         129 RFEAVIEVDTTNRSPEEVAEEIIDIIGG  156 (180)
T ss_pred             hcCceEEEECCCCCHHHHHHHHHHHHcc
Confidence            10     034567888888888877663

>PRK06851 hypothetical protein; Provisional

Probab=97.55  E-value=0.00028  Score=70.22  Aligned_cols=25  Identities=32%  Similarity=0.535  Sum_probs=22.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      +++.|+|||||||+++.+++++...
T Consensus       217 ~~i~G~pG~GKstl~~~i~~~a~~~  241 (367)
T PRK06851        217 YFLKGRPGTGKSTMLKKIAKAAEER  241 (367)
T ss_pred             EEEeCCCCCcHHHHHHHHHHHHHhC
Confidence            8999999999999999999998554

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.55  E-value=6.2e-05  Score=69.54  Aligned_cols=21  Identities=52%  Similarity=0.762  Sum_probs=18.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~  328 (533)
                      .++|||+||+||||+|+.++.
T Consensus        14 ~~liyG~~G~GKtt~a~~~~~   34 (220)
T TIGR01618        14 MYLIYGKPGTGKTSTIKYLPG   34 (220)
T ss_pred             EEEEECCCCCCHHHHHHhcCC
Confidence            389999999999999998863

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.54  E-value=0.00048  Score=70.94  Aligned_cols=96  Identities=13%  Similarity=0.122  Sum_probs=76.0

Q ss_pred             ceEEEEEcCC-C---CcCchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Q psy4285           7 NVRFCIICNY-L---SKITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNIL   79 (533)
Q Consensus         7 ~~~~il~~~~-~---~~i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l   79 (533)
                      +..+|+++|. +   ..+.+.|+||+   .++.|.+|+.++...+|++.+...++.++++.++.|+....||+|.....|
T Consensus       232 ~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~r~l~~~l  311 (405)
T TIGR00362       232 GKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQKKAEEEGLELPDEVLEFIAKNIRSNVRELEGAL  311 (405)
T ss_pred             CCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Confidence            3457777764 2   24668899998   579999999999999999999999999999999999999999999866555


Q ss_pred             HHH---HHhCCCCcchhhHHhhhhhh
Q psy4285          80 QSA---ATAHADEVNEDTIFTLLVSR  102 (533)
Q Consensus        80 ~~~---~~~~~~~i~~~~i~~~~~~~  102 (533)
                      +.+   +...+..||.+.+.+++...
T Consensus       312 ~~l~~~a~~~~~~it~~~~~~~L~~~  337 (405)
T TIGR00362       312 NRLLAYASLTGKPITLELAKEALKDL  337 (405)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHh
Confidence            554   33344568888877766543

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).

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=97.53  E-value=0.00027  Score=64.03  Aligned_cols=92  Identities=22%  Similarity=0.320  Sum_probs=52.5

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHHccccc--cCcceEEecCCCC-----Cch---------hHHH------HHHHHHHh
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKLYTKAQ--FNAMVLELNASDD-----RGI---------GIVR------DQIFQFAS  363 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l~~~~~--~~~~~~~~~~~~~-----~~~---------~~~~------~~~~~~~~  363 (533)
                      ..|.|+.|||||||||+.+-+|+.+...-.  ....+.-++....     .+.         +..+      ..+.... 
T Consensus       137 ~lntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDersEIag~~~gvpq~~~g~R~dVld~cpk~~gmmmaIr-  215 (308)
T COG3854         137 WLNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQHGRGRRMDVLDPCPKAEGMMMAIR-  215 (308)
T ss_pred             ceeeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEeccchhhccccCCchhhhhhhhhhcccchHHHHHHHHHH-
Confidence            346899999999999999999998743210  1112222222110     111         1111      1111111 


Q ss_pred             cccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEe
Q psy4285         364 TKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIIC  408 (533)
Q Consensus       364 ~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~  408 (533)
                           .-.+.|+|+||+....  ..-+++.+++   ..+.+|.|.
T Consensus       216 -----sm~PEViIvDEIGt~~--d~~A~~ta~~---~GVkli~Ta  250 (308)
T COG3854         216 -----SMSPEVIIVDEIGTEE--DALAILTALH---AGVKLITTA  250 (308)
T ss_pred             -----hcCCcEEEEeccccHH--HHHHHHHHHh---cCcEEEEee
Confidence                 1246799999999853  3356667774   667888776

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=97.52  E-value=0.00081  Score=68.28  Aligned_cols=92  Identities=23%  Similarity=0.278  Sum_probs=70.7

Q ss_pred             CceEEEEEcCCCC---cCchhhhccc--eeEEeCCCCHHHHHHHHHHHHhh--cCCCCCHHHHHHH---HHhcCCCHHHH
Q psy4285           6 TNVRFCIICNYLS---KITPAIQSRC--TRFRFGPLDSSLIMSRLDYVIEQ--EKVNVTPDGKKAI---IDLSDGDMRKV   75 (533)
Q Consensus         6 ~~~~~il~~~~~~---~i~~~i~SRc--~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~~~---~~~~~g~~r~a   75 (533)
                      .++.+|+++|.+.   .+.+.++|||  ..+.|+|++.+++.++|+..++.  ....+++++++.+   +..++||+|+|
T Consensus       164 ~~v~lI~i~n~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~a  243 (365)
T TIGR02928       164 AKVGVIGISNDLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKA  243 (365)
T ss_pred             CeEEEEEEECCcchHhhcCHHHhccCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHH
Confidence            6788999998775   6889999998  47999999999999999987752  2234677776664   44557999999


Q ss_pred             HHHHHHHHHh----CCCCcchhhHHh
Q psy4285          76 LNILQSAATA----HADEVNEDTIFT   97 (533)
Q Consensus        76 ~~~l~~~~~~----~~~~i~~~~i~~   97 (533)
                      ++++..+...    ....|+.+.+..
T Consensus       244 l~~l~~a~~~a~~~~~~~it~~~v~~  269 (365)
T TIGR02928       244 IDLLRVAGEIAEREGAERVTEDHVEK  269 (365)
T ss_pred             HHHHHHHHHHHHHcCCCCCCHHHHHH
Confidence            9999987643    223588877654

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.51  E-value=0.0021  Score=73.62  Aligned_cols=140  Identities=16%  Similarity=0.145  Sum_probs=81.2

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHH-----------------------------
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQ-----------------------------  357 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------------  357 (533)
                      +-++++||+|.||||++..+++...     ...++.+...+..........                             
T Consensus        33 ~~~~v~apaG~GKTtl~~~~~~~~~-----~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  107 (903)
T PRK04841         33 RLVLVTSPAGYGKTTLISQWAAGKN-----NLGWYSLDESDNQPERFASYLIAALQQATNGHCSKSEALAQKRQYASLSS  107 (903)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCC-----CeEEEecCcccCCHHHHHHHHHHHHHHhcCcccchhhhhhccCCcCCHHH
Confidence            4589999999999999999876431     223444443332111110110                             


Q ss_pred             -HHHHHhcccCCCCCcEEEEEeCCCCCCHHH-HHHHHHHHHhcCCCcEEEEEeCCCCCCC-hhhh--ccceeeeec--CC
Q psy4285         358 -IFQFASTKTMHKSSYKLIILDEADAMTNDA-QNALRRIIEKFTTNVRFCIICNYLSKIP-PAIQ--SRCTRFRFG--PL  430 (533)
Q Consensus       358 -~~~~~~~~~~~~~~~~vliiDE~d~l~~~~-~~~Ll~~le~~~~~~~~I~~~n~~~~l~-~~l~--sR~~~i~~~--~~  430 (533)
                       +..+..... ....+-+||||+++.++... ...+..+++..+.+..+|+++.....+. ..++  ..+..+...  ++
T Consensus       108 ~~~~~~~~l~-~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~~~~~~~l~~~~~~~~l~~~~l~f  186 (903)
T PRK04841        108 LFAQLFIELA-DWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLPPLGIANLRVRDQLLEIGSQQLAF  186 (903)
T ss_pred             HHHHHHHHHh-cCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCCCCchHhHHhcCcceecCHHhCCC
Confidence             111100000 01356799999999997544 4466666777788889988886533231 1222  222333333  88


Q ss_pred             CHHHHHHHhhcC------HHHHHHHHHH
Q psy4285         431 DSSLIMSRLDYD------DISFFNIIIW  452 (533)
Q Consensus       431 ~~~~~~~~l~~~------~~~~~~ll~~  452 (533)
                      +.++....+...      ++++..+.+.
T Consensus       187 ~~~e~~~ll~~~~~~~~~~~~~~~l~~~  214 (903)
T PRK04841        187 DHQEAQQFFDQRLSSPIEAAESSRLCDD  214 (903)
T ss_pred             CHHHHHHHHHhccCCCCCHHHHHHHHHH
Confidence            999999988654      5566666654

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=97.49  E-value=9.8e-05  Score=61.92  Aligned_cols=22  Identities=41%  Similarity=0.791  Sum_probs=20.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++.||||+||||+|+.+++.+
T Consensus         2 I~I~G~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERL   23 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999999987

...

>KOG3347|consensus

Probab=97.49  E-value=0.0001  Score=61.99  Aligned_cols=27  Identities=44%  Similarity=0.623  Sum_probs=24.1

Q ss_pred             cCCCceeEeCCCCCChHHHHHHHHHHH
Q psy4285         304 NELPHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       304 ~~~~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ...|++|++|-|||||||++..+|...
T Consensus         5 r~~PNILvtGTPG~GKstl~~~lae~~   31 (176)
T KOG3347|consen    5 RERPNILVTGTPGTGKSTLAERLAEKT   31 (176)
T ss_pred             hcCCCEEEeCCCCCCchhHHHHHHHHh
Confidence            345789999999999999999999776

>PF14516 AAA_35: AAA-like domain

Probab=97.48  E-value=0.0046  Score=61.61  Aligned_cols=142  Identities=12%  Similarity=0.136  Sum_probs=79.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC--C---Cchh-HHHHHHHH---------------------
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD--D---RGIG-IVRDQIFQ---------------------  360 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~--~---~~~~-~~~~~~~~---------------------  360 (533)
                      .+.+.||..+|||++...+.+.+...   +...+.++...  .   .... -.+.....                     
T Consensus        33 ~~~I~apRq~GKTSll~~l~~~l~~~---~~~~v~id~~~~~~~~~~~~~~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~  109 (331)
T PF14516_consen   33 YIRIKAPRQMGKTSLLLRLLERLQQQ---GYRCVYIDLQQLGSAIFSDLEQFLRWFCEEISRQLKLDEKLDEYWDEEIGS  109 (331)
T ss_pred             EEEEECcccCCHHHHHHHHHHHHHHC---CCEEEEEEeecCCCcccCCHHHHHHHHHHHHHHHcCCChhHHHHHHHhcCC
Confidence            58999999999999999999887544   23333333221  1   1110 00000000                     


Q ss_pred             ------HHhc-ccCCCCCcEEEEEeCCCCCCH--HHHHHHHHHH----Hhc-----CCCcEEEEEeCCCCCCChhh-hc-
Q psy4285         361 ------FAST-KTMHKSSYKLIILDEADAMTN--DAQNALRRII----EKF-----TTNVRFCIICNYLSKIPPAI-QS-  420 (533)
Q Consensus       361 ------~~~~-~~~~~~~~~vliiDE~d~l~~--~~~~~Ll~~l----e~~-----~~~~~~I~~~n~~~~l~~~l-~s-  420 (533)
                            +... .......+-||+|||+|.+..  .....++..+    ++.     ....++|+++.....+.... .| 
T Consensus       110 ~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~~~~~~~~~~SP  189 (331)
T PF14516_consen  110 KISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPIWQKLRLILAGSTEDYIILDINQSP  189 (331)
T ss_pred             hhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCcccceEEEEEecCcccccccCCCCCC
Confidence                  0000 000014577999999999865  3333444443    332     23466777765333222222 12 


Q ss_pred             --cceeeeecCCCHHHHHHHhhcC-----HHHHHHHHHH
Q psy4285         421 --RCTRFRFGPLDSSLIMSRLDYD-----DISFFNIIIW  452 (533)
Q Consensus       421 --R~~~i~~~~~~~~~~~~~l~~~-----~~~~~~ll~~  452 (533)
                        -...+.+++.+.+++.+.+...     ++.+..+.++
T Consensus       190 FNIg~~i~L~~Ft~~ev~~L~~~~~~~~~~~~~~~l~~~  228 (331)
T PF14516_consen  190 FNIGQPIELPDFTPEEVQELAQRYGLEFSQEQLEQLMDW  228 (331)
T ss_pred             cccccceeCCCCCHHHHHHHHHhhhccCCHHHHHHHHHH
Confidence              2357888999999999888877     4556666665

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=97.47  E-value=0.00055  Score=58.40  Aligned_cols=25  Identities=32%  Similarity=0.468  Sum_probs=22.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +++++||+|+|||+++..++..+..
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~~   26 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLD   26 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHh
Confidence            5899999999999999999888754

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=97.46  E-value=0.00047  Score=66.13  Aligned_cols=28  Identities=39%  Similarity=0.494  Sum_probs=24.0

Q ss_pred             cCCCceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         304 NELPHLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       304 ~~~~~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +...++++.||||+||||+.+.++..+.
T Consensus       109 ~~~~~~~i~g~~g~GKttl~~~l~~~~~  136 (270)
T TIGR02858       109 NRVLNTLIISPPQCGKTTLLRDLARILS  136 (270)
T ss_pred             CCeeEEEEEcCCCCCHHHHHHHHhCccC
Confidence            3335799999999999999999998763

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

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

Probab=97.46  E-value=0.00016  Score=66.49  Aligned_cols=124  Identities=19%  Similarity=0.278  Sum_probs=81.9

Q ss_pred             hHHHHHhchHHHHhhcCCChhhH--HHHHh-h-ccCccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhh
Q psy4285         109 STLDELVSHQDIISTIEIPESML--VDLVL-K-MSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGI  184 (533)
Q Consensus       109 ~~l~~lls~~~~l~~l~~~~~~~--~~~~~-~-~~~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~  184 (533)
                      -++++++++++...++++..+..  +..+. + ...+.++||||||||..+.+++....     ..++-++|...-|..+
T Consensus       118 it~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~k-----vp~l~vkat~liGehV  192 (368)
T COG1223         118 ITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAK-----VPLLLVKATELIGEHV  192 (368)
T ss_pred             ccHhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccC-----CceEEechHHHHHHHh
Confidence            36889998887765543211111  11111 1 13567999999999988888777665     7889999999888888


Q ss_pred             hH--HHHhhhhhcccccCCCceEEEEcCccccC-HHHHHHHHccCCCChhHHHHHHHhccCchHHhhcHHHHHHhh
Q psy4285         185 VR--DQIFQFASTKTMHKSSYKLIILDEADAMT-NDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATA  257 (533)
Q Consensus       185 ~~--d~i~~~a~~~~l~~~~~~~iilDE~d~l~-~~a~~~LRr~~~~~~~~l~~l~~~s~~di~~~L~~L~~~~~~  257 (533)
                      +.  .+|.+.-..-.  ..+|-++++||.|.+. +.-++-||                  ||+.+.+|.|...--.
T Consensus       193 Gdgar~Ihely~rA~--~~aPcivFiDE~DAiaLdRryQelR------------------GDVsEiVNALLTelDg  248 (368)
T COG1223         193 GDGARRIHELYERAR--KAAPCIVFIDELDAIALDRRYQELR------------------GDVSEIVNALLTELDG  248 (368)
T ss_pred             hhHHHHHHHHHHHHH--hcCCeEEEehhhhhhhhhhhHHHhc------------------ccHHHHHHHHHHhccC
Confidence            87  55533322111  2356699999999885 44444453                  8888888888765433

>PRK06585 holA DNA polymerase III subunit delta; Reviewed

Probab=97.45  E-value=0.0018  Score=65.06  Aligned_cols=104  Identities=14%  Similarity=0.164  Sum_probs=82.4

Q ss_pred             CCCCCCceEEEEEcCCCC---cCchhhh--ccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLS---KITPAIQ--SRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKV   75 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~---~i~~~i~--SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a   75 (533)
                      ++.|++.+++|+.+....   ++...+.  -....+.|.+++..++.+|+.+.+++.|+.+++++++.++..++||++.+
T Consensus       102 l~~~~~~~~lil~~~~~~~~~kl~k~~~~~~~~~~v~~~~~~~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l  181 (343)
T PRK06585        102 LESPPGDAFIVIEAGDLKKGSSLRKLFETAAYAAAIPCYADDERDLARLIDDELAEAGLRITPDARALLVALLGGDRLAS  181 (343)
T ss_pred             HcCCCCCcEEEEEcCCCCcccHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHhCCCHHHH
Confidence            356788888888765432   2222221  23467899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCC--CCcchhhHHhhhhhhcc
Q psy4285          76 LNILQSAATAHA--DEVNEDTIFTLLVSRVE  104 (533)
Q Consensus        76 ~~~l~~~~~~~~--~~i~~~~i~~~~~~~~e  104 (533)
                      .|-|+.++...+  ..||.++|.++++...+
T Consensus       182 ~~EleKL~ly~~~~~~It~edV~~lv~~~~e  212 (343)
T PRK06585        182 RNEIEKLALYAHGKGEITLDDVRAVVGDASA  212 (343)
T ss_pred             HHHHHHHHHhcCCCCCCCHHHHHHHhCCccc
Confidence            999999987633  46999999877666544

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.43  E-value=0.00041  Score=71.76  Aligned_cols=93  Identities=14%  Similarity=0.154  Sum_probs=76.2

Q ss_pred             eEEEEEcC-CCC---cCchhhhccce---eEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           8 VRFCIICN-YLS---KITPAIQSRCT---RFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         8 ~~~il~~~-~~~---~i~~~i~SRc~---~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ..++++|+ ++.   .+.+.++|||.   ++.|.+|+.+....+|++.++.+++.++++.++.|+..+.||+|.....|.
T Consensus       228 k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~~~~~R~L~g~l~  307 (440)
T PRK14088        228 KQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAII  307 (440)
T ss_pred             CeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhccccCHHHHHHHHH
Confidence            35666664 433   46788999997   999999999999999999999889999999999999999999999888887


Q ss_pred             HHHHh---CCCCcchhhHHhhhh
Q psy4285          81 SAATA---HADEVNEDTIFTLLV  100 (533)
Q Consensus        81 ~~~~~---~~~~i~~~~i~~~~~  100 (533)
                      .+...   .+..||.+.+.+++.
T Consensus       308 ~l~~~~~~~~~~it~~~a~~~L~  330 (440)
T PRK14088        308 KLLVYKETTGEEVDLKEAILLLK  330 (440)
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHH
Confidence            76432   345688888766654

>TIGR01613 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain

Probab=97.43  E-value=0.0014  Score=64.64  Aligned_cols=138  Identities=19%  Similarity=0.225  Sum_probs=74.5

Q ss_pred             HHHHHHHHhhhchhhhhhhccccc----c-cCCCc-eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchh
Q psy4285         279 ITNILRWLLNESMDLCYKINRFID----E-NELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIG  352 (533)
Q Consensus       279 ~~~~l~~~~~~~~~~~~~l~~~~~----~-~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~  352 (533)
                      +..++.+...+..+....+.+++.    . ..... ++++|+.|+|||++...+...+ +..     ......+..  ..
T Consensus        43 ~~~~L~~~~~~d~~~~~~l~~~lg~~L~~~~~~~~~~~l~G~g~nGKStl~~~l~~l~-G~~-----~~~~~~~~~--~~  114 (304)
T TIGR01613        43 WNGFLLETFGGDNELIEYLQRVIGYSLTGNYTEQKLFFLYGNGGNGKSTFQNLLSNLL-GDY-----ATTAVASLK--MN  114 (304)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHhHHhcCCCCceEEEEEECCCCCcHHHHHHHHHHHh-Chh-----hccCCcchh--hh
Confidence            445555555555555555544432    2 11122 7999999999999999887655 332     111011100  00


Q ss_pred             HHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh--------------cCCCcEEEEEeCCCCCC---C
Q psy4285         353 IVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEK--------------FTTNVRFCIICNYLSKI---P  415 (533)
Q Consensus       353 ~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~--------------~~~~~~~I~~~n~~~~l---~  415 (533)
                      ...+  ..+....   -.+..+++.||++.-.....+.|..+...              ......+|++||....+   +
T Consensus       115 ~~~~--~~f~~a~---l~gk~l~~~~E~~~~~~~~~~~lK~lt~gd~i~~~~k~k~~~~~~~~~~~i~~tN~~P~~~~~~  189 (304)
T TIGR01613       115 EFQE--HRFGLAR---LEGKRAVIGDEVQKGYRDDESTFKSLTGGDTITARFKNKDPFEFTPKFTLVQSTNHLPRIRGFD  189 (304)
T ss_pred             hccC--CCchhhh---hcCCEEEEecCCCCCccccHHhhhhhhcCCeEEeecccCCcEEEEEeeEEEEEcCCCCccCCCC
Confidence            0000  0000000   13567999999975322222334333321              13457799999987655   5


Q ss_pred             hhhhccceeeeecC
Q psy4285         416 PAIQSRCTRFRFGP  429 (533)
Q Consensus       416 ~~l~sR~~~i~~~~  429 (533)
                      .++.+|+..+.|..
T Consensus       190 ~a~~RR~~vi~f~~  203 (304)
T TIGR01613       190 GGIKRRLRIIPFTK  203 (304)
T ss_pred             hhheeeEEEEeccC
Confidence            68999998888753

This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus.

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

Probab=97.41  E-value=0.00034  Score=62.68  Aligned_cols=83  Identities=12%  Similarity=0.199  Sum_probs=65.5

Q ss_pred             CCCCCCceEEEEEcC-CCC---cCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHH
Q psy4285           1 IEKFTTNVRFCIICN-YLS---KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVL   76 (533)
Q Consensus         1 ~E~~~~~~~~il~~~-~~~---~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~   76 (533)
                      ++.|++++.+|+.++ ...   ++..++...+.++.|.+++..++..|++..+.+.|+.+++++++.++...+||++.+.
T Consensus        85 l~~~~~~~~lii~~~~~~~~~~k~~k~l~~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~  164 (172)
T PF06144_consen   85 LSNPPPDCILIIFSEEKLDKRKKLYKALKKQAIVIECKKPKEQELPRWIKERAKKNGLKIDPDAAQYLIERVGNDLSLLQ  164 (172)
T ss_dssp             TTT--SSEEEEEEES-S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHH
T ss_pred             HhCCCCCEEEEEEeCCchhhhhhHHHHHhcccceEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhChHHHHHH
Confidence            467888999998888 444   5788999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q psy4285          77 NILQSAA   83 (533)
Q Consensus        77 ~~l~~~~   83 (533)
                      +-++-++
T Consensus       165 ~EleKL~  171 (172)
T PF06144_consen  165 NELEKLS  171 (172)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHhc
Confidence            9988764

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

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=97.39  E-value=0.001  Score=60.79  Aligned_cols=102  Identities=20%  Similarity=0.332  Sum_probs=54.4

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhc---cc---------------CCCC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAST---KT---------------MHKS  370 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~---------------~~~~  370 (533)
                      ++|.||+|+||||++-.+|..+... .....++..+.......++++...+...-.   ..               ....
T Consensus         4 i~lvGptGvGKTTt~aKLAa~~~~~-~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~~~~~l~~~~~~   82 (196)
T PF00448_consen    4 IALVGPTGVGKTTTIAKLAARLKLK-GKKVALISADTYRIGAVEQLKTYAEILGVPFYVARTESDPAEIAREALEKFRKK   82 (196)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEESTSSTHHHHHHHHHHHHHTEEEEESSTTSCHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCchHhHHHHHHHHHhhc-cccceeecCCCCCccHHHHHHHHHHHhccccchhhcchhhHHHHHHHHHHHhhc
Confidence            7899999999999999999887554 223334443332222222222221111000   00               0012


Q ss_pred             CcEEEEEeCCCCCCH--HHHHHHHHHHHhc-CCCcEEEEEeCCC
Q psy4285         371 SYKLIILDEADAMTN--DAQNALRRIIEKF-TTNVRFCIICNYL  411 (533)
Q Consensus       371 ~~~vliiDE~d~l~~--~~~~~Ll~~le~~-~~~~~~I~~~n~~  411 (533)
                      +.++++||=..+...  +....+.++++.. +..+.+++.++..
T Consensus        83 ~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~  126 (196)
T PF00448_consen   83 GYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMG  126 (196)
T ss_dssp             TSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGG
T ss_pred             CCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccC
Confidence            467999999988764  3344555555432 4456666665443

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>PF13245 AAA_19: Part of AAA domain

Probab=97.37  E-value=0.00033  Score=53.14  Aligned_cols=24  Identities=50%  Similarity=0.751  Sum_probs=17.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+++.||||||||+++...+..+.
T Consensus        12 ~~vv~g~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen   12 LFVVQGPPGTGKTTTLAARIAELL   35 (76)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHH
Confidence            367799999999966655555554

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.37  E-value=0.00091  Score=62.06  Aligned_cols=35  Identities=29%  Similarity=0.509  Sum_probs=26.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS  346 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~  346 (533)
                      +.++||||+|||+++..++......   +..++.++..
T Consensus        15 ~~i~G~~GsGKT~l~~~~~~~~~~~---g~~v~yi~~e   49 (209)
T TIGR02237        15 TQIYGPPGSGKTNICMILAVNAARQ---GKKVVYIDTE   49 (209)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECC
Confidence            7999999999999999998876443   3344444443

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

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.35  E-value=0.0076  Score=59.93  Aligned_cols=29  Identities=24%  Similarity=0.288  Sum_probs=24.6

Q ss_pred             cCCCceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         304 NELPHLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       304 ~~~~~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      ++....+++||||||||++++.+++.+..
T Consensus       131 GkGQR~LIvG~pGtGKTTLl~~la~~i~~  159 (380)
T PRK12608        131 GKGQRGLIVAPPRAGKTVLLQQIAAAVAA  159 (380)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHHHh
Confidence            44446899999999999999999998744

>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=97.35  E-value=0.00021  Score=65.39  Aligned_cols=52  Identities=17%  Similarity=0.181  Sum_probs=33.2

Q ss_pred             CcEEEEEeCCCCCCHHHH------HHHHHHHHh-cCCCcEEEEEeCCCCCCChhhhccc
Q psy4285         371 SYKLIILDEADAMTNDAQ------NALRRIIEK-FTTNVRFCIICNYLSKIPPAIQSRC  422 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~------~~Ll~~le~-~~~~~~~I~~~n~~~~l~~~l~sR~  422 (533)
                      ...++||||++...+...      ....+.+.. +..+.-++++|..+..+++.++..+
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~~~~~~~~l~~hRh~g~diiliTQ~~~~id~~ir~lv  137 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKKVPEIIEFLAQHRHYGWDIILITQSPSQIDKFIRDLV  137 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T----HHHHGGGGCCCTT-EEEEEES-GGGB-HHHHCCE
T ss_pred             CCcEEEEECChhhcCCCccccccchHHHHHHHHhCcCCcEEEEEeCCHHHHhHHHHHHH
Confidence            568999999997743322      223355543 4567889999999999999998765

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.

>PRK13695 putative NTPase; Provisional

Probab=97.34  E-value=0.0016  Score=58.54  Aligned_cols=65  Identities=17%  Similarity=0.230  Sum_probs=39.8

Q ss_pred             CCcEEEEEeCCCCC---CHHHHHHHHHHHHhcCCCcEEEEEeCCCC--CCChhhhccc--eeeeecCCCHHHHHH
Q psy4285         370 SSYKLIILDEADAM---TNDAQNALRRIIEKFTTNVRFCIICNYLS--KIPPAIQSRC--TRFRFGPLDSSLIMS  437 (533)
Q Consensus       370 ~~~~vliiDE~d~l---~~~~~~~Ll~~le~~~~~~~~I~~~n~~~--~l~~~l~sR~--~~i~~~~~~~~~~~~  437 (533)
                      .+++++++||+..+   +....+.+.++++   .+..+|++++...  ...+.+.+|.  ..+.+.+-+.+++..
T Consensus        95 ~~~~~lllDE~~~~e~~~~~~~~~l~~~~~---~~~~~i~v~h~~~~~~~~~~i~~~~~~~i~~~~~~~r~~~~~  166 (174)
T PRK13695         95 EEADVIIIDEIGKMELKSPKFVKAVEEVLD---SEKPVIATLHRRSVHPFVQEIKSRPGGRVYELTPENRDSLPF  166 (174)
T ss_pred             CCCCEEEEECCCcchhhhHHHHHHHHHHHh---CCCeEEEEECchhhHHHHHHHhccCCcEEEEEcchhhhhHHH
Confidence            36789999997654   3344556666663   3467888887643  3456676665  355555555444443

>cd01131 PilT Pilus retraction ATPase PilT

Probab=97.34  E-value=0.0023  Score=58.79  Aligned_cols=24  Identities=38%  Similarity=0.585  Sum_probs=21.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+++.||+|+||||++++++..+.
T Consensus         3 lilI~GptGSGKTTll~~ll~~~~   26 (198)
T cd01131           3 LVLVTGPTGSGKSTTLAAMIDYIN   26 (198)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            379999999999999999998874

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.33  E-value=0.0027  Score=64.04  Aligned_cols=127  Identities=15%  Similarity=0.203  Sum_probs=64.6

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccc---cccCcceEEecCCCCCchhHHHHHHHH-------------HHhcccCCCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTK---AQFNAMVLELNASDDRGIGIVRDQIFQ-------------FASTKTMHKS  370 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~  370 (533)
                      ..++|+||+|+||||++..+|..+...   .+....++..+.-......+++.....             +...... ..
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~-~~  253 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQ-SK  253 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHH-hC
Confidence            348999999999999999999876422   111222333332111111111111000             0000000 14


Q ss_pred             CcEEEEEeCCCCCCHHH--HHHHHHHHHhcC--CCcEEEEEeCCCCCCChhhhccc-----eeeeecCCCHHH
Q psy4285         371 SYKLIILDEADAMTNDA--QNALRRIIEKFT--TNVRFCIICNYLSKIPPAIQSRC-----TRFRFGPLDSSL  434 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~--~~~Ll~~le~~~--~~~~~I~~~n~~~~l~~~l~sR~-----~~i~~~~~~~~~  434 (533)
                      +.++++||++++...+.  ...+.+.++...  ..+.+++.++.-..-...+..++     ..+.|..+++..
T Consensus       254 ~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~~~~~~~~~~~~~~~~I~TKlDet~  326 (388)
T PRK12723        254 DFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDVKEIFHQFSPFSYKTVIFTKLDETT  326 (388)
T ss_pred             CCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHHHHHHHHhcCCCCCEEEEEeccCCC
Confidence            57899999999986543  345566665432  24556665543322222333333     456666666544

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=97.33  E-value=0.001  Score=60.09  Aligned_cols=41  Identities=12%  Similarity=0.344  Sum_probs=30.4

Q ss_pred             CcEEEEEeCC-CCCCHHHHHHHHHHHHhc-CCCcEEEEEeCCC
Q psy4285         371 SYKLIILDEA-DAMTNDAQNALRRIIEKF-TTNVRFCIICNYL  411 (533)
Q Consensus       371 ~~~vliiDE~-d~l~~~~~~~Ll~~le~~-~~~~~~I~~~n~~  411 (533)
                      .++++++||. +.|+++.....+..|.+. ..+...|++|...
T Consensus       154 ~P~vmLFDEPTSALDPElv~EVL~vm~~LA~eGmTMivVTHEM  196 (240)
T COG1126         154 DPKVMLFDEPTSALDPELVGEVLDVMKDLAEEGMTMIIVTHEM  196 (240)
T ss_pred             CCCEEeecCCcccCCHHHHHHHHHHHHHHHHcCCeEEEEechh
Confidence            5789999998 567999999988888653 2445666666543

>COG1485 Predicted ATPase [General function prediction only]

Probab=97.33  E-value=9.3e-05  Score=71.51  Aligned_cols=116  Identities=16%  Similarity=0.171  Sum_probs=63.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC-------CCCCcEEEEEeCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM-------HKSSYKLIILDEA  380 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~vliiDE~  380 (533)
                      .+.+|||-|.|||.+.-.+-..+-........+-.       -...+++.+.........       .....+||+|||+
T Consensus        67 GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R~HFh~-------FM~~vH~~l~~l~g~~dpl~~iA~~~~~~~~vLCfDEF  139 (367)
T COG1485          67 GLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFHR-------FMARVHQRLHTLQGQTDPLPPIADELAAETRVLCFDEF  139 (367)
T ss_pred             eEEEECCCCccHHHHHHHHHhhCCccccccccHHH-------HHHHHHHHHHHHcCCCCccHHHHHHHHhcCCEEEeeee
Confidence            49999999999999999988876332210000000       001111111111110000       0134679999999


Q ss_pred             CCCCHHHHHHHHHHHHh-cCCCcEEEEEeCCCC-----------CCC---hhhhccceeeeecCC
Q psy4285         381 DAMTNDAQNALRRIIEK-FTTNVRFCIICNYLS-----------KIP---PAIQSRCTRFRFGPL  430 (533)
Q Consensus       381 d~l~~~~~~~Ll~~le~-~~~~~~~I~~~n~~~-----------~l~---~~l~sR~~~i~~~~~  430 (533)
                      .--+....-.|-+++++ ...++.+++|+|...           ...   ..|.++|.++.+..+
T Consensus       140 ~VtDI~DAMiL~rL~~~Lf~~GV~lvaTSN~~P~~LY~dGlqR~~FLP~I~li~~~~~v~~vD~~  204 (367)
T COG1485         140 EVTDIADAMILGRLLEALFARGVVLVATSNTAPDNLYKDGLQRERFLPAIDLIKSHFEVVNVDGP  204 (367)
T ss_pred             eecChHHHHHHHHHHHHHHHCCcEEEEeCCCChHHhcccchhHHhhHHHHHHHHHheEEEEecCC
Confidence            76655444444444443 246788888888543           122   345567776666655

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.32  E-value=0.00048  Score=83.13  Aligned_cols=96  Identities=16%  Similarity=0.213  Sum_probs=63.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHH-----------HHHHHhc-----------c
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQ-----------IFQFAST-----------K  365 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~-----------~  365 (533)
                      ..++.|+|||||||+++.+.+.+...   +..+.-+ +++++....+.+.           +......           .
T Consensus       448 v~ii~G~aGTGKTt~l~~l~~~~~~~---G~~V~~l-APTgrAA~~L~e~~g~~A~Ti~~~l~~l~~~~~~~tv~~fl~~  523 (1960)
T TIGR02760       448 FIIINGFGGTGSTEIAQLLLHLASEQ---GYEIQII-TAGSLSAQELRQKIPRLASTFITWVKNLFNDDQDHTVQGLLDK  523 (1960)
T ss_pred             eEEEEECCCCCHHHHHHHHHHHHHhc---CCeEEEE-eCCHHHHHHHHHHhcchhhhHHHHHHhhcccccchhHHHhhcc
Confidence            47999999999999999999876333   3344433 4443433333332           1110000           0


Q ss_pred             cCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeC
Q psy4285         366 TMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN  409 (533)
Q Consensus       366 ~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n  409 (533)
                      .....+.++|||||+++++......|++..+.  .+.++|++++
T Consensus       524 ~~~l~~~~vlIVDEAsMl~~~~~~~Ll~~a~~--~garvVlvGD  565 (1960)
T TIGR02760       524 SSPFSNKDIFVVDEANKLSNNELLKLIDKAEQ--HNSKLILLND  565 (1960)
T ss_pred             cCCCCCCCEEEEECCCCCCHHHHHHHHHHHhh--cCCEEEEEcC
Confidence            00013578999999999999998899887753  5688999885

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PRK14974 cell division protein FtsY; Provisional

Probab=97.30  E-value=0.0046  Score=61.19  Aligned_cols=25  Identities=48%  Similarity=0.537  Sum_probs=22.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .++|+||||+||||++..+|..+..
T Consensus       142 vi~~~G~~GvGKTTtiakLA~~l~~  166 (336)
T PRK14974        142 VIVFVGVNGTGKTTTIAKLAYYLKK  166 (336)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            3899999999999999999987643

>PRK08487 DNA polymerase III subunit delta; Validated

Probab=97.29  E-value=0.002  Score=64.18  Aligned_cols=102  Identities=16%  Similarity=0.114  Sum_probs=80.8

Q ss_pred             CCCCCCceEEEEEcCCCCc---Cchhhhcc--ceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSK---ITPAIQSR--CTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKV   75 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~---i~~~i~SR--c~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a   75 (533)
                      +|.||+.+.+|++.+...+   +...+...  ..++.|.+++..++..|++..+++.|+.+++++++.++...+||+..+
T Consensus        95 l~~~~~~~~lv~~~~~~~k~kkl~k~~~~~k~~~~v~~~~~~~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l  174 (328)
T PRK08487         95 CEKNSDNYFIIELYGADSKTKDIEKLFQKKDEAVFVRFFKPNAREALELLQERAKELGLDIDQNALNHLYFIHNEDLALA  174 (328)
T ss_pred             HhcCCCCEEEEEecCCcchhHHHHHHhccCCCceEEEeeCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCcHHHHH
Confidence            3667888877775544432   22222222  568999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCCCcchhhHHhhhhhhc
Q psy4285          76 LNILQSAATAHADEVNEDTIFTLLVSRV  103 (533)
Q Consensus        76 ~~~l~~~~~~~~~~i~~~~i~~~~~~~~  103 (533)
                      .+-|+-+....+ .||.+.|..++....
T Consensus       175 ~~ELeKL~ly~~-~It~edV~~~v~~~~  201 (328)
T PRK08487        175 ANELEKLAILNE-PITLKDIQELVFGLG  201 (328)
T ss_pred             HHHHHHHHHhcC-CCCHHHHHHHhcccc
Confidence            999999987543 799999877665543

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=97.28  E-value=0.00044  Score=65.40  Aligned_cols=21  Identities=33%  Similarity=0.596  Sum_probs=19.4

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|+||+|||++++.++..
T Consensus         1 ~vv~G~pGsGKSt~i~~~~~~   21 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKKLLKD   21 (234)
T ss_pred             CEEEcCCCCCHHHHHHHHHHh
Confidence            478999999999999999987

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.28  E-value=0.0024  Score=60.40  Aligned_cols=22  Identities=27%  Similarity=0.314  Sum_probs=20.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++|+||+|||+++..++...
T Consensus        28 ~~i~G~~GsGKt~l~~~~~~~~   49 (234)
T PRK06067         28 ILIEGDHGTGKSVLSQQFVYGA   49 (234)
T ss_pred             EEEECCCCCChHHHHHHHHHHH
Confidence            7999999999999999998764

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=97.27  E-value=0.012  Score=59.01  Aligned_cols=71  Identities=6%  Similarity=0.095  Sum_probs=44.7

Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHh------cCCCcEEEEEeCCCC---CCChhhhcc-ceeeeecCCCHHHHHHHhh
Q psy4285         371 SYKLIILDEADAMTNDAQNALRRIIEK------FTTNVRFCIICNYLS---KIPPAIQSR-CTRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~~le~------~~~~~~~I~~~n~~~---~l~~~l~sR-~~~i~~~~~~~~~~~~~l~  440 (533)
                      ...|++||.+..-... .+.++..|-+      ...-.++|+.|+...   .|..++=+| |..+.+...+++..+.++.
T Consensus       148 ~~PVVVIdnF~~k~~~-~~~iy~~laeWAa~Lv~~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak~yV~  226 (431)
T PF10443_consen  148 RRPVVVIDNFLHKAEE-NDFIYDKLAEWAASLVQNNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAKQYVL  226 (431)
T ss_pred             cCCEEEEcchhccCcc-cchHHHHHHHHHHHHHhcCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHHHHHH
Confidence            4679999999765433 3344443322      134467888886554   455566555 4678888888777776665


Q ss_pred             cC
Q psy4285         441 YD  442 (533)
Q Consensus       441 ~~  442 (533)
                      ..
T Consensus       227 ~~  228 (431)
T PF10443_consen  227 SQ  228 (431)
T ss_pred             HH
Confidence            54

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>PF00519 PPV_E1_C: Papillomavirus helicase; InterPro: IPR001177 Papillomaviruses are a large family of DNA tumour viruses which give rise to warts in their host species

Probab=97.27  E-value=0.0012  Score=64.96  Aligned_cols=134  Identities=24%  Similarity=0.297  Sum_probs=72.2

Q ss_pred             HHHHHHHHHHHhhhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccccCcceEE-ecCCCCCchhH
Q psy4285         276 KTEITNILRWLLNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLE-LNASDDRGIGI  353 (533)
Q Consensus       276 ~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~-~~~~~~~~~~~  353 (533)
                      -+.+..++...-..--.....++.+++.-...+ ++|+|||+||||..+..+.+-+      +..++. +|....     
T Consensus       231 Wk~Iv~FLryQ~v~~i~Fl~~lk~~Lkg~PKKnClvi~GPPdTGKS~F~~SLi~Fl------~GkViSf~Ns~Sh-----  299 (432)
T PF00519_consen  231 WKPIVKFLRYQGVEFISFLIALKQFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFL------KGKVISFVNSKSH-----  299 (432)
T ss_dssp             CHHHHHHHHHTT--HHHHHHHHHHHHHTBTTSSEEEEESSCCCSHHHHHHHHHHHH------TSEEE-GGGTTSC-----
T ss_pred             HHHHHHHHhhcCccHHHHHHHHHHHHhCCCcccEEEEECCCCCchhHHHHHHHHHh------CCEEEEecCCCCc-----
Confidence            344555554332222333455666776543344 8999999999999999999988      333443 333221     


Q ss_pred             HHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHH-HHHHHHHHHhcC-------------CCcEEEEEeCCCCCC---Ch
Q psy4285         354 VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDA-QNALRRIIEKFT-------------TNVRFCIICNYLSKI---PP  416 (533)
Q Consensus       354 ~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~-~~~Ll~~le~~~-------------~~~~~I~~~n~~~~l---~~  416 (533)
                             |--.+.   ...++-+|||+-.-.=.- -..|..+++..+             .-..+++|||..-.-   ..
T Consensus       300 -------FWLqPL---~d~Ki~llDDAT~~cW~Y~D~ylRNaLDGN~vsiD~KHkap~Qik~PPLlITsN~dv~~~~~~~  369 (432)
T PF00519_consen  300 -------FWLQPL---ADAKIALLDDATYPCWDYIDTYLRNALDGNPVSIDCKHKAPVQIKCPPLLITSNIDVKKDDRWK  369 (432)
T ss_dssp             -------GGGGGG---CT-SSEEEEEE-HHHHHHHHHHTHHHHCTSEEEEEESSSEEEEEE---EEEEESS-TTTSCCCH
T ss_pred             -------ccccch---hcCcEEEEcCCcccHHHHHHHHHHhccCCCeeeeeccCCCceEeecCceEEecCCCCCcchhhh
Confidence                   111111   356799999984321111 133566666321             113478888855433   44


Q ss_pred             hhhccceeeeecCC
Q psy4285         417 AIQSRCTRFRFGPL  430 (533)
Q Consensus       417 ~l~sR~~~i~~~~~  430 (533)
                      -|.||...+.|+.+
T Consensus       370 YLhSRi~~f~F~n~  383 (432)
T PF00519_consen  370 YLHSRITCFEFPNP  383 (432)
T ss_dssp             HHCTTEEEEE--S-
T ss_pred             hhhheEEEEEcCCc
Confidence            67789988888654

The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication []. It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins []. The E1 protein is a 70 kDa polypeptide with a central DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase []. In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other []. Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity []. The entry represents the C-terminal region of E1, containing both the DNA-binding and ATPase/helical domains.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1TUE_K 1R9W_A 2V9P_B 2GXA_I 1KSX_J 1KSY_A 1F08_B.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=97.26  E-value=0.0022  Score=57.20  Aligned_cols=23  Identities=22%  Similarity=0.195  Sum_probs=20.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++++||||+|||++|..++..+
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~   25 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQS   25 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHc
Confidence            37999999999999999999875

>COG1119 ModF ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]

Probab=97.25  E-value=0.0016  Score=59.98  Aligned_cols=53  Identities=25%  Similarity=0.341  Sum_probs=41.7

Q ss_pred             CCcEEEEEeC-CCCCCHHHHHHHHHHHHh---cCCCcEEEEEeCCCCCCChhhhccc
Q psy4285         370 SSYKLIILDE-ADAMTNDAQNALRRIIEK---FTTNVRFCIICNYLSKIPPAIQSRC  422 (533)
Q Consensus       370 ~~~~vliiDE-~d~l~~~~~~~Ll~~le~---~~~~~~~I~~~n~~~~l~~~l~sR~  422 (533)
                      ..+.+||+|| +..++....+.|++.+++   .+....++++|...+.++|-+-.++
T Consensus       188 ~~P~LLiLDEP~~GLDl~~re~ll~~l~~~~~~~~~~~ll~VtHh~eEi~~~~th~l  244 (257)
T COG1119         188 KDPELLILDEPAQGLDLIAREQLLNRLEELAASPGAPALLFVTHHAEEIPPCFTHRL  244 (257)
T ss_pred             cCCCEEEecCccccCChHHHHHHHHHHHHHhcCCCCceEEEEEcchhhcccccceEE
Confidence            4578999999 467888888888888875   3456789999999998888776654

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=97.25  E-value=0.00062  Score=60.99  Aligned_cols=45  Identities=22%  Similarity=0.369  Sum_probs=34.1

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKI  414 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l  414 (533)
                      ..++++++||- ..++......+.+.+.+......+|++|+....+
T Consensus       113 ~~p~llllDEP~~gLD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~  158 (171)
T cd03228         113 RDPPILILDEATSALDPETEALILEALRALAKGKTVIVIAHRLSTI  158 (171)
T ss_pred             cCCCEEEEECCCcCCCHHHHHHHHHHHHHhcCCCEEEEEecCHHHH
Confidence            46789999996 4778888888888887655557788888776533

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.25  E-value=0.0025  Score=65.47  Aligned_cols=93  Identities=22%  Similarity=0.298  Sum_probs=72.1

Q ss_pred             ceEEEEEcCCCC---cCchhhhccc--eeEEeCCCCHHHHHHHHHHHHhhc--CCCCCHHHHHHHHHhc---CCCHHHHH
Q psy4285           7 NVRFCIICNYLS---KITPAIQSRC--TRFRFGPLDSSLIMSRLDYVIEQE--KVNVTPDGKKAIIDLS---DGDMRKVL   76 (533)
Q Consensus         7 ~~~~il~~~~~~---~i~~~i~SRc--~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~~~~~~~~---~g~~r~a~   76 (533)
                      ++.+|+++|+..   .+.|.++||+  ..+.|+|++.+++.++|+..++..  ...+++++++.+++.+   .||+|+|+
T Consensus       173 ~v~vI~i~~~~~~~~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~  252 (394)
T PRK00411        173 RIGVIGISSDLTFLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAI  252 (394)
T ss_pred             eEEEEEEECCcchhhhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHH
Confidence            677899988763   5778899997  578999999999999998876532  2357889999998888   89999999


Q ss_pred             HHHHHHHHh----CCCCcchhhHHhhh
Q psy4285          77 NILQSAATA----HADEVNEDTIFTLL   99 (533)
Q Consensus        77 ~~l~~~~~~----~~~~i~~~~i~~~~   99 (533)
                      +++..+...    +...|+.+.+...+
T Consensus       253 ~ll~~a~~~a~~~~~~~I~~~~v~~a~  279 (394)
T PRK00411        253 DLLRRAGLIAEREGSRKVTEEDVRKAY  279 (394)
T ss_pred             HHHHHHHHHHHHcCCCCcCHHHHHHHH
Confidence            999876432    23458887775433

>PRK00279 adk adenylate kinase; Reviewed

Probab=97.25  E-value=0.0047  Score=57.55  Aligned_cols=22  Identities=45%  Similarity=0.738  Sum_probs=21.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++||||+||||+++.+|+.+
T Consensus         3 I~v~G~pGsGKsT~a~~la~~~   24 (215)
T PRK00279          3 LILLGPPGAGKGTQAKFIAEKY   24 (215)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            7899999999999999999987

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

Probab=97.25  E-value=0.00055  Score=64.85  Aligned_cols=26  Identities=31%  Similarity=0.425  Sum_probs=22.7

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      ..++|+||+|+||||+++.+++.+..
T Consensus        17 qr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          17 QRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcccc
Confidence            35999999999999999999987643

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

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.25  E-value=0.0058  Score=55.29  Aligned_cols=22  Identities=27%  Similarity=0.536  Sum_probs=20.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++||||+||||+|+.+++.+
T Consensus         2 i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            6899999999999999999987

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

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

Probab=97.23  E-value=0.0055  Score=53.89  Aligned_cols=32  Identities=28%  Similarity=0.367  Sum_probs=27.0

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEec
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELN  344 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~  344 (533)
                      .+++|.|++|+||||+.+.+|+.+      +..|+..+
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L------~~~F~D~D   34 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKAL------NLPFIDTD   34 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHc------CCCcccch
Confidence            368999999999999999999998      56665543

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.22  E-value=0.0012  Score=67.85  Aligned_cols=112  Identities=18%  Similarity=0.175  Sum_probs=59.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc-cccccCcceEEecCCCCCc--hhHHHHHHH-------------HHHhcccCCCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY-TKAQFNAMVLELNASDDRG--IGIVRDQIF-------------QFASTKTMHKSS  371 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~-~~~~~~~~~~~~~~~~~~~--~~~~~~~~~-------------~~~~~~~~~~~~  371 (533)
                      .++|.||+|+||||++..+|..+. ...  +..+..++....+.  ...++....             .+...... ...
T Consensus       223 ~i~~vGptGvGKTTt~~kLA~~~~~~~~--g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~-~~~  299 (424)
T PRK05703        223 VVALVGPTGVGKTTTLAKLAARYALLYG--KKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQ-LRD  299 (424)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcC--CCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHH-hCC
Confidence            489999999999999999998774 222  23333333332221  111111000             00000000 135


Q ss_pred             cEEEEEeCCCCCC--HHHHHHHHHHHHh--cCCCcEEEEEeCCCCCCChhhhccc
Q psy4285         372 YKLIILDEADAMT--NDAQNALRRIIEK--FTTNVRFCIICNYLSKIPPAIQSRC  422 (533)
Q Consensus       372 ~~vliiDE~d~l~--~~~~~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~sR~  422 (533)
                      ++++|||...+..  ......|.++++.  .+....+++.++....-...+.++|
T Consensus       300 ~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~~~~~~f  354 (424)
T PRK05703        300 CDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLKDIYKHF  354 (424)
T ss_pred             CCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHHHHHHHh
Confidence            7899999987754  4455667777762  2334566666655433333333433

>PRK08118 topology modulation protein; Reviewed

Probab=97.22  E-value=0.00032  Score=62.47  Aligned_cols=23  Identities=30%  Similarity=0.535  Sum_probs=21.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.||||+||||+|+.+++.+
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l   25 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKL   25 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999987

>PTZ00202 tuzin; Provisional

Probab=97.22  E-value=0.019  Score=57.95  Aligned_cols=37  Identities=8%  Similarity=0.035  Sum_probs=29.1

Q ss_pred             hhhhccceeeeecCCCHHHHHHHhhcC--HHHHHHHHHH
Q psy4285         416 PAIQSRCTRFRFGPLDSSLIMSRLDYD--DISFFNIIIW  452 (533)
Q Consensus       416 ~~l~sR~~~i~~~~~~~~~~~~~l~~~--~~~~~~ll~~  452 (533)
                      ...+-|++.+.+++.+.+|......+.  +-++..+++.
T Consensus       407 ~~~lprldf~~vp~fsr~qaf~y~~h~~dal~l~~fve~  445 (550)
T PTZ00202        407 NTLLPRLDFYLVPNFSRSQAFAYTQHAIDALSLEHFVDV  445 (550)
T ss_pred             cccCccceeEecCCCCHHHHHHHHhhccchHHhhHHHHh
Confidence            345568899999999999999999998  5566666654

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=97.20  E-value=0.0012  Score=59.71  Aligned_cols=43  Identities=14%  Similarity=0.273  Sum_probs=32.2

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhcCC--CcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEAD-AMTNDAQNALRRIIEKFTT--NVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~d-~l~~~~~~~Ll~~le~~~~--~~~~I~~~n~~~  412 (533)
                      ..++++++||.- .++......+.+.+.+...  +..+|+++....
T Consensus       114 ~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~  159 (180)
T cd03214         114 QEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLN  159 (180)
T ss_pred             cCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            457899999964 7788888888888876433  467788887655

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=97.19  E-value=0.0013  Score=58.29  Aligned_cols=100  Identities=18%  Similarity=0.223  Sum_probs=56.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc--h-hHHHH-----------HHHHHHhcccCCCCCcE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG--I-GIVRD-----------QIFQFASTKTMHKSSYK  373 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~--~-~~~~~-----------~~~~~~~~~~~~~~~~~  373 (533)
                      .+.+.||.|+||||+.+.++.......  +  -+.++..+...  . ...+.           ..+...-... .-..++
T Consensus        28 ~~~l~G~nGsGKSTLl~~i~G~~~~~~--G--~v~~~g~~~~~~~~~~~~~~~i~~~~qLS~G~~qrl~lara-l~~~p~  102 (163)
T cd03216          28 VHALLGENGAGKSTLMKILSGLYKPDS--G--EILVDGKEVSFASPRDARRAGIAMVYQLSVGERQMVEIARA-LARNAR  102 (163)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCC--e--EEEECCEECCcCCHHHHHhcCeEEEEecCHHHHHHHHHHHH-HhcCCC
Confidence            588999999999999999987542111  1  12222211100  0 00000           0001000000 124578


Q ss_pred             EEEEeCCC-CCCHHHHHHHHHHHHhcC-CCcEEEEEeCCCC
Q psy4285         374 LIILDEAD-AMTNDAQNALRRIIEKFT-TNVRFCIICNYLS  412 (533)
Q Consensus       374 vliiDE~d-~l~~~~~~~Ll~~le~~~-~~~~~I~~~n~~~  412 (533)
                      ++++||.. .++......+.+.+.+.. .+..+|++|....
T Consensus       103 illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~  143 (163)
T cd03216         103 LLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLD  143 (163)
T ss_pred             EEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence            99999974 678888888888886542 3566777776544

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>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=97.19  E-value=0.0011  Score=64.95  Aligned_cols=78  Identities=15%  Similarity=0.198  Sum_probs=58.7

Q ss_pred             CceEEEEEcC------------CCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcC-CCH
Q psy4285           6 TNVRFCIICN------------YLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSD-GDM   72 (533)
Q Consensus         6 ~~~~~il~~~------------~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-g~~   72 (533)
                      -...+||+||            .++-|..-+.+||.+++..|.+.+|+.++|+--|+.|++.+++++++.+...+. -++
T Consensus       306 ~sPiiIlATNRg~~~irGt~~~sphGiP~DlLDRllII~t~py~~~ei~~Il~iR~~~E~v~i~~~al~~L~~ig~~~SL  385 (398)
T PF06068_consen  306 LSPIIILATNRGITKIRGTDIISPHGIPLDLLDRLLIIRTKPYSEEEIKQILKIRAKEEDVEISEDALDLLTKIGVETSL  385 (398)
T ss_dssp             T--EEEEEES-SEEE-BTTS-EEETT--HHHHTTEEEEEE----HHHHHHHHHHHHHHCT--B-HHHHHHHHHHHHHS-H
T ss_pred             CCcEEEEecCceeeeccCccCcCCCCCCcchHhhcEEEECCCCCHHHHHHHHHhhhhhhcCcCCHHHHHHHHHHhhhccH
Confidence            3456888887            788899999999999999999999999999999999999999999999877654 789


Q ss_pred             HHHHHHHHHHH
Q psy4285          73 RKVLNILQSAA   83 (533)
Q Consensus        73 r~a~~~l~~~~   83 (533)
                      |.|++++..+.
T Consensus       386 RYAiqLi~~a~  396 (398)
T PF06068_consen  386 RYAIQLITPAS  396 (398)
T ss_dssp             HHHHHCHHHHH
T ss_pred             HHHHHhhhhhh
Confidence            99999997764

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.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=97.18  E-value=0.00058  Score=61.65  Aligned_cols=45  Identities=18%  Similarity=0.240  Sum_probs=34.4

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKI  414 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l  414 (533)
                      .+++++++||. ..++......+.+.+.+...+..+|++|.....+
T Consensus       115 ~~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~  160 (178)
T cd03247         115 QDAPIVLLDEPTVGLDPITERQLLSLIFEVLKDKTLIWITHHLTGI  160 (178)
T ss_pred             cCCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEecCHHHH
Confidence            46789999997 4778888888888887654567788888766543

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.18  E-value=0.0031  Score=59.29  Aligned_cols=23  Identities=26%  Similarity=0.274  Sum_probs=19.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      ++++||||||||+++..++..+.
T Consensus        27 ~~i~G~~G~GKTtl~~~~~~~~~   49 (230)
T PRK08533         27 ILIEGDESTGKSILSQRLAYGFL   49 (230)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH
Confidence            89999999999999877766553

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=97.18  E-value=0.00081  Score=61.21  Aligned_cols=41  Identities=22%  Similarity=0.430  Sum_probs=24.6

Q ss_pred             CcEEEEEeCCCCCCH-HHHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         371 SYKLIILDEADAMTN-DAQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       371 ~~~vliiDE~d~l~~-~~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      ..+++|+||++.+.. .....+..++...+...++++.|..+
T Consensus       129 ~~~~iIiDE~h~~~~~~~~~~~~~~~~~~~~~~~~v~~saT~  170 (201)
T smart00487      129 NVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATP  170 (201)
T ss_pred             HCCEEEEECHHHHhcCCcHHHHHHHHHhCCccceEEEEecCC
Confidence            356999999999986 44444444444333445555555444

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.17  E-value=0.0026  Score=64.08  Aligned_cols=34  Identities=35%  Similarity=0.578  Sum_probs=25.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNA  345 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~  345 (533)
                      ++++|+||+|||+++..++..+...   +..++.++.
T Consensus        85 vLI~G~pG~GKStLllq~a~~~a~~---g~~VlYvs~  118 (372)
T cd01121          85 ILIGGDPGIGKSTLLLQVAARLAKR---GGKVLYVSG  118 (372)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhc---CCeEEEEEC
Confidence            7999999999999999999876433   234444443

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PLN02674 adenylate kinase

Probab=97.16  E-value=0.0048  Score=58.07  Aligned_cols=24  Identities=33%  Similarity=0.607  Sum_probs=22.2

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++|.||||+||||.++.+++.+
T Consensus        32 ~~i~l~G~PGsGKgT~a~~La~~~   55 (244)
T PLN02674         32 KRLILIGPPGSGKGTQSPIIKDEY   55 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHc
Confidence            459999999999999999999986

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=97.16  E-value=0.0046  Score=53.56  Aligned_cols=94  Identities=16%  Similarity=0.207  Sum_probs=56.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC------CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS------DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+.+.||+|+||||+.+.++.......  +.  +.++..      ...+....+.. . .+..-   ...++++++||-.
T Consensus        28 ~~~i~G~nGsGKStLl~~l~G~~~~~~--G~--i~~~~~~~i~~~~~lS~G~~~rv-~-laral---~~~p~illlDEP~   98 (144)
T cd03221          28 RIGLVGRNGAGKSTLLKLIAGELEPDE--GI--VTWGSTVKIGYFEQLSGGEKMRL-A-LAKLL---LENPNLLLLDEPT   98 (144)
T ss_pred             EEEEECCCCCCHHHHHHHHcCCCCCCc--eE--EEECCeEEEEEEccCCHHHHHHH-H-HHHHH---hcCCCEEEEeCCc
Confidence            478999999999999999987652211  11  111110      00111121111 1 11111   1356799999974


Q ss_pred             -CCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         382 -AMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       382 -~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                       .++......+.+.+.+.  +..++++++..+
T Consensus        99 ~~LD~~~~~~l~~~l~~~--~~til~~th~~~  128 (144)
T cd03221          99 NHLDLESIEALEEALKEY--PGTVILVSHDRY  128 (144)
T ss_pred             cCCCHHHHHHHHHHHHHc--CCEEEEEECCHH
Confidence             78888888888888765  356777776654

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=97.13  E-value=0.0012  Score=59.14  Aligned_cols=43  Identities=16%  Similarity=0.329  Sum_probs=32.0

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcC-CCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFT-TNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~-~~~~~I~~~n~~~  412 (533)
                      ..++++++||. ..++......+.+.+.+.. .+..+|++|....
T Consensus       113 ~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~~  157 (173)
T cd03246         113 GNPRILVLDEPNSHLDVEGERALNQAIAALKAAGATRIVIAHRPE  157 (173)
T ss_pred             cCCCEEEEECCccccCHHHHHHHHHHHHHHHhCCCEEEEEeCCHH
Confidence            46789999996 4778888888888876542 3567888887654

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>PRK14700 recombination factor protein RarA; Provisional

Probab=97.12  E-value=0.0033  Score=60.06  Aligned_cols=113  Identities=14%  Similarity=0.065  Sum_probs=77.2

Q ss_pred             CCcEEEEEe--CCCCCCChhhhccceeeeecCCCHHHHHHHhhcC--------------------------HHHHHHHHH
Q psy4285         400 TNVRFCIIC--NYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD--------------------------DISFFNIII  451 (533)
Q Consensus       400 ~~~~~I~~~--n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~--------------------------~~~~~~ll~  451 (533)
                      ..+.+|.+|  |+...+.++|+|||..+.|.+++.+++..++.+.                          .+|.+..++
T Consensus         7 G~i~LIGATTENP~f~vn~ALlSR~~v~~l~~L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~~a~GDaR~aLN   86 (300)
T PRK14700          7 GKIILIGATTENPTYYLNDALVSRLFILRLKRLSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHNYNEGDCRKILN   86 (300)
T ss_pred             CcEEEEeecCCCccceecHhhhhhhheeeecCCCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHHhcCCHHHHHHH
Confidence            345666665  7777999999999999999999999998888765                          233333333


Q ss_pred             HHHHH-----------------HHHH-------HhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHH-------HHHH
Q psy4285         452 WYIKI-----------------QEIK-------IEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMS-------DIEY  500 (533)
Q Consensus       452 ~~~~l-----------------~~l~-------~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~  500 (533)
                      ..+..                 .+..       ...|-.+.|+++.+++.++.++  ++...+++.++-       ++.+
T Consensus        87 ~LE~a~~~~~~~~~~~it~~~~~~~~~~~~~~yDk~gd~HYd~iSAf~KSiRGSD--pDAAlYyLArml~~GEDp~~IaR  164 (300)
T PRK14700         87 LLERMFLISTRGDEIYLNKELFDQAVGETSRDFHREGKEFYEQLSAFHKSVRGTD--PDAAIFWLSVMLDNGVDPLVIAR  164 (300)
T ss_pred             HHHHHHhhccccCCCccCHHHHHHHHhHHHhcccCCcchhHHHHHHHHHHhhcCC--ccHHHHHHHHHHHcCCCHHHHHH
Confidence            32221                 1111       1134567889999999999877  333445554443       6788


Q ss_pred             HHhCCCChHHHHHH
Q psy4285         501 RLAAGTSEKIQLSA  514 (533)
Q Consensus       501 ~l~~g~~~~~~l~~  514 (533)
                      ||..-+++.+++++
T Consensus       165 RLii~AsEDIGlAd  178 (300)
T PRK14700        165 RMLCIASEDIGNAD  178 (300)
T ss_pred             HHHHHHHhhccCCC
Confidence            99998998888654

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.12  E-value=0.002  Score=60.56  Aligned_cols=25  Identities=40%  Similarity=0.644  Sum_probs=21.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ++++||||+|||+++..++......
T Consensus        26 ~~i~G~~GsGKT~l~~~la~~~~~~   50 (225)
T PRK09361         26 TQIYGPPGSGKTNICLQLAVEAAKN   50 (225)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC
Confidence            7999999999999999999876433

>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=97.10  E-value=0.0066  Score=60.49  Aligned_cols=41  Identities=20%  Similarity=0.267  Sum_probs=31.6

Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhc--CCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTNDAQNALRRIIEKF--TTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~~Ll~~le~~--~~~~~~I~~~n~  410 (533)
                      ...-|+||||+|++.++....+++.+...  -+++.+|++.+.
T Consensus       171 ~~~iViiIDdLDR~~~~~i~~~l~~ik~~~~~~~i~~Il~~D~  213 (325)
T PF07693_consen  171 KKRIVIIIDDLDRCSPEEIVELLEAIKLLLDFPNIIFILAFDP  213 (325)
T ss_pred             CceEEEEEcchhcCCcHHHHHHHHHHHHhcCCCCeEEEEEecH
Confidence            45679999999999998887777776532  257888888763

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 [].

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.08  E-value=0.0023  Score=66.36  Aligned_cols=92  Identities=12%  Similarity=0.160  Sum_probs=74.9

Q ss_pred             EEEEEcCCCC----cCchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCC--CCCHHHHHHHHHhcCCCHHHHHHHH
Q psy4285           9 RFCIICNYLS----KITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKV--NVTPDGKKAIIDLSDGDMRKVLNIL   79 (533)
Q Consensus         9 ~~il~~~~~~----~i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~--~~~~~~~~~~~~~~~g~~r~a~~~l   79 (533)
                      .+|++++.+-    .+.+-|+||+   .++.+++|+.++...+|++.++..++  .+++++++.|+..++||+|.+++.|
T Consensus       241 ~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~~~~~~gl~~~l~~evl~~Ia~~~~gd~R~L~gaL  320 (450)
T PRK14087        241 QLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKKEIKNQNIKQEVTEEAINFISNYYSDDVRKIKGSV  320 (450)
T ss_pred             cEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHccCCCHHHHHHHH
Confidence            5677776432    3458899998   59999999999999999999987775  6999999999999999999999999


Q ss_pred             HHHHHh--C---CCCcchhhHHhhhh
Q psy4285          80 QSAATA--H---ADEVNEDTIFTLLV  100 (533)
Q Consensus        80 ~~~~~~--~---~~~i~~~~i~~~~~  100 (533)
                      ..+...  .   +..||.+.+.+++.
T Consensus       321 ~~l~~~a~~~~~~~~it~~~v~~~l~  346 (450)
T PRK14087        321 SRLNFWSQQNPEEKIITIEIVSDLFR  346 (450)
T ss_pred             HHHHHHHhcccCCCCCCHHHHHHHHh
Confidence            888532  1   24588888776654

>PRK03839 putative kinase; Provisional

Probab=97.06  E-value=0.00056  Score=61.84  Aligned_cols=23  Identities=43%  Similarity=0.546  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+|+.+
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~   24 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKL   24 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999998

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=97.06  E-value=0.0034  Score=59.49  Aligned_cols=34  Identities=21%  Similarity=0.188  Sum_probs=24.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNA  345 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~  345 (533)
                      ++++||||+|||+++..++......   +...+.++.
T Consensus        24 ~lI~G~pGsGKT~la~~~l~~~~~~---ge~~lyvs~   57 (237)
T TIGR03877        24 VLLSGGPGTGKSIFSQQFLWNGLQM---GEPGIYVAL   57 (237)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHc---CCcEEEEEe
Confidence            8999999999999999887664332   344444443

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

>PRK00625 shikimate kinase; Provisional

Probab=97.06  E-value=0.00059  Score=60.99  Aligned_cols=31  Identities=26%  Similarity=0.356  Sum_probs=25.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEec
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELN  344 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~  344 (533)
                      +++|+|.||+||||+++.+|+.+      +..++.++
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l------~~~~id~D   32 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFL------SLPFFDTD   32 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh------CCCEEEhh
Confidence            48999999999999999999998      55555543

>PF13479 AAA_24: AAA domain

Probab=97.06  E-value=0.0005  Score=63.93  Aligned_cols=63  Identities=22%  Similarity=0.447  Sum_probs=38.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC-------------CCCchhHHHHHHHHHHhcccCCCCCcEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS-------------DDRGIGIVRDQIFQFASTKTMHKSSYKL  374 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~v  374 (533)
                      .+++||+||+|||+++..+-+-+         ++.+...             ...+...+.+.+..+...    ...+++
T Consensus         5 ~~lIyG~~G~GKTt~a~~~~k~l---------~id~E~g~~~~~~~~~~~~i~i~s~~~~~~~~~~l~~~----~~~y~t   71 (213)
T PF13479_consen    5 KILIYGPPGSGKTTLAASLPKPL---------FIDTENGSDSLKFLDDGDVIPITSWEDFLEALDELEED----EADYDT   71 (213)
T ss_pred             EEEEECCCCCCHHHHHHhCCCeE---------EEEeCCCccchhhhcCCCeeCcCCHHHHHHHHHHHHhc----cCCCCE
Confidence            38999999999999998883332         2222222             112333444444333222    257899


Q ss_pred             EEEeCCCCC
Q psy4285         375 IILDEADAM  383 (533)
Q Consensus       375 liiDE~d~l  383 (533)
                      ||||-++.+
T Consensus        72 iVIDsis~~   80 (213)
T PF13479_consen   72 IVIDSISWL   80 (213)
T ss_pred             EEEECHHHH
Confidence            999988665

>PRK00131 aroK shikimate kinase; Reviewed

Probab=97.05  E-value=0.00067  Score=60.85  Aligned_cols=23  Identities=30%  Similarity=0.440  Sum_probs=21.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|+|+||+||||+|+.+++.+
T Consensus         6 ~i~l~G~~GsGKstla~~La~~l   28 (175)
T PRK00131          6 NIVLIGFMGAGKSTIGRLLAKRL   28 (175)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999998

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=97.05  E-value=0.0018  Score=59.53  Aligned_cols=52  Identities=21%  Similarity=0.354  Sum_probs=34.1

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc--CCCcEEEEEeCCCCCCChhhhccc
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF--TTNVRFCIICNYLSKIPPAIQSRC  422 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~--~~~~~~I~~~n~~~~l~~~l~sR~  422 (533)
                      ..+++||+||. .+++...|..+++++.+-  ..+..++++|.... +..-+-+|+
T Consensus       158 ~~PklLIlDEptSaLD~siQa~IlnlL~~l~~~~~lt~l~IsHdl~-~v~~~cdRi  212 (252)
T COG1124         158 PEPKLLILDEPTSALDVSVQAQILNLLLELKKERGLTYLFISHDLA-LVEHMCDRI  212 (252)
T ss_pred             cCCCEEEecCchhhhcHHHHHHHHHHHHHHHHhcCceEEEEeCcHH-HHHHHhhhe
Confidence            45889999996 567788888777776532  34467788876543 233344454

>PRK11823 DNA repair protein RadA; Provisional

Probab=97.05  E-value=0.0034  Score=65.05  Aligned_cols=34  Identities=35%  Similarity=0.543  Sum_probs=25.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNA  345 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~  345 (533)
                      ++++|+||+|||+++..++......   +..+++++.
T Consensus        83 ~lI~G~pG~GKTtL~lq~a~~~a~~---g~~vlYvs~  116 (446)
T PRK11823         83 VLIGGDPGIGKSTLLLQVAARLAAA---GGKVLYVSG  116 (446)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEc
Confidence            7999999999999999999876422   334444443

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=97.04  E-value=0.0037  Score=60.05  Aligned_cols=87  Identities=21%  Similarity=0.295  Sum_probs=46.3

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEec-------CC---CCCchhHHHHHHHHHHhcccCCCCCcEEEE
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELN-------AS---DDRGIGIVRDQIFQFASTKTMHKSSYKLII  376 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~-------~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~vli  376 (533)
                      |-++++|.||+||||+|+.+.+.+-..   +..+..++       ..   +....+..|..++.......   +...++|
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~~~~~---~~~v~~i~~~~~~~~~~~y~~~~~Ek~~R~~l~s~v~r~l---s~~~iVI   75 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKYLEEK---GKEVVIISDDSLGIDRNDYADSKKEKEARGSLKSAVERAL---SKDTIVI   75 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHHHHHT---T--EEEE-THHHH-TTSSS--GGGHHHHHHHHHHHHHHHH---TT-SEEE
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHHHhc---CCEEEEEcccccccchhhhhchhhhHHHHHHHHHHHHHhh---ccCeEEE
Confidence            458999999999999999999987442   22232222       11   22334555555544333221   3447999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhcCC
Q psy4285         377 LDEADAMTNDAQNALRRIIEKFTT  400 (533)
Q Consensus       377 iDE~d~l~~~~~~~Ll~~le~~~~  400 (533)
                      +|+..++ ......|+.+=.....
T Consensus        76 ~Dd~nYi-Kg~RYelyclAr~~~~   98 (270)
T PF08433_consen   76 LDDNNYI-KGMRYELYCLARAYGT   98 (270)
T ss_dssp             E-S---S-HHHHHHHHHHHHHTT-
T ss_pred             EeCCchH-HHHHHHHHHHHHHcCC
Confidence            9998877 4556677776555443

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PRK13947 shikimate kinase; Provisional

Probab=97.04  E-value=0.00069  Score=60.67  Aligned_cols=23  Identities=39%  Similarity=0.443  Sum_probs=22.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++.|+||+||||+++.+|+.+
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~l   25 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTL   25 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHh
Confidence            68999999999999999999998

>PRK13808 adenylate kinase; Provisional

Probab=97.04  E-value=0.0069  Score=59.51  Aligned_cols=23  Identities=35%  Similarity=0.699  Sum_probs=21.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|+||||+||||+++.|++.+
T Consensus         2 rIiv~GpPGSGK~T~a~~LA~~y   24 (333)
T PRK13808          2 RLILLGPPGAGKGTQAQRLVQQY   24 (333)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            38999999999999999999986

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.03  E-value=0.001  Score=66.18  Aligned_cols=29  Identities=28%  Similarity=0.338  Sum_probs=24.2

Q ss_pred             cCCCceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         304 NELPHLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       304 ~~~~~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +.....++.||||+||||+++.+++.+..
T Consensus       167 GkGQR~lIvgppGvGKTTLaK~Ian~I~~  195 (416)
T PRK09376        167 GKGQRGLIVAPPKAGKTVLLQNIANSITT  195 (416)
T ss_pred             ccCceEEEeCCCCCChhHHHHHHHHHHHh
Confidence            34345899999999999999999988754

>PLN03210 Resistant to P

Probab=97.03  E-value=0.0046  Score=72.23  Aligned_cols=128  Identities=18%  Similarity=0.193  Sum_probs=64.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEe---cCCC--C-------Cc--hhHHHHHHHHHHhc---------
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLEL---NASD--D-------RG--IGIVRDQIFQFAST---------  364 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~---~~~~--~-------~~--~~~~~~~~~~~~~~---------  364 (533)
                      .+-++|++|+||||+|++++..+..... +..++..   ....  .       ..  .....+.+......         
T Consensus       209 vvgI~G~gGiGKTTLA~~l~~~l~~~F~-g~vfv~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~~~~  287 (1153)
T PLN03210        209 MVGIWGSSGIGKTTIARALFSRLSRQFQ-SSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIYHLG  287 (1153)
T ss_pred             EEEEEcCCCCchHHHHHHHHHHHhhcCC-eEEEeeccccccchhhcccccccccchhHHHHHHHHHHHhCCCCcccCCHH
Confidence            4789999999999999999887644321 1111110   0000  0       00  00001111111100         


Q ss_pred             --ccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccc-eeeeecCCCHHHHHHHhhc
Q psy4285         365 --KTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRC-TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       365 --~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~  441 (533)
                        ......++-+||+|+++..  ...+.|....+....+.++|+||.....+..   ..+ ..+....++.++..+.+..
T Consensus       288 ~~~~~L~~krvLLVLDdv~~~--~~l~~L~~~~~~~~~GsrIIiTTrd~~vl~~---~~~~~~~~v~~l~~~ea~~LF~~  362 (1153)
T PLN03210        288 AMEERLKHRKVLIFIDDLDDQ--DVLDALAGQTQWFGSGSRIIVITKDKHFLRA---HGIDHIYEVCLPSNELALEMFCR  362 (1153)
T ss_pred             HHHHHHhCCeEEEEEeCCCCH--HHHHHHHhhCccCCCCcEEEEEeCcHHHHHh---cCCCeEEEecCCCHHHHHHHHHH
Confidence              0001235678999998753  3334444333333456788888875432111   111 3566667777766666544

syringae 6; Provisional

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=97.02  E-value=0.0042  Score=54.69  Aligned_cols=96  Identities=19%  Similarity=0.240  Sum_probs=56.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC-----------------CchhHHHHHHHHHHhcccCCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD-----------------RGIGIVRDQIFQFASTKTMHKS  370 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~  370 (533)
                      .+.+.||.|+||||+.++++..+....    .-+.++....                 .+....+.. . ++...   ..
T Consensus        27 ~~~i~G~nGsGKStll~~l~g~~~~~~----G~i~~~~~~~~~~~~~~~~~~i~~~~qlS~G~~~r~-~-l~~~l---~~   97 (157)
T cd00267          27 IVALVGPNGSGKSTLLRAIAGLLKPTS----GEILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQRV-A-LARAL---LL   97 (157)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCc----cEEEECCEEcccCCHHHHHhceEEEeeCCHHHHHHH-H-HHHHH---hc
Confidence            488999999999999999987652211    1122222110                 011111111 0 11110   13


Q ss_pred             CcEEEEEeCCC-CCCHHHHHHHHHHHHhcCC-CcEEEEEeCCCC
Q psy4285         371 SYKLIILDEAD-AMTNDAQNALRRIIEKFTT-NVRFCIICNYLS  412 (533)
Q Consensus       371 ~~~vliiDE~d-~l~~~~~~~Ll~~le~~~~-~~~~I~~~n~~~  412 (533)
                      .++++++||.. .++......+.+.+.+... +..+++++....
T Consensus        98 ~~~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~  141 (157)
T cd00267          98 NPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPE  141 (157)
T ss_pred             CCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence            46899999986 6778888888888765432 356777876654

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK05907 hypothetical protein; Provisional

Probab=97.02  E-value=0.0091  Score=58.65  Aligned_cols=101  Identities=6%  Similarity=0.052  Sum_probs=78.0

Q ss_pred             CCCCCCceEEE-EEcCCCC---cCchhhhccceeE----EeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhc-CCC
Q psy4285           1 IEKFTTNVRFC-IICNYLS---KITPAIQSRCTRF----RFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLS-DGD   71 (533)
Q Consensus         1 ~E~~~~~~~~i-l~~~~~~---~i~~~i~SRc~~~----~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~g~   71 (533)
                      +|+||+.+.++ ++.+ ..   ++-..|. .+..+    .|+++.+.++.+|+.+.++++|..+++++++.++..+ +||
T Consensus        93 l~np~~~~~liv~~~~-~d~~kkl~K~i~-k~~~v~~~~e~~~l~e~~L~~Wi~~~~~~~g~~i~~~a~~~L~~~~~~~n  170 (311)
T PRK05907         93 ARNPNPHLTLFLFTTK-QECFSSLSKKLS-SALCLSLFGEWFADRDKRIAQLLIQRAKELGISCSLGLASLFVSKFPQTG  170 (311)
T ss_pred             HhCCCCCeEEEEEEec-ccHHHHHHHHHh-hcceeccccccCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHccCCC
Confidence            47888875555 5552 22   2334454 35555    8999999999999999999999999999999999999 699


Q ss_pred             HHHHHHHHHHHHHh-C-CCCcchhhHHhhhhhhc
Q psy4285          72 MRKVLNILQSAATA-H-ADEVNEDTIFTLLVSRV  103 (533)
Q Consensus        72 ~r~a~~~l~~~~~~-~-~~~i~~~~i~~~~~~~~  103 (533)
                      +..+.+-++-+... . +..||.+.|..++....
T Consensus       171 L~~l~~EleKL~ly~g~~~~It~e~V~~lv~~s~  204 (311)
T PRK05907        171 LFEILSEFQKLLCQMGKKESLEASDIQSFVVKKE  204 (311)
T ss_pred             HHHHHHHHHHHHHhcCCCCeECHHHHHHHhcCcc
Confidence            99999999998775 3 34599999876655433

>PRK14527 adenylate kinase; Provisional

Probab=97.01  E-value=0.0064  Score=55.49  Aligned_cols=23  Identities=43%  Similarity=0.771  Sum_probs=21.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.||||+||||+++.+++.+
T Consensus         8 ~i~i~G~pGsGKsT~a~~La~~~   30 (191)
T PRK14527          8 VVIFLGPPGAGKGTQAERLAQEL   30 (191)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999876

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=96.99  E-value=0.0067  Score=54.43  Aligned_cols=100  Identities=18%  Similarity=0.228  Sum_probs=55.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccc---c-CcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC-C
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQ---F-NAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD-A  382 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~---~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d-~  382 (533)
                      .+.+.||.|+||||+.+.++..+....+   + +..+..+......+...-+ .+. ++..   ....++++++||-- .
T Consensus        27 ~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~i~~~~q~~~LSgGq~q-rv~-lara---l~~~p~lllLDEPts~  101 (177)
T cd03222          27 VIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQYIDLSGGELQ-RVA-IAAA---LLRNATFYLFDEPSAY  101 (177)
T ss_pred             EEEEECCCCChHHHHHHHHHcCCCCCCcEEEECCEEEEEEcccCCCCHHHHH-HHH-HHHH---HhcCCCEEEEECCccc
Confidence            4789999999999999999876422110   0 0001111110001111111 111 1111   11356899999974 6


Q ss_pred             CCHHHHHHHHHHHHhcC-C-CcEEEEEeCCCC
Q psy4285         383 MTNDAQNALRRIIEKFT-T-NVRFCIICNYLS  412 (533)
Q Consensus       383 l~~~~~~~Ll~~le~~~-~-~~~~I~~~n~~~  412 (533)
                      ++......+.+.+.+.. . +..+|++|....
T Consensus       102 LD~~~~~~l~~~l~~~~~~~~~tiiivsH~~~  133 (177)
T cd03222         102 LDIEQRLNAARAIRRLSEEGKKTALVVEHDLA  133 (177)
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCEEEEEECCHH
Confidence            78888888777776532 2 256777776543

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=96.99  E-value=0.0039  Score=57.69  Aligned_cols=23  Identities=43%  Similarity=0.739  Sum_probs=20.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||+||||||+.+.|-+.+
T Consensus        29 f~vliGpSGsGKTTtLkMINrLi   51 (309)
T COG1125          29 FLVLIGPSGSGKTTTLKMINRLI   51 (309)
T ss_pred             EEEEECCCCCcHHHHHHHHhccc
Confidence            47899999999999999887654

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=96.99  E-value=0.0081  Score=53.43  Aligned_cols=21  Identities=24%  Similarity=0.271  Sum_probs=19.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      ++++|+||+|||++|..++..
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~   22 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE   22 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            589999999999999999876

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=96.99  E-value=0.011  Score=51.20  Aligned_cols=22  Identities=41%  Similarity=0.650  Sum_probs=20.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.+.|+||+||||+|+.+++.+
T Consensus         2 I~i~G~~GsGKst~a~~la~~~   23 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKKL   23 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5799999999999999999987

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=96.98  E-value=0.00046  Score=59.68  Aligned_cols=22  Identities=41%  Similarity=0.853  Sum_probs=20.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++.||||+||||+|+.+++.+
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~   23 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRL   23 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHC
Confidence            6899999999999999999876

...

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=96.98  E-value=0.0019  Score=78.04  Aligned_cols=99  Identities=17%  Similarity=0.233  Sum_probs=58.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH---ccccccCcceEEecCCCCCc----------hhHHHHHHHHHHh-cccCCCCCcE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL---YTKAQFNAMVLELNASDDRG----------IGIVRDQIFQFAS-TKTMHKSSYK  373 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l---~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~-~~~~~~~~~~  373 (533)
                      .+++.|++||||||+.+.+.+.+   ....  +..++-+ +++++.          ...+...+..+.. ..........
T Consensus      1038 ~~~i~G~AGtGKTt~l~~~~~~i~~~~~~~--g~~v~gl-ApT~~Aa~~L~~~g~~a~Ti~s~l~~~~~~~~~~~~~~~~ 1114 (1960)
T TIGR02760      1038 FVAVQGLAGVGKTTMLESRYKPVLQAFESE--QLQVIGL-APTHEAVGELKSAGVQAQTLDSFLTDISLYRNSGGDFRNT 1114 (1960)
T ss_pred             EEEEEeCCCCCHHHhHHHHHHHHHHHHHhc--CCeEEEE-eChHHHHHHHHhcCCchHhHHHHhcCcccccccCCCCccc
Confidence            37899999999999995443322   1111  2334333 222222          2233322211100 0000123568


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         374 LIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       374 vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      |+||||+++++......|++..+.  .+.++|++++..
T Consensus      1115 v~ivDEasMv~~~~~~~l~~~~~~--~~ak~vlvGD~~ 1150 (1960)
T TIGR02760      1115 LFILDESSMVSNFQLTHATELVQK--SGSRAVSLGDIA 1150 (1960)
T ss_pred             EEEEEccccccHHHHHHHHHhccC--CCCEEEEeCChh
Confidence            999999999999999999888764  458899999643

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PRK04328 hypothetical protein; Provisional

Probab=96.97  E-value=0.0043  Score=59.18  Aligned_cols=22  Identities=32%  Similarity=0.385  Sum_probs=19.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++||||+|||+++..++...
T Consensus        26 ili~G~pGsGKT~l~~~fl~~~   47 (249)
T PRK04328         26 VLLSGGPGTGKSIFSQQFLWNG   47 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHH
Confidence            8999999999999999887664

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=96.96  E-value=0.0051  Score=61.66  Aligned_cols=25  Identities=32%  Similarity=0.537  Sum_probs=22.4

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      ..++++||+|+||||+.+++...+.
T Consensus       123 g~ili~G~tGSGKTT~l~al~~~i~  147 (343)
T TIGR01420       123 GLILVTGPTGSGKSTTLASMIDYIN  147 (343)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhhC
Confidence            3589999999999999999998774

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

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.96  E-value=0.001  Score=56.22  Aligned_cols=25  Identities=32%  Similarity=0.363  Sum_probs=22.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .++|.|+.|+||||+++.+++.+..
T Consensus        24 ~i~l~G~lGaGKTtl~~~l~~~lg~   48 (133)
T TIGR00150        24 VVLLKGDLGAGKTTLVQGLLQGLGI   48 (133)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            4889999999999999999998743

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

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=96.95  E-value=0.0014  Score=60.76  Aligned_cols=23  Identities=30%  Similarity=0.429  Sum_probs=20.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.+.||+||||||+.+.+|-..
T Consensus        31 fvsilGpSGcGKSTLLriiAGL~   53 (248)
T COG1116          31 FVAILGPSGCGKSTLLRLIAGLE   53 (248)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            47899999999999999999654

>KOG1808|consensus

Probab=96.95  E-value=0.003  Score=73.79  Aligned_cols=126  Identities=19%  Similarity=0.296  Sum_probs=88.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC---C--------CCCcEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM---H--------KSSYKLII  376 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~--------~~~~~vli  376 (533)
                      .++|-||.|+|||++++.+|+..      +..+++++.....   ..++.++.+......   +        ..+++.+|
T Consensus       442 pillqG~tssGKtsii~~la~~~------g~~~vrinnheht---d~qeyig~y~~~~~g~l~freg~LV~Alr~G~~~v  512 (1856)
T KOG1808|consen  442 PILLQGPTSSGKTSIIKELARAT------GKNIVRINNHEHT---DLQEYIGTYVADDNGDLVFREGVLVQALRNGDWIV  512 (1856)
T ss_pred             CeEEecCcCcCchhHHHHHHHHh------ccCceehhccccc---hHHHHHHhhhcCCCCCeeeehhHHHHHHHhCCEEE
Confidence            38999999999999999999998      6666666654322   223333321110000   0        12467999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhc-----C---------CCcEEEEEeCCCC------CCChhhhccceeeeecCCCHHHHH
Q psy4285         377 LDEADAMTNDAQNALRRIIEKF-----T---------TNVRFCIICNYLS------KIPPAIQSRCTRFRFGPLDSSLIM  436 (533)
Q Consensus       377 iDE~d~l~~~~~~~Ll~~le~~-----~---------~~~~~I~~~n~~~------~l~~~l~sR~~~i~~~~~~~~~~~  436 (533)
                      +||++....+..++|.++++..     +         .+.++..|=|.+.      .+..++++||..++|...+++++.
T Consensus       513 lD~lnla~~dvL~aLnrllddnRel~ipe~~rlv~~h~~f~lfatqn~~~~y~grk~lsRa~~~rf~e~~f~~~~e~e~~  592 (1856)
T KOG1808|consen  513 LDELNLAPHDVLEALNRLLDDNRELFIPETQRLVKAHPEFMLFATQNPPGTYGGRKILSRALRNRFIELHFDDIGEEELE  592 (1856)
T ss_pred             eccccccchHHHHHHHhhhhhhccccccccceeeccCcchhhhhhccCccccchhhhhhhcccccchhhhhhhcCchhhh
Confidence            9999999999999999999851     1         2222333334442      467788899999999999999999


Q ss_pred             HHhhcC
Q psy4285         437 SRLDYD  442 (533)
Q Consensus       437 ~~l~~~  442 (533)
                      .++.+.
T Consensus       593 ~i~~~~  598 (1856)
T KOG1808|consen  593 EILEHR  598 (1856)
T ss_pred             hhhccc
Confidence            999887

>KOG2543|consensus

Probab=96.95  E-value=0.0096  Score=58.29  Aligned_cols=135  Identities=20%  Similarity=0.200  Sum_probs=70.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcce-------------EEe--cCCCCCch----hHHHHHHHHHHhcccCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMV-------------LEL--NASDDRGI----GIVRDQIFQFASTKTMH  368 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~-------------~~~--~~~~~~~~----~~~~~~~~~~~~~~~~~  368 (533)
                      ++.++|..|||||.+++.+.+.+..+..+-.++             ..+  ...++...    ..+...+..+.+.....
T Consensus        32 ~~~iyG~sgTGKT~~~r~~l~~~n~~~vw~n~~ecft~~~lle~IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t  111 (438)
T KOG2543|consen   32 IVHIYGHSGTGKTYLVRQLLRKLNLENVWLNCVECFTYAILLEKILNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAAT  111 (438)
T ss_pred             eEEEeccCCCchhHHHHHHHhhcCCcceeeehHHhccHHHHHHHHHHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhh
Confidence            479999999999999999999873332111000             001  01111111    12222233333311111


Q ss_pred             -CCCcEEEEEeCCCCCCH---HHHHHHHHHHHhcC-CCcEEEEEeCCCCCCChhhhc--cceeeeecCCCHHHHHHHhhc
Q psy4285         369 -KSSYKLIILDEADAMTN---DAQNALRRIIEKFT-TNVRFCIICNYLSKIPPAIQS--RCTRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       369 -~~~~~vliiDE~d~l~~---~~~~~Ll~~le~~~-~~~~~I~~~n~~~~l~~~l~s--R~~~i~~~~~~~~~~~~~l~~  441 (533)
                       ....-+||+|.+|.+..   ...+.|++.-+--+ ..+.++++.-.....-..=.+  -...++|+.|+.++...++.+
T Consensus       112 ~~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i~iils~~~~e~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~  191 (438)
T KOG2543|consen  112 NRDQKVFLILDNADALRDMDAILLQCLFRLYELLNEPTIVIILSAPSCEKQYLINTGTLEIVVLHFPQYSVEETQVILSR  191 (438)
T ss_pred             ccCceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCceEEEEeccccHHHhhcccCCCCceEEecCCCCHHHHHHHHhc
Confidence             12467899999998853   33344444333212 244555543222110000001  125799999999999999998


Q ss_pred             C
Q psy4285         442 D  442 (533)
Q Consensus       442 ~  442 (533)
                      -
T Consensus       192 ~  192 (438)
T KOG2543|consen  192 D  192 (438)
T ss_pred             C
Confidence            7

>KOG0479|consensus

Probab=96.94  E-value=0.0016  Score=66.65  Aligned_cols=112  Identities=15%  Similarity=0.214  Sum_probs=71.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc---cccCcceEEecCC----CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK---AQFNAMVLELNAS----DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~---~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      |+|+.|.|.|.||-+.+.+.+..-..   .+.+..-+-+.+.    ...+...+.       ..... -+..+|++|||+
T Consensus       336 NiLlvGDPSvAKSQLLRyVLntAplAI~TTGRGSSGVGLTAAVTtD~eTGERRLE-------AGAMV-LADRGVVCIDEF  407 (818)
T KOG0479|consen  336 NILLVGDPSVAKSQLLRYVLNTAPLAIATTGRGSSGVGLTAAVTTDQETGERRLE-------AGAMV-LADRGVVCIDEF  407 (818)
T ss_pred             eEEEecCchHHHHHHHHHHHhcccccccccCCCCCCccceeEEeeccccchhhhh-------cCceE-EccCceEEehhc
Confidence            59999999999999999998764211   0001111111110    011121111       11111 145789999999


Q ss_pred             CCCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC-------------CCChhhhccceeeee
Q psy4285         381 DAMTNDAQNALRRIIEKF-------------TTNVRFCIICNYLS-------------KIPPAIQSRCTRFRF  427 (533)
Q Consensus       381 d~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~-------------~l~~~l~sR~~~i~~  427 (533)
                      |+|+.-..-++.+.||+.             ...|.++.+.|+..             .++..|+|||+.+++
T Consensus       408 DKMsDiDRvAIHEVMEQqtVTIaKAGIHasLNARCSVlAAANPvyG~Yd~~k~P~eNIgLpDSLLSRFDLlFv  480 (818)
T KOG0479|consen  408 DKMSDIDRVAIHEVMEQQTVTIAKAGIHASLNARCSVLAAANPVYGQYDQSKTPMENIGLPDSLLSRFDLLFV  480 (818)
T ss_pred             ccccchhHHHHHHHHhcceEEeEeccchhhhccceeeeeecCccccccCCCCChhhccCCcHHHHhhhcEEEE
Confidence            999988888999999863             45688999988643             478899999974443

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=96.93  E-value=0.0017  Score=69.41  Aligned_cols=41  Identities=12%  Similarity=0.204  Sum_probs=31.5

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEAD-AMTNDAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d-~l~~~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      .+++++++||+- .++.+....+.+.+.+..++..+|++|.+
T Consensus       487 ~~~~iliLDE~TSaLD~~te~~I~~~l~~~~~~~TvIiItHr  528 (529)
T TIGR02868       487 ADAPILLLDEPTEHLDAGTESELLEDLLAALSGKTVVVITHH  528 (529)
T ss_pred             cCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEecC
Confidence            457899999985 57888888888888876556667777654

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

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

Probab=96.93  E-value=0.00088  Score=49.86  Aligned_cols=22  Identities=32%  Similarity=0.478  Sum_probs=20.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.+.|+||+||||+++.+++.+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999999999999987

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

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

Probab=96.93  E-value=0.0086  Score=56.34  Aligned_cols=89  Identities=10%  Similarity=0.074  Sum_probs=76.2

Q ss_pred             ceEEEEEcCCCCcCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHh
Q psy4285           7 NVRFCIICNYLSKITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATA   85 (533)
Q Consensus         7 ~~~~il~~~~~~~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~~~~   85 (533)
                      ...+|-+|+....+..|||.|+ .+.++.-.+.+|+.+++.+.+...++++++++...|++.|.|-+|-|..+|......
T Consensus       151 pFTLIGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~~~a~eIA~rSRGTPRIAnRLLrRVRDf  230 (332)
T COG2255         151 PFTLIGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGIEIDEEAALEIARRSRGTPRIANRLLRRVRDF  230 (332)
T ss_pred             CeeEeeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCCCCChHHHHHHHHhccCCcHHHHHHHHHHHHH
Confidence            3458889999999999999998 778888899999999999999999999999999999999999999999999887443


Q ss_pred             ----CCCCcchhhH
Q psy4285          86 ----HADEVNEDTI   95 (533)
Q Consensus        86 ----~~~~i~~~~i   95 (533)
                          ....|+.+..
T Consensus       231 a~V~~~~~I~~~ia  244 (332)
T COG2255         231 AQVKGDGDIDRDIA  244 (332)
T ss_pred             HHHhcCCcccHHHH
Confidence                2334665543

>TIGR00767 rho transcription termination factor Rho

Probab=96.92  E-value=0.0024  Score=63.91  Aligned_cols=29  Identities=24%  Similarity=0.314  Sum_probs=23.9

Q ss_pred             cCCCceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         304 NELPHLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       304 ~~~~~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +....+++.||||+|||++++.+++.+..
T Consensus       166 g~Gq~~~IvG~~g~GKTtL~~~i~~~I~~  194 (415)
T TIGR00767       166 GKGQRGLIVAPPKAGKTVLLQKIAQAITR  194 (415)
T ss_pred             CCCCEEEEECCCCCChhHHHHHHHHhhcc
Confidence            33345899999999999999999998643

Members of this family differ in the specificity of RNA binding.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=96.91  E-value=0.011  Score=58.09  Aligned_cols=22  Identities=18%  Similarity=0.089  Sum_probs=19.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ..++||||+|||+++..++-..
T Consensus        99 teI~G~~GsGKTql~lqla~~~  120 (313)
T TIGR02238        99 TEVFGEFRCGKTQLSHTLCVTA  120 (313)
T ss_pred             EEEECCCCCCcCHHHHHHHHHH
Confidence            6899999999999999887543

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

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=96.90  E-value=0.00069  Score=57.25  Aligned_cols=22  Identities=41%  Similarity=0.554  Sum_probs=20.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|.|+||+||||+|+.+++.+
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            5799999999999999999986

...

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	533
1sxj_C	340	Crystal Structure Of The Eukaryotic Clamp Loader (R		1e-50
1iqp_A	327	Crystal Structure Of The Clamp Loader Small Subunit		5e-40
1sxj_D	353	Crystal Structure Of The Eukaryotic Clamp Loader (R		3e-37
2chq_A	319	Replication Factor C Adpnp Complex Length = 319		8e-35
2chg_A	226	Replication Factor C Domains 1 And 2 Length = 226		1e-34
1sxj_B	323	Crystal Structure Of The Eukaryotic Clamp Loader (R		2e-27
1sxj_E	354	Crystal Structure Of The Eukaryotic Clamp Loader (R		7e-15
3u5z_B	324	Structure Of T4 Bacteriophage Clamp Loader Bound To		1e-09
1xxi_B	368	Adp Bound E. Coli Clamp Loader Complex Length = 368		7e-05
3glh_B	376	Crystal Structure Of The E. Coli Clamp Loader Bound		8e-05
1jr3_A	373	Crystal Structure Of The Processivity Clamp Loader		8e-05
3glf_B	395	Crystal Structure Of The Ecoli Clamp Loader Bound T		8e-05
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		9e-05
3glg_B	395	Crystal Structure Of A Mutant (Gammat157a) E. Coli		1e-04
1njg_A	250	Nucleotide-Free Form Of An Isolated E. Coli Clamp L		1e-04
4b4t_M	434	Near-Atomic Resolution Structural Model Of The Yeas		6e-04

>pdb|1SXJ|C Chain C, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 340

Iteration: 1
 Score =  197 bits (501), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 93/158 (58%), Positives = 118/158 (74%), Gaps = 8/158 (5%)
Query: 289 ESMDLCYKIN-------RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVL 341
           E++D  Y  N       +F+DE +LPHLLFYGPPGTGKT+TI+A AR++Y K  ++ MVL
Sbjct: 22  ETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGK-NYSNMVL 80
Query: 342 ELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTN 401
           ELNASDDRGI +VR+QI  FAST+ +    +KLIILDEADAMTN AQNALRR+IE++T N
Sbjct: 81  ELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKN 140
Query: 402 VRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
            RFC++ NY  K+ PA+ S+CTRFRF PL    I  R+
Sbjct: 141 TRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRI 178

>pdb|1IQP|A Chain A, Crystal Structure Of The Clamp Loader Small Subunit From Pyrococcus Furiosus Length = 327

Iteration: 1
 Score =  162 bits (410), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 76/149 (51%), Positives = 102/149 (68%), Gaps = 1/149 (0%)
Query: 293 LCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIG 352
           +  ++  ++    +PHLLF GPPG GKTT  LA AR+L+ +  +    LELNASD+RGI 
Sbjct: 33  IVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGE-NWRHNFLELNASDERGIN 91
Query: 353 IVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS 412
           ++R+++ +FA TK +  +S+K+I LDEADA+T DAQ ALRR +E F++NVRF + CNY S
Sbjct: 92  VIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSS 151
Query: 413 KIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
           KI   IQSRC  FRF PL    I  RL Y
Sbjct: 152 KIIEPIQSRCAIFRFRPLRDEDIAKRLRY 180

>pdb|1SXJ|D Chain D, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 353

Iteration: 1
 Score =  152 bits (385), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 75/147 (51%), Positives = 103/147 (70%), Gaps = 12/147 (8%)
Query: 306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTK 365
           LPH+LFYGPPGTGKT+TILA  ++LY      + +LELNASD+RGI IVR+++  FA   
Sbjct: 58  LPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARL- 116
Query: 366 TMHKSS-----------YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKI 414
           T+ K S           YK+IILDEAD+MT DAQ+ALRR +E ++   RFC+ICNY+++I
Sbjct: 117 TVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRI 176
Query: 415 PPAIQSRCTRFRFGPLDSSLIMSRLDY 441
              + S+C++FRF  LD+S  + RL +
Sbjct: 177 IDPLASQCSKFRFKALDASNAIDRLRF 203

>pdb|2CHQ|A Chain A, Replication Factor C Adpnp Complex Length = 319

Iteration: 1
 Score =  145 bits (365), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 67/148 (45%), Positives = 99/148 (66%), Gaps = 1/148 (0%)
Query: 292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
           ++  ++  +++   +PHLLF GPPGTGKT T +A AR L+ +  +    +E+NASD+RGI
Sbjct: 24  EVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGE-NWRDNFIEMNASDERGI 82
Query: 352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
            +VR +I +FA T  +  + +K+I LDEADA+T DAQ ALRR +E ++ + RF + CNY+
Sbjct: 83  DVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYV 142
Query: 412 SKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
           S+I   IQSRC  FRF P+    +  RL
Sbjct: 143 SRIIEPIQSRCAVFRFKPVPKEAMKKRL 170

>pdb|2CHG|A Chain A, Replication Factor C Domains 1 And 2 Length = 226

Iteration: 1
 Score =  144 bits (363), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 67/148 (45%), Positives = 99/148 (66%), Gaps = 1/148 (0%)
Query: 292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI 351
           ++  ++  +++   +PHLLF GPPGTGKT T +A AR L+ +  +    +E+NASD+RGI
Sbjct: 24  EVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGE-NWRDNFIEMNASDERGI 82
Query: 352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
            +VR +I +FA T  +  + +K+I LDEADA+T DAQ ALRR +E ++ + RF + CNY+
Sbjct: 83  DVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYV 142
Query: 412 SKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
           S+I   IQSRC  FRF P+    +  RL
Sbjct: 143 SRIIEPIQSRCAVFRFKPVPKEAMKKRL 170

>pdb|1SXJ|B Chain B, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 323

Iteration: 1
 Score =  120 bits (301), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 94/158 (59%), Gaps = 6/158 (3%)
Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
           ++ +   +  +PH++  G PG GKTT++   A +L  ++  +  VLELNASDDRGI +VR
Sbjct: 32  RLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADG-VLELNASDDRGIDVVR 90
Query: 356 DQIFQFASTK-TMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKI 414
           +QI  FA  K  +    +K++ILDEAD+MT  AQ ALRR +E ++ + RF   CN  +KI
Sbjct: 91  NQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKI 150
Query: 415 PPAIQSRCTRFRFGPLDSSLIMSRL----DYDDISFFN 448
              +QS+C   R+  L    ++ RL      +D+ + N
Sbjct: 151 IEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTN 188

>pdb|1SXJ|E Chain E, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 354

Iteration: 1
 Score = 78.6 bits (192), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 55/191 (28%), Positives = 88/191 (46%), Gaps = 47/191 (24%)
Query: 278 EITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFN 337
           E+TN L+ L ++  DL             PHLL YGP GTGK T  +A    ++    + 
Sbjct: 21  ELTNFLKSLSDQPRDL-------------PHLLLYGPNGTGKKTRCMALLESIFGPGVYR 67
Query: 338 AMV------------LELN---------------ASDDRGI------GIVRDQIFQFAST 364
             +            LELN                ++DR +       + + +   F  +
Sbjct: 68  LKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDS 127
Query: 365 KTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTR 424
           K      YK +I++EA+++T DAQ ALRR +EK++ N+R  ++C+ +S I   I+S+C  
Sbjct: 128 KDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLL 187
Query: 425 FRF-GPLDSSL 434
            R   P DS +
Sbjct: 188 IRCPAPSDSEI 198

>pdb|3U5Z|B Chain B, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4 Clamp, Primer-Template Dna, And Atp Analog Length = 324

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 44/136 (32%), Positives = 69/136 (50%), Gaps = 11/136 (8%)
Query: 303 ENELPHLLFYGP-PGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQF 361
           + ++PH++ + P PGTGKTT   A    +      NA ++ +N SD + I  VR  +  F
Sbjct: 44  KGKIPHIILHSPSPGTGKTTVAKALCHDV------NADMMFVNGSDCK-IDFVRGPLTNF 96
Query: 362 ASTKTMHKSSYKLIILDEAD-AMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQS 420
           AS  +      K+I++DE D +   ++Q  LR  +E +++N    I  N +  I   +QS
Sbjct: 97  ASAASF-DGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQS 155
Query: 421 RCTRFRFG-PLDSSLI 435
           RC    FG P D   I
Sbjct: 156 RCRVITFGQPTDEDKI 171

>pdb|1XXI|B Chain B, Adp Bound E. Coli Clamp Loader Complex Length = 368

Iteration: 1
 Score = 45.4 bits (106), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 36/152 (23%), Positives = 66/152 (43%), Gaps = 24/152 (15%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VLELNASDDRGI 351
           LF G  G GKT+     A+ L  +    A                   ++E++A+    +
Sbjct: 42  LFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKV 101
Query: 352 GIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN 409
              RD +   Q+A  +      +K+ ++DE   ++  + NAL + +E+   +V+F +   
Sbjct: 102 EDTRDLLDNVQYAPAR----GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATT 157
Query: 410 YLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
              K+P  I SRC +F    LD   I  +L++
Sbjct: 158 DPQKLPVTILSRCLQFHLKALDVEQIRHQLEH 189

>pdb|3GLH|B Chain B, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi Peptide Length = 376

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 36/152 (23%), Positives = 66/152 (43%), Gaps = 24/152 (15%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VLELNASDDRGI 351
           LF G  G GKT+     A+ L  +    A                   ++E++A+    +
Sbjct: 45  LFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKV 104
Query: 352 GIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN 409
              RD +   Q+A  +      +K+ ++DE   ++  + NAL + +E+   +V+F +   
Sbjct: 105 EDTRDLLDNVQYAPAR----GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATT 160
Query: 410 YLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
              K+P  I SRC +F    LD   I  +L++
Sbjct: 161 DPQKLPVTILSRCLQFHLKALDVEQIRHQLEH 192

>pdb|1JR3|A Chain A, Crystal Structure Of The Processivity Clamp Loader Gamma Complex Of E. Coli Dna Polymerase Iii Length = 373

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 36/152 (23%), Positives = 66/152 (43%), Gaps = 24/152 (15%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VLELNASDDRGI 351
           LF G  G GKT+     A+ L  +    A                   ++E++A+    +
Sbjct: 42  LFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKV 101
Query: 352 GIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN 409
              RD +   Q+A  +      +K+ ++DE   ++  + NAL + +E+   +V+F +   
Sbjct: 102 EDTRDLLDNVQYAPAR----GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATT 157
Query: 410 YLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
              K+P  I SRC +F    LD   I  +L++
Sbjct: 158 DPQKLPVTILSRCLQFHLKALDVEQIRHQLEH 189

>pdb|3GLF|B Chain B, Crystal Structure Of The Ecoli Clamp Loader Bound To Primer-template Dna Length = 395

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 36/152 (23%), Positives = 66/152 (43%), Gaps = 24/152 (15%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VLELNASDDRGI 351
           LF G  G GKT+     A+ L  +    A                   ++E++A+    +
Sbjct: 64  LFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKV 123
Query: 352 GIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN 409
              RD +   Q+A  +      +K+ ++DE   ++  + NAL + +E+   +V+F +   
Sbjct: 124 EDTRDLLDNVQYAPAR----GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATT 179
Query: 410 YLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
              K+P  I SRC +F    LD   I  +L++
Sbjct: 180 DPQKLPVTILSRCLQFHLKALDVEQIRHQLEH 211

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 42/148 (28%), Positives = 66/148 (44%), Gaps = 40/148 (27%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD------DRGIGIVRDQIFQFA 362
           +L YGPPGTGKT  + A A    TKA F    + +N S+        G  +VRD +F+ A
Sbjct: 209 VLLYGPPGTGKTMLVKAVANS--TKAAF----IRVNGSEFVHKYLGEGPRMVRD-VFRLA 261
Query: 363 STKTMHKSSYKLIILDEADAMTN---DAQNALRRIIEKF-------------TTNVRFCI 406
                 +++  +I +DE D++     DAQ    R +++              +TNV+  +
Sbjct: 262 -----RENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIM 316
Query: 407 ICNYLSKIPPAIQSRCTRFRFGPLDSSL 434
             N    + PA+       R G LD  +
Sbjct: 317 ATNRADTLDPAL------LRPGRLDRKI 338

>pdb|3GLG|B Chain B, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp Loader Bound To Primer-Template Dna Length = 395

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/152 (23%), Positives = 66/152 (43%), Gaps = 24/152 (15%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VLELNASDDRGI 351
           LF G  G GKT+     A+ L  +    A                   ++E++A+    +
Sbjct: 64  LFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKV 123
Query: 352 GIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN 409
              RD +   Q+A  +      +K+ ++DE   ++  + NAL + +E+   +V+F +   
Sbjct: 124 EDTRDLLDNVQYAPAR----GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATA 179
Query: 410 YLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
              K+P  I SRC +F    LD   I  +L++
Sbjct: 180 DPQKLPVTILSRCLQFHLKALDVEQIRHQLEH 211

>pdb|1NJG|A Chain A, Nucleotide-Free Form Of An Isolated E. Coli Clamp Loader Gamma Subunit Length = 250

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/152 (23%), Positives = 66/152 (43%), Gaps = 24/152 (15%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VLELNASDDRGI 351
           LF G  G GKT+     A+ L  +    A                   ++E++A+    +
Sbjct: 49  LFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKV 108
Query: 352 GIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN 409
              RD +   Q+A  +      +K+ ++DE   ++  + NAL + +E+   +V+F +   
Sbjct: 109 EDTRDLLDNVQYAPAR----GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATT 164
Query: 410 YLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
              K+P  I SRC +F    LD   I  +L++
Sbjct: 165 DPQKLPVTILSRCLQFHLKALDVEQIRHQLEH 196

>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/80 (40%), Positives = 38/80 (47%), Gaps = 18/80 (22%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD------DRGIGIVRDQIFQFAS 363
           L YGPPGTGKT    ACA      AQ NA  L+L A          G  +VRD  F  A 
Sbjct: 219 LMYGPPGTGKTLLARACA------AQTNATFLKLAAPQLVQMYIGEGAKLVRD-AFALAK 271
Query: 364 TKTMHKSSYKLIILDEADAM 383
            K     +  +I +DE DA+
Sbjct: 272 EK-----APTIIFIDELDAI 286

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	533
2chg_A	226	Replication factor C small subunit; DNA-binding pr	4e-80
2chg_A	226	Replication factor C small subunit; DNA-binding pr	3e-43
2chg_A	226	Replication factor C small subunit; DNA-binding pr	3e-39
2chq_A	319	Replication factor C small subunit; DNA-binding pr	4e-76
2chq_A	319	Replication factor C small subunit; DNA-binding pr	6e-49
2chq_A	319	Replication factor C small subunit; DNA-binding pr	4e-46
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	2e-75
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	2e-48
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	7e-46
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	1e-72
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	3e-50
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	1e-43
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	3e-70
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	1e-47
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	3e-46
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	2e-12
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	7e-65
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	8e-46
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	1e-40
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	3e-10
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	2e-58
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	5e-42
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	2e-26
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	1e-08
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	3e-07
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	1e-52
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	1e-43
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	7e-29
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	3e-10
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	7e-52
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	3e-26
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	2e-24
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	7e-19
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	6e-09
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	3e-12
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	2e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	5e-10
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	6e-09
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	3e-07
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	6e-07
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	8e-07
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	1e-06
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	2e-06
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	5e-06
3pvs_A	447	Replication-associated recombination protein A; ma	1e-05
3pvs_A	447	Replication-associated recombination protein A; ma	8e-05
3pvs_A	447	Replication-associated recombination protein A; ma	1e-04
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	3e-05
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	3e-05
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	6e-05
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	7e-05
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	9e-05

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus} Length = 226

 Score =  249 bits (637), Expect = 4e-80
 Identities = 67/146 (45%), Positives = 97/146 (66%), Gaps = 1/146 (0%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
           ++  +++   +PHLLF GPPGTGKT T +A AR L+ +  +    +E+NASD+RGI +VR
Sbjct: 28  RLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGE-NWRDNFIEMNASDERGIDVVR 86

Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
            +I +FA T  +  + +K+I LDEADA+T DAQ ALRR +E ++ + RF + CNY+S+I 
Sbjct: 87  HKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRII 146

Query: 416 PAIQSRCTRFRFGPLDSSLIMSRLDY 441
             IQSRC  FRF P+    +  RL  
Sbjct: 147 EPIQSRCAVFRFKPVPKEAMKKRLLE 172

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus} Length = 226

 Score =  152 bits (386), Expect = 3e-43
 Identities = 66/225 (29%), Positives = 96/225 (42%), Gaps = 63/225 (28%)

Query: 103 VEKYRPSTLDELVSHQDIISTIE--IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIA 160
           VEKYRP TLDE+V   ++I  ++  +    +  L+            GT +     AL  
Sbjct: 8   VEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGP-------PGTGKTATAIALAR 60

Query: 161 AFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQN 220
                  +   +E+NASD+RGI +VR +I +FA T  +  + +K+I LDEADA+T DAQ 
Sbjct: 61  DLFGENWRDNFIEMNASDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQA 120

Query: 221 ALRR-----------------------------------------------------KLP 227
           ALRR                                                      + 
Sbjct: 121 ALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVK 180

Query: 228 VTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVG 272
           +T DG +A+I +S GD RK +N LQ AA    + V+ DT+Y    
Sbjct: 181 ITEDGLEALIYISGGDFRKAINALQGAAAIG-EVVDADTIYQITA 224

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus} Length = 226

 Score =  141 bits (358), Expect = 3e-39
 Identities = 41/98 (41%), Positives = 61/98 (62%), Gaps = 1/98 (1%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           +E ++ + RF + CNY+S+I   IQSRC  FRF P+    +  RL  + E+E V +T DG
Sbjct: 126 MEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDG 185

Query: 61  KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTL 98
            +A+I +S GD RK +N LQ AA    + V+ DTI+ +
Sbjct: 186 LEALIYISGGDFRKAINALQGAAAIG-EVVDADTIYQI 222

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A Length = 319

 Score =  242 bits (619), Expect = 4e-76
 Identities = 67/146 (45%), Positives = 97/146 (66%), Gaps = 1/146 (0%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
           ++  +++   +PHLLF GPPGTGKT T +A AR L+ +  +    +E+NASD+RGI +VR
Sbjct: 28  RLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGE-NWRDNFIEMNASDERGIDVVR 86

Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
            +I +FA T  +  + +K+I LDEADA+T DAQ ALRR +E ++ + RF + CNY+S+I 
Sbjct: 87  HKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRII 146

Query: 416 PAIQSRCTRFRFGPLDSSLIMSRLDY 441
             IQSRC  FRF P+    +  RL  
Sbjct: 147 EPIQSRCAVFRFKPVPKEAMKKRLLE 172

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A Length = 319

 Score =  170 bits (433), Expect = 6e-49
 Identities = 62/199 (31%), Positives = 102/199 (51%), Gaps = 36/199 (18%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           +E ++ + RF + CNY+S+I   IQSRC  FRF P+    +  RL  + E+E V +T DG
Sbjct: 126 MEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDG 185

Query: 61  KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSH--- 117
            +A+I +S GD RK +N LQ AA    + V+ DTI+ +        RP  + EL+     
Sbjct: 186 LEALIYISGGDFRKAINALQGAAAIG-EVVDADTIYQI----TATARPEEMTELIQTALK 240

Query: 118 ---------------------QDIIS-------TIEIPESMLVDLVLKMSDIEYRLAAGT 149
                                +DI++       ++ I +S+ V L+ K+ ++++RL  G 
Sbjct: 241 GNFMEARELLDRLMVEYGMSGEDIVAQLFREIISMPIKDSLKVQLIDKLGEVDFRLTEGA 300

Query: 150 SEKIQLSALIAAFNSARDK 168
           +E+IQL A +A  ++   K
Sbjct: 301 NERIQLDAYLAYLSTLAKK 319

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A Length = 319

 Score =  163 bits (414), Expect = 4e-46
 Identities = 71/261 (27%), Positives = 111/261 (42%), Gaps = 64/261 (24%)

Query: 103 VEKYRPSTLDELVSHQDIISTIE--IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIA 160
           VEKYRP TLDE+V   ++I  ++  +    +  L+            GT +     AL  
Sbjct: 8   VEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGP-------PGTGKTATAIALAR 60

Query: 161 AFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQN 220
                  +   +E+NASD+RGI +VR +I +FA T  +  + +K+I LDEADA+T DAQ 
Sbjct: 61  DLFGENWRDNFIEMNASDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQA 120

Query: 221 ALRR-----------------------------------------------------KLP 227
           ALRR                                                      + 
Sbjct: 121 ALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVK 180

Query: 228 VTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLL 287
           +T DG +A+I +S GD RK +N LQ AA    + V+ DT+Y         E+T +++  L
Sbjct: 181 ITEDGLEALIYISGGDFRKAINALQGAAAIG-EVVDADTIYQITATARPEEMTELIQTAL 239

Query: 288 NESMDLCYK-INRFIDENELP 307
             +     + ++R + E  + 
Sbjct: 240 KGNFMEARELLDRLMVEYGMS 260

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20 Length = 327

 Score =  241 bits (616), Expect = 2e-75
 Identities = 76/146 (52%), Positives = 101/146 (69%), Gaps = 1/146 (0%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
           ++  ++    +PHLLF GPPG GKTT  LA AR+L+ +  +    LELNASD+RGI ++R
Sbjct: 36  RLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGE-NWRHNFLELNASDERGINVIR 94

Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
           +++ +FA TK +  +S+K+I LDEADA+T DAQ ALRR +E F++NVRF + CNY SKI 
Sbjct: 95  EKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKII 154

Query: 416 PAIQSRCTRFRFGPLDSSLIMSRLDY 441
             IQSRC  FRF PL    I  RL Y
Sbjct: 155 EPIQSRCAIFRFRPLRDEDIAKRLRY 180

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20 Length = 327

 Score =  169 bits (431), Expect = 2e-48
 Identities = 64/199 (32%), Positives = 99/199 (49%), Gaps = 36/199 (18%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           +E F++NVRF + CNY SKI   IQSRC  FRF PL    I  RL Y+ E E + +T +G
Sbjct: 134 MEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEG 193

Query: 61  KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSH--- 117
            +AI+ +++GDMR+ +NILQ+AA     ++ ++ +F +      + RP  + E++     
Sbjct: 194 LQAILYIAEGDMRRAINILQAAAALD-KKITDENVFMV----ASRARPEDIREMMLLALK 248

Query: 118 ---------------------QDIIS-------TIEIPESMLVDLVLKMSDIEYRLAAGT 149
                                +D++         + I E   V L  K+ +  +RL  G 
Sbjct: 249 GNFLKAREKLREILLKQGLSGEDVLVQMHKEVFNLPIEEPKKVLLADKIGEYNFRLVEGA 308

Query: 150 SEKIQLSALIAAFNSARDK 168
           +E IQL AL+A F     K
Sbjct: 309 NEIIQLEALLAQFTLIGKK 327

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20 Length = 327

 Score =  162 bits (413), Expect = 7e-46
 Identities = 65/261 (24%), Positives = 111/261 (42%), Gaps = 64/261 (24%)

Query: 103 VEKYRPSTLDELVSHQDIISTIE--IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIA 160
           VEKYRP  LD++V  + I+  ++  +    +  L+            G  +     AL  
Sbjct: 16  VEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGP-------PGVGKTTAALALAR 68

Query: 161 AFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQN 220
                  +   LELNASD+RGI ++R+++ +FA TK +  +S+K+I LDEADA+T DAQ 
Sbjct: 69  ELFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQ 128

Query: 221 ALRR-----------------------------------------------------KLP 227
           ALRR                                                      L 
Sbjct: 129 ALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLE 188

Query: 228 VTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLL 287
           +T +G +AI+ +++GDMR+ +NILQ+AA     ++ ++ V+         +I  ++   L
Sbjct: 189 LTEEGLQAILYIAEGDMRRAINILQAAAALD-KKITDENVFMVASRARPEDIREMMLLAL 247

Query: 288 NESMDLCYK-INRFIDENELP 307
             +     + +   + +  L 
Sbjct: 248 KGNFLKAREKLREILLKQGLS 268

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 323

 Score =  233 bits (596), Expect = 1e-72
 Identities = 76/292 (26%), Positives = 123/292 (42%), Gaps = 63/292 (21%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
           ++ +   +  +PH++  G PG GKTT++   A +L     +   VLELNASDDRGI +VR
Sbjct: 32  RLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELL-GRSYADGVLELNASDDRGIDVVR 90

Query: 356 DQIFQFASTK-TMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKI 414
           +QI  FA  K  +    +K++ILDEAD+MT  AQ ALRR +E ++ + RF   CN  +KI
Sbjct: 91  NQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKI 150

Query: 415 PPAIQSRCTRFRFGPLDSSLIMSRL---------DYDDISFFNIIIWYI--------KIQ 457
              +QS+C   R+  L    ++ RL          Y +     II             +Q
Sbjct: 151 IEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQ 210

Query: 458 EIKIEKGLALTDILTEISLLVHRLEIPESMLV---------------------------- 489
                 GL   D + +I    H L + + +L                             
Sbjct: 211 STVAGHGLVNADNVFKIVDSPHPLIVKKMLLASNLEDSIQILRTDLWKKGYSSIDIVTTS 270

Query: 490 -DLVLKMSDI---------------EYRLAAGTSEKIQLSALIAAFNSARDK 525
             +   ++ +                 R+  G    +QL++++A  +   +K
Sbjct: 271 FRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQLASMLAKIHKLNNK 322

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 323

 Score =  174 bits (443), Expect = 3e-50
 Identities = 53/193 (27%), Positives = 92/193 (47%), Gaps = 26/193 (13%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           +E ++ + RF   CN  +KI   +QS+C   R+  L    ++ RL  +I+ E V  T DG
Sbjct: 131 MELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDG 190

Query: 61  KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFT-------------LLVSRVEKYR 107
            +AII  ++GDMR+ +N LQS    H   VN D +F              LL S +E   
Sbjct: 191 LEAIIFTAEGDMRQAINNLQSTVAGH-GLVNADNVFKIVDSPHPLIVKKMLLASNLEDSI 249

Query: 108 PSTLDELV----SHQDIISTI--------EIPESMLVDLVLKMSDIEYRLAAGTSEKIQL 155
                +L     S  DI++T         ++ ES+ ++++ ++     R+  G    +QL
Sbjct: 250 QILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQL 309

Query: 156 SALIAAFNSARDK 168
           ++++A  +   +K
Sbjct: 310 ASMLAKIHKLNNK 322

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 323

 Score =  156 bits (396), Expect = 1e-43
 Identities = 70/252 (27%), Positives = 103/252 (40%), Gaps = 69/252 (27%)

Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRL---AAGTSEKIQLSALI 159
           VEKYRP  L ++V +++ I  ++         + K  ++ + +     G  +   +  L 
Sbjct: 12  VEKYRPQVLSDIVGNKETIDRLQQ--------IAKDGNMPHMIISGMPGIGKTTSVHCLA 63

Query: 160 AAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTK-TMHKSSYKLIILDEADAMTNDA 218
                      VLELNASDDRGI +VR+QI  FA  K  +    +K++ILDEAD+MT  A
Sbjct: 64  HELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGA 123

Query: 219 QNALRR-----------------------------------------------------K 225
           Q ALRR                                                      
Sbjct: 124 QQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLED 183

Query: 226 LPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRW 285
           +  T DG +AII  ++GDMR+ +N LQS    H   VN D V+  V  P    +      
Sbjct: 184 VKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGH-GLVNADNVFKIVDSPHPLIVKK---M 239

Query: 286 LLNESMDLCYKI 297
           LL  +++   +I
Sbjct: 240 LLASNLEDSIQI 251

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 340

 Score =  227 bits (581), Expect = 3e-70
 Identities = 88/146 (60%), Positives = 112/146 (76%), Gaps = 1/146 (0%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
            + +F+DE +LPHLLFYGPPGTGKT+TI+A AR++Y    ++ MVLELNASDDRGI +VR
Sbjct: 36  TVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIY-GKNYSNMVLELNASDDRGIDVVR 94

Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
           +QI  FAST+ +    +KLIILDEADAMTN AQNALRR+IE++T N RFC++ NY  K+ 
Sbjct: 95  NQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLT 154

Query: 416 PAIQSRCTRFRFGPLDSSLIMSRLDY 441
           PA+ S+CTRFRF PL    I  R+  
Sbjct: 155 PALLSQCTRFRFQPLPQEAIERRIAN 180

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 340

 Score =  167 bits (426), Expect = 1e-47
 Identities = 86/262 (32%), Positives = 123/262 (46%), Gaps = 67/262 (25%)

Query: 103 VEKYRPSTLDELVSHQDIISTIE--IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIA 160
           VEKYRP TLDE+    ++I+T+   + E  L  L+            GT +   + AL  
Sbjct: 16  VEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGP-------PGTGKTSTIVALAR 68

Query: 161 AFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQN 220
                     VLELNASDDRGI +VR+QI  FAST+ +    +KLIILDEADAMTN AQN
Sbjct: 69  EIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQN 128

Query: 221 ALRR-----------------------------------------------------KLP 227
           ALRR                                                     KL 
Sbjct: 129 ALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLK 188

Query: 228 VTPDGKKAIIDLSDGDMRKVLNILQSAA----TAHADEVNEDTVYNSVGYPTKTEITNIL 283
           ++P+ +KA+I+LS+GDMR+VLN+LQS          DE+++D +Y   G P  +++  +L
Sbjct: 189 LSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRPSDLKAVL 248

Query: 284 RWLLNESMDLCYK-INRFIDEN 304
           + +L +     +  +N+     
Sbjct: 249 KSILEDDWGTAHYTLNKVRSAK 270

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 340

 Score =  164 bits (416), Expect = 3e-46
 Identities = 66/199 (33%), Positives = 106/199 (53%), Gaps = 32/199 (16%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           IE++T N RFC++ NY  K+TPA+ S+CTRFRF PL    I  R+  V+  EK+ ++P+ 
Sbjct: 134 IERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNA 193

Query: 61  KKAIIDLSDGDMRKVLNILQSAA----TAHADEVNEDTIFTLLVSRVEKYRPSTLDELVS 116
           +KA+I+LS+GDMR+VLN+LQS          DE+++D I+    +       + L  ++ 
Sbjct: 194 EKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRPSDLKAVLKSILE 253

Query: 117 H--------------------QDIISTI--------EIPESMLVDLVLKMSDIEYRLAAG 148
                                 D+I  I           E   V L+ K++DIEY ++ G
Sbjct: 254 DDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSISKG 313

Query: 149 TSEKIQLSALIAAFNSARD 167
            +++IQ SA+I A  ++ +
Sbjct: 314 GNDQIQGSAVIGAIKASFE 332

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 340

 Score = 67.5 bits (165), Expect = 2e-12
 Identities = 23/73 (31%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 453 YIKIQEIKIEKGLALTDILTEISLLVHRLEIP-ESMLVDLVLKMSDIEYRLAAGTSEKIQ 511
           +  + +++  KGLAL D++  I  ++   E+  E   V L+ K++DIEY ++ G +++IQ
Sbjct: 260 HYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSISKGGNDQIQ 319

Query: 512 LSALIAAFNSARD 524
            SA+I A  ++ +
Sbjct: 320 GSAVIGAIKASFE 332

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 353

 Score =  213 bits (545), Expect = 7e-65
 Identities = 72/156 (46%), Positives = 102/156 (65%), Gaps = 10/156 (6%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
            + + +    LPH+LFYGPPGTGKT+TILA  ++LY      + +LELNASD+RGI IVR
Sbjct: 48  VLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVR 107

Query: 356 DQIFQFASTKTMH----------KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFC 405
           +++  FA                   YK+IILDEAD+MT DAQ+ALRR +E ++   RFC
Sbjct: 108 EKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFC 167

Query: 406 IICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
           +ICNY+++I   + S+C++FRF  LD+S  + RL +
Sbjct: 168 LICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRF 203

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 353

 Score =  163 bits (414), Expect = 8e-46
 Identities = 47/194 (24%), Positives = 84/194 (43%), Gaps = 32/194 (16%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           +E ++   RFC+ICNY+++I   + S+C++FRF  LD+S  + RL ++ EQE V      
Sbjct: 157 METYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENVKCDDGV 216

Query: 61  KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRV-EKYRPSTLDELVSH-- 117
            + I+D+S GD+R+ + +LQSA+       +   I +  V  +        L E+V    
Sbjct: 217 LERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVK 276

Query: 118 ---------------------QDIISTI--------EIPESMLVDLVLKMSDIEYRLAAG 148
                                  +++ +            +    +   +   + RL  G
Sbjct: 277 SGDFDEIKKYVNTFMKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNG 336

Query: 149 TSEKIQLSALIAAF 162
           T+E IQL  L+   
Sbjct: 337 TNEHIQLLNLLVKI 350

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 353

 Score =  149 bits (377), Expect = 1e-40
 Identities = 64/267 (23%), Positives = 100/267 (37%), Gaps = 80/267 (29%)

Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAA- 161
           VEKYRP  LDE+ +    ++ ++          LK +++ + L  G     + S ++A  
Sbjct: 28  VEKYRPKNLDEVTAQDHAVTVLKK--------TLKSANLPHMLFYGPPGTGKTSTILALT 79

Query: 162 ---FNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMH----------KSSYKLIIL 208
              +     K  +LELNASD+RGI IVR+++  FA                   YK+IIL
Sbjct: 80  KELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIIL 139

Query: 209 DEADAMTNDAQNALRR-------------------------------------------- 224
           DEAD+MT DAQ+ALRR                                            
Sbjct: 140 DEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAID 199

Query: 225 ---------KLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAH-----ADEVNEDTVYNS 270
                     +       + I+D+S GD+R+ + +LQSA+           +    V   
Sbjct: 200 RLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEEL 259

Query: 271 VGYPTKTEITNILRWLLNESMDLCYKI 297
            G      +  I+  + +   D   K 
Sbjct: 260 AGVVPHDILIEIVEKVKSGDFDEIKKY 286

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 353

 Score = 61.0 bits (148), Expect = 3e-10
 Identities = 10/68 (14%), Positives = 25/68 (36%), Gaps = 2/68 (2%)

Query: 453 YIKIQEIKIEKGLALTDILTEIS-LLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQ 511
              +    ++ G +   ++ ++    +       +    +   +   + RL  GT+E IQ
Sbjct: 284 KKYVNTF-MKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQ 342

Query: 512 LSALIAAF 519
           L  L+   
Sbjct: 343 LLNLLVKI 350

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B* Length = 324

 Score =  196 bits (499), Expect = 2e-58
 Identities = 42/155 (27%), Positives = 68/155 (43%), Gaps = 17/155 (10%)

Query: 296 KINRFIDENELPHLLFYGP-PGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIV 354
                  + ++PH++ + P PGTGKTT   A    +       A ++ +N SD + I  V
Sbjct: 37  TFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVN------ADMMFVNGSDCK-IDFV 89

Query: 355 RDQIFQFASTKTMHKSSYKLIILDEADAM-TNDAQNALRRIIEKFTTNVRFCIICNYLSK 413
           R  +  FAS  +      K+I++DE D     ++Q  LR  +E +++N    I  N +  
Sbjct: 90  RGPLTNFASAASF-DGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDG 148

Query: 414 IPPAIQSRCTRFRFGPLD-------SSLIMSRLDY 441
           I   +QSRC    FG             ++ RL  
Sbjct: 149 IIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTE 183

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B* Length = 324

 Score =  152 bits (385), Expect = 5e-42
 Identities = 25/188 (13%), Positives = 61/188 (32%), Gaps = 30/188 (15%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLD-------SSLIMSRLDYVIEQEK 53
           +E +++N    I  N +  I   +QSRC    FG             ++ RL  + + E 
Sbjct: 130 MEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEG 189

Query: 54  VNVT-PDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFT--------------L 98
           + +       A++  +  D RK +  L S ++     ++   +                L
Sbjct: 190 IAIADMKVVAALVKKNFPDFRKTIGELDSYSS--KGVLDAGILSLVTNDRGAIDDVLESL 247

Query: 99  LVSRVEKYRPSTLDELVSHQDIISTI------EIPESMLVDLVLKMSDIEYRLAAGTSEK 152
               V++ R         +   +  +       +    ++ +   + +         + +
Sbjct: 248 KNKDVKQLRALAPKYAADYSWFVGKLAEEIYSRVTPQSIIRMYEIVGENNQYHGIAANTE 307

Query: 153 IQLSALIA 160
           + L+ L  
Sbjct: 308 LHLAYLFI 315

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B* Length = 324

 Score =  108 bits (272), Expect = 2e-26
 Identities = 30/124 (24%), Positives = 51/124 (41%), Gaps = 14/124 (11%)

Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAF 162
            +KYRPST+DE +       T +         +     I + +    S     + +  A 
Sbjct: 17  EQKYRPSTIDECILPAFDKETFKS--------ITSKGKIPHIILHSPSPGTGKTTVAKAL 68

Query: 163 NSARD-KLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAM-TNDAQN 220
               D   +++ +N SD + I  VR  +  FAS  +      K+I++DE D     ++Q 
Sbjct: 69  --CHDVNADMMFVNGSDCK-IDFVRGPLTNFASAASF-DGRQKVIVIDEFDRSGLAESQR 124

Query: 221 ALRR 224
            LR 
Sbjct: 125 HLRS 128

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B* Length = 324

 Score = 55.8 bits (135), Expect = 1e-08
 Identities = 10/68 (14%), Positives = 24/68 (35%), Gaps = 4/68 (5%)

Query: 230 PDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNE 289
                A++  +  D RK +  L S ++     ++   +           I ++L  L N+
Sbjct: 195 MKVVAALVKKNFPDFRKTIGELDSYSS--KGVLDAGILSLVTNDR--GAIDDVLESLKNK 250

Query: 290 SMDLCYKI 297
            +     +
Sbjct: 251 DVKQLRAL 258

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B* Length = 324

 Score = 51.2 bits (123), Expect = 3e-07
 Identities = 4/65 (6%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 453 YIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQL 512
             +++ +  +     +  + +++  ++    P+S+ + +   + +         + ++ L
Sbjct: 252 VKQLRALAPKYAADYSWFVGKLAEEIYSRVTPQSI-IRMYEIVGENNQYHGIAANTELHL 310

Query: 513 SALIA 517
           + L  
Sbjct: 311 AYLFI 315

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 354

 Score =  181 bits (462), Expect = 1e-52
 Identities = 47/180 (26%), Positives = 80/180 (44%), Gaps = 34/180 (18%)

Query: 296 KINRFIDENE-LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV-------------- 340
            +    D+   LPHLL YGP GTGK T  +A    ++    +   +              
Sbjct: 25  FLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLE 84

Query: 341 ---------LELNASDDRGI--GIVRDQIFQFASTKTM--------HKSSYKLIILDEAD 381
                    LE+  SD       ++++ + + A  + +            YK +I++EA+
Sbjct: 85  LNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEAN 144

Query: 382 AMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
           ++T DAQ ALRR +EK++ N+R  ++C+ +S I   I+S+C   R      S I + L  
Sbjct: 145 SLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSD 204

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 354

 Score =  157 bits (398), Expect = 1e-43
 Identities = 40/193 (20%), Positives = 79/193 (40%), Gaps = 32/193 (16%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNV-TPD 59
           +EK++ N+R  ++C+ +S I   I+S+C   R      S I + L  V+  E++ + T D
Sbjct: 158 MEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKD 217

Query: 60  GKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDT------------------IFTLLVS 101
             K I   S+G++R  L +L+S A  +   +   +                  +    V+
Sbjct: 218 ILKRIAQASNGNLRVSLLMLESMALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVN 277

Query: 102 RVEKYRPSTLDELVSH----QDIISTI--------EIPESMLVDLVLKMSDIEYRLAAGT 149
            + + R + L +L++H      I+  +         +  +    ++   S  + RL+ G 
Sbjct: 278 SLIECR-AVLYDLLAHCIPANIILKELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGN 336

Query: 150 SEKIQLSALIAAF 162
                L   IA  
Sbjct: 337 KAIFHLEGFIAKV 349

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 354

 Score =  116 bits (292), Expect = 7e-29
 Identities = 46/278 (16%), Positives = 94/278 (33%), Gaps = 100/278 (35%)

Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAA- 161
           V+KYRP +L+ L  ++++ +        L  L  +  D+ + L  G +   + +  +A  
Sbjct: 5   VDKYRPKSLNALSHNEELTNF-------LKSLSDQPRDLPHLLLYGPNGTGKKTRCMALL 57

Query: 162 ---FNSARDKLEV-----------------------LELNASDDRGI--GIVRDQIFQFA 193
              F     +L++                       LE+  SD       ++++ + + A
Sbjct: 58  ESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVA 117

Query: 194 STKTM--------HKSSYKLIILDEADAMTNDAQNALRR--------------------- 224
             + +            YK +I++EA+++T DAQ ALRR                     
Sbjct: 118 QMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPI 177

Query: 225 --------------------------------KLPVTPD-GKKAIIDLSDGDMRKVLNIL 251
                                           ++ +      K I   S+G++R  L +L
Sbjct: 178 IAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLML 237

Query: 252 QSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNE 289
           +S A  +  E+   +    +       I  + R ++ E
Sbjct: 238 ESMALNN--ELALKSSSPIIKPDWIIVIHKLTRKIVKE 273

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 354

 Score = 60.7 bits (147), Expect = 3e-10
 Identities = 11/66 (16%), Positives = 26/66 (39%), Gaps = 2/66 (3%)

Query: 455 KIQEIKIEKGLALTDILTEISLLVHRLE-IPESMLVDLVLKMSDIEYRLAAGTSEKIQLS 513
            + ++ +   +    IL E++  +  +E +  +    ++   S  + RL+ G      L 
Sbjct: 285 VLYDL-LAHCIPANIILKELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLE 343

Query: 514 ALIAAF 519
             IA  
Sbjct: 344 GFIAKV 349

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 516

 Score =  183 bits (467), Expect = 7e-52
 Identities = 40/182 (21%), Positives = 67/182 (36%), Gaps = 22/182 (12%)

Query: 276 KTEITNILRWLLN--ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTK 333
           K  +  +  WL N   S    +K             + YGPPG GKTT     A+     
Sbjct: 45  KGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQ----- 99

Query: 334 AQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH------------KSSYKLIILDEAD 381
            +    +LE NASD R   ++   +       ++                + +II+DE D
Sbjct: 100 -ELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVD 158

Query: 382 AMTNDAQNALRRIIEKFT-TNVRFCIICNYLS-KIPPAIQSRCTRFRFGPLDSSLIMSRL 439
            M+   +  + ++ +    T+    +ICN  +          C   +F   D++ I SRL
Sbjct: 159 GMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRL 218

Query: 440 DY 441
             
Sbjct: 219 MT 220

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 516

 Score =  111 bits (279), Expect = 3e-26
 Identities = 25/116 (21%), Positives = 49/116 (42%), Gaps = 3/116 (2%)

Query: 1   IEKFT-TNVRFCIICNYLS-KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTP 58
            +    T+    +ICN  +          C   +F   D++ I SRL  +  +EK  + P
Sbjct: 172 AQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDP 231

Query: 59  DGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDEL 114
           +    +I  + GD+R+V+N+L + +T     +N + I  +  +  +       D  
Sbjct: 232 NVIDRLIQTTRGDIRQVINLLSTISTTT-KTINHENINEISKAWEKNIALKPFDIA 286

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 516

 Score =  105 bits (264), Expect = 2e-24
 Identities = 41/342 (11%), Positives = 83/342 (24%), Gaps = 113/342 (33%)

Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSD---IEYRLAAGTSEKIQLSALI 159
             KY P+ L ++  ++  +  ++          L   +         AG        A +
Sbjct: 30  TVKYAPTNLQQVCGNKGSVMKLK--------NWLANWENSKKNSFKHAGKDGSGVFRAAM 81

Query: 160 -----------AAFNSARD-KLEVLELNASDDRGIGIVRDQIFQFASTKTMH-------- 199
                      AA   A++   ++LE NASD R   ++   +       ++         
Sbjct: 82  LYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEE 141

Query: 200 ----KSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAII------------------ 237
                  + +II+DE D M+   +  + +           +I                  
Sbjct: 142 AQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVC 201

Query: 238 ------DLSDGDMRK-------------------------------VLNILQSAATAHAD 260
                       ++                                V+N+L + +T    
Sbjct: 202 LDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTT-K 260

Query: 261 EVNEDTVYNSVGYPTKTEITNILRWL------------------LNESMDLCY----KIN 298
            +N + +        K                            LN+ + L +       
Sbjct: 261 TINHENINEISKAWEKNIALKPFDIAHKMLDGQIYSDIGSRNFTLNDKIALYFDDFDFTP 320

Query: 299 RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV 340
             I EN L        PG      +   A  +         +
Sbjct: 321 LMIQENYLSTRPSVLKPGQSHLEAVAEAANCISLGDIVEKKI 362

>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* Length = 334

 Score = 87.1 bits (216), Expect = 7e-19
 Identities = 28/161 (17%), Positives = 53/161 (32%), Gaps = 24/161 (14%)

Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VL 341
                  H LL    PG G    I A +R L  +                          
Sbjct: 18  YQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYY 77

Query: 342 ELNASDDRG-IGI--VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF 398
            L     +  +G+  VR ++ +  +         K++ + +A  +T+ A NAL + +E+ 
Sbjct: 78  TLAPEKGKNTLGVDAVR-EVTEKLNEHA-RLGGAKVVWVTDAALLTDAAANALLKTLEEP 135

Query: 399 TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
                F +      ++   ++SRC      P      ++ L
Sbjct: 136 PAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWL 176

>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* Length = 334

 Score = 56.7 bits (137), Expect = 6e-09
 Identities = 24/174 (13%), Positives = 54/174 (31%), Gaps = 20/174 (11%)

Query: 7   NVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIID 66
              F +      ++   ++SRC      P      ++ L       +V ++ D   A + 
Sbjct: 138 ETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWL-----SREVTMSQDALLAALR 192

Query: 67  LSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEI 126
           LS G     L + Q       + +        L   V      +L   ++H+   + +  
Sbjct: 193 LSAGSPGAALALFQGDNWQARETL-----CQALAYSVPSGDWYSLLAALNHEQAPARLHW 247

Query: 127 PESMLVDLVLKMSDIEYRLAAGTSEKIQ----------LSALIAAFNSARDKLE 170
             ++L+D + +               +           L A++      R++L 
Sbjct: 248 LATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQLM 301

>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* Length = 250

 Score = 65.7 bits (161), Expect = 3e-12
 Identities = 40/171 (23%), Positives = 71/171 (41%), Gaps = 43/171 (25%)

Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----CARKLYTK-----------AQFNAM-VL 341
           +    + H  LF G  G GKT+   +LA    C   +               Q   + ++
Sbjct: 39  LSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLI 98

Query: 342 ELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIE--- 396
           E++A+    +   RD +   Q+A  +      +K+ ++DE   ++  + NAL + +E   
Sbjct: 99  EIDAASRTKVEDTRDLLDNVQYAPAR----GRFKVYLIDEVHMLSRHSFNALLKTLEEPP 154

Query: 397 ---KF---TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
              KF   TT+ +         K+P  I SRC +F    LD   I  +L++
Sbjct: 155 EHVKFLLATTDPQ---------KLPVTILSRCLQFHLKALDVEQIRHQLEH 196

>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* Length = 250

 Score = 59.9 bits (146), Expect = 2e-10
 Identities = 18/81 (22%), Positives = 39/81 (48%)

Query: 19  KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
           K+   I SRC +F    LD   I  +L++++ +E +   P   + +   ++G +R  L++
Sbjct: 168 KLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSL 227

Query: 79  LQSAATAHADEVNEDTIFTLL 99
              A  +   +V+   +  +L
Sbjct: 228 TDQAIASGDGQVSTQAVSAML 248

>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 = 62.9 bits (152), Expect = 2e-10
 Identities = 89/494 (18%), Positives = 175/494 (35%), Gaps = 120/494 (24%)

Query: 91  NEDTIFT-LLVSRVEKYRP--STLDELVSHQDIISTIE----IPESMLVDLVLKMSDIEY 143
           N++ +F    VSR++ Y      L EL   ++++  I+      ++ +   V     ++ 
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVL--IDGVLGSGKTWVALDVCLSYKVQC 178

Query: 144 RLAAGTSEKIQ-LSALIAAFNSARDKLEVLE---------LNASDDRGIGI-VRDQIFQF 192
           ++       I  L+  +   NS    LE+L+           +  D    I +R    Q 
Sbjct: 179 KMDFK----IFWLN--LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232

Query: 193 ASTKTMHKSSYK--LIILDE-ADAMTNDAQNALR-RKLPVTPDGKKAIIDLSDGDMRKVL 248
              + +    Y+  L++L    +A   +A N L  + L  T               ++V 
Sbjct: 233 ELRRLLKSKPYENCLLVLLNVQNAKAWNAFN-LSCKILLTTRF-------------KQVT 278

Query: 249 NILQSAATAHADEVNEDTVYNSVGYPTKTEITNIL-RWLLNESMDL----CYKINRF--- 300
           + L +A T H    +           T  E+ ++L ++L     DL        N     
Sbjct: 279 DFLSAATTTHISLDHHSMTL------TPDEVKSLLLKYLDCRPQDLPREVL-TTNPRRLS 331

Query: 301 -IDE---NELPHLLFYGPPGTGKTTTILACA---------RKLYTK-AQFN------AMV 340
            I E   + L     +      K TTI+  +         RK++ + + F        ++
Sbjct: 332 IIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTIL 391

Query: 341 LEL--NASDDRGIGIVRDQIFQFAS-TKTMHKSSYKL--IILDEADAMTNDAQNAL-RRI 394
           L L         + +V +++ +++   K   +S+  +  I L+    + N+   AL R I
Sbjct: 392 LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEY--ALHRSI 449

Query: 395 IEKFTTNVRFCI-----------ICNY----LSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
           ++ +     F               ++    L  I      R T FR   LD   +  ++
Sbjct: 450 VDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHP--ERMTLFRMVFLDFRFLEQKI 507

Query: 440 DYDDI------SFFNIII------WYIKIQEIKIEKGL-ALTDILTEISLLVHRLEIPES 486
            +D        S  N +        YI   + K E+ + A+ D L +I   +       +
Sbjct: 508 RHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLIC--SKYT 565

Query: 487 MLVDLVLKMSDIEY 500
            L+ + L M++ E 
Sbjct: 566 DLLRIAL-MAEDEA 578

>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 = 61.4 bits (148), Expect = 6e-10
 Identities = 67/405 (16%), Positives = 119/405 (29%), Gaps = 116/405 (28%)

Query: 199 HKSSYKLIILDEADAMT-----NDAQNALRRKLPVTPDGKKAIIDLSDGD--MRKVLNIL 251
           H+  YK I+    DA        D Q+  +  L  + +    II   D      ++   L
Sbjct: 14  HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSIL--SKEEIDHIIMSKDAVSGTLRLFWTL 71

Query: 252 QSAATAHADEVNEDTV---YNSVGYPTKTE--ITNILRWLLNESMD-LC--------YKI 297
            S       +  E+ +   Y  +  P KTE    +++  +  E  D L         Y +
Sbjct: 72  LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV 131

Query: 298 NRFIDENEL----------PHLLFYGPPGTGKTTTILACARKLYTKAQFN---------- 337
           +R     +L           ++L  G  G+GKT   L        + + +          
Sbjct: 132 SRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKN 191

Query: 338 ----AMVLE------------LNASDDRGIGI-VRDQIFQFASTKTMHKSSYK--LIILD 378
                 VLE              +  D    I +R    Q    + +    Y+  L++L 
Sbjct: 192 CNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL 251

Query: 379 EADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSR 438
                  + QNA  +    F  N+  C       KI                   L+ +R
Sbjct: 252 -------NVQNA--KAWNAF--NLS-C-------KI-------------------LLTTR 273

Query: 439 LDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML----VD---L 491
                    + +              + LT    + SLL+  L+     L    +     
Sbjct: 274 ----FKQVTDFLSAATTTHISLDHHSMTLTPDEVK-SLLLKYLDCRPQDLPREVLTTNPR 328

Query: 492 VLKM---SDIEYRLAAGTSEKIQLSALIAAFNSARDKLEAPPDPQ 533
            L +   S  +        + +    L     S+ + LE P + +
Sbjct: 329 RLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLE-PAEYR 372

>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 = 53.3 bits (127), Expect = 2e-07
 Identities = 70/447 (15%), Positives = 138/447 (30%), Gaps = 129/447 (28%)

Query: 15  NYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRK 74
             L +I P   SR        L    I + L  +++          +  ++ L +     
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS------KPYENCLLVLLN----- 252

Query: 75  VLNILQSAATAHADEVNEDTIF-----TLLVSR---VEKYRPSTLDELVSHQDIISTIEI 126
               +Q+A   +A        F      LL +R   V  +  +     +S      T+  
Sbjct: 253 ----VQNAKAWNA--------FNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTP 300

Query: 127 PESMLVDLVLKMSDIEY----RLAAGTSEKIQLSALIAAF------------NSARDKL- 169
            E     L+LK  D       R    T+   +  ++IA              +   DKL 
Sbjct: 301 DEVK--SLLLKYLDCRPQDLPREVLTTNP--RRLSIIAESIRDGLATWDNWKHVNCDKLT 356

Query: 170 EVLE-----LNASDDRG----IGIVRD--QIFQFASTKTMHKSSYKLIIL----DEADAM 214
            ++E     L  ++ R     + +      I     T         L ++     ++D M
Sbjct: 357 TIIESSLNVLEPAEYRKMFDRLSVFPPSAHI----PTIL-------LSLIWFDVIKSDVM 405

Query: 215 TNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVN----------- 263
                N L +   V    K++ I +    +   + +    A  H   V+           
Sbjct: 406 --VVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYA-LHRSIVDHYNIPKTFDSD 462

Query: 264 ------EDT-VYNSVGY----PTKTEITNILRWLLNESMDLCYKINRFIDENELPH--LL 310
                  D   Y+ +G+        E   + R +    +D      RF+ E ++ H    
Sbjct: 463 DLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVF---LDF-----RFL-EQKIRHDSTA 513

Query: 311 FYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKS 370
           +        T   L    K Y        + + +   +R +  + D  F     + +  S
Sbjct: 514 WNASGSILNTLQQL----KFYKP-----YICDNDPKYERLVNAILD--FLPKIEENLICS 562

Query: 371 SY----KLIILDEADAMTNDAQNALRR 393
            Y    ++ ++ E +A+  +A   ++R
Sbjct: 563 KYTDLLRIALMAEDEAIFEEAHKQVQR 589

>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* Length = 373

 Score = 60.3 bits (147), Expect = 5e-10
 Identities = 40/171 (23%), Positives = 71/171 (41%), Gaps = 43/171 (25%)

Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----CARKLYTK-----------AQFNAM-VL 341
           +    + H  LF G  G GKT+   +LA    C   +               Q   + ++
Sbjct: 32  LSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLI 91

Query: 342 ELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIE--- 396
           E++A+    +   RD +   Q+A  +      +K+ ++DE   ++  + NAL + +E   
Sbjct: 92  EIDAASRTKVEDTRDLLDNVQYAPAR----GRFKVYLIDEVHMLSRHSFNALLKTLEEPP 147

Query: 397 ---KF---TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
              KF   TT+ +         K+P  I SRC +F    LD   I  +L++
Sbjct: 148 EHVKFLLATTDPQ---------KLPVTILSRCLQFHLKALDVEQIRHQLEH 189

>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* Length = 373

 Score = 56.8 bits (138), Expect = 6e-09
 Identities = 20/113 (17%), Positives = 49/113 (43%), Gaps = 1/113 (0%)

Query: 19  KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
           K+   I SRC +F    LD   I  +L++++ +E +   P   + +   ++G +R  L++
Sbjct: 161 KLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSL 220

Query: 79  LQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESML 131
              A  +   +V+   +  +L   ++  +  +L E +   +    + +     
Sbjct: 221 TDQAIASGDGQVSTQAVSAML-GTLDDDQALSLVEAMVEANGERVMALINEAA 272

>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 Length = 389

 Score = 51.3 bits (122), Expect = 3e-07
 Identities = 26/165 (15%), Positives = 51/165 (30%), Gaps = 33/165 (20%)

Query: 307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT 366
           P     G PGTGKT T+         K       + +N    R    +  +I +  +   
Sbjct: 45  PRATLLGRPGTGKTVTLRKLWELYKDKTTAR--FVYINGFIYRNFTAIIGEIARSLNIPF 102

Query: 367 MHKS------------------SYKLIILDEADAMTNDAQNALRRIIEKFTT--NVRFCI 406
             +                    Y  ++LD+A  +  D  +   R+ ++       R  +
Sbjct: 103 PRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIAL 162

Query: 407 IC-----NYLSKIPPAIQSRC--TRFRFGPLDSS----LIMSRLD 440
           +        L+ + P+ +        RF P        +++ R  
Sbjct: 163 VIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAK 207

>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} Length = 384

 Score = 50.9 bits (121), Expect = 6e-07
 Identities = 28/181 (15%), Positives = 51/181 (28%), Gaps = 30/181 (16%)

Query: 288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAM-----VLE 342
           +   D    I  F+        LF G  GTGKT        ++    + +          
Sbjct: 27  DILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAY 86

Query: 343 LN---------------ASDDRGIGIVR---DQIFQFASTKTMHKSSYKLIILDEADAMT 384
           +N               A    G  + +   +        K   ++   +I LDE D + 
Sbjct: 87  VNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLV 146

Query: 385 NDAQNALRRIIEKFTTNVRFCIIC-----NYLSKIPPAIQSRC-TRFRFGPLDSSLIMSR 438
                    + +   ++    +I      N    + P + S       F P D+  +   
Sbjct: 147 KRRGG-DIVLYQLLRSDANISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFI 205

Query: 439 L 439
           L
Sbjct: 206 L 206

>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} Length = 386

 Score = 50.4 bits (120), Expect = 8e-07
 Identities = 27/185 (14%), Positives = 59/185 (31%), Gaps = 32/185 (17%)

Query: 288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD 347
           ++   +   +     E +  ++  YG  GTGKT  +     KL+ K       + +N   
Sbjct: 27  DQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQ 86

Query: 348 DR------------------GIGIVRDQIFQFASTKTMHKSSYKLIILDEADAM-TNDAQ 388
                                 G+   ++++          S  +I+LDE DA       
Sbjct: 87  IDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYND 146

Query: 389 NALRRIIEKFT--TNVRFCIIC-----NYLSKIPPAIQSRC--TRFRFGPLDS----SLI 435
           + L ++    +     +   I       ++  + P ++S        F P ++     ++
Sbjct: 147 DILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDIL 206

Query: 436 MSRLD 440
             R  
Sbjct: 207 TKRAQ 211

>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 Length = 305

 Score = 49.3 bits (118), Expect = 1e-06
 Identities = 24/148 (16%), Positives = 47/148 (31%), Gaps = 25/148 (16%)

Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELN-ASDDRGIGIVRDQI--FQFASTK 365
           +L  G   +      L     +       + VLE++   ++ GI  +R       ++   
Sbjct: 21  ILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPEL 80

Query: 366 TMHKSSYKLIILDEADAMTNDAQNALRRIIE------KF---TTNVRFCIICNYLSKIPP 416
                + K +I+ + + MT  A NA  + +E           T              + P
Sbjct: 81  ----YTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWH---------YLLP 127

Query: 417 AIQSRCTRFRFGPLDSSLIMSRLDYDDI 444
            I+SR  R           + +    D+
Sbjct: 128 TIKSRVFRVVVNVPKEFRDLVKEKIGDL 155

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

 Score = 48.8 bits (116), Expect = 2e-06
 Identities = 35/198 (17%), Positives = 55/198 (27%), Gaps = 67/198 (33%)

Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAM------------------------------ 339
           L  G PGTGKT   +  A+ L     F A+                              
Sbjct: 74  LIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKA 133

Query: 340 -------VLELNASDDRGIGI--------------VRDQIFQFASTKTMHKSSYKLI--- 375
                  + E++  + R  G               VR+QI      +   +   ++I   
Sbjct: 134 GAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQI-NAKVAEWREEGKAEIIPGV 192

Query: 376 -ILDEADAMTNDAQNALRRIIEK-------FTTNVRFCIIC--NYLS--KIPPAIQSRCT 423
             +DE   +  ++ + L R +E          TN     I   +Y S   IP  +  R  
Sbjct: 193 LFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLL 252

Query: 424 RFRFGPLDSSLIMSRLDY 441
                P         L  
Sbjct: 253 IVSTTPYSEKDTKQILRI 270

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

 Score = 47.6 bits (113), Expect = 5e-06
 Identities = 13/89 (14%), Positives = 29/89 (32%), Gaps = 2/89 (2%)

Query: 19  KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL-SDGDMRKVLN 77
            I   +  R       P         L    E+E V ++ D    +  +  +  +R  + 
Sbjct: 242 GIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQ 301

Query: 78  ILQSAATAHADEVNEDTIFTLLVSRVEKY 106
           ++ +AA+    +     +    + RV   
Sbjct: 302 LI-TAASLVCRKRKGTEVQVDDIKRVYSL 329

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli} Length = 447

 Score = 47.1 bits (113), Expect = 1e-05
 Identities = 23/112 (20%), Positives = 46/112 (41%), Gaps = 13/112 (11%)

Query: 22  PAIQSRCTRFRFGPLDSSLIMSRLDYVIEQE-------KVNVTPDGKKAIIDLSDGDMRK 74
            A+ SR   +    L +  I   L   +E +        + +  + ++AI +L +GD R+
Sbjct: 151 SALLSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARR 210

Query: 75  VLNILQSAATAHADEVNEDTIFTL-LVSRVEKYRPSTLD---ELVSHQDIIS 122
            LN L+  A     + +   +    L++ +   R +  D   +     D+IS
Sbjct: 211 ALNTLEMMADMAEVDDSGKRVLKPELLTEIAGERSARFDNKGD--RFYDLIS 260

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli} Length = 447

 Score = 44.1 bits (105), Expect = 8e-05
 Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 10/49 (20%)

Query: 299 RFIDENELPHLLFYGPPGTGKTTTILA--CARKLYTKAQFNAMVLELNA 345
           R I+   L  ++ +GPPGTGKTT  LA   AR  Y  A        ++A
Sbjct: 43  RAIEAGHLHSMILWGPPGTGKTT--LAEVIAR--YANADV----ERISA 83

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli} Length = 447

 Score = 43.7 bits (104), Expect = 1e-04
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 203 YKLIILDEAD-------AMTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAA 255
           Y L  L   D       AM +  +    + + +  + ++AI +L +GD R+ LN L+  A
Sbjct: 160 YLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTLEMMA 219

Query: 256 TAHADEVNEDTV 267
                + +   V
Sbjct: 220 DMAEVDDSGKRV 231

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae} Length = 318

 Score = 44.9 bits (105), Expect = 3e-05
 Identities = 24/230 (10%), Positives = 71/230 (30%), Gaps = 37/230 (16%)

Query: 288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAM----VLEL 343
            +   +   I   +  ++           + K   +     +L T +    +     + +
Sbjct: 27  EDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHI 86

Query: 344 NASDDRG------------------IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN 385
           +A +  G                    I  + +  + +     K    LI++   + + +
Sbjct: 87  DALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLS 146

Query: 386 DAQNALRRIIEKFTT-NVRFCIIC--NYL----SKIPPAIQSRC--TRFRFGPLDSS--- 433
             +  L+   +  ++ N +  IIC   +      +I      +   T  +   +D +   
Sbjct: 147 --EKILQYFEKWISSKNSKLSIICVGGHNVTIREQINIMPSLKAHFTEIKLNKVDKNELQ 204

Query: 434 -LIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLE 482
            +I++RL      F   +    ++      +      I   + ++ H++ 
Sbjct: 205 QMIITRLKSLLKPFHVKVNDKKEMTIYNNIREGQNQKIPDNVIVINHKIN 254

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A* Length = 309

 Score = 44.4 bits (104), Expect = 6e-05
 Identities = 35/177 (19%), Positives = 62/177 (35%), Gaps = 28/177 (15%)

Query: 274 PTKTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTK 333
           P K  I      LL   ++   +      E    H+ F G PGTGKTT  L  A  L+  
Sbjct: 38  PVKDRIRETAALLL---VERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRL 94

Query: 334 -AQFNAMVLELNASDDRGIGIVRDQIFQFAS--TKTMHKSSYKLIILDEADAMTN----- 385
                  ++ +   D     +V   I   A    + + ++   ++ +DEA  +       
Sbjct: 95  GYVRKGHLVSVTRDD-----LVGQYIGHTAPKTKEVLKRAMGGVLFIDEAYYLYRPDNER 149

Query: 386 ----DAQNALRRIIEKFTTNVRFCIICNYLSKI------PPAIQSR-CTRFRFGPLD 431
               +A   L +++E    ++   I+  Y  ++       P  +SR      F    
Sbjct: 150 DYGQEAIEILLQVMENNRDDL-VVILAGYADRMENFFQSNPGFRSRIAHHIEFPDYS 205

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix} Length = 387

 Score = 44.4 bits (104), Expect = 7e-05
 Identities = 31/191 (16%), Positives = 60/191 (31%), Gaps = 37/191 (19%)

Query: 288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAM---VLELN 344
            E   L   +   +   +  + L YG  GTGKT       R+L  +A    +    + +N
Sbjct: 26  AELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVN 85

Query: 345 ASDDRGIGIVRDQIFQFAS------------------TKTMHKSSYKLIILDEADAMT-- 384
           A        V   I +                      +        +I+LDE D +   
Sbjct: 86  ARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKR 145

Query: 385 ---NDAQNALRRIIEKFTTNVRFCIIC-----NYLSKIPPAIQSRC--TRFRFGPLDSS- 433
               D    + RI ++    V   ++       ++  + P ++S        F P  +  
Sbjct: 146 PGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQ 205

Query: 434 ---LIMSRLDY 441
              ++ +R + 
Sbjct: 206 LRDILETRAEE 216

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A* Length = 180

 Score = 42.4 bits (100), Expect = 9e-05
 Identities = 25/125 (20%), Positives = 48/125 (38%), Gaps = 16/125 (12%)

Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH 368
           L F G PG GKT   +A  + +Y K          +  D   I  ++  + +   TK + 
Sbjct: 41  LTFVGSPGVGKTHLAVATLKAIYEKKGIR--GYFFDTKD--LIFRLKHLMDEGKDTKFLK 96

Query: 369 K-SSYKLIILDE--ADAMTNDAQNALRRIIEK---------FTTNVRFCIICNYLSKIPP 416
              +  +++LD+  ++ +++  +  +  II            TTN           +I  
Sbjct: 97  TVLNSPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNYSLQREEESSVRISA 156

Query: 417 AIQSR 421
            + SR
Sbjct: 157 DLASR 161

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	533
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.93
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.92
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.91
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.91
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.9
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.89
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.89
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.88
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.87
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.85
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.79
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.77
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.77
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.76
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.75
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.75
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	99.75
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.74
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	99.74
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	99.73
3pvs_A	447	Replication-associated recombination protein A; ma	99.73
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.69
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.69
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.69
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.68
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.67
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.65
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.64
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.63
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.63
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.63
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.63
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.62
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.61
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.61
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.61
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.6
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.59
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.58
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.58
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.58
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.57
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.57
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.55
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.54
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.54
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.53
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.53
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.52
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.52
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.52
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.51
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.5
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.49
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.49
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.48
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.48
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.48
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.47
3bos_A	242	Putative DNA replication factor; P-loop containing	99.46
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.46
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.46
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.45
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.44
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.43
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.41
3co5_A	143	Putative two-component system transcriptional RES	99.4
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.4
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.39
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	99.39
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.39
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.37
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.37
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.37
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.34
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.33
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.32
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	99.31
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.3
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.3
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.29
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.28
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.28
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	99.26
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.24
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.24
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.23
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.22
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.22
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.19
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.19
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.18
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	99.16
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.15
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.15
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.14
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.12
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	99.11
1tue_A	212	Replication protein E1; helicase, replication, E1E	99.04
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	99.02
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	99.02
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.98
3pvs_A	447	Replication-associated recombination protein A; ma	98.94
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.93
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.93
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.93
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	98.8
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.69
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.69
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.69
3f8t_A	506	Predicted ATPase involved in replication control,	98.64
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.63
2qgz_A	308	Helicase loader, putative primosome component; str	98.6
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.54
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	98.51
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.48
2fna_A	357	Conserved hypothetical protein; structural genomic	98.46
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.42
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	98.34
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.33
3bos_A	242	Putative DNA replication factor; P-loop containing	98.3
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	98.28
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.24
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	98.22
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.2
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.2
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	98.12
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	98.11
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.11
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.09
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.07
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.02
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.01
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	97.98
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	97.91
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.9
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	97.84
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.7
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	97.67
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.66
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	97.51
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.47
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	97.46
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.45
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	97.42
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	97.41
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	97.41
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	97.37
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	97.32
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	97.3
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.29
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.28
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	97.25
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	97.23
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	97.2
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.18
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.18
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.18
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.16
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.16
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.16
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	97.13
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.12
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	97.12
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.12
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	97.11
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	97.08
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.08
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.08
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.08
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	97.08
1u94_A	356	RECA protein, recombinase A; homologous recombinat	97.04
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.04
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	97.03
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	97.02
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	97.02
2r44_A	331	Uncharacterized protein; putative ATPase, structur	96.99
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	96.98
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	96.96
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	96.95
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	96.95
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	96.95
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	96.95
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.95
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.93
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.92
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	96.91
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.9
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	96.89
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.86
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	96.84
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.84
1via_A	175	Shikimate kinase; structural genomics, transferase	96.82
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.81
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	96.81
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.81
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	96.8
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.72
2eyu_A	261	Twitching motility protein PILT; pilus retraction	96.72
4a74_A	231	DNA repair and recombination protein RADA; hydrola	96.71
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	96.69
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	96.68
1nrj_B	218	SR-beta, signal recognition particle receptor beta	96.67
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	96.65
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	96.64
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	96.63
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.62
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.62
3b6e_A	216	Interferon-induced helicase C domain-containing P;	96.61
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	96.61
3h1t_A	590	Type I site-specific restriction-modification syst	96.61
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	96.59
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.59
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.59
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	96.58
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.58
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	96.56
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	96.55
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.55
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.54
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	96.53
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	96.53
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	96.53
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	96.53
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	96.52
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	96.51
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	96.51
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	96.51
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	96.5
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.48
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.47
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.46
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	96.46
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	96.45
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	96.42
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.42
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	96.4
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	96.37
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	96.36
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	96.35
2vli_A	183	Antibiotic resistance protein; transferase, tunica	96.33
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	96.33
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.33
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	96.32
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	96.31
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	96.3
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	96.3
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.29
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	96.29
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	96.28
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.28
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	96.27
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	96.27
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	96.27
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	96.26
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	96.24
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	96.21
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.21
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	96.2
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.19
3bor_A	237	Human initiation factor 4A-II; translation initiat	96.19
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	96.19
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.18
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	96.16
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	96.16
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	96.13
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.12
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	96.11
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	96.09
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	96.08
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.08
2ewv_A	372	Twitching motility protein PILT; pilus retraction	96.08
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	96.07
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	96.06
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	96.06
2r6a_A	454	DNAB helicase, replicative helicase; replication,	96.05
3io5_A	333	Recombination and repair protein; storage dimer, i	96.04
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.04
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.02
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	96.02
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.98
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	95.97
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	95.97
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	95.97
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	95.97
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	95.97
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	95.97
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	95.96
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	95.96
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	95.96
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.94
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	95.94
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	95.93
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	95.9
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	95.9
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	95.86
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	95.85
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	95.85
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	95.83
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	95.83
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	95.83
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	95.82
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	95.8
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	95.78
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	95.77
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	95.76
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	95.76
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.73
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	95.72
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.72
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	95.72
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	95.71
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.69
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	95.68
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	95.67
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	95.63
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	95.59
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.58
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	95.57
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.57
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	95.54
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	95.53
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.53
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	95.52
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	95.51
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	95.47
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.45
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	95.45
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	95.45
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	95.41
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	95.41
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	95.4
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	95.35
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	95.33
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	95.32
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	95.31
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	95.31
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.29
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	95.28
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	95.28
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.26
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	95.25
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	95.23
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	95.22
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	95.22
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	95.21
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	95.19
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	95.18
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	95.18
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	95.17
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.17
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	95.16
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	95.13
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	95.08
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	95.08
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	95.08
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	95.08
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	95.08
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	95.07
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	95.07
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	95.06
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	95.06
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	95.05
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	95.05
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.02
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	95.0
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	94.99
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	94.99
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	94.98
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	94.98
2z43_A	324	DNA repair and recombination protein RADA; archaea	94.96
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	94.96
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	94.96
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	94.95
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	94.94
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	94.94
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	94.9
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	94.9
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.88
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	94.86
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	94.85
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	94.84
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	94.84
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	94.81
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	94.8
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	94.79
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	94.79
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	94.79
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	94.79
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	94.79
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	94.78
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	94.78
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	94.77
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	94.76
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	94.76
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	94.74
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	94.73
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	94.73
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	94.7
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	94.69
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	94.69
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	94.68
2hf9_A	226	Probable hydrogenase nickel incorporation protein	94.68
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	94.64
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	94.59
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	94.56
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	94.55
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	94.52
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	94.51
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	94.51
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	94.48
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	94.47
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	94.47
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	94.47
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	94.47
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	94.46
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	94.46
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	94.45
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	94.45
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	94.36
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	94.35
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	94.34
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	94.33
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	94.32
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	94.3
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	94.27
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	94.25
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	94.23
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	94.21
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	94.21
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	94.21
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	94.21
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	94.21
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	94.21
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	94.2
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	94.19
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	94.17
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	94.15
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	94.15
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	94.14
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	94.12
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	94.12
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	94.1
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	94.1
1yks_A	440	Genome polyprotein [contains: flavivirin protease	94.09
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	94.09
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	94.08
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	94.08
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	94.08
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	94.06
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	94.06
2fh5_B	214	SR-beta, signal recognition particle receptor beta	94.05
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	94.05
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	94.03
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	94.0
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	93.98
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	93.97
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	93.96
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	93.93
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	93.92
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	93.9
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	93.84
2xxa_A	433	Signal recognition particle protein; protein trans	93.84
3llu_A	196	RAS-related GTP-binding protein C; structural geno	93.82
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	93.81
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	93.8
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	93.8
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	93.8
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	93.78
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	93.78
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	93.77
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	93.77
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	93.75
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	93.73
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	93.73
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	93.71
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	93.69
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	93.66
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	93.64
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	93.63
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	93.63
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	93.6
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	93.59
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	93.58
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	93.56
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	93.55
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	93.54
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	93.53
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	93.51
3gee_A	476	MNME, tRNA modification GTPase MNME; G protein, cy	93.44
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	93.34
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	93.34
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	93.34
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	93.33
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	93.28
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	93.26
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	93.26
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	93.25
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	93.25
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	93.19

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.93  E-value=8.3e-25  Score=218.51  Aligned_cols=238  Identities=47%  Similarity=0.783  Sum_probs=195.7

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM  367 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (533)
                      .|++.+...+..++..+..+|++|+|||||||||+++++++.+.+.. ....+..+++++..+.+.+++.++.+.+....
T Consensus        28 ~g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~~~~-~~~~~~~~~~~~~~~~~~ir~~i~~~~~~~~~  106 (340)
T 1sxj_C           28 YGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKN-YSNMVLELNASDDRGIDVVRNQIKDFASTRQI  106 (340)
T ss_dssp             CSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTS-HHHHEEEECTTSCCSHHHHHTHHHHHHHBCCS
T ss_pred             cCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-ccceEEEEcCcccccHHHHHHHHHHHHhhccc
Confidence            45677777788888888888999999999999999999999987653 23467888888777778888877777654433


Q ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC-----
Q psy4285         368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD-----  442 (533)
Q Consensus       368 ~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~-----  442 (533)
                      ..++++++||||+|.++.+.+++|++++|+++.++.+|++||.+..++++++|||..+.|.+++.+++.+++.++     
T Consensus       107 ~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~~~~~~~~l~~~~~~~~l~~~~~~~~  186 (340)
T 1sxj_C          107 FSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEK  186 (340)
T ss_dssp             SSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTT
T ss_pred             CCCCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhceeEeccCCCHHHHHHHHHHHHHHcC
Confidence            345689999999999999999999999999999999999999999999999999999999999999999888743     


Q ss_pred             ------------------------------------------------------HHHHHHHHHH---------HHHHHHH
Q psy4285         443 ------------------------------------------------------DISFFNIIIW---------YIKIQEI  459 (533)
Q Consensus       443 ------------------------------------------------------~~~~~~ll~~---------~~~l~~l  459 (533)
                                                                            +..+.++++.         ...+..+
T Consensus       187 ~~i~~~~~~~i~~~s~G~~r~~~~~l~~~~~~~~~~~~~~it~~~v~~~~~~~~~~~i~~l~~~i~~~~~~~al~~l~~l  266 (340)
T 1sxj_C          187 LKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRPSDLKAVLKSILEDDWGTAHYTLNKV  266 (340)
T ss_dssp             CCBCHHHHHHHHHHHTTCHHHHHHHTTTTTTTTCSSSCCCBCHHHHHHHTTCCCHHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCcccccccHHHHHHHhCCCCHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence                                                                  1122222222         3334444


Q ss_pred             HHhcCCCHHHHHHHHHHHHHhcCCC-hhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhHh
Q psy4285         460 KIEKGLALTDILTEISLLVHRLEIP-ESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKL  526 (533)
Q Consensus       460 ~~~~~~~~~di~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~~~~  526 (533)
                      ....|+++.+++..+...++...++ ...+..++..+.++++++..|+++.++++.|+.+++.+....
T Consensus       267 ~~~~g~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~l~~~l~~~~~~~  334 (340)
T 1sxj_C          267 RSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSISKGGNDQIQGSAVIGAIKASFENE  334 (340)
T ss_dssp             HHTTTCCHHHHHHHHHHHHTTSCCSSHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHCCC-
T ss_pred             HHHcCCCHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhhc
Confidence            3327999999999999998887777 888899999999999999999999999999999998876543

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=99.92  E-value=4.9e-24  Score=207.77  Aligned_cols=231  Identities=15%  Similarity=0.130  Sum_probs=178.7

Q ss_pred             hchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC-CCchhHHHHHHHHHHhcccC
Q psy4285         289 ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD-DRGIGIVRDQIFQFASTKTM  367 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  367 (533)
                      ||++++..+...++.++.|++||+||||+|||++|+++++.+.........+..+++++ ..+.+.+++.+..+... +.
T Consensus         1 g~~~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~id~ir~li~~~~~~-p~   79 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYS-PE   79 (305)
T ss_dssp             ---CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSC-CS
T ss_pred             ChHHHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCCHHHHHHHHHHHhhc-cc
Confidence            56778888888888888667999999999999999999987421111244678888764 57788899877665433 32


Q ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC-----
Q psy4285         368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD-----  442 (533)
Q Consensus       368 ~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~-----  442 (533)
                       .++++|+||||+|+|+.+++++|++.||+|++++.||++|+.+.++.|+++||  .+.|.+++++++.+++.+.     
T Consensus        80 -~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR--~~~f~~l~~~~i~~~L~~~~~i~~  156 (305)
T 2gno_A           80 -LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR--VFRVVVNVPKEFRDLVKEKIGDLW  156 (305)
T ss_dssp             -SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT--SEEEECCCCHHHHHHHHHHHTTHH
T ss_pred             -cCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce--eEeCCCCCHHHHHHHHHHHhCCCH
Confidence             35789999999999999999999999999999999999999999999999999  9999999999999988664     


Q ss_pred             ---------HH-----------------------------------------HHHHHHHH---------HHHHHHHHHh-
Q psy4285         443 ---------DI-----------------------------------------SFFNIIIW---------YIKIQEIKIE-  462 (533)
Q Consensus       443 ---------~~-----------------------------------------~~~~ll~~---------~~~l~~l~~~-  462 (533)
                               +.                                         ++.++++.         +..+.++... 
T Consensus       157 ~~~~~~~g~~~~al~~l~~~~~~~~~l~~~~~~~~~~~~v~~~~~~~~~~~~~v~~l~~ai~~~~~~~a~~~~~~l~~~~  236 (305)
T 2gno_A          157 EELPLLERDFKTALEAYKLGAEKLSGLMESLKVLETEKLLKKVLSKGLEGYLACRELLERFSKVESKEFFALFDQVTNTI  236 (305)
T ss_dssp             HHCGGGGTCHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHTTTTTCSHHHHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHS
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHccCCcchHHHHHHHHHHHCCCHHHHHHHHHHHHHhh
Confidence                     00                                         22222222         3445555433 


Q ss_pred             cCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhC---CCChHHHHHHHHHHHHHHHhH
Q psy4285         463 KGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAA---GTSEKIQLSALIAAFNSARDK  525 (533)
Q Consensus       463 ~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~---g~~~~~~l~~~~~~~~~~~~~  525 (533)
                      .|+++.+++..+++.+...+  ...+.+.++.++.+++++..   |.++.++++++++++....+-
T Consensus       237 ~g~~~~~~i~~~~r~l~~~~--~~~~~~~l~~~~~~~~~~~~k~~g~~~~lql~~l~~~~~~~~~~  300 (305)
T 2gno_A          237 TGKDAFLLIQRLTRIILHEN--TWESVEDQKSVSFLDSILRVKIANLNNKLTLMNILAIHRERKRG  300 (305)
T ss_dssp             CTHHHHHHHHHHHHHHHHTS--CCCSHHHHHHHHHHHHHHTCCGGGCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCHHHHHHHHHHHHHhhc--hhhhHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhccc
Confidence            67777788888887776443  33446677799999999999   999999999999999866543

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=99.91  E-value=2.7e-23  Score=206.47  Aligned_cols=235  Identities=43%  Similarity=0.688  Sum_probs=189.2

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM  367 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (533)
                      .|++.....+..++..+..+|++|+||||||||++|+++++.+.+.. ....++.+++++..+.+.+++.+..+....+.
T Consensus        28 ~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  106 (327)
T 1iqp_A           28 VGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGEN-WRHNFLELNASDERGINVIREKVKEFARTKPI  106 (327)
T ss_dssp             CSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGG-HHHHEEEEETTCHHHHHTTHHHHHHHHHSCCG
T ss_pred             hCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCc-ccCceEEeeccccCchHHHHHHHHHHHhhCCc
Confidence            45666667777777777778899999999999999999999986542 23457788887765556666666666544333


Q ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC-----
Q psy4285         368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD-----  442 (533)
Q Consensus       368 ~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~-----  442 (533)
                      ..++++++||||+|.++.+.+++|++.+++++.++++|++||.+..+++++.+||..+.|.+++.+++..++.++     
T Consensus       107 ~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~~~~~~l~~~~~~~~l~~~~~~~~  186 (327)
T 1iqp_A          107 GGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEG  186 (327)
T ss_dssp             GGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTT
T ss_pred             CCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhCcEEEecCCCHHHHHHHHHHHHHhcC
Confidence            235689999999999999999999999999989999999999999999999999999999999999999888753     


Q ss_pred             -------------------------------------------------HHHHHHHHHH---------HHHHHHHHHhcC
Q psy4285         443 -------------------------------------------------DISFFNIIIW---------YIKIQEIKIEKG  464 (533)
Q Consensus       443 -------------------------------------------------~~~~~~ll~~---------~~~l~~l~~~~~  464 (533)
                                                                       +.++.++++.         ...+..+....|
T Consensus       187 ~~~~~~~~~~l~~~~~g~~r~~~~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~ll~~~g  266 (327)
T 1iqp_A          187 LELTEEGLQAILYIAEGDMRRAINILQAAAALDKKITDENVFMVASRARPEDIREMMLLALKGNFLKAREKLREILLKQG  266 (327)
T ss_dssp             CEECHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSEECHHHHHHHTTCCCHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcC
Confidence                                                             2222222222         233333322569


Q ss_pred             CCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHH
Q psy4285         465 LALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSAR  523 (533)
Q Consensus       465 ~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~  523 (533)
                      .++.+++..+...++...|+......++..+.++++++..|+++.++++.|+.+++.+.
T Consensus       267 ~~~~~i~~~l~~~~~~~~~~~~~l~~~~~~l~~~~~~lk~~~~~~~~le~l~~~l~~~~  325 (327)
T 1iqp_A          267 LSGEDVLVQMHKEVFNLPIEEPKKVLLADKIGEYNFRLVEGANEIIQLEALLAQFTLIG  325 (327)
T ss_dssp             CCHHHHHHHHHHHGGGSSSCHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhh
Confidence            99999999999888877789999999999999999999999999999999999998765

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=99.91  E-value=3.1e-23  Score=205.20  Aligned_cols=236  Identities=36%  Similarity=0.635  Sum_probs=190.4

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM  367 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (533)
                      .|++.....+..++..+..++++|+||||||||++|+++++.+.+.. ....++.+++++..+.+.+++.+..+....+.
T Consensus        20 ~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (319)
T 2chq_A           20 VGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGEN-WRDNFIEMNASDERGIDVVRHKIKEFARTAPI   98 (319)
T ss_dssp             CSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHHHTTC-HHHHCEEEETTSTTCTTTSSHHHHHHHHSCCS
T ss_pred             hCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHhcCCc-ccCCeEEEeCccccChHHHHHHHHHHHhcCCC
Confidence            46677777888888888888899999999999999999999986543 23457788887766666666666666533333


Q ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC-----
Q psy4285         368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD-----  442 (533)
Q Consensus       368 ~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~-----  442 (533)
                      ..+.++++||||+|.++.+.++.|++.+++++.++++|++||.+..+++++.+||..+.|.+++.+++.+++.++     
T Consensus        99 ~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~  178 (319)
T 2chq_A           99 GGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEG  178 (319)
T ss_dssp             SSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCEEEECCCCCHHHHHHHHHHHHHTTC
T ss_pred             CCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCeEEEecCCCHHHHHHHHHHHHHHcC
Confidence            235689999999999999999999999999889999999999999999999999999999999999999988753     


Q ss_pred             -------------------------------------------------HHHHHHHHHH---------HHHHHHHHHhcC
Q psy4285         443 -------------------------------------------------DISFFNIIIW---------YIKIQEIKIEKG  464 (533)
Q Consensus       443 -------------------------------------------------~~~~~~ll~~---------~~~l~~l~~~~~  464 (533)
                                                                       +.++.++++.         ...+..+....|
T Consensus       179 ~~i~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~i~~~~v~~~~~~~~~~~~~~l~~~~~~~~~~~a~~~l~~l~~~~g  258 (319)
T 2chq_A          179 VKITEDGLEALIYISGGDFRKAINALQGAAAIGEVVDADTIYQITATARPEEMTELIQTALKGNFMEARELLDRLMVEYG  258 (319)
T ss_dssp             CCBCHHHHHHHHHTTTTCHHHHHHHHHHHHHSSSCBCHHHHHHHTTCCCHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSC
T ss_pred             CCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcC
Confidence                                                             1112222221         233444433369


Q ss_pred             CCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHh
Q psy4285         465 LALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD  524 (533)
Q Consensus       465 ~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~~  524 (533)
                      .++.+++..+.+.++...|+.....+++..+.+++.++..|+++.++++.++.+++.++.
T Consensus       259 ~~~~~i~~~l~~~~~~l~~~~~~l~~~~~~l~~~~~~lk~~~~~~~~le~l~~~l~~~~~  318 (319)
T 2chq_A          259 MSGEDIVAQLFREIISMPIKDSLKVQLIDKLGEVDFRLTEGANERIQLDAYLAYLSTLAK  318 (319)
T ss_dssp             CCHHHHHHHHHHHHHTSCSCTTHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhhc
Confidence            999999999998888767888889999999999999999999999999999999987653

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.90  E-value=6.7e-22  Score=198.71  Aligned_cols=236  Identities=25%  Similarity=0.426  Sum_probs=178.4

Q ss_pred             hhchhhhhhhcccc-cccCCCceeEeCCCCCChHHHHHHHHHHHcccccc-----------------------CcceEEe
Q psy4285         288 NESMDLCYKINRFI-DENELPHLLFYGPPGTGKTTTILACARKLYTKAQF-----------------------NAMVLEL  343 (533)
Q Consensus       288 ~~~~~~~~~l~~~~-~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~-----------------------~~~~~~~  343 (533)
                      .|++.+...+..++ ..+..+|++|+||||+||||+++++++.+.++...                       ...++.+
T Consensus        17 vg~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (354)
T 1sxj_E           17 SHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEI   96 (354)
T ss_dssp             CSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------CCEECSSEEEE
T ss_pred             cCCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceeecccccccceeeeecccceEEe
Confidence            46777777888888 77777889999999999999999999987654310                       0123445


Q ss_pred             cCCCCCchh--HHHHHHHHHHhcccCC--------CCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCC
Q psy4285         344 NASDDRGIG--IVRDQIFQFASTKTMH--------KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSK  413 (533)
Q Consensus       344 ~~~~~~~~~--~~~~~~~~~~~~~~~~--------~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~  413 (533)
                      ++++.....  .+++.+..+.......        ..+++++||||++.++...+++|++.+++++.++.+|++|+.+..
T Consensus        97 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~vlilDE~~~L~~~~~~~L~~~le~~~~~~~~Il~t~~~~~  176 (354)
T 1sxj_E           97 TPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSP  176 (354)
T ss_dssp             CCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTEEEEEEESCSCS
T ss_pred             cHhhcCCcchHHHHHHHHHHHHhccccccccccccCCCCeEEEEeCccccCHHHHHHHHHHHHhhcCCCEEEEEeCCHHH
Confidence            544322111  3566666554432211        236889999999999999999999999999889999999999999


Q ss_pred             CChhhhccceeeeecCCCHHHHHHHhhcC--------H------------------------------------------
Q psy4285         414 IPPAIQSRCTRFRFGPLDSSLIMSRLDYD--------D------------------------------------------  443 (533)
Q Consensus       414 l~~~l~sR~~~i~~~~~~~~~~~~~l~~~--------~------------------------------------------  443 (533)
                      ++++++|||..+.|.+++.+++.+++.++        +                                          
T Consensus       177 l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~i~~~~~G~~r~a~~~l~~~~~~~~~~i~~~~~~~~  256 (354)
T 1sxj_E          177 IIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMALNNELALKSSSPIIK  256 (354)
T ss_dssp             SCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHHHHHTHHHHTTTTEECSSCCCCC
T ss_pred             HHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCCCcCcCcCCCC
Confidence            99999999999999999999999998753        0                                          


Q ss_pred             ----HHHHHHHHH-------------HHHHHHHHHhcCCCHHHHHHHHHHHHHhc-CCChhHHHHHHHHHHHHHHHHhCC
Q psy4285         444 ----ISFFNIIIW-------------YIKIQEIKIEKGLALTDILTEISLLVHRL-EIPESMLVDLVLKMSDIEYRLAAG  505 (533)
Q Consensus       444 ----~~~~~ll~~-------------~~~l~~l~~~~~~~~~di~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~g  505 (533)
                          ..+.++++.             +..+..+ ...|+++.+++..+...+... .+++..+.+++..++++++++..|
T Consensus       257 ~~~~~~~~~l~~~i~~~~~~~~~~~~~~~l~~l-~~~g~~~~~i~~~l~~~~~~~~~~~~~~l~~~~~~l~~~d~~l~~g  335 (354)
T 1sxj_E          257 PDWIIVIHKLTRKIVKERSVNSLIECRAVLYDL-LAHCIPANIILKELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLG  335 (354)
T ss_dssp             CHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHH-HTTTCCHHHHHHHHHHTTTTCTTSCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             ccHHHHHHHHHHHHHHhcchhHHHHHHHHHHHH-HHcCCCHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence                112222221             1122222 336899999998888776654 478899999999999999999999


Q ss_pred             CChHHHHHHHHHHHHHHHh
Q psy4285         506 TSEKIQLSALIAAFNSARD  524 (533)
Q Consensus       506 ~~~~~~l~~~~~~~~~~~~  524 (533)
                      .++.++++.|+++++.+++
T Consensus       336 ~~~~~~le~~~~~~~~~~~  354 (354)
T 1sxj_E          336 NKAIFHLEGFIAKVMCCLD  354 (354)
T ss_dssp             SCHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHHHhC
Confidence            9999999999999998753

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.89  E-value=7.9e-22  Score=198.07  Aligned_cols=233  Identities=36%  Similarity=0.617  Sum_probs=180.8

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhccc-
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT-  366 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  366 (533)
                      .|+++..+.+..++..+..+|++|+||||||||++++++++.+.+.......+..+++++..+...+++.+..+..... 
T Consensus        40 ~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (353)
T 1sxj_D           40 TAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVS  119 (353)
T ss_dssp             CSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHHSCCC
T ss_pred             hCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHHHHHHHHHHhhhccc
Confidence            5677778888888888877889999999999999999999998654323456788888876677767666655543211 


Q ss_pred             ---------CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHH
Q psy4285         367 ---------MHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMS  437 (533)
Q Consensus       367 ---------~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~  437 (533)
                               .....+++++|||+|.++...+++|++.+++++.++++|++||.+..+++++++||..+.|.+++.+++..
T Consensus       120 ~~~~~~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~~i~~~~~~~~~~~~  199 (353)
T 1sxj_D          120 KPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAID  199 (353)
T ss_dssp             CCCTTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHH
T ss_pred             ccchhhcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCceEEeCCCCHHHHHH
Confidence                     01245689999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             HhhcC---------HHHHHHHHHH--------------------------------------------------------
Q psy4285         438 RLDYD---------DISFFNIIIW--------------------------------------------------------  452 (533)
Q Consensus       438 ~l~~~---------~~~~~~ll~~--------------------------------------------------------  452 (533)
                      ++.++         ++.+..+.+.                                                        
T Consensus       200 ~l~~~~~~~~~~i~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~~~~~~It~~~v~~~~~~~~~~~~~~l~~~~~~~~  279 (353)
T 1sxj_D          200 RLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGD  279 (353)
T ss_dssp             HHHHHHHTTTCCCCHHHHHHHHHHTSSCHHHHHHHHHHTHHHHHHHCSCCCCCHHHHHHHHTCCCSHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCccCccccHHHHHHHhCCCCHHHHHHHHHHHhcCC
Confidence            98763         1111111111                                                        


Q ss_pred             ----HHHHHHHHHhcCCCHHHHHHHHHHHHHhc-CCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHH
Q psy4285         453 ----YIKIQEIKIEKGLALTDILTEISLLVHRL-EIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNS  521 (533)
Q Consensus       453 ----~~~l~~l~~~~~~~~~di~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~  521 (533)
                          ...+..+ ...|.++.+++..+.+.+... .+++..+..++..++++++++..|+++.++++.|++++++
T Consensus       280 ~~~a~~~l~~l-~~~g~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~l~~~~~~~~~  352 (353)
T 1sxj_D          280 FDEIKKYVNTF-MKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQ  352 (353)
T ss_dssp             HHHHHHHHHHH-HHTSCCCTTHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH-HHhCCCHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHh
Confidence                1111112 234666666777777766554 5778888899999999999999999999999999999875

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

Probab=99.89  E-value=1.7e-21  Score=193.28  Aligned_cols=226  Identities=19%  Similarity=0.249  Sum_probs=170.7

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhccc
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT  366 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  366 (533)
                      .|++.....+..++..+..++ ++++||||||||++++++++.+      +..++++++++. +.+.+++.+..+....+
T Consensus        29 vg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l------~~~~~~i~~~~~-~~~~i~~~~~~~~~~~~  101 (324)
T 3u61_B           29 ILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDV------NADMMFVNGSDC-KIDFVRGPLTNFASAAS  101 (324)
T ss_dssp             CCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHT------TEEEEEEETTTC-CHHHHHTHHHHHHHBCC
T ss_pred             hCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHh------CCCEEEEccccc-CHHHHHHHHHHHHhhcc
Confidence            466677777888888888777 5777889999999999999988      667888998774 36677777776665543


Q ss_pred             CCCCCcEEEEEeCCCCCC-HHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC---
Q psy4285         367 MHKSSYKLIILDEADAMT-NDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD---  442 (533)
Q Consensus       367 ~~~~~~~vliiDE~d~l~-~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~---  442 (533)
                      . .+.++++||||+|.++ .+.++.|++.+++++.++++|++||.+..++++++|||..+.|.+|+.++..+++..+   
T Consensus       102 ~-~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~~~~~  180 (324)
T 3u61_B          102 F-DGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRR  180 (324)
T ss_dssp             C-SSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHHSEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             c-CCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhhCcEEEeCCCCHHHHHHHHHHHHHH
Confidence            2 3478999999999999 9999999999999888999999999999999999999999999999988743332221   


Q ss_pred             -------------H-HHHHHHHHH-----------------------------------------------H-HHHHHHH
Q psy4285         443 -------------D-ISFFNIIIW-----------------------------------------------Y-IKIQEIK  460 (533)
Q Consensus       443 -------------~-~~~~~ll~~-----------------------------------------------~-~~l~~l~  460 (533)
                                   + +.+..++..                                               . ..+..+.
T Consensus       181 l~~~~~~~~~~~~~~~~~~~l~~~~~gd~R~a~~~L~~~~~~~~i~~~~v~~~~~~~~~i~~~~~~~~~~~~~~a~~~~~  260 (324)
T 3u61_B          181 LTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGELDSYSSKGVLDAGILSLVTNDRGAIDDVLESLKNKDVKQLRALAP  260 (324)
T ss_dssp             HHHHHHHHTCCBSCHHHHHHHHHHTCSCTTHHHHHHHHHGGGTCBCC------------CHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCcHHHHHHHHHhCCCCHHHHHHHHHHHhccCCCCHHHHHHHhCCHHHHHHHHHHHHcCCHHHHHHHHH
Confidence                         2 222222222                                               0 0000000


Q ss_pred             HhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHH
Q psy4285         461 IEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSAR  523 (533)
Q Consensus       461 ~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~  523 (533)
                      ..-. ++.+++..+...+.. .+++....+++..++..++++..|.++.++++.|++++|..+
T Consensus       261 ~l~~-~~~~i~~~l~~~~~~-~~~~~~l~~i~~~l~~~d~~l~~g~~~~~~le~~~~~~~~~~  321 (324)
T 3u61_B          261 KYAA-DYSWFVGKLAEEIYS-RVTPQSIIRMYEIVGENNQYHGIAANTELHLAYLFIQLACEM  321 (324)
T ss_dssp             HHSS-CHHHHHHHHHHHHHH-HSCHHHHHHHHHHHHHHHHHTTTCSCHHHHHHHHHHHHHHHC
T ss_pred             Hhcc-CHHHHHHHHHHHHHH-hCCHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhc
Confidence            1111 555666666555544 456778889999999999999999999999999999999753

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.88  E-value=1.3e-21  Score=193.88  Aligned_cols=236  Identities=32%  Similarity=0.496  Sum_probs=186.0

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM  367 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (533)
                      .|++.....+..++..+..+|++|+||||+|||++|+++++.+.+.. ....++.+++++..+.+.+++.+..+......
T Consensus        24 ~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~-~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~  102 (323)
T 1sxj_B           24 VGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRS-YADGVLELNASDDRGIDVVRNQIKHFAQKKLH  102 (323)
T ss_dssp             CSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGG-HHHHEEEECTTSCCSHHHHHTHHHHHHHBCCC
T ss_pred             HCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCc-ccCCEEEecCccccChHHHHHHHHHHHhcccc
Confidence            46667777777888878878899999999999999999999986643 23457788888766777787777766533222


Q ss_pred             C-CCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC----
Q psy4285         368 H-KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD----  442 (533)
Q Consensus       368 ~-~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~----  442 (533)
                      . .++++++||||+|.++...++.|++.+++++.++.+|++||.+..+++++++||..+.|.+++.+++.+++..+    
T Consensus       103 ~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~  182 (323)
T 1sxj_B          103 LPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLE  182 (323)
T ss_dssp             CCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhceEEeecCCCHHHHHHHHHHHHHHc
Confidence            2 23589999999999999999999999999999999999999999999999999999999999999999998753    


Q ss_pred             -------------------HHHHHHHHHH----------------------------------HHHHHHHH---HhcCCC
Q psy4285         443 -------------------DISFFNIIIW----------------------------------YIKIQEIK---IEKGLA  466 (533)
Q Consensus       443 -------------------~~~~~~ll~~----------------------------------~~~l~~l~---~~~~~~  466 (533)
                                         +..+..+++.                                  ...+..+.   ...|.+
T Consensus       183 ~~~~~~~~~~~l~~~~~G~~r~a~~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~~~~~~~~~~~l~~l~~dl~~~g~~  262 (323)
T 1sxj_B          183 DVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKMLLASNLEDSIQILRTDLWKKGYS  262 (323)
T ss_dssp             TCCBCHHHHHHHHHHHTTCHHHHHHHHHHHHHHHSSBCHHHHHHHHTSCCHHHHHHHHSCSSHHHHHHHHHHTTTTTTCC
T ss_pred             CCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHCCCCHHHHHHHHhcCCHHHHHHHHHHHHHHcCCC
Confidence                               1111111110                                  01111111   125888


Q ss_pred             HHHHHHHHHHHHHhcC-CChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHh
Q psy4285         467 LTDILTEISLLVHRLE-IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD  524 (533)
Q Consensus       467 ~~di~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~~  524 (533)
                      +.++...+...++... ++......++..+.++++++..|+++.++++.++.+++.+..
T Consensus       263 ~~~i~~~l~~~~~~l~~~~~~~l~~~l~~l~~~~~~l~~~~~~~l~le~l~~~~~~~~~  321 (323)
T 1sxj_B          263 SIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQLASMLAKIHKLNN  321 (323)
T ss_dssp             HHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHHHhhcc
Confidence            8898888888777654 788888899999999999999999999999999999987654

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=99.87  E-value=6.3e-21  Score=189.51  Aligned_cols=233  Identities=16%  Similarity=0.189  Sum_probs=168.6

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCC--
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNAS--  346 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~--  346 (533)
                      .|+++..+.+...+..++.+| ++|+||||+|||++|+++++.+.|....                  ...+..+++.  
T Consensus         5 pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~   84 (334)
T 1a5t_A            5 PWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKG   84 (334)
T ss_dssp             GGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTT
T ss_pred             CchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEecccc
Confidence            466777788888888888888 8999999999999999999999875421                  1345666654  


Q ss_pred             -CCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceee
Q psy4285         347 -DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRF  425 (533)
Q Consensus       347 -~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i  425 (533)
                       ...+.+.+++.+..+...+  ..++++|+||||+|+|+.+++++|++.+|+++.++.+|++||.+..++++++|||..+
T Consensus        85 ~~~~~i~~ir~l~~~~~~~~--~~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~~~l~~ti~SRc~~~  162 (334)
T 1a5t_A           85 KNTLGVDAVREVTEKLNEHA--RLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLH  162 (334)
T ss_dssp             CSSBCHHHHHHHHHHTTSCC--TTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEE
T ss_pred             CCCCCHHHHHHHHHHHhhcc--ccCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHhhcceee
Confidence             3456777888776654332  2357899999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCHHHHHHHhhcC----HHHHHHHHHH-----------------------HHHHHHHHH----------hcCCCHH
Q psy4285         426 RFGPLDSSLIMSRLDYD----DISFFNIIIW-----------------------YIKIQEIKI----------EKGLALT  468 (533)
Q Consensus       426 ~~~~~~~~~~~~~l~~~----~~~~~~ll~~-----------------------~~~l~~l~~----------~~~~~~~  468 (533)
                      .|.+++.+++.+++.+.    ++.+..++..                       ...+..+..          ..+.+..
T Consensus       163 ~~~~~~~~~~~~~L~~~~~~~~~~~~~l~~~s~G~~r~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  242 (334)
T 1a5t_A          163 YLAPPPEQYAVTWLSREVTMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALNHEQAP  242 (334)
T ss_dssp             ECCCCCHHHHHHHHHHHCCCCHHHHHHHHHHTTTCHHHHHHTTSSHHHHHHHHHHHHHHHHHHHCCCGGGHHHHCSTTHH
T ss_pred             eCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHHhccchHHHHHHHHHHHHHHHhChHHHHHHHHHhcccHH
Confidence            99999999999988775    2222222211                       011111100          0112333


Q ss_pred             HHHHHHHHHHHhc------------------------CCChhHHHHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHHH
Q psy4285         469 DILTEISLLVHRL------------------------EIPESMLVDLVLKMSDIEYRLA--AGTSEKIQLSALIAAFNSA  522 (533)
Q Consensus       469 di~~~~~~~~~~~------------------------~~~~~~~~~~~~~~~~~~~~l~--~g~~~~~~l~~~~~~~~~~  522 (533)
                      .++..+...++..                        .++......+++.+.+.+.++.  .++++.+.++.++.++..+
T Consensus       243 ~~l~~l~~~~rdll~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~l~~~~~~l~~~~~~n~~l~le~ll~~l~~~  322 (334)
T 1a5t_A          243 ARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQLMSVTGINRELLITDLLLRIEHY  322 (334)
T ss_dssp             HHHHHHHHHHHHHTCC------CCCTTCHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccCCccccCHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHh
Confidence            3333333221110                        1233444567777888888998  8999999999999999864

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

Probab=99.85  E-value=3.1e-21  Score=208.22  Aligned_cols=150  Identities=21%  Similarity=0.264  Sum_probs=95.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC------CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD------DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      ++|||||||||||++|+++|.++      +.+++.+++++      +.+...+++.+.....      ..++||||||+|
T Consensus       513 gvLl~GPPGtGKT~lAkaiA~e~------~~~f~~v~~~~l~s~~vGese~~vr~lF~~Ar~------~~P~IifiDEiD  580 (806)
T 3cf2_A          513 GVLFYGPPGCGKTLLAKAIANEC------QANFISIKGPELLTMWFGESEANVREIFDKARQ------AAPCVLFFDELD  580 (806)
T ss_dssp             CCEEESSTTSSHHHHHHHHHHTT------TCEEEECCHHHHHTTTCSSCHHHHHHHHHHHHT------TCSEEEECSCGG
T ss_pred             eEEEecCCCCCchHHHHHHHHHh------CCceEEeccchhhccccchHHHHHHHHHHHHHH------cCCceeechhhh
Confidence            49999999999999999999998      67777776543      3445566666554332      356899999999


Q ss_pred             CCCHH--------------HHHHHHHHHHhc--CCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC
Q psy4285         382 AMTND--------------AQNALRRIIEKF--TTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       382 ~l~~~--------------~~~~Ll~~le~~--~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+...              ..+.|+..|+..  ..++.+|.+||+++.+|+++++  ||. .+.++.|+.++..++++..
T Consensus       581 sl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~~~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~  660 (806)
T 3cf2_A          581 SIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKAN  660 (806)
T ss_dssp             GCC--------------CHHHHHHHHHHHSSCSSSSEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTT
T ss_pred             HHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHH
Confidence            98532              246688888843  4567788899999999999999  995 6777777777777777665


Q ss_pred             --------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q psy4285         443 --------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLV  478 (533)
Q Consensus       443 --------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~  478 (533)
                              ..++..+.+         .+.|||+.||..-+.++.
T Consensus       661 l~~~~~~~~~dl~~la~---------~t~g~SGadi~~l~~~A~  695 (806)
T 3cf2_A          661 LRKSPVAKDVDLEFLAK---------MTNGFSGADLTEICQRAC  695 (806)
T ss_dssp             SSCC--CCC-------------------------CHHHHHHHHH
T ss_pred             hcCCCCCCCCCHHHHHH---------hCCCCCHHHHHHHHHHHH
Confidence                    234444444         677999999877665543

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

Probab=99.79  E-value=1.4e-18  Score=172.47  Aligned_cols=189  Identities=21%  Similarity=0.310  Sum_probs=129.5

Q ss_pred             CccccccccCCCC--HHHHHHHHHHHhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcce
Q psy4285         263 NEDTVYNSVGYPT--KTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV  340 (533)
Q Consensus       263 ~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~  340 (533)
                      .++..|.++++..  ...+.+.+.+... +.+....+.    ...+.++|||||||||||++|+++|.++      +.++
T Consensus       142 ~p~v~~~dIgGl~~~k~~l~e~v~~Pl~-~pe~f~~~g----i~~prGvLL~GPPGTGKTllAkAiA~e~------~~~f  210 (405)
T 4b4t_J          142 VPDSTYDMVGGLTKQIKEIKEVIELPVK-HPELFESLG----IAQPKGVILYGPPGTGKTLLARAVAHHT------DCKF  210 (405)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHTHHHHH-CHHHHHHHT----CCCCCCEEEESCSSSSHHHHHHHHHHHH------TCEE
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHHh-CHHHHHhCC----CCCCCceEEeCCCCCCHHHHHHHHHHhh------CCCc
Confidence            3556788888753  2344554444332 222222211    1122359999999999999999999998      7788


Q ss_pred             EEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHh--c
Q psy4285         341 LELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN--------------DAQNALRRIIEK--F  398 (533)
Q Consensus       341 ~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------------~~~~~Ll~~le~--~  398 (533)
                      +.+++++..      +...++..+.....      ..++||||||+|.+..              ...+.|+..|+.  .
T Consensus       211 ~~v~~s~l~sk~vGese~~vr~lF~~Ar~------~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~  284 (405)
T 4b4t_J          211 IRVSGAELVQKYIGEGSRMVRELFVMARE------HAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFET  284 (405)
T ss_dssp             EEEEGGGGSCSSTTHHHHHHHHHHHHHHH------TCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTC
T ss_pred             eEEEhHHhhccccchHHHHHHHHHHHHHH------hCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCC
Confidence            888877643      23445554433322      3568999999999853              124557777774  3


Q ss_pred             CCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC--------HHHHHHHHHHHHHHHHHHHhcCCCH
Q psy4285         399 TTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD--------DISFFNIIIWYIKIQEIKIEKGLAL  467 (533)
Q Consensus       399 ~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~--------~~~~~~ll~~~~~l~~l~~~~~~~~  467 (533)
                      ..++.+|++||+++.+||++++  ||+ .+.|+.|+.++..+++...        ..++..+.+         .+.|+++
T Consensus       285 ~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl~~lA~---------~t~G~SG  355 (405)
T 4b4t_J          285 SKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAE---------KMNGCSG  355 (405)
T ss_dssp             CCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCCHHHHHH---------HCCSCCH
T ss_pred             CCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHH---------HCCCCCH
Confidence            4578899999999999999998  995 8888889988888887654        123444444         7789999


Q ss_pred             HHHHHHHHHH
Q psy4285         468 TDILTEISLL  477 (533)
Q Consensus       468 ~di~~~~~~~  477 (533)
                      .||..-+.++
T Consensus       356 ADi~~l~~eA  365 (405)
T 4b4t_J          356 ADVKGVCTEA  365 (405)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9987766554

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=99.77  E-value=3.6e-17  Score=165.26  Aligned_cols=153  Identities=22%  Similarity=0.340  Sum_probs=120.3

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCCC
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASDD  348 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~~  348 (533)
                      .|++.....+..++..+..+| ++|+||||||||++++++++.+.+....                  ...++.+++...
T Consensus        19 vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (373)
T 1jr3_A           19 VGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASR   98 (373)
T ss_dssp             CSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSSHHHHHHHTSCCSSCEEEETTCS
T ss_pred             cCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhccCCCceEEeccccc
Confidence            455666666777777777777 7999999999999999999998764311                  012355555443


Q ss_pred             CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeec
Q psy4285         349 RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFG  428 (533)
Q Consensus       349 ~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~  428 (533)
                      .+.+.+++.+.......  ..+++.|+||||+|.++...++.|++.+++++.++.+|++|+....+.+++++||..+.|.
T Consensus        99 ~~~~~~~~l~~~~~~~~--~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~~~l~sr~~~i~~~  176 (373)
T 1jr3_A           99 TKVEDTRDLLDNVQYAP--ARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLK  176 (373)
T ss_dssp             CCSSCHHHHHHHTTSCC--SSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSCHHHHTTSEEEECC
T ss_pred             CCHHHHHHHHHHHhhcc--ccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCcHHHHhheeEeeCC
Confidence            44556666655543222  1356789999999999999999999999999899999999999999999999999999999


Q ss_pred             CCCHHHHHHHhhcC
Q psy4285         429 PLDSSLIMSRLDYD  442 (533)
Q Consensus       429 ~~~~~~~~~~l~~~  442 (533)
                      +++.+++.+++.++
T Consensus       177 ~l~~~~~~~~l~~~  190 (373)
T 1jr3_A          177 ALDVEQIRHQLEHI  190 (373)
T ss_dssp             CCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999998754

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

Probab=99.77  E-value=1.9e-17  Score=154.30  Aligned_cols=153  Identities=44%  Similarity=0.769  Sum_probs=124.0

Q ss_pred             hchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCC
Q psy4285         289 ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH  368 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  368 (533)
                      |++.....+..++..+..++++|+||||||||++++.+++.+.+.. ....++.++++...+...+...+..+.......
T Consensus        21 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (226)
T 2chg_A           21 GQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGEN-WRDNFIEMNASDERGIDVVRHKIKEFARTAPIG   99 (226)
T ss_dssp             SCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHGGG-GGGGEEEEETTCTTCHHHHHHHHHHHHTSCCST
T ss_pred             CcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHhccc-cccceEEeccccccChHHHHHHHHHHhcccCCC
Confidence            4455556666666666666799999999999999999999875543 345677888877667666766666665443322


Q ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         369 KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       369 ~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ...+.+|+|||++.+....++.|++.+++++.++.+|++||.+..+++++.+||..+.|.+++.+++.+++.+.
T Consensus       100 ~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~  173 (226)
T 2chg_A          100 GAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEI  173 (226)
T ss_dssp             TCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHH
T ss_pred             ccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCceeecCCCCHHHHHHHHHHH
Confidence            35688999999999999999999999999888899999999999999999999999999999999988887754

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

Probab=99.76  E-value=8.2e-18  Score=167.35  Aligned_cols=189  Identities=20%  Similarity=0.259  Sum_probs=127.0

Q ss_pred             CccccccccCCCC--HHHHHHHHHHHhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcce
Q psy4285         263 NEDTVYNSVGYPT--KTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV  340 (533)
Q Consensus       263 ~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~  340 (533)
                      .+...|.+++...  ...+.+.+.+.... .+....+.    ...+..+|||||||||||++|+++|.++      +.++
T Consensus       176 ~p~v~~~DIgGld~~k~~L~e~v~~Pl~~-pe~f~~~G----i~~prGvLLyGPPGTGKTlLAkAiA~e~------~~~f  244 (437)
T 4b4t_I          176 SPTESYSDIGGLESQIQEIKESVELPLTH-PELYEEMG----IKPPKGVILYGAPGTGKTLLAKAVANQT------SATF  244 (437)
T ss_dssp             SCCCCGGGTCSCHHHHHHHHHHHHHHHHC-CHHHHHHT----CCCCSEEEEESSTTTTHHHHHHHHHHHH------TCEE
T ss_pred             CCCCcceecCcHHHHHHHHHHHHHHHHhC-HHHHHhCC----CCCCCCCceECCCCchHHHHHHHHHHHh------CCCE
Confidence            4555788887753  23455544443322 22222111    1122349999999999999999999998      7788


Q ss_pred             EEecCCCCCc------hhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHh--c
Q psy4285         341 LELNASDDRG------IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN--------------DAQNALRRIIEK--F  398 (533)
Q Consensus       341 ~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------------~~~~~Ll~~le~--~  398 (533)
                      +.+++++..+      ...++..+.....      ..++||||||+|.+..              ...+.|+..++.  .
T Consensus       245 i~v~~s~l~sk~vGesek~ir~lF~~Ar~------~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~  318 (437)
T 4b4t_I          245 LRIVGSELIQKYLGDGPRLCRQIFKVAGE------NAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDD  318 (437)
T ss_dssp             EEEESGGGCCSSSSHHHHHHHHHHHHHHH------TCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCC
T ss_pred             EEEEHHHhhhccCchHHHHHHHHHHHHHh------cCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCC
Confidence            8888766432      3344444433322      3568999999998842              123456666664  3


Q ss_pred             CCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC--------HHHHHHHHHHHHHHHHHHHhcCCCH
Q psy4285         399 TTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD--------DISFFNIIIWYIKIQEIKIEKGLAL  467 (533)
Q Consensus       399 ~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~--------~~~~~~ll~~~~~l~~l~~~~~~~~  467 (533)
                      ..++.+|+|||+++.+||++++  ||+ .+.|+.|+.++..+++...        ..++..+..         .+.|+|+
T Consensus       319 ~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dvdl~~LA~---------~T~GfSG  389 (437)
T 4b4t_I          319 RGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVT---------TKDDLSG  389 (437)
T ss_dssp             SSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCCCHHHHHH---------HCCSCCH
T ss_pred             CCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHH---------hCCCCCH
Confidence            4568899999999999999998  995 7888888888888887654        123444444         6789999


Q ss_pred             HHHHHHHHHH
Q psy4285         468 TDILTEISLL  477 (533)
Q Consensus       468 ~di~~~~~~~  477 (533)
                      .||..-+.++
T Consensus       390 ADI~~l~~eA  399 (437)
T 4b4t_I          390 ADIQAMCTEA  399 (437)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9987666554

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

Probab=99.75  E-value=1.1e-17  Score=184.26  Aligned_cols=127  Identities=19%  Similarity=0.298  Sum_probs=94.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHH-HHHHHHHHhcccCCCCCcEEEEEeCCCCCCHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIV-RDQIFQFASTKTMHKSSYKLIILDEADAMTND  386 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~  386 (533)
                      +++|+||||||||++|+++++.+.+.   +.+++.+++++....... ...+......     .+++||||||++.+.++
T Consensus       523 ~~Ll~Gp~GtGKT~lA~ala~~l~~~---~~~~i~i~~s~~~~~~~~~~~~l~~~~~~-----~~~~vl~lDEi~~~~~~  594 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELARALAESIFGD---EESMIRIDMSEYMEKHSTSGGQLTEKVRR-----KPYSVVLLDAIEKAHPD  594 (758)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHHHSC---TTCEEEEEGGGGCSSCCCC---CHHHHHH-----CSSSEEEEECGGGSCHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcCC---CcceEEEechhcccccccccchhhHHHHh-----CCCeEEEEeCccccCHH
Confidence            59999999999999999999998554   456777777654321110 1111111111     24579999999999999


Q ss_pred             HHHHHHHHHHh-----------cCCCcEEEEEeCCCCC------------CChhhhccc-eeeeecCCCHHHHHHHhhcC
Q psy4285         387 AQNALRRIIEK-----------FTTNVRFCIICNYLSK------------IPPAIQSRC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       387 ~~~~Ll~~le~-----------~~~~~~~I~~~n~~~~------------l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .++.|++.|++           ...++++|+|||....            +.|++++|| ..+.|+|++.+++..++...
T Consensus       595 ~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~~~~~f~p~l~~Rl~~~i~~~~l~~~~~~~i~~~~  674 (758)
T 3pxi_A          595 VFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKVMGELKRAFRPEFINRIDEIIVFHSLEKKHLTEIVSLM  674 (758)
T ss_dssp             HHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHHHHHHHHHSCHHHHTTSSEEEECC--CHHHHHHHHHHH
T ss_pred             HHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHHHHHHHhhCCHHHHhhCCeEEecCCCCHHHHHHHHHHH
Confidence            99999999997           3457899999997554            789999999 79999999998888887765

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

Probab=99.75  E-value=2e-17  Score=167.07  Aligned_cols=189  Identities=19%  Similarity=0.271  Sum_probs=125.9

Q ss_pred             CccccccccCCCC--HHHHHHHHHHHhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcce
Q psy4285         263 NEDTVYNSVGYPT--KTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV  340 (533)
Q Consensus       263 ~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~  340 (533)
                      .++..|.++++..  ...+.+.+.+... +.+....+.    ...+.++|||||||||||++|+++|.++      +.++
T Consensus       175 ~p~v~~~digGl~~~k~~l~e~v~~pl~-~p~~f~~~g----~~~prGvLL~GPPGtGKTllAkAiA~e~------~~~~  243 (437)
T 4b4t_L          175 QGEITFDGIGGLTEQIRELREVIELPLK-NPEIFQRVG----IKPPKGVLLYGPPGTGKTLLAKAVAATI------GANF  243 (437)
T ss_dssp             SCSSCSGGGCSCHHHHHHHHHHHHHHHH-CHHHHHHHC----CCCCCEEEEESCTTSSHHHHHHHHHHHH------TCEE
T ss_pred             CCCCChhHhCChHHHHHHHHHHHHHHHh-CHHHHHhCC----CCCCCeEEEECCCCCcHHHHHHHHHHHh------CCCE
Confidence            3445677777753  2344554444332 222222221    1122349999999999999999999998      7788


Q ss_pred             EEecCCCCCc------hhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhc--
Q psy4285         341 LELNASDDRG------IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN--------------DAQNALRRIIEKF--  398 (533)
Q Consensus       341 ~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------------~~~~~Ll~~le~~--  398 (533)
                      +.+++++..+      ...++..+.....      ..++||||||+|.+..              ...+.|+..|+..  
T Consensus       244 ~~v~~s~l~sk~~Gese~~ir~~F~~A~~------~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~  317 (437)
T 4b4t_L          244 IFSPASGIVDKYIGESARIIREMFAYAKE------HEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDN  317 (437)
T ss_dssp             EEEEGGGTCCSSSSHHHHHHHHHHHHHHH------SCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSC
T ss_pred             EEEehhhhccccchHHHHHHHHHHHHHHh------cCCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhcccC
Confidence            8888766432      2334443332221      3578999999998842              1245677777753  


Q ss_pred             CCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC--------HHHHHHHHHHHHHHHHHHHhcCCCH
Q psy4285         399 TTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD--------DISFFNIIIWYIKIQEIKIEKGLAL  467 (533)
Q Consensus       399 ~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~--------~~~~~~ll~~~~~l~~l~~~~~~~~  467 (533)
                      ..++.+|+|||+++.+||++++  ||+ .+.|+.|+.++..+++...        ..++..+..         .+.|+++
T Consensus       318 ~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl~~lA~---------~t~G~sG  388 (437)
T 4b4t_L          318 LGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVK---------MSDGFNG  388 (437)
T ss_dssp             TTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCCHHHHHH---------TCCSCCH
T ss_pred             CCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccCHHHHHH---------hCCCCCH
Confidence            3568899999999999999998  474 7888888888888877654        123444433         6789999


Q ss_pred             HHHHHHHHHH
Q psy4285         468 TDILTEISLL  477 (533)
Q Consensus       468 ~di~~~~~~~  477 (533)
                      .||..-+.++
T Consensus       389 ADi~~l~~eA  398 (437)
T 4b4t_L          389 ADIRNCATEA  398 (437)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9987766554

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

Probab=99.75  E-value=9.7e-18  Score=169.22  Aligned_cols=189  Identities=23%  Similarity=0.311  Sum_probs=124.3

Q ss_pred             CccccccccCCCCH--HHHHHHHHHHhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcce
Q psy4285         263 NEDTVYNSVGYPTK--TEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV  340 (533)
Q Consensus       263 ~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~  340 (533)
                      .+...|.++++...  ..+.+.+.+.... .+....+.    ...+.++|||||||||||++|+++|.++      +.++
T Consensus       175 ~p~~t~~digGl~~~k~~l~e~v~~pl~~-pe~f~~~g----~~~prGvLLyGPPGTGKTllAkAiA~e~------~~~f  243 (434)
T 4b4t_M          175 KPTETYSDVGGLDKQIEELVEAIVLPMKR-ADKFKDMG----IRAPKGALMYGPPGTGKTLLARACAAQT------NATF  243 (434)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHTHHHHHC-SHHHHHHC----CCCCCEEEEESCTTSSHHHHHHHHHHHH------TCEE
T ss_pred             CCCCChHhcCcHHHHHHHHHHHHHHHHhC-HHHHHhCC----CCCCCeeEEECcCCCCHHHHHHHHHHHh------CCCE
Confidence            34557888877642  2344433333322 22221111    1122349999999999999999999998      7788


Q ss_pred             EEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH-----------H---HHHHHHHHHHhc--
Q psy4285         341 LELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN-----------D---AQNALRRIIEKF--  398 (533)
Q Consensus       341 ~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~---~~~~Ll~~le~~--  398 (533)
                      +.+++++..      +...++..+.....      ..++||||||+|.+..           .   ..+.|+..|+..  
T Consensus       244 ~~v~~s~l~~~~vGese~~ir~lF~~A~~------~aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~~  317 (434)
T 4b4t_M          244 LKLAAPQLVQMYIGEGAKLVRDAFALAKE------KAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSS  317 (434)
T ss_dssp             EEEEGGGGCSSCSSHHHHHHHHHHHHHHH------HCSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTSCS
T ss_pred             EEEehhhhhhcccchHHHHHHHHHHHHHh------cCCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhccCC
Confidence            888876542      23344444433322      2468999999998721           1   234566777643  


Q ss_pred             CCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC--------HHHHHHHHHHHHHHHHHHHhcCCCH
Q psy4285         399 TTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD--------DISFFNIIIWYIKIQEIKIEKGLAL  467 (533)
Q Consensus       399 ~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~--------~~~~~~ll~~~~~l~~l~~~~~~~~  467 (533)
                      ..++.+|+|||+++.+||++++  ||+ .+.|+.|+.++..+++...        .-++..+..         .+.|+++
T Consensus       318 ~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvdl~~lA~---------~t~G~sG  388 (434)
T 4b4t_M          318 DDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELAR---------STDEFNG  388 (434)
T ss_dssp             SCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCCHHHHHH---------HCSSCCH
T ss_pred             CCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHH---------hCCCCCH
Confidence            3567899999999999999988  995 7888888888888887654        112333333         6789999


Q ss_pred             HHHHHHHHHH
Q psy4285         468 TDILTEISLL  477 (533)
Q Consensus       468 ~di~~~~~~~  477 (533)
                      .||..-+.++
T Consensus       389 ADi~~l~~eA  398 (434)
T 4b4t_M          389 AQLKAVTVEA  398 (434)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9987666544

>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=99.74  E-value=3.6e-17  Score=180.44  Aligned_cols=144  Identities=22%  Similarity=0.252  Sum_probs=102.9

Q ss_pred             hhhchhhhhhhccccccc--------CC-CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch------
Q psy4285         287 LNESMDLCYKINRFIDEN--------EL-PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI------  351 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~--------~~-~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~------  351 (533)
                      ..|++..+..+...+...        ++ .+++|+||||||||++|+++++.+      +..++.+++++....      
T Consensus       460 v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l------~~~~~~i~~s~~~~~~~~~~l  533 (758)
T 1r6b_X          460 VFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL------GIELLRFDMSEYMERHTVSRL  533 (758)
T ss_dssp             SCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH------TCEEEEEEGGGCSSSSCCSSS
T ss_pred             ccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHh------cCCEEEEechhhcchhhHhhh
Confidence            456776666555544322        11 259999999999999999999988      445566655432110      


Q ss_pred             -----hHH-----HHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcC-----------CCcEEEEEeCC
Q psy4285         352 -----GIV-----RDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT-----------TNVRFCIICNY  410 (533)
Q Consensus       352 -----~~~-----~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~-----------~~~~~I~~~n~  410 (533)
                           ..+     ......+.      ..+++||+|||++++.++.++.|++.|++..           .++.+|+|||.
T Consensus       534 ~g~~~g~~g~~~~~~l~~~~~------~~~~~vl~lDEi~~~~~~~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~  607 (758)
T 1r6b_X          534 IGAPPGYVGFDQGGLLTDAVI------KHPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNA  607 (758)
T ss_dssp             CCCCSCSHHHHHTTHHHHHHH------HCSSEEEEEETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECS
T ss_pred             cCCCCCCcCccccchHHHHHH------hCCCcEEEEeCccccCHHHHHHHHHHhcCcEEEcCCCCEEecCCeEEEEecCc
Confidence                 011     01111111      1356899999999999999999999999642           46789999997


Q ss_pred             CC-------------------------CCChhhhccc-eeeeecCCCHHHHHHHhhcC
Q psy4285         411 LS-------------------------KIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       411 ~~-------------------------~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..                         .+.|++++|| ..+.|++++.+++..++...
T Consensus       608 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~l~~~~~~~i~~~~  665 (758)
T 1r6b_X          608 GVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKF  665 (758)
T ss_dssp             SCC-----------------CHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHH
T ss_pred             chhhhhhcccCccccchHHHHHHHHHHhcCHHHHhhCCcceeeCCCCHHHHHHHHHHH
Confidence            43                         5789999999 68999999998888887765

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

Probab=99.74  E-value=3e-17  Score=165.00  Aligned_cols=189  Identities=21%  Similarity=0.261  Sum_probs=125.0

Q ss_pred             CccccccccCCCCH--HHHHHHHHHHhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcce
Q psy4285         263 NEDTVYNSVGYPTK--TEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV  340 (533)
Q Consensus       263 ~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~  340 (533)
                      .++..|.++++...  ..+.+.+.+.+. +.+....+.    -..+..+|||||||||||++|+++|.++      +.++
T Consensus       203 ~P~vt~~DIgGl~~~k~~L~e~V~~pl~-~pe~f~~~G----i~pprGILLyGPPGTGKTlLAkAiA~e~------~~~f  271 (467)
T 4b4t_H          203 KPDVTYSDVGGCKDQIEKLREVVELPLL-SPERFATLG----IDPPKGILLYGPPGTGKTLCARAVANRT------DATF  271 (467)
T ss_dssp             SCSCCCSSCTTCHHHHHHHHHHTHHHHH-CHHHHHHHT----CCCCSEEEECSCTTSSHHHHHHHHHHHH------TCEE
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHhc-CHHHHHHCC----CCCCCceEeeCCCCCcHHHHHHHHHhcc------CCCe
Confidence            44556777777532  234444333222 222222211    1122349999999999999999999998      7788


Q ss_pred             EEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhc--
Q psy4285         341 LELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN--------------DAQNALRRIIEKF--  398 (533)
Q Consensus       341 ~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------------~~~~~Ll~~le~~--  398 (533)
                      +.+++++..      +...++..+.....      ..++||||||+|.+..              ...+.++..|+..  
T Consensus       272 i~vs~s~L~sk~vGesek~ir~lF~~Ar~------~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~  345 (467)
T 4b4t_H          272 IRVIGSELVQKYVGEGARMVRELFEMART------KKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDP  345 (467)
T ss_dssp             EEEEGGGGCCCSSSHHHHHHHHHHHHHHH------TCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCC
T ss_pred             EEEEhHHhhcccCCHHHHHHHHHHHHHHh------cCCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCC
Confidence            888876543      23345544433322      3568999999998842              1234556666633  


Q ss_pred             CCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC--------HHHHHHHHHHHHHHHHHHHhcCCCH
Q psy4285         399 TTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD--------DISFFNIIIWYIKIQEIKIEKGLAL  467 (533)
Q Consensus       399 ~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~--------~~~~~~ll~~~~~l~~l~~~~~~~~  467 (533)
                      ..++.+|+|||+++.+|+++++  ||+ .+.|+.|+.++..+++...        ..++..+.+         .+.|+++
T Consensus       346 ~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl~~LA~---------~T~GfSG  416 (467)
T 4b4t_H          346 RGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISR---------LCPNSTG  416 (467)
T ss_dssp             TTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHH---------HCCSCCH
T ss_pred             CCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHH---------HCCCCCH
Confidence            4567899999999999999998  994 7888888888888887644        123344333         6789999


Q ss_pred             HHHHHHHHHH
Q psy4285         468 TDILTEISLL  477 (533)
Q Consensus       468 ~di~~~~~~~  477 (533)
                      .||..-+.++
T Consensus       417 ADI~~l~~eA  426 (467)
T 4b4t_H          417 AELRSVCTEA  426 (467)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9987766554

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

Probab=99.73  E-value=3.8e-17  Score=164.79  Aligned_cols=189  Identities=26%  Similarity=0.325  Sum_probs=125.2

Q ss_pred             CccccccccCCCC--HHHHHHHHHHHhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcce
Q psy4285         263 NEDTVYNSVGYPT--KTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV  340 (533)
Q Consensus       263 ~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~  340 (533)
                      .++..|.++++..  ...+.+.+.+... +.+....+.    ...+..+|||||||||||++|+++|+++      +.++
T Consensus       166 ~p~v~~~digGl~~~k~~l~e~v~~pl~-~p~~~~~~g----~~~prGiLL~GPPGtGKT~lakAiA~~~------~~~~  234 (428)
T 4b4t_K          166 KPDVTYADVGGLDMQKQEIREAVELPLV-QADLYEQIG----IDPPRGVLLYGPPGTGKTMLVKAVANST------KAAF  234 (428)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHHHHHHH-CHHHHHHHC----CCCCCEEEEESCTTTTHHHHHHHHHHHH------TCEE
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHHh-CHHHHHhCC----CCCCceEEEECCCCCCHHHHHHHHHHHh------CCCe
Confidence            3455788887754  2334444444332 222222221    1122249999999999999999999998      7788


Q ss_pred             EEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhc--
Q psy4285         341 LELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN--------------DAQNALRRIIEKF--  398 (533)
Q Consensus       341 ~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------------~~~~~Ll~~le~~--  398 (533)
                      +.+++++..      +...++..+.....      ..++|+||||+|.+..              ...+.|+..|+..  
T Consensus       235 ~~v~~~~l~~~~~Ge~e~~ir~lF~~A~~------~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~  308 (428)
T 4b4t_K          235 IRVNGSEFVHKYLGEGPRMVRDVFRLARE------NAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQ  308 (428)
T ss_dssp             EEEEGGGTCCSSCSHHHHHHHHHHHHHHH------TCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCS
T ss_pred             EEEecchhhccccchhHHHHHHHHHHHHH------cCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCC
Confidence            888876543      23345554433322      3568999999987621              2356677788753  


Q ss_pred             CCCcEEEEEeCCCCCCChhhhc--cce-eeeec-CCCHHHHHHHhhcC--------HHHHHHHHHHHHHHHHHHHhcCCC
Q psy4285         399 TTNVRFCIICNYLSKIPPAIQS--RCT-RFRFG-PLDSSLIMSRLDYD--------DISFFNIIIWYIKIQEIKIEKGLA  466 (533)
Q Consensus       399 ~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~-~~~~~~~~~~l~~~--------~~~~~~ll~~~~~l~~l~~~~~~~  466 (533)
                      ..++.+|+|||+++.+||++++  ||+ .+.|+ .|+.++...++...        ..++..+..         .+.|++
T Consensus       309 ~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~dl~~lA~---------~t~G~s  379 (428)
T 4b4t_K          309 STNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLII---------RNDSLS  379 (428)
T ss_dssp             SCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTCCHHHHHH---------HTTTCC
T ss_pred             CCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHH---------HCCCCC
Confidence            4568899999999999999998  885 67785 56777766666544        123444444         678999


Q ss_pred             HHHHHHHHHHH
Q psy4285         467 LTDILTEISLL  477 (533)
Q Consensus       467 ~~di~~~~~~~  477 (533)
                      +.||..-+.++
T Consensus       380 gadi~~l~~eA  390 (428)
T 4b4t_K          380 GAVIAAIMQEA  390 (428)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99987766554

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

Probab=99.73  E-value=5.1e-17  Score=166.61  Aligned_cols=144  Identities=25%  Similarity=0.331  Sum_probs=108.0

Q ss_pred             hhchhhh---hhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhc
Q psy4285         288 NESMDLC---YKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAST  364 (533)
Q Consensus       288 ~~~~~~~---~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  364 (533)
                      .|++++.   ..+...+..+..++++|+||||||||++|+++++.+      +..+..+++.. .+...+++.+......
T Consensus        29 vGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~------~~~f~~l~a~~-~~~~~ir~~~~~a~~~  101 (447)
T 3pvs_A           29 IGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYA------NADVERISAVT-SGVKEIREAIERARQN  101 (447)
T ss_dssp             CSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHHHT------TCEEEEEETTT-CCHHHHHHHHHHHHHH
T ss_pred             CCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHHHh------CCCeEEEEecc-CCHHHHHHHHHHHHHh
Confidence            4555555   567777777777789999999999999999999987      55677777655 4555566655543322


Q ss_pred             ccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEe--CCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         365 KTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIIC--NYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       365 ~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~--n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..  .....+|||||+|.++...++.|++.+++  ..+.+|++|  |....++++++|||..+.|.+++.+++..++.+.
T Consensus       102 ~~--~~~~~iLfIDEI~~l~~~~q~~LL~~le~--~~v~lI~att~n~~~~l~~aL~sR~~v~~l~~l~~edi~~il~~~  177 (447)
T 3pvs_A          102 RN--AGRRTILFVDEVHRFNKSQQDAFLPHIED--GTITFIGATTENPSFELNSALLSRARVYLLKSLSTEDIEQVLTQA  177 (447)
T ss_dssp             HH--TTCCEEEEEETTTCC------CCHHHHHT--TSCEEEEEESSCGGGSSCHHHHTTEEEEECCCCCHHHHHHHHHHH
T ss_pred             hh--cCCCcEEEEeChhhhCHHHHHHHHHHHhc--CceEEEecCCCCcccccCHHHhCceeEEeeCCcCHHHHHHHHHHH
Confidence            21  24678999999999999999999999997  447788777  5556899999999999999999999999888654

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

Probab=99.69  E-value=5.2e-16  Score=152.95  Aligned_cols=151  Identities=18%  Similarity=0.215  Sum_probs=110.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      +++|+||||||||++|+++|+++.     +..++.+++++..      ....++..+.....      ..++||||||+|
T Consensus        47 ~iLL~GppGtGKT~la~ala~~~~-----~~~~~~i~~~~l~~~~~g~~~~~~~~lf~~a~~------~~~~vl~iDEid  115 (322)
T 1xwi_A           47 GILLFGPPGTGKSYLAKAVATEAN-----NSTFFSISSSDLVSKWLGESEKLVKNLFQLARE------NKPSIIFIDEID  115 (322)
T ss_dssp             EEEEESSSSSCHHHHHHHHHHHTT-----SCEEEEEECCSSCCSSCCSCHHHHHHHHHHHHH------TSSEEEEEETTT
T ss_pred             eEEEECCCCccHHHHHHHHHHHcC-----CCcEEEEEhHHHHhhhhhHHHHHHHHHHHHHHh------cCCcEEEeecHH
Confidence            599999999999999999999872     3456666665432      23344444333221      356899999999


Q ss_pred             CCC-----------HHHHHHHHHHHHh---cCCCcEEEEEeCCCCCCChhhhccc-eeeeecCCCHHHHHHHhhcC----
Q psy4285         382 AMT-----------NDAQNALRRIIEK---FTTNVRFCIICNYLSKIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD----  442 (533)
Q Consensus       382 ~l~-----------~~~~~~Ll~~le~---~~~~~~~I~~~n~~~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~----  442 (533)
                      .+.           ....+.|+..++.   ...++.+|++||.+..++++++||| ..+.++.|+.++..+++...    
T Consensus       116 ~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~  195 (322)
T 1xwi_A          116 SLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHLGTT  195 (322)
T ss_dssp             GGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTTEEEEEEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTC
T ss_pred             HhccccccccchHHHHHHHHHHHHHhcccccCCCEEEEEecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHHhcC
Confidence            983           2345678888875   3467889999999999999999999 57888889988888888764    


Q ss_pred             -----HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q psy4285         443 -----DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLV  478 (533)
Q Consensus       443 -----~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~  478 (533)
                           +.++..+..         .+.|+++.|+..-+.+++
T Consensus       196 ~~~l~~~~l~~la~---------~t~G~sgadl~~l~~~A~  227 (322)
T 1xwi_A          196 QNSLTEADFRELGR---------KTDGYSGADISIIVRDAL  227 (322)
T ss_dssp             CBCCCHHHHHHHHH---------TCTTCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHH---------HcCCCCHHHHHHHHHHHH
Confidence                 334444444         678999999877665554

>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=99.69  E-value=3.4e-16  Score=156.46  Aligned_cols=150  Identities=21%  Similarity=0.266  Sum_probs=109.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      ++||+||||||||++|+++|+.+      +..++.+++++.      .....++..+.....      ..++||||||+|
T Consensus        86 ~iLL~GppGtGKT~la~ala~~~------~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~------~~~~vl~iDEid  153 (355)
T 2qp9_X           86 GILLYGPPGTGKSYLAKAVATEA------NSTFFSVSSSDLVSKWMGESEKLVKQLFAMARE------NKPSIIFIDQVD  153 (355)
T ss_dssp             CEEEECSTTSCHHHHHHHHHHHH------TCEEEEEEHHHHHSCC---CHHHHHHHHHHHHH------TSSEEEEEECGG
T ss_pred             eEEEECCCCCcHHHHHHHHHHHh------CCCEEEeeHHHHhhhhcchHHHHHHHHHHHHHH------cCCeEEEEechH
Confidence            59999999999999999999998      556666665431      122333333322211      356899999999


Q ss_pred             CCCH-----------HHHHHHHHHHHh---cCCCcEEEEEeCCCCCCChhhhccc-eeeeecCCCHHHHHHHhhcC----
Q psy4285         382 AMTN-----------DAQNALRRIIEK---FTTNVRFCIICNYLSKIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD----  442 (533)
Q Consensus       382 ~l~~-----------~~~~~Ll~~le~---~~~~~~~I~~~n~~~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~----  442 (533)
                      .+..           ..++.|+..|+.   ...++.+|++||.+..+++++++|| ..+.+.+|+.++...++...    
T Consensus       154 ~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~  233 (355)
T 2qp9_X          154 ALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDT  233 (355)
T ss_dssp             GGTC------CTHHHHHHHHHHHHHHHCC---CCEEEEEEESCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTS
T ss_pred             hhcccCCCCcchHHHHHHHHHHHHhhcccccCCCeEEEeecCCcccCCHHHHcccCEEEEeCCcCHHHHHHHHHHHHhhC
Confidence            9863           246778888874   3467889999999999999999999 57888889999888888764    


Q ss_pred             -----HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q psy4285         443 -----DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLV  478 (533)
Q Consensus       443 -----~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~  478 (533)
                           +.++..+..         .+.|+++.|+..-+.+++
T Consensus       234 ~~~~~~~~l~~la~---------~t~G~sg~dl~~l~~~A~  265 (355)
T 2qp9_X          234 PSVLTKEDYRTLGA---------MTEGYSGSDIAVVVKDAL  265 (355)
T ss_dssp             CBCCCHHHHHHHHH---------HTTTCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHH---------HcCCCCHHHHHHHHHHHH
Confidence                 334444444         677999999877665544

>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=99.69  E-value=2.5e-16  Score=175.26  Aligned_cols=151  Identities=20%  Similarity=0.294  Sum_probs=104.4

Q ss_pred             hhhchhhhhhhcccccccC--------C-CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHH
Q psy4285         287 LNESMDLCYKINRFIDENE--------L-PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQ  357 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~--------~-~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  357 (533)
                      +.|++..+..+...+....        + .+++|+||||||||++|+++++.+.+.   +..++.++++...........
T Consensus       560 viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~~~---~~~~i~i~~~~~~~~~~~s~l  636 (854)
T 1qvr_A          560 VVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT---EEAMIRIDMTEYMEKHAVSRL  636 (854)
T ss_dssp             SCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSS---GGGEEEECTTTCCSSGGGGGC
T ss_pred             cCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCC---CCcEEEEechhccchhHHHHH
Confidence            4566666666555544321        1 258999999999999999999998664   356777777654322111110


Q ss_pred             H------------HHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcC-----------CCcEEEEEeCC----
Q psy4285         358 I------------FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT-----------TNVRFCIICNY----  410 (533)
Q Consensus       358 ~------------~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~-----------~~~~~I~~~n~----  410 (533)
                      +            +.+....  ....+++|||||++.+..+.++.|++.|+++.           .++.+|+|||.    
T Consensus       637 ~g~~~~~~G~~~~g~l~~~~--~~~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~~~~~  714 (854)
T 1qvr_A          637 IGAPPGYVGYEEGGQLTEAV--RRRPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPL  714 (854)
T ss_dssp             --------------CHHHHH--HHCSSEEEEESSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHH
T ss_pred             cCCCCCCcCccccchHHHHH--HhCCCeEEEEecccccCHHHHHHHHHHhccCceECCCCCEeccCCeEEEEecCcChHH
Confidence            0            0000000  01246899999999999999999999998652           36779999996    


Q ss_pred             ----------------------CCCCChhhhccc-eeeeecCCCHHHHHHHhhcC
Q psy4285         411 ----------------------LSKIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       411 ----------------------~~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                                            ...+.|++.+|| ..+.|.|++.+++..++...
T Consensus       715 ~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~Rl~~~i~~~pl~~edi~~i~~~~  769 (854)
T 1qvr_A          715 ILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQ  769 (854)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHTCSBCCBCCCCCHHHHHHHHHHH
T ss_pred             HhhhcccccchHHHHHHHHHHHHhhCCHHHHHhcCeEEeCCCCCHHHHHHHHHHH
Confidence                                  235789999999 68888999988877776654

>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=99.68  E-value=1.9e-16  Score=156.49  Aligned_cols=150  Identities=21%  Similarity=0.257  Sum_probs=109.6

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .++||+||||||||++|+++|+.+      +..++.+++++..      ....++..+.....      ..++||||||+
T Consensus        52 ~~vLl~GppGtGKT~la~aia~~~------~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~------~~~~vl~iDEi  119 (322)
T 3eie_A           52 SGILLYGPPGTGKSYLAKAVATEA------NSTFFSVSSSDLVSKWMGESEKLVKQLFAMARE------NKPSIIFIDQV  119 (322)
T ss_dssp             CEEEEECSSSSCHHHHHHHHHHHH------TCEEEEEEHHHHHTTTGGGHHHHHHHHHHHHHH------TSSEEEEEECG
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHH------CCCEEEEchHHHhhcccchHHHHHHHHHHHHHh------cCCeEEEechh
Confidence            359999999999999999999997      5667777764421      12223333222221      35689999999


Q ss_pred             CCCCH-----------HHHHHHHHHHHh---cCCCcEEEEEeCCCCCCChhhhccc-eeeeecCCCHHHHHHHhhcC---
Q psy4285         381 DAMTN-----------DAQNALRRIIEK---FTTNVRFCIICNYLSKIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD---  442 (533)
Q Consensus       381 d~l~~-----------~~~~~Ll~~le~---~~~~~~~I~~~n~~~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~---  442 (533)
                      |.+..           ..++.|+..++.   ...++.+|++||.+..++++++||| ..+.+..|+.++..+++...   
T Consensus       120 d~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~~  199 (322)
T 3eie_A          120 DALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGD  199 (322)
T ss_dssp             GGGSCC------CCTHHHHHHHHHHHGGGGTSCCCEEEEEEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHHHHHHTT
T ss_pred             hhhhccCCCCcchHHHHHHHHHHHHhccccccCCceEEEEecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHHHHHhcc
Confidence            98854           346778888874   3567888999999999999999999 57888999999998888765   


Q ss_pred             ------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 ------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 ------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                            +.++..+..         .+.|+++.|+..-+..+
T Consensus       200 ~~~~~~~~~l~~la~---------~t~g~sg~di~~l~~~a  231 (322)
T 3eie_A          200 TPCVLTKEDYRTLGA---------MTEGYSGSDIAVVVKDA  231 (322)
T ss_dssp             CCCCCCHHHHHHHHH---------TTTTCCHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHH---------HcCCCCHHHHHHHHHHH
Confidence                  334444444         66799999887555443

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=99.67  E-value=1.1e-15  Score=144.34  Aligned_cols=152  Identities=22%  Similarity=0.347  Sum_probs=110.6

Q ss_pred             hchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCCCC
Q psy4285         289 ESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASDDR  349 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~~~  349 (533)
                      |++.....+..++..+..++ ++|+||||||||++++.+++.+.+....                  ...++.++.....
T Consensus        27 g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  106 (250)
T 1njg_A           27 GQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRT  106 (250)
T ss_dssp             SCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHTTCCSSEEEEETTCGG
T ss_pred             CcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhccCCcceEEecCcccc
Confidence            44555555656666555555 8999999999999999999987543210                  0122334433323


Q ss_pred             chhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecC
Q psy4285         350 GIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGP  429 (533)
Q Consensus       350 ~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~  429 (533)
                      ....++..+.......  ...++.+|||||+|.++...++.|++.+++.+.++.+|++||....+++++.+|+..+.+.+
T Consensus       107 ~~~~~~~~~~~~~~~~--~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~~~l~~r~~~i~l~~  184 (250)
T 1njg_A          107 KVEDTRDLLDNVQYAP--ARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKA  184 (250)
T ss_dssp             GHHHHHHHHHSCCCSC--SSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCC
T ss_pred             cHHHHHHHHHHhhhch--hcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCCHHHHHHhhhccCCC
Confidence            3333444333221111  12457899999999999999999999999888889999999999999999999999999999


Q ss_pred             CCHHHHHHHhhcC
Q psy4285         430 LDSSLIMSRLDYD  442 (533)
Q Consensus       430 ~~~~~~~~~l~~~  442 (533)
                      ++.+++.+++.+.
T Consensus       185 l~~~e~~~~l~~~  197 (250)
T 1njg_A          185 LDVEQIRHQLEHI  197 (250)
T ss_dssp             CCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH
Confidence            9999998888754

>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=99.65  E-value=1.6e-15  Score=156.14  Aligned_cols=152  Identities=18%  Similarity=0.212  Sum_probs=109.6

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc------hhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG------IGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .++||+||||||||++|+++|+.+.     +..++.+++++..+      ...++..+.....      ..++||||||+
T Consensus       168 ~~vLL~GppGtGKT~lA~aia~~~~-----~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~------~~~~vl~iDEi  236 (444)
T 2zan_A          168 RGILLFGPPGTGKSYLAKAVATEAN-----NSTFFSISSSDLVSKWLGESEKLVKNLFQLARE------NKPSIIFIDEI  236 (444)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHCC-----SSEEEEECCC---------CCCTHHHHHHHHHH------SCSEEEEESCT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHcC-----CCCEEEEeHHHHHhhhcchHHHHHHHHHHHHHH------cCCeEEEEech
Confidence            3599999999999999999999872     34566777655321      2234444333221      35689999999


Q ss_pred             CCCC-----------HHHHHHHHHHHHh---cCCCcEEEEEeCCCCCCChhhhccce-eeeecCCCHHHHHHHhhcC---
Q psy4285         381 DAMT-----------NDAQNALRRIIEK---FTTNVRFCIICNYLSKIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD---  442 (533)
Q Consensus       381 d~l~-----------~~~~~~Ll~~le~---~~~~~~~I~~~n~~~~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~---  442 (533)
                      |.+.           ....+.|+..++.   .+.++.||++||.+..++++++|||. .+.++.|+.++...++...   
T Consensus       237 d~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~  316 (444)
T 2zan_A          237 DSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGS  316 (444)
T ss_dssp             TTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCSSCEEEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTT
T ss_pred             HhhccCCCCccccHHHHHHHHHHHHHhCcccCCCCEEEEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhc
Confidence            9983           2456777777765   35678999999999999999999995 7888888888888877664   


Q ss_pred             ------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q psy4285         443 ------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLV  478 (533)
Q Consensus       443 ------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~  478 (533)
                            +.++..+..         .+.|+++.|+..-+..++
T Consensus       317 ~~~~l~~~~l~~la~---------~t~G~sgadl~~l~~~a~  349 (444)
T 2zan_A          317 TQNSLTEADFQELGR---------KTDGYSGADISIIVRDAL  349 (444)
T ss_dssp             SCEECCHHHHHHHHH---------HTTTCCHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHH---------HcCCCCHHHHHHHHHHHH
Confidence                  334444444         678999999877666554

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

Probab=99.64  E-value=1.1e-15  Score=148.49  Aligned_cols=150  Identities=23%  Similarity=0.305  Sum_probs=105.4

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc------hhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG------IGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .+++|+||||||||++|+++++.+      +..++.+++++..+      ...++..+.....      ..++||||||+
T Consensus        52 ~~~ll~G~~GtGKT~la~~la~~~------~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~vl~iDEi  119 (285)
T 3h4m_A           52 KGILLYGPPGTGKTLLAKAVATET------NATFIRVVGSELVKKFIGEGASLVKDIFKLAKE------KAPSIIFIDEI  119 (285)
T ss_dssp             SEEEEESSSSSSHHHHHHHHHHHT------TCEEEEEEGGGGCCCSTTHHHHHHHHHHHHHHH------TCSEEEEEETT
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHh------CCCEEEEehHHHHHhccchHHHHHHHHHHHHHH------cCCeEEEEECH
Confidence            459999999999999999999987      55666666544321      1222222222211      34679999999


Q ss_pred             CCC-----------CHHHHHHHHHHHHh-----cCCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhc
Q psy4285         381 DAM-----------TNDAQNALRRIIEK-----FTTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       381 d~l-----------~~~~~~~Ll~~le~-----~~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~  441 (533)
                      |.+           ....+..+..+++.     ...++.+|++||.+..+++++++  ||. .+.+++|+.++..+++..
T Consensus       120 d~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~  199 (285)
T 3h4m_A          120 DAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKI  199 (285)
T ss_dssp             HHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSSSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHH
T ss_pred             HHhcccCccccCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHH
Confidence            987           44556666666653     34578899999999999999999  884 899999999999988876


Q ss_pred             C--------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         442 D--------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       442 ~--------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                      .        +.++..+..         ...|+++.++..-+..+
T Consensus       200 ~~~~~~~~~~~~~~~l~~---------~~~g~~~~~i~~l~~~a  234 (285)
T 3h4m_A          200 HTRKMNLAEDVNLEEIAK---------MTEGCVGAELKAICTEA  234 (285)
T ss_dssp             HHTTSCBCTTCCHHHHHH---------HCTTCCHHHHHHHHHHH
T ss_pred             HHhcCCCCCcCCHHHHHH---------HcCCCCHHHHHHHHHHH
Confidence            5        112333333         56678887776654443

>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=99.63  E-value=1.5e-15  Score=148.52  Aligned_cols=150  Identities=21%  Similarity=0.254  Sum_probs=106.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      +++|+||||||||++|+++++.+      +..++.+++++.      .....++..+.....      ..++++||||+|
T Consensus        51 ~vLL~Gp~GtGKT~la~ala~~~------~~~~i~v~~~~l~~~~~g~~~~~~~~~f~~a~~------~~p~il~iDEid  118 (301)
T 3cf0_A           51 GVLFYGPPGCGKTLLAKAIANEC------QANFISIKGPELLTMWFGESEANVREIFDKARQ------AAPCVLFFDELD  118 (301)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHT------TCEEEEECHHHHHHHHHTTCTTHHHHHHHHHHH------TCSEEEEECSTT
T ss_pred             eEEEECCCCcCHHHHHHHHHHHh------CCCEEEEEhHHHHhhhcCchHHHHHHHHHHHHh------cCCeEEEEEChH
Confidence            59999999999999999999987      556677765432      122233333332221      246899999999


Q ss_pred             CCCHH--------------HHHHHHHHHHh--cCCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhcC
Q psy4285         382 AMTND--------------AQNALRRIIEK--FTTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       382 ~l~~~--------------~~~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+...              .++.|++.++.  ...++.+|++||.++.+++++++  || ..+.+++|+.++..+++...
T Consensus       119 ~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~  198 (301)
T 3cf0_A          119 SIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKAN  198 (301)
T ss_dssp             HHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCTTSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHH
T ss_pred             HHhhccCCCcCCcchHHHHHHHHHHHHhhcccCCCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHH
Confidence            87654              35778888874  34578999999999999999998  99 47888999998888877654


Q ss_pred             --------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q psy4285         443 --------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLV  478 (533)
Q Consensus       443 --------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~  478 (533)
                              +.++..+.       .  .+.|+++.|+..-+.+++
T Consensus       199 l~~~~~~~~~~~~~la-------~--~~~g~sg~dl~~l~~~a~  233 (301)
T 3cf0_A          199 LRKSPVAKDVDLEFLA-------K--MTNGFSGADLTEICQRAC  233 (301)
T ss_dssp             HTTSCBCSSCCHHHHH-------H--TCSSCCHHHHHHHHHHHH
T ss_pred             HccCCCCccchHHHHH-------H--HcCCCCHHHHHHHHHHHH
Confidence                    11122222       2  467888888776655544

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

Probab=99.63  E-value=5.3e-15  Score=150.00  Aligned_cols=148  Identities=18%  Similarity=0.210  Sum_probs=106.7

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc------hhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG------IGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .++||+||||||||++|+++++.+      +..++.+++++..+      ...++..+.....      ..++||||||+
T Consensus       149 ~~vLL~GppGtGKT~la~aia~~~------~~~~~~v~~~~l~~~~~g~~~~~~~~~~~~a~~------~~~~il~iDEi  216 (389)
T 3vfd_A          149 RGLLLFGPPGNGKTMLAKAVAAES------NATFFNISAASLTSKYVGEGEKLVRALFAVARE------LQPSIIFIDQV  216 (389)
T ss_dssp             SEEEEESSTTSCHHHHHHHHHHHT------TCEEEEECSCCC-------CHHHHHHHHHHHHH------SSSEEEEEETG
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhh------cCcEEEeeHHHhhccccchHHHHHHHHHHHHHh------cCCeEEEEECc
Confidence            469999999999999999999987      67788888876433      2223333222221      24579999999


Q ss_pred             CCCC-----------HHHHHHHHHHHHhc----CCCcEEEEEeCCCCCCChhhhccce-eeeecCCCHHHHHHHhhcC--
Q psy4285         381 DAMT-----------NDAQNALRRIIEKF----TTNVRFCIICNYLSKIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD--  442 (533)
Q Consensus       381 d~l~-----------~~~~~~Ll~~le~~----~~~~~~I~~~n~~~~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~--  442 (533)
                      |.+.           ...++.|+..++..    +.++++|++||.+..+++++++||. .+.|..|+.++...++..+  
T Consensus       217 d~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~  296 (389)
T 3vfd_A          217 DSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLC  296 (389)
T ss_dssp             GGGC--------CTHHHHHHHHHHHHHHHC-----CEEEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHT
T ss_pred             hhhcccCCCccchHHHHHHHHHHHHhhcccccCCCCEEEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHH
Confidence            9883           34566778877743    4568899999999999999999995 7899999999998888754  


Q ss_pred             -------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285         443 -------DISFFNIIIWYIKIQEIKIEKGLALTDILTEIS  475 (533)
Q Consensus       443 -------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~  475 (533)
                             +.++..+..         ...|++..++..-+.
T Consensus       297 ~~~~~l~~~~~~~la~---------~~~g~~~~~l~~L~~  327 (389)
T 3vfd_A          297 KQGSPLTQKELAQLAR---------MTDGYSGSDLTALAK  327 (389)
T ss_dssp             TSCCCSCHHHHHHHHH---------HTTTCCHHHHHHHHH
T ss_pred             hcCCCCCHHHHHHHHH---------HcCCCCHHHHHHHHH
Confidence                   333444333         567888877755443

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

Probab=99.63  E-value=3e-15  Score=147.04  Aligned_cols=127  Identities=20%  Similarity=0.241  Sum_probs=96.6

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHcccccc-CcceEEecCCCCCc------hhHHHHHHHHHHhcccCCCCCcEEEEEeC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQF-NAMVLELNASDDRG------IGIVRDQIFQFASTKTMHKSSYKLIILDE  379 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~-~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~vliiDE  379 (533)
                      .+++|+||||||||++|+++++.+...... ...++.+++++..+      .......+..   .      .+++|||||
T Consensus        68 ~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~~~~~~~~---~------~~~vl~iDE  138 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEVLKR---A------MGGVLFIDE  138 (309)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGGGTCCSSTTCHHHHHHHHHHH---H------TTSEEEEET
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHHHhhhhcccccHHHHHHHHHh---c------CCCEEEEEC
Confidence            359999999999999999999998654321 23566776654322      1122222221   1      346999999


Q ss_pred             CCCC---------CHHHHHHHHHHHHhcCCCcEEEEEeCCCC-----CCChhhhccc-eeeeecCCCHHHHHHHhhcC
Q psy4285         380 ADAM---------TNDAQNALRRIIEKFTTNVRFCIICNYLS-----KIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       380 ~d~l---------~~~~~~~Ll~~le~~~~~~~~I~~~n~~~-----~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +|.+         ....++.|++.+++.+.++.+|++||...     .++|++++|| ..+.|++|+.+++..++.+.
T Consensus       139 id~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~~~~~~~~~il~~~  216 (309)
T 3syl_A          139 AYYLYRPDNERDYGQEAIEILLQVMENNRDDLVVILAGYADRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHM  216 (309)
T ss_dssp             GGGSCCCC---CCTHHHHHHHHHHHHHCTTTCEEEEEECHHHHHHHHHHSTTHHHHEEEEEEECCCCHHHHHHHHHHH
T ss_pred             hhhhccCCCcccccHHHHHHHHHHHhcCCCCEEEEEeCChHHHHHHHhhCHHHHHhCCeEEEcCCcCHHHHHHHHHHH
Confidence            9987         78889999999999888899999997543     3579999999 89999999999999888665

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

Probab=99.63  E-value=6.1e-15  Score=146.83  Aligned_cols=123  Identities=20%  Similarity=0.256  Sum_probs=100.8

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN  385 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~  385 (533)
                      .++++|+||||||||++|+++++.+      +..++.++++.......+...+..        ...+.+|||||++.+..
T Consensus        55 ~~~vll~G~~GtGKT~la~~ia~~~------~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~vl~lDEi~~l~~  120 (338)
T 3pfi_A           55 LDHILFSGPAGLGKTTLANIISYEM------SANIKTTAAPMIEKSGDLAAILTN--------LSEGDILFIDEIHRLSP  120 (338)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHT------TCCEEEEEGGGCCSHHHHHHHHHT--------CCTTCEEEEETGGGCCH
T ss_pred             CCeEEEECcCCCCHHHHHHHHHHHh------CCCeEEecchhccchhHHHHHHHh--------ccCCCEEEEechhhcCH
Confidence            3469999999999999999999987      556777777665554444443322        14568999999999999


Q ss_pred             HHHHHHHHHHHhcC------------------CCcEEEEEeCCCCCCChhhhccc-eeeeecCCCHHHHHHHhhcC
Q psy4285         386 DAQNALRRIIEKFT------------------TNVRFCIICNYLSKIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       386 ~~~~~Ll~~le~~~------------------~~~~~I~~~n~~~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..++.|++.+++..                  +.+++|++||....+++++++|| ..+.|.+|+.+++..++.+.
T Consensus       121 ~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~  196 (338)
T 3pfi_A          121 AIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRAGMLSNPLRDRFGMQFRLEFYKDSELALILQKA  196 (338)
T ss_dssp             HHHHHHHHHHHTSCC---------CCCCCCCCCCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccchhhcccCccccceecCCCCeEEEEeCCCccccCHHHHhhcCEEeeCCCcCHHHHHHHHHHH
Confidence            99999999998742                  13789999999999999999999 79999999999999888765

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

Probab=99.62  E-value=9.1e-15  Score=142.80  Aligned_cols=148  Identities=20%  Similarity=0.216  Sum_probs=104.7

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc------hhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG------IGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .+++|+||||||||++|+++++.+      +..++.+++++..+      ....+..+.....      ..+++|||||+
T Consensus        55 ~~vll~Gp~GtGKT~la~~la~~~------~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~------~~~~vl~iDEi  122 (297)
T 3b9p_A           55 KGLLLFGPPGNGKTLLARAVATEC------SATFLNISAASLTSKYVGDGEKLVRALFAVARH------MQPSIIFIDEV  122 (297)
T ss_dssp             SEEEEESSSSSCHHHHHHHHHHHT------TCEEEEEESTTTSSSSCSCHHHHHHHHHHHHHH------TCSEEEEEETG
T ss_pred             CeEEEECcCCCCHHHHHHHHHHHh------CCCeEEeeHHHHhhcccchHHHHHHHHHHHHHH------cCCcEEEeccH
Confidence            359999999999999999999987      55677777665322      2223333322211      35689999999


Q ss_pred             CCCC-----------HHHHHHHHHHHHhcC-----CCcEEEEEeCCCCCCChhhhccc-eeeeecCCCHHHHHHHhhcC-
Q psy4285         381 DAMT-----------NDAQNALRRIIEKFT-----TNVRFCIICNYLSKIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD-  442 (533)
Q Consensus       381 d~l~-----------~~~~~~Ll~~le~~~-----~~~~~I~~~n~~~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~-  442 (533)
                      |.+.           ...++.|+..++..+     .++.+|++||.+..+++++++|| ..+.++.|+.++...++... 
T Consensus       123 d~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~~~l~~~l~~R~~~~i~~~~p~~~~r~~il~~~~  202 (297)
T 3b9p_A          123 DSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALRRFTKRVYVSLPDEQTRELLLNRLL  202 (297)
T ss_dssp             GGTSBCC-----CCSHHHHHHHHHHHHHCC------CEEEEEEESCGGGBCHHHHHHCCEEEECCCCCHHHHHHHHHHHH
T ss_pred             HHhccccccCcchHHHHHHHHHHHHHhcccccCCCCcEEEEeecCChhhCCHHHHhhCCeEEEeCCcCHHHHHHHHHHHH
Confidence            9883           345677888888754     35789999999999999999999 57778888888877776553 


Q ss_pred             --------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285         443 --------DISFFNIIIWYIKIQEIKIEKGLALTDILTEIS  475 (533)
Q Consensus       443 --------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~  475 (533)
                              +..+..+..         .+.|++..++..-+.
T Consensus       203 ~~~~~~~~~~~~~~la~---------~~~g~~~~~l~~l~~  234 (297)
T 3b9p_A          203 QKQGSPLDTEALRRLAK---------ITDGYSGSDLTALAK  234 (297)
T ss_dssp             GGGSCCSCHHHHHHHHH---------HTTTCCHHHHHHHHH
T ss_pred             HhcCCCCCHHHHHHHHH---------HcCCCCHHHHHHHHH
Confidence                    223333333         567888887755443

>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=99.61  E-value=9.6e-15  Score=139.81  Aligned_cols=153  Identities=18%  Similarity=0.184  Sum_probs=98.8

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc------hhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG------IGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .+++|+||||||||++|+++++.+      +..++.+++++...      ...++..+.....      ..+.+|||||+
T Consensus        40 ~~vll~G~~GtGKT~la~~la~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~------~~~~vl~iDei  107 (262)
T 2qz4_A           40 KGALLLGPPGCGKTLLAKAVATEA------QVPFLAMAGAEFVEVIGGLGAARVRSLFKEARA------RAPCIVYIDEI  107 (262)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHH------TCCEEEEETTTTSSSSTTHHHHHHHHHHHHHHH------TCSEEEEEECC
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh------CCCEEEechHHHHhhccChhHHHHHHHHHHHHh------cCCeEEEEeCc
Confidence            459999999999999999999987      55677777665322      1223332222211      24689999999


Q ss_pred             CCCCH------------HHHHH---HHHHHHh--cCCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhh
Q psy4285         381 DAMTN------------DAQNA---LRRIIEK--FTTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       381 d~l~~------------~~~~~---Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~  440 (533)
                      |.+..            ..+..   ++..++.  .+.++.+|++||.+..+++++++  || ..+.+.+|+.++..+++.
T Consensus       108 d~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~  187 (262)
T 2qz4_A          108 DAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFE  187 (262)
T ss_dssp             -------------------CHHHHHHHHHHHTCCTTCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHH
T ss_pred             chhhccccccccCccchhHHHHHHHHHHHhhCcCCCCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHH
Confidence            99832            22333   4444443  34578899999999999999999  99 588899999999888877


Q ss_pred             cC--------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q psy4285         441 YD--------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLV  478 (533)
Q Consensus       441 ~~--------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~  478 (533)
                      +.        +.+.  .   ...+..  ...|+++.++..-+..++
T Consensus       188 ~~~~~~~~~~~~~~--~---~~~l~~--~~~g~~~~~l~~l~~~a~  226 (262)
T 2qz4_A          188 QHLKSLKLTQSSTF--Y---SQRLAE--LTPGFSGADIANICNEAA  226 (262)
T ss_dssp             HHHHHTTCCBTHHH--H---HHHHHH--TCTTCCHHHHHHHHHHHH
T ss_pred             HHHHhCCCCcchhh--H---HHHHHH--HCCCCCHHHHHHHHHHHH
Confidence            65        1111  0   011111  456788887766665544

>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=99.61  E-value=5.8e-15  Score=147.75  Aligned_cols=150  Identities=18%  Similarity=0.158  Sum_probs=107.1

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc------hhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG------IGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .+++|+||||||||++|+++|+.+      +..++.+++++...      ...++..+....      ...+.+|||||+
T Consensus       118 ~~vLl~GppGtGKT~la~aia~~~------~~~~~~i~~~~l~~~~~g~~~~~~~~~~~~a~------~~~~~vl~iDEi  185 (357)
T 3d8b_A          118 KGILLFGPPGTGKTLIGKCIASQS------GATFFSISASSLTSKWVGEGEKMVRALFAVAR------CQQPAVIFIDEI  185 (357)
T ss_dssp             SEEEEESSTTSSHHHHHHHHHHHT------TCEEEEEEGGGGCCSSTTHHHHHHHHHHHHHH------HTCSEEEEEETH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHc------CCeEEEEehHHhhccccchHHHHHHHHHHHHH------hcCCeEEEEeCc
Confidence            359999999999999999999987      56677777665322      122232222221      135689999999


Q ss_pred             CCCCH-----------HHHHHHHHHHHh----cCCCcEEEEEeCCCCCCChhhhccce-eeeecCCCHHHHHHHhhcC--
Q psy4285         381 DAMTN-----------DAQNALRRIIEK----FTTNVRFCIICNYLSKIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD--  442 (533)
Q Consensus       381 d~l~~-----------~~~~~Ll~~le~----~~~~~~~I~~~n~~~~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~--  442 (533)
                      |.+..           ..++.|+..++.    ...++.+|++||.+..+++++++||. .+.+..|+.++..+++...  
T Consensus       186 d~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~  265 (357)
T 3d8b_A          186 DSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMS  265 (357)
T ss_dssp             HHHTBC------CHHHHHHHHHHHHHHC----CCCCEEEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHH
T ss_pred             hhhhccCCCCcchHHHHHHHHHHHHHhcccccCCCCEEEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHh
Confidence            88732           345677777764    24578899999999999999999996 7788889988888877654  


Q ss_pred             -------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 -------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 -------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                             +.++..+..         .+.|+++.++..-+...
T Consensus       266 ~~~~~l~~~~l~~la~---------~t~G~s~~dl~~l~~~a  298 (357)
T 3d8b_A          266 KEQCCLSEEEIEQIVQ---------QSDAFSGADMTQLCREA  298 (357)
T ss_dssp             TSCBCCCHHHHHHHHH---------HTTTCCHHHHHHHHHHH
T ss_pred             hcCCCccHHHHHHHHH---------HcCCCCHHHHHHHHHHH
Confidence                   333444433         56789988876655443

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

Probab=99.60  E-value=9.8e-15  Score=157.77  Aligned_cols=186  Identities=22%  Similarity=0.287  Sum_probs=126.9

Q ss_pred             ccccccCCCC--HHHHHHHHHHHhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEe
Q psy4285         266 TVYNSVGYPT--KTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLEL  343 (533)
Q Consensus       266 ~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~  343 (533)
                      .-|.+++...  ...+.+.+.+.+. +.+....+    ....+.++|||||||||||++|+++|+++      +..++.+
T Consensus       201 v~~~dIgGl~~~~~~l~e~v~~pl~-~p~~f~~~----g~~~p~GILL~GPPGTGKT~LAraiA~el------g~~~~~v  269 (806)
T 3cf2_A          201 VGYDDIGGCRKQLAQIKEMVELPLR-HPALFKAI----GVKPPRGILLYGPPGTGKTLIARAVANET------GAFFFLI  269 (806)
T ss_dssp             CCGGGCCSCCTTHHHHHHHHHHHHH-CCGGGTSC----CCCCCCEEEEECCTTSCHHHHHHHHHTTT------TCEEEEE
T ss_pred             CChhhhcCHHHHHHHHHHHHHHHcc-CHHHHhhc----CCCCCCeEEEECCCCCCHHHHHHHHHHHh------CCeEEEE
Confidence            4566666543  3455555544332 22222221    11122359999999999999999999987      6777888


Q ss_pred             cCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH-----------HHHHHHHHHHHhc--CCCcEE
Q psy4285         344 NASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN-----------DAQNALRRIIEKF--TTNVRF  404 (533)
Q Consensus       344 ~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~Ll~~le~~--~~~~~~  404 (533)
                      ++++.      .+...++..+....      ...++||||||+|.+.+           ...+.|+..|+..  ..++.+
T Consensus       270 ~~~~l~sk~~gese~~lr~lF~~A~------~~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~V  343 (806)
T 3cf2_A          270 NGPEIMSKLAGESESNLRKAFEEAE------KNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIV  343 (806)
T ss_dssp             EHHHHHSSCTTHHHHHHHHHHHHHT------TSCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEE
T ss_pred             EhHHhhcccchHHHHHHHHHHHHHH------HcCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCEEE
Confidence            76542      22334444433322      13578999999999853           2356677788753  345788


Q ss_pred             EEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhcC--------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHH
Q psy4285         405 CIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDYD--------DISFFNIIIWYIKIQEIKIEKGLALTDILTE  473 (533)
Q Consensus       405 I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~--------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~  473 (533)
                      |++||.++.+|+++++  || ..+.+..|+.++..+++...        ..++..+..         .+.|+++.|+..-
T Consensus       344 IaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl~~lA~---------~T~GfsgaDL~~L  414 (806)
T 3cf2_A          344 MAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVAN---------ETHGHVGADLAAL  414 (806)
T ss_dssp             EEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTCCHHHHHH---------HCCSCCHHHHHHH
T ss_pred             EEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHH---------hcCCCCHHHHHHH
Confidence            9999999999999999  89 47899999999999888766        234555555         7889999998765


Q ss_pred             HHHH
Q psy4285         474 ISLL  477 (533)
Q Consensus       474 ~~~~  477 (533)
                      +.++
T Consensus       415 v~eA  418 (806)
T 3cf2_A          415 CSEA  418 (806)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5444

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

Probab=99.59  E-value=7.1e-15  Score=148.13  Aligned_cols=70  Identities=17%  Similarity=0.167  Sum_probs=60.1

Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeC------------CCCCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         372 YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN------------YLSKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       372 ~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n------------~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      ++||||||+|.++.+.++.|++.++++...+ ++++++            .+..++++++|||..+.|++|+.+++.+++
T Consensus       190 ~~vl~IDEi~~l~~~~~~~L~~~le~~~~~~-~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~~i~~~~~~~~e~~~il  268 (368)
T 3uk6_A          190 PGVLFIDEVHMLDIESFSFLNRALESDMAPV-LIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQIL  268 (368)
T ss_dssp             BCEEEEESGGGSBHHHHHHHHHHTTCTTCCE-EEEEESCSEEECBTSSCEEETTCCHHHHTTEEEEEECCCCHHHHHHHH
T ss_pred             CceEEEhhccccChHHHHHHHHHhhCcCCCe-eeeecccceeeeeccCCCCcccCCHHHHhhccEEEecCCCHHHHHHHH
Confidence            4699999999999999999999999876554 444554            366899999999999999999999999999


Q ss_pred             hcC
Q psy4285         440 DYD  442 (533)
Q Consensus       440 ~~~  442 (533)
                      .+.
T Consensus       269 ~~~  271 (368)
T 3uk6_A          269 RIR  271 (368)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            854

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.58  E-value=5.8e-15  Score=147.97  Aligned_cols=165  Identities=24%  Similarity=0.355  Sum_probs=127.5

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCC-HHHHHHHHHhcCCCHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVT-PDGKKAIIDLSDGDMRKVLNIL   79 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-~~~~~~~~~~~~g~~r~a~~~l   79 (533)
                      ||+|+.+++||++||.+.+++|+|+|||+.++|++++.+++.++|++++.++++.++ +++++.+++.++||+|+|++.|
T Consensus       158 le~~~~~~~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~i~~~~~G~~r~a~~~l  237 (354)
T 1sxj_E          158 MEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLML  237 (354)
T ss_dssp             HHHSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHhhcCCCEEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCCHHHHHHHH
Confidence            477889999999999999999999999999999999999999999999999999999 9999999999999999999999


Q ss_pred             HHHHHhCCCCcchh----------hHHhhhhhhccccch-------hHHHHHh----chHHHHhhc--------CCChhh
Q psy4285          80 QSAATAHADEVNED----------TIFTLLVSRVEKYRP-------STLDELV----SHQDIISTI--------EIPESM  130 (533)
Q Consensus        80 ~~~~~~~~~~i~~~----------~i~~~~~~~~ek~~~-------~~l~~ll----s~~~~l~~l--------~~~~~~  130 (533)
                      +.++......|+.+          .+.+++.....+-.+       +.+++++    +..+++..+        +++...
T Consensus       238 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~l~~l~~~g~~~~~i~~~l~~~~~~~~~~~~~~  317 (354)
T 1sxj_E          238 ESMALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIILKELTFSLLDVETLNTTN  317 (354)
T ss_dssp             THHHHTTTTEECSSCCCCCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHTTTTCTTSCHHH
T ss_pred             HHHHHhCCCCcCcCcCCCCccHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCCHHH
Confidence            99987543234432          222222211111111       1233432    222333222        256667


Q ss_pred             HHHHHhhccCccccccCCCChhhHHHHHHHHHhcc
Q psy4285         131 LVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSA  165 (533)
Q Consensus       131 ~~~~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~~  165 (533)
                      +..++..++++++++..|.++.++++++++.++..
T Consensus       318 l~~~~~~l~~~d~~l~~g~~~~~~le~~~~~~~~~  352 (354)
T 1sxj_E          318 KSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCC  352 (354)
T ss_dssp             HHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHH
Confidence            78888889999999999999999999999998753

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

Probab=99.58  E-value=3.2e-15  Score=147.04  Aligned_cols=127  Identities=20%  Similarity=0.342  Sum_probs=94.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH---------------HHHHhcccCCCCCc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI---------------FQFASTKTMHKSSY  372 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~~~~~~  372 (533)
                      +++|+||||||||++|+++++.+.+.   +..++.++++...........+               .....     ...+
T Consensus        49 ~~ll~G~~GtGKt~la~~la~~~~~~---~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~~~-----~~~~  120 (311)
T 4fcw_A           49 SFLFLGPTGVGKTELAKTLAATLFDT---EEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVR-----RRPY  120 (311)
T ss_dssp             EEEEESCSSSSHHHHHHHHHHHHHSC---GGGEEEEEGGGCCSTTHHHHHHCCCTTSTTTTTCCHHHHHHH-----HCSS
T ss_pred             EEEEECCCCcCHHHHHHHHHHHHcCC---CcceEEeecccccccccHHHhcCCCCccccccccchHHHHHH-----hCCC
Confidence            59999999999999999999998554   2345666654433222222211               11111     1245


Q ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHhcC-----------CCcEEEEEeCC--------------------------CCCCC
Q psy4285         373 KLIILDEADAMTNDAQNALRRIIEKFT-----------TNVRFCIICNY--------------------------LSKIP  415 (533)
Q Consensus       373 ~vliiDE~d~l~~~~~~~Ll~~le~~~-----------~~~~~I~~~n~--------------------------~~~l~  415 (533)
                      +++||||+|.++.+.++.|++.|++..           .++.+|+|||.                          ...++
T Consensus       121 ~vl~lDEi~~l~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~  200 (311)
T 4fcw_A          121 SVILFDAIEKAHPDVFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFR  200 (311)
T ss_dssp             EEEEEETGGGSCHHHHHHHHHHHHHSEEECTTSCEEECTTEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSC
T ss_pred             eEEEEeChhhcCHHHHHHHHHHHhcCEEEcCCCCEEECCCcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCC
Confidence            799999999999999999999999753           36669999998                          44689


Q ss_pred             hhhhccc-eeeeecCCCHHHHHHHhhcC
Q psy4285         416 PAIQSRC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       416 ~~l~sR~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +++.+|| ..+.|.||+.+++..++.+.
T Consensus       201 ~~l~~R~~~~~~~~p~~~~~~~~i~~~~  228 (311)
T 4fcw_A          201 PEFLNRLDEIVVFRPLTKEQIRQIVEIQ  228 (311)
T ss_dssp             HHHHTTCSEEEECCCCCHHHHHHHHHHH
T ss_pred             HHHHhcCCeEEEeCCCCHHHHHHHHHHH
Confidence            9999999 68889999988888777664

>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=99.58  E-value=4e-15  Score=146.17  Aligned_cols=160  Identities=21%  Similarity=0.223  Sum_probs=107.3

Q ss_pred             HHHHHHHHHHHhhhchhhhhhhcccccc--------------cCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceE
Q psy4285         276 KTEITNILRWLLNESMDLCYKINRFIDE--------------NELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVL  341 (533)
Q Consensus       276 ~~~~~~~l~~~~~~~~~~~~~l~~~~~~--------------~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~  341 (533)
                      +..+...+.....|++.....+...+..              ....+++|+||||||||++|+++++.+      +..++
T Consensus         6 ~~~l~~~l~~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l------~~~~~   79 (310)
T 1ofh_A            6 PREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA------NAPFI   79 (310)
T ss_dssp             HHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH------TCCEE
T ss_pred             HHHHHHHHhhhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHh------CCCEE
Confidence            4445555554455666666555544432              223469999999999999999999988      44566


Q ss_pred             EecCCCCCc--------hhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHH------------HHHHHHHHHhc---
Q psy4285         342 ELNASDDRG--------IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDA------------QNALRRIIEKF---  398 (533)
Q Consensus       342 ~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~------------~~~Ll~~le~~---  398 (533)
                      .++++....        ...+++.......... ....++||||||+|.+....            ++.|++.+++.   
T Consensus        80 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~  158 (310)
T 1ofh_A           80 KVEATKFTEVGYVGKEVDSIIRDLTDSAGGAID-AVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVS  158 (310)
T ss_dssp             EEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHH-HHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEE
T ss_pred             EEcchhcccCCccCccHHHHHHHHHHHhhHHHh-hccCCCEEEEEChhhcCccccccccchhHHHHHHHHHHHhcCCeEe
Confidence            666544221        1123332221100000 00136799999999997654            88999999863   


Q ss_pred             -------CCCcEEEEEe----CCCCCCChhhhccce-eeeecCCCHHHHHHHhhcC
Q psy4285         399 -------TTNVRFCIIC----NYLSKIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       399 -------~~~~~~I~~~----n~~~~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                             ..++.+|+++    +.+..+++++++||. .+.|++|+.+++..++.+.
T Consensus       159 ~~~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~R~~~~i~~~~~~~~~~~~il~~~  214 (310)
T 1ofh_A          159 TKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLPIRVELTALSAADFERILTEP  214 (310)
T ss_dssp             ETTEEEECTTCEEEEEECCSSSCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHSS
T ss_pred             cccccccCCcEEEEEcCCcccCCcccCCHHHHhhCCceEEcCCcCHHHHHHHHHhh
Confidence                   3467888885    456689999999995 6999999999999999864

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

Probab=99.57  E-value=3.6e-14  Score=140.31  Aligned_cols=123  Identities=20%  Similarity=0.256  Sum_probs=98.7

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTND  386 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~  386 (533)
                      .+++|+||||||||++|+++++.+      +..++.++++.......+.+.   +...    ...+.+|||||++.++..
T Consensus        39 ~~vll~G~~GtGKT~la~~i~~~~------~~~~~~~~~~~~~~~~~l~~~---l~~~----~~~~~~l~lDEi~~l~~~  105 (324)
T 1hqc_A           39 EHLLLFGPPGLGKTTLAHVIAHEL------GVNLRVTSGPAIEKPGDLAAI---LANS----LEEGDILFIDEIHRLSRQ  105 (324)
T ss_dssp             CCCEEECCTTCCCHHHHHHHHHHH------TCCEEEECTTTCCSHHHHHHH---HTTT----CCTTCEEEETTTTSCCHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHh------CCCEEEEeccccCChHHHHHH---HHHh----ccCCCEEEEECCcccccc
Confidence            469999999999999999999987      456667777665444333332   2210    135679999999999999


Q ss_pred             HHHHHHHHHHhcC------------------CCcEEEEEeCCCCCCChhhhccc-eeeeecCCCHHHHHHHhhcC
Q psy4285         387 AQNALRRIIEKFT------------------TNVRFCIICNYLSKIPPAIQSRC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       387 ~~~~Ll~~le~~~------------------~~~~~I~~~n~~~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .++.|++.+++..                  .++++|++||....+++++.+|| ..+.+.+|+.+++..++.+.
T Consensus       106 ~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~  180 (324)
T 1hqc_A          106 AEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRD  180 (324)
T ss_dssp             HHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEEEEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHhhhhHHhccccccccccccCCCCEEEEEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHHHHH
Confidence            9999999998742                  35789999999999999999999 59999999999998887764

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.57  E-value=1.2e-14  Score=140.99  Aligned_cols=155  Identities=8%  Similarity=0.084  Sum_probs=104.3

Q ss_pred             HhhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCCCchhH-HHH----
Q psy4285         286 LLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDDRGIGI-VRD----  356 (533)
Q Consensus       286 ~~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~~~~~~-~~~----  356 (533)
                      +......+...+...+..+.+++++|+||||||||++++.+++.+.....    ....++++|+........ +..    
T Consensus        25 Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I~~~  104 (318)
T 3te6_A           25 QVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFA  104 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHHHHH
Confidence            33344455566777777777788999999999999999999999854321    123567788765433211 111    


Q ss_pred             -------------HHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHH---hcCCCcEEEEEeCCCCC----CCh
Q psy4285         357 -------------QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIE---KFTTNVRFCIICNYLSK----IPP  416 (533)
Q Consensus       357 -------------~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le---~~~~~~~~I~~~n~~~~----l~~  416 (533)
                                   .+..+............|+++||+|.+.  .++.|+.+++   ....++.+|+++|..+.    +++
T Consensus       105 L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~--~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~~~~L~~  182 (318)
T 3te6_A          105 ISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLL--SEKILQYFEKWISSKNSKLSIICVGGHNVTIREQINI  182 (318)
T ss_dssp             HSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSC--CTHHHHHHHHHHHCSSCCEEEEEECCSSCCCHHHHHT
T ss_pred             hcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhh--cchHHHHHHhcccccCCcEEEEEEecCcccchhhcch
Confidence                         1111111110012456899999999998  5666666664   33456788889988753    566


Q ss_pred             hhhccc--eeeeecCCCHHHHHHHhhcC
Q psy4285         417 AIQSRC--TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       417 ~l~sR~--~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +++|||  ..+.|.||+.+++.+++.+.
T Consensus       183 ~v~SR~~~~~i~F~pYt~~el~~Il~~R  210 (318)
T 3te6_A          183 MPSLKAHFTEIKLNKVDKNELQQMIITR  210 (318)
T ss_dssp             CHHHHTTEEEEECCCCCHHHHHHHHHHH
T ss_pred             hhhccCCceEEEeCCCCHHHHHHHHHHH
Confidence            778998  57999999999999988876

>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=99.55  E-value=1.1e-14  Score=150.77  Aligned_cols=150  Identities=23%  Similarity=0.309  Sum_probs=108.5

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC----Cc--hhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD----RG--IGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~----~~--~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .++||+||||||||++|+++++.+      +..++.+++++.    .+  ...++..+.....      ..+++|||||+
T Consensus       239 ~~vLL~GppGtGKT~lAraia~~~------~~~fv~vn~~~l~~~~~g~~~~~~~~~f~~A~~------~~p~iLfLDEI  306 (489)
T 3hu3_A          239 RGILLYGPPGTGKTLIARAVANET------GAFFFLINGPEIMSKLAGESESNLRKAFEEAEK------NAPAIIFIDEL  306 (489)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHC------SSEEEEEEHHHHHTSCTTHHHHHHHHHHHHHHH------TCSEEEEEESH
T ss_pred             CcEEEECcCCCCHHHHHHHHHHHh------CCCEEEEEchHhhhhhcchhHHHHHHHHHHHHh------cCCcEEEecch
Confidence            359999999999999999999987      567777775432    11  2223333322211      34689999999


Q ss_pred             CCCCH-----------HHHHHHHHHHHh--cCCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC--
Q psy4285         381 DAMTN-----------DAQNALRRIIEK--FTTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD--  442 (533)
Q Consensus       381 d~l~~-----------~~~~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~--  442 (533)
                      |.+..           ..++.|++.|+.  ...++++|++||.+..+++++++  ||. .+.|.+|+.++..+++...  
T Consensus       307 d~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~  386 (489)
T 3hu3_A          307 DAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTK  386 (489)
T ss_dssp             HHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTT
T ss_pred             hhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHh
Confidence            77643           567889999985  34578899999999999999999  774 6899999999999888765  


Q ss_pred             ------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 ------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 ------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                            +.++..+..         .+.|+++.|+..-+..+
T Consensus       387 ~~~l~~~~~l~~la~---------~t~g~s~~dL~~L~~~A  418 (489)
T 3hu3_A          387 NMKLADDVDLEQVAN---------ETHGHVGADLAALCSEA  418 (489)
T ss_dssp             TSCBCTTCCHHHHHH---------TCTTCCHHHHHHHHHHH
T ss_pred             cCCCcchhhHHHHHH---------HccCCcHHHHHHHHHHH
Confidence                  222344333         56788888876554443

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.54  E-value=1.6e-14  Score=143.75  Aligned_cols=167  Identities=40%  Similarity=0.687  Sum_probs=129.9

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+.+++||++||++++++|+|+|||+.++|++++.+++.++|.++++++++.++++++..++..|+||+|+|++.|+
T Consensus       134 le~~~~~~~~il~~n~~~~i~~~i~sR~~~~~~~~l~~~~~~~~l~~~~~~~~~~i~~~~~~~i~~~s~G~~r~~~~~l~  213 (340)
T 1sxj_C          134 IERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQ  213 (340)
T ss_dssp             HHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTTCHHHHHHHTT
T ss_pred             HhcCCCCeEEEEEecCccccchhHHhhceeEeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            57899999999999999999999999999999999999999999999999899999999999999999999999999999


Q ss_pred             HHHHhCCC----CcchhhHHhhhhhh-----------ccccch----hHHHHHhc-----hHHHHh-------hcCCC-h
Q psy4285          81 SAATAHAD----EVNEDTIFTLLVSR-----------VEKYRP----STLDELVS-----HQDIIS-------TIEIP-E  128 (533)
Q Consensus        81 ~~~~~~~~----~i~~~~i~~~~~~~-----------~ek~~~----~~l~~lls-----~~~~l~-------~l~~~-~  128 (533)
                      .++.....    .|+.+.+.++++..           +.+-..    ..+++++.     ..+++.       .+.++ .
T Consensus       214 ~~~~~~~~~~~~~it~~~v~~~~~~~~~~~i~~l~~~i~~~~~~~al~~l~~l~~~~g~~~~~i~~~l~~~~~~~~~~~~  293 (340)
T 1sxj_C          214 SCKATLDNPDEDEISDDVIYECCGAPRPSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNE  293 (340)
T ss_dssp             TTTTTTCSSSCCCBCHHHHHHHTTCCCHHHHHHHHHHHHTSCHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTTSCCSSH
T ss_pred             HHHHhcCCcccccccHHHHHHHhCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCcH
Confidence            88654331    58887765543311           111111    11233321     122222       12344 6


Q ss_pred             hhHHHHHhhccCccccccCCCChhhHHHHHHHHHhcccc
Q psy4285         129 SMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD  167 (533)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~~~~  167 (533)
                      ..+..++..++++++++..|+++..+++.++..++....
T Consensus       294 ~~~~~~~~~l~~~~~~l~~g~~~~l~le~l~~~l~~~~~  332 (340)
T 1sxj_C          294 ETRVHLLTKLADIEYSISKGGNDQIQGSAVIGAIKASFE  332 (340)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhh
Confidence            677788888999999999999999999999999875443

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

Probab=99.54  E-value=7.3e-14  Score=133.29  Aligned_cols=124  Identities=27%  Similarity=0.298  Sum_probs=89.7

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .+++|+||||||||++|+++++.+      +.+++.+++++..      ....++..+....      ...+.+++|||+
T Consensus        46 ~~vll~G~~GtGKT~la~~la~~~------~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~a~------~~~~~il~iDei  113 (257)
T 1lv7_A           46 KGVLMVGPPGTGKTLLAKAIAGEA------KVPFFTISGSDFVEMFVGVGASRVRDMFEQAK------KAAPCIIFIDEI  113 (257)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH------TCCEEEECSCSSTTSCCCCCHHHHHHHHHHHH------TTCSEEEEETTH
T ss_pred             CeEEEECcCCCCHHHHHHHHHHHc------CCCEEEEeHHHHHHHhhhhhHHHHHHHHHHHH------HcCCeeehhhhh
Confidence            359999999999999999999987      4556777766532      2233443333321      134679999999


Q ss_pred             CCCCH--------------HHHHHHHHHHHhc--CCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhc
Q psy4285         381 DAMTN--------------DAQNALRRIIEKF--TTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       381 d~l~~--------------~~~~~Ll~~le~~--~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~  441 (533)
                      |.+..              ...+.++..++..  ..++.+|++||.++.+++++.+  || ..+.+.+|+.++..+++..
T Consensus       114 d~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~  193 (257)
T 1lv7_A          114 DAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKV  193 (257)
T ss_dssp             HHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHH
T ss_pred             hhhccCCCCCcCCCchHHHHHHHHHHHHhhCcccCCCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHH
Confidence            87642              3456677777643  4567899999999999999998  88 4778888888887776654


Q ss_pred             C
Q psy4285         442 D  442 (533)
Q Consensus       442 ~  442 (533)
                      .
T Consensus       194 ~  194 (257)
T 1lv7_A          194 H  194 (257)
T ss_dssp             H
T ss_pred             H
Confidence            3

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.53  E-value=4.6e-14  Score=148.21  Aligned_cols=128  Identities=28%  Similarity=0.390  Sum_probs=96.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC------------CCCCcEE
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM------------HKSSYKL  374 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~v  374 (533)
                      ++++|+||||||||++|+++++++      +..++.+++++......+...+.........            ....+.|
T Consensus        78 ~~lLL~GppGtGKTtla~~la~~l------~~~~i~in~s~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~v  151 (516)
T 1sxj_A           78 RAAMLYGPPGIGKTTAAHLVAQEL------GYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFV  151 (516)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHT------TCEEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc------CCCEEEEeCCCcchHHHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeE
Confidence            459999999999999999999998      6778899998877665554443322111100            1245789


Q ss_pred             EEEeCCCCCCHHHH---HHHHHHHHhcCCCcEEEEEeCCCC-CCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         375 IILDEADAMTNDAQ---NALRRIIEKFTTNVRFCIICNYLS-KIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       375 liiDE~d~l~~~~~---~~Ll~~le~~~~~~~~I~~~n~~~-~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      |||||+|.+....+   +.|++++++.  +..+|++||... ...+++.+||..+.|.+|+.+++.+++..+
T Consensus       152 liIDEid~l~~~~~~~l~~L~~~l~~~--~~~iIli~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i  221 (516)
T 1sxj_A          152 IIMDEVDGMSGGDRGGVGQLAQFCRKT--STPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTI  221 (516)
T ss_dssp             EEECSGGGCCTTSTTHHHHHHHHHHHC--SSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHH
T ss_pred             EEEECCCccchhhHHHHHHHHHHHHhc--CCCEEEEEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHH
Confidence            99999999976544   7888888864  456788887654 456789999999999999999999988765

>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=99.53  E-value=9.2e-14  Score=143.70  Aligned_cols=69  Identities=14%  Similarity=0.142  Sum_probs=62.5

Q ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC-------------CCCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         373 KLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY-------------LSKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       373 ~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~-------------~~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                      +|+||||+++|+.+++++|+++||+++.+ .||++||.             +..++|+++|||..+.|.+++.+++.++|
T Consensus       297 ~VliIDEa~~l~~~a~~aLlk~lEe~~~~-~~il~tn~~~~~i~~~~~~~~~~~l~~~i~sR~~~~~~~~~~~~e~~~iL  375 (456)
T 2c9o_A          297 GVLFVDEVHMLDIECFTYLHRALESSIAP-IVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQII  375 (456)
T ss_dssp             CEEEEESGGGCBHHHHHHHHHHTTSTTCC-EEEEEECCSEEECBTTSSCEEETTCCHHHHTTEEEEECCCCCHHHHHHHH
T ss_pred             eEEEEechhhcCHHHHHHHHHHhhccCCC-EEEEecCCccccccccccccccccCChhHHhhcceeeCCCCCHHHHHHHH
Confidence            69999999999999999999999998887 57777743             66899999999999999999999999999


Q ss_pred             hcC
Q psy4285         440 DYD  442 (533)
Q Consensus       440 ~~~  442 (533)
                      .+.
T Consensus       376 ~~~  378 (456)
T 2c9o_A          376 KIR  378 (456)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            865

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

Probab=99.52  E-value=3.1e-14  Score=138.35  Aligned_cols=126  Identities=16%  Similarity=0.161  Sum_probs=85.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .++|+||||||||++|+++|+.+      +..++.+++++..      ....+++.+........  ...++||+|||+|
T Consensus        38 ~lLl~GppGtGKT~la~aiA~~l------~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~--~~~~~vl~iDEiD  109 (293)
T 3t15_A           38 ILGIWGGKGQGKSFQCELVFRKM------GINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIR--KGNMCCLFINDLD  109 (293)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH------TCCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHHT--TSSCCCEEEECCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh------CCCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHHh--cCCCeEEEEechh
Confidence            48999999999999999999998      6667777754321      12233333333211101  2357899999999


Q ss_pred             CCCH-------------HHHHHHHHHHHh-------------cCCCcEEEEEeCCCCCCChhhhc--cceeeeecCCCHH
Q psy4285         382 AMTN-------------DAQNALRRIIEK-------------FTTNVRFCIICNYLSKIPPAIQS--RCTRFRFGPLDSS  433 (533)
Q Consensus       382 ~l~~-------------~~~~~Ll~~le~-------------~~~~~~~I~~~n~~~~l~~~l~s--R~~~i~~~~~~~~  433 (533)
                      .+.+             ..++.|++.|+.             ...++.+|+|||.++.+++++++  ||....+ .|+.+
T Consensus       110 ~~~~~~~~~~~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~R~d~~i~-~P~~~  188 (293)
T 3t15_A          110 AGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYW-APTRE  188 (293)
T ss_dssp             --------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCCC--CHHHHHHHEEEEEE-CCCHH
T ss_pred             hhcCCCCCCccccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcccCCHHHhCCCCCceeEe-CcCHH
Confidence            8865             234788888862             23568999999999999999997  7865555 45888


Q ss_pred             HHHHHhhcC
Q psy4285         434 LIMSRLDYD  442 (533)
Q Consensus       434 ~~~~~l~~~  442 (533)
                      +..+++...
T Consensus       189 ~r~~Il~~~  197 (293)
T 3t15_A          189 DRIGVCTGI  197 (293)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            888888755

>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=99.52  E-value=4.1e-14  Score=142.89  Aligned_cols=163  Identities=17%  Similarity=0.207  Sum_probs=106.6

Q ss_pred             cCCCCHHHHHHHHHHHhhhchhhhhhhccccc----c--------------------------cCCCceeEeCCCCCChH
Q psy4285         271 VGYPTKTEITNILRWLLNESMDLCYKINRFID----E--------------------------NELPHLLFYGPPGTGKT  320 (533)
Q Consensus       271 ~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~----~--------------------------~~~~~~ll~GppGtGKT  320 (533)
                      ...+....+...+.....|++.+.+.+..++.    .                          ...++++|+||||||||
T Consensus         7 ~~~~~~~~l~~~L~~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT   86 (376)
T 1um8_A            7 SYIPAPKELKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKT   86 (376)
T ss_dssp             SCCCCHHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHH
T ss_pred             cCCCCHHHHHHHHhhHccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHH
Confidence            34556666766666666677776666655441    0                          12346999999999999


Q ss_pred             HHHHHHHHHHccccccCcceEEecCCCCCc--------hhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHH------
Q psy4285         321 TTILACARKLYTKAQFNAMVLELNASDDRG--------IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTND------  386 (533)
Q Consensus       321 ~la~~la~~l~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~------  386 (533)
                      ++|+++|+.+      +..++.++++....        ...+...+......  .....++++||||+|.+...      
T Consensus        87 ~la~~la~~l------~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~--~~~~~~~vl~iDEi~~l~~~~~~~~~  158 (376)
T 1um8_A           87 LMAQTLAKHL------DIPIAISDATSLTEAGYVGEDVENILTRLLQASDWN--VQKAQKGIVFIDEIDKISRLSENRSI  158 (376)
T ss_dssp             HHHHHHHHHT------TCCEEEEEGGGCC--------CTHHHHHHHHHTTTC--HHHHTTSEEEEETGGGC---------
T ss_pred             HHHHHHHHHh------CCCEEEecchhhhhcCcCCccHHHHHHHHHhhccch--hhhcCCeEEEEcCHHHHhhhcCCCce
Confidence            9999999987      44556665543221        11122222111000  00124679999999999887      


Q ss_pred             --------HHHHHHHHHHhcC---------------------CCcEEEEEeCC---------------------------
Q psy4285         387 --------AQNALRRIIEKFT---------------------TNVRFCIICNY---------------------------  410 (533)
Q Consensus       387 --------~~~~Ll~~le~~~---------------------~~~~~I~~~n~---------------------------  410 (533)
                              .++.|+++|++..                     .++.+|+++|.                           
T Consensus       159 ~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~R~~~~~~g~~~~~~~~~~  238 (376)
T 1um8_A          159 TRDVSGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKE  238 (376)
T ss_dssp             -----CHHHHHHHHHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTT
T ss_pred             ecccchHHHHHHHHHHhhccceecccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHHHhcccccCCCchhhhccc
Confidence                    8999999999541                     45678888762                           


Q ss_pred             --------------CCCCChhhhccc-eeeeecCCCHHHHHHHhhc
Q psy4285         411 --------------LSKIPPAIQSRC-TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       411 --------------~~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~  441 (533)
                                    ...+.|++.+|| ..+.|.+++.+++..++..
T Consensus       239 ~~~~~~~~~~~~l~~~~~~p~l~~R~~~~i~~~~l~~~~l~~i~~~  284 (376)
T 1um8_A          239 QEAILHLVQTHDLVTYGLIPELIGRLPVLSTLDSISLEAMVDILQK  284 (376)
T ss_dssp             TTTSGGGCCHHHHHHTTCCHHHHTTCCEEEECCCCCHHHHHHHHHS
T ss_pred             hhHHHhhcCHHHHhhcCCChHHhcCCCceeeccCCCHHHHHHHHhh
Confidence                          113678899999 6899999999999888874

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.52  E-value=2.4e-14  Score=129.91  Aligned_cols=141  Identities=15%  Similarity=0.208  Sum_probs=93.6

Q ss_pred             hhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCC----Cchh----HHHHHHH
Q psy4285         292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDD----RGIG----IVRDQIF  359 (533)
Q Consensus       292 ~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~----~~~~----~~~~~~~  359 (533)
                      .....+...+..+...+++|+||||||||++++++++.+.+...    .+..++.++....    ....    .+...+.
T Consensus        29 ~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (195)
T 1jbk_A           29 EEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLN  108 (195)
T ss_dssp             HHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeHHHHhccCCccccHHHHHHHHHH
Confidence            33344444444455557999999999999999999998754211    1234444443221    1111    2222222


Q ss_pred             HHHhcccCCCCCcEEEEEeCCCCCCHH--------HHHHHHHHHHhcCCCcEEEEEeCCCC-----CCChhhhccceeee
Q psy4285         360 QFASTKTMHKSSYKLIILDEADAMTND--------AQNALRRIIEKFTTNVRFCIICNYLS-----KIPPAIQSRCTRFR  426 (533)
Q Consensus       360 ~~~~~~~~~~~~~~vliiDE~d~l~~~--------~~~~Ll~~le~~~~~~~~I~~~n~~~-----~l~~~l~sR~~~i~  426 (533)
                      ....     ...+.+|+|||+|.+...        .++.|...++.  .++.+|++||...     .+++++++||..+.
T Consensus       109 ~~~~-----~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~l~~~~~~--~~~~~i~~~~~~~~~~~~~~~~~l~~r~~~i~  181 (195)
T 1jbk_A          109 DLAK-----QEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR--GELHCVGATTLDEYRQYIEKDAALERRFQKVF  181 (195)
T ss_dssp             HHHH-----STTTEEEEEETGGGGTT------CCCCHHHHHHHHHT--TSCCEEEEECHHHHHHHTTTCHHHHTTEEEEE
T ss_pred             HHhh-----cCCCeEEEEeCHHHHhccCcccchHHHHHHHHHhhcc--CCeEEEEeCCHHHHHHHHhcCHHHHHHhceee
Confidence            2221     135679999999999632        35667777764  4578899998765     78999999999999


Q ss_pred             ecCCCHHHHHHHh
Q psy4285         427 FGPLDSSLIMSRL  439 (533)
Q Consensus       427 ~~~~~~~~~~~~l  439 (533)
                      +.+|+.++..+++
T Consensus       182 ~~~p~~~~~~~il  194 (195)
T 1jbk_A          182 VAEPSVEDTIAIL  194 (195)
T ss_dssp             CCCCCHHHHHTTC
T ss_pred             cCCCCHHHHHHHh
Confidence            9999999988765

>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=99.51  E-value=6.5e-14  Score=147.46  Aligned_cols=128  Identities=22%  Similarity=0.309  Sum_probs=88.5

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHH-----------HHHHHHHHhcccCCCCCcEE
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIV-----------RDQIFQFASTKTMHKSSYKL  374 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~v  374 (533)
                      .++++|+||||||||++|++++..+      +..+..++.........+           ...+.......   .....+
T Consensus       108 g~~vll~Gp~GtGKTtlar~ia~~l------~~~~~~i~~~~~~~~~~~~g~~~~~ig~~~~~~~~~~~~a---~~~~~v  178 (543)
T 3m6a_A          108 GPILCLAGPPGVGKTSLAKSIAKSL------GRKFVRISLGGVRDESEIRGHRRTYVGAMPGRIIQGMKKA---GKLNPV  178 (543)
T ss_dssp             SCEEEEESSSSSSHHHHHHHHHHHH------TCEEEEECCCC--------------------CHHHHHHTT---CSSSEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhc------CCCeEEEEecccchhhhhhhHHHHHhccCchHHHHHHHHh---hccCCE
Confidence            3469999999999999999999998      445555555432211111           11111111111   123459


Q ss_pred             EEEeCCCCCCHHH----HHHHHHHHHhcC---------------CCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHH
Q psy4285         375 IILDEADAMTNDA----QNALRRIIEKFT---------------TNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLI  435 (533)
Q Consensus       375 liiDE~d~l~~~~----~~~Ll~~le~~~---------------~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~  435 (533)
                      ++|||+|.+..+.    ++.|++.|++..               .+++||+|||.+..++++|++||..+.|++|+.++.
T Consensus       179 l~lDEid~l~~~~~~~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~ttN~~~~l~~aL~~R~~vi~~~~~~~~e~  258 (543)
T 3m6a_A          179 FLLDEIDKMSSDFRGDPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATANNLATIPGPLRDRMEIINIAGYTEIEK  258 (543)
T ss_dssp             EEEEESSSCC---------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEECSSTTTSCHHHHHHEEEEECCCCCHHHH
T ss_pred             EEEhhhhhhhhhhccCHHHHHHHHHhhhhcceeecccCCeeecccceEEEeccCccccCCHHHHhhcceeeeCCCCHHHH
Confidence            9999999998874    488888886432               567899999999999999999999999999999999


Q ss_pred             HHHhhcC
Q psy4285         436 MSRLDYD  442 (533)
Q Consensus       436 ~~~l~~~  442 (533)
                      ..++...
T Consensus       259 ~~Il~~~  265 (543)
T 3m6a_A          259 LEIVKDH  265 (543)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHH
Confidence            8888766

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

Probab=99.50  E-value=1.3e-13  Score=141.42  Aligned_cols=149  Identities=23%  Similarity=0.246  Sum_probs=103.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      +++|+||||||||++|++++..+      +.+++.+++++..      +...++..+.....      ..+++|||||+|
T Consensus        51 gvLL~GppGtGKT~Laraia~~~------~~~f~~is~~~~~~~~~g~~~~~~r~lf~~A~~------~~p~ILfIDEid  118 (476)
T 2ce7_A           51 GILLVGPPGTGKTLLARAVAGEA------NVPFFHISGSDFVELFVGVGAARVRDLFAQAKA------HAPCIVFIDEID  118 (476)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH------TCCEEEEEGGGTTTCCTTHHHHHHHHHHHHHHH------TCSEEEEEETGG
T ss_pred             eEEEECCCCCCHHHHHHHHHHHc------CCCeeeCCHHHHHHHHhcccHHHHHHHHHHHHh------cCCCEEEEechh
Confidence            49999999999999999999987      5667777765432      12234443333221      356899999999


Q ss_pred             CCCH--------------HHHHHHHHHHHh--cCCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC
Q psy4285         382 AMTN--------------DAQNALRRIIEK--FTTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       382 ~l~~--------------~~~~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+..              ..++.|+..|+.  ...++.+|++||.++.+++++++  ||. .+.+.+|+.++..+++...
T Consensus       119 ~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~  198 (476)
T 2ce7_A          119 AVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIH  198 (476)
T ss_dssp             GTCCC---------CHHHHHHHHHHHHHHHSCGGGTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHH
T ss_pred             hhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCCCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHH
Confidence            9843              245667777764  23568899999999999999987  885 7888999988888877543


Q ss_pred             ------HH--HHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 ------DI--SFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 ------~~--~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                            +.  ++..+..         .+.|+++.|+...+.++
T Consensus       199 ~~~~~l~~~v~l~~la~---------~t~G~sgadL~~lv~~A  232 (476)
T 2ce7_A          199 TRNKPLAEDVNLEIIAK---------RTPGFVGADLENLVNEA  232 (476)
T ss_dssp             HTTSCBCTTCCHHHHHH---------TCTTCCHHHHHHHHHHH
T ss_pred             HHhCCCcchhhHHHHHH---------hcCCCcHHHHHHHHHHH
Confidence                  11  1222211         45677777766655544

>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=99.49  E-value=8.9e-14  Score=139.69  Aligned_cols=163  Identities=21%  Similarity=0.246  Sum_probs=108.6

Q ss_pred             CCCHHHHHHHHHHHhhhchhhhhhhccccc-------------cc--CCCceeEeCCCCCChHHHHHHHHHHHccccccC
Q psy4285         273 YPTKTEITNILRWLLNESMDLCYKINRFID-------------EN--ELPHLLFYGPPGTGKTTTILACARKLYTKAQFN  337 (533)
Q Consensus       273 ~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~-------------~~--~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~  337 (533)
                      ++.+..+...+.....|++.+...+...+.             ..  ...+++|+||||||||++|+++|+.+      +
T Consensus         3 ~~~~~~l~~~l~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~------~   76 (363)
T 3hws_A            3 LPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLL------D   76 (363)
T ss_dssp             CCCHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHT------T
T ss_pred             CCCHHHHHHHHHhhccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHc------C
Confidence            345666666666666777777776665552             11  22459999999999999999999988      5


Q ss_pred             cceEEecCCCCCchhHH----HHHHHHHHhcccC--CCCCcEEEEEeCCCCCCHH--------------HHHHHHHHHHh
Q psy4285         338 AMVLELNASDDRGIGIV----RDQIFQFASTKTM--HKSSYKLIILDEADAMTND--------------AQNALRRIIEK  397 (533)
Q Consensus       338 ~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~--~~~~~~vliiDE~d~l~~~--------------~~~~Ll~~le~  397 (533)
                      .+++.+++++.......    ...+.........  ....+++|||||+|.+...              .++.|++.|+.
T Consensus        77 ~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~~~~~~~~~~~~~~~~~~~~Ll~~leg  156 (363)
T 3hws_A           77 VPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEG  156 (363)
T ss_dssp             CCEEEEEHHHHTTCHHHHHHHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCCCSSCC---CHHHHHHHHHHHHHHHHC
T ss_pred             CCEEEechHHhcccccccccHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhcccccccccccccchHHHHHHHHHHhcC
Confidence            67777776543221111    1111111111100  0124679999999988765              89999999982


Q ss_pred             c---------------------CCCcEEEEEeCCC----------CC---------------------------------
Q psy4285         398 F---------------------TTNVRFCIICNYL----------SK---------------------------------  413 (533)
Q Consensus       398 ~---------------------~~~~~~I~~~n~~----------~~---------------------------------  413 (533)
                      .                     ..+..||+++|..          ..                                 
T Consensus       157 ~~~~~~~~~~~~~~~~~~~~i~tsn~~~i~~g~~~~l~~~i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~  236 (363)
T 3hws_A          157 TVAAVPPQGGRKHPQQEFLQVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIK  236 (363)
T ss_dssp             C----------------CCCCCTTSSEEEEEECCTTHHHHHHHHHCCCC------------CCSCHHHHHHTCCHHHHHH
T ss_pred             ceeeccCccccccCCCceEEEECCCceEEecCCcHHHHHHHHHhhhccccCCccccccccccchhhHHHHHhCCHHHHHH
Confidence            1                     2445667776643          11                                 


Q ss_pred             --CChhhhcccee-eeecCCCHHHHHHHhhc
Q psy4285         414 --IPPAIQSRCTR-FRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       414 --l~~~l~sR~~~-i~~~~~~~~~~~~~l~~  441 (533)
                        +.|++.+|+.. +.|.|++.+++.+++..
T Consensus       237 ~~~~~~l~~R~~~~~~~~pl~~~~~~~I~~~  267 (363)
T 3hws_A          237 FGLIPEFIGRLPVVATLNELSEEALIQILKE  267 (363)
T ss_dssp             HTCCHHHHTTCCEEEECCCCCHHHHHHHHHS
T ss_pred             cCCCHHHhcccCeeeecCCCCHHHHHHHHHH
Confidence              78999999964 55899999999888876

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.49  E-value=6.9e-14  Score=136.50  Aligned_cols=167  Identities=14%  Similarity=0.152  Sum_probs=101.6

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCC------------CCCcEE
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH------------KSSYKL  374 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~v  374 (533)
                      .+++|+||||||||++|+++++.....   +.+++.++++.... ..+...+  |......+            ....++
T Consensus        26 ~~vLi~Ge~GtGKt~lAr~i~~~~~~~---~~~~v~v~~~~~~~-~l~~~~l--fg~~~g~~tg~~~~~~g~~~~a~~g~   99 (304)
T 1ojl_A           26 ATVLIHGDSGTGKELVARALHACSARS---DRPLVTLNCAALNE-SLLESEL--FGHEKGAFTGADKRREGRFVEADGGT   99 (304)
T ss_dssp             SCEEEESCTTSCHHHHHHHHHHHSSCS---SSCCCEEECSSCCH-HHHHHHH--TCCCSSCCC---CCCCCHHHHHTTSE
T ss_pred             CcEEEECCCCchHHHHHHHHHHhCccc---CCCeEEEeCCCCCh-HHHHHHh--cCccccccCchhhhhcCHHHhcCCCE
Confidence            469999999999999999999875332   45677777765422 1111111  10000000            123469


Q ss_pred             EEEeCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHH
Q psy4285         375 IILDEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIM  436 (533)
Q Consensus       375 liiDE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~  436 (533)
                      |||||++.++.+.+..|++.+++.           +.++++|++||..       ..+.+.|.+|+..+.+.-|+     
T Consensus       100 L~LDEi~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~l~~~v~~g~fr~~L~~Rl~~~~i~lPp-----  174 (304)
T 1ojl_A          100 LFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPS-----  174 (304)
T ss_dssp             EEEESCTTCCHHHHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSCHHHHHHHTSSCHHHHHHHSSEEEECCC-----
T ss_pred             EEEeccccCCHHHHHHHHHHHhcCEeeecCCcccccCCeEEEEecCccHHHHHHhCCcHHHHHhhcCeeEEeccC-----
Confidence            999999999999999999999864           3568999999975       35788999998655544444     


Q ss_pred             HHhhcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHH
Q psy4285         437 SRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       437 ~~l~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~  488 (533)
                        +...++|+..++..+-  .......+.....+.......+..+.||++++
T Consensus       175 --L~eR~edi~~l~~~~l--~~~~~~~~~~~~~~s~~a~~~L~~~~wpGnvR  222 (304)
T 1ojl_A          175 --LRQRREDIPLLADHFL--RRFAERNRKVVKGFTPQAMDLLIHYDWPGNIR  222 (304)
T ss_dssp             --SGGGGGGHHHHHHHHH--HHHHHHTTCCCCCBCHHHHHHHHHCCCSSHHH
T ss_pred             --HHHhHhhHHHHHHHHH--HHHHHHhccCccCCCHHHHHHHHcCCCCCCHH
Confidence              1111222333333211  11111222222223345566667778888876

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=99.48  E-value=2.5e-13  Score=130.24  Aligned_cols=169  Identities=15%  Similarity=0.113  Sum_probs=101.7

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH-H----HHHhc----ccCC-CCCcEEEE
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI-F----QFAST----KTMH-KSSYKLII  376 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~----~~~~~----~~~~-~~~~~vli  376 (533)
                      .+++|+||||||||++|+++++.+...   +.+++.++++.... ..+...+ +    .+...    .... ....++||
T Consensus        30 ~~vll~G~~GtGKt~la~~i~~~~~~~---~~~~~~v~~~~~~~-~~~~~~l~g~~~~~~~g~~~~~~~~l~~a~~~~l~  105 (265)
T 2bjv_A           30 KPVLIIGERGTGKELIASRLHYLSSRW---QGPFISLNCAALNE-NLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLF  105 (265)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHTSTTT---TSCEEEEEGGGSCH-HHHHHHHHCCC---------CCCCHHHHTTTSEEE
T ss_pred             CCEEEECCCCCcHHHHHHHHHHhcCcc---CCCeEEEecCCCCh-hHHHHHhcCCcccccccccccccchhhhcCCcEEE
Confidence            469999999999999999999876332   35677787765422 2221111 0    00000    0000 12457999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHH
Q psy4285         377 LDEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSR  438 (533)
Q Consensus       377 iDE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~  438 (533)
                      |||++.++.+.++.|++++++.           +.++++|++||..       ..+.+++.+||..+.+.-|+       
T Consensus       106 lDEi~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~~~~~~~~~~~~~~~L~~Rl~~~~i~lp~-------  178 (265)
T 2bjv_A          106 LDELATAPMMVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLDALAFDVVQLPP-------  178 (265)
T ss_dssp             EESGGGSCHHHHHHHHHHHHHCEECCCCC--CEECCCEEEEEESSCHHHHHHHTSSCHHHHHHHCSEEEECCC-------
T ss_pred             EechHhcCHHHHHHHHHHHHhCCeecCCCcccccCCeEEEEecCcCHHHHHHcCCccHHHHHhhcCcEEeCCC-------
Confidence            9999999999999999999863           3568999999975       25789999999654444333       


Q ss_pred             hhcCHHHHHHHHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHhcCCChhHH
Q psy4285         439 LDYDDISFFNIIIWYIKIQEIKIEKGLAL-TDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       439 l~~~~~~~~~ll~~~~~l~~l~~~~~~~~-~di~~~~~~~~~~~~~~~~~~  488 (533)
                      +....+++..+++.+  +.......+... ..+-....+.+..+.|+++++
T Consensus       179 L~~R~~di~~l~~~~--l~~~~~~~~~~~~~~~~~~a~~~L~~~~~~gn~r  227 (265)
T 2bjv_A          179 LRERESDIMLMAEYF--AIQMCREIKLPLFPGFTERARETLLNYRWPGNIR  227 (265)
T ss_dssp             GGGCHHHHHHHHHHH--HHHHHHHTTCSSCCCBCHHHHHHHHHSCCTTHHH
T ss_pred             hhhhhHHHHHHHHHH--HHHHHHHhCCCcccCcCHHHHHHHHhCCCCCCHH
Confidence            112222333333321  111112223211 122344556666778998876

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.48  E-value=6.4e-14  Score=121.19  Aligned_cols=111  Identities=16%  Similarity=0.157  Sum_probs=81.5

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTND  386 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~  386 (533)
                      .+++|+||||||||++|+++++.....   +.+++ ++++...........+..         ...++|||||+|.++.+
T Consensus        25 ~~vll~G~~GtGKt~lA~~i~~~~~~~---~~~~v-~~~~~~~~~~~~~~~~~~---------a~~g~l~ldei~~l~~~   91 (145)
T 3n70_A           25 IAVWLYGAPGTGRMTGARYLHQFGRNA---QGEFV-YRELTPDNAPQLNDFIAL---------AQGGTLVLSHPEHLTRE   91 (145)
T ss_dssp             SCEEEESSTTSSHHHHHHHHHHSSTTT---TSCCE-EEECCTTTSSCHHHHHHH---------HTTSCEEEECGGGSCHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHhCCcc---CCCEE-EECCCCCcchhhhcHHHH---------cCCcEEEEcChHHCCHH
Confidence            469999999999999999999865332   34555 666554333223332221         13369999999999999


Q ss_pred             HHHHHHHHHHhcCCCcEEEEEeCCC-------CCCChhhhccce--eeeecCC
Q psy4285         387 AQNALRRIIEKFTTNVRFCIICNYL-------SKIPPAIQSRCT--RFRFGPL  430 (533)
Q Consensus       387 ~~~~Ll~~le~~~~~~~~I~~~n~~-------~~l~~~l~sR~~--~i~~~~~  430 (533)
                      .|..|++.|+..+.++++|++||..       ..+.+.+..|+.  .+.++|+
T Consensus        92 ~q~~Ll~~l~~~~~~~~~I~~t~~~~~~~~~~~~~~~~L~~rl~~~~i~lPpL  144 (145)
T 3n70_A           92 QQYHLVQLQSQEHRPFRLIGIGDTSLVELAASNHIIAELYYCFAMTQIACLPL  144 (145)
T ss_dssp             HHHHHHHHHHSSSCSSCEEEEESSCHHHHHHHSCCCHHHHHHHHHHEEECCCC
T ss_pred             HHHHHHHHHhhcCCCEEEEEECCcCHHHHHHcCCCCHHHHHHhcCCEEeCCCC
Confidence            9999999998888889999999965       357788888875  4555543

>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=99.48  E-value=4.7e-15  Score=142.58  Aligned_cols=123  Identities=25%  Similarity=0.276  Sum_probs=85.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      +++|+||||||||++|+++++.+      +.+++.+++++..      +...++..+.....      ..+++|||||+|
T Consensus        46 ~vll~G~~GtGKT~la~~la~~~------~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~a~~------~~~~vl~iDEid  113 (268)
T 2r62_A           46 GVLLVGPPGTGKTLLAKAVAGEA------HVPFFSMGGSSFIEMFVGLGASRVRDLFETAKK------QAPSIIFIDEID  113 (268)
T ss_dssp             CCCCBCSSCSSHHHHHHHHHHHH------TCCCCCCCSCTTTTSCSSSCSSSSSTTHHHHHH------SCSCEEEESCGG
T ss_pred             eEEEECCCCCcHHHHHHHHHHHh------CCCEEEechHHHHHhhcchHHHHHHHHHHHHHh------cCCeEEEEeChh
Confidence            59999999999999999999987      3344445543321      11112222222211      245799999999


Q ss_pred             CCCHHH---------------HHHHHHHHHhcC---CCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhh
Q psy4285         382 AMTNDA---------------QNALRRIIEKFT---TNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       382 ~l~~~~---------------~~~Ll~~le~~~---~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~  440 (533)
                      .+....               ++.|+..++...   ..+.+|++||.+..+++++++  || ..+.|.+|+.++..+++.
T Consensus       114 ~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~  193 (268)
T 2r62_A          114 AIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILK  193 (268)
T ss_dssp             GTTC----------CCCSCSSTTTTTTTTTCSSCSCSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHH
T ss_pred             hhcccccccccCCCchhHHHHHHHHHHHhhCcccCCCCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHH
Confidence            996542               345666665432   347889999999999999999  77 578999999998888876


Q ss_pred             cC
Q psy4285         441 YD  442 (533)
Q Consensus       441 ~~  442 (533)
                      ..
T Consensus       194 ~~  195 (268)
T 2r62_A          194 VH  195 (268)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

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

Probab=99.47  E-value=4.8e-14  Score=139.89  Aligned_cols=144  Identities=17%  Similarity=0.132  Sum_probs=96.9

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhc--c
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAST--K  365 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~  365 (533)
                      .|++.....+...+..+  .+++|+||||||||++|+++++.+      +..+..++.........   .++.....  .
T Consensus        30 ~g~~~~~~~l~~~l~~~--~~vll~G~pGtGKT~la~~la~~~------~~~~~~i~~~~~~~~~~---l~g~~~~~~~~   98 (331)
T 2r44_A           30 VGQKYMINRLLIGICTG--GHILLEGVPGLAKTLSVNTLAKTM------DLDFHRIQFTPDLLPSD---LIGTMIYNQHK   98 (331)
T ss_dssp             CSCHHHHHHHHHHHHHT--CCEEEESCCCHHHHHHHHHHHHHT------TCCEEEEECCTTCCHHH---HHEEEEEETTT
T ss_pred             eCcHHHHHHHHHHHHcC--CeEEEECCCCCcHHHHHHHHHHHh------CCCeEEEecCCCCChhh---cCCceeecCCC
Confidence            34555555554444443  379999999999999999999987      33445555432211111   11000000  0


Q ss_pred             ---cCC--CCCcEEEEEeCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCCC-----CCChhhhccce-
Q psy4285         366 ---TMH--KSSYKLIILDEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYLS-----KIPPAIQSRCT-  423 (533)
Q Consensus       366 ---~~~--~~~~~vliiDE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~~-----~l~~~l~sR~~-  423 (533)
                         ...  .-..++++|||++.++...++.|++.+++.           +..+.+|.|+|...     .+++++++||. 
T Consensus        99 ~~~~~~~g~l~~~vl~iDEi~~~~~~~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~~~~~~~~l~~~l~~Rf~~  178 (331)
T 2r44_A           99 GNFEVKKGPVFSNFILADEVNRSPAKVQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPVEQEGTYPLPEAQVDRFMM  178 (331)
T ss_dssp             TEEEEEECTTCSSEEEEETGGGSCHHHHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTTCCSCCCCCCHHHHTTSSE
T ss_pred             CceEeccCcccccEEEEEccccCCHHHHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCCcccCcccCCHHHHhheeE
Confidence               000  011369999999999999999999999863           44567777777443     38999999997 


Q ss_pred             eeeecCCCHHHHHHHhhcC
Q psy4285         424 RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 ~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.+.+|+.++..+++.+.
T Consensus       179 ~i~i~~p~~~~~~~il~~~  197 (331)
T 2r44_A          179 KIHLTYLDKESELEVMRRV  197 (331)
T ss_dssp             EEECCCCCHHHHHHHHHHH
T ss_pred             EEEcCCCCHHHHHHHHHhc
Confidence            5999999999999888653

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=99.46  E-value=2.5e-13  Score=128.03  Aligned_cols=138  Identities=14%  Similarity=0.237  Sum_probs=94.2

Q ss_pred             hhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCC
Q psy4285         292 DLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSS  371 (533)
Q Consensus       292 ~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  371 (533)
                      .....+..+......++++|+||||||||++++++++.+...   +..+..++..+....  +.+.+.    .    ...
T Consensus        38 ~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~---~~~~~~~~~~~~~~~--~~~~~~----~----~~~  104 (242)
T 3bos_A           38 ELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANEL---ERRSFYIPLGIHASI--STALLE----G----LEQ  104 (242)
T ss_dssp             HHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEEGGGGGGS--CGGGGT----T----GGG
T ss_pred             HHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEEHHHHHHH--HHHHHH----h----ccC
Confidence            344455555554444579999999999999999999988544   334555554432111  000000    0    134


Q ss_pred             cEEEEEeCCCCCCHHH--HHHHHHHHHhcCC--CcEEEEEeCCCC----CCChhhhccc---eeeeecCCCHHHHHHHhh
Q psy4285         372 YKLIILDEADAMTNDA--QNALRRIIEKFTT--NVRFCIICNYLS----KIPPAIQSRC---TRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       372 ~~vliiDE~d~l~~~~--~~~Ll~~le~~~~--~~~~I~~~n~~~----~l~~~l~sR~---~~i~~~~~~~~~~~~~l~  440 (533)
                      +.+|||||++.+....  ++.|+..++....  ...+|++||...    .+++++.+||   ..+.|.+|+.++..+++.
T Consensus       105 ~~vliiDe~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~~r~~~~~~i~l~~~~~~~~~~~l~  184 (242)
T 3bos_A          105 FDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVSRMHWGLTYQLQPMMDDEKLAALQ  184 (242)
T ss_dssp             SSEEEEETGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCCHHHHHHHHHSEEEECCCCCGGGHHHHHH
T ss_pred             CCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhhhhhhHhhcCceEEeCCCCHHHHHHHHH
Confidence            6799999999997655  7888888775432  235888887544    4569999999   899999999998888776


Q ss_pred             cC
Q psy4285         441 YD  442 (533)
Q Consensus       441 ~~  442 (533)
                      ..
T Consensus       185 ~~  186 (242)
T 3bos_A          185 RR  186 (242)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>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=99.46  E-value=1.6e-13  Score=132.19  Aligned_cols=121  Identities=17%  Similarity=0.223  Sum_probs=81.4

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC-Cc--h----hHHHHHHHHHHhcccCCCCCcEEEEEeC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD-RG--I----GIVRDQIFQFASTKTMHKSSYKLIILDE  379 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~-~~--~----~~~~~~~~~~~~~~~~~~~~~~vliiDE  379 (533)
                      .+++|+||||||||++|+++++.+      +..++.+++++. .+  .    ..++..+....      ...+++|||||
T Consensus        65 ~~vLl~G~~GtGKT~la~~ia~~~------~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~------~~~~~vl~iDE  132 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALAAKIAEES------NFPFIKICSPDKMIGFSETAKCQAMKKIFDDAY------KSQLSCVVVDD  132 (272)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHH------TCSEEEEECGGGCTTCCHHHHHHHHHHHHHHHH------TSSEEEEEECC
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHh------CCCEEEEeCHHHhcCCchHHHHHHHHHHHHHHH------hcCCcEEEEEC
Confidence            459999999999999999999986      556666665431 11  1    12223222221      13578999999


Q ss_pred             CCCC----------CHHHHHHHHHHHHh---cCCCcEEEEEeCCCCCCCh-hhhccc-eeeeecCCCH-HHHHHHh
Q psy4285         380 ADAM----------TNDAQNALRRIIEK---FTTNVRFCIICNYLSKIPP-AIQSRC-TRFRFGPLDS-SLIMSRL  439 (533)
Q Consensus       380 ~d~l----------~~~~~~~Ll~~le~---~~~~~~~I~~~n~~~~l~~-~l~sR~-~~i~~~~~~~-~~~~~~l  439 (533)
                      +|.+          .....+.|...++.   ....+.+|++||.+..+++ .+.+|| ..+.+++++. +++..++
T Consensus       133 id~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~~l~~~~l~~rf~~~i~~p~l~~r~~i~~i~  208 (272)
T 1d2n_A          133 IERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEAL  208 (272)
T ss_dssp             HHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTTTSSEEEECCCEEEHHHHHHHH
T ss_pred             hhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCEEEEEecCChhhcchhhhhcccceEEcCCCccHHHHHHHHH
Confidence            9987          34455666666653   3345678888998877777 688897 6778877776 4444443

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

Probab=99.46  E-value=6.4e-14  Score=138.54  Aligned_cols=162  Identities=14%  Similarity=0.246  Sum_probs=119.1

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHH-------HHHHHHHHHhhcCCCCCH-HHHHHHHHhcCCCH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSL-------IMSRLDYVIEQEKVNVTP-DGKKAIIDLSDGDM   72 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~-------~~~~l~~~~~~~~~~~~~-~~~~~~~~~~~g~~   72 (533)
                      ||+|+.+++||++||++.++.|+|+|||.+++|++|+.++       +..++.+++.++++.+++ ++++.++..++||+
T Consensus       130 le~~~~~~~iI~~~n~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~gd~  209 (324)
T 3u61_B          130 MEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDF  209 (324)
T ss_dssp             HHHHGGGCEEEEEESSGGGSCTTHHHHSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCBSCHHHHHHHHHHTCSCT
T ss_pred             HHhCCCCcEEEEEeCCccccCHHHHhhCcEEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHhCCCCH
Confidence            4678889999999999999999999999999999999887       566777778889999988 99999999999999


Q ss_pred             HHHHHHHHHHHHhCCCCcchhhHHhhhhh--hcccc-------ch----hHHHHHhc-hHHHHhhc------CCChhhHH
Q psy4285          73 RKVLNILQSAATAHADEVNEDTIFTLLVS--RVEKY-------RP----STLDELVS-HQDIISTI------EIPESMLV  132 (533)
Q Consensus        73 r~a~~~l~~~~~~~~~~i~~~~i~~~~~~--~~ek~-------~~----~~l~~lls-~~~~l~~l------~~~~~~~~  132 (533)
                      |.|+|.|+.++  ....|+.+.+.+++..  .+..+       ..    ..+++++. ...++..+      ........
T Consensus       210 R~a~~~L~~~~--~~~~i~~~~v~~~~~~~~~i~~~~~~~~~~~~~~a~~~~~~l~~~~~~i~~~l~~~~~~~~~~~~l~  287 (324)
T 3u61_B          210 RKTIGELDSYS--SKGVLDAGILSLVTNDRGAIDDVLESLKNKDVKQLRALAPKYAADYSWFVGKLAEEIYSRVTPQSII  287 (324)
T ss_dssp             THHHHHHHHHG--GGTCBCC------------CHHHHHHHHTTCHHHHHHHHHHHSSCHHHHHHHHHHHHHHHSCHHHHH
T ss_pred             HHHHHHHHHHh--ccCCCCHHHHHHHhCCHHHHHHHHHHHHcCCHHHHHHHHHHhccCHHHHHHHHHHHHHHhCCHHHHH
Confidence            99999999988  3345777766544332  11100       11    12333332 11222211      24555667


Q ss_pred             HHHhhccCccccccCCCChhhHHHHHHHHHhc
Q psy4285         133 DLVLKMSDIEYRLAAGTSEKIQLSALIAAFNS  164 (533)
Q Consensus       133 ~~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~  164 (533)
                      .+...+++.++++..|.++..++++|++.+++
T Consensus       288 ~i~~~l~~~d~~l~~g~~~~~~le~~~~~~~~  319 (324)
T 3u61_B          288 RMYEIVGENNQYHGIAANTELHLAYLFIQLAC  319 (324)
T ss_dssp             HHHHHHHHHHHHTTTCSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            78888899999999999999999999999985

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

Probab=99.45  E-value=3.3e-12  Score=129.23  Aligned_cols=139  Identities=22%  Similarity=0.265  Sum_probs=95.0

Q ss_pred             ccCCCceeEeCCCCCChHHHHHHHHHHHcccc---ccCcceEEecCCCCCchhH-H------------------HHHHHH
Q psy4285         303 ENELPHLLFYGPPGTGKTTTILACARKLYTKA---QFNAMVLELNASDDRGIGI-V------------------RDQIFQ  360 (533)
Q Consensus       303 ~~~~~~~ll~GppGtGKT~la~~la~~l~~~~---~~~~~~~~~~~~~~~~~~~-~------------------~~~~~~  360 (533)
                      .+..++++|+||||||||++++.+++.+....   ..+..++.+++........ +                  .+....
T Consensus        41 ~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~  120 (387)
T 2v1u_A           41 GEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYER  120 (387)
T ss_dssp             SCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHH
T ss_pred             CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHH
Confidence            34455699999999999999999999874321   1134567777654332211 1                  111111


Q ss_pred             HHhcccCCCCCcEEEEEeCCCCCCHH--HHHHHHHHHHhc-----CCCcEEEEEeCCC---CCCChhhhccc--eeeeec
Q psy4285         361 FASTKTMHKSSYKLIILDEADAMTND--AQNALRRIIEKF-----TTNVRFCIICNYL---SKIPPAIQSRC--TRFRFG  428 (533)
Q Consensus       361 ~~~~~~~~~~~~~vliiDE~d~l~~~--~~~~Ll~~le~~-----~~~~~~I~~~n~~---~~l~~~l~sR~--~~i~~~  428 (533)
                      +..... ....+.+|||||+|.+...  .++.|..+++..     +.++.+|++||..   ..+++++.+||  ..+.|+
T Consensus       121 l~~~l~-~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~~~~~l~~~l~~r~~~~~i~l~  199 (387)
T 2v1u_A          121 LVKRLS-RLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLGEVELVFP  199 (387)
T ss_dssp             HHHHHT-TSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEECSCSTTSSSSCHHHHTTTTSEECCBC
T ss_pred             HHHHHh-ccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEECCCchHhhhCHHHHhcCCCeEEeeC
Confidence            111110 1234779999999999776  677777777643     5578899999877   67899999999  689999


Q ss_pred             CCCHHHHHHHhhcC
Q psy4285         429 PLDSSLIMSRLDYD  442 (533)
Q Consensus       429 ~~~~~~~~~~l~~~  442 (533)
                      +++.+++.+++.+.
T Consensus       200 ~l~~~~~~~il~~~  213 (387)
T 2v1u_A          200 PYTAPQLRDILETR  213 (387)
T ss_dssp             CCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999888754

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=99.44  E-value=5.5e-12  Score=124.94  Aligned_cols=122  Identities=17%  Similarity=0.199  Sum_probs=90.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTND  386 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~  386 (533)
                      .+++|+||||+||||++++++..+.      ..+...+++.......+......   .     ...+|++|||++.+.+.
T Consensus        52 ~~~ll~Gp~G~GKTTLa~~ia~~l~------~~~~~~sg~~~~~~~~l~~~~~~---~-----~~~~v~~iDE~~~l~~~  117 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAHIIASELQ------TNIHVTSGPVLVKQGDMAAILTS---L-----ERGDVLFIDEIHRLNKA  117 (334)
T ss_dssp             CCEEEESSTTSSHHHHHHHHHHHHT------CCEEEEETTTCCSHHHHHHHHHH---C-----CTTCEEEEETGGGCCHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHhC------CCEEEEechHhcCHHHHHHHHHH---c-----cCCCEEEEcchhhcCHH
Confidence            5699999999999999999999883      33333444333333333322211   1     24579999999999998


Q ss_pred             HHHHHHHHHHhcC------------------CCcEEEEEeCCCCCCChhhhccce-eeeecCCCHHHHHHHhhcC
Q psy4285         387 AQNALRRIIEKFT------------------TNVRFCIICNYLSKIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       387 ~~~~Ll~~le~~~------------------~~~~~I~~~n~~~~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                      .++.|+..++.+.                  ..+.++.+++.+..+++++++||. ...|.+++.+++.+++.+.
T Consensus       118 ~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l~~~~li~at~~~~~Ls~~l~sR~~l~~~Ld~~~~~~l~~iL~~~  192 (334)
T 1in4_A          118 VEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRA  192 (334)
T ss_dssp             HHHHHHHHHHTSCCCC---------------CCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccceeeccCcccccccccCCCeEEEEecCCcccCCHHHHHhcCceeeCCCCCHHHHHHHHHHH
Confidence            8888888876532                  135677788889999999999995 6889999999999999875

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=99.43  E-value=2e-12  Score=127.33  Aligned_cols=163  Identities=37%  Similarity=0.644  Sum_probs=128.9

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+.+++||++||.+.++.|+|+|||+.++|++++.+++.++|.+++.++++.+++++++.++..++||+|.+++.++
T Consensus       126 le~~~~~~~~i~~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G~~r~~~~~l~  205 (319)
T 2chq_A          126 MEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQ  205 (319)
T ss_dssp             TSSSSSSEEEEEEESCGGGSCHHHHTTCEEEECCCCCHHHHHHHHHHHHHTTCCCBCHHHHHHHHHTTTTCHHHHHHHHH
T ss_pred             HHhcCCCCeEEEEeCChhhcchHHHhhCeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhcc-----------ccch----hHHHHHhc-----hHHHH-------hhcCCChhhHHH
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRVE-----------KYRP----STLDELVS-----HQDII-------STIEIPESMLVD  133 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~e-----------k~~~----~~l~~lls-----~~~~l-------~~l~~~~~~~~~  133 (533)
                      .++.. ...|+.+.+.++++....           .-..    ..+.+++.     ..+++       ..++++...+..
T Consensus       206 ~~~~~-~~~i~~~~v~~~~~~~~~~~~~~l~~~~~~~~~~~a~~~l~~l~~~~g~~~~~i~~~l~~~~~~l~~~~~~l~~  284 (319)
T 2chq_A          206 GAAAI-GEVVDADTIYQITATARPEEMTELIQTALKGNFMEARELLDRLMVEYGMSGEDIVAQLFREIISMPIKDSLKVQ  284 (319)
T ss_dssp             HHHHS-SSCBCHHHHHHHTTCCCHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTSCSCTTHHHH
T ss_pred             HHHHc-CCCCCHHHHHHHHCCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCHHHHHH
Confidence            98874 446888776654432110           0000    11223321     11222       122466667777


Q ss_pred             HHhhccCccccccCCCChhhHHHHHHHHHhc
Q psy4285         134 LVLKMSDIEYRLAAGTSEKIQLSALIAAFNS  164 (533)
Q Consensus       134 ~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~  164 (533)
                      .+..+++++.++..|.+...+++.++..++.
T Consensus       285 ~~~~l~~~~~~lk~~~~~~~~le~l~~~l~~  315 (319)
T 2chq_A          285 LIDKLGEVDFRLTEGANERIQLDAYLAYLST  315 (319)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            8888899999999999999999999998864

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.41  E-value=1.7e-13  Score=123.59  Aligned_cols=135  Identities=15%  Similarity=0.191  Sum_probs=87.3

Q ss_pred             chhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCC----Cchh----HHHHH
Q psy4285         290 SMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDD----RGIG----IVRDQ  357 (533)
Q Consensus       290 ~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~----~~~~----~~~~~  357 (533)
                      ++.....+...+......+++|+||||||||++|+++++.+.....    .+..++.++....    ....    .+...
T Consensus        27 ~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  106 (187)
T 2p65_A           27 RDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLDLSSLIAGAKYRGDFEERLKSI  106 (187)
T ss_dssp             CHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEEECHHHHHHHCCSHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEEEeHHHhhcCCCchhHHHHHHHHH
Confidence            3334444444444455567999999999999999999998744210    1234444443211    0111    12222


Q ss_pred             HHHHHhcccCCCCCcEEEEEeCCCCCC---------HHHHHHHHHHHHhcCCCcEEEEEeCCCC-----CCChhhhccce
Q psy4285         358 IFQFASTKTMHKSSYKLIILDEADAMT---------NDAQNALRRIIEKFTTNVRFCIICNYLS-----KIPPAIQSRCT  423 (533)
Q Consensus       358 ~~~~~~~~~~~~~~~~vliiDE~d~l~---------~~~~~~Ll~~le~~~~~~~~I~~~n~~~-----~l~~~l~sR~~  423 (533)
                      +......     ..+.+|||||++.+.         .+..+.|...+++  ..+.+|+++|...     .+++++++||.
T Consensus       107 ~~~~~~~-----~~~~vl~iDe~~~l~~~~~~~~~~~~~~~~l~~~~~~--~~~~ii~~~~~~~~~~~~~~~~~l~~R~~  179 (187)
T 2p65_A          107 LKEVQDA-----EGQVVMFIDEIHTVVGAGAVAEGALDAGNILKPMLAR--GELRCIGATTVSEYRQFIEKDKALERRFQ  179 (187)
T ss_dssp             HHHHHHT-----TTSEEEEETTGGGGSSSSSSCTTSCCTHHHHHHHHHT--TCSCEEEEECHHHHHHHTTTCHHHHHHEE
T ss_pred             HHHHHhc-----CCceEEEEeCHHHhcccccccccchHHHHHHHHHHhc--CCeeEEEecCHHHHHHHHhccHHHHHhcC
Confidence            2222211     346799999999986         4556677777764  5588999998664     68999999999


Q ss_pred             eeeecCCC
Q psy4285         424 RFRFGPLD  431 (533)
Q Consensus       424 ~i~~~~~~  431 (533)
                      .+.+.+|+
T Consensus       180 ~i~i~~p~  187 (187)
T 2p65_A          180 QILVEQPS  187 (187)
T ss_dssp             EEECCSCC
T ss_pred             cccCCCCC
Confidence            88888774

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.40  E-value=1.2e-13  Score=119.11  Aligned_cols=107  Identities=13%  Similarity=0.163  Sum_probs=76.1

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTND  386 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~  386 (533)
                      .+++|+||||||||++|+++++..      . .++.+++++... ......+.   .      ...++|||||+|.++.+
T Consensus        28 ~~vll~G~~GtGKt~lA~~i~~~~------~-~~~~~~~~~~~~-~~~~~~~~---~------a~~~~l~lDei~~l~~~   90 (143)
T 3co5_A           28 SPVFLTGEAGSPFETVARYFHKNG------T-PWVSPARVEYLI-DMPMELLQ---K------AEGGVLYVGDIAQYSRN   90 (143)
T ss_dssp             SCEEEEEETTCCHHHHHGGGCCTT------S-CEECCSSTTHHH-HCHHHHHH---H------TTTSEEEEEECTTCCHH
T ss_pred             CcEEEECCCCccHHHHHHHHHHhC------C-CeEEechhhCCh-HhhhhHHH---h------CCCCeEEEeChHHCCHH
Confidence            469999999999999999998765      2 677777765321 11222211   1      23469999999999999


Q ss_pred             HHHHHHHHHHhc-CCCcEEEEEeCCCC-C----CChhhhcccee--eeecCC
Q psy4285         387 AQNALRRIIEKF-TTNVRFCIICNYLS-K----IPPAIQSRCTR--FRFGPL  430 (533)
Q Consensus       387 ~~~~Ll~~le~~-~~~~~~I~~~n~~~-~----l~~~l~sR~~~--i~~~~~  430 (533)
                      .+..|++.+++. +.++++|++||... .    +.+.+..|+..  +.++|+
T Consensus        91 ~q~~Ll~~l~~~~~~~~~iI~~tn~~~~~~~~~~~~~L~~rl~~~~i~lPpL  142 (143)
T 3co5_A           91 IQTGITFIIGKAERCRVRVIASCSYAAGSDGISCEEKLAGLFSESVVRIPPL  142 (143)
T ss_dssp             HHHHHHHHHHHHTTTTCEEEEEEEECTTTC--CHHHHHHHHSSSEEEEECCC
T ss_pred             HHHHHHHHHHhCCCCCEEEEEecCCCHHHHHhCccHHHHHHhcCcEEeCCCC
Confidence            999999999875 46789999998542 2    44566777643  444443

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

Probab=99.40  E-value=2.4e-12  Score=123.48  Aligned_cols=156  Identities=21%  Similarity=0.175  Sum_probs=102.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch--hHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI--GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN  385 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~  385 (533)
                      +++|+|||||||||++++++..+      +..++.+++.+....  ......+....+...  ...+.++++||+|.+..
T Consensus        46 GvlL~Gp~GtGKTtLakala~~~------~~~~i~i~g~~l~~~~~~~~~~~i~~vf~~a~--~~~p~i~~~Deid~~~~  117 (274)
T 2x8a_A           46 GVLLAGPPGCGKTLLAKAVANES------GLNFISVKGPELLNMYVGESERAVRQVFQRAK--NSAPCVIFFDEVDALCP  117 (274)
T ss_dssp             EEEEESSTTSCHHHHHHHHHHHT------TCEEEEEETTTTCSSTTHHHHHHHHHHHHHHH--HTCSEEEEEETCTTTCC
T ss_pred             eEEEECCCCCcHHHHHHHHHHHc------CCCEEEEEcHHHHhhhhhHHHHHHHHHHHHHH--hcCCCeEeeehhhhhhc
Confidence            39999999999999999999986      445777777654321  222222332222210  12467999999998742


Q ss_pred             -----------HHHHHHHHHHHhc--CCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC-------
Q psy4285         386 -----------DAQNALRRIIEKF--TTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD-------  442 (533)
Q Consensus       386 -----------~~~~~Ll~~le~~--~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~-------  442 (533)
                                 ...+.++..|+..  ...+.++.++|.+..+|+++++  ||. .+.++.|+.++..+++...       
T Consensus       118 ~r~~~~~~~~~~~~~~~l~~Lsgg~~~~~~i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~~~~  197 (274)
T 2x8a_A          118 RRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKP  197 (274)
T ss_dssp             ---------CTTHHHHHHHHHHTCCSTTCEEEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTTBTT
T ss_pred             ccCCCcchHHHHHHHHHHHhhhcccccCCEEEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcccCC
Confidence                       1235566666532  2446677889999999999998  994 7788888888888887654       


Q ss_pred             ----HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q psy4285         443 ----DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLV  478 (533)
Q Consensus       443 ----~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~  478 (533)
                          ..++..+..       ...+.||++.|+..-+.++.
T Consensus       198 ~~~~~~~~~~la~-------~~~~~g~sgadl~~l~~~a~  230 (274)
T 2x8a_A          198 PLDADVNLEAIAG-------DLRCDCYTGADLSALVREAS  230 (274)
T ss_dssp             BBCTTCCHHHHHT-------CSGGGSCCHHHHHHHHHHHH
T ss_pred             CCccccCHHHHHH-------hhccCCcCHHHHHHHHHHHH
Confidence                011222211       11245999999987665554

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.39  E-value=1.2e-12  Score=130.81  Aligned_cols=163  Identities=26%  Similarity=0.490  Sum_probs=127.0

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+++.+++||++||++..++|+++|||..+.|++++.+++..+|.+++.++++.+++++++.++..++||+|.+++.++
T Consensus       157 le~~~~~~~~il~~~~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G~~r~~~~~l~  236 (353)
T 1sxj_D          157 METYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQ  236 (353)
T ss_dssp             HHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSSCHHHHHHHHH
T ss_pred             HHhcCCCceEEEEeCchhhCcchhhccCceEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            47788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCC-----CcchhhHHhhhhhhcccc-----------chh----HHHHHhc----hHHHHh--------hcCCCh
Q psy4285          81 SAATAHAD-----EVNEDTIFTLLVSRVEKY-----------RPS----TLDELVS----HQDIIS--------TIEIPE  128 (533)
Q Consensus        81 ~~~~~~~~-----~i~~~~i~~~~~~~~ek~-----------~~~----~l~~lls----~~~~l~--------~l~~~~  128 (533)
                      .++.....     .|+.+.|.++++......           .+.    .+.+++.    ...++.        .-+++.
T Consensus       237 ~~~~~~~~~~~~~~It~~~v~~~~~~~~~~~~~~l~~~~~~~~~~~a~~~l~~l~~~g~~~~~i~~~l~~~~~~~~~~~~  316 (353)
T 1sxj_D          237 SASKGAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASVVNQLHEYYITNDNFDT  316 (353)
T ss_dssp             HTHHHHHHHCSCCCCCHHHHHHHHTCCCSHHHHHHHHHHHSCCHHHHHHHHHHHHHTSCCCTTHHHHHHHHHHHCSSSCH
T ss_pred             HHHHhcCCCccCccccHHHHHHHhCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccCCH
Confidence            88654321     588888766544211100           011    1222211    111111        114556


Q ss_pred             hhHHHHHhhccCccccccCCCChhhHHHHHHHHHh
Q psy4285         129 SMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFN  163 (533)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~  163 (533)
                      ..+..++..++++++++..|.++..+++.++..++
T Consensus       317 ~~~~~~~~~l~~~~~~l~~g~~~~l~l~~~~~~~~  351 (353)
T 1sxj_D          317 NFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKIS  351 (353)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHH
Confidence            66777888889999999999999999999999875

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

Probab=99.39  E-value=2.8e-12  Score=132.74  Aligned_cols=143  Identities=13%  Similarity=0.138  Sum_probs=95.2

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCC-CC--chhHHHHHHHH
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASD-DR--GIGIVRDQIFQ  360 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~-~~--~~~~~~~~~~~  360 (533)
                      .|++..+..+...+.....+|++|+||||||||++|+++++.+.+...    .+..++.++++. ..  ....++..+..
T Consensus       183 iGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~~~~g~~e~~~~~~~~~  262 (468)
T 3pxg_A          183 IGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMGTKYRGEFEDRLKKVMDE  262 (468)
T ss_dssp             CCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC----------CTTHHHHHHH
T ss_pred             cCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeCCccccchHHHHHHHHHHH
Confidence            345555555556665566678999999999999999999999854321    144566666541 11  12234444443


Q ss_pred             HHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC-----CCChhhhccceeeeecCCCHHHH
Q psy4285         361 FASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS-----KIPPAIQSRCTRFRFGPLDSSLI  435 (533)
Q Consensus       361 ~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~-----~l~~~l~sR~~~i~~~~~~~~~~  435 (533)
                      ...      .++.|||||    ...+.++.|+..|++  ..+++|++||...     .+++++++||..+.|.+|+.++.
T Consensus       263 ~~~------~~~~iLfiD----~~~~a~~~L~~~L~~--g~v~vI~at~~~e~~~~~~~~~al~~Rf~~i~v~~p~~e~~  330 (468)
T 3pxg_A          263 IRQ------AGNIILFID----AAIDASNILKPSLAR--GELQCIGATTLDEYRKYIEKDAALERRFQPIQVDQPSVDES  330 (468)
T ss_dssp             HHT------CCCCEEEEC----C--------CCCTTS--SSCEEEEECCTTTTHHHHTTCSHHHHSEEEEECCCCCHHHH
T ss_pred             HHh------cCCeEEEEe----CchhHHHHHHHhhcC--CCEEEEecCCHHHHHHHhhcCHHHHHhCccceeCCCCHHHH
Confidence            322      245799999    455677888888874  4689999999886     68999999999999999999999


Q ss_pred             HHHhhcC
Q psy4285         436 MSRLDYD  442 (533)
Q Consensus       436 ~~~l~~~  442 (533)
                      ..++..+
T Consensus       331 ~~iL~~~  337 (468)
T 3pxg_A          331 IQILQGL  337 (468)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHH
Confidence            9999865

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=99.39  E-value=4.3e-12  Score=126.74  Aligned_cols=71  Identities=8%  Similarity=0.051  Sum_probs=57.7

Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC-CCChhhhcccee-eeecCCCHH-H
Q psy4285         371 SYKLIILDEADAMTNDAQNALRRIIEKF-------------TTNVRFCIICNYLS-KIPPAIQSRCTR-FRFGPLDSS-L  434 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~-~l~~~l~sR~~~-i~~~~~~~~-~  434 (533)
                      ..++|||||++.++.+.++.|++.+++.             +.++.+|+++|... .+++++++||.. +.+.+|+.. +
T Consensus       144 ~~~vl~iDEi~~l~~~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~R~~~~~~l~~~~~~~~  223 (350)
T 1g8p_A          144 NRGYLYIDECNLLEDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLDRFGLSVEVLSPRDVET  223 (350)
T ss_dssp             TTEEEEETTGGGSCHHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHTTCSEEEECCCCCSHHH
T ss_pred             CCCEEEEeChhhCCHHHHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCCCCCCCCHHHHhhcceEEEcCCCCcHHH
Confidence            3679999999999999999999999863             24678888999754 899999999965 899988544 4


Q ss_pred             HHHHhhc
Q psy4285         435 IMSRLDY  441 (533)
Q Consensus       435 ~~~~l~~  441 (533)
                      ..+++.+
T Consensus       224 ~~~il~~  230 (350)
T 1g8p_A          224 RVEVIRR  230 (350)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            4466655

>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=99.37  E-value=7.3e-13  Score=135.96  Aligned_cols=131  Identities=15%  Similarity=0.199  Sum_probs=91.3

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHH-----HHHhcccCCCCCcEEEEEeCC
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIF-----QFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .++++|+|||||||||+++++++.+.... .+..++.+++.+..  ..+...+.     .+...   ....+++|||||+
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~l~~~~-~~~~v~~v~~~~~~--~~~~~~~~~~~~~~~~~~---~~~~~~vL~IDEi  203 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNE-PDLRVMYITSEKFL--NDLVDSMKEGKLNEFREK---YRKKVDILLIDDV  203 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHHHHHHC-CSSCEEEEEHHHHH--HHHHHHHHTTCHHHHHHH---HTTTCSEEEEECG
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhC-CCCeEEEeeHHHHH--HHHHHHHHcccHHHHHHH---hcCCCCEEEEeCc
Confidence            44699999999999999999999875432 13455566554321  11111111     11111   0115679999999


Q ss_pred             CCCCH--HHHHHHHHHHHhc-CCCcEEEEEeCCCC----CCChhhhccc---eeeeecCCCHHHHHHHhhcC
Q psy4285         381 DAMTN--DAQNALRRIIEKF-TTNVRFCIICNYLS----KIPPAIQSRC---TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       381 d~l~~--~~~~~Ll~~le~~-~~~~~~I~~~n~~~----~l~~~l~sR~---~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +.+..  ..++.|+..++.. ..+..+|++|+.+.    .++++++|||   ..+.+.+|+.++...++.+.
T Consensus       204 ~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~sR~~~g~~i~l~~p~~e~r~~iL~~~  275 (440)
T 2z4s_A          204 QFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKM  275 (440)
T ss_dssp             GGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHHHHHSSBCCBCCCCCHHHHHHHHHHH
T ss_pred             ccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHhhccCCeEEEeCCCCHHHHHHHHHHH
Confidence            99976  6788899988763 34567888887643    3889999999   58999999999999888764

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=99.37  E-value=2e-12  Score=130.97  Aligned_cols=133  Identities=20%  Similarity=0.254  Sum_probs=96.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch-hHHHHHHHHHHhcccC-----------------CC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI-GIVRDQIFQFASTKTM-----------------HK  369 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-----------------~~  369 (533)
                      +++|+||||||||++++++++.+....  +..++.+++...... ..+......+....+.                 ..
T Consensus        46 ~~li~G~~G~GKTtl~~~l~~~~~~~~--~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~  123 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLRKLWELYKDKT--TARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRER  123 (389)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTTSC--CCEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHhhhc--CeeEEEEeCccCCCHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhc
Confidence            699999999999999999999885432  345666775543322 1222211111000000                 01


Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhcC----CCcEEEEEeCCC---CCCChhhhccce--eeeecCCCHHHHHHHhh
Q psy4285         370 SSYKLIILDEADAMTNDAQNALRRIIEKFT----TNVRFCIICNYL---SKIPPAIQSRCT--RFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~~Ll~~le~~~----~~~~~I~~~n~~---~~l~~~l~sR~~--~i~~~~~~~~~~~~~l~  440 (533)
                      .++.+|+|||++.++...++.|++++++.+    .++.+|++||.+   ..+++.+.+||.  .+.|+|++.+++.+++.
T Consensus       124 ~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~  203 (389)
T 1fnn_A          124 DLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILL  203 (389)
T ss_dssp             TCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHH
T ss_pred             CCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHH
Confidence            346799999999999999999999987643    478999999987   678999999996  69999999999998886


Q ss_pred             cC
Q psy4285         441 YD  442 (533)
Q Consensus       441 ~~  442 (533)
                      +.
T Consensus       204 ~~  205 (389)
T 1fnn_A          204 DR  205 (389)
T ss_dssp             HH
T ss_pred             HH
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=99.37  E-value=1.1e-12  Score=129.56  Aligned_cols=127  Identities=17%  Similarity=0.238  Sum_probs=87.9

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH-----HHHHhcccCCCCCcEEEEEeCC
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI-----FQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .++++|+|||||||||+++++++.+...   +..++.+++.+..  ..+...+     ..+....    ..+++|||||+
T Consensus        37 ~~~lll~G~~GtGKT~la~~i~~~~~~~---~~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~----~~~~vL~iDEi  107 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQAAGNEAKKR---GYRVIYSSADDFA--QAMVEHLKKGTINEFRNMY----KSVDLLLLDDV  107 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHHHHHHHHHHT---TCCEEEEEHHHHH--HHHHHHHHHTCHHHHHHHH----HTCSEEEEECG
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHC---CCEEEEEEHHHHH--HHHHHHHHcCcHHHHHHHh----cCCCEEEEcCc
Confidence            3469999999999999999999987543   3456666654321  1111111     1111110    13579999999


Q ss_pred             CCCCH--HHHHHHHHHHHhc-CCCcEEEEEeCCC-C---CCChhhhccc---eeeeecCCCHHHHHHHhhcC
Q psy4285         381 DAMTN--DAQNALRRIIEKF-TTNVRFCIICNYL-S---KIPPAIQSRC---TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       381 d~l~~--~~~~~Ll~~le~~-~~~~~~I~~~n~~-~---~l~~~l~sR~---~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +.+..  ..++.++..++.. ..+..+|++++.+ .   .+++++.+||   ..+.++| +.++...++...
T Consensus       108 ~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~sR~~~~~~i~l~~-~~~e~~~il~~~  178 (324)
T 1l8q_A          108 QFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIEL-DNKTRFKIIKEK  178 (324)
T ss_dssp             GGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECCC-CHHHHHHHHHHH
T ss_pred             ccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhhcccCceEEEeCC-CHHHHHHHHHHH
Confidence            99976  6778888887653 2445677777644 2   5899999999   6789999 999998888765

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

Probab=99.34  E-value=3.7e-12  Score=131.42  Aligned_cols=154  Identities=19%  Similarity=0.227  Sum_probs=101.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc--hhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG--IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN  385 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~  385 (533)
                      +++|+||||||||+++++++..+      +..++.+++++...  .......+....+...  ...++++||||+|.+..
T Consensus        66 GvLL~GppGtGKTtLaraIa~~~------~~~~i~i~g~~~~~~~~g~~~~~v~~lfq~a~--~~~p~il~IDEId~l~~  137 (499)
T 2dhr_A           66 GVLLVGPPGVGKTHLARAVAGEA------RVPFITASGSDFVEMFVGVGAARVRDLFETAK--RHAPCIVFIDEIDAVGR  137 (499)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHT------TCCEEEEEGGGGTSSCTTHHHHHHHHHTTTSS--SSSSCEEEEECGGGTCC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh------CCCEEEEehhHHHHhhhhhHHHHHHHHHHHHH--hcCCCEEEEehHHHHHH
Confidence            49999999999999999999987      45677777655322  1222222333222221  12468999999998742


Q ss_pred             --------------HHHHHHHHHHHhc--CCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhcC----
Q psy4285         386 --------------DAQNALRRIIEKF--TTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDYD----  442 (533)
Q Consensus       386 --------------~~~~~Ll~~le~~--~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~----  442 (533)
                                    ...+.|+..|+..  ...+.++.+||.+..+|+++++  || ..+.+..|+.++..+++...    
T Consensus       138 ~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~  217 (499)
T 2dhr_A          138 KRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGK  217 (499)
T ss_dssp             CSSSSTTTSSHHHHHHHHHHHHHGGGCCSSCCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSS
T ss_pred             hhccCcCCCcHHHHHHHHHHHHHhcccccCccEEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcC
Confidence                          2234555555532  3456788888999999999998  66 47889999999888888654    


Q ss_pred             --HH--HHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q psy4285         443 --DI--SFFNIIIWYIKIQEIKIEKGLALTDILTEISLLV  478 (533)
Q Consensus       443 --~~--~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~  478 (533)
                        +.  ++..+..         .+.|+++.|+...+.++.
T Consensus       218 ~l~~dv~l~~lA~---------~t~G~~gadL~~lv~~Aa  248 (499)
T 2dhr_A          218 PLAEDVDLALLAK---------RTPGFVGADLENLLNEAA  248 (499)
T ss_dssp             CCCCSSTTHHHHT---------TSCSCCHHHHHHHHHHHH
T ss_pred             CCChHHHHHHHHH---------hcCCCCHHHHHHHHHHHH
Confidence              11  1222222         456777777766665543

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=99.33  E-value=4.8e-12  Score=125.02  Aligned_cols=163  Identities=39%  Similarity=0.650  Sum_probs=127.1

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+.+++||++||++.++.|+++|||..++|++++.+++.+++.+++.++++.+++++++.++..++||+|.+++.++
T Consensus       134 le~~~~~~~~i~~~~~~~~l~~~l~sr~~~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~~~~~l~  213 (327)
T 1iqp_A          134 MEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQ  213 (327)
T ss_dssp             HHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHhcCCCCeEEEEeCCccccCHHHHhhCcEEEecCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHCCCCHHHHHHHHH
Confidence            47789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhh-----------ccccch----hHHHHHh-----chHHHHh-------hcCCChhhHHH
Q psy4285          81 SAATAHADEVNEDTIFTLLVSR-----------VEKYRP----STLDELV-----SHQDIIS-------TIEIPESMLVD  133 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~-----------~ek~~~----~~l~~ll-----s~~~~l~-------~l~~~~~~~~~  133 (533)
                      .++.. ...|+.+.+.+..+..           +...+.    ..+++++     +..+++.       .++++......
T Consensus       214 ~~~~~-~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~ll~~~g~~~~~i~~~l~~~~~~~~~~~~~l~~  292 (327)
T 1iqp_A          214 AAAAL-DKKITDENVFMVASRARPEDIREMMLLALKGNFLKAREKLREILLKQGLSGEDVLVQMHKEVFNLPIEEPKKVL  292 (327)
T ss_dssp             HHHTT-CSEECHHHHHHHTTCCCHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHGGGSSSCHHHHHH
T ss_pred             HHHhc-CCCCCHHHHHHHHCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCHHHHHH
Confidence            88763 3357776665433210           000011    1233333     1122221       22477777778


Q ss_pred             HHhhccCccccccCCCChhhHHHHHHHHHhc
Q psy4285         134 LVLKMSDIEYRLAAGTSEKIQLSALIAAFNS  164 (533)
Q Consensus       134 ~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~  164 (533)
                      ++..+++++.++..|.++..+++.++..++.
T Consensus       293 ~~~~l~~~~~~lk~~~~~~~~le~l~~~l~~  323 (327)
T 1iqp_A          293 LADKIGEYNFRLVEGANEIIQLEALLAQFTL  323 (327)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            8888899999999999999999999988764

>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=99.32  E-value=1.2e-11  Score=125.11  Aligned_cols=71  Identities=20%  Similarity=0.245  Sum_probs=56.6

Q ss_pred             CcEEEEEeCCCCCCH------------HHHHHHHHHHHh----------cCCCcEEEEEe----CCCCCCChhhhcccee
Q psy4285         371 SYKLIILDEADAMTN------------DAQNALRRIIEK----------FTTNVRFCIIC----NYLSKIPPAIQSRCTR  424 (533)
Q Consensus       371 ~~~vliiDE~d~l~~------------~~~~~Ll~~le~----------~~~~~~~I~~~----n~~~~l~~~l~sR~~~  424 (533)
                      ...++++||+|++..            ..|++|++.||.          ..+++.||+++    +.+..+.|.+++|+..
T Consensus       250 ~~~il~~DEidki~~~~~~~~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dlipel~~R~~i  329 (444)
T 1g41_A          250 QNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLPI  329 (444)
T ss_dssp             HHCEEEEETGGGGSCCSSCSSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHTTCCE
T ss_pred             cCCeeeHHHHHHHhhccCCCCCCchHHHHHHHHHHHhcccccccccceecCCcEEEEeccccccCChhhcchHHhcccce
Confidence            356999999999853            267899999984          13567788887    2344577999999975


Q ss_pred             -eeecCCCHHHHHHHhhc
Q psy4285         425 -FRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       425 -i~~~~~~~~~~~~~l~~  441 (533)
                       +.|++++.++...++..
T Consensus       330 ~i~l~~lt~~e~~~Il~~  347 (444)
T 1g41_A          330 RVELTALSAADFERILTE  347 (444)
T ss_dssp             EEECCCCCHHHHHHHHHS
T ss_pred             eeeCCCCCHHHHHHHHHH
Confidence             89999999999999953

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=99.31  E-value=3.8e-12  Score=126.81  Aligned_cols=103  Identities=6%  Similarity=0.054  Sum_probs=93.0

Q ss_pred             CCCCCCceEEEEEcCC------CCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHH
Q psy4285           1 IEKFTTNVRFCIICNY------LSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRK   74 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~------~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~   74 (533)
                      +|+||++++||++|+.      .+++.++|+|||++++|++++.+++.+|+++++.++|+.+++++++.++..++||+|.
T Consensus       101 le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~gdl~~  180 (343)
T 1jr3_D          101 TGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLA  180 (343)
T ss_dssp             HTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTTHHHHHHHHHHHHTTCEECHHHHHHHHHSSTTCHHH
T ss_pred             HhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhchHHHH
Confidence            5899999999999976      4679999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhC-CCCcchhhHHhhhhhhc
Q psy4285          75 VLNILQSAATAH-ADEVNEDTIFTLLVSRV  103 (533)
Q Consensus        75 a~~~l~~~~~~~-~~~i~~~~i~~~~~~~~  103 (533)
                      +.+.||.++... +..||.+.|.++++...
T Consensus       181 ~~~elekl~l~~~~~~It~e~V~~~~~~~~  210 (343)
T 1jr3_D          181 LAQALERLSLLWPDGKLTLPRVEQAVNDAA  210 (343)
T ss_dssp             HHHHHHHHHHHCTTCEECHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhcCCCCCCHHHHHHHHhhhh
Confidence            999999998753 44699999887766543

>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=99.30  E-value=7.3e-12  Score=119.12  Aligned_cols=153  Identities=20%  Similarity=0.218  Sum_probs=94.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC--chhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR--GIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN  385 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~  385 (533)
                      +++|+|||||||||++++++..+      ...++.+++.+..  ........+....+...  ...+.++++||+|.+..
T Consensus        51 g~ll~G~~G~GKTtl~~~i~~~~------~~~~i~~~~~~~~~~~~~~~~~~i~~~~~~~~--~~~~~i~~~Deid~l~~  122 (254)
T 1ixz_A           51 GVLLVGPPGVGKTHLARAVAGEA------RVPFITASGSDFVEMFVGVGAARVRDLFETAK--RHAPCIVFIDEIDAVGR  122 (254)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT------TCCEEEEEHHHHHHSCTTHHHHHHHHHHHHHT--TSSSEEEEEETHHHHHC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh------CCCEEEeeHHHHHHHHhhHHHHHHHHHHHHHH--hcCCeEEEehhhhhhhc
Confidence            49999999999999999999987      3445555543210  01111112222222111  12457999999987631


Q ss_pred             --------------HHHHHHHHHHHhcC--CCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhcC----
Q psy4285         386 --------------DAQNALRRIIEKFT--TNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDYD----  442 (533)
Q Consensus       386 --------------~~~~~Ll~~le~~~--~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~----  442 (533)
                                    ...+.++..++...  ....++.++|.+..+++++++  || ..+.+.+|+.++..+++...    
T Consensus       123 ~~~~~~~~~~~~~~~~~~~ll~~l~g~~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~  202 (254)
T 1ixz_A          123 KRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGK  202 (254)
T ss_dssp             ---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTS
T ss_pred             ccCccccccchHHHHHHHHHHHHHhCCCCCCCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCC
Confidence                          12345566665432  335677788999999999998  67 47888999988888877643    


Q ss_pred             --HH--HHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 --DI--SFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 --~~--~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                        +.  ++..+..         ...|+++.|+...+.++
T Consensus       203 ~~~~~~~~~~la~---------~~~G~~~~dl~~~~~~a  232 (254)
T 1ixz_A          203 PLAEDVDLALLAK---------RTPGFVGADLENLLNEA  232 (254)
T ss_dssp             CBCTTCCHHHHHH---------TCTTCCHHHHHHHHHHH
T ss_pred             CCCcccCHHHHHH---------HcCCCCHHHHHHHHHHH
Confidence              11  1222222         45677777766555444

>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=99.30  E-value=1.8e-11  Score=136.27  Aligned_cols=147  Identities=14%  Similarity=0.164  Sum_probs=93.1

Q ss_pred             hchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCCCc--------hhHHHH
Q psy4285         289 ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDDRG--------IGIVRD  356 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~~~--------~~~~~~  356 (533)
                      |++..+..+...+..+..++++|+||||||||++|+++++.+.+...    .+..++.++.+....        ...++.
T Consensus       174 Gr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~g~~~~g~~~~~l~~  253 (854)
T 1qvr_A          174 GRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKA  253 (854)
T ss_dssp             SCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHH
T ss_pred             CcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhccCccchHHHHHHHH
Confidence            33444444545555556667999999999999999999998844221    144566666544321        112333


Q ss_pred             HHHHHHhcccCCCCCcEEEEEeCCCCCC--------HHHHHHHHHHHHhcCCCcEEEEEeCCCC----CCChhhhcccee
Q psy4285         357 QIFQFASTKTMHKSSYKLIILDEADAMT--------NDAQNALRRIIEKFTTNVRFCIICNYLS----KIPPAIQSRCTR  424 (533)
Q Consensus       357 ~~~~~~~~~~~~~~~~~vliiDE~d~l~--------~~~~~~Ll~~le~~~~~~~~I~~~n~~~----~l~~~l~sR~~~  424 (533)
                      .+......     .++.||||||++.+.        .+..+.|..+++.  ..+.+|++||...    .+++++.+||..
T Consensus       254 ~~~~~~~~-----~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l~~--~~i~~I~at~~~~~~~~~~d~aL~rRf~~  326 (854)
T 1qvr_A          254 VIQEVVQS-----QGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALAR--GELRLIGATTLDEYREIEKDPALERRFQP  326 (854)
T ss_dssp             HHHHHHTT-----CSSEEEEECCC-------------------HHHHHT--TCCCEEEEECHHHHHHHTTCTTTCSCCCC
T ss_pred             HHHHHHhc-----CCCeEEEEecHHHHhccCCccchHHHHHHHHHHHhC--CCeEEEEecCchHHhhhccCHHHHhCCce
Confidence            33332211     246799999999997        4456678888875  4577888888653    579999999999


Q ss_pred             eeecCCCHHHHHHHhhcC
Q psy4285         425 FRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       425 i~~~~~~~~~~~~~l~~~  442 (533)
                      +.+.+|+.++...++..+
T Consensus       327 i~l~~p~~~e~~~iL~~~  344 (854)
T 1qvr_A          327 VYVDEPTVEETISILRGL  344 (854)
T ss_dssp             EEECCCCHHHHHHHHHHH
T ss_pred             EEeCCCCHHHHHHHHHhh
Confidence            999999999999998754

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.29  E-value=1.6e-12  Score=134.33  Aligned_cols=149  Identities=15%  Similarity=0.056  Sum_probs=91.4

Q ss_pred             hhhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHH------HHH--H
Q psy4285         287 LNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIV------RDQ--I  358 (533)
Q Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~------~~~--~  358 (533)
                      ..|++++...+...+..+.  |++|+||||||||++|+++++.+..    +..+...+..- .....+      ...  .
T Consensus        24 ivGq~~~i~~l~~al~~~~--~VLL~GpPGtGKT~LAraLa~~l~~----~~~f~~~~~~~-~t~~dL~G~~~~~~~~~~   96 (500)
T 3nbx_X           24 LYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAFQN----ARAFEYLMTRF-STPEEVFGPLSIQALKDE   96 (500)
T ss_dssp             CSSCHHHHHHHHHHHHHTC--EEEEECCSSSSHHHHHHHGGGGBSS----CCEEEEECCTT-CCHHHHHCCBC-------
T ss_pred             hHHHHHHHHHHHHHHhcCC--eeEeecCchHHHHHHHHHHHHHHhh----hhHHHHHHHhc-CCHHHhcCcccHHHHhhc
Confidence            4566666666665555543  8999999999999999999987622    12222222211 011100      000  1


Q ss_pred             HHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcC----------CCcEEEEEeCCCCC---CChhhhccce-e
Q psy4285         359 FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT----------TNVRFCIICNYLSK---IPPAIQSRCT-R  424 (533)
Q Consensus       359 ~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~----------~~~~~I~~~n~~~~---l~~~l~sR~~-~  424 (533)
                      +.+..........++||||||++++++..++.|+..|++..          +...+|++||....   ..+++.+||. .
T Consensus        97 g~~~~~~~g~l~~~~IL~IDEI~r~~~~~q~~LL~~lee~~v~i~G~~~~~~~~~iI~ATN~lpe~~~~~~aLldRF~~~  176 (500)
T 3nbx_X           97 GRYERLTSGYLPEAEIVFLDEIWKAGPAILNTLLTAINERQFRNGAHVEKIPMRLLVAASNELPEADSSLEALYDRMLIR  176 (500)
T ss_dssp             ---CBCCTTSGGGCSEEEEESGGGCCHHHHHHHHHHHHSSEEECSSSEEECCCCEEEEEESSCCCTTCTTHHHHTTCCEE
T ss_pred             hhHHhhhccCCCcceeeeHHhHhhhcHHHHHHHHHHHHHHhccCCCCcCCcchhhhhhccccCCCccccHHHHHHHHHHH
Confidence            11111111000135699999999999999999999998531          12235888886432   4569999994 5


Q ss_pred             eeecCCCH-HHHHHHhhcC
Q psy4285         425 FRFGPLDS-SLIMSRLDYD  442 (533)
Q Consensus       425 i~~~~~~~-~~~~~~l~~~  442 (533)
                      +.+++|+. ++...++...
T Consensus       177 i~v~~p~~~ee~~~IL~~~  195 (500)
T 3nbx_X          177 LWLDKVQDKANFRSMLTSQ  195 (500)
T ss_dssp             EECCSCCCHHHHHHHHTCC
T ss_pred             HHHHHhhhhhhHHHHHhcc
Confidence            77788877 5566676653

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.28  E-value=8.4e-12  Score=123.02  Aligned_cols=163  Identities=31%  Similarity=0.508  Sum_probs=124.7

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      +|+|+.+++||++||++.++.|+|+|||+.++|++++.+++.++|.+++.++++.+++++++.++..++||+|.|++.++
T Consensus       131 le~~~~~~~~il~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~a~~~l~  210 (323)
T 1sxj_B          131 MELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQ  210 (323)
T ss_dssp             HHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HhccCCCceEEEEeCChhhchhHHHhhceEEeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            47789999999999999999999999999999999999999999999998899999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhhhc--------cccc-hh---HHHH-Hh----chHHHHhh-------cC-CChhhHHHHH
Q psy4285          81 SAATAHADEVNEDTIFTLLVSRV--------EKYR-PS---TLDE-LV----SHQDIIST-------IE-IPESMLVDLV  135 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~~~--------ek~~-~~---~l~~-ll----s~~~~l~~-------l~-~~~~~~~~~~  135 (533)
                      .++... ..|+.+.+.+.++...        ..-. ..   .+.. ++    +..+++..       +. ++.......+
T Consensus       211 ~~~~~~-~~i~~~~v~~~~~~~~~~~i~~~~~~~~~~~~l~~l~~dl~~~g~~~~~i~~~l~~~~~~l~~~~~~~l~~~l  289 (323)
T 1sxj_B          211 STVAGH-GLVNADNVFKIVDSPHPLIVKKMLLASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMI  289 (323)
T ss_dssp             HHHHHH-SSBCHHHHHHHHTSCCHHHHHHHHSCSSHHHHHHHHHHTTTTTTCCHHHHHHHHHHHHHTCTTSCHHHHHHHH
T ss_pred             HHHhcC-CCcCHHHHHHHHCCCCHHHHHHHHhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcccCCHHHHHHHH
Confidence            987533 4588777665443211        1000 01   1222 22    11222221       12 5556666777


Q ss_pred             hhccCccccccCCCChhhHHHHHHHHHhc
Q psy4285         136 LKMSDIEYRLAAGTSEKIQLSALIAAFNS  164 (533)
Q Consensus       136 ~~~~~~~~~~~~G~~~~~~l~~~~~~~~~  164 (533)
                      ..+.+++.++..|.++..+++.++..+..
T Consensus       290 ~~l~~~~~~l~~~~~~~l~le~l~~~~~~  318 (323)
T 1sxj_B          290 KEIGLTHMRILEGVGTYLQLASMLAKIHK  318 (323)
T ss_dssp             HHHHHHHHHHHTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccChHHHHHHHHHHHHh
Confidence            77788888888999999999999988753

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.28  E-value=2.3e-12  Score=130.41  Aligned_cols=137  Identities=18%  Similarity=0.217  Sum_probs=90.7

Q ss_pred             cccCCCceeEeCCCCCChHHHHHHHHHHHcccc----cc-CcceEEecCCCCC-ch-hHHHHHHH---------------
Q psy4285         302 DENELPHLLFYGPPGTGKTTTILACARKLYTKA----QF-NAMVLELNASDDR-GI-GIVRDQIF---------------  359 (533)
Q Consensus       302 ~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~----~~-~~~~~~~~~~~~~-~~-~~~~~~~~---------------  359 (533)
                      ..+..++++|+||||||||++++++++.+....    .. +..++.+++.... .. ..+...+.               
T Consensus        41 ~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~  120 (384)
T 2qby_B           41 KNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLG  120 (384)
T ss_dssp             TTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHHHHHHHHHHHCSCCCSSSSCTH
T ss_pred             cCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHHHHHHHHHhcCCCCCCCCCCHH
Confidence            334445699999999999999999999874431    11 3456666643322 11 11111111               


Q ss_pred             ----HHHhcccCCCCCcEEEEEeCCCCCCHHH-HHH-HHHHHHhcCCCcEEEEEeCCC---CCCChhhhccc-eeeeecC
Q psy4285         360 ----QFASTKTMHKSSYKLIILDEADAMTNDA-QNA-LRRIIEKFTTNVRFCIICNYL---SKIPPAIQSRC-TRFRFGP  429 (533)
Q Consensus       360 ----~~~~~~~~~~~~~~vliiDE~d~l~~~~-~~~-Ll~~le~~~~~~~~I~~~n~~---~~l~~~l~sR~-~~i~~~~  429 (533)
                          .+....   .....+|||||+|.+.... ++. +..+++.. .++.+|++||..   ..+++++.+|+ ..+.|+|
T Consensus       121 ~~~~~l~~~l---~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~-~~~~iI~~t~~~~~~~~l~~~l~sr~~~~i~l~~  196 (384)
T 2qby_B          121 EYIDKIKNGT---RNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSD-ANISVIMISNDINVRDYMEPRVLSSLGPSVIFKP  196 (384)
T ss_dssp             HHHHHHHHHH---SSSCEEEEEETTHHHHHSTTSHHHHHHHHTSS-SCEEEEEECSSTTTTTTSCHHHHHTCCCEEEECC
T ss_pred             HHHHHHHHHh---ccCCCEEEEECHHHhccCCCCceeHHHHhcCC-cceEEEEEECCCchHhhhCHHHHhcCCCeEEECC
Confidence                111111   1122399999999986542 455 55555443 678999999877   67899999996 6999999


Q ss_pred             CCHHHHHHHhhcC
Q psy4285         430 LDSSLIMSRLDYD  442 (533)
Q Consensus       430 ~~~~~~~~~l~~~  442 (533)
                      ++.+++.+++.+.
T Consensus       197 l~~~~~~~il~~~  209 (384)
T 2qby_B          197 YDAEQLKFILSKY  209 (384)
T ss_dssp             CCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH
Confidence            9999999988763

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=99.26  E-value=1.4e-11  Score=122.76  Aligned_cols=136  Identities=8%  Similarity=0.012  Sum_probs=102.0

Q ss_pred             ccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEE
Q psy4285         299 RFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIIL  377 (533)
Q Consensus       299 ~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlii  377 (533)
                      ..++ ++.+| ++|+||+|+||++.+..+++.+.+.+......+.+++     ...+++...... ..+. .++.+|++|
T Consensus        11 ~~l~-~~~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~-----~~~~~~l~~~~~-~~pl-f~~~kvvii   82 (343)
T 1jr3_D           11 AQLN-EGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDP-----NTDWNAIFSLCQ-AMSL-FASRQTLLL   82 (343)
T ss_dssp             HHHH-HCCCSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECCT-----TCCHHHHHHHHH-HHHH-CCSCEEEEE
T ss_pred             HHHh-cCCCcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEecC-----CCCHHHHHHHhc-CcCC-ccCCeEEEE
Confidence            3344 33444 8999999999999999999988765311112334432     133444443332 2222 257899999


Q ss_pred             eCCCC-CCHHHHHHHHHHHHhcCCCcEEEEEeCCC------CCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         378 DEADA-MTNDAQNALRRIIEKFTTNVRFCIICNYL------SKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       378 DE~d~-l~~~~~~~Ll~~le~~~~~~~~I~~~n~~------~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ||++. ++.+.+++|++.++++++++.+|++++..      .++.+++.+||..+.|.+++..++..++.++
T Consensus        83 ~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~~~~l~~~l~~~  154 (343)
T 1jr3_D           83 LLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAAR  154 (343)
T ss_dssp             ECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTTHHHHHHHHH
T ss_pred             ECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCCHHHHHHHHHHH
Confidence            99999 99999999999999999999999998764      3577899999999999999999999888775

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

Probab=99.24  E-value=1.2e-11  Score=136.24  Aligned_cols=143  Identities=12%  Similarity=0.135  Sum_probs=95.6

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCC-C--CCchhHHHHHHHH
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNAS-D--DRGIGIVRDQIFQ  360 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~-~--~~~~~~~~~~~~~  360 (533)
                      .|++..+..+...+.....+|+||+||||||||++|+++|+.+.+...    .+..++.++.. .  +.....++..+..
T Consensus       183 iG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~~~~g~~~~G~~e~~l~~~~~~  262 (758)
T 3pxi_A          183 IGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMGTKYRGEFEDRLKKVMDE  262 (758)
T ss_dssp             CCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC----------CTTHHHHHHH
T ss_pred             cCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEEecccccccchHHHHHHHHHHH
Confidence            345555555666666666678999999999999999999999854321    13345555441 1  1112244554444


Q ss_pred             HHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC-----CCChhhhccceeeeecCCCHHHH
Q psy4285         361 FASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS-----KIPPAIQSRCTRFRFGPLDSSLI  435 (533)
Q Consensus       361 ~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~-----~l~~~l~sR~~~i~~~~~~~~~~  435 (533)
                      ...      ..+.|||||    ...+.++.|+..+++  ..+++|++||...     .+++++++||..+.|.+|+.++.
T Consensus       263 ~~~------~~~~iLfiD----~~~~~~~~L~~~l~~--~~v~~I~at~~~~~~~~~~~d~al~rRf~~i~v~~p~~~~~  330 (758)
T 3pxi_A          263 IRQ------AGNIILFID----AAIDASNILKPSLAR--GELQCIGATTLDEYRKYIEKDAALERRFQPIQVDQPSVDES  330 (758)
T ss_dssp             HHT------CCCCEEEEC----C--------CCCTTS--SSCEEEEECCTTTTHHHHTTCSHHHHSEEEEECCCCCHHHH
T ss_pred             HHh------cCCEEEEEc----CchhHHHHHHHHHhc--CCEEEEeCCChHHHHHHhhccHHHHhhCcEEEeCCCCHHHH
Confidence            432      346799999    445677888888874  5689999999887     79999999999999999999999


Q ss_pred             HHHhhcC
Q psy4285         436 MSRLDYD  442 (533)
Q Consensus       436 ~~~l~~~  442 (533)
                      ..++..+
T Consensus       331 ~~il~~~  337 (758)
T 3pxi_A          331 IQILQGL  337 (758)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHH
Confidence            9999854

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.24  E-value=1.7e-11  Score=123.86  Aligned_cols=135  Identities=24%  Similarity=0.301  Sum_probs=89.3

Q ss_pred             ccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC----------------------CCchhHHHHHHHH
Q psy4285         303 ENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD----------------------DRGIGIVRDQIFQ  360 (533)
Q Consensus       303 ~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~----------------------~~~~~~~~~~~~~  360 (533)
                      .....+++|+||||||||++++.+++.+......+..++.+++..                      ........+.+..
T Consensus        42 ~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~  121 (386)
T 2qby_A           42 EEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVK  121 (386)
T ss_dssp             TCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHH
T ss_pred             CCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHH
Confidence            334446999999999999999999998743210022344444221                      0111222222222


Q ss_pred             HHhcccCCCCCcEEEEEeCCCCCC----HHHHHHHHHHHHh-cCCCcEEEEEeCCC---CCCChhhhccc--eeeeecCC
Q psy4285         361 FASTKTMHKSSYKLIILDEADAMT----NDAQNALRRIIEK-FTTNVRFCIICNYL---SKIPPAIQSRC--TRFRFGPL  430 (533)
Q Consensus       361 ~~~~~~~~~~~~~vliiDE~d~l~----~~~~~~Ll~~le~-~~~~~~~I~~~n~~---~~l~~~l~sR~--~~i~~~~~  430 (533)
                      ....    ...+.+|+|||++.+.    .+....|++.++. ...++.+|++||..   ..+++.+.+||  ..+.|.|+
T Consensus       122 ~l~~----~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~~~r~~~~~i~l~~l  197 (386)
T 2qby_A          122 AVRD----YGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPY  197 (386)
T ss_dssp             HHHT----CCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGGGGGGCTTHHHHTTTTEEEEECCC
T ss_pred             HHhc----cCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCChHhhhCHHHhccCCCeeEEeCCC
Confidence            2211    1347899999999885    4456667777764 24568889999876   46889999999  68999999


Q ss_pred             CHHHHHHHhhc
Q psy4285         431 DSSLIMSRLDY  441 (533)
Q Consensus       431 ~~~~~~~~l~~  441 (533)
                      +.+++.+++.+
T Consensus       198 ~~~~~~~il~~  208 (386)
T 2qby_A          198 NAEELEDILTK  208 (386)
T ss_dssp             CHHHHHHHHHH
T ss_pred             CHHHHHHHHHH
Confidence            99999998875

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

Probab=99.23  E-value=3.7e-11  Score=115.83  Aligned_cols=127  Identities=22%  Similarity=0.283  Sum_probs=80.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC--chhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCC-
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR--GIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMT-  384 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~-  384 (533)
                      +++|+|||||||||++++++..+      ...++.+++.+..  ........+....+...  ...+.++++||+|.+. 
T Consensus        75 gvll~Gp~GtGKTtl~~~i~~~~------~~~~i~~~~~~~~~~~~~~~~~~i~~~~~~~~--~~~~~i~~iDeid~l~~  146 (278)
T 1iy2_A           75 GVLLVGPPGVGKTHLARAVAGEA------RVPFITASGSDFVEMFVGVGAARVRDLFETAK--RHAPCIVFIDEIDAVGR  146 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT------TCCEEEEEHHHHHHSTTTHHHHHHHHHHHHHH--TSCSEEEEEETHHHHHC
T ss_pred             eEEEECCCcChHHHHHHHHHHHc------CCCEEEecHHHHHHHHhhHHHHHHHHHHHHHH--hcCCcEEehhhhHhhhc
Confidence            49999999999999999999987      3445555543210  01111111222111111  1245799999998652 


Q ss_pred             ----------HHHH---HHHHHHHHhc--CCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhcC
Q psy4285         385 ----------NDAQ---NALRRIIEKF--TTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       385 ----------~~~~---~~Ll~~le~~--~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                                .+..   +.++..++..  .....++.++|.+..+++++++  || ..+.+.+|+.++..+++...
T Consensus       147 ~~~~~~~~~~~~~~~~~~~ll~~lsgg~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~  222 (278)
T 1iy2_A          147 KRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIH  222 (278)
T ss_dssp             C--------CHHHHHHHHHHHHHHTTCCTTCCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHH
T ss_pred             ccccccCCcchHHHHHHHHHHHHHhCCCCCCCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHH
Confidence                      1122   3344444432  2335677788999999999998  67 47889999998888887643

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=99.22  E-value=8.9e-12  Score=123.42  Aligned_cols=78  Identities=18%  Similarity=0.307  Sum_probs=72.5

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++||++||.+++++|||+|||++++|++++.+++.++|.+.+     .++++++..+++.++||+|+|+++++
T Consensus       132 lEep~~~~~~Il~t~~~~~l~~ti~SRc~~~~~~~~~~~~~~~~L~~~~-----~~~~~~~~~l~~~s~G~~r~a~~~l~  206 (334)
T 1a5t_A          132 LEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREV-----TMSQDALLAALRLSAGSPGAALALFQ  206 (334)
T ss_dssp             HTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHC-----CCCHHHHHHHHHHTTTCHHHHHHTTS
T ss_pred             hcCCCCCeEEEEEeCChHhCcHHHhhcceeeeCCCCCHHHHHHHHHHhc-----CCCHHHHHHHHHHcCCCHHHHHHHhc
Confidence            5999999999999999999999999999999999999999999998654     56789999999999999999999998


Q ss_pred             HHH
Q psy4285          81 SAA   83 (533)
Q Consensus        81 ~~~   83 (533)
                      ...
T Consensus       207 ~~~  209 (334)
T 1a5t_A          207 GDN  209 (334)
T ss_dssp             SHH
T ss_pred             cch
Confidence            754

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=99.22  E-value=9.9e-12  Score=120.80  Aligned_cols=150  Identities=15%  Similarity=0.086  Sum_probs=99.0

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+||++++++|||+||  +++|++++++++.+||.+++   +  ++++++    ..++||+|+|+|+++
T Consensus       106 LEep~~~t~fIl~t~~~~kl~~tI~SR--~~~f~~l~~~~i~~~L~~~~---~--i~~~~~----~~~~g~~~~al~~l~  174 (305)
T 2gno_A          106 LEEPPEYAVIVLNTRRWHYLLPTIKSR--VFRVVVNVPKEFRDLVKEKI---G--DLWEEL----PLLERDFKTALEAYK  174 (305)
T ss_dssp             HHSCCTTEEEEEEESCGGGSCHHHHTT--SEEEECCCCHHHHHHHHHHH---T--THHHHC----GGGGTCHHHHHHHHH
T ss_pred             HhCCCCCeEEEEEECChHhChHHHHce--eEeCCCCCHHHHHHHHHHHh---C--CCHHHH----HHHCCCHHHHHHHHH
Confidence            699999999999999999999999999  99999999999999999887   2  455544    568999999999997


Q ss_pred             HHHHh---------CCCCcchhhHHhhh--------------hhhccccc---hhHHHHHhc---h---HHHHhhc----
Q psy4285          81 SAATA---------HADEVNEDTIFTLL--------------VSRVEKYR---PSTLDELVS---H---QDIISTI----  124 (533)
Q Consensus        81 ~~~~~---------~~~~i~~~~i~~~~--------------~~~~ek~~---~~~l~~lls---~---~~~l~~l----  124 (533)
                      .....         ...  +.+.|..++              .....+-.   .+.+++++.   .   .+++..+    
T Consensus       175 ~~~~~~~~l~~~~~~~~--~~~~v~~~~~~~~~~~~~v~~l~~ai~~~~~~~a~~~~~~l~~~~~g~~~~~~i~~~~r~l  252 (305)
T 2gno_A          175 LGAEKLSGLMESLKVLE--TEKLLKKVLSKGLEGYLACRELLERFSKVESKEFFALFDQVTNTITGKDAFLLIQRLTRII  252 (305)
T ss_dssp             HHHHHHHHHHHHHHHSC--HHHHTTTTTCSHHHHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHSCTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcc--cHHHHHHHHccCCcchHHHHHHHHHHHCCCHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHH
Confidence            43210         000  122222211              11111000   122333332   1   1111111    


Q ss_pred             -CCChhhHHHHHhhccCccccccC---CCChhhHHHHHHHHHh
Q psy4285         125 -EIPESMLVDLVLKMSDIEYRLAA---GTSEKIQLSALIAAFN  163 (533)
Q Consensus       125 -~~~~~~~~~~~~~~~~~~~~~~~---G~~~~~~l~~~~~~~~  163 (533)
                       ......+...+..++.+++++..   |.++..|++++++.+.
T Consensus       253 ~~~~~~~~~~~l~~~~~~~~~~~~k~~g~~~~lql~~l~~~~~  295 (305)
T 2gno_A          253 LHENTWESVEDQKSVSFLDSILRVKIANLNNKLTLMNILAIHR  295 (305)
T ss_dssp             HHTSCCCSHHHHHHHHHHHHHHTCCGGGCCHHHHHHHHHHHHH
T ss_pred             HhhchhhhHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence             01112224556677888899999   9999999999999985

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.19  E-value=2.8e-12  Score=136.22  Aligned_cols=126  Identities=19%  Similarity=0.237  Sum_probs=78.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH-HHHHhcc-cCCCCCcEEEEEeCCCCCCH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI-FQFASTK-TMHKSSYKLIILDEADAMTN  385 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~-~~~~~~~~vliiDE~d~l~~  385 (533)
                      |+||+||||||||++|+++++.+.... +. .....++.+..+. ...... +.+.... ....+..++++|||+|+++.
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~~~r~~-~~-~~~~~~~~~l~~~-~~~~~~~g~~~~~~G~l~~A~~gil~IDEid~l~~  405 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRVAPRAV-YT-TGKGSTAAGLTAA-VVREKGTGEYYLEAGALVLADGGIAVIDEIDKMRD  405 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTTCSCEE-CC-CTTCSTTTTSEEE-CSSGGGTSSCSEEECHHHHHSSSEECCTTTTCCCS
T ss_pred             ceEEECCCchHHHHHHHHHHHhCCCce-ec-CCCccccccccce-eeeccccccccccCCeeEecCCCcEEeehhhhCCH
Confidence            799999999999999999998762211 00 0000111111100 000000 0000000 00012347999999999999


Q ss_pred             HHHHHHHHHHHhc-------------CCCcEEEEEeCCCC-------------CCChhhhccce-eeeecCCCHHHHH
Q psy4285         386 DAQNALRRIIEKF-------------TTNVRFCIICNYLS-------------KIPPAIQSRCT-RFRFGPLDSSLIM  436 (533)
Q Consensus       386 ~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~-------------~l~~~l~sR~~-~i~~~~~~~~~~~  436 (533)
                      +.+++|++.|++.             +.++.+|+|+|...             .++++++|||+ .+.+.+++.++..
T Consensus       406 ~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaatNp~~G~~~~~~~~~~ni~l~~aLl~RFDl~~~~~~~~~~e~~  483 (595)
T 3f9v_A          406 EDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPKFGRYISERPVSDNINLPPTILSRFDLIFILKDQPGEQDR  483 (595)
T ss_dssp             HHHHHHHHHHHSSSEEEESSSSEEEECCCCEEEEEECCTTCCSCTTSCSCTTTCSCSSSGGGCSCCEEECCTTHHHHH
T ss_pred             hHhhhhHHHHhCCEEEEecCCcEEEecCceEEEEEcCCcCCccCcccCchhccCCCHHHHhhCeEEEEeCCCCCHHHH
Confidence            9999999999863             35678999999876             89999999995 5556666655533

>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=99.19  E-value=4.2e-11  Score=131.94  Aligned_cols=147  Identities=14%  Similarity=0.163  Sum_probs=98.3

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCC------Cc--hhHHH
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDD------RG--IGIVR  355 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~------~~--~~~~~  355 (533)
                      .|++..+..+...+......+++|+||||||||++|+++++.+.+...    .+..++.++....      .+  ...++
T Consensus       189 iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l~~~~~~~g~~e~~l~  268 (758)
T 1r6b_X          189 IGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFK  268 (758)
T ss_dssp             CSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHH
T ss_pred             cCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHHhccccccchHHHHHH
Confidence            345555555666666666667999999999999999999998854321    1233444443221      11  22333


Q ss_pred             HHHHHHHhcccCCCCCcEEEEEeCCCCC---------CHHHHHHHHHHHHhcCCCcEEEEEeCCC-----CCCChhhhcc
Q psy4285         356 DQIFQFASTKTMHKSSYKLIILDEADAM---------TNDAQNALRRIIEKFTTNVRFCIICNYL-----SKIPPAIQSR  421 (533)
Q Consensus       356 ~~~~~~~~~~~~~~~~~~vliiDE~d~l---------~~~~~~~Ll~~le~~~~~~~~I~~~n~~-----~~l~~~l~sR  421 (533)
                      ..+....      ...+.+|||||++.+         ..+..+.|..+++.  ..+.+|++||.+     ..+++++.+|
T Consensus       269 ~~~~~~~------~~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~~--~~~~~I~at~~~~~~~~~~~d~aL~~R  340 (758)
T 1r6b_X          269 ALLKQLE------QDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSS--GKIRVIGSTTYQEFSNIFEKDRALARR  340 (758)
T ss_dssp             HHHHHHS------SSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSS--CCCEEEEEECHHHHHCCCCCTTSSGGG
T ss_pred             HHHHHHH------hcCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHHhC--CCeEEEEEeCchHHhhhhhcCHHHHhC
Confidence            3333221      124689999999998         23444555555553  457888888753     3678999999


Q ss_pred             ceeeeecCCCHHHHHHHhhcC
Q psy4285         422 CTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       422 ~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      |..+.|.+|+.++..+++..+
T Consensus       341 f~~i~v~~p~~~e~~~il~~l  361 (758)
T 1r6b_X          341 FQKIDITEPSIEETVQIINGL  361 (758)
T ss_dssp             EEEEECCCCCHHHHHHHHHHH
T ss_pred             ceEEEcCCCCHHHHHHHHHHH
Confidence            999999999999998888765

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=99.16  E-value=6.1e-12  Score=132.87  Aligned_cols=208  Identities=16%  Similarity=0.224  Sum_probs=116.5

Q ss_pred             CcccchhhhH-HHHhhhhhcccccCCCce------EEEE-cCc----------cccCHHHHHHHHccCCCChhHHHHHHH
Q psy4285         177 SDDRGIGIVR-DQIFQFASTKTMHKSSYK------LIIL-DEA----------DAMTNDAQNALRRKLPVTPDGKKAIID  238 (533)
Q Consensus       177 sd~~g~~~~~-d~i~~~a~~~~l~~~~~~------~iil-DE~----------d~l~~~a~~~LRr~~~~~~~~l~~l~~  238 (533)
                      .|+.|++|.+ |+|   |.+.|+..+++.      +++| .++          +.|.+.+..+|               +
T Consensus        47 ~~i~gigf~~aD~i---a~~~g~~~~~~~R~~a~~~~~l~~~~~~~Ght~~~~~~l~~~~~~~l---------------~  108 (574)
T 3e1s_A           47 TEVEGIGFLTADKL---WQARGGALDDPRRLTAAAVYALQLAGTQAGHSFLPRSRAEKGVVHYT---------------R  108 (574)
T ss_dssp             GTSSSCCHHHHHTT---C-------CCHHHHHHHHHHHHHHHHHHTCCSCEEHHHHHHHHHHHH---------------C
T ss_pred             CCcCCCCHHHHHHH---HHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCEeecHHHHHHHHHHHh---------------C
Confidence            4889999999 999   999998877765      3444 222          22223333322               4


Q ss_pred             hccCchHHhhcHHHHHHhhcCCC-C---------CccccccccCCCCHHHHHHHHHHHhhhchh----------------
Q psy4285         239 LSDGDMRKVLNILQSAATAHADE-V---------NEDTVYNSVGYPTKTEITNILRWLLNESMD----------------  292 (533)
Q Consensus       239 ~s~~di~~~L~~L~~~~~~~~~~-~---------~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------------  292 (533)
                      ++...+.+++..+...+....+. .         ....+|....+..+..+...+..+......                
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~yl~~~~~~E~~ia~~l~~~~~~~~~~~~~~~~~~~l~~~~~  188 (574)
T 3e1s_A          109 VTPGQARLAVETAVELGRLSEDDSPLFAAEAAATGEGRIYLPHVLRAEKKLASLIRTLLATPPADGAGNDDWAVPKKARK  188 (574)
T ss_dssp             CCHHHHHHHHHHHHHHTSSEEECCCCSCC---CCSCCEEECHHHHHHHHHHHHHHHHHHHSCCCC-CCCCCCCCCTTTTT
T ss_pred             CCHHHHHHHHHHHHhCCCEEEEeccccccccccCCCcEEEcHHHHHHHHHHHHHHHHHhccCCccCCChhhHHHHHhhcC
Confidence            45556677777777766553322 1         112355555555666676666554432111                


Q ss_pred             -----hhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH-------HH
Q psy4285         293 -----LCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI-------FQ  360 (533)
Q Consensus       293 -----~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~  360 (533)
                           ....+....   ..+.++++|||||||||++.+++..+...   +..+. +.+++.+....+.+.+       ..
T Consensus       189 ~L~~~Q~~Av~~~~---~~~~~~I~G~pGTGKTt~i~~l~~~l~~~---g~~Vl-~~ApT~~Aa~~L~e~~~~~a~Tih~  261 (574)
T 3e1s_A          189 GLSEEQASVLDQLA---GHRLVVLTGGPGTGKSTTTKAVADLAESL---GLEVG-LCAPTGKAARRLGEVTGRTASTVHR  261 (574)
T ss_dssp             TCCHHHHHHHHHHT---TCSEEEEECCTTSCHHHHHHHHHHHHHHT---TCCEE-EEESSHHHHHHHHHHHTSCEEEHHH
T ss_pred             CCCHHHHHHHHHHH---hCCEEEEEcCCCCCHHHHHHHHHHHHHhc---CCeEE-EecCcHHHHHHhHhhhcccHHHHHH
Confidence                 001111111   12358999999999999999999877443   33333 3344444444444321       11


Q ss_pred             HHhccc-------CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         361 FASTKT-------MHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       361 ~~~~~~-------~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      +....+       ......++|||||+++++......|++.+   +.+.++|++++...
T Consensus       262 ll~~~~~~~~~~~~~~~~~dvlIIDEasml~~~~~~~Ll~~~---~~~~~lilvGD~~Q  317 (574)
T 3e1s_A          262 LLGYGPQGFRHNHLEPAPYDLLIVDEVSMMGDALMLSLLAAV---PPGARVLLVGDTDQ  317 (574)
T ss_dssp             HTTEETTEESCSSSSCCSCSEEEECCGGGCCHHHHHHHHTTS---CTTCEEEEEECTTS
T ss_pred             HHcCCcchhhhhhcccccCCEEEEcCccCCCHHHHHHHHHhC---cCCCEEEEEecccc
Confidence            211110       01235789999999999998777777666   46788999987544

>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=99.15  E-value=3.8e-10  Score=113.78  Aligned_cols=176  Identities=15%  Similarity=0.106  Sum_probs=114.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHH----HHhcccC-----CCCCcEEEEEe
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQ----FASTKTM-----HKSSYKLIILD  378 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~-----~~~~~~vliiD  378 (533)
                      +++++|++||||+++|++++......   ..+++.++++.......-.++++.    |......     ..+..++||+|
T Consensus       162 ~vli~Ge~GtGK~~lAr~ih~~s~r~---~~~fv~v~~~~~~~~~~~~elfg~~~g~~tga~~~~~g~~~~a~~gtlfld  238 (387)
T 1ny5_A          162 PVLITGESGVGKEVVARLIHKLSDRS---KEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLD  238 (387)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHSTTT---TSCEEEEETTTSCHHHHHHHHHCBCTTSSTTCCSCBCCHHHHTTTSEEEEE
T ss_pred             CeEEecCCCcCHHHHHHHHHHhcCCC---CCCeEEEecCCCCHHHHHHHhcCCCCCCCCCcccccCCceeeCCCcEEEEc
Confidence            48999999999999999998865332   457888888764322211121110    0000000     01346799999


Q ss_pred             CCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHhh
Q psy4285         379 EADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       379 E~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l~  440 (533)
                      |++.++.+.|..|++.+++.           +.++++|++||..       ..+.+.+..|+..+.+.-|+       |+
T Consensus       239 ei~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~l~~~~~~g~fr~dl~~rl~~~~i~lPp-------Lr  311 (387)
T 1ny5_A          239 EIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYRLGVIEIEIPP-------LR  311 (387)
T ss_dssp             SGGGCCHHHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSCHHHHHHTTSSCHHHHHHHTTEEEECCC-------GG
T ss_pred             ChhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCCCCHHHHHHcCCccHHHHHhhcCCeecCCc-------ch
Confidence            99999999999999999863           2478899999863       45778888888777776666       55


Q ss_pred             cCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHH
Q psy4285         441 YDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMS  496 (533)
Q Consensus       441 ~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~  496 (533)
                      ..++|+..+++.+-.  ......+.....+.......+..+.||++++ ++-+.+.
T Consensus       312 eR~~Di~~l~~~~l~--~~~~~~~~~~~~~~~~a~~~l~~~~wpGNvr-eL~~~i~  364 (387)
T 1ny5_A          312 ERKEDIIPLANHFLK--KFSRKYAKEVEGFTKSAQELLLSYPWYGNVR-ELKNVIE  364 (387)
T ss_dssp             GCHHHHHHHHHHHHH--HHHHHTTCCCCEECHHHHHHHHHSCCTTHHH-HHHHHHH
T ss_pred             hccccHHHHHHHHHH--HHHHHcCCCCCCCCHHHHHHHHhCCCCcHHH-HHHHHHH
Confidence            555666666654221  1112233333334456777788899999987 4333333

>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=99.15  E-value=1.1e-10  Score=120.54  Aligned_cols=99  Identities=11%  Similarity=0.135  Sum_probs=87.0

Q ss_pred             CCCCCCceEEEEEcCC-------------CCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHh
Q psy4285           1 IEKFTTNVRFCIICNY-------------LSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL   67 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~-------------~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   67 (533)
                      ||+|+.+ .|||.||+             ++++.|+|+|||+.++|++++.+++.++|++.+..+++.++++++..+++.
T Consensus       319 lEe~~~~-~~il~tn~~~~~i~~~~~~~~~~~l~~~i~sR~~~~~~~~~~~~e~~~iL~~~~~~~~~~~~~~~~~~i~~~  397 (456)
T 2c9o_A          319 LESSIAP-IVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEI  397 (456)
T ss_dssp             TTSTTCC-EEEEEECCSEEECBTTSSCEEETTCCHHHHTTEEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHH
T ss_pred             hhccCCC-EEEEecCCccccccccccccccccCChhHHhhcceeeCCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence            7999999 68889844             889999999999999999999999999999999999999999999999999


Q ss_pred             c-CCCHHHHHHHHHHHHHh----CCCCcchhhHHhhhh
Q psy4285          68 S-DGDMRKVLNILQSAATA----HADEVNEDTIFTLLV  100 (533)
Q Consensus        68 ~-~g~~r~a~~~l~~~~~~----~~~~i~~~~i~~~~~  100 (533)
                      + +|++|.|+++++.+...    ....|+.+.|.+.+.
T Consensus       398 a~~g~~r~a~~ll~~a~~~A~~~~~~~v~~~~v~~~~~  435 (456)
T 2c9o_A          398 GTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISE  435 (456)
T ss_dssp             HHHSCHHHHHHTHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             ccCCCHHHHHHHHHHHHHHHhhcCCCccCHHHHHHHHH
Confidence            9 99999999999987332    334688888876543

>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=99.14  E-value=9.3e-10  Score=110.03  Aligned_cols=165  Identities=16%  Similarity=0.130  Sum_probs=111.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCC------------CCCcEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH------------KSSYKLI  375 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~vl  375 (533)
                      .++++|++||||+++|++++......   + .++.++++.........++++   .....+            .+..++|
T Consensus       154 ~vli~GesGtGKe~lAr~ih~~s~r~---~-~fv~vnc~~~~~~~~~~~lfg---~~~g~~tga~~~~~g~~~~a~~gtl  226 (368)
T 3dzd_A          154 PVLITGESGTGKEIVARLIHRYSGRK---G-AFVDLNCASIPQELAESELFG---HEKGAFTGALTRKKGKLELADQGTL  226 (368)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHCCC---S-CEEEEESSSSCTTTHHHHHHE---ECSCSSSSCCCCEECHHHHTTTSEE
T ss_pred             hheEEeCCCchHHHHHHHHHHhcccc---C-CcEEEEcccCChHHHHHHhcC---ccccccCCcccccCChHhhcCCCeE
Confidence            58999999999999999999876333   2 388888876533322222211   111100            1345799


Q ss_pred             EEeCCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHH
Q psy4285         376 ILDEADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMS  437 (533)
Q Consensus       376 iiDE~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~  437 (533)
                      |+||++.++.+.|..|++.+++.           +.++++|++||..       ..+.+.|..|+..+.+.-|+      
T Consensus       227 fldei~~l~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~l~~~v~~g~fr~dL~~rl~~~~i~lPp------  300 (368)
T 3dzd_A          227 FLDEVGELDQRVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNKNLEEEIKKGNFREDLYYRLSVFQIYLPP------  300 (368)
T ss_dssp             EEETGGGSCHHHHHHHHHHHHHSEECCBTCCCBEECCCEEEEEESSCHHHHHHTTSSCHHHHHHHTSEEEECCC------
T ss_pred             EecChhhCCHHHHHHHHHHHHhCCcccCCCCcceeeeeEEEEecCCCHHHHHHcCCccHHHHHHhCCeEEeCCC------
Confidence            99999999999999999999863           2368899999854       35778899999877766666      


Q ss_pred             HhhcCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHH
Q psy4285         438 RLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       438 ~l~~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~  488 (533)
                       |+..++|+..+++.+-  .+.....+.....+.....+.+..+.||++++
T Consensus       301 -LreR~~Di~~l~~~~l--~~~~~~~~~~~~~~~~~a~~~L~~~~wpGNvr  348 (368)
T 3dzd_A          301 -LRERGKDVILLAEYFL--KKFAKEYKKNCFELSEETKEYLMKQEWKGNVR  348 (368)
T ss_dssp             -GGGSTTHHHHHHHHHH--HHHHHHTTCCCCCBCHHHHHHHHTCCCTTHHH
T ss_pred             -hhhchhhHHHHHHHHH--HHHHHHcCCCCCCcCHHHHHHHHhCCCCcHHH
Confidence             5555555555555321  12212234333345566778889999999986

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=99.12  E-value=2e-10  Score=115.62  Aligned_cols=101  Identities=21%  Similarity=0.411  Sum_probs=92.0

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      +|+|+.+++||++|+...++.++|+|||+.++|++++.+++.++|.+.+.++++.++++++..++..++||+|.+.+.++
T Consensus       143 le~~~~~~~~Il~~~~~~~l~~~l~sr~~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~a~~~l~~~~~G~~r~~~~~l~  222 (373)
T 1jr3_A          143 LEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTD  222 (373)
T ss_dssp             HHSCCSSEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHSSSCHHHHHHHHH
T ss_pred             HhcCCCceEEEEEeCChHhCcHHHHhheeEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHCCCCHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLVS  101 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~~  101 (533)
                      .+.......|+.+.|.++++.
T Consensus       223 ~~~~~~~~~i~~~~v~~~~~~  243 (373)
T 1jr3_A          223 QAIASGDGQVSTQAVSAMLGT  243 (373)
T ss_dssp             HHHHHTTTCBCHHHHHHHTTC
T ss_pred             HHHHhcCCcccHHHHHHHhCC
Confidence            987655567898888765543

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=99.11  E-value=1.4e-10  Score=100.31  Aligned_cols=98  Identities=14%  Similarity=0.252  Sum_probs=69.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDA  387 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~  387 (533)
                      .++|+||+|+||||++++++..+...   +...+.++..+....        .+       ...+++|+|||++.+....
T Consensus        38 ~~~l~G~~G~GKTtL~~~i~~~~~~~---g~~~~~~~~~~~~~~--------~~-------~~~~~lLilDE~~~~~~~~   99 (149)
T 2kjq_A           38 FIYVWGEEGAGKSHLLQAWVAQALEA---GKNAAYIDAASMPLT--------DA-------AFEAEYLAVDQVEKLGNEE   99 (149)
T ss_dssp             EEEEESSSTTTTCHHHHHHHHHHHTT---TCCEEEEETTTSCCC--------GG-------GGGCSEEEEESTTCCCSHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc---CCcEEEEcHHHhhHH--------HH-------HhCCCEEEEeCccccChHH
Confidence            58999999999999999999987432   344566666554332        11       1245799999999998777


Q ss_pred             HHHHHHHHHhcCC-Cc-EEEEEeCCCC-CC--Chhhhccce
Q psy4285         388 QNALRRIIEKFTT-NV-RFCIICNYLS-KI--PPAIQSRCT  423 (533)
Q Consensus       388 ~~~Ll~~le~~~~-~~-~~I~~~n~~~-~l--~~~l~sR~~  423 (533)
                      +..|+.+++.... +. ++|++||.+. .+  .+.+.||+.
T Consensus       100 ~~~l~~li~~~~~~g~~~iiits~~~p~~l~~~~~L~SRl~  140 (149)
T 2kjq_A          100 QALLFSIFNRFRNSGKGFLLLGSEYTPQQLVIREDLRTRMA  140 (149)
T ss_dssp             HHHHHHHHHHHHHHTCCEEEEEESSCTTTSSCCHHHHHHGG
T ss_pred             HHHHHHHHHHHHHcCCcEEEEECCCCHHHccccHHHHHHHh
Confidence            8888888875322 23 4788888532 22  289999984

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=99.04  E-value=3.5e-10  Score=101.01  Aligned_cols=116  Identities=19%  Similarity=0.225  Sum_probs=70.3

Q ss_pred             hhhhcccccccC-CCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCc
Q psy4285         294 CYKINRFIDENE-LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSY  372 (533)
Q Consensus       294 ~~~l~~~~~~~~-~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  372 (533)
                      ...++.++..-. ..+++|+||||||||++|.++++.+.+      .++.+..+.  ..-        ....    -.+.
T Consensus        45 ~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a~ala~~l~g------~i~~fans~--s~f--------~l~~----l~~~  104 (212)
T 1tue_A           45 LGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQG------AVISFVNST--SHF--------WLEP----LTDT  104 (212)
T ss_dssp             HHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHTC------EECCCCCSS--SCG--------GGGG----GTTC
T ss_pred             HHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhCC------CeeeEEecc--chh--------hhcc----cCCC
Confidence            445555554311 125999999999999999999998832      122111110  000        0000    0235


Q ss_pred             EEEEEeCCCCCCHHH-HHHHHHHHHhcC-------------CCcEEEEEeCCC---CCCChhhhccceeeeecC
Q psy4285         373 KLIILDEADAMTNDA-QNALRRIIEKFT-------------TNVRFCIICNYL---SKIPPAIQSRCTRFRFGP  429 (533)
Q Consensus       373 ~vliiDE~d~l~~~~-~~~Ll~~le~~~-------------~~~~~I~~~n~~---~~l~~~l~sR~~~i~~~~  429 (533)
                      +++++||++.-..+. ...+..+++..+             ....+|+|||..   ....+.|.||+..+.|+.
T Consensus       105 kIiiLDEad~~~~~~~d~~lrn~ldG~~~~iD~Khr~~~~~~~~PlIITtN~~~~~~~~~~~L~SRi~~f~F~~  178 (212)
T 1tue_A          105 KVAMLDDATTTCWTYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLESRITVFEFPN  178 (212)
T ss_dssp             SSEEEEEECHHHHHHHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHTSCEEEECCS
T ss_pred             CEEEEECCCchhHHHHHHHHHHHhCCCcccHHHhhcCccccCCCCEEEecCCCcccccchhhhhhhEEEEEcCC
Confidence            699999998532121 234666666532             235799999974   344578999999888874

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=99.02  E-value=6.3e-10  Score=104.34  Aligned_cols=126  Identities=14%  Similarity=0.143  Sum_probs=77.8

Q ss_pred             hhhhhcccccccCC-C-ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCC
Q psy4285         293 LCYKINRFIDENEL-P-HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKS  370 (533)
Q Consensus       293 ~~~~l~~~~~~~~~-~-~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  370 (533)
                      ....+..+++...+ . +++|+||||||||++|.++|+.+...       ..++.+..           .+....   -.
T Consensus        89 ~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~~~l~-------G~vn~~~~-----------~f~l~~---~~  147 (267)
T 1u0j_A           89 AASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVPFY-------GCVNWTNE-----------NFPFND---CV  147 (267)
T ss_dssp             HHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHSSCE-------EECCTTCS-----------SCTTGG---GS
T ss_pred             HHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhhhccc-------ceeecccc-----------cccccc---cc
Confidence            34456667665422 2 49999999999999999999974111       12222110           010000   02


Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHH--------hcC-----CCcEEEEEeCCC-----------CCCChhhhccceeee
Q psy4285         371 SYKLIILDEADAMTNDAQNALRRIIE--------KFT-----TNVRFCIICNYL-----------SKIPPAIQSRCTRFR  426 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~~le--------~~~-----~~~~~I~~~n~~-----------~~l~~~l~sR~~~i~  426 (533)
                      ...+++.||..+. .+.++.+.++++        +..     ..+.+|+|||..           ....++|+||+..+.
T Consensus       148 ~k~i~l~Ee~~~~-~d~~~~lr~i~~G~~~~id~K~k~~~~v~~tPvIitsN~~i~~~~~g~~~s~~~~~~L~sR~~~f~  226 (267)
T 1u0j_A          148 DKMVIWWEEGKMT-AKVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFE  226 (267)
T ss_dssp             SCSEEEECSCCEE-TTTHHHHHHHHTTCCEEC------CCEECCCCEEEEESSCTTCEEETTEEECTTHHHHHTTEEEEE
T ss_pred             ccEEEEeccccch-hHHHHHHHHHhCCCcEEEecCcCCcccccCCCEEEEecCCcccccccCccchhhhHHHhhhEEEEE
Confidence            3456666666655 456667777776        322     567899999972           245689999999999


Q ss_pred             ec--------CCCHHHHHHHhh
Q psy4285         427 FG--------PLDSSLIMSRLD  440 (533)
Q Consensus       427 ~~--------~~~~~~~~~~l~  440 (533)
                      |.        +++++++...+.
T Consensus       227 F~~~~p~~~~~lt~~~~~~f~~  248 (267)
T 1u0j_A          227 LTRRLDHDFGKVTKQEVKDFFR  248 (267)
T ss_dssp             CCSCCCTTSCCCCHHHHHHHHH
T ss_pred             CCCcCCcccCCCCHHHHHHHHH
Confidence            98        555555555443

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=99.02  E-value=2.6e-10  Score=121.94  Aligned_cols=53  Identities=19%  Similarity=0.281  Sum_probs=45.7

Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhc---------------------CCCcEEEEEeCCC--CCCChhhhccce
Q psy4285         371 SYKLIILDEADAMTNDAQNALRRIIEKF---------------------TTNVRFCIICNYL--SKIPPAIQSRCT  423 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~~le~~---------------------~~~~~~I~~~n~~--~~l~~~l~sR~~  423 (533)
                      .+++|||||++.+++..++.|++.|++.                     +.++++|++||..  ..++++|++||.
T Consensus       201 ~~gvL~LDEi~~l~~~~q~~Ll~~Le~~~~~~~g~~~~~~~~~l~~~~~p~~~~vI~atn~~~~~~l~~~l~~R~~  276 (604)
T 3k1j_A          201 HKGVLFIDEIATLSLKMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNLDTVDKMHPALRSRIR  276 (604)
T ss_dssp             TTSEEEETTGGGSCHHHHHHHHHHHHHSEECCBCSCTTSGGGGCBCSCEECCCEEEEEECHHHHHHSCHHHHHHHH
T ss_pred             CCCEEEEechhhCCHHHHHHHHHHHHcCcEEecccccccccccCCCCccceeEEEEEecCHHHHhhcCHHHHHHhh
Confidence            4569999999999999999999999842                     2467899999976  579999999994

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=98.98  E-value=6.8e-10  Score=99.48  Aligned_cols=99  Identities=20%  Similarity=0.259  Sum_probs=62.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC----CCCCcEEEEEeCCC--
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM----HKSSYKLIILDEAD--  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~vliiDE~d--  381 (533)
                      +++|+|||||||||++++++..+....  +..+..++..+     ........+......    ....+++|||||++  
T Consensus        40 ~~~l~G~~G~GKTtL~~~i~~~~~~~~--g~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~llilDE~~~~  112 (180)
T 3ec2_A           40 GLTFVGSPGVGKTHLAVATLKAIYEKK--GIRGYFFDTKD-----LIFRLKHLMDEGKDTKFLKTVLNSPVLVLDDLGSE  112 (180)
T ss_dssp             EEEECCSSSSSHHHHHHHHHHHHHHHS--CCCCCEEEHHH-----HHHHHHHHHHHTCCSHHHHHHHTCSEEEEETCSSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHc--CCeEEEEEHHH-----HHHHHHHHhcCchHHHHHHHhcCCCEEEEeCCCCC
Confidence            589999999999999999999874222  22222222211     111111111100000    00246799999998  


Q ss_pred             CCCHHHHHHHHHHHHhcC-CCcEEEEEeCCCCC
Q psy4285         382 AMTNDAQNALRRIIEKFT-TNVRFCIICNYLSK  413 (533)
Q Consensus       382 ~l~~~~~~~Ll~~le~~~-~~~~~I~~~n~~~~  413 (533)
                      .++...+..|++++++.. .+..+|++||.+..
T Consensus       113 ~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~~~~  145 (180)
T 3ec2_A          113 RLSDWQRELISYIITYRYNNLKSTIITTNYSLQ  145 (180)
T ss_dssp             CCCHHHHHHHHHHHHHHHHTTCEEEEECCCCSC
T ss_pred             cCCHHHHHHHHHHHHHHHHcCCCEEEEcCCChh
Confidence            567888888888887643 56789999998764

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

Probab=98.94  E-value=1.7e-09  Score=110.66  Aligned_cols=112  Identities=20%  Similarity=0.310  Sum_probs=92.5

Q ss_pred             CceEEEEEc--CCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhh-------cCCCCCHHHHHHHHHhcCCCHHHHH
Q psy4285           6 TNVRFCIIC--NYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQ-------EKVNVTPDGKKAIIDLSDGDMRKVL   76 (533)
Q Consensus         6 ~~~~~il~~--~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~-------~~~~~~~~~~~~~~~~~~g~~r~a~   76 (533)
                      +.++||.+|  |+.+.+.++|+|||+++.|++++.+++..++.+.+.+       +++.+++++++.++..++||+|.++
T Consensus       133 ~~v~lI~att~n~~~~l~~aL~sR~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~Gd~R~ll  212 (447)
T 3pvs_A          133 GTITFIGATTENPSFELNSALLSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRAL  212 (447)
T ss_dssp             TSCEEEEEESSCGGGSSCHHHHTTEEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCSCHHHHH
T ss_pred             CceEEEecCCCCcccccCHHHhCceeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCCCHHHHH
Confidence            457788777  7778999999999999999999999999999999876       5577999999999999999999999


Q ss_pred             HHHHHHHHhCC------CCcchhhHHhhhhhhccccch--hHHHHHhch
Q psy4285          77 NILQSAATAHA------DEVNEDTIFTLLVSRVEKYRP--STLDELVSH  117 (533)
Q Consensus        77 ~~l~~~~~~~~------~~i~~~~i~~~~~~~~ek~~~--~~l~~lls~  117 (533)
                      |+|+.+.....      ..||.+.+.++++.....|+.  +.+|++++.
T Consensus       213 n~Le~a~~~a~~~~~~~~~It~e~v~~~l~~~~~~~dk~gd~~yd~isa  261 (447)
T 3pvs_A          213 NTLEMMADMAEVDDSGKRVLKPELLTEIAGERSARFDNKGDRFYDLISA  261 (447)
T ss_dssp             HHHHHHHHHSCBCTTSCEECCHHHHHHHHTCCCCC---CCHHHHHHHHH
T ss_pred             HHHHHHHHhcccccCCCCccCHHHHHHHHhhhhhccCCccchHHHHHHH
Confidence            99999987643      249999998888766655554  357777653

>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=98.93  E-value=3.7e-09  Score=99.08  Aligned_cols=98  Identities=21%  Similarity=0.420  Sum_probs=89.1

Q ss_pred             CCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q psy4285           2 EKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQS   81 (533)
Q Consensus         2 E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~   81 (533)
                      |+++.++++|++||....+.++++|||..++|++++.+++.+++.+.+.++++.++++.++.+++.++||+|.+.++++.
T Consensus       151 ~~~~~~~~~i~~t~~~~~~~~~l~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~~~~~~~~~~  230 (250)
T 1njg_A          151 EEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQ  230 (250)
T ss_dssp             HSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             hcCCCceEEEEEeCChHhCCHHHHHHhhhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            56788999999999999999999999999999999999999999999988888999999999999999999999999999


Q ss_pred             HHHhCCCCcchhhHHhhh
Q psy4285          82 AATAHADEVNEDTIFTLL   99 (533)
Q Consensus        82 ~~~~~~~~i~~~~i~~~~   99 (533)
                      +.......|+.+.+.+++
T Consensus       231 ~~~~~~~~i~~~~v~~~~  248 (250)
T 1njg_A          231 AIASGDGQVSTQAVSAML  248 (250)
T ss_dssp             HHTTTTSSBCHHHHHHHS
T ss_pred             HHhccCceecHHHHHHHh
Confidence            877555578888876654

>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=98.93  E-value=2.6e-09  Score=128.76  Aligned_cols=130  Identities=16%  Similarity=0.207  Sum_probs=94.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcc---------cCCCCCcEEEEEe
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTK---------TMHKSSYKLIILD  378 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~vliiD  378 (533)
                      ++||+||||||||++|+.++...     .+..+..++.+...+...+.+.+.......         +...+...|+|||
T Consensus      1269 ~vLL~GPpGtGKT~la~~~l~~~-----~~~~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~~~~P~~~gk~~VlFiD 1343 (2695)
T 4akg_A         1269 GIILCGPPGSGKTMIMNNALRNS-----SLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCD 1343 (2695)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC-----SSCEEEEEECCTTCCHHHHHHHHHHHBCCEEETTTEEEEEBSSSSCEEEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHhcC-----CCCceEEEEeecCCCHHHHHHHHHHHhhhccccCCccccCCCCCceEEEEec
Confidence            69999999999999996665543     145666777776666666665555432111         1012346799999


Q ss_pred             CCCCCCH------HHHHHHHHHHHhcC------------CCcEEEEEeCCCC-----CCChhhhccceeeeecCCCHHHH
Q psy4285         379 EADAMTN------DAQNALRRIIEKFT------------TNVRFCIICNYLS-----KIPPAIQSRCTRFRFGPLDSSLI  435 (533)
Q Consensus       379 E~d~l~~------~~~~~Ll~~le~~~------------~~~~~I~~~n~~~-----~l~~~l~sR~~~i~~~~~~~~~~  435 (533)
                      |+++-..      ...+.|.+.+|...            .++.+|+++|++.     .++++++|||..+.++.|+.+++
T Consensus      1344 Einmp~~d~yg~q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllRrf~vi~i~~P~~~~l 1423 (2695)
T 4akg_A         1344 EINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYLGYPSGKSL 1423 (2695)
T ss_dssp             TTTCSCCCSSSCCHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHTTEEEEECCCCTTTHH
T ss_pred             ccccccccccCchhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhheeeEEEeCCCCHHHH
Confidence            9987643      35667777777421            2478999999984     79999999999999999999999


Q ss_pred             HHHhhcC
Q psy4285         436 MSRLDYD  442 (533)
Q Consensus       436 ~~~l~~~  442 (533)
                      ..++..+
T Consensus      1424 ~~I~~~i 1430 (2695)
T 4akg_A         1424 SQIYEIY 1430 (2695)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9888765

>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=98.93  E-value=3.4e-09  Score=97.89  Aligned_cols=98  Identities=42%  Similarity=0.710  Sum_probs=89.1

Q ss_pred             CCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q psy4285           2 EKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQS   81 (533)
Q Consensus         2 E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~   81 (533)
                      |+++.++++|++||.+..+.++++|||..+.|++++.+++.+++.+.+.+.++.+++++++.+++.++||+|.+++.++.
T Consensus       127 ~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~l~~~l~~  206 (226)
T 2chg_A          127 EMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQG  206 (226)
T ss_dssp             HHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HhcCCCCeEEEEeCChhhcCHHHHHhCceeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            56778899999999999999999999999999999999999999999988888899999999999999999999999999


Q ss_pred             HHHhCCCCcchhhHHhhhh
Q psy4285          82 AATAHADEVNEDTIFTLLV  100 (533)
Q Consensus        82 ~~~~~~~~i~~~~i~~~~~  100 (533)
                      ++... ..|+.+.+.++++
T Consensus       207 ~~~~~-~~I~~~~v~~~~~  224 (226)
T 2chg_A          207 AAAIG-EVVDADTIYQITA  224 (226)
T ss_dssp             HHHTC-SCBCHHHHHHHHH
T ss_pred             HHhcC-ceecHHHHHHHhc
Confidence            98754 5789888876554

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=98.80  E-value=6e-09  Score=106.16  Aligned_cols=132  Identities=19%  Similarity=0.296  Sum_probs=83.2

Q ss_pred             CCceeE--eCCCCCChHHHHHHHHHHHcccc---ccCcceEEecCCCCCch-hHHHHH---------------------H
Q psy4285         306 LPHLLF--YGPPGTGKTTTILACARKLYTKA---QFNAMVLELNASDDRGI-GIVRDQ---------------------I  358 (533)
Q Consensus       306 ~~~~ll--~GppGtGKT~la~~la~~l~~~~---~~~~~~~~~~~~~~~~~-~~~~~~---------------------~  358 (533)
                      ..++++  +||||+|||++++.+++.+....   ..+..++.+++...... ......                     +
T Consensus        50 ~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l  129 (412)
T 1w5s_A           50 DVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKAL  129 (412)
T ss_dssp             CEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHH
T ss_pred             CCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHH
Confidence            345888  99999999999999998874320   01223445553221111 111111                     1


Q ss_pred             HHHHhcccCCCCCcEEEEEeCCCCCC------HHHHHHHHHHHHhcC-----CCcEEEEEeCCCC---CCC---hhhhcc
Q psy4285         359 FQFASTKTMHKSSYKLIILDEADAMT------NDAQNALRRIIEKFT-----TNVRFCIICNYLS---KIP---PAIQSR  421 (533)
Q Consensus       359 ~~~~~~~~~~~~~~~vliiDE~d~l~------~~~~~~Ll~~le~~~-----~~~~~I~~~n~~~---~l~---~~l~sR  421 (533)
                      ......    ...+.+|||||++.+.      .+....|++.++..+     .++.+|++|+.+.   .++   +.+.+|
T Consensus       130 ~~~l~~----~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~~  205 (412)
T 1w5s_A          130 VDNLYV----ENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQ  205 (412)
T ss_dssp             HHHHHH----HTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTT
T ss_pred             HHHHHh----cCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCceEEEEEEeccccHHHHHhhhcchhhhh
Confidence            111110    1346799999999974      356666777777643     5677888887554   233   666677


Q ss_pred             c-eeeeecCCCHHHHHHHhhc
Q psy4285         422 C-TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       422 ~-~~i~~~~~~~~~~~~~l~~  441 (533)
                      + ..+.+.|++.+++.+++.+
T Consensus       206 ~~~~i~l~~l~~~e~~~ll~~  226 (412)
T 1w5s_A          206 IGFKLHLPAYKSRELYTILEQ  226 (412)
T ss_dssp             CSEEEECCCCCHHHHHHHHHH
T ss_pred             cCCeeeeCCCCHHHHHHHHHH
Confidence            6 3499999999999998854

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.69  E-value=9.4e-09  Score=93.77  Aligned_cols=94  Identities=18%  Similarity=0.170  Sum_probs=55.0

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc-------hhHHHHHHHHHHhcccCCCCCcEEEEEeC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG-------IGIVRDQIFQFASTKTMHKSSYKLIILDE  379 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~vliiDE  379 (533)
                      .+++|+||||||||++++++++.+...   +..+..++.++...       .......+..+        ...++|||||
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~lilDe  123 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELAKR---NVSSLIVYVPELFRELKHSLQDQTMNEKLDYI--------KKVPVLMLDD  123 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHTT---TCCEEEEEHHHHHHHHHHC---CCCHHHHHHH--------HHSSEEEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEEhHHHHHHHHHHhccchHHHHHHHh--------cCCCEEEEcC
Confidence            469999999999999999999988543   23343333321100       00001111111        1235999999


Q ss_pred             CCCCCH--HHHHHHH-HHHHhc-CCCcEEEEEeCCC
Q psy4285         380 ADAMTN--DAQNALR-RIIEKF-TTNVRFCIICNYL  411 (533)
Q Consensus       380 ~d~l~~--~~~~~Ll-~~le~~-~~~~~~I~~~n~~  411 (533)
                      ++....  +.+..++ .+++.. ..+..+|+|||..
T Consensus       124 i~~~~~~~~~~~~ll~~~l~~~~~~~~~~i~tsn~~  159 (202)
T 2w58_A          124 LGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNFD  159 (202)
T ss_dssp             ECCC---CCGGGTTHHHHHHHHHHTTCCEEEEESSC
T ss_pred             CCCCcCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCC
Confidence            977543  3344344 466543 4567899999864

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

Probab=98.69  E-value=6.8e-08  Score=96.80  Aligned_cols=99  Identities=17%  Similarity=0.187  Sum_probs=83.5

Q ss_pred             CCCCCCceEEEEEcC------------CCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhc
Q psy4285           1 IEKFTTNVRFCIICN------------YLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLS   68 (533)
Q Consensus         1 ~E~~~~~~~~il~~~------------~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   68 (533)
                      +|+++..+ ++++++            ++..+.|+|+|||.++.|++|+.+++.++|++.+..+++.+++++++.++..+
T Consensus       213 le~~~~~~-~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~  291 (368)
T 3uk6_A          213 LESDMAPV-LIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIG  291 (368)
T ss_dssp             TTCTTCCE-EEEEESCSEEECBTSSCEEETTCCHHHHTTEEEEEECCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHH
T ss_pred             hhCcCCCe-eeeecccceeeeeccCCCCcccCCHHHHhhccEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHh
Confidence            46776665 455554            57889999999999999999999999999999999899999999999999999


Q ss_pred             C-CCHHHHHHHHHHHHHh----CCCCcchhhHHhhhh
Q psy4285          69 D-GDMRKVLNILQSAATA----HADEVNEDTIFTLLV  100 (533)
Q Consensus        69 ~-g~~r~a~~~l~~~~~~----~~~~i~~~~i~~~~~  100 (533)
                      . ||+|.++++++.+...    ....|+.+.+.+.+.
T Consensus       292 ~~G~~r~~~~ll~~a~~~A~~~~~~~It~~~v~~a~~  328 (368)
T 3uk6_A          292 LETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYS  328 (368)
T ss_dssp             HHSCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence            9 9999999999997653    234688888766543

>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=98.69  E-value=2.2e-07  Score=112.27  Aligned_cols=121  Identities=20%  Similarity=0.266  Sum_probs=96.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDA  387 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~  387 (533)
                      ..++.||||||||++++.+|+.+      +..++.+++++......+.+.+....+.       +..+++||++++..+.
T Consensus       647 ~~~l~GpaGtGKTe~vk~LA~~l------g~~~v~~nc~e~ld~~~lg~~~~g~~~~-------Gaw~~~DE~nr~~~ev  713 (2695)
T 4akg_A          647 GGCFFGPAGTGKTETVKAFGQNL------GRVVVVFNCDDSFDYQVLSRLLVGITQI-------GAWGCFDEFNRLDEKV  713 (2695)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHTT------TCCCEEEETTSSCCHHHHHHHHHHHHHH-------TCEEEEETTTSSCHHH
T ss_pred             CCcccCCCCCCcHHHHHHHHHHh------CCcEEEEECCCCCChhHhhHHHHHHHhc-------CCEeeehhhhhcChHH
Confidence            37899999999999999999998      8888999999888877776665554433       3599999999999988


Q ss_pred             HHHHHHH-------HHhc-------------CCCcEEEEEeCC----CCCCChhhhccceeeeecCCCHHHHHHHhhc
Q psy4285         388 QNALRRI-------IEKF-------------TTNVRFCIICNY----LSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       388 ~~~Ll~~-------le~~-------------~~~~~~I~~~n~----~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~  441 (533)
                      .+.+-..       +.+.             .+++.+++|.|.    ...+++++++||..+.+..|+.+.+.+++..
T Consensus       714 Ls~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy~g~~eLP~~Lk~~Fr~v~m~~Pd~~~i~ei~l~  791 (2695)
T 4akg_A          714 LSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKKSFREFSMKSPQSGTIAEMILQ  791 (2695)
T ss_dssp             HHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCSSSSCCCCHHHHTTEEEEECCCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCccCcccccHHHHhheEEEEeeCCCHHHHHHHHHH
Confidence            7776333       3221             345678888883    4579999999999999999999999888644

>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=98.64  E-value=3.8e-07  Score=91.58  Aligned_cols=112  Identities=11%  Similarity=0.112  Sum_probs=71.2

Q ss_pred             CceeEeCCCCCChHHHHHHH-HHHHccccccCcceEEecCCCCCchh-HHHHHHHHHHhccc-CCCCCcEEEEEeCCCCC
Q psy4285         307 PHLLFYGPPGTGKTTTILAC-ARKLYTKAQFNAMVLELNASDDRGIG-IVRDQIFQFASTKT-MHKSSYKLIILDEADAM  383 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~l-a~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~-~~~~~~~vliiDE~d~l  383 (533)
                      .|+|+.|+||| ||.+++++ ++.+ ...    .+.....+...+.. .+++..+ +..... ...+...++++||++.+
T Consensus       240 ihVLL~G~PGt-KS~Lar~i~~~i~-pR~----~ft~g~~ss~~gLt~s~r~~tG-~~~~~G~l~LAdgGvl~lDEIn~~  312 (506)
T 3f8t_A          240 LHVLLAGYPVV-CSEILHHVLDHLA-PRG----VYVDLRRTELTDLTAVLKEDRG-WALRAGAAVLADGGILAVDHLEGA  312 (506)
T ss_dssp             CCEEEESCHHH-HHHHHHHHHHHTC-SSE----EEEEGGGCCHHHHSEEEEESSS-EEEEECHHHHTTTSEEEEECCTTC
T ss_pred             eeEEEECCCCh-HHHHHHHHHHHhC-CCe----EEecCCCCCccCceEEEEcCCC-cccCCCeeEEcCCCeeehHhhhhC
Confidence            37999999999 99999999 6643 111    11111111000000 0000000 000000 00134679999999999


Q ss_pred             CHHHHHHHHHHHHhc---------CCCcEEEEEeCCCC-----------CCChhhhccceee
Q psy4285         384 TNDAQNALRRIIEKF---------TTNVRFCIICNYLS-----------KIPPAIQSRCTRF  425 (533)
Q Consensus       384 ~~~~~~~Ll~~le~~---------~~~~~~I~~~n~~~-----------~l~~~l~sR~~~i  425 (533)
                      +...+.+|++.||+.         +..+.+|.++|...           .+++++++||+.+
T Consensus       313 ~~~~qsaLlEaMEe~~VtI~G~~lparf~VIAA~NP~~~yd~~~s~~~~~Lp~alLDRFDLi  374 (506)
T 3f8t_A          313 PEPHRWALMEAMDKGTVTVDGIALNARCAVLAAINPGEQWPSDPPIARIDLDQDFLSHFDLI  374 (506)
T ss_dssp             CHHHHHHHHHHHHHSEEEETTEEEECCCEEEEEECCCC--CCSCGGGGCCSCHHHHTTCSEE
T ss_pred             CHHHHHHHHHHHhCCcEEECCEEcCCCeEEEEEeCcccccCCCCCccccCCChHHhhheeeE
Confidence            999999999999963         56788999999764           7899999999543

>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=98.63  E-value=1.1e-07  Score=99.67  Aligned_cols=96  Identities=24%  Similarity=0.403  Sum_probs=82.8

Q ss_pred             ceEEEEEcCCCC-cCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHh
Q psy4285           7 NVRFCIICNYLS-KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATA   85 (533)
Q Consensus         7 ~~~~il~~~~~~-~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~~~~   85 (533)
                      ++.+|++||... ..++++++||+.++|++|+.+++.++|.+++.++++.++++++..|+..++||+|.+++.|+.++. 
T Consensus       179 ~~~iIli~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~~~l~~la~~s~GdiR~~i~~L~~~~~-  257 (516)
T 1sxj_A          179 STPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTIST-  257 (516)
T ss_dssp             SSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTTCHHHHHHHHTHHHH-
T ss_pred             CCCEEEEEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh-
Confidence            345777776554 678999999999999999999999999999999999999999999999999999999999999876 


Q ss_pred             CCCCcchhhHHhhhhhhc
Q psy4285          86 HADEVNEDTIFTLLVSRV  103 (533)
Q Consensus        86 ~~~~i~~~~i~~~~~~~~  103 (533)
                      ....|+.+.+.+++..|.
T Consensus       258 ~~~~It~~~v~~~~~~~~  275 (516)
T 1sxj_A          258 TTKTINHENINEISKAWE  275 (516)
T ss_dssp             HSSCCCTTHHHHHHHHHH
T ss_pred             cCCCCchHHHHHHHHhhc
Confidence            445688888877666554

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=98.60  E-value=1.4e-08  Score=98.91  Aligned_cols=97  Identities=21%  Similarity=0.216  Sum_probs=53.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHc-cccccCcceEEecCCCCCchhHHHHHHHHHHh--cccCC--CCCcEEEEEeCCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLY-TKAQFNAMVLELNASDDRGIGIVRDQIFQFAS--TKTMH--KSSYKLIILDEAD  381 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~--~~~~~vliiDE~d  381 (533)
                      .+++|+||||||||++|.++++.+. ..   +..+..++.++.     +.+....+..  .....  -...++|||||++
T Consensus       153 ~~lll~G~~GtGKT~La~aia~~~~~~~---g~~v~~~~~~~l-----~~~l~~~~~~~~~~~~~~~~~~~~lLiiDdig  224 (308)
T 2qgz_A          153 KGLYLYGDMGIGKSYLLAAMAHELSEKK---GVSTTLLHFPSF-----AIDVKNAISNGSVKEEIDAVKNVPVLILDDIG  224 (308)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHHS---CCCEEEEEHHHH-----HHHHHCCCC----CCTTHHHHTSSEEEEETCC
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHhc---CCcEEEEEHHHH-----HHHHHHHhccchHHHHHHHhcCCCEEEEcCCC
Confidence            4699999999999999999999885 33   334443333210     1110000000  00000  0135699999997


Q ss_pred             CCC--HHHHHHHHH-HHHhc-CCCcEEEEEeCCC
Q psy4285         382 AMT--NDAQNALRR-IIEKF-TTNVRFCIICNYL  411 (533)
Q Consensus       382 ~l~--~~~~~~Ll~-~le~~-~~~~~~I~~~n~~  411 (533)
                      ...  .+.+..|+. +++.. ..+..+|+|||.+
T Consensus       225 ~~~~~~~~~~~ll~~ll~~r~~~~~~~IitSN~~  258 (308)
T 2qgz_A          225 AEQATSWVRDEVLQVILQYRMLEELPTFFTSNYS  258 (308)
T ss_dssp             C------CTTTTHHHHHHHHHHHTCCEEEEESSC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHCCCcEEEECCCC
Confidence            653  333443443 66543 3456899999854

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.54  E-value=2.4e-07  Score=112.53  Aligned_cols=128  Identities=19%  Similarity=0.265  Sum_probs=92.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcc----------cCCCCCcEEEEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTK----------TMHKSSYKLIIL  377 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~vlii  377 (533)
                      ++||+||||||||.++......+     .+..++.++.+.......+.+.+.......          +...+++.|+||
T Consensus      1306 pvLL~GptGtGKT~li~~~L~~l-----~~~~~~~infS~~Tta~~l~~~~e~~~e~~~~~~~G~~~~p~~~Gk~~VlFi 1380 (3245)
T 3vkg_A         1306 PLILCGPPGSGKTMTLTSTLRAF-----PDFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFC 1380 (3245)
T ss_dssp             CCEEESSTTSSHHHHHHHHGGGC-----TTEEEEEECCCTTCCHHHHHHHHHHHEEEEECTTSCEEEEESSTTCEEEEEE
T ss_pred             cEEEECCCCCCHHHHHHHHHHhC-----CCCceEEEEeeCCCCHHHHHHHHhhcceEEeccCCCcccCCCcCCceEEEEe
Confidence            69999999999998876554433     134567788877777666666554422111          100144679999


Q ss_pred             eCCCCCCH------HHHHHHHHHHHhc------------CCCcEEEEEeCCC-----CCCChhhhccceeeeecCCCHHH
Q psy4285         378 DEADAMTN------DAQNALRRIIEKF------------TTNVRFCIICNYL-----SKIPPAIQSRCTRFRFGPLDSSL  434 (533)
Q Consensus       378 DE~d~l~~------~~~~~Ll~~le~~------------~~~~~~I~~~n~~-----~~l~~~l~sR~~~i~~~~~~~~~  434 (533)
                      ||+++-..      ...+.|.+++|..            ..++.+|+++|.+     ..++++++|||..+.++.|+.++
T Consensus      1381 DDiNmp~~D~yGtQ~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp~~gGr~~l~~Rf~r~F~vi~i~~ps~es 1460 (3245)
T 3vkg_A         1381 DEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLRHAPILLVDFPSTSS 1460 (3245)
T ss_dssp             TTTTCCCCCTTSCCHHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECCTTSTTCCCCCHHHHTTCCEEECCCCCHHH
T ss_pred             cccCCCCccccccccHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCCCCCCCccCCHHHHhhceEEEeCCCCHHH
Confidence            99988654      3567778888742            2457789999977     36999999999999999999999


Q ss_pred             HHHHhh
Q psy4285         435 IMSRLD  440 (533)
Q Consensus       435 ~~~~l~  440 (533)
                      +..+..
T Consensus      1461 L~~If~ 1466 (3245)
T 3vkg_A         1461 LTQIYG 1466 (3245)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            998844

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=98.51  E-value=6.3e-08  Score=87.57  Aligned_cols=118  Identities=10%  Similarity=0.163  Sum_probs=67.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcc--ccccC-cceEEecCCCCC--c---------------hhHHHHHHHHHHhcccCC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYT--KAQFN-AMVLELNASDDR--G---------------IGIVRDQIFQFASTKTMH  368 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~--~~~~~-~~~~~~~~~~~~--~---------------~~~~~~~~~~~~~~~~~~  368 (533)
                      .+++|+||+|||+.|..++.....  ....+ ..++..+..+..  .               .....+....+...+   
T Consensus         8 ~l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~~gL~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~---   84 (199)
T 2r2a_A            8 CLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIPHTYIETDAKKLPKSTDEQLSAHDMYEWIKKP---   84 (199)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECCTTBCSCCEEEECCTTTCSSCCSSCEEGGGHHHHTTSG---
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecCCCccccccccchhhhhccccCcccccHHHHHHHhhcc---
Confidence            689999999999999887655420  00012 333222222110  0               000001111221111   


Q ss_pred             CCCcEEEEEeCCCCCCH---HH--HHHHHHHHHh-cCCCcEEEEEeCCCCCCChhhhccce-eeeecC
Q psy4285         369 KSSYKLIILDEADAMTN---DA--QNALRRIIEK-FTTNVRFCIICNYLSKIPPAIQSRCT-RFRFGP  429 (533)
Q Consensus       369 ~~~~~vliiDE~d~l~~---~~--~~~Ll~~le~-~~~~~~~I~~~n~~~~l~~~l~sR~~-~i~~~~  429 (533)
                      .+...||||||++.+.+   +.  ...++..++. ......+|++|+.+..++.++++|+. .+++.+
T Consensus        85 ~~~~~vliIDEAq~l~~~~~~~~e~~rll~~l~~~r~~~~~iil~tq~~~~l~~~lr~ri~~~~~l~~  152 (199)
T 2r2a_A           85 ENIGSIVIVDEAQDVWPARSAGSKIPENVQWLNTHRHQGIDIFVLTQGPKLLDQNLRTLVRKHYHIAS  152 (199)
T ss_dssp             GGTTCEEEETTGGGTSBCCCTTCCCCHHHHGGGGTTTTTCEEEEEESCGGGBCHHHHTTEEEEEEEEE
T ss_pred             ccCceEEEEEChhhhccCccccchhHHHHHHHHhcCcCCeEEEEECCCHHHHhHHHHHHhheEEEEcC
Confidence            13467999999999832   11  1134444443 34567899999999999999999984 566655

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.48  E-value=4.2e-07  Score=90.08  Aligned_cols=69  Identities=12%  Similarity=0.169  Sum_probs=48.4

Q ss_pred             cEEEEEeCCCCCCH-------HHHHHHHHHHHhcCCCcEEEEEeCCCC---------CCChhhhccc-eeeeecCCCHHH
Q psy4285         372 YKLIILDEADAMTN-------DAQNALRRIIEKFTTNVRFCIICNYLS---------KIPPAIQSRC-TRFRFGPLDSSL  434 (533)
Q Consensus       372 ~~vliiDE~d~l~~-------~~~~~Ll~~le~~~~~~~~I~~~n~~~---------~l~~~l~sR~-~~i~~~~~~~~~  434 (533)
                      +.+|+|||++.+..       +....|...++.. .++.+|+++....         ....++..|. ..+.+.|++.++
T Consensus       129 ~~vlvlDe~~~~~~~~~~~~~~~~~~L~~~~~~~-~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e  207 (350)
T 2qen_A          129 EFIVAFDEAQYLRFYGSRGGKELLALFAYAYDSL-PNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDT  207 (350)
T ss_dssp             CEEEEEETGGGGGGBTTTTTHHHHHHHHHHHHHC-TTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHH
T ss_pred             CEEEEEeCHHHHhccCccchhhHHHHHHHHHHhc-CCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHH
Confidence            57999999999864       4445555555553 4788888886431         2233455455 589999999999


Q ss_pred             HHHHhhc
Q psy4285         435 IMSRLDY  441 (533)
Q Consensus       435 ~~~~l~~  441 (533)
                      ..+.+.+
T Consensus       208 ~~~~l~~  214 (350)
T 2qen_A          208 SVEFLKR  214 (350)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9988865

>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=98.46  E-value=5.9e-07  Score=89.24  Aligned_cols=69  Identities=16%  Similarity=0.288  Sum_probs=48.0

Q ss_pred             cEEEEEeCCCCCCH----HHHHHHHHHHHhcCCCcEEEEEeCCCC---------CCChhhhccc-eeeeecCCCHHHHHH
Q psy4285         372 YKLIILDEADAMTN----DAQNALRRIIEKFTTNVRFCIICNYLS---------KIPPAIQSRC-TRFRFGPLDSSLIMS  437 (533)
Q Consensus       372 ~~vliiDE~d~l~~----~~~~~Ll~~le~~~~~~~~I~~~n~~~---------~l~~~l~sR~-~~i~~~~~~~~~~~~  437 (533)
                      +.+|+|||++.+..    +....|....+.. .++.+|++++...         ....++..|+ ..+.+.|++.++..+
T Consensus       138 ~~vlvlDe~~~~~~~~~~~~~~~l~~~~~~~-~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~  216 (357)
T 2fna_A          138 NVIIVLDEAQELVKLRGVNLLPALAYAYDNL-KRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIE  216 (357)
T ss_dssp             CEEEEEETGGGGGGCTTCCCHHHHHHHHHHC-TTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHH
T ss_pred             CeEEEEECHHHhhccCchhHHHHHHHHHHcC-CCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHH
Confidence            67999999999753    2334454455543 4688888887532         2223455565 689999999999998


Q ss_pred             Hhhc
Q psy4285         438 RLDY  441 (533)
Q Consensus       438 ~l~~  441 (533)
                      .+.+
T Consensus       217 ~l~~  220 (357)
T 2fna_A          217 FLRR  220 (357)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8875

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=98.42  E-value=6.1e-07  Score=92.55  Aligned_cols=117  Identities=16%  Similarity=0.157  Sum_probs=73.8

Q ss_pred             hchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHH-------HHH
Q psy4285         289 ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI-------FQF  361 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~  361 (533)
                      +|..++..+..++..+. +++++.||||||||+++.+++..+....  ...++.+ +.+......+++.+       ..+
T Consensus        29 ~Q~~av~~~~~~i~~~~-~~~li~G~aGTGKT~ll~~~~~~l~~~~--~~~il~~-a~T~~Aa~~l~~~~~~~~~T~h~~  104 (459)
T 3upu_A           29 GQKNAFNIVMKAIKEKK-HHVTINGPAGTGATTLTKFIIEALISTG--ETGIILA-APTHAAKKILSKLSGKEASTIHSI  104 (459)
T ss_dssp             HHHHHHHHHHHHHHSSS-CEEEEECCTTSCHHHHHHHHHHHHHHTT--CCCEEEE-ESSHHHHHHHHHHHSSCEEEHHHH
T ss_pred             HHHHHHHHHHHHHhcCC-CEEEEEeCCCCCHHHHHHHHHHHHHhcC--CceEEEe-cCcHHHHHHHHhhhccchhhHHHH
Confidence            45555555555555443 3799999999999999999999886553  1123333 33333333333322       111


Q ss_pred             Hhcc--------------cCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         362 ASTK--------------TMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       362 ~~~~--------------~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      ....              .......+++||||+++++......|++.+.   .+..++++++...
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiDE~~~~~~~~~~~l~~~~~---~~~~~~~vGD~~Q  166 (459)
T 3upu_A          105 LKINPVTYEENVLFEQKEVPDLAKCRVLICDEVSMYDRKLFKILLSTIP---PWCTIIGIGDNKQ  166 (459)
T ss_dssp             HTEEEEECSSCEEEEECSCCCCSSCSEEEESCGGGCCHHHHHHHHHHSC---TTCEEEEEECTTS
T ss_pred             hccCcccccccchhcccccccccCCCEEEEECchhCCHHHHHHHHHhcc---CCCEEEEECCHHH
Confidence            1110              0011357899999999999998888888773   5678899886443

>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=98.34  E-value=1.7e-06  Score=76.77  Aligned_cols=68  Identities=18%  Similarity=0.337  Sum_probs=47.9

Q ss_pred             CCcEEEEEeCC---CCCCHHHHHHHHHHHHhcCCCcEEEEEeC--CCCCCChhhhcc--ceeeeecCCCHHHHHHHh
Q psy4285         370 SSYKLIILDEA---DAMTNDAQNALRRIIEKFTTNVRFCIICN--YLSKIPPAIQSR--CTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       370 ~~~~vliiDE~---d~l~~~~~~~Ll~~le~~~~~~~~I~~~n--~~~~l~~~l~sR--~~~i~~~~~~~~~~~~~l  439 (533)
                      ..++++++||+   ..++...+..+.+.+++  .+..+|+++.  ....+...+.+|  +..+.+.+.+.+++...+
T Consensus        98 ~~p~llilDEigp~~~ld~~~~~~l~~~l~~--~~~~~i~~~H~~h~~~~~~~i~~r~~~~i~~~~~~~r~~~~~~l  172 (178)
T 1ye8_A           98 DRRKVIIIDEIGKMELFSKKFRDLVRQIMHD--PNVNVVATIPIRDVHPLVKEIRRLPGAVLIELTPENRDVILEDI  172 (178)
T ss_dssp             CTTCEEEECCCSTTGGGCHHHHHHHHHHHTC--TTSEEEEECCSSCCSHHHHHHHTCTTCEEEECCTTTTTTHHHHH
T ss_pred             cCCCEEEEeCCCCcccCCHHHHHHHHHHHhc--CCCeEEEEEccCCCchHHHHHHhcCCcEEEEecCcCHHHHHHHH
Confidence            35689999995   45577888999999976  3455777773  344556677777  678888877766555443

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.33  E-value=3.6e-06  Score=102.52  Aligned_cols=121  Identities=18%  Similarity=0.252  Sum_probs=96.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQ  388 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~  388 (533)
                      ..+.||+|||||++++.+|+.+      +..++.+++++......+.+.+...++.       +.-.++||++++..+..
T Consensus       607 g~~~GPaGtGKTet~k~La~~l------gr~~~vfnC~~~~d~~~~g~i~~G~~~~-------GaW~cfDEfNrl~~~vL  673 (3245)
T 3vkg_A          607 GNPFGPAGTGKTETVKALGSQL------GRFVLVFCCDEGFDLQAMSRIFVGLCQC-------GAWGCFDEFNRLEERIL  673 (3245)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHT------TCCEEEEECSSCCCHHHHHHHHHHHHHH-------TCEEEEETTTSSCHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHh------CCeEEEEeCCCCCCHHHHHHHHhhHhhc-------CcEEEehhhhcCCHHHH
Confidence            4789999999999999999998      7888999999888777776665555433       34779999999999887


Q ss_pred             HHHHHHHH-------h--------------cCCCcEEEEEeCC----CCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         389 NALRRIIE-------K--------------FTTNVRFCIICNY----LSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       389 ~~Ll~~le-------~--------------~~~~~~~I~~~n~----~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      +.+.+.+.       .              ..+++.+++|.|.    ...+++++++||..+.+..|+.+.+.+++...
T Consensus       674 Svv~~qi~~I~~a~~~~~~~~~~~~G~~i~l~~~~~vfiTmNpgY~gr~eLP~nLk~lFr~v~m~~Pd~~~i~ei~L~s  752 (3245)
T 3vkg_A          674 SAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGYAGRSNLPDNLKKLFRSMAMIKPDREMIAQVMLYS  752 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHTCSEECCC---CEECCTTCEEEECBCCCGGGCCCSCHHHHTTEEEEECCSCCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHcCCCeEEecCCCEEeecCCeEEEEEeCCCccCcccChHHHHhhcEEEEEeCCCHHHHHHHHHHH
Confidence            77666543       1              1245778888884    45899999999999999999999999986554

>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=98.30  E-value=2.9e-06  Score=79.07  Aligned_cols=91  Identities=12%  Similarity=0.230  Sum_probs=77.4

Q ss_pred             EEEEEcCCCC----cCchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q psy4285           9 RFCIICNYLS----KITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQS   81 (533)
Q Consensus         9 ~~il~~~~~~----~i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~   81 (533)
                      ++|++|+...    .+.+.++|||   .++.|++|+.+++.+++.+.+...++.++++.++.++..++||+|.+.+.++.
T Consensus       140 ~ii~~~~~~~~~~~~~~~~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~l~~~l~~  219 (242)
T 3bos_A          140 SLIVSASASPMEAGFVLPDLVSRMHWGLTYQLQPMMDDEKLAALQRRAAMRGLQLPEDVGRFLLNRMARDLRTLFDVLDR  219 (242)
T ss_dssp             EEEEEESSCTTTTTCCCHHHHHHHHHSEEEECCCCCGGGHHHHHHHHHHHTTCCCCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             eEEEEcCCCHHHHHHhhhhhhhHhhcCceEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccCCHHHHHHHHHH
Confidence            5777776444    4569999999   99999999999999999999988889999999999999999999999999998


Q ss_pred             HHHhC---CCCcchhhHHhhh
Q psy4285          82 AATAH---ADEVNEDTIFTLL   99 (533)
Q Consensus        82 ~~~~~---~~~i~~~~i~~~~   99 (533)
                      +....   +..|+.+.+.+++
T Consensus       220 ~~~~a~~~~~~It~~~v~~~l  240 (242)
T 3bos_A          220 LDKASMVHQRKLTIPFVKEML  240 (242)
T ss_dssp             HHHHHHHHTCCCCHHHHHHHH
T ss_pred             HHHHHHHhCCCCcHHHHHHHh
Confidence            86542   4458888876544

>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=98.28  E-value=4.1e-06  Score=82.55  Aligned_cols=95  Identities=12%  Similarity=0.145  Sum_probs=81.1

Q ss_pred             ceEEEEEcCCCCcCchhhhccce-eEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHh
Q psy4285           7 NVRFCIICNYLSKITPAIQSRCT-RFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATA   85 (533)
Q Consensus         7 ~~~~il~~~~~~~i~~~i~SRc~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~~~~   85 (533)
                      .+.++.+++.+..+.++++|||. .+.|.+++.+++.++|++.+...++.++++++..|+..++||+|.|+++|+.+...
T Consensus       150 ~~~li~at~~~~~Ls~~l~sR~~l~~~Ld~~~~~~l~~iL~~~~~~~~~~~~~~~~~~ia~~~~G~~R~a~~ll~~~~~~  229 (334)
T 1in4_A          150 PFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDM  229 (334)
T ss_dssp             CCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHHHHHHHH
T ss_pred             CeEEEEecCCcccCCHHHHHhcCceeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhcCCChHHHHHHHHHHHHH
Confidence            46677789999999999999995 68999999999999999999888899999999999999999999999999876432


Q ss_pred             ----CCCCcchhhHHhhhhh
Q psy4285          86 ----HADEVNEDTIFTLLVS  101 (533)
Q Consensus        86 ----~~~~i~~~~i~~~~~~  101 (533)
                          ....||.+.+.+.+..
T Consensus       230 a~~~~~~~It~~~v~~al~~  249 (334)
T 1in4_A          230 LTVVKADRINTDIVLKTMEV  249 (334)
T ss_dssp             HHHHTCSSBCHHHHHHHHHH
T ss_pred             HHHcCCCCcCHHHHHHHHHH
Confidence                2346888877665543

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=98.24  E-value=1.3e-06  Score=93.11  Aligned_cols=101  Identities=19%  Similarity=0.201  Sum_probs=63.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHh-----------------ccc----
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAS-----------------TKT----  366 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~----  366 (533)
                      .++++|||||||||++..+...+.........-+.+.+++......+.+.++....                 +.+    
T Consensus       166 ~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vll~APTg~AA~~L~e~~~~~~~~l~l~~~~~~~~~~~~~Tih~ll~  245 (608)
T 1w36_D          166 ISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEDASTLHRLLG  245 (608)
T ss_dssp             EEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCCSCCCCSCSCCCBTTTSCC-
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHHhhhcCCCeEEEEeCChhHHHHHHHHHHHHHhcCCCCHHHHhccchhhhhhHhhhc
Confidence            58999999999999999988877431100111233444444444444443332100                 000    


Q ss_pred             ------------CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         367 ------------MHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       367 ------------~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                                  ......++|||||+++++......|++.+   +.+.++|+.++..
T Consensus       246 ~~~~~~~~~~~~~~~l~~d~lIIDEAsml~~~~~~~Ll~~l---~~~~~liLvGD~~  299 (608)
T 1w36_D          246 AQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLIDAL---PDHARVIFLGDRD  299 (608)
T ss_dssp             ----------CTTSCCSCSEEEECSGGGCBHHHHHHHHHTC---CTTCEEEEEECTT
T ss_pred             cCCCchHHHhccCCCCCCCEEEEechhhCCHHHHHHHHHhC---CCCCEEEEEcchh
Confidence                        00124679999999999977766676655   6778999999654

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=98.22  E-value=4.5e-07  Score=81.08  Aligned_cols=106  Identities=12%  Similarity=0.146  Sum_probs=59.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC-CCC-chhHHHHH------------HHHHHhcccCCCCCcEE
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS-DDR-GIGIVRDQ------------IFQFASTKTMHKSSYKL  374 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~-~~~-~~~~~~~~------------~~~~~~~~~~~~~~~~v  374 (533)
                      .+++||||+||||++..++..+...+   ..++.+.+. +.+ +...+...            ...+...   .....++
T Consensus         6 ~vi~G~~gsGKTT~ll~~~~~~~~~g---~~v~~~~~~~d~r~~~~~i~s~~g~~~~~~~~~~~~~~~~~---~~~~~dv   79 (184)
T 2orw_A            6 TVITGPMYSGKTTELLSFVEIYKLGK---KKVAVFKPKIDSRYHSTMIVSHSGNGVEAHVIERPEEMRKY---IEEDTRG   79 (184)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTT---CEEEEEEEC-----CCCEECC----CEECEEESSGGGGGGG---CCTTEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCC---CeEEEEeeccccccCcccEEecCCCceeeEEECCHHHHHHH---hcCCCCE
Confidence            68999999999999987777664332   222222111 000 00000000            0001110   1135789


Q ss_pred             EEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeC------CCCCCChhhhccce
Q psy4285         375 IILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN------YLSKIPPAIQSRCT  423 (533)
Q Consensus       375 liiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n------~~~~l~~~l~sR~~  423 (533)
                      |+|||++.++++....|..+.++   +..+|+++.      .+....+.++++.+
T Consensus        80 viIDE~Q~~~~~~~~~l~~l~~~---~~~Vi~~Gl~~~f~~~~f~~~~~ll~~ad  131 (184)
T 2orw_A           80 VFIDEVQFFNPSLFEVVKDLLDR---GIDVFCAGLDLTHKQNPFETTALLLSLAD  131 (184)
T ss_dssp             EEECCGGGSCTTHHHHHHHHHHT---TCEEEEEEESBCTTSCBCHHHHHHHHHCS
T ss_pred             EEEECcccCCHHHHHHHHHHHHC---CCCEEEEeeccccccCCccchHHHHHHhh
Confidence            99999999987777777767764   567887774      33344566777664

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

Probab=98.20  E-value=4.5e-06  Score=82.41  Aligned_cols=93  Identities=13%  Similarity=0.108  Sum_probs=80.9

Q ss_pred             ceEEEEEcCCCCcCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHh
Q psy4285           7 NVRFCIICNYLSKITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATA   85 (533)
Q Consensus         7 ~~~~il~~~~~~~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~~~~   85 (533)
                      +++||.+||....+.|+|+||| .++.|++|+.+++..++.+.+...++.+++++++.++..+.||+|.+.+.++.+...
T Consensus       154 ~~~~i~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l~~~~~~  233 (338)
T 3pfi_A          154 KFTLIGATTRAGMLSNPLRDRFGMQFRLEFYKDSELALILQKAALKLNKTCEEKAALEIAKRSRSTPRIALRLLKRVRDF  233 (338)
T ss_dssp             CCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHTTTTCHHHHHHHHHHHHHH
T ss_pred             CeEEEEeCCCccccCHHHHhhcCEEeeCCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            4889999999999999999999 999999999999999999999888888999999999999999999999999986432


Q ss_pred             ---C-CCCcchhhHHhhh
Q psy4285          86 ---H-ADEVNEDTIFTLL   99 (533)
Q Consensus        86 ---~-~~~i~~~~i~~~~   99 (533)
                         . ...|+.+.+...+
T Consensus       234 a~~~~~~~i~~~~~~~~~  251 (338)
T 3pfi_A          234 ADVNDEEIITEKRANEAL  251 (338)
T ss_dssp             HHHTTCSEECHHHHHHHH
T ss_pred             HHhhcCCccCHHHHHHHH
Confidence               1 3347777765443

>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=98.20  E-value=6.8e-06  Score=80.52  Aligned_cols=93  Identities=12%  Similarity=0.054  Sum_probs=81.2

Q ss_pred             CceEEEEEcCCCCcCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHH
Q psy4285           6 TNVRFCIICNYLSKITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAAT   84 (533)
Q Consensus         6 ~~~~~il~~~~~~~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~~~   84 (533)
                      .++++|.+||....+.+++.||| .++.|++|+.+++..++.+.+...++.+++++++.++..+.|++|.+.++++.+..
T Consensus       137 ~~~~~i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l~~~~~  216 (324)
T 1hqc_A          137 PRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRD  216 (324)
T ss_dssp             CCCEEEEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHSCSCHHHHHHHHHHHTT
T ss_pred             CCEEEEEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHH
Confidence            46889999999999999999999 69999999999999999999988888999999999999999999999999998865


Q ss_pred             hC----CCCcchhhHHhh
Q psy4285          85 AH----ADEVNEDTIFTL   98 (533)
Q Consensus        85 ~~----~~~i~~~~i~~~   98 (533)
                      ..    ...|+.+.+...
T Consensus       217 ~a~~~~~~~i~~~~~~~~  234 (324)
T 1hqc_A          217 FAQVAGEEVITRERALEA  234 (324)
T ss_dssp             TSTTTSCSCCCHHHHHHH
T ss_pred             HHHHhcCCCCCHHHHHHH
Confidence            33    234777666543

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=98.12  E-value=1.8e-05  Score=70.45  Aligned_cols=107  Identities=14%  Similarity=0.129  Sum_probs=65.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC-CCch-----------------------------hHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD-DRGI-----------------------------GIVRD  356 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~-~~~~-----------------------------~~~~~  356 (533)
                      +.+++++++|.||||+|-.+|....+.+ ....++.+.... ..+.                             .....
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G-~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~~  107 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHG-KNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMA  107 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTT-CCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCC-CeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHHH
Confidence            4699999999999999999998886653 222222221110 0000                             01111


Q ss_pred             HHHHHHhcccCCCCCcEEEEEeCC------CCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccc
Q psy4285         357 QIFQFASTKTMHKSSYKLIILDEA------DAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRC  422 (533)
Q Consensus       357 ~~~~~~~~~~~~~~~~~vliiDE~------d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~  422 (533)
                      ........  .....+++||+||+      +.++.+   .+++++...+.+..+|+|+|...   +.|....
T Consensus       108 ~l~~a~~~--l~~~~yDlvILDEi~~al~~g~l~~~---ev~~~l~~Rp~~~~vIlTGr~ap---~~l~e~A  171 (196)
T 1g5t_A          108 VWQHGKRM--LADPLLDMVVLDELTYMVAYDYLPLE---EVISALNARPGHQTVIITGRGCH---RDILDLA  171 (196)
T ss_dssp             HHHHHHHH--TTCTTCSEEEEETHHHHHHTTSSCHH---HHHHHHHTSCTTCEEEEECSSCC---HHHHHHC
T ss_pred             HHHHHHHH--HhcCCCCEEEEeCCCccccCCCCCHH---HHHHHHHhCcCCCEEEEECCCCc---HHHHHhC
Confidence            11111111  11356899999999      445444   58888998899999999999764   4555443

>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=98.11  E-value=9.7e-06  Score=77.83  Aligned_cols=21  Identities=24%  Similarity=0.363  Sum_probs=20.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      ++|+||||||||++|..++..
T Consensus       126 iLI~GpPGsGKTtLAlqlA~~  146 (331)
T 2vhj_A          126 VIVTGKGNSGKTPLVHALGEA  146 (331)
T ss_dssp             EEEECSCSSSHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHh
Confidence            799999999999999999987

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=98.11  E-value=7.6e-06  Score=83.68  Aligned_cols=97  Identities=15%  Similarity=0.150  Sum_probs=80.9

Q ss_pred             CceEEEEEcCC-CCc---Cchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHH
Q psy4285           6 TNVRFCIICNY-LSK---ITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI   78 (533)
Q Consensus         6 ~~~~~il~~~~-~~~---i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~   78 (533)
                      .+..+|++|+. +..   +.+.|+|||   +++.|.+|+.++...+|++.+...++.+++++++.|+..++||+|.+.+.
T Consensus       226 ~~~~iIitt~~~~~~l~~l~~~L~sR~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~~e~l~~la~~~~gn~R~l~~~  305 (440)
T 2z4s_A          226 SGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGA  305 (440)
T ss_dssp             TTCEEEEEESSCGGGCSSCCHHHHHHHHSSBCCBCCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHCCSCHHHHHHH
T ss_pred             CCCeEEEEECCCHHHHHHHHHHHHhhccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHH
Confidence            34567777765 443   889999999   79999999999999999999988899999999999999999999999999


Q ss_pred             HHHHHHh---CCCCcchhhHHhhhhhh
Q psy4285          79 LQSAATA---HADEVNEDTIFTLLVSR  102 (533)
Q Consensus        79 l~~~~~~---~~~~i~~~~i~~~~~~~  102 (533)
                      |+.+...   .+..||.+.+.+.+...
T Consensus       306 L~~~~~~a~~~~~~It~~~~~~~l~~~  332 (440)
T 2z4s_A          306 IIKLLVYKETTGKEVDLKEAILLLKDF  332 (440)
T ss_dssp             HHHHHHHHHHSSSCCCHHHHHHHTSTT
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence            9988653   24458888877666543

>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=98.09  E-value=1.6e-05  Score=79.71  Aligned_cols=94  Identities=22%  Similarity=0.265  Sum_probs=79.1

Q ss_pred             CceEEEEEcCCC---CcCchhhhcc-ceeEEeCCCCHHHHHHHHHHHHhh--cCCCCCHHHHHHHHHhcC---CCHHHHH
Q psy4285           6 TNVRFCIICNYL---SKITPAIQSR-CTRFRFGPLDSSLIMSRLDYVIEQ--EKVNVTPDGKKAIIDLSD---GDMRKVL   76 (533)
Q Consensus         6 ~~~~~il~~~~~---~~i~~~i~SR-c~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~~~~~~~~---g~~r~a~   76 (533)
                      .+++||++||..   ..+.++++|| |..+.|+|++.+++.+++.+.+..  .+..+++++++.+++.++   ||+|.|+
T Consensus       163 ~~~~iI~~t~~~~~~~~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~G~~r~a~  242 (384)
T 2qby_B          163 ANISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAV  242 (384)
T ss_dssp             SCEEEEEECSSTTTTTTSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCCSHHHHHHHHHHHTTCCCHHHHH
T ss_pred             cceEEEEEECCCchHhhhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcCHHHHHHHHHHHHhccCCHHHHH
Confidence            578899999987   7899999999 689999999999999999988764  345788999999999998   9999999


Q ss_pred             HHHHHHHHhCC--CCcchhhHHhhh
Q psy4285          77 NILQSAATAHA--DEVNEDTIFTLL   99 (533)
Q Consensus        77 ~~l~~~~~~~~--~~i~~~~i~~~~   99 (533)
                      ++++.+.....  ..|+.+.+.+.+
T Consensus       243 ~~l~~a~~~a~~~~~i~~~~v~~~~  267 (384)
T 2qby_B          243 NLLFRAAQLASGGGIIRKEHVDKAI  267 (384)
T ss_dssp             HHHHHHHHHTTSSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCccCHHHHHHHH
Confidence            99999876442  357877775543

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.07  E-value=8.1e-06  Score=79.01  Aligned_cols=82  Identities=10%  Similarity=0.099  Sum_probs=66.2

Q ss_pred             CCCceEEEEEcCCCC----cCchhhhccc--eeEEeCCCCHHHHHHHHHHHHhhc--C----------------------
Q psy4285           4 FTTNVRFCIICNYLS----KITPAIQSRC--TRFRFGPLDSSLIMSRLDYVIEQE--K----------------------   53 (533)
Q Consensus         4 ~~~~~~~il~~~~~~----~i~~~i~SRc--~~~~~~~~~~~~~~~~l~~~~~~~--~----------------------   53 (533)
                      +..++.+|+++|...    .+.+.++|||  .++.|+|++.+++.++|++.+...  +                      
T Consensus       160 ~~s~~~vI~i~n~~d~~~~~L~~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl~~~~~~~f~~~~~~~~~~~~~~~~~~~~  239 (318)
T 3te6_A          160 KNSKLSIICVGGHNVTIREQINIMPSLKAHFTEIKLNKVDKNELQQMIITRLKSLLKPFHVKVNDKKEMTIYNNIREGQN  239 (318)
T ss_dssp             SSCCEEEEEECCSSCCCHHHHHTCHHHHTTEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEECTTCCEEECCCC-----
T ss_pred             cCCcEEEEEEecCcccchhhcchhhhccCCceEEEeCCCCHHHHHHHHHHHHHhhhcccccccccccccccccccccccc
Confidence            345677888887653    3667889998  689999999999999998887542  1                      


Q ss_pred             -----------CCCCHHHHHHHHH---hcCCCHHHHHHHHHHHHHh
Q psy4285          54 -----------VNVTPDGKKAIID---LSDGDMRKVLNILQSAATA   85 (533)
Q Consensus        54 -----------~~~~~~~~~~~~~---~~~g~~r~a~~~l~~~~~~   85 (533)
                                 +.+++++++.+++   .++||+|+|+++|+.+...
T Consensus       240 ~~~~~~~~~~~~~i~~~ai~~~A~~vA~~~GD~R~Al~ilr~A~~~  285 (318)
T 3te6_A          240 QKIPDNVIVINHKINNKITQLIAKNVANVSGSTEKAFKICEAAVEI  285 (318)
T ss_dssp             ---CTTEEEECEECCHHHHHHHHHHHHHHHCSHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccCHHHHHHHHHHHHhhCChHHHHHHHHHHHHHH
Confidence                       1368999999998   6899999999999998753

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

Probab=98.02  E-value=2.1e-06  Score=83.66  Aligned_cols=84  Identities=14%  Similarity=0.222  Sum_probs=73.6

Q ss_pred             CCCCCCceEEEEEcCCCC-----cCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhc------
Q psy4285           1 IEKFTTNVRFCIICNYLS-----KITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLS------   68 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~-----~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~------   68 (533)
                      ||+++.++++|+++|+..     .+.|+|+||| ..+.|++|+.+++.+++++.+.+.++.++++++..++..+      
T Consensus       163 l~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~~~~~~~~~il~~~l~~~~~~~~~~~~~~l~~~~~~~~~~  242 (309)
T 3syl_A          163 MENNRDDLVVILAGYADRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRAYIGLRRNQ  242 (309)
T ss_dssp             HHHCTTTCEEEEEECHHHHHHHHHHSTTHHHHEEEEEEECCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHTTS
T ss_pred             HhcCCCCEEEEEeCChHHHHHHHhhCHHHHHhCCeEEEcCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhccC
Confidence            356678899999997543     4579999999 9999999999999999999999889999999999998864      


Q ss_pred             --CCCHHHHHHHHHHHHH
Q psy4285          69 --DGDMRKVLNILQSAAT   84 (533)
Q Consensus        69 --~g~~r~a~~~l~~~~~   84 (533)
                        .||+|.+.++++.+..
T Consensus       243 ~~~gn~r~l~~~l~~a~~  260 (309)
T 3syl_A          243 PHFANARSIRNALDRARL  260 (309)
T ss_dssp             SSCCHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHH
Confidence              4999999999999875

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

Probab=98.01  E-value=1.8e-05  Score=79.32  Aligned_cols=95  Identities=21%  Similarity=0.341  Sum_probs=77.8

Q ss_pred             CCceEEEEEcCCC---CcCchhhhccc--eeEEeCCCCHHHHHHHHHHHHhh--cCCCCCHHHHHHHHHhcC---CCHHH
Q psy4285           5 TTNVRFCIICNYL---SKITPAIQSRC--TRFRFGPLDSSLIMSRLDYVIEQ--EKVNVTPDGKKAIIDLSD---GDMRK   74 (533)
Q Consensus         5 ~~~~~~il~~~~~---~~i~~~i~SRc--~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~~~~~~~~---g~~r~   74 (533)
                      +.++.+|++||..   ..+.++++|||  ..+.|++++.+++.+++.+.+..  .+..+++++++.+++.++   ||+|.
T Consensus       165 ~~~~~~I~~t~~~~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~  244 (387)
T 2v1u_A          165 RVWVSLVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARR  244 (387)
T ss_dssp             ---CEEEEECSCSTTSSSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSSHHHHHHHHHHSSSCCHHH
T ss_pred             CceEEEEEEECCCchHhhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhccCHHH
Confidence            5678899999887   78999999999  78999999999999999988765  456788999999999998   99999


Q ss_pred             HHHHHHHHHHh----CCCCcchhhHHhhh
Q psy4285          75 VLNILQSAATA----HADEVNEDTIFTLL   99 (533)
Q Consensus        75 a~~~l~~~~~~----~~~~i~~~~i~~~~   99 (533)
                      ++++++.+...    ....|+.+.+.+.+
T Consensus       245 ~~~~l~~a~~~a~~~~~~~i~~~~v~~a~  273 (387)
T 2v1u_A          245 ALDLLRVAGEIAERRREERVRREHVYSAR  273 (387)
T ss_dssp             HHHHHHHHHHHHHHTTCSCBCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Confidence            99999998653    22457877765543

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=97.98  E-value=1.4e-05  Score=72.73  Aligned_cols=128  Identities=13%  Similarity=0.201  Sum_probs=75.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcc-------------cC----CCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTK-------------TM----HKS  370 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~----~~~  370 (533)
                      ++++.|+||+||||++..+|..+...+ +...+..++...  ... ............             ..    ...
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~G-~~V~v~d~D~q~--~~~-~~al~~gl~~~~~~~~~~~~~~~~e~~l~~~L~~   83 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQG-VRVMAGVVETHG--RAE-TEALLNGLPQQPLLRTEYRGMTLEEMDLDALLKA   83 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTT-CCEEEEECCCTT--CHH-HHHHHTTSCBCCCEEEEETTEEEEECCHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCC-CCEEEEEeCCCC--Chh-HHHHhcCccccCcceeecCCcccccccHHHHHhc
Confidence            489999999999999999999885442 222233333210  000 000000000000             00    002


Q ss_pred             CcEEEEEeCCCCCCHH------HHHHHHHHHHhcCCCcEEEEEeCCC------------------CCCChhhhccceeee
Q psy4285         371 SYKLIILDEADAMTND------AQNALRRIIEKFTTNVRFCIICNYL------------------SKIPPAIQSRCTRFR  426 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~------~~~~Ll~~le~~~~~~~~I~~~n~~------------------~~l~~~l~sR~~~i~  426 (533)
                      .+++++|||+.+.+..      ....+...+   +....++.|+|..                  +.++..+..++..+.
T Consensus        84 ~pdlvIVDElG~~~~~~~r~~~~~qDV~~~l---~sgidVitT~Nlqh~esl~d~v~~itg~~v~e~vpd~~~~~a~~v~  160 (228)
T 2r8r_A           84 APSLVLVDELAHTNAPGSRHTKRWQDIQELL---AAGIDVYTTVNVQHLESLNDQVRGITGVQVRETLPDWVLQEAFDLV  160 (228)
T ss_dssp             CCSEEEESCTTCBCCTTCSSSBHHHHHHHHH---HTTCEEEEEEEGGGBGGGHHHHHHHHSCCCCSCBCHHHHHTCSEEE
T ss_pred             CCCEEEEeCCCCCCcccchhHHHHHHHHHHH---cCCCCEEEEccccccccHHHHHHHHcCCCcCCcCccHHHhhCCeEE
Confidence            4679999999875321      222222233   4556788888721                  356777888888888


Q ss_pred             ecCCCHHHHHHHhhcC
Q psy4285         427 FGPLDSSLIMSRLDYD  442 (533)
Q Consensus       427 ~~~~~~~~~~~~l~~~  442 (533)
                      +-..+++++.+++..=
T Consensus       161 lvD~~p~~l~~rl~~g  176 (228)
T 2r8r_A          161 LIDLPPRELLERLRDG  176 (228)
T ss_dssp             EBCCCHHHHHHHHHTT
T ss_pred             EecCCHHHHHHHHHCC
Confidence            8888888899988763

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=97.91  E-value=4.7e-05  Score=76.40  Aligned_cols=94  Identities=18%  Similarity=0.243  Sum_probs=77.8

Q ss_pred             CceEEEEEcCCC---CcCchhhhccce--eEEeCCCCHHHHHHHHHHHHhh--cCCCCCHHHHHHHHHhc---------C
Q psy4285           6 TNVRFCIICNYL---SKITPAIQSRCT--RFRFGPLDSSLIMSRLDYVIEQ--EKVNVTPDGKKAIIDLS---------D   69 (533)
Q Consensus         6 ~~~~~il~~~~~---~~i~~~i~SRc~--~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~~~~~~~---------~   69 (533)
                      .++.+|++||.+   ..+.++++|||.  .+.|+|++.+++.+++.+.+..  ....+++++++.++..+         +
T Consensus       158 ~~~~iI~~~~~~~~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  237 (389)
T 1fnn_A          158 FRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNR  237 (389)
T ss_dssp             CCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTS
T ss_pred             CCEEEEEEECCchHHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCC
Confidence            588999999988   789999999997  6999999999999999988764  22368899999999999         8


Q ss_pred             CCHHHHHHHHHHHHHh----CCCCcchhhHHhhh
Q psy4285          70 GDMRKVLNILQSAATA----HADEVNEDTIFTLL   99 (533)
Q Consensus        70 g~~r~a~~~l~~~~~~----~~~~i~~~~i~~~~   99 (533)
                      ||+|.++++++.+...    ....++.+.+...+
T Consensus       238 G~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~~~  271 (389)
T 1fnn_A          238 GDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSS  271 (389)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHH
Confidence            9999999999987653    23457777765543

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=97.90  E-value=4.2e-05  Score=70.08  Aligned_cols=93  Identities=16%  Similarity=0.153  Sum_probs=54.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC---C-------Cc-------hhHHHHHHHHHHhcccCCCCC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD---D-------RG-------IGIVRDQIFQFASTKTMHKSS  371 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~---~-------~~-------~~~~~~~~~~~~~~~~~~~~~  371 (533)
                      ++++||||+||||++..++..+...+   ..++.+.+..   +       .+       .....+.........  ....
T Consensus        15 ~litG~mGsGKTT~ll~~~~r~~~~g---~kVli~~~~~d~r~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~--~~~~   89 (223)
T 2b8t_A           15 EFITGPMFAGKTAELIRRLHRLEYAD---VKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNS--FNDE   89 (223)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTT---CCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTT--SCTT
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHhcC---CEEEEEEeccCchHHHHHHHhcCCCccccccCCHHHHHHHHHHHh--hCCC
Confidence            78999999999999999998875442   1222221110   0       00       001112222111111  1235


Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeC
Q psy4285         372 YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN  409 (533)
Q Consensus       372 ~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n  409 (533)
                      +++|+|||+..++.+....+..+.+   .++.+|+++.
T Consensus        90 ~dvViIDEaQ~l~~~~ve~l~~L~~---~gi~Vil~Gl  124 (223)
T 2b8t_A           90 TKVIGIDEVQFFDDRICEVANILAE---NGFVVIISGL  124 (223)
T ss_dssp             CCEEEECSGGGSCTHHHHHHHHHHH---TTCEEEEECC
T ss_pred             CCEEEEecCccCcHHHHHHHHHHHh---CCCeEEEEec
Confidence            7899999999998776555544443   2688999985

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

Probab=97.84  E-value=4.3e-05  Score=74.07  Aligned_cols=80  Identities=19%  Similarity=0.266  Sum_probs=66.2

Q ss_pred             CCCceEEEEE----cCCCCcCchhhhccce-eEEeCCCCHHHHHHHHHH-----------HHhhcC--CCCCHHHHHHHH
Q psy4285           4 FTTNVRFCII----CNYLSKITPAIQSRCT-RFRFGPLDSSLIMSRLDY-----------VIEQEK--VNVTPDGKKAII   65 (533)
Q Consensus         4 ~~~~~~~il~----~~~~~~i~~~i~SRc~-~~~~~~~~~~~~~~~l~~-----------~~~~~~--~~~~~~~~~~~~   65 (533)
                      ++.+++||.+    ++.+..+.|+++|||. .+.|++|+.+++.+++++           .+...+  +.+++++++.++
T Consensus       165 ~~~~~~~i~~~~~~~~~~~~l~~~l~~R~~~~i~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~  244 (310)
T 1ofh_A          165 KTDHILFIASGAFQVARPSDLIPELQGRLPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIA  244 (310)
T ss_dssp             ECTTCEEEEEECCSSSCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHHTTCEEEECHHHHHHHH
T ss_pred             cCCcEEEEEcCCcccCCcccCCHHHHhhCCceEEcCCcCHHHHHHHHHhhHHHHHHHHHHHHHhcCCeeccCHHHHHHHH
Confidence            3467888888    4577899999999995 699999999999999872           222344  358999999999


Q ss_pred             Hhc--------CCCHHHHHHHHHHHH
Q psy4285          66 DLS--------DGDMRKVLNILQSAA   83 (533)
Q Consensus        66 ~~~--------~g~~r~a~~~l~~~~   83 (533)
                      +.+        .||+|.+.++++.+.
T Consensus       245 ~~~~~~~~~~~~g~~R~l~~~l~~~~  270 (310)
T 1ofh_A          245 EAAFRVNEKTENIGARRLHTVMERLM  270 (310)
T ss_dssp             HHHHHHHHHSCCCTTHHHHHHHHHHS
T ss_pred             HHhhhhcccccccCcHHHHHHHHHHH
Confidence            998        899999999999875

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.70  E-value=9.8e-05  Score=86.84  Aligned_cols=26  Identities=31%  Similarity=0.439  Sum_probs=22.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      +++|+||||||||++|.+++.+....
T Consensus      1429 ~vll~GppGtGKT~LA~ala~ea~~~ 1454 (2050)
T 3cmu_A         1429 IVEIYGPESSGKTTLTLQVIAAAQRE 1454 (2050)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            59999999999999999999886443

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=97.67  E-value=0.0002  Score=71.62  Aligned_cols=95  Identities=18%  Similarity=0.282  Sum_probs=76.0

Q ss_pred             CCCceEEEEEcCCC---CcCchhhhccc--eeEEeCCCCHHHHHHHHHHHHhhc--CCCCCHHHHHHHHHhcC---CCHH
Q psy4285           4 FTTNVRFCIICNYL---SKITPAIQSRC--TRFRFGPLDSSLIMSRLDYVIEQE--KVNVTPDGKKAIIDLSD---GDMR   73 (533)
Q Consensus         4 ~~~~~~~il~~~~~---~~i~~~i~SRc--~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~~~~~~~~~---g~~r   73 (533)
                      +..++.+|+++|..   ..+.+.++|||  ..+.|+|++.+++.+++.+.+...  ...++++.++.++..+.   ||+|
T Consensus       160 ~~~~~~~I~~~~~~~~~~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r  239 (386)
T 2qby_A          160 NKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDAR  239 (386)
T ss_dssp             CC--EEEEEEESCGGGGGGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCCHH
T ss_pred             CCCeEEEEEEECCCChHhhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCCHH
Confidence            35678899999877   57889999999  799999999999999999876532  35688999999999998   9999


Q ss_pred             HHHHHHHHHHHh----CCCCcchhhHHhh
Q psy4285          74 KVLNILQSAATA----HADEVNEDTIFTL   98 (533)
Q Consensus        74 ~a~~~l~~~~~~----~~~~i~~~~i~~~   98 (533)
                      .++++++.+...    ....|+.+.+...
T Consensus       240 ~~~~ll~~a~~~a~~~~~~~i~~~~v~~a  268 (386)
T 2qby_A          240 RALDLLRVSGEIAERMKDTKVKEEYVYMA  268 (386)
T ss_dssp             HHHHHHHHHHHHHHHTTCSSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCccCHHHHHHH
Confidence            999999988653    2235787776543

>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=97.66  E-value=0.00017  Score=70.43  Aligned_cols=77  Identities=5%  Similarity=0.094  Sum_probs=67.5

Q ss_pred             ceEEEEEcC-CCC---cCchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Q psy4285           7 NVRFCIICN-YLS---KITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNIL   79 (533)
Q Consensus         7 ~~~~il~~~-~~~---~i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l   79 (533)
                      +.++|++++ ++.   .+.+.++|||   .++.|+| +.++...+|++.+...++.+++++++.++..+ ||+|.+.+.|
T Consensus       131 ~~~iii~~~~~~~~l~~l~~~L~sR~~~~~~i~l~~-~~~e~~~il~~~~~~~~~~l~~~~l~~l~~~~-g~~r~l~~~l  208 (324)
T 1l8q_A          131 EKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIEL-DNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-KNVREIEGKI  208 (324)
T ss_dssp             TCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECCC-CHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-SSHHHHHHHH
T ss_pred             CCeEEEEecCChHHHHHhhhHhhhcccCceEEEeCC-CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhC-CCHHHHHHHH
Confidence            345666665 433   6899999999   8999999 99999999999998889999999999999999 9999999999


Q ss_pred             HHHHHh
Q psy4285          80 QSAATA   85 (533)
Q Consensus        80 ~~~~~~   85 (533)
                      +.+...
T Consensus       209 ~~~~~~  214 (324)
T 1l8q_A          209 KLIKLK  214 (324)
T ss_dssp             HHHHHH
T ss_pred             HHHHHc
Confidence            998764

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=97.51  E-value=0.00088  Score=71.22  Aligned_cols=62  Identities=13%  Similarity=0.070  Sum_probs=35.8

Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeee-ecCCCHHHHHHHhhcC
Q psy4285         371 SYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFR-FGPLDSSLIMSRLDYD  442 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~-~~~~~~~~~~~~l~~~  442 (533)
                      ++-+||+|+++..  .       .++..+.++++|+||....... ........+. ..+++.++..+.+...
T Consensus       236 ~~~LLVLDdv~~~--~-------~l~~l~~~~~ilvTsR~~~~~~-~~~~~~~~v~~l~~L~~~ea~~L~~~~  298 (591)
T 1z6t_A          236 PRSLLILDDVWDS--W-------VLKAFDSQCQILLTTRDKSVTD-SVMGPKYVVPVESSLGKEKGLEILSLF  298 (591)
T ss_dssp             TTCEEEEEEECCH--H-------HHHTTCSSCEEEEEESCGGGGT-TCCSCEEEEECCSSCCHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCH--H-------HHHHhcCCCeEEEECCCcHHHH-hcCCCceEeecCCCCCHHHHHHHHHHH
Confidence            4579999999862  1       2333467789999986543111 1111111222 2478888887777654

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

Probab=97.47  E-value=0.00033  Score=70.40  Aligned_cols=79  Identities=14%  Similarity=0.082  Sum_probs=69.3

Q ss_pred             CCCceEEEEEcCCCCcCchhhhccce-eEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285           4 FTTNVRFCIICNYLSKITPAIQSRCT-RFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSA   82 (533)
Q Consensus         4 ~~~~~~~il~~~~~~~i~~~i~SRc~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~   82 (533)
                      ++.++++|.+||.+..+.++++|||. .+.|+.|+.++...+|+..+.+.+..++++.+..++..+.|..+.+++.|...
T Consensus       249 ~~~~v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~~~~g~~~~~l~~L~~~  328 (389)
T 3vfd_A          249 GDDRVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAKD  328 (389)
T ss_dssp             ---CEEEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             CCCCEEEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            46778999999999999999999995 79999999999999999999888888999999999999999998888766543

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

Probab=97.46  E-value=0.00024  Score=74.56  Aligned_cols=79  Identities=13%  Similarity=0.151  Sum_probs=65.7

Q ss_pred             CceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHh-----h-----cCCCCCHHHHHHHHHhcC--CCHH
Q psy4285           6 TNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIE-----Q-----EKVNVTPDGKKAIIDLSD--GDMR   73 (533)
Q Consensus         6 ~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~-----~-----~~~~~~~~~~~~~~~~~~--g~~r   73 (533)
                      .+++||.+||+++.+.|+++|||.+++|++|+.++..+++.+...     .     .++.++++++..++..+.  |++|
T Consensus       223 ~~v~iI~ttN~~~~l~~aL~~R~~vi~~~~~~~~e~~~Il~~~l~~~~~~~~~~~~~~i~i~~~~l~~l~~~~~~~~~vR  302 (543)
T 3m6a_A          223 SKVLFIATANNLATIPGPLRDRMEIINIAGYTEIEKLEIVKDHLLPKQIKEHGLKKSNLQLRDQAILDIIRYYTREAGVR  302 (543)
T ss_dssp             SSCEEEEECSSTTTSCHHHHHHEEEEECCCCCHHHHHHHHHHTHHHHHHHHTTCCGGGCEECHHHHHHHHHHHCCCSSSH
T ss_pred             cceEEEeccCccccCCHHHHhhcceeeeCCCCHHHHHHHHHHHHHHHHHHHcCCCcccccCCHHHHHHHHHhCChhhchh
Confidence            678999999999999999999999999999999999988877541     2     245678999999877555  7889


Q ss_pred             HHHHHHHHHHH
Q psy4285          74 KVLNILQSAAT   84 (533)
Q Consensus        74 ~a~~~l~~~~~   84 (533)
                      ...+.++.++.
T Consensus       303 ~L~~~i~~~~~  313 (543)
T 3m6a_A          303 SLERQLAAICR  313 (543)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            88888887654

>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=97.45  E-value=0.00052  Score=67.91  Aligned_cols=82  Identities=12%  Similarity=0.119  Sum_probs=68.5

Q ss_pred             CCCCceEEEEEcCCCCcCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCC-CHHHHHHHHH
Q psy4285           3 KFTTNVRFCIICNYLSKITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDG-DMRKVLNILQ   80 (533)
Q Consensus         3 ~~~~~~~~il~~~~~~~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g-~~r~a~~~l~   80 (533)
                      +++.++++|.+||.+..+.|++++|| ..+.|+.|+.++..++|+..+...+..+++..+..|+..+.| +.+..-++++
T Consensus       183 ~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~~t~G~sg~dl~~l~~  262 (355)
T 2qp9_X          183 NDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVK  262 (355)
T ss_dssp             ---CCEEEEEEESCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             ccCCCeEEEeecCCcccCCHHHHcccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            45678999999999999999999999 789999999999999999888777767788899999999998 6666666666


Q ss_pred             HHHH
Q psy4285          81 SAAT   84 (533)
Q Consensus        81 ~~~~   84 (533)
                      .+..
T Consensus       263 ~A~~  266 (355)
T 2qp9_X          263 DALM  266 (355)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6544

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=97.42  E-value=0.00012  Score=68.02  Aligned_cols=23  Identities=30%  Similarity=0.401  Sum_probs=20.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++.||+|+|||.++..++..+
T Consensus       110 ~~ll~~~tG~GKT~~a~~~~~~~  132 (237)
T 2fz4_A          110 RGCIVLPTGSGKTHVAMAAINEL  132 (237)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHc
Confidence            48999999999999999888765

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=97.41  E-value=0.002  Score=58.73  Aligned_cols=22  Identities=36%  Similarity=0.495  Sum_probs=20.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|+||||+||||+++.+++.+
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            3 LVLMGLPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            7899999999999999999876

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=97.41  E-value=0.00031  Score=73.99  Aligned_cols=126  Identities=13%  Similarity=0.147  Sum_probs=66.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHH---HHccccccCcceEEecCCC-CCchhHHHHHHHHHHhcc------------------
Q psy4285         308 HLLFYGPPGTGKTTTILACAR---KLYTKAQFNAMVLELNASD-DRGIGIVRDQIFQFASTK------------------  365 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~---~l~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~------------------  365 (533)
                      .+.++|++|+||||+|+.+++   .-.........++.+.... ..........+..+....                  
T Consensus       154 vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~~~l~~  233 (549)
T 2a5y_B          154 FLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKR  233 (549)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHHHhcCcccccccccccccHHHHHH
Confidence            478999999999999999996   2222211112223222211 001112222222221110                  


Q ss_pred             ---cCCCCC-cEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhc
Q psy4285         366 ---TMHKSS-YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       366 ---~~~~~~-~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~  441 (533)
                         .....+ .-+||+|+++.....   .+   ..  ..+.++|+||....- ......-...+.+.+++.++..+.+.+
T Consensus       234 ~l~~~L~~~kr~LlVLDdv~~~~~~---~~---~~--~~gs~ilvTTR~~~v-~~~~~~~~~~~~l~~L~~~ea~~Lf~~  304 (549)
T 2a5y_B          234 MICNALIDRPNTLFVFDDVVQEETI---RW---AQ--ELRLRCLVTTRDVEI-SNAASQTCEFIEVTSLEIDECYDFLEA  304 (549)
T ss_dssp             HHHHHHTTSTTEEEEEEEECCHHHH---HH---HH--HTTCEEEEEESBGGG-GGGCCSCEEEEECCCCCHHHHHHHHHH
T ss_pred             HHHHHHcCCCcEEEEEECCCCchhh---cc---cc--cCCCEEEEEcCCHHH-HHHcCCCCeEEECCCCCHHHHHHHHHH
Confidence               000233 679999999884221   11   11  156888988875331 111101114588889999998888877


Q ss_pred             C
Q psy4285         442 D  442 (533)
Q Consensus       442 ~  442 (533)
                      .
T Consensus       305 ~  305 (549)
T 2a5y_B          305 Y  305 (549)
T ss_dssp             T
T ss_pred             H
Confidence            6

>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=97.37  E-value=0.0032  Score=65.26  Aligned_cols=69  Identities=20%  Similarity=0.244  Sum_probs=51.9

Q ss_pred             cEEEEEeCCCCCC----HHHHHHHHHHHHh-cCCCcEEEEEeCCCC--CCChhhhccc-eeeeecCCCHHHHHHHhh
Q psy4285         372 YKLIILDEADAMT----NDAQNALRRIIEK-FTTNVRFCIICNYLS--KIPPAIQSRC-TRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       372 ~~vliiDE~d~l~----~~~~~~Ll~~le~-~~~~~~~I~~~n~~~--~l~~~l~sR~-~~i~~~~~~~~~~~~~l~  440 (533)
                      +-+|||||++.+.    .+....|.++..+ +..++.+|++|.++.  .++..+++-| ..+.|...+..+...++.
T Consensus       344 ~ivvVIDE~~~L~~~~~~~~~~~L~~Iar~GRa~GIhLIlaTQRPs~d~I~~~Iran~~~RI~lrv~s~~Dsr~ILd  420 (574)
T 2iut_A          344 TIVVVVDEFADMMMIVGKKVEELIARIAQKARAAGIHLILATQRPSVDVITGLIKANIPTRIAFQVSSKIDSRTILD  420 (574)
T ss_dssp             EEEEEESCCTTHHHHTCHHHHHHHHHHHHHCTTTTEEEEEEESCCCTTTSCHHHHHTCCEEEEECCSCHHHHHHHHS
T ss_pred             cEEEEEeCHHHHhhhhhHHHHHHHHHHHHHHhhCCeEEEEEecCcccccccHHHHhhhccEEEEEcCCHHHHHHhcC
Confidence            5699999998773    3445556666654 356788999999887  7888888888 577888888888877764

>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=97.32  E-value=0.00076  Score=66.48  Aligned_cols=94  Identities=14%  Similarity=0.075  Sum_probs=69.1

Q ss_pred             CCceEEEEEcCCCC-cCchhhhcccee-EEeCCCCHH-HHHHHHHHH-----------------------------Hhhc
Q psy4285           5 TTNVRFCIICNYLS-KITPAIQSRCTR-FRFGPLDSS-LIMSRLDYV-----------------------------IEQE   52 (533)
Q Consensus         5 ~~~~~~il~~~~~~-~i~~~i~SRc~~-~~~~~~~~~-~~~~~l~~~-----------------------------~~~~   52 (533)
                      +.++++|.++|+.. .+.|+|+|||.+ +.|++|++. +-.+++++.                             ....
T Consensus       185 ~~~~~li~~~n~~~~~l~~~L~~R~~~~~~l~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~  264 (350)
T 1g8p_A          185 PARFVLVGSGNPEEGDLRPQLLDRFGLSVEVLSPRDVETRVEVIRRRDTYDADPKAFLEEWRPKDMDIRNQILEARERLP  264 (350)
T ss_dssp             ECCEEEEEEECSCSCCCCHHHHTTCSEEEECCCCCSHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHGG
T ss_pred             CCceEEEEEeCCCCCCCCHHHHhhcceEEEcCCCCcHHHHHHHHHHHHhcccCchhhccccccchHHHHHHHHHHHHhCC
Confidence            34788888899854 899999999976 999999543 333444331                             2234


Q ss_pred             CCCCCHHHHHHHHHhcCC----CHHHHHHHHHHHHHh---CC-CCcchhhHHhh
Q psy4285          53 KVNVTPDGKKAIIDLSDG----DMRKVLNILQSAATA---HA-DEVNEDTIFTL   98 (533)
Q Consensus        53 ~~~~~~~~~~~~~~~~~g----~~r~a~~~l~~~~~~---~~-~~i~~~~i~~~   98 (533)
                      ++.+++++++.|+.++.|    ++|.++++++.+...   .+ ..|+.+.+.+.
T Consensus       265 ~~~ls~~~~~~l~~~~~~~~~~~~R~~~~ll~~a~~~A~~~~~~~v~~~~v~~a  318 (350)
T 1g8p_A          265 KVEAPNTALYDCAALCIALGSDGLRGELTLLRSARALAALEGATAVGRDHLKRV  318 (350)
T ss_dssp             GCBCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHHHHHHHTTCSBCCHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHH
Confidence            568999999999999887    999999999877543   22 34888776543

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=97.30  E-value=0.00051  Score=75.73  Aligned_cols=22  Identities=32%  Similarity=0.394  Sum_probs=19.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+.++|++|+||||+|+.+++.
T Consensus       152 VV~IvGmGGIGKTTLAk~Vy~d  173 (1221)
T 1vt4_I          152 NVLIDGVLGSGKTWVALDVCLS  173 (1221)
T ss_dssp             EEEECCSTTSSHHHHHHHHHHH
T ss_pred             EEEEEcCCCccHHHHHHHHHHh
Confidence            4889999999999999999853

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=97.29  E-value=0.00057  Score=61.64  Aligned_cols=95  Identities=12%  Similarity=0.089  Sum_probs=52.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC-CC-chhHHHHHHHHHH---------hcccCCCCCcEEEEE
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD-DR-GIGIVRDQIFQFA---------STKTMHKSSYKLIIL  377 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~---------~~~~~~~~~~~vlii  377 (533)
                      .+++||.|+||||.+...+......   +..++.+.+.. .+ +...+...++.-.         ..........++|+|
T Consensus        31 ~vitG~MgsGKTT~lL~~a~r~~~~---g~kVli~k~~~d~R~ge~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~dvViI  107 (214)
T 2j9r_A           31 EVICGSMFSGKSEELIRRVRRTQFA---KQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSASKDIFKHITEEMDVIAI  107 (214)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHT---TCCEEEEECC-----------------CCEEECSSGGGGGGGCCSSCCEEEE
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHC---CCEEEEEEeccCCcchHHHHHhhcCCeeEEeecCCHHHHHHHHhcCCCEEEE
Confidence            5789999999999999998887544   23333333221 11 1111111111000         000000124789999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeC
Q psy4285         378 DEADAMTNDAQNALRRIIEKFTTNVRFCIICN  409 (533)
Q Consensus       378 DE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n  409 (533)
                      ||+..++.+....+..+.+   .+..+|+++-
T Consensus       108 DEaQF~~~~~V~~l~~l~~---~~~~Vi~~Gl  136 (214)
T 2j9r_A          108 DEVQFFDGDIVEVVQVLAN---RGYRVIVAGL  136 (214)
T ss_dssp             CCGGGSCTTHHHHHHHHHH---TTCEEEEEEC
T ss_pred             ECcccCCHHHHHHHHHHhh---CCCEEEEEec
Confidence            9999998776644444333   3678999885

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=97.28  E-value=0.0015  Score=59.59  Aligned_cols=20  Identities=40%  Similarity=0.541  Sum_probs=19.2

Q ss_pred             eeEeCCCCCChHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~  328 (533)
                      ++++||||+||||+++.++.
T Consensus        23 ~~i~G~~GsGKTtl~~~l~~   42 (220)
T 2cvh_A           23 TQVYGPYASGKTTLALQTGL   42 (220)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999999998

>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=97.25  E-value=0.0002  Score=71.07  Aligned_cols=91  Identities=22%  Similarity=0.250  Sum_probs=54.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCH--
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN--  385 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--  385 (533)
                      .++++||||+||||+++.++...      +..++.++.+...    .+-.++..        ....++++||++....  
T Consensus       171 ~i~l~G~~GsGKSTl~~~l~~~~------~g~~~~~~~~~~~----~~~~lg~~--------~q~~~~l~dd~~~~~~~~  232 (377)
T 1svm_A          171 YWLFKGPIDSGKTTLAAALLELC------GGKALNVNLPLDR----LNFELGVA--------IDQFLVVFEDVKGTGGES  232 (377)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH------CCEEECCSSCTTT----HHHHHGGG--------TTCSCEEETTCCCSTTTT
T ss_pred             EEEEECCCCCCHHHHHHHHHhhc------CCcEEEEeccchh----HHHHHHHh--------cchhHHHHHHHHHHHHHH
Confidence            48999999999999999999876      2223333333211    11111111        1224679999987753  


Q ss_pred             ------H---HHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhc
Q psy4285         386 ------D---AQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQS  420 (533)
Q Consensus       386 ------~---~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~s  420 (533)
                            .   ....+...++   ..+.+++++|+++.+ +++.+
T Consensus       233 r~l~~~~~~~~~~~l~~~ld---G~v~v~~~tn~~~~l-~alf~  272 (377)
T 1svm_A          233 RDLPSGQGINNLDNLRDYLD---GSVKVNLEKKHLNKR-TQIFP  272 (377)
T ss_dssp             TTCCCCSHHHHHHTTHHHHH---CSSCEEECCSSSCCE-EECCC
T ss_pred             hhccccCcchHHHHHHHHhc---CCCeEeeccCchhhH-HHhhc
Confidence                  1   1133444453   345678888888877 55555

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

Probab=97.23  E-value=0.00042  Score=71.33  Aligned_cols=80  Identities=15%  Similarity=0.198  Sum_probs=69.1

Q ss_pred             CCceEEEEEcCCCC-----cCchhhhccceeEEeCCCCHHHHHHHHHHHHhh----cCCCCCHHHHHHHHHhcCCC----
Q psy4285           5 TTNVRFCIICNYLS-----KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQ----EKVNVTPDGKKAIIDLSDGD----   71 (533)
Q Consensus         5 ~~~~~~il~~~~~~-----~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~~~~~~~~~~~~~g~----   71 (533)
                      .+.+++|.+||+..     .+.|+++|||+++.|.+|+.+++..+|+.++.+    .++.++++++..++.++.+.    
T Consensus       289 ~g~v~vI~at~~~e~~~~~~~~~al~~Rf~~i~v~~p~~e~~~~iL~~~~~~~~~~~~~~i~~~al~~l~~~s~~~~~~~  368 (468)
T 3pxg_A          289 RGELQCIGATTLDEYRKYIEKDAALERRFQPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDR  368 (468)
T ss_dssp             SSSCEEEEECCTTTTHHHHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCS
T ss_pred             CCCEEEEecCCHHHHHHHhhcCHHHHHhCccceeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhccC
Confidence            35788999999886     689999999999999999999999999988765    67889999999999887754    


Q ss_pred             --HHHHHHHHHHHHH
Q psy4285          72 --MRKVLNILQSAAT   84 (533)
Q Consensus        72 --~r~a~~~l~~~~~   84 (533)
                        +++|+.+++.+..
T Consensus       369 ~lp~~ai~ll~~a~~  383 (468)
T 3pxg_A          369 FLPDKAIDLIDEAGS  383 (468)
T ss_dssp             CTTHHHHHHHHHHHH
T ss_pred             cCCcHHHHHHHHHHH
Confidence              4689999988765

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=97.20  E-value=0.0019  Score=58.79  Aligned_cols=22  Identities=32%  Similarity=0.525  Sum_probs=20.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|+||||+||||+++.+++.+
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            3 IVLMGLPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            7899999999999999999887

>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=97.18  E-value=0.00066  Score=79.04  Aligned_cols=25  Identities=32%  Similarity=0.486  Sum_probs=22.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      +++|||||||||++|++++.+....
T Consensus      1085 ~l~~G~~g~GKT~la~~~~~~~~~~ 1109 (1706)
T 3cmw_A         1085 VEIYGPESSGKTTLTLQVIAAAQRE 1109 (1706)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEcCCCCChHHHHHHHHHHhhhc
Confidence            8999999999999999999876443

>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=97.18  E-value=0.0012  Score=67.45  Aligned_cols=81  Identities=12%  Similarity=0.061  Sum_probs=68.6

Q ss_pred             CCCceEEEEEcCCCCcCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHH
Q psy4285           4 FTTNVRFCIICNYLSKITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDG-DMRKVLNILQS   81 (533)
Q Consensus         4 ~~~~~~~il~~~~~~~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g-~~r~a~~~l~~   81 (533)
                      ++.+++||.+||.+..+.|+++||| .++.|+.|+.++...+++..+...+..+++..+..|+..+.| +.+...+++..
T Consensus       268 ~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~  347 (444)
T 2zan_A          268 DNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRD  347 (444)
T ss_dssp             CCSSCEEEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             CCCCEEEEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            5678999999999999999999999 589999999999999999888776666788899999999999 56666666655


Q ss_pred             HHH
Q psy4285          82 AAT   84 (533)
Q Consensus        82 ~~~   84 (533)
                      +..
T Consensus       348 a~~  350 (444)
T 2zan_A          348 ALM  350 (444)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            543

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

Probab=97.18  E-value=0.00092  Score=64.28  Aligned_cols=74  Identities=14%  Similarity=0.150  Sum_probs=65.4

Q ss_pred             CceEEEEEcCCCCcCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Q psy4285           6 TNVRFCIICNYLSKITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNIL   79 (533)
Q Consensus         6 ~~~~~il~~~~~~~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l   79 (533)
                      .++++|.+||.+..+.|+++||| ..+.|+.|+.++...+++..+.+.+..++++.+..+++.+.|..+..+..|
T Consensus       158 ~~v~vi~~tn~~~~l~~~l~~R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~l~~l  232 (297)
T 3b9p_A          158 DRIVVLAATNRPQELDEAALRRFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTAL  232 (297)
T ss_dssp             -CEEEEEEESCGGGBCHHHHHHCCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHHHHHH
T ss_pred             CcEEEEeecCChhhCCHHHHhhCCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHH
Confidence            46889999999999999999999 788999999999999999888888888889999999999999988777444

>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=97.16  E-value=0.0016  Score=64.41  Aligned_cols=80  Identities=14%  Similarity=0.125  Sum_probs=67.4

Q ss_pred             CCCceEEEEEcCCCCcCchhhhccce-eEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHH
Q psy4285           4 FTTNVRFCIICNYLSKITPAIQSRCT-RFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDG-DMRKVLNILQS   81 (533)
Q Consensus         4 ~~~~~~~il~~~~~~~i~~~i~SRc~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g-~~r~a~~~l~~   81 (533)
                      ++.++++|.+||.+..+.++++|||. .+.|+.|+.++..+++...+...+..++++.++.++..+.| +.+...++.+.
T Consensus       218 ~~~~v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~~  297 (357)
T 3d8b_A          218 SEDRILVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCRE  297 (357)
T ss_dssp             CCCCEEEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             CCCCEEEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            45788999999999999999999995 78999999999999999988888888899999999999999 44444444444


Q ss_pred             HH
Q psy4285          82 AA   83 (533)
Q Consensus        82 ~~   83 (533)
                      +.
T Consensus       298 a~  299 (357)
T 3d8b_A          298 AS  299 (357)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=97.16  E-value=0.0015  Score=63.62  Aligned_cols=81  Identities=12%  Similarity=0.127  Sum_probs=69.0

Q ss_pred             CCCCceEEEEEcCCCCcCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCC-CHHHHHHHHH
Q psy4285           3 KFTTNVRFCIICNYLSKITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDG-DMRKVLNILQ   80 (533)
Q Consensus         3 ~~~~~~~~il~~~~~~~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g-~~r~a~~~l~   80 (533)
                      .+..++++|.+||.+..+.|+++||| ..+.|+.|+.++..++++..+.+.+..+++..+..++..+.| +.+..-++++
T Consensus       150 ~~~~~v~vi~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~~t~g~sg~di~~l~~  229 (322)
T 3eie_A          150 NDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVK  229 (322)
T ss_dssp             TSCCCEEEEEEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHHTTTTCCHHHHHHHHH
T ss_pred             ccCCceEEEEecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            45678999999999999999999999 678999999999999999988877777889999999999988 5666555555


Q ss_pred             HHH
Q psy4285          81 SAA   83 (533)
Q Consensus        81 ~~~   83 (533)
                      .+.
T Consensus       230 ~a~  232 (322)
T 3eie_A          230 DAL  232 (322)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.16  E-value=0.00089  Score=78.92  Aligned_cols=96  Identities=20%  Similarity=0.275  Sum_probs=56.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch---------------------hHHHHHHHHHHhccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI---------------------GIVRDQIFQFASTKT  366 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~~~~~~~~  366 (533)
                      +++++||||||||++|.+++.+....   +.....++..+....                     .............  
T Consensus      1083 ~vll~G~~GtGKT~la~~~~~ea~k~---Ge~~~Fit~ee~~~~L~a~~~G~dl~~l~~~~pd~~e~~~~i~~~l~~~-- 1157 (2050)
T 3cmu_A         1083 IVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARS-- 1157 (2050)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTT---TCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHHH--
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEEccccHHHHHHHHcCCChhHheeecCcchHHHHHHHHHHHHh--
Confidence            49999999999999999999887544   333444443332111                     1111222222211  


Q ss_pred             CCCCCcEEEEEeCCCCCCHHH------------------HHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         367 MHKSSYKLIILDEADAMTNDA------------------QNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       367 ~~~~~~~vliiDE~d~l~~~~------------------~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                         ..++++|||++..+.+..                  .+.|++++........+++++|..
T Consensus      1158 ---~~~dlvVIDsl~~L~~~~e~~~~~g~~~~gl~aR~~~~~L~~L~~~l~e~~stiI~tN~~ 1217 (2050)
T 3cmu_A         1158 ---GAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQI 1217 (2050)
T ss_dssp             ---TCCSEEEESCGGGCCCHHHHHSCTTCCCTTHHHHHHHHHHHHHHHHHHTTTCEEEEEECC
T ss_pred             ---CCCCEEEECCcccccccccccccccccchhHHHHHHHHHHHHHHHHHHhCCeEEEEecCC
Confidence               357899999999984321                  234666665444444555566654

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=97.13  E-value=0.0046  Score=71.67  Aligned_cols=60  Identities=13%  Similarity=0.127  Sum_probs=36.9

Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecC-CCHHHHHHHhhc
Q psy4285         372 YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGP-LDSSLIMSRLDY  441 (533)
Q Consensus       372 ~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~-~~~~~~~~~l~~  441 (533)
                      .-+||+|+++..         ..++....+.++|+||....-. .........+...+ ++.++..+.+..
T Consensus       237 ~~LlvlDd~~~~---------~~~~~~~~~~~ilvTtR~~~~~-~~~~~~~~~~~~~~~l~~~~a~~l~~~  297 (1249)
T 3sfz_A          237 RSLLILDDVWDP---------WVLKAFDNQCQILLTTRDKSVT-DSVMGPKHVVPVESGLGREKGLEILSL  297 (1249)
T ss_dssp             SCEEEEESCCCH---------HHHTTTCSSCEEEEEESSTTTT-TTCCSCBCCEECCSSCCHHHHHHHHHH
T ss_pred             CEEEEEecCCCH---------HHHHhhcCCCEEEEEcCCHHHH-HhhcCCceEEEecCCCCHHHHHHHHHH
Confidence            679999999863         1233346778999999765421 11112224556664 777777776664

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=97.12  E-value=0.0023  Score=62.79  Aligned_cols=24  Identities=25%  Similarity=0.367  Sum_probs=21.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      ++++||||+||||++..++..+..
T Consensus        64 ~~I~GppGsGKSTLal~la~~~~~   87 (356)
T 3hr8_A           64 VEIFGQESSGKTTLALHAIAEAQK   87 (356)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHh
Confidence            799999999999999999987643

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=97.12  E-value=0.0022  Score=59.70  Aligned_cols=23  Identities=35%  Similarity=0.654  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|+||||+||||+++.+++.+
T Consensus        31 ~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           31 RYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999887

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=97.12  E-value=0.0025  Score=62.68  Aligned_cols=25  Identities=32%  Similarity=0.509  Sum_probs=21.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .++++||||+||||++..++..+..
T Consensus        63 iv~I~G~pGsGKTtLal~la~~~~~   87 (349)
T 2zr9_A           63 VIEIYGPESSGKTTVALHAVANAQA   87 (349)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHh
Confidence            3799999999999999999977643

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=97.11  E-value=0.002  Score=57.35  Aligned_cols=24  Identities=46%  Similarity=0.773  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+.|.||+|+||||+++.++..+.
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~~   26 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhhcc
Confidence            478999999999999999998773

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=97.08  E-value=0.0018  Score=57.44  Aligned_cols=92  Identities=13%  Similarity=0.094  Sum_probs=50.5

Q ss_pred             eeEeCCCCCChH-HHHHHHHHHHccccccCcceEEecCC-CCCchhHHHHHHHHHHhcc------cC--CCCCcEEEEEe
Q psy4285         309 LLFYGPPGTGKT-TTILACARKLYTKAQFNAMVLELNAS-DDRGIGIVRDQIFQFASTK------TM--HKSSYKLIILD  378 (533)
Q Consensus       309 ~ll~GppGtGKT-~la~~la~~l~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~------~~--~~~~~~vliiD  378 (533)
                      .++|||.|+||| ++.+++.+....    +..++.+.+. +.+....+...++......      ..  .....++|+||
T Consensus        23 ~fiyG~MgsGKTt~Ll~~i~n~~~~----~~kvl~~kp~~D~R~~~~i~S~~g~~~~A~~~~~~~d~~~~~~~~DvIlID   98 (195)
T 1w4r_A           23 QVILGPMFSGKSTELMRRVRRFQIA----QYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGID   98 (195)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHT----TCCEEEEEETTCCCGGGSCCHHHHHHSEEEEESSGGGGHHHHHTCSEEEES
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHc----CCeEEEEccccCccchhhhhhccCCcccceecCCHHHHHHhccCCCEEEEE
Confidence            689999999999 888888876533    2334444332 1111010111111000000      00  00235799999


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCcEEEEEe
Q psy4285         379 EADAMTNDAQNALRRIIEKFTTNVRFCIIC  408 (533)
Q Consensus       379 E~d~l~~~~~~~Ll~~le~~~~~~~~I~~~  408 (533)
                      |++.+ ++ +..+++.+.+  .+..||+++
T Consensus        99 EaQFf-k~-~ve~~~~L~~--~gk~VI~~G  124 (195)
T 1w4r_A           99 EGQFF-PD-IVEFCEAMAN--AGKTVIVAA  124 (195)
T ss_dssp             SGGGC-TT-HHHHHHHHHH--TTCEEEEEE
T ss_pred             chhhh-HH-HHHHHHHHHH--CCCeEEEEe
Confidence            99999 55 5555565543  456788887

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=97.08  E-value=0.00071  Score=60.36  Aligned_cols=88  Identities=17%  Similarity=0.257  Sum_probs=51.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC-C------------CCc-----hhHHHHHHHHHHhcccCCCC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS-D------------DRG-----IGIVRDQIFQFASTKTMHKS  370 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~-~------------~~~-----~~~~~~~~~~~~~~~~~~~~  370 (533)
                      .+++||+|+||||.+..+++.+...+   ..+..+.+. +            +..     .....+.....       ..
T Consensus        11 ~v~~G~mgsGKTT~ll~~a~r~~~~g---~kV~v~k~~~d~r~~~~~i~s~~g~~~~a~~~~~~~~i~~~~-------~~   80 (191)
T 1xx6_A           11 EVIVGPMYSGKSEELIRRIRRAKIAK---QKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYF-------EE   80 (191)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTT---CCEEEEEEC-------CEEECTTSCEEECEEESSSTHHHHHC-------CT
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCC---CEEEEEEeccCccchHHHHHhhcCCceeeEeeCCHHHHHHHH-------hc
Confidence            68999999999999999998874332   122211110 0            000     00001111111       12


Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeC
Q psy4285         371 SYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN  409 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n  409 (533)
                      ..++|+|||++.++++....+..+.+   .+..+|+++-
T Consensus        81 ~~dvViIDEaqfl~~~~v~~l~~l~~---~~~~Vi~~Gl  116 (191)
T 1xx6_A           81 DTEVIAIDEVQFFDDEIVEIVNKIAE---SGRRVICAGL  116 (191)
T ss_dssp             TCSEEEECSGGGSCTHHHHHHHHHHH---TTCEEEEEEC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHHh---CCCEEEEEec
Confidence            46899999999998776555444443   3678888874

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.08  E-value=0.0011  Score=66.62  Aligned_cols=90  Identities=20%  Similarity=0.211  Sum_probs=52.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHH----------------HHHhccc-CCCCC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIF----------------QFASTKT-MHKSS  371 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~~-~~~~~  371 (533)
                      .++.|+||||||+++..++..        .....+.+.. .....+++.+.                .+..... .....
T Consensus       164 ~~I~G~aGsGKTt~I~~~~~~--------~~~lVlTpT~-~aa~~l~~kl~~~~~~~~~~~~V~T~dsfL~~~~~~~~~~  234 (446)
T 3vkw_A          164 VLVDGVPGCGKTKEILSRVNF--------EEDLILVPGR-QAAEMIRRRANASGIIVATKDNVRTVDSFLMNYGKGARCQ  234 (446)
T ss_dssp             EEEEECTTSCHHHHHHHHCCT--------TTCEEEESCH-HHHHHHHHHHTTTSCCCCCTTTEEEHHHHHHTTTSSCCCC
T ss_pred             EEEEcCCCCCHHHHHHHHhcc--------CCeEEEeCCH-HHHHHHHHHhhhcCccccccceEEEeHHhhcCCCCCCCCc
Confidence            689999999999999877531        1112222221 12222222221                1111110 00113


Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         372 YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       372 ~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      .+++||||+.+++......++..+    ...++|++++..
T Consensus       235 ~d~liiDE~sm~~~~~l~~l~~~~----~~~~vilvGD~~  270 (446)
T 3vkw_A          235 FKRLFIDEGLMLHTGCVNFLVEMS----LCDIAYVYGDTQ  270 (446)
T ss_dssp             CSEEEEETGGGSCHHHHHHHHHHT----TCSEEEEEECTT
T ss_pred             CCEEEEeCcccCCHHHHHHHHHhC----CCCEEEEecCcc
Confidence            689999999999988887777665    227899998644

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

Probab=97.08  E-value=0.002  Score=62.80  Aligned_cols=80  Identities=13%  Similarity=0.055  Sum_probs=67.1

Q ss_pred             CCCceEEEEEcCCCCcCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCC-HHHHHHHHHH
Q psy4285           4 FTTNVRFCIICNYLSKITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGD-MRKVLNILQS   81 (533)
Q Consensus         4 ~~~~~~~il~~~~~~~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~-~r~a~~~l~~   81 (533)
                      ++.++++|.+||.+..+.|++++|| ..+.|+.|+.++..++|+..+.+.+..+++..+..+++.+.|- .+..-++...
T Consensus       146 ~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~  225 (322)
T 1xwi_A          146 DNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVRD  225 (322)
T ss_dssp             CCTTEEEEEEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHHTCTTCCHHHHHHHHHH
T ss_pred             cCCCEEEEEecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            5678999999999999999999999 7899999999999999998887777777889999999999985 4444444444


Q ss_pred             HH
Q psy4285          82 AA   83 (533)
Q Consensus        82 ~~   83 (533)
                      +.
T Consensus       226 A~  227 (322)
T 1xwi_A          226 AL  227 (322)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=97.08  E-value=0.00034  Score=62.10  Aligned_cols=24  Identities=25%  Similarity=0.303  Sum_probs=22.3

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++|+||||+||||+++.+++.+
T Consensus         6 ~~i~l~G~~GsGKst~a~~La~~l   29 (185)
T 3trf_A            6 TNIYLIGLMGAGKTSVGSQLAKLT   29 (185)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            358999999999999999999988

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=97.04  E-value=0.0036  Score=61.62  Aligned_cols=25  Identities=32%  Similarity=0.441  Sum_probs=22.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .++++||||+|||++|..++..+..
T Consensus        65 ii~I~G~pGsGKTtLal~la~~~~~   89 (356)
T 1u94_A           65 IVEIYGPESSGKTTLTLQVIAAAQR   89 (356)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3799999999999999999987643

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.04  E-value=0.0029  Score=58.02  Aligned_cols=24  Identities=38%  Similarity=0.444  Sum_probs=21.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++++||||+||||+++.++..+.
T Consensus        25 ~~~i~G~~GsGKTtl~~~l~~~~~   48 (235)
T 2w0m_A           25 FIALTGEPGTGKTIFSLHFIAKGL   48 (235)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999997653

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=97.03  E-value=0.00042  Score=61.03  Aligned_cols=23  Identities=17%  Similarity=0.330  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++++|+||+||||+++.+++.+
T Consensus         5 ~i~l~G~~GsGKST~a~~La~~l   27 (178)
T 1qhx_A            5 MIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            48999999999999999999987

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=97.02  E-value=0.0013  Score=59.86  Aligned_cols=23  Identities=30%  Similarity=0.520  Sum_probs=21.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||||+||+|.|+.+++.+
T Consensus        31 iI~llGpPGsGKgTqa~~L~~~~   53 (217)
T 3umf_A           31 VIFVLGGPGSGKGTQCEKLVQKF   53 (217)
T ss_dssp             EEEEECCTTCCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37889999999999999999987

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=97.02  E-value=0.0036  Score=56.91  Aligned_cols=95  Identities=13%  Similarity=0.126  Sum_probs=52.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC-CCCchhHHHHHHHHHHhc------ccCC--CCCcEEEEEeC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS-DDRGIGIVRDQIFQFAST------KTMH--KSSYKLIILDE  379 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~------~~~~--~~~~~vliiDE  379 (533)
                      .+++|+.|+||||.+...+......+   ..++.+... +.+....+....+.-...      ....  ....++|+|||
T Consensus        22 ~v~~G~MgsGKTT~lL~~~~r~~~~g---~kvli~kp~~D~Ryg~~i~sr~G~~~~a~~i~~~~di~~~~~~~dvViIDE   98 (234)
T 2orv_A           22 QVILGPMFSGKSTELMRRVRRFQIAQ---YKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDE   98 (234)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTT---CCEEEEEETTCCCC-----------CEEEEESSGGGGHHHHTTCSEEEESS
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCC---CeEEEEeecCCccchHHHHhhcCCeeEEEecCCHHHHHHHhccCCEEEEEc
Confidence            58899999999988888777664442   222222211 111001111111100000      0000  03468999999


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         380 ADAMTNDAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       380 ~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      +..+..  ...+.+.++.  .+..+|+++-.
T Consensus        99 aQF~~~--v~el~~~l~~--~gi~VI~~GL~  125 (234)
T 2orv_A           99 GQFFPD--IVEFCEAMAN--AGKTVIVAALD  125 (234)
T ss_dssp             GGGCTT--HHHHHHHHHH--TTCEEEEECCS
T ss_pred             hhhhhh--HHHHHHHHHh--CCCEEEEEecc
Confidence            999974  6667777776  56789998844

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

Probab=96.99  E-value=0.0051  Score=60.01  Aligned_cols=95  Identities=19%  Similarity=0.171  Sum_probs=71.8

Q ss_pred             CCceEEEEEcCCCC-----cCchhhhcccee-EEeCCCCHHHHHHHHHHHHhhc----------------------CCCC
Q psy4285           5 TTNVRFCIICNYLS-----KITPAIQSRCTR-FRFGPLDSSLIMSRLDYVIEQE----------------------KVNV   56 (533)
Q Consensus         5 ~~~~~~il~~~~~~-----~i~~~i~SRc~~-~~~~~~~~~~~~~~l~~~~~~~----------------------~~~~   56 (533)
                      +.++.+|.++|+..     .+.++++|||.+ +.|.+|+.++..++|++.+..+                      ++.+
T Consensus       148 ~~~~~viat~np~~~~~~~~l~~~l~~Rf~~~i~i~~p~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~v~~  227 (331)
T 2r44_A          148 DNPFLVLATQNPVEQEGTYPLPEAQVDRFMMKIHLTYLDKESELEVMRRVSNMNFNYQVQKIVSKNDVLEIRNEINKVTI  227 (331)
T ss_dssp             CSSCEEEEEECTTCCSCCCCCCHHHHTTSSEEEECCCCCHHHHHHHHHHHHCTTCCCCCCCCSCHHHHHHHHHHHHTCBC
T ss_pred             CCCEEEEEecCCCcccCcccCCHHHHhheeEEEEcCCCCHHHHHHHHHhccccCcchhccccCCHHHHHHHHHHhccCCC
Confidence            55677777777654     489999999974 9999999999999998876542                      6778


Q ss_pred             CHHHHHHHHHhc-----CC---------------CHHHHHHHHHHHHHh----CCCCcchhhHHhhh
Q psy4285          57 TPDGKKAIIDLS-----DG---------------DMRKVLNILQSAATA----HADEVNEDTIFTLL   99 (533)
Q Consensus        57 ~~~~~~~~~~~~-----~g---------------~~r~a~~~l~~~~~~----~~~~i~~~~i~~~~   99 (533)
                      +++.++.++..+     .|               ++|.+++++..+...    ....++.+.+.+++
T Consensus       228 ~~~~~~~i~~~~~~~r~~~~~~~~~~~~~~~~~~s~R~~~~ll~~a~a~A~l~g~~~v~~~dv~~~~  294 (331)
T 2r44_A          228 SESLEKYIIELVFATRFPAEYGLEAEASYILYGASTRAAINLNRVAKAMAFFNNRDYVLPEDIKEVA  294 (331)
T ss_dssp             CHHHHHHHHHHHHHHHSGGGGTCHHHHHHEEECCCHHHHHHHHHHHHHHHHHTTCSBCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhccccccccccccccccCcChhHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence            999898887765     23               799999999876432    23347888776544

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=96.98  E-value=0.0087  Score=61.54  Aligned_cols=69  Identities=17%  Similarity=0.223  Sum_probs=47.3

Q ss_pred             EEEEEeCCCCCCHH----HHHHHHHHHHhc-CCCcEEEEEeCCCC--CCChhhhccc-eeeeecCCCHHHHHHHhhc
Q psy4285         373 KLIILDEADAMTND----AQNALRRIIEKF-TTNVRFCIICNYLS--KIPPAIQSRC-TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       373 ~vliiDE~d~l~~~----~~~~Ll~~le~~-~~~~~~I~~~n~~~--~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~  441 (533)
                      -+++|||+..+...    ....+.++.... ..++.+|++|.++.  .+...+++.| ..+.|.-.+..+.+.++..
T Consensus       299 ivlvIDE~~~ll~~~~~~~~~~l~~Lar~gRa~GI~LIlaTQrp~~dvl~~~i~~n~~~RI~lrv~s~~dsr~ilg~  375 (512)
T 2ius_A          299 IVVLVDEFADLMMTVGKKVEELIARLAQKARAAGIHLVLATQRPSVDVITGLIKANIPTRIAFTVSSKIDSRTILDQ  375 (512)
T ss_dssp             EEEEEETHHHHHHHHHHHHHHHHHHHHHHCGGGTEEEEEEESCCCTTTSCHHHHHHCCEEEEECCSSHHHHHHHHSS
T ss_pred             EEEEEeCHHHHHhhhhHHHHHHHHHHHHHhhhCCcEEEEEecCCccccccHHHHhhcCCeEEEEcCCHHHHHHhcCC
Confidence            48999999665432    223333443433 34788999998887  5777788877 5778888888888877654

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=96.96  E-value=0.0019  Score=59.75  Aligned_cols=21  Identities=29%  Similarity=0.422  Sum_probs=17.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~  328 (533)
                      .+++.||+|+|||++...+.-
T Consensus        78 ~~~i~g~TGsGKTt~~~~~~~   98 (235)
T 3llm_A           78 VVIIRGATGCGKTTQVPQFIL   98 (235)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEeCCCCCcHHhHHHHHh
Confidence            589999999999987766543

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=96.95  E-value=0.0045  Score=60.92  Aligned_cols=92  Identities=17%  Similarity=0.174  Sum_probs=53.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC-C---------------CCchhHHHHHHHHHHhcccCCCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS-D---------------DRGIGIVRDQIFQFASTKTMHKSS  371 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~-~---------------~~~~~~~~~~~~~~~~~~~~~~~~  371 (533)
                      .+++.||+|+||||+.++++..+....  +..++.+..+ +               ......+.+.+....      ...
T Consensus       125 ~i~I~GptGSGKTTlL~~l~g~~~~~~--~~~i~t~ed~~e~~~~~~~~~v~q~~~~~~~~~~~~~La~aL------~~~  196 (356)
T 3jvv_A          125 LVLVTGPTGSGKSTTLAAMLDYLNNTK--YHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSAL------RED  196 (356)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHHC--CCEEEEEESSCCSCCCCSSSEEEEEEBTTTBSCHHHHHHHHT------TSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhcccCCC--CcEEEEccCcHHhhhhccccceeeeeeccccCCHHHHHHHHh------hhC
Confidence            589999999999999999998774321  1111111100 0               000112233333222      246


Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         372 YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       372 ~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      ++++++||+-  +.+....+++..+.   +..+++|+...+
T Consensus       197 PdvillDEp~--d~e~~~~~~~~~~~---G~~vl~t~H~~~  232 (356)
T 3jvv_A          197 PDIILVGEMR--DLETIRLALTAAET---GHLVFGTLHTTS  232 (356)
T ss_dssp             CSEEEESCCC--SHHHHHHHHHHHHT---TCEEEEEESCSS
T ss_pred             cCEEecCCCC--CHHHHHHHHHHHhc---CCEEEEEEccCh
Confidence            7899999996  46666666666543   345666765544

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

Probab=96.95  E-value=0.00057  Score=66.16  Aligned_cols=79  Identities=15%  Similarity=0.190  Sum_probs=66.8

Q ss_pred             CceEEEEEcCC--------------------------CCcCchhhhccc-eeEEeCCCCHHHHHHHHHHHHhhc------
Q psy4285           6 TNVRFCIICNY--------------------------LSKITPAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQE------   52 (533)
Q Consensus         6 ~~~~~il~~~~--------------------------~~~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~------   52 (533)
                      .+++||++||.                          ...+.|++.||| .++.|.||+.+++..++++.+.+.      
T Consensus       159 ~~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~R~~~~~~~~p~~~~~~~~i~~~~l~~~~~~~~~  238 (311)
T 4fcw_A          159 RNTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQMSYLRARLAE  238 (311)
T ss_dssp             TTEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHHTHHHHHHHHT
T ss_pred             CCcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHhcCCeEEEeCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            36779999998                          557899999999 899999999999999998876531      


Q ss_pred             ---CCCCCHHHHHHHHHhcC---CCHHHHHHHHHHHHH
Q psy4285          53 ---KVNVTPDGKKAIIDLSD---GDMRKVLNILQSAAT   84 (533)
Q Consensus        53 ---~~~~~~~~~~~~~~~~~---g~~r~a~~~l~~~~~   84 (533)
                         .+.+++++++.++..+-   ||+|...+.++.+..
T Consensus       239 ~~~~~~~~~~~~~~l~~~~~~~~gn~R~L~~~i~~~~~  276 (311)
T 4fcw_A          239 KRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELE  276 (311)
T ss_dssp             TTCEEEECHHHHHHHHHHSCBTTTBTTTHHHHHHHHTH
T ss_pred             CCcEEEeCHHHHHHHHHhCCCccCCchhHHHHHHHHHH
Confidence               34688999999998764   999999999998755

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=96.95  E-value=0.00051  Score=59.94  Aligned_cols=24  Identities=29%  Similarity=0.430  Sum_probs=22.4

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++|+|+||+||||+++.+++.+
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~l   31 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLAL   31 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            458999999999999999999988

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=96.95  E-value=0.0042  Score=56.64  Aligned_cols=52  Identities=23%  Similarity=0.267  Sum_probs=31.7

Q ss_pred             CCcEEEEEeCCCCCC--HHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhcc
Q psy4285         370 SSYKLIILDEADAMT--NDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSR  421 (533)
Q Consensus       370 ~~~~vliiDE~d~l~--~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR  421 (533)
                      ...+++|+||+|.+.  ......+..++...+.+..+++.|..+..-...+.++
T Consensus       157 ~~~~~lViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~  210 (220)
T 1t6n_A          157 KHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRK  210 (220)
T ss_dssp             TTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHT
T ss_pred             ccCCEEEEcCHHHHhcccCcHHHHHHHHHhCCCcCeEEEEEeecCHHHHHHHHH
Confidence            457899999999874  3444555566665555677776665444323334333

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=96.95  E-value=0.0046  Score=61.09  Aligned_cols=25  Identities=36%  Similarity=0.424  Sum_probs=21.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .++++||||+|||++|..++..+..
T Consensus        76 li~I~G~pGsGKTtlal~la~~~~~  100 (366)
T 1xp8_A           76 ITEIYGPESGGKTTLALAIVAQAQK  100 (366)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCChHHHHHHHHHHHHH
Confidence            3789999999999999999987643

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=96.93  E-value=0.00063  Score=59.40  Aligned_cols=23  Identities=22%  Similarity=0.307  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||||+||||+++.+++.+
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l   25 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKEL   25 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999987

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=96.92  E-value=0.0029  Score=58.61  Aligned_cols=23  Identities=26%  Similarity=0.161  Sum_probs=20.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|+||||+||||+++.++...
T Consensus        26 ~~~i~G~~GsGKTtl~~~l~~~~   48 (243)
T 1n0w_A           26 ITEMFGEFRTGKTQICHTLAVTC   48 (243)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHH
Confidence            37999999999999999999864

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=96.91  E-value=0.0019  Score=69.02  Aligned_cols=25  Identities=44%  Similarity=0.561  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      ..++.||||||||+++..++..+..
T Consensus       197 ~~li~GppGTGKT~~~~~~i~~l~~  221 (624)
T 2gk6_A          197 LSLIQGPPGTGKTVTSATIVYHLAR  221 (624)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CeEEECCCCCCHHHHHHHHHHHHHH
Confidence            5799999999999999988877653

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

Probab=96.90  E-value=0.00065  Score=64.49  Aligned_cols=76  Identities=9%  Similarity=0.147  Sum_probs=61.7

Q ss_pred             CCCceEEEEEcCCCCcCch-hhhcc-ceeEEeCCCCH-HHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCC-----CHHHH
Q psy4285           4 FTTNVRFCIICNYLSKITP-AIQSR-CTRFRFGPLDS-SLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDG-----DMRKV   75 (533)
Q Consensus         4 ~~~~~~~il~~~~~~~i~~-~i~SR-c~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g-----~~r~a   75 (533)
                      ++.++++|.+||.+..+-+ .++|| |..+.|++++. +++..++.+    . ..++++.+..++..+.|     |+|++
T Consensus       164 ~~~~~~ii~ttn~~~~l~~~~l~~rf~~~i~~p~l~~r~~i~~i~~~----~-~~~~~~~~~~l~~~~~g~~~~g~ir~l  238 (272)
T 1d2n_A          164 QGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEALEL----L-GNFKDKERTTIAQQVKGKKVWIGIKKL  238 (272)
T ss_dssp             TTCEEEEEEEESCHHHHHHTTCTTTSSEEEECCCEEEHHHHHHHHHH----H-TCSCHHHHHHHHHHHTTSEEEECHHHH
T ss_pred             CCCCEEEEEecCChhhcchhhhhcccceEEcCCCccHHHHHHHHHHh----c-CCCCHHHHHHHHHHhcCCCccccHHHH
Confidence            4566778888888876666 68999 79999999988 777777653    2 24678899999999988     99999


Q ss_pred             HHHHHHHHH
Q psy4285          76 LNILQSAAT   84 (533)
Q Consensus        76 ~~~l~~~~~   84 (533)
                      +|+++.+..
T Consensus       239 ~~~l~~a~~  247 (272)
T 1d2n_A          239 LMLIEMSLQ  247 (272)
T ss_dssp             HHHHHHHTT
T ss_pred             HHHHHHHhh
Confidence            999999865

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=96.89  E-value=0.00068  Score=59.87  Aligned_cols=24  Identities=46%  Similarity=0.630  Sum_probs=22.3

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.++|+|+||+||||+++.+++.+
T Consensus        12 ~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           12 PNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHh
Confidence            468999999999999999999987

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.86  E-value=0.0081  Score=55.62  Aligned_cols=24  Identities=33%  Similarity=0.339  Sum_probs=20.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++++||||+|||+++..++....
T Consensus        25 ~~~i~G~~GsGKTtl~~~~~~~~~   48 (247)
T 2dr3_A           25 VVLLSGGPGTGKTIFSQQFLWNGL   48 (247)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            379999999999999998887654

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=96.84  E-value=0.00075  Score=59.78  Aligned_cols=23  Identities=35%  Similarity=0.511  Sum_probs=21.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|+|+||+||||+++.+++.+
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~l   26 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAKAL   26 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999987

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.84  E-value=0.00076  Score=60.71  Aligned_cols=23  Identities=48%  Similarity=0.531  Sum_probs=21.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||||+||||+++.+++.+
T Consensus        27 ~i~l~G~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           27 RIFLTGYMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999988

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=96.82  E-value=0.00092  Score=58.72  Aligned_cols=23  Identities=39%  Similarity=0.589  Sum_probs=21.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l   28 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDL   28 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999987

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=96.81  E-value=0.0015  Score=61.44  Aligned_cols=23  Identities=35%  Similarity=0.511  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus         6 lIvl~G~pGSGKSTla~~La~~L   28 (260)
T 3a4m_A            6 LIILTGLPGVGKSTFSKNLAKIL   28 (260)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            48999999999999999999985

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=96.81  E-value=0.00076  Score=59.86  Aligned_cols=23  Identities=39%  Similarity=0.562  Sum_probs=21.4

Q ss_pred             CceeEeCCCCCChHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~  329 (533)
                      ..++|+|+||+||||+++.+++.
T Consensus        11 ~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A           11 INILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            35899999999999999999998

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=96.81  E-value=0.0046  Score=60.70  Aligned_cols=22  Identities=23%  Similarity=0.098  Sum_probs=20.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++||||+|||+++..++...
T Consensus       125 ~~I~G~~GsGKTtla~~la~~~  146 (343)
T 1v5w_A          125 TEAFGEFRTGKTQLSHTLCVTA  146 (343)
T ss_dssp             EEEECCTTCTHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7999999999999999999874

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=96.80  E-value=0.0026  Score=69.57  Aligned_cols=26  Identities=46%  Similarity=0.636  Sum_probs=22.2

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +..++.||||||||+++..++..+..
T Consensus       372 ~~~lI~GppGTGKT~ti~~~i~~l~~  397 (800)
T 2wjy_A          372 PLSLIQGPPGTGKTVTSATIVYHLAR  397 (800)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            35799999999999999988887654

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.72  E-value=0.0011  Score=58.04  Aligned_cols=23  Identities=35%  Similarity=0.582  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|+||||+||||+++.++..+
T Consensus         6 ~i~l~G~~GsGKSTl~~~La~~l   28 (173)
T 1kag_A            6 NIFLVGPMGAGKSTIGRQLAQQL   28 (173)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999986

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=96.72  E-value=0.01  Score=55.71  Aligned_cols=24  Identities=38%  Similarity=0.598  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+.+.||+|+||||+.+.++..+.
T Consensus        27 ~v~i~Gp~GsGKSTll~~l~g~~~   50 (261)
T 2eyu_A           27 LILVTGPTGSGKSTTIASMIDYIN   50 (261)
T ss_dssp             EEEEECSTTCSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCccHHHHHHHHHHhCC
Confidence            489999999999999999998763

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=96.71  E-value=0.0053  Score=56.25  Aligned_cols=24  Identities=25%  Similarity=0.221  Sum_probs=21.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+.|.||+|+||||+++.++..+.
T Consensus        27 ~~~l~G~nGsGKSTll~~l~g~~~   50 (231)
T 4a74_A           27 ITEVFGEFGSGKTQLAHTLAVMVQ   50 (231)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            379999999999999999998653

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=96.69  E-value=0.00096  Score=65.01  Aligned_cols=38  Identities=21%  Similarity=0.349  Sum_probs=29.9

Q ss_pred             hhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         294 CYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       294 ~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      ...+...+..+..++++|.|+||+||||+++.+++.+.
T Consensus        12 l~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~~l~   49 (359)
T 2ga8_A           12 LQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQIIN   49 (359)
T ss_dssp             HHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHHHhC
Confidence            33444455666666799999999999999999999874

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=96.68  E-value=0.0037  Score=68.44  Aligned_cols=42  Identities=14%  Similarity=0.379  Sum_probs=28.6

Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhh
Q psy4285         371 SYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAI  418 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l  418 (533)
                      ..+++||||+..++..  +.+..++   ....++|++++... +.|.+
T Consensus       517 ~fd~viIDEA~q~~e~--~~li~l~---~~~~~lilvGD~~Q-L~pvv  558 (802)
T 2xzl_A          517 KFRTVLIDESTQASEP--ECLIPIV---KGAKQVILVGDHQQ-LGPVI  558 (802)
T ss_dssp             CCSEEEETTGGGSCHH--HHHHHHT---TTBSEEEEEECTTS-CCCCC
T ss_pred             cCCEEEEECccccchH--HHHHHHH---hCCCEEEEEeCccc-cCCee
Confidence            6889999999888754  2455555   23468999998544 44433

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=96.67  E-value=0.0057  Score=55.49  Aligned_cols=105  Identities=16%  Similarity=0.217  Sum_probs=56.2

Q ss_pred             CCCceeEeCCCCCChHHHHHHHHHHHccccc--cCc---------ceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcE
Q psy4285         305 ELPHLLFYGPPGTGKTTTILACARKLYTKAQ--FNA---------MVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYK  373 (533)
Q Consensus       305 ~~~~~ll~GppGtGKT~la~~la~~l~~~~~--~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  373 (533)
                      ..+++++.|++|+|||+++..+....+....  ...         .+..++.   .+....+.....+..... .....-
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~Dt---~G~~~~~~~~~~~~~~~~-~~~~~~   86 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTDSVRPTVVSQEPLSAADYDGSGVTLVDF---PGHVKLRYKLSDYLKTRA-KFVKGL   86 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHSSCCCBCCCSSCEEETTGGGSSCEEEEC---CCCGGGTHHHHHHHHHHG-GGEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCCCCeeeecCceEEEEeeCceEEEEEC---CCcHHHHHHHHHHHHhcc-ccCCEE
Confidence            3456999999999999999999876532210  000         0111111   122222233333332210 001345


Q ss_pred             EEEEeCC-CCC-CHHHHHHHHHHHHh----cCCCcEEEEEeCCCCC
Q psy4285         374 LIILDEA-DAM-TNDAQNALRRIIEK----FTTNVRFCIICNYLSK  413 (533)
Q Consensus       374 vliiDE~-d~l-~~~~~~~Ll~~le~----~~~~~~~I~~~n~~~~  413 (533)
                      ++++|-. +.- .......+..++..    .+.+..+++++|..+.
T Consensus        87 i~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl  132 (218)
T 1nrj_B           87 IFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSEL  132 (218)
T ss_dssp             EEEEETTSCTTCCHHHHHHHHHHHHHHHHHSTTCCCEEEEEECTTS
T ss_pred             EEEEECCCChHHHHHHHHHHHHHHhcccccccCCCCEEEEEEchHh
Confidence            7888876 222 23444556566543    3456788999998774

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

Probab=96.65  E-value=0.01  Score=56.46  Aligned_cols=95  Identities=16%  Similarity=0.112  Sum_probs=69.9

Q ss_pred             CCCceEEEEEcCCCCcCchhhhc--cc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCC-CHHHHHHHH
Q psy4285           4 FTTNVRFCIICNYLSKITPAIQS--RC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDG-DMRKVLNIL   79 (533)
Q Consensus         4 ~~~~~~~il~~~~~~~i~~~i~S--Rc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g-~~r~a~~~l   79 (533)
                      +..++++|.+||.+..+.|++++  |+ ..+.|++|+.++..++++..+...+.. ++..+..++..+.| +.|...+++
T Consensus       153 ~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~-~~~~~~~l~~~~~g~~~~~i~~l~  231 (285)
T 3h4m_A          153 ARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLA-EDVNLEEIAKMTEGCVGAELKAIC  231 (285)
T ss_dssp             SSSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBC-TTCCHHHHHHHCTTCCHHHHHHHH
T ss_pred             CCCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCC-CcCCHHHHHHHcCCCCHHHHHHHH
Confidence            45688999999999999999999  88 589999999999999999887655443 22346788888877 555555555


Q ss_pred             HHHHH---hC-CCCcchhhHHhhh
Q psy4285          80 QSAAT---AH-ADEVNEDTIFTLL   99 (533)
Q Consensus        80 ~~~~~---~~-~~~i~~~~i~~~~   99 (533)
                      +.+..   .. ...|+.+.+.+.+
T Consensus       232 ~~a~~~a~~~~~~~I~~~d~~~al  255 (285)
T 3h4m_A          232 TEAGMNAIRELRDYVTMDDFRKAV  255 (285)
T ss_dssp             HHHHHHHHHTTCSSBCHHHHHHHH
T ss_pred             HHHHHHHHHhccCcCCHHHHHHHH
Confidence            55433   22 3458888765543

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=96.64  E-value=0.0012  Score=57.73  Aligned_cols=23  Identities=35%  Similarity=0.421  Sum_probs=21.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|+|+||+||||+++.+++.+
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~l   26 (173)
T 1e6c_A            4 PIFMVGARGCGMTTVGRELARAL   26 (173)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999987

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=96.63  E-value=0.0014  Score=62.60  Aligned_cols=23  Identities=35%  Similarity=0.473  Sum_probs=21.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.||||+||||+++.+++.+
T Consensus        35 livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           35 AFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             EEEEECCTTSCTHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            38999999999999999999876

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=96.62  E-value=0.0076  Score=60.24  Aligned_cols=23  Identities=22%  Similarity=0.143  Sum_probs=19.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|+||||+||||+++.++...
T Consensus       180 i~~I~G~sGsGKTTLl~~la~~~  202 (400)
T 3lda_A          180 ITELFGEFRTGKSQLCHTLAVTC  202 (400)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCChHHHHHHHHHHh
Confidence            37999999999999999887554

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=96.62  E-value=0.0084  Score=60.37  Aligned_cols=24  Identities=33%  Similarity=0.344  Sum_probs=21.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +++.||+|+||||++..+|..+..
T Consensus       100 I~lvG~~GsGKTTt~~kLA~~l~~  123 (433)
T 3kl4_A          100 IMLVGVQGSGKTTTAGKLAYFYKK  123 (433)
T ss_dssp             EEECCCTTSCHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH
Confidence            789999999999999999988744

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=96.61  E-value=0.0015  Score=59.19  Aligned_cols=23  Identities=26%  Similarity=0.468  Sum_probs=20.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++.+|+|+|||.++...+...
T Consensus        50 ~~li~~~tGsGKT~~~~~~~~~~   72 (216)
T 3b6e_A           50 NIIICLPTGSGKTRVAVYIAKDH   72 (216)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHH
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHH
Confidence            69999999999999998887654

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=96.61  E-value=0.0015  Score=61.19  Aligned_cols=23  Identities=35%  Similarity=0.566  Sum_probs=21.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.||||+||||+|+.+|+.+
T Consensus         3 li~I~G~~GSGKSTla~~La~~~   25 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQET   25 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHhcC
Confidence            37899999999999999999987

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=96.61  E-value=0.0023  Score=67.94  Aligned_cols=26  Identities=31%  Similarity=0.405  Sum_probs=22.0

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .++++.+|+|+|||.++-.++..+..
T Consensus       199 ~~~ll~~~TGsGKT~~~~~~~~~l~~  224 (590)
T 3h1t_A          199 KRSLITMATGTGKTVVAFQISWKLWS  224 (590)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             CceEEEecCCCChHHHHHHHHHHHHh
Confidence            35899999999999999888877754

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=96.59  E-value=0.0017  Score=59.42  Aligned_cols=23  Identities=30%  Similarity=0.677  Sum_probs=21.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus         6 ~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            6 RMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999987

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

Probab=96.59  E-value=0.0025  Score=63.26  Aligned_cols=68  Identities=15%  Similarity=0.212  Sum_probs=52.3

Q ss_pred             cCccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhhhH--H---HHhhhhhcccccCCCceEEEEcCccc
Q psy4285         139 SDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVR--D---QIFQFASTKTMHKSSYKLIILDEADA  213 (533)
Q Consensus       139 ~~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~~~--d---~i~~~a~~~~l~~~~~~~iilDE~d~  213 (533)
                      ..+..+||||||||..+.|++..+.     ..++.++++++.+...+.  .   .+...|..     .+|.++++||+|.
T Consensus       183 rGvLL~GPPGTGKTllAkAiA~e~~-----~~f~~v~~s~l~sk~vGese~~vr~lF~~Ar~-----~aP~IIFiDEiDa  252 (405)
T 4b4t_J          183 KGVILYGPPGTGKTLLARAVAHHTD-----CKFIRVSGAELVQKYIGEGSRMVRELFVMARE-----HAPSIIFMDEIDS  252 (405)
T ss_dssp             CCEEEESCSSSSHHHHHHHHHHHHT-----CEEEEEEGGGGSCSSTTHHHHHHHHHHHHHHH-----TCSEEEEEESSSC
T ss_pred             CceEEeCCCCCCHHHHHHHHHHhhC-----CCceEEEhHHhhccccchHHHHHHHHHHHHHH-----hCCceEeeecchh
Confidence            4577899999999999999999988     688999999887776655  2   23222322     3577999999999


Q ss_pred             cCH
Q psy4285         214 MTN  216 (533)
Q Consensus       214 l~~  216 (533)
                      +..
T Consensus       253 i~~  255 (405)
T 4b4t_J          253 IGS  255 (405)
T ss_dssp             CTT
T ss_pred             hcc
Confidence            873

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=96.59  E-value=0.0012  Score=57.71  Aligned_cols=22  Identities=27%  Similarity=0.439  Sum_probs=19.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||||+||||+++.+ +.+
T Consensus         3 ~I~l~G~~GsGKsT~a~~L-~~~   24 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL-KER   24 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH-HHT
T ss_pred             EEEEECCCCCCHHHHHHHH-HHC
Confidence            4789999999999999999 655

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=96.58  E-value=0.0031  Score=63.75  Aligned_cols=82  Identities=13%  Similarity=0.091  Sum_probs=44.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQ  388 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~  388 (533)
                      ++++|+||+||||+++.+++.+      +..  .++...................       ....+|+|-... .....
T Consensus       261 Iil~G~pGSGKSTla~~L~~~~------~~~--~i~~D~~~~~~~~~~~~~~~l~-------~g~~vIiD~~~~-~~~~r  324 (416)
T 3zvl_A          261 VVAVGFPGAGKSTFIQEHLVSA------GYV--HVNRDTLGSWQRCVSSCQAALR-------QGKRVVIDNTNP-DVPSR  324 (416)
T ss_dssp             EEEESCTTSSHHHHHHHHTGGG------TCE--ECCGGGSCSHHHHHHHHHHHHH-------TTCCEEEESCCC-SHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHhc------CcE--EEccchHHHHHHHHHHHHHHHh-------cCCcEEEeCCCC-CHHHH
Confidence            7899999999999999998765      322  2333222222222222222221       123466776543 34445


Q ss_pred             HHHHHHHHhcCCCcEEEE
Q psy4285         389 NALRRIIEKFTTNVRFCI  406 (533)
Q Consensus       389 ~~Ll~~le~~~~~~~~I~  406 (533)
                      ..+.+...+....+.+|.
T Consensus       325 ~~~~~~~~~~~~~~~~v~  342 (416)
T 3zvl_A          325 ARYIQCAKDAGVPCRCFN  342 (416)
T ss_dssp             HHHHHHHHHHTCCEEEEE
T ss_pred             HHHHHHHHHcCCeEEEEE
Confidence            556666655443344433

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=96.58  E-value=0.016  Score=58.40  Aligned_cols=26  Identities=42%  Similarity=0.560  Sum_probs=22.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      .+++.|++|+||||++..+|..+...
T Consensus       102 vIlivG~~G~GKTTt~~kLA~~l~~~  127 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTVAKLARYFQKR  127 (443)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             EEEEECcCCCCHHHHHHHHHHHHHHC
Confidence            38999999999999999999887543

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=96.56  E-value=0.0014  Score=58.96  Aligned_cols=23  Identities=48%  Similarity=0.836  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|+|+||+||||+++.+++.+
T Consensus        22 ~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           22 RVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999987

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=96.55  E-value=0.0014  Score=58.31  Aligned_cols=23  Identities=43%  Similarity=0.495  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus         7 ~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            7 LIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999987

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.55  E-value=0.0017  Score=58.51  Aligned_cols=23  Identities=26%  Similarity=0.368  Sum_probs=21.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus        20 ~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           20 SIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             CEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999987

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=96.54  E-value=0.0051  Score=59.82  Aligned_cols=22  Identities=32%  Similarity=0.385  Sum_probs=20.4

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++||||+|||+++..++...
T Consensus       101 ~~i~G~~gsGKT~la~~la~~~  122 (322)
T 2i1q_A          101 TEFAGVFGSGKTQIMHQSCVNL  122 (322)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7999999999999999999764

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=96.53  E-value=0.0013  Score=58.43  Aligned_cols=24  Identities=29%  Similarity=0.416  Sum_probs=22.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++|.|+||+||||+++.+++.+.
T Consensus         5 ~I~i~G~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A            5 VVVVTGVPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999999873

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=96.53  E-value=0.0016  Score=57.66  Aligned_cols=23  Identities=43%  Similarity=0.798  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|+|+||+||||+++.+++.+
T Consensus         6 ~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            6 AVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999887

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=96.53  E-value=0.0016  Score=56.67  Aligned_cols=23  Identities=26%  Similarity=0.277  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|+|+||+||||+++.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l   24 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSL   24 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999987

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=96.53  E-value=0.0058  Score=60.08  Aligned_cols=22  Identities=27%  Similarity=0.300  Sum_probs=20.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.++||||+||||+++.++...
T Consensus       134 ~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          134 TEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            7899999999999999999875

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=96.52  E-value=0.0015  Score=58.37  Aligned_cols=23  Identities=30%  Similarity=0.478  Sum_probs=21.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus        11 ~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A           11 IIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999987

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=96.51  E-value=0.0079  Score=57.18  Aligned_cols=24  Identities=17%  Similarity=0.199  Sum_probs=20.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +.++.+|+|+|||.++..++....
T Consensus       130 ~~ll~~~tGsGKT~~~~~~~~~~~  153 (282)
T 1rif_A          130 RRILNLPTSAGRSLIQALLARYYL  153 (282)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             CeEEEcCCCCCcHHHHHHHHHHHH
Confidence            468899999999999988777653

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=96.51  E-value=0.008  Score=53.99  Aligned_cols=42  Identities=24%  Similarity=0.382  Sum_probs=26.3

Q ss_pred             CCcEEEEEeCCCCCCH-HHHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         370 SSYKLIILDEADAMTN-DAQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~-~~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      ...+++|+||+|.+.. .....+..++...+.+..+++.|...
T Consensus       145 ~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~  187 (206)
T 1vec_A          145 DHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATF  187 (206)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHHHSCTTCEEEEEESCC
T ss_pred             ccCCEEEEEChHHhHhhCcHHHHHHHHHhCCccceEEEEEeeC
Confidence            4578999999997643 33344555555555566666665443

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=96.51  E-value=0.0075  Score=55.01  Aligned_cols=42  Identities=21%  Similarity=0.402  Sum_probs=26.5

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      ...+++|+||+|.+... ....+..++...+.+..+++.|...
T Consensus       154 ~~~~~iViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~lSAT~  196 (224)
T 1qde_A          154 DKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATM  196 (224)
T ss_dssp             TTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESSC
T ss_pred             hhCcEEEEcChhHHhhhhhHHHHHHHHHhCCccCeEEEEEeec
Confidence            45689999999987542 2334555555555566666665443

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=96.50  E-value=0.0017  Score=57.94  Aligned_cols=23  Identities=30%  Similarity=0.473  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus         5 ~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            5 VVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37999999999999999999987

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.48  E-value=0.0013  Score=57.73  Aligned_cols=21  Identities=33%  Similarity=0.414  Sum_probs=19.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~  328 (533)
                      .+++.|+||+||||+++.+++
T Consensus         4 ~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEecCCCCCHHHHHHHHHh
Confidence            378999999999999999998

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.47  E-value=0.0013  Score=58.58  Aligned_cols=24  Identities=29%  Similarity=0.372  Sum_probs=22.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++|.|+||+||||+++.+++.+.
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~   26 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999999874

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.46  E-value=0.0023  Score=57.51  Aligned_cols=23  Identities=35%  Similarity=0.534  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|.||+|+||||+++.++..+
T Consensus        31 ~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           31 HVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhh
Confidence            48999999999999999999887

>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=96.46  E-value=0.006  Score=57.44  Aligned_cols=91  Identities=19%  Similarity=0.282  Sum_probs=67.3

Q ss_pred             CCceEEEEEcCCC-------CcCchhhhccce--eEEeCCCCH--HHHHHHH----HHHHhhcCC----CCCHHHHHHHH
Q psy4285           5 TTNVRFCIICNYL-------SKITPAIQSRCT--RFRFGPLDS--SLIMSRL----DYVIEQEKV----NVTPDGKKAII   65 (533)
Q Consensus         5 ~~~~~~il~~~~~-------~~i~~~i~SRc~--~~~~~~~~~--~~~~~~l----~~~~~~~~~----~~~~~~~~~~~   65 (533)
                      +.++++|++||+.       ..+.+.+.+|+.  .+.++++++  +++...+    ++.+...+.    .+++++++.+.
T Consensus       139 ~~~~~iI~atn~~~~~~~~~~~~~~~L~~Rl~~~~i~lp~L~~R~~di~~l~~~~l~~~~~~~~~~~~~~~~~~a~~~L~  218 (265)
T 2bjv_A          139 QVNVRLVCATNADLPAMVNEGTFRADLLDALAFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTERARETLL  218 (265)
T ss_dssp             ECCCEEEEEESSCHHHHHHHTSSCHHHHHHHCSEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCSSCCCBCHHHHHHHH
T ss_pred             cCCeEEEEecCcCHHHHHHcCCccHHHHHhhcCcEEeCCChhhhhHHHHHHHHHHHHHHHHHhCCCcccCcCHHHHHHHH
Confidence            4578999999985       346799999984  588888876  6666544    444444444    67899999998


Q ss_pred             Hhc-CCCHHHHHHHHHHHHHhC-CCCcchhhH
Q psy4285          66 DLS-DGDMRKVLNILQSAATAH-ADEVNEDTI   95 (533)
Q Consensus        66 ~~~-~g~~r~a~~~l~~~~~~~-~~~i~~~~i   95 (533)
                      .++ .||+|...+.++.++... +..|+.+.+
T Consensus       219 ~~~~~gn~reL~~~l~~~~~~~~~~~i~~~~l  250 (265)
T 2bjv_A          219 NYRWPGNIRELKNVVERSVYRHGTSDYPLDDI  250 (265)
T ss_dssp             HSCCTTHHHHHHHHHHHHHHHHCCSSSCBCCC
T ss_pred             hCCCCCCHHHHHHHHHHHHHhCCCCcCcHHHc
Confidence            776 899999999999987543 334666554

>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=96.45  E-value=0.0033  Score=62.63  Aligned_cols=66  Identities=14%  Similarity=0.194  Sum_probs=54.9

Q ss_pred             cCchhhhccc-eeEEeCCCCHHHHHHHHHH----HHh---------hcCCCCCHHHHHHHHHhcC---CCHHHHHHHHHH
Q psy4285          19 KITPAIQSRC-TRFRFGPLDSSLIMSRLDY----VIE---------QEKVNVTPDGKKAIIDLSD---GDMRKVLNILQS   81 (533)
Q Consensus        19 ~i~~~i~SRc-~~~~~~~~~~~~~~~~l~~----~~~---------~~~~~~~~~~~~~~~~~~~---g~~r~a~~~l~~   81 (533)
                      .+.|++.||| .++.|++++.+++..++..    ++.         ..++.+++++++.|+..+.   |++|...+.++.
T Consensus       255 ~~~p~l~~R~~~~i~~~~l~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~L~~~le~  334 (376)
T 1um8_A          255 GLIPELIGRLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKTGARGLRAIIED  334 (376)
T ss_dssp             TCCHHHHTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTGGGHHHHHHH
T ss_pred             CCChHHhcCCCceeeccCCCHHHHHHHHhhhHHHHHHHHHHHHhhcCceEEECHHHHHHHHHHhcccccCcHHHHHHHHH
Confidence            4789999999 9999999999999998862    221         1235688999999999876   999999999998


Q ss_pred             HHH
Q psy4285          82 AAT   84 (533)
Q Consensus        82 ~~~   84 (533)
                      +..
T Consensus       335 ~~~  337 (376)
T 1um8_A          335 FCL  337 (376)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            865

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=96.42  E-value=0.0025  Score=58.81  Aligned_cols=23  Identities=35%  Similarity=0.671  Sum_probs=21.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus        18 ~I~l~G~~GsGKsT~a~~La~~l   40 (233)
T 1ak2_A           18 RAVLLGPPGAGKGTQAPKLAKNF   40 (233)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999987

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=96.42  E-value=0.0023  Score=57.81  Aligned_cols=22  Identities=45%  Similarity=0.791  Sum_probs=20.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|.||||+||+|.|+.+++.+
T Consensus         3 Iil~GpPGsGKgTqa~~La~~~   24 (206)
T 3sr0_A            3 LVFLGPPGAGKGTQAKRLAKEK   24 (206)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999999987

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=96.40  E-value=0.002  Score=58.79  Aligned_cols=23  Identities=30%  Similarity=0.570  Sum_probs=21.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus         7 ~I~l~G~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A            7 NLILIGAPGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999987

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=96.37  E-value=0.0018  Score=57.93  Aligned_cols=23  Identities=30%  Similarity=0.475  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus        14 ~I~l~G~~GsGKsT~a~~L~~~l   36 (199)
T 2bwj_A           14 IIFIIGGPGSGKGTQCEKLVEKY   36 (199)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999987

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=96.36  E-value=0.002  Score=60.33  Aligned_cols=23  Identities=30%  Similarity=0.434  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|+||+||||+++.+++.+
T Consensus        34 ~i~l~G~~GsGKSTla~~L~~~l   56 (253)
T 2p5t_B           34 AILLGGQSGAGKTTIHRIKQKEF   56 (253)
T ss_dssp             EEEEESCGGGTTHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            38999999999999999999987

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=96.35  E-value=0.011  Score=58.77  Aligned_cols=41  Identities=20%  Similarity=0.346  Sum_probs=26.2

Q ss_pred             CCcEEEEEeCCCCCCH--HHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTN--DAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~--~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...+++|+||+|.+..  .....+..++...+.+..+++.|..
T Consensus       144 ~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT  186 (395)
T 3pey_A          144 QKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSAT  186 (395)
T ss_dssp             TTCCEEEEETHHHHHHSTTHHHHHHHHHHTSCTTCEEEEEESC
T ss_pred             ccCCEEEEEChhhhcCccccHHHHHHHHHhCCCCcEEEEEEec
Confidence            4578999999998754  2233444455544566677766643

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=96.33  E-value=0.0015  Score=57.62  Aligned_cols=23  Identities=35%  Similarity=0.489  Sum_probs=17.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|+|+||+||||+++.+++.+
T Consensus         7 ~I~l~G~~GsGKST~a~~La~~l   29 (183)
T 2vli_A            7 IIWINGPFGVGKTHTAHTLHERL   29 (183)
T ss_dssp             EEEEECCC----CHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            48999999999999999999887

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=96.33  E-value=0.0022  Score=57.76  Aligned_cols=23  Identities=26%  Similarity=0.456  Sum_probs=21.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|+|+||+||||+++.+++.+
T Consensus        17 ~I~l~G~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           17 VIFVLGGPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999886

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=96.33  E-value=0.0028  Score=55.49  Aligned_cols=23  Identities=26%  Similarity=0.468  Sum_probs=21.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||||+||||+++.++..+
T Consensus        10 ~i~l~G~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A           10 IYVLMGVSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHhh
Confidence            48899999999999999999876

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

Probab=96.32  E-value=0.0031  Score=63.56  Aligned_cols=68  Identities=21%  Similarity=0.221  Sum_probs=51.8

Q ss_pred             cCccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhhhH-----HHHhhhhhcccccCCCceEEEEcCccc
Q psy4285         139 SDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVR-----DQIFQFASTKTMHKSSYKLIILDEADA  213 (533)
Q Consensus       139 ~~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~~~-----d~i~~~a~~~~l~~~~~~~iilDE~d~  213 (533)
                      ..+..+||||||||..+.+++..+.     ..++.++++++.+...+.     ..+...|.     ...|.++++||+|.
T Consensus       216 rGvLL~GPPGtGKTllAkAiA~e~~-----~~~~~v~~s~l~sk~~Gese~~ir~~F~~A~-----~~~P~IifiDEiDa  285 (437)
T 4b4t_L          216 KGVLLYGPPGTGKTLLAKAVAATIG-----ANFIFSPASGIVDKYIGESARIIREMFAYAK-----EHEPCIIFMDEVDA  285 (437)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHHT-----CEEEEEEGGGTCCSSSSHHHHHHHHHHHHHH-----HSCSEEEEEECCCS
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHhC-----CCEEEEehhhhccccchHHHHHHHHHHHHHH-----hcCCceeeeecccc
Confidence            4467889999999999999999988     688999999887766655     22222222     23577999999999


Q ss_pred             cCH
Q psy4285         214 MTN  216 (533)
Q Consensus       214 l~~  216 (533)
                      +..
T Consensus       286 i~~  288 (437)
T 4b4t_L          286 IGG  288 (437)
T ss_dssp             SSC
T ss_pred             ccc
Confidence            863

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=96.31  E-value=0.0024  Score=56.78  Aligned_cols=23  Identities=30%  Similarity=0.543  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|+|+||+||||+++.+++.+
T Consensus         8 ~I~l~G~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A            8 VVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999987

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=96.30  E-value=0.0073  Score=52.72  Aligned_cols=18  Identities=28%  Similarity=0.497  Sum_probs=16.3

Q ss_pred             ceeEeCCCCCChHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILA  325 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~  325 (533)
                      .+.+.||+|+||||+++.
T Consensus        11 i~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A           11 LVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             EEEEECCTTSCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            378999999999999993

>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=96.30  E-value=0.01  Score=69.37  Aligned_cols=70  Identities=20%  Similarity=0.233  Sum_probs=43.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc---------------------hhHHHHHHHHHHhccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG---------------------IGIVRDQIFQFASTKT  366 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~~~~~~~~~  366 (533)
                      .++++||||||||++|..++......   +..++.++......                     ...+.+.+..+...  
T Consensus        36 i~lI~G~pGsGKT~LAlqla~~~~~~---G~~vlYI~te~~~~~l~~~~lg~dl~~i~i~~p~t~e~l~~ll~~L~~~--  110 (1706)
T 3cmw_A           36 IVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARS--  110 (1706)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHH--
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhC---CCceEEEEecCccHHHHHHhhccCccceeeeccCcHHHHHHHHHHHHhc--
Confidence            48999999999999999998775433   33344444332211                     12222333332221  


Q ss_pred             CCCCCcEEEEEeCCCCCCH
Q psy4285         367 MHKSSYKLIILDEADAMTN  385 (533)
Q Consensus       367 ~~~~~~~vliiDE~d~l~~  385 (533)
                         ...++||||++..+..
T Consensus       111 ---~~~~LVVIDSLt~L~~  126 (1706)
T 3cmw_A          111 ---GAVDVIVVDSVAALTP  126 (1706)
T ss_dssp             ---TCCSEEEESCSTTCCC
T ss_pred             ---cCCCEEEEcchhhhcc
Confidence               3467999999998854

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

Probab=96.29  E-value=0.0029  Score=63.74  Aligned_cols=67  Identities=24%  Similarity=0.224  Sum_probs=51.1

Q ss_pred             cCccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhhhH-H----HHhhhhhcccccCCCceEEEEcCccc
Q psy4285         139 SDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVR-D----QIFQFASTKTMHKSSYKLIILDEADA  213 (533)
Q Consensus       139 ~~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~~~-d----~i~~~a~~~~l~~~~~~~iilDE~d~  213 (533)
                      ..+.++||||||||..+.|++..+.     ..++.++++++.+..++. .    .+...|..     .+|.++++||+|.
T Consensus       216 rGvLLyGPPGTGKTllAkAiA~e~~-----~~f~~v~~s~l~~~~vGese~~ir~lF~~A~~-----~aP~IifiDEiDa  285 (434)
T 4b4t_M          216 KGALMYGPPGTGKTLLARACAAQTN-----ATFLKLAAPQLVQMYIGEGAKLVRDAFALAKE-----KAPTIIFIDELDA  285 (434)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHHT-----CEEEEEEGGGGCSSCSSHHHHHHHHHHHHHHH-----HCSEEEEEECTHH
T ss_pred             CeeEEECcCCCCHHHHHHHHHHHhC-----CCEEEEehhhhhhcccchHHHHHHHHHHHHHh-----cCCeEEeecchhh
Confidence            3477899999999999999999988     689999999987776655 2    22222322     2467999999998


Q ss_pred             cC
Q psy4285         214 MT  215 (533)
Q Consensus       214 l~  215 (533)
                      +.
T Consensus       286 l~  287 (434)
T 4b4t_M          286 IG  287 (434)
T ss_dssp             HH
T ss_pred             hh
Confidence            74

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

Probab=96.29  E-value=0.029  Score=52.37  Aligned_cols=93  Identities=16%  Similarity=0.094  Sum_probs=71.0

Q ss_pred             CCCceEEEEEcCCCCcCchhhhc--cc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHH-HHHHHHHhcCC-CHHHHHHH
Q psy4285           4 FTTNVRFCIICNYLSKITPAIQS--RC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPD-GKKAIIDLSDG-DMRKVLNI   78 (533)
Q Consensus         4 ~~~~~~~il~~~~~~~i~~~i~S--Rc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~-~~~~~~~~~~g-~~r~a~~~   78 (533)
                      .+.++++|.+||.+..+-|++++  |+ ..+.|+.|+.++..++++..+....  ++++ .+..++..+.| +.|...++
T Consensus       147 ~~~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~--l~~~~~~~~la~~~~G~~~~dl~~l  224 (257)
T 1lv7_A          147 GNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVP--LAPDIDAAIIARGTPGFSGADLANL  224 (257)
T ss_dssp             SSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSC--BCTTCCHHHHHHTCTTCCHHHHHHH
T ss_pred             cCCCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCC--CCccccHHHHHHHcCCCCHHHHHHH
Confidence            35678899999999999999988  76 6788999999998888887765433  3333 36778999999 99999999


Q ss_pred             HHHHHHhC----CCCcchhhHHhh
Q psy4285          79 LQSAATAH----ADEVNEDTIFTL   98 (533)
Q Consensus        79 l~~~~~~~----~~~i~~~~i~~~   98 (533)
                      ++.+....    ...|+.+.+.+.
T Consensus       225 ~~~a~~~a~~~~~~~i~~~~~~~a  248 (257)
T 1lv7_A          225 VNEAALFAARGNKRVVSMVEFEKA  248 (257)
T ss_dssp             HHHHHHHHHHTTCSSBCHHHHHHH
T ss_pred             HHHHHHHHHHhCCCcccHHHHHHH
Confidence            88875532    245777776543

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=96.28  E-value=0.0022  Score=58.69  Aligned_cols=24  Identities=25%  Similarity=0.364  Sum_probs=22.2

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ..++|.||||+||||+++.+++.+
T Consensus         6 ~~I~l~G~~GsGKsT~~~~La~~l   29 (222)
T 1zak_A            6 LKVMISGAPASGKGTQCELIKTKY   29 (222)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            358999999999999999999987

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.28  E-value=0.0023  Score=57.94  Aligned_cols=24  Identities=21%  Similarity=0.270  Sum_probs=22.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++|.|+||+||||+++.+++.+.
T Consensus         6 ~I~i~G~~GsGKsT~~~~L~~~l~   29 (213)
T 2plr_A            6 LIAFEGIDGSGKSSQATLLKDWIE   29 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHh
Confidence            489999999999999999999874

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=96.27  E-value=0.0099  Score=56.21  Aligned_cols=43  Identities=14%  Similarity=0.278  Sum_probs=32.3

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcC--CCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFT--TNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~--~~~~~I~~~n~~~  412 (533)
                      ..+++|++||- ..+++..+..+.+.+.+..  .+..+|++|....
T Consensus       160 ~~P~lLlLDEPts~LD~~~~~~i~~~l~~l~~~~g~tvi~vtHdl~  205 (275)
T 3gfo_A          160 MEPKVLILDEPTAGLDPMGVSEIMKLLVEMQKELGITIIIATHDID  205 (275)
T ss_dssp             TCCSEEEEECTTTTCCHHHHHHHHHHHHHHHHHHCCEEEEEESCCS
T ss_pred             cCCCEEEEECccccCCHHHHHHHHHHHHHHHhhCCCEEEEEecCHH
Confidence            45889999996 5688888888888776532  2567888887765

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=96.27  E-value=0.0012  Score=63.43  Aligned_cols=42  Identities=26%  Similarity=0.404  Sum_probs=31.5

Q ss_pred             CcEEEEEeCC-CCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         371 SYKLIILDEA-DAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       371 ~~~vliiDE~-d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      .+++|++||. ..++......+.+.+.+...+..+|++|.+..
T Consensus       208 ~p~iLlLDEPts~LD~~~~~~i~~~l~~l~~~~Tvi~itH~l~  250 (306)
T 3nh6_A          208 APGIILLDEATSALDTSNERAIQASLAKVCANRTTIVVAHRLS  250 (306)
T ss_dssp             CCSEEEEECCSSCCCHHHHHHHHHHHHHHHTTSEEEEECCSHH
T ss_pred             CCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEEcChH
Confidence            4789999997 56788888888888776545567788887554

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=96.27  E-value=0.01  Score=64.82  Aligned_cols=22  Identities=36%  Similarity=0.496  Sum_probs=18.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      ++++.||+|+|||+++..++..
T Consensus       111 ~vii~gpTGSGKTtllp~ll~~  132 (773)
T 2xau_A          111 IMVFVGETGSGKTTQIPQFVLF  132 (773)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999977666443

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=96.26  E-value=0.002  Score=59.25  Aligned_cols=23  Identities=26%  Similarity=0.482  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus         9 ~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            9 RAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999886

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=96.24  E-value=0.01  Score=62.69  Aligned_cols=78  Identities=12%  Similarity=0.062  Sum_probs=52.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhc-cc----CCCCCcEEEEEeCCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAST-KT----MHKSSYKLIILDEADA  382 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~----~~~~~~~vliiDE~d~  382 (533)
                      ..+++|++|.|||+++-.++..+..      . ..+.+++....+.+.+........ .+    ......++|||||+-+
T Consensus       194 ~~vlta~RGRGKSa~lG~~~a~~~~------~-~~vtAP~~~a~~~l~~~~~~~i~~~~Pd~~~~~~~~~dlliVDEAAa  266 (671)
T 2zpa_A          194 VAAVTAARGRGKSALAGQLISRIAG------R-AIVTAPAKASTDVLAQFAGEKFRFIAPDALLASDEQADWLVVDEAAA  266 (671)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHSSS------C-EEEECSSCCSCHHHHHHHGGGCCBCCHHHHHHSCCCCSEEEEETGGG
T ss_pred             eEEEecCCCCCHHHHHHHHHHHHHh------C-cEEECCCHHHHHHHHHHhhCCeEEeCchhhhhCcccCCEEEEEchhc
Confidence            4799999999999999999887732      2 256677767777666543221110 00    0123478999999999


Q ss_pred             CCHHHHHHHH
Q psy4285         383 MTNDAQNALR  392 (533)
Q Consensus       383 l~~~~~~~Ll  392 (533)
                      ++......|+
T Consensus       267 Ip~pll~~ll  276 (671)
T 2zpa_A          267 IPAPLLHQLV  276 (671)
T ss_dssp             SCHHHHHHHH
T ss_pred             CCHHHHHHHH
Confidence            9987554444

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=96.21  E-value=0.0026  Score=57.82  Aligned_cols=23  Identities=26%  Similarity=0.411  Sum_probs=21.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999987

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.21  E-value=0.0029  Score=56.04  Aligned_cols=24  Identities=38%  Similarity=0.438  Sum_probs=22.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++|.|+||+||||+++.++..+.
T Consensus        15 ~i~l~G~~GsGKsT~~~~L~~~l~   38 (186)
T 2yvu_A           15 VVWLTGLPGSGKTTIATRLADLLQ   38 (186)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999999874

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=96.20  E-value=0.018  Score=51.75  Aligned_cols=36  Identities=11%  Similarity=0.238  Sum_probs=28.3

Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEe
Q psy4285         370 SSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIIC  408 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~  408 (533)
                      ...++++|||++.++.+....+.++.+   .+..+|+.+
T Consensus       100 ~~~dvV~IDEaQFf~~~~v~~l~~la~---~gi~Vi~~G  135 (219)
T 3e2i_A          100 TNVDVIGIDEVQFFDDEIVSIVEKLSA---DGHRVIVAG  135 (219)
T ss_dssp             TTCSEEEECCGGGSCTHHHHHHHHHHH---TTCEEEEEE
T ss_pred             cCCCEEEEechhcCCHHHHHHHHHHHH---CCCEEEEee
Confidence            456899999999999887777777663   457777776

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=96.19  E-value=0.0026  Score=57.13  Aligned_cols=24  Identities=33%  Similarity=0.470  Sum_probs=22.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+.|.||+|+||||+++.++..+.
T Consensus        27 ~i~l~G~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           27 VIWVTGLSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            488999999999999999999884

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=96.19  E-value=0.0068  Score=55.99  Aligned_cols=42  Identities=24%  Similarity=0.466  Sum_probs=26.4

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      ...+++|+||+|.+... ....+..++...+.+..+++.|...
T Consensus       172 ~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT~  214 (237)
T 3bor_A          172 KWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATM  214 (237)
T ss_dssp             TTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSC
T ss_pred             ccCcEEEECCchHhhccCcHHHHHHHHHhCCCCCeEEEEEEec
Confidence            45689999999987432 2234455555555667777766543

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

Probab=96.19  E-value=0.0048  Score=61.57  Aligned_cols=68  Identities=19%  Similarity=0.233  Sum_probs=52.1

Q ss_pred             cCccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhhhH-HH----HhhhhhcccccCCCceEEEEcCccc
Q psy4285         139 SDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVR-DQ----IFQFASTKTMHKSSYKLIILDEADA  213 (533)
Q Consensus       139 ~~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~~~-d~----i~~~a~~~~l~~~~~~~iilDE~d~  213 (533)
                      ..+.++||||||||..+.|++..+.     ..++.++++++.+..++. .+    +...|.     ..+|.++++||+|.
T Consensus       217 rGvLLyGPPGTGKTlLAkAiA~e~~-----~~fi~v~~s~l~sk~vGesek~ir~lF~~Ar-----~~aP~IIfiDEiDa  286 (437)
T 4b4t_I          217 KGVILYGAPGTGKTLLAKAVANQTS-----ATFLRIVGSELIQKYLGDGPRLCRQIFKVAG-----ENAPSIVFIDEIDA  286 (437)
T ss_dssp             SEEEEESSTTTTHHHHHHHHHHHHT-----CEEEEEESGGGCCSSSSHHHHHHHHHHHHHH-----HTCSEEEEEEEESS
T ss_pred             CCCceECCCCchHHHHHHHHHHHhC-----CCEEEEEHHHhhhccCchHHHHHHHHHHHHH-----hcCCcEEEEehhhh
Confidence            4477899999999999999999988     688999999987776666 22    222222     23577999999999


Q ss_pred             cCH
Q psy4285         214 MTN  216 (533)
Q Consensus       214 l~~  216 (533)
                      +..
T Consensus       287 i~~  289 (437)
T 4b4t_I          287 IGT  289 (437)
T ss_dssp             SSC
T ss_pred             hcc
Confidence            863

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.18  E-value=0.0032  Score=67.62  Aligned_cols=26  Identities=38%  Similarity=0.620  Sum_probs=21.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ..|+.||||||||+++-.+...+...
T Consensus       207 ~~lI~GPPGTGKT~ti~~~I~~l~~~  232 (646)
T 4b3f_X          207 LAIIHGPPGTGKTTTVVEIILQAVKQ  232 (646)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHhC
Confidence            47999999999999888777776543

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=96.16  E-value=0.0037  Score=57.24  Aligned_cols=22  Identities=36%  Similarity=0.596  Sum_probs=20.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|.|+||+||||+++.+++.+
T Consensus         3 I~l~G~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            3 ILIFGPNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            7899999999999999999987

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

Probab=96.16  E-value=0.025  Score=52.78  Aligned_cols=81  Identities=15%  Similarity=0.056  Sum_probs=65.6

Q ss_pred             CCCceEEEEEcCCCCcCchhhhc--cc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHH-HHHHHHhcCCC-HHHHHHH
Q psy4285           4 FTTNVRFCIICNYLSKITPAIQS--RC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG-KKAIIDLSDGD-MRKVLNI   78 (533)
Q Consensus         4 ~~~~~~~il~~~~~~~i~~~i~S--Rc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-~~~~~~~~~g~-~r~a~~~   78 (533)
                      ++.++++|.+||.+..+.+++++  |+ ..+.|++|+.++..+++++.+.+.+...+.+. ...++..+.|. .+...++
T Consensus       142 ~~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l  221 (262)
T 2qz4_A          142 TTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANI  221 (262)
T ss_dssp             TTCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHH
T ss_pred             CCCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHH
Confidence            35678999999999999999999  98 78999999999999999998888777766553 47788888875 4566666


Q ss_pred             HHHHHH
Q psy4285          79 LQSAAT   84 (533)
Q Consensus        79 l~~~~~   84 (533)
                      ++.+..
T Consensus       222 ~~~a~~  227 (262)
T 2qz4_A          222 CNEAAL  227 (262)
T ss_dssp             HHHHHT
T ss_pred             HHHHHH
Confidence            666654

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=96.13  E-value=0.003  Score=56.73  Aligned_cols=23  Identities=30%  Similarity=0.588  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l   24 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKL   24 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHhc
Confidence            37899999999999999999987

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=96.11  E-value=0.003  Score=56.16  Aligned_cols=22  Identities=36%  Similarity=0.416  Sum_probs=20.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.|+|+||+||||+++.+++.+
T Consensus         3 I~l~G~~GsGKsT~~~~L~~~l   24 (195)
T 2pbr_A            3 IAFEGIDGSGKTTQAKKLYEYL   24 (195)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999999987

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=96.09  E-value=0.0087  Score=53.76  Aligned_cols=42  Identities=19%  Similarity=0.273  Sum_probs=26.5

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      ...+++|+||+|.+... ....+..++...+.+..+++.|...
T Consensus       143 ~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  185 (207)
T 2gxq_A          143 SRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATL  185 (207)
T ss_dssp             TTCSEEEEESHHHHHHTTCHHHHHHHHHTSCTTSEEEEECSSC
T ss_pred             hhceEEEEEChhHhhccchHHHHHHHHHhCCccCeEEEEEEec
Confidence            45789999999987432 2334455555555566666666443

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=96.08  E-value=0.013  Score=57.17  Aligned_cols=90  Identities=17%  Similarity=0.204  Sum_probs=49.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------C--------chhHHHHHHHHHHhcccCCCCCcE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------R--------GIGIVRDQIFQFASTKTMHKSSYK  373 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~--------~~~~~~~~~~~~~~~~~~~~~~~~  373 (533)
                      .+.+.||+|+||||+.++++..+...    ...+.++....      .        +....+..+....      ...++
T Consensus       173 ~v~i~G~~GsGKTTll~~l~g~~~~~----~g~i~i~~~~e~~~~~~~~~i~~~~ggg~~~r~~la~aL------~~~p~  242 (330)
T 2pt7_A          173 NVIVCGGTGSGKTTYIKSIMEFIPKE----ERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCL------RMRPD  242 (330)
T ss_dssp             CEEEEESTTSCHHHHHHHGGGGSCTT----SCEEEEESSCCCCCSSCSSEEEEECBTTBCHHHHHHHHT------TSCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCcCC----CcEEEECCeeccccccchhEEEEEeCCChhHHHHHHHHh------hhCCC
Confidence            68999999999999999998765221    12222222110      0        1112222232221      13578


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         374 LIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       374 vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      ++++||.-.  .+... +++.+..  .+..+++++...+
T Consensus       243 ilildE~~~--~e~~~-~l~~~~~--g~~tvi~t~H~~~  276 (330)
T 2pt7_A          243 RIILGELRS--SEAYD-FYNVLCS--GHKGTLTTLHAGS  276 (330)
T ss_dssp             EEEECCCCS--THHHH-HHHHHHT--TCCCEEEEEECSS
T ss_pred             EEEEcCCCh--HHHHH-HHHHHhc--CCCEEEEEEcccH
Confidence            999999876  33333 3444432  2334666766544

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.08  E-value=0.0027  Score=57.48  Aligned_cols=25  Identities=24%  Similarity=0.280  Sum_probs=22.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .++|+|+||+||||+++.+++.+..
T Consensus        12 ~I~l~G~~GsGKST~~~~L~~~l~~   36 (212)
T 2wwf_A           12 FIVFEGLDRSGKSTQSKLLVEYLKN   36 (212)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            4899999999999999999998743

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=96.08  E-value=0.023  Score=56.35  Aligned_cols=24  Identities=38%  Similarity=0.598  Sum_probs=21.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+++.||+|+||||++++++..+.
T Consensus       138 ~i~ivG~~GsGKTTll~~l~~~~~  161 (372)
T 2ewv_A          138 LILVTGPTGSGKSTTIASMIDYIN  161 (372)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhhcC
Confidence            489999999999999999998764

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=96.07  E-value=0.019  Score=56.31  Aligned_cols=43  Identities=14%  Similarity=0.301  Sum_probs=30.5

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcC--CCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFT--TNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~--~~~~~I~~~n~~~  412 (533)
                      ..+++|++||- ..|+......+.+.+.+..  .+..+|++|....
T Consensus       162 ~~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  207 (355)
T 1z47_A          162 PRPQVLLFDEPFAAIDTQIRRELRTFVRQVHDEMGVTSVFVTHDQE  207 (355)
T ss_dssp             TCCSEEEEESTTCCSSHHHHHHHHHHHHHHHHHHTCEEEEECSCHH
T ss_pred             cCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEECCCHH
Confidence            45789999995 6788888777777765432  2467888886543

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=96.06  E-value=0.024  Score=52.91  Aligned_cols=42  Identities=17%  Similarity=0.319  Sum_probs=31.0

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcC-CCcEEEEEeCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFT-TNVRFCIICNYL  411 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~-~~~~~I~~~n~~  411 (533)
                      ..++++++||- ..+++..+..+.+.+.+.. .+..+|++|...
T Consensus       163 ~~p~lllLDEPts~LD~~~~~~l~~~l~~l~~~g~tiiivtHd~  206 (256)
T 1vpl_A          163 VNPRLAILDEPTSGLDVLNAREVRKILKQASQEGLTILVSSHNM  206 (256)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEEECCH
T ss_pred             cCCCEEEEeCCccccCHHHHHHHHHHHHHHHhCCCEEEEEcCCH
Confidence            45789999996 5778888888888776542 356778887654

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=96.06  E-value=0.0045  Score=56.68  Aligned_cols=23  Identities=39%  Similarity=0.495  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|+||+|+||||+++.+++.+
T Consensus         7 ~i~i~G~~GsGKSTl~~~L~~~~   29 (227)
T 1cke_A            7 VITIDGPSGAGKGTLCKAMAEAL   29 (227)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999999999999877

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=96.05  E-value=0.031  Score=57.01  Aligned_cols=24  Identities=29%  Similarity=0.423  Sum_probs=21.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +++.|+||+|||+++..++..+..
T Consensus       206 iiI~G~pG~GKTtl~l~ia~~~~~  229 (454)
T 2r6a_A          206 IIVAARPSVGKTAFALNIAQNVAT  229 (454)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH
Confidence            899999999999999999987754

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=96.04  E-value=0.013  Score=55.98  Aligned_cols=24  Identities=21%  Similarity=0.254  Sum_probs=21.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      ++++||||+|||+++..++.....
T Consensus        31 teI~G~pGsGKTtL~Lq~~~~~~~   54 (333)
T 3io5_A           31 LILAGPSKSFKSNFGLTMVSSYMR   54 (333)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHh
Confidence            799999999999999998877643

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.04  E-value=0.0031  Score=56.90  Aligned_cols=23  Identities=35%  Similarity=0.562  Sum_probs=21.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||||+||||+++.+++.+
T Consensus        14 ~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           14 PLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            48999999999999999999876

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=96.02  E-value=0.0026  Score=56.55  Aligned_cols=22  Identities=45%  Similarity=0.579  Sum_probs=20.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+.+.||||+||||+++.++..
T Consensus        11 ~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A           11 ILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             EEEEEECTTSCHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHhc
Confidence            4889999999999999999875

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=96.02  E-value=0.015  Score=57.07  Aligned_cols=42  Identities=26%  Similarity=0.388  Sum_probs=26.8

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      ...+++|+||+|.+... ....+.+++...+.+..+++.|..+
T Consensus       146 ~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~  188 (367)
T 1hv8_A          146 KNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATM  188 (367)
T ss_dssp             TSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECSSC
T ss_pred             ccCCEEEEeCchHhhhhchHHHHHHHHHhCCCCceEEEEeecc
Confidence            45689999999987432 2344555555555667777666443

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=95.98  E-value=0.0045  Score=55.19  Aligned_cols=22  Identities=32%  Similarity=0.302  Sum_probs=20.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.++|++|+||||+++.+++.+
T Consensus        15 IgltG~~GSGKSTva~~L~~~l   36 (192)
T 2grj_A           15 IGVTGKIGTGKSTVCEILKNKY   36 (192)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHhc
Confidence            7899999999999999999976

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=95.97  E-value=0.018  Score=58.15  Aligned_cols=25  Identities=40%  Similarity=0.484  Sum_probs=22.4

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      ..+++.|+||+||||++..+|..+.
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~l~  124 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARYIQ  124 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4589999999999999999998874

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

Probab=95.97  E-value=0.0078  Score=60.65  Aligned_cols=67  Identities=18%  Similarity=0.193  Sum_probs=51.3

Q ss_pred             cCccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhhhH-H----HHhhhhhcccccCCCceEEEEcCccc
Q psy4285         139 SDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVR-D----QIFQFASTKTMHKSSYKLIILDEADA  213 (533)
Q Consensus       139 ~~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~~~-d----~i~~~a~~~~l~~~~~~~iilDE~d~  213 (533)
                      ..+.++||||||||..+.+++..+.     ..++.++++++.+..++. .    .+...|.     ..+|.++++||+|.
T Consensus       244 rGILLyGPPGTGKTlLAkAiA~e~~-----~~fi~vs~s~L~sk~vGesek~ir~lF~~Ar-----~~aP~IIfiDEiDa  313 (467)
T 4b4t_H          244 KGILLYGPPGTGKTLCARAVANRTD-----ATFIRVIGSELVQKYVGEGARMVRELFEMAR-----TKKACIIFFDEIDA  313 (467)
T ss_dssp             SEEEECSCTTSSHHHHHHHHHHHHT-----CEEEEEEGGGGCCCSSSHHHHHHHHHHHHHH-----HTCSEEEEEECCTT
T ss_pred             CceEeeCCCCCcHHHHHHHHHhccC-----CCeEEEEhHHhhcccCCHHHHHHHHHHHHHH-----hcCCceEeeccccc
Confidence            3467899999999999999999988     688999999887776655 2    2222222     23567999999998


Q ss_pred             cC
Q psy4285         214 MT  215 (533)
Q Consensus       214 l~  215 (533)
                      +.
T Consensus       314 i~  315 (467)
T 4b4t_H          314 VG  315 (467)
T ss_dssp             TS
T ss_pred             cc
Confidence            86

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=95.97  E-value=0.014  Score=54.31  Aligned_cols=41  Identities=17%  Similarity=0.347  Sum_probs=25.4

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...+++|+||+|.+... ....+.+++...+.+..+++.|..
T Consensus       185 ~~~~~lViDEah~l~~~~~~~~l~~i~~~~~~~~~~l~~SAT  226 (249)
T 3ber_A          185 RALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSAT  226 (249)
T ss_dssp             TTCCEEEECSHHHHHHTTCHHHHHHHHHSSCSSSEEEEEESS
T ss_pred             cccCEEEEcChhhhhccChHHHHHHHHHhCCCCCeEEEEecc
Confidence            45679999999977442 233455555554555666655543

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=95.97  E-value=0.0094  Score=56.02  Aligned_cols=40  Identities=20%  Similarity=0.380  Sum_probs=25.6

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICN  409 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n  409 (533)
                      ...+++||||+|.+... ....+..++...+....+++.|-
T Consensus       200 ~~l~~lViDEah~l~~~~~~~~l~~i~~~~~~~~q~l~~SA  240 (262)
T 3ly5_A          200 KNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSA  240 (262)
T ss_dssp             TTCCEEEECSHHHHHHTTCHHHHHHHHHHSCSSSEEEEECS
T ss_pred             ccCCEEEEcChHHHhhhhHHHHHHHHHHhCCCCCeEEEEEe
Confidence            45789999999987543 23344555555556666666554

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=95.97  E-value=0.0046  Score=59.59  Aligned_cols=23  Identities=35%  Similarity=0.592  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.||+|+||||+++.+|+.+
T Consensus         7 ~i~i~GptGsGKTtla~~La~~l   29 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLAMALADAL   29 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999987

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=95.97  E-value=0.0043  Score=60.74  Aligned_cols=42  Identities=19%  Similarity=0.326  Sum_probs=30.6

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcC--CCcEEEEEeCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFT--TNVRFCIICNYL  411 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~--~~~~~I~~~n~~  411 (533)
                      ..+++|++||- ..++......+.+.+.+..  .+..+|++|...
T Consensus       144 ~~P~lLLLDEP~s~LD~~~~~~l~~~l~~l~~~~g~tii~vTHd~  188 (348)
T 3d31_A          144 TNPKILLLDEPLSALDPRTQENAREMLSVLHKKNKLTVLHITHDQ  188 (348)
T ss_dssp             SCCSEEEEESSSTTSCHHHHHHHHHHHHHHHHHTTCEEEEEESCH
T ss_pred             cCCCEEEEECccccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            45789999995 6788888877777776532  256788888654

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=95.96  E-value=0.0053  Score=57.19  Aligned_cols=23  Identities=39%  Similarity=0.452  Sum_probs=22.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|.|++|+||||+++.++..+
T Consensus        50 ~i~l~G~~GsGKSTl~~~La~~l   72 (250)
T 3nwj_A           50 SMYLVGMMGSGKTTVGKIMARSL   72 (250)
T ss_dssp             CEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            69999999999999999999987

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=95.96  E-value=0.024  Score=55.68  Aligned_cols=43  Identities=9%  Similarity=0.203  Sum_probs=30.7

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcC--CCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFT--TNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~--~~~~~I~~~n~~~  412 (533)
                      ..++++++||- ..++......+.+.+.+..  .+..+|++|....
T Consensus       150 ~~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  195 (362)
T 2it1_A          150 KEPEVLLLDEPLSNLDALLRLEVRAELKRLQKELGITTVYVTHDQA  195 (362)
T ss_dssp             TCCSEEEEESGGGGSCHHHHHHHHHHHHHHHHHHTCEEEEEESCHH
T ss_pred             cCCCEEEEECccccCCHHHHHHHHHHHHHHHHhCCCEEEEECCCHH
Confidence            45789999995 6788888777777775432  2467888887543

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=95.94  E-value=0.0034  Score=56.90  Aligned_cols=24  Identities=21%  Similarity=0.241  Sum_probs=22.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++|+|+||+||||+++.+++.+.
T Consensus        11 ~I~l~G~~GsGKsT~~~~L~~~l~   34 (215)
T 1nn5_A           11 LIVLEGVDRAGKSTQSRKLVEALC   34 (215)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999999874

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=95.94  E-value=0.016  Score=55.72  Aligned_cols=41  Identities=27%  Similarity=0.374  Sum_probs=26.1

Q ss_pred             CCcEEEEEeCCCCCCH--HHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTN--DAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~--~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...++|||||+|.+..  .....+..++...+.++.+++.|-.
T Consensus       234 ~~l~~lVlDEad~l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT  276 (300)
T 3fmo_B          234 KKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSAT  276 (300)
T ss_dssp             GGCSEEEETTHHHHHHSTTHHHHHHHHHTTSCTTCEEEEEESC
T ss_pred             hhceEEEEeCHHHHhhccCcHHHHHHHHHhCCCCCEEEEEecc
Confidence            3567999999998754  2334444555544566777766643

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=95.93  E-value=0.023  Score=55.80  Aligned_cols=43  Identities=12%  Similarity=0.247  Sum_probs=30.5

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcC--CCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFT--TNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~--~~~~~I~~~n~~~  412 (533)
                      ..+++|++||- ..++......+.+.+.+..  .+..+|++|....
T Consensus       150 ~~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  195 (359)
T 2yyz_A          150 KQPKVLLFDEPLSNLDANLRMIMRAEIKHLQQELGITSVYVTHDQA  195 (359)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHCCEEEEEESCHH
T ss_pred             cCCCEEEEECCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEcCCHH
Confidence            45789999995 5788888777777765432  2467888886543

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=95.90  E-value=0.03  Score=54.92  Aligned_cols=43  Identities=14%  Similarity=0.325  Sum_probs=32.3

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc--CCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF--TTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~--~~~~~~I~~~n~~~  412 (533)
                      ..+++|++||. ..|++..+..+++++.+.  ..+..+|++|....
T Consensus       180 ~~P~lLLlDEPTs~LD~~~~~~i~~lL~~l~~~~g~Tii~vTHdl~  225 (366)
T 3tui_C          180 SNPKVLLCDQATSALDPATTRSILELLKDINRRLGLTILLITHEMD  225 (366)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHSCCEEEEEESCHH
T ss_pred             cCCCEEEEECCCccCCHHHHHHHHHHHHHHHHhCCCEEEEEecCHH
Confidence            46889999996 567888888888887653  23577888887544

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=95.90  E-value=0.023  Score=51.93  Aligned_cols=41  Identities=20%  Similarity=0.342  Sum_probs=26.2

Q ss_pred             CCcEEEEEeCCCCCCHHH-HHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTNDA-QNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~-~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...+++|+||+|.+.... ...+.+++...+.+..+++.|-.
T Consensus       166 ~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT  207 (228)
T 3iuy_A          166 RSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSAT  207 (228)
T ss_dssp             TTCCEEEECCHHHHHHTTCHHHHHHHHHHSCSSCEEEEEESC
T ss_pred             ccceEEEEECHHHHhccchHHHHHHHHHhCCcCCeEEEEEee
Confidence            457899999999875432 33455555555556666666543

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=95.86  E-value=0.0077  Score=55.34  Aligned_cols=40  Identities=25%  Similarity=0.395  Sum_probs=23.8

Q ss_pred             CcEEEEEeCCCCCCHH--HHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         371 SYKLIILDEADAMTND--AQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~--~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ..+++|+||+|.+...  ....+..++...+....+++.|..
T Consensus       166 ~~~~lViDEah~~~~~~~~~~~~~~i~~~~~~~~~~l~lSAT  207 (230)
T 2oxc_A          166 SIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSAT  207 (230)
T ss_dssp             GCCEEEESSHHHHHSTTSSHHHHHHHHHHSCSSCEEEEEESC
T ss_pred             cCCEEEeCCchHhhcCcchHHHHHHHHHhCCCCCeEEEEEec
Confidence            4579999999987322  233444445544555666655543

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=95.85  E-value=0.0066  Score=56.71  Aligned_cols=53  Identities=11%  Similarity=0.163  Sum_probs=44.1

Q ss_pred             CCceEEEEEcCC----------C-CcCchhhhccceeEEeC--------CCCHHHHHHHHHHHHhhcCCCCCH
Q psy4285           5 TTNVRFCIICNY----------L-SKITPAIQSRCTRFRFG--------PLDSSLIMSRLDYVIEQEKVNVTP   58 (533)
Q Consensus         5 ~~~~~~il~~~~----------~-~~i~~~i~SRc~~~~~~--------~~~~~~~~~~l~~~~~~~~~~~~~   58 (533)
                      ...+.+|++||.          . ....++|+|||.+|+|.        +++++++..++..+ +.+.+++++
T Consensus       188 v~~tPvIitsN~~i~~~~~g~~~s~~~~~~L~sR~~~f~F~~~~p~~~~~lt~~~~~~f~~w~-~~~~~~~~~  259 (267)
T 1u0j_A          188 IDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRRLDHDFGKVTKQEVKDFFRWA-KDHVVEVEH  259 (267)
T ss_dssp             ECCCCEEEEESSCTTCEEETTEEECTTHHHHHTTEEEEECCSCCCTTSCCCCHHHHHHHHHHH-HHTCCCCCC
T ss_pred             ccCCCEEEEecCCcccccccCccchhhhHHHhhhEEEEECCCcCCcccCCCCHHHHHHHHHHH-HHcCCCCcc
Confidence            367789999987          2 37889999999999999        89999999999966 667666554

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=95.85  E-value=0.0035  Score=56.29  Aligned_cols=23  Identities=26%  Similarity=0.417  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|+||+||||+++.+++.+
T Consensus         6 ~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            6 LIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHTS
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            48999999999999999999876

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=95.83  E-value=0.0067  Score=55.72  Aligned_cols=23  Identities=39%  Similarity=0.551  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.+.||||+||||+++.+++.+
T Consensus        11 ~i~i~G~~GsGKsTla~~la~~l   33 (233)
T 3r20_A           11 VVAVDGPAGTGKSSVSRGLARAL   33 (233)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999987

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=95.83  E-value=0.0044  Score=54.60  Aligned_cols=23  Identities=22%  Similarity=0.326  Sum_probs=20.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|.||+|+||||+++.++..+
T Consensus         7 ~i~i~GpsGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A            7 TLVLLGAHGVGRRHIKNTLITKH   29 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            37899999999999999999865

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

Probab=95.83  E-value=0.0072  Score=60.79  Aligned_cols=65  Identities=17%  Similarity=0.275  Sum_probs=49.9

Q ss_pred             ccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhhhH--H---HHhhhhhcccccCCCceEEEEcCccccC
Q psy4285         141 IEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVR--D---QIFQFASTKTMHKSSYKLIILDEADAMT  215 (533)
Q Consensus       141 ~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~~~--d---~i~~~a~~~~l~~~~~~~iilDE~d~l~  215 (533)
                      +..+||||||||..+.+++..+.     ..++.+++++..+...+.  .   .+-..|..     ..|.++++||+|.+.
T Consensus       209 iLL~GPPGtGKT~lakAiA~~~~-----~~~~~v~~~~l~~~~~Ge~e~~ir~lF~~A~~-----~aP~IifiDEiD~i~  278 (428)
T 4b4t_K          209 VLLYGPPGTGKTMLVKAVANSTK-----AAFIRVNGSEFVHKYLGEGPRMVRDVFRLARE-----NAPSIIFIDEVDSIA  278 (428)
T ss_dssp             EEEESCTTTTHHHHHHHHHHHHT-----CEEEEEEGGGTCCSSCSHHHHHHHHHHHHHHH-----TCSEEEEEECTHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC-----CCeEEEecchhhccccchhHHHHHHHHHHHHH-----cCCCeeechhhhhhh
Confidence            67899999999999999999987     689999999887766555  2   23222322     357799999999774

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=95.82  E-value=0.0042  Score=55.87  Aligned_cols=22  Identities=27%  Similarity=0.335  Sum_probs=20.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.++|++|+||||+++.++. +
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-~   24 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-L   24 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-T
T ss_pred             EEEEECCCCcCHHHHHHHHHH-C
Confidence            478999999999999999998 6

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=95.80  E-value=0.005  Score=57.28  Aligned_cols=23  Identities=35%  Similarity=0.661  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|.||+|+||||+++.+++.+
T Consensus        29 ~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           29 RAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999876

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=95.78  E-value=0.0048  Score=54.76  Aligned_cols=22  Identities=41%  Similarity=0.626  Sum_probs=19.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|.||+|+||||+++.++...
T Consensus         5 i~l~G~~GaGKSTl~~~L~~~~   26 (189)
T 2bdt_A            5 YIITGPAGVGKSTTCKRLAAQL   26 (189)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCcHHHHHHHHhccc
Confidence            6899999999999999998743

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=95.77  E-value=0.033  Score=53.53  Aligned_cols=92  Identities=16%  Similarity=0.247  Sum_probs=67.9

Q ss_pred             CCceEEEEEcCCC-------CcCchhhhccc--eeEEeCCCC--HHHHHHHHHHHH----hhcC---CCCCHHHHHHHHH
Q psy4285           5 TTNVRFCIICNYL-------SKITPAIQSRC--TRFRFGPLD--SSLIMSRLDYVI----EQEK---VNVTPDGKKAIID   66 (533)
Q Consensus         5 ~~~~~~il~~~~~-------~~i~~~i~SRc--~~~~~~~~~--~~~~~~~l~~~~----~~~~---~~~~~~~~~~~~~   66 (533)
                      +.++++|++||..       ...-+.|.+|+  ..+.++|+.  .+|+...+.+.+    ...+   ..+++++++.+..
T Consensus       135 ~~~~riI~atn~~l~~~v~~g~fr~~L~~Rl~~~~i~lPpL~eR~edi~~l~~~~l~~~~~~~~~~~~~~s~~a~~~L~~  214 (304)
T 1ojl_A          135 SVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIH  214 (304)
T ss_dssp             BCCCEEEEEESSCHHHHHHHTSSCHHHHHHHSSEEEECCCSGGGGGGHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHH
T ss_pred             cCCeEEEEecCccHHHHHHhCCcHHHHHhhcCeeEEeccCHHHhHhhHHHHHHHHHHHHHHHhccCccCCCHHHHHHHHc
Confidence            4578999999976       24567899997  446688887  566666555443    3332   4688999999999


Q ss_pred             hc-CCCHHHHHHHHHHHHHhCC-CCcchhhHH
Q psy4285          67 LS-DGDMRKVLNILQSAATAHA-DEVNEDTIF   96 (533)
Q Consensus        67 ~~-~g~~r~a~~~l~~~~~~~~-~~i~~~~i~   96 (533)
                      ++ .||+|...|.++.++.... ..|+.+.+.
T Consensus       215 ~~wpGnvReL~~~l~~~~~~~~~~~i~~~~l~  246 (304)
T 1ojl_A          215 YDWPGNIRELENAIERAVVLLTGEYISERELP  246 (304)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHCCSSSBCGGGSC
T ss_pred             CCCCCCHHHHHHHHHHHHHhCCCCcccHHhhh
Confidence            98 9999999999999887543 347666653

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=95.76  E-value=0.0087  Score=54.45  Aligned_cols=42  Identities=14%  Similarity=0.348  Sum_probs=26.1

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      ...+++|+||+|.+... ....+..++...+.+..+++.|...
T Consensus       149 ~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~  191 (219)
T 1q0u_A          149 HTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSATI  191 (219)
T ss_dssp             GGCCEEEECSHHHHHHTTCHHHHHHHHHTSCTTCEEEEEESCC
T ss_pred             CcceEEEEcCchHHhhhChHHHHHHHHHhCCcccEEEEEecCC
Confidence            34679999999987542 2334555555555566666655433

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=95.76  E-value=0.0074  Score=54.30  Aligned_cols=23  Identities=26%  Similarity=0.403  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.++|++|+||||+++.+++.+
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~l   26 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAAL   26 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            47899999999999999999987

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.73  E-value=0.0068  Score=54.80  Aligned_cols=24  Identities=33%  Similarity=0.437  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+.+.||+|+||||+++.++..+.
T Consensus        24 ~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           24 LVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             EEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            378999999999999999998873

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=95.72  E-value=0.027  Score=55.90  Aligned_cols=41  Identities=22%  Similarity=0.315  Sum_probs=27.2

Q ss_pred             CCcEEEEEeCCCCCCH--HHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTN--DAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~--~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...+++|+||+|.+..  .....+..++...+....+++.|..
T Consensus       151 ~~~~~vViDEaH~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT  193 (391)
T 1xti_A          151 KHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSAT  193 (391)
T ss_dssp             TTCSEEEECSHHHHTSSHHHHHHHHHHHHTSCSSSEEEEEESS
T ss_pred             cccCEEEEeCHHHHhhccchHHHHHHHHhhCCCCceEEEEEee
Confidence            4678999999998854  4445555666555556666666543

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=95.72  E-value=0.006  Score=53.59  Aligned_cols=23  Identities=35%  Similarity=0.462  Sum_probs=21.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|+|++|+||||+++.++..+
T Consensus         7 ~i~l~G~~GsGKST~~~~L~~~l   29 (179)
T 2pez_A            7 TVWLTGLSGAGKTTVSMALEEYL   29 (179)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37899999999999999999976

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=95.72  E-value=0.042  Score=54.80  Aligned_cols=23  Identities=26%  Similarity=0.307  Sum_probs=18.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++.+|+|+|||..+-..+...
T Consensus        60 ~~li~a~TGsGKT~~~~~~~~~~   82 (400)
T 1s2m_A           60 DILARAKNGTGKTAAFVIPTLEK   82 (400)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEECCCCcHHHHHHHHHHHHH
Confidence            59999999999998766555443

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=95.71  E-value=0.0057  Score=55.10  Aligned_cols=20  Identities=30%  Similarity=0.280  Sum_probs=18.9

Q ss_pred             eeEeCCCCCChHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~  328 (533)
                      +.|+||+|+||||+++.++.
T Consensus         5 i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            5 VGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEECSTTSCHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999987

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=95.69  E-value=0.0054  Score=55.45  Aligned_cols=23  Identities=30%  Similarity=0.450  Sum_probs=20.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|.||+|+||||+++.++..+
T Consensus        10 ~i~l~GpsGsGKsTl~~~L~~~~   32 (208)
T 3tau_A           10 LIVLSGPSGVGKGTVREAVFKDP   32 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHST
T ss_pred             EEEEECcCCCCHHHHHHHHHhhC
Confidence            37899999999999999999865

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=95.68  E-value=0.022  Score=54.52  Aligned_cols=24  Identities=33%  Similarity=0.531  Sum_probs=21.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+.|.||+|+||||++..+|..+.
T Consensus       107 vi~lvG~~GsGKTTl~~~LA~~l~  130 (296)
T 2px0_A          107 YIVLFGSTGAGKTTTLAKLAAISM  130 (296)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            488999999999999999998875

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=95.67  E-value=0.0062  Score=53.87  Aligned_cols=23  Identities=30%  Similarity=0.521  Sum_probs=20.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||+|+||||+++.+.+..
T Consensus         3 pIVi~GPSG~GK~Tl~~~L~~~~   25 (186)
T 1ex7_A            3 PIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            38999999999999999998765

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=95.63  E-value=0.0055  Score=65.02  Aligned_cols=43  Identities=23%  Similarity=0.361  Sum_probs=33.1

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      .+++++++||. ..+++.....+.+.+.+...+..+|++|.+.+
T Consensus       508 ~~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~t~i~itH~l~  551 (598)
T 3qf4_B          508 ANPKILILDEATSNVDTKTEKSIQAAMWKLMEGKTSIIIAHRLN  551 (598)
T ss_dssp             TCCSEEEECCCCTTCCHHHHHHHHHHHHHHHTTSEEEEESCCTT
T ss_pred             cCCCEEEEECCccCCCHHHHHHHHHHHHHHcCCCEEEEEecCHH
Confidence            35789999997 56788888888887776545677888888765

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=95.59  E-value=0.021  Score=57.30  Aligned_cols=41  Identities=24%  Similarity=0.451  Sum_probs=27.0

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...+++|+||+|.+... ....+..++...+.+..+|+.|-.
T Consensus       182 ~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT  223 (414)
T 3eiq_A          182 KYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSAT  223 (414)
T ss_dssp             TTCCEEEECSHHHHHHTTTHHHHHHHHTTSCTTCEEEEECSC
T ss_pred             ccCcEEEEECHHHhhccCcHHHHHHHHHhCCCCCeEEEEEEe
Confidence            34689999999987433 234455566655567777776643

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.58  E-value=0.0061  Score=54.79  Aligned_cols=23  Identities=26%  Similarity=0.368  Sum_probs=20.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|.||+|+||||+++.++..+
T Consensus         8 ~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            8 LIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHCT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhh
Confidence            47899999999999999999865

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=95.57  E-value=0.022  Score=48.93  Aligned_cols=23  Identities=17%  Similarity=0.392  Sum_probs=20.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus         8 ~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            8 KVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            48999999999999999998654

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.57  E-value=0.0068  Score=54.43  Aligned_cols=23  Identities=30%  Similarity=0.557  Sum_probs=20.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|.||+|+||||+++.++..+
T Consensus         9 ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            9 LFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHhhC
Confidence            37899999999999999999864

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=95.54  E-value=0.034  Score=55.64  Aligned_cols=41  Identities=27%  Similarity=0.374  Sum_probs=24.9

Q ss_pred             CCcEEEEEeCCCCCCH--HHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTN--DAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~--~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...+++|+||+|.+..  .....+..++...+.+..+++.|-.
T Consensus       167 ~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT  209 (412)
T 3fht_A          167 KKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSAT  209 (412)
T ss_dssp             GGCCEEEEETHHHHHSTTTTHHHHHHHHHTSCTTCEEEEEESC
T ss_pred             hhCcEEEEeCHHHHhhcCCcHHHHHHHHhhCCCCceEEEEEee
Confidence            3578999999997632  2233344444444566677766643

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=95.53  E-value=0.026  Score=52.23  Aligned_cols=40  Identities=23%  Similarity=0.388  Sum_probs=24.5

Q ss_pred             CCcEEEEEeCCCCCCHH----HHHHHHHHHHhc-CCCcEEEEEeC
Q psy4285         370 SSYKLIILDEADAMTND----AQNALRRIIEKF-TTNVRFCIICN  409 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~----~~~~Ll~~le~~-~~~~~~I~~~n  409 (533)
                      ...+++|+||+|.+..+    ....+..++... +.+..+++.|-
T Consensus       174 ~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SA  218 (245)
T 3dkp_A          174 ASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSA  218 (245)
T ss_dssp             TTCCEEEESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEES
T ss_pred             ccCcEEEEeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEec
Confidence            35679999999998652    344555555442 23455555543

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=95.53  E-value=0.0074  Score=54.65  Aligned_cols=24  Identities=21%  Similarity=0.357  Sum_probs=21.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++|.|+||+||||+++.+++.+.
T Consensus        27 ~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           27 TIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhc
Confidence            488999999999999999999874

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=95.52  E-value=0.083  Score=50.96  Aligned_cols=24  Identities=29%  Similarity=0.411  Sum_probs=21.4

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +++.|+||+|||+++..++.....
T Consensus        71 ~li~G~pG~GKTtl~l~ia~~~a~   94 (315)
T 3bh0_A           71 VLIAARPSMGKTAFALKQAKNMSD   94 (315)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHH
Confidence            899999999999999999977643

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=95.51  E-value=0.022  Score=60.50  Aligned_cols=96  Identities=15%  Similarity=0.203  Sum_probs=70.2

Q ss_pred             CCCceEEEEEcCCC--CcCchhhhccce----eEEeCC---CCHHHHHHHHHHHHhhc-----CCCCCHHHHHHHHHhc-
Q psy4285           4 FTTNVRFCIICNYL--SKITPAIQSRCT----RFRFGP---LDSSLIMSRLDYVIEQE-----KVNVTPDGKKAIIDLS-   68 (533)
Q Consensus         4 ~~~~~~~il~~~~~--~~i~~~i~SRc~----~~~~~~---~~~~~~~~~l~~~~~~~-----~~~~~~~~~~~~~~~~-   68 (533)
                      .|.++++|++||+.  +.+.|+++|||.    .+.|++   -+.+.+..+++.++...     ...++++++..+++.+ 
T Consensus       249 ~p~~~~vI~atn~~~~~~l~~~l~~R~~v~~i~i~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ls~eAl~~Li~~~~  328 (604)
T 3k1j_A          249 VPCDFVLVAAGNLDTVDKMHPALRSRIRGYGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEIVREAQ  328 (604)
T ss_dssp             EECCCEEEEEECHHHHHHSCHHHHHHHHHHSEEEECCSEEECCHHHHHHHHHHHHHHHHHHCSSCCBBHHHHHHHHHHHH
T ss_pred             cceeEEEEEecCHHHHhhcCHHHHHHhhccceEeeccccccCCHHHHHHHHHHHHHHHhhccCcccCCHHHHHHHHHHHh
Confidence            35689999999987  789999999994    556543   35556777776665432     2568899999998876 


Q ss_pred             --CC-------CHHHHHHHHHHHHHh----CCCCcchhhHHhhh
Q psy4285          69 --DG-------DMRKVLNILQSAATA----HADEVNEDTIFTLL   99 (533)
Q Consensus        69 --~g-------~~r~a~~~l~~~~~~----~~~~i~~~~i~~~~   99 (533)
                        .|       ++|.+.++++.+...    ....|+.+.+.+.+
T Consensus       329 r~~g~r~~l~~~~R~l~~llr~A~~~A~~~~~~~I~~edv~~A~  372 (604)
T 3k1j_A          329 KRAGRKGHLTLRLRDLGGIVRAAGDIAVKKGKKYVEREDVIEAV  372 (604)
T ss_dssp             HTTCSTTEEECCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHH
T ss_pred             hhhccccccccCHHHHHHHHHHHHHHHHhcCcccccHHHHHHHH
Confidence              56       699999999987542    23458888776544

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=95.47  E-value=0.035  Score=56.60  Aligned_cols=24  Identities=29%  Similarity=0.297  Sum_probs=20.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      ++++.+|+|+|||..+-.++....
T Consensus        25 ~~ll~~~tG~GKT~~~~~~~~~~~   48 (494)
T 1wp9_A           25 NCLIVLPTGLGKTLIAMMIAEYRL   48 (494)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHH
Confidence            689999999999999988876653

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=95.45  E-value=0.011  Score=54.90  Aligned_cols=22  Identities=41%  Similarity=0.394  Sum_probs=19.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++|+||+|||+++..++...
T Consensus        33 ~~i~G~pG~GKT~l~l~~~~~~   54 (251)
T 2zts_A           33 VLLTGGTGTGKTTFAAQFIYKG   54 (251)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHH
Confidence            7999999999999999887654

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=95.45  E-value=0.014  Score=61.63  Aligned_cols=43  Identities=26%  Similarity=0.471  Sum_probs=33.0

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      .+++++++||. ..+++.....+.+.+.+...+..+|++|.+.+
T Consensus       497 ~~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~tvi~itH~~~  540 (582)
T 3b5x_A          497 RDAPVLILDEATSALDTESERAIQAALDELQKNKTVLVIAHRLS  540 (582)
T ss_pred             cCCCEEEEECccccCCHHHHHHHHHHHHHHcCCCEEEEEecCHH
Confidence            45789999997 46788888888888876555677888887654

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=95.45  E-value=0.024  Score=52.09  Aligned_cols=41  Identities=17%  Similarity=0.377  Sum_probs=26.0

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...+++|+||+|.+... ....+..++...+.+..+++.|..
T Consensus       170 ~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT  211 (236)
T 2pl3_A          170 TDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSAT  211 (236)
T ss_dssp             TTCCEEEETTHHHHHHTTTHHHHHHHHHTSCTTSEEEEEESS
T ss_pred             ccccEEEEeChHHHhcCCcHHHHHHHHHhCCCCCeEEEEEee
Confidence            45679999999987532 234455556555556666655543

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=95.41  E-value=0.079  Score=44.84  Aligned_cols=23  Identities=22%  Similarity=0.418  Sum_probs=20.4

Q ss_pred             CceeEeCCCCCChHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~  329 (533)
                      +.+++.|++|+|||++++.+...
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            35899999999999999999864

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=95.41  E-value=0.0076  Score=69.87  Aligned_cols=45  Identities=27%  Similarity=0.431  Sum_probs=30.0

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC
Q psy4285         370 SSYKLIILDEAD-AMTNDAQNALRRIIEKFTTNVRFCIICNYLSKI  414 (533)
Q Consensus       370 ~~~~vliiDE~d-~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l  414 (533)
                      .+++++++||+- .++......+.+.+++...+..+|++|++.+.+
T Consensus       571 ~~~~IliLDE~tSaLD~~te~~i~~~l~~~~~~~T~iiiaHrls~i  616 (1321)
T 4f4c_A          571 RNPKILLLDEATSALDAESEGIVQQALDKAAKGRTTIIIAHRLSTI  616 (1321)
T ss_dssp             TCCSEEEEESTTTTSCTTTHHHHHHHHHHHHTTSEEEEECSCTTTT
T ss_pred             cCCCEEEEecccccCCHHHHHHHHHHHHHHhCCCEEEEEcccHHHH
Confidence            457899999983 455554555556665544566778888877643

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=95.40  E-value=0.0087  Score=63.31  Aligned_cols=42  Identities=17%  Similarity=0.306  Sum_probs=33.5

Q ss_pred             CcEEEEEeCC-CCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         371 SYKLIILDEA-DAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       371 ~~~vliiDE~-d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      +++++++||. ..+++.....+.+.+.+...+..+|++|.+.+
T Consensus       497 ~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~tvi~itH~l~  539 (587)
T 3qf4_A          497 KPKVLILDDCTSSVDPITEKRILDGLKRYTKGCTTFIITQKIP  539 (587)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHSTTCEEEEEESCHH
T ss_pred             CCCEEEEECCcccCCHHHHHHHHHHHHHhCCCCEEEEEecChH
Confidence            5789999997 56788888888888877656778888887654

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=95.35  E-value=0.0074  Score=58.39  Aligned_cols=23  Identities=30%  Similarity=0.511  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||+|+|||+++..+|+.+
T Consensus        42 lIvI~GPTgsGKTtLa~~LA~~l   64 (339)
T 3a8t_A           42 LLVLMGATGTGKSRLSIDLAAHF   64 (339)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTTS
T ss_pred             eEEEECCCCCCHHHHHHHHHHHC
Confidence            48999999999999999999987

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=95.33  E-value=0.023  Score=52.52  Aligned_cols=41  Identities=20%  Similarity=0.343  Sum_probs=26.3

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...+++|+||+|.+... ....+..++...+.+..+++.|-.
T Consensus       175 ~~~~~lViDEah~l~~~~~~~~~~~i~~~~~~~~q~~~~SAT  216 (242)
T 3fe2_A          175 RRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSAT  216 (242)
T ss_dssp             TTCCEEEETTHHHHHHTTCHHHHHHHHTTSCSSCEEEEEESC
T ss_pred             ccccEEEEeCHHHHhhhCcHHHHHHHHHhCCccceEEEEEee
Confidence            45689999999987543 234455555555556666665543

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=95.32  E-value=0.037  Score=55.45  Aligned_cols=41  Identities=22%  Similarity=0.394  Sum_probs=26.1

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...+++|+||+|.+... ....+..++...+....+++.|-.
T Consensus       178 ~~~~~vViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  219 (410)
T 2j0s_A          178 RAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISAT  219 (410)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESC
T ss_pred             hheeEEEEccHHHHHhhhhHHHHHHHHHhCccCceEEEEEcC
Confidence            45789999999976432 334555555554556666666543

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=95.31  E-value=0.0062  Score=55.45  Aligned_cols=41  Identities=22%  Similarity=0.237  Sum_probs=29.8

Q ss_pred             chhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHH
Q psy4285         290 SMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       290 ~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.+....+.........+.+++.|++|+||||++..++..+
T Consensus        14 ~~~~~~~~~~~~~~~~~~~i~i~G~~g~GKTTl~~~l~~~~   54 (221)
T 2wsm_A           14 NKRLAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERI   54 (221)
T ss_dssp             HHHHHHHHHHHHHHHTCEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHhhcccCceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            33344444444444455679999999999999999999886

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=95.31  E-value=0.0088  Score=55.86  Aligned_cols=24  Identities=17%  Similarity=0.145  Sum_probs=21.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+.++|++|+||||+++.+++.+.
T Consensus        24 iI~I~G~~GSGKST~a~~L~~~lg   47 (252)
T 1uj2_A           24 LIGVSGGTASGKSSVCAKIVQLLG   47 (252)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            378999999999999999999873

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=95.28  E-value=0.043  Score=47.48  Aligned_cols=23  Identities=22%  Similarity=0.368  Sum_probs=20.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus        17 ~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           17 KYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            48999999999999999998654

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=95.28  E-value=0.0097  Score=53.41  Aligned_cols=22  Identities=32%  Similarity=0.270  Sum_probs=20.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.++||+|+||||+++.++..+
T Consensus        25 i~i~G~~GsGKstl~~~l~~~~   46 (201)
T 1rz3_A           25 LGIDGLSRSGKTTLANQLSQTL   46 (201)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7899999999999999999876

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=95.26  E-value=0.01  Score=52.89  Aligned_cols=23  Identities=22%  Similarity=0.342  Sum_probs=20.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||+|+||||+++.++...
T Consensus        21 ~ivl~GPSGaGKsTL~~~L~~~~   43 (197)
T 3ney_A           21 TLVLIGASGVGRSHIKNALLSQN   43 (197)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHhhC
Confidence            37899999999999999999864

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=95.25  E-value=0.021  Score=57.77  Aligned_cols=35  Identities=20%  Similarity=0.354  Sum_probs=26.3

Q ss_pred             hhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         294 CYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       294 ~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      ++.+..+.+.+   .++|+||+|+|||+++..++....
T Consensus       142 ID~L~pi~kGq---~~~i~G~sGvGKTtL~~~l~~~~~  176 (473)
T 1sky_E          142 VDLLAPYIKGG---KIGLFGGAGVGKTVLIQELIHNIA  176 (473)
T ss_dssp             HHHHSCEETTC---EEEEECCSSSCHHHHHHHHHHHHH
T ss_pred             HHHHhhhccCC---EEEEECCCCCCccHHHHHHHhhhh
Confidence            44454554433   489999999999999999987653

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=95.23  E-value=0.013  Score=54.68  Aligned_cols=23  Identities=39%  Similarity=0.481  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|.||+|+||||+++.+++.+
T Consensus        29 ~I~I~G~~GsGKSTl~k~La~~L   51 (252)
T 4e22_A           29 VITVDGPSGAGKGTLCKALAESL   51 (252)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            48899999999999999999887

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=95.22  E-value=0.035  Score=48.95  Aligned_cols=23  Identities=30%  Similarity=0.465  Sum_probs=20.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus        25 ki~v~G~~~~GKSsli~~l~~~~   47 (191)
T 3dz8_A           25 KLLIIGNSSVGKTSFLFRYADDT   47 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCcCHHHHHHHHhcCC
Confidence            38999999999999999998764

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=95.22  E-value=0.012  Score=56.00  Aligned_cols=23  Identities=26%  Similarity=0.521  Sum_probs=21.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +++.||+|+|||+++..+|+.+.
T Consensus        13 i~i~GptgsGKt~la~~La~~~~   35 (316)
T 3foz_A           13 IFLMGPTASGKTALAIELRKILP   35 (316)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHSC
T ss_pred             EEEECCCccCHHHHHHHHHHhCC
Confidence            78999999999999999999873

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=95.21  E-value=0.013  Score=56.89  Aligned_cols=23  Identities=30%  Similarity=0.596  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.||+|+||||+++.+++.+
T Consensus         9 lI~I~GptgSGKTtla~~La~~l   31 (340)
T 3d3q_A            9 LIVIVGPTASGKTELSIEVAKKF   31 (340)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT
T ss_pred             eEEEECCCcCcHHHHHHHHHHHc
Confidence            47899999999999999999987

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=95.19  E-value=0.013  Score=53.20  Aligned_cols=21  Identities=33%  Similarity=0.362  Sum_probs=19.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~  328 (533)
                      .+.|+|++|+||||+++.++.
T Consensus         6 ~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            6 IVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999987

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

Probab=95.18  E-value=0.0071  Score=57.94  Aligned_cols=71  Identities=10%  Similarity=0.160  Sum_probs=43.6

Q ss_pred             ccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhhhH--HHHh-hhhhcccc-cCCCceEEEEcCccccCH
Q psy4285         141 IEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVR--DQIF-QFASTKTM-HKSSYKLIILDEADAMTN  216 (533)
Q Consensus       141 ~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~~~--d~i~-~~a~~~~l-~~~~~~~iilDE~d~l~~  216 (533)
                      +...|+||+|||..+.+++..+.     ..++.+++++..+...+.  ..+. .|...... ....+.++++||+|.+..
T Consensus        39 lLl~GppGtGKT~la~aiA~~l~-----~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~~~~~~vl~iDEiD~~~~  113 (293)
T 3t15_A           39 LGIWGGKGQGKSFQCELVFRKMG-----INPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDAGAG  113 (293)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHT-----CCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHHTTSSCCCEEEECCC----
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC-----CCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHHhcCCCeEEEEechhhhcC
Confidence            45679999999999999988886     788999987765543333  2221 12222111 133566999999999875

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=95.18  E-value=0.059  Score=58.52  Aligned_cols=24  Identities=25%  Similarity=0.387  Sum_probs=18.5

Q ss_pred             CceeEeCCCCCChHHHH-HHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTI-LACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la-~~la~~l  330 (533)
                      .++++.||+|+|||+.+ ..+.+.+
T Consensus        40 ~~~lv~apTGsGKT~~~~l~il~~~   64 (720)
T 2zj8_A           40 KNALISIPTASGKTLIAEIAMVHRI   64 (720)
T ss_dssp             CEEEEECCGGGCHHHHHHHHHHHHH
T ss_pred             CcEEEEcCCccHHHHHHHHHHHHHH
Confidence            36999999999999988 4444443

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=95.17  E-value=0.032  Score=57.31  Aligned_cols=42  Identities=26%  Similarity=0.381  Sum_probs=25.7

Q ss_pred             CCcEEEEEeCCCCCCH--HHHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         370 SSYKLIILDEADAMTN--DAQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~--~~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      ...++|||||+|.+..  .....+..++...+.+..+++.|-.+
T Consensus       234 ~~~~~iViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  277 (479)
T 3fmp_B          234 KKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATF  277 (479)
T ss_dssp             GGCCEEEECCHHHHHTSTTHHHHHHHHHTTSCTTSEEEEEESCC
T ss_pred             ccCCEEEEECHHHHhhcCCcHHHHHHHHhhCCccceEEEEeCCC
Confidence            4578999999997632  23333444444445667777766443

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.17  E-value=0.012  Score=52.76  Aligned_cols=23  Identities=26%  Similarity=0.496  Sum_probs=21.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|.||+|+||||+++.++..+
T Consensus         6 ~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            6 PVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            48999999999999999999865

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=95.16  E-value=0.012  Score=54.19  Aligned_cols=24  Identities=42%  Similarity=0.657  Sum_probs=22.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++|.||||+||||+++.+++.+.
T Consensus        28 ~i~i~G~~GsGKsT~~~~l~~~l~   51 (229)
T 4eaq_A           28 FITFEGPEGSGKTTVINEVYHRLV   51 (229)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHh
Confidence            388999999999999999999884

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=95.13  E-value=0.067  Score=61.03  Aligned_cols=39  Identities=18%  Similarity=0.060  Sum_probs=24.5

Q ss_pred             hhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHH
Q psy4285         291 MDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       291 ~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~  329 (533)
                      ...+..+.....++.+.+.++.||+|+|||.++-..+-.
T Consensus       609 ~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~  647 (1151)
T 2eyq_A          609 AQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFL  647 (1151)
T ss_dssp             HHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHH
Confidence            333333333333344446899999999999887655433

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=95.08  E-value=0.011  Score=56.80  Aligned_cols=23  Identities=35%  Similarity=0.381  Sum_probs=20.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|+||+||||+++.+++.+
T Consensus         4 ~I~l~G~~GsGKST~a~~L~~~~   26 (301)
T 1ltq_A            4 IILTIGCPGSGKSTWAREFIAKN   26 (301)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            37899999999999999999853

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=95.08  E-value=0.0099  Score=53.20  Aligned_cols=22  Identities=23%  Similarity=0.173  Sum_probs=20.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+.|+|++|+||||+++.+++.
T Consensus        10 ~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A           10 IIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
Confidence            4889999999999999999984

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=95.08  E-value=0.033  Score=48.22  Aligned_cols=22  Identities=18%  Similarity=0.436  Sum_probs=19.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||++++.+...
T Consensus         9 ~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            9 KVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999999754

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=95.08  E-value=0.012  Score=56.20  Aligned_cols=24  Identities=33%  Similarity=0.508  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+++.||+|+|||+++..+|+.+.
T Consensus         5 ~i~i~GptgsGKt~la~~La~~~~   28 (322)
T 3exa_A            5 LVAIVGPTAVGKTKTSVMLAKRLN   28 (322)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHTTT
T ss_pred             EEEEECCCcCCHHHHHHHHHHhCc
Confidence            378999999999999999999873

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=95.08  E-value=0.1  Score=53.00  Aligned_cols=35  Identities=23%  Similarity=0.148  Sum_probs=26.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNA  345 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~  345 (533)
                      +++.|+||+|||+++..++.......  +.+++.++.
T Consensus       203 ~ii~G~pg~GKT~lal~ia~~~a~~~--g~~vl~~sl  237 (444)
T 2q6t_A          203 NIIAARPAMGKTAFALTIAQNAALKE--GVGVGIYSL  237 (444)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTT--CCCEEEEES
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHhC--CCeEEEEEC
Confidence            79999999999999999998765432  334444443

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=95.07  E-value=0.046  Score=56.64  Aligned_cols=24  Identities=17%  Similarity=0.199  Sum_probs=20.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +.++.||+|+|||..+-.++....
T Consensus       130 ~~ll~~~tGsGKT~~~~~~~~~~~  153 (510)
T 2oca_A          130 RRILNLPTSAGRSLIQALLARYYL  153 (510)
T ss_dssp             EEEEECCSTTTHHHHHHHHHHHHH
T ss_pred             CcEEEeCCCCCHHHHHHHHHHHHH
Confidence            589999999999999987776654

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=95.07  E-value=0.045  Score=49.66  Aligned_cols=21  Identities=33%  Similarity=0.491  Sum_probs=19.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.+|+|||+++..+...
T Consensus        16 ivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           16 LVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCcCHHHHHHHHHhC
Confidence            899999999999999998754

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=95.06  E-value=0.049  Score=55.17  Aligned_cols=23  Identities=26%  Similarity=0.333  Sum_probs=17.9

Q ss_pred             ceeEeCCCCCChHHHH-HHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTI-LACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la-~~la~~l  330 (533)
                      ++++.||+|+|||..+ ..+.+.+
T Consensus         4 ~~lv~a~TGsGKT~~~l~~~l~~~   27 (431)
T 2v6i_A            4 LTVLDLHPGAGKTRRVLPQLVREA   27 (431)
T ss_dssp             EEEEECCTTSCTTTTHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            5899999999999986 5455333

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=95.06  E-value=0.033  Score=55.34  Aligned_cols=42  Identities=21%  Similarity=0.402  Sum_probs=26.4

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      ...+++|+||+|.+... ....+.+++...+....+++.|..+
T Consensus       161 ~~~~~vIiDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~  203 (394)
T 1fuu_A          161 DKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATM  203 (394)
T ss_dssp             TTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSC
T ss_pred             hhCcEEEEEChHHhhCCCcHHHHHHHHHhCCCCceEEEEEEec
Confidence            45789999999987432 2334445555545666677666443

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=95.05  E-value=0.056  Score=46.92  Aligned_cols=22  Identities=27%  Similarity=0.610  Sum_probs=19.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||++++.+...
T Consensus        14 ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           14 KLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            3899999999999999999864

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=95.05  E-value=0.0099  Score=52.71  Aligned_cols=23  Identities=30%  Similarity=0.460  Sum_probs=21.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||+|+|||++|..+++..
T Consensus        36 ~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           36 GVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             EEEEECCCTTTTHHHHHHHHTTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            38999999999999999999875

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=95.02  E-value=0.015  Score=55.37  Aligned_cols=23  Identities=35%  Similarity=0.664  Sum_probs=21.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +.+.||+|+||||+++.++..+.
T Consensus        34 i~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           34 IFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhh
Confidence            78999999999999999998874

>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.05A {Homo sapiens}

Probab=95.00  E-value=0.063  Score=47.83  Aligned_cols=22  Identities=23%  Similarity=0.366  Sum_probs=19.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||++++.+...
T Consensus        31 ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           31 KLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhhC
Confidence            4899999999999999999754

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=94.99  E-value=0.042  Score=46.87  Aligned_cols=23  Identities=22%  Similarity=0.377  Sum_probs=20.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus         6 ~i~v~G~~~~GKssl~~~l~~~~   28 (168)
T 1u8z_A            6 KVIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            48999999999999999998643

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=94.99  E-value=0.0053  Score=55.60  Aligned_cols=23  Identities=22%  Similarity=0.296  Sum_probs=21.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +.|.|++|+||||+++.+++.+.
T Consensus         3 I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            3 IAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH
Confidence            68999999999999999999874

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=94.98  E-value=0.016  Score=50.21  Aligned_cols=25  Identities=20%  Similarity=0.074  Sum_probs=22.2

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +.+.|.|++|+||||++..++..+.
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~l~   29 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAAAV   29 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhhH
Confidence            3478999999999999999999874

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=94.98  E-value=0.017  Score=59.34  Aligned_cols=23  Identities=30%  Similarity=0.401  Sum_probs=20.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.++.||+|+|||..+-..+...
T Consensus       110 ~~ll~~~TGsGKT~~~l~~i~~~  132 (472)
T 2fwr_A          110 RGCIVLPTGSGKTHVAMAAINEL  132 (472)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHc
Confidence            48999999999999998887765

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=94.96  E-value=0.038  Score=53.61  Aligned_cols=24  Identities=25%  Similarity=0.326  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++++||||+|||+++..++....
T Consensus       109 i~~i~G~~GsGKT~la~~la~~~~  132 (324)
T 2z43_A          109 MTEFFGEFGSGKTQLCHQLSVNVQ  132 (324)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHhHHHHHHHHHHh
Confidence            379999999999999999998753

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=94.96  E-value=0.019  Score=62.37  Aligned_cols=21  Identities=33%  Similarity=0.434  Sum_probs=17.5

Q ss_pred             CceeEeCCCCCChHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACA  327 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la  327 (533)
                      .++++.||+|+|||+.+-..+
T Consensus        47 ~~~lv~apTGsGKT~~~~l~i   67 (715)
T 2va8_A           47 NRLLLTSPTGSGKTLIAEMGI   67 (715)
T ss_dssp             CCEEEECCTTSCHHHHHHHHH
T ss_pred             CcEEEEcCCCCcHHHHHHHHH
Confidence            379999999999999985443

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=94.96  E-value=0.018  Score=52.30  Aligned_cols=23  Identities=30%  Similarity=0.504  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.++|++|+||||+++.+++.+
T Consensus         5 ~i~i~G~~gsGkst~~~~l~~~~   27 (219)
T 2h92_A            5 NIALDGPAAAGKSTIAKRVASEL   27 (219)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            48899999999999999999987

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=94.95  E-value=0.051  Score=52.57  Aligned_cols=22  Identities=18%  Similarity=0.261  Sum_probs=18.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      ++++.+|+|+|||..+-..+..
T Consensus        33 ~~lv~~~TGsGKT~~~~~~~~~   54 (337)
T 2z0m_A           33 NVVVRAKTGSGKTAAYAIPILE   54 (337)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEcCCCCcHHHHHHHHHHh
Confidence            6999999999999877665543

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=94.94  E-value=0.026  Score=54.46  Aligned_cols=23  Identities=26%  Similarity=0.187  Sum_probs=20.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +-+.||+|+||||+++.++..+.
T Consensus        95 igI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           95 IGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Confidence            68999999999999999998763

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=94.90  E-value=0.013  Score=52.99  Aligned_cols=22  Identities=41%  Similarity=0.418  Sum_probs=20.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.+.||+|+||||+++.++..+
T Consensus         9 i~i~G~~GsGKSTl~~~l~~~~   30 (211)
T 3asz_A            9 IGIAGGTASGKTTLAQALARTL   30 (211)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            7899999999999999999876

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=94.90  E-value=0.014  Score=52.43  Aligned_cols=24  Identities=17%  Similarity=0.263  Sum_probs=20.6

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      -.+++.|++|+|||+++..+....
T Consensus        31 ~ki~vvG~~~~GKSsLi~~l~~~~   54 (204)
T 4gzl_A           31 IKCVVVGDGAVGKTCLLISYTTNA   54 (204)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECcCCCCHHHHHHHHHhCC
Confidence            349999999999999999988643

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.88  E-value=0.066  Score=52.00  Aligned_cols=24  Identities=17%  Similarity=0.314  Sum_probs=21.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +++.|+||+|||+++..+|..+..
T Consensus        49 iiIaG~pG~GKTt~al~ia~~~a~   72 (338)
T 4a1f_A           49 VIIGARPSMGKTSLMMNMVLSALN   72 (338)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHH
Confidence            899999999999999999987644

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=94.86  E-value=0.023  Score=48.68  Aligned_cols=23  Identities=17%  Similarity=0.395  Sum_probs=20.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+||||+++.+...-
T Consensus         7 ~i~v~G~~~~GKssl~~~l~~~~   29 (168)
T 1z2a_A            7 KMVVVGNGAVGKSSMIQRYCKGI   29 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            48999999999999999998653

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=94.85  E-value=0.024  Score=52.27  Aligned_cols=23  Identities=26%  Similarity=0.494  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|+|++|+||||+++.+++.+
T Consensus        18 ~i~i~G~~gsGKst~~~~l~~~l   40 (236)
T 1q3t_A           18 QIAIDGPASSGKSTVAKIIAKDF   40 (236)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48899999999999999999987

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=94.84  E-value=0.038  Score=46.96  Aligned_cols=23  Identities=22%  Similarity=0.407  Sum_probs=20.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+||||+++.+...-
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~~   27 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            48999999999999999998653

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=94.84  E-value=0.06  Score=47.87  Aligned_cols=23  Identities=22%  Similarity=0.377  Sum_probs=20.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||+++..+...-
T Consensus        16 ki~v~G~~~~GKSsli~~l~~~~   38 (206)
T 2bov_A           16 KVIMVGSGGVGKSALTLQFMYDE   38 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            48999999999999999987643

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=94.81  E-value=0.014  Score=55.37  Aligned_cols=20  Identities=25%  Similarity=0.341  Sum_probs=18.9

Q ss_pred             eeEeCCCCCChHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~  328 (533)
                      +.|+|++|+||||+++.++.
T Consensus        78 I~I~G~~GSGKSTva~~La~   97 (281)
T 2f6r_A           78 LGLTGISGSGKSSVAQRLKN   97 (281)
T ss_dssp             EEEEECTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            78999999999999999994

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=94.80  E-value=0.039  Score=58.16  Aligned_cols=43  Identities=21%  Similarity=0.394  Sum_probs=33.3

Q ss_pred             CcEEEEEeCC-CCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCC
Q psy4285         371 SYKLIILDEA-DAMTNDAQNALRRIIEKFTTNVRFCIICNYLSK  413 (533)
Q Consensus       371 ~~~vliiDE~-d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~  413 (533)
                      +++++++||. ..+++.....+.+.+.+...+..+|++|.+.+.
T Consensus       495 ~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~t~i~itH~l~~  538 (578)
T 4a82_A          495 NPPILILDEATSALDLESESIIQEALDVLSKDRTTLIVAHRLST  538 (578)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHHHTTTSEEEEECSSGGG
T ss_pred             CCCEEEEECccccCCHHHHHHHHHHHHHHcCCCEEEEEecCHHH
Confidence            4789999997 567888888888888765556778888877664

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8

Probab=94.79  E-value=0.064  Score=47.69  Aligned_cols=22  Identities=27%  Similarity=0.487  Sum_probs=19.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||+++..+...
T Consensus        10 ki~v~G~~~~GKSsli~~l~~~   31 (203)
T 1zbd_A           10 KILIIGNSSVGKTSFLFRYADD   31 (203)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999998754

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=94.79  E-value=0.22  Score=47.45  Aligned_cols=25  Identities=32%  Similarity=0.279  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .+.++|++|+||||++..+|..+..
T Consensus       100 ~i~i~g~~G~GKTT~~~~la~~~~~  124 (295)
T 1ls1_A          100 LWFLVGLQGSGKTTTAAKLALYYKG  124 (295)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3678899999999999999988743

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=94.79  E-value=0.011  Score=53.36  Aligned_cols=23  Identities=26%  Similarity=0.263  Sum_probs=20.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.++|++|+||||+++.++..+
T Consensus        23 ~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           23 IIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTTS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            37899999999999999998754

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=94.79  E-value=0.012  Score=68.31  Aligned_cols=44  Identities=18%  Similarity=0.426  Sum_probs=35.3

Q ss_pred             CcEEEEEeCCC-CCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC
Q psy4285         371 SYKLIILDEAD-AMTNDAQNALRRIIEKFTTNVRFCIICNYLSKI  414 (533)
Q Consensus       371 ~~~vliiDE~d-~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l  414 (533)
                      +++||++||+- .++.+....+.+.+++...+..+|+++.+.+.+
T Consensus      1235 ~~~ILiLDEaTSaLD~~tE~~Iq~~l~~~~~~~TvI~IAHRLsTi 1279 (1321)
T 4f4c_A         1235 NPKILLLDEATSALDTESEKVVQEALDRAREGRTCIVIAHRLNTV 1279 (1321)
T ss_dssp             CCSEEEEESCCCSTTSHHHHHHHHHHTTTSSSSEEEEECSSSSTT
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHHcCCCEEEEeccCHHHH
Confidence            46899999984 567777888888898777788889999877643

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=94.79  E-value=0.051  Score=46.46  Aligned_cols=22  Identities=23%  Similarity=0.520  Sum_probs=19.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||++++.+...
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3899999999999999999864

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=94.78  E-value=0.049  Score=48.06  Aligned_cols=23  Identities=35%  Similarity=0.566  Sum_probs=20.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus        18 ki~v~G~~~~GKSsli~~l~~~~   40 (196)
T 3tkl_A           18 KLLLIGDSGVGKSCLLLRFADDT   40 (196)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            48999999999999999998643

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=94.78  E-value=0.06  Score=45.80  Aligned_cols=23  Identities=17%  Similarity=0.358  Sum_probs=20.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||+++..+...-
T Consensus         5 ~i~v~G~~~~GKSsli~~l~~~~   27 (167)
T 1kao_A            5 KVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            48999999999999999987643

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=94.77  E-value=0.053  Score=46.38  Aligned_cols=23  Identities=22%  Similarity=0.434  Sum_probs=20.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            38999999999999999997653

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=94.76  E-value=0.016  Score=59.67  Aligned_cols=25  Identities=4%  Similarity=0.057  Sum_probs=22.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .++|+|.+|+||||+++++++.+..
T Consensus       397 ~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          397 SIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             EEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             EEEecccCCCCHHHHHHHHHHHHHH
Confidence            4899999999999999999999953

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=94.76  E-value=0.055  Score=47.51  Aligned_cols=23  Identities=22%  Similarity=0.407  Sum_probs=20.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+||||++..++..-
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~~   45 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQNH   45 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            48999999999999999998653

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=94.74  E-value=0.034  Score=63.14  Aligned_cols=39  Identities=18%  Similarity=0.307  Sum_probs=24.5

Q ss_pred             CcEEEEEeCCCCCCHHH-HHHHHHHHHhcCCCcEEEEEeC
Q psy4285         371 SYKLIILDEADAMTNDA-QNALRRIIEKFTTNVRFCIICN  409 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~-~~~Ll~~le~~~~~~~~I~~~n  409 (533)
                      ..++|||||+|++.... ...+..++...+.+..+|+.|-
T Consensus       290 ~l~lVVIDEaH~l~d~~rg~~~e~ii~~l~~~~qvl~lSA  329 (1108)
T 3l9o_A          290 EVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSA  329 (1108)
T ss_dssp             HEEEEEEETGGGTTSHHHHHHHHHHHHHSCTTSEEEEEEC
T ss_pred             cCCEEEEhhhhhccccchHHHHHHHHHhcCCCceEEEEcC
Confidence            46899999999996543 2233334444455666666553

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=94.73  E-value=0.033  Score=47.64  Aligned_cols=21  Identities=29%  Similarity=0.556  Sum_probs=18.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~  328 (533)
                      .+++.|+||+|||++++.+..
T Consensus         4 ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            489999999999999998853

>3b60_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; HET: ANP; 3.70A {Salmonella typhimurium} SCOP: c.37.1.12 f.37.1.1 PDB: 3b5y_A* 3b5z_A* 3b5w_A

Probab=94.73  E-value=0.013  Score=62.02  Aligned_cols=43  Identities=26%  Similarity=0.458  Sum_probs=32.7

Q ss_pred             CcEEEEEeCC-CCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCC
Q psy4285         371 SYKLIILDEA-DAMTNDAQNALRRIIEKFTTNVRFCIICNYLSK  413 (533)
Q Consensus       371 ~~~vliiDE~-d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~  413 (533)
                      +++++++||. ..+++.....+.+.+.+...+..+|++|.+.+.
T Consensus       498 ~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~tvi~itH~~~~  541 (582)
T 3b60_A          498 DSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRLST  541 (582)
T ss_dssp             CCSEEEEETTTSSCCHHHHHHHHHHHHHHHTTSEEEEECSCGGG
T ss_pred             CCCEEEEECccccCCHHHHHHHHHHHHHHhCCCEEEEEeccHHH
Confidence            4789999997 467888888888887765446678888877653

>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein, mostly mixed alpha-beta structures, one domain is entirely helical; HET: DNA; 2.20A {Thermus aquaticus} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A* 1fw6_A* 1ewr_A*

Probab=94.70  E-value=0.049  Score=59.06  Aligned_cols=100  Identities=21%  Similarity=0.284  Sum_probs=51.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc-cccc-c-----------CcceEEecCCCCC--chh-HHHHHHHHHHhcccCCCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY-TKAQ-F-----------NAMVLELNASDDR--GIG-IVRDQIFQFASTKTMHKSS  371 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~-~~~~-~-----------~~~~~~~~~~~~~--~~~-~~~~~~~~~~~~~~~~~~~  371 (533)
                      .++++||.|+||||+.+.++.... ...+ +           ...+..+...+..  +.. ...+... ...... ....
T Consensus       578 i~~I~GpNGsGKSTlLr~iagl~~~~~~G~~vpa~~~~i~~v~~i~~~~~~~d~l~~g~S~~~~e~~~-la~il~-~a~~  655 (765)
T 1ewq_A          578 LVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEE-VALILK-EATE  655 (765)
T ss_dssp             EEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSEEEEECCC------CCSHHHHHHHH-HHHHHH-HCCT
T ss_pred             EEEEECCCCCChHHHHHHHHhhhhhcccCceeehhccceeeHHHhhccCCHHHHHHhcccHHHHHHHH-HHHHHH-hccC
Confidence            478999999999999999997642 1110 0           0001111211110  111 1111111 111000 0246


Q ss_pred             cEEEEEeCCCC----CCHHH-HHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         372 YKLIILDEADA----MTNDA-QNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       372 ~~vliiDE~d~----l~~~~-~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      ++++++||..+    ++... ..++++.+.+  .+..+|++|...
T Consensus       656 p~LlLLDEpgrGTs~lD~~~~~~~i~~~L~~--~g~~vl~~TH~~  698 (765)
T 1ewq_A          656 NSLVLLDEVGRGTSSLDGVAIATAVAEALHE--RRAYTLFATHYF  698 (765)
T ss_dssp             TEEEEEESTTTTSCHHHHHHHHHHHHHHHHH--HTCEEEEECCCH
T ss_pred             CCEEEEECCCCCCCCcCHHHHHHHHHHHHHh--CCCEEEEEeCCH
Confidence            78999999843    33333 2456777765  457788888653

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=94.69  E-value=0.068  Score=46.88  Aligned_cols=22  Identities=27%  Similarity=0.490  Sum_probs=19.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||++++.+...
T Consensus        13 ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           13 KFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999999864

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=94.69  E-value=0.19  Score=51.67  Aligned_cols=25  Identities=36%  Similarity=0.408  Sum_probs=22.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .+.|.|+||+||||++..++..+..
T Consensus       103 vI~ivG~~GvGKTTl~~kLA~~l~~  127 (504)
T 2j37_W          103 VIMFVGLQGSGKTTTCSKLAYYYQR  127 (504)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHh
Confidence            4889999999999999999987743

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=94.68  E-value=0.063  Score=57.00  Aligned_cols=29  Identities=17%  Similarity=0.407  Sum_probs=21.1

Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhc
Q psy4285         370 SSYKLIILDEADAMTNDAQNALRRIIEKF  398 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~~Ll~~le~~  398 (533)
                      ...+++||||+++++......+..+++..
T Consensus       317 ~~l~~lVlDEAH~l~~~~~~~l~~Il~~l  345 (666)
T 3o8b_A          317 GAYDIIICDECHSTDSTTILGIGTVLDQA  345 (666)
T ss_dssp             TSCSEEEETTTTCCSHHHHHHHHHHHHHT
T ss_pred             CcccEEEEccchhcCccHHHHHHHHHHhh
Confidence            45789999999998877655555555543

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=94.68  E-value=0.014  Score=53.12  Aligned_cols=37  Identities=24%  Similarity=0.353  Sum_probs=27.1

Q ss_pred             hhcccccccCCCceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       296 ~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .++........+.+++.|++|+||||++..++.....
T Consensus        28 ~~r~~~~~~~~~~i~ivG~~gvGKTtl~~~l~~~~~~   64 (226)
T 2hf9_A           28 KNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDNLKD   64 (226)
T ss_dssp             HHHHHHHHTTCEEEEEEESTTSSHHHHHHHHHHHHTT
T ss_pred             HHHHHHHhCCCeEEEEEcCCCCCHHHHHHHHHHHhcc
Confidence            3333333334456899999999999999999988643

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=94.64  E-value=0.075  Score=46.66  Aligned_cols=22  Identities=18%  Similarity=0.299  Sum_probs=19.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||++++.+...
T Consensus        22 ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           22 KIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999998754

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=94.59  E-value=0.02  Score=49.17  Aligned_cols=23  Identities=26%  Similarity=0.352  Sum_probs=21.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|.||.|+||||+++.++..+
T Consensus        35 ~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           35 MVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            37899999999999999999987

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=94.56  E-value=0.037  Score=50.07  Aligned_cols=26  Identities=31%  Similarity=0.451  Sum_probs=22.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      .++|.|++|+||||.++.+++.+...
T Consensus         8 ~i~~eG~~gsGKsT~~~~l~~~l~~~   33 (213)
T 4edh_A            8 FVTLEGPEGAGKSTNRDYLAERLRER   33 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHTT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            37899999999999999999988443

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=94.55  E-value=0.073  Score=47.07  Aligned_cols=22  Identities=18%  Similarity=0.471  Sum_probs=20.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||+++.++...
T Consensus         9 ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            9 KTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999999875

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=94.52  E-value=0.024  Score=49.49  Aligned_cols=25  Identities=40%  Similarity=0.428  Sum_probs=22.1

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +.+.|.|++|+||||+++.++..+.
T Consensus         7 ~~i~i~G~sGsGKTTl~~~l~~~l~   31 (174)
T 1np6_A            7 PLLAFAAWSGTGKTTLLKKLIPALC   31 (174)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhcc
Confidence            4588999999999999999998764

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=94.51  E-value=0.019  Score=52.29  Aligned_cols=23  Identities=35%  Similarity=0.560  Sum_probs=20.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|.||+|+||||+++.++...
T Consensus        25 ~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           25 PLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            47899999999999999999865

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=94.51  E-value=0.18  Score=44.27  Aligned_cols=24  Identities=25%  Similarity=0.463  Sum_probs=20.7

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHH
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~  329 (533)
                      ...+++.|++|+||||++..+...
T Consensus        23 ~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           23 LPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            345999999999999999999754

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=94.48  E-value=0.19  Score=44.00  Aligned_cols=23  Identities=22%  Similarity=0.359  Sum_probs=20.2

Q ss_pred             CceeEeCCCCCChHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~  329 (533)
                      +.+++.|++|+||||++..+...
T Consensus        24 ~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 3pqc_A           24 GEVAFVGRSNVGKSSLLNALFNR   46 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHTS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            45999999999999999998754

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=94.47  E-value=0.083  Score=45.42  Aligned_cols=22  Identities=36%  Similarity=0.584  Sum_probs=19.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|+||+|||++++.+...
T Consensus         6 ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            6 RVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCccHHHHHHHHhcC
Confidence            4899999999999999998743

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=94.47  E-value=0.061  Score=46.88  Aligned_cols=23  Identities=22%  Similarity=0.377  Sum_probs=20.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus        20 ki~v~G~~~~GKSsli~~l~~~~   42 (187)
T 2a9k_A           20 KVIMVGSGGVGKSALTLQFMYDE   42 (187)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhhCC
Confidence            48999999999999999998643

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=94.47  E-value=0.02  Score=51.64  Aligned_cols=23  Identities=22%  Similarity=0.520  Sum_probs=20.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|.||+|+||||+++.++..+
T Consensus        22 i~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           22 VVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            37899999999999999999875

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=94.47  E-value=0.024  Score=49.72  Aligned_cols=23  Identities=22%  Similarity=0.362  Sum_probs=20.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus         9 ki~v~G~~~vGKSsli~~l~~~~   31 (184)
T 1m7b_A            9 KIVVVGDSQCGKTALLHVFAKDC   31 (184)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            38999999999999999998753

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=94.46  E-value=0.035  Score=48.43  Aligned_cols=23  Identities=17%  Similarity=0.312  Sum_probs=20.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus         7 ~i~~~G~~~~GKssl~~~l~~~~   29 (186)
T 1mh1_A            7 KCVVVGDGAVGKTCLLISYTTNA   29 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            48999999999999999987643

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=94.46  E-value=0.19  Score=51.00  Aligned_cols=25  Identities=28%  Similarity=0.405  Sum_probs=22.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      +++.|+||+|||+++..+|......
T Consensus       200 iiIaG~pG~GKTtlal~ia~~~a~~  224 (444)
T 3bgw_A          200 VLIAARPSMGKTAFALKQAKNMSDN  224 (444)
T ss_dssp             EEEEECSSSSHHHHHHHHHHHHHHT
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHc
Confidence            8999999999999999999877543

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=94.45  E-value=0.017  Score=50.27  Aligned_cols=21  Identities=38%  Similarity=0.648  Sum_probs=18.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~  328 (533)
                      .+++.|++|+|||++++.+..
T Consensus        11 ~i~v~G~~~~GKssl~~~l~~   31 (181)
T 3tw8_B           11 KLLIIGDSGVGKSSLLLRFAD   31 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHCS
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999998864

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=94.45  E-value=0.02  Score=52.12  Aligned_cols=22  Identities=27%  Similarity=0.478  Sum_probs=20.4

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.|.||+|+||||+.+.++...
T Consensus        19 i~l~GpsGsGKSTLlk~L~g~~   40 (219)
T 1s96_A           19 YIVSAPSGAGKSSLIQALLKTQ   40 (219)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhccC
Confidence            7899999999999999999865

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=94.36  E-value=0.074  Score=46.44  Aligned_cols=23  Identities=22%  Similarity=0.420  Sum_probs=20.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||+++..+...-
T Consensus         6 ki~v~G~~~~GKSsli~~l~~~~   28 (189)
T 4dsu_A            6 KLVVVGADGVGKSALTIQLIQNH   28 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            38999999999999999998653

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=94.35  E-value=0.034  Score=62.40  Aligned_cols=41  Identities=15%  Similarity=0.341  Sum_probs=24.6

Q ss_pred             CCcEEEEEeCCCCCCHHH-HHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTNDA-QNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~-~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...+++||||+|.+.... ...+.+++...+.++.+|+.|-.
T Consensus       146 ~~l~lvViDEaH~l~d~~~g~~~e~ii~~l~~~v~iIlLSAT  187 (997)
T 4a4z_A          146 RDVEFVIFDEVHYVNDQDRGVVWEEVIIMLPQHVKFILLSAT  187 (997)
T ss_dssp             GGEEEEEECCTTCCCTTCTTCCHHHHHHHSCTTCEEEEEECC
T ss_pred             cCCCEEEEECcccccccchHHHHHHHHHhcccCCCEEEEcCC
Confidence            457899999999986431 11122333334566776666543

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=94.34  E-value=0.026  Score=51.43  Aligned_cols=25  Identities=36%  Similarity=0.377  Sum_probs=22.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .+.|.|++|+||||+++.+++.+..
T Consensus        23 ~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           23 FITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhh
Confidence            4889999999999999999998854

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=94.33  E-value=0.048  Score=57.89  Aligned_cols=39  Identities=21%  Similarity=0.239  Sum_probs=23.1

Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhc-CCCcEEEEEe
Q psy4285         370 SSYKLIILDEADAMTNDAQNALRRIIEKF-TTNVRFCIIC  408 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~~Ll~~le~~-~~~~~~I~~~  408 (533)
                      ...+++||||+|.++......+..+++.. ..+..+++.|
T Consensus       276 ~~~~~iViDEah~~~~~~~~~~~~i~~~l~~~~~q~il~S  315 (618)
T 2whx_A          276 PNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAAAIFMT  315 (618)
T ss_dssp             CCCSEEEEESTTCCSHHHHHHHHHHHHHHHHTSCEEEEEC
T ss_pred             cCCeEEEEECCCCCCccHHHHHHHHHHHhcccCccEEEEE
Confidence            46789999999999765433333333221 1345555555

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=94.32  E-value=0.25  Score=41.75  Aligned_cols=23  Identities=26%  Similarity=0.309  Sum_probs=20.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||+++..+...-
T Consensus         2 ki~~~G~~~~GKssl~~~l~~~~   24 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKLGE   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            37899999999999999997654

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=94.30  E-value=0.029  Score=51.23  Aligned_cols=22  Identities=36%  Similarity=0.602  Sum_probs=20.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +-|.||||+||||.++.+++.+
T Consensus        11 ~~~~G~pGsGKsT~a~~L~~~~   32 (230)
T 3gmt_A           11 LILLGAPGAGKGTQANFIKEKF   32 (230)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             eeeECCCCCCHHHHHHHHHHHh
Confidence            6799999999999999999987

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=94.27  E-value=0.025  Score=52.41  Aligned_cols=22  Identities=23%  Similarity=0.209  Sum_probs=20.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +-|.||+|+||||+++.++..+
T Consensus        28 igI~G~~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           28 IGVSGGTASGKSTVCEKIMELL   49 (245)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            7899999999999999999876

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=94.25  E-value=0.077  Score=45.94  Aligned_cols=23  Identities=22%  Similarity=0.432  Sum_probs=20.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||+++..+...-
T Consensus        12 ~i~v~G~~~~GKssli~~l~~~~   34 (180)
T 2g6b_A           12 KVMLVGDSGVGKTCLLVRFKDGA   34 (180)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHHhCC
Confidence            48999999999999999997654

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=94.23  E-value=0.059  Score=46.93  Aligned_cols=23  Identities=26%  Similarity=0.483  Sum_probs=20.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+....
T Consensus        20 ki~v~G~~~~GKSsl~~~l~~~~   42 (183)
T 3kkq_A           20 KLVVVGDGGVGKSALTIQFFQKI   42 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            38999999999999999998653

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=94.21  E-value=0.057  Score=47.14  Aligned_cols=23  Identities=30%  Similarity=0.453  Sum_probs=20.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus        12 ki~v~G~~~~GKSsli~~l~~~~   34 (186)
T 2bme_A           12 KFLVIGNAGTGKSCLLHQFIEKK   34 (186)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            48999999999999999997653

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=94.21  E-value=0.066  Score=47.24  Aligned_cols=22  Identities=23%  Similarity=0.462  Sum_probs=19.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||++++.+...
T Consensus        28 ki~vvG~~~~GKSsLi~~l~~~   49 (192)
T 2il1_A           28 QVIIIGSRGVGKTSLMERFTDD   49 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHCC-
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3899999999999999998744

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A*

Probab=94.21  E-value=0.037  Score=50.05  Aligned_cols=23  Identities=26%  Similarity=0.379  Sum_probs=20.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus        29 ki~vvG~~~vGKSsL~~~l~~~~   51 (214)
T 3q3j_B           29 KLVLVGDVQCGKTAMLQVLAKDC   51 (214)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            38999999999999999987653

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=94.21  E-value=0.058  Score=46.21  Aligned_cols=20  Identities=25%  Similarity=0.448  Sum_probs=18.4

Q ss_pred             ceeEeCCCCCChHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACA  327 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la  327 (533)
                      .+++.|+||+|||++++.+.
T Consensus         4 ki~ivG~~~~GKSsli~~l~   23 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFG   23 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            48999999999999999986

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=94.21  E-value=0.12  Score=45.28  Aligned_cols=23  Identities=35%  Similarity=0.605  Sum_probs=19.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+....
T Consensus        16 ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           16 KIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhc
Confidence            38999999999999998776544

>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=94.21  E-value=0.15  Score=48.80  Aligned_cols=79  Identities=19%  Similarity=0.134  Sum_probs=57.7

Q ss_pred             CCceEEEEEcCCCCcCchhhhc--cc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCC-CHHHHHHHHH
Q psy4285           5 TTNVRFCIICNYLSKITPAIQS--RC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDG-DMRKVLNILQ   80 (533)
Q Consensus         5 ~~~~~~il~~~~~~~i~~~i~S--Rc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g-~~r~a~~~l~   80 (533)
                      ..++++|.+||.+..+.|++++  |+ ..+.|+.|+.++..++++..+.+.+.. ++..+..++..+.| +.+...++++
T Consensus       152 ~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~-~~~~~~~la~~~~g~sg~dl~~l~~  230 (301)
T 3cf0_A          152 KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVA-KDVDLEFLAKMTNGFSGADLTEICQ  230 (301)
T ss_dssp             TSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC-SSCCHHHHHHTCSSCCHHHHHHHHH
T ss_pred             CCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCC-ccchHHHHHHHcCCCCHHHHHHHHH
Confidence            4678999999999999999988  88 689999999999999998888765543 12235566666654 3445555555


Q ss_pred             HHHH
Q psy4285          81 SAAT   84 (533)
Q Consensus        81 ~~~~   84 (533)
                      .++.
T Consensus       231 ~a~~  234 (301)
T 3cf0_A          231 RACK  234 (301)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=94.20  E-value=0.015  Score=53.40  Aligned_cols=23  Identities=30%  Similarity=0.410  Sum_probs=14.7

Q ss_pred             ceeEeCCCCCChHHHHHHHH-HHH
Q psy4285         308 HLLFYGPPGTGKTTTILACA-RKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la-~~l  330 (533)
                      .+.|.||+|+||||+++.++ ..+
T Consensus        29 ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           29 ILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             EEEEECSCC----CHHHHHHC---
T ss_pred             EEEEECCCCCCHHHHHHHHHhcCC
Confidence            37899999999999999999 754

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=94.19  E-value=0.03  Score=53.63  Aligned_cols=23  Identities=39%  Similarity=0.550  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|+||+|+||||+++.++..+
T Consensus       128 ~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          128 CLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHhhhc
Confidence            48899999999999999999876

>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=94.17  E-value=0.036  Score=51.98  Aligned_cols=92  Identities=18%  Similarity=0.157  Sum_probs=65.7

Q ss_pred             CceEEEEEcCCCCcCchhhhc--cc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHH
Q psy4285           6 TNVRFCIICNYLSKITPAIQS--RC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDG-DMRKVLNILQS   81 (533)
Q Consensus         6 ~~~~~il~~~~~~~i~~~i~S--Rc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g-~~r~a~~~l~~   81 (533)
                      .++++|.+||.+..+-|++++  |+ ..+.|++|+.++..+.|+..+....+. ++..+..++..+.| +.|...++++.
T Consensus       150 ~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~-~~~~~~~la~~~~g~~g~dl~~l~~~  228 (268)
T 2r62_A          150 APVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLA-NDVNLQEVAKLTAGLAGADLANIINE  228 (268)
T ss_dssp             SCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCC-SSCCTTTTTSSSCSSCHHHHHHHHHH
T ss_pred             CCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCC-CccCHHHHHHHcCCCCHHHHHHHHHH
Confidence            457899999999999999998  54 679999999999999998776543322 22235667777776 45677777777


Q ss_pred             HHHhC----CCCcchhhHHhh
Q psy4285          82 AATAH----ADEVNEDTIFTL   98 (533)
Q Consensus        82 ~~~~~----~~~i~~~~i~~~   98 (533)
                      +....    ...|+.+.+.+.
T Consensus       229 a~~~a~~~~~~~i~~~~~~~a  249 (268)
T 2r62_A          229 AALLAGRNNQKEVRQQHLKEA  249 (268)
T ss_dssp             HHHTTSSSCCCSCCHHHHHTS
T ss_pred             HHHHHHHhccCCcCHHHHHHH
Confidence            76543    234777776543

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=94.15  E-value=0.062  Score=45.79  Aligned_cols=22  Identities=23%  Similarity=0.453  Sum_probs=19.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||++++.+...
T Consensus         5 ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999999864

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=94.15  E-value=0.03  Score=50.24  Aligned_cols=23  Identities=22%  Similarity=0.362  Sum_probs=20.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus        30 ki~vvG~~~vGKSsLi~~l~~~~   52 (205)
T 1gwn_A           30 KIVVVGDSQCGKTALLHVFAKDC   52 (205)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            48999999999999999998753

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=94.14  E-value=0.064  Score=47.61  Aligned_cols=22  Identities=14%  Similarity=0.452  Sum_probs=19.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||++++.+...
T Consensus        30 ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           30 KIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            4899999999999999999754

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=94.12  E-value=0.063  Score=58.43  Aligned_cols=42  Identities=17%  Similarity=0.090  Sum_probs=28.1

Q ss_pred             hchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHH
Q psy4285         289 ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .|..++..+..-...+...+.++.||+|+|||..+-..+...
T Consensus       372 ~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~  413 (780)
T 1gm5_A          372 AQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDN  413 (780)
T ss_dssp             HHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHH
Confidence            445555555444444444568999999999999886655443

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=94.12  E-value=0.075  Score=46.84  Aligned_cols=23  Identities=17%  Similarity=0.408  Sum_probs=20.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus        25 ki~vvG~~~~GKSsli~~l~~~~   47 (192)
T 2fg5_A           25 KVCLLGDTGVGKSSIVCRFVQDH   47 (192)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHCC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            48999999999999999997643

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=94.10  E-value=0.031  Score=55.36  Aligned_cols=22  Identities=27%  Similarity=0.534  Sum_probs=21.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++.||+|+|||+++..+++.+
T Consensus         5 i~i~GptgsGKttla~~La~~~   26 (409)
T 3eph_A            5 IVIAGTTGVGKSQLSIQLAQKF   26 (409)
T ss_dssp             EEEEECSSSSHHHHHHHHHHHH
T ss_pred             EEEECcchhhHHHHHHHHHHHC
Confidence            7899999999999999999987

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=94.10  E-value=0.099  Score=57.87  Aligned_cols=22  Identities=27%  Similarity=0.274  Sum_probs=19.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .++|+||.|+||||+.+.++..
T Consensus       664 i~~ItGpNGsGKSTlLr~ial~  685 (934)
T 3thx_A          664 FHIITGPNMGGKSTYIRQTGVI  685 (934)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3799999999999999999543

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=94.09  E-value=0.072  Score=54.08  Aligned_cols=23  Identities=22%  Similarity=0.221  Sum_probs=17.7

Q ss_pred             ceeEeCCCCCChHHHH-HHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTI-LACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la-~~la~~l  330 (533)
                      ++++.||+|+|||..+ ..+...+
T Consensus        10 ~vlv~a~TGSGKT~~~l~~~l~~~   33 (440)
T 1yks_A           10 TTVLDFHPGAGKTRRFLPQILAEC   33 (440)
T ss_dssp             EEEECCCTTSSTTTTHHHHHHHHH
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHH
Confidence            6999999999999985 4444433

>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=94.09  E-value=0.095  Score=52.41  Aligned_cols=91  Identities=18%  Similarity=0.273  Sum_probs=66.5

Q ss_pred             CceEEEEEcCCCC---cCc---hhhhccc-eeEEeCCCCHHHHHHHHHHHHhhcC--CCCCHHHHHHHHHhcC------C
Q psy4285           6 TNVRFCIICNYLS---KIT---PAIQSRC-TRFRFGPLDSSLIMSRLDYVIEQEK--VNVTPDGKKAIIDLSD------G   70 (533)
Q Consensus         6 ~~~~~il~~~~~~---~i~---~~i~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~~~~~~~~~~~~~------g   70 (533)
                      .++.+|++++.+.   .+.   +.+.||. ..++|+|++.+++.+++.+.+...+  ..++++.+..++..++      |
T Consensus       178 ~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~G  257 (412)
T 1w5s_A          178 NRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDG  257 (412)
T ss_dssp             CBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCC
T ss_pred             ceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHhccCCC
Confidence            6778888887554   233   6677774 4499999999999999987654322  3477889999999999      9


Q ss_pred             CHHHHHHHHHHHHHh----CCCCcchhhHH
Q psy4285          71 DMRKVLNILQSAATA----HADEVNEDTIF   96 (533)
Q Consensus        71 ~~r~a~~~l~~~~~~----~~~~i~~~~i~   96 (533)
                      ++|.+++++..+...    ....++.+.+.
T Consensus       258 ~p~~~~~l~~~a~~~a~~~~~~~i~~~~v~  287 (412)
T 1w5s_A          258 SARRAIVALKMACEMAEAMGRDSLSEDLVR  287 (412)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCSSCCHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHcCCCCCCHHHHH
Confidence            999999999876432    12246655543

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=94.08  E-value=0.076  Score=57.46  Aligned_cols=41  Identities=10%  Similarity=0.201  Sum_probs=25.8

Q ss_pred             CCcEEEEEeCCCCCCH----HHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTN----DAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~----~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...+++||||+|.+..    .....++..+.....+.++|+.|-.
T Consensus       137 ~~~~~vIiDE~H~l~~~~r~~~~~~ll~~l~~~~~~~~ii~lSAT  181 (702)
T 2p6r_A          137 KAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSAT  181 (702)
T ss_dssp             GGCCEEEETTGGGGGCTTTHHHHHHHHHHHHHHCTTCEEEEEECC
T ss_pred             hhcCEEEEeeeeecCCCCcccHHHHHHHHHHhcCcCceEEEECCC
Confidence            3568999999998743    3334455545433456777776644

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=94.08  E-value=0.035  Score=49.05  Aligned_cols=23  Identities=26%  Similarity=0.404  Sum_probs=20.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus        25 ki~~vG~~~~GKSsl~~~l~~~~   47 (194)
T 3reg_A           25 KIVVVGDGAVGKTCLLLAFSKGE   47 (194)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            48999999999999999998754

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=94.08  E-value=0.024  Score=51.79  Aligned_cols=25  Identities=32%  Similarity=0.436  Sum_probs=19.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .++|.|++|+||||+++.+++.+..
T Consensus        27 ~I~~eG~~GsGKsT~~~~l~~~l~~   51 (227)
T 3v9p_A           27 FITFEGIDGAGKTTHLQWFCDRLQE   51 (227)
T ss_dssp             EEEEECCC---CHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHh
Confidence            3889999999999999999998843

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=94.06  E-value=0.031  Score=50.11  Aligned_cols=23  Identities=13%  Similarity=0.027  Sum_probs=21.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.+.|++|+||||+++.+|+.+
T Consensus         8 iI~i~g~~GsGk~ti~~~la~~l   30 (201)
T 3fdi_A            8 IIAIGREFGSGGHLVAKKLAEHY   30 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHT
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999998

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=94.06  E-value=0.043  Score=47.01  Aligned_cols=22  Identities=23%  Similarity=0.536  Sum_probs=19.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||+++..+...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            5 KILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            4899999999999999999754

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=94.05  E-value=0.17  Score=45.38  Aligned_cols=24  Identities=25%  Similarity=0.267  Sum_probs=20.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ..+++.|++|+|||+++..+...-
T Consensus         8 ~ki~vvG~~~~GKTsli~~l~~~~   31 (214)
T 2fh5_B            8 RAVLFVGLCDSGKTLLFVRLLTGQ   31 (214)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            358999999999999999998654

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=94.05  E-value=0.06  Score=48.10  Aligned_cols=23  Identities=26%  Similarity=0.495  Sum_probs=20.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+....
T Consensus        28 ki~lvG~~~vGKSsLi~~l~~~~   50 (201)
T 2ew1_A           28 KIVLIGNAGVGKTCLVRRFTQGL   50 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECcCCCCHHHHHHHHHhCC
Confidence            48999999999999999988654

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=94.03  E-value=0.025  Score=53.59  Aligned_cols=24  Identities=25%  Similarity=0.303  Sum_probs=21.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++++||||+||||+++.++..+.
T Consensus        32 i~~i~G~~GsGKTtl~~~l~~~~~   55 (279)
T 1nlf_A           32 VGALVSPGGAGKSMLALQLAAQIA   55 (279)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHh
Confidence            379999999999999999997653

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=94.00  E-value=0.068  Score=60.05  Aligned_cols=22  Identities=18%  Similarity=0.175  Sum_probs=17.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      ++++.+|+|+|||.++...+..
T Consensus       103 ~vLV~apTGSGKTlva~lai~~  124 (1010)
T 2xgj_A          103 SVLVSAHTSAGKTVVAEYAIAQ  124 (1010)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEECCCCCChHHHHHHHHHH
Confidence            6999999999999987544433

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=93.97  E-value=0.092  Score=54.19  Aligned_cols=101  Identities=15%  Similarity=0.242  Sum_probs=56.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhccc---------------------
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT---------------------  366 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------  366 (533)
                      +.++.-++|+|||..+-+++..+..... ...++.+.+...  .....+.+..+.....                     
T Consensus        58 ~~ilad~~GlGKT~~ai~~i~~~~~~~~-~~~~LIv~P~~l--~~qw~~e~~~~~~~~~v~~~~g~~~~~~~~~~~ivi~  134 (500)
T 1z63_A           58 GICLADDMGLGKTLQTIAVFSDAKKENE-LTPSLVICPLSV--LKNWEEELSKFAPHLRFAVFHEDRSKIKLEDYDIILT  134 (500)
T ss_dssp             CEEECCCTTSCHHHHHHHHHHHHHHTTC-CSSEEEEECSTT--HHHHHHHHHHHCTTSCEEECSSSTTSCCGGGSSEEEE
T ss_pred             CEEEEeCCCCcHHHHHHHHHHHHHhcCC-CCCEEEEccHHH--HHHHHHHHHHHCCCceEEEEecCchhccccCCcEEEe
Confidence            5789999999999999888877653321 223444444322  1222222222211000                     


Q ss_pred             ----------CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         367 ----------MHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       367 ----------~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                                .....++++|+||++.+.... ....+.+.......++.+|+....
T Consensus       135 t~~~l~~~~~l~~~~~~~vIvDEaH~~kn~~-~~~~~~l~~l~~~~~l~LTaTP~~  189 (500)
T 1z63_A          135 TYAVLLRDTRLKEVEWKYIVIDEAQNIKNPQ-TKIFKAVKELKSKYRIALTGTPIE  189 (500)
T ss_dssp             EHHHHTTCHHHHTCCEEEEEEETGGGGSCTT-SHHHHHHHTSCEEEEEEECSSCST
T ss_pred             eHHHHhccchhcCCCcCEEEEeCccccCCHh-HHHHHHHHhhccCcEEEEecCCCC
Confidence                      002357899999999984321 223444444444556777766543

>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B* 3thy_B* 3thz_B*

Probab=93.96  E-value=0.1  Score=57.62  Aligned_cols=100  Identities=20%  Similarity=0.271  Sum_probs=51.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcccc-----c--------cCcceEEecCCCC--Cch----hHHHHHHHHHHhcccCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKA-----Q--------FNAMVLELNASDD--RGI----GIVRDQIFQFASTKTMH  368 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~-----~--------~~~~~~~~~~~~~--~~~----~~~~~~~~~~~~~~~~~  368 (533)
                      .++|+||.|+||||+.+.++.......     +        ....+..+...+.  .+.    ..+.+...... .    
T Consensus       675 i~~ItGPNGaGKSTlLr~i~~i~~~aq~g~~vpa~~~~i~~~d~i~~~ig~~d~l~~~~stfs~em~~~~~il~-~----  749 (918)
T 3thx_B          675 VMIITGPNMGGKSSYIKQVALITIMAQIGSYVPAEEATIGIVDGIFTRMGAADNIYKGRSTFMEELTDTAEIIR-K----  749 (918)
T ss_dssp             EEEEESCCCHHHHHHHHHHHHHHHHHHHTCCBSSSEEEEECCSEEEEEC----------CCHHHHHHHHHHHHH-H----
T ss_pred             EEEEECCCCCchHHHHHHHHHHHHHhhcCccccchhhhhhHHHHHHHhCChHHHHHHhHHHhhHHHHHHHHHHH-h----
Confidence            379999999999999999875432110     0        0001111121111  111    11122111111 1    


Q ss_pred             CCCcEEEEEeCCCC-CCHHHHHHHH-HHHHhc--CCCcEEEEEeCCCC
Q psy4285         369 KSSYKLIILDEADA-MTNDAQNALR-RIIEKF--TTNVRFCIICNYLS  412 (533)
Q Consensus       369 ~~~~~vliiDE~d~-l~~~~~~~Ll-~~le~~--~~~~~~I~~~n~~~  412 (533)
                      ...+.++++||... +++.....+. .+++..  ..++.+|++|...+
T Consensus       750 a~~p~LlLLDEP~~GlD~~~~~~i~~~il~~L~~~~g~tvl~vTH~~e  797 (918)
T 3thx_B          750 ATSQSLVILDELGRGTSTHDGIAIAYATLEYFIRDVKSLTLFVTHYPP  797 (918)
T ss_dssp             CCTTCEEEEESTTTTSCHHHHHHHHHHHHHHHHHTTCCEEEEECSCGG
T ss_pred             ccCCCEEEEeCCCCCCCHHHHHHHHHHHHHHHHHhcCCeEEEEeCcHH
Confidence            14578999999864 5555454444 344332  24678888887654

>1zd9_A ADP-ribosylation factor-like 10B; transport protein, GDP-binding, membrane trafficking, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2al7_A* 2h18_A*

Probab=93.93  E-value=0.15  Score=44.61  Aligned_cols=23  Identities=30%  Similarity=0.245  Sum_probs=20.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus        24 ki~v~G~~~~GKSsli~~l~~~~   46 (188)
T 1zd9_A           24 ELTLVGLQYSGKTTFVNVIASGQ   46 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            48999999999999999998643

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=93.92  E-value=0.038  Score=53.02  Aligned_cols=24  Identities=42%  Similarity=0.458  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+.+.||+|+||||+++.++..+.
T Consensus       104 vi~lvG~nGsGKTTll~~Lagll~  127 (304)
T 1rj9_A          104 VVLVVGVNGVGKTTTIAKLGRYYQ  127 (304)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHH
Confidence            478999999999999999998764

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=93.90  E-value=0.14  Score=47.33  Aligned_cols=19  Identities=26%  Similarity=0.462  Sum_probs=15.6

Q ss_pred             ceeEeCCCCCChHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILAC  326 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~l  326 (533)
                      ++++.+|+|+|||..+-..
T Consensus        62 ~~l~~a~TGsGKT~~~~~~   80 (253)
T 1wrb_A           62 DIMACAQTGSGKTAAFLIP   80 (253)
T ss_dssp             CEEEECCTTSSHHHHHHHH
T ss_pred             CEEEECCCCChHHHHHHHH
Confidence            6999999999999865443

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=93.84  E-value=0.028  Score=48.48  Aligned_cols=22  Identities=27%  Similarity=0.369  Sum_probs=20.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .++|.|++|+||||+|..+.+.
T Consensus        18 gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           18 GVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHc
Confidence            4899999999999999999874

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=93.84  E-value=0.49  Score=47.64  Aligned_cols=26  Identities=35%  Similarity=0.422  Sum_probs=22.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      .+++.|++|+||||++..+|..+...
T Consensus       102 vI~ivG~~GvGKTT~a~~LA~~l~~~  127 (433)
T 2xxa_A          102 VVLMAGLQGAGKTTSVGKLGKFLREK  127 (433)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            37888999999999999999888544

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=93.82  E-value=0.055  Score=47.98  Aligned_cols=43  Identities=14%  Similarity=0.275  Sum_probs=27.2

Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHh---cCCCcEEEEEeCCCCCC
Q psy4285         371 SYKLIILDEADAMTNDAQNALRRIIEK---FTTNVRFCIICNYLSKI  414 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~~le~---~~~~~~~I~~~n~~~~l  414 (533)
                      ..-++++|=-+. ..+....+..++.+   ...+..+++++|..+.+
T Consensus        97 ~~~i~v~d~~~~-~~~~~~~~~~~l~~~~~~~~~~piilv~nK~Dl~  142 (196)
T 3llu_A           97 GALIYVIDAQDD-YMEALTRLHITVSKAYKVNPDMNFEVFIHKVDGL  142 (196)
T ss_dssp             SEEEEEEETTSC-CHHHHHHHHHHHHHHHHHCTTCEEEEEEECGGGS
T ss_pred             CEEEEEEECCCc-hHHHHHHHHHHHHHHHhcCCCCcEEEEEeccccC
Confidence            445777776555 44454555555554   34578899999987744

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=93.81  E-value=0.05  Score=47.99  Aligned_cols=23  Identities=22%  Similarity=0.341  Sum_probs=20.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus        20 ki~v~G~~~~GKssli~~l~~~~   42 (194)
T 2atx_A           20 KCVVVGDGAVGKTCLLMSYANDA   42 (194)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            48999999999999999998653

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=93.80  E-value=0.078  Score=46.66  Aligned_cols=21  Identities=29%  Similarity=0.548  Sum_probs=19.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|++|+|||++++.+...
T Consensus        24 i~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           24 YIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            899999999999999999764

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=93.80  E-value=0.029  Score=53.64  Aligned_cols=25  Identities=24%  Similarity=0.220  Sum_probs=22.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .+++.||||+||||+++.++..+..
T Consensus        37 ~~~i~G~~G~GKTTl~~~ia~~~~~   61 (296)
T 1cr0_A           37 VIMVTSGSGMGKSTFVRQQALQWGT   61 (296)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            3789999999999999999987643

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=93.80  E-value=0.043  Score=49.51  Aligned_cols=22  Identities=27%  Similarity=0.514  Sum_probs=19.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||+++..+...
T Consensus        36 ki~vvG~~~vGKSsli~~l~~~   57 (214)
T 2j1l_A           36 KVVLVGDGGCGKTSLLMVFADG   57 (214)
T ss_dssp             EEEEEECTTSSHHHHHHHHHC-
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            4899999999999999999753

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=93.78  E-value=0.037  Score=58.01  Aligned_cols=23  Identities=22%  Similarity=0.235  Sum_probs=21.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      ++|+|+||+||||+|+.+++.+.
T Consensus       399 I~l~GlsGSGKSTiA~~La~~L~  421 (573)
T 1m8p_A          399 IFLTGYMNSGKDAIARALQVTLN  421 (573)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEeecCCCCCHHHHHHHHHHHhc
Confidence            79999999999999999999884

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=93.78  E-value=0.019  Score=54.86  Aligned_cols=24  Identities=17%  Similarity=0.239  Sum_probs=18.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+.++||+|+||||+++.+++.+.
T Consensus         7 iIgItG~sGSGKSTva~~L~~~lg   30 (290)
T 1a7j_A            7 IISVTGSSGAGTSTVKHTFDQIFR   30 (290)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            378999999999999999998763

>1upt_A ARL1, ADP-ribosylation factor-like protein 1; hydrolase/protein-binding, complex (GTPase/golgin), golgin-245, GRIP, golgin, GTPase, G-protein; HET: GTP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1r4a_A*

Probab=93.77  E-value=0.17  Score=43.28  Aligned_cols=22  Identities=32%  Similarity=0.468  Sum_probs=19.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||+++..+...
T Consensus         9 ~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            9 RILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999999754

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=93.77  E-value=0.035  Score=53.46  Aligned_cols=23  Identities=26%  Similarity=0.187  Sum_probs=21.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +.|.||+|+||||+++.++..+.
T Consensus        93 vgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           93 IGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEECCCCchHHHHHHHHHhhcc
Confidence            78999999999999999998763

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=93.75  E-value=0.13  Score=47.19  Aligned_cols=23  Identities=22%  Similarity=0.359  Sum_probs=20.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.|++|+||||++.++...-
T Consensus        31 ~i~lvG~~g~GKStlin~l~g~~   53 (239)
T 3lxx_A           31 RIVLVGKTGAGKSATGNSILGRK   53 (239)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSC
T ss_pred             EEEEECCCCCCHHHHHHHHcCCC
Confidence            48999999999999999998643

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=93.73  E-value=0.16  Score=51.76  Aligned_cols=23  Identities=22%  Similarity=0.309  Sum_probs=17.8

Q ss_pred             ceeEeCCCCCChHHH-HHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTT-ILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~l-a~~la~~l  330 (533)
                      ++++.||+|+|||+. ...+...+
T Consensus        23 ~vlv~a~TGsGKT~~~~l~il~~~   46 (459)
T 2z83_A           23 MTVLDLHPGSGKTRKILPQIIKDA   46 (459)
T ss_dssp             EEEECCCTTSCTTTTHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHH
Confidence            699999999999997 44554443

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

Probab=93.73  E-value=0.31  Score=45.08  Aligned_cols=90  Identities=13%  Similarity=0.072  Sum_probs=65.4

Q ss_pred             CceEEEEEcCCCCcCchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHH-HHHHHHhcCCCH-HHHHHHHH
Q psy4285           6 TNVRFCIICNYLSKITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG-KKAIIDLSDGDM-RKVLNILQ   80 (533)
Q Consensus         6 ~~~~~il~~~~~~~i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-~~~~~~~~~g~~-r~a~~~l~   80 (533)
                      ..+.++.++|.+..+-|++++|+   ..+.|+.|+.++..++|+..+..  ..++++. +..++..+.|+. |...++++
T Consensus       153 ~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~--~~~~~~~~~~~la~~~~G~~~~dl~~~~~  230 (254)
T 1ixz_A          153 TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARG--KPLAEDVDLALLAKRTPGFVGADLENLLN  230 (254)
T ss_dssp             CCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTT--SCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcC--CCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            34567778899999999999954   56899999999999988866543  3444433 778999999866 77777777


Q ss_pred             HHHHh---C-CCCcchhhHHh
Q psy4285          81 SAATA---H-ADEVNEDTIFT   97 (533)
Q Consensus        81 ~~~~~---~-~~~i~~~~i~~   97 (533)
                      .++..   . ...|+.+.+.+
T Consensus       231 ~a~~~a~~~~~~~I~~~dl~~  251 (254)
T 1ixz_A          231 EAALLAAREGRRKITMKDLEE  251 (254)
T ss_dssp             HHHHHHHHTTCSSBCHHHHHH
T ss_pred             HHHHHHHHhcCCCcCHHHHHH
Confidence            66542   2 23477777654

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=93.71  E-value=0.038  Score=53.06  Aligned_cols=24  Identities=33%  Similarity=0.405  Sum_probs=21.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++++||+|+||||++..+|..+.
T Consensus       106 vi~ivG~~GsGKTTl~~~LA~~l~  129 (306)
T 1vma_A          106 VIMVVGVNGTGKTTSCGKLAKMFV  129 (306)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCChHHHHHHHHHHHHH
Confidence            378999999999999999998874

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=93.69  E-value=0.078  Score=46.60  Aligned_cols=23  Identities=26%  Similarity=0.540  Sum_probs=20.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||++++.+...-
T Consensus        17 ~i~v~G~~~~GKssli~~l~~~~   39 (195)
T 1x3s_A           17 KILIIGESGVGKSSLLLRFTDDT   39 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            48999999999999999998653

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=93.66  E-value=0.055  Score=47.15  Aligned_cols=22  Identities=32%  Similarity=0.607  Sum_probs=9.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||+++..+...
T Consensus        10 ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C           10 KLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEECCCCC------------
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999998754

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=93.64  E-value=0.021  Score=49.88  Aligned_cols=107  Identities=10%  Similarity=0.116  Sum_probs=57.9

Q ss_pred             hhccccchhHHHHHhchHHHHhhcCCChhhHHHHH--hhccCccccccCCCChhhHHHHHHHHHhccc-----ccceeee
Q psy4285         101 SRVEKYRPSTLDELVSHQDIISTIEIPESMLVDLV--LKMSDIEYRLAAGTSEKIQLSALIAAFNSAR-----DKLEVLE  173 (533)
Q Consensus       101 ~~~ek~~~~~l~~lls~~~~l~~l~~~~~~~~~~~--~~~~~~~~~~~~G~~~~~~l~~~~~~~~~~~-----~~~~~~e  173 (533)
                      +|.+++++..+.++++..+.+..+.       ..+  .....+...|++|+|||+.+.+++..+....     ....++.
T Consensus        11 ~l~~~~~~~~~~~~~g~~~~~~~l~-------~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~   83 (187)
T 2p65_A           11 DLTALARAGKLDPVIGRDTEIRRAI-------QILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVS   83 (187)
T ss_dssp             EHHHHHHTTCSCCCCSCHHHHHHHH-------HHHTSSSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEE
T ss_pred             HHHHHHhccccchhhcchHHHHHHH-------HHHhCCCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEE
Confidence            4556666666666666554443321       000  1123456889999999999998888764321     1356666


Q ss_pred             ecCCcccc----hhhhHHHHhhhhhcccccCCCceEEEEcCccccC
Q psy4285         174 LNASDDRG----IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMT  215 (533)
Q Consensus       174 ~nasd~~g----~~~~~d~i~~~a~~~~l~~~~~~~iilDE~d~l~  215 (533)
                      +++++...    .+...+.+........ ..+.+.++++||++.+.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~vl~iDe~~~l~  128 (187)
T 2p65_A           84 LDLSSLIAGAKYRGDFEERLKSILKEVQ-DAEGQVVMFIDEIHTVV  128 (187)
T ss_dssp             ECHHHHHHHCCSHHHHHHHHHHHHHHHH-HTTTSEEEEETTGGGGS
T ss_pred             EeHHHhhcCCCchhHHHHHHHHHHHHHH-hcCCceEEEEeCHHHhc
Confidence            66544211    1111112211111111 11345699999999886

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.63  E-value=0.097  Score=46.82  Aligned_cols=22  Identities=23%  Similarity=0.536  Sum_probs=19.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||+++..+...
T Consensus        22 ~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           22 KILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999998854

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

Probab=93.63  E-value=0.35  Score=45.49  Aligned_cols=90  Identities=13%  Similarity=0.084  Sum_probs=65.4

Q ss_pred             CceEEEEEcCCCCcCchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHH-HHHHHHHhcCCCH-HHHHHHHH
Q psy4285           6 TNVRFCIICNYLSKITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPD-GKKAIIDLSDGDM-RKVLNILQ   80 (533)
Q Consensus         6 ~~~~~il~~~~~~~i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~-~~~~~~~~~~g~~-r~a~~~l~   80 (533)
                      ..+.++.++|.+..+-|++++|+   ..+.|++|+.++..++|+..+..  ..++++ .+..++..+.|+. |...++++
T Consensus       177 ~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~--~~~~~~~~~~~la~~~~G~~~~dl~~l~~  254 (278)
T 1iy2_A          177 TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARG--KPLAEDVDLALLAKRTPGFVGADLENLLN  254 (278)
T ss_dssp             CCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTT--SCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHcc--CCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            34667778899999999999854   56899999999999988866543  444443 3778999999977 66667777


Q ss_pred             HHHHh---C-CCCcchhhHHh
Q psy4285          81 SAATA---H-ADEVNEDTIFT   97 (533)
Q Consensus        81 ~~~~~---~-~~~i~~~~i~~   97 (533)
                      .+...   . ...|+.+.+.+
T Consensus       255 ~a~~~a~~~~~~~I~~~dl~~  275 (278)
T 1iy2_A          255 EAALLAAREGRRKITMKDLEE  275 (278)
T ss_dssp             HHHHHHHHTTCCSBCHHHHHH
T ss_pred             HHHHHHHHhCCCCcCHHHHHH
Confidence            66542   1 23577777654

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=93.60  E-value=0.037  Score=57.39  Aligned_cols=23  Identities=30%  Similarity=0.394  Sum_probs=21.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +++.|.||+||||+++.+++.+.
T Consensus        38 IvlvGlpGSGKSTia~~La~~L~   60 (520)
T 2axn_A           38 IVMVGLPARGKTYISKKLTRYLN   60 (520)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHh
Confidence            78999999999999999999873

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=93.59  E-value=0.17  Score=51.53  Aligned_cols=22  Identities=27%  Similarity=0.401  Sum_probs=16.2

Q ss_pred             ceeEeCCCCCChHHH-HHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTT-ILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~l-a~~la~~  329 (533)
                      .+++.||+|+|||+. +-.+...
T Consensus        21 ~~lv~a~TGsGKT~~~~~~~l~~   43 (451)
T 2jlq_A           21 LTIMDLHPGAGKTKRILPSIVRE   43 (451)
T ss_dssp             EEEECCCTTSSCCTTHHHHHHHH
T ss_pred             eEEEECCCCCCHhhHHHHHHHHH
Confidence            469999999999993 4444433

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=93.58  E-value=0.035  Score=51.08  Aligned_cols=26  Identities=27%  Similarity=0.442  Sum_probs=22.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      .++|.|++|+||||+++.+++.+...
T Consensus        29 ~i~~eG~~GsGKsT~~~~l~~~l~~~   54 (236)
T 3lv8_A           29 FIVIEGLEGAGKSTAIQVVVETLQQN   54 (236)
T ss_dssp             EEEEEESTTSCHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            37899999999999999999988443

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=93.56  E-value=0.072  Score=47.53  Aligned_cols=23  Identities=30%  Similarity=0.544  Sum_probs=20.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||+++..+...-
T Consensus        10 ki~v~G~~~~GKSsli~~l~~~~   32 (206)
T 2bcg_Y           10 KLLLIGNSGVGKSCLLLRFSDDT   32 (206)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            48999999999999999997643

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*

Probab=93.55  E-value=0.37  Score=52.48  Aligned_cols=23  Identities=30%  Similarity=0.316  Sum_probs=20.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++++||.|+||||+.+.++...
T Consensus       609 i~~ItGpNGsGKSTlLr~iagl~  631 (800)
T 1wb9_A          609 MLIITGPNMGGKSTYMRQTALIA  631 (800)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCChHHHHHHHHHHH
Confidence            48999999999999999998764

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C

Probab=93.54  E-value=0.077  Score=47.22  Aligned_cols=22  Identities=23%  Similarity=0.306  Sum_probs=4.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||+++..+...
T Consensus        22 ~i~v~G~~~~GKssli~~l~~~   43 (208)
T 2yc2_C           22 KVAVVGEATVGKSALISMFTSK   43 (208)
T ss_dssp             EEEEC-----------------
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999998765

>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=93.53  E-value=0.12  Score=51.98  Aligned_cols=80  Identities=18%  Similarity=0.238  Sum_probs=59.7

Q ss_pred             CCceEEEEEc----CCCCcCchhhhcccee-EEeCCCCHHHHHHHHHH-----------HHhhcC--CCCCHHHHHHHHH
Q psy4285           5 TTNVRFCIIC----NYLSKITPAIQSRCTR-FRFGPLDSSLIMSRLDY-----------VIEQEK--VNVTPDGKKAIID   66 (533)
Q Consensus         5 ~~~~~~il~~----~~~~~i~~~i~SRc~~-~~~~~~~~~~~~~~l~~-----------~~~~~~--~~~~~~~~~~~~~   66 (533)
                      ..++.||.++    +.++.++|.+++|+-+ +.|++++.+++.+++..           ....++  +.++++++..|++
T Consensus       300 ~~~ilfI~~gaf~~~~~~dlipel~~R~~i~i~l~~lt~~e~~~Il~~~~~~l~~q~~~~~~~~~~~l~~~~~al~~i~~  379 (444)
T 1g41_A          300 TDHILFIASGAFQVARPSDLIPELQGRLPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAE  379 (444)
T ss_dssp             CTTCEEEEEECCSSCCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHH
T ss_pred             CCcEEEEeccccccCChhhcchHHhcccceeeeCCCCCHHHHHHHHHHHHHhHHHHHHHHhcccCceEEECHHHHHHHHH
Confidence            4567788886    2445578999999865 89999999999999831           111234  4578999999988


Q ss_pred             h--------cCCCHHHHHHHHHHHHH
Q psy4285          67 L--------SDGDMRKVLNILQSAAT   84 (533)
Q Consensus        67 ~--------~~g~~r~a~~~l~~~~~   84 (533)
                      .        -++.+|...+.++.+..
T Consensus       380 ~a~~~~~~t~~~GaR~L~~~ie~~~~  405 (444)
T 1g41_A          380 AAFRVNEKTENIGARRLHTVMERLMD  405 (444)
T ss_dssp             HHHHHHHHSCCCGGGHHHHHHHHHHH
T ss_pred             HHHHhccCCccCCchHHHHHHHHHHH
Confidence            6        35778998888887643

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=93.51  E-value=0.032  Score=51.54  Aligned_cols=23  Identities=22%  Similarity=0.258  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.|.|++|+||||+++.+++.+
T Consensus         4 ~i~~~G~~g~GKtt~~~~l~~~l   26 (241)
T 2ocp_A            4 RLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHC
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc
Confidence            37899999999999999999987

>3gee_A MNME, tRNA modification GTPase MNME; G protein, cytoplasm, GTP- binding, hydrolase, magnesium, metal-binding, nucleotide- binding, potassium; HET: GDP FON; 2.95A {Chlorobium tepidum} PDB: 3gei_A*

Probab=93.44  E-value=0.51  Score=48.15  Aligned_cols=22  Identities=23%  Similarity=0.371  Sum_probs=18.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+.+.|+||+||||+..++...
T Consensus       235 kV~ivG~~nvGKSSLln~L~~~  256 (476)
T 3gee_A          235 STVIAGKPNAGKSTLLNTLLGQ  256 (476)
T ss_dssp             EEEEECCTTSSHHHHHHHCC--
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999998765

>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2iez_A*

Probab=93.34  E-value=0.097  Score=47.10  Aligned_cols=22  Identities=36%  Similarity=0.525  Sum_probs=19.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||++++.+...
T Consensus        27 ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           27 KLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4899999999999999988753

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=93.34  E-value=0.029  Score=58.01  Aligned_cols=35  Identities=23%  Similarity=0.164  Sum_probs=26.1

Q ss_pred             hhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHH
Q psy4285         294 CYKINRFIDENELPHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       294 ~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ...+.-.+..+.  ++++.||+|+||||+.++++..+
T Consensus       250 l~~l~~~v~~g~--~i~I~GptGSGKTTlL~aL~~~i  284 (511)
T 2oap_1          250 LAYLWLAIEHKF--SAIVVGETASGKTTTLNAIMMFI  284 (511)
T ss_dssp             HHHHHHHHHTTC--CEEEEESTTSSHHHHHHHHGGGS
T ss_pred             HHHHHHHHhCCC--EEEEECCCCCCHHHHHHHHHhhC
Confidence            344444444443  58999999999999999998765

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=93.34  E-value=0.1  Score=45.96  Aligned_cols=22  Identities=23%  Similarity=0.610  Sum_probs=19.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|++|+|||+++..+...
T Consensus        10 ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A           10 RVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCcHHHHHHHHHcC
Confidence            4899999999999999999864

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=93.33  E-value=0.041  Score=49.82  Aligned_cols=24  Identities=38%  Similarity=0.317  Sum_probs=22.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++|.|++|+||||.++.+++.+.
T Consensus         7 ~i~~eG~~g~GKst~~~~l~~~l~   30 (216)
T 3tmk_A            7 LILIEGLDRTGKTTQCNILYKKLQ   30 (216)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhc
Confidence            489999999999999999999983

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=93.28  E-value=0.35  Score=47.44  Aligned_cols=23  Identities=30%  Similarity=0.541  Sum_probs=20.2

Q ss_pred             CceeEeCCCCCChHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~  329 (533)
                      ..+++.|+||+||||+...++..
T Consensus       168 ~~v~lvG~~gvGKSTLin~L~~~  190 (357)
T 2e87_A          168 PTVVIAGHPNVGKSTLLKALTTA  190 (357)
T ss_dssp             CEEEEECSTTSSHHHHHHHHCSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            35899999999999999998764

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=93.26  E-value=0.052  Score=49.46  Aligned_cols=23  Identities=17%  Similarity=0.079  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.+.|++|||||++++.+|+.+
T Consensus        16 iI~i~g~~gsGk~~i~~~la~~l   38 (223)
T 3hdt_A           16 IITIEREYGSGGRIVGKKLAEEL   38 (223)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHc
Confidence            37899999999999999999998

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=93.26  E-value=0.073  Score=55.36  Aligned_cols=100  Identities=15%  Similarity=0.160  Sum_probs=0.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcc-------------------------------------------------
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAM-------------------------------------------------  339 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~-------------------------------------------------  339 (533)
                      +-|.||.|+||||+.+.++..+....  +..                                                 
T Consensus        28 ~gLiGpNGaGKSTLlkiL~Gl~~p~~--G~i~~~~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (538)
T 3ozx_A           28 LGVLGKNGVGKTTVLKILAGEIIPNF--GDPNSKVGKDEVLKRFRGKEIYNYFKELYSNELKIVHKIQYVEYASKFLKGT  105 (538)
T ss_dssp             EEEECCTTSSHHHHHHHHTTSSCCCT--TCTTSCCCHHHHHHHHTTSTTHHHHHHHHTTCCCEEEECSCTTGGGTTCCSB
T ss_pred             EEEECCCCCcHHHHHHHHhcCCCCCC--CccccccchhhHHhhcCCeeHHHHHHHHhhcccchhhccchhhhhhhhccCc


Q ss_pred             -------------------eEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeC-CCCCCHHHHHHHHHHHHhcC
Q psy4285         340 -------------------VLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDE-ADAMTNDAQNALRRIIEKFT  399 (533)
Q Consensus       340 -------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE-~d~l~~~~~~~Ll~~le~~~  399 (533)
                                         .+.+.....+....+..-.++-..........+++|++|| ...|+...+..+++++.+..
T Consensus       106 v~~~l~~~~~~~~~~~~l~~l~l~~~~~~~~~~LSgGe~Qrv~iA~aL~~~p~illlDEPts~LD~~~~~~l~~~l~~l~  185 (538)
T 3ozx_A          106 VNEILTKIDERGKKDEVKELLNMTNLWNKDANILSGGGLQRLLVAASLLREADVYIFDQPSSYLDVRERMNMAKAIRELL  185 (538)
T ss_dssp             HHHHHHHHCCSSCHHHHHHHTTCGGGTTSBGGGCCHHHHHHHHHHHHHHSCCSEEEEESTTTTCCHHHHHHHHHHHHHHC
T ss_pred             HHHHhhcchhHHHHHHHHHHcCCchhhcCChhhCCHHHHHHHHHHHHHHcCCCEEEEECCcccCCHHHHHHHHHHHHHHh


Q ss_pred             CCcEEEEEeCC
Q psy4285         400 TNVRFCIICNY  410 (533)
Q Consensus       400 ~~~~~I~~~n~  410 (533)
                      .+..+|+++..
T Consensus       186 ~g~tii~vsHd  196 (538)
T 3ozx_A          186 KNKYVIVVDHD  196 (538)
T ss_dssp             TTSEEEEECSC
T ss_pred             CCCEEEEEEeC

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=93.25  E-value=0.049  Score=52.19  Aligned_cols=24  Identities=33%  Similarity=0.463  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+.|.||+|+||||+++.++..+.
T Consensus       102 vi~lvG~nGsGKTTll~~Lag~l~  125 (302)
T 3b9q_A          102 VIMIVGVNGGGKTTSLGKLAHRLK  125 (302)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            378999999999999999998764

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=93.25  E-value=0.062  Score=47.84  Aligned_cols=23  Identities=22%  Similarity=0.417  Sum_probs=20.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.|++|+|||+++..+...-
T Consensus        27 ki~vvG~~~~GKSsli~~l~~~~   49 (201)
T 2gco_A           27 KLVIVGDGACGKTCLLIVFSKDQ   49 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            48999999999999999998643

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=93.19  E-value=0.045  Score=49.48  Aligned_cols=26  Identities=27%  Similarity=0.278  Sum_probs=22.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      .+.|.|++|+||||.++.+++.+...
T Consensus         5 ~i~~eG~~gsGKsT~~~~l~~~l~~~   30 (213)
T 4tmk_A            5 YIVIEGLEGAGKTTARNVVVETLEQL   30 (213)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            47899999999999999999988544

---

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	533
d1njfa_	239	c.37.1.20 (A:) delta prime subunit of DNA polymera	3e-25
d1njfa_	239	c.37.1.20 (A:) delta prime subunit of DNA polymera	3e-19
d1njfa_	239	c.37.1.20 (A:) delta prime subunit of DNA polymera	2e-13
d2gnoa2	198	c.37.1.20 (A:11-208) gamma subunit of DNA polymera	3e-25
d2gnoa2	198	c.37.1.20 (A:11-208) gamma subunit of DNA polymera	1e-04
d1iqpa2	231	c.37.1.20 (A:2-232) Replication factor C {Archaeon	1e-22
d1iqpa2	231	c.37.1.20 (A:2-232) Replication factor C {Archaeon	4e-14
d1iqpa2	231	c.37.1.20 (A:2-232) Replication factor C {Archaeon	6e-11
d1sxjc2	227	c.37.1.20 (C:12-238) Replication factor C3 {Baker'	5e-18
d1sxjc2	227	c.37.1.20 (C:12-238) Replication factor C3 {Baker'	3e-09
d1sxjc2	227	c.37.1.20 (C:12-238) Replication factor C3 {Baker'	2e-08
d1sxjc2	227	c.37.1.20 (C:12-238) Replication factor C3 {Baker'	1e-05
d1sxjd2	237	c.37.1.20 (D:26-262) Replication factor C2 {Baker'	6e-18
d1sxjd2	237	c.37.1.20 (D:26-262) Replication factor C2 {Baker'	2e-08
d1sxjd2	237	c.37.1.20 (D:26-262) Replication factor C2 {Baker'	3e-06
d1sxjd2	237	c.37.1.20 (D:26-262) Replication factor C2 {Baker'	0.001
d1sxjb2	224	c.37.1.20 (B:7-230) Replication factor C4 {Baker's	7e-17
d1sxjb2	224	c.37.1.20 (B:7-230) Replication factor C4 {Baker's	2e-12
d1sxjb2	224	c.37.1.20 (B:7-230) Replication factor C4 {Baker's	3e-07
d1sxjb2	224	c.37.1.20 (B:7-230) Replication factor C4 {Baker's	1e-06
d1sxjc1	95	a.80.1.1 (C:239-333) Replication factor C3 {Baker'	8e-15
d1sxjc1	95	a.80.1.1 (C:239-333) Replication factor C3 {Baker'	5e-07
d1iqpa1	95	a.80.1.1 (A:233-327) Replication factor C {Archaeo	1e-14
d1iqpa1	95	a.80.1.1 (A:233-327) Replication factor C {Archaeo	2e-08
d1a5ta2	207	c.37.1.20 (A:1-207) delta prime subunit of DNA pol	2e-11
d1a5ta2	207	c.37.1.20 (A:1-207) delta prime subunit of DNA pol	5e-09
d1a5ta2	207	c.37.1.20 (A:1-207) delta prime subunit of DNA pol	3e-05
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	4e-11
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	6e-05
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	3e-10
d1sxjb1	92	a.80.1.1 (B:231-322) Replication factor C4 {Baker'	1e-09
d1sxjb1	92	a.80.1.1 (B:231-322) Replication factor C4 {Baker'	8e-06
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	3e-09
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	1e-04
d1sxjd1	91	a.80.1.1 (D:263-353) Replication factor C2 {Baker'	4e-09
d1sxjd1	91	a.80.1.1 (D:263-353) Replication factor C2 {Baker'	2e-06
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	7e-08
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	4e-06
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	1e-05
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	2e-07
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	1e-06
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	2e-04
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	0.003
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	2e-05
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	6e-05
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	8e-05
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	9e-05
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	0.001
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	0.002

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 239

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

 Score =  102 bits (254), Expect = 3e-25
 Identities = 35/174 (20%), Positives = 67/174 (38%), Gaps = 21/174 (12%)

Query: 296 KINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAM--------------- 339
            +   +    + H  LF G  G GKT+     A+ L  +    A                
Sbjct: 23  ALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGR 82

Query: 340 ---VLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIE 396
              ++E++A+    +   RD +          +  +K+ ++DE   ++  + NAL + +E
Sbjct: 83  FVDLIEIDAASRTKVEDTRDLLDNVQYAPARGR--FKVYLIDEVHMLSRHSFNALLKTLE 140

Query: 397 KFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNII 450
           +   +V+F +      K+P  I SRC +F    LD   I  +L++         
Sbjct: 141 EPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAH 194

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 239

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

 Score = 84.8 bits (209), Expect = 3e-19
 Identities = 35/237 (14%), Positives = 77/237 (32%), Gaps = 70/237 (29%)

Query: 104 EKYRPSTLDELVSHQDIISTIE-------IPESMLV---DLVLKMSDIEYRLAAGTSEKI 153
            K+RP T  ++V  + +++ +        I  + L      V K S           E  
Sbjct: 4   RKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETG 63

Query: 154 QLSALIAAFNSARD-----KLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIIL 208
             +      ++ R+      ++++E++A+    +   RD +          +  +K+ ++
Sbjct: 64  ITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGR--FKVYLI 121

Query: 209 DEADAMTNDAQNALRR-------------------KLPVT-------------------- 229
           DE   ++  + NAL +                   KLPVT                    
Sbjct: 122 DEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRH 181

Query: 230 --------------PDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVG 272
                         P   + +   ++G +R  L++   A  +   +V+   V   +G
Sbjct: 182 QLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLG 238

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 239

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

 Score = 67.8 bits (165), Expect = 2e-13
 Identities = 21/99 (21%), Positives = 47/99 (47%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           +E+   +V+F +      K+   I SRC +F    LD   I  +L++++ +E +   P  
Sbjct: 139 LEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRA 198

Query: 61  KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLL 99
            + +   ++G +R  L++   A  +   +V+   +  +L
Sbjct: 199 LQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAML 237

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]} Length = 198

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]

 Score =  100 bits (251), Expect = 3e-25
 Identities = 28/149 (18%), Positives = 56/149 (37%), Gaps = 3/149 (2%)

Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNA-SDDRGIGIVR 355
           + R I+++E   +L  G   +      L     +       + VLE++   ++ GI  +R
Sbjct: 6   LKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIR 65

Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
             I  F +       + K +I+ + + MT  A NA  + +E+        +       + 
Sbjct: 66  T-IKDFLNYSPEL-YTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLL 123

Query: 416 PAIQSRCTRFRFGPLDSSLIMSRLDYDDI 444
           P I+SR  R           + +    D+
Sbjct: 124 PTIKSRVFRVVVNVPKEFRDLVKEKIGDL 152

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]} Length = 198

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]

 Score = 41.2 bits (96), Expect = 1e-04
 Identities = 10/90 (11%), Positives = 26/90 (28%), Gaps = 8/90 (8%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYV-------IEQEK 53
           +E+        +       + P I+SR  R           + +           + +  
Sbjct: 103 LEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVPKEFRDLVKEKIGDLWEELPLLERD 162

Query: 54  VNVTPDGKKAIIDLSDGDMRKVLNILQSAA 83
                +  K   +   G + + L +L++  
Sbjct: 163 FKTALEAYKLGAEKLSG-LMESLKVLETEK 191

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 231

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 94.6 bits (234), Expect = 1e-22
 Identities = 70/132 (53%), Positives = 95/132 (71%), Gaps = 1/132 (0%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
           ++  ++    +PHLLF GPPG GKTT  LA AR+L+ +  +    LELNASD+RGI ++R
Sbjct: 35  RLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGE-NWRHNFLELNASDERGINVIR 93

Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
           +++ +FA TK +  +S+K+I LDEADA+T DAQ ALRR +E F++NVRF + CNY SKI 
Sbjct: 94  EKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKII 153

Query: 416 PAIQSRCTRFRF 427
             IQSRC  FRF
Sbjct: 154 EPIQSRCAIFRF 165

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 231

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 70.0 bits (170), Expect = 4e-14
 Identities = 44/96 (45%), Positives = 65/96 (67%), Gaps = 1/96 (1%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           +E F++NVRF + CNY SKI   IQSRC  FRF PL    I  RL Y+ E E + +T +G
Sbjct: 133 MEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEG 192

Query: 61  KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIF 96
            +AI+ +++GDMR+ +NILQ+AA A   ++ ++ +F
Sbjct: 193 LQAILYIAEGDMRRAINILQAAA-ALDKKITDENVF 227

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 231

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 60.3 bits (145), Expect = 6e-11
 Identities = 53/222 (23%), Positives = 88/222 (39%), Gaps = 65/222 (29%)

Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRL---AAGTSEKIQLSALI 159
           VEKYRP  LD++V  + I+  ++          +K   + + L     G  +     AL 
Sbjct: 15  VEKYRPQRLDDIVGQEHIVKRLKH--------YVKTGSMPHLLFAGPPGVGKTTAALALA 66

Query: 160 AAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTK----------------------- 196
                   +   LELNASD+RGI ++R+++ +FA TK                       
Sbjct: 67  RELFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQ 126

Query: 197 -----------------TMHKSSYKLI-------------ILDEADAMTNDAQNALRRKL 226
                                 S K+I              L + D        A    L
Sbjct: 127 QALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGL 186

Query: 227 PVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVY 268
            +T +G +AI+ +++GDMR+ +NILQ+AA A   ++ ++ V+
Sbjct: 187 ELTEEGLQAILYIAEGDMRRAINILQAAA-ALDKKITDENVF 227

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 227

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]

 Score = 80.9 bits (198), Expect = 5e-18
 Identities = 85/132 (64%), Positives = 108/132 (81%), Gaps = 1/132 (0%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
            + +F+DE +LPHLLFYGPPGTGKT+TI+A AR++Y K  ++ MVLELNASDDRGI +VR
Sbjct: 25  TVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGK-NYSNMVLELNASDDRGIDVVR 83

Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
           +QI  FAST+ +    +KLIILDEADAMTN AQNALRR+IE++T N RFC++ NY  K+ 
Sbjct: 84  NQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLT 143

Query: 416 PAIQSRCTRFRF 427
           PA+ S+CTRFRF
Sbjct: 144 PALLSQCTRFRF 155

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 227

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]

 Score = 55.1 bits (131), Expect = 3e-09
 Identities = 47/103 (45%), Positives = 70/103 (67%), Gaps = 4/103 (3%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           IE++T N RFC++ NY  K+TPA+ S+CTRFRF PL    I  R+  V+  EK+ ++P+ 
Sbjct: 123 IERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNA 182

Query: 61  KKAIIDLSDGDMRKVLNILQSAA----TAHADEVNEDTIFTLL 99
           +KA+I+LS+GDMR+VLN+LQS          DE+++D I+   
Sbjct: 183 EKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECC 225

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 227

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]

 Score = 52.4 bits (124), Expect = 2e-08
 Identities = 59/127 (46%), Positives = 74/127 (58%), Gaps = 9/127 (7%)

Query: 103 VEKYRPSTLDELVSHQDIISTIE--IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIA 160
           VEKYRP TLDE+    ++I+T+   + E  L  L+            GT +   + AL  
Sbjct: 5   VEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGP-------PGTGKTSTIVALAR 57

Query: 161 AFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQN 220
                     VLELNASDDRGI +VR+QI  FAST+ +    +KLIILDEADAMTN AQN
Sbjct: 58  EIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQN 117

Query: 221 ALRRKLP 227
           ALRR + 
Sbjct: 118 ALRRVIE 124

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 227

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]

 Score = 44.7 bits (104), Expect = 1e-05
 Identities = 21/48 (43%), Positives = 33/48 (68%), Gaps = 4/48 (8%)

Query: 229 TPDGKKAIIDLSDGDMRKVLNILQSAA----TAHADEVNEDTVYNSVG 272
           +P+ +KA+I+LS+GDMR+VLN+LQS          DE+++D +Y   G
Sbjct: 179 SPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCG 226

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 80.9 bits (198), Expect = 6e-18
 Identities = 67/142 (47%), Positives = 95/142 (66%), Gaps = 10/142 (7%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
            + + +    LPH+LFYGPPGTGKT+TILA  ++LY      + +LELNASD+RGI IVR
Sbjct: 23  VLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVR 82

Query: 356 DQIFQFAST----------KTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFC 405
           +++  FA            +      YK+IILDEAD+MT DAQ+ALRR +E ++   RFC
Sbjct: 83  EKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFC 142

Query: 406 IICNYLSKIPPAIQSRCTRFRF 427
           +ICNY+++I   + S+C++FRF
Sbjct: 143 LICNYVTRIIDPLASQCSKFRF 164

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 53.2 bits (126), Expect = 2e-08
 Identities = 47/135 (34%), Positives = 68/135 (50%), Gaps = 22/135 (16%)

Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSE--KIQLSALIA 160
           VEKYRP  LDE+ +    ++ ++          LK +++ + L  G     K      + 
Sbjct: 3   VEKYRPKNLDEVTAQDHAVTVLKK--------TLKSANLPHMLFYGPPGTGKTSTILALT 54

Query: 161 A--FNSARDKLEVLELNASDDRGIGIVRDQIFQFAST----------KTMHKSSYKLIIL 208
              +     K  +LELNASD+RGI IVR+++  FA            +      YK+IIL
Sbjct: 55  KELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIIL 114

Query: 209 DEADAMTNDAQNALR 223
           DEAD+MT DAQ+ALR
Sbjct: 115 DEADSMTADAQSALR 129

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 46.2 bits (108), Expect = 3e-06
 Identities = 32/86 (37%), Positives = 53/86 (61%)

Query: 10  FCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSD 69
           FC+ICNY+++I   + S+C++FRF  LD+S  + RL ++ EQE V       + I+D+S 
Sbjct: 141 FCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISA 200

Query: 70  GDMRKVLNILQSAATAHADEVNEDTI 95
           GD+R+ + +LQSA+       +   I
Sbjct: 201 GDLRRGITLLQSASKGAQYLGDGKNI 226

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.2 bits (87), Expect = 0.001
 Identities = 16/91 (17%), Positives = 36/91 (39%), Gaps = 5/91 (5%)

Query: 187 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRK 246
           + + +         S ++   LD ++A+      + +  +       + I+D+S GD+R+
Sbjct: 146 NYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRR 205

Query: 247 VLNILQSAA-----TAHADEVNEDTVYNSVG 272
            + +LQSA+           +    V    G
Sbjct: 206 GITLLQSASKGAQYLGDGKNITSTQVEELAG 236

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 224

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]

 Score = 77.4 bits (189), Expect = 7e-17
 Identities = 54/133 (40%), Positives = 83/133 (62%), Gaps = 2/133 (1%)

Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
           ++ +   +  +PH++  G PG GKTT++   A +L  ++  + ++ ELNASDDRGI +VR
Sbjct: 26  RLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVL-ELNASDDRGIDVVR 84

Query: 356 DQIFQFASTKTMHKSS-YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKI 414
           +QI  FA  K       +K++ILDEAD+MT  AQ ALRR +E ++ + RF   CN  +KI
Sbjct: 85  NQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKI 144

Query: 415 PPAIQSRCTRFRF 427
              +QS+C   R+
Sbjct: 145 IEPLQSQCAILRY 157

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 224

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]

 Score = 64.3 bits (155), Expect = 2e-12
 Identities = 35/97 (36%), Positives = 54/97 (55%), Gaps = 1/97 (1%)

Query: 3   KFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKK 62
            ++ + RF   CN  +KI   +QS+C   R+  L    ++ RL  +I+ E V  T DG +
Sbjct: 127 LYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLE 186

Query: 63  AIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLL 99
           AII  ++GDMR+ +N LQS    H   VN D +F ++
Sbjct: 187 AIIFTAEGDMRQAINNLQSTVAGH-GLVNADNVFKIV 222

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 224

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]

 Score = 49.3 bits (116), Expect = 3e-07
 Identities = 49/154 (31%), Positives = 75/154 (48%), Gaps = 14/154 (9%)

Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRL---AAGTSEKIQLSALI 159
           VEKYRP  L ++V +++ I  ++         + K  ++ + +     G  +   +  L 
Sbjct: 6   VEKYRPQVLSDIVGNKETIDRLQQ--------IAKDGNMPHMIISGMPGIGKTTSVHCLA 57

Query: 160 AAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSS-YKLIILDEADAMTNDA 218
                      VLELNASDDRGI +VR+QI  FA  K       +K++ILDEAD+MT  A
Sbjct: 58  HELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGA 117

Query: 219 QNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQ 252
           Q ALRR + +  +        +     K++  LQ
Sbjct: 118 QQALRRTMELYSN--STRFAFACNQSNKIIEPLQ 149

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 224

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]

 Score = 47.3 bits (111), Expect = 1e-06
 Identities = 23/79 (29%), Positives = 34/79 (43%), Gaps = 1/79 (1%)

Query: 194 STKTMHKSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQS 253
                  +  +   L + D +    Q      +  T DG +AII  ++GDMR+ +N LQS
Sbjct: 146 EPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQS 205

Query: 254 AATAHADEVNEDTVYNSVG 272
               H   VN D V+  V 
Sbjct: 206 TVAGH-GLVNADNVFKIVD 223

>d1sxjc1 a.80.1.1 (C:239-333) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 95

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 67.9 bits (166), Expect = 8e-15
 Identities = 23/73 (31%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 453 YIKIQEIKIEKGLALTDILTEISLLVHRLEIP-ESMLVDLVLKMSDIEYRLAAGTSEKIQ 511
           +  + +++  KGLAL D++  I  ++   E+  E   V L+ K++DIEY ++ G +++IQ
Sbjct: 22  HYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSISKGGNDQIQ 81

Query: 512 LSALIAAFNSARD 524
            SA+I A  ++ +
Sbjct: 82  GSAVIGAIKASFE 94

>d1sxjc1 a.80.1.1 (C:239-333) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 95

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.9 bits (109), Expect = 5e-07
 Identities = 15/51 (29%), Positives = 29/51 (56%)

Query: 117 HQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD 167
            + +       E   V L+ K++DIEY ++ G +++IQ SA+I A  ++ +
Sbjct: 44  VKILEDYELQNEETRVHLLTKLADIEYSISKGGNDQIQGSAVIGAIKASFE 94

>d1iqpa1 a.80.1.1 (A:233-327) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 95

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 67.5 bits (165), Expect = 1e-14
 Identities = 27/78 (34%), Positives = 42/78 (53%)

Query: 448 NIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTS 507
           N +    K++EI +++GL+  D+L ++   V  L I E   V L  K+ +  +RL  G +
Sbjct: 18  NFLKAREKLREILLKQGLSGEDVLVQMHKEVFNLPIEEPKKVLLADKIGEYNFRLVEGAN 77

Query: 508 EKIQLSALIAAFNSARDK 525
           E IQL AL+A F     K
Sbjct: 78  EIIQLEALLAQFTLIGKK 95

>d1iqpa1 a.80.1.1 (A:233-327) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 95

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 49.4 bits (118), Expect = 2e-08
 Identities = 25/96 (26%), Positives = 40/96 (41%), Gaps = 14/96 (14%)

Query: 85  AHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQ-----DIISTI-------EIPESMLV 132
           A  +++  + +   L     K R   L E++  Q     D++  +        I E   V
Sbjct: 2   ARPEDI-REMMLLALKGNFLKAR-EKLREILLKQGLSGEDVLVQMHKEVFNLPIEEPKKV 59

Query: 133 DLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDK 168
            L  K+ +  +RL  G +E IQL AL+A F     K
Sbjct: 60  LLADKIGEYNFRLVEGANEIIQLEALLAQFTLIGKK 95

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

 Score = 61.3 bits (147), Expect = 2e-11
 Identities = 26/164 (15%), Positives = 48/164 (29%), Gaps = 20/164 (12%)

Query: 296 KINRFIDENELPH-LLFYGPPGTGKTTTILACARK-------------------LYTKAQ 335
           K+          H LL    PG G    I A +R                    L     
Sbjct: 13  KLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGT 72

Query: 336 FNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRII 395
                          +G+   +       +       K++ + +A  +T+ A NAL + +
Sbjct: 73  HPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTL 132

Query: 396 EKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
           E+      F +      ++   ++SRC      P      ++ L
Sbjct: 133 EEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWL 176

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

 Score = 54.3 bits (129), Expect = 5e-09
 Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 5/80 (6%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
           +E+      F +      ++   ++SRC      P      ++ L       +V ++ D 
Sbjct: 132 LEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWL-----SREVTMSQDA 186

Query: 61  KKAIIDLSDGDMRKVLNILQ 80
             A + LS G     L + Q
Sbjct: 187 LLAALRLSAGSPGAALALFQ 206

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

 Score = 42.8 bits (99), Expect = 3e-05
 Identities = 11/57 (19%), Positives = 21/57 (36%)

Query: 196 KTMHKSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQ 252
           + +     +  +   A      A   L R++ ++ D   A + LS G     L + Q
Sbjct: 150 RLLATLRSRCRLHYLAPPPEQYAVTWLSREVTMSQDALLAALRLSAGSPGAALALFQ 206

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]} Length = 239

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

 Score = 60.7 bits (146), Expect = 4e-11
 Identities = 32/177 (18%), Positives = 53/177 (29%), Gaps = 31/177 (17%)

Query: 301 IDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQ 360
             +  L HLL +GPPG GKTT               + + + L  +    I    D    
Sbjct: 30  ARKEPLEHLLLFGPPGLGKTTLAHVI---------AHELGVNLRVTSGPAIEKPGDLAAI 80

Query: 361 FASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF----------------TTNVRF 404
            A+          ++ +DE   ++  A+  L   +E F                    RF
Sbjct: 81  LAN----SLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRF 136

Query: 405 CIICNYLS--KIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQEI 459
            +I        I   + SR          +   +++    D     + I      EI
Sbjct: 137 TLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEI 193

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]} Length = 239

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

 Score = 42.3 bits (98), Expect = 6e-05
 Identities = 14/95 (14%), Positives = 23/95 (24%), Gaps = 4/95 (4%)

Query: 4   FTTNVRFCIICNYLS---KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
                RF +I           P +                +   +        V +T + 
Sbjct: 130 RLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEA 189

Query: 61  KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTI 95
              I   S G MR    + +      A    E+ I
Sbjct: 190 ALEIGRRSRGTMRVAKRLFRRVRDF-AQVAGEEVI 223

>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 = 59.7 bits (144), Expect = 3e-10
 Identities = 19/149 (12%), Positives = 37/149 (24%), Gaps = 20/149 (13%)

Query: 307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIV-------RDQIF 359
            + LF GP  +GKTT   A       K       L +N   DR    +            
Sbjct: 155 RYWLFKGPIDSGKTTLAAALLELCGGK------ALNVNLPLDRLNFELGVAIDQFLVVFE 208

Query: 360 QFASTKTMHKSSYKLIILDEADAMTND------AQNALRRIIEKFTTNVRFCIICN-YLS 412
               T    +       ++  D + +            + + ++        +  N Y  
Sbjct: 209 DVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSV 268

Query: 413 KIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
                 +                + R ++
Sbjct: 269 PKTLQARFVKQIDFRPKDYLKHCLERSEF 297

>d1sxjb1 a.80.1.1 (B:231-322) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 92

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 52.9 bits (127), Expect = 1e-09
 Identities = 14/74 (18%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 453 YIKIQEIKIEKGLALTDILTEISLLVHRLE-IPESMLVDLVLKMSDIEYRLAAGTSEKIQ 511
              ++    +KG +  DI+T    +   L  + ES+ ++++ ++     R+  G    +Q
Sbjct: 19  IQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQ 78

Query: 512 LSALIAAFNSARDK 525
           L++++A  +   +K
Sbjct: 79  LASMLAKIHKLNNK 92

>d1sxjb1 a.80.1.1 (B:231-322) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 92

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 42.1 bits (99), Expect = 8e-06
 Identities = 12/65 (18%), Positives = 32/65 (49%), Gaps = 8/65 (12%)

Query: 112 DELVSHQDIISTI--------EIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFN 163
            +  S  DI++T         ++ ES+ ++++ ++     R+  G    +QL++++A  +
Sbjct: 28  KKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQLASMLAKIH 87

Query: 164 SARDK 168
              +K
Sbjct: 88  KLNNK 92

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]} Length = 238

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]

 Score = 55.0 bits (131), Expect = 3e-09
 Identities = 30/160 (18%), Positives = 49/160 (30%), Gaps = 8/160 (5%)

Query: 306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI------GIVRDQIF 359
           L H+L  GPPG GKTT     A +L T     +  + +   D   I      G V     
Sbjct: 35  LDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDE 94

Query: 360 QFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQ 419
                K + +  Y  I   + D M     +A  + I                  +   ++
Sbjct: 95  IHRLNKAVEELLYSAIEDFQIDIMIGKGPSA--KSIRIDIQPFTLVGATTRSGLLSSPLR 152

Query: 420 SRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQEI 459
           SR          +   +  +     S  ++ I     + I
Sbjct: 153 SRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMI 192

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]} Length = 238

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]

 Score = 41.5 bits (96), Expect = 1e-04
 Identities = 12/104 (11%), Positives = 26/104 (25%), Gaps = 5/104 (4%)

Query: 1   IEKFTTNVRFCIICNYLSKITPAIQSRCTR-FRFGPLDSSLIMSRLDYVIEQEKVNVTPD 59
           I                  ++  ++SR              +   +        V +   
Sbjct: 128 IRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDA 187

Query: 60  GKKAIIDLSDGDMRKVLNILQ----SAATAHADEVNEDTIFTLL 99
             + I   S G  R  + + +          AD +N D +   +
Sbjct: 188 AAEMIAKRSRGTPRIAIRLTKRVRDMLTVVKADRINTDIVLKTM 231

>d1sxjd1 a.80.1.1 (D:263-353) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 91

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 51.3 bits (123), Expect = 4e-09
 Identities = 10/68 (14%), Positives = 25/68 (36%), Gaps = 2/68 (2%)

Query: 453 YIKIQEIKIEKGLALTDILTEIS-LLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQ 511
              +    ++ G +   ++ ++    +       +    +   +   + RL  GT+E IQ
Sbjct: 22  KKYVNTF-MKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQ 80

Query: 512 LSALIAAF 519
           L  L+   
Sbjct: 81  LLNLLVKI 88

>d1sxjd1 a.80.1.1 (D:263-353) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 91

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.0 bits (104), Expect = 2e-06
 Identities = 11/46 (23%), Positives = 19/46 (41%)

Query: 117 HQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAF 162
           H+  I+      +    +   +   + RL  GT+E IQL  L+   
Sbjct: 43  HEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKI 88

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 253

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 51.3 bits (121), Expect = 7e-08
 Identities = 22/96 (22%), Positives = 41/96 (42%), Gaps = 1/96 (1%)

Query: 4   FTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKA 63
            T+     I               C   +F   D++ I SRL  +  +EK  + P+    
Sbjct: 152 KTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDR 211

Query: 64  IIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLL 99
           +I  + GD+R+V+N+L + +T     +N + I  + 
Sbjct: 212 LIQTTRGDIRQVINLLSTISTTT-KTINHENINEIS 246

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 253

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 46.3 bits (108), Expect = 4e-06
 Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 214 MTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGY 273
            +     A+R K  + P+    +I  + GD+R+V+N+L + +T     +N + +      
Sbjct: 190 KSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTT-KTINHENINEISKA 248

Query: 274 PTK 276
             K
Sbjct: 249 WEK 251

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 253

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.8 bits (104), Expect = 1e-05
 Identities = 24/159 (15%), Positives = 47/159 (29%), Gaps = 7/159 (4%)

Query: 275 TKTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKA 334
           +  ++ N L    N   +  +K             + YGPPG GKTT     A++L    
Sbjct: 22  SVMKLKNWLANWENSKKNS-FKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDI 80

Query: 335 QFNAMVLELNASDDRGI------GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQ 388
                    + +            +     F+           + +II+DE D M+   +
Sbjct: 81  LEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDR 140

Query: 389 NALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF 427
             + ++ +         I+      +P            
Sbjct: 141 GGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDI 179

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 252

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]

 Score = 50.2 bits (118), Expect = 2e-07
 Identities = 25/90 (27%), Positives = 45/90 (50%), Gaps = 1/90 (1%)

Query: 7   NVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNV-TPDGKKAII 65
           N+R  ++C+ +S I   I+S+C   R      S I + L  V+  E++ + T D  K I 
Sbjct: 161 NIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIA 220

Query: 66  DLSDGDMRKVLNILQSAATAHADEVNEDTI 95
             S+G++R  L +L+S A  +   +   + 
Sbjct: 221 QASNGNLRVSLLMLESMALNNELALKSSSP 250

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 252

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]

 Score = 47.9 bits (112), Expect = 1e-06
 Identities = 48/209 (22%), Positives = 80/209 (38%), Gaps = 45/209 (21%)

Query: 296 KINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAMV-------------- 340
            +    D+      LL YGP GTGK T  +A    ++    +   +              
Sbjct: 22  FLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLE 81

Query: 341 ---------LELNASDDRGIGIVRD----------QIFQFASTKTMHKSSYKLIILDEAD 381
                    LE+  SD      +            +   F  +K      YK +I++EA+
Sbjct: 82  LNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEAN 141

Query: 382 AMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
           ++T DAQ ALRR +EK++ N+R  ++C+ +S I   I+S+C   R               
Sbjct: 142 SLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPA-----------P 190

Query: 442 DDISFFNIIIWYIKIQEIKIEKGLALTDI 470
            D     I+   +  + I++E    L  I
Sbjct: 191 SDSEISTILSDVVTNERIQLETKDILKRI 219

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 252

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]

 Score = 40.5 bits (93), Expect = 2e-04
 Identities = 11/39 (28%), Positives = 19/39 (48%)

Query: 229 TPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTV 267
           T D  K I   S+G++R  L +L+S A  +   +   + 
Sbjct: 212 TKDILKRIAQASNGNLRVSLLMLESMALNNELALKSSSP 250

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 252

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]

 Score = 37.5 bits (85), Expect = 0.003
 Identities = 7/23 (30%), Positives = 17/23 (73%)

Query: 103 VEKYRPSTLDELVSHQDIISTIE 125
           V+KYRP +L+ L  ++++ + ++
Sbjct: 2   VDKYRPKSLNALSHNEELTNFLK 24

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 276

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]

 Score = 44.4 bits (103), Expect = 2e-05
 Identities = 22/141 (15%), Positives = 35/141 (24%), Gaps = 16/141 (11%)

Query: 302 DENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNA---MVLELNASDDRGIGIVRDQI 358
             +  P     G PGTGKT T+         K                      I R   
Sbjct: 39  PGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLN 98

Query: 359 FQFASTKTMHKSSYKLII-------------LDEADAMTNDAQNALRRIIEKFTTNVRFC 405
             F            L++             LD+A  +  D  +   R+ ++      F 
Sbjct: 99  IPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFR 158

Query: 406 IICNYLSKIPPAIQSRCTRFR 426
           I    +      + +     R
Sbjct: 159 IALVIVGHNDAVLNNLDPSTR 179

>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 = 42.9 bits (100), Expect = 6e-05
 Identities = 17/119 (14%), Positives = 34/119 (28%), Gaps = 13/119 (10%)

Query: 302 DENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV-LELNASDDRGIGIVRDQIFQ 360
            E    ++L  GP G GKT      A+                     + +  +   +  
Sbjct: 45  HEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTD 104

Query: 361 FASTKTMHKSSYKLIILDEADAMTNDA------------QNALRRIIEKFTTNVRFCII 407
            A           ++ +DE D +                Q  L  ++E  T + +  ++
Sbjct: 105 SAGGAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMV 163

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]} Length = 287

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]

 Score = 42.4 bits (98), Expect = 8e-05
 Identities = 25/254 (9%), Positives = 62/254 (24%), Gaps = 36/254 (14%)

Query: 278 EITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLY------ 331
           E   + R  LN  +      +     +        G  G GKTT      +++       
Sbjct: 24  EAEALARIYLNRLL------SGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKE 77

Query: 332 ---------------TKAQFNAMVLELNASDDRGIGIVRDQIFQF------ASTKTMHKS 370
                                ++++       +  G     I +            +   
Sbjct: 78  GLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVI 137

Query: 371 SYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPL 430
             +   +  +  +  +    L R+ E+  +      I      +   +++        P 
Sbjct: 138 LDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIG--FLLVASDVRALSYMREKIPQ 195

Query: 431 DSSLIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVD 490
             S I  +L         +     +  E+ +   +     L  IS +    +        
Sbjct: 196 VESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGE-DKGGDGSAR 254

Query: 491 LVLKMSDIEYRLAA 504
             +    +   +A 
Sbjct: 255 RAIVALKMACEMAE 268

>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 = 41.7 bits (98), Expect = 9e-05
 Identities = 37/184 (20%), Positives = 65/184 (35%), Gaps = 44/184 (23%)

Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD--DRGIG----IVRDQIFQFA 362
           +L  GPPGTGKT    A A +             ++ SD  +  +G     VR  +F+ A
Sbjct: 48  VLMVGPPGTGKTLLAKAIAGEA------KVPFFTISGSDFVEMFVGVGASRVR-DMFEQA 100

Query: 363 STKTMHKSSYKLIILDEADAM--------------TNDAQNALRRIIEKFTTNVRFCIIC 408
                 K++  +I +DE DA+                   N +   ++ F  N    +I 
Sbjct: 101 K-----KAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIA 155

Query: 409 --NYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLA 466
             N    + PA+       R G  D  +++   D          I  + ++ + +   + 
Sbjct: 156 ATNRPDVLDPAL------LRPGRFDRQVVVGLPDVRGR----EQILKVHMRRVPLAPDID 205

Query: 467 LTDI 470
              I
Sbjct: 206 AAII 209

>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 = 38.7 bits (90), Expect = 0.001
 Identities = 41/217 (18%), Positives = 72/217 (33%), Gaps = 50/217 (23%)

Query: 276 KTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ 335
           K E+  I+ +L N S                  +L  GPPG GKT    A A +      
Sbjct: 18  KEELKEIVEFLKNPSRFHEMGARIP------KGVLLVGPPGVGKTHLARAVAGEA----- 66

Query: 336 FNAMVLELNASD--DRGIG----IVRDQIFQFASTKTMHKSSYKLIILDEADAM------ 383
                +  + SD  +  +G     VRD +F+ A      + +  ++ +DE DA+      
Sbjct: 67  -RVPFITASGSDFVEMFVGVGAARVRD-LFETA-----KRHAPCIVFIDEIDAVGRKRGS 119

Query: 384 --------TNDAQNALRRIIEKFTTNVRFCIIC--NYLSKIPPAIQSRCTRFRFGPLDSS 433
                        N L   ++ F  +    ++   N    + PA+       R G  D  
Sbjct: 120 GVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPAL------LRPGRFDRQ 173

Query: 434 LIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDI 470
           + +   D          I  I  +   + + + L  +
Sbjct: 174 IAIDAPDVKGR----EQILRIHARGKPLAEDVDLALL 206

>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 = 37.6 bits (86), Expect = 0.002
 Identities = 19/132 (14%), Positives = 37/132 (28%), Gaps = 8/132 (6%)

Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH 368
           +L  GPP +GKT   LA      +   F  +               +     F      +
Sbjct: 43  VLLEGPPHSGKTA--LAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIF---DDAY 97

Query: 369 KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFG 428
           KS    +++D+ + + +      R         +          +    I    T  R  
Sbjct: 98  KSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLII---GTTSRKD 154

Query: 429 PLDSSLIMSRLD 440
            L    +++   
Sbjct: 155 VLQEMEMLNAFS 166

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	533
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.88
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.87
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.87
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.86
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.86
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.84
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.82
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.78
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.75
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.74
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.71
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.7
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.69
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.69
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.64
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.62
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.6
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.58
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.58
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.57
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.49
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.48
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.43
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.43
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.41
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.4
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.36
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.32
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	99.31
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.31
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.31
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.26
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.24
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.19
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.17
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.13
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	99.04
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	99.04
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.0
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.94
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.87
d1iqpa1	95	Replication factor C {Archaeon Pyrococcus furiosus	98.83
d1sxjc1	95	Replication factor C3 {Baker's yeast (Saccharomyce	98.66
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.64
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	98.61
d1sxjb1	92	Replication factor C4 {Baker's yeast (Saccharomyce	98.58
d1sxje1	99	Replication factor C5 {Baker's yeast (Saccharomyce	98.53
d1sxjd1	91	Replication factor C2 {Baker's yeast (Saccharomyce	98.28
d1tuea_	205	Replication protein E1 helicase domain {Human papi	98.27
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.23
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.15
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.14
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	98.01
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.84
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.8
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	97.78
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.75
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.71
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	97.69
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.68
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.68
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	97.66
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.56
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.55
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.54
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.48
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.48
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.46
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	97.45
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.41
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.4
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.36
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.36
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.36
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	97.3
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.26
d1sxje1	99	Replication factor C5 {Baker's yeast (Saccharomyce	97.26
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.23
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.17
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.17
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.16
d1okkd2	207	GTPase domain of the signal recognition particle r	97.16
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	97.15
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	97.13
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	97.13
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	97.1
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	97.05
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.04
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.02
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.01
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.01
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.0
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	96.98
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.97
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	96.95
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.93
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	96.92
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.82
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	96.82
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.82
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	96.81
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	96.81
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.81
d2awna2	232	Maltose transport protein MalK, N-terminal domain	96.81
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.8
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.79
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.76
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	96.75
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	96.62
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.59
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	96.59
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.58
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	96.57
d1g2912	240	Maltose transport protein MalK, N-terminal domain	96.52
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.5
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	96.5
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	96.48
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.48
d1sxjd1	91	Replication factor C2 {Baker's yeast (Saccharomyce	96.46
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	96.42
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.32
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	96.31
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.24
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	96.18
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	96.16
d1iqpa1	95	Replication factor C {Archaeon Pyrococcus furiosus	96.12
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	96.07
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.05
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	96.03
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	96.03
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	96.0
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	96.0
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	95.99
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	95.98
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	95.95
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	95.93
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	95.89
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	95.87
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	95.87
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	95.86
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	95.84
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	95.79
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	95.79
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	95.76
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	95.75
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.73
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	95.72
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.71
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	95.7
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	95.67
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	95.67
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.67
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	95.64
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.63
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	95.63
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	95.57
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	95.56
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	95.53
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	95.46
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	95.45
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	95.44
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	95.43
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	95.42
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	95.33
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.32
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	95.32
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	95.28
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	95.23
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	95.19
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	95.16
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	95.15
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	95.15
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.11
d1sxjc1	95	Replication factor C3 {Baker's yeast (Saccharomyce	95.11
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	95.09
d2fh5b1	207	Signal recognition particle receptor beta-subunit	95.07
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	95.07
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	95.05
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	95.03
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	94.99
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	94.94
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	94.94
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	94.88
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	94.85
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	94.82
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.79
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	94.78
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	94.77
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	94.75
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	94.73
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	94.72
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	94.68
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	94.67
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	94.65
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	94.63
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.62
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	94.61
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	94.6
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	94.6
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	94.58
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.57
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	94.57
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	94.56
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	94.54
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	94.52
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.52
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	94.35
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	94.31
d1sxjb1	92	Replication factor C4 {Baker's yeast (Saccharomyce	94.26
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	94.16
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	94.12
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	94.12
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	94.05
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.0
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	93.94
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	93.93
d1nrjb_	209	Signal recognition particle receptor beta-subunit	93.93
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.89
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	93.87
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	93.86
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	93.79
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	93.66
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	93.65
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	93.64
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	93.62
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	93.58
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	93.48
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	93.46
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	93.35
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	93.32
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	93.2
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	93.14
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	93.06
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	93.03
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	92.95
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	92.79
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	92.78
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	92.76
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	92.75
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	92.74
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	92.66
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	92.64
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	92.64
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	92.51
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	92.49
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	92.28
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	92.16
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	92.15
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	92.07
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	91.93
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	91.82
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	91.76
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	91.72
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	91.69
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	91.63
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	91.63
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	91.56
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	91.4
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	91.31
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	91.18
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	91.07
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	91.03
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	91.0
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.84
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	90.66
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	90.53
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	90.53
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	90.45
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	90.06
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	89.9
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	89.71
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	89.31
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	89.24
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	89.2
d1c9ka_	180	Adenosylcobinamide kinase/adenosylcobinamide phosp	88.82
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	88.8
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	88.75
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	88.4
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	88.32
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	88.28
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	87.95
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	87.65
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	87.6
d1xpua3	289	Transcription termination factor Rho, ATPase domai	87.57
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	87.42
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	86.91
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	86.59
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	86.13
d1jqlb_	140	delta subunit of DNA polymerase III, N-domain {Esc	85.3
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	85.18
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	84.7
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	84.57
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	84.15
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	84.03
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	83.84
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	83.56
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	83.3
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	83.02
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	82.96
d2olra1	313	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	82.87
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	82.18
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	81.99
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	81.89
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	81.85
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	81.61
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	81.4
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	81.18
d1lkxa_	684	Myosin S1, motor domain {Dictyostelium discoideum,	81.15
d1ii2a1	323	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	80.97
d1d0xa2	712	Myosin S1, motor domain {Dictyostelium discoideum	80.64
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	80.32

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=99.88  E-value=4.9e-22  Score=185.64  Aligned_cols=153  Identities=22%  Similarity=0.348  Sum_probs=129.6

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccccC------------------cceEEecCCCC
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFN------------------AMVLELNASDD  348 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~~------------------~~~~~~~~~~~  348 (533)
                      .|++++.+.|..++..++.|| +||+||||||||++|+++++.+.+.....                  ..++++++++.
T Consensus        15 ig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~   94 (239)
T d1njfa_          15 VGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASR   94 (239)
T ss_dssp             CSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHTCCTTEEEEETTCS
T ss_pred             cChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchHHHHHHcCCCCeEEEecchhc
Confidence            467777888888888888888 89999999999999999999987643211                  13677888777


Q ss_pred             CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeec
Q psy4285         349 RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFG  428 (533)
Q Consensus       349 ~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~  428 (533)
                      .+.+.+++.++.+....  ..++.+|+||||+|.|+.+++++|++.||+++.+++||++||..+.+.++++|||..+.|.
T Consensus        95 ~~i~~ir~~~~~~~~~~--~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~~~i~~~i~SRc~~i~~~  172 (239)
T d1njfa_          95 TKVEDTRDLLDNVQYAP--ARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLK  172 (239)
T ss_dssp             SSHHHHHHHHHSCCCSC--SSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECC
T ss_pred             CCHHHHHHHHHHHHhcc--ccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCCccccChhHhhhhcccccc
Confidence            77888887766553332  2356789999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHhhcC
Q psy4285         429 PLDSSLIMSRLDYD  442 (533)
Q Consensus       429 ~~~~~~~~~~l~~~  442 (533)
                      +++.+++.+++.++
T Consensus       173 ~~~~~~i~~~l~~i  186 (239)
T d1njfa_         173 ALDVEQIRHQLEHI  186 (239)
T ss_dssp             CCCHHHHHHHHHHH
T ss_pred             cCcHHHhhhHHHHH
Confidence            99999999988876

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=99.87  E-value=1e-21  Score=178.64  Aligned_cols=153  Identities=19%  Similarity=0.236  Sum_probs=125.2

Q ss_pred             hhchhhhhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHcccccc------------------CcceEEecCCC-
Q psy4285         288 NESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQF------------------NAMVLELNASD-  347 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~------------------~~~~~~~~~~~-  347 (533)
                      .|++...+.+...+..++.|| +||+||||+|||++|+.+|+.+.|....                  ...+..+.... 
T Consensus         5 Pw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~   84 (207)
T d1a5ta2           5 PWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKG   84 (207)
T ss_dssp             GGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTT
T ss_pred             cccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhc
Confidence            467777888888888889898 8999999999999999999999765421                  12234443322 


Q ss_pred             --CCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceee
Q psy4285         348 --DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRF  425 (533)
Q Consensus       348 --~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i  425 (533)
                        ....+.+++....+.....  .++.+|+||||+|.|+.+++++|+++||+++.++.||++||.+.+++++++|||..+
T Consensus        85 ~~~i~~~~ir~l~~~~~~~~~--~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~tI~SRc~~i  162 (207)
T d1a5ta2          85 KNTLGVDAVREVTEKLNEHAR--LGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLH  162 (207)
T ss_dssp             CSSBCHHHHHHHHHHTTSCCT--TSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEE
T ss_pred             ccccccchhhHHhhhhhhccc--cCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChhhhhhhhcceeEEE
Confidence              2345677777665543322  357899999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCHHHHHHHhhcC
Q psy4285         426 RFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       426 ~~~~~~~~~~~~~l~~~  442 (533)
                      .|.+++.+++..+|.+.
T Consensus       163 ~~~~~~~~~~~~~L~~~  179 (207)
T d1a5ta2         163 YLAPPPEQYAVTWLSRE  179 (207)
T ss_dssp             ECCCCCHHHHHHHHHHH
T ss_pred             ecCCCCHHHHHHHHHHc
Confidence            99999999998888654

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.87  E-value=9.5e-22  Score=181.98  Aligned_cols=154  Identities=38%  Similarity=0.620  Sum_probs=135.3

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM  367 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (533)
                      .||+++...|..++..+..||+||+||||+|||++|+.+++++.+.. ....+.++++++.++...+......+......
T Consensus        18 ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~-~~~~~~~~n~~~~~~~~~i~~~~~~~~~~~~~   96 (224)
T d1sxjb2          18 VGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRS-YADGVLELNASDDRGIDVVRNQIKHFAQKKLH   96 (224)
T ss_dssp             CSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGG-HHHHEEEECTTSCCSHHHHHTHHHHHHHBCCC
T ss_pred             cCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHhccc-cccccccccccccCCceehhhHHHHHHHhhcc
Confidence            56778888899999999999999999999999999999999987653 34568899999999888888777776654322


Q ss_pred             -CCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         368 -HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       368 -~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                       ....++++|+||+|.+....+++|+..+++++.++.++++++..+.+.++++|||..+.|.+|+.+++..++.++
T Consensus        97 ~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~~~~~~~~~i~~~l~~i  172 (224)
T d1sxjb2          97 LPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQI  172 (224)
T ss_dssp             CCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHH
T ss_pred             CCCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHHHhhhcccchhhhHHHHHHH
Confidence             234678999999999999999999999999999999999999999999999999999999999999999999876

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.86  E-value=1.8e-21  Score=180.61  Aligned_cols=154  Identities=58%  Similarity=0.969  Sum_probs=133.9

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM  367 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (533)
                      .|++++.+.+..++..+..||+||+||||+|||++|+++|+++.+.. +...+.+.+.++..+.+...............
T Consensus        17 vg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~-~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~   95 (227)
T d1sxjc2          17 YGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKN-YSNMVLELNASDDRGIDVVRNQIKDFASTRQI   95 (227)
T ss_dssp             CSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTS-HHHHEEEECTTSCCSHHHHHTHHHHHHHBCCS
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhhcCC-CcceeEEecccccCCeeeeecchhhccccccc
Confidence            46777888888899999999999999999999999999999986543 24457788888888877777666666555544


Q ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       368 ~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ...+.+++||||+|.+....+++|++.+++++.++++++++|....++++++|||..+.|.+++.+++..++.++
T Consensus        96 ~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~~~~~~~~i~~~l~~I  170 (227)
T d1sxjc2          96 FSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANV  170 (227)
T ss_dssp             SSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHH
T ss_pred             cCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhhhccccccccccccccccc
Confidence            456778999999999999999999999999999999999999999999999999999999999999999998875

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.86  E-value=2.2e-21  Score=180.49  Aligned_cols=154  Identities=49%  Similarity=0.825  Sum_probs=132.8

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM  367 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (533)
                      .|+++....+..+++.+..||++|+||||+|||++|+++|+++.+.. ....++++++++.++.+.++............
T Consensus        27 ig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l~~~~-~~~~~~e~n~s~~~~~~~~~~~~~~~~~~~~~  105 (231)
T d1iqpa2          27 VGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGEN-WRHNFLELNASDERGINVIREKVKEFARTKPI  105 (231)
T ss_dssp             CSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGG-HHHHEEEEETTCHHHHHTTHHHHHHHHHSCCG
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHHhcc-cCCCeeEEecCcccchhHHHHHHHHHHhhhhc
Confidence            46777788888888888889999999999999999999999987643 35578889998877766666666655544433


Q ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       368 ~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ......++++||+|.+....++.|++.++++..++.+|+++|....++++++|||..+.|.+++..++..++.++
T Consensus       106 ~~~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~~  180 (231)
T d1iqpa2         106 GGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYI  180 (231)
T ss_dssp             GGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHH
T ss_pred             cCCCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccccccccccchhhHHHHHHHH
Confidence            345688999999999999999999999999999999999999999999999999999999999999999998776

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.84  E-value=4.3e-21  Score=172.48  Aligned_cols=137  Identities=18%  Similarity=0.180  Sum_probs=113.7

Q ss_pred             hhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC-CCchhHHHHHHHHHHhcccCCCCCc
Q psy4285         294 CYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD-DRGIGIVRDQIFQFASTKTMHKSSY  372 (533)
Q Consensus       294 ~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  372 (533)
                      .+.++++++++..++++|+||||+|||++|..+++.+.........++.+.+.. ..+.+.+|+....+... + ..+++
T Consensus         3 ~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~-~-~~~~~   80 (198)
T d2gnoa2           3 LETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYS-P-ELYTR   80 (198)
T ss_dssp             HHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSC-C-SSSSS
T ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCCCHHHHHHHHHHHhhC-c-ccCCC
Confidence            345677788888888999999999999999999998754433344677777643 35788999876655433 3 34678


Q ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCH
Q psy4285         373 KLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDS  432 (533)
Q Consensus       373 ~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~  432 (533)
                      +|+||||+|+|+.+++++|+++||+||.+++||++|+.+..+.|+++|||..+.|.+|.+
T Consensus        81 KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~TI~SRC~~i~~~~p~~  140 (198)
T d2gnoa2          81 KYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVPKE  140 (198)
T ss_dssp             EEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCHH
T ss_pred             EEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChhhCHHHHhcceEEEeCCCchH
Confidence            999999999999999999999999999999999999999999999999999999986653

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.82  E-value=1e-19  Score=169.71  Aligned_cols=155  Identities=46%  Similarity=0.823  Sum_probs=129.7

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccC
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM  367 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  367 (533)
                      .|+++..+.+..++..+..+|++|+|||||||||+++++++++.+...........+.+...+.......++.+......
T Consensus        15 ig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   94 (237)
T d1sxjd2          15 TAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVS   94 (237)
T ss_dssp             CSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHHSCCC
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHHHHHhhhhhh
Confidence            46677788888888888889999999999999999999999987665456667788887777766655555554322211


Q ss_pred             ----------CCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHH
Q psy4285         368 ----------HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMS  437 (533)
Q Consensus       368 ----------~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~  437 (533)
                                .....+++||||+|.+....++.+++.++.++.++.+|++++....++++++|||..+.|.+++.+++..
T Consensus        95 ~~~~~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i~f~~~~~~~~~~  174 (237)
T d1sxjd2          95 KPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAID  174 (237)
T ss_dssp             CCCTTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHH
T ss_pred             hhhHHHHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccccccccccccccccchhhhhccccccccccch
Confidence                      1245679999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhcC
Q psy4285         438 RLDYD  442 (533)
Q Consensus       438 ~l~~~  442 (533)
                      +|.++
T Consensus       175 ~L~~i  179 (237)
T d1sxjd2         175 RLRFI  179 (237)
T ss_dssp             HHHHH
T ss_pred             hhhhh
Confidence            88765

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.78  E-value=3.8e-18  Score=160.40  Aligned_cols=155  Identities=31%  Similarity=0.521  Sum_probs=110.9

Q ss_pred             hhchhhhhhhccccccc-CCCceeEeCCCCCChHHHHHHHHHHHccccccC-----------------------cceEEe
Q psy4285         288 NESMDLCYKINRFIDEN-ELPHLLFYGPPGTGKTTTILACARKLYTKAQFN-----------------------AMVLEL  343 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~-~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~-----------------------~~~~~~  343 (533)
                      .|++++...+..++..+ ..|+++|+||||||||++|+++|+.+.+.....                       .....+
T Consensus        14 ig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (252)
T d1sxje2          14 SHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEI   93 (252)
T ss_dssp             CSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------CCEECSSEEEE
T ss_pred             cCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccccccccccchhhhhhccCCcccee
Confidence            45566667777777655 456799999999999999999999985433100                       011111


Q ss_pred             cCCCCC--chhHHHHHHHHHHhccc--------CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCC
Q psy4285         344 NASDDR--GIGIVRDQIFQFASTKT--------MHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSK  413 (533)
Q Consensus       344 ~~~~~~--~~~~~~~~~~~~~~~~~--------~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~  413 (533)
                      ...+..  .................        .......+++|||+|.++.+.++.|++.+++++.+++||++||..+.
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d~l~~~~~~~l~~~~e~~~~~~~~Il~tn~~~~  173 (252)
T d1sxje2          94 TPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSP  173 (252)
T ss_dssp             CCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTEEEEEEESCSCS
T ss_pred             eecccccCCcceeeehhhhhhhhhhhhhhhcccccCCCceEEEeccccccccccchhhhcccccccccccceeeeccccc
Confidence            222111  11122222222222111        11245679999999999999999999999999999999999999999


Q ss_pred             CChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         414 IPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       414 l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ++++++|||..++|.+|+.+++.+++..+
T Consensus       174 i~~~l~sR~~~i~~~~~~~~~~~~~l~~i  202 (252)
T d1sxje2         174 IIAPIKSQCLLIRCPAPSDSEISTILSDV  202 (252)
T ss_dssp             SCHHHHTTSEEEECCCCCHHHHHHHHHHH
T ss_pred             hhhhhhcchheeeecccchhhHHHHHHHH
Confidence            99999999999999999999999998876

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=99.75  E-value=7.1e-18  Score=157.31  Aligned_cols=150  Identities=24%  Similarity=0.229  Sum_probs=111.3

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      .++||+||||||||++|+++|+++      +.+++.+++++..      +...++..+.....      ..++||+|||+
T Consensus        46 ~~iLL~GppGtGKT~la~~iA~~~------~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~A~~------~~P~il~iDei  113 (256)
T d1lv7a_          46 KGVLMVGPPGTGKTLLAKAIAGEA------KVPFFTISGSDFVEMFVGVGASRVRDMFEQAKK------AAPCIIFIDEI  113 (256)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH------TCCEEEECSCSSTTSCCCCCHHHHHHHHHHHHT------TCSEEEEETTH
T ss_pred             CeEEeeCCCCCCccHHHHHHHHHc------CCCEEEEEhHHhhhcchhHHHHHHHHHHHHHHH------cCCEEEEEECh
Confidence            349999999999999999999998      7788888887643      23445555443322      35689999999


Q ss_pred             CCCCH--------------HHHHHHHHHHHh--cCCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhc
Q psy4285         381 DAMTN--------------DAQNALRRIIEK--FTTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDY  441 (533)
Q Consensus       381 d~l~~--------------~~~~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~  441 (533)
                      |.+..              ...+.|+..++.  ...++.+|+|||.++.+|+++++  || ..+.|++|+.++..+++..
T Consensus       114 D~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~  193 (256)
T d1lv7a_         114 DAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKV  193 (256)
T ss_dssp             HHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHH
T ss_pred             hhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHH
Confidence            87632              234567777874  34567889999999999999997  89 5899999999998888876


Q ss_pred             C--------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         442 D--------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       442 ~--------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                      .        ..++..+.+         .+.|+++.|+..-+.++
T Consensus       194 ~l~~~~~~~~~~~~~la~---------~t~G~s~adi~~l~~~A  228 (256)
T d1lv7a_         194 HMRRVPLAPDIDAAIIAR---------GTPGFSGADLANLVNEA  228 (256)
T ss_dssp             HHTTSCBCTTCCHHHHHH---------TCTTCCHHHHHHHHHHH
T ss_pred             hccCCCcCcccCHHHHHH---------hCCCCCHHHHHHHHHHH
Confidence            5        122333333         67899999886665443

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=99.74  E-value=1.6e-17  Score=154.76  Aligned_cols=141  Identities=16%  Similarity=0.193  Sum_probs=110.7

Q ss_pred             hhchhhhhhhccccc-----ccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHH
Q psy4285         288 NESMDLCYKINRFID-----ENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFA  362 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~-----~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (533)
                      .||+++.+.+..++.     ....+|+|||||||||||++|+++|+++      +..+..+++++......+...+... 
T Consensus        12 vGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~------~~~~~~~~~~~~~~~~~~~~~~~~~-   84 (238)
T d1in4a2          12 IGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL------QTNIHVTSGPVLVKQGDMAAILTSL-   84 (238)
T ss_dssp             CSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHH------TCCEEEEETTTCCSHHHHHHHHHHC-
T ss_pred             CChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhcc------CCCcccccCcccccHHHHHHHHHhh-
Confidence            355555555555443     2345789999999999999999999998      5667788888877666555543321 


Q ss_pred             hcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc------------------CCCcEEEEEeCCCCCCChhhhccce-
Q psy4285         363 STKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF------------------TTNVRFCIICNYLSKIPPAIQSRCT-  423 (533)
Q Consensus       363 ~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~------------------~~~~~~I~~~n~~~~l~~~l~sR~~-  423 (533)
                             ....++++||++.+....++.++..++..                  ..++.+|++||....+++++++||. 
T Consensus        85 -------~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~at~~~~~~~~~~~~r~~~  157 (238)
T d1in4a2          85 -------ERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRSRFGI  157 (238)
T ss_dssp             -------CTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEEEEEESCGGGSCHHHHTTCSE
T ss_pred             -------ccCCchHHHHHHHhhhHHHhhcccceeeeeeeeeecCcccccccccCCCCeEEEEecCCCccccccceeeeeE
Confidence                   34579999999999999999999888753                  2467899999999999999999995 


Q ss_pred             eeeecCCCHHHHHHHhhcC
Q psy4285         424 RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       424 ~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+.|.+++.+++..++..+
T Consensus       158 ~~~~~~~~~~~~~~~l~~~  176 (238)
T d1in4a2         158 ILELDFYTVKELKEIIKRA  176 (238)
T ss_dssp             EEECCCCCHHHHHHHHHHH
T ss_pred             EEEecCCCHHHHHHHHHHh
Confidence            5789999999999888876

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=99.71  E-value=1e-17  Score=155.65  Aligned_cols=149  Identities=22%  Similarity=0.252  Sum_probs=106.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      ++||+||||||||++|+++|+++      +.+++.+++++..      ....++..+....      ...+.||+|||+|
T Consensus        44 giLl~GppGtGKT~la~aia~~~------~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~a~------~~~p~Ii~iDeid  111 (247)
T d1ixza_          44 GVLLVGPPGVGKTHLARAVAGEA------RVPFITASGSDFVEMFVGVGAARVRDLFETAK------RHAPCIVFIDEID  111 (247)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT------TCCEEEEEHHHHHHSCTTHHHHHHHHHHHHHT------TSSSEEEEEETHH
T ss_pred             eEEEecCCCCChhHHHHHHHHHc------CCCEEEEEhHHhhhccccHHHHHHHHHHHHHH------HcCCEEEEEEChh
Confidence            49999999999999999999987      6778888765432      1223333332221      1356899999999


Q ss_pred             CCCH--------------HHHHHHHHHHHhc--CCCcEEEEEeCCCCCCChhhhc--cce-eeeecCCCHHHHHHHhhcC
Q psy4285         382 AMTN--------------DAQNALRRIIEKF--TTNVRFCIICNYLSKIPPAIQS--RCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       382 ~l~~--------------~~~~~Ll~~le~~--~~~~~~I~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+..              ...+.|+..|+..  ..++.+|+|||.++.+|+++++  ||. .+.|++|+.++..+++...
T Consensus       112 ~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~  191 (247)
T d1ixza_         112 AVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIH  191 (247)
T ss_dssp             HHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHH
T ss_pred             hhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHH
Confidence            7631              1345677778743  3456788899999999999985  894 8999999999999888765


Q ss_pred             --------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 --------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 --------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                              ..++..+.+         .+.|+++.|+..-+..+
T Consensus       192 l~~~~~~~~~~~~~la~---------~t~g~s~~di~~lv~~A  225 (247)
T d1ixza_         192 ARGKPLAEDVDLALLAK---------RTPGFVGADLENLLNEA  225 (247)
T ss_dssp             HTTSCBCTTCCHHHHHH---------TCTTCCHHHHHHHHHHH
T ss_pred             hcccCCccccCHHHHHH---------HCCCCCHHHHHHHHHHH
Confidence                    112333322         56799999876655433

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=99.70  E-value=2.1e-17  Score=153.75  Aligned_cols=100  Identities=21%  Similarity=0.410  Sum_probs=94.6

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+|+.+++||++||+++++++||+|||+.++|++++.+++..++.+++.+|++.+++++++.+++.|+||+|+|+|+||
T Consensus       139 lE~~~~~~~~il~tn~~~~i~~~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~~~~~~~l~~i~~~s~Gd~R~ain~l~  218 (239)
T d1njfa_         139 LEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTD  218 (239)
T ss_dssp             HHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HhcCCCCeEEEEEcCCccccChhHhhhhcccccccCcHHHhhhHHHHHHhhhccCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhhh
Q psy4285          81 SAATAHADEVNEDTIFTLLV  100 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~~  100 (533)
                      .+.....++|+.+.|.+++|
T Consensus       219 ~~~~~~~~~I~~~~v~~~lg  238 (239)
T d1njfa_         219 QAIASGDGQVSTQAVSAMLG  238 (239)
T ss_dssp             HHHHHTTTSBCHHHHHHHHT
T ss_pred             HHHHhCCCCcCHHHHHHHhC
Confidence            88776777899999887765

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=99.69  E-value=3e-16  Score=146.02  Aligned_cols=141  Identities=18%  Similarity=0.232  Sum_probs=104.1

Q ss_pred             hchhhhhhhccccc-----ccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHh
Q psy4285         289 ESMDLCYKINRFID-----ENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAS  363 (533)
Q Consensus       289 ~~~~~~~~l~~~~~-----~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  363 (533)
                      ||+++.+.++.++.     ....+|+||+||||||||++|+++|+++      +..+..+++++..........+...  
T Consensus        13 Gq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~------~~~~~~~~~~~~~~~~~~~~~~~~~--   84 (239)
T d1ixsb2          13 GQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL------GVNLRVTSGPAIEKPGDLAAILANS--   84 (239)
T ss_dssp             SCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHH------TCCEEEEETTTCCSHHHHHHHHHTT--
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHh------CCCeEeccCCccccchhhHHHHHhh--
Confidence            44444444444433     2345789999999999999999999998      6667778887766554444333221  


Q ss_pred             cccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc------------------CCCcEEEEEeCCCCCCC-hhhhcccee
Q psy4285         364 TKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF------------------TTNVRFCIICNYLSKIP-PAIQSRCTR  424 (533)
Q Consensus       364 ~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~------------------~~~~~~I~~~n~~~~l~-~~l~sR~~~  424 (533)
                           .....++++||+|.+....++.++..++..                  .+++.+|++||.+...+ +.++++|..
T Consensus        85 -----~~~~~i~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~~~~  159 (239)
T d1ixsb2          85 -----LEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIV  159 (239)
T ss_dssp             -----CCTTCEEEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTTCCCEEEEECCCCEEEEEESCCSSCSCGGGGGCSEE
T ss_pred             -----ccCCCeeeeecccccchhHHHhhhhhhhhhhhhhhhccchhhhhcccCCCCEEEEeeccCcccccchhhccccee
Confidence                 134569999999999999999999999752                  34566888888777655 556567789


Q ss_pred             eeecCCCHHHHHHHhhcC
Q psy4285         425 FRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       425 i~~~~~~~~~~~~~l~~~  442 (533)
                      +.|.+++.++...++..+
T Consensus       160 ~~~~~~~~~~~~~i~~~~  177 (239)
T d1ixsb2         160 EHLEYYTPEELAQGVMRD  177 (239)
T ss_dssp             EECCCCCHHHHHHHHHHH
T ss_pred             eEeeccChhhhhHHHHHH
Confidence            999999999999888766

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=1.2e-16  Score=149.86  Aligned_cols=149  Identities=23%  Similarity=0.298  Sum_probs=108.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      .+|||||||||||++++++|+++      +.+++.+++++..      ....++..+.....      ..++||+|||+|
T Consensus        40 giLL~GppGtGKT~l~~ala~~~------~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~A~~------~~p~il~iDeid  107 (258)
T d1e32a2          40 GILLYGPPGTGKTLIARAVANET------GAFFFLINGPEIMSKLAGESESNLRKAFEEAEK------NAPAIIFIDELD  107 (258)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT------TCEEEEECHHHHTTSCTTHHHHHHHHHHHHHHH------TCSEEEEESSGG
T ss_pred             eeEEecCCCCCchHHHHHHHHHh------CCeEEEEEchhhcccccccHHHHHHHHHHHHHh------cCCeEEEehhhh
Confidence            49999999999999999999998      6777777765321      22334433332221      356899999999


Q ss_pred             CCCHH-----------HHHHHHHHHHh--cCCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhcC---
Q psy4285         382 AMTND-----------AQNALRRIIEK--FTTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDYD---  442 (533)
Q Consensus       382 ~l~~~-----------~~~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~---  442 (533)
                      .+...           ..+.++..++.  ...++.+|+|||.+..+|+++++  || ..+.|++|+.++...++...   
T Consensus       108 ~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~  187 (258)
T d1e32a2         108 AIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKN  187 (258)
T ss_dssp             GTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTT
T ss_pred             hhccCCCCCCCchHHHHHHHhccccccccccCCccEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccC
Confidence            99643           23344444442  34567889999999999999998  89 58999999999999999877   


Q ss_pred             -----HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 -----DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 -----~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                           ..++..+.+         .+.|+++.|+..-+..+
T Consensus       188 ~~~~~~~~~~~la~---------~t~G~s~adl~~lv~~A  218 (258)
T d1e32a2         188 MKLADDVDLEQVAN---------ETHGHVGADLAALCSEA  218 (258)
T ss_dssp             SCBCTTCCHHHHHH---------HCTTCCHHHHHHHHHHH
T ss_pred             cccccccchhhhhh---------cccCCCHHHHHHHHHHH
Confidence                 223444444         78899999987665544

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.64  E-value=1.7e-15  Score=142.10  Aligned_cols=133  Identities=26%  Similarity=0.355  Sum_probs=97.8

Q ss_pred             cCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhccc------------CCCCC
Q psy4285         304 NELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT------------MHKSS  371 (533)
Q Consensus       304 ~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~  371 (533)
                      +..++++|+||||||||++|+++|+++      +..+..++.++..+...++...+.+.....            .....
T Consensus        50 ~~~~~lll~GPpG~GKTt~a~~la~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (253)
T d1sxja2          50 GVFRAAMLYGPPGIGKTTAAHLVAQEL------GYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGK  123 (253)
T ss_dssp             TSCSEEEEECSTTSSHHHHHHHHHHHT------TCEEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTT
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHH------HhhhhccccccchhhHHHHHHHHHHhhcchhhhhhhhhhhccccccc
Confidence            344579999999999999999999998      667788888887776666554433322211            01245


Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhc-CCCcEEEEEeCC-CCCCChhhhccceeeeecCCCHHHHHHHhhcC
Q psy4285         372 YKLIILDEADAMTNDAQNALRRIIEKF-TTNVRFCIICNY-LSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       372 ~~vliiDE~d~l~~~~~~~Ll~~le~~-~~~~~~I~~~n~-~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~  442 (533)
                      ..++++||++.+....+..+...++.. .....+++++|. .....++++|||..+.|.+|+.+++..++..+
T Consensus       124 ~~vi~ide~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i  196 (253)
T d1sxja2         124 HFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTI  196 (253)
T ss_dssp             SEEEEECSGGGCCTTSTTHHHHHHHHHHHCSSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHH
T ss_pred             ceEEEeeeccccccchhhhhHHHhhhhcccccccccccccccccccccccceeeeeeccccchhHHHHHHHHH
Confidence            789999999999887776666665531 233456666654 44567789999999999999999999998876

>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=99.62  E-value=5.2e-16  Score=145.92  Aligned_cols=149  Identities=21%  Similarity=0.248  Sum_probs=104.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC------CchhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD------RGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      ++||+||||||||++|+++|.++      +.+++.+++++.      .....++..+.....      ..+++|+|||+|
T Consensus        43 giLL~Gp~GtGKT~l~~ala~~~------~~~~~~~~~~~l~~~~~~~~~~~l~~~f~~A~~------~~p~il~ideid  110 (265)
T d1r7ra3          43 GVLFYGPPGCGKTLLAKAIANEC------QANFISIKGPELLTMWFGESEANVREIFDKARQ------AAPCVLFFDELD  110 (265)
T ss_dssp             EEEEBCCTTSSHHHHHHHHHHHT------TCEEEEECHHHHHTSCTTTHHHHHHHHHHHHHH------TCSEEEEESSGG
T ss_pred             eEEEECCCCCcchhHHHHHHHHh------CCcEEEEEHHHhhhccccchHHHHHHHHHHHHh------cCCcceeHHhhh
Confidence            59999999999999999999998      677777775432      122334444333221      356899999999


Q ss_pred             CCCHH--------------HHHHHHHHHHh--cCCCcEEEEEeCCCCCCChhhhc--cc-eeeeecCCCHHHHHHHhhcC
Q psy4285         382 AMTND--------------AQNALRRIIEK--FTTNVRFCIICNYLSKIPPAIQS--RC-TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       382 ~l~~~--------------~~~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+...              ..+.|+..++.  ...++.+|+|||.++.+|+++++  || ..+.|++|+.++..+++...
T Consensus       111 ~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~  190 (265)
T d1r7ra3         111 SIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKAN  190 (265)
T ss_dssp             GTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHH
T ss_pred             hccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHHHHHHHHH
Confidence            88532              22455555542  23457899999999999999987  88 48999999999988888755


Q ss_pred             --------HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy4285         443 --------DISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL  477 (533)
Q Consensus       443 --------~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~  477 (533)
                              +.++..+..         .+.|+++.|+..-+..+
T Consensus       191 l~~~~~~~~~~l~~la~---------~t~g~s~~di~~lv~~A  224 (265)
T d1r7ra3         191 LRKSPVAKDVDLEFLAK---------MTNGFSGADLTEICQRA  224 (265)
T ss_dssp             TTCC----CCCCHHHHH---------HHCSSCCHHHHHHHHHH
T ss_pred             hccCCchhhhhHHHHHh---------cCCCCCHHHHHHHHHHH
Confidence                    112222222         67899999987665544

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.60  E-value=7.3e-16  Score=141.79  Aligned_cols=98  Identities=37%  Similarity=0.630  Sum_probs=91.0

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+++.+++|+++|++.+++++||+|||+.++|++|+.+++..+|.+++++|++.+++++++.|+..|+||+|+|++.||
T Consensus       125 ~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~~~~~~~~~i~~~l~~i~~~e~~~i~~~~l~~I~~~s~Gd~R~ai~~Lq  204 (224)
T d1sxjb2         125 MELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQ  204 (224)
T ss_dssp             HHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ccccccceeeeeccCchhhhhhHHHHHHHHhhhcccchhhhHHHHHHHHHhcccCCCHHHHHHHHHHcCCcHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhhh
Q psy4285          81 SAATAHADEVNEDTIFTLL   99 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~~   99 (533)
                      .++... +.|+.+.|++++
T Consensus       205 ~~~~~~-~~i~~~~i~~~~  222 (224)
T d1sxjb2         205 STVAGH-GLVNADNVFKIV  222 (224)
T ss_dssp             HHHHHH-SSBCHHHHHHHH
T ss_pred             HHHHcC-CCcCHHHHHHHh
Confidence            987643 468888876653

>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=99.58  E-value=8.5e-16  Score=147.94  Aligned_cols=162  Identities=20%  Similarity=0.228  Sum_probs=108.4

Q ss_pred             CHHHHHHHHHHHhhhchhhhhhhcccccc-------------c-CCCceeEeCCCCCChHHHHHHHHHHHccccccCcce
Q psy4285         275 TKTEITNILRWLLNESMDLCYKINRFIDE-------------N-ELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV  340 (533)
Q Consensus       275 ~~~~~~~~l~~~~~~~~~~~~~l~~~~~~-------------~-~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~  340 (533)
                      .|+++...+.....||+++.+.+..++..             . .+.++||+||||||||++|+++|+.+      +.++
T Consensus         4 ~p~~i~~~L~~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~------~~~~   77 (309)
T d1ofha_           4 TPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA------NAPF   77 (309)
T ss_dssp             CHHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH------TCCE
T ss_pred             CHHHHHHHhcCcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhcc------ccch
Confidence            46777777777778888877776544411             1 23459999999999999999999998      5567


Q ss_pred             EEecCCCCCch----hHHHHHHHHHHhcccCC---CCCcEEEEEeCCCCCCHH------------HHHHHHHHHHhc---
Q psy4285         341 LELNASDDRGI----GIVRDQIFQFASTKTMH---KSSYKLIILDEADAMTND------------AQNALRRIIEKF---  398 (533)
Q Consensus       341 ~~~~~~~~~~~----~~~~~~~~~~~~~~~~~---~~~~~vliiDE~d~l~~~------------~~~~Ll~~le~~---  398 (533)
                      +.++.++....    .......+.........   ...++|+||||+|++.+.            .++.|+..++..   
T Consensus        78 ~~i~~s~~~~~~~~~~~~~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~~~~~~~~~~~~~gv~~~LL~~~dg~~~~  157 (309)
T d1ofha_          78 IKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVS  157 (309)
T ss_dssp             EEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEE
T ss_pred             hcccccccccceeEeeeccccccccchhhhcccccccCCceEEehhhhhhhhhccCcccchhhhHHHHHhhHHhcCCEEe
Confidence            77776553211    11111112211111100   013579999999998532            456788888741   


Q ss_pred             -------CCCcEEEEEe----CCCCCCChhhhccce-eeeecCCCHHHHHHHhhcC
Q psy4285         399 -------TTNVRFCIIC----NYLSKIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       399 -------~~~~~~I~~~----n~~~~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                             ..++.||+++    +.+..++|+++.|+. .+.|.+|+..+..+++...
T Consensus       158 ~~~~~i~~s~ilfi~~ga~~~~~~~~~~p~l~~R~~~~i~~~~~~~~~~~~Il~~~  213 (309)
T d1ofha_         158 TKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLPIRVELTALSAADFERILTEP  213 (309)
T ss_dssp             ETTEEEECTTCEEEEEECCSSSCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHSS
T ss_pred             cCCeEEEccceeEEeccchhhcCcccchhhhhhhhheeeeccCCCHHHHHHHHHHH
Confidence                   2345566553    566789999999994 6889999999999988765

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.58  E-value=8.9e-16  Score=141.53  Aligned_cols=100  Identities=47%  Similarity=0.867  Sum_probs=91.6

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+++.+++|+++||.+++++++|+|||+.++|++++.+++.++|.+++.+|++.+++++++.|++.|+||+|+|+|.||
T Consensus       123 le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~~~~~~~~i~~~l~~I~~~e~i~i~~~~l~~i~~~s~Gd~R~ain~Lq  202 (227)
T d1sxjc2         123 IERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQ  202 (227)
T ss_dssp             HHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTTCHHHHHHHTT
T ss_pred             hhhcccceeeccccCcHHHhHHHHHHHHhhhccccccccccccccccccccccccCCHHHHHHHHHHcCCcHHHHHHHHH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhC----CCCcchhhHHhhhh
Q psy4285          81 SAATAH----ADEVNEDTIFTLLV  100 (533)
Q Consensus        81 ~~~~~~----~~~i~~~~i~~~~~  100 (533)
                      .+....    ...||.+.|.+++|
T Consensus       203 ~~~~~~~~~~~~~It~~~v~e~~g  226 (227)
T d1sxjc2         203 SCKATLDNPDEDEISDDVIYECCG  226 (227)
T ss_dssp             TTTTTTCSSSCCCBCHHHHHHHTT
T ss_pred             HHHHhcCCCCCCeeCHHHHHHHhC
Confidence            876532    23488888887765

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=99.57  E-value=8.7e-16  Score=138.98  Aligned_cols=75  Identities=20%  Similarity=0.344  Sum_probs=70.8

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      |||||++++|||+||++++|+|||+|||+.++|++++.+++..+|+     +++.++++++..+++.|+||+|+|+++||
T Consensus       132 lEep~~~~~fIl~t~~~~~ll~tI~SRc~~i~~~~~~~~~~~~~L~-----~~~~~~~~~~~~i~~~s~Gs~r~al~~le  206 (207)
T d1a5ta2         132 LEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLS-----REVTMSQDALLAALRLSAGSPGAALALFQ  206 (207)
T ss_dssp             HTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHH-----HHCCCCHHHHHHHHHHTTTCHHHHHHTTS
T ss_pred             HHhhcccceeeeeecChhhhhhhhcceeEEEecCCCCHHHHHHHHH-----HcCCCCHHHHHHHHHHcCCCHHHHHHHhC
Confidence            6999999999999999999999999999999999999999999996     45678899999999999999999999986

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.49  E-value=3.3e-14  Score=131.69  Aligned_cols=100  Identities=34%  Similarity=0.684  Sum_probs=90.5

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      +|+++.+++||++++.+.+++++|+|||+.++|++++.+++..+|++++.++++.+++++++.|++.++||+|+|+|.||
T Consensus       132 ~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i~f~~~~~~~~~~~L~~i~~~e~i~i~~~~l~~ia~~s~gd~R~ai~~L~  211 (237)
T d1sxjd2         132 METYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQ  211 (237)
T ss_dssp             HHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSSCHHHHHHHHH
T ss_pred             cccccccccccccccccccccccccchhhhhccccccccccchhhhhhhhhhcCcCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            36788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHh-----CCCCcchhhHHhhhh
Q psy4285          81 SAATA-----HADEVNEDTIFTLLV  100 (533)
Q Consensus        81 ~~~~~-----~~~~i~~~~i~~~~~  100 (533)
                      .++..     ..+.||.+.|.+++|
T Consensus       212 ~~~~~~~~~~~~~~It~~~i~e~~g  236 (237)
T d1sxjd2         212 SASKGAQYLGDGKNITSTQVEELAG  236 (237)
T ss_dssp             HTHHHHHHHCSCCCCCHHHHHHHHT
T ss_pred             HHHHhchhcCCCCccCHHHHHHhhC
Confidence            87443     234588888877664

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.48  E-value=1.7e-14  Score=135.03  Aligned_cols=86  Identities=30%  Similarity=0.502  Sum_probs=80.4

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCC-HHHHHHHHHhcCCCHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVT-PDGKKAIIDLSDGDMRKVLNIL   79 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-~~~~~~~~~~~~g~~r~a~~~l   79 (533)
                      +|+|+.+++||++||.+++++|||+|||+.++|++++.+++.++|.+++.+|++.++ +++++.|+..|+||+|+|++.|
T Consensus       155 ~e~~~~~~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~~~~~~~~l~~i~~~s~Gd~R~ai~~L  234 (252)
T d1sxje2         155 MEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLML  234 (252)
T ss_dssp             HHHSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cccccccccceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCcHHHHHHHH
Confidence            478999999999999999999999999999999999999999999999999998775 6778999999999999999999


Q ss_pred             HHHHHhC
Q psy4285          80 QSAATAH   86 (533)
Q Consensus        80 ~~~~~~~   86 (533)
                      |.++..+
T Consensus       235 q~~~~~~  241 (252)
T d1sxje2         235 ESMALNN  241 (252)
T ss_dssp             THHHHTT
T ss_pred             HHHHHcC
Confidence            9988743

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.43  E-value=9.3e-14  Score=128.08  Aligned_cols=97  Identities=44%  Similarity=0.811  Sum_probs=89.4

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ   80 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~   80 (533)
                      ||+++.+++||++||.+++++++|+|||..++|++++.+++..+|++++.++++.+++++++.|++.++||+|+|+|.||
T Consensus       133 l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~e~i~i~~~~l~~I~~~~~gdiR~ai~~Lq  212 (231)
T d1iqpa2         133 MEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQ  212 (231)
T ss_dssp             HHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             cccCCcceEEEeccCChhhchHhHhCccccccccccchhhHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCcchhhHHhh
Q psy4285          81 SAATAHADEVNEDTIFTL   98 (533)
Q Consensus        81 ~~~~~~~~~i~~~~i~~~   98 (533)
                      .++. .++.++.+.|..+
T Consensus       213 ~~~~-~~~~it~e~v~~v  229 (231)
T d1iqpa2         213 AAAA-LDKKITDENVFMV  229 (231)
T ss_dssp             HHHT-TCSEECHHHHHHH
T ss_pred             HHHH-cCCCcCHHHHHhh
Confidence            9876 4556888887543

>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=99.43  E-value=5.1e-14  Score=130.39  Aligned_cols=112  Identities=15%  Similarity=0.193  Sum_probs=76.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC---ch----hHHHHHHHHHHhcccCCCCCcEEEEEeCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR---GI----GIVRDQIFQFASTKTMHKSSYKLIILDEA  380 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~---~~----~~~~~~~~~~~~~~~~~~~~~~vliiDE~  380 (533)
                      ++||+||||||||++|+++|+++      +.+++.+++++..   ..    ..++..+....      ...++||+|||+
T Consensus        42 ~vLL~GppGtGKT~la~alA~~~------~~~~~~i~~~~~~~g~~~~~~~~~i~~if~~A~------~~~p~il~iDEi  109 (246)
T d1d2na_          42 SVLLEGPPHSGKTALAAKIAEES------NFPFIKICSPDKMIGFSETAKCQAMKKIFDDAY------KSQLSCVVVDDI  109 (246)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH------TCSEEEEECGGGCTTCCHHHHHHHHHHHHHHHH------TSSEEEEEECCH
T ss_pred             EEEEECcCCCCHHHHHHHHhhcc------cccccccccccccccccccchhhhhhhhhhhhh------hcccceeehhhh
Confidence            49999999999999999999998      7778888765421   11    22333322221      135789999999


Q ss_pred             CCCC----------HHHHHHHHHHHHhcC---CCcEEEEEeCCCCCCChh-hhccce-eeeecCCC
Q psy4285         381 DAMT----------NDAQNALRRIIEKFT---TNVRFCIICNYLSKIPPA-IQSRCT-RFRFGPLD  431 (533)
Q Consensus       381 d~l~----------~~~~~~Ll~~le~~~---~~~~~I~~~n~~~~l~~~-l~sR~~-~i~~~~~~  431 (533)
                      |.+.          ....+.|+..++...   .++.+|+|||.++.++++ +++||. .+.++.++
T Consensus       110 d~l~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~tTn~~~~ld~~~~~~rF~~~i~~P~~~  175 (246)
T d1d2na_         110 ERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIA  175 (246)
T ss_dssp             HHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTTTSSEEEECCCEE
T ss_pred             hhHhhhcccccchhHHHHHHHHHHhcCCCccccceeeeeccCChhhccchhhcCccceEEecCCch
Confidence            8752          334566777776543   246788899999888765 677885 56664443

>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=99.41  E-value=3.2e-13  Score=129.44  Aligned_cols=156  Identities=20%  Similarity=0.307  Sum_probs=108.6

Q ss_pred             HHHHHHHHhhhchhhhhhhccccc-------ccCCC--ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC
Q psy4285         279 ITNILRWLLNESMDLCYKINRFID-------ENELP--HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR  349 (533)
Q Consensus       279 ~~~~l~~~~~~~~~~~~~l~~~~~-------~~~~~--~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~  349 (533)
                      +.+.+.....||+++++.+...+.       ....|  .++|+||||+|||.+|+.+|+.+++.   ...++.++.++..
T Consensus        17 l~~~L~~~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~---~~~~~~~~~~~~~   93 (315)
T d1qvra3          17 LEEELHKRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT---EEAMIRIDMTEYM   93 (315)
T ss_dssp             HHHHHHHHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSS---GGGEEEECTTTCC
T ss_pred             HHHHhcCeEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCC---CcceEEEeccccc
Confidence            445555556777766655433322       12223  37899999999999999999998655   3467777765543


Q ss_pred             chhHHH---------------HHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc-----------CCCcE
Q psy4285         350 GIGIVR---------------DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF-----------TTNVR  403 (533)
Q Consensus       350 ~~~~~~---------------~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~-----------~~~~~  403 (533)
                      ......               ..+.....     ..+.+|+++||+|++.++.++.|++++++.           ..++.
T Consensus        94 ~~~~~~~L~g~~~gyvG~~~~~~l~~~~~-----~~p~~Vvl~DEieK~~~~v~~~ll~~l~~g~~~~~~gr~v~~~~~i  168 (315)
T d1qvra3          94 EKHAVSRLIGAPPGYVGYEEGGQLTEAVR-----RRPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTV  168 (315)
T ss_dssp             SSGGGGGC--------------CHHHHHH-----HCSSEEEEESSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEE
T ss_pred             cchhhhhhcCCCCCCcCcccCChHHHHHH-----hCCCcEEEEehHhhcCHHHHHHHHHHhccCceeCCCCcEecCcceE
Confidence            211111               01111111     135689999999999999999999999863           35688


Q ss_pred             EEEEeCC--------------------------CCCCChhhhccce-eeeecCCCHHHHHHHhhcC
Q psy4285         404 FCIICNY--------------------------LSKIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       404 ~I~~~n~--------------------------~~~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                      +|+|||.                          ...+.|.+++|+. .+.|.|++.+++.+++...
T Consensus       169 ~i~tsnlG~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~pEflnRid~Ii~F~~L~~~~~~~I~~~~  234 (315)
T d1qvra3         169 IILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQ  234 (315)
T ss_dssp             EEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHTCSBCCBCCCCCHHHHHHHHHHH
T ss_pred             EEEecccChHHHhhhcccccchhhhhHHHHHHHHhhcCHHHHhcCCeeeeccchhhhhhHHHHHHH
Confidence            9999984                          2458999999996 6689999999988887654

>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=99.40  E-value=1.6e-12  Score=124.81  Aligned_cols=154  Identities=21%  Similarity=0.275  Sum_probs=105.1

Q ss_pred             HHHHHHHHHhhhchhhhhhhccccc-------c-cCCC-ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCC
Q psy4285         278 EITNILRWLLNESMDLCYKINRFID-------E-NELP-HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD  348 (533)
Q Consensus       278 ~~~~~l~~~~~~~~~~~~~l~~~~~-------~-~~~~-~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~  348 (533)
                      .+...+.....||+++++.+...+.       . .++. .++|.||||+|||.+|+.+|+.+      +.+++.+++++.
T Consensus        15 ~l~~~L~~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l------~~~~i~~d~s~~   88 (315)
T d1r6bx3          15 NLGDRLKMLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL------GIELLRFDMSEY   88 (315)
T ss_dssp             HHHHHHTTTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH------TCEEEEEEGGGC
T ss_pred             HHHHHhCCeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhc------cCCeeEeccccc
Confidence            3444555556777777665544332       1 1222 38999999999999999999987      445666654432


Q ss_pred             Cc-----------hhHHH----HHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc-----------CCCc
Q psy4285         349 RG-----------IGIVR----DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF-----------TTNV  402 (533)
Q Consensus       349 ~~-----------~~~~~----~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~-----------~~~~  402 (533)
                      ..           .+.+.    ..+.....     ..+..|+++||+|++.++.++.|++++++.           -.++
T Consensus        89 ~~~~~~~~l~g~~~gy~g~~~~~~l~~~~~-----~~~~~vvl~DeieKa~~~V~~~lLqild~G~ltd~~Gr~vdf~n~  163 (315)
T d1r6bx3          89 MERHTVSRLIGAPPGYVGFDQGGLLTDAVI-----KHPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNV  163 (315)
T ss_dssp             SSSSCCSSSCCCCSCSHHHHHTTHHHHHHH-----HCSSEEEEEETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTTE
T ss_pred             cchhhhhhhcccCCCccccccCChhhHHHH-----hCccchhhhcccccccchHhhhhHHhhccceecCCCCCccCccce
Confidence            11           01110    11111111     135689999999999999999999999862           3668


Q ss_pred             EEEEEeCCCC-------------------------CCChhhhccce-eeeecCCCHHHHHHHhhcC
Q psy4285         403 RFCIICNYLS-------------------------KIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       403 ~~I~~~n~~~-------------------------~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                      .+|+|+|...                         .+.|.++.|+. .+.|.|++.+++..++...
T Consensus       164 iiI~Tsnig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEflnRid~ii~f~~l~~~~~~~I~~~~  229 (315)
T d1r6bx3         164 VLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKF  229 (315)
T ss_dssp             EEEEEECSSCC-----------------CHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHH
T ss_pred             EEEeccchhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHHHhhhhhhhcccchhhhHHHHHHHHH
Confidence            8999998431                         26888999995 7888999999988887544

>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=99.36  E-value=3e-12  Score=124.74  Aligned_cols=163  Identities=17%  Similarity=0.189  Sum_probs=110.5

Q ss_pred             CCCCHHHHHHHHHHHhhhchhhhhhhccccc------------------------------ccCCCceeEeCCCCCChHH
Q psy4285         272 GYPTKTEITNILRWLLNESMDLCYKINRFID------------------------------ENELPHLLFYGPPGTGKTT  321 (533)
Q Consensus       272 ~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~------------------------------~~~~~~~ll~GppGtGKT~  321 (533)
                      ..|.|.++...+.....||+++.+.+..++.                              ...+.++||.||+|||||.
T Consensus         4 ~~~tP~ei~~~L~~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTE   83 (364)
T d1um8a_           4 YIPAPKELKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTL   83 (364)
T ss_dssp             CCCCHHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHH
T ss_pred             CCCCHHHHHHHhCCeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHH
Confidence            4578999999999888999998877765442                              1134469999999999999


Q ss_pred             HHHHHHHHHccccccCcceEEecCCCCCch--------hHHHHHHHHHHhcccCCCCCcEEEEEeCCCCC----------
Q psy4285         322 TILACARKLYTKAQFNAMVLELNASDDRGI--------GIVRDQIFQFASTKTMHKSSYKLIILDEADAM----------  383 (533)
Q Consensus       322 la~~la~~l~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l----------  383 (533)
                      +|+++|+.+      ..+++.++++.....        ..+++.+......  ......+++++||+++.          
T Consensus        84 lAk~LA~~~------~~~~ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~--v~~~~~~iv~lDEieK~~~~s~~~~~~  155 (364)
T d1um8a_          84 MAQTLAKHL------DIPIAISDATSLTEAGYVGEDVENILTRLLQASDWN--VQKAQKGIVFIDEIDKISRLSENRSIT  155 (364)
T ss_dssp             HHHHHHHHT------TCCEEEEEGGGCC--------CTHHHHHHHHHTTTC--HHHHTTSEEEEETGGGC----------
T ss_pred             HHHHHHhhc------ccceeehhhhhcccchhhHhhhccchhhhhhhchhH--HHHhhcccchhhhhhhhcccccccccc
Confidence            999999986      556777776654332        2333333221100  00134679999999994          


Q ss_pred             ----CHHHHHHHHHHHHhc-------------CCCcEEEEEeCC------------------------------------
Q psy4285         384 ----TNDAQNALRRIIEKF-------------TTNVRFCIICNY------------------------------------  410 (533)
Q Consensus       384 ----~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~------------------------------------  410 (533)
                          .+..++.|++.++..             ..+..++.|+|-                                    
T Consensus       156 ~d~a~~~V~~~lLqild~~~~~~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (364)
T d1um8a_         156 RDVSGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQ  235 (364)
T ss_dssp             ----CHHHHHHHHHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTT
T ss_pred             ccccchHHHHhhhhhhcCceeccCCCCCCcCCcceeEEEeehhhhhhhcccchhhhhhhhhhcccccccccccccchhhh
Confidence                456799999999831             122333433332                                    


Q ss_pred             -------------CCCCChhhhccce-eeeecCCCHHHHHHHhhcC
Q psy4285         411 -------------LSKIPPAIQSRCT-RFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       411 -------------~~~l~~~l~sR~~-~i~~~~~~~~~~~~~l~~~  442 (533)
                                   ...+.|.++.|+. .+.|.+++.+++.+++...
T Consensus       236 ~~~~~~~~~~~~~~~~f~PEf~gRi~~iv~f~~L~~~~l~~Il~~~  281 (364)
T d1um8a_         236 EAILHLVQTHDLVTYGLIPELIGRLPVLSTLDSISLEAMVDILQKP  281 (364)
T ss_dssp             TTSGGGCCHHHHHHTTCCHHHHTTCCEEEECCCCCHHHHHHHHHSS
T ss_pred             hhhhccccHHHHhhhhhHHHHHHHhcchhhHhhhhHHHHHHHHHHH
Confidence                         1136788889994 7889999999999988764

>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=99.32  E-value=3.2e-11  Score=111.46  Aligned_cols=150  Identities=11%  Similarity=0.125  Sum_probs=100.7

Q ss_pred             hchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCCC----chhHHHHHHHH
Q psy4285         289 ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDDR----GIGIVRDQIFQ  360 (533)
Q Consensus       289 ~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~~----~~~~~~~~~~~  360 (533)
                      |.++.++++...+.+....|+++.||||+|||++++.+|+.+.....    .+..++.++.+...    ..+...+.++.
T Consensus        22 gRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~liag~~~~g~~e~r~~~  101 (268)
T d1r6bx2          22 GREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKA  101 (268)
T ss_dssp             SCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHH
T ss_pred             ChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHhccCccchhHHHHHHH
Confidence            34444555556666666678999999999999999999998754321    23456777654321    12233333332


Q ss_pred             HHhcccCCCCCcEEEEEeCCCCCCH---------HHHHHHHHHHHhcCCCcEEEEEeC-----CCCCCChhhhccceeee
Q psy4285         361 FASTKTMHKSSYKLIILDEADAMTN---------DAQNALRRIIEKFTTNVRFCIICN-----YLSKIPPAIQSRCTRFR  426 (533)
Q Consensus       361 ~~~~~~~~~~~~~vliiDE~d~l~~---------~~~~~Ll~~le~~~~~~~~I~~~n-----~~~~l~~~l~sR~~~i~  426 (533)
                      ......  ..+..|+||||++.+..         +..+.|...|.  ....++|.+|.     ....-++++.+||..+.
T Consensus       102 i~~~~~--~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~--rg~i~vIgatT~eey~~~~e~d~al~rrF~~I~  177 (268)
T d1r6bx2         102 LLKQLE--QDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTYQEFSNIFEKDRALARRFQKID  177 (268)
T ss_dssp             HHHHHS--SSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS--SCCCEEEEEECHHHHHCCCCCTTSSGGGEEEEE
T ss_pred             HHHHhh--ccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHh--CCCCeEEEeCCHHHHHHHHhhcHHHHhhhcccc
Confidence            222111  23567999999999832         34445555555  35688999885     33467999999999999


Q ss_pred             ecCCCHHHHHHHhhcC
Q psy4285         427 FGPLDSSLIMSRLDYD  442 (533)
Q Consensus       427 ~~~~~~~~~~~~l~~~  442 (533)
                      +.+|+.++...+|...
T Consensus       178 V~Eps~e~t~~IL~~~  193 (268)
T d1r6bx2         178 ITEPSIEETVQIINGL  193 (268)
T ss_dssp             CCCCCHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHh
Confidence            9999999999988765

>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=99.31  E-value=1e-11  Score=114.66  Aligned_cols=169  Identities=14%  Similarity=0.085  Sum_probs=109.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHH----Hhccc-----CCCCCcEEEEEe
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQF----ASTKT-----MHKSSYKLIILD  378 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~-----~~~~~~~vliiD  378 (533)
                      +++++|++|||||++|++++......   ...++.+++...........+.+..    .....     ......++|+||
T Consensus        25 pvlI~Ge~GtGK~~~A~~ih~~s~~~---~~~~~~~~~~~~~~~~~~~~lfg~~~~~~~~~~~~~~g~l~~a~gGtL~l~  101 (247)
T d1ny5a2          25 PVLITGESGVGKEVVARLIHKLSDRS---KEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLD  101 (247)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHSTTT---TSCEEEEETTTSCHHHHHHHHHCBCTTSSTTCCSCBCCHHHHTTTSEEEEE
T ss_pred             CEEEECCCCcCHHHHHHHHHHhcCCc---ccccccchhhhhhhcccHHHhcCcccCCcCCcccccCCHHHccCCCEEEEe
Confidence            59999999999999999998754222   4566677766543332222221110    00000     001335699999


Q ss_pred             CCCCCCHHHHHHHHHHHHhc-----------CCCcEEEEEeCCC-------CCCChhhhccceeeeecCCCHHHHHHHhh
Q psy4285         379 EADAMTNDAQNALRRIIEKF-----------TTNVRFCIICNYL-------SKIPPAIQSRCTRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       379 E~d~l~~~~~~~Ll~~le~~-----------~~~~~~I~~~n~~-------~~l~~~l~sR~~~i~~~~~~~~~~~~~l~  440 (533)
                      |+|.++...|..|++.+++.           ..++++|++|+..       ..+.+.|..|+....+.-|+       |+
T Consensus       102 ~i~~L~~~~Q~~L~~~l~~~~~~~~~~~~~~~~~~RlI~~s~~~l~~l~~~~~f~~~L~~~l~~~~i~lPp-------Lr  174 (247)
T d1ny5a2         102 EIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYRLGVIEIEIPP-------LR  174 (247)
T ss_dssp             SGGGCCHHHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSCHHHHHHTTSSCHHHHHHHTTEEEECCC-------GG
T ss_pred             ChHhCCHHHHHHHHHHHHhCCEEECCCCCceecCeEEEEecCCCHHHHHHcCCCcHHHHhhcCeeeecCCC-------hh
Confidence            99999999999999999752           2357899998754       25788888888666666555       45


Q ss_pred             cCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHH
Q psy4285         441 YDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML  488 (533)
Q Consensus       441 ~~~~~~~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~  488 (533)
                      ..++|+..++..+  +.++....+.....+.......+..+.||++++
T Consensus       175 eR~~Di~~l~~~~--l~~~~~~~~~~~~~ls~~al~~L~~~~WPGNl~  220 (247)
T d1ny5a2         175 ERKEDIIPLANHF--LKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVR  220 (247)
T ss_dssp             GCHHHHHHHHHHH--HHHHHHHTTCCCCEECHHHHHHHHHSCCTTHHH
T ss_pred             hchhhHhhhhhhh--hhhhhhhcCCCCCCCCHHHHHHHHhCCCCCHHH
Confidence            5555666555532  122223345444445566778889999999976

>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=99.31  E-value=8.3e-13  Score=125.13  Aligned_cols=122  Identities=16%  Similarity=0.039  Sum_probs=82.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCC------chhHHHHHHHHHHhcccCCCCCcEEEEEeCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR------GIGIVRDQIFQFASTKTMHKSSYKLIILDEAD  381 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d  381 (533)
                      ++||+||||||||.+|+++|.++..    ..+++.+++++..      ....+++.+....        .++||||||+|
T Consensus       125 ~~l~~G~pG~GKT~la~ala~~~~~----~~~~~~~~~~~~~~~~~G~~e~~~~~~f~~a~--------~~~ilf~DEid  192 (321)
T d1w44a_         125 MVIVTGKGNSGKTPLVHALGEALGG----KDKYATVRFGEPLSGYNTDFNVFVDDIARAML--------QHRVIVIDSLK  192 (321)
T ss_dssp             EEEEECSSSSCHHHHHHHHHHHHHT----TSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHH--------HCSEEEEECCT
T ss_pred             eEEEECCCCccHHHHHHHHHHHhcC----CCCeEEEEhhHhhhcccchHHHHHHHHHHHHh--------hccEEEeehhh
Confidence            4778999999999999999999842    2356667776643      3445555544432        13599999999


Q ss_pred             CCCHHH------------HHHHHHHHHh--cCCCcEEEEEeCCCCCCChhhh------ccc-eeeeecCCCHHHHHHHhh
Q psy4285         382 AMTNDA------------QNALRRIIEK--FTTNVRFCIICNYLSKIPPAIQ------SRC-TRFRFGPLDSSLIMSRLD  440 (533)
Q Consensus       382 ~l~~~~------------~~~Ll~~le~--~~~~~~~I~~~n~~~~l~~~l~------sR~-~~i~~~~~~~~~~~~~l~  440 (533)
                      .+.+..            .+.|+..|+.  ...++.+|.+|| +..+++++-      .|| ..+.+.+|+.+...++|.
T Consensus       193 ~~~~~r~~~~~~~~~~r~v~~lL~e~dg~~~~~~v~viaatN-~~~~~~~i~~~~~r~~Rf~~~v~v~~pd~~~r~~il~  271 (321)
T d1w44a_         193 NVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLN-PTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLT  271 (321)
T ss_dssp             TTC-----------CCHHHHHHHHHHHHHHHHHTCEEEEECC-CCCCCHHHHHHHHHHHHHSCSEEEEECSSTTEEEEEE
T ss_pred             hhccccccCCCCCcchhhhhhhhhhccccccCCCeEEEEeCC-CcccccchhhhhhccCcccceeecCCCChHHHHHHHH
Confidence            996432            3456666652  235688888998 455666553      266 577888888777776665


Q ss_pred             cC
Q psy4285         441 YD  442 (533)
Q Consensus       441 ~~  442 (533)
                      ..
T Consensus       272 ~~  273 (321)
T d1w44a_         272 RT  273 (321)
T ss_dssp             EC
T ss_pred             Hh
Confidence            44

>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=99.31  E-value=3.4e-12  Score=111.44  Aligned_cols=147  Identities=14%  Similarity=0.173  Sum_probs=98.4

Q ss_pred             hhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHcccc----ccCcceEEecCCCC----CchhHHHHHHHHHH
Q psy4285         291 MDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKA----QFNAMVLELNASDD----RGIGIVRDQIFQFA  362 (533)
Q Consensus       291 ~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~----~~~~~~~~~~~~~~----~~~~~~~~~~~~~~  362 (533)
                      ++.++.+...+.+....|++|.||||+|||+++..+|+.+....    ..+..++.++.+..    .......+.++...
T Consensus        28 d~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~rG~~E~rl~~il  107 (195)
T d1jbka_          28 DEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVL  107 (195)
T ss_dssp             HHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHHhccCCccHHHHHHHHHHH
Confidence            33444455556666667899999999999999999999875432    12455777764321    22233333333222


Q ss_pred             hcccCCCCCcEEEEEeCCCCCCHH--------HHHHHHHHHHhcCCCcEEEEEeCCC-----CCCChhhhccceeeeecC
Q psy4285         363 STKTMHKSSYKLIILDEADAMTND--------AQNALRRIIEKFTTNVRFCIICNYL-----SKIPPAIQSRCTRFRFGP  429 (533)
Q Consensus       363 ~~~~~~~~~~~vliiDE~d~l~~~--------~~~~Ll~~le~~~~~~~~I~~~n~~-----~~l~~~l~sR~~~i~~~~  429 (533)
                      .... ...+.-||||||++.+...        +.+.|...|+.  ...++|.+|...     ..-+++|.+||..+.+.+
T Consensus       108 ~e~~-~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~r--g~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~E  184 (195)
T d1jbka_         108 NDLA-KQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR--GELHCVGATTLDEYRQYIEKDAALERRFQKVFVAE  184 (195)
T ss_dssp             HHHH-HSTTTEEEEEETGGGGTT------CCCCHHHHHHHHHT--TSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCC
T ss_pred             HHHh-cCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHhC--CCceEEecCCHHHHHHHHHcCHHHHhcCCEeecCC
Confidence            1110 0124569999999998432        34667778874  558888888532     356999999999999999


Q ss_pred             CCHHHHHHHhh
Q psy4285         430 LDSSLIMSRLD  440 (533)
Q Consensus       430 ~~~~~~~~~l~  440 (533)
                      |+.++...+|+
T Consensus       185 p~~e~t~~IL~  195 (195)
T d1jbka_         185 PSVEDTIAILR  195 (195)
T ss_dssp             CCHHHHHTTCC
T ss_pred             CCHHHHHHHhC
Confidence            99999887763

>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=99.26  E-value=8e-11  Score=110.58  Aligned_cols=132  Identities=20%  Similarity=0.253  Sum_probs=89.6

Q ss_pred             CCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc----------------------hhHHHHHHHHHH
Q psy4285         305 ELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG----------------------IGIVRDQIFQFA  362 (533)
Q Consensus       305 ~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~----------------------~~~~~~~~~~~~  362 (533)
                      .+++++|+||||||||++++++++.+....  ...++.+++.....                      .......+....
T Consensus        42 ~~~~lll~GppGtGKT~l~~~l~~~l~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (276)
T d1fnna2          42 HYPRATLLGRPGTGKTVTLRKLWELYKDKT--TARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHL  119 (276)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHHTTSC--CCEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHH
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHHHhccc--CCcEEEecchhhhhhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHH
Confidence            345699999999999999999999986543  33444444432221                      111111111111


Q ss_pred             hcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh----cCCCcEEEEEeCCC---CCCChhhhccc--eeeeecCCCHH
Q psy4285         363 STKTMHKSSYKLIILDEADAMTNDAQNALRRIIEK----FTTNVRFCIICNYL---SKIPPAIQSRC--TRFRFGPLDSS  433 (533)
Q Consensus       363 ~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~----~~~~~~~I~~~n~~---~~l~~~l~sR~--~~i~~~~~~~~  433 (533)
                      ..    .....+.++|++|.+.....+.+...+..    ......+|++++..   +.+++.+.+|+  ..+.|.+++.+
T Consensus       120 ~~----~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~r~~~~~i~~~~~~~~  195 (276)
T d1fnna2         120 RE----RDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKD  195 (276)
T ss_dssp             HH----TTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHH
T ss_pred             hh----cccccccchhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchhhhhhcchhhhhhhcchhccccchhHH
Confidence            11    13567889999999988777666655432    24556778888764   47889999987  56899999999


Q ss_pred             HHHHHhhcC
Q psy4285         434 LIMSRLDYD  442 (533)
Q Consensus       434 ~~~~~l~~~  442 (533)
                      ++.+++.+.
T Consensus       196 e~~~il~~r  204 (276)
T d1fnna2         196 QIFDILLDR  204 (276)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999998775

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.24  E-value=1.1e-11  Score=111.82  Aligned_cols=126  Identities=18%  Similarity=0.263  Sum_probs=82.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCch--hHHHH-HHHHHHhcccCCCCCcEEEEEeCCCCCC-
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGI--GIVRD-QIFQFASTKTMHKSSYKLIILDEADAMT-  384 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~-~~~~~~~~~~~~~~~~~vliiDE~d~l~-  384 (533)
                      ++++|||||||||++.++++++...   +..++.++..+....  ..+.. ....+....    ...++|+|||+|.+. 
T Consensus        39 l~l~G~~G~GKTHLl~A~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~dll~iDDi~~i~~  111 (213)
T d1l8qa2          39 IFIYGSVGTGKTHLLQAAGNEAKKR---GYRVIYSSADDFAQAMVEHLKKGTINEFRNMY----KSVDLLLLDDVQFLSG  111 (213)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHHHT---TCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHH----HTCSEEEEECGGGGTT
T ss_pred             EEEECCCCCcHHHHHHHHHHHhccC---ccceEEechHHHHHHHHHHHHccchhhHHHHH----hhccchhhhhhhhhcC
Confidence            8999999999999999999998544   334444444321100  00000 000111000    245799999999985 


Q ss_pred             -HHHHHHHHHHHHhc-CCCcEEEEEeCCCC----CCChhhhccc---eeeeecCCCHHHHHHHhhcC
Q psy4285         385 -NDAQNALRRIIEKF-TTNVRFCIICNYLS----KIPPAIQSRC---TRFRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       385 -~~~~~~Ll~~le~~-~~~~~~I~~~n~~~----~l~~~l~sR~---~~i~~~~~~~~~~~~~l~~~  442 (533)
                       .+.+..|+.+++.. ..+..+|+|++.+.    .+.+.|+||+   ..+.+. |++++..+++.+.
T Consensus       112 ~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i~-p~d~~~~~iL~~~  177 (213)
T d1l8qa2         112 KERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIE-LDNKTRFKIIKEK  177 (213)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECC-CCHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHHHhhCceEEEEC-CCcHHHHHHHHHH
Confidence             56677888888753 35677888886543    4678999998   356664 6777777777765

>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=99.19  E-value=1.5e-10  Score=113.12  Aligned_cols=146  Identities=14%  Similarity=0.168  Sum_probs=92.3

Q ss_pred             chhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc----cCcceEEecCCCCCc--------hhHHHHH
Q psy4285         290 SMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ----FNAMVLELNASDDRG--------IGIVRDQ  357 (533)
Q Consensus       290 ~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~----~~~~~~~~~~~~~~~--------~~~~~~~  357 (533)
                      .+.-+..+...+.+....|.+|.||||+|||+++..+|+.+.....    .+..++.++......        ...+...
T Consensus        27 r~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~~e~r~~~i  106 (387)
T d1qvra2          27 RDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAV  106 (387)
T ss_dssp             CHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHHH
T ss_pred             cHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhcccCcchhHHHHHHHH
Confidence            3334444555555566667999999999999999999998754321    234577777654321        1233333


Q ss_pred             HHHHHhcccCCCCCcEEEEEeCCCCCCH--------HHHHHHHHHHHhcCCCcEEEEEeCCC----CCCChhhhccceee
Q psy4285         358 IFQFASTKTMHKSSYKLIILDEADAMTN--------DAQNALRRIIEKFTTNVRFCIICNYL----SKIPPAIQSRCTRF  425 (533)
Q Consensus       358 ~~~~~~~~~~~~~~~~vliiDE~d~l~~--------~~~~~Ll~~le~~~~~~~~I~~~n~~----~~l~~~l~sR~~~i  425 (533)
                      +......     .+..||||||++.+..        ++.+.|...|..  ..+++|.+|...    ..-|++|.+||..+
T Consensus       107 ~~~~~~~-----~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~r--g~~~~I~~tT~~ey~~~e~d~al~rrF~~v  179 (387)
T d1qvra2         107 IQEVVQS-----QGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALAR--GELRLIGATTLDEYREIEKDPALERRFQPV  179 (387)
T ss_dssp             HHHHHTT-----CSSEEEEECCC-------------------HHHHHT--TCCCEEEEECHHHHHHHTTCTTTCSCCCCE
T ss_pred             HHHhccC-----CCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhC--CCcceeeecCHHHHHHhcccHHHHHhcccc
Confidence            3333221     2456899999999832        445667777875  458888888422    13489999999999


Q ss_pred             eecCCCHHHHHHHhhcC
Q psy4285         426 RFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       426 ~~~~~~~~~~~~~l~~~  442 (533)
                      .+.+|+.++...+|..+
T Consensus       180 ~v~ep~~~~~~~il~~~  196 (387)
T d1qvra2         180 YVDEPTVEETISILRGL  196 (387)
T ss_dssp             EECCCCHHHHHHHHHHH
T ss_pred             cCCCCcHHHHHHHHHHH
Confidence            99999999999999877

>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=99.17  E-value=1.1e-10  Score=113.16  Aligned_cols=62  Identities=10%  Similarity=0.091  Sum_probs=49.8

Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhc-------------CCCcEEEEEeCCCC-CCChhhhccce-eeeecCCCH
Q psy4285         371 SYKLIILDEADAMTNDAQNALRRIIEKF-------------TTNVRFCIICNYLS-KIPPAIQSRCT-RFRFGPLDS  432 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~~le~~-------------~~~~~~I~~~n~~~-~l~~~l~sR~~-~i~~~~~~~  432 (533)
                      ..+|+++||++.+.+..+++|++.||+.             +..+.++.++|... .+.+++++||. .+.+..+.+
T Consensus       127 ~~gvl~iDEi~~~~~~~~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~~l~~~llDRf~~~i~v~~~~~  203 (333)
T d1g8pa_         127 NRGYLYIDECNLLEDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLDRFGLSVEVLSPRD  203 (333)
T ss_dssp             TTEEEEETTGGGSCHHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHTTCSEEEECCCCCS
T ss_pred             cccEeecccHHHHHHHHHHHHhhhhcCCeEEecccCceecCCCCEEEEEecCccccccccchhhhhcceeeccCcch
Confidence            3689999999999999999999999964             35567777778654 79999999995 456655543

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.13  E-value=7.2e-11  Score=109.80  Aligned_cols=93  Identities=24%  Similarity=0.402  Sum_probs=79.9

Q ss_pred             EEEEEc-CCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHhCC
Q psy4285           9 RFCIIC-NYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATAHA   87 (533)
Q Consensus         9 ~~il~~-~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~~~~~~   87 (533)
                      .++++| ++....+++|+|||..++|++|+.+++..+|++++.+|++.+++++++.|+..++||+|+|++.||.++.. .
T Consensus       156 ~ii~i~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~~~l~~i~~~s~GDiR~ai~~L~~~~~~-~  234 (253)
T d1sxja2         156 PLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTT-T  234 (253)
T ss_dssp             CEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTTCHHHHHHHHTHHHHH-S
T ss_pred             ccccccccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCCHHHHHHHHHhCCCcHHHHHHHHHHHHHc-C
Confidence            344444 56677899999999999999999999999999999999999999999999999999999999999998774 4


Q ss_pred             CCcchhhHHhhhhhh
Q psy4285          88 DEVNEDTIFTLLVSR  102 (533)
Q Consensus        88 ~~i~~~~i~~~~~~~  102 (533)
                      +.++.+.+.++...+
T Consensus       235 ~~i~~~~~~~~~~~~  249 (253)
T d1sxja2         235 KTINHENINEISKAW  249 (253)
T ss_dssp             SCCCTTHHHHHHHHH
T ss_pred             CCCCHHHHHHHhchh
Confidence            468888776655443

>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=99.04  E-value=1.3e-10  Score=109.75  Aligned_cols=130  Identities=18%  Similarity=0.245  Sum_probs=80.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccc---cCcceEEecCCCCCch----------------------hHHHHHHHHHHh
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQ---FNAMVLELNASDDRGI----------------------GIVRDQIFQFAS  363 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~---~~~~~~~~~~~~~~~~----------------------~~~~~~~~~~~~  363 (533)
                      ++|+||||||||++++++++.+.....   ....+..++.......                      ....+.+.....
T Consensus        49 l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  128 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLY  128 (287)
T ss_dssp             EECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHH
T ss_pred             EEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHH
Confidence            678999999999999999999853221   1122333333222111                      111111111111


Q ss_pred             cccCCCCCcEEEEEeCCCCCC------HHHHHHHHHHHHhc-----CCCcEEEEEeCCCC------CCChhhhccc-eee
Q psy4285         364 TKTMHKSSYKLIILDEADAMT------NDAQNALRRIIEKF-----TTNVRFCIICNYLS------KIPPAIQSRC-TRF  425 (533)
Q Consensus       364 ~~~~~~~~~~vliiDE~d~l~------~~~~~~Ll~~le~~-----~~~~~~I~~~n~~~------~l~~~l~sR~-~~i  425 (533)
                      .    .....++++||+|.+.      .+....+.++++..     .....+|+++|...      ..++.+.+|+ ..+
T Consensus       129 ~----~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i  204 (287)
T d1w5sa2         129 V----ENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKL  204 (287)
T ss_dssp             H----HTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEE
T ss_pred             h----ccCccccceeEEEEeccccccchhHHHHHHHHHHhcchhhcccceeEEeecccHHHHHHHHhhccchhcccceee
Confidence            1    1356788999998763      34555666666542     24566777776554      3456777775 799


Q ss_pred             eecCCCHHHHHHHhhcC
Q psy4285         426 RFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       426 ~~~~~~~~~~~~~l~~~  442 (533)
                      .|.+|+.+++.+++...
T Consensus       205 ~f~~y~~~el~~Il~~r  221 (287)
T d1w5sa2         205 HLPAYKSRELYTILEQR  221 (287)
T ss_dssp             ECCCCCHHHHHHHHHHH
T ss_pred             eccCCcHHHHHHHHhhh
Confidence            99999999999999865

>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=99.04  E-value=4.5e-12  Score=123.31  Aligned_cols=40  Identities=33%  Similarity=0.225  Sum_probs=34.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGI  353 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~  353 (533)
                      .++|+||||||||++|+++|+.+      +..++.+++++.++...
T Consensus       156 ~~~~~g~~~~gk~~~~~~~~~~~------~~~~i~in~s~~rs~~~  195 (362)
T d1svma_         156 YWLFKGPIDSGKTTLAAALLELC------GGKALNVNLPLDRLNFE  195 (362)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH------CCEEECCSSCTTTHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHc------CCCEEEEECcchhhHHH
Confidence            49999999999999999999998      77889999988655433

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.00  E-value=4.3e-11  Score=106.36  Aligned_cols=38  Identities=16%  Similarity=0.145  Sum_probs=35.9

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccceeEEeCCCCH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDS   38 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~~~~~~~~~~   38 (533)
                      |||||++++|||+|+++++|+|||+|||+.++|++|.+
T Consensus       103 LEEPp~~t~fiLit~~~~~ll~TI~SRC~~i~~~~p~~  140 (198)
T d2gnoa2         103 LEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVPKE  140 (198)
T ss_dssp             HHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCHH
T ss_pred             HhCCCCCceeeeccCChhhCHHHHhcceEEEeCCCchH
Confidence            69999999999999999999999999999999987754

>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=98.94  E-value=2.2e-09  Score=98.54  Aligned_cols=98  Identities=12%  Similarity=0.134  Sum_probs=82.2

Q ss_pred             CCCCCCceEEEEEcCCCCcCchhhhccce-eEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Q psy4285           1 IEKFTTNVRFCIICNYLSKITPAIQSRCT-RFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNIL   79 (533)
Q Consensus         1 ~E~~~~~~~~il~~~~~~~i~~~i~SRc~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l   79 (533)
                      +|.+..+++||++||++..+.++++|||. +++|++++.+++...++.++..+++.++++++..+++.++||+|.|+|+|
T Consensus       128 ~~~~~~~~~~I~at~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~~s~gd~R~ai~~l  207 (238)
T d1in4a2         128 IRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLT  207 (238)
T ss_dssp             -----CCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             cccCCCCeEEEEecCCCccccccceeeeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHHhCCCCHHHHHHHH
Confidence            35677889999999999999999999985 57999999999999999999999999999999999999999999999999


Q ss_pred             HHHHH----hCCCCcchhhHHhh
Q psy4285          80 QSAAT----AHADEVNEDTIFTL   98 (533)
Q Consensus        80 ~~~~~----~~~~~i~~~~i~~~   98 (533)
                      +.+..    .....||.+.+.+.
T Consensus       208 ~~~~~~~~~~~~~~it~~~~~~a  230 (238)
T d1in4a2         208 KRVRDMLTVVKADRINTDIVLKT  230 (238)
T ss_dssp             HHHHHHHHHHTCSSBCHHHHHHH
T ss_pred             HHHHHHHHHhcCCccCHHHHHHH
Confidence            97642    23446777766543

>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=98.87  E-value=7.6e-09  Score=94.85  Aligned_cols=95  Identities=9%  Similarity=0.002  Sum_probs=78.7

Q ss_pred             CCceEEEEEc-CCCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHH
Q psy4285           5 TTNVRFCIIC-NYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAA   83 (533)
Q Consensus         5 ~~~~~~il~~-~~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l~~~~   83 (533)
                      ++++.|+++| +++....+++++||..++|.+++.+++.+++.+++.++++.++++.++.+++.++||+|.|+|+|+.+.
T Consensus       133 ~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~~~~~l~~ia~~s~gd~R~a~~~l~~~~  212 (239)
T d1ixsb2         133 LPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVR  212 (239)
T ss_dssp             CCCCEEEEEESCCSSCSCGGGGGCSEEEECCCCCHHHHHHHHHHHHGGGCCCBCHHHHHHHHHHTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEeeccCcccccchhhcccceeeEeeccChhhhhHHHHHHHHHhCCccchHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            3445566555 556677788999999999999999999999999999999999999999999999999999999999875


Q ss_pred             Hh----CCCCcchhhHHhhh
Q psy4285          84 TA----HADEVNEDTIFTLL   99 (533)
Q Consensus        84 ~~----~~~~i~~~~i~~~~   99 (533)
                      ..    ....||.+.+.+.+
T Consensus       213 ~~a~~~~~~~It~~~~~~~l  232 (239)
T d1ixsb2         213 DFAQVAGEEVITRERALEAL  232 (239)
T ss_dssp             HHHTTSCCSCBCHHHHHHHH
T ss_pred             HHHHHhCCCCcCHHHHHHHH
Confidence            42    22348887766544

>d1iqpa1 a.80.1.1 (A:233-327) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.83  E-value=1.9e-08  Score=77.35  Aligned_cols=81  Identities=31%  Similarity=0.429  Sum_probs=71.4

Q ss_pred             HHHHHHHHHH---------HHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHhCCCChHHHHH
Q psy4285         443 DISFFNIIIW---------YIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLS  513 (533)
Q Consensus       443 ~~~~~~ll~~---------~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~  513 (533)
                      |+++.++++.         +..+.++....|+++.|++..+++.+...++|+..+.+++..++.+++||..|+++.+|++
T Consensus         4 P~~I~~il~~~l~~~f~~a~~~l~~l~~~~G~s~~dIl~~l~~~v~~~~~~~~~k~~ll~~la~~d~rL~~G~~e~iQL~   83 (95)
T d1iqpa1           4 PEDIREMMLLALKGNFLKAREKLREILLKQGLSGEDVLVQMHKEVFNLPIEEPKKVLLADKIGEYNFRLVEGANEIIQLE   83 (95)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHGGGSSSCHHHHHHHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             cHHHHHHHHHHHcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHcCCChHHHHH
Confidence            5566666655         6667776667899999999999999998899999999999999999999999999999999


Q ss_pred             HHHHHHHHHH
Q psy4285         514 ALIAAFNSAR  523 (533)
Q Consensus       514 ~~~~~~~~~~  523 (533)
                      +|+++|..+-
T Consensus        84 alla~~~~i~   93 (95)
T d1iqpa1          84 ALLAQFTLIG   93 (95)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999998764

>d1sxjc1 a.80.1.1 (C:239-333) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.66  E-value=1.2e-07  Score=72.73  Aligned_cols=71  Identities=32%  Similarity=0.534  Sum_probs=63.5

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCC-hhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHH
Q psy4285         453 YIKIQEIKIEKGLALTDILTEISLLVHRLEIP-ESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSAR  523 (533)
Q Consensus       453 ~~~l~~l~~~~~~~~~di~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~  523 (533)
                      +..+..+....|+++.|++..+++.+...+++ +..+.+++..++++++||..|+++.+|+.++++++..+.
T Consensus        22 ~~~l~~l~~~~G~s~~dIl~~l~~~i~~~~~~~~~~k~~ll~~la~~e~rL~~G~~e~lQL~~lla~~~~~~   93 (95)
T d1sxjc1          22 HYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSISKGGNDQIQGSAVIGAIKASF   93 (95)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHHTTSCCSSHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHh
Confidence            66666766678999999999999999988876 567899999999999999999999999999999998764

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=98.64  E-value=2.8e-08  Score=96.06  Aligned_cols=102  Identities=18%  Similarity=0.193  Sum_probs=66.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhccc---------------------
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT---------------------  366 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------  366 (533)
                      ..+++||||||||+++..+...+.........-+.+.+++++..+.+.+.+........                     
T Consensus       165 ~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~~~~~~~~~~~~~~~~t~~~ll~  244 (359)
T d1w36d1         165 ISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEDASTLHRLLG  244 (359)
T ss_dssp             EEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCCSCCCCSCSCCCBTTTSCC-
T ss_pred             eEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHHHHHhhcCchhhhhhhhhhhhhHHHHHHh
Confidence            48999999999999987776655332111222345556666666665555433211000                     


Q ss_pred             ------------CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         367 ------------MHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       367 ------------~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                                  ......+++||||+.+++......++..+   +.+.++|++++...
T Consensus       245 ~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~~~l~~~ll~~~---~~~~~lILvGD~~Q  299 (359)
T d1w36d1         245 AQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLIDAL---PDHARVIFLGDRDQ  299 (359)
T ss_dssp             ----------CTTSCCSCSEEEECSGGGCBHHHHHHHHHTC---CTTCEEEEEECTTS
T ss_pred             hhhcchHHHHhhhcccccceeeehhhhccCHHHHHHHHHHh---cCCCEEEEECChhh
Confidence                        01124689999999999988766666655   67789999997654

>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=98.61  E-value=6.1e-07  Score=88.82  Aligned_cols=71  Identities=21%  Similarity=0.273  Sum_probs=49.6

Q ss_pred             cEEEEEeCCCCCC------------HHHHHHHHHHHHhc----------CCCcEEEEEeC----CCCCCChhhhccc-ee
Q psy4285         372 YKLIILDEADAMT------------NDAQNALRRIIEKF----------TTNVRFCIICN----YLSKIPPAIQSRC-TR  424 (533)
Q Consensus       372 ~~vliiDE~d~l~------------~~~~~~Ll~~le~~----------~~~~~~I~~~n----~~~~l~~~l~sR~-~~  424 (533)
                      ..++++||++...            ...+..++..++..          ..+..+|..+.    .++.+.|.+..|+ ..
T Consensus       250 ~~~~~~dei~k~~~~~~~~g~d~~~eg~~~~ll~~~e~~~v~~~~~~~~~~~~l~i~~~~~~~~~~~gliPEliGRlPi~  329 (443)
T d1g41a_         250 NGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLPIR  329 (443)
T ss_dssp             HCEEEEETGGGGSCCSSCSSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHTTCCEE
T ss_pred             cCccccchhhhhhhcccCCCCCcccchhhhhhhhhccccccccccccccccchhhccccchhhcccccchhhhccceEEE
Confidence            3578899988763            12355666776531          23344554442    2346899999999 58


Q ss_pred             eeecCCCHHHHHHHhhcC
Q psy4285         425 FRFGPLDSSLIMSRLDYD  442 (533)
Q Consensus       425 i~~~~~~~~~~~~~l~~~  442 (533)
                      +.+.+++.+++..+|..-
T Consensus       330 v~L~~L~~~dL~rILtEP  347 (443)
T d1g41a_         330 VELTALSAADFERILTEP  347 (443)
T ss_dssp             EECCCCCHHHHHHHHHSS
T ss_pred             EEccCccHHHHHHHHHhh
Confidence            899999999999999876

>d1sxjb1 a.80.1.1 (B:231-322) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.58  E-value=1.2e-07  Score=72.22  Aligned_cols=71  Identities=18%  Similarity=0.298  Sum_probs=62.8

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHhc-CCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHH
Q psy4285         453 YIKIQEIKIEKGLALTDILTEISLLVHRL-EIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSAR  523 (533)
Q Consensus       453 ~~~l~~l~~~~~~~~~di~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~  523 (533)
                      +..+.++....|++..|++..+++.+... .+++..+.+++..++.+++|+..|+++.+||.++++++..+.
T Consensus        19 ~~~l~~~l~~~Gys~~DIi~~l~~~i~~~~~~~e~~k~~il~~la~~~~rl~~G~~e~lQL~~lla~i~~i~   90 (92)
T d1sxjb1          19 IQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQLASMLAKIHKLN   90 (92)
T ss_dssp             HHHHHHTTTTTTCCHHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHh
Confidence            44555544567999999999999999875 788999999999999999999999999999999999998875

>d1sxje1 a.80.1.1 (E:256-354) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.53  E-value=3e-07  Score=69.30  Aligned_cols=77  Identities=16%  Similarity=0.192  Sum_probs=66.9

Q ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHh-cCCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHh
Q psy4285         447 FNIIIWYIKIQEIKIEKGLALTDILTEISLLVHR-LEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARD  524 (533)
Q Consensus       447 ~~ll~~~~~l~~l~~~~~~~~~di~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~~~  524 (533)
                      ..+.+-+..++++ ..+++++.-|+..+...+.. ...++..+.+++.+++.+++|+..|.++.+|||+|+|++|.+.+
T Consensus        22 ~~L~~iR~~lYeL-L~~cIpp~~Ilk~L~~~Ll~~~~~d~~lk~eii~~aa~yE~Rl~~GsK~IfHLEaFvAkfM~~l~   99 (99)
T d1sxje1          22 NSLIECRAVLYDL-LAHCIPANIILKELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD   99 (99)
T ss_dssp             HHHHHHHHHHHHH-HTTTCCHHHHHHHHHHTTTTCTTSCHHHHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHH-HHhcCCHHHHHHHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHhhcC
Confidence            4455568888887 77899999999999887753 46678899999999999999999999999999999999999864

>d1sxjd1 a.80.1.1 (D:263-353) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.28  E-value=1.4e-06  Score=66.04  Aligned_cols=69  Identities=14%  Similarity=0.235  Sum_probs=59.7

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHH-HhcCCChhHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHH
Q psy4285         453 YIKIQEIKIEKGLALTDILTEISLLV-HRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSA  522 (533)
Q Consensus       453 ~~~l~~l~~~~~~~~~di~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~~~l~~~~~~~~~~  522 (533)
                      +..+..+ ...|++..|++.++++.+ ....+|+..+.+++..++++++||..|+++.+||.+++++++.+
T Consensus        22 ~~~i~~l-~~~Gys~~dIl~~l~~~vv~~~~i~~~~k~~i~~~la~~d~rL~~G~~e~lQL~~lla~i~~i   91 (91)
T d1sxjd1          22 KKYVNTF-MKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL   91 (91)
T ss_dssp             HHHHHHH-HHTSCCCTTHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHH-HHcCCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHcC
Confidence            4455555 456999999999999875 44568999999999999999999999999999999999998763

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

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 protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=98.27  E-value=7e-07  Score=76.92  Aligned_cols=116  Identities=20%  Similarity=0.252  Sum_probs=70.1

Q ss_pred             hhhhcccccccCCCc-eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCc
Q psy4285         294 CYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSY  372 (533)
Q Consensus       294 ~~~l~~~~~~~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  372 (533)
                      ...++.++......+ ++|+|||+||||+++.++++.+.+      .++....+.  +         .|.-...   ...
T Consensus        40 l~~l~~~l~~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~G------~vis~~N~~--s---------~F~Lq~l---~~~   99 (205)
T d1tuea_          40 LGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQG------AVISFVNST--S---------HFWLEPL---TDT   99 (205)
T ss_dssp             HHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHTC------EECCCCCSS--S---------CGGGGGG---TTC
T ss_pred             HHHHHHHHcCCCCceEEEEECCCCccHHHHHHHHHHHhCC------EEEeccCCC--C---------Ccccccc---cCC
Confidence            445555664332234 899999999999999999998732      222222111  0         0111111   245


Q ss_pred             EEEEEeCCCCCCHHHHHH-HHHHHHhc-------------CCCcEEEEEeCCCC---CCChhhhccceeeeecC
Q psy4285         373 KLIILDEADAMTNDAQNA-LRRIIEKF-------------TTNVRFCIICNYLS---KIPPAIQSRCTRFRFGP  429 (533)
Q Consensus       373 ~vliiDE~d~l~~~~~~~-Ll~~le~~-------------~~~~~~I~~~n~~~---~l~~~l~sR~~~i~~~~  429 (533)
                      +++++||+......-... +..+++..             -..+.+|+|||..-   .-.+.|.||...+.|..
T Consensus       100 kv~l~dD~t~~~~~~~d~~lK~ll~G~~vsvd~KhK~~vqi~~pPliITsN~~~~~~d~~~~L~sRi~~f~F~~  173 (205)
T d1tuea_         100 KVAMLDDATTTCWTYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLESRITVFEFPN  173 (205)
T ss_dssp             SSEEEEEECHHHHHHHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHTSCEEEECCS
T ss_pred             eEEEEeccccchHHHHHHHHHhccCCCeeeeecccCCcccccCCCEEEEcCCCCCccccchhhhheEEEEECCC
Confidence            799999987765444444 44455531             01245788888543   33467999999888873

>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=98.23  E-value=9.1e-07  Score=76.36  Aligned_cols=25  Identities=32%  Similarity=0.559  Sum_probs=22.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +++++||||+||||+++.++..+..
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGG
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCCC
Confidence            4899999999999999999998743

>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=98.15  E-value=2e-05  Score=72.73  Aligned_cols=72  Identities=14%  Similarity=0.209  Sum_probs=43.4

Q ss_pred             CCcEEEEEeCCCCCCHH----HHHHHHHHHHhcCCCcEEEEEeCCCC---------CCChhh-hccceeeeecCCCHHHH
Q psy4285         370 SSYKLIILDEADAMTND----AQNALRRIIEKFTTNVRFCIICNYLS---------KIPPAI-QSRCTRFRFGPLDSSLI  435 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~----~~~~Ll~~le~~~~~~~~I~~~n~~~---------~l~~~l-~sR~~~i~~~~~~~~~~  435 (533)
                      ....++++||++.+...    ....+...... ......++++....         .....+ .+++..+.+.+++.++.
T Consensus       135 ~~~~~i~id~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~  213 (283)
T d2fnaa2         135 KDNVIIVLDEAQELVKLRGVNLLPALAYAYDN-LKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEA  213 (283)
T ss_dssp             SSCEEEEEETGGGGGGCTTCCCHHHHHHHHHH-CTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHH
T ss_pred             ccccccccchhhhhcccchHHHHHHHHHHHHh-hhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHH
Confidence            35678999999876432    23334444443 34566666653221         112222 23457789999999999


Q ss_pred             HHHhhcC
Q psy4285         436 MSRLDYD  442 (533)
Q Consensus       436 ~~~l~~~  442 (533)
                      .+.+.+.
T Consensus       214 ~~~l~~~  220 (283)
T d2fnaa2         214 IEFLRRG  220 (283)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHhh
Confidence            9888765

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.14  E-value=7e-07  Score=82.86  Aligned_cols=34  Identities=26%  Similarity=0.404  Sum_probs=28.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD  347 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~  347 (533)
                      .+||+||||||||++|+++|.++      +..++.+++++
T Consensus        34 ~ilL~GpPGtGKT~la~~la~~~------~~~~~~i~~d~   67 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSLRSAIFEET------QGNVIVIDNDT   67 (273)
T ss_dssp             EEEEECCTTSCTHHHHHHHHHHT------TTCCEEECTHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh------hcceEEEecHH
Confidence            38999999999999999999998      45566777643

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=98.01  E-value=4.4e-05  Score=70.58  Aligned_cols=124  Identities=13%  Similarity=0.133  Sum_probs=69.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc--cccC-cceEEecCCCCCchhHHHHHHHHHHhc--------------------
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK--AQFN-AMVLELNASDDRGIGIVRDQIFQFAST--------------------  364 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~--~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------  364 (533)
                      .+.++|++|+||||+|+.+.+.....  ..+. ..++.+..  ......+...+......                    
T Consensus        46 ~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~--~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (277)
T d2a5yb3          46 FLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSG--TAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVL  123 (277)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCC--CSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecC--CCCHHHHHHHHHHHHHHhcchhhcCCccchhhhhHHH
Confidence            37899999999999999998764211  1111 12222222  11111111111111000                    


Q ss_pred             -----ccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccceeeeecCCCHHHHHHHh
Q psy4285         365 -----KTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL  439 (533)
Q Consensus       365 -----~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l  439 (533)
                           ......+..++|+|+++..  +..    +.+.  ....++|+||.... +...+.+++..+.+.+++.++..+.+
T Consensus       124 ~~~~~~~~L~~kr~LlVLDDv~~~--~~~----~~~~--~~~srilvTTR~~~-v~~~~~~~~~~~~l~~L~~~ea~~Lf  194 (277)
T d2a5yb3         124 KRMICNALIDRPNTLFVFDDVVQE--ETI----RWAQ--ELRLRCLVTTRDVE-ISNAASQTCEFIEVTSLEIDECYDFL  194 (277)
T ss_dssp             HHHHHHHHTTSTTEEEEEEEECCH--HHH----HHHH--HTTCEEEEEESBGG-GGGGCCSCEEEEECCCCCHHHHHHHH
T ss_pred             HHHHHHHHhccCCeeEecchhhHH--hhh----hhhc--ccCceEEEEeehHH-HHHhcCCCCceEECCCCCHHHHHHHH
Confidence                 0001235679999999853  211    2222  23568888887553 33344456677889999999999988


Q ss_pred             hcC
Q psy4285         440 DYD  442 (533)
Q Consensus       440 ~~~  442 (533)
                      ...
T Consensus       195 ~~~  197 (277)
T d2a5yb3         195 EAY  197 (277)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            765

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=97.84  E-value=2.2e-05  Score=64.21  Aligned_cols=39  Identities=13%  Similarity=0.269  Sum_probs=26.2

Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHh--cCCCcEEEEEe
Q psy4285         370 SSYKLIILDEADAMTNDAQNALRRIIEK--FTTNVRFCIIC  408 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~~Ll~~le~--~~~~~~~I~~~  408 (533)
                      ...+++|+||++.++......+..+++.  +.....+++.|
T Consensus        93 ~~~~~vIiDE~H~~~~~~~~~~~~~l~~~~~~~~~~~l~~T  133 (136)
T d1a1va1          93 GAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLAT  133 (136)
T ss_dssp             CCCSEEEEETTTCCSHHHHHHHHHHHHHTTTTTCSEEEEEE
T ss_pred             hcCCEEEEecccccCHHHHHHHHHHHHHHHHCCCCcEEEEe
Confidence            4578999999999988766666555553  22344555544

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=97.80  E-value=5.8e-06  Score=70.51  Aligned_cols=25  Identities=48%  Similarity=0.658  Sum_probs=23.3

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHH
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .|+++|+||||+||||+|+.+++.+
T Consensus         4 ~~~I~i~G~pGsGKTTia~~La~~l   28 (173)
T d1rkba_           4 LPNILLTGTPGVGKTTLGKELASKS   28 (173)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            4679999999999999999999998

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=97.78  E-value=1e-05  Score=66.22  Aligned_cols=38  Identities=13%  Similarity=0.202  Sum_probs=24.4

Q ss_pred             CCcEEEEEeCCCCCCHHHHH--HHHHHHHhcCCCcEEEEEe
Q psy4285         370 SSYKLIILDEADAMTNDAQN--ALRRIIEKFTTNVRFCIIC  408 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~--~Ll~~le~~~~~~~~I~~~  408 (533)
                      ...+++|+||++.+.+....  .+...+... ++.++|+.|
T Consensus        97 ~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~~-~~~~~l~lT  136 (140)
T d1yksa1          97 VNWEVIIMDEAHFLDPASIAARGWAAHRARA-NESATILMT  136 (140)
T ss_dssp             CCCSEEEETTTTCCSHHHHHHHHHHHHHHHT-TSCEEEEEC
T ss_pred             cceeEEEEccccccChhhHHHHHHHHHHhhC-CCCCEEEEE
Confidence            56889999999999776432  334444433 455666554

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=97.75  E-value=0.00015  Score=60.02  Aligned_cols=22  Identities=36%  Similarity=0.431  Sum_probs=19.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++||||+||||+|+.+++..
T Consensus         5 Iii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           5 ILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHhC
Confidence            7899999999999999987654

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=97.71  E-value=1e-05  Score=68.19  Aligned_cols=23  Identities=35%  Similarity=0.582  Sum_probs=22.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++|+||||+||||+|+.+|+.+
T Consensus         4 ~I~l~G~~GsGKSTvak~La~~L   26 (169)
T d1kaga_           4 NIFLVGPMGAGKSTIGRQLAQQL   26 (169)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999998

>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=97.69  E-value=8.7e-05  Score=67.98  Aligned_cols=93  Identities=19%  Similarity=0.286  Sum_probs=73.0

Q ss_pred             CCceEEEEEcCC---CCcCchhhhccc--eeEEeCCCCHHHHHHHHHHHHhh--cCCCCCHHHHHHHHHh---------c
Q psy4285           5 TTNVRFCIICNY---LSKITPAIQSRC--TRFRFGPLDSSLIMSRLDYVIEQ--EKVNVTPDGKKAIIDL---------S   68 (533)
Q Consensus         5 ~~~~~~il~~~~---~~~i~~~i~SRc--~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~~~~~~---------~   68 (533)
                      ..++.+|.+++.   ...+.|.++|||  ..++|++++.+++.++|++.++.  .+..+++++++.+++.         +
T Consensus       156 ~~~~~~i~~~~~~~~~~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~~~~~~~~~~~~~~l~~ia~~~~~~~~~~~~  235 (276)
T d1fnna2         156 AFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTN  235 (276)
T ss_dssp             SCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTT
T ss_pred             ccceEEeecCCchhhhhhcchhhhhhhcchhccccchhHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhhhhhhhhhc
Confidence            456778888876   457899999998  55899999999999999887654  3345789999988775         4


Q ss_pred             CCCHHHHHHHHHHHHHh----CCCCcchhhHHh
Q psy4285          69 DGDMRKVLNILQSAATA----HADEVNEDTIFT   97 (533)
Q Consensus        69 ~g~~r~a~~~l~~~~~~----~~~~i~~~~i~~   97 (533)
                      .||+|+|+++++.+...    ....|+.++|.+
T Consensus       236 ~G~~R~a~~ll~~a~~~A~~~~~~~I~~edv~~  268 (276)
T d1fnna2         236 RGDARLAIDILYRSAYAAQQNGRKHIAPEDVRK  268 (276)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHH
Confidence            79999999999987543    234588888765

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.68  E-value=1.2e-05  Score=68.36  Aligned_cols=31  Identities=32%  Similarity=0.506  Sum_probs=26.8

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccccccCcceEEe
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLEL  343 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~  343 (533)
                      |+++|.|+||+||||+++.+|+.+      +.+++..
T Consensus         2 p~IvliG~~G~GKSTig~~La~~l------~~~fiD~   32 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGRRLAKAL------GVGLLDT   32 (165)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH------TCCEEEH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHh------CCCeEee
Confidence            678899999999999999999998      6666654

>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=97.68  E-value=7.8e-05  Score=68.77  Aligned_cols=94  Identities=18%  Similarity=0.283  Sum_probs=72.4

Q ss_pred             CceEEEEEcCCCC------cCchhhhcc-ceeEEeCCCCHHHHHHHHHHHHhhc--CCCCCHHHHHHHHHhc------CC
Q psy4285           6 TNVRFCIICNYLS------KITPAIQSR-CTRFRFGPLDSSLIMSRLDYVIEQE--KVNVTPDGKKAIIDLS------DG   70 (533)
Q Consensus         6 ~~~~~il~~~~~~------~i~~~i~SR-c~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~~~~~~~~------~g   70 (533)
                      .+..+|++++...      ..+|.++|| +..+.|++++.+++.++++..++..  ...+++++++.+++.+      .|
T Consensus       172 ~~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~~~~~~~~~g  251 (287)
T d1w5sa2         172 NRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDG  251 (287)
T ss_dssp             CBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCC
T ss_pred             cceeEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHHHhccccCCC
Confidence            4566777776543      445788877 7999999999999999999887653  3357899999999876      69


Q ss_pred             CHHHHHHHHHHHHHh----CCCCcchhhHHhhh
Q psy4285          71 DMRKVLNILQSAATA----HADEVNEDTIFTLL   99 (533)
Q Consensus        71 ~~r~a~~~l~~~~~~----~~~~i~~~~i~~~~   99 (533)
                      |+|+|+++|+.+...    +...|+.+.|.+.+
T Consensus       252 d~R~ai~~l~~a~~~A~~~~~~~It~~~V~~A~  284 (287)
T d1w5sa2         252 SARRAIVALKMACEMAEAMGRDSLSEDLVRKAV  284 (287)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence            999999999887532    33468888876543

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

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: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=97.66  E-value=7.3e-05  Score=68.30  Aligned_cols=132  Identities=13%  Similarity=0.141  Sum_probs=77.1

Q ss_pred             hhhcccccccC-CCc-eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCc
Q psy4285         295 YKINRFIDENE-LPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSY  372 (533)
Q Consensus       295 ~~l~~~~~~~~-~~~-~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  372 (533)
                      ..+..++..+. ..+ ++|+|||+||||+++.++++.+ +.     . ..++.+...           |.-..   -.+.
T Consensus        91 ~~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l-g~-----~-~~~~~~~~~-----------f~l~~---l~~k  149 (267)
T d1u0ja_          91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV-PF-----Y-GCVNWTNEN-----------FPFND---CVDK  149 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS-SC-----E-EECCTTCSS-----------CTTGG---GSSC
T ss_pred             HHHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh-cc-----h-hhccccCCC-----------ccccc---cCCC
Confidence            34455554332 223 8999999999999999999876 21     1 122222110           10000   1356


Q ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHh--------------cCCCcEEEEEeCCCCC----------CChhhhccceeeeec
Q psy4285         373 KLIILDEADAMTNDAQNALRRIIEK--------------FTTNVRFCIICNYLSK----------IPPAIQSRCTRFRFG  428 (533)
Q Consensus       373 ~vliiDE~d~l~~~~~~~Ll~~le~--------------~~~~~~~I~~~n~~~~----------l~~~l~sR~~~i~~~  428 (533)
                      .++++||...-. ...+.+.+++..              ......+|+++|....          -..++.||+..+.|.
T Consensus       150 ~~~~~~e~~~~~-~~~~~~K~l~gGd~i~v~~K~k~~~~~~~~p~li~s~n~i~~~~~~~~~~~~~~~~l~~R~~~~~F~  228 (267)
T d1u0ja_         150 MVIWWEEGKMTA-KVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELT  228 (267)
T ss_dssp             SEEEECSCCEET-TTHHHHHHHHTTCCEEC------CCEECCCCEEEEESSCTTCEEETTEEECTTHHHHHTTEEEEECC
T ss_pred             EEEEEeCCCccc-cHHHHHHHhcCCCceEeecccCCCcEeeCCeEEEEeCCCcccccCCCccccccchHhhhhEEEEECC
Confidence            799999987543 334455555532              1244667777776543          246899999988886


Q ss_pred             CCCHHHHHHHhhcC-HHHHHHHHHH
Q psy4285         429 PLDSSLIMSRLDYD-DISFFNIIIW  452 (533)
Q Consensus       429 ~~~~~~~~~~l~~~-~~~~~~ll~~  452 (533)
                      ..-+.+.    ..+ ++++..++.|
T Consensus       229 ~~~p~~~----~~i~~~e~k~f~~W  249 (267)
T d1u0ja_         229 RRLDHDF----GKVTKQEVKDFFRW  249 (267)
T ss_dssp             SCCCTTS----CCCCHHHHHHHHHH
T ss_pred             CcCCCcc----CCCCHHHHHHHHHH
Confidence            6433221    112 6777777765

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.56  E-value=1.6e-05  Score=68.50  Aligned_cols=23  Identities=17%  Similarity=0.262  Sum_probs=21.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|+|||||||||+|+++++.+
T Consensus         9 ~I~i~G~~GsGKTTla~~La~~~   31 (192)
T d1lw7a2           9 TVAILGGESSGKSVLVNKLAAVF   31 (192)
T ss_dssp             EEEEECCTTSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            49999999999999999999987

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.55  E-value=1.8e-05  Score=68.01  Aligned_cols=26  Identities=42%  Similarity=0.735  Sum_probs=23.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      |++|+|||||||||+++.++..+...
T Consensus         3 ~v~ItG~~GtGKTtl~~~i~~~l~~~   28 (189)
T d2i3ba1           3 HVFLTGPPGVGKTTLIHKASEVLKSS   28 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHC
Confidence            79999999999999999999998543

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.54  E-value=9.5e-05  Score=62.91  Aligned_cols=82  Identities=13%  Similarity=0.085  Sum_probs=46.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeCCCCCCHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQ  388 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~  388 (533)
                      +++.|+||+||||+|+.++...      +  +..++..+..........++....       ...-+|+|... ......
T Consensus        17 iil~G~pGsGKST~a~~l~~~~------~--~~~i~~D~~~~~~~~~~~~~~~l~-------~g~~vIiD~t~-~~~~~R   80 (172)
T d1yj5a2          17 VVAVGFPGAGKSTFIQEHLVSA------G--YVHVNRDTLGSWQRCVSSCQAALR-------QGKRVVIDNTN-PDVPSR   80 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHTGGG------T--CEEEEHHHHCSHHHHHHHHHHHHH-------TTCCEEEESCC-CSHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHhc------C--CEEEchHHHHHHHHHHHHHHHHHH-------CCCCceeeCcC-CCHHHH
Confidence            8999999999999998886543      2  233433333333333333333222       22357778654 445555


Q ss_pred             HHHHHHHHhcCCCcEEEE
Q psy4285         389 NALRRIIEKFTTNVRFCI  406 (533)
Q Consensus       389 ~~Ll~~le~~~~~~~~I~  406 (533)
                      ..+.++..+....+.+|.
T Consensus        81 ~~~~~~a~~~~~~~~~v~   98 (172)
T d1yj5a2          81 ARYIQCAKDAGVPCRCFN   98 (172)
T ss_dssp             HHHHHHHHHHTCCEEEEE
T ss_pred             HHHHHHHHhcCCCEEEEE
Confidence            667776665444444443

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=97.48  E-value=3.2e-05  Score=65.23  Aligned_cols=30  Identities=33%  Similarity=0.533  Sum_probs=26.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEe
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLEL  343 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~  343 (533)
                      +++|.|+||+||||+++.+|+.+      +.+++.+
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l------~~~~~d~   31 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDL------DLVFLDS   31 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH------TCEEEEH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHh------CCCEEec
Confidence            58899999999999999999998      6666654

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=97.48  E-value=2.8e-05  Score=66.24  Aligned_cols=24  Identities=42%  Similarity=0.594  Sum_probs=22.1

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      -+++|+||||+||||+++.+++.+
T Consensus         6 ~~I~i~G~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_           6 INILITGTPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHh
Confidence            359999999999999999999987

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=97.46  E-value=4.4e-05  Score=64.77  Aligned_cols=22  Identities=27%  Similarity=0.522  Sum_probs=21.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|.||||+||||+|+.+++.+
T Consensus         9 ivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           9 YVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            7889999999999999999998

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {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: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=97.45  E-value=4.2e-05  Score=68.64  Aligned_cols=44  Identities=27%  Similarity=0.428  Sum_probs=34.4

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFTTNVRFCIICNYLSK  413 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~  413 (533)
                      ..++++++||. ..++......+++.+.+...+..+|++|.+.+.
T Consensus       156 ~~p~ililDEpts~LD~~~~~~i~~~l~~l~~~~Tvi~itH~l~~  200 (241)
T d2pmka1         156 NNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLST  200 (241)
T ss_dssp             TCCSEEEECCCCSCCCHHHHHHHHHHHHHHHTTSEEEEECSSGGG
T ss_pred             cccchhhhhCCccccCHHHHHHHHHHHHHHhCCCEEEEEECCHHH
Confidence            45789999998 467888888888888775566788888887653

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=97.41  E-value=4.3e-05  Score=65.00  Aligned_cols=29  Identities=28%  Similarity=0.344  Sum_probs=25.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLE  342 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~  342 (533)
                      +++|.|+||+||||+++.+|+.+      +.+++.
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~L------g~~~id   32 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARAL------GYEFVD   32 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHH------TCEEEE
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh------CCCEEe
Confidence            47889999999999999999998      666664

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=97.40  E-value=3.3e-05  Score=65.61  Aligned_cols=22  Identities=41%  Similarity=0.626  Sum_probs=21.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++||||+||||+|+.+++.+
T Consensus         5 I~i~G~~GsGKTTva~~L~~~~   26 (176)
T d2bdta1           5 YIITGPAGVGKSTTCKRLAAQL   26 (176)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7899999999999999999987

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=97.36  E-value=5.5e-05  Score=64.36  Aligned_cols=23  Identities=17%  Similarity=0.330  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      -++|+||||+||||+|+++++.+
T Consensus         5 iI~l~G~~GsGKsTva~~L~~~l   27 (178)
T d1qhxa_           5 MIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            37899999999999999999987

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.36  E-value=4.3e-05  Score=65.28  Aligned_cols=25  Identities=20%  Similarity=0.236  Sum_probs=22.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ++|+|+||+||||+|+++++.+...
T Consensus         9 I~l~G~~GsGKTTia~~La~~L~~~   33 (183)
T d1m8pa3           9 IFLTGYMNSGKDAIARALQVTLNQQ   33 (183)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhhc
Confidence            7899999999999999999998543

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.36  E-value=3.2e-05  Score=65.89  Aligned_cols=31  Identities=32%  Similarity=0.442  Sum_probs=25.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNA  345 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~  345 (533)
                      ++|.||||+||||+|+.+++.+      +.+++.++.
T Consensus         7 I~l~G~~GsGKSTia~~La~~l------g~~~~~~~~   37 (176)
T d1zp6a1           7 LLLSGHPGSGKSTIAEALANLP------GVPKVHFHS   37 (176)
T ss_dssp             EEEEECTTSCHHHHHHHHHTCS------SSCEEEECT
T ss_pred             EEEECCCCCCHHHHHHHHHHHh------CCCEEEecH
Confidence            7899999999999999999876      555665544

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=97.30  E-value=0.00018  Score=62.69  Aligned_cols=23  Identities=30%  Similarity=0.310  Sum_probs=18.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.++.+|+|+|||.++-.++...
T Consensus        25 n~lv~~pTGsGKT~i~~~~~~~~   47 (200)
T d1wp9a1          25 NCLIVLPTGLGKTLIAMMIAEYR   47 (200)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEeCCCCcHHHHHHHHHHHH
Confidence            58899999999998777666543

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.26  E-value=3.2e-05  Score=67.23  Aligned_cols=25  Identities=32%  Similarity=0.416  Sum_probs=22.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ++|+|+||+||||+|+.+++.+...
T Consensus        22 I~L~G~pGSGKTTiAk~La~~l~~~   46 (195)
T d1x6va3          22 VWLTGLSGAGKTTVSMALEEYLVCH   46 (195)
T ss_dssp             EEEESSCHHHHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhc
Confidence            6799999999999999999988543

>d1sxje1 a.80.1.1 (E:256-354) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.26  E-value=0.00013  Score=54.49  Aligned_cols=57  Identities=19%  Similarity=0.310  Sum_probs=44.1

Q ss_pred             hHHHHHhchH---H-HHhh----c----CCChhhHHHHHhhccCccccccCCCChhhHHHHHHHHHhcc
Q psy4285         109 STLDELVSHQ---D-IIST----I----EIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSA  165 (533)
Q Consensus       109 ~~l~~lls~~---~-~l~~----l----~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~~  165 (533)
                      ..+|++++++   + +++.    +    +.+...+..++...+++++|+..|++..+|++||+|+||+.
T Consensus        29 ~~lYeLL~~cIpp~~Ilk~L~~~Ll~~~~~d~~lk~eii~~aa~yE~Rl~~GsK~IfHLEaFvAkfM~~   97 (99)
T d1sxje1          29 AVLYDLLAHCIPANIILKELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCC   97 (99)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHTTTTCTTSCHHHHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHhh
Confidence            3577777654   2 2322    2    24555678888999999999999999999999999999974

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {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: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=97.23  E-value=0.00071  Score=59.02  Aligned_cols=29  Identities=34%  Similarity=0.473  Sum_probs=23.8

Q ss_pred             CCCc-eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         305 ELPH-LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       305 ~~~~-~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ..|+ ++|.||+|+||||++-.+|..+...
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLAa~~~~~   38 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLAKMFVDE   38 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            4456 7899999999999999999887443

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=97.17  E-value=0.00011  Score=63.72  Aligned_cols=26  Identities=27%  Similarity=0.455  Sum_probs=22.6

Q ss_pred             CCCceeEeCCCCCChHHHHHHHHHHH
Q psy4285         305 ELPHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       305 ~~~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++.+++.||||+||||+|+.+|+.+
T Consensus         5 kp~iI~i~G~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_           5 KPNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            33347899999999999999999987

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {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: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=97.17  E-value=0.0012  Score=57.37  Aligned_cols=41  Identities=32%  Similarity=0.421  Sum_probs=28.5

Q ss_pred             cCCCc-eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC
Q psy4285         304 NELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD  347 (533)
Q Consensus       304 ~~~~~-~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~  347 (533)
                      +..|+ ++|.||+|+||||++-.+|..+...   +..+.-++..+
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~~~---g~kV~lit~Dt   47 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFEQQ---GKSVMLAAGDT   47 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHHTT---TCCEEEECCCT
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEEeccc
Confidence            34456 6899999999999999999876433   33444444433

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {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: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=97.16  E-value=0.00011  Score=62.10  Aligned_cols=27  Identities=37%  Similarity=0.437  Sum_probs=24.0

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      |.+.|+|+||+||||+++.+++.+...
T Consensus         3 Pvi~itG~~GSGKTTL~~~L~~~l~~~   29 (170)
T d1np6a_           3 PLLAFAAWSGTGKTTLLKKLIPALCAR   29 (170)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHC
Confidence            568999999999999999999987544

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=97.16  E-value=0.0017  Score=56.35  Aligned_cols=26  Identities=38%  Similarity=0.402  Sum_probs=22.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      .++|.||+|+||||++-.+|..+...
T Consensus         8 vi~lvGptGvGKTTTiaKLA~~~~~~   33 (207)
T d1okkd2           8 VVLVVGVNGVGKTTTIAKLGRYYQNL   33 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            37899999999999999999877533

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.15  E-value=7.9e-05  Score=67.44  Aligned_cols=42  Identities=26%  Similarity=0.468  Sum_probs=32.7

Q ss_pred             CcEEEEEeCC-CCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         371 SYKLIILDEA-DAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       371 ~~~vliiDE~-d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      .++++++||. ..++......+++.+.+...+..+|++|.+..
T Consensus       170 ~p~ililDEpts~LD~~~~~~i~~~l~~l~~~~Tvi~itH~l~  212 (253)
T d3b60a1         170 DSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRLS  212 (253)
T ss_dssp             CCSEEEEETTTSSCCHHHHHHHHHHHHHHHTTSEEEEECSCGG
T ss_pred             CCCEEEeccccccCCHHHHHHHHHHHHHhccCCEEEEEECCHH
Confidence            4789999997 56788888888888876555677888887655

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=97.13  E-value=0.0001  Score=63.72  Aligned_cols=25  Identities=24%  Similarity=0.319  Sum_probs=22.7

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHH
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.+++|.||||+||||+|+.+++.+
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3458999999999999999999988

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.13  E-value=0.00014  Score=62.20  Aligned_cols=23  Identities=30%  Similarity=0.481  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++.||||+||||+|+.+|+.+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37899999999999999999988

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.10  E-value=0.00014  Score=62.37  Aligned_cols=23  Identities=48%  Similarity=0.836  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++|.||||+||||+|+.+++.+
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999999998

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.05  E-value=5.8e-05  Score=68.29  Aligned_cols=43  Identities=21%  Similarity=0.394  Sum_probs=34.1

Q ss_pred             CcEEEEEeCC-CCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCCC
Q psy4285         371 SYKLIILDEA-DAMTNDAQNALRRIIEKFTTNVRFCIICNYLSK  413 (533)
Q Consensus       371 ~~~vliiDE~-d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~~  413 (533)
                      .++++++||. ..++......+++.+.+...+..+|++|.+...
T Consensus       172 ~p~ililDEpts~LD~~t~~~i~~~l~~l~~~~TvI~itH~~~~  215 (255)
T d2hyda1         172 NPPILILDEATSALDLESESIIQEALDVLSKDRTTLIVAHRLST  215 (255)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHHHTTTSEEEEECSSGGG
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHHhcCCEEEEEeCCHHH
Confidence            4789999997 467888888888888876666778888876653

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.04  E-value=0.00048  Score=60.25  Aligned_cols=23  Identities=30%  Similarity=0.401  Sum_probs=19.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.++.+|+|+|||.++-.++..+
T Consensus        87 ~~ll~~~tG~GKT~~a~~~~~~~  109 (206)
T d2fz4a1          87 RGCIVLPTGSGKTHVAMAAINEL  109 (206)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CcEEEeCCCCCceehHHhHHHHh
Confidence            46788999999999998888775

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=97.02  E-value=0.00021  Score=61.74  Aligned_cols=24  Identities=25%  Similarity=0.429  Sum_probs=21.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      -.++|.||||+||||+|+.+|+.+
T Consensus         7 mrIiliG~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSRITKHF   30 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHB
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHH
Confidence            358899999999999999999986

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=97.01  E-value=0.002  Score=55.88  Aligned_cols=98  Identities=21%  Similarity=0.171  Sum_probs=52.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCc--hhHHHHHHHHHHh---cc--c-------------CC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG--IGIVRDQIFQFAS---TK--T-------------MH  368 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~---~~--~-------------~~  368 (533)
                      ++|.||+|+||||++-.+|..+...   +..+.-++....+.  .++++..-+...-   ..  .             ..
T Consensus        13 i~lvGp~GvGKTTTiaKLA~~~~~~---g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~~~~~~~   89 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAAKLALYYKGK---GRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKAR   89 (207)
T ss_dssp             EEEECCTTTTHHHHHHHHHHHHHHT---TCCEEEEECCSSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEEecccccchHHHHHHHHHHhcCCccccccccchhhHHHHHHHHHHh
Confidence            6889999999999999999887543   33333333333221  1122211111000   00  0             00


Q ss_pred             CCCcEEEEEeCCCCCC--HHHHHHHHHHHHhc-CCCcEEEEEeC
Q psy4285         369 KSSYKLIILDEADAMT--NDAQNALRRIIEKF-TTNVRFCIICN  409 (533)
Q Consensus       369 ~~~~~vliiDE~d~l~--~~~~~~Ll~~le~~-~~~~~~I~~~n  409 (533)
                      ....++++||=+.+..  .+....|.++.+.. +..+.+++.++
T Consensus        90 ~~~~d~vlIDTaGr~~~d~~~~~el~~~~~~~~~~~~llv~~a~  133 (207)
T d1ls1a2          90 LEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAM  133 (207)
T ss_dssp             HHTCCEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGG
T ss_pred             hccCcceeecccccchhhhhhHHHHHHHHhhcCCceEEEEeccc
Confidence            1245799999988764  44555555554432 33444555543

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=97.01  E-value=0.00022  Score=61.52  Aligned_cols=23  Identities=35%  Similarity=0.671  Sum_probs=21.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||||+||||.|+.+|+.+
T Consensus         5 riil~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           5 RAVLLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37889999999999999999987

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.00  E-value=0.00022  Score=61.74  Aligned_cols=23  Identities=30%  Similarity=0.473  Sum_probs=21.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+++.||||+||||.|+.+|+.+
T Consensus         3 iI~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47999999999999999999987

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.98  E-value=0.00024  Score=64.03  Aligned_cols=43  Identities=21%  Similarity=0.295  Sum_probs=32.2

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhcCC--CcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKFTT--NVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~~~--~~~~I~~~n~~~  412 (533)
                      ..++|+++||. ..++......+.+.+.+...  +..+|++|.+..
T Consensus       168 ~~p~ililDEpTs~LD~~~~~~i~~~l~~l~~~~~~Tvi~itH~l~  213 (251)
T d1jj7a_         168 RKPCVLILDDATSALDANSQLQVEQLLYESPERYSRSVLLITQHLS  213 (251)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHTCGGGGGCEEEEECSCHH
T ss_pred             cCCcEEEecCcCcccChhhHHHHHHHHHHHhhhcCCEEEEEeCCHH
Confidence            45789999997 57788888888888875432  567888887643

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.97  E-value=0.00023  Score=61.81  Aligned_cols=24  Identities=25%  Similarity=0.443  Sum_probs=21.8

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      +-++|.||||+||||+|+.+++.+
T Consensus         9 ~iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_           9 SVIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            348899999999999999999987

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.95  E-value=0.00028  Score=60.37  Aligned_cols=22  Identities=32%  Similarity=0.699  Sum_probs=20.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|.||||+||||+|+.+|+.+
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            7888999999999999999987

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=96.93  E-value=0.00096  Score=58.06  Aligned_cols=27  Identities=33%  Similarity=0.410  Sum_probs=18.7

Q ss_pred             CCCc-eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         305 ELPH-LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       305 ~~~~-~ll~GppGtGKT~la~~la~~l~  331 (533)
                      ..|+ ++|.||+|+||||++-.+|..+.
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~~~~   37 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAYFYK   37 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3456 78899999999999999998764

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=96.92  E-value=0.0003  Score=60.23  Aligned_cols=22  Identities=32%  Similarity=0.514  Sum_probs=21.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|.||||+||||+|+.+|+.+
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7899999999999999999998

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.82  E-value=0.0015  Score=58.26  Aligned_cols=25  Identities=28%  Similarity=0.388  Sum_probs=22.4

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ++++||||+|||+++..++......
T Consensus        29 ~li~G~pGsGKT~l~~qia~~~~~~   53 (242)
T d1tf7a2          29 ILATGATGTGKTLLVSRFVENACAN   53 (242)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHTT
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            7999999999999999999887544

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=96.82  E-value=0.00044  Score=60.96  Aligned_cols=43  Identities=19%  Similarity=0.333  Sum_probs=31.3

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc--CCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF--TTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~--~~~~~~I~~~n~~~  412 (533)
                      ..+++|++||- ..+++.....+.+.+.+.  ..+..+|++|....
T Consensus       144 ~~P~iLllDEPts~LD~~~~~~i~~~l~~l~~~~g~tii~vtHd~~  189 (229)
T d3d31a2         144 TNPKILLLDEPLSALDPRTQENAREMLSVLHKKNKLTVLHITHDQT  189 (229)
T ss_dssp             SCCSEEEEESSSTTSCHHHHHHHHHHHHHHHHHTTCEEEEEESCHH
T ss_pred             ccCCceeecCCCcCCCHHHHHHHHHHHHHHHhcCCcEEEEEcCCHH
Confidence            46899999996 577888887777776542  23577888887554

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.82  E-value=0.00031  Score=61.52  Aligned_cols=23  Identities=30%  Similarity=0.394  Sum_probs=21.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      ++++|.||+||||+|+.+++.+.
T Consensus         5 i~l~GlpgsGKSTla~~L~~~l~   27 (213)
T d1bifa1           5 IVMVGLPARGKTYISKKLTRYLN   27 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH
Confidence            78999999999999999998874

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=96.81  E-value=0.00036  Score=60.45  Aligned_cols=24  Identities=29%  Similarity=0.450  Sum_probs=21.8

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.++|.||||+||||.|+.+++.+
T Consensus         9 ~iI~l~G~pGSGKsT~a~~La~~~   32 (194)
T d3adka_           9 KIIFVVGGPGSGKGTQCEKIVQKY   32 (194)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            348899999999999999999986

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.81  E-value=0.00035  Score=59.60  Aligned_cols=23  Identities=26%  Similarity=0.411  Sum_probs=21.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++|.||||+||||.|+.+++.+
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999987

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.81  E-value=0.0003  Score=60.09  Aligned_cols=25  Identities=28%  Similarity=0.444  Sum_probs=22.4

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ++|.|+||+||||+++.+++.+...
T Consensus         4 I~i~G~~GsGKsT~~~~L~~~l~~~   28 (190)
T d1khta_           4 VVVTGVPGVGSTTSSQLAMDNLRKE   28 (190)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHc
Confidence            7899999999999999999988443

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal 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: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.81  E-value=0.0014  Score=57.90  Aligned_cols=43  Identities=12%  Similarity=0.180  Sum_probs=29.6

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc--CCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF--TTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~--~~~~~~I~~~n~~~  412 (533)
                      ..+++|++||- ..+++.....+...+.+.  ..+..+|++|....
T Consensus       147 ~~P~illlDEPts~LD~~~~~~i~~~l~~l~~~~g~tii~vTHd~~  192 (232)
T d2awna2         147 AEPSVFLLDEPLSNLDAALRVQMRIEISRLHKRLGRTMIYVTHDQV  192 (232)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHSCCEEEEEESCHH
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            35789999996 567887777666665432  24577888886543

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=96.80  E-value=0.0034  Score=55.33  Aligned_cols=46  Identities=15%  Similarity=0.054  Sum_probs=33.8

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ..|......+...+....+.+.|++|.+|+|||.++-..+......
T Consensus        58 ~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~  103 (233)
T d2eyqa3          58 PDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN  103 (233)
T ss_dssp             HHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHc
Confidence            3455556666666666665568999999999999998887765443

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=96.79  E-value=0.00045  Score=61.01  Aligned_cols=24  Identities=42%  Similarity=0.580  Sum_probs=21.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      |-+.+.||||+||+|.|+.+++.+
T Consensus         4 piI~I~GppGSGKgT~ak~La~~~   27 (225)
T d1ckea_           4 PVITIDGPSGAGKGTLCKAMAEAL   27 (225)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            457888999999999999999998

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=96.76  E-value=0.0003  Score=61.65  Aligned_cols=25  Identities=20%  Similarity=0.351  Sum_probs=22.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ++|+|.||+||||+|+.+++.+...
T Consensus        27 IwltGlsGsGKTTia~~L~~~l~~~   51 (208)
T d1m7ga_          27 IWLTGLSASGKSTLAVELEHQLVRD   51 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHh
Confidence            8999999999999999999887543

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=96.75  E-value=0.00027  Score=62.79  Aligned_cols=43  Identities=16%  Similarity=0.241  Sum_probs=31.2

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc--CCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF--TTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~--~~~~~~I~~~n~~~  412 (533)
                      ..+++|++||- ..+++.....+.+.+.+.  ..+..+|++|....
T Consensus       153 ~~P~iLllDEPts~LD~~~~~~i~~ll~~l~~~~g~tii~vTHd~~  198 (239)
T d1v43a3         153 VEPDVLLMDEPLSNLDAKLRVAMRAEIKKLQQKLKVTTIYVTHDQV  198 (239)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHTCEEEEEESCHH
T ss_pred             cCCCceeecCCcccCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCHH
Confidence            45889999996 577888777777776553  23677888887544

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=96.62  E-value=0.00066  Score=59.97  Aligned_cols=22  Identities=27%  Similarity=0.498  Sum_probs=20.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.+.||||+||||.|+.||+.+
T Consensus         6 IaIdGp~GsGKgT~ak~La~~l   27 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAKDF   27 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4567999999999999999998

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.59  E-value=0.0035  Score=55.16  Aligned_cols=42  Identities=10%  Similarity=0.319  Sum_probs=31.7

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc--CCCcEEEEEeCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF--TTNVRFCIICNYL  411 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~--~~~~~~I~~~n~~  411 (533)
                      ..+++|++||- ..+++..+..+++.+.+.  ..++.+|++|...
T Consensus       162 ~~P~lLllDEPTs~LD~~~~~~i~~~l~~l~~~~g~tii~vTHd~  206 (230)
T d1l2ta_         162 NNPPIILADQPTGALDSKTGEKIMQLLKKLNEEDGKTVVVVTHDI  206 (230)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHTTCCEEEEECSCH
T ss_pred             cCCCEEEecCCccccCHHHHHHHHHHHHHHHHhhCCEEEEECCCH
Confidence            45789999996 567888888887777653  3467888888754

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.59  E-value=0.0004  Score=60.55  Aligned_cols=39  Identities=10%  Similarity=0.252  Sum_probs=26.5

Q ss_pred             CcEEEEEeCCCCCCHH----HHHHHHHHHHhcCCCcEEEEEeC
Q psy4285         371 SYKLIILDEADAMTND----AQNALRRIIEKFTTNVRFCIICN  409 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~----~~~~Ll~~le~~~~~~~~I~~~n  409 (533)
                      ..+++|+||+|.+..+    ....++..+.+.++++++|+.|-
T Consensus       138 ~~~~ii~DE~h~~~~~~r~~~~~~~l~~i~~~~~~~~~l~lSA  180 (202)
T d2p6ra3         138 AVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSA  180 (202)
T ss_dssp             GCCEEEETTGGGGGCTTTHHHHHHHHHHHHHHCTTCEEEEEEC
T ss_pred             hhhhccccHHHHhcccccchHHHHHHHHHHhcCCCCcEEEEcC
Confidence            5679999999988532    23446666666566777776554

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=96.58  E-value=0.0011  Score=62.08  Aligned_cols=91  Identities=19%  Similarity=0.133  Sum_probs=52.8

Q ss_pred             hhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccc-------------cCcceEEecCCCCCchhHHHHHHHH
Q psy4285         294 CYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ-------------FNAMVLELNASDDRGIGIVRDQIFQ  360 (533)
Q Consensus       294 ~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~  360 (533)
                      ...+..++..+.  +++++||+|+||||+.++++..+-....             ....+..+...   +.-.+.+.++.
T Consensus       156 ~~~l~~~v~~~~--nili~G~tgSGKTT~l~al~~~i~~~~rivtiEd~~El~l~~~~~~~~~~~~---~~~~~~~ll~~  230 (323)
T d1g6oa_         156 ISAIKDGIAIGK--NVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFG---GNITSADCLKS  230 (323)
T ss_dssp             HHHHHHHHHHTC--CEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCCCCSSCSSEEEEECB---TTBCHHHHHHH
T ss_pred             HHHHHHHHHhCC--CEEEEeeccccchHHHHHHhhhcccccceeeccchhhhhcccccccceeccc---cchhHHHHHHH
Confidence            344555555554  7999999999999999999876522110             00111111111   11133444444


Q ss_pred             HHhcccCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhc
Q psy4285         361 FASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF  398 (533)
Q Consensus       361 ~~~~~~~~~~~~~vliiDE~d~l~~~~~~~Ll~~le~~  398 (533)
                      ...      ..++.+++.|+-.  .++. .+++.+...
T Consensus       231 ~lR------~~pd~iivgEiR~--~ea~-~~l~a~~tG  259 (323)
T d1g6oa_         231 CLR------MRPDRIILGELRS--SEAY-DFYNVLCSG  259 (323)
T ss_dssp             HTT------SCCSEEEESCCCS--THHH-HHHHHHHTT
T ss_pred             Hhc------cCCCcccCCccCc--hhHH-HHHHHHHhc
Confidence            322      3578999999974  4554 467788654

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=96.57  E-value=0.00093  Score=59.70  Aligned_cols=23  Identities=35%  Similarity=0.509  Sum_probs=20.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+-+.||+|+||||+++.++..+
T Consensus        30 ~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          30 IIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhh
Confidence            47899999999999999998754

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=96.52  E-value=0.0039  Score=55.14  Aligned_cols=43  Identities=12%  Similarity=0.204  Sum_probs=31.2

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc--CCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF--TTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~--~~~~~~I~~~n~~~  412 (533)
                      ..+++|++||- ..+++.....+.+.+.+.  ..+..+|++|...+
T Consensus       156 ~~P~iLllDEPt~~LD~~~~~~i~~~l~~l~~~~g~tvi~vTHd~~  201 (240)
T d1g2912         156 RKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIYVTHDQV  201 (240)
T ss_dssp             TCCSEEEEECTTTTSCHHHHHHHHHHHHHHHHHHTCEEEEEESCHH
T ss_pred             cCCCEEEecCCCcccCHHHHHHHHHHHHHHHhccCCEEEEEcCCHH
Confidence            45889999996 567888887777777542  22577888887543

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=96.50  E-value=0.00056  Score=58.61  Aligned_cols=25  Identities=28%  Similarity=0.413  Sum_probs=22.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ++|.|+||+||||+++.+++.+...
T Consensus         4 ivi~G~~GsGKTT~~~~La~~L~~~   28 (194)
T d1nksa_           4 GIVTGIPGVGKSTVLAKVKEILDNQ   28 (194)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHc
Confidence            6789999999999999999988443

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.50  E-value=0.00036  Score=61.91  Aligned_cols=43  Identities=19%  Similarity=0.216  Sum_probs=30.3

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc--CCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF--TTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~--~~~~~~I~~~n~~~  412 (533)
                      ..+++|++||- ..+++..+..+.+.+.+.  ..+..+|++|....
T Consensus       143 ~~P~illlDEPts~LD~~~~~~i~~~i~~l~~~~g~tvi~vtHd~~  188 (240)
T d2onka1         143 IQPRLLLLDEPLSAVDLKTKGVLMEELRFVQREFDVPILHVTHDLI  188 (240)
T ss_dssp             TCCSSBEEESTTSSCCHHHHHHHHHHHHHHHHHHTCCEEEEESCHH
T ss_pred             ccCCceEecCccccCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCHH
Confidence            46889999996 567888887777776543  22466777776543

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.48  E-value=0.0037  Score=56.95  Aligned_cols=42  Identities=12%  Similarity=0.147  Sum_probs=29.4

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHH-HHhcCCCcEEEEEeCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRI-IEKFTTNVRFCIICNYL  411 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~-le~~~~~~~~I~~~n~~  411 (533)
                      ..++++++||. ..++......+++. +.....+..+|++|.+.
T Consensus       175 ~~p~illLDEPts~LD~~~~~~i~~~~~~~~~~~~tvi~itH~~  218 (281)
T d1r0wa_         175 KDADLYLLDSPFGYLDVFTEEQVFESCVCKLMANKTRILVTSKM  218 (281)
T ss_dssp             SCCSEEEEESCCCSSCHHHHHHHHHHCCCCCTTTSEEEEECSCH
T ss_pred             hCccchhhcCccccCCHHHHHHHHHHHHHHhhCCCEEEEEechH
Confidence            34789999997 46777777777764 44444556778888654

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=96.48  E-value=0.0049  Score=59.41  Aligned_cols=66  Identities=20%  Similarity=0.284  Sum_probs=41.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC-CC------------CchhHHHHHHHHHHhcccCCCCCcEE
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS-DD------------RGIGIVRDQIFQFASTKTMHKSSYKL  374 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~-~~------------~~~~~~~~~~~~~~~~~~~~~~~~~v  374 (533)
                      -+|++||+|+||||+..++...+....   ..++.+..+ +.            .........++....      ..+++
T Consensus       160 liLvtGpTGSGKSTTl~~~l~~~~~~~---~~i~tiEdPiE~~~~~~~q~~v~~~~~~~~~~~l~~~lR------~dPDv  230 (401)
T d1p9ra_         160 IILVTGPTGSGKSTTLYAGLQELNSSE---RNILTVEDPIEFDIDGIGQTQVNPRVDMTFARGLRAILR------QDPDV  230 (401)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHCCTT---SCEEEEESSCCSCCSSSEEEECBGGGTBCHHHHHHHHGG------GCCSE
T ss_pred             eEEEEcCCCCCccHHHHHHhhhhcCCC---ceEEEeccCcccccCCCCeeeecCCcCCCHHHHHHHHHh------hcCCE
Confidence            389999999999999999999885432   233333321 10            011123444444332      35789


Q ss_pred             EEEeCCCC
Q psy4285         375 IILDEADA  382 (533)
Q Consensus       375 liiDE~d~  382 (533)
                      ++|.|+-.
T Consensus       231 i~igEiRd  238 (401)
T d1p9ra_         231 VMVGEIRD  238 (401)
T ss_dssp             EEESCCCS
T ss_pred             EEecCcCC
Confidence            99999965

>d1sxjd1 a.80.1.1 (D:263-353) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.46  E-value=0.0046  Score=45.77  Aligned_cols=87  Identities=18%  Similarity=0.289  Sum_probs=59.0

Q ss_pred             CHHHHHHHH-HhcCCCHHHHHHHHHHHHHhCCCCcchhhHHhhhhhhccccchhHHHHHhchHHHHhhcCCChhhHHHHH
Q psy4285          57 TPDGKKAII-DLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESMLVDLV  135 (533)
Q Consensus        57 ~~~~~~~~~-~~~~g~~r~a~~~l~~~~~~~~~~i~~~~i~~~~~~~~ek~~~~~l~~lls~~~~l~~l~~~~~~~~~~~  135 (533)
                      |++.++.+. ..-+||...|.+.++.+... +  .+...|.            ..+     +.+++....+++..+..++
T Consensus         2 P~~~i~~il~~~~~~~f~~a~~~i~~l~~~-G--ys~~dIl------------~~l-----~~~vv~~~~i~~~~k~~i~   61 (91)
T d1sxjd1           2 PHDILIEIVEKVKSGDFDEIKKYVNTFMKS-G--WSAASVV------------NQL-----HEYYITNDNFDTNFKNQIS   61 (91)
T ss_dssp             CSHHHHHHHHHHHSCCHHHHHHHHHHHHHT-S--CCCTTHH------------HHH-----HHHHHHCSSSCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHc-C--CCHHHHH------------HHH-----HHHHHhcCCCCHHHHHHHH
Confidence            444444433 33458888888888876542 2  2222211            011     1223445567888889999


Q ss_pred             hhccCccccccCCCChhhHHHHHHHHHh
Q psy4285         136 LKMSDIEYRLAAGTSEKIQLSALIAAFN  163 (533)
Q Consensus       136 ~~~~~~~~~~~~G~~~~~~l~~~~~~~~  163 (533)
                      ..++++++|+..|+++..|+.++++.+.
T Consensus        62 ~~la~~d~rL~~G~~e~lQL~~lla~i~   89 (91)
T d1sxjd1          62 WLLFTTDSRLNNGTNEHIQLLNLLVKIS   89 (91)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHH
Confidence            9999999999999999999999999875

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

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: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=96.42  E-value=0.005  Score=50.38  Aligned_cols=52  Identities=12%  Similarity=0.059  Sum_probs=36.6

Q ss_pred             CCCcEEEEEeCCCCCCH---HHHHHHHHHHHhcCCCcEEEEEeCCCCCCChhhhccce
Q psy4285         369 KSSYKLIILDEADAMTN---DAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCT  423 (533)
Q Consensus       369 ~~~~~vliiDE~d~l~~---~~~~~Ll~~le~~~~~~~~I~~~n~~~~l~~~l~sR~~  423 (533)
                      ...+++||+||+...-.   =..+.++.+++..|...-+|+|++...   +.|..+.+
T Consensus        92 ~~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~p---~~L~e~AD  146 (157)
T d1g5ta_          92 DPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCH---RDILDLAD  146 (157)
T ss_dssp             CTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCC---HHHHHHCS
T ss_pred             cCccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCCC---HHHHHhcc
Confidence            35689999999843211   012467788888899999999998654   56666554

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=96.32  E-value=0.009  Score=53.30  Aligned_cols=92  Identities=13%  Similarity=0.095  Sum_probs=64.0

Q ss_pred             CCceEEEEEcCCCCcCchhhh--ccc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCC----CHHHHHH
Q psy4285           5 TTNVRFCIICNYLSKITPAIQ--SRC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDG----DMRKVLN   77 (533)
Q Consensus         5 ~~~~~~il~~~~~~~i~~~i~--SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g----~~r~a~~   77 (533)
                      ..++.+|.+||.+..+-|+++  +|+ ..+.|++|+.++..++++..+.+.... .+..+..+++.+.|    |++.+++
T Consensus       145 ~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~lv~  223 (247)
T d1ixza_         145 DTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLA-EDVDLALLAKRTPGFVGADLENLLN  223 (247)
T ss_dssp             TCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBC-TTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CCCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCc-cccCHHHHHHHCCCCCHHHHHHHHH
Confidence            456778889999999999997  577 699999999999999998877654433 33347788888877    4544443


Q ss_pred             HHHHHHHh-CCCCcchhhHHh
Q psy4285          78 ILQSAATA-HADEVNEDTIFT   97 (533)
Q Consensus        78 ~l~~~~~~-~~~~i~~~~i~~   97 (533)
                      .--..+.. ....|+.+++.+
T Consensus       224 ~A~l~a~~~~~~~i~~~d~~~  244 (247)
T d1ixza_         224 EAALLAAREGRRKITMKDLEE  244 (247)
T ss_dssp             HHHHHHHHTTCSSBCHHHHHH
T ss_pred             HHHHHHHHcCCCCcCHHHHHH
Confidence            22122222 234577777654

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.31  E-value=0.0039  Score=55.81  Aligned_cols=24  Identities=21%  Similarity=0.048  Sum_probs=21.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      ++++||||+|||+++..++.....
T Consensus        40 ~~i~G~~GsGKT~lalq~~~~~~~   63 (258)
T d1v5wa_          40 TEAFGEFRTGKTQLSHTLCVTAQL   63 (258)
T ss_dssp             EEEECCTTCTHHHHHHHHHHHTTS
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHh
Confidence            799999999999999999987644

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.24  E-value=0.0011  Score=57.01  Aligned_cols=24  Identities=29%  Similarity=0.221  Sum_probs=21.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +-+.||+|+||||+|+.++..+..
T Consensus        25 IgI~G~~GSGKSTla~~L~~~l~~   48 (198)
T d1rz3a_          25 LGIDGLSRSGKTTLANQLSQTLRE   48 (198)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcc
Confidence            459999999999999999987743

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {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: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.18  E-value=0.0019  Score=53.92  Aligned_cols=21  Identities=19%  Similarity=0.379  Sum_probs=18.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|+||+|||+++..+...
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988753

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.16  E-value=0.0018  Score=57.69  Aligned_cols=23  Identities=35%  Similarity=0.340  Sum_probs=18.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++++.+|+|+|||+++-..+...
T Consensus        60 ~~~i~apTGsGKT~~~~~~~~~~   82 (237)
T d1gkub1          60 SFAATAPTGVGKTSFGLAMSLFL   82 (237)
T ss_dssp             CEECCCCBTSCSHHHHHHHHHHH
T ss_pred             CEEEEecCCChHHHHHHHHHHHH
Confidence            68999999999998776655444

>d1iqpa1 a.80.1.1 (A:233-327) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.12  E-value=0.006  Score=45.53  Aligned_cols=45  Identities=36%  Similarity=0.476  Sum_probs=40.0

Q ss_pred             HHhhcCCChhhHHHHHhhccCccccccCCCChhhHHHHHHHHHhc
Q psy4285         120 IISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNS  164 (533)
Q Consensus       120 ~l~~l~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~  164 (533)
                      .+...++++..+..++..++++++|+..|+++.+|+.++++.|..
T Consensus        47 ~v~~~~~~~~~k~~ll~~la~~d~rL~~G~~e~iQL~alla~~~~   91 (95)
T d1iqpa1          47 EVFNLPIEEPKKVLLADKIGEYNFRLVEGANEIIQLEALLAQFTL   91 (95)
T ss_dssp             HGGGSSSCHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHhhcCCCHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH
Confidence            344667888899999999999999999999999999999999864

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=96.07  E-value=0.022  Score=52.16  Aligned_cols=18  Identities=39%  Similarity=0.608  Sum_probs=15.0

Q ss_pred             CCcEEEEEeCCCCCCHHH
Q psy4285         370 SSYKLIILDEADAMTNDA  387 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~  387 (533)
                      ...+++|+||+|.+..+.
T Consensus        99 ~~~~~vViDE~H~~~~~~  116 (305)
T d2bmfa2          99 PNYNLIIMDEAHFTDPAS  116 (305)
T ss_dssp             CCCSEEEEESTTCCSHHH
T ss_pred             cceeEEEeeeeeecchhh
Confidence            457899999999998754

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=96.05  E-value=0.015  Score=47.43  Aligned_cols=22  Identities=27%  Similarity=0.314  Sum_probs=19.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++.|+||+||||+++.+...-
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            7899999999999999987653

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.03  E-value=0.0074  Score=52.37  Aligned_cols=40  Identities=25%  Similarity=0.391  Sum_probs=29.1

Q ss_pred             CCcEEEEEeCCCCC-CHHHHHHHHHHHHhcCCCcEEEEEeC
Q psy4285         370 SSYKLIILDEADAM-TNDAQNALRRIIEKFTTNVRFCIICN  409 (533)
Q Consensus       370 ~~~~vliiDE~d~l-~~~~~~~Ll~~le~~~~~~~~I~~~n  409 (533)
                      ..-+.+++||+|.+ +......+.++++..+.+..+++.|.
T Consensus       144 ~~l~~lViDEad~l~~~~~~~~i~~I~~~~~~~~Q~i~~SA  184 (208)
T d1hv8a1         144 KNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSA  184 (208)
T ss_dssp             TSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECS
T ss_pred             ccCcEEEEEChHHhhcCCChHHHHHHHHhCCCCCeEEEEEc
Confidence            55679999999975 33344567777777677788887764

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.03  E-value=0.016  Score=50.23  Aligned_cols=41  Identities=22%  Similarity=0.389  Sum_probs=29.8

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ...+.+++||+|.+... ..+.+.++++..+.+..+++.|..
T Consensus       150 ~~l~~lVlDEad~lld~~f~~~v~~I~~~~~~~~Q~vl~SAT  191 (212)
T d1qdea_         150 DKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSAT  191 (212)
T ss_dssp             TTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESS
T ss_pred             CcceEEeehhhhhhcccchHHHHHHHHHhCCCCCeEEEEEee
Confidence            46789999999988543 456677777776777777776643

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.00  E-value=0.0063  Score=53.26  Aligned_cols=43  Identities=23%  Similarity=0.447  Sum_probs=31.0

Q ss_pred             CCCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCCC
Q psy4285         369 KSSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNYL  411 (533)
Q Consensus       369 ~~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~~  411 (533)
                      ....+.+|+||+|.+... ..+.+.++++..+.+..+++.|...
T Consensus       153 ~~~l~~lVlDEaD~ll~~~f~~~~~~Il~~~~~~~Q~il~SAT~  196 (218)
T d2g9na1         153 PKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATM  196 (218)
T ss_dssp             STTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESCC
T ss_pred             cccceEEEeeecchhhcCchHHHHHHHHHhCCCCCeEEEEEecC
Confidence            356789999999998543 3556666677667778888877643

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {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: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=96.00  E-value=0.015  Score=48.78  Aligned_cols=102  Identities=12%  Similarity=0.136  Sum_probs=51.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc---ccc-------------cCcceEEecCCCC-CchhHHHHHHHH-HHhcccCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT---KAQ-------------FNAMVLELNASDD-RGIGIVRDQIFQ-FASTKTMHK  369 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~---~~~-------------~~~~~~~~~~~~~-~~~~~~~~~~~~-~~~~~~~~~  369 (533)
                      .+.|.|.||+||||+++++...-..   ...             .+..+..++.+.. .......+.... .....  ..
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~~~~~~~~~~~~tt~~~~~~~~~~~~~~~~~~DtpG~~~~~~~~~~~~~~~~~~~~--~~   84 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLGVKVAPISPRPQTTRKRLRGILTEGRRQIVFVDTPGLHKPMDALGEFMDQEVYEAL--AD   84 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSCCSCCCSSSCCCCSCEEEEEEETTEEEEEEECCCCCCCCSHHHHHHHHHHHHHT--SS
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCceeecccCCcccccccceeeeeeeeeeecccccccccccccchhccccccccc--cc
Confidence            4899999999999999998753110   000             0011122222211 111111111111 11111  12


Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      ...-++++|--+..... ...+.+.+.+...+..+|++.|..+
T Consensus        85 ad~il~v~D~~~~~~~~-~~~i~~~l~~~~~~~piilv~NK~D  126 (178)
T d1wf3a1          85 VNAVVWVVDLRHPPTPE-DELVARALKPLVGKVPILLVGNKLD  126 (178)
T ss_dssp             CSEEEEEEETTSCCCHH-HHHHHHHHGGGTTTSCEEEEEECGG
T ss_pred             ccceeeeechhhhhccc-ccchhhheeccccchhhhhhhcccc
Confidence            34457777765555543 3456667766555667888888665

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=95.99  E-value=0.012  Score=52.07  Aligned_cols=43  Identities=16%  Similarity=0.284  Sum_probs=30.7

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc-CCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF-TTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~-~~~~~~I~~~n~~~  412 (533)
                      ..++++++||- ..+++..+..+.+++.+. ..+..+|++|...+
T Consensus       150 ~~p~illLDEPt~gLD~~~~~~i~~~i~~~~~~g~tii~~tH~l~  194 (238)
T d1vpla_         150 VNPRLAILDEPTSGLDVLNAREVRKILKQASQEGLTILVSSHNML  194 (238)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEEECCHH
T ss_pred             cCCCEEEecCCCCCCCHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            46889999996 567887777777777543 24567888876544

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.98  E-value=0.0059  Score=51.02  Aligned_cols=22  Identities=23%  Similarity=0.487  Sum_probs=19.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++.|.+|+|||+++..+...-
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~~   30 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7999999999999999988643

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.95  E-value=0.002  Score=55.36  Aligned_cols=22  Identities=27%  Similarity=0.536  Sum_probs=20.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|.||+|+||||+++.+++..
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHhC
Confidence            7899999999999999999886

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.93  E-value=0.013  Score=50.66  Aligned_cols=40  Identities=25%  Similarity=0.389  Sum_probs=29.0

Q ss_pred             CCcEEEEEeCCCCCCH-HHHHHHHHHHHhcCCCcEEEEEeC
Q psy4285         370 SSYKLIILDEADAMTN-DAQNALRRIIEKFTTNVRFCIICN  409 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~-~~~~~Ll~~le~~~~~~~~I~~~n  409 (533)
                      ..-+.+|+||+|.|.. +....+..+++..+....+++.|.
T Consensus       142 ~~l~~lV~DEaD~l~~~~f~~~v~~I~~~l~~~~Q~il~SA  182 (206)
T d1s2ma1         142 SDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSA  182 (206)
T ss_dssp             TTCCEEEEESHHHHSSHHHHHHHHHHHTTSCSSCEEEEEES
T ss_pred             ccceEEEeechhhhhhhhhHHHHHHHHHhCCCCCEEEEEEE
Confidence            4567899999998754 456667777776677777777664

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.89  E-value=0.0021  Score=55.00  Aligned_cols=23  Identities=30%  Similarity=0.521  Sum_probs=21.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||+|+||||+++.+++..
T Consensus         3 pIvl~GpsG~GK~tl~~~L~~~~   25 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHC
T ss_pred             eEEEECCCCCCHHHHHHHHHHhC
Confidence            38999999999999999999876

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=95.87  E-value=0.0097  Score=52.71  Aligned_cols=43  Identities=16%  Similarity=0.209  Sum_probs=31.6

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc-CCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF-TTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~-~~~~~~I~~~n~~~  412 (533)
                      ..+++|++||- ..+++.....+.+++.+. ..+..+|++|....
T Consensus       156 ~~P~lLllDEPt~gLD~~~~~~i~~~i~~l~~~g~til~~tH~l~  200 (240)
T d1ji0a_         156 SRPKLLMMDEPSLGLAPILVSEVFEVIQKINQEGTTILLVEQNAL  200 (240)
T ss_dssp             TCCSEEEEECTTTTCCHHHHHHHHHHHHHHHHTTCCEEEEESCHH
T ss_pred             hCCCEeeecCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHH
Confidence            46889999996 568888888888887653 23566778876543

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal 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: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.87  E-value=0.016  Score=51.00  Aligned_cols=99  Identities=18%  Similarity=0.245  Sum_probs=51.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcccc-c------------cCcceEEecCCCC--Cchh----HHHHHHHHHHhcccCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKA-Q------------FNAMVLELNASDD--RGIG----IVRDQIFQFASTKTMH  368 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~-~------------~~~~~~~~~~~~~--~~~~----~~~~~~~~~~~~~~~~  368 (533)
                      .++++||.+.|||++.|.++-...-.. +            +..-+..+...+.  .+..    .+.+. +......   
T Consensus        43 ~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d~I~~~~~~~d~~~~~~S~F~~E~~~~-~~il~~~---  118 (234)
T d1wb9a2          43 MLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTET-ANILHNA---  118 (234)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCCEEEEEEC-----------CHHHHHHH-HHHHHHC---
T ss_pred             EEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccchhheeEEccCcccccchhHHHHHHHHH-HHHHHhc---
Confidence            479999999999999999987643211 0            1112233333321  1111    22222 1121111   


Q ss_pred             CCCcEEEEEeCCCCCCH-----HHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         369 KSSYKLIILDEADAMTN-----DAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       369 ~~~~~vliiDE~d~l~~-----~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                       .+..++++||+.+=+.     ....++++.+.. ..++.+|+||....
T Consensus       119 -~~~sLvliDE~~~gT~~~eg~~l~~a~l~~l~~-~~~~~~i~tTH~~~  165 (234)
T d1wb9a2         119 -TEYSLVLMDEIGRGTSTYDGLSLAWACAENLAN-KIKALTLFATHYFE  165 (234)
T ss_dssp             -CTTEEEEEESCCCCSSSSHHHHHHHHHHHHHHH-TTCCEEEEECSCGG
T ss_pred             -ccccEEeecccccCCChhhhhHHHHHhhhhhhc-cccceEEEecchHH
Confidence             3467999999987653     223344444422 24567777776543

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G 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: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=95.86  E-value=0.0071  Score=49.84  Aligned_cols=43  Identities=12%  Similarity=0.228  Sum_probs=27.3

Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      ....++++|.-+.........+.+.+.....+..+|++.|..+
T Consensus        81 ~d~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~iilv~NK~D  123 (161)
T d2gj8a1          81 ADRVLFMVDGTTTDAVDPAEIWPEFIARLPAKLPITVVRNKAD  123 (161)
T ss_dssp             CSEEEEEEETTTCCCCSHHHHCHHHHHHSCTTCCEEEEEECHH
T ss_pred             ccccceeeccccccchhhhhhhhhhhhhcccccceeeccchhh
Confidence            3456777776666554444555566666566677888888654

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.84  E-value=0.0053  Score=51.35  Aligned_cols=21  Identities=24%  Similarity=0.469  Sum_probs=19.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|++|+|||++++.+...
T Consensus         8 i~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999998864

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase 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: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.79  E-value=0.007  Score=54.31  Aligned_cols=46  Identities=20%  Similarity=0.163  Sum_probs=34.6

Q ss_pred             hhchhhhhhhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       288 ~~~~~~~~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ..|..+...+..-+.++.+-+-|+.|..|+|||.++-..+......
T Consensus        86 ~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~  131 (264)
T d1gm5a3          86 NAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA  131 (264)
T ss_dssp             HHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc
Confidence            4566667777666666665568999999999999998887665433

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.79  E-value=0.029  Score=48.57  Aligned_cols=75  Identities=7%  Similarity=0.133  Sum_probs=58.7

Q ss_pred             ceEEEEEcC-CC---CcCchhhhccc---eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Q psy4285           7 NVRFCIICN-YL---SKITPAIQSRC---TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNIL   79 (533)
Q Consensus         7 ~~~~il~~~-~~---~~i~~~i~SRc---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~r~a~~~l   79 (533)
                      +..+|++++ ++   ....|-|+||+   .++.++ |++++..++|++.+...++.++++.++.|++.+ .|+|.....|
T Consensus       130 ~~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~yl~~~~-~~~R~L~~~l  207 (213)
T d1l8qa2         130 EKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIE-LDNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-KNVREIEGKI  207 (213)
T ss_dssp             TCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECC-CCHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-SSHHHHHHHH
T ss_pred             cceEEEecCCcchhccccchHHHHHhhCceEEEEC-CCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc-CcHHHHHHHH
Confidence            345566664 33   34678899996   788886 678889999999999999999999999999987 5788766666


Q ss_pred             HHHH
Q psy4285          80 QSAA   83 (533)
Q Consensus        80 ~~~~   83 (533)
                      ..+.
T Consensus       208 ~~l~  211 (213)
T d1l8qa2         208 KLIK  211 (213)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            5544

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.76  E-value=0.0023  Score=55.91  Aligned_cols=25  Identities=24%  Similarity=0.130  Sum_probs=22.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ++++||||+|||+++..++......
T Consensus        26 ~~i~G~~GsGKT~l~l~la~~~~~~   50 (242)
T d1n0wa_          26 TEMFGEFRTGKTQICHTLAVTCQLP   50 (242)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHTTSC
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            7999999999999999999876544

>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=95.75  E-value=0.00087  Score=63.76  Aligned_cols=43  Identities=14%  Similarity=-0.006  Sum_probs=36.6

Q ss_pred             CccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhhhHH
Q psy4285         140 DIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVRD  187 (533)
Q Consensus       140 ~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~~~d  187 (533)
                      .+.+.||||+|||+.+.+++..+.     ..++++|++|+++...+..
T Consensus       156 ~~~~~g~~~~gk~~~~~~~~~~~~-----~~~i~in~s~~rs~~~l~~  198 (362)
T d1svma_         156 YWLFKGPIDSGKTTLAAALLELCG-----GKALNVNLPLDRLNFELGV  198 (362)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC-----CEEECCSSCTTTHHHHHGG
T ss_pred             eEEEECCCCCCHHHHHHHHHHHcC-----CCEEEEECcchhhHHHHHh
Confidence            467899999999999999988887     7999999999887765553

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.73  E-value=0.0029  Score=56.34  Aligned_cols=22  Identities=23%  Similarity=0.182  Sum_probs=19.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|+||||||||+++..++...
T Consensus        37 ~li~G~pGsGKT~l~lq~~~~~   58 (251)
T d1szpa2          37 TELFGEFRTGKSQLCHTLAVTC   58 (251)
T ss_dssp             EEEEESTTSSHHHHHHHHTTTT
T ss_pred             EEEEcCCCCCHHHHHHHHHHHh
Confidence            7999999999999999887654

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=95.72  E-value=0.024  Score=49.44  Aligned_cols=99  Identities=21%  Similarity=0.252  Sum_probs=52.4

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcccc-c------------cCcceEEecCCCC--CchhHHHHHHHHHHhcccCCCCCcE
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKA-Q------------FNAMVLELNASDD--RGIGIVRDQIFQFASTKTMHKSSYK  373 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~-~------------~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~  373 (533)
                      ++++||...|||++.|.++-...-.. +            +..-+..+...+.  .+.......++........ .....
T Consensus        38 ~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~I~~~~~~~d~~~~~~StF~~el~~~~~il~~-~~~~s  116 (224)
T d1ewqa2          38 VLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKE-ATENS  116 (224)
T ss_dssp             EEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSEEEEECCC------CCSHHHHHHHHHHHHHHH-CCTTE
T ss_pred             EEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecceEEEEECCCccccCCccHHHHhHHHHHHHhcc-CCCCc
Confidence            79999999999999999986643211 0            1111233333332  1222222222221111000 13568


Q ss_pred             EEEEeCCCCCCHH-----HHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         374 LIILDEADAMTND-----AQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       374 vliiDE~d~l~~~-----~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      +++|||+.+=+..     ...++++.+.+.  +..++++|..
T Consensus       117 LvliDE~~~gT~~~eg~ala~aile~L~~~--~~~~i~tTH~  156 (224)
T d1ewqa2         117 LVLLDEVGRGTSSLDGVAIATAVAEALHER--RAYTLFATHY  156 (224)
T ss_dssp             EEEEESTTTTSCHHHHHHHHHHHHHHHHHH--TCEEEEECCC
T ss_pred             EEeecccccCcchhhhcchHHHHHHHHhhc--CcceEEeeec
Confidence            9999999887542     234455555543  3567778764

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.71  E-value=0.0029  Score=52.78  Aligned_cols=25  Identities=20%  Similarity=0.126  Sum_probs=22.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      +-++|++|+||||++..++..+...
T Consensus         4 i~I~G~~gSGKTTli~~l~~~L~~~   28 (165)
T d1xjca_           4 WQVVGYKHSGKTTLMEKWVAAAVRE   28 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhC
Confidence            4589999999999999999988544

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.70  E-value=0.013  Score=48.54  Aligned_cols=21  Identities=24%  Similarity=0.426  Sum_probs=19.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.||+|||++++.+...
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998764

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {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: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=95.67  E-value=0.0052  Score=57.26  Aligned_cols=39  Identities=28%  Similarity=0.428  Sum_probs=28.2

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCC
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD  347 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~  347 (533)
                      .+=++||||+||||++..+++.+...+ ....++.++++.
T Consensus        56 ~IgitG~pGaGKSTLi~~l~~~~~~~g-~~vavlavDpss   94 (327)
T d2p67a1          56 RLGVTGTPGAGKSTFLEAFGMLLIREG-LKVAVIAVDPSS   94 (327)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTT-CCEEEEEECCC-
T ss_pred             EEEeeCCCCCCHHHHHHHHHHHHHhcC-CceeeecCCCce
Confidence            378999999999999999998875443 233455555443

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.67  E-value=0.031  Score=48.17  Aligned_cols=41  Identities=22%  Similarity=0.315  Sum_probs=28.9

Q ss_pred             CCcEEEEEeCCCCCCH--HHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTN--DAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~--~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ..-+.+++||+|.|..  ...+.+.++++..+....+++.|..
T Consensus       144 ~~l~~lVlDEaD~ll~~~~~~~~i~~I~~~~~~~~Q~il~SAT  186 (207)
T d1t6na_         144 KHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSAT  186 (207)
T ss_dssp             TTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESC
T ss_pred             cccceeehhhhhhhhhcCCcHHHHHHHHHhCCCCCEEEEEeee
Confidence            5577999999997642  4555666677666677777776643

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.67  E-value=0.005  Score=54.99  Aligned_cols=23  Identities=26%  Similarity=0.262  Sum_probs=21.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      ++++||||+|||+++..++....
T Consensus        39 ~li~G~pGsGKT~~~lq~~~~~~   61 (254)
T d1pzna2          39 TEVFGEFGSGKTQLAHTLAVMVQ   61 (254)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhh
Confidence            79999999999999999988764

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.64  E-value=0.0073  Score=50.59  Aligned_cols=21  Identities=29%  Similarity=0.548  Sum_probs=18.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|+||+|||+++..+...
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            789999999999999988754

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.63  E-value=0.003  Score=53.69  Aligned_cols=22  Identities=23%  Similarity=0.573  Sum_probs=20.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|.||+|+||||+++.+.+..
T Consensus         5 ivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           5 VVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhhC
Confidence            7899999999999999998875

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.63  E-value=0.034  Score=48.45  Aligned_cols=41  Identities=22%  Similarity=0.391  Sum_probs=29.5

Q ss_pred             CCcEEEEEeCCCCCCH-HHHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTN-DAQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~-~~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ..-+.+|+||+|.|.. .....+.++++..+.+..+++.|-.
T Consensus       158 ~~l~~lVlDEaD~ll~~~f~~~i~~I~~~l~~~~Q~ilfSAT  199 (222)
T d2j0sa1         158 RAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISAT  199 (222)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESC
T ss_pred             ccceeeeecchhHhhhcCcHHHHHHHHHhCCCCCEEEEEEEe
Confidence            4577999999998754 3456677777766777777776643

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {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: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=95.57  E-value=0.016  Score=50.95  Aligned_cols=41  Identities=22%  Similarity=0.416  Sum_probs=29.4

Q ss_pred             CcEEEEEeCC-CCCCHHHHHHHHHHHHhc-CCCcEEEEEeCCC
Q psy4285         371 SYKLIILDEA-DAMTNDAQNALRRIIEKF-TTNVRFCIICNYL  411 (533)
Q Consensus       371 ~~~vliiDE~-d~l~~~~~~~Ll~~le~~-~~~~~~I~~~n~~  411 (533)
                      .++++++||- ..++...+..+.+++.+. ..+..+|++|...
T Consensus       150 ~p~llllDEPt~gLD~~~~~~i~~~i~~l~~~g~tii~vtHdl  192 (231)
T d1l7vc_         150 AGQLLLLDEPMNSLDVAQQSALDKILSALCQQGLAIVMSSHDL  192 (231)
T ss_dssp             TCCEEEESSCSTTCCHHHHHHHHHHHHHHHHTTCEEEECCCCH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            4589999996 567888877777777643 3456677777654

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.56  E-value=0.016  Score=50.09  Aligned_cols=40  Identities=25%  Similarity=0.399  Sum_probs=28.1

Q ss_pred             CCcEEEEEeCCCCCC-HHHHHHHHHHHHhcCCCcEEEEEeC
Q psy4285         370 SSYKLIILDEADAMT-NDAQNALRRIIEKFTTNVRFCIICN  409 (533)
Q Consensus       370 ~~~~vliiDE~d~l~-~~~~~~Ll~~le~~~~~~~~I~~~n  409 (533)
                      ..-+.+|+||+|.|. ......+.++++..+.+..+++.|-
T Consensus       145 ~~l~~lVlDEaD~ll~~~f~~~i~~I~~~~~~~~Q~~l~SA  185 (206)
T d1veca_         145 DHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSA  185 (206)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHHHSCTTCEEEEEES
T ss_pred             cccceEEEeccccccccchHHHHHHHHHhCCCCCEEEEEEe
Confidence            457899999999775 3345556666666677777777664

>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=95.53  E-value=0.048  Score=48.58  Aligned_cols=93  Identities=14%  Similarity=0.049  Sum_probs=64.1

Q ss_pred             CCCceEEEEEcCCCCcCchhhhc--cc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCC-CHHHHHHHH
Q psy4285           4 FTTNVRFCIICNYLSKITPAIQS--RC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDG-DMRKVLNIL   79 (533)
Q Consensus         4 ~~~~~~~il~~~~~~~i~~~i~S--Rc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g-~~r~a~~~l   79 (533)
                      ...++.+|.+||.+..|-|+++.  |. ..+.|++|+.++-.++++....+..+. .+..+..+++.+.| +.+..-+++
T Consensus       147 ~~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~G~s~adi~~l~  225 (256)
T d1lv7a_         147 GNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLA-PDIDAAIIARGTPGFSGADLANLV  225 (256)
T ss_dssp             SSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC-TTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             CCCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcC-cccCHHHHHHhCCCCCHHHHHHHH
Confidence            34567888899999999999973  77 799999999999999998777655443 33457788887776 444444555


Q ss_pred             HHHHH---h-CCCCcchhhHHh
Q psy4285          80 QSAAT---A-HADEVNEDTIFT   97 (533)
Q Consensus        80 ~~~~~---~-~~~~i~~~~i~~   97 (533)
                      +.+..   . ....|+.+++.+
T Consensus       226 ~~A~~~a~~~~~~~i~~~d~~~  247 (256)
T d1lv7a_         226 NEAALFAARGNKRVVSMVEFEK  247 (256)
T ss_dssp             HHHHHHHHHTTCSSBCHHHHHH
T ss_pred             HHHHHHHHHcCCCccCHHHHHH
Confidence            43322   1 223466665543

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.46  E-value=0.013  Score=48.50  Aligned_cols=21  Identities=19%  Similarity=0.403  Sum_probs=19.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|++|+|||+++..+...
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999998764

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=95.45  E-value=0.014  Score=48.45  Aligned_cols=21  Identities=24%  Similarity=0.447  Sum_probs=19.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.+|+|||++++.+...
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           7 VIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999998753

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=95.44  E-value=0.011  Score=48.93  Aligned_cols=100  Identities=19%  Similarity=0.214  Sum_probs=51.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccccc--cCcceEEecCC-------CCCchhHHHHHHHHHHhcccCCCCCcEEEEEe
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTKAQ--FNAMVLELNAS-------DDRGIGIVRDQIFQFASTKTMHKSSYKLIILD  378 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~~~--~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiD  378 (533)
                      .+++.|+||+|||++.+.+...-.....  .+.....++..       +..+....+.....+.     .....-++++|
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~~~~~~~~t~~~~~~~~~~~~~~~~~~D~~G~~~~~~~~~~~~-----~~~~~~i~v~d   78 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGEDVDTISPTLGFNIKTLEHRGFKLNIWDVGGQKSLRSYWRNYF-----ESTDGLIWVVD   78 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTCCCSSCCCCSSEEEEEEEETTEEEEEEEECCSHHHHTTGGGGC-----TTCSEEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHcCCCCCcccceEeeeeeeccccccceeeeecCcchhhhhHHHhhh-----hhhhcceeeee
Confidence            3899999999999999988643221110  01111111111       1112222222111111     12345688888


Q ss_pred             CCCCCCH-HHHHHHHHHHHh-cCCCcEEEEEeCCCC
Q psy4285         379 EADAMTN-DAQNALRRIIEK-FTTNVRFCIICNYLS  412 (533)
Q Consensus       379 E~d~l~~-~~~~~Ll~~le~-~~~~~~~I~~~n~~~  412 (533)
                      -.|.-.. +....+.+.+.. ...+..+++++|..+
T Consensus        79 ~~d~~~~~~~~~~~~~~~~~~~~~~~p~iiv~nK~D  114 (165)
T d1ksha_          79 SADRQRMQDCQRELQSLLVEERLAGATLLIFANKQD  114 (165)
T ss_dssp             TTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTT
T ss_pred             cccchhHHHHHHhhhhhhhhcccCCCceEEEEeccc
Confidence            8876554 334444455432 235677888887665

>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=95.43  E-value=0.0042  Score=55.57  Aligned_cols=66  Identities=14%  Similarity=0.244  Sum_probs=45.1

Q ss_pred             CccccccCCCChhhHHHHHHHHHhcccccceeeeecCCccc-chhhhH-----HHHhhhhhcccccCCCceEEEEcCccc
Q psy4285         140 DIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDR-GIGIVR-----DQIFQFASTKTMHKSSYKLIILDEADA  213 (533)
Q Consensus       140 ~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~-g~~~~~-----d~i~~~a~~~~l~~~~~~~iilDE~d~  213 (533)
                      .+...||||+|||+.+.+++..+.     ..++++++++.. |.....     ..+..-|.     ...|.++++||+|.
T Consensus        42 ~vLL~GppGtGKT~la~alA~~~~-----~~~~~i~~~~~~~g~~~~~~~~~i~~if~~A~-----~~~p~il~iDEid~  111 (246)
T d1d2na_          42 SVLLEGPPHSGKTALAAKIAEESN-----FPFIKICSPDKMIGFSETAKCQAMKKIFDDAY-----KSQLSCVVVDDIER  111 (246)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHT-----CSEEEEECGGGCTTCCHHHHHHHHHHHHHHHH-----TSSEEEEEECCHHH
T ss_pred             EEEEECcCCCCHHHHHHHHhhccc-----ccccccccccccccccccchhhhhhhhhhhhh-----hcccceeehhhhhh
Confidence            367889999999999999888876     788999987643 221111     12212222     23567999999998


Q ss_pred             cC
Q psy4285         214 MT  215 (533)
Q Consensus       214 l~  215 (533)
                      +.
T Consensus       112 l~  113 (246)
T d1d2na_         112 LL  113 (246)
T ss_dssp             HT
T ss_pred             Hh
Confidence            75

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.42  E-value=0.014  Score=48.44  Aligned_cols=21  Identities=29%  Similarity=0.501  Sum_probs=19.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|++|+|||+++..+...
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            899999999999999998764

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=95.33  E-value=0.039  Score=49.47  Aligned_cols=25  Identities=36%  Similarity=0.448  Sum_probs=22.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ..++||||||||++|..++......
T Consensus        60 tei~G~~~sGKT~l~l~~~~~aqk~   84 (268)
T d1xp8a1          60 TEIYGPESGGKTTLALAIVAQAQKA   84 (268)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEecCCccchHHHHHHHHHHHHhC
Confidence            6899999999999999999887544

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.32  E-value=0.0042  Score=54.16  Aligned_cols=23  Identities=17%  Similarity=0.179  Sum_probs=20.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +-++||+|+||||+|+.+++.+.
T Consensus         5 IgI~G~~gSGKSTla~~L~~~l~   27 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQLLG   27 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Confidence            45899999999999999999874

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.32  E-value=0.0098  Score=49.87  Aligned_cols=21  Identities=24%  Similarity=0.536  Sum_probs=18.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|+||+|||++++.+...
T Consensus         7 i~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999988653

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.28  E-value=0.035  Score=46.68  Aligned_cols=20  Identities=40%  Similarity=0.554  Sum_probs=18.2

Q ss_pred             eeEeCCCCCChHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~  328 (533)
                      +++.|+||+|||++++.+..
T Consensus         8 i~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhc
Confidence            78999999999999998864

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.23  E-value=0.013  Score=48.49  Aligned_cols=21  Identities=24%  Similarity=0.466  Sum_probs=19.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|++|+|||+++..+...
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            799999999999999998764

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=95.19  E-value=0.0046  Score=54.57  Aligned_cols=22  Identities=32%  Similarity=0.294  Sum_probs=19.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|+|+||+|||+++..++...
T Consensus        29 ~~I~G~~G~GKT~la~~~~~~~   50 (242)
T d1tf7a1          29 TLVSGTSGTGKTLFSIQFLYNG   50 (242)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHH
Confidence            7999999999999998876543

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.16  E-value=0.032  Score=50.00  Aligned_cols=25  Identities=32%  Similarity=0.530  Sum_probs=21.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ..|+||||+|||++|..++......
T Consensus        63 ~e~~G~~~~GKT~l~l~~~~~~q~~   87 (269)
T d1mo6a1          63 IEIYGPESSGKTTVALHAVANAQAA   87 (269)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHHHT
T ss_pred             EEEecCCCcHHHHHHHHHHHHHhcC
Confidence            6899999999999998888766444

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.15  E-value=0.0085  Score=50.17  Aligned_cols=21  Identities=24%  Similarity=0.436  Sum_probs=19.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.+|+|||++++.+...
T Consensus         9 v~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           9 LVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999988754

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.15  E-value=0.013  Score=48.35  Aligned_cols=21  Identities=33%  Similarity=0.491  Sum_probs=18.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.+|+|||++++.+...
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998753

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=95.11  E-value=0.022  Score=46.99  Aligned_cols=22  Identities=32%  Similarity=0.250  Sum_probs=19.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|.|++|+|||++...+...-
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~~   26 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASGQ   26 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            7899999999999999987643

>d1sxjc1 a.80.1.1 (C:239-333) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.11  E-value=0.04  Score=40.77  Aligned_cols=78  Identities=26%  Similarity=0.374  Sum_probs=53.1

Q ss_pred             hcCCCHHHHHHHHHHHHHhCCCCcchhhHHhhhhhhccccchhHHHHHhchHHHHhhcCCC-hhhHHHHHhhccCccccc
Q psy4285          67 LSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIP-ESMLVDLVLKMSDIEYRL  145 (533)
Q Consensus        67 ~~~g~~r~a~~~l~~~~~~~~~~i~~~~i~~~~~~~~ek~~~~~l~~lls~~~~l~~l~~~-~~~~~~~~~~~~~~~~~~  145 (533)
                      .-+|+...|.+.++.+....+  .+..+|.                  ....+.+...+++ +..+..++..++++++|+
T Consensus        13 ~l~~~f~~a~~~l~~l~~~~G--~s~~dIl------------------~~l~~~i~~~~~~~~~~k~~ll~~la~~e~rL   72 (95)
T d1sxjc1          13 ILEDDWGTAHYTLNKVRSAKG--LALIDLI------------------EGIVKILEDYELQNEETRVHLLTKLADIEYSI   72 (95)
T ss_dssp             HHTSCHHHHHHHHHHHHHTTT--CCHHHHH------------------HHHHHHHTTSCCSSHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHcC--CCHHHHH------------------HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence            345788888888877653222  2222211                  1112333444554 456788899999999999


Q ss_pred             cCCCChhhHHHHHHHHHhc
Q psy4285         146 AAGTSEKIQLSALIAAFNS  164 (533)
Q Consensus       146 ~~G~~~~~~l~~~~~~~~~  164 (533)
                      ..|+++..|+.++++.+..
T Consensus        73 ~~G~~e~lQL~~lla~~~~   91 (95)
T d1sxjc1          73 SKGGNDQIQGSAVIGAIKA   91 (95)
T ss_dssp             TTCCCHHHHHHHHHHHHHH
T ss_pred             HcCCCcHHHHHHHHHHHHH
Confidence            9999999999999999864

>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=95.09  E-value=0.0077  Score=55.60  Aligned_cols=73  Identities=11%  Similarity=0.021  Sum_probs=45.9

Q ss_pred             ccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhhhH--HHHhhhhhcccccCCCceEEEEcCccccCHHH
Q psy4285         141 IEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVR--DQIFQFASTKTMHKSSYKLIILDEADAMTNDA  218 (533)
Q Consensus       141 ~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~~~--d~i~~~a~~~~l~~~~~~~iilDE~d~l~~~a  218 (533)
                      ....|+||+|||..+.+++..+..   +...+.++.+++.+...+.  .+++..-..-.    .+.++|+||+|.+....
T Consensus       126 ~l~~G~pG~GKT~la~ala~~~~~---~~~~~~~~~~~~~~~~~G~~e~~~~~~f~~a~----~~~ilf~DEid~~~~~r  198 (321)
T d1w44a_         126 VIVTGKGNSGKTPLVHALGEALGG---KDKYATVRFGEPLSGYNTDFNVFVDDIARAML----QHRVIVIDSLKNVIGAA  198 (321)
T ss_dssp             EEEECSSSSCHHHHHHHHHHHHHT---TSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHH----HCSEEEEECCTTTC---
T ss_pred             EEEECCCCccHHHHHHHHHHHhcC---CCCeEEEEhhHhhhcccchHHHHHHHHHHHHh----hccEEEeehhhhhcccc
Confidence            456899999999999999998752   1245667888887664443  33322211110    23499999999998655


Q ss_pred             HH
Q psy4285         219 QN  220 (533)
Q Consensus       219 ~~  220 (533)
                      ..
T Consensus       199 ~~  200 (321)
T d1w44a_         199 GG  200 (321)
T ss_dssp             --
T ss_pred             cc
Confidence            43

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {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: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.07  E-value=0.031  Score=47.97  Aligned_cols=22  Identities=27%  Similarity=0.329  Sum_probs=19.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      ++++.|+||+|||++.+.+...
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999764

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.07  E-value=0.019  Score=47.66  Aligned_cols=21  Identities=29%  Similarity=0.520  Sum_probs=18.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|++|+|||++++.+...
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            789999999999999988653

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=95.05  E-value=0.014  Score=54.15  Aligned_cols=36  Identities=33%  Similarity=0.422  Sum_probs=26.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNA  345 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~  345 (533)
                      +=++||||+||||++..+++.+...+ ....++.+++
T Consensus        54 igitG~pGaGKSTli~~l~~~~~~~g-~~vaViavDp   89 (323)
T d2qm8a1          54 VGITGVPGVGKSTTIDALGSLLTAAG-HKVAVLAVDP   89 (323)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHTT-CCEEEEEECG
T ss_pred             EeeeCCCCCCHHHHHHHHHHHHhhcC-Cceeeeeccc
Confidence            77999999999999999998764432 2334444443

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=95.03  E-value=0.0069  Score=55.79  Aligned_cols=18  Identities=33%  Similarity=0.433  Sum_probs=15.0

Q ss_pred             ceeEeCCCCCChHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILA  325 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~  325 (533)
                      ++++.||||||||+++-.
T Consensus        16 ~~lI~g~aGTGKTt~l~~   33 (306)
T d1uaaa1          16 PCLVLAGAGSGKTRVITN   33 (306)
T ss_dssp             EEEECCCTTSCHHHHHHH
T ss_pred             CEEEEeeCCccHHHHHHH
Confidence            588999999999987543

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {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: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.99  E-value=0.017  Score=48.25  Aligned_cols=21  Identities=24%  Similarity=0.499  Sum_probs=18.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|+||+|||++++.+...
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999998753

>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=94.94  E-value=0.0083  Score=55.58  Aligned_cols=74  Identities=15%  Similarity=0.145  Sum_probs=45.3

Q ss_pred             ccCccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhh--hH--HHHhhh-hhccccc--CCCceEEEEcC
Q psy4285         138 MSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGI--VR--DQIFQF-ASTKTMH--KSSYKLIILDE  210 (533)
Q Consensus       138 ~~~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~--~~--d~i~~~-a~~~~l~--~~~~~~iilDE  210 (533)
                      .+.+.+.||||+|||..+.+++..+.     ...+.+++++....+.  ..  ..++.. ....+..  ...+.++++||
T Consensus        49 ~~~iLl~GPpG~GKT~lAkalA~~~~-----~~~~~i~~s~~~~~~~~~~~~~~~~~~~f~~a~~~~~~~~~~~IIf~DE  123 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIARRLAKLAN-----APFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDE  123 (309)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHHT-----CCEEEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEEC
T ss_pred             CceEEEECCCCCCHHHHHHHHhhccc-----cchhcccccccccceeEeeeccccccccchhhhcccccccCCceEEehh
Confidence            36678899999999999998888765     5667777666532221  11  222111 1111110  11245999999


Q ss_pred             ccccCH
Q psy4285         211 ADAMTN  216 (533)
Q Consensus       211 ~d~l~~  216 (533)
                      +|.+..
T Consensus       124 Idki~~  129 (309)
T d1ofha_         124 IDKICK  129 (309)
T ss_dssp             GGGGSC
T ss_pred             hhhhhh
Confidence            999874

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {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: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=94.94  E-value=0.0089  Score=48.92  Aligned_cols=25  Identities=24%  Similarity=0.304  Sum_probs=22.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ++|.|+=|+||||+++.+++.+...
T Consensus        36 i~L~G~LGaGKTtfvr~~~~~lg~~   60 (158)
T d1htwa_          36 VYLNGDLGAGKTTLTRGMLQGIGHQ   60 (158)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTCC
T ss_pred             EEEecCCCccHHHHHHHHHhhcccc
Confidence            7899999999999999999998543

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=94.88  E-value=0.025  Score=50.46  Aligned_cols=52  Identities=15%  Similarity=0.257  Sum_probs=34.7

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc-CCCcEEEEEeCCCCCCChhhhccc
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF-TTNVRFCIICNYLSKIPPAIQSRC  422 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~-~~~~~~I~~~n~~~~l~~~l~sR~  422 (533)
                      ..+++|++||- ..+++.....+++.+.+. ..++.++++|...+.+ ..+-+|.
T Consensus       167 ~~P~llilDEPt~gLD~~~~~~i~~~i~~l~~~g~til~vsHdl~~~-~~~~Drv  220 (254)
T d1g6ha_         167 TNPKMIVMDEPIAGVAPGLAHDIFNHVLELKAKGITFLIIEHRLDIV-LNYIDHL  220 (254)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEECSCCSTT-GGGCSEE
T ss_pred             hCcCchhhcCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEeCcHHHH-HHhCCEE
Confidence            45789999996 467887777777776543 3457788888766533 2344554

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=94.85  E-value=0.012  Score=50.91  Aligned_cols=41  Identities=15%  Similarity=0.334  Sum_probs=29.0

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhcCCCcEEEEEeCC
Q psy4285         370 SSYKLIILDEADAMTND-AQNALRRIIEKFTTNVRFCIICNY  410 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~-~~~~Ll~~le~~~~~~~~I~~~n~  410 (533)
                      ..-+.+++||+|.+... ....+..++...+++..+++.|..
T Consensus       146 ~~l~~lViDEad~ll~~~f~~~v~~I~~~~~~~~Q~il~SAT  187 (209)
T d1q0ua_         146 HTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSAT  187 (209)
T ss_dssp             GGCCEEEECSHHHHHHTTCHHHHHHHHHTSCTTCEEEEEESC
T ss_pred             ccceEEEEeecccccccccHHHHHHHHHHCCCCCEEEEEEcc
Confidence            45679999999998654 244566666666677888877643

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=94.82  E-value=0.012  Score=52.14  Aligned_cols=23  Identities=39%  Similarity=0.533  Sum_probs=20.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      ++++|++|+||||+...+.+.+.
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~~~   25 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRYLE   25 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHh
Confidence            68999999999999999998763

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.79  E-value=0.014  Score=48.58  Aligned_cols=21  Identities=24%  Similarity=0.581  Sum_probs=18.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.+|+|||+++..+...
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999988753

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.78  E-value=0.028  Score=46.80  Aligned_cols=21  Identities=19%  Similarity=0.447  Sum_probs=19.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|+||+|||+++..+...
T Consensus         9 I~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            899999999999999888764

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {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: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.77  E-value=0.014  Score=49.80  Aligned_cols=21  Identities=33%  Similarity=0.607  Sum_probs=19.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|++|+|||+++..+...
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            789999999999999988754

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=94.75  E-value=0.015  Score=52.99  Aligned_cols=25  Identities=16%  Similarity=0.190  Sum_probs=20.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +.++.-|+|+|||.++..+++.+..
T Consensus       130 ~~il~~pTGsGKT~i~~~i~~~~~~  154 (282)
T d1rifa_         130 RRILNLPTSAGRSLIQALLARYYLE  154 (282)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHH
T ss_pred             CceeEEEcccCccHHHHHHHHHhhh
Confidence            3678889999999999888876543

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.73  E-value=0.0084  Score=50.59  Aligned_cols=23  Identities=22%  Similarity=0.326  Sum_probs=20.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .++|.||+|+||||+++.+.+..
T Consensus         5 ~ivl~Gpsg~GK~tl~~~L~~~~   27 (178)
T d1kgda_           5 TLVLLGAHGVGRRHIKNTLITKH   27 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             cEEEECCCCCCHHHHHHHHHHhC
Confidence            38899999999999999988764

>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=94.72  E-value=0.0088  Score=54.03  Aligned_cols=71  Identities=8%  Similarity=0.214  Sum_probs=51.2

Q ss_pred             cCccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhhhH--HHHhh-hhhcccccCCCceEEEEcCccccC
Q psy4285         139 SDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVR--DQIFQ-FASTKTMHKSSYKLIILDEADAMT  215 (533)
Q Consensus       139 ~~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~~~--d~i~~-~a~~~~l~~~~~~~iilDE~d~l~  215 (533)
                      ..+..+|+||+|||+.+.+++..+.     ..++.++++++.+.....  .++.. |..+.   ...|.++++||+|.+.
T Consensus        42 ~giLL~Gp~GtGKT~l~~ala~~~~-----~~~~~~~~~~l~~~~~~~~~~~l~~~f~~A~---~~~p~il~ideid~l~  113 (265)
T d1r7ra3          42 KGVLFYGPPGCGKTLLAKAIANECQ-----ANFISIKGPELLTMWFGESEANVREIFDKAR---QAAPCVLFFDELDSIA  113 (265)
T ss_dssp             CEEEEBCCTTSSHHHHHHHHHHHTT-----CEEEEECHHHHHTSCTTTHHHHHHHHHHHHH---HTCSEEEEESSGGGTC
T ss_pred             CeEEEECCCCCcchhHHHHHHHHhC-----CcEEEEEHHHhhhccccchHHHHHHHHHHHH---hcCCcceeHHhhhhcc
Confidence            3467899999999999999999987     688999988876654444  33311 22222   2356799999999998


Q ss_pred             HH
Q psy4285         216 ND  217 (533)
Q Consensus       216 ~~  217 (533)
                      ..
T Consensus       114 ~~  115 (265)
T d1r7ra3         114 KA  115 (265)
T ss_dssp             CH
T ss_pred             cc
Confidence            54

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.68  E-value=0.019  Score=47.53  Aligned_cols=22  Identities=23%  Similarity=0.486  Sum_probs=19.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++.|.+|+|||++++.+...-
T Consensus         6 ivvvG~~~vGKTsli~r~~~~~   27 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            8999999999999999987643

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.67  E-value=0.013  Score=49.71  Aligned_cols=22  Identities=23%  Similarity=0.347  Sum_probs=19.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++.|.+|+|||++++.+...-
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~~   33 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYANDA   33 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHhhCC
Confidence            7999999999999999887643

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {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: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.65  E-value=0.019  Score=47.65  Aligned_cols=21  Identities=29%  Similarity=0.475  Sum_probs=19.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.+|+|||+++..+...
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998764

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.63  E-value=0.0065  Score=50.80  Aligned_cols=21  Identities=38%  Similarity=0.466  Sum_probs=17.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|++|+|||+++..+...
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999887654

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.62  E-value=0.021  Score=47.47  Aligned_cols=21  Identities=24%  Similarity=0.436  Sum_probs=19.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.||+|||++++.+...
T Consensus         8 i~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            899999999999999988753

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=94.61  E-value=0.0091  Score=51.63  Aligned_cols=23  Identities=26%  Similarity=0.430  Sum_probs=20.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      -++|.||+|+||||+.+.+.+..
T Consensus         4 livi~GPSG~GK~tl~~~L~~~~   26 (205)
T d1s96a_           4 LYIVSAPSGAGKSSLIQALLKTQ   26 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            37899999999999999998874

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {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: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=94.60  E-value=0.014  Score=53.58  Aligned_cols=23  Identities=26%  Similarity=0.238  Sum_probs=21.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +-+.|++|+||||+|+.+...+.
T Consensus        83 IGIaG~sgSGKSTla~~L~~lL~  105 (308)
T d1sq5a_          83 ISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHT
T ss_pred             EEEeCCCCCCCcHHHHHHHHHHh
Confidence            56999999999999999998874

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.60  E-value=0.018  Score=48.56  Aligned_cols=22  Identities=18%  Similarity=0.317  Sum_probs=19.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++.|.+|+|||++++.+...-
T Consensus         8 ivviG~~~vGKTsli~~~~~~~   29 (183)
T d1mh1a_           8 CVVVGDGAVGKTCLLISYTTNA   29 (183)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            8999999999999999987643

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=94.58  E-value=0.02  Score=51.32  Aligned_cols=25  Identities=32%  Similarity=0.486  Sum_probs=22.4

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ..|+||||+|||+++..++.....+
T Consensus        57 tei~G~~gsGKTtl~l~~~~~~q~~   81 (263)
T d1u94a1          57 VEIYGPESSGKTTLTLQVIAAAQRE   81 (263)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEecCCCcHHHHHHHHHHHHHHcC
Confidence            7999999999999999999887554

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=94.57  E-value=0.061  Score=44.48  Aligned_cols=22  Identities=23%  Similarity=0.394  Sum_probs=19.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .+++.|.||+||||++..+...
T Consensus        17 kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          17 KVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999988653

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.57  E-value=0.022  Score=47.44  Aligned_cols=21  Identities=33%  Similarity=0.520  Sum_probs=18.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.||+|||++++.+...
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999988753

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=94.56  E-value=0.0072  Score=53.67  Aligned_cols=25  Identities=28%  Similarity=0.315  Sum_probs=22.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ++++|+||+|||+++..+|..+...
T Consensus        37 ~~i~G~~G~GKT~~~l~~a~~~~~~   61 (258)
T d2i1qa2          37 TEFAGVFGSGKTQIMHQSCVNLQNP   61 (258)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTCG
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            7999999999999999999876543

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.54  E-value=0.0089  Score=50.23  Aligned_cols=22  Identities=23%  Similarity=0.412  Sum_probs=19.4

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++.|++|+|||+++..+...-
T Consensus         5 ivvvG~~~vGKTsLi~~~~~~~   26 (177)
T d1kmqa_           5 LVIVGDGACGKTCLLIVNSKDQ   26 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7899999999999999887653

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=94.52  E-value=0.033  Score=49.82  Aligned_cols=22  Identities=27%  Similarity=0.489  Sum_probs=19.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      +++|.|.||+||||++.++...
T Consensus        34 ~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          34 TILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCcHHHHHHHHhCC
Confidence            4899999999999999999753

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=94.52  E-value=0.025  Score=47.07  Aligned_cols=100  Identities=18%  Similarity=0.192  Sum_probs=49.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccc--cCcceEEec-------CCCCCchhHHHHHHHHHHhcccCCCCCcEEEEEeC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQ--FNAMVLELN-------ASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDE  379 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~--~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE  379 (533)
                      +++.|+||+|||++++.+...-+....  .+.....++       -.+..+....+.....+...     ...-++++|=
T Consensus        19 I~vvG~~~vGKSsLi~~l~~~~~~~~~~~~~~~~~~i~~~~~~~~i~d~~g~~~~~~~~~~~~~~-----~~~ii~v~d~   93 (176)
T d1fzqa_          19 ILLLGLDNAGKTTLLKQLASEDISHITPTQGFNIKSVQSQGFKLNVWDIGGQRKIRPYWRSYFEN-----TDILIYVIDS   93 (176)
T ss_dssp             EEEEESTTSSHHHHHHHHCCSCCEEEEEETTEEEEEEEETTEEEEEEECSSCGGGHHHHHHHHTT-----CSEEEEEEET
T ss_pred             EEEECCCCCCHHHHHHHHhcCCCCcceeeeeeeEEEeccCCeeEeEeeccccccchhHHHHHhhc-----cceeEEeecc
Confidence            899999999999999887542211100  011111111       11112223333333333222     3455777776


Q ss_pred             CCCCCHH-HHHHHHHHHHh-cCCCcEEEEEeCCCCC
Q psy4285         380 ADAMTND-AQNALRRIIEK-FTTNVRFCIICNYLSK  413 (533)
Q Consensus       380 ~d~l~~~-~~~~Ll~~le~-~~~~~~~I~~~n~~~~  413 (533)
                      .|.-+.. ....+...... ...+..+++++|..+.
T Consensus        94 ~d~~s~~~~~~~~~~~~~~~~~~~~pillv~nK~Dl  129 (176)
T d1fzqa_          94 ADRKRFEETGQELTELLEEEKLSCVPVLIFANKQDL  129 (176)
T ss_dssp             TCGGGHHHHHHHHHHHTTCGGGTTCCEEEEEECTTS
T ss_pred             ccccchhhhhhhhhhhhhhhccCCCeEEEEEEeccc
Confidence            5544332 23333333322 2345668888887664

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.35  E-value=0.033  Score=46.14  Aligned_cols=21  Identities=24%  Similarity=0.482  Sum_probs=19.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|++|+|||++++.+...
T Consensus         9 i~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999988764

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=94.31  E-value=0.016  Score=53.64  Aligned_cols=23  Identities=30%  Similarity=0.407  Sum_probs=17.3

Q ss_pred             ceeEeCCCCCChHHHHHH-HHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILA-CARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~-la~~l  330 (533)
                      ++++.|+|||||||++-. +++.+
T Consensus        26 ~~lV~g~aGSGKTt~l~~ri~~ll   49 (318)
T d1pjra1          26 PLLIMAGAGSGKTRVLTHRIAYLM   49 (318)
T ss_dssp             CEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CEEEEecCCccHHHHHHHHHHHHH
Confidence            589999999999987654 44433

>d1sxjb1 a.80.1.1 (B:231-322) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.26  E-value=0.068  Score=39.19  Aligned_cols=45  Identities=16%  Similarity=0.416  Sum_probs=38.6

Q ss_pred             HHhhc-CCChhhHHHHHhhccCccccccCCCChhhHHHHHHHHHhc
Q psy4285         120 IISTI-EIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNS  164 (533)
Q Consensus       120 ~l~~l-~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~l~~~~~~~~~  164 (533)
                      .+... .+++..+..++..++++++|+..|+++..|+.++++.+..
T Consensus        43 ~i~~~~~~~e~~k~~il~~la~~~~rl~~G~~e~lQL~~lla~i~~   88 (92)
T d1sxjb1          43 VTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQLASMLAKIHK   88 (92)
T ss_dssp             HHHTCTTSCHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHcccccHHHHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Confidence            33343 5788888999999999999999999999999999999863

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {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: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.16  E-value=0.048  Score=44.93  Aligned_cols=21  Identities=19%  Similarity=0.453  Sum_probs=19.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.+|+|||++++.+...
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            889999999999999998764

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.12  E-value=0.018  Score=49.82  Aligned_cols=25  Identities=20%  Similarity=0.259  Sum_probs=22.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      +.|.|+.|+||||.++.+++.+...
T Consensus         6 I~ieG~dGsGKsT~~~~L~~~L~~~   30 (209)
T d1nn5a_           6 IVLEGVDRAGKSTQSRKLVEALCAA   30 (209)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC
Confidence            6788999999999999999988554

>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=94.12  E-value=0.063  Score=47.87  Aligned_cols=78  Identities=15%  Similarity=0.148  Sum_probs=57.9

Q ss_pred             CCCCceEEEEEcCCCCcCchhhhc--cc-eeEEeCCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHHHhcCC-CHHHHHHH
Q psy4285           3 KFTTNVRFCIICNYLSKITPAIQS--RC-TRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDG-DMRKVLNI   78 (533)
Q Consensus         3 ~~~~~~~~il~~~~~~~i~~~i~S--Rc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~g-~~r~a~~~   78 (533)
                      +...++.+|.+||.+..+-|++++  |+ ..+.|+.|+.++-.++|+..+.+..+. ++..+..|++.+.| +.+..-++
T Consensus       136 ~~~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~G~s~adl~~l  214 (258)
T d1e32a2         136 KQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLA-DDVDLEQVANETHGHVGADLAAL  214 (258)
T ss_dssp             CCSSCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBC-TTCCHHHHHHHCTTCCHHHHHHH
T ss_pred             cccCCccEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccc-cccchhhhhhcccCCCHHHHHHH
Confidence            345678899999999999999997  78 889999999999999998776554332 22247788888877 33333334


Q ss_pred             HHH
Q psy4285          79 LQS   81 (533)
Q Consensus        79 l~~   81 (533)
                      .+.
T Consensus       215 v~~  217 (258)
T d1e32a2         215 CSE  217 (258)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            333

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {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: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.05  E-value=0.016  Score=48.79  Aligned_cols=22  Identities=23%  Similarity=0.369  Sum_probs=19.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      ++|.|.+|+|||++++.+...-
T Consensus         5 ivliG~~~vGKTsli~r~~~~~   26 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKDC   26 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7899999999999999887653

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=94.00  E-value=0.013  Score=49.00  Aligned_cols=21  Identities=29%  Similarity=0.417  Sum_probs=18.6

Q ss_pred             ceeEeCCCCCChHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~  328 (533)
                      .+++.|+||+|||++.+.+..
T Consensus        14 kIvlvG~~~vGKTSli~rl~~   34 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKL   34 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999998754

>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=93.94  E-value=0.089  Score=46.94  Aligned_cols=80  Identities=11%  Similarity=0.138  Sum_probs=66.8

Q ss_pred             CCceEEEEEcC-----CCCcCchhhhccceeEEeCCCCHHHHHHHHHHHHh----hcCCCCCHHHHHHHHHhcC------
Q psy4285           5 TTNVRFCIICN-----YLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIE----QEKVNVTPDGKKAIIDLSD------   69 (533)
Q Consensus         5 ~~~~~~il~~~-----~~~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~----~~~~~~~~~~~~~~~~~~~------   69 (533)
                      .+.+++|.+|+     .+..-.|++..|++.+.+.+|+.++...+|+....    ..++.++++++..++.+|+      
T Consensus       145 rg~i~vIgatT~eey~~~~e~d~al~rrF~~I~V~Eps~e~t~~IL~~~~~~~e~~h~v~~~~~al~~~v~ls~ryi~~~  224 (268)
T d1r6bx2         145 SGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDR  224 (268)
T ss_dssp             SCCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTS
T ss_pred             CCCCeEEEeCCHHHHHHHHhhcHHHHhhhcccccCCCCHHHHHHHHHHhhHHHhccCCEEeChHHHHHHHHHHHhhccCC
Confidence            46788888885     44566899999999999999999999999987653    4579999999999888776      


Q ss_pred             CCHHHHHHHHHHHHH
Q psy4285          70 GDMRKVLNILQSAAT   84 (533)
Q Consensus        70 g~~r~a~~~l~~~~~   84 (533)
                      .=+.+|+.+|+.+..
T Consensus       225 ~~PdKAIdllDea~a  239 (268)
T d1r6bx2         225 HLPDKAIDVIDEAGA  239 (268)
T ss_dssp             CTTHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHH
Confidence            457899999988764

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=93.93  E-value=0.0076  Score=51.62  Aligned_cols=23  Identities=30%  Similarity=0.358  Sum_probs=21.0

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      -+.|.|+.|+||||+++.+++.+
T Consensus        11 ~I~ieG~~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGGT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999876

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {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: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.93  E-value=0.014  Score=50.15  Aligned_cols=24  Identities=25%  Similarity=0.533  Sum_probs=21.4

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHH
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~  329 (533)
                      .|.++|.|+||+||||+..++...
T Consensus         3 ~p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           3 QPSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            467999999999999999999865

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=93.89  E-value=0.015  Score=47.83  Aligned_cols=21  Identities=33%  Similarity=0.480  Sum_probs=19.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      ++|.|+||+||||+.+.+...
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999998754

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=93.87  E-value=0.025  Score=48.54  Aligned_cols=25  Identities=20%  Similarity=0.275  Sum_probs=21.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      +.|.|+.|+||||+++.+++.+...
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~   27 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAA   27 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC
Confidence            5788999999999999999987443

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {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: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.86  E-value=0.022  Score=51.60  Aligned_cols=24  Identities=33%  Similarity=0.635  Sum_probs=20.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +-+.|++|+||||++..+...+..
T Consensus        30 IGi~G~qGSGKSTl~~~l~~~L~~   53 (286)
T d1odfa_          30 IFFSGPQGSGKSFTSIQIYNHLME   53 (286)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             EEeECCCCCCHHHHHHHHHHHHHH
Confidence            458999999999999999887644

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {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: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.79  E-value=0.016  Score=47.32  Aligned_cols=21  Identities=38%  Similarity=0.512  Sum_probs=19.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|+||+|||+++..+...
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999998764

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=93.66  E-value=0.026  Score=50.97  Aligned_cols=23  Identities=22%  Similarity=0.232  Sum_probs=20.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +++.|+||+|||+++..++..+.
T Consensus        38 ~vi~G~~G~GKT~~~~~la~~~a   60 (277)
T d1cr2a_          38 IMVTSGSGMGKSTFVRQQALQWG   60 (277)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHhhh
Confidence            79999999999999999997653

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.65  E-value=0.016  Score=50.14  Aligned_cols=26  Identities=27%  Similarity=0.278  Sum_probs=22.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      .+.|.|++|+||||.++.+++.+...
T Consensus         4 fIviEG~dGsGKsT~~~~L~~~L~~~   29 (210)
T d4tmka_           4 YIVIEGLEGAGKTTARNVVVETLEQL   29 (210)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            47889999999999999999988544

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=93.64  E-value=0.019  Score=47.92  Aligned_cols=22  Identities=32%  Similarity=0.548  Sum_probs=19.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .++|.|++|+|||++|..+.+.
T Consensus        16 gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          16 GVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHc
Confidence            3899999999999999887764

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal 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: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.62  E-value=0.19  Score=41.37  Aligned_cols=23  Identities=22%  Similarity=0.338  Sum_probs=20.1

Q ss_pred             CceeEeCCCCCChHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~  329 (533)
                      +.+.|.|.||+||||+.+++.+.
T Consensus         6 ~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           6 GFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            35889999999999999999753

>d1ek0a_ c.37.1.8 (A:) Ypt51 {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: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.58  E-value=0.07  Score=43.97  Aligned_cols=21  Identities=24%  Similarity=0.529  Sum_probs=18.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.+|+|||+++..+...
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988754

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=93.48  E-value=0.017  Score=52.25  Aligned_cols=23  Identities=26%  Similarity=0.345  Sum_probs=20.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+|+|+||+|||+++..+|..+.
T Consensus        32 ~~i~G~~G~GKS~l~l~la~~ia   54 (274)
T d1nlfa_          32 GALVSPGGAGKSMLALQLAAQIA   54 (274)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHH
Confidence            78999999999999999998764

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {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: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.46  E-value=0.031  Score=46.44  Aligned_cols=21  Identities=33%  Similarity=0.626  Sum_probs=8.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.||+|||+++..+...
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988754

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {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: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.35  E-value=0.028  Score=46.37  Aligned_cols=21  Identities=24%  Similarity=0.551  Sum_probs=19.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|+||+|||++++.+...
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998764

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {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: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=93.32  E-value=0.018  Score=48.92  Aligned_cols=19  Identities=26%  Similarity=0.303  Sum_probs=16.8

Q ss_pred             eeEeCCCCCChHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACA  327 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la  327 (533)
                      +-++|++|+||||+|+.+.
T Consensus         6 IgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           6 IGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             EEEEECTTSCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            4589999999999999884

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {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: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=93.20  E-value=0.021  Score=49.02  Aligned_cols=23  Identities=39%  Similarity=0.543  Sum_probs=20.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      .+.+.||.|+||||+.+.++..+
T Consensus        29 i~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          29 VVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             CEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEEEECCCCChHHHHHHHHhccc
Confidence            47899999999999999998754

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase 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: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=93.14  E-value=0.043  Score=47.07  Aligned_cols=20  Identities=30%  Similarity=0.290  Sum_probs=16.4

Q ss_pred             ceeEeCCCCCChHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACA  327 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la  327 (533)
                      ++++.-|+|+|||..+....
T Consensus        42 ~vlv~apTGsGKT~~~~~~~   61 (206)
T d1oywa2          42 DCLVVMPTGGGKSLCYQIPA   61 (206)
T ss_dssp             CEEEECSCHHHHHHHHHHHH
T ss_pred             CEEEEcCCCCCCcchhhhhh
Confidence            69999999999998765443

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=93.06  E-value=0.021  Score=48.62  Aligned_cols=24  Identities=25%  Similarity=0.415  Sum_probs=20.8

Q ss_pred             CCCceeEeCCCCCChHHHHHHHHH
Q psy4285         305 ELPHLLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       305 ~~~~~ll~GppGtGKT~la~~la~  328 (533)
                      ..|.+.+.|+||+||||+.+++..
T Consensus        22 ~~~~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          22 GLPEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHhcC
Confidence            345699999999999999999974

>d1f6ba_ c.37.1.8 (A:) SAR1 {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: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=93.03  E-value=0.016  Score=48.52  Aligned_cols=21  Identities=33%  Similarity=0.469  Sum_probs=18.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~  328 (533)
                      .++|.|+||+||||+..++..
T Consensus        15 kI~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_          15 KLVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             EEEEEEETTSSHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            399999999999999988754

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal 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: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=92.95  E-value=0.022  Score=49.49  Aligned_cols=21  Identities=24%  Similarity=0.264  Sum_probs=18.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~  328 (533)
                      ..+|.|++|+||||++.++..
T Consensus        97 t~~~~G~SGVGKSTLiN~L~~  117 (225)
T d1u0la2          97 ISTMAGLSGVGKSSLLNAINP  117 (225)
T ss_dssp             EEEEECSTTSSHHHHHHHHST
T ss_pred             eEEEECCCCCCHHHHHHhhcc
Confidence            368999999999999998853

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=92.79  E-value=0.02  Score=47.72  Aligned_cols=22  Identities=32%  Similarity=0.477  Sum_probs=19.3

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .++|.|++|+|||++|..+.+.
T Consensus        17 gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          17 GVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHc
Confidence            4899999999999999887653

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {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: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=92.78  E-value=0.13  Score=44.66  Aligned_cols=26  Identities=19%  Similarity=0.176  Sum_probs=21.4

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ..+|.=++|+|||..+-+++..+...
T Consensus        33 g~iLaDe~GlGKT~~~i~~~~~~~~~   58 (230)
T d1z63a1          33 GICLADDMGLGKTLQTIAVFSDAKKE   58 (230)
T ss_dssp             CEEECCCTTSCHHHHHHHHHHHHHHT
T ss_pred             CEEEEeCCCCChHHHHHHhhhhhhhc
Confidence            46788899999999999888776544

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.76  E-value=0.31  Score=38.21  Aligned_cols=93  Identities=15%  Similarity=0.174  Sum_probs=46.5

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC-CCCchhHH--HHHHHHH-HhcccC-----CCCCcEEEEEeC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS-DDRGIGIV--RDQIFQF-ASTKTM-----HKSSYKLIILDE  379 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~-~~~~~~~~--~~~~~~~-~~~~~~-----~~~~~~vliiDE  379 (533)
                      -+++||-.+|||+-.-..++.....   +..++.++++ +.+.....  +...... ......     .....++++|||
T Consensus         5 ~li~GpMfsGKTt~Li~~~~~~~~~---g~~v~~ikp~~D~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~I~IDE   81 (133)
T d1xbta1           5 QVILGPMFSGKSTELMRRVRRFQIA---QYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDE   81 (133)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTT---TCCEEEEEETTCCC--------------CEEESSGGGGHHHHHTCSEEEESS
T ss_pred             EEEEecccCHHHHHHHHHHHHHHHc---CCcEEEEecccccCCcceeeecCCCcceeeeeechhhhhhhhcccceEEeeh
Confidence            3789999999999776666654322   3344444433 22221110  0000000 000000     012467999999


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCcEEEEEe
Q psy4285         380 ADAMTNDAQNALRRIIEKFTTNVRFCIIC  408 (533)
Q Consensus       380 ~d~l~~~~~~~Ll~~le~~~~~~~~I~~~  408 (533)
                      ++.+. +.. .+.+.+.+  .+..+++.+
T Consensus        82 aQFf~-dl~-~~~~~~~~--~~~~Viv~G  106 (133)
T d1xbta1          82 GQFFP-DIV-EFCEAMAN--AGKTVIVAA  106 (133)
T ss_dssp             GGGCT-THH-HHHHHHHH--TTCEEEEEC
T ss_pred             hHHHH-HHH-HHHHHHHh--cCCcEEEEE
Confidence            99996 333 34455543  346677776

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.75  E-value=0.03  Score=46.35  Aligned_cols=21  Identities=29%  Similarity=0.594  Sum_probs=19.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|++|+|||++++.+...
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999998864

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=92.74  E-value=0.029  Score=48.41  Aligned_cols=20  Identities=35%  Similarity=0.416  Sum_probs=17.3

Q ss_pred             eeEeCCCCCChHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~  328 (533)
                      +-++|++|+||||+++.+.+
T Consensus         6 IgitG~igSGKStv~~~l~~   25 (208)
T d1vhta_           6 VALTGGIGSGKSTVANAFAD   25 (208)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCcCCHHHHHHHHHH
Confidence            45899999999999998753

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=92.66  E-value=0.026  Score=46.66  Aligned_cols=22  Identities=32%  Similarity=0.543  Sum_probs=19.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~  329 (533)
                      .++|.|++|+|||++|..+.+.
T Consensus        17 gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          17 GVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHc
Confidence            4899999999999999887765

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {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: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=92.64  E-value=0.03  Score=46.47  Aligned_cols=20  Identities=30%  Similarity=0.514  Sum_probs=18.4

Q ss_pred             eeEeCCCCCChHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~  328 (533)
                      +.+.|+||+||||+++++..
T Consensus         3 V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           3 VLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            68999999999999999974

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.64  E-value=0.03  Score=47.46  Aligned_cols=22  Identities=18%  Similarity=0.303  Sum_probs=19.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++.|++|+|||+++..+...-
T Consensus         6 vvllG~~~vGKTSli~r~~~~~   27 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTNK   27 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7899999999999998887643

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=92.51  E-value=0.021  Score=51.65  Aligned_cols=27  Identities=19%  Similarity=0.281  Sum_probs=19.9

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      .|-+-++|++|+||||+++++.+.+..
T Consensus         4 ~pIIgIaG~SGSGKTTva~~l~~i~~~   30 (288)
T d1a7ja_           4 HPIISVTGSSGAGTSTVKHTFDQIFRR   30 (288)
T ss_dssp             SCEEEEESCC---CCTHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHHHhh
Confidence            344789999999999999999987743

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.49  E-value=0.034  Score=45.92  Aligned_cols=21  Identities=24%  Similarity=0.450  Sum_probs=19.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.+|+|||++++.+...
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            799999999999999988754

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {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: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=92.28  E-value=0.023  Score=49.93  Aligned_cols=43  Identities=16%  Similarity=0.340  Sum_probs=30.1

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc--CCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF--TTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~--~~~~~~I~~~n~~~  412 (533)
                      ..+++|++||- ..+++..+..+.+.+.+.  ..+..+|++|....
T Consensus       157 ~~P~lLllDEPt~~LD~~~~~~i~~~l~~l~~~~g~tvi~vTHdl~  202 (240)
T d3dhwc1         157 SNPKVLLCDEATSALDPATTRSILELLKDINRRLGLTILLITHEMD  202 (240)
T ss_dssp             TCCSEEEEESGGGSSCHHHHHHHHHHHHHHHHHHCCEEEEEBSCHH
T ss_pred             cCCCeEEeccccccCCHHHhhHHHHHHHHHHhccCCEEEEEcCCHH
Confidence            45789999995 567887777777776542  12577888886543

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {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: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.16  E-value=0.039  Score=45.27  Aligned_cols=21  Identities=19%  Similarity=0.303  Sum_probs=19.1

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|++|+|||++++.+...
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998754

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=92.15  E-value=0.51  Score=37.16  Aligned_cols=36  Identities=17%  Similarity=0.190  Sum_probs=25.5

Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEe
Q psy4285         370 SSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIIC  408 (533)
Q Consensus       370 ~~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~  408 (533)
                      ...++++|||++.++. ....+...+.+  .+..+++.+
T Consensus        78 ~~~dvI~IDE~QFf~d-~i~~~~~~~~~--~g~~Viv~G  113 (139)
T d2b8ta1          78 DETKVIGIDEVQFFDD-RICEVANILAE--NGFVVIISG  113 (139)
T ss_dssp             TTCCEEEECSGGGSCT-HHHHHHHHHHH--TTCEEEEEC
T ss_pred             cCcCEEEechhhhcch-hHHHHHHHHHh--cCceEEEEE
Confidence            3578999999999974 45556666654  345677776

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=92.07  E-value=0.032  Score=47.93  Aligned_cols=19  Identities=32%  Similarity=0.300  Sum_probs=16.6

Q ss_pred             eeEeCCCCCChHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACA  327 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la  327 (533)
                      +-++|++|+||||+++.+.
T Consensus         5 IgITG~igSGKStv~~~l~   23 (205)
T d1jjva_           5 VGLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEEECSTTSCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            4489999999999998775

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=91.93  E-value=0.043  Score=46.07  Aligned_cols=21  Identities=29%  Similarity=0.531  Sum_probs=18.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.||+|||+++..+...
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988753

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=91.82  E-value=0.029  Score=50.04  Aligned_cols=43  Identities=12%  Similarity=0.332  Sum_probs=29.0

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc-CCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF-TTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~-~~~~~~I~~~n~~~  412 (533)
                      ..+++||+||- ..++...+..+++.+.+. ..+..+|++|....
T Consensus       166 ~~P~llilDEPT~gLD~~~~~~i~~ll~~l~~~g~til~vtHdl~  210 (258)
T d1b0ua_         166 MEPDVLLFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEMG  210 (258)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHTTCCEEEECSCHH
T ss_pred             cCCCEEEeccccccCCHHHHHHHHHhhhhhcccCCceEEEeCCHH
Confidence            35789999996 467887777777766542 13456777776543

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.76  E-value=0.044  Score=47.45  Aligned_cols=24  Identities=38%  Similarity=0.317  Sum_probs=21.8

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+.|.|+-|+||||+++.+++.+.
T Consensus         5 ~I~iEG~DGsGKST~~~~L~~~L~   28 (214)
T d1tmka_           5 LILIEGLDRTGKTTQCNILYKKLQ   28 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHH
Confidence            478999999999999999999873

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon 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: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=91.72  E-value=0.02  Score=50.46  Aligned_cols=43  Identities=14%  Similarity=0.340  Sum_probs=28.5

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhc--CCCcEEEEEeCCCC
Q psy4285         370 SSYKLIILDEA-DAMTNDAQNALRRIIEKF--TTNVRFCIICNYLS  412 (533)
Q Consensus       370 ~~~~vliiDE~-d~l~~~~~~~Ll~~le~~--~~~~~~I~~~n~~~  412 (533)
                      ..+++|++||- ..+++.....+.+.+.+.  ..+..+|++|....
T Consensus       157 ~~P~llllDEPt~~LD~~~~~~i~~~i~~l~~~~g~tvi~vTHd~~  202 (242)
T d1oxxk2         157 KDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLLVVSHDPA  202 (242)
T ss_dssp             TCCSEEEEESTTTTSCGGGHHHHHHHHHHHHHHHCCEEEEEESCHH
T ss_pred             hcccceeecCCccCCCHHHHHHHHHHHHHHHhccCCEEEEEECCHH
Confidence            46889999996 456766666666665432  12567888886543

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=91.69  E-value=0.034  Score=46.57  Aligned_cols=21  Identities=33%  Similarity=0.542  Sum_probs=18.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      ++|.|+||+||||+..++...
T Consensus         3 I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           3 IIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999753

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.63  E-value=0.037  Score=48.68  Aligned_cols=24  Identities=21%  Similarity=0.195  Sum_probs=21.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +.|.|+-|+||||+++.+++.+..
T Consensus         5 IviEG~~GsGKST~~~~L~~~l~~   28 (241)
T d2ocpa1           5 LSIEGNIAVGKSTFVKLLTKTYPE   28 (241)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHCTT
T ss_pred             EEEECCCCCcHHHHHHHHHHHHhh
Confidence            789999999999999999998743

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.63  E-value=0.048  Score=45.45  Aligned_cols=21  Identities=29%  Similarity=0.602  Sum_probs=19.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|.+|+|||++++.+...
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999998764

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.56  E-value=0.041  Score=45.31  Aligned_cols=21  Identities=14%  Similarity=0.283  Sum_probs=19.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|++|+|||++++.+...
T Consensus         7 v~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           7 IAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            889999999999999998754

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=91.40  E-value=0.012  Score=51.44  Aligned_cols=32  Identities=22%  Similarity=0.379  Sum_probs=22.4

Q ss_pred             hhhcccccccCCCceeEeCCCCCChHHHHHHHHHH
Q psy4285         295 YKINRFIDENELPHLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       295 ~~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~  329 (533)
                      +.|..++...   ..+|.|++|+||||++.++...
T Consensus        89 ~~L~~~l~~~---~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          89 ADIIPHFQDK---TTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             TTTGGGGTTS---EEEEEESHHHHHHHHHHHHCC-
T ss_pred             HHHHHhhccc---eEEEECCCCccHHHHHHhhccH
Confidence            3344444432   3688999999999999988643

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.31  E-value=0.019  Score=50.54  Aligned_cols=24  Identities=17%  Similarity=0.113  Sum_probs=21.5

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      -+.|.|+-|+||||+++.+++.+.
T Consensus         4 ~I~ieG~dGsGKST~~~~L~~~l~   27 (241)
T d1p5zb_           4 KISIEGNIAAGKSTFVNILKQLCE   27 (241)
T ss_dssp             EEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            478999999999999999998763

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.18  E-value=0.054  Score=44.88  Aligned_cols=20  Identities=30%  Similarity=0.433  Sum_probs=18.2

Q ss_pred             eeEeCCCCCChHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~  328 (533)
                      +++.|.+|+|||++++.+..
T Consensus         6 v~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999988764

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=91.07  E-value=0.35  Score=38.29  Aligned_cols=87  Identities=17%  Similarity=0.294  Sum_probs=47.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCC-CCC------------c-----hhHHHHHHHHHHhcccCCCC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS-DDR------------G-----IGIVRDQIFQFASTKTMHKS  370 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~-~~~------------~-----~~~~~~~~~~~~~~~~~~~~  370 (533)
                      -+++||-.+||||-.-..++.....   +..++.+++. +.+            .     .....+.....       ..
T Consensus        10 ~lI~GpMfSGKTteLi~~~~~~~~~---g~~vl~i~~~~D~Ry~~~~i~sh~g~~~~a~~~~~~~~~~~~~-------~~   79 (141)
T d1xx6a1          10 EVIVGPMYSGKSEELIRRIRRAKIA---KQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYF-------EE   79 (141)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEEEC-------CEEECTTSCEEECEEESSSTHHHHHC-------CT
T ss_pred             EEEEeccccHHHHHHHHHHHHhhhc---CCcEEEEEeccccccccceeeecccceEEEEEecchhhhhhhh-------cc
Confidence            3789999999999877777654322   2223333221 100            0     00111111111       13


Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhcCCCcEEEEEe
Q psy4285         371 SYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIIC  408 (533)
Q Consensus       371 ~~~vliiDE~d~l~~~~~~~Ll~~le~~~~~~~~I~~~  408 (533)
                      ..++++|||++.++......+.. +..  .+..+++.+
T Consensus        80 ~~dvI~IDE~QFf~d~~~~~~~~-l~~--~g~~Viv~G  114 (141)
T d1xx6a1          80 DTEVIAIDEVQFFDDEIVEIVNK-IAE--SGRRVICAG  114 (141)
T ss_dssp             TCSEEEECSGGGSCTHHHHHHHH-HHH--TTCEEEEEE
T ss_pred             cccEEEEeehhhccccHHHHHHh-hee--CCcEEEEEE
Confidence            56899999999998665554444 443  345677766

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=91.03  E-value=0.061  Score=47.28  Aligned_cols=22  Identities=23%  Similarity=0.246  Sum_probs=19.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +-|+|+.|+||||+|+.++...
T Consensus         4 IgiTG~igSGKsTva~~l~e~~   25 (241)
T d1deka_           4 IFLSGVKRSGKDTTADFIMSNY   25 (241)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHhC
Confidence            5789999999999999998764

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=91.00  E-value=0.039  Score=46.19  Aligned_cols=20  Identities=35%  Similarity=0.566  Sum_probs=17.9

Q ss_pred             ceeEeCCCCCChHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACA  327 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la  327 (533)
                      .+++.|+||+||||+.+.+.
T Consensus        19 KI~lvG~~~vGKTsLi~~l~   38 (182)
T d1moza_          19 RILILGLDGAGKTTILYRLQ   38 (182)
T ss_dssp             EEEEEEETTSSHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            38999999999999998764

>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=90.66  E-value=0.43  Score=41.80  Aligned_cols=92  Identities=15%  Similarity=0.209  Sum_probs=64.9

Q ss_pred             CceEEEEEcCCC-------CcCchhhhccc--eeEEeCCCC--HHHHHHHHHHH----HhhcCC---CCCHHHHHHHHHh
Q psy4285           6 TNVRFCIICNYL-------SKITPAIQSRC--TRFRFGPLD--SSLIMSRLDYV----IEQEKV---NVTPDGKKAIIDL   67 (533)
Q Consensus         6 ~~~~~il~~~~~-------~~i~~~i~SRc--~~~~~~~~~--~~~~~~~l~~~----~~~~~~---~~~~~~~~~~~~~   67 (533)
                      .++|+|++++..       ....+.+..|+  ..+.++|+.  .+|+..+++..    +.+.+.   .++++++..|..+
T Consensus       134 ~~~RlI~~s~~~l~~l~~~~~f~~~L~~~l~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~ls~~al~~L~~~  213 (247)
T d1ny5a2         134 VNVRILAATNRNIKELVKEGKFREDLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSY  213 (247)
T ss_dssp             CCCEEEEEESSCHHHHHHTTSSCHHHHHHHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHHHHS
T ss_pred             cCeEEEEecCCCHHHHHHcCCCcHHHHhhcCeeeecCCChhhchhhHhhhhhhhhhhhhhhcCCCCCCCCHHHHHHHHhC
Confidence            468899988743       24566677775  457788885  46776555544    444343   3689999998777


Q ss_pred             c-CCCHHHHHHHHHHHHHhCCC-CcchhhHHh
Q psy4285          68 S-DGDMRKVLNILQSAATAHAD-EVNEDTIFT   97 (533)
Q Consensus        68 ~-~g~~r~a~~~l~~~~~~~~~-~i~~~~i~~   97 (533)
                      . .||+|...+.++.++..... .|+.+++..
T Consensus       214 ~WPGNl~EL~~~l~~a~~~~~~~~I~~~dl~~  245 (247)
T d1ny5a2         214 PWYGNVRELKNVIERAVLFSEGKFIDRGELSC  245 (247)
T ss_dssp             CCTTHHHHHHHHHHHHHHHCCSSEECHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCCeECHHHccc
Confidence            6 79999999999999876543 488877644

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {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: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=90.53  E-value=0.11  Score=46.84  Aligned_cols=26  Identities=38%  Similarity=0.483  Sum_probs=22.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      .++++|.-|+||||++-++|..+...
T Consensus        10 ~i~~sGKGGVGKTTvaa~lA~~lA~~   35 (296)
T d1ihua1          10 YLFFTGKGGVGKTSISCATAIRLAEQ   35 (296)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCcChHHHHHHHHHHHHHHC
Confidence            37899999999999999999988654

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {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: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=90.53  E-value=0.051  Score=45.33  Aligned_cols=22  Identities=27%  Similarity=0.471  Sum_probs=19.3

Q ss_pred             CceeEeCCCCCChHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~  328 (533)
                      +++.|.|.||+||||+++++..
T Consensus         2 ~~VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           2 ADVGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             CSEEEECCGGGCHHHHHHHHCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4688999999999999999864

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=90.45  E-value=0.072  Score=51.36  Aligned_cols=37  Identities=24%  Similarity=0.324  Sum_probs=27.0

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecC
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNA  345 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~  345 (533)
                      ..|+++.|++|+|||++++.+...+...   +..++.+++
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li~~~~~~---g~~~iiiD~   86 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELAYTGLLR---GDRMVIVDP   86 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHT---TCEEEEEEE
T ss_pred             cceEEEEeCCCCcHHHHHHHHHHHHHhC---CCCEEEEeC
Confidence            3489999999999999998887776543   334444443

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {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: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=90.06  E-value=0.1  Score=44.72  Aligned_cols=26  Identities=19%  Similarity=0.183  Sum_probs=22.4

Q ss_pred             ceeEeCC-CCCChHHHHHHHHHHHccc
Q psy4285         308 HLLFYGP-PGTGKTTTILACARKLYTK  333 (533)
Q Consensus       308 ~~ll~Gp-pGtGKT~la~~la~~l~~~  333 (533)
                      .++++|- +|+||||++-.+|..+...
T Consensus         3 ~~~i~gt~~GVGKTtvs~~La~aLa~~   29 (224)
T d1byia_           3 RYFVTGTDTEVGKTVASCALLQAAKAA   29 (224)
T ss_dssp             EEEEEESSTTSCHHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCccHHHHHHHHHHHHHHC
Confidence            3788888 6999999999999998655

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {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: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=89.90  E-value=0.044  Score=45.74  Aligned_cols=23  Identities=17%  Similarity=0.273  Sum_probs=19.8

Q ss_pred             CCCceeEeCCCCCChHHHHHHHH
Q psy4285         305 ELPHLLFYGPPGTGKTTTILACA  327 (533)
Q Consensus       305 ~~~~~ll~GppGtGKT~la~~la  327 (533)
                      ..+.+.|.|+|++||||+.+++.
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~   37 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLT   37 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHh
Confidence            34569999999999999998884

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=89.71  E-value=0.068  Score=44.73  Aligned_cols=21  Identities=24%  Similarity=0.385  Sum_probs=18.3

Q ss_pred             CceeEeCCCCCChHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACA  327 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la  327 (533)
                      +.+-|.|+||+||||+.+++.
T Consensus         2 ~~VaiiG~~nvGKSSLin~L~   22 (185)
T d1lnza2           2 ADVGLVGFPSVGKSTLLSVVS   22 (185)
T ss_dssp             CCEEEESSTTSSHHHHHHHSE
T ss_pred             CeEEEECCCCCCHHHHHHHHh
Confidence            357899999999999998875

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal 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: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.31  E-value=0.066  Score=46.56  Aligned_cols=24  Identities=29%  Similarity=0.336  Sum_probs=20.7

Q ss_pred             CCceeEeCCCCCChHHHHHHHHHH
Q psy4285         306 LPHLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       306 ~~~~ll~GppGtGKT~la~~la~~  329 (533)
                      .|-.+++|..|+||||+.+.+.+.
T Consensus         3 iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           3 IAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             EEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCEEEEeeCCCCCHHHHHHHHHhc
Confidence            355799999999999999988875

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {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: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=89.24  E-value=0.096  Score=43.72  Aligned_cols=20  Identities=30%  Similarity=0.419  Sum_probs=18.5

Q ss_pred             eeEeCCCCCChHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~  328 (533)
                      +.+.|.+|+||||++.++..
T Consensus        11 V~iiG~~~~GKSTLin~l~~   30 (186)
T d1mkya2          11 VAIVGRPNVGKSTLFNAILN   30 (186)
T ss_dssp             EEEECSTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHC
Confidence            88999999999999999875

>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=89.20  E-value=0.23  Score=46.73  Aligned_cols=80  Identities=18%  Similarity=0.142  Sum_probs=65.3

Q ss_pred             CceEEEEEcCCC----CcCchhhhccceeEEeCCCCHHHHHHHHHHHHh----hcCCCCCHHHHHHHHHhcC------CC
Q psy4285           6 TNVRFCIICNYL----SKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIE----QEKVNVTPDGKKAIIDLSD------GD   71 (533)
Q Consensus         6 ~~~~~il~~~~~----~~i~~~i~SRc~~~~~~~~~~~~~~~~l~~~~~----~~~~~~~~~~~~~~~~~~~------g~   71 (533)
                      +.+++|.+|++.    +.-.|++..|++.+.+.+|+.++...+|+.+..    ..++.++++++..++..|+      .=
T Consensus       150 g~~~~I~~tT~~ey~~~e~d~al~rrF~~v~v~ep~~~~~~~il~~~~~~~e~~h~v~~~~~ai~~~v~ls~ryi~~r~~  229 (387)
T d1qvra2         150 GELRLIGATTLDEYREIEKDPALERRFQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRL  229 (387)
T ss_dssp             TCCCEEEEECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCT
T ss_pred             CCcceeeecCHHHHHHhcccHHHHHhcccccCCCCcHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHhcccccccccC
Confidence            456777777421    123789999999999999999999999997764    4578999999999988776      67


Q ss_pred             HHHHHHHHHHHHHh
Q psy4285          72 MRKVLNILQSAATA   85 (533)
Q Consensus        72 ~r~a~~~l~~~~~~   85 (533)
                      +.+|+.+|+.++..
T Consensus       230 PdKAidlld~a~a~  243 (387)
T d1qvra2         230 PDKAIDLIDEAAAR  243 (387)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHH
Confidence            89999999998764

>d1c9ka_ c.37.1.11 (A:) Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU {Salmonella typhimurium [TaxId: 90371]}

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: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU
species: Salmonella typhimurium [TaxId: 90371]

Probab=88.82  E-value=0.43  Score=39.46  Aligned_cols=19  Identities=26%  Similarity=0.319  Sum_probs=17.1

Q ss_pred             eeEeCCCCCChHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACA  327 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la  327 (533)
                      +|++|+.++|||..|..++
T Consensus         2 iLVtGGarSGKS~~AE~l~   20 (180)
T d1c9ka_           2 ILVTGGARSGKSRHAEALI   20 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHH
T ss_pred             EEEECCCCccHHHHHHHHH
Confidence            5899999999999998775

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {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: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=88.80  E-value=0.043  Score=46.53  Aligned_cols=25  Identities=32%  Similarity=0.420  Sum_probs=22.0

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      .+|+||.|+||||+..||.-.+.+.
T Consensus        27 tvi~G~NGsGKStil~Ai~~~L~g~   51 (222)
T d1qhla_          27 TTLSGGNGAGKSTTMAAFVTALIPD   51 (222)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHHSCC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcCC
Confidence            6899999999999999999877543

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {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: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=88.75  E-value=0.15  Score=45.60  Aligned_cols=25  Identities=36%  Similarity=0.473  Sum_probs=22.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK  333 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~  333 (533)
                      ++++|.=|+||||++-.+|..+...
T Consensus        23 ii~sGKGGVGKTT~a~nLA~~lA~~   47 (279)
T d1ihua2          23 IMLMGKGGVGKTTMAAAIAVRLADM   47 (279)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC
Confidence            7888999999999999999988654

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

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: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=88.40  E-value=1.7  Score=38.29  Aligned_cols=24  Identities=25%  Similarity=0.484  Sum_probs=21.4

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.+++.|++|+|||+++..+++..
T Consensus        69 Qr~~If~~~g~GKt~l~~~i~~~~   92 (276)
T d2jdid3          69 GKIGLFGGAGVGKTVLIMELINNV   92 (276)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CEEEeeCCCCCCHHHHHHHHHHHH
Confidence            359999999999999999998875

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase 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: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=88.32  E-value=0.039  Score=44.95  Aligned_cols=21  Identities=24%  Similarity=0.461  Sum_probs=19.3

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +.|.|.||+||||+++++...
T Consensus         3 I~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            689999999999999999765

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {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: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.28  E-value=0.11  Score=43.73  Aligned_cols=18  Identities=28%  Similarity=0.482  Sum_probs=17.3

Q ss_pred             eeEeCCCCCChHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILAC  326 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~l  326 (533)
                      +++.|.+|+|||++++.+
T Consensus         5 ivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            799999999999999998

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.95  E-value=0.15  Score=42.33  Aligned_cols=22  Identities=23%  Similarity=0.214  Sum_probs=19.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++.|++|+|||+++..+...-
T Consensus         8 i~vlG~~~vGKTsLi~~~~~~~   29 (175)
T d2bmja1           8 LGVLGDARSGKSSLIHRFLTGS   29 (175)
T ss_dssp             EEEECCTTTTHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            8999999999999999887643

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=87.60  E-value=1.4  Score=39.50  Aligned_cols=24  Identities=21%  Similarity=0.214  Sum_probs=19.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         308 HLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +.+|.=..|+|||..+-++...+.
T Consensus        81 g~iLaDemGlGKT~qaia~l~~l~  104 (298)
T d1z3ix2          81 GCIMADEMGLGKTLQCITLIWTLL  104 (298)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             ceEEEeCCCCCHHHHHHHHHHHHH
Confidence            478888999999998877766554

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=87.57  E-value=0.16  Score=45.64  Aligned_cols=25  Identities=28%  Similarity=0.400  Sum_probs=22.0

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +..++.||+|||||+++..+++...
T Consensus        44 Qr~~I~g~~g~GKT~l~~~i~~~~~   68 (289)
T d1xpua3          44 QRGLIVAPPKAGKTMLLQNIAQSIA   68 (289)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHHHH
T ss_pred             CeeeEeCCCCCCHHHHHHHHHHHHh
Confidence            3599999999999999999998663

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=87.42  E-value=1.4  Score=35.92  Aligned_cols=21  Identities=29%  Similarity=0.300  Sum_probs=18.9

Q ss_pred             ceeEeCCCCCChHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACAR  328 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~  328 (533)
                      ++-+.|.|++||||+..++.+
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            478999999999999999974

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=86.59  E-value=0.13  Score=47.41  Aligned_cols=23  Identities=30%  Similarity=0.251  Sum_probs=21.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~  331 (533)
                      +.|-|+-|+||||+++.+++.+.
T Consensus         9 I~iEG~iGsGKSTl~~~L~~~l~   31 (333)
T d1p6xa_           9 IYLDGVYGIGKSTTGRVMASAAS   31 (333)
T ss_dssp             EEEECSTTSSHHHHHHHHHSGGG
T ss_pred             EEEECCccCCHHHHHHHHHHHhc
Confidence            78999999999999999999873

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=86.13  E-value=0.18  Score=43.58  Aligned_cols=21  Identities=29%  Similarity=0.382  Sum_probs=18.8

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|++|+|||++++.+...
T Consensus         9 illlG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           9 LLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            899999999999999988543

>d1jqlb_ c.37.1.20 (B:) delta 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 subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=85.30  E-value=1.7  Score=33.90  Aligned_cols=110  Identities=10%  Similarity=0.036  Sum_probs=66.0

Q ss_pred             hhcccccccCCCceeEeCCCCCChHHHHHHHHHHHccccccCcceEEecCCCCCchhHHHHHHHHHHhcccCCCCCcEEE
Q psy4285         296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLI  375 (533)
Q Consensus       296 ~l~~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl  375 (533)
                      ++.+.++.+-.|-.+|+|+---=+......+-+.+...+ +. .........   .....+.+.. ..+.+.+ +..+++
T Consensus         8 ~L~~~l~k~l~~vyll~G~E~~L~~~~~~~i~~~~~~~~-~~-~~~~~~~~~---~~~~~~l~~~-~~t~slF-~~krli   80 (140)
T d1jqlb_           8 QLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQG-FE-EHHTFSIDP---NTDWNAIFSL-CQAMSLF-ASRQTL   80 (140)
T ss_dssp             GHHHHHHHCCCSEEEEESSCHHHHHHHHHHHHHHHHHTT-CC-EEECCCCST---TCCHHHHHHH-HHCCCTT-CCCEEE
T ss_pred             HHHHHHhcCCCcEEEEEcChHHHHHHHHHHHHHHHHhCC-cc-eeeeecccc---cCCHHHHHHH-HcCCCcc-cCcEEE
Confidence            344455555344489999887777777777766554332 11 111111111   1123333333 3333333 678899


Q ss_pred             EEeCCCCC-CHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q psy4285         376 ILDEADAM-TNDAQNALRRIIEKFTTNVRFCIICNYLS  412 (533)
Q Consensus       376 iiDE~d~l-~~~~~~~Ll~~le~~~~~~~~I~~~n~~~  412 (533)
                      +|++.+.. +......|.+.++.+++.+.+|++++..+
T Consensus        81 ~i~~~~~~~~k~~~~~L~~~~~~~~~~~~lii~~~~~~  118 (140)
T d1jqlb_          81 LLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLS  118 (140)
T ss_dssp             EEECCTTCSCTTHHHHHHHHHHHCCSSCCEEEECSSCC
T ss_pred             EEEcCCCCCcHHHHHHHHHHHhCCCCCEEEEEEcCCCC
Confidence            99988655 45667789999999888898998887554

>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=85.18  E-value=0.67  Score=42.16  Aligned_cols=77  Identities=16%  Similarity=0.239  Sum_probs=47.7

Q ss_pred             cCccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhhhH---------------HHHhhhhhcccccCCCc
Q psy4285         139 SDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVR---------------DQIFQFASTKTMHKSSY  203 (533)
Q Consensus       139 ~~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~~~---------------d~i~~~a~~~~l~~~~~  203 (533)
                      +-+.+.||+|+|||..+..++..+.+.  ...++.+|.++........               ..+.++..     ....
T Consensus        54 ~~~lf~Gp~G~GKt~lak~la~~l~~~--~~~~~~~~~~~~~~~~~~~~L~g~~~gyvG~~~~~~l~~~~~-----~~p~  126 (315)
T d1qvra3          54 GSFLFLGPTGVGKTELAKTLAATLFDT--EEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVR-----RRPY  126 (315)
T ss_dssp             EEEEEBSCSSSSHHHHHHHHHHHHHSS--GGGEEEECTTTCCSSGGGGGC--------------CHHHHHH-----HCSS
T ss_pred             eEEEEECCCcchHHHHHHHHHHHhcCC--CcceEEEeccccccchhhhhhcCCCCCCcCcccCChHHHHHH-----hCCC
Confidence            346788999999888777776665321  2467777766544322211               12211111     1223


Q ss_pred             eEEEEcCccccCHHHHHHH
Q psy4285         204 KLIILDEADAMTNDAQNAL  222 (533)
Q Consensus       204 ~~iilDE~d~l~~~a~~~L  222 (533)
                      .++++||+|.+..+.+..|
T Consensus       127 ~Vvl~DEieK~~~~v~~~l  145 (315)
T d1qvra3         127 SVILFDEIEKAHPDVFNIL  145 (315)
T ss_dssp             EEEEESSGGGSCHHHHHHH
T ss_pred             cEEEEehHhhcCHHHHHHH
Confidence            4999999999999888865

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {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: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.70  E-value=0.22  Score=41.74  Aligned_cols=22  Identities=32%  Similarity=0.323  Sum_probs=19.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      +++.|.+|+|||++.+.+...-
T Consensus         5 iv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            7999999999999999986654

>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=84.57  E-value=0.41  Score=43.64  Aligned_cols=74  Identities=18%  Similarity=0.194  Sum_probs=45.3

Q ss_pred             cCccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchh---------h-----hH-HHHhhhhhcccccCCCc
Q psy4285         139 SDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIG---------I-----VR-DQIFQFASTKTMHKSSY  203 (533)
Q Consensus       139 ~~~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~---------~-----~~-d~i~~~a~~~~l~~~~~  203 (533)
                      +.+.+.||+|+|||..+.+++..+.     ..++.+|+++....+         .     .. ..+..+     +.....
T Consensus        53 ~~~lf~Gp~GvGKT~lak~la~~l~-----~~~i~~d~s~~~~~~~~~~l~g~~~gy~g~~~~~~l~~~-----~~~~~~  122 (315)
T d1r6bx3          53 GSFLFAGPTGVGKTEVTVQLSKALG-----IELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDA-----VIKHPH  122 (315)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHT-----CEEEEEEGGGCSSSSCCSSSCCCCSCSHHHHHTTHHHHH-----HHHCSS
T ss_pred             eEEEEECCCcchhHHHHHHHHhhcc-----CCeeEeccccccchhhhhhhcccCCCccccccCChhhHH-----HHhCcc
Confidence            4567899999999888888776654     455556654432111         1     11 111111     111233


Q ss_pred             eEEEEcCccccCHHHHHHH
Q psy4285         204 KLIILDEADAMTNDAQNAL  222 (533)
Q Consensus       204 ~~iilDE~d~l~~~a~~~L  222 (533)
                      .++++||+|.+.++.+.+|
T Consensus       123 ~vvl~DeieKa~~~V~~~l  141 (315)
T d1r6bx3         123 AVLLLDEIEKAHPDVFNIL  141 (315)
T ss_dssp             EEEEEETGGGSCHHHHHHH
T ss_pred             chhhhcccccccchHhhhh
Confidence            4999999999998888755

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=84.15  E-value=1.3  Score=37.97  Aligned_cols=24  Identities=25%  Similarity=0.230  Sum_probs=20.7

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      |-+-+.|.|++||||++.++....
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~~~   29 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRGSA   29 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEeCCCccHHHHHHHHHhhc
Confidence            448889999999999999998764

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=84.03  E-value=0.6  Score=35.47  Aligned_cols=35  Identities=3%  Similarity=-0.023  Sum_probs=26.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccc-cccCcceEEecC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTK-AQFNAMVLELNA  345 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~-~~~~~~~~~~~~  345 (533)
                      ++|+|-+|+||+++|+++...+... +  ++.+--++.
T Consensus         9 i~~tg~~~~gk~~ia~al~~~l~q~~G--~R~vtll~~   44 (122)
T d1g8fa3           9 IVLGNSLTVSREQLSIALLSTFLQFGG--GRYYKIFEH   44 (122)
T ss_dssp             EEECTTCCSCHHHHHHHHHHHHTTSCS--CCCEEECCC
T ss_pred             EEEeCCCCCCHHHHHHHHHHHHHHhcC--CcceEEecC
Confidence            8999999999999999998888552 3  344444433

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=83.84  E-value=0.26  Score=45.31  Aligned_cols=24  Identities=25%  Similarity=0.307  Sum_probs=21.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHcc
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYT  332 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~  332 (533)
                      +.|-|+-|+||||+++.+++.+..
T Consensus         8 I~IEG~iGsGKSTl~~~L~~~l~~   31 (331)
T d1osna_           8 IYLDGAYGIGKTTAAEEFLHHFAI   31 (331)
T ss_dssp             EEEEESSSSCTTHHHHHHHHTTTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhh
Confidence            789999999999999999998743

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=83.56  E-value=0.18  Score=44.65  Aligned_cols=39  Identities=10%  Similarity=0.014  Sum_probs=31.4

Q ss_pred             ccccccCCCChhhHHHHHHHHHhcccccceeeeecCCcccchhh
Q psy4285         141 IEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGI  184 (533)
Q Consensus       141 ~~~~~~~G~~~~~~l~~~~~~~~~~~~~~~~~e~nasd~~g~~~  184 (533)
                      +...||||+|||+.+.+++..+.     ..++.+|+++++....
T Consensus        35 ilL~GpPGtGKT~la~~la~~~~-----~~~~~i~~d~~~~~~~   73 (273)
T d1gvnb_          35 FLLGGQPGSGKTSLRSAIFEETQ-----GNVIVIDNDTFKQQHP   73 (273)
T ss_dssp             EEEECCTTSCTHHHHHHHHHHTT-----TCCEEECTHHHHTTST
T ss_pred             EEEECCCCCCHHHHHHHHHHHhh-----cceEEEecHHHHHHhc
Confidence            66889999999999998888876     5788899977654433

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

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: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=83.02  E-value=1.5  Score=38.70  Aligned_cols=23  Identities=26%  Similarity=0.237  Sum_probs=18.9

Q ss_pred             CceeEeCCCCCChHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~  329 (533)
                      +.+++.|++|+|||+++..++..
T Consensus        68 Qr~~Ifg~~g~GKt~l~~~~~~~   90 (276)
T d1fx0a3          68 QRELIIGDRQTGKTAVATDTILN   90 (276)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHT
T ss_pred             ceEeeccCCCCChHHHHHHHHhh
Confidence            35899999999999999876543

>d1j3ba1 c.91.1.1 (A:212-529) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Thermus thermophilus [TaxId: 274]

Probab=82.96  E-value=0.19  Score=45.58  Aligned_cols=17  Identities=47%  Similarity=0.718  Sum_probs=14.9

Q ss_pred             eeEeCCCCCChHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILA  325 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~  325 (533)
                      .+|+|.+|||||||...
T Consensus        17 alffGLSGTGKTTLs~~   33 (318)
T d1j3ba1          17 AVFFGLSGTGKTTLSTD   33 (318)
T ss_dssp             EEEEECTTSCHHHHTCB
T ss_pred             EEEEccCCCCccccccC
Confidence            69999999999997743

>d2olra1 c.91.1.1 (A:228-540) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Escherichia coli [TaxId: 562]

Probab=82.87  E-value=0.24  Score=44.67  Aligned_cols=16  Identities=50%  Similarity=0.769  Sum_probs=14.4

Q ss_pred             eeEeCCCCCChHHHHH
Q psy4285         309 LLFYGPPGTGKTTTIL  324 (533)
Q Consensus       309 ~ll~GppGtGKT~la~  324 (533)
                      .+|.|.+|||||||..
T Consensus        17 alfFGLSGTGKTTLs~   32 (313)
T d2olra1          17 AVFFGLSGTGKTTLST   32 (313)
T ss_dssp             EEEECSTTSSHHHHHC
T ss_pred             EEEEccCCCCccccee
Confidence            6999999999999874

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=82.18  E-value=0.33  Score=40.26  Aligned_cols=21  Identities=29%  Similarity=0.385  Sum_probs=18.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      +++.|..|+|||++++.+...
T Consensus         5 ivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            799999999999999987644

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=81.99  E-value=5.9  Score=34.50  Aligned_cols=23  Identities=35%  Similarity=0.364  Sum_probs=20.1

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      |+.+.|..|+||||++.++....
T Consensus         4 Nv~iiGh~~~GKTtL~e~ll~~~   26 (267)
T d2dy1a2           4 TVALVGHAGSGKTTLTEALLYKT   26 (267)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHc
Confidence            68889999999999999997543

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

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: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=81.89  E-value=3.4  Score=36.50  Aligned_cols=24  Identities=25%  Similarity=0.263  Sum_probs=20.1

Q ss_pred             CceeEeCCCCCChHHHHHHHHHHH
Q psy4285         307 PHLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       307 ~~~ll~GppGtGKT~la~~la~~l  330 (533)
                      +.+.+.|++|+|||+++..++...
T Consensus        69 Qr~~If~~~g~GKt~ll~~~~~~~   92 (285)
T d2jdia3          69 QRELIIGDRQTGKTSIAIDTIINQ   92 (285)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHHT
T ss_pred             CEEEeecCCCCChHHHHHHHHHhH
Confidence            358999999999999998887653

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {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: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=81.85  E-value=9.9  Score=31.34  Aligned_cols=23  Identities=26%  Similarity=0.114  Sum_probs=19.7

Q ss_pred             ceeEeCCCCCChHHHHHHHHHHH
Q psy4285         308 HLLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       308 ~~ll~GppGtGKT~la~~la~~l  330 (533)
                      |+.+.|-++.|||||+.++....
T Consensus         5 ni~iiGhvd~GKSTL~~~Ll~~~   27 (204)
T d2c78a3           5 NVGTIGHVDHGKTTLTAALTYVA   27 (204)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHh
Confidence            37889999999999999997543

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=81.61  E-value=0.26  Score=44.58  Aligned_cols=21  Identities=33%  Similarity=0.439  Sum_probs=18.6

Q ss_pred             eeEeCCCCCChHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARK  329 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~  329 (533)
                      -+|+||.|+|||++..|+.-.
T Consensus        27 nvlvG~NgsGKS~iL~Ai~~~   47 (308)
T d1e69a_          27 TAIVGPNGSGKSNIIDAIKWV   47 (308)
T ss_dssp             EEEECCTTTCSTHHHHHHHHT
T ss_pred             EEEECCCCCcHHHHHHHHHHH
Confidence            589999999999999999643

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=81.40  E-value=0.24  Score=45.36  Aligned_cols=22  Identities=36%  Similarity=0.372  Sum_probs=18.9

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      |.|-|+-|+||||+++.+++.+
T Consensus         7 I~IEG~iGsGKTTl~~~La~~l   28 (329)
T d1e2ka_           7 VYIDGPHGMGKTTTTQLLVALG   28 (329)
T ss_dssp             EEECSCTTSSHHHHHHHHTC--
T ss_pred             EEEECCcCCCHHHHHHHHHHHh
Confidence            6789999999999999998876

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.18  E-value=0.34  Score=45.89  Aligned_cols=22  Identities=32%  Similarity=0.448  Sum_probs=19.2

Q ss_pred             eeEeCCCCCChHHHHHHHHHHH
Q psy4285         309 LLFYGPPGTGKTTTILACARKL  330 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l  330 (533)
                      -+|+||.|+|||++..||.-.+
T Consensus        28 ~~i~G~NGsGKS~ileAi~~~l   49 (427)
T d1w1wa_          28 TSIIGPNGSGKSNMMDAISFVL   49 (427)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4899999999999999997443

>d1lkxa_ c.37.1.9 (A:) Myosin S1, motor domain {Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]

Probab=81.15  E-value=0.36  Score=49.08  Aligned_cols=33  Identities=21%  Similarity=0.247  Sum_probs=26.2

Q ss_pred             ccccccCCCceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         299 RFIDENELPHLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       299 ~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .+...++...+++.|.+|+|||+.++.+.+.+.
T Consensus        79 ~l~~~~~~QsIiisGeSGsGKTe~~k~il~yL~  111 (684)
T d1lkxa_          79 SMRQSQENQCVIISGESGAGKTEASKKIMQFLT  111 (684)
T ss_dssp             HHHHHCCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HHHHcCCCeEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            344444545699999999999999999998873

>d1ii2a1 c.91.1.1 (A:201-523) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Trypanosoma cruzi [TaxId: 5693]

Probab=80.97  E-value=0.31  Score=44.08  Aligned_cols=16  Identities=50%  Similarity=0.769  Sum_probs=14.7

Q ss_pred             eeEeCCCCCChHHHHH
Q psy4285         309 LLFYGPPGTGKTTTIL  324 (533)
Q Consensus       309 ~ll~GppGtGKT~la~  324 (533)
                      .+|.|-+||||||+..
T Consensus        17 alfFGLSGTGKTTLs~   32 (323)
T d1ii2a1          17 TVFFGLSGTGKTTLSA   32 (323)
T ss_dssp             EEEECCTTSSHHHHHC
T ss_pred             EEEEccCCCCccccee
Confidence            6899999999999984

>d1d0xa2 c.37.1.9 (A:2-33,A:80-759) Myosin S1, motor domain {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=80.64  E-value=0.39  Score=49.04  Aligned_cols=33  Identities=27%  Similarity=0.415  Sum_probs=26.0

Q ss_pred             ccccccCCCceeEeCCCCCChHHHHHHHHHHHc
Q psy4285         299 RFIDENELPHLLFYGPPGTGKTTTILACARKLY  331 (533)
Q Consensus       299 ~~~~~~~~~~~ll~GppGtGKT~la~~la~~l~  331 (533)
                      .++..++...+++.|.+|+|||..++.+.+.+.
T Consensus       118 ~m~~~~~nQsIiisGeSGaGKTe~~k~il~yL~  150 (712)
T d1d0xa2         118 SMLDDRQNQSLLITGESGAGKTENTKKVIQYLA  150 (712)
T ss_dssp             HHHHHTCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HHHHhCCCceEEEeCCCCCCHHHHHHHHHHHHH
Confidence            344444444699999999999999999988764

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=80.32  E-value=0.56  Score=41.45  Aligned_cols=36  Identities=28%  Similarity=0.362  Sum_probs=26.7

Q ss_pred             eeEeCCCCCChHHHHHHHHHHHccccccCcceEEecC
Q psy4285         309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNA  345 (533)
Q Consensus       309 ~ll~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~  345 (533)
                      +-++|.=|+||||++-.+|..+...+ ....++.++.
T Consensus         4 Iai~gKGGvGKTT~a~nLA~~LA~~G-~rVllID~D~   39 (269)
T d1cp2a_           4 VAIYGKGGIGKSTTTQNLTSGLHAMG-KTIMVVGCDP   39 (269)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHTTT-CCEEEEEECT
T ss_pred             EEEECCCcCCHHHHHHHHHHHHHhCC-CcEEEEecCC
Confidence            55789999999999999999986542 3344555543