Citrus Sinensis ID: 042806

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390
Protein Sequence
MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQKEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQLTLKIYNQRHIKL
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHcHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHccccccEEEEEccccccHHHHHHHHHHHHHHcccccEEEEEEEcccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccEEEEEEccccccccccccccccccccccEEEEEEccHHHHHccccccccEEcccccHHHHHHHHHHHHccccccccHHHHHHHHHHHccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHcccccEEccccccccccccccccccccccHHHHHHHHHHHHHccccEEEEEEEcccccHHHHHHHHHHHHHHcccccEEEEEEEcccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHccccEEEEEcccccHccHHHccccccccccccEEEEEEccHHHHHHHccccccEEEccccHHHHHHHHHHHcccccccccHHHHHHHHHHHccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccccccccc
Coil and Loop (DISEMBL)
MADIILSVVVEVAKclappiycqmsylrkskytsnlqnlktevgipeaervSKQREVDKAKRRGEEIEEYVEKWLTSVNGIIDeaekftgvdarankrcfkglcpnlktRRRLSKEAERQKEAIVKVREVgrfdrisyniipddtllLSIKDYEACESRMSTLNDILDalknpdvnmlgiygmggiVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLtlheesdsGRARSLRNRLKKEKTILVILDNIwgnldfqavgiphgddrkgCKVLLTARSLDVLSRkmdsqqnfsvgvLKEDEAWSLFKKMAGdyiegsefKWVAKDVARECAGLPVSIVTVARALgtrdylngrthwnswgGLLQLTLKIYNQRHIKL
Flexible Loop (DISEMBL)
MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLktevgipeaervskqrevdkakrrgeeIEEYVEKWLTSVNGIIDEAEKftgvdarankrcfkglcpnlktrrrlskeaerqkeaivkvrevgrfdrisyniipddtllLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAeteklfdqvIFVEVSKIQDIRKIQGEIADKlgltlheesdsgrarslrnrlkkekTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLdvlsrkmdsqqnfsvgvlkeDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQLTLKIYNQRHIKL
Low Complexity Region (SEG)
MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQKEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQLTLKIYNQRHIKL
Disordered region (IsUnstruct)
***IILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNL******************************IEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLK**************AIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTL******************EKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQLTLKIYNQ*****
Disordered Region (DISOPRED)
MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAER**************************************SRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL*****************NRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQLT***********
Disordered Region (DISEMBL)
MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEA***************GEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTR**********KEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLH**********LRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQLTLKIYNQRHIKL
Disordered Region (DISPRO)
MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQKEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQL************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTxxxxxxxxxxxxxxxxxxxxxGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQLTLKIYNQRHIKL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	390	2.2.26 [Sep-21-2011]
Q9T048	985	Disease resistance protei	yes	no	0.497	0.196	0.407	3e-32
O64973	889	Disease resistance protei	no	no	0.869	0.381	0.304	3e-30
O22727	967	Probable disease resistan	no	no	0.884	0.356	0.287	1e-29
Q940K0	889	Probable disease resistan	no	no	0.864	0.379	0.295	1e-28
O64789	925	Probable disease resistan	no	no	0.843	0.355	0.293	2e-28
O81825	919	Probable disease resistan	no	no	0.466	0.198	0.380	6e-28
Q8L3R3	885	Disease resistance protei	no	no	0.858	0.378	0.269	2e-27
O23317	719	Probable disease resistan	no	no	0.776	0.421	0.267	3e-27
P60838	894	Probable disease resistan	no	no	0.828	0.361	0.295	4e-27
Q9C8T9	898	Putative disease resistan	no	no	0.830	0.360	0.276	4e-27

>sp|Q9T048|DRL27_ARATH Disease resistance protein At4g27190 OS=Arabidopsis thaliana GN=At4g27190 PE=2 SV=1

 Score =  139 bits (351), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 81/199 (40%), Positives = 121/199 (60%), Gaps = 5/199 (2%)

Query: 163 LNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETE---KLFDQVIFVEVSKIQDI 219
           L  I D L +     +G++GMGG+ KTTL + +  K   E   + F  VIFV VSK  D 
Sbjct: 152 LAKIRDGLTSEKAQKIGVWGMGGVGKTTLVRTLNNKLREEGATQPFGLVIFVIVSKEFDP 211

Query: 220 RKIQGEIADKLGL-TLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGD 278
           R++Q +IA++L + T  EES+   AR +   L KE+  L+ILD++W  +D   +GIP  +
Sbjct: 212 REVQKQIAERLDIDTQMEESEEKLARRIYVGLMKERKFLLILDDVWKPIDLDLLGIPRTE 271

Query: 279 DRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKD 338
           + KG KV+LT+R L+V  R M +  +  V  L E++AW LF K AGD +     + +AK 
Sbjct: 272 ENKGSKVILTSRFLEV-CRSMKTDLDVRVDCLLEEDAWELFCKNAGDVVRSDHVRKIAKA 330

Query: 339 VARECAGLPVSIVTVARAL 357
           V++EC GLP++I+TV  A+
Sbjct: 331 VSQECGGLPLAIITVGTAM 349

Disease resistance protein.
Arabidopsis thaliana (taxid: 3702)

>sp|O64973|RPS5_ARATH Disease resistance protein RPS5 OS=Arabidopsis thaliana GN=RPS5 PE=1 SV=2

 Score =  133 bits (334), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 111/365 (30%), Positives = 178/365 (48%), Gaps = 26/365 (7%)

Query: 21  YCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEY---------V 71
           + Q+  +R S Y  NL   K    + +A R+ K R+ D  +R   E EE+         V
Sbjct: 18  FSQLLCVRGS-YIHNLS--KNLASLQKAMRMLKARQYDVIRRL--ETEEFTGRQQRLSQV 72

Query: 72  EKWLTSVNGIIDEAEKFT-GVDARANKRCFKGLCP-NLKTRRRLSKEAERQKEAIVKVRE 129
           + WLTSV  I ++        +    + C  G C  +LK   R  K      + +  +  
Sbjct: 73  QVWLTSVLIIQNQFNDLLRSNEVELQRLCLCGFCSKDLKLSYRYGKRVIMMLKEVESLSS 132

Query: 130 VGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKT 189
            G FD +S      D   +  +     +  M  L    + L      +LG+YGMGG+ KT
Sbjct: 133 QGFFDVVSEATPFADVDEIPFQPTIVGQEIM--LEKAWNRLMEDGSGILGLYGMGGVGKT 190

Query: 190 TLAKEVARK-AETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGL---TLHEESDSGRARS 245
           TL  ++  K ++ +  FD VI+V VS+   +RKIQ +IA+K+GL      E++D+  A  
Sbjct: 191 TLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGMEWSEKNDNQIAVD 250

Query: 246 LRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNF 305
           + N L++ K +L +LD+IW  ++ +AVG+P+     GCKV  T RS DV  R M      
Sbjct: 251 IHNVLRRRKFVL-LLDDIWEKVNLKAVGVPYPSKDNGCKVAFTTRSRDVCGR-MGVDDPM 308

Query: 306 SVGVLKEDEAWSLFKKMAGDYIEGS--EFKWVAKDVARECAGLPVSIVTVARALGTRDYL 363
            V  L+ +E+W LF+   G    GS  +   +A+ VAR+C GLP+++  +  A+  +  +
Sbjct: 309 EVSCLQPEESWDLFQMKVGKNTLGSHPDIPGLARKVARKCRGLPLALNVIGEAMACKRTV 368

Query: 364 NGRTH 368
           +   H
Sbjct: 369 HEWCH 373

Disease resistance (R) protein that specifically recognizes the avrPphB type III effector avirulence protein from Pseudomonas syringae. Also confers resistance against Hyaloperonospora parasitica (downy mildew). Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. Requires PBS1 to trigger the defense reaction against avrPphB. Probably triggers the defense mechanism when PBS1 is cleaved by avrPphB, suggesting that it detects indirectly the protease activity of avrPphB, and possibly binds to the cleaved RPS5.

Arabidopsis thaliana (taxid: 3702)

>sp|O22727|DRL16_ARATH Probable disease resistance protein At1g61190 OS=Arabidopsis thaliana GN=At1g61190 PE=3 SV=1

 Score =  131 bits (329), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 105/365 (28%), Positives = 180/365 (49%), Gaps = 20/365 (5%)

Query: 12  VAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEYV 71
           + +CL     C   Y+R  +   NL+ L+ E+    A +   Q +V + + R ++  E V
Sbjct: 18  IIRCL-----CGKGYIRNLE--KNLRALQREMEDLRATQHEVQNKVAREESRHQQRLEAV 70

Query: 72  EKWLTSVNGIIDEAEKFTGVDA-RANKRCFKGLCPN-LKTRRRLSKEAERQKEAIVKVRE 129
           + WL  VN I  E +    V      K C  GLC   + +  +  K      E + K++ 
Sbjct: 71  QVWLDRVNSIDIECKDLLSVSPVELQKLCLCGLCSKYVCSSYKYGKRVFLLLEEVTKLKS 130

Query: 130 VGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKT 189
            G FD +S    P     +  +  +    +   L    + L    V ++G++GMGG+ KT
Sbjct: 131 EGNFDEVSQ---PPPRSEVEERPTQPTIGQEEMLKKAWNRLMEDGVGIMGLHGMGGVGKT 187

Query: 190 TLAKEVARK-AETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLT---LHEESDSGRARS 245
           TL K++  K AET   FD VI++ VS+   + K+Q +IA+KL L       +++S +A  
Sbjct: 188 TLFKKIHNKFAETGGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLCDDLWKNKNESDKATD 247

Query: 246 LRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNF 305
           + +R+ K K  +++LD+IW  +D +A+GIP+  +   CKV  T R   V   +M   +  
Sbjct: 248 I-HRVLKGKRFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRDQKVCG-QMGDHKPM 305

Query: 306 SVGVLKEDEAWSLFKKMAGDYIEGSEFKWV--AKDVARECAGLPVSIVTVARALGTRDYL 363
            V  L+ ++AW LFK   GD    S+   V  A++VA++C GLP+++  +   + ++  +
Sbjct: 306 QVKCLEPEDAWELFKNKVGDNTLRSDPVIVGLAREVAQKCRGLPLALSCIGETMASKTMV 365

Query: 364 NGRTH 368
               H
Sbjct: 366 QEWEH 370

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q940K0|DRL15_ARATH Probable disease resistance protein At1g61180 OS=Arabidopsis thaliana GN=At1g61180 PE=2 SV=2

 Score =  127 bits (320), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 104/352 (29%), Positives = 176/352 (50%), Gaps = 15/352 (4%)

Query: 25  SYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNGIIDE 84
           SY+R  +   NL+ L+ E+    A +   Q +V + + R +   E V+ WL  VN +  E
Sbjct: 25  SYIRTLE--KNLRALQREMEDLRAIQHEVQNKVARDEARHQRRLEAVQVWLDRVNSVDIE 82

Query: 85  AEKFTGV-DARANKRCFKGLCPN-LKTRRRLSKEAERQKEAIVKVREVGRFDRISYNIIP 142
            +    V      K C  GLC   + +  +  K+     E + K+   G FD +S    P
Sbjct: 83  CKDLLSVTPVELQKLCLCGLCSKYVCSSYKYGKKVFLLLEEVKKLNSEGNFDEVSQ---P 139

Query: 143 DDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARK-AET 201
                +  +  +    +   L    + L    V ++G++GMGG+ KTTL K++  K AE 
Sbjct: 140 PPRSEVEERPTQPTIGQEDMLEKAWNRLMEDGVGIMGLHGMGGVGKTTLFKKIHNKFAEI 199

Query: 202 EKLFDQVIFVEVSKIQDIRKIQGEIADKLGLT---LHEESDSGRARSLRNRLKKEKTILV 258
              FD VI++ VSK   I K+Q +IA+KL L       +++S +A  + +R+ K K  ++
Sbjct: 200 GGTFDIVIWIVVSKGVMISKLQEDIAEKLHLCDDLWKNKNESDKATDI-HRVLKGKRFVL 258

Query: 259 ILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSL 318
           +LD+IW  +D +A+GIP+  +   CKV  T RS +V   +M   +   V  L+ ++AW L
Sbjct: 259 MLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRSREVCG-EMGDHKPMQVNCLEPEDAWEL 317

Query: 319 FKKMAGDYIEGSEFKWV--AKDVARECAGLPVSIVTVARALGTRDYLNGRTH 368
           FK   GD    S+   V  A++VA++C GLP+++  +   + ++  +    H
Sbjct: 318 FKNKVGDNTLSSDPVIVELAREVAQKCRGLPLALNVIGETMSSKTMVQEWEH 369

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O64789|DRL18_ARATH Probable disease resistance protein At1g61310 OS=Arabidopsis thaliana GN=At1g61310 PE=2 SV=1

 Score =  127 bits (319), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 101/344 (29%), Positives = 175/344 (50%), Gaps = 15/344 (4%)

Query: 25  SYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNGIIDE 84
           SY+R  +   NL+ L+ E+    A +   Q +V + + R ++  E V+ WL  VN I  E
Sbjct: 27  SYIRTLE--KNLRALQREMEDLRATQHEVQNKVAREESRHQQRLEAVQVWLDRVNSIDIE 84

Query: 85  AEKFTGVDA-RANKRCFKGLCPN-LKTRRRLSKEAERQKEAIVKVREVGRFDRISYNIIP 142
            +    V      K C  GLC   + +  +  K+     E +  ++  G FD +S    P
Sbjct: 85  CKDLLSVSPVELQKLCLCGLCTKYVCSSYKYGKKVFLLLEEVKILKSEGNFDEVSQ---P 141

Query: 143 DDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARK-AET 201
                +  +  +    +   L    + L    V ++G++GMGG+ KTTL K++  K AE 
Sbjct: 142 PPRSEVEERPTQPTIGQEEMLEKAWNRLMEDGVGIMGLHGMGGVGKTTLFKKIHNKFAEI 201

Query: 202 EKLFDQVIFVEVSKIQDIRKIQGEIADKLGLT---LHEESDSGRARSLRNRLKKEKTILV 258
              FD VI++ VS+   + K+Q +IA+KL L       +++S +A  + +R+ K K  ++
Sbjct: 202 GGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLCDDLWKNKNESDKATDI-HRVLKGKRFVL 260

Query: 259 ILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSL 318
           +LD+IW  +D +A+GIP+  +   CKV  T RS +V   +M   +   V  L+ ++AW L
Sbjct: 261 MLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRSREVCG-EMGDHKPMQVNCLEPEDAWEL 319

Query: 319 FKKMAGDYIEGSEFKWV--AKDVARECAGLPVSIVTVARALGTR 360
           FK   GD    S+   V  A++VA++C GLP+++  +   + ++
Sbjct: 320 FKNKVGDNTLSSDPVIVGLAREVAQKCRGLPLALNVIGETMASK 363

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O81825|DRL28_ARATH Probable disease resistance protein At4g27220 OS=Arabidopsis thaliana GN=At4g27220 PE=2 SV=1

 Score =  125 bits (313), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 72/189 (38%), Positives = 114/189 (60%), Gaps = 7/189 (3%)

Query: 174 DVNMLGIYGMGGIVKTTLAK----EVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADK 229
           +V  +G++GMGG+ KTTL +    ++ + A T++ F  VI+V VSK  D++++Q +IA +
Sbjct: 133 NVQKIGVWGMGGVGKTTLVRTLNNDLLKYAATQQ-FALVIWVTVSKDFDLKRVQMDIAKR 191

Query: 230 LGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDR-KGCKVLLT 288
           LG     E  +    ++  RL   K  L+ILD++W  +D   +GIP   +R K  KV+LT
Sbjct: 192 LGKRFTREQMNQLGLTICERLIDLKNFLLILDDVWHPIDLDQLGIPLALERSKDSKVVLT 251

Query: 289 ARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV 348
           +R L+V  ++M + +N  V  L+E EAW LF    G+       K +AKDV+ EC GLP+
Sbjct: 252 SRRLEV-CQQMMTNENIKVACLQEKEAWELFCHNVGEVANSDNVKPIAKDVSHECCGLPL 310

Query: 349 SIVTVARAL 357
           +I+T+ R L
Sbjct: 311 AIITIGRTL 319

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L3R3|RFL1_ARATH Disease resistance protein RFL1 OS=Arabidopsis thaliana GN=RFL1 PE=3 SV=2

 Score =  123 bits (309), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 96/356 (26%), Positives = 175/356 (49%), Gaps = 21/356 (5%)

Query: 25  SYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIE-EYVEKWLTSVNGIID 83
           SY++    + NL +L+  +G+  A+R   Q  +++ +  G       V+ WLT +  I +
Sbjct: 27  SYIQN--LSENLASLQKAMGVLNAKRDDVQGRINREEFTGHRRRLAQVQVWLTRIQTIEN 84

Query: 84  EA-EKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQKEAIVKVREV-GRFDRISYNII 141
           +  +  +  +A   + C  G C      + +       K  IV +REV G   +  ++I+
Sbjct: 85  QFNDLLSTCNAEIQRLCLCGFC-----SKNVKMSYLYGKRVIVLLREVEGLSSQGVFDIV 139

Query: 142 PDDTLLLSIKDYEACESRM---STLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARK 198
            +   +  +++     + +   S L+ + + L    V ++G+YGMGG+ KTTL  ++  K
Sbjct: 140 TEAAPIAEVEELPIQSTIVGQDSMLDKVWNCLMEDKVWIVGLYGMGGVGKTTLLTQINNK 199

Query: 199 -AETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLT---LHEESDSGRARSLRNRLKKEK 254
            ++    FD VI+V VSK   + KIQ  I +KLGL      E++ + RA  + N L+++K
Sbjct: 200 FSKLGGGFDVVIWVVVSKNATVHKIQKSIGEKLGLVGKNWDEKNKNQRALDIHNVLRRKK 259

Query: 255 TILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDE 314
            +L +LD+IW  ++ + +G+P+     GCKV  T  S +V  R M       +  L    
Sbjct: 260 FVL-LLDDIWEKVELKVIGVPYPSGENGCKVAFTTHSKEVCGR-MGVDNPMEISCLDTGN 317

Query: 315 AWSLFKKMAGDYIEGS--EFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTH 368
           AW L KK  G+   GS  +   +A+ V+ +C GLP+++  +   +  +  +    H
Sbjct: 318 AWDLLKKKVGENTLGSHPDIPQLARKVSEKCCGLPLALNVIGETMSFKRTIQEWRH 373

Disease resistance (R) protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O23317|DRL24_ARATH Probable disease resistance protein At4g14610 OS=Arabidopsis thaliana GN=At4g14610 PE=3 SV=1

 Score =  123 bits (308), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 87/325 (26%), Positives = 163/325 (50%), Gaps = 22/325 (6%)

Query: 54  QREVDKAKRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRL 113
           Q+ ++  K + ++++  V+K        +    + + V     + CF G C      +  
Sbjct: 34  QKAIEVLKTKHDDVKRRVDK-----EEFLGRRHRLSQVQVEIERLCFCGFC-----SKSF 83

Query: 114 SKEAERQKEAIVKVREVGRFD-RISYNIIPDDTLLLSIKDYEACES---RMSTLNDILDA 169
            K     K   V ++EV     R  ++++ ++ L+  +++     +   + + L  + + 
Sbjct: 84  GKSYHYGKMVSVMLKEVENLSSRGVFDVVTEENLVAQVEEMPIQSTVVGQETMLERVWNT 143

Query: 170 LKNPDVNMLGIYGMGGIVKTTLAKEVARK-AETEKLFDQVIFVEVSKIQDIRKIQGEIAD 228
           L      ++G+YGMGG+ KTTL  ++ +K +ET+  FD V++V VSK  +I +IQ +IA 
Sbjct: 144 LMKDGFKIMGLYGMGGVGKTTLLTQINKKFSETDGGFDIVMWVVVSKTSEIYRIQEDIAK 203

Query: 229 KLGLTLHE---ESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKV 285
           +LGLT  E   ++++ RA  + N L++ K +L +LD+IW  ++ + VG+P+     G  V
Sbjct: 204 RLGLTGEEWDKKNENKRAVDIHNVLRRHKFVL-LLDDIWEKVNLELVGVPYPSRENGSIV 262

Query: 286 LLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGS--EFKWVAKDVAREC 343
             T RS DV  R M       V  L+ ++AW LF+   G+    S  +   +AK VA +C
Sbjct: 263 AFTTRSRDVCGR-MGVDDPMQVSCLEPEDAWDLFQNKVGENTLKSHPDIPELAKQVAEKC 321

Query: 344 AGLPVSIVTVARALGTRDYLNGRTH 368
            GLP+++  +   +  +  +    H
Sbjct: 322 RGLPLALNVIGETMACKSTVQEWRH 346

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|P60838|DRL1_ARATH Probable disease resistance protein At1g12280 OS=Arabidopsis thaliana GN=At1g12280 PE=3 SV=1

 Score =  122 bits (306), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 100/338 (29%), Positives = 170/338 (50%), Gaps = 15/338 (4%)

Query: 33  TSNLQNLKTEVGIPEAERVSKQREVD--KAKRRGEEIEEYVEKWLTSVNGIIDEA-EKFT 89
           + N+  +K ++ + + +R   +R VD  +  RR E + + V+ WLT+V+ + ++  E  T
Sbjct: 33  SKNVVAMKKDMEVLKKKRDDVKRRVDIEEFTRRRERLSQ-VQGWLTNVSTVENKFNELLT 91

Query: 90  GVDARANKRCFKGLCP-NLKTRRRLSKEAERQKEAIVKVREVGRFDRISYNIIPDDTLLL 148
             DA   + C  G C  N+K      K      + I  +   G FD ++          +
Sbjct: 92  TNDAELQRLCLFGFCSKNVKMSYLYGKRVVLMLKEIESLSSQGDFDTVTLATPIARIEEM 151

Query: 149 SIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARK-AETEKLFDQ 207
            I+     +  M  L  +   L      ++G+YGMGG+ KTTL   +  K +E    F  
Sbjct: 152 PIQPTIVGQETM--LERVWTRLTEDGDEIVGLYGMGGVGKTTLLTRINNKFSEKCSGFGV 209

Query: 208 VIFVEVSKIQDIRKIQGEIADKLGLTLHE---ESDSGRARSLRNRLKKEKTILVILDNIW 264
           VI+V VSK  DI +IQG+I  +L L   E    +++ RA  + N L K+K +L +LD+IW
Sbjct: 210 VIWVVVSKSPDIHRIQGDIGKRLDLGGEEWDNVNENQRALDIYNVLGKQKFVL-LLDDIW 268

Query: 265 GNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAG 324
             ++ + +G+P+   + GCKV+ T RS DV  R M       V  L+ +EAW LF+   G
Sbjct: 269 EKVNLEVLGVPYPSRQNGCKVVFTTRSRDVCGR-MRVDDPMEVSCLEPNEAWELFQMKVG 327

Query: 325 -DYIEG-SEFKWVAKDVARECAGLPVSIVTVARALGTR 360
            + ++G  +   +A+ VA +C GLP+++  +   +  +
Sbjct: 328 ENTLKGHPDIPELARKVAGKCCGLPLALNVIGETMACK 365

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C8T9|DRL19_ARATH Putative disease resistance protein At1g63350 OS=Arabidopsis thaliana GN=At1g63350 PE=2 SV=1

 Score =  122 bits (306), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 96/347 (27%), Positives = 173/347 (49%), Gaps = 23/347 (6%)

Query: 29  KSKYTSNLQN----LKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNGIIDE 84
           K  YT NL+     L+T +   +A+R    R++ + + RG +    ++ WL  V  I   
Sbjct: 23  KVSYTHNLEKNLVALETTMEELKAKRDDLLRKLKREEDRGLQTLGEIKVWLNRVETIESR 82

Query: 85  AEKFTGV-DARANKRCFKGLCPNLKTRRRLSKEAERQKEAIVKVREVGRFDRISYNIIPD 143
                   +A   + C  G C      + L+      K   +K+REV + +R  + +I D
Sbjct: 83  VNDLLNARNAELQRLCLCGFCS-----KSLTTSYRYGKSVFLKLREVEKLERRVFEVISD 137

Query: 144 DTLLLSIKDYEACES---RMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAE 200
                 +++ +   +   + + L++  + L    V ++G+YGMGG+ KTTL  ++  K  
Sbjct: 138 QASTSEVEEQQLQPTIVGQETMLDNAWNHLMEDGVGIMGLYGMGGVGKTTLLTQINNKFS 197

Query: 201 TEKL-FDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDS----GRARSLRNRLKKEKT 255
                FD VI+V VSK  ++  I  EIA K+ ++  E+ D+     +   L N L+K + 
Sbjct: 198 KYMCGFDSVIWVVVSKEVNVENILDEIAQKVHIS-GEKWDTKYKYQKGVYLYNFLRKMRF 256

Query: 256 ILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEA 315
           +L  LD+IW  ++   +G+P    +  CKV+ T RSLDV +  M  ++   V  L +++A
Sbjct: 257 VL-FLDDIWEKVNLVEIGVPFPTIKNKCKVVFTTRSLDVCT-SMGVEKPMEVQCLADNDA 314

Query: 316 WSLFKKMAGDYIEGS--EFKWVAKDVARECAGLPVSIVTVARALGTR 360
           + LF+K  G    GS  E + +++ VA++C GLP+++  V+  +  +
Sbjct: 315 YDLFQKKVGQITLGSDPEIRELSRVVAKKCCGLPLALNVVSETMSCK 361

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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	390
359488027	1520	PREDICTED: disease resistance protein At	0.917	0.235	0.469	3e-88
147802546	1409	hypothetical protein VITISV_007222 [Viti	0.917	0.254	0.469	6e-88
147833354	1494	hypothetical protein VITISV_041837 [Viti	0.907	0.236	0.460	4e-85
359487988	1297	PREDICTED: disease resistance protein RP	0.892	0.268	0.486	9e-85
359488288	1340	PREDICTED: LOW QUALITY PROTEIN: probable	0.920	0.267	0.448	9e-85
147865073	1694	hypothetical protein VITISV_021876 [Viti	0.912	0.210	0.448	5e-83
147772601	1392	hypothetical protein VITISV_013427 [Viti	0.9	0.252	0.453	5e-83
147787802	1517	hypothetical protein VITISV_005047 [Viti	0.9	0.231	0.453	2e-82
302143590	948	unnamed protein product [Vitis vinifera]	0.9	0.370	0.453	2e-82
359488025	1781	PREDICTED: uncharacterized protein LOC10	0.897	0.196	0.456	2e-82

>gi|359488027|ref|XP_002269288.2| PREDICTED: disease resistance protein At4g27190-like [Vitis vinifera]

 Score =  331 bits (849), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 169/360 (46%), Positives = 250/360 (69%), Gaps = 2/360 (0%)

Query: 1   MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKA 60
           M +I++++  +VA+ L  PI     YL    Y SN+ +L+ +V      R   +R VD+A
Sbjct: 1   MEEIVVTIAAKVAEYLVAPIGRSFGYL--FNYRSNIDDLRQQVEKLGDARARLERSVDEA 58

Query: 61  KRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQ 120
            R G+EIE  V+KWL  V+G ++EA  F  V+ +AN+ CF G CPNLK++ +LS+EA+++
Sbjct: 59  IRNGDEIEADVDKWLLRVSGFMEEAGIFFEVEKKANQSCFNGSCPNLKSQYQLSREAKKR 118

Query: 121 KEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGI 180
              + +++  G+F+R+SY            K +EA ESRM+TL++I++AL++  VN++G+
Sbjct: 119 ARVVAEIQGDGKFERVSYRAPLPGIGSAPFKGHEALESRMTTLDEIMEALRDAHVNIIGV 178

Query: 181 YGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDS 240
           +GM G+ KTTL K+VA++AE EKLFD+V+   +S   +++KIQGE+AD LGL   EES+ 
Sbjct: 179 WGMAGVGKTTLMKQVAKQAEEEKLFDKVVMAYISSTPELKKIQGELADMLGLKFEEESEM 238

Query: 241 GRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMD 300
           GRA  L  RLKK K IL+ILD+IW  LD + VGIP GDD KGCK++LT+R+  +LS +M 
Sbjct: 239 GRAARLCERLKKVKKILIILDDIWTELDLEKVGIPFGDDHKGCKMVLTSRNKHILSNEMG 298

Query: 301 SQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTR 360
           +Q++F V  L+E+EA  LFKKMAGD IE  + + +A DVA+ECAGLP++IVTVA+AL  +
Sbjct: 299 TQKDFPVEHLQEEEALILFKKMAGDSIEEPDLQSIAIDVAKECAGLPIAIVTVAKALKNK 358

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147802546|emb|CAN77665.1| hypothetical protein VITISV_007222 [Vitis vinifera]

 Score =  330 bits (847), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 169/360 (46%), Positives = 249/360 (69%), Gaps = 2/360 (0%)

Query: 1   MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKA 60
           M +I++++  +VA+ L  PI     YL    Y SN+ +L+ +V      R   +R VD+A
Sbjct: 1   MEEIVVTIAAKVAEYLVAPIGRSFGYL--FNYRSNIDDLRQQVEKLGDARARLERSVDEA 58

Query: 61  KRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQ 120
            R G+EIE  V+KWL  V+G ++EA  F  V+ +AN+ CF G CPNLK++ +LS+EA+++
Sbjct: 59  IRNGDEIEADVDKWLLRVSGFMEEAGIFFEVEKKANQSCFNGSCPNLKSQYQLSREAKKR 118

Query: 121 KEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGI 180
              + +++  G+F+R+SY            K +EA ESRM+TL++I++AL++  VN++G+
Sbjct: 119 ARVVAEIQGDGKFERVSYRAPLPGIGSAPFKGHEALESRMTTLDEIMEALRDAHVNIIGV 178

Query: 181 YGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDS 240
           +GM G+ KTTL K+VA++ E EKLFD+V+   +S   +++KIQGE+AD LGL   EES+ 
Sbjct: 179 WGMAGVGKTTLMKQVAKQVEEEKLFDKVVMAYISSTPELKKIQGELADMLGLKFEEESEM 238

Query: 241 GRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMD 300
           GRA  L  RLKK K IL+ILD+IW  LD + VGIP GDD KGCK++LT+R+  VLS +M 
Sbjct: 239 GRAARLCERLKKVKKILIILDDIWTELDLEKVGIPFGDDHKGCKMVLTSRNKHVLSNEMG 298

Query: 301 SQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTR 360
           +Q++F V  L+E+EA  LFKKMAGD IE  + + +A DVA+ECAGLP++IVTVA+AL  +
Sbjct: 299 TQKDFPVEHLQEEEALILFKKMAGDSIEEPDLQSIAIDVAKECAGLPIAIVTVAKALKNK 358

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147833354|emb|CAN66237.1| hypothetical protein VITISV_041837 [Vitis vinifera]

 Score =  321 bits (823), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 167/363 (46%), Positives = 243/363 (66%), Gaps = 9/363 (2%)

Query: 1   MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKA 60
           M DI+ SV  +V++ L  P+  Q+ YL    Y +N+++L  EV      R   Q  V++A
Sbjct: 1   MVDIVFSVAAKVSEYLVVPVVRQLGYL--FNYRTNIEDLSQEVEKLRDARDRHQHSVNEA 58

Query: 61  KRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQ 120
              G +IE+YV KWLT  +G I +A KF   +  A K CF GLCPNLK+R +LS+EA ++
Sbjct: 59  IGNGHKIEDYVCKWLTRADGFIQDACKFLEDEKEAQKSCFNGLCPNLKSRHQLSREARKK 118

Query: 121 KEAIVKVREVGRFDRISYNIIPDDTLLLSIK--DYEACESRMSTLNDILDALKNPDVNML 178
               V++ E G+F+++SY      T L  I+    EA ESRM TLN++++AL++ ++N +
Sbjct: 119 AGVSVQILENGQFEKVSYR-----TPLQGIRTAPSEALESRMLTLNEVMEALRDANINRI 173

Query: 179 GIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEES 238
           G++GMGG+ K+TL K +A +A  EKLFD+V+ V V +  D+ +IQ E+AD LG+   EES
Sbjct: 174 GLWGMGGVGKSTLVKHLAEQANQEKLFDKVVKVSVLQTPDLERIQRELADGLGMKFEEES 233

Query: 239 DSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRK 298
           + GRA  L  R++ EKTIL+ILD++W  L+ + VGIP  DD KGCK++LT+R+  VLS +
Sbjct: 234 EQGRAARLLQRMEAEKTILIILDDLWAELELEKVGIPSPDDHKGCKLVLTSRNKQVLSNE 293

Query: 299 MDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALG 358
           M +Q++F V  L+EDE W LFK  AGD IE  E + +A DVA+ECAGLP++IVTVA+AL 
Sbjct: 294 MSTQKDFRVRHLQEDETWILFKNTAGDSIENPELQPIAVDVAKECAGLPLAIVTVAKALK 353

Query: 359 TRD 361
            ++
Sbjct: 354 NKN 356

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487988|ref|XP_002262896.2| PREDICTED: disease resistance protein RPS2-like [Vitis vinifera]

 Score =  320 bits (819), Expect = 9e-85,   Method: Compositional matrix adjust.
 Identities = 174/358 (48%), Positives = 242/358 (67%), Gaps = 10/358 (2%)

Query: 1   MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKA 60
           MA+I++S+  +VA+ L  PI   + YL    Y SNL NL+ +V      R  +QR+VD A
Sbjct: 1   MAEILISIAAKVAEYLVAPIVRPLGYL--FNYRSNLDNLEEQVDKLGDARERRQRDVDDA 58

Query: 61  KRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQ 120
            R+G+EIE  V+KWLT   GII  A++    +  A+  CF     NLK R + S++A++Q
Sbjct: 59  NRQGDEIEPDVQKWLTRTEGIIQTAKELIEDEKAASTSCF-----NLKLRYQRSRQAKKQ 113

Query: 121 KEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGI 180
              I K++E  +F+R+SY + P       ++D  A ESR S LN+I++AL+N D+ M+G+
Sbjct: 114 SGDIGKIQEENKFNRVSYGLPPQGIWSPRLRDCGALESRASILNEIMEALRNDDIRMIGV 173

Query: 181 YGMGGIVKTTLAKEVARKAETEKLFDQVIF-VEVSKIQDIRKIQGEIADKLGLTLHEESD 239
           +GMGG+ KTTLA +VA+KAE +KLF++V+  + +S++ ++ KIQGEIA  LGL   EE +
Sbjct: 174 WGMGGVGKTTLANQVAKKAEEDKLFEKVVMALNISRVPNVTKIQGEIASMLGLKFEEEEE 233

Query: 240 SGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKM 299
           SGRA  L   L+K KT+LVILD+IW  L  + +GIPHGD  +GCKVLLT+R   VLSRKM
Sbjct: 234 SGRAARLSKSLQKNKTVLVILDDIWEELSLENIGIPHGDAHRGCKVLLTSRKQGVLSRKM 293

Query: 300 DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARAL 357
            +Q+NF V  L E+EAWSLFKK AGD +E  + K +A  V REC GLPV+IVTVA+AL
Sbjct: 294 ATQKNFRVQHLCEEEAWSLFKKTAGDSVE--QLKSIAIKVLRECDGLPVAIVTVAKAL 349

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488288|ref|XP_003633735.1| PREDICTED: LOW QUALITY PROTEIN: probable disease resistance protein At1g61310-like [Vitis vinifera]

 Score =  320 bits (819), Expect = 9e-85,   Method: Compositional matrix adjust.
 Identities = 162/361 (44%), Positives = 237/361 (65%), Gaps = 2/361 (0%)

Query: 1   MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKA 60
           M +I++SV  +V++ L  P+  Q+ +L    Y +N+++L  +V      R  +Q  VD+A
Sbjct: 1   MVEIVVSVAAKVSEYLVAPVGRQLGHL--FNYRTNVEDLSQQVAKLRDARARQQHSVDEA 58

Query: 61  KRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQ 120
            R+G +IE+ V KW T  +G I  A KF   +  A K CF GLCPNLK+R +LSKEA ++
Sbjct: 59  IRKGHKIEDDVCKWFTRADGFIQVACKFLEEEKEAQKTCFNGLCPNLKSRYQLSKEARKK 118

Query: 121 KEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGI 180
               V++   G+F+R+SY     +      K  +  ESRM TLN+++ AL++ D+N +GI
Sbjct: 119 AGVAVEIHGDGQFERVSYRPPLLEIGSAPPKASKVLESRMLTLNEVMKALRDADINTIGI 178

Query: 181 YGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDS 240
           +GMGG+ K TL K+VA +A  EKLFD+V+   V +  D R+IQGEIAD LG+   EES+ 
Sbjct: 179 WGMGGVGKNTLVKQVAEQAAQEKLFDKVVMTSVFQTPDFRRIQGEIADMLGMKFEEESEQ 238

Query: 241 GRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMD 300
           GRA  L  ++ +EKTIL+ILD+IW  L+ + +GIP  D+ KGCK++LT+R+  VLS +M 
Sbjct: 239 GRAARLHRKINEEKTILIILDDIWAELELEKIGIPSPDNHKGCKLVLTSRNKHVLSNEMS 298

Query: 301 SQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTR 360
           +Q++F V  L+ DEAW LFK M GD IE  +   +A DVA+EC GLP++IVTVA+AL  +
Sbjct: 299 TQKDFGVEHLQGDEAWILFKNMVGDSIENPDLLLIATDVAKECTGLPIAIVTVAKALKNK 358

Query: 361 D 361
           +
Sbjct: 359 N 359

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147865073|emb|CAN83232.1| hypothetical protein VITISV_021876 [Vitis vinifera]

 Score =  314 bits (805), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 162/361 (44%), Positives = 236/361 (65%), Gaps = 5/361 (1%)

Query: 1   MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKA 60
           M +I+LSV  +V++ L  P   Q+ YL    Y +N+++L  +V      R   Q  VD+A
Sbjct: 1   MVEIVLSVAAKVSEYLVDPAIRQLGYL--FNYRANIEDLSQQVEKLRDARARLQHSVDEA 58

Query: 61  KRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQ 120
              G  IE+ V KW+   +G I  A KF   +  A K CF GLCPNLK+R +LS+EA ++
Sbjct: 59  IGNGHIIEDDVRKWMKRADGFIQNACKFLEDEKEARKSCFNGLCPNLKSRYQLSREARKK 118

Query: 121 KEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGI 180
               V++   G+F+R+SY     +   +     EA ESRM TLN++++AL++ ++N +G+
Sbjct: 119 AGVAVEIHGAGQFERVSYRAPLQE---IRTAPSEALESRMLTLNEVMEALRDANINRIGV 175

Query: 181 YGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDS 240
           +GMGG+ K+TL K+VA +AE EKLF +V+ V V +  D + IQ +IADKLG+   E S+ 
Sbjct: 176 WGMGGVGKSTLVKQVAEQAEQEKLFRKVVMVPVIQTPDFKGIQQQIADKLGMKFEEVSEQ 235

Query: 241 GRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMD 300
           GRA  L  R+K+E TIL+ILD++W  L+ + VGIP  DD KGCK++LT+R+  VLS +M 
Sbjct: 236 GRADRLHQRIKQENTILIILDDLWAELELEKVGIPSPDDHKGCKLVLTSRNKQVLSNEMS 295

Query: 301 SQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTR 360
           +Q++F V  L+EDE W LFK  AGD IE  E + +A DVA+ECAGLP++IVTVA+AL  +
Sbjct: 296 TQKDFRVQHLQEDETWILFKNTAGDSIENPELQPIAVDVAKECAGLPIAIVTVAKALKNK 355

Query: 361 D 361
           +
Sbjct: 356 N 356

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147772601|emb|CAN62857.1| hypothetical protein VITISV_013427 [Vitis vinifera]

 Score =  314 bits (804), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 162/357 (45%), Positives = 235/357 (65%), Gaps = 6/357 (1%)

Query: 1   MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKA 60
           M +I+ SV  +V +CL  P+  Q+ YL    Y +N+++L  EV      R   Q  V++A
Sbjct: 1   MVEIVASVAAKVLECLVVPVKRQLGYL--FNYRTNIEDLSQEVEKLRHARDGHQHSVNEA 58

Query: 61  KRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQ 120
              G +IE+YV KWLT  +G I +A KF   +  A K CF GLCPNLK+R +LS+EA ++
Sbjct: 59  SGNGHKIEDYVCKWLTRADGFIQDACKFLEDEKEAQKSCFNGLCPNLKSRYQLSREARKK 118

Query: 121 KEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGI 180
               V++   G+F+R+SY     +   +     EA  SR+ TL+++++AL++  +N +G+
Sbjct: 119 ARVAVQMLGDGQFERVSYRAPLQE---IRSAPSEALRSRVLTLDEVMEALRDAKINKIGV 175

Query: 181 YGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDS 240
           +G+GG+ KTTL K+VA  A  EKLFD+V+   V +  D++KIQGE+AD LG+   EES+ 
Sbjct: 176 WGLGGVGKTTLVKQVAEHAAQEKLFDKVVTAAVLQTPDLKKIQGELADLLGMKFEEESEQ 235

Query: 241 GRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMD 300
           GRA  L  R+ +EKTIL+ILD+IW  LD + +GIP  D  KGCK++LT+R+  +LS +MD
Sbjct: 236 GRAARLYQRMNEEKTILIILDDIWATLDLEKIGIPSPDHHKGCKLVLTSRNEHILSNEMD 295

Query: 301 SQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARAL 357
           +Q++F V  L+EDE W LFK  AG  IE  E K +A DVA+ECAGLP+++VTVA AL
Sbjct: 296 TQKDFRVQPLQEDETWILFKNTAGS-IENPELKHIAVDVAKECAGLPLAMVTVATAL 351

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147787802|emb|CAN71755.1| hypothetical protein VITISV_005047 [Vitis vinifera]

 Score =  312 bits (799), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 162/357 (45%), Positives = 234/357 (65%), Gaps = 6/357 (1%)

Query: 1   MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKA 60
           M +I+  V  +V+KCL  P+  Q+ YL    Y +N+++L  EV      R   Q  V++A
Sbjct: 1   MEEIVAKVAAKVSKCLVVPVKRQLGYL--FNYRTNIEDLSQEVEKLRHARDGHQHSVNEA 58

Query: 61  KRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQ 120
              G +IE+YV KWLT  +G I +A KF   +  A K CF GLCPNLK+R +LS+EA ++
Sbjct: 59  IGNGHKIEDYVCKWLTRADGFIQDACKFLEDEKEAQKSCFNGLCPNLKSRYQLSREARKK 118

Query: 121 KEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGI 180
               V++   G+F R+SY     +   +     EA  SR+ TL+++++AL++  +N +G+
Sbjct: 119 ARVAVQMHGDGQFVRVSYRAPLQE---IRSAPSEALRSRVLTLDEVMEALRDAKINKIGV 175

Query: 181 YGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDS 240
           +G+GG+ KTTL K+VA +A  EKLFD+V+   V +  D++KIQGE+AD LG+   EES+ 
Sbjct: 176 WGLGGVGKTTLVKQVAEQAAQEKLFDKVVTAAVLQTPDLKKIQGELADLLGMKFEEESEQ 235

Query: 241 GRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMD 300
           GRA  L  R+  EKTIL+ILD+IW  LD + +GIP  D  KGCK++LT+R+  +LS +MD
Sbjct: 236 GRAARLYQRMNNEKTILIILDDIWAKLDLEKIGIPSPDHHKGCKLVLTSRNEHILSNEMD 295

Query: 301 SQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARAL 357
           +Q++F V  L+EDE W LFK  AG  IE  E + +A DVA+ECAGLP++IVTVA AL
Sbjct: 296 TQKDFRVQPLQEDETWILFKNTAGS-IENPELQPIAVDVAKECAGLPLAIVTVATAL 351

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143590|emb|CBI22343.3| unnamed protein product [Vitis vinifera]

 Score =  312 bits (799), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 162/357 (45%), Positives = 234/357 (65%), Gaps = 6/357 (1%)

Query: 1   MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKA 60
           M +I+  V  +V+KCL  P+  Q+ YL    Y +N+++L  EV      R   Q  V++A
Sbjct: 1   MEEIVAKVAAKVSKCLVVPVKRQLGYL--FNYRTNIEDLSQEVEKLRHARDGHQHSVNEA 58

Query: 61  KRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQ 120
              G +IE+YV KWLT  +G I +A KF   +  A K CF GLCPNLK+R +LS+EA ++
Sbjct: 59  IGNGHKIEDYVCKWLTRADGFIQDACKFLEDEKEAQKSCFNGLCPNLKSRYQLSREARKK 118

Query: 121 KEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGI 180
               V++   G+F R+SY     +   +     EA  SR+ TL+++++AL++  +N +G+
Sbjct: 119 ARVAVQMHGDGQFVRVSYRAPLQE---IRSAPSEALRSRVLTLDEVMEALRDAKINKIGV 175

Query: 181 YGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDS 240
           +G+GG+ KTTL K+VA +A  EKLFD+V+   V +  D++KIQGE+AD LG+   EES+ 
Sbjct: 176 WGLGGVGKTTLVKQVAEQAAQEKLFDKVVTAAVLQTPDLKKIQGELADLLGMKFEEESEQ 235

Query: 241 GRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMD 300
           GRA  L  R+  EKTIL+ILD+IW  LD + +GIP  D  KGCK++LT+R+  +LS +MD
Sbjct: 236 GRAARLYQRMNNEKTILIILDDIWAKLDLEKIGIPSPDHHKGCKLVLTSRNEHILSNEMD 295

Query: 301 SQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARAL 357
           +Q++F V  L+EDE W LFK  AG  IE  E + +A DVA+ECAGLP++IVTVA AL
Sbjct: 296 TQKDFRVQPLQEDETWILFKNTAGS-IENPELQPIAVDVAKECAGLPLAIVTVATAL 351

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488025|ref|XP_003633688.1| PREDICTED: uncharacterized protein LOC100852821 [Vitis vinifera]

 Score =  312 bits (799), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 163/357 (45%), Positives = 236/357 (66%), Gaps = 7/357 (1%)

Query: 1   MADIILSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKA 60
           M +I++SV  +V++ L  P+  Q+ YL    Y +N+++L  +V      R   Q  VD+A
Sbjct: 1   MVEIVVSVAAKVSEYLVGPVVRQLGYL--FNYRTNIEDLSQKVEKLRGARARLQHSVDEA 58

Query: 61  KRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQ 120
            R G +IE+ V KW+T  +G I +  KF   D  A K CF GLCPNLK+R +LS+EA ++
Sbjct: 59  IRNGHKIEDDVCKWMTRADGFIQKDCKFLE-DEEARKSCFNGLCPNLKSRYQLSREARKK 117

Query: 121 KEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGI 180
               V++ E G+F+R SY     +   +     EA ESRM TLN+++ AL++  +N +G+
Sbjct: 118 AGVAVEIHEAGQFERASYRAPLQE---IRSAPSEALESRMLTLNEVMKALRDAKINKIGV 174

Query: 181 YGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDS 240
           +G+GG+ KTTL K+VA +A  EKLFD+V+   V +  D++KIQGE+AD LG+   EES+ 
Sbjct: 175 WGLGGVGKTTLVKQVAEQAAQEKLFDKVVTAAVLETPDLKKIQGELADLLGMKFEEESEQ 234

Query: 241 GRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMD 300
           GRA  L  R+ +EKTIL+ILD+IW  LD + +GIP  D  KGCK++LT+R+  +LS +MD
Sbjct: 235 GRAARLYQRMNEEKTILIILDDIWAKLDLEKIGIPSPDHHKGCKLVLTSRNEHILSNEMD 294

Query: 301 SQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARAL 357
           +Q++F V  L+EDE W LFK  AG  IE  E + +A DVA+ECAGLP+++VTVA AL
Sbjct: 295 TQKDFRVQPLQEDETWILFKNTAGS-IENPELQPIAVDVAKECAGLPLAVVTVATAL 350

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	390
TAIR|locus:2008510	967	AT1G61190 "AT1G61190" [Arabido	0.871	0.351	0.287	3.9e-33
TAIR|locus:2008440	899	AT1G61180 [Arabidopsis thalian	0.864	0.374	0.292	1.5e-32
TAIR|locus:2136447	985	AT4G27190 [Arabidopsis thalian	0.712	0.282	0.335	3.7e-32
TAIR|locus:2201996	889	RPS5 "AT1G12220" [Arabidopsis	0.848	0.372	0.308	8.1e-32
TAIR|locus:2034770	894	SUMM2 "AT1G12280" [Arabidopsis	0.876	0.382	0.282	9.7e-31
TAIR|locus:2201986	885	RFL1 "AT1G12210" [Arabidopsis	0.828	0.364	0.280	4.2e-30
TAIR|locus:2131689	919	AT4G27220 [Arabidopsis thalian	0.756	0.321	0.312	9.5e-30
TAIR|locus:2166320	888	AT5G63020 [Arabidopsis thalian	0.843	0.370	0.272	1.1e-29
TAIR|locus:2031366	898	AT1G63350 "AT1G63350" [Arabido	0.830	0.360	0.276	1.8e-28
TAIR|locus:2203881	893	AT1G62630 [Arabidopsis thalian	0.828	0.361	0.287	7.6e-28

TAIR|locus:2008510 AT1G61190 "AT1G61190" [Arabidopsis thaliana (taxid:3702)]

 Score = 372 (136.0 bits), Expect = 3.9e-33, P = 3.9e-33
 Identities = 102/355 (28%), Positives = 176/355 (49%)

Query:    22 CQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNGI 81
             C   Y+R  +   NL+ L+ E+    A +   Q +V + + R ++  E V+ WL  VN I
Sbjct:    23 CGKGYIRNLE--KNLRALQREMEDLRATQHEVQNKVAREESRHQQRLEAVQVWLDRVNSI 80

Query:    82 IDEAEKFTGVD-ARANKRCFKGLCPN-LKTRRRLSKEAERQKEAIVKVREVGRFDRISYN 139
               E +    V      K C  GLC   + +  +  K      E + K++  G FD +S  
Sbjct:    81 DIECKDLLSVSPVELQKLCLCGLCSKYVCSSYKYGKRVFLLLEEVTKLKSEGNFDEVSQ- 139

Query:   140 IIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARK- 198
               P     +  +  +    +   L    + L    V ++G++GMGG+ KTTL K++  K 
Sbjct:   140 --PPPRSEVEERPTQPTIGQEEMLKKAWNRLMEDGVGIMGLHGMGGVGKTTLFKKIHNKF 197

Query:   199 AETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLT---LHEESDSGRARSLRNRLKKEKT 255
             AET   FD VI++ VS+   + K+Q +IA+KL L       +++S +A  + +R+ K K 
Sbjct:   198 AETGGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLCDDLWKNKNESDKATDI-HRVLKGKR 256

Query:   256 ILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEA 315
              +++LD+IW  +D +A+GIP+  +   CKV  T R   V  + M   +   V  L+ ++A
Sbjct:   257 FVLMLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRDQKVCGQ-MGDHKPMQVKCLEPEDA 315

Query:   316 WSLFKKMAGDYIEGSE--FKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTH 368
             W LFK   GD    S+     +A++VA++C GLP+++  +   + ++  +    H
Sbjct:   316 WELFKNKVGDNTLRSDPVIVGLAREVAQKCRGLPLALSCIGETMASKTMVQEWEH 370

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2008440 AT1G61180 [Arabidopsis thaliana (taxid:3702)]

 Score = 366 (133.9 bits), Expect = 1.5e-32, P = 1.5e-32
 Identities = 103/352 (29%), Positives = 176/352 (50%)

Query:    25 SYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNGIIDE 84
             SY+R  +   NL+ L+ E+    A +   Q +V + + R +   E V+ WL  VN +  E
Sbjct:    25 SYIRTLE--KNLRALQREMEDLRAIQHEVQNKVARDEARHQRRLEAVQVWLDRVNSVDIE 82

Query:    85 AEKFTGVD-ARANKRCFKGLCPN-LKTRRRLSKEAERQKEAIVKVREVGRFDRISYNIIP 142
              +    V      K C  GLC   + +  +  K+     E + K+   G FD +S    P
Sbjct:    83 CKDLLSVTPVELQKLCLCGLCSKYVCSSYKYGKKVFLLLEEVKKLNSEGNFDEVSQ---P 139

Query:   143 DDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARK-AET 201
                  +  +  +    +   L    + L    V ++G++GMGG+ KTTL K++  K AE 
Sbjct:   140 PPRSEVEERPTQPTIGQEDMLEKAWNRLMEDGVGIMGLHGMGGVGKTTLFKKIHNKFAEI 199

Query:   202 EKLFDQVIFVEVSKIQDIRKIQGEIADKLGLT---LHEESDSGRARSLRNRLKKEKTILV 258
                FD VI++ VSK   I K+Q +IA+KL L       +++S +A  + +R+ K K  ++
Sbjct:   200 GGTFDIVIWIVVSKGVMISKLQEDIAEKLHLCDDLWKNKNESDKATDI-HRVLKGKRFVL 258

Query:   259 ILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSL 318
             +LD+IW  +D +A+GIP+  +   CKV  T RS +V   +M   +   V  L+ ++AW L
Sbjct:   259 MLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRSREVCG-EMGDHKPMQVNCLEPEDAWEL 317

Query:   319 FKKMAGDYIEGSE--FKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTH 368
             FK   GD    S+     +A++VA++C GLP+++  +   + ++  +    H
Sbjct:   318 FKNKVGDNTLSSDPVIVELAREVAQKCRGLPLALNVIGETMSSKTMVQEWEH 369

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

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2136447 AT4G27190 [Arabidopsis thaliana (taxid:3702)]

 Score = 363 (132.8 bits), Expect = 3.7e-32, P = 3.7e-32
 Identities = 99/295 (33%), Positives = 161/295 (54%)

Query:    84 EAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQKEAIVKVREVG-RF-DRISYNII 141
             EAE+   V ++A  +  + +   +  R R+S++  +  + +  + + G  F D +S    
Sbjct:    74 EAEE---VISKARLKLEERVSCGMSLRPRMSRKLVKILDEVKMLEKDGIEFVDMLSVEST 130

Query:   142 PDDTLLLSIKDYEACESRMST--LNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKA 199
             P+   +  +         M++  L  I D L +     +G++GMGG+ KTTL + +  K 
Sbjct:   131 PER--VEHVPGVSVVHQTMASNMLAKIRDGLTSEKAQKIGVWGMGGVGKTTLVRTLNNKL 188

Query:   200 ETE---KLFDQVIFVEVSKIQDIRKIQGEIADKLGL-TLHEESDSGRARSLRNRLKKEKT 255
               E   + F  VIFV VSK  D R++Q +IA++L + T  EES+   AR +   L KE+ 
Sbjct:   189 REEGATQPFGLVIFVIVSKEFDPREVQKQIAERLDIDTQMEESEEKLARRIYVGLMKERK 248

Query:   256 ILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEA 315
              L+ILD++W  +D   +GIP  ++ KG KV+LT+R L+V  R M +  +  V  L E++A
Sbjct:   249 FLLILDDVWKPIDLDLLGIPRTEENKGSKVILTSRFLEVC-RSMKTDLDVRVDCLLEEDA 307

Query:   316 WSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWN 370
             W LF K AGD +     + +AK V++EC GLP++I+TV  A+  R   N +  WN
Sbjct:   308 WELFCKNAGDVVRSDHVRKIAKAVSQECGGLPLAIITVGTAM--RGKKNVKL-WN 359

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2201996 RPS5 "AT1G12220" [Arabidopsis thaliana (taxid:3702)]

 Score = 359 (131.4 bits), Expect = 8.1e-32, P = 8.1e-32
 Identities = 110/357 (30%), Positives = 176/357 (49%)

Query:    21 YCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEY---------V 71
             + Q+  +R S Y  NL   K    + +A R+ K R+ D  +R   E EE+         V
Sbjct:    18 FSQLLCVRGS-YIHNLS--KNLASLQKAMRMLKARQYDVIRRL--ETEEFTGRQQRLSQV 72

Query:    72 EKWLTSVNGIIDEA-EKFTGVDARANKRCFKGLCP-NLKTRRRLSKEAERQKEAIVKVRE 129
             + WLTSV  I ++  +     +    + C  G C  +LK   R  K      + +  +  
Sbjct:    73 QVWLTSVLIIQNQFNDLLRSNEVELQRLCLCGFCSKDLKLSYRYGKRVIMMLKEVESLSS 132

Query:   130 VGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKT 189
              G FD +S      D   +  +     +  M  L    + L      +LG+YGMGG+ KT
Sbjct:   133 QGFFDVVSEATPFADVDEIPFQPTIVGQEIM--LEKAWNRLMEDGSGILGLYGMGGVGKT 190

Query:   190 TLAKEVARK-AETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGL---TLHEESDSGRARS 245
             TL  ++  K ++ +  FD VI+V VS+   +RKIQ +IA+K+GL      E++D+  A  
Sbjct:   191 TLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGMEWSEKNDNQIAVD 250

Query:   246 LRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNF 305
             + N L++ K +L +LD+IW  ++ +AVG+P+     GCKV  T RS DV  R M      
Sbjct:   251 IHNVLRRRKFVL-LLDDIWEKVNLKAVGVPYPSKDNGCKVAFTTRSRDVCGR-MGVDDPM 308

Query:   306 SVGVLKEDEAWSLFKKMAGDYIEGS--EFKWVAKDVARECAGLPVSIVTVARALGTR 360
              V  L+ +E+W LF+   G    GS  +   +A+ VAR+C GLP+++  +  A+  +
Sbjct:   309 EVSCLQPEESWDLFQMKVGKNTLGSHPDIPGLARKVARKCRGLPLALNVIGEAMACK 365

GO:0009626 "plant-type hypersensitive response" evidence=IMP

GO:0006952 "defense response" evidence=IMP;TAS

GO:0009816 "defense response to bacterium, incompatible interaction" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0008219 "cell death" evidence=IMP

GO:0038023 "signaling receptor activity" evidence=IMP

GO:0000166 "nucleotide binding" evidence=IMP

GO:0005622 "intracellular" evidence=ISS

TAIR|locus:2034770 SUMM2 "AT1G12280" [Arabidopsis thaliana (taxid:3702)]

 Score = 349 (127.9 bits), Expect = 9.7e-31, P = 9.7e-31
 Identities = 102/361 (28%), Positives = 180/361 (49%)

Query:    11 EVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVD--KAKRRGEEIE 68
             EV   ++  +   + Y+   + + N+  +K ++ + + +R   +R VD  +  RR E + 
Sbjct:    13 EVVNQISQGLCINVGYI--CELSKNVVAMKKDMEVLKKKRDDVKRRVDIEEFTRRRERLS 70

Query:    69 EYVEKWLTSVNGIIDEA-EKFTGVDARANKRCFKGLCP-NLKTRRRLSKEAERQKEAIVK 126
             + V+ WLT+V+ + ++  E  T  DA   + C  G C  N+K      K      + I  
Sbjct:    71 Q-VQGWLTNVSTVENKFNELLTTNDAELQRLCLFGFCSKNVKMSYLYGKRVVLMLKEIES 129

Query:   127 VREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGI 186
             +   G FD ++  +      +  +        + + L  +   L      ++G+YGMGG+
Sbjct:   130 LSSQGDFDTVT--LATPIARIEEMPIQPTIVGQETMLERVWTRLTEDGDEIVGLYGMGGV 187

Query:   187 VKTTLAKEVARKAETEKL--FDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE---ESDSG 241
              KTTL   +  K  +EK   F  VI+V VSK  DI +IQG+I  +L L   E    +++ 
Sbjct:   188 GKTTLLTRINNKF-SEKCSGFGVVIWVVVSKSPDIHRIQGDIGKRLDLGGEEWDNVNENQ 246

Query:   242 RARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDS 301
             RA  + N L K+K +L +LD+IW  ++ + +G+P+   + GCKV+ T RS DV  R M  
Sbjct:   247 RALDIYNVLGKQKFVL-LLDDIWEKVNLEVLGVPYPSRQNGCKVVFTTRSRDVCGR-MRV 304

Query:   302 QQNFSVGVLKEDEAWSLFKKMAGDY-IEGS-EFKWVAKDVARECAGLPVSIVTVARALGT 359
                  V  L+ +EAW LF+   G+  ++G  +   +A+ VA +C GLP+++  +   +  
Sbjct:   305 DDPMEVSCLEPNEAWELFQMKVGENTLKGHPDIPELARKVAGKCCGLPLALNVIGETMAC 364

Query:   360 R 360
             +
Sbjct:   365 K 365

GO:0006952 "defense response" evidence=IGI;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2201986 RFL1 "AT1G12210" [Arabidopsis thaliana (taxid:3702)]

 Score = 343 (125.8 bits), Expect = 4.2e-30, P = 4.2e-30
 Identities = 97/346 (28%), Positives = 170/346 (49%)

Query:    25 SYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIE-EYVEKWLTSVNGIID 83
             SY++    + NL +L+  +G+  A+R   Q  +++ +  G       V+ WLT +  I +
Sbjct:    27 SYIQN--LSENLASLQKAMGVLNAKRDDVQGRINREEFTGHRRRLAQVQVWLTRIQTIEN 84

Query:    84 EAEKFTGV-DARANKRCFKGLCP-NLKTRRRLSKEAERQKEAIVKVREV-GRFDRISYNI 140
             +        +A   + C  G C  N+K      K        IV +REV G   +  ++I
Sbjct:    85 QFNDLLSTCNAEIQRLCLCGFCSKNVKMSYLYGKRV------IVLLREVEGLSSQGVFDI 138

Query:   141 IPDDTLLLSIKDY---EACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVAR 197
             + +   +  +++         + S L+ + + L    V ++G+YGMGG+ KTTL  ++  
Sbjct:   139 VTEAAPIAEVEELPIQSTIVGQDSMLDKVWNCLMEDKVWIVGLYGMGGVGKTTLLTQINN 198

Query:   198 K-AETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLT---LHEESDSGRARSLRNRLKKE 253
             K ++    FD VI+V VSK   + KIQ  I +KLGL      E++ + RA  + N L+++
Sbjct:   199 KFSKLGGGFDVVIWVVVSKNATVHKIQKSIGEKLGLVGKNWDEKNKNQRALDIHNVLRRK 258

Query:   254 KTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKED 313
             K +L +LD+IW  ++ + +G+P+     GCKV  T  S +V  R M       +  L   
Sbjct:   259 KFVL-LLDDIWEKVELKVIGVPYPSGENGCKVAFTTHSKEVCGR-MGVDNPMEISCLDTG 316

Query:   314 EAWSLFKKMAGDYIEGS--EFKWVAKDVARECAGLPVSIVTVARAL 357
              AW L KK  G+   GS  +   +A+ V+ +C GLP+++  +   +
Sbjct:   317 NAWDLLKKKVGENTLGSHPDIPQLARKVSEKCCGLPLALNVIGETM 362

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0009617 "response to bacterium" evidence=ISS

GO:0006499 "N-terminal protein myristoylation" evidence=RCA

TAIR|locus:2131689 AT4G27220 [Arabidopsis thaliana (taxid:3702)]

 Score = 340 (124.7 bits), Expect = 9.5e-30, P = 9.5e-30
 Identities = 100/320 (31%), Positives = 170/320 (53%)

Query:    49 ERVSK-QREVDKA-KRRG---EEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGL 103
             ER+   Q +V++A KR G   + +E  +  WL  V   +   E    ++ R++  C   L
Sbjct:    14 ERLKNVQTKVNEALKRSGIQEKSLERKLRIWLRKVEENVPLGELI--LEKRSS--CAIWL 69

Query:   104 CP-NLKTRRRLSKEAERQKEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMST 162
                +++   ++ K  E Q + ++K   V +  R    I+     +L    +   ++ +  
Sbjct:    70 SDKDVEILEKV-KRLEEQGQDLIKKISVNKSSR---EIVER---VLG-PSFHPQKTALEM 121

Query:   163 LNDILDALKNPDVNMLGIYGMGGIVKTTLAK----EVARKAETEKLFDQVIFVEVSKIQD 218
             L+ + D LK  +V  +G++GMGG+ KTTL +    ++ + A T++ F  VI+V VSK  D
Sbjct:   122 LDKLKDCLKKKNVQKIGVWGMGGVGKTTLVRTLNNDLLKYAATQQ-FALVIWVTVSKDFD 180

Query:   219 IRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGD 278
             ++++Q +IA +LG     E  +    ++  RL   K  L+ILD++W  +D   +GIP   
Sbjct:   181 LKRVQMDIAKRLGKRFTREQMNQLGLTICERLIDLKNFLLILDDVWHPIDLDQLGIPLAL 240

Query:   279 DR-KGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAK 337
             +R K  KV+LT+R L+V  + M + +N  V  L+E EAW LF    G+       K +AK
Sbjct:   241 ERSKDSKVVLTSRRLEVCQQMM-TNENIKVACLQEKEAWELFCHNVGEVANSDNVKPIAK 299

Query:   338 DVARECAGLPVSIVTVARAL 357
             DV+ EC GLP++I+T+ R L
Sbjct:   300 DVSHECCGLPLAIITIGRTL 319

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2166320 AT5G63020 [Arabidopsis thaliana (taxid:3702)]

 Score = 339 (124.4 bits), Expect = 1.1e-29, P = 1.1e-29
 Identities = 94/345 (27%), Positives = 162/345 (46%)

Query:    35 NLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNGIIDEAEKFTGV-DA 93
             NL  L+  +   E  R    R++   +RRG +    V+ W++ V  I+    +   +   
Sbjct:    35 NLTALQRALEQIEQRREDLLRKILSEERRGLQRLSVVQGWVSKVEAIVPRVNELVRMRSV 94

Query:    94 RANKRCFKGLCP-NLKTRRRLSKEAERQKEAIVKVREVGRFDRISYNIIPDDTLLLSIKD 152
             +  + C  G C  NL +  R  K   +  E +  +R  G F  ++  +   D   +  + 
Sbjct:    95 QVQRLCLCGFCSKNLVSSYRYGKRVMKMIEEVEVLRYQGDFAVVAERV---DAARVEERP 151

Query:   153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARK-AETEKLFDQVIFV 211
                  +    L    + L   ++ +LG++GMGG+ KTTL   +  + +     FD VI++
Sbjct:   152 TRPMVAMDPMLESAWNRLMEDEIGILGLHGMGGVGKTTLLSHINNRFSRVGGEFDIVIWI 211

Query:   212 EVSKIQDIRKIQGEIADKL---GLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD 268
              VSK   I++IQ EI +KL        ++++  +A ++ N LK ++ +L +LD+IW  +D
Sbjct:   212 VVSKELQIQRIQDEIWEKLRSDNEKWKQKTEDIKASNIYNVLKHKRFVL-LLDDIWSKVD 270

Query:   269 FQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIE 328
                VG+P      GCK++ T R  ++  R M    +  V  L  D+AW LF K  G+   
Sbjct:   271 LTEVGVPFPSRENGCKIVFTTRLKEICGR-MGVDSDMEVRCLAPDDAWDLFTKKVGEITL 329

Query:   329 GS--EFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNS 371
             GS  E   VA+ VA++C GLP+++  +   +    Y      W S
Sbjct:   330 GSHPEIPTVARTVAKKCRGLPLALNVIGETMA---YKRTVQEWRS 371

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2031366 AT1G63350 "AT1G63350" [Arabidopsis thaliana (taxid:3702)]

 Score = 328 (120.5 bits), Expect = 1.8e-28, P = 1.8e-28
 Identities = 96/347 (27%), Positives = 172/347 (49%)

Query:    29 KSKYTSNLQN----LKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNGIIDE 84
             K  YT NL+     L+T +   +A+R    R++ + + RG +    ++ WL  V  I   
Sbjct:    23 KVSYTHNLEKNLVALETTMEELKAKRDDLLRKLKREEDRGLQTLGEIKVWLNRVETIESR 82

Query:    85 AEKFTGV-DARANKRCFKGLCPNLKTRRRLSKEAERQKEAIVKVREVGRFDRISYNIIPD 143
                     +A   + C  G C      + L+      K   +K+REV + +R  + +I D
Sbjct:    83 VNDLLNARNAELQRLCLCGFCS-----KSLTTSYRYGKSVFLKLREVEKLERRVFEVISD 137

Query:   144 DTLLLSIKDYE---ACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAE 200
                   +++ +       + + L++  + L    V ++G+YGMGG+ KTTL  ++  K  
Sbjct:   138 QASTSEVEEQQLQPTIVGQETMLDNAWNHLMEDGVGIMGLYGMGGVGKTTLLTQINNKFS 197

Query:   201 TEKL-FDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSG----RARSLRNRLKKEKT 255
                  FD VI+V VSK  ++  I  EIA K+ ++  E+ D+     +   L N L+K + 
Sbjct:   198 KYMCGFDSVIWVVVSKEVNVENILDEIAQKVHIS-GEKWDTKYKYQKGVYLYNFLRKMRF 256

Query:   256 ILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEA 315
             +L  LD+IW  ++   +G+P    +  CKV+ T RSLDV +  M  ++   V  L +++A
Sbjct:   257 VL-FLDDIWEKVNLVEIGVPFPTIKNKCKVVFTTRSLDVCT-SMGVEKPMEVQCLADNDA 314

Query:   316 WSLFKKMAGDYIEGS--EFKWVAKDVARECAGLPVSIVTVARALGTR 360
             + LF+K  G    GS  E + +++ VA++C GLP+++  V+  +  +
Sbjct:   315 YDLFQKKVGQITLGSDPEIRELSRVVAKKCCGLPLALNVVSETMSCK 361

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2203881 AT1G62630 [Arabidopsis thaliana (taxid:3702)]

 Score = 322 (118.4 bits), Expect = 7.6e-28, P = 7.6e-28
 Identities = 100/348 (28%), Positives = 169/348 (48%)

Query:    29 KSKYTSNLQN----LKTEVGIPEAERVSKQREVDKAKRRG-EEIEEYVEKWLTSVNGIID 83
             K  YT NL+     L+T +   +A+R    R + + + RG + + E+ + WL  V  + D
Sbjct:    23 KGSYTHNLEKNLVALETTMEELKAKRDDLLRRLKREEDRGLQRLSEF-QVWLNRVATVED 81

Query:    84 EA-EKFTGVDARANKRCFKGLCP-NLKTRRRLSKEAERQKEAIVKVREVGRFDRISYNII 141
                      D    + C    C  NL T  R  K         +++REV +     + +I
Sbjct:    82 IIITLLRDRDVEIQRLCLCRFCSKNLTTSYRYGKSV------FLRLREVEKLKGEVFGVI 135

Query:   142 PDDTLLLSIKD---YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARK 198
              +     + ++         +   L+     L      ++G+YGMGG+ KTTL  ++   
Sbjct:   136 TEQASTSAFEERPLQPTIVGQKKMLDKAWKHLMEDGTGIMGMYGMGGVGKTTLLTQLFNM 195

Query:   199 AETEKL-FDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE--ESD-SGRARSLRNRLKKEK 254
                +K  FD  I+V VS+  ++ KIQ EIA KLGL  HE  + D S +   L N LK +K
Sbjct:   196 FNKDKCGFDIGIWVVVSQEVNVEKIQDEIAQKLGLGGHEWTQRDISQKGVHLFNFLKNKK 255

Query:   255 TILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDE 314
              +L  LD++W  ++   +G+P    +KGCK+  T+RSL+V +  M  ++   V  L+E+ 
Sbjct:   256 FVL-FLDDLWDKVELANIGVPDPRTQKGCKLAFTSRSLNVCT-SMGDEEPMEVQCLEENV 313

Query:   315 AWSLFKKMAGDYIEGSE--FKWVAKDVARECAGLPVSIVTVARALGTR 360
             A+ LF+K  G    GS+     +A+ VA++C GLP+++  +   +  +
Sbjct:   314 AFDLFQKKVGQKTLGSDPGIPQLARIVAKKCCGLPLALNVIGETMSCK 361

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	390
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	2e-40
pfam13401	124	pfam13401, AAA_22, AAA domain	2e-04

>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain

 Score =  144 bits (365), Expect = 2e-40
 Identities = 61/213 (28%), Positives = 109/213 (51%), Gaps = 8/213 (3%)

Query: 159 RMSTLNDILDAL--KNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI 216
           R   +  +++ L   + ++ ++GI GMGG+ KTTLAK++         FD V +V VSK 
Sbjct: 1   REDMIEALIEKLLEMSDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKT 60

Query: 217 QDIRKIQGEIADKLGLT---LHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVG 273
               ++Q +I  +LGL      E+++S  A  ++  L   K  L++LD++W   D+  +G
Sbjct: 61  YTEFRLQKDILQELGLDDSDWVEKNESELAVKIKEALL-RKRFLLVLDDVWEKNDWDKIG 119

Query: 274 IPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAG--DYIEGSE 331
           +P  D   G +V++T RS  V  R   + +   V  L+ +E+W LF       +     E
Sbjct: 120 VPFPDGENGSRVIVTTRSESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKELPPCPE 179

Query: 332 FKWVAKDVARECAGLPVSIVTVARALGTRDYLN 364
            + VAK++  +C GLP+++  +   L  +  + 
Sbjct: 180 LEEVAKEIVEKCKGLPLALKVLGGLLAFKSTVQ 212

Length = 285

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

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 4/84 (4%)

Query: 180 IYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESD 239
           + G  G  KTTL + +AR+        +V++VE   +   + +  +I   LGL L   + 
Sbjct: 9   LTGESGSGKTTLLRRLARQLPN----RRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTT 64

Query: 240 SGRARSLRNRLKKEKTILVILDNI 263
           +    ++ + LK+    L+I+D  
Sbjct: 65  AELLEAILDALKRRGRPLLIIDEA 88

Length = 124

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	390
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.96
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.52
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.48
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.4
PF05729	166	NACHT: NACHT domain	99.39
PRK04841	903	transcriptional regulator MalT; Provisional	99.37
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.32
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.15
PRK06893	229	DNA replication initiation factor; Validated	99.09
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.07
PRK13342	413	recombination factor protein RarA; Reviewed	99.06
PF13173	128	AAA_14: AAA domain	99.03
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	99.0
PRK12402	337	replication factor C small subunit 2; Reviewed	99.0
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.97
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.95
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.94
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.93
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.93
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.9
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.89
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.89
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.88
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.86
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.86
PLN03025	319	replication factor C subunit; Provisional	98.85
PTZ00202	550	tuzin; Provisional	98.84
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.84
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.82
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.81
PRK04195	482	replication factor C large subunit; Provisional	98.81
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.8
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.8
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.79
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.76
PRK08084	235	DNA replication initiation factor; Provisional	98.75
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.75
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	98.74
PRK09087	226	hypothetical protein; Validated	98.73
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	98.72
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.71
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	98.71
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.7
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.7
PRK08727	233	hypothetical protein; Validated	98.7
PRK09112	351	DNA polymerase III subunit delta'; Validated	98.69
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.69
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.69
PRK07471	365	DNA polymerase III subunit delta'; Validated	98.69
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.68
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.67
COG3899	849	Predicted ATPase [General function prediction only	98.66
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	98.66
cd01128	249	rho_factor Transcription termination factor rho is	98.65
PRK13341	725	recombination factor protein RarA/unknown domain f	98.65
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.63
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	98.61
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.6
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	98.6
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	98.6
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	98.6
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.59
PRK05642	234	DNA replication initiation factor; Validated	98.59
PF14516	331	AAA_35: AAA-like domain	98.58
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.57
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	98.57
KOG2028	554	consensus ATPase related to the helicase subunit o	98.56
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	98.55
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	98.55
PRK09376	416	rho transcription termination factor Rho; Provisio	98.52
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	98.51
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	98.5
PRK03992	389	proteasome-activating nucleotidase; Provisional	98.5
PHA02544	316	44 clamp loader, small subunit; Provisional	98.48
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	98.48
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.47
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.46
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	98.44
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	98.44
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.42
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	98.42
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.41
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	98.41
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.41
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.39
COG3903	414	Predicted ATPase [General function prediction only	98.39
CHL00095	821	clpC Clp protease ATP binding subunit	98.38
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	98.38
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	98.38
PRK14086	617	dnaA chromosomal replication initiation protein; P	98.38
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	98.37
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	98.36
TIGR00767	415	rho transcription termination factor Rho. Members	98.36
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	98.33
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	98.33
PRK00149	450	dnaA chromosomal replication initiation protein; R	98.32
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.3
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	98.3
PRK06620	214	hypothetical protein; Validated	98.28
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	98.26
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.25
CHL00181	287	cbbX CbbX; Provisional	98.25
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	98.24
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.22
PRK12422	445	chromosomal replication initiation protein; Provis	98.2
PRK10865	857	protein disaggregation chaperone; Provisional	98.19
PF00004	132	AAA: ATPase family associated with various cellula	98.19
PRK07399	314	DNA polymerase III subunit delta'; Validated	98.19
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	98.19
smart00382	148	AAA ATPases associated with a variety of cellular	98.17
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.14
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	98.14
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	98.09
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	98.09
PRK05707	328	DNA polymerase III subunit delta'; Validated	98.09
COG0593	408	DnaA ATPase involved in DNA replication initiation	98.08
CHL00176	638	ftsH cell division protein; Validated	98.06
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	98.05
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	98.05
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	98.02
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	98.01
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	97.98
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.98
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.96
PRK08116	268	hypothetical protein; Validated	97.95
PRK08058	329	DNA polymerase III subunit delta'; Validated	97.95
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.95
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.94
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.92
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.92
PRK08181	269	transposase; Validated	97.92
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	97.92
PHA00729	226	NTP-binding motif containing protein	97.89
CHL00195	489	ycf46 Ycf46; Provisional	97.87
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	97.83
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.81
PRK10536	262	hypothetical protein; Provisional	97.78
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	97.78
PRK06090	319	DNA polymerase III subunit delta'; Validated	97.78
PRK12608	380	transcription termination factor Rho; Provisional	97.75
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.75
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.73
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.73
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.69
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.69
PRK07993	334	DNA polymerase III subunit delta'; Validated	97.67
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.65
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.65
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.64
PRK08939	306	primosomal protein DnaI; Reviewed	97.64
PRK08118	167	topology modulation protein; Reviewed	97.63
PRK07261	171	topology modulation protein; Provisional	97.63
PRK04132	846	replication factor C small subunit; Provisional	97.61
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.61
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	97.6
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	97.59
PRK10865	857	protein disaggregation chaperone; Provisional	97.56
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.55
PRK06526	254	transposase; Provisional	97.55
PRK06964	342	DNA polymerase III subunit delta'; Validated	97.55
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.54
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	97.54
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	97.54
PRK12377	248	putative replication protein; Provisional	97.52
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.52
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.52
KOG1969	877	consensus DNA replication checkpoint protein CHL12	97.5
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.47
PRK06921	266	hypothetical protein; Provisional	97.47
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.46
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.44
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	97.43
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	97.42
PRK07952	244	DNA replication protein DnaC; Validated	97.42
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.42
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.41
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	97.41
PRK09183	259	transposase/IS protein; Provisional	97.4
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	97.39
cd00983	325	recA RecA is a bacterial enzyme which has roles in	97.37
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	97.36
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	97.35
PRK09354	349	recA recombinase A; Provisional	97.35
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.34
KOG1514	767	consensus Origin recognition complex, subunit 1, a	97.32
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.31
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	97.31
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	97.29
CHL00095	821	clpC Clp protease ATP binding subunit	97.27
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.27
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	97.27
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.26
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	97.26
PRK04296	190	thymidine kinase; Provisional	97.24
PRK08699	325	DNA polymerase III subunit delta'; Validated	97.22
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.2
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	97.2
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.2
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.19
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	97.18
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	97.17
PRK06696	223	uridine kinase; Validated	97.16
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	97.16
TIGR02236	310	recomb_radA DNA repair and recombination protein R	97.13
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.12
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	97.1
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.1
PRK04301	317	radA DNA repair and recombination protein RadA; Va	97.1
PHA02244	383	ATPase-like protein	97.1
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.1
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	97.09
PRK06835	329	DNA replication protein DnaC; Validated	97.09
KOG0736	953	consensus Peroxisome assembly factor 2 containing	97.07
PRK05541	176	adenylylsulfate kinase; Provisional	97.04
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	97.03
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	97.01
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	97.01
PTZ00035	337	Rad51 protein; Provisional	97.0
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	97.0
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	96.99
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.99
cd01394	218	radB RadB. The archaeal protein radB shares simila	96.99
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.99
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.99
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.98
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.98
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	96.98
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	96.94
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.94
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	96.93
TIGR00959	428	ffh signal recognition particle protein. This mode	96.93
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.92
PF00154	322	RecA: recA bacterial DNA recombination protein; In	96.92
PRK06067	234	flagellar accessory protein FlaH; Validated	96.92
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	96.92
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	96.9
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	96.9
PRK04328	249	hypothetical protein; Provisional	96.9
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	96.88
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.87
PRK10867	433	signal recognition particle protein; Provisional	96.86
PTZ00494	664	tuzin-like protein; Provisional	96.86
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.85
PRK06547	172	hypothetical protein; Provisional	96.84
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	96.83
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	96.82
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	96.82
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.8
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	96.8
PRK07132	299	DNA polymerase III subunit delta'; Validated	96.79
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	96.79
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	96.78
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	96.78
PRK11823	446	DNA repair protein RadA; Provisional	96.75
PRK14527	191	adenylate kinase; Provisional	96.74
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.74
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	96.73
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.73
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.72
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	96.72
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.71
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.71
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.71
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.68
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.67
PRK09519	790	recA DNA recombination protein RecA; Reviewed	96.66
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.65
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.65
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	96.64
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.64
PRK15455	644	PrkA family serine protein kinase; Provisional	96.64
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.64
PRK05439	311	pantothenate kinase; Provisional	96.63
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.63
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	96.63
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.62
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.61
PRK14974	336	cell division protein FtsY; Provisional	96.61
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	96.6
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	96.58
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.58
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	96.56
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	96.55
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.55
PRK07667	193	uridine kinase; Provisional	96.54
PRK08233	182	hypothetical protein; Provisional	96.53
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.51
PTZ00301	210	uridine kinase; Provisional	96.5
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	96.49
PRK05480	209	uridine/cytidine kinase; Provisional	96.48
PRK11608	326	pspF phage shock protein operon transcriptional ac	96.47
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	96.46
PRK06762	166	hypothetical protein; Provisional	96.46
CHL00206	2281	ycf2 Ycf2; Provisional	96.46
COG2884	223	FtsE Predicted ATPase involved in cell division [C	96.45
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.44
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.44
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	96.42
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.42
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.42
PRK13531	498	regulatory ATPase RavA; Provisional	96.41
PRK05973	237	replicative DNA helicase; Provisional	96.4
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.39
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	96.39
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	96.39
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	96.37
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	96.37
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	96.36
PF13245	76	AAA_19: Part of AAA domain	96.36
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.35
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.29
PRK00409	782	recombination and DNA strand exchange inhibitor pr	96.29
PF07726	131	AAA_3: ATPase family associated with various cellu	96.28
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.27
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.27
PF05659	147	RPW8: Arabidopsis broad-spectrum mildew resistance	96.27
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	96.26
PRK05917	290	DNA polymerase III subunit delta'; Validated	96.25
PRK13765	637	ATP-dependent protease Lon; Provisional	96.25
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	96.25
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.24
PTZ00088	229	adenylate kinase 1; Provisional	96.24
PRK04040	188	adenylate kinase; Provisional	96.24
PRK06217	183	hypothetical protein; Validated	96.24
PRK00131	175	aroK shikimate kinase; Reviewed	96.24
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.24
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	96.23
PRK03839	180	putative kinase; Provisional	96.21
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	96.21
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	96.21
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	96.2
PLN02924	220	thymidylate kinase	96.18
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	96.17
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	96.17
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	96.16
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	96.16
PRK00279	215	adk adenylate kinase; Reviewed	96.15
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.15
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	96.15
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	96.15
PRK14531	183	adenylate kinase; Provisional	96.14
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.13
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.11
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	96.11
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	96.11
PRK01184	184	hypothetical protein; Provisional	96.1
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	96.1
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	96.09
PRK14532	188	adenylate kinase; Provisional	96.09
PRK08149	428	ATP synthase SpaL; Validated	96.09
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	96.08
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	96.07
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	96.07
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	96.05
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	96.04
PRK14528	186	adenylate kinase; Provisional	96.04
PRK05022	509	anaerobic nitric oxide reductase transcription reg	96.04
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	96.03
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	96.02
COG4240	300	Predicted kinase [General function prediction only	96.02
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	96.02
PRK15424	538	propionate catabolism operon regulatory protein Pr	96.02
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	96.01
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	96.01
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	96.0
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.0
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	95.99
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	95.99
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.99
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	95.98
PRK00625	173	shikimate kinase; Provisional	95.98
COG0714	329	MoxR-like ATPases [General function prediction onl	95.98
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	95.94
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	95.94
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	95.93
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	95.93
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	95.93
PRK06936	439	type III secretion system ATPase; Provisional	95.92
PLN02165	334	adenylate isopentenyltransferase	95.91
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	95.91
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	95.9
PRK14529	223	adenylate kinase; Provisional	95.89
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	95.89
PHA02774	613	E1; Provisional	95.87
PRK14737	186	gmk guanylate kinase; Provisional	95.86
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	95.86
PRK12678	672	transcription termination factor Rho; Provisional	95.85
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.83
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	95.83
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	95.82
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	95.82
PRK05922	434	type III secretion system ATPase; Validated	95.82
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	95.82
CHL00060	494	atpB ATP synthase CF1 beta subunit	95.81
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.79
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	95.79
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	95.79
PRK00300	205	gmk guanylate kinase; Provisional	95.77
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	95.77
PRK09302	509	circadian clock protein KaiC; Reviewed	95.76
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	95.76
TIGR01040	466	V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. Th	95.76
PRK09302	509	circadian clock protein KaiC; Reviewed	95.75
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	95.74
COG3598	402	RepA RecA-family ATPase [DNA replication, recombin	95.73
PTZ00185	574	ATPase alpha subunit; Provisional	95.73
PRK14738	206	gmk guanylate kinase; Provisional	95.71
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	95.71
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.71
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	95.7
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	95.7
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.7
PRK07933	213	thymidylate kinase; Validated	95.7
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	95.7
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	95.69
PRK00889	175	adenylylsulfate kinase; Provisional	95.69
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	95.69
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	95.68
PRK10875	615	recD exonuclease V subunit alpha; Provisional	95.66
PRK14530	215	adenylate kinase; Provisional	95.66
PRK05748	448	replicative DNA helicase; Provisional	95.65
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	95.65
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	95.63
PRK13975	196	thymidylate kinase; Provisional	95.63
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	95.63
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	95.62
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	95.6
PRK00698	205	tmk thymidylate kinase; Validated	95.6
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	95.59
PRK13949	169	shikimate kinase; Provisional	95.59
PRK13947	171	shikimate kinase; Provisional	95.59
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	95.57
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	95.56
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	95.56
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	95.55
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	95.55
PRK15453	290	phosphoribulokinase; Provisional	95.55
PRK07594	433	type III secretion system ATPase SsaN; Validated	95.55
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	95.54
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	95.53
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	95.53
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.52
) 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	95.5
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	95.5
PRK12339	197	2-phosphoglycerate kinase; Provisional	95.5
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	95.49
PRK04196	460	V-type ATP synthase subunit B; Provisional	95.48
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	95.48
PRK03846	198	adenylylsulfate kinase; Provisional	95.48
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	95.47
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	95.47
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	95.46
PRK13695	174	putative NTPase; Provisional	95.46
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	95.45
PRK09099	441	type III secretion system ATPase; Provisional	95.45
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	95.43
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	95.43
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	95.43
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	95.38
PRK05057	172	aroK shikimate kinase I; Reviewed	95.37
PRK06851	367	hypothetical protein; Provisional	95.37
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	95.36
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	95.36
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	95.36
PLN02200	234	adenylate kinase family protein	95.35
PRK06851	367	hypothetical protein; Provisional	95.35
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	95.35
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	95.34
KOG0736	953	consensus Peroxisome assembly factor 2 containing	95.33
COG3910	233	Predicted ATPase [General function prediction only	95.33
COG0055	468	AtpD F0F1-type ATP synthase, beta subunit [Energy	95.32
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	95.31
PRK09435	332	membrane ATPase/protein kinase; Provisional	95.29
TIGR01287	275	nifH nitrogenase iron protein. This model describe	95.27
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	95.25
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	95.23
PRK13974	212	thymidylate kinase; Provisional	95.23
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	95.22
PLN02674	244	adenylate kinase	95.2
PRK07721	438	fliI flagellum-specific ATP synthase; Validated	95.19
PRK06761	282	hypothetical protein; Provisional	95.17
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	95.17
PRK08760	476	replicative DNA helicase; Provisional	95.17
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	95.15
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	95.15
PLN02459	261	probable adenylate kinase	95.15
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	95.14
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	95.13
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	95.12
PF00005	137	ABC_tran: ABC transporter This structure is on hol	95.12
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	95.1
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	95.09
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	95.07
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	95.07
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	95.06
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	95.06
TIGR02546	422	III_secr_ATP type III secretion apparatus H+-trans	95.06
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	95.05

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=2.3e-45  Score=377.91  Aligned_cols=336  Identities=27%  Similarity=0.440  Sum_probs=259.8

Q ss_pred             HHHHHHhchHHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHHHHHhhhhhhhhc-----------------cccc
Q 042806           38 NLKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNGIIDEAEKFTGVDARAN-----------------KRCF  100 (390)
Q Consensus        38 ~l~~~l~~l~~~l~~i~~~l~~a~~~~~~~~~~~~~wl~~l~~~~~d~ed~ld~~~~~~-----------------~~~~  100 (390)
                      ..++.+..|+..|..+++++++++.+. .....+..|...++++.|++||.++.+.-..                 ..|+
T Consensus        25 ~~~~~i~~Lk~~L~~l~~~l~d~~a~~-~~~~~~~~~~e~~~~~~~~~e~~~~~~~v~~~~~~~~~~l~~~~~~~~~~c~  103 (889)
T KOG4658|consen   25 GKDNYILELKENLKALQSALEDLDAKR-DDLERRVNWEEDVGDLVYLAEDIIWLFLVEEIERKANDLLSTRSVERQRLCL  103 (889)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhhc-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhhhHHHHHHHhh
Confidence            444455566666666666788888775 3478899999999999999999998643111                 1122


Q ss_pred             cCcCC-ChhHHhhHHHHHHHHHHHHHHHHhcCCCCccccccCCCC-cccccccCcccccchhHHHHHHHHHhcCCCccEE
Q 042806          101 KGLCP-NLKTRRRLSKEAERQKEAIVKVREVGRFDRISYNIIPDD-TLLLSIKDYEACESRMSTLNDILDALKNPDVNML  178 (390)
Q Consensus       101 ~~~~~-~~~~r~~~~~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~gR~~~~~~l~~~L~~~~~~vi  178 (390)
                      ...+. .+..-+.+++++.++...++.+...+.|..+.....|.+ ....+..+... +|.+..++++.+.|.+++..++
T Consensus       104 ~~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~~~~~~~~~~~~~~~~~e~~~~~~~~~-VG~e~~~~kl~~~L~~d~~~iv  182 (889)
T KOG4658|consen  104 CGFCSKNVSDSYKYGKRVSKVLREVESLGSKGVFEVVGESLDPREKVETRPIQSESD-VGLETMLEKLWNRLMEDDVGIV  182 (889)
T ss_pred             hhhHhHhhhhhHhHHHHHHHHHHHHHHhccccceecccccccchhhcccCCCCcccc-ccHHHHHHHHHHHhccCCCCEE
Confidence            11111 122233444444444444554433333433332111111 11122222223 9999999999999999888999


Q ss_pred             EEEcCCCCcHHHHHHHHHHHhh-hcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CchHHHHHHHHHHhCCC
Q 042806          179 GIYGMGGIVKTTLAKEVARKAE-TEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE---SDSGRARSLRNRLKKEK  254 (390)
Q Consensus       179 ~I~G~~GvGKTtLa~~v~~~~~-~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~l~~~l~~~~  254 (390)
                      +|+||||+||||||++++|+.. ++.+|+..+||.||+.++...++.+|+..++......   ........+.+.|..+|
T Consensus       183 ~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~~kr  262 (889)
T KOG4658|consen  183 GIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLLDEEWEDKEEDELASKLLNLLEGKR  262 (889)
T ss_pred             EEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccCCcccchhhHHHHHHHHHHHhccCc
Confidence            9999999999999999999998 8889999999999999999999999999998744332   33567778888888766


Q ss_pred             eEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCC--CCCCch
Q 042806          255 TILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDY--IEGSEF  332 (390)
Q Consensus       255 ~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~--~~~~~~  332 (390)
                       |||||||||+..+|+.++.++|...+||+|++|||+..|+...++....+++.+|+++|||+||++.++..  ...+.+
T Consensus       263 -fllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~~~~~~i  341 (889)
T KOG4658|consen  263 -FLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTLGSHPDI  341 (889)
T ss_pred             -eEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccccccCccccHHHHHHhhccccccccccH
Confidence             99999999999999999999999999999999999999988768888899999999999999999999833  334558


Q ss_pred             HHHHHHHHHHcCCChHHHHHHHHHhcCCCCCCCcccchhHHHHHhhh
Q 042806          333 KWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQLT  379 (390)
Q Consensus       333 ~~~~~~i~~~~~GlPLai~~l~~~L~~~~~~~~~~~w~~~~~~l~~~  379 (390)
                      +++|++++++|+|+|||+.++|+.|++|..   ..+|+++...|.+.
T Consensus       342 ~~lak~v~~kC~GLPLAl~viG~~ma~K~t---~~eW~~~~~~l~s~  385 (889)
T KOG4658|consen  342 EELAKEVAEKCGGLPLALNVLGGLLACKKT---VQEWRRALNVLKSS  385 (889)
T ss_pred             HHHHHHHHHHhCChHHHHHHHHHHhcCCCc---HHHHHHHHcccccc
Confidence            999999999999999999999999999987   78999999988776

>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=100.00  E-value=2.3e-35  Score=273.42  Aligned_cols=218  Identities=30%  Similarity=0.465  Sum_probs=173.5

Q ss_pred             hhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC-
Q 042806          159 RMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLH-  235 (390)
Q Consensus       159 R~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~-  235 (390)
                      |+.++++|.+.|.+  ++.++|+|+|+||+||||||..++++...+.+|+.++|+.++...+..+++..|+..++.... 
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~   80 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSS   80 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-ST
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccc
Confidence            78899999999988  789999999999999999999999997777889999999999999999999999999988743 


Q ss_pred             ---CCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhhhhcCCCcceEecCCCCH
Q 042806          236 ---EESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKE  312 (390)
Q Consensus       236 ---~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~~~~~~~~~~~~l~~L~~  312 (390)
                         ..+.......+.+.|.+++ +||||||||+...|+.+...++....|++||+|||+..++.........|++++|+.
T Consensus        81 ~~~~~~~~~~~~~l~~~L~~~~-~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~~  159 (287)
T PF00931_consen   81 ISDPKDIEELQDQLRELLKDKR-CLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLSE  159 (287)
T ss_dssp             SSCCSSHHHHHHHHHHHHCCTS-EEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--H
T ss_pred             cccccccccccccchhhhcccc-ceeeeeeeccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence               2345567788888888875 999999999999998888888777789999999999888654333367999999999


Q ss_pred             HHHHHHHHHhhCCCC--CCCchHHHHHHHHHHcCCChHHHHHHHHHhcCCCCCCCcccchhHHHHHhhhh
Q 042806          313 DEAWSLFKKMAGDYI--EGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQLTL  380 (390)
Q Consensus       313 ~ea~~lf~~~~~~~~--~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~~~~~~~~~w~~~~~~l~~~~  380 (390)
                      ++|++||.+.++...  ..+..++.+++|+++|+|+||||.++|++|+.++.   ..+|+++...+....
T Consensus       160 ~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~---~~~w~~~~~~l~~~~  226 (287)
T PF00931_consen  160 EEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKST---VDEWEEALEELENSL  226 (287)
T ss_dssp             HHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHS---SSSHHHHHHHHHHCH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccc---ccccccccccccccc
Confidence            999999999997332  34555678899999999999999999999977664   789998887776655

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.

>PLN03210 Resistant to P

Probab=99.96  E-value=4.3e-28  Score=261.71  Aligned_cols=218  Identities=20%  Similarity=0.277  Sum_probs=166.3

Q ss_pred             cccccchhHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEe---CCC-----------
Q 042806          153 YEACESRMSTLNDILDALK--NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEV---SKI-----------  216 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~--~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v---~~~-----------  216 (390)
                      .+.++||+..++++..+|.  .++.++|+|+||||+||||||+.+|+....  +|++.+|+..   +..           
T Consensus       183 ~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~--~F~g~vfv~~~~v~~~~~~~~~~~~~~  260 (1153)
T PLN03210        183 FEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLSR--QFQSSVFIDRAFISKSMEIYSSANPDD  260 (1153)
T ss_pred             cccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHHhh--cCCeEEEeeccccccchhhcccccccc
Confidence            4579999999999988875  356899999999999999999999998764  4998888742   110           


Q ss_pred             CC-HHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhh
Q 042806          217 QD-IRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVL  295 (390)
Q Consensus       217 ~~-~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~  295 (390)
                      +. ...+...++..+.......  ......+.+.+..++ +||||||||+...|+.+.......++||+||||||+..++
T Consensus       261 ~~~~~~l~~~~l~~il~~~~~~--~~~~~~~~~~L~~kr-vLLVLDdv~~~~~l~~L~~~~~~~~~GsrIIiTTrd~~vl  337 (1153)
T PLN03210        261 YNMKLHLQRAFLSEILDKKDIK--IYHLGAMEERLKHRK-VLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITKDKHFL  337 (1153)
T ss_pred             cchhHHHHHHHHHHHhCCCCcc--cCCHHHHHHHHhCCe-EEEEEeCCCCHHHHHHHHhhCccCCCCcEEEEEeCcHHHH
Confidence            00 1223344444432211110  011245667777655 9999999999989988876655557899999999999886


Q ss_pred             hhcCCCcceEecCCCCHHHHHHHHHHhhCC-CCCCCchHHHHHHHHHHcCCChHHHHHHHHHhcCCCCCCCcccchhHHH
Q 042806          296 SRKMDSQQNFSVGVLKEDEAWSLFKKMAGD-YIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGG  374 (390)
Q Consensus       296 ~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~-~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~~~~~~~~~w~~~~~  374 (390)
                      . ..+..+.|+++.|+.++||+||+.+||. ..++.++.+++++|+++|+|+||||+++|++|+.++    ..+|+.+..
T Consensus       338 ~-~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k~----~~~W~~~l~  412 (1153)
T PLN03210        338 R-AHGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLGSYLRGRD----KEDWMDMLP  412 (1153)
T ss_pred             H-hcCCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCCC----HHHHHHHHH
Confidence            4 3445679999999999999999999984 334556788999999999999999999999999875    689999888


Q ss_pred             HHhhhh
Q 042806          375 LLQLTL  380 (390)
Q Consensus       375 ~l~~~~  380 (390)
                      .|+...
T Consensus       413 ~L~~~~  418 (1153)
T PLN03210        413 RLRNGL  418 (1153)
T ss_pred             HHHhCc
Confidence            887643

syringae 6; Provisional

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

Probab=99.52  E-value=2.4e-12  Score=118.09  Aligned_cols=182  Identities=16%  Similarity=0.166  Sum_probs=117.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHH---
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNR---  249 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~---  249 (390)
                      ....++.|+|++|+|||||++.+++...... + ..+|+ +....+..+++..++..++......+.......+...   
T Consensus        41 ~~~~~~~l~G~~G~GKTtl~~~l~~~l~~~~-~-~~~~~-~~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~  117 (269)
T TIGR03015        41 QREGFILITGEVGAGKTTLIRNLLKRLDQER-V-VAAKL-VNTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLIE  117 (269)
T ss_pred             cCCCEEEEEcCCCCCHHHHHHHHHHhcCCCC-e-EEeee-eCCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHH
Confidence            3456899999999999999999998875321 1 12333 3334577889999999998765443333333444433   


Q ss_pred             -HhCCCeEEEEEeCCCCCc--ccccccC---CCCCCCCCcEEEEEecchhhhh--------hcCCCcceEecCCCCHHHH
Q 042806          250 -LKKEKTILVILDNIWGNL--DFQAVGI---PHGDDRKGCKVLLTARSLDVLS--------RKMDSQQNFSVGVLKEDEA  315 (390)
Q Consensus       250 -l~~~~~~LlVlDdv~~~~--~~~~l~~---~l~~~~~~s~IivTtr~~~v~~--------~~~~~~~~~~l~~L~~~ea  315 (390)
                       ...++++++|+||++...  .++.+..   ....+.....|++|........        ........+++.+|+.+|.
T Consensus       118 ~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~r~~~~~~l~~l~~~e~  197 (269)
T TIGR03015       118 QFAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPEFRETLQSPQLQQLRQRIIASCHLGPLDREET  197 (269)
T ss_pred             HHhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHHHHHHHcCchhHHHHhheeeeeeCCCCCHHHH
Confidence             334566999999998753  3444322   1111223345667765432100        0011134788999999999


Q ss_pred             HHHHHHhhC--CCC-CCCchHHHHHHHHHHcCCChHHHHHHHHHh
Q 042806          316 WSLFKKMAG--DYI-EGSEFKWVAKDVARECAGLPVSIVTVARAL  357 (390)
Q Consensus       316 ~~lf~~~~~--~~~-~~~~~~~~~~~i~~~~~GlPLai~~l~~~L  357 (390)
                      .+++.+.+.  +.. ...-.++..+.|++.|+|.|..|..++..+
T Consensus       198 ~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~  242 (269)
T TIGR03015       198 REYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRL  242 (269)
T ss_pred             HHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence            999988774  111 112235678999999999999999998776

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.

>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=99.48  E-value=2.6e-13  Score=121.39  Aligned_cols=194  Identities=15%  Similarity=0.229  Sum_probs=105.9

Q ss_pred             ccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH---------
Q 042806          156 CESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEI---------  226 (390)
Q Consensus       156 ~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i---------  226 (390)
                      |+||+.++++|.+++..+..+.+.|+|+.|+|||+|++.+.+.....+ + ..+|+......+. .....+         
T Consensus         1 F~gR~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~~~~~~~-~-~~~y~~~~~~~~~-~~~~~~~~~~~~~~~   77 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFINELKEKG-Y-KVVYIDFLEESNE-SSLRSFIEETSLADE   77 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHHHCT--E-E-CCCHHCCTTBSHH-HHHHHHHHHHHHHCH
T ss_pred             CCCHHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHHHhhhcC-C-cEEEEecccchhh-hHHHHHHHHHHHHHH
Confidence            789999999999999877788999999999999999999999884421 2 2344444333322 222221         


Q ss_pred             -HHHhCCCCC-----------CCCchHHHHHHHHHHhC-CCeEEEEEeCCCCCc-cc----------ccccCCCCCCCCC
Q 042806          227 -ADKLGLTLH-----------EESDSGRARSLRNRLKK-EKTILVILDNIWGNL-DF----------QAVGIPHGDDRKG  282 (390)
Q Consensus       227 -~~~l~~~~~-----------~~~~~~~~~~l~~~l~~-~~~~LlVlDdv~~~~-~~----------~~l~~~l~~~~~~  282 (390)
                       ...+....+           ..........+.+.+.. +++++||+||++... ..          ..+..... ....
T Consensus        78 l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~  156 (234)
T PF01637_consen   78 LSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLL-SQQN  156 (234)
T ss_dssp             CHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH-----TT
T ss_pred             HHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhcc-ccCC
Confidence             111211100           11223344555555543 234999999997554 11          11111221 2334


Q ss_pred             cEEEEEecchhhhhh-------cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          283 CKVLLTARSLDVLSR-------KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       283 s~IivTtr~~~v~~~-------~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      ..+|+++.+......       ..+....+.+++|+.+++++++...+.....-+.-++..++|+..+||+|..|..+
T Consensus       157 ~~~v~~~S~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~e~~~~~~~~~~~~~~~~~~~~~~~~i~~~~gG~P~~l~~~  234 (234)
T PF01637_consen  157 VSIVITGSSDSLMEEFLDDKSPLFGRFSHIELKPLSKEEAREFLKELFKELIKLPFSDEDIEEIYSLTGGNPRYLQEL  234 (234)
T ss_dssp             EEEEEEESSHHHHHHTT-TTSTTTT---EEEE----HHHHHHHHHHHHHCC------HHHHHHHHHHHTT-HHHHHHH
T ss_pred             ceEEEECCchHHHHHhhcccCccccccceEEEeeCCHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHhCCCHHHHhcC
Confidence            455566555444322       22333469999999999999999976433111122455789999999999998753

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

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.40  E-value=3.6e-11  Score=116.52  Aligned_cols=202  Identities=19%  Similarity=0.165  Sum_probs=128.8

Q ss_pred             cccccchhHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALK----NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~----~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      ++.++||+.++++|...+.    +.....+.|+|++|+|||++++.+++........-..+++++....+...++..++.
T Consensus        29 P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~  108 (394)
T PRK00411         29 PENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIAR  108 (394)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHH
Confidence            4579999999999988873    234567889999999999999999998765432234677777777788899999999


Q ss_pred             HhCCC-CCC--CCchHHHHHHHHHHhC-CCeEEEEEeCCCCCc------ccccccCCCCCCCC--CcEEEEEecchhhhh
Q 042806          229 KLGLT-LHE--ESDSGRARSLRNRLKK-EKTILVILDNIWGNL------DFQAVGIPHGDDRK--GCKVLLTARSLDVLS  296 (390)
Q Consensus       229 ~l~~~-~~~--~~~~~~~~~l~~~l~~-~~~~LlVlDdv~~~~------~~~~l~~~l~~~~~--~s~IivTtr~~~v~~  296 (390)
                      ++... .+.  .+.......+.+.+.. +++.+||||+++...      .+..+...+ ....  +..+|.++....+..
T Consensus       109 ~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~-~~~~~~~v~vI~i~~~~~~~~  187 (394)
T PRK00411        109 QLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAH-EEYPGARIGVIGISSDLTFLY  187 (394)
T ss_pred             HhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhh-hccCCCeEEEEEEECCcchhh
Confidence            98652 211  1334455666676654 456899999997642      122222211 1112  233666666543221


Q ss_pred             h------cCCCcceEecCCCCHHHHHHHHHHhhCC-----CCCCCchHHHHHHHHHHcCCChHHHHHHHH
Q 042806          297 R------KMDSQQNFSVGVLKEDEAWSLFKKMAGD-----YIEGSEFKWVAKDVARECAGLPVSIVTVAR  355 (390)
Q Consensus       297 ~------~~~~~~~~~l~~L~~~ea~~lf~~~~~~-----~~~~~~~~~~~~~i~~~~~GlPLai~~l~~  355 (390)
                      .      ..-....+.+.+++.++..+++...+..     ...+..++.+++......|..+.|+..+-.
T Consensus       188 ~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~  257 (394)
T PRK00411        188 ILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRR  257 (394)
T ss_pred             hcCHHHHhcCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            1      1112357899999999999999887631     122222233333333334668888877754

>PF05729 NACHT: NACHT domain

Probab=99.39  E-value=4e-12  Score=107.50  Aligned_cols=143  Identities=22%  Similarity=0.306  Sum_probs=92.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCC----CCeEEEEEeCCCCCHH---HHHHHHHHHhCCCCCCCCchHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKL----FDQVIFVEVSKIQDIR---KIQGEIADKLGLTLHEESDSGRARSLRN  248 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~---~l~~~i~~~l~~~~~~~~~~~~~~~l~~  248 (390)
                      +++.|+|.+|+||||+++.++........    +...+|+..+......   .+...+..........     ....+..
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~-----~~~~~~~   75 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAP-----IEELLQE   75 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhh-----hHHHHHH
Confidence            57899999999999999999998876543    3456677665543322   3444444444322111     1113334


Q ss_pred             HHhCCCeEEEEEeCCCCCcc---------ccc-ccCCCCC-CCCCcEEEEEecchhh--hhhcCCCcceEecCCCCHHHH
Q 042806          249 RLKKEKTILVILDNIWGNLD---------FQA-VGIPHGD-DRKGCKVLLTARSLDV--LSRKMDSQQNFSVGVLKEDEA  315 (390)
Q Consensus       249 ~l~~~~~~LlVlDdv~~~~~---------~~~-l~~~l~~-~~~~s~IivTtr~~~v--~~~~~~~~~~~~l~~L~~~ea  315 (390)
                      .+...++++||||+++....         +.. +...++. ..+++++++|+|+...  ..........+++.+|++++.
T Consensus        76 ~~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~~  155 (166)
T PF05729_consen   76 LLEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEEDI  155 (166)
T ss_pred             HHHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHHH
Confidence            44455669999999975432         111 2112222 3568999999998665  222344457899999999999


Q ss_pred             HHHHHHhh
Q 042806          316 WSLFKKMA  323 (390)
Q Consensus       316 ~~lf~~~~  323 (390)
                      .+++++.+
T Consensus       156 ~~~~~~~f  163 (166)
T PF05729_consen  156 KQYLRKYF  163 (166)
T ss_pred             HHHHHHHh
Confidence            99998876

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.37  E-value=1.2e-11  Score=132.39  Aligned_cols=195  Identities=14%  Similarity=0.149  Sum_probs=125.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhC
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-IQDIRKIQGEIADKLG  231 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~l~~~i~~~l~  231 (390)
                      ...++.|..-.+.+-+   ....+++.|+||+|.||||++.++....      +.++|+++.. +.++..+...++..++
T Consensus        13 ~~~~~~R~rl~~~l~~---~~~~~~~~v~apaG~GKTtl~~~~~~~~------~~~~w~~l~~~d~~~~~f~~~l~~~l~   83 (903)
T PRK04841         13 LHNTVVRERLLAKLSG---ANNYRLVLVTSPAGYGKTTLISQWAAGK------NNLGWYSLDESDNQPERFASYLIAALQ   83 (903)
T ss_pred             ccccCcchHHHHHHhc---ccCCCeEEEECCCCCCHHHHHHHHHHhC------CCeEEEecCcccCCHHHHHHHHHHHHH
Confidence            4467888765555432   2357899999999999999999988532      2589999964 4466667777777764


Q ss_pred             CCCCC--------------CCchHHHHHHHHHHhC-CCeEEEEEeCCCCCc--ccc-cccCCCCCCCCCcEEEEEecchh
Q 042806          232 LTLHE--------------ESDSGRARSLRNRLKK-EKTILVILDNIWGNL--DFQ-AVGIPHGDDRKGCKVLLTARSLD  293 (390)
Q Consensus       232 ~~~~~--------------~~~~~~~~~l~~~l~~-~~~~LlVlDdv~~~~--~~~-~l~~~l~~~~~~s~IivTtr~~~  293 (390)
                      .....              .+.......+...+.. +++++|||||++..+  ... .+...+....++.++|+|||...
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~  163 (903)
T PRK04841         84 QATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLP  163 (903)
T ss_pred             HhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCC
Confidence            21111              0111233344445543 667999999997542  222 22222333455678989999732


Q ss_pred             hhh--hcCCCcceEecC----CCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhcCC
Q 042806          294 VLS--RKMDSQQNFSVG----VLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTR  360 (390)
Q Consensus       294 v~~--~~~~~~~~~~l~----~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~  360 (390)
                      ...  .........++.    +|+.+|+.++|....+....    .+....|.+.|+|+|+++..++..+...
T Consensus       164 ~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~~~~~~~----~~~~~~l~~~t~Gwp~~l~l~~~~~~~~  232 (903)
T PRK04841        164 PLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQRLSSPIE----AAESSRLCDDVEGWATALQLIALSARQN  232 (903)
T ss_pred             CCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhccCCCCC----HHHHHHHHHHhCChHHHHHHHHHHHhhC
Confidence            111  001112345555    99999999999887653321    3346789999999999999998777543

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.32  E-value=2.7e-10  Score=109.31  Aligned_cols=198  Identities=17%  Similarity=0.185  Sum_probs=124.6

Q ss_pred             ccccchhHHHHHHHHHhcC----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcC-CC---CeEEEEEeCCCCCHHHHHHH
Q 042806          154 EACESRMSTLNDILDALKN----PDVNMLGIYGMGGIVKTTLAKEVARKAETEK-LF---DQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~----~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~-~f---~~~~wv~v~~~~~~~~l~~~  225 (390)
                      +.++||+.++++|...+..    .....+.|+|++|+|||++++.+++...... ..   -..+|+++....+...++..
T Consensus        15 ~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~   94 (365)
T TIGR02928        15 DRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVE   94 (365)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHHH
Confidence            4689999999999998763    3456789999999999999999999864321 11   24677888777788899999


Q ss_pred             HHHHhC---CCCCC--CCchHHHHHHHHHHh-CCCeEEEEEeCCCCCc-c----cccccCCC-CCCC--CCcEEEEEecc
Q 042806          226 IADKLG---LTLHE--ESDSGRARSLRNRLK-KEKTILVILDNIWGNL-D----FQAVGIPH-GDDR--KGCKVLLTARS  291 (390)
Q Consensus       226 i~~~l~---~~~~~--~~~~~~~~~l~~~l~-~~~~~LlVlDdv~~~~-~----~~~l~~~l-~~~~--~~s~IivTtr~  291 (390)
                      ++.++.   ...+.  .+.......+.+.+. .+++++||||+++... .    +..+.... ....  ....+|+++..
T Consensus        95 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~n~  174 (365)
T TIGR02928        95 LANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGISND  174 (365)
T ss_pred             HHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEECC
Confidence            999883   32221  123344555666664 3556899999997651 1    11221110 1111  23445555544


Q ss_pred             hhhhhh----c--CCCcceEecCCCCHHHHHHHHHHhhC----CCCCCCchHHHHHHHHHHcCCChHHHH
Q 042806          292 LDVLSR----K--MDSQQNFSVGVLKEDEAWSLFKKMAG----DYIEGSEFKWVAKDVARECAGLPVSIV  351 (390)
Q Consensus       292 ~~v~~~----~--~~~~~~~~l~~L~~~ea~~lf~~~~~----~~~~~~~~~~~~~~i~~~~~GlPLai~  351 (390)
                      ......    .  .-....+++.+++.++..+++..++.    .....++..+.+..++..+.|.|-.+.
T Consensus       175 ~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al  244 (365)
T TIGR02928       175 LKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAI  244 (365)
T ss_pred             cchHhhcCHHHhccCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHH
Confidence            322111    0  11125789999999999999988863    111222222344556777778885443

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.15  E-value=2e-09  Score=100.62  Aligned_cols=188  Identities=15%  Similarity=0.066  Sum_probs=107.9

Q ss_pred             ccccchhHHHHHHHHHhc-----CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          154 EACESRMSTLNDILDALK-----NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~-----~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      ..|+|++..++.|..++.     ......+.++|++|+|||+||+.+++.....  +   ..+..+......++. ..+.
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~~~--~---~~~~~~~~~~~~~l~-~~l~   77 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVN--L---KITSGPALEKPGDLA-AILT   77 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCC--E---EEeccchhcCchhHH-HHHH
Confidence            479999999999888876     2345668899999999999999999987532  2   222222212222222 2222


Q ss_pred             HhCCCC-------CCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhhhhc-CC
Q 042806          229 KLGLTL-------HEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRK-MD  300 (390)
Q Consensus       229 ~l~~~~-------~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~~~~-~~  300 (390)
                      .++...       ...+ ......+...+.+.+ ..+|+++..+...+..   .+   .+.+-|..||+...+.... ..
T Consensus        78 ~~~~~~vl~iDEi~~l~-~~~~e~l~~~~~~~~-~~~v~~~~~~~~~~~~---~~---~~~~li~~t~~~~~l~~~l~sR  149 (305)
T TIGR00635        78 NLEEGDVLFIDEIHRLS-PAVEELLYPAMEDFR-LDIVIGKGPSARSVRL---DL---PPFTLVGATTRAGMLTSPLRDR  149 (305)
T ss_pred             hcccCCEEEEehHhhhC-HHHHHHhhHHHhhhh-eeeeeccCccccceee---cC---CCeEEEEecCCccccCHHHHhh
Confidence            222111       0001 112223334443333 4555555433333221   11   2245566666654332211 11


Q ss_pred             CcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHH
Q 042806          301 SQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARA  356 (390)
Q Consensus       301 ~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~  356 (390)
                      ....+++.+++.++..+++.+.+...... -.++....|++.|+|.|-.+..+...
T Consensus       150 ~~~~~~l~~l~~~e~~~il~~~~~~~~~~-~~~~al~~ia~~~~G~pR~~~~ll~~  204 (305)
T TIGR00635       150 FGIILRLEFYTVEELAEIVSRSAGLLNVE-IEPEAALEIARRSRGTPRIANRLLRR  204 (305)
T ss_pred             cceEEEeCCCCHHHHHHHHHHHHHHhCCC-cCHHHHHHHHHHhCCCcchHHHHHHH
Confidence            23578999999999999999887522222 22456789999999999877666544

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=99.09  E-value=1.8e-09  Score=96.38  Aligned_cols=155  Identities=16%  Similarity=0.147  Sum_probs=96.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      ..+.+.|+|++|+|||+|++.+++....+  .....|+.+...   .....                    .+.+.+.+ 
T Consensus        38 ~~~~l~l~G~~G~GKThL~~ai~~~~~~~--~~~~~y~~~~~~---~~~~~--------------------~~~~~~~~-   91 (229)
T PRK06893         38 QQPFFYIWGGKSSGKSHLLKAVSNHYLLN--QRTAIYIPLSKS---QYFSP--------------------AVLENLEQ-   91 (229)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEeeHHHh---hhhhH--------------------HHHhhccc-
Confidence            34678999999999999999999987543  234567665321   00000                    11222222 


Q ss_pred             CeEEEEEeCCCCC---ccccc-ccCCCCC-CCCCcEEEE-Eecc---------hhhhhhcCCCcceEecCCCCHHHHHHH
Q 042806          254 KTILVILDNIWGN---LDFQA-VGIPHGD-DRKGCKVLL-TARS---------LDVLSRKMDSQQNFSVGVLKEDEAWSL  318 (390)
Q Consensus       254 ~~~LlVlDdv~~~---~~~~~-l~~~l~~-~~~~s~Iiv-Ttr~---------~~v~~~~~~~~~~~~l~~L~~~ea~~l  318 (390)
                       .-+|++||+|..   ..|+. +...+.. ...|..+|+ |+..         ..+.+ ....+..+++++++.++.+++
T Consensus        92 -~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~s-Rl~~g~~~~l~~pd~e~~~~i  169 (229)
T PRK06893         92 -QDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLAS-RLTWGEIYQLNDLTDEQKIIV  169 (229)
T ss_pred             -CCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHH-HHhcCCeeeCCCCCHHHHHHH
Confidence             249999999864   34442 2222221 123555554 4443         23322 234557899999999999999


Q ss_pred             HHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHh
Q 042806          319 FKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARAL  357 (390)
Q Consensus       319 f~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L  357 (390)
                      +++.+....... -+++...|++.+.|-.-.+..+-..|
T Consensus       170 L~~~a~~~~l~l-~~~v~~~L~~~~~~d~r~l~~~l~~l  207 (229)
T PRK06893        170 LQRNAYQRGIEL-SDEVANFLLKRLDRDMHTLFDALDLL  207 (229)
T ss_pred             HHHHHHHcCCCC-CHHHHHHHHHhccCCHHHHHHHHHHH
Confidence            998886332222 25678899999998877766655444

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.07  E-value=7.2e-09  Score=97.77  Aligned_cols=191  Identities=13%  Similarity=0.014  Sum_probs=104.1

Q ss_pred             CcccccchhHHHHHHHHHhc-----CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 042806          152 DYEACESRMSTLNDILDALK-----NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~-----~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      ....|+||+..++.+...+.     ....+.+.|+|++|+|||+||+.+++.....  +   .++..+..... .-+..+
T Consensus        23 ~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~~~--~---~~~~~~~~~~~-~~l~~~   96 (328)
T PRK00080         23 SLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVN--I---RITSGPALEKP-GDLAAI   96 (328)
T ss_pred             CHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhCCC--e---EEEecccccCh-HHHHHH
Confidence            45679999999988877664     2335678899999999999999999987532  2   22222211111 112222


Q ss_pred             HHHhCCCC----CCCC--chHHHHHHHHHHhCCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhhhhc-C
Q 042806          227 ADKLGLTL----HEES--DSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRK-M  299 (390)
Q Consensus       227 ~~~l~~~~----~~~~--~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~~~~-~  299 (390)
                      +..+....    ++.+  .....+.+...+.+.+ ..+|+|+-.+...+..   .+   .+.+-|..|++...+.... .
T Consensus        97 l~~l~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~-~~~~l~~~~~~~~~~~---~l---~~~~li~at~~~~~l~~~L~s  169 (328)
T PRK00080         97 LTNLEEGDVLFIDEIHRLSPVVEEILYPAMEDFR-LDIMIGKGPAARSIRL---DL---PPFTLIGATTRAGLLTSPLRD  169 (328)
T ss_pred             HHhcccCCEEEEecHhhcchHHHHHHHHHHHhcc-eeeeeccCccccceee---cC---CCceEEeecCCcccCCHHHHH
Confidence            22221110    0000  0001112222222222 3344443322211110   11   1234455666644332211 1


Q ss_pred             CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHH
Q 042806          300 DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARA  356 (390)
Q Consensus       300 ~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~  356 (390)
                      .....+++.+++.++..+++...+...... -.++....|++.|+|.|-.+..+...
T Consensus       170 Rf~~~~~l~~~~~~e~~~il~~~~~~~~~~-~~~~~~~~ia~~~~G~pR~a~~~l~~  225 (328)
T PRK00080        170 RFGIVQRLEFYTVEELEKIVKRSARILGVE-IDEEGALEIARRSRGTPRIANRLLRR  225 (328)
T ss_pred             hcCeeeecCCCCHHHHHHHHHHHHHHcCCC-cCHHHHHHHHHHcCCCchHHHHHHHH
Confidence            123578999999999999999887632222 22457889999999999866666553

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.06  E-value=2.9e-09  Score=103.49  Aligned_cols=180  Identities=18%  Similarity=0.164  Sum_probs=107.6

Q ss_pred             CcccccchhHHHHH---HHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          152 DYEACESRMSTLND---ILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       152 ~~~~~~gR~~~~~~---l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      ..+.++|++..+..   +..++..+..+.+.|+|++|+||||||+.+++.....  |     +.++.......-++.+..
T Consensus        10 ~l~d~vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~~~~--~-----~~l~a~~~~~~~ir~ii~   82 (413)
T PRK13342         10 TLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAP--F-----EALSAVTSGVKDLREVIE   82 (413)
T ss_pred             CHHHhcCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHhCCC--E-----EEEecccccHHHHHHHHH
Confidence            34568888877655   7777777777788899999999999999999876422  2     222221111111112211


Q ss_pred             HhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEE--Eecchh--hhhhcCCCc
Q 042806          229 KLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLL--TARSLD--VLSRKMDSQ  302 (390)
Q Consensus       229 ~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~Iiv--Ttr~~~--v~~~~~~~~  302 (390)
                                      ........+++.+|++|+++...  ..+.+...+   ..+..+++  ||.+..  +......-.
T Consensus        83 ----------------~~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~l---e~~~iilI~att~n~~~~l~~aL~SR~  143 (413)
T PRK13342         83 ----------------EARQRRSAGRRTILFIDEIHRFNKAQQDALLPHV---EDGTITLIGATTENPSFEVNPALLSRA  143 (413)
T ss_pred             ----------------HHHHhhhcCCceEEEEechhhhCHHHHHHHHHHh---hcCcEEEEEeCCCChhhhccHHHhccc
Confidence                            11111122344899999998652  333343333   22444444  344322  111122233


Q ss_pred             ceEecCCCCHHHHHHHHHHhhCC--CCCCCchHHHHHHHHHHcCCChHHHHHHHHHh
Q 042806          303 QNFSVGVLKEDEAWSLFKKMAGD--YIEGSEFKWVAKDVARECAGLPVSIVTVARAL  357 (390)
Q Consensus       303 ~~~~l~~L~~~ea~~lf~~~~~~--~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L  357 (390)
                      ..+++.+++.++...++.+.+..  .....-.++....|++.|+|.|..+..+....
T Consensus       144 ~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~Le~~  200 (413)
T PRK13342        144 QVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLLELA  200 (413)
T ss_pred             eeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            68999999999999999987642  11102235567889999999998776554443

>PF13173 AAA_14: AAA domain

Probab=99.03  E-value=8e-10  Score=89.39  Aligned_cols=121  Identities=20%  Similarity=0.197  Sum_probs=81.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      .+++.|.|+.|+|||||+++++.+..   ....++|+++...........+                ....+.+....++
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~   62 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDRRLADPD----------------LLEYFLELIKPGK   62 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHHHHhhhh----------------hHHHHHHhhccCC
Confidence            46899999999999999999998875   1345677776654321110000                1222333322334


Q ss_pred             eEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhhhh-----cCCCcceEecCCCCHHHH
Q 042806          255 TILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSR-----KMDSQQNFSVGVLKEDEA  315 (390)
Q Consensus       255 ~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~~~-----~~~~~~~~~l~~L~~~ea  315 (390)
                       .+++||+++...+|......+.+..+..+|++|+.+......     ..+-...+++.||+..|.
T Consensus        63 -~~i~iDEiq~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   63 -KYIFIDEIQYLPDWEDALKFLVDNGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             -cEEEEehhhhhccHHHHHHHHHHhccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence             899999999988888876666565567899999998655422     222335789999998774

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=99.00  E-value=1.3e-08  Score=102.30  Aligned_cols=204  Identities=16%  Similarity=0.127  Sum_probs=134.3

Q ss_pred             cccccCcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHH
Q 042806          147 LLSIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-IQDIRKIQGE  225 (390)
Q Consensus       147 ~~~~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~l~~~  225 (390)
                      ..+|.+....+-|..-.+.|-+   ..+.+++.|..|+|.|||||+.++......   =..+.|++++. +.++..++..
T Consensus        12 ~~~P~~~~~~v~R~rL~~~L~~---~~~~RL~li~APAGfGKttl~aq~~~~~~~---~~~v~Wlslde~dndp~rF~~y   85 (894)
T COG2909          12 LVRPVRPDNYVVRPRLLDRLRR---ANDYRLILISAPAGFGKTTLLAQWRELAAD---GAAVAWLSLDESDNDPARFLSY   85 (894)
T ss_pred             cCCCCCcccccccHHHHHHHhc---CCCceEEEEeCCCCCcHHHHHHHHHHhcCc---ccceeEeecCCccCCHHHHHHH
Confidence            3445556677888655544433   247899999999999999999999873322   33589999975 4578888888


Q ss_pred             HHHHhCCCCCCCC--------------chHHHHHHHHHHhC-CCeEEEEEeCCCCC--ccccc-ccCCCCCCCCCcEEEE
Q 042806          226 IADKLGLTLHEES--------------DSGRARSLRNRLKK-EKTILVILDNIWGN--LDFQA-VGIPHGDDRKGCKVLL  287 (390)
Q Consensus       226 i~~~l~~~~~~~~--------------~~~~~~~l~~~l~~-~~~~LlVlDdv~~~--~~~~~-l~~~l~~~~~~s~Iiv  287 (390)
                      ++..++...+...              .......+...+.+ .+|+++||||.+-.  ..+.. +...+....++...|+
T Consensus        86 Li~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv  165 (894)
T COG2909          86 LIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVV  165 (894)
T ss_pred             HHHHHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEE
Confidence            8888874433221              11233344444432 45699999998633  22322 2223334566889999


Q ss_pred             Eecchhhhhh--cCCCcceEecC----CCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhcCC
Q 042806          288 TARSLDVLSR--KMDSQQNFSVG----VLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTR  360 (390)
Q Consensus       288 Ttr~~~v~~~--~~~~~~~~~l~----~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~  360 (390)
                      |||+.--...  ..-....++++    .|+.+|+.++|....+...+    +...+.+.+..+|.+-|+..++-.++++
T Consensus       166 ~SR~rP~l~la~lRlr~~llEi~~~~Lrf~~eE~~~fl~~~~~l~Ld----~~~~~~L~~~teGW~~al~L~aLa~~~~  240 (894)
T COG2909         166 TSRSRPQLGLARLRLRDELLEIGSEELRFDTEEAAAFLNDRGSLPLD----AADLKALYDRTEGWAAALQLIALALRNN  240 (894)
T ss_pred             EeccCCCCcccceeehhhHHhcChHhhcCChHHHHHHHHHcCCCCCC----hHHHHHHHhhcccHHHHHHHHHHHccCC
Confidence            9997432110  11112244443    58999999999887743332    2346789999999999999999888833

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.00  E-value=1.2e-08  Score=96.74  Aligned_cols=201  Identities=14%  Similarity=0.102  Sum_probs=112.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCH--HHHHH--HHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFD-QVIFVEVSKIQDI--RKIQG--EIA  227 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~--~~l~~--~i~  227 (390)
                      ...++|++..++.+..++..+..+.+.++|++|+||||+|+.+.+..... .+. ..++++++.....  ..+..  ...
T Consensus        14 ~~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~~-~~~~~~~~i~~~~~~~~~~~~~~~~~~~~   92 (337)
T PRK12402         14 LEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGD-PWENNFTEFNVADFFDQGKKYLVEDPRFA   92 (337)
T ss_pred             HHHhcCCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcCc-ccccceEEechhhhhhcchhhhhcCcchh
Confidence            45788999999999999888776778899999999999999999886432 122 2344444321100  00000  000


Q ss_pred             HHhCCC-CCCCCchHHHHHHHHHHhC-----CCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEecchh-hhhhc
Q 042806          228 DKLGLT-LHEESDSGRARSLRNRLKK-----EKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTARSLD-VLSRK  298 (390)
Q Consensus       228 ~~l~~~-~~~~~~~~~~~~l~~~l~~-----~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTtr~~~-v~~~~  298 (390)
                      ..++.. ............+.+....     ..+-+||+||++...  ....+...+......+++|+|+.... +....
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~~~~~~~L  172 (337)
T PRK12402         93 HFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPI  172 (337)
T ss_pred             hhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCChhhCchhh
Confidence            000000 0000111122222222211     222589999997552  22233322222234567877775432 21212


Q ss_pred             CCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHH
Q 042806          299 MDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVAR  355 (390)
Q Consensus       299 ~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~  355 (390)
                      ......+++.+++.++...++.+.+......- ..+....+++.++|.+-.+.....
T Consensus       173 ~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~~-~~~al~~l~~~~~gdlr~l~~~l~  228 (337)
T PRK12402        173 RSRCLPLFFRAPTDDELVDVLESIAEAEGVDY-DDDGLELIAYYAGGDLRKAILTLQ  228 (337)
T ss_pred             cCCceEEEecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHHH
Confidence            22345888999999999999988764222111 245678899999887766655443

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.97  E-value=9e-09  Score=91.81  Aligned_cols=170  Identities=16%  Similarity=0.151  Sum_probs=104.1

Q ss_pred             hhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCC
Q 042806          159 RMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEES  238 (390)
Q Consensus       159 R~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~  238 (390)
                      ....++.+.+++.......+.|+|++|+|||+||+.+++.....  ....+|++++.-.+      ..            
T Consensus        22 ~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~~~--~~~~~~i~~~~~~~------~~------------   81 (226)
T TIGR03420        22 NAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEER--GKSAIYLPLAELAQ------AD------------   81 (226)
T ss_pred             cHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHHhc--CCcEEEEeHHHHHH------hH------------
Confidence            44566777777655667789999999999999999999887543  33455665543211      00            


Q ss_pred             chHHHHHHHHHHhCCCeEEEEEeCCCCCc---ccc-cccCCCCC-CCCCcEEEEEecchhhh--------hhcCCCcceE
Q 042806          239 DSGRARSLRNRLKKEKTILVILDNIWGNL---DFQ-AVGIPHGD-DRKGCKVLLTARSLDVL--------SRKMDSQQNF  305 (390)
Q Consensus       239 ~~~~~~~l~~~l~~~~~~LlVlDdv~~~~---~~~-~l~~~l~~-~~~~s~IivTtr~~~v~--------~~~~~~~~~~  305 (390)
                           ..+.+.+.. . -+||+||++...   .|. .+...+.. ...+..+|+||+.....        .........+
T Consensus        82 -----~~~~~~~~~-~-~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~~~i  154 (226)
T TIGR03420        82 -----PEVLEGLEQ-A-DLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWGLVF  154 (226)
T ss_pred             -----HHHHhhccc-C-CEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcCeeE
Confidence                 011122222 2 489999997553   222 23222211 12234788888743210        1112234689


Q ss_pred             ecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHH
Q 042806          306 SVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARA  356 (390)
Q Consensus       306 ~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~  356 (390)
                      ++.+++.++...++++.+...... -.++..+.+.+.++|.|..+..+...
T Consensus       155 ~l~~l~~~e~~~~l~~~~~~~~~~-~~~~~l~~L~~~~~gn~r~L~~~l~~  204 (226)
T TIGR03420       155 QLPPLSDEEKIAALQSRAARRGLQ-LPDEVADYLLRHGSRDMGSLMALLDA  204 (226)
T ss_pred             ecCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHhccCCHHHHHHHHHH
Confidence            999999999999998765321111 12456788888999999988777443

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.95  E-value=4.3e-08  Score=93.65  Aligned_cols=179  Identities=13%  Similarity=0.192  Sum_probs=109.7

Q ss_pred             cccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC-------------------eEEEEE
Q 042806          153 YEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFD-------------------QVIFVE  212 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~-------------------~~~wv~  212 (390)
                      ...++|.+..++.+...+..++. ..+.++|+.|+||||+|+.+.+.......+.                   ...++.
T Consensus        15 ~~~iiGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~~c~~~~~~~~~d~~~~~   94 (363)
T PRK14961         15 FRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCIICKEIEKGLCLDLIEID   94 (363)
T ss_pred             hhhccChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceEEec
Confidence            45789999999999998887654 5678999999999999999998864221110                   111111


Q ss_pred             eCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEE
Q 042806          213 VSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVL  286 (390)
Q Consensus       213 v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~Ii  286 (390)
                      .+.....                     .....+.+.+.    .++.-++|+|+++...  .++.+...+.......++|
T Consensus        95 ~~~~~~v---------------------~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fI  153 (363)
T PRK14961         95 AASRTKV---------------------EEMREILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFI  153 (363)
T ss_pred             ccccCCH---------------------HHHHHHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEE
Confidence            1111111                     11222222221    1233599999998653  3555544444444566677


Q ss_pred             EEecc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          287 LTARS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       287 vTtr~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      ++|.+ ..+.....+-...+++.+++.++..+.+.+.+....... .++.+..|++.++|.|-.+..+
T Consensus       154 l~t~~~~~l~~tI~SRc~~~~~~~l~~~el~~~L~~~~~~~g~~i-~~~al~~ia~~s~G~~R~al~~  220 (363)
T PRK14961        154 LATTDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKESIDT-DEYALKLIAYHAHGSMRDALNL  220 (363)
T ss_pred             EEcCChHhhhHHHHhhceEEeCCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHH
Confidence            76654 333222223346899999999999999888764221111 2346778999999988644443

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

Probab=98.94  E-value=1e-08  Score=95.02  Aligned_cols=176  Identities=16%  Similarity=0.155  Sum_probs=104.7

Q ss_pred             CcccccchhHHH---HHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC-HHHHHHHHH
Q 042806          152 DYEACESRMSTL---NDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD-IRKIQGEIA  227 (390)
Q Consensus       152 ~~~~~~gR~~~~---~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~l~~~i~  227 (390)
                      ..+.++|.+..+   .-|-.++..+++.-..+|||+|+||||||+.+.......  |     ..+|...+ ..++ +.+ 
T Consensus        22 ~lde~vGQ~HLlg~~~~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~~~~--f-----~~~sAv~~gvkdl-r~i-   92 (436)
T COG2256          22 SLDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTTNAA--F-----EALSAVTSGVKDL-REI-   92 (436)
T ss_pred             CHHHhcChHhhhCCCchHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhhCCc--e-----EEeccccccHHHH-HHH-
Confidence            345566655443   234455556777777799999999999999999876532  3     33343322 2222 111 


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc-ccccccCCCCCCCCCcEEEE--Eecchhhh--hhcCCCc
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL-DFQAVGIPHGDDRKGCKVLL--TARSLDVL--SRKMDSQ  302 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~-~~~~l~~~l~~~~~~s~Iiv--Ttr~~~v~--~~~~~~~  302 (390)
                                     ++.-.+....+++.+|.+|.|+... .-++..  +|.-.+|.-|+|  ||.+....  ....+-.
T Consensus        93 ---------------~e~a~~~~~~gr~tiLflDEIHRfnK~QQD~l--Lp~vE~G~iilIGATTENPsF~ln~ALlSR~  155 (436)
T COG2256          93 ---------------IEEARKNRLLGRRTILFLDEIHRFNKAQQDAL--LPHVENGTIILIGATTENPSFELNPALLSRA  155 (436)
T ss_pred             ---------------HHHHHHHHhcCCceEEEEehhhhcChhhhhhh--hhhhcCCeEEEEeccCCCCCeeecHHHhhhh
Confidence                           1222233334667999999997542 222332  333556766665  55554321  2233455


Q ss_pred             ceEecCCCCHHHHHHHHHHhhC------CCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          303 QNFSVGVLKEDEAWSLFKKMAG------DYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       303 ~~~~l~~L~~~ea~~lf~~~~~------~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      .++.+++|+.++..+++.+.+.      +.....-.++....++..++|---+.-..
T Consensus       156 ~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~GD~R~aLN~  212 (436)
T COG2256         156 RVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRALNL  212 (436)
T ss_pred             heeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCchHHHHHHH
Confidence            7999999999999999988442      11111122456778899988866544333

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

Probab=98.93  E-value=3.3e-09  Score=85.95  Aligned_cols=116  Identities=26%  Similarity=0.322  Sum_probs=82.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc---CCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-CCchHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE---KLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE-ESDSGRARSLRNR  249 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~---~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~-~~~~~~~~~l~~~  249 (390)
                      +.+.+.|+|++|+|||++++.+.+.....   ..-..++|+.++...+...+...++..++..... .+.......+.+.
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~   82 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDA   82 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHH
Confidence            34678999999999999999999987431   0123467999988889999999999999987766 4556667788888


Q ss_pred             HhCCCeEEEEEeCCCCC---cccccccCCCCCCCCCcEEEEEecc
Q 042806          250 LKKEKTILVILDNIWGN---LDFQAVGIPHGDDRKGCKVLLTARS  291 (390)
Q Consensus       250 l~~~~~~LlVlDdv~~~---~~~~~l~~~l~~~~~~s~IivTtr~  291 (390)
                      +...+..+||+|+++..   ..++.+....  +..+.++|+..+.
T Consensus        83 l~~~~~~~lviDe~~~l~~~~~l~~l~~l~--~~~~~~vvl~G~~  125 (131)
T PF13401_consen   83 LDRRRVVLLVIDEADHLFSDEFLEFLRSLL--NESNIKVVLVGTP  125 (131)
T ss_dssp             HHHCTEEEEEEETTHHHHTHHHHHHHHHHT--CSCBEEEEEEESS
T ss_pred             HHhcCCeEEEEeChHhcCCHHHHHHHHHHH--hCCCCeEEEEECh
Confidence            88777579999999754   2233333222  2667788888775

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.93  E-value=3.5e-08  Score=99.37  Aligned_cols=183  Identities=14%  Similarity=0.157  Sum_probs=114.9

Q ss_pred             cCcccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCC-------------------CCeEEE
Q 042806          151 KDYEACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKL-------------------FDQVIF  210 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~-------------------f~~~~w  210 (390)
                      ....+++|.+..++.|.+++..++ ...+.++|+.|+||||+++.+.+.......                   |...++
T Consensus        13 qtFdEVIGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~G~h~DviE   92 (830)
T PRK07003         13 KDFASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRFVDYVE   92 (830)
T ss_pred             CcHHHHcCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHHHHHHhcCCCceEEE
Confidence            335678999999999999998776 456789999999999999999887642211                   111222


Q ss_pred             EEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcE
Q 042806          211 VEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCK  284 (390)
Q Consensus       211 v~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~  284 (390)
                      ++.+....+++                     +..+.+.+.    .++.-++|||+++...  .++.+...+-.-..+.+
T Consensus        93 IDAas~rgVDd---------------------IReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~  151 (830)
T PRK07003         93 MDAASNRGVDE---------------------MAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVK  151 (830)
T ss_pred             ecccccccHHH---------------------HHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeE
Confidence            22221111111                     112222211    2333588999998663  46666555534445677


Q ss_pred             EEEEecch-hhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh-HHHHHHHH
Q 042806          285 VLLTARSL-DVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP-VSIVTVAR  355 (390)
Q Consensus       285 IivTtr~~-~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP-Lai~~l~~  355 (390)
                      +|+||.+. .+......-...+++++++.++..+.+.+.+....... .++....|++.++|.. -++..+-.
T Consensus       152 FILaTtd~~KIp~TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI~i-d~eAL~lIA~~A~GsmRdALsLLdQ  223 (830)
T PRK07003        152 FILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERILGEERIAF-EPQALRLLARAAQGSMRDALSLTDQ  223 (830)
T ss_pred             EEEEECChhhccchhhhheEEEecCCcCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            78777763 33222233346899999999999999998875322222 2456778999998855 56665443

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.90  E-value=4.1e-07  Score=92.43  Aligned_cols=202  Identities=16%  Similarity=0.089  Sum_probs=120.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCC---CeEEEEEeCCC---CCHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLF---DQVIFVEVSKI---QDIRKIQGEI  226 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f---~~~~wv~v~~~---~~~~~l~~~i  226 (390)
                      .+.++|+...+..+.+.+..+....+.|+|++|+||||||+.+++.......+   ....|+.+...   .+...+...+
T Consensus       153 ~~~iiGqs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~~l  232 (615)
T TIGR02903       153 FSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTNPL  232 (615)
T ss_pred             HHhceeCcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHhHHh
Confidence            45688999888888888876667789999999999999999998876443322   12345544321   1222221111


Q ss_pred             ---------------HHHhCCC------------------CCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--ccccc
Q 042806          227 ---------------ADKLGLT------------------LHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQA  271 (390)
Q Consensus       227 ---------------~~~l~~~------------------~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~  271 (390)
                                     +...+..                  ....-+......+...+..++ +.++-|+.|..  ..|+.
T Consensus       233 lg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~~Le~~~-v~~~~~~~~~~~~~~~~~  311 (615)
T TIGR02903       233 LGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLEDKR-VEFSSSYYDPDDPNVPKY  311 (615)
T ss_pred             cCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCHHHHHHHHHHHhhCe-EEeecceeccCCcccchh
Confidence                           1111110                  000112234556777777755 77777666543  45777


Q ss_pred             ccCCCCCCCCCcEEEE--Eecchhh-hhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH
Q 042806          272 VGIPHGDDRKGCKVLL--TARSLDV-LSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV  348 (390)
Q Consensus       272 l~~~l~~~~~~s~Iiv--Ttr~~~v-~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL  348 (390)
                      +...+....+...+++  ||++... ......-...+.+.+++.++.+.++.+.+......- .+++.+.|.+.+..-+-
T Consensus       312 ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~Il~~~a~~~~v~l-s~eal~~L~~ys~~gRr  390 (615)
T TIGR02903       312 IKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIALIVLNAAEKINVHL-AAGVEELIARYTIEGRK  390 (615)
T ss_pred             hhhhcccCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHCCCcHHH
Confidence            7666655555544554  4554321 111112234778999999999999999875221111 14456667776666677


Q ss_pred             HHHHHHHH
Q 042806          349 SIVTVARA  356 (390)
Q Consensus       349 ai~~l~~~  356 (390)
                      ++..++.+
T Consensus       391 aln~L~~~  398 (615)
T TIGR02903       391 AVNILADV  398 (615)
T ss_pred             HHHHHHHH
Confidence            88777544

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.

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.89  E-value=8.5e-08  Score=90.15  Aligned_cols=186  Identities=14%  Similarity=0.086  Sum_probs=110.1

Q ss_pred             CcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEe--CCCCCHHHHHHHHHHH
Q 042806          152 DYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEV--SKIQDIRKIQGEIADK  229 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v--~~~~~~~~l~~~i~~~  229 (390)
                      ....++|++..++.+..++..+..+.+.++|++|+||||+++.+.+...... +. ..++.+  +...... .....+..
T Consensus        15 ~~~~~~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~-~~-~~~i~~~~~~~~~~~-~~~~~i~~   91 (319)
T PRK00440         15 TLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGED-WR-ENFLELNASDERGID-VIRNKIKE   91 (319)
T ss_pred             cHHHhcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCc-cc-cceEEeccccccchH-HHHHHHHH
Confidence            3456889999999999999877777789999999999999999999864332 22 122222  2222211 11121111


Q ss_pred             hCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEecch-hhhhhcCCCcceEe
Q 042806          230 LGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTARSL-DVLSRKMDSQQNFS  306 (390)
Q Consensus       230 l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTtr~~-~v~~~~~~~~~~~~  306 (390)
                      +....+              .....+-++++|+++...  ....+...+....+.+.+|+++... .+..........++
T Consensus        92 ~~~~~~--------------~~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~  157 (319)
T PRK00440         92 FARTAP--------------VGGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFR  157 (319)
T ss_pred             HHhcCC--------------CCCCCceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhheee
Confidence            111000              001123689999986542  2233333333333456777776432 11111112234789


Q ss_pred             cCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHH
Q 042806          307 VGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVAR  355 (390)
Q Consensus       307 l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~  355 (390)
                      +.+++.++...++.+.+......- .++....+++.++|.+--+...-.
T Consensus       158 ~~~l~~~ei~~~l~~~~~~~~~~i-~~~al~~l~~~~~gd~r~~~~~l~  205 (319)
T PRK00440        158 FSPLKKEAVAERLRYIAENEGIEI-TDDALEAIYYVSEGDMRKAINALQ  205 (319)
T ss_pred             eCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHHH
Confidence            999999999999988775222211 244678899999998877544433

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.89  E-value=7.5e-08  Score=90.24  Aligned_cols=177  Identities=19%  Similarity=0.175  Sum_probs=114.8

Q ss_pred             ccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhh----hcCCCCeEEEEEe-CCCCCHHHHHHHHH
Q 042806          154 EACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAE----TEKLFDQVIFVEV-SKIQDIRKIQGEIA  227 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~----~~~~f~~~~wv~v-~~~~~~~~l~~~i~  227 (390)
                      ..++|.+..++.+..++..++ .+.+.++|+.|+||||+|+.++...-    ...|+|...|... +.....++ .+++.
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~-ir~~~   82 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDD-IRNII   82 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHH-HHHHH
Confidence            356788888888999988765 46778999999999999999998752    2346676555442 23333434 23333


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCC--CCcccccccCCCCCCCCCcEEEEEecchhh-hhhcCCCcce
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIW--GNLDFQAVGIPHGDDRKGCKVLLTARSLDV-LSRKMDSQQN  304 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~--~~~~~~~l~~~l~~~~~~s~IivTtr~~~v-~~~~~~~~~~  304 (390)
                      ..+...+-               .+++ -++|+|+++  +...++.+...+..-.+++.+|++|.+.+. ......-...
T Consensus        83 ~~~~~~p~---------------~~~~-kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~  146 (313)
T PRK05564         83 EEVNKKPY---------------EGDK-KVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQI  146 (313)
T ss_pred             HHHhcCcc---------------cCCc-eEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhcee
Confidence            33322111               1233 477777765  335677777777666678888888876432 2222333469


Q ss_pred             EecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHH
Q 042806          305 FSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVT  352 (390)
Q Consensus       305 ~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~  352 (390)
                      +++.+++.++....+.+.... .    .++.+..++..++|.|..+..
T Consensus       147 ~~~~~~~~~~~~~~l~~~~~~-~----~~~~~~~l~~~~~g~~~~a~~  189 (313)
T PRK05564        147 YKLNRLSKEEIEKFISYKYND-I----KEEEKKSAIAFSDGIPGKVEK  189 (313)
T ss_pred             eeCCCcCHHHHHHHHHHHhcC-C----CHHHHHHHHHHcCCCHHHHHH
Confidence            999999999998888765521 1    123466889999998875543

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.88  E-value=4.3e-08  Score=100.54  Aligned_cols=184  Identities=16%  Similarity=0.179  Sum_probs=111.6

Q ss_pred             CcccccchhHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCCCC-------------------eEEEE
Q 042806          152 DYEACESRMSTLNDILDALKNPDVN-MLGIYGMGGIVKTTLAKEVARKAETEKLFD-------------------QVIFV  211 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~-------------------~~~wv  211 (390)
                      ....++|.+..+..|.+++..++.. .+.++|+.|+||||+|+.+++.........                   .++++
T Consensus        14 tFddIIGQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~DviEi   93 (944)
T PRK14949         14 TFEQMVGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDLIEV   93 (944)
T ss_pred             CHHHhcCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceEEEe
Confidence            3567899999999999988877654 568999999999999999998874321111                   11222


Q ss_pred             EeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEe
Q 042806          212 EVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTA  289 (390)
Q Consensus       212 ~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTt  289 (390)
                      .......+.+ ++++...+.                ..-..++.-++|||+++..  ..++.|...+-.-...+++|++|
T Consensus        94 dAas~~kVDd-IReLie~v~----------------~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaT  156 (944)
T PRK14949         94 DAASRTKVDD-TRELLDNVQ----------------YRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLAT  156 (944)
T ss_pred             ccccccCHHH-HHHHHHHHH----------------hhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEEC
Confidence            1111111111 122222111                0001234469999999755  44555544443333456666555


Q ss_pred             cc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          290 RS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       290 r~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      .+ ..+......-...|++++|+.++..+++.+.+..... .-.++....|++.++|.|--+..+
T Consensus       157 Te~~kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il~~EgI-~~edeAL~lIA~~S~Gd~R~ALnL  220 (944)
T PRK14949        157 TDPQKLPVTVLSRCLQFNLKSLTQDEIGTQLNHILTQEQL-PFEAEALTLLAKAANGSMRDALSL  220 (944)
T ss_pred             CCchhchHHHHHhheEEeCCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHH
Confidence            44 4443222333469999999999999999887742211 122456788999999988655444

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.86  E-value=9.8e-08  Score=96.93  Aligned_cols=207  Identities=16%  Similarity=0.147  Sum_probs=124.5

Q ss_pred             cccccchhHHHHHHHHHhcC----C-CccEEEEEcCCCCcHHHHHHHHHHHhhhc---CCCC--eEEEEEeCCCCCHHHH
Q 042806          153 YEACESRMSTLNDILDALKN----P-DVNMLGIYGMGGIVKTTLAKEVARKAETE---KLFD--QVIFVEVSKIQDIRKI  222 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~----~-~~~vi~I~G~~GvGKTtLa~~v~~~~~~~---~~f~--~~~wv~v~~~~~~~~l  222 (390)
                      ++.+.+|+.++++|...|..    . ...++.|+|++|.|||++++.|...+...   ....  ..++|++....+...+
T Consensus       754 PD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sI  833 (1164)
T PTZ00112        754 PKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAA  833 (1164)
T ss_pred             CCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHH
Confidence            45688999999999887753    2 23567899999999999999999876432   1122  3567777777788899


Q ss_pred             HHHHHHHhCCCCCCC--CchHHHHHHHHHHhC--CCeEEEEEeCCCCCcc--cccccCCCC-CCCCCcEEEE--Eecchh
Q 042806          223 QGEIADKLGLTLHEE--SDSGRARSLRNRLKK--EKTILVILDNIWGNLD--FQAVGIPHG-DDRKGCKVLL--TARSLD  293 (390)
Q Consensus       223 ~~~i~~~l~~~~~~~--~~~~~~~~l~~~l~~--~~~~LlVlDdv~~~~~--~~~l~~~l~-~~~~~s~Iiv--Ttr~~~  293 (390)
                      +..|+.++....+..  +.......+...+..  +...+||||+++....  -+.|...+. ....+++|++  ++....
T Consensus       834 YqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLIGISNdlD  913 (1164)
T PTZ00112        834 YQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLIAISNTMD  913 (1164)
T ss_pred             HHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEEEecCchh
Confidence            999998884433321  223344555555422  2336999999975421  111111110 1123444433  343221


Q ss_pred             hh----hhc--CCCcceEecCCCCHHHHHHHHHHhhCC---CCCCCchHHHHHHHHHHcCCChHHHHHHHHHhcC
Q 042806          294 VL----SRK--MDSQQNFSVGVLKEDEAWSLFKKMAGD---YIEGSEFKWVAKDVARECAGLPVSIVTVARALGT  359 (390)
Q Consensus       294 v~----~~~--~~~~~~~~l~~L~~~ea~~lf~~~~~~---~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~  359 (390)
                      ..    ...  .-....+...|++.++..+++..++..   ...+..++-+++.++...|-.-.||..+-.+...
T Consensus       914 LperLdPRLRSRLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIArkVAq~SGDARKALDILRrAgEi  988 (1164)
T PTZ00112        914 LPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCARKVANVSGDIRKALQICRKAFEN  988 (1164)
T ss_pred             cchhhhhhhhhccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhhcCCHHHHHHHHHHHHHhh
Confidence            11    111  111234778999999999999998852   1222333344444445556677788777666554

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.86  E-value=5.6e-08  Score=96.64  Aligned_cols=181  Identities=13%  Similarity=0.168  Sum_probs=112.8

Q ss_pred             cCcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcC------------------------CC
Q 042806          151 KDYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEK------------------------LF  205 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~------------------------~f  205 (390)
                      ....+++|.+..+..|.+++..++. ..+.++|+.|+||||+|+.+.+.....+                        .|
T Consensus        13 qtFddVIGQe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG~h   92 (700)
T PRK12323         13 RDFTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGRF   92 (700)
T ss_pred             CcHHHHcCcHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHHcCCC
Confidence            3356789999999999999988764 4678999999999999999998764310                        00


Q ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCC
Q 042806          206 DQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDD  279 (390)
Q Consensus       206 ~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~  279 (390)
                      ...++++......+                     +.+..+.+.+.    .++.-++|||+++..  ..++.|...+-.-
T Consensus        93 pDviEIdAas~~gV---------------------DdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEP  151 (700)
T PRK12323         93 VDYIEMDAASNRGV---------------------DEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEP  151 (700)
T ss_pred             CcceEecccccCCH---------------------HHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccC
Confidence            01112211111111                     11222222221    234469999999855  4455555555333


Q ss_pred             CCCcEEEEEecc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          280 RKGCKVLLTARS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       280 ~~~s~IivTtr~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      ..++++|++|.+ ..+.....+-...+++++++.++..+.+.+.+.......+ ++..+.|++.++|.|.-...+
T Consensus       152 P~~v~FILaTtep~kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~Egi~~d-~eAL~~IA~~A~Gs~RdALsL  225 (700)
T PRK12323        152 PEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEGIAHE-VNALRLLAQAAQGSMRDALSL  225 (700)
T ss_pred             CCCceEEEEeCChHhhhhHHHHHHHhcccCCCChHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHHH
Confidence            445665555554 4443333333469999999999999998887752222222 345678999999999755544

>PLN03025 replication factor C subunit; Provisional

Probab=98.85  E-value=8.4e-08  Score=90.14  Aligned_cols=186  Identities=12%  Similarity=0.026  Sum_probs=108.8

Q ss_pred             CcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          152 DYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFD-QVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ....++|.+..+..|..++..++.+-+.++|++|+||||+|+.+++..... .|. ..+-++.+...... .++.+.+.+
T Consensus        11 ~l~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~~-~~~~~~~eln~sd~~~~~-~vr~~i~~~   88 (319)
T PLN03025         11 KLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGP-NYKEAVLELNASDDRGID-VVRNKIKMF   88 (319)
T ss_pred             CHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhcc-cCccceeeecccccccHH-HHHHHHHHH
Confidence            345788888888888888877777778899999999999999999986432 132 22222333222222 222222222


Q ss_pred             CCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEecch-hhhhhcCCCcceEec
Q 042806          231 GLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTARSL-DVLSRKMDSQQNFSV  307 (390)
Q Consensus       231 ~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTtr~~-~v~~~~~~~~~~~~l  307 (390)
                      ......             +..++.-++++|+++...  ....+...+......+++|+++... .+......-...+++
T Consensus        89 ~~~~~~-------------~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~f  155 (319)
T PLN03025         89 AQKKVT-------------LPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRF  155 (319)
T ss_pred             Hhcccc-------------CCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhcccC
Confidence            110000             011234699999997652  2222322222223456677766542 221111122358999


Q ss_pred             CCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          308 GVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       308 ~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      .+++.++....+...+......-+ ++....|++.++|-.-.+...
T Consensus       156 ~~l~~~~l~~~L~~i~~~egi~i~-~~~l~~i~~~~~gDlR~aln~  200 (319)
T PLN03025        156 SRLSDQEILGRLMKVVEAEKVPYV-PEGLEAIIFTADGDMRQALNN  200 (319)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHHH
Confidence            999999999999888752222222 346788999998877554433

>PTZ00202 tuzin; Provisional

Probab=98.84  E-value=4.5e-07  Score=85.85  Aligned_cols=165  Identities=16%  Similarity=0.213  Sum_probs=106.7

Q ss_pred             cccCcccccchhHHHHHHHHHhcC---CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          149 SIKDYEACESRMSTLNDILDALKN---PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       149 ~~~~~~~~~gR~~~~~~l~~~L~~---~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      .|.+...|+||+.++..|...|.+   +.++++.|.|++|+|||||++.+.....    + ...+++. .  +..++++.
T Consensus       257 lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l~----~-~qL~vNp-r--g~eElLr~  328 (550)
T PTZ00202        257 APAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKEG----M-PAVFVDV-R--GTEDTLRS  328 (550)
T ss_pred             CCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcCC----c-eEEEECC-C--CHHHHHHH
Confidence            455567899999999999988864   2356899999999999999999986653    1 1222222 2  67999999


Q ss_pred             HHHHhCCCCCCCCchHHHHHHHHHHh----C-CCeEEEEEeCCCCCccccccc---CCCCCCCCCcEEEEEecchhhhh-
Q 042806          226 IADKLGLTLHEESDSGRARSLRNRLK----K-EKTILVILDNIWGNLDFQAVG---IPHGDDRKGCKVLLTARSLDVLS-  296 (390)
Q Consensus       226 i~~~l~~~~~~~~~~~~~~~l~~~l~----~-~~~~LlVlDdv~~~~~~~~l~---~~l~~~~~~s~IivTtr~~~v~~-  296 (390)
                      ++..||.... .....+...|.+.+.    . +++.+||+- +.+-..+..+.   ..+.....-|.|++----+++-. 
T Consensus       329 LL~ALGV~p~-~~k~dLLrqIqeaLl~~~~e~GrtPVLII~-lreg~~l~rvyne~v~la~drr~ch~v~evpleslt~~  406 (550)
T PTZ00202        329 VVKALGVPNV-EACGDLLDFISEACRRAKKMNGETPLLVLK-LREGSSLQRVYNEVVALACDRRLCHVVIEVPLESLTIA  406 (550)
T ss_pred             HHHHcCCCCc-ccHHHHHHHHHHHHHHHHHhCCCCEEEEEE-ecCCCcHHHHHHHHHHHHccchhheeeeeehHhhcchh
Confidence            9999997433 333455555555542    2 454666653 22222222211   12333445677877665544321 


Q ss_pred             -hcCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          297 -RKMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       297 -~~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                       ...+--..|-+.+|+.++|..+-++..
T Consensus       407 ~~~lprldf~~vp~fsr~qaf~y~~h~~  434 (550)
T PTZ00202        407 NTLLPRLDFYLVPNFSRSQAFAYTQHAI  434 (550)
T ss_pred             cccCccceeEecCCCCHHHHHHHHhhcc
Confidence             123344688899999999988877765

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.84  E-value=7.4e-08  Score=95.98  Aligned_cols=181  Identities=13%  Similarity=0.149  Sum_probs=112.2

Q ss_pred             cCcccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCC-------------------CeEEE
Q 042806          151 KDYEACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLF-------------------DQVIF  210 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f-------------------~~~~w  210 (390)
                      .....++|.+.....|..++..++ ...+.++|+.|+||||+|+.+++........                   -..+.
T Consensus        12 ktFddVIGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDviE   91 (702)
T PRK14960         12 RNFNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLIE   91 (702)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCceEE
Confidence            335678999999999999998776 4577899999999999999998876421111                   11122


Q ss_pred             EEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcE
Q 042806          211 VEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCK  284 (390)
Q Consensus       211 v~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~  284 (390)
                      +..+......                     .+..+...+.    .++.-++|+|+++..  ...+.+...+-.-..+.+
T Consensus        92 IDAAs~~~Vd---------------------dIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~  150 (702)
T PRK14960         92 IDAASRTKVE---------------------DTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVK  150 (702)
T ss_pred             ecccccCCHH---------------------HHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcE
Confidence            2221111111                     1222222211    133368999999865  344445444433345567


Q ss_pred             EEEEecc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          285 VLLTARS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       285 IivTtr~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      +|++|.+ ..+......-...+++++++.++..+.+.+.+.......+ .+....|++.++|.+-.+..+
T Consensus       151 FILaTtd~~kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~kEgI~id-~eAL~~IA~~S~GdLRdALnL  219 (702)
T PRK14960        151 FLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQIAAD-QDAIWQIAESAQGSLRDALSL  219 (702)
T ss_pred             EEEEECChHhhhHHHHHhhheeeccCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHHH
Confidence            7777765 3332222344469999999999999999888753222222 345778999999988555444

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

Probab=98.82  E-value=6.1e-07  Score=85.14  Aligned_cols=202  Identities=20%  Similarity=0.240  Sum_probs=131.4

Q ss_pred             cccchhHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          155 ACESRMSTLNDILDALK----NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~----~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      .+.+|+.+++++...|.    +..+.-+.|+|++|+|||+.++.+.........=...++|++....+..+++..|++.+
T Consensus        18 ~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~   97 (366)
T COG1474          18 ELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKL   97 (366)
T ss_pred             cccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHHc
Confidence            48899999999987765    33445599999999999999999999987642222289999999999999999999999


Q ss_pred             CCC-CCCCCchHHHHHHHHHHhC-CCeEEEEEeCCCCCccc--ccccCCCCC-CCCCcE--EEEEecchhhhhh------
Q 042806          231 GLT-LHEESDSGRARSLRNRLKK-EKTILVILDNIWGNLDF--QAVGIPHGD-DRKGCK--VLLTARSLDVLSR------  297 (390)
Q Consensus       231 ~~~-~~~~~~~~~~~~l~~~l~~-~~~~LlVlDdv~~~~~~--~~l~~~l~~-~~~~s~--IivTtr~~~v~~~------  297 (390)
                      +.. ....+.......+.+.+.. ++.+++|||++.....-  +.+...+.. ..+.++  +|..+.+......      
T Consensus        98 ~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~~~LY~L~r~~~~~~~~v~vi~i~n~~~~~~~ld~rv~  177 (366)
T COG1474          98 GKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPRVK  177 (366)
T ss_pred             CCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccchHHHHHHhhccccceeEEEEEEeccHHHHHHhhhhhh
Confidence            633 2234566677777777754 55689999999754222  122111111 112343  3333433322111      


Q ss_pred             cCCCcceEecCCCCHHHHHHHHHHhhC-----CCCCCCchHHHHHHHHHHcCCChHHHHHHHHH
Q 042806          298 KMDSQQNFSVGVLKEDEAWSLFKKMAG-----DYIEGSEFKWVAKDVARECAGLPVSIVTVARA  356 (390)
Q Consensus       298 ~~~~~~~~~l~~L~~~ea~~lf~~~~~-----~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~  356 (390)
                      ..-....+...|-+.+|-.+++..++.     +...+.-++-++...++..|-.-.||..+-..
T Consensus       178 s~l~~~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A  241 (366)
T COG1474         178 SSLGPSEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRA  241 (366)
T ss_pred             hccCcceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHH
Confidence            111223588999999999999988874     22333344444545555555666777766433

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.81  E-value=2e-07  Score=92.22  Aligned_cols=203  Identities=16%  Similarity=0.105  Sum_probs=114.4

Q ss_pred             CcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          152 DYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ..+.++|.+..++.|..++..++. ..+.++|++|+||||+|+.+++.....+.+...+|.|.+.. .+.......+..+
T Consensus        12 ~~~dvvGq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~-~i~~~~h~dv~el   90 (504)
T PRK14963         12 TFDEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCL-AVRRGAHPDVLEI   90 (504)
T ss_pred             CHHHhcChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhH-HHhcCCCCceEEe
Confidence            355789998888889888887764 46689999999999999999988753222222222221110 0000000000000


Q ss_pred             CCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEec-chhhhhhcCCCcc
Q 042806          231 GLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTAR-SLDVLSRKMDSQQ  303 (390)
Q Consensus       231 ~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr-~~~v~~~~~~~~~  303 (390)
                      .  .........+..+.+.+.    .+++-++|+|+++..  ..++.+...+......+.+|++|. ...+.........
T Consensus        91 ~--~~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SRc~  168 (504)
T PRK14963         91 D--AASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQ  168 (504)
T ss_pred             c--ccccCCHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcceE
Confidence            0  000011112223333221    123469999999754  335555444433334555555554 3443322333456


Q ss_pred             eEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHH-HHHHHhc
Q 042806          304 NFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIV-TVARALG  358 (390)
Q Consensus       304 ~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~-~l~~~L~  358 (390)
                      .+++.+++.++..+.+.+.+....... .++....|++.++|.+--+. .+-.++.
T Consensus       169 ~~~f~~ls~~el~~~L~~i~~~egi~i-~~~Al~~ia~~s~GdlR~aln~Lekl~~  223 (504)
T PRK14963        169 HFRFRRLTEEEIAGKLRRLLEAEGREA-EPEALQLVARLADGAMRDAESLLERLLA  223 (504)
T ss_pred             EEEecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            899999999999999998875222222 24567889999999986554 4434333

>PRK04195 replication factor C large subunit; Provisional

Probab=98.81  E-value=1.2e-07  Score=93.94  Aligned_cols=184  Identities=16%  Similarity=0.145  Sum_probs=111.1

Q ss_pred             cCcccccchhHHHHHHHHHhcC----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 042806          151 KDYEACESRMSTLNDILDALKN----PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~----~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      .....++|++..++.|.+|+..    ...+.+.|+|++|+||||+|+.+++...    |+ .+-++.+...+.. .+..+
T Consensus        11 ~~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el~----~~-~ielnasd~r~~~-~i~~~   84 (482)
T PRK04195         11 KTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDYG----WE-VIELNASDQRTAD-VIERV   84 (482)
T ss_pred             CCHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHcC----CC-EEEEcccccccHH-HHHHH
Confidence            3356789999999999888763    2267899999999999999999999874    33 3344555433332 22333


Q ss_pred             HHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc------cccccCCCCCCCCCcEEEEEecchh-hhh-hc
Q 042806          227 ADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD------FQAVGIPHGDDRKGCKVLLTARSLD-VLS-RK  298 (390)
Q Consensus       227 ~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~------~~~l~~~l~~~~~~s~IivTtr~~~-v~~-~~  298 (390)
                      +........              +.+.++-+||||+++....      +..+...+.  ..+..||+|+.... ... ..
T Consensus        85 i~~~~~~~s--------------l~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~--~~~~~iIli~n~~~~~~~k~L  148 (482)
T PRK04195         85 AGEAATSGS--------------LFGARRKLILLDEVDGIHGNEDRGGARAILELIK--KAKQPIILTANDPYDPSLREL  148 (482)
T ss_pred             HHHhhccCc--------------ccCCCCeEEEEecCcccccccchhHHHHHHHHHH--cCCCCEEEeccCccccchhhH
Confidence            222211100              0111347999999976422      333333322  23344666665422 111 12


Q ss_pred             CCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHh
Q 042806          299 MDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARAL  357 (390)
Q Consensus       299 ~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L  357 (390)
                      ......+++.+++.++....+...+.......+ .++...|++.++|-.-.+......+
T Consensus       149 rsr~~~I~f~~~~~~~i~~~L~~i~~~egi~i~-~eaL~~Ia~~s~GDlR~ain~Lq~~  206 (482)
T PRK04195        149 RNACLMIEFKRLSTRSIVPVLKRICRKEGIECD-DEALKEIAERSGGDLRSAINDLQAI  206 (482)
T ss_pred             hccceEEEecCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            234468999999999999998887742222122 4567889999988766655443333

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.80  E-value=2.7e-07  Score=90.98  Aligned_cols=197  Identities=12%  Similarity=0.127  Sum_probs=111.5

Q ss_pred             CcccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCe-EEEEEeCCCCCHHHHHHHHHHH
Q 042806          152 DYEACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQ-VIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~-~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      ....++|.+..+..|...+..++ ...+.++|+.|+||||+|+.+++.......... ..+..+..+.+    ...+...
T Consensus        19 ~f~dliGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~----C~~i~~~   94 (507)
T PRK06645         19 NFAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTN----CISFNNH   94 (507)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChH----HHHHhcC
Confidence            35578899988888888777665 467889999999999999999988643211100 00000010000    0001000


Q ss_pred             hCC-----CCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEE-Eecchhhhhh
Q 042806          230 LGL-----TLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLL-TARSLDVLSR  297 (390)
Q Consensus       230 l~~-----~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~Iiv-Ttr~~~v~~~  297 (390)
                      ...     +.........+..+.+...    .+++-++|+|+++..  ..++.+...+....+.+.+|+ ||+...+...
T Consensus        95 ~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI~~t  174 (507)
T PRK06645         95 NHPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPAT  174 (507)
T ss_pred             CCCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHhhHH
Confidence            000     0000001111222222221    123368999999865  346666555544445556554 4444454433


Q ss_pred             cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          298 KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       298 ~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      .......+++.+++.++....+.+.+.......+ ++....|++.++|.+--+..+
T Consensus       175 I~SRc~~~ef~~ls~~el~~~L~~i~~~egi~ie-~eAL~~Ia~~s~GslR~al~~  229 (507)
T PRK06645        175 IISRCQRYDLRRLSFEEIFKLLEYITKQENLKTD-IEALRIIAYKSEGSARDAVSI  229 (507)
T ss_pred             HHhcceEEEccCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHHH
Confidence            3334468999999999999999988853222222 345678999999987555443

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.80  E-value=2.1e-07  Score=91.35  Aligned_cols=188  Identities=16%  Similarity=0.161  Sum_probs=110.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCC--C-----------------CeEEEEE
Q 042806          153 YEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKL--F-----------------DQVIFVE  212 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~--f-----------------~~~~wv~  212 (390)
                      ...++|.+.....|...+..++. +.+.++|++|+||||+|+.+++.......  +                 .....++
T Consensus        13 ~~divGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~el~   92 (472)
T PRK14962         13 FSEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVIELD   92 (472)
T ss_pred             HHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccEEEe
Confidence            45789998888888888887765 45889999999999999999887643211  0                 0112222


Q ss_pred             eCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEec
Q 042806          213 VSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTAR  290 (390)
Q Consensus       213 v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr  290 (390)
                      .+......++ +.+.......               -. .+++-++|+|+++..  ...+.+...+......+.+|++|.
T Consensus        93 aa~~~gid~i-R~i~~~~~~~---------------p~-~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Ilatt  155 (472)
T PRK14962         93 AASNRGIDEI-RKIRDAVGYR---------------PM-EGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATT  155 (472)
T ss_pred             CcccCCHHHH-HHHHHHHhhC---------------hh-cCCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEEEEEeC
Confidence            2211122211 1222111100               00 123369999999754  233444333333233444444444


Q ss_pred             c-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcC-CChHHHHHHHHHhc
Q 042806          291 S-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECA-GLPVSIVTVARALG  358 (390)
Q Consensus       291 ~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~-GlPLai~~l~~~L~  358 (390)
                      + ..+..........+++.+++.++....+...+......- .++....|++.++ +++.++..+-.+..
T Consensus       156 n~~kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi~i-~~eal~~Ia~~s~GdlR~aln~Le~l~~  224 (472)
T PRK14962        156 NLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGIEI-DREALSFIAKRASGGLRDALTMLEQVWK  224 (472)
T ss_pred             ChHhhhHHHhcCcEEEEECCccHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            3 444333334456899999999999999888774221111 2446778888775 56778777766543

>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=98.79  E-value=5.2e-08  Score=79.97  Aligned_cols=123  Identities=20%  Similarity=0.183  Sum_probs=72.5

Q ss_pred             cchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC
Q 042806          157 ESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE  236 (390)
Q Consensus       157 ~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~  236 (390)
                      .|++..+..+...+..+..+.+.|+|++|+|||++++.+++.....  -..++++..+...........+...       
T Consensus         1 ~~~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~--~~~v~~~~~~~~~~~~~~~~~~~~~-------   71 (151)
T cd00009           1 VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP--GAPFLYLNASDLLEGLVVAELFGHF-------   71 (151)
T ss_pred             CchHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhcC--CCCeEEEehhhhhhhhHHHHHhhhh-------
Confidence            3677888888888877677889999999999999999999987532  2345666665543322221111100       


Q ss_pred             CCchHHHHHHHHHHhCCCeEEEEEeCCCCC-----cccccccCCCCC---CCCCcEEEEEecchh
Q 042806          237 ESDSGRARSLRNRLKKEKTILVILDNIWGN-----LDFQAVGIPHGD---DRKGCKVLLTARSLD  293 (390)
Q Consensus       237 ~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~-----~~~~~l~~~l~~---~~~~s~IivTtr~~~  293 (390)
                           ............++.++++||++..     ..+..+...+..   ...+..||+||....
T Consensus        72 -----~~~~~~~~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009          72 -----LVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             -----hHhHHHHhhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence                 0001111111234489999999853     122222122211   135778888888643

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.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.76  E-value=1.3e-07  Score=91.57  Aligned_cols=199  Identities=14%  Similarity=0.109  Sum_probs=114.2

Q ss_pred             cCcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 042806          151 KDYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      .....++|.+..+..|..++..++. ..+.++|+.|+||||+|+.+++.........   ...+..+.+-..+.......
T Consensus        15 ~~f~dvVGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~---~~pCg~C~sC~~i~~g~~~d   91 (484)
T PRK14956         15 QFFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPIG---NEPCNECTSCLEITKGISSD   91 (484)
T ss_pred             CCHHHHhChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhcCcccccC---ccccCCCcHHHHHHccCCcc
Confidence            3356789999999999999888775 4688999999999999999998864321111   00111111111111110000


Q ss_pred             hC-CCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEec-chhhhhhcCCC
Q 042806          230 LG-LTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTAR-SLDVLSRKMDS  301 (390)
Q Consensus       230 l~-~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr-~~~v~~~~~~~  301 (390)
                      +. .+.........+..+.+.+.    .++.-++|+|+++..  ..++.+...+-.-.....+|++|. ...+......-
T Consensus        92 viEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~TI~SR  171 (484)
T PRK14956         92 VLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSR  171 (484)
T ss_pred             ceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHHHHhh
Confidence            00 00000011122233333332    234469999999855  446666544433334455554444 44443333334


Q ss_pred             cceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          302 QQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       302 ~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      ...|.+.+++.++..+.+.+.+......- .++....|++.++|.+--...+
T Consensus       172 Cq~~~f~~ls~~~i~~~L~~i~~~Egi~~-e~eAL~~Ia~~S~Gd~RdAL~l  222 (484)
T PRK14956        172 CQDFIFKKVPLSVLQDYSEKLCKIENVQY-DQEGLFWIAKKGDGSVRDMLSF  222 (484)
T ss_pred             hheeeecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCChHHHHHHH
Confidence            46899999999999999988875222222 2456789999999998544433

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.75  E-value=4.1e-07  Score=81.54  Aligned_cols=167  Identities=13%  Similarity=0.067  Sum_probs=100.7

Q ss_pred             HHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHH
Q 042806          163 LNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGR  242 (390)
Q Consensus       163 ~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~  242 (390)
                      +..+..+...+..+.+.|+|++|+|||+|++.+++.....  -..+.|+.+....+                       .
T Consensus        33 ~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~--~~~v~y~~~~~~~~-----------------------~   87 (235)
T PRK08084         33 LAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAELSQR--GRAVGYVPLDKRAW-----------------------F   87 (235)
T ss_pred             HHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEEHHHHhh-----------------------h
Confidence            3444444444555788999999999999999999986543  23456665533100                       0


Q ss_pred             HHHHHHHHhCCCeEEEEEeCCCCC---ccccc-ccCCCCC--CCCCcEEEEEecchhhh--------hhcCCCcceEecC
Q 042806          243 ARSLRNRLKKEKTILVILDNIWGN---LDFQA-VGIPHGD--DRKGCKVLLTARSLDVL--------SRKMDSQQNFSVG  308 (390)
Q Consensus       243 ~~~l~~~l~~~~~~LlVlDdv~~~---~~~~~-l~~~l~~--~~~~s~IivTtr~~~v~--------~~~~~~~~~~~l~  308 (390)
                      ...+.+.+..-  -+|++||++..   ..|+. +...+..  ...+.++|+||+.....        ......+.+++++
T Consensus        88 ~~~~~~~~~~~--dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~  165 (235)
T PRK08084         88 VPEVLEGMEQL--SLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQ  165 (235)
T ss_pred             hHHHHHHhhhC--CEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHHHhCCceeeec
Confidence            01112222221  38899999753   33432 2111111  12234788888853211        1134556799999


Q ss_pred             CCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHh
Q 042806          309 VLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARAL  357 (390)
Q Consensus       309 ~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L  357 (390)
                      +++.++-.+++.+.+..... .--+++...|++.+.|..-.+..+-..|
T Consensus       166 ~~~~~~~~~~l~~~a~~~~~-~l~~~v~~~L~~~~~~d~r~l~~~l~~l  213 (235)
T PRK08084        166 PLSDEEKLQALQLRARLRGF-ELPEDVGRFLLKRLDREMRTLFMTLDQL  213 (235)
T ss_pred             CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHhhcCCHHHHHHHHHHH
Confidence            99999999999886643212 2225688899999998777766655444

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.75  E-value=1.7e-07  Score=94.48  Aligned_cols=196  Identities=13%  Similarity=0.131  Sum_probs=111.4

Q ss_pred             cCcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 042806          151 KDYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      .....++|.+..+..|...+..++. ..+.++|+.|+||||+|+.+.+.......+...   .+..+    ...+.|...
T Consensus        13 ~~f~divGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~---pCg~C----~~C~~i~~g   85 (647)
T PRK07994         13 QTFAEVVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITAT---PCGEC----DNCREIEQG   85 (647)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCC---CCCCC----HHHHHHHcC
Confidence            3356789999999999998887765 457899999999999999998876432111000   00000    111111100


Q ss_pred             hC-----CCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecc-hhhhhh
Q 042806          230 LG-----LTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARS-LDVLSR  297 (390)
Q Consensus       230 l~-----~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~-~~v~~~  297 (390)
                      -.     .+.......+.+..+.+.+.    .++.-++|+|+++..  ...+.+...+-.-....++|++|.+ ..+...
T Consensus        86 ~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~T  165 (647)
T PRK07994         86 RFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVT  165 (647)
T ss_pred             CCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccchH
Confidence            00     00000001112222222221    234469999999754  3455554444333345555555544 444322


Q ss_pred             cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          298 KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       298 ~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      ...-...|++++++.++....+.+.+....... .+.....|++.++|.|--+..+.
T Consensus       166 I~SRC~~~~f~~Ls~~ei~~~L~~il~~e~i~~-e~~aL~~Ia~~s~Gs~R~Al~ll  221 (647)
T PRK07994        166 ILSRCLQFHLKALDVEQIRQQLEHILQAEQIPF-EPRALQLLARAADGSMRDALSLT  221 (647)
T ss_pred             HHhhheEeeCCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHH
Confidence            233347999999999999999988764221112 23456789999999887554443

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.74  E-value=3.4e-07  Score=92.05  Aligned_cols=197  Identities=11%  Similarity=0.111  Sum_probs=111.6

Q ss_pred             CcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCC--CCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          152 DYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKL--FDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~--f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      ...+++|.+..+..|.+++..++. ..+.++|+.|+||||+|+.+.+...-.+.  ......-.++.+    ...+.|..
T Consensus        14 ~f~dviGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C----~~C~~i~~   89 (618)
T PRK14951         14 SFSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVC----QACRDIDS   89 (618)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCcc----HHHHHHHc
Confidence            355789988888999999887765 56789999999999999999777532110  000000001111    11111100


Q ss_pred             HhC-----CCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEec-chhhhh
Q 042806          229 KLG-----LTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTAR-SLDVLS  296 (390)
Q Consensus       229 ~l~-----~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr-~~~v~~  296 (390)
                      .-.     .+.......+.+..+.+.+.    .++.-++|||+++..  ..++.+...+-.-...+++|++|. ...+..
T Consensus        90 g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~kil~  169 (618)
T PRK14951         90 GRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPV  169 (618)
T ss_pred             CCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhhhH
Confidence            000     00000001111222222221    123358999999855  345555555544344556665554 344433


Q ss_pred             hcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          297 RKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       297 ~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      ....-...+++++++.++..+.+.+.+.......+ .+....|++.++|.+--+..+
T Consensus       170 TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi~ie-~~AL~~La~~s~GslR~al~l  225 (618)
T PRK14951        170 TVLSRCLQFNLRPMAPETVLEHLTQVLAAENVPAE-PQALRLLARAARGSMRDALSL  225 (618)
T ss_pred             HHHHhceeeecCCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHHH
Confidence            23344579999999999999999887752222222 346788999999987655554

>PRK09087 hypothetical protein; Validated

Probab=98.73  E-value=2.3e-07  Score=82.40  Aligned_cols=143  Identities=16%  Similarity=0.118  Sum_probs=88.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      ..+.+.|+|++|+|||+|++.+++....       .|++..      ++..++..                    .+.. 
T Consensus        43 ~~~~l~l~G~~GsGKThLl~~~~~~~~~-------~~i~~~------~~~~~~~~--------------------~~~~-   88 (226)
T PRK09087         43 PSPVVVLAGPVGSGKTHLASIWREKSDA-------LLIHPN------EIGSDAAN--------------------AAAE-   88 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHhcCC-------EEecHH------HcchHHHH--------------------hhhc-
Confidence            3567899999999999999998876421       233221      11111111                    1111 


Q ss_pred             CeEEEEEeCCCCCc-ccccccCCCCC-CCCCcEEEEEecch---------hhhhhcCCCcceEecCCCCHHHHHHHHHHh
Q 042806          254 KTILVILDNIWGNL-DFQAVGIPHGD-DRKGCKVLLTARSL---------DVLSRKMDSQQNFSVGVLKEDEAWSLFKKM  322 (390)
Q Consensus       254 ~~~LlVlDdv~~~~-~~~~l~~~l~~-~~~~s~IivTtr~~---------~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~  322 (390)
                        -+|++||+.... .-+.+...+.. ...|..+|+|++..         .+.+ .+..+..+++++++.++-.+++.+.
T Consensus        89 --~~l~iDDi~~~~~~~~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~S-Rl~~gl~~~l~~pd~e~~~~iL~~~  165 (226)
T PRK09087         89 --GPVLIEDIDAGGFDETGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKS-RLKAATVVEIGEPDDALLSQVIFKL  165 (226)
T ss_pred             --CeEEEECCCCCCCCHHHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHH-HHhCCceeecCCCCHHHHHHHHHHH
Confidence              278889996432 11122222211 23366788888742         1211 3456679999999999999999988


Q ss_pred             hCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          323 AGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       323 ~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      +...... --+++...|++.+.|..-++..+-
T Consensus       166 ~~~~~~~-l~~ev~~~La~~~~r~~~~l~~~l  196 (226)
T PRK09087        166 FADRQLY-VDPHVVYYLVSRMERSLFAAQTIV  196 (226)
T ss_pred             HHHcCCC-CCHHHHHHHHHHhhhhHHHHHHHH
Confidence            8532221 225678899999999888877543

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.72  E-value=2.8e-07  Score=91.33  Aligned_cols=186  Identities=13%  Similarity=0.146  Sum_probs=112.3

Q ss_pred             cCcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCC-------------------CeEEE
Q 042806          151 KDYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLF-------------------DQVIF  210 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f-------------------~~~~w  210 (390)
                      ....+++|-+..+..|.+++..++. ..+.++|+.|+||||+|+.+.+...-...+                   ...+.
T Consensus        13 ~~f~divGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~e   92 (509)
T PRK14958         13 RCFQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLFE   92 (509)
T ss_pred             CCHHHhcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEEE
Confidence            3356789999999999999987765 457899999999999999999876432111                   11233


Q ss_pred             EEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEE
Q 042806          211 VEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLT  288 (390)
Q Consensus       211 v~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivT  288 (390)
                      +..+....++++ +++...+....                ..++.-++|+|+++..  ...+.+...+-.-.+.+++|++
T Consensus        93 idaas~~~v~~i-R~l~~~~~~~p----------------~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIla  155 (509)
T PRK14958         93 VDAASRTKVEDT-RELLDNIPYAP----------------TKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILA  155 (509)
T ss_pred             EcccccCCHHHH-HHHHHHHhhcc----------------ccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEE
Confidence            332222222221 22222221110                1234358999999854  3444454444333446666665


Q ss_pred             ecc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          289 ARS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       289 tr~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      |.+ ..+......-...+++++++.++....+.+.+.......+ ++....|++.++|.|--+..+-
T Consensus       156 ttd~~kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi~~~-~~al~~ia~~s~GslR~al~lL  221 (509)
T PRK14958        156 TTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEENVEFE-NAALDLLARAANGSVRDALSLL  221 (509)
T ss_pred             ECChHhchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCcHHHHHHHH
Confidence            544 3333222233468899999999988887777642222222 3456789999999886555443

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.71  E-value=8.8e-07  Score=84.61  Aligned_cols=184  Identities=15%  Similarity=0.158  Sum_probs=110.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcC--------------------CCCeEEEE
Q 042806          153 YEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEK--------------------LFDQVIFV  211 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~--------------------~f~~~~wv  211 (390)
                      ...++|.+..++.+.+++..++. +.+.++|++|+||||+|+.+........                    +++. .++
T Consensus        13 ~~~iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~-~~~   91 (355)
T TIGR02397        13 FEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDV-IEI   91 (355)
T ss_pred             HhhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCE-EEe
Confidence            45789999999999999987664 4678999999999999999988864211                    1221 222


Q ss_pred             EeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEe
Q 042806          212 EVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTA  289 (390)
Q Consensus       212 ~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTt  289 (390)
                      ..+......+ .+.+...+...+               ..+++ -++|+|+++..  ...+.+...+....+.+.+|++|
T Consensus        92 ~~~~~~~~~~-~~~l~~~~~~~p---------------~~~~~-~vviidea~~l~~~~~~~Ll~~le~~~~~~~lIl~~  154 (355)
T TIGR02397        92 DAASNNGVDD-IREILDNVKYAP---------------SSGKY-KVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILAT  154 (355)
T ss_pred             eccccCCHHH-HHHHHHHHhcCc---------------ccCCc-eEEEEeChhhcCHHHHHHHHHHHhCCccceeEEEEe
Confidence            2221111111 122222221100               01223 58899998654  33444444443334456666676


Q ss_pred             cchh-hhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHH
Q 042806          290 RSLD-VLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVAR  355 (390)
Q Consensus       290 r~~~-v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~  355 (390)
                      .+.. +..........+++.+++.++..+++...+.......+ ++.+..+++.++|.|..+.....
T Consensus       155 ~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~~i~-~~a~~~l~~~~~g~~~~a~~~le  220 (355)
T TIGR02397       155 TEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGIKIE-DEALELIARAADGSLRDALSLLD  220 (355)
T ss_pred             CCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCChHHHHHHHH
Confidence            5433 22222233468899999999999999887742211111 35678899999999976665543

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.

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.71  E-value=6.4e-07  Score=88.91  Aligned_cols=187  Identities=14%  Similarity=0.173  Sum_probs=110.3

Q ss_pred             CcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcC-------------------CCCeEEEE
Q 042806          152 DYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEK-------------------LFDQVIFV  211 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~-------------------~f~~~~wv  211 (390)
                      ....++|.+..++.|...+..++. ..+.++|+.|+||||+|+.+++......                   .|...+++
T Consensus        14 ~f~diiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dliei   93 (546)
T PRK14957         14 SFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEI   93 (546)
T ss_pred             cHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEe
Confidence            355788999999999999887654 5578999999999999999998754211                   11122222


Q ss_pred             EeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEe
Q 042806          212 EVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTA  289 (390)
Q Consensus       212 ~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTt  289 (390)
                      ........+++ +.+...+                ...-..+++-++|+|+++..  ..++.+...+-.....+.+|++|
T Consensus        94 daas~~gvd~i-r~ii~~~----------------~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~T  156 (546)
T PRK14957         94 DAASRTGVEET-KEILDNI----------------QYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILAT  156 (546)
T ss_pred             ecccccCHHHH-HHHHHHH----------------HhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEEE
Confidence            22111111111 1111111                11101123369999999754  34555554443333455566555


Q ss_pred             cc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH-HHHHHHHH
Q 042806          290 RS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV-SIVTVARA  356 (390)
Q Consensus       290 r~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL-ai~~l~~~  356 (390)
                      .+ ..+......-...+++++++.++....+.+.+....... .+.....|++.++|-+- |+..+-.+
T Consensus       157 td~~kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~egi~~-e~~Al~~Ia~~s~GdlR~alnlLek~  224 (546)
T PRK14957        157 TDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENINS-DEQSLEYIAYHAKGSLRDALSLLDQA  224 (546)
T ss_pred             CChhhhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            43 333322233457999999999999888887664222222 24456789999999664 55555433

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.70  E-value=6e-07  Score=87.89  Aligned_cols=184  Identities=13%  Similarity=0.108  Sum_probs=112.5

Q ss_pred             CcccccchhHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhc-------------------CCCCeEEEE
Q 042806          152 DYEACESRMSTLNDILDALKNPDVN-MLGIYGMGGIVKTTLAKEVARKAETE-------------------KLFDQVIFV  211 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~~GvGKTtLa~~v~~~~~~~-------------------~~f~~~~wv  211 (390)
                      ...+++|.+..+..|.+.+..++.. .+.++|+.|+||||+|+.+.....-.                   +.+..++.+
T Consensus        11 ~f~dliGQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~ei   90 (491)
T PRK14964         11 SFKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEI   90 (491)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEE
Confidence            3557899998888888888877654 78999999999999999998754211                   011123344


Q ss_pred             EeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEe
Q 042806          212 EVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTA  289 (390)
Q Consensus       212 ~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTt  289 (390)
                      +.+......+ .+.+.......+               + .++.-++|+|+++..  ...+.+...+-.-.+.+++|++|
T Consensus        91 daas~~~vdd-IR~Iie~~~~~P---------------~-~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlat  153 (491)
T PRK14964         91 DAASNTSVDD-IKVILENSCYLP---------------I-SSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILAT  153 (491)
T ss_pred             ecccCCCHHH-HHHHHHHHHhcc---------------c-cCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEe
Confidence            4433333332 222222221100               0 123358999999754  33445544443334556666655


Q ss_pred             cc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          290 RS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       290 r~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      .. ..+......-...+++.+++.++..+.+.+.+......-+ ++....|++.++|.+-.+..+
T Consensus       154 te~~Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~Egi~i~-~eAL~lIa~~s~GslR~alsl  217 (491)
T PRK14964        154 TEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENIEHD-EESLKLIAENSSGSMRNALFL  217 (491)
T ss_pred             CChHHHHHHHHHhheeeecccccHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHHH
Confidence            43 4443333344578999999999999999888753222222 345678999999988654443

>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=98.70  E-value=2e-07  Score=82.45  Aligned_cols=164  Identities=20%  Similarity=0.199  Sum_probs=100.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      ...+.|+|+.|+|||.|++.+++.......-..++|+      +..++...+...+..        .....+.+.+..-.
T Consensus        34 ~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~------~~~~f~~~~~~~~~~--------~~~~~~~~~~~~~D   99 (219)
T PF00308_consen   34 YNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYL------SAEEFIREFADALRD--------GEIEEFKDRLRSAD   99 (219)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEE------EHHHHHHHHHHHHHT--------TSHHHHHHHHCTSS
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHHHhccccccceee------cHHHHHHHHHHHHHc--------ccchhhhhhhhcCC
Confidence            4568899999999999999999997653222235554      445666666665543        12345666666544


Q ss_pred             eEEEEEeCCCCCc---cccc-ccCCCCC-CCCCcEEEEEecchhh-h-------hhcCCCcceEecCCCCHHHHHHHHHH
Q 042806          255 TILVILDNIWGNL---DFQA-VGIPHGD-DRKGCKVLLTARSLDV-L-------SRKMDSQQNFSVGVLKEDEAWSLFKK  321 (390)
Q Consensus       255 ~~LlVlDdv~~~~---~~~~-l~~~l~~-~~~~s~IivTtr~~~v-~-------~~~~~~~~~~~l~~L~~~ea~~lf~~  321 (390)
                        +|++||++...   .|+. +...+.. ...|.+||+|+...-. .       ...+..+..+++.+++.++-..++.+
T Consensus       100 --lL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~  177 (219)
T PF00308_consen  100 --LLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDEDRRRILQK  177 (219)
T ss_dssp             --EEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHHHHHHHHH
T ss_pred             --EEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHHHHHHHHH
Confidence              99999997542   2322 2111111 1346689999964211 0       11344667999999999999999999


Q ss_pred             hhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHH
Q 042806          322 MAGDYIEGSEFKWVAKDVARECAGLPVSIVTVAR  355 (390)
Q Consensus       322 ~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~  355 (390)
                      .+...... --++++..|++.+.+..-.+..+-.
T Consensus       178 ~a~~~~~~-l~~~v~~~l~~~~~~~~r~L~~~l~  210 (219)
T PF00308_consen  178 KAKERGIE-LPEEVIEYLARRFRRDVRELEGALN  210 (219)
T ss_dssp             HHHHTT---S-HHHHHHHHHHTTSSHHHHHHHHH
T ss_pred             HHHHhCCC-CcHHHHHHHHHhhcCCHHHHHHHHH
Confidence            88622222 2256788899998877766665543

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.

>PRK08727 hypothetical protein; Validated

Probab=98.70  E-value=3.8e-07  Score=81.65  Aligned_cols=152  Identities=16%  Similarity=0.103  Sum_probs=92.3

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHh
Q 042806          172 NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK  251 (390)
Q Consensus       172 ~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~  251 (390)
                      +.....+.|+|++|+|||+|++.+++.....  ...+.|+++..      ....+.                 ...+.+.
T Consensus        38 ~~~~~~l~l~G~~G~GKThL~~a~~~~~~~~--~~~~~y~~~~~------~~~~~~-----------------~~~~~l~   92 (233)
T PRK08727         38 GQSSDWLYLSGPAGTGKTHLALALCAAAEQA--GRSSAYLPLQA------AAGRLR-----------------DALEALE   92 (233)
T ss_pred             ccCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEEeHHH------hhhhHH-----------------HHHHHHh
Confidence            3344569999999999999999999987644  22455665422      111111                 1122332


Q ss_pred             CCCeEEEEEeCCCCCc---cccc-ccCCCCC-CCCCcEEEEEecchhhh--------hhcCCCcceEecCCCCHHHHHHH
Q 042806          252 KEKTILVILDNIWGNL---DFQA-VGIPHGD-DRKGCKVLLTARSLDVL--------SRKMDSQQNFSVGVLKEDEAWSL  318 (390)
Q Consensus       252 ~~~~~LlVlDdv~~~~---~~~~-l~~~l~~-~~~~s~IivTtr~~~v~--------~~~~~~~~~~~l~~L~~~ea~~l  318 (390)
                      +  .-+||+||+....   .|.. +...+.. ...+..||+|++...-.        ...+.....+++++++.++-.++
T Consensus        93 ~--~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~SRl~~~~~~~l~~~~~e~~~~i  170 (233)
T PRK08727         93 G--RSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSRLAQCIRIGLPVLDDVARAAV  170 (233)
T ss_pred             c--CCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHHHHhcCceEEecCCCHHHHHHH
Confidence            2  2599999997442   2332 2211111 12456799999852110        11233456899999999999999


Q ss_pred             HHHhhCCCCCCCchHHHHHHHHHHcCCChHHHH
Q 042806          319 FKKMAGDYIEGSEFKWVAKDVARECAGLPVSIV  351 (390)
Q Consensus       319 f~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~  351 (390)
                      +.+.+....... .++....|++.++|-.-.+.
T Consensus       171 L~~~a~~~~l~l-~~e~~~~La~~~~rd~r~~l  202 (233)
T PRK08727        171 LRERAQRRGLAL-DEAAIDWLLTHGERELAGLV  202 (233)
T ss_pred             HHHHHHHcCCCC-CHHHHHHHHHhCCCCHHHHH
Confidence            998775222212 24577899999987766653

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=98.69  E-value=8.8e-07  Score=83.75  Aligned_cols=199  Identities=14%  Similarity=0.060  Sum_probs=115.2

Q ss_pred             ccCcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCC--CCeEEEEEeCCCCCHHHHHHHH
Q 042806          150 IKDYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKL--FDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       150 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~--f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      |.....++|.+.....+...+..++. ..+.|+|+.|+||||+|..+....-....  +...   .....+..-...+.+
T Consensus        19 P~~~~~l~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~---~~~~~~~~c~~c~~i   95 (351)
T PRK09112         19 PSENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPE---TLADPDPASPVWRQI   95 (351)
T ss_pred             CCchhhccCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCcc---ccCCCCCCCHHHHHH
Confidence            33456789999999999999987764 46889999999999999999988643110  1111   001011111122333


Q ss_pred             HHHhC-------CCCCCC----C---chHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcE-E
Q 042806          227 ADKLG-------LTLHEE----S---DSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCK-V  285 (390)
Q Consensus       227 ~~~l~-------~~~~~~----~---~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~-I  285 (390)
                      ...-.       ...+..    .   ..+.+..+.+++.    .+++-++|+|+++..  ...+.+...+..-..++. |
T Consensus        96 ~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~~~fi  175 (351)
T PRK09112         96 AQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPARALFI  175 (351)
T ss_pred             HcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcCCCCceEE
Confidence            22110       000000    0   1123445555553    234469999999754  233334333322223344 4


Q ss_pred             EEEecchhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          286 LLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       286 ivTtr~~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      ++|++...+.....+-...+++.+++.++..+++.+......   -.++....+++.++|.|.....+.
T Consensus       176 Lit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~~~---~~~~~~~~i~~~s~G~pr~Al~ll  241 (351)
T PRK09112        176 LISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSSQG---SDGEITEALLQRSKGSVRKALLLL  241 (351)
T ss_pred             EEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcccC---CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            455444444333333446999999999999999988542211   113456789999999998766554

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.69  E-value=8.1e-07  Score=76.85  Aligned_cols=160  Identities=18%  Similarity=0.122  Sum_probs=93.9

Q ss_pred             HHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhc--------------------CCCCeEEEEEeCC-CCCHHHH
Q 042806          165 DILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETE--------------------KLFDQVIFVEVSK-IQDIRKI  222 (390)
Q Consensus       165 ~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~--------------------~~f~~~~wv~v~~-~~~~~~l  222 (390)
                      .+.+.+..++. ..+.++|+.|+||||+|+.+....-..                    .+.+. .++.... ....++ 
T Consensus         3 ~l~~~i~~~~~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~-~~~~~~~~~~~~~~-   80 (188)
T TIGR00678         3 QLKRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDL-HRLEPEGQSIKVDQ-   80 (188)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcE-EEeccccCcCCHHH-
Confidence            35555656655 678999999999999999998886432                    11221 2221111 111111 


Q ss_pred             HHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecch-hhhhhcC
Q 042806          223 QGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSL-DVLSRKM  299 (390)
Q Consensus       223 ~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~-~v~~~~~  299 (390)
                      .+.+...+.....                .+.+-++|+|+++..  ...+.+...+......+.+|++|++. .+.....
T Consensus        81 i~~i~~~~~~~~~----------------~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~  144 (188)
T TIGR00678        81 VRELVEFLSRTPQ----------------ESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIR  144 (188)
T ss_pred             HHHHHHHHccCcc----------------cCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHH
Confidence            1222222211100                123368999999754  23444544443334456677766643 3322222


Q ss_pred             CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHH
Q 042806          300 DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVS  349 (390)
Q Consensus       300 ~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLa  349 (390)
                      .....+++.+++.++..+.+.+. +  ..    ++.+..|++.++|.|..
T Consensus       145 sr~~~~~~~~~~~~~~~~~l~~~-g--i~----~~~~~~i~~~~~g~~r~  187 (188)
T TIGR00678       145 SRCQVLPFPPLSEEALLQWLIRQ-G--IS----EEAAELLLALAGGSPGA  187 (188)
T ss_pred             hhcEEeeCCCCCHHHHHHHHHHc-C--CC----HHHHHHHHHHcCCCccc
Confidence            33469999999999999998876 2  11    35678999999998853

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.

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.69  E-value=7.3e-07  Score=85.47  Aligned_cols=172  Identities=14%  Similarity=0.072  Sum_probs=103.5

Q ss_pred             ccccchhHHHHHHHHHhcCCC----------ccEEEEEcCCCCcHHHHHHHHHHHhhhcC-------------------C
Q 042806          154 EACESRMSTLNDILDALKNPD----------VNMLGIYGMGGIVKTTLAKEVARKAETEK-------------------L  204 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~~~----------~~vi~I~G~~GvGKTtLa~~v~~~~~~~~-------------------~  204 (390)
                      ..++|.+..++.|.+++..+.          .+.+.++|++|+|||++|+.+....--..                   |
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~h   84 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGTH   84 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCC
Confidence            457888888888888887653          46688999999999999999987643211                   1


Q ss_pred             CCeEEEEEeC-CCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCC
Q 042806          205 FDQVIFVEVS-KIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHG  277 (390)
Q Consensus       205 f~~~~wv~v~-~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~  277 (390)
                      .| ..++... ....+++                     +..+.+.+.    .+++-++++|+++..  ...+.+...+-
T Consensus        85 pD-~~~i~~~~~~i~i~~---------------------iR~l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk~LE  142 (394)
T PRK07940         85 PD-VRVVAPEGLSIGVDE---------------------VRELVTIAARRPSTGRWRIVVIEDADRLTERAANALLKAVE  142 (394)
T ss_pred             CC-EEEeccccccCCHHH---------------------HHHHHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHHHhh
Confidence            22 1122111 1111111                     222222221    123358888999754  23333433333


Q ss_pred             CCCCCcEEEEEecc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          278 DDRKGCKVLLTARS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       278 ~~~~~s~IivTtr~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      .-.++..+|++|.+ ..+......-...+.+.+++.++..+.+.+..+   ..   .+.+..++..++|.|.....+
T Consensus       143 ep~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~~~~---~~---~~~a~~la~~s~G~~~~A~~l  213 (394)
T PRK07940        143 EPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVRRDG---VD---PETARRAARASQGHIGRARRL  213 (394)
T ss_pred             cCCCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHHhcC---CC---HHHHHHHHHHcCCCHHHHHHH
Confidence            33345556666655 444333333446999999999999988875432   11   345678999999999755433

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=98.69  E-value=1.2e-06  Score=83.19  Aligned_cols=196  Identities=16%  Similarity=0.054  Sum_probs=113.1

Q ss_pred             cCcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEE------EEEeCCCCCHHHHH
Q 042806          151 KDYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVI------FVEVSKIQDIRKIQ  223 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~------wv~v~~~~~~~~l~  223 (390)
                      .....++|.+.....|.+.+..++. ..+.++|+.|+||+|+|..+....--........      -..+...+   ...
T Consensus        16 ~~~~~iiGq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~~~~c---~~c   92 (365)
T PRK07471         16 RETTALFGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDH---PVA   92 (365)
T ss_pred             CchhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccCCCCC---hHH
Confidence            3356789999999999999888764 4688999999999999999988764321110000      00000000   011


Q ss_pred             HHHHHHhCCC-------CCCCC-------chHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCc
Q 042806          224 GEIADKLGLT-------LHEES-------DSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGC  283 (390)
Q Consensus       224 ~~i~~~l~~~-------~~~~~-------~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s  283 (390)
                      +.+...-..+       .++..       ..+.+..+.+.+.    .+++-++|+|+++..  ...+.+...+..-.+++
T Consensus        93 ~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m~~~aanaLLK~LEepp~~~  172 (365)
T PRK07471         93 RRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEEPPARS  172 (365)
T ss_pred             HHHHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhcCHHHHHHHHHHHhcCCCCe
Confidence            1111100000       00000       0122334444442    244479999999754  33444444443333456


Q ss_pred             EEEEEecch-hhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          284 KVLLTARSL-DVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       284 ~IivTtr~~-~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      .+|++|.+. .+......-...+.+.+++.++..+++.+....   ..  +.....++..++|.|+....+.
T Consensus       173 ~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~~~---~~--~~~~~~l~~~s~Gsp~~Al~ll  239 (365)
T PRK07471        173 LFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAGPD---LP--DDPRAALAALAEGSVGRALRLA  239 (365)
T ss_pred             EEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhccc---CC--HHHHHHHHHHcCCCHHHHHHHh
Confidence            667766654 443333445579999999999999999876521   11  1122578999999998665553

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

Probab=98.68  E-value=9.2e-08  Score=82.27  Aligned_cols=48  Identities=19%  Similarity=0.212  Sum_probs=34.7

Q ss_pred             cccchhHHHHHHHHHhc---CCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          155 ACESRMSTLNDILDALK---NPDVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~---~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      .|+||+.+++++...+.   ....+.+.|+|++|+|||+|++.++......
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            38999999999999982   3457899999999999999999999998776

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.67  E-value=5.3e-07  Score=89.73  Aligned_cols=195  Identities=13%  Similarity=0.099  Sum_probs=108.6

Q ss_pred             CcccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          152 DYEACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ....++|++..++.+.+++..++ .+.+.++|+.|+||||+|+.+.+......+..      ... +..-...+.+....
T Consensus        14 ~F~dIIGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~------~~~-Cg~C~sCr~i~~~~   86 (605)
T PRK05896         14 NFKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKD------GDC-CNSCSVCESINTNQ   86 (605)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCC------CCC-CcccHHHHHHHcCC
Confidence            35578999999999999987765 45788999999999999999998864321111      000 00001111111110


Q ss_pred             CCC-----CCCCCchHHHHHHHHHHh-----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEe-cchhhhhh
Q 042806          231 GLT-----LHEESDSGRARSLRNRLK-----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTA-RSLDVLSR  297 (390)
Q Consensus       231 ~~~-----~~~~~~~~~~~~l~~~l~-----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTt-r~~~v~~~  297 (390)
                      ...     .......+.+..+.+.+.     .++ -++|+|+++..  ..++.+...+-.-...+.+|++| ....+...
T Consensus        87 h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~-KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~T  165 (605)
T PRK05896         87 SVDIVELDAASNNGVDEIRNIIDNINYLPTTFKY-KVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLT  165 (605)
T ss_pred             CCceEEeccccccCHHHHHHHHHHHHhchhhCCc-EEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhHH
Confidence            000     000000111222222211     233 47999999754  34455544443323345555444 43444322


Q ss_pred             cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH-HHHHHHH
Q 042806          298 KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV-SIVTVAR  355 (390)
Q Consensus       298 ~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL-ai~~l~~  355 (390)
                      .......+++.+++.++....+...+......-+ .+.+..+++.++|.+- |+..+-.
T Consensus       166 I~SRcq~ieF~~Ls~~eL~~~L~~il~kegi~Is-~eal~~La~lS~GdlR~AlnlLek  223 (605)
T PRK05896        166 IISRCQRYNFKKLNNSELQELLKSIAKKEKIKIE-DNAIDKIADLADGSLRDGLSILDQ  223 (605)
T ss_pred             HHhhhhhcccCCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCcHHHHHHHHHH
Confidence            2333468999999999999999887742211111 3457789999999664 5555444

>COG3899 Predicted ATPase [General function prediction only]

Probab=98.66  E-value=2.8e-07  Score=96.72  Aligned_cols=204  Identities=14%  Similarity=0.126  Sum_probs=119.5

Q ss_pred             cccchhHHHHHHHHHhcC---CCccEEEEEcCCCCcHHHHHHHHHHHhhhc-CCCCeEEEEEeCCCC---CHHHHHHHHH
Q 042806          155 ACESRMSTLNDILDALKN---PDVNMLGIYGMGGIVKTTLAKEVARKAETE-KLFDQVIFVEVSKIQ---DIRKIQGEIA  227 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~---~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~~---~~~~l~~~i~  227 (390)
                      +++||+.+++.|...+.+   +...++.|.|.+|+|||+|++.|......+ +.|-...+-......   ...+.+++++
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~~i~~~~~~~i~~~f~q~~~~ipl~~lvq~~r~l~   80 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKPITQQRGYFIKGKFDQFERNIPLSPLVQAFRDLM   80 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHHHHhccceeeeHhhcccccCCCchHHHHHHHHHHH
Confidence            368999999999888764   567799999999999999999999887544 111111111112222   2233334444


Q ss_pred             HHh-------------------CCCCC------------------CC--Cc------h--HHHHHHHHHHhCCCeEEEEE
Q 042806          228 DKL-------------------GLTLH------------------EE--SD------S--GRARSLRNRLKKEKTILVIL  260 (390)
Q Consensus       228 ~~l-------------------~~~~~------------------~~--~~------~--~~~~~l~~~l~~~~~~LlVl  260 (390)
                      .++                   +....                  ..  +.      .  .....+.......+|.++|+
T Consensus        81 ~~ll~~~~~~~~~~~~~il~~~g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~~~~plVi~l  160 (849)
T COG3899          81 GQLLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTAEEHPLVIVL  160 (849)
T ss_pred             HHHhhccchHHHHHHHHHHHHhcccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHhccCCeEEEE
Confidence            433                   11000                  00  00      0  01123333444566799999


Q ss_pred             eCCC-C-Ccccccc---cCCCC---CCCCCcEEEEEecch-hhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCc
Q 042806          261 DNIW-G-NLDFQAV---GIPHG---DDRKGCKVLLTARSL-DVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSE  331 (390)
Q Consensus       261 Ddv~-~-~~~~~~l---~~~l~---~~~~~s~IivTtr~~-~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~  331 (390)
                      ||++ - ...++-+   ....+   ...+..-.+.|.+.. ............|.|.||+..+...+....++.....  
T Consensus       161 eDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l~~~~~~--  238 (849)
T COG3899         161 EDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATLGCTKLL--  238 (849)
T ss_pred             ecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHhCCcccc--
Confidence            9994 2 2222222   11111   001111233333332 1112234455799999999999999999998742222  


Q ss_pred             hHHHHHHHHHHcCCChHHHHHHHHHhcCC
Q 042806          332 FKWVAKDVARECAGLPVSIVTVARALGTR  360 (390)
Q Consensus       332 ~~~~~~~i~~~~~GlPLai~~l~~~L~~~  360 (390)
                      ..+....|+++..|+|+-+..+-..|...
T Consensus       239 ~~p~~~~i~~kt~GnPfFi~e~lk~l~~~  267 (849)
T COG3899         239 PAPLLELIFEKTKGNPFFIEEFLKALYEE  267 (849)
T ss_pred             cchHHHHHHHHhcCCCccHHHHHHHHHhC
Confidence            23457899999999999999999888764

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=98.66  E-value=5.3e-07  Score=90.71  Aligned_cols=182  Identities=14%  Similarity=0.140  Sum_probs=109.4

Q ss_pred             cCcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCC-------------------CeEEE
Q 042806          151 KDYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLF-------------------DQVIF  210 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f-------------------~~~~w  210 (390)
                      .....++|.+..+..|..++..++. ..+.++|+.|+||||+|+.+.+........                   -..+.
T Consensus        13 ~tFddIIGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~DvlE   92 (709)
T PRK08691         13 KTFADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLLE   92 (709)
T ss_pred             CCHHHHcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccceEE
Confidence            3356789999999999999987764 568899999999999999998875322111                   01112


Q ss_pred             EEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcE
Q 042806          211 VEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCK  284 (390)
Q Consensus       211 v~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~  284 (390)
                      +.......+                     ..+..+.+...    .++.-++|+|+++...  ..+.+...+-.-...++
T Consensus        93 idaAs~~gV---------------------d~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~  151 (709)
T PRK08691         93 IDAASNTGI---------------------DNIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVK  151 (709)
T ss_pred             EeccccCCH---------------------HHHHHHHHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHhCCCCcE
Confidence            221111111                     11222222110    1233699999997543  23334333322234566


Q ss_pred             EEEEecc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          285 VLLTARS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       285 IivTtr~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      +|++|.+ ..+.....+-...+++++++.++....+.+.+....... .++....|++.++|.+.-+..+-
T Consensus       152 fILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi~i-d~eAL~~Ia~~A~GslRdAlnLL  221 (709)
T PRK08691        152 FILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIAY-EPPALQLLGRAAAGSMRDALSLL  221 (709)
T ss_pred             EEEEeCCccccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHcCCCc-CHHHHHHHHHHhCCCHHHHHHHH
Confidence            7766654 333222222335788899999999999988875322222 24467899999999986555543

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=98.65  E-value=7.2e-08  Score=86.55  Aligned_cols=91  Identities=14%  Similarity=0.137  Sum_probs=62.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC--CCHHHHHHHHHHHhCCCCCCCCchH---H----HH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI--QDIRKIQGEIADKLGLTLHEESDSG---R----AR  244 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~--~~~~~l~~~i~~~l~~~~~~~~~~~---~----~~  244 (390)
                      ....+.|+|++|+|||||++.+++..... +|+..+|+.+.+.  ++..++++.+...+-....+.+...   .    ..
T Consensus        15 ~Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~   93 (249)
T cd01128          15 KGQRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLE   93 (249)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHH
Confidence            45678899999999999999999998764 7999999997766  7899999998333221111111111   1    11


Q ss_pred             HHHHHHhCCCeEEEEEeCCCC
Q 042806          245 SLRNRLKKEKTILVILDNIWG  265 (390)
Q Consensus       245 ~l~~~l~~~~~~LlVlDdv~~  265 (390)
                      ........+++.++++|++..
T Consensus        94 ~a~~~~~~G~~vll~iDei~r  114 (249)
T cd01128          94 KAKRLVEHGKDVVILLDSITR  114 (249)
T ss_pred             HHHHHHHCCCCEEEEEECHHH
Confidence            222222346679999999964

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.

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

Probab=98.65  E-value=5.2e-07  Score=92.69  Aligned_cols=177  Identities=18%  Similarity=0.208  Sum_probs=101.2

Q ss_pred             cCcccccchhHHHH---HHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          151 KDYEACESRMSTLN---DILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       151 ~~~~~~~gR~~~~~---~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      ...+.|+|++..+.   .+...+..++...+.++|++|+||||||+.+++....  +|.   .++... ....++ +.  
T Consensus        25 ~tldd~vGQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~~~--~f~---~lna~~-~~i~di-r~--   95 (725)
T PRK13341         25 RTLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHTRA--HFS---SLNAVL-AGVKDL-RA--   95 (725)
T ss_pred             CcHHHhcCcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHhcC--cce---eehhhh-hhhHHH-HH--
Confidence            34557889887764   4666677777777889999999999999999987642  231   111110 011111 11  


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHh-CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEE--ecchh--hhhhcCC
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLK-KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLT--ARSLD--VLSRKMD  300 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~-~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivT--tr~~~--v~~~~~~  300 (390)
                                    ......+.+. .+++.+|+|||++..  ..++.+...+   ..++.++++  |.+..  +......
T Consensus        96 --------------~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~l---E~g~IiLI~aTTenp~~~l~~aL~S  158 (725)
T PRK13341         96 --------------EVDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPWV---ENGTITLIGATTENPYFEVNKALVS  158 (725)
T ss_pred             --------------HHHHHHHHhhhcCCceEEEEeChhhCCHHHHHHHHHHh---cCceEEEEEecCCChHhhhhhHhhc
Confidence                          1111111121 123479999999754  2334443322   235545553  33321  2111222


Q ss_pred             CcceEecCCCCHHHHHHHHHHhhCC------CCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          301 SQQNFSVGVLKEDEAWSLFKKMAGD------YIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       301 ~~~~~~l~~L~~~ea~~lf~~~~~~------~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      -...+.+++|+.++...++.+.+..      .....-.++....|++.+.|..-.+..+
T Consensus       159 R~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD~R~lln~  217 (725)
T PRK13341        159 RSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDARSLLNA  217 (725)
T ss_pred             cccceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCCHHHHHHH
Confidence            2458999999999999999887641      1111222456788999998865444333

>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=98.63  E-value=3.7e-06  Score=73.06  Aligned_cols=180  Identities=18%  Similarity=0.149  Sum_probs=94.7

Q ss_pred             ccCcccccchhHHHHHHHHHhc-----CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 042806          150 IKDYEACESRMSTLNDILDALK-----NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQG  224 (390)
Q Consensus       150 ~~~~~~~~gR~~~~~~l~~~L~-----~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~  224 (390)
                      |...++|+|.+.-+..+.-.+.     ++...-+.+|||+|+||||||..+.+.....  |.   +.+.+......++. 
T Consensus        20 P~~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~--~~---~~sg~~i~k~~dl~-   93 (233)
T PF05496_consen   20 PKSLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELGVN--FK---ITSGPAIEKAGDLA-   93 (233)
T ss_dssp             -SSCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT----EE---EEECCC--SCHHHH-
T ss_pred             CCCHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccCCC--eE---eccchhhhhHHHHH-
Confidence            3446789999887776544332     2346678899999999999999999998754  32   22222111122221 


Q ss_pred             HHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc---------ccccccC--CCCCC----------CCCc
Q 042806          225 EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL---------DFQAVGI--PHGDD----------RKGC  283 (390)
Q Consensus       225 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~---------~~~~l~~--~l~~~----------~~~s  283 (390)
                                          .+...+.. + -+|.+|+++...         ..++...  ....+          .+-+
T Consensus        94 --------------------~il~~l~~-~-~ILFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FT  151 (233)
T PF05496_consen   94 --------------------AILTNLKE-G-DILFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFT  151 (233)
T ss_dssp             --------------------HHHHT--T-T--EEEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----E
T ss_pred             --------------------HHHHhcCC-C-cEEEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCCCce
Confidence                                11112222 2 467778886441         1111110  00000          1234


Q ss_pred             EEEEEecchhhhhhcCC-CcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhc
Q 042806          284 KVLLTARSLDVLSRKMD-SQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALG  358 (390)
Q Consensus       284 ~IivTtr~~~v~~~~~~-~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~  358 (390)
                      -|=.|||...+.....+ .+-..+++..+.+|-.+++.+.+.--... -.++.+.+|+++|.|-|--..-+-+-.+
T Consensus       152 ligATTr~g~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~-i~~~~~~~Ia~rsrGtPRiAnrll~rvr  226 (233)
T PF05496_consen  152 LIGATTRAGLLSSPLRDRFGIVLRLEFYSEEELAKIVKRSARILNIE-IDEDAAEEIARRSRGTPRIANRLLRRVR  226 (233)
T ss_dssp             EEEEESSGCCTSHCCCTTSSEEEE----THHHHHHHHHHCCHCTT-E-E-HHHHHHHHHCTTTSHHHHHHHHHHHC
T ss_pred             EeeeeccccccchhHHhhcceecchhcCCHHHHHHHHHHHHHHhCCC-cCHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence            46678887555321122 22356899999999999998877422221 2245789999999999988777665554

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.

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.61  E-value=1.9e-06  Score=82.72  Aligned_cols=182  Identities=14%  Similarity=0.136  Sum_probs=104.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhc------CCCCeE-EEEEeCCCCCHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETE------KLFDQV-IFVEVSKIQDIRKIQG  224 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~------~~f~~~-~wv~v~~~~~~~~l~~  224 (390)
                      ..+++|.+..++.+.+.+..++. +.+.++|++|+||||+|+.+.+.....      ..|... +.+.........+ ..
T Consensus        16 ~~~iig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-i~   94 (367)
T PRK14970         16 FDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDD-IR   94 (367)
T ss_pred             HHhcCCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCHHH-HH
Confidence            45788999999999999987664 578899999999999999998876431      112211 1111111111111 12


Q ss_pred             HHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEecc-hhhhhhcCCC
Q 042806          225 EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTARS-LDVLSRKMDS  301 (390)
Q Consensus       225 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTtr~-~~v~~~~~~~  301 (390)
                      .+...+...+               ..+++ -++++|+++...  .++.+...+......+.+|+++.. ..+.......
T Consensus        95 ~l~~~~~~~p---------------~~~~~-kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~sr  158 (367)
T PRK14970         95 NLIDQVRIPP---------------QTGKY-KIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILSR  158 (367)
T ss_pred             HHHHHHhhcc---------------ccCCc-EEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHHhc
Confidence            2222221100               01233 589999986542  244443333222334555555533 2322222233


Q ss_pred             cceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHH
Q 042806          302 QQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVT  352 (390)
Q Consensus       302 ~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~  352 (390)
                      ...+++.+++.++....+...+......- .++.+..+++.++|.+-.+..
T Consensus       159 ~~~v~~~~~~~~~l~~~l~~~~~~~g~~i-~~~al~~l~~~~~gdlr~~~~  208 (367)
T PRK14970        159 CQIFDFKRITIKDIKEHLAGIAVKEGIKF-EDDALHIIAQKADGALRDALS  208 (367)
T ss_pred             ceeEecCCccHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHhCCCCHHHHHH
Confidence            45899999999999998888764222111 135678899999996654433

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.60  E-value=8.5e-07  Score=79.16  Aligned_cols=153  Identities=12%  Similarity=0.057  Sum_probs=90.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      ..+.+.|+|++|+|||+||+.+++.....+ . ...+++.....      ..    +                 ..... 
T Consensus        41 ~~~~~~l~G~~G~GKT~La~ai~~~~~~~~-~-~~~~i~~~~~~------~~----~-----------------~~~~~-   90 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHLLQALVADASYGG-R-NARYLDAASPL------LA----F-----------------DFDPE-   90 (227)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHhCC-C-cEEEEehHHhH------HH----H-----------------hhccc-
Confidence            456788999999999999999999864321 2 24455443311      00    0                 11112 


Q ss_pred             CeEEEEEeCCCCCcccc--cccCCCCC-CCCCc-EEEEEecchhhhhh-------cCCCcceEecCCCCHHHHHHHHHHh
Q 042806          254 KTILVILDNIWGNLDFQ--AVGIPHGD-DRKGC-KVLLTARSLDVLSR-------KMDSQQNFSVGVLKEDEAWSLFKKM  322 (390)
Q Consensus       254 ~~~LlVlDdv~~~~~~~--~l~~~l~~-~~~~s-~IivTtr~~~v~~~-------~~~~~~~~~l~~L~~~ea~~lf~~~  322 (390)
                      . -+|++||++....+.  .+...+.. ...+. .+|+|++.......       .......+++.+++.++-..++.+.
T Consensus        91 ~-~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~~~~~~~~l~~~  169 (227)
T PRK08903         91 A-ELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLSDADKIAALKAA  169 (227)
T ss_pred             C-CEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCCHHHHHHHHHHH
Confidence            2 478899997543222  22222211 12233 46666654221110       1223468999999998877777765


Q ss_pred             hCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhc
Q 042806          323 AGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALG  358 (390)
Q Consensus       323 ~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~  358 (390)
                      +....... .++....+++.+.|.+..+..+...|.
T Consensus       170 ~~~~~v~l-~~~al~~L~~~~~gn~~~l~~~l~~l~  204 (227)
T PRK08903        170 AAERGLQL-ADEVPDYLLTHFRRDMPSLMALLDALD  204 (227)
T ss_pred             HHHcCCCC-CHHHHHHHHHhccCCHHHHHHHHHHHH
Confidence            53221222 245788899999999999888776654

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.60  E-value=8.9e-07  Score=85.64  Aligned_cols=200  Identities=13%  Similarity=0.127  Sum_probs=110.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEE-eCCCCCHHHHHHHHHHHh
Q 042806          153 YEACESRMSTLNDILDALKNPDVN-MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVE-VSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~-v~~~~~~~~l~~~i~~~l  230 (390)
                      ...++|.+..++.|..++.+++.+ .+.++|+.|+||||+|+.+.+...-...+....|.. ....+..=...+.+...-
T Consensus        15 ~~eiiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~~~~~~~   94 (397)
T PRK14955         15 FADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCRDFDAGT   94 (397)
T ss_pred             HhhccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHHHHhcCC
Confidence            457889988888899988877654 588999999999999999998874321111111110 000000000011111000


Q ss_pred             CC-----CCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEe-cchhhhhhc
Q 042806          231 GL-----TLHEESDSGRARSLRNRLK----KEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTA-RSLDVLSRK  298 (390)
Q Consensus       231 ~~-----~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTt-r~~~v~~~~  298 (390)
                      ..     ........+.+..+.+.+.    .+++-++|+|+++...  .++.+...+..-.+.+.+|++| +...+....
T Consensus        95 ~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~kl~~tl  174 (397)
T PRK14955         95 SLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATI  174 (397)
T ss_pred             CCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHHhHHHH
Confidence            00     0000011122233333331    1233589999997553  4555544444334456666555 333332211


Q ss_pred             CCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          299 MDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       299 ~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      ......+++.+++.++..+.+...+......- .++.+..|++.++|.+--+...
T Consensus       175 ~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~~i-~~~al~~l~~~s~g~lr~a~~~  228 (397)
T PRK14955        175 ASRCQRFNFKRIPLEEIQQQLQGICEAEGISV-DADALQLIGRKAQGSMRDAQSI  228 (397)
T ss_pred             HHHHHHhhcCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHH
Confidence            22235889999999999988888764221111 1456789999999977644443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.60  E-value=1e-06  Score=87.83  Aligned_cols=184  Identities=15%  Similarity=0.148  Sum_probs=107.8

Q ss_pred             CcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCC-------------------CCeEEEE
Q 042806          152 DYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKL-------------------FDQVIFV  211 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~-------------------f~~~~wv  211 (390)
                      ....++|.+..+..|..++..++. ..+.++|+.|+||||+|+.+.........                   |...+++
T Consensus        14 ~f~divGq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~ei   93 (527)
T PRK14969         14 SFSELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLIEV   93 (527)
T ss_pred             cHHHhcCcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceeEe
Confidence            345788999999999999887665 45789999999999999999887632110                   1112222


Q ss_pred             EeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEe
Q 042806          212 EVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTA  289 (390)
Q Consensus       212 ~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTt  289 (390)
                      ..+......+ ++.+........                ..+++-++|+|+++...  ..+.+...+-.-...+.+|++|
T Consensus        94 ~~~~~~~vd~-ir~l~~~~~~~p----------------~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t  156 (527)
T PRK14969         94 DAASNTQVDA-MRELLDNAQYAP----------------TRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILAT  156 (527)
T ss_pred             eccccCCHHH-HHHHHHHHhhCc----------------ccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEe
Confidence            2221111111 112222111100                01334699999997553  3444444443333456666655


Q ss_pred             cc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH-HHHHH
Q 042806          290 RS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV-SIVTV  353 (390)
Q Consensus       290 r~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL-ai~~l  353 (390)
                      .+ ..+......-...+++++++.++..+.+.+.+....... .+.....|++.++|.+- ++..+
T Consensus       157 ~d~~kil~tI~SRc~~~~f~~l~~~~i~~~L~~il~~egi~~-~~~al~~la~~s~Gslr~al~ll  221 (527)
T PRK14969        157 TDPQKIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQENIPF-DATALQLLARAAAGSMRDALSLL  221 (527)
T ss_pred             CChhhCchhHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHH
Confidence            44 333211122236899999999999988888764221212 23456789999999775 44444

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=98.60  E-value=1.4e-06  Score=90.76  Aligned_cols=177  Identities=14%  Similarity=0.119  Sum_probs=108.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC---------------------eEEE
Q 042806          153 YEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFD---------------------QVIF  210 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~---------------------~~~w  210 (390)
                      ...++|.+..++.|..++..++. ..+.++|+.|+||||+|+.+.+.+.-.....                     .+++
T Consensus        14 f~eiiGqe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~~~~dv~e   93 (824)
T PRK07764         14 FAEVIGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGPGSLDVTE   93 (824)
T ss_pred             HHHhcCcHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCCCCCcEEE
Confidence            45789999999999999987665 4688999999999999999988874211110                     0112


Q ss_pred             EEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHH----hCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcE
Q 042806          211 VEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRL----KKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCK  284 (390)
Q Consensus       211 v~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l----~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~  284 (390)
                      +.......++                     .+..+.+.+    ..++.-++|||+++..  ..++.|...+-.-...+.
T Consensus        94 idaas~~~Vd---------------------~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~  152 (824)
T PRK07764         94 IDAASHGGVD---------------------DARELRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLK  152 (824)
T ss_pred             ecccccCCHH---------------------HHHHHHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeE
Confidence            2111111111                     122222221    1123358899999755  344555545544345566


Q ss_pred             EEEEecc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHH
Q 042806          285 VLLTARS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIV  351 (390)
Q Consensus       285 IivTtr~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~  351 (390)
                      +|++|.+ ..+......-...|++.+++.++..+++.+.+....... ..+....|++.++|.+..+.
T Consensus       153 fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~EGv~i-d~eal~lLa~~sgGdlR~Al  219 (824)
T PRK07764        153 FIFATTEPDKVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQEGVPV-EPGVLPLVIRAGGGSVRDSL  219 (824)
T ss_pred             EEEEeCChhhhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHH
Confidence            6655543 444333344457899999999999988888764222212 23456789999999884443

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.59  E-value=1.1e-06  Score=86.13  Aligned_cols=168  Identities=14%  Similarity=0.074  Sum_probs=105.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      ..+.|+|+.|+|||+|++.+.+.......-..++++      +..++...+...++...      .....+.+.+..-  
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv------~~~~f~~~~~~~l~~~~------~~~~~~~~~~~~~--  207 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYM------SGDEFARKAVDILQKTH------KEIEQFKNEICQN--  207 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEE------EHHHHHHHHHHHHHHhh------hHHHHHHHHhccC--
Confidence            458899999999999999999976543212234443      34567777766664210      2233444444432  


Q ss_pred             EEEEEeCCCCCc---cc-ccccCCCCC-CCCCcEEEEEecch--hhh------hhcCCCcceEecCCCCHHHHHHHHHHh
Q 042806          256 ILVILDNIWGNL---DF-QAVGIPHGD-DRKGCKVLLTARSL--DVL------SRKMDSQQNFSVGVLKEDEAWSLFKKM  322 (390)
Q Consensus       256 ~LlVlDdv~~~~---~~-~~l~~~l~~-~~~~s~IivTtr~~--~v~------~~~~~~~~~~~l~~L~~~ea~~lf~~~  322 (390)
                      -+||+||+....   .+ +.+...+.. ...+..||+|+...  ...      ...+..+-.+.+++++.++-.+++.+.
T Consensus       208 dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~~  287 (450)
T PRK14087        208 DVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKKE  287 (450)
T ss_pred             CEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHHHH
Confidence            489999997542   12 223222211 12345688887632  110      113445678899999999999999998


Q ss_pred             hCCCCC-CCchHHHHHHHHHHcCCChHHHHHHHHHh
Q 042806          323 AGDYIE-GSEFKWVAKDVARECAGLPVSIVTVARAL  357 (390)
Q Consensus       323 ~~~~~~-~~~~~~~~~~i~~~~~GlPLai~~l~~~L  357 (390)
                      +..... ..-.+++...|++.++|.|-.+.-+..-+
T Consensus       288 ~~~~gl~~~l~~evl~~Ia~~~~gd~R~L~gaL~~l  323 (450)
T PRK14087        288 IKNQNIKQEVTEEAINFISNYYSDDVRKIKGSVSRL  323 (450)
T ss_pred             HHhcCCCCCCCHHHHHHHHHccCCCHHHHHHHHHHH
Confidence            852211 12235688999999999998887765333

>PRK05642 DNA replication initiation factor; Validated

Probab=98.59  E-value=1.3e-06  Score=78.23  Aligned_cols=155  Identities=13%  Similarity=0.153  Sum_probs=95.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      ...+.|+|+.|+|||+|++.+++....+  -..++|++..      ++...                 ...+.+.+.+-.
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~~~--~~~v~y~~~~------~~~~~-----------------~~~~~~~~~~~d   99 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFEQR--GEPAVYLPLA------ELLDR-----------------GPELLDNLEQYE   99 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhC--CCcEEEeeHH------HHHhh-----------------hHHHHHhhhhCC
Confidence            3578899999999999999999876543  2345666543      22211                 012334444333


Q ss_pred             eEEEEEeCCCCC---ccccc-ccCCCCC-CCCCcEEEEEecchhhhh--------hcCCCcceEecCCCCHHHHHHHHHH
Q 042806          255 TILVILDNIWGN---LDFQA-VGIPHGD-DRKGCKVLLTARSLDVLS--------RKMDSQQNFSVGVLKEDEAWSLFKK  321 (390)
Q Consensus       255 ~~LlVlDdv~~~---~~~~~-l~~~l~~-~~~~s~IivTtr~~~v~~--------~~~~~~~~~~l~~L~~~ea~~lf~~  321 (390)
                        +|++||+...   ..|+. +...+.. ...|..+|+|++......        .....+..+++++++.++-.++++.
T Consensus       100 --~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~  177 (234)
T PRK05642        100 --LVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQL  177 (234)
T ss_pred             --EEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHH
Confidence              7889999633   34433 3332211 234567888887422110        1223456899999999999999986


Q ss_pred             hhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHh
Q 042806          322 MAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARAL  357 (390)
Q Consensus       322 ~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L  357 (390)
                      .+...... --+++...|++.+.|-.-.+..+-..|
T Consensus       178 ka~~~~~~-l~~ev~~~L~~~~~~d~r~l~~~l~~l  212 (234)
T PRK05642        178 RASRRGLH-LTDEVGHFILTRGTRSMSALFDLLERL  212 (234)
T ss_pred             HHHHcCCC-CCHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence            66422111 125688899999998877666655444

>PF14516 AAA_35: AAA-like domain

Probab=98.58  E-value=5.7e-06  Score=78.02  Aligned_cols=200  Identities=12%  Similarity=0.134  Sum_probs=120.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-----CCHHHHHHH--
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-----QDIRKIQGE--  225 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-----~~~~~l~~~--  225 (390)
                      .+.++.|...-.++.+.+.++ ...+.|.|+..+|||||...+.+..... .|. .+++++...     .+.+.+++.  
T Consensus        10 ~~~Yi~R~~~e~~~~~~i~~~-G~~~~I~apRq~GKTSll~~l~~~l~~~-~~~-~v~id~~~~~~~~~~~~~~f~~~~~   86 (331)
T PF14516_consen   10 SPFYIERPPAEQECYQEIVQP-GSYIRIKAPRQMGKTSLLLRLLERLQQQ-GYR-CVYIDLQQLGSAIFSDLEQFLRWFC   86 (331)
T ss_pred             CCcccCchHHHHHHHHHHhcC-CCEEEEECcccCCHHHHHHHHHHHHHHC-CCE-EEEEEeecCCCcccCCHHHHHHHHH
Confidence            456789986667777777653 4688999999999999999999988764 354 457777542     245555544  


Q ss_pred             --HHHHhCCCCCCC--------CchHHHHHHHHHH-h-CCCeEEEEEeCCCCCccc----ccccCCCC----C---C-CC
Q 042806          226 --IADKLGLTLHEE--------SDSGRARSLRNRL-K-KEKTILVILDNIWGNLDF----QAVGIPHG----D---D-RK  281 (390)
Q Consensus       226 --i~~~l~~~~~~~--------~~~~~~~~l~~~l-~-~~~~~LlVlDdv~~~~~~----~~l~~~l~----~---~-~~  281 (390)
                        +.++++....-.        +......-+.+.+ . ..++.+|+||+++.....    +++...+.    .   . ..
T Consensus        87 ~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~~  166 (331)
T PF14516_consen   87 EEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPIW  166 (331)
T ss_pred             HHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCccc
Confidence              455555432110        1122222333333 2 246699999999744221    11111000    0   0 01


Q ss_pred             Cc-EEEEEecc-hhh----hhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHH
Q 042806          282 GC-KVLLTARS-LDV----LSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVAR  355 (390)
Q Consensus       282 ~s-~IivTtr~-~~v----~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~  355 (390)
                      .. ++++.... ...    ....+..+..++|.+|+.+|...|+..+-..    .. ....+.|...+||+|.-+..++.
T Consensus       167 ~~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~----~~-~~~~~~l~~~tgGhP~Lv~~~~~  241 (331)
T PF14516_consen  167 QKLRLILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRYGLE----FS-QEQLEQLMDWTGGHPYLVQKACY  241 (331)
T ss_pred             ceEEEEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhhhcc----CC-HHHHHHHHHHHCCCHHHHHHHHH
Confidence            11 22222211 111    1113344568999999999999998876422    11 22378999999999999999999


Q ss_pred             HhcCC
Q 042806          356 ALGTR  360 (390)
Q Consensus       356 ~L~~~  360 (390)
                      .+..+
T Consensus       242 ~l~~~  246 (331)
T PF14516_consen  242 LLVEE  246 (331)
T ss_pred             HHHHc
Confidence            99764

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.57  E-value=8.3e-07  Score=84.99  Aligned_cols=173  Identities=18%  Similarity=0.228  Sum_probs=101.3

Q ss_pred             cccccchhHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALKN-------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ...+.|++..+++|.+.+..             ..++-+.|+|++|+|||++|+.+++.....  |     +.+..    
T Consensus       121 ~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~~--~-----~~v~~----  189 (364)
T TIGR01242       121 YEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNAT--F-----IRVVG----  189 (364)
T ss_pred             HHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCCC--E-----Eecch----
Confidence            45688999988888876532             124568899999999999999999977532  2     22221    


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc----------------ccccccCCCC--CCCC
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL----------------DFQAVGIPHG--DDRK  281 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~----------------~~~~l~~~l~--~~~~  281 (390)
                      .++....   ++      ........+.+......+.+|+||+++...                .+..+...+.  ....
T Consensus       190 ~~l~~~~---~g------~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~  260 (364)
T TIGR01242       190 SELVRKY---IG------EGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRG  260 (364)
T ss_pred             HHHHHHh---hh------HHHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCCCC
Confidence            1121110   11      111223344444444556899999996431                0111111111  1234


Q ss_pred             CcEEEEEecchhhhh-hcC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh
Q 042806          282 GCKVLLTARSLDVLS-RKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       282 ~s~IivTtr~~~v~~-~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      +..||.||....... ...   .....+++...+.++..++|+.++.......+.  -...+++.+.|..
T Consensus       261 ~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~--~~~~la~~t~g~s  328 (364)
T TIGR01242       261 NVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDV--DLEAIAKMTEGAS  328 (364)
T ss_pred             CEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccC--CHHHHHHHcCCCC
Confidence            677888887543211 111   224578999999999999999887532222211  1357888887765

Many proteins may score above the trusted cutoff because an internal

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.57  E-value=1.6e-06  Score=86.85  Aligned_cols=198  Identities=14%  Similarity=0.107  Sum_probs=111.1

Q ss_pred             cccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 042806          153 YEACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLG  231 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~  231 (390)
                      ...++|.+..+..|...+..++ ...+.++|+.|+||||+|+.+.+...-....+..       .+..=...+.+...-.
T Consensus        15 f~dIiGQe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~-------pCg~C~sC~~i~~g~h   87 (624)
T PRK14959         15 FAEVAGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGE-------PCNTCEQCRKVTQGMH   87 (624)
T ss_pred             HHHhcCCHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCC-------CCcccHHHHHHhcCCC
Confidence            4567888888888888887766 5778899999999999999999887432111000       0000001111110000


Q ss_pred             CCC-----CCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecc-hhhhhhcC
Q 042806          232 LTL-----HEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARS-LDVLSRKM  299 (390)
Q Consensus       232 ~~~-----~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~-~~v~~~~~  299 (390)
                      .+.     ........+..+.+.+.    .+++-++|+|+++..  ...+.|...+..-.....+|++|.. ..+.....
T Consensus        88 pDv~eId~a~~~~Id~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll~TI~  167 (624)
T PRK14959         88 VDVVEIDGASNRGIDDAKRLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIV  167 (624)
T ss_pred             CceEEEecccccCHHHHHHHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhhHHHH
Confidence            000     00000111222222221    223369999999755  3344454444222334556665544 44432222


Q ss_pred             CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh-HHHHHHHHHhc
Q 042806          300 DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP-VSIVTVARALG  358 (390)
Q Consensus       300 ~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP-Lai~~l~~~L~  358 (390)
                      .-...+++++++.++....+...+....... .++.+..|++.++|.+ .|+..+..++.
T Consensus       168 SRcq~i~F~pLs~~eL~~~L~~il~~egi~i-d~eal~lIA~~s~GdlR~Al~lLeqll~  226 (624)
T PRK14959        168 SRCQHFTFTRLSEAGLEAHLTKVLGREGVDY-DPAAVRLIARRAAGSVRDSMSLLGQVLA  226 (624)
T ss_pred             hhhhccccCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            3345889999999999999988765222111 2446778999999954 67777765553

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

Probab=98.56  E-value=9.2e-07  Score=81.00  Aligned_cols=173  Identities=15%  Similarity=0.147  Sum_probs=105.4

Q ss_pred             cccchhHHH---HHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 042806          155 ACESRMSTL---NDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLG  231 (390)
Q Consensus       155 ~~~gR~~~~---~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~  231 (390)
                      ++||.+..+   ..|...+..+..+.+.+||++|+||||||+.+.+..+...    ..||..|....-..-++.|+.+-.
T Consensus       139 dyvGQ~hlv~q~gllrs~ieq~~ipSmIlWGppG~GKTtlArlia~tsk~~S----yrfvelSAt~a~t~dvR~ife~aq  214 (554)
T KOG2028|consen  139 DYVGQSHLVGQDGLLRSLIEQNRIPSMILWGPPGTGKTTLARLIASTSKKHS----YRFVELSATNAKTNDVRDIFEQAQ  214 (554)
T ss_pred             HhcchhhhcCcchHHHHHHHcCCCCceEEecCCCCchHHHHHHHHhhcCCCc----eEEEEEeccccchHHHHHHHHHHH
Confidence            455544332   2334445567788888999999999999999999876542    567777765433222333332211


Q ss_pred             CCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC-cccccccCCCCCCCCCcEEEE--Eecchhhh--hhcCCCcceEe
Q 042806          232 LTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN-LDFQAVGIPHGDDRKGCKVLL--TARSLDVL--SRKMDSQQNFS  306 (390)
Q Consensus       232 ~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~-~~~~~l~~~l~~~~~~s~Iiv--Ttr~~~v~--~~~~~~~~~~~  306 (390)
                                     ......+|+-+|.+|.|+.. ...+++  .+|...+|.-++|  ||.+.+.-  .....-..++-
T Consensus       215 ---------------~~~~l~krkTilFiDEiHRFNksQQD~--fLP~VE~G~I~lIGATTENPSFqln~aLlSRC~Vfv  277 (554)
T KOG2028|consen  215 ---------------NEKSLTKRKTILFIDEIHRFNKSQQDT--FLPHVENGDITLIGATTENPSFQLNAALLSRCRVFV  277 (554)
T ss_pred             ---------------HHHhhhcceeEEEeHHhhhhhhhhhhc--ccceeccCceEEEecccCCCccchhHHHHhccceeE
Confidence                           01112356689999999744 222333  2445667775554  66654331  11234456899


Q ss_pred             cCCCCHHHHHHHHHHhh---C------CCCCCC---chHHHHHHHHHHcCCChH
Q 042806          307 VGVLKEDEAWSLFKKMA---G------DYIEGS---EFKWVAKDVARECAGLPV  348 (390)
Q Consensus       307 l~~L~~~ea~~lf~~~~---~------~~~~~~---~~~~~~~~i~~~~~GlPL  348 (390)
                      |++|..++-..++.+..   +      ...+.+   -...+.+.++..|+|-.-
T Consensus       278 LekL~~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyla~lsdGDaR  331 (554)
T KOG2028|consen  278 LEKLPVNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDGDAR  331 (554)
T ss_pred             eccCCHHHHHHHHHHHHHhhccccccCCCCCCcchhhhHHHHHHHHHhcCchHH
Confidence            99999999999998733   1      112221   224578888999988654

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.55  E-value=3.6e-06  Score=85.37  Aligned_cols=197  Identities=14%  Similarity=0.120  Sum_probs=112.3

Q ss_pred             cccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 042806          153 YEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLG  231 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~  231 (390)
                      ...++|.+..++.|..++..++. ..+.++|+.|+||||+|+.+.+.........  -    ...+..-...+.+....+
T Consensus        15 ~~eiiGq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~--~----~~~c~~c~~c~~i~~~~~   88 (585)
T PRK14950         15 FAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDP--K----GRPCGTCEMCRAIAEGSA   88 (585)
T ss_pred             HHHhcCCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCC--C----CCCCccCHHHHHHhcCCC
Confidence            45789999999999888887654 5678999999999999999998764211100  0    001111122223322111


Q ss_pred             CCC-----CCCCchHHHHHHHHHHhC----CCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecc-hhhhhhcC
Q 042806          232 LTL-----HEESDSGRARSLRNRLKK----EKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARS-LDVLSRKM  299 (390)
Q Consensus       232 ~~~-----~~~~~~~~~~~l~~~l~~----~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~-~~v~~~~~  299 (390)
                      .+.     ......+.+..+.+.+..    .++-++|+|+++..  ...+.|...+......+.+|+++.+ ..+.....
T Consensus        89 ~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll~tI~  168 (585)
T PRK14950         89 VDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATIL  168 (585)
T ss_pred             CeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhhHHHH
Confidence            110     000111122233332221    23369999999754  3344454444333345666666543 33322222


Q ss_pred             CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHH
Q 042806          300 DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARA  356 (390)
Q Consensus       300 ~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~  356 (390)
                      .-...+++.+++.++....+...+.......+ ++.+..|++.++|.+..+...-..
T Consensus       169 SR~~~i~f~~l~~~el~~~L~~~a~~egl~i~-~eal~~La~~s~Gdlr~al~~Lek  224 (585)
T PRK14950        169 SRCQRFDFHRHSVADMAAHLRKIAAAEGINLE-PGALEAIARAATGSMRDAENLLQQ  224 (585)
T ss_pred             hccceeeCCCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHHHHHH
Confidence            33468889999999998888887752222121 356789999999999765554433

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=98.55  E-value=2.5e-06  Score=85.95  Aligned_cols=198  Identities=13%  Similarity=0.096  Sum_probs=113.2

Q ss_pred             CcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC--eEEEEEeCCCCCHHHHHHHHHH
Q 042806          152 DYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFD--QVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~--~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      ....++|.+..++.|.+++..++. ..+.++|+.|+||||+|+.+.+.........  ...+-.+..+    .-.+.|..
T Consensus        22 ~f~dliGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~c----~~C~~i~~   97 (598)
T PRK09111         22 TFDDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGVG----EHCQAIME   97 (598)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCccc----HHHHHHhc
Confidence            356789999999999999987764 4688999999999999999998764321110  0000001111    01111111


Q ss_pred             HhCCC-----CCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEe-cchhhhh
Q 042806          229 KLGLT-----LHEESDSGRARSLRNRLK----KEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTA-RSLDVLS  296 (390)
Q Consensus       229 ~l~~~-----~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTt-r~~~v~~  296 (390)
                      .-..+     .......+.+..+.+.+.    ..++-++|+|+++...  ..+.+...+-.-.+++.+|++| ....+..
T Consensus        98 g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kll~  177 (598)
T PRK09111         98 GRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKVPV  177 (598)
T ss_pred             CCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhhhH
Confidence            11000     000011112233333332    1233589999997553  3444444443334456666555 3344433


Q ss_pred             hcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          297 RKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       297 ~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      ....-...+++.+++.++....+.+.+....... .++....|++.++|.+.-+....
T Consensus       178 tI~SRcq~~~f~~l~~~el~~~L~~i~~kegi~i-~~eAl~lIa~~a~Gdlr~al~~L  234 (598)
T PRK09111        178 TVLSRCQRFDLRRIEADVLAAHLSRIAAKEGVEV-EDEALALIARAAEGSVRDGLSLL  234 (598)
T ss_pred             HHHhheeEEEecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHH
Confidence            2233446899999999999999988774222111 13567889999999997766554

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.52  E-value=3.4e-07  Score=86.01  Aligned_cols=90  Identities=17%  Similarity=0.172  Sum_probs=61.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC--CHHHHHHHHHHHhCCCCCCCCchHH------HHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ--DIRKIQGEIADKLGLTLHEESDSGR------ARS  245 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~--~~~~l~~~i~~~l~~~~~~~~~~~~------~~~  245 (390)
                      ...-..|+|++|+|||||++.+++..... +|++.+||.+.+..  ...++++.+...+-....+.+....      +..
T Consensus       168 kGQR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~ie  246 (416)
T PRK09376        168 KGQRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVIE  246 (416)
T ss_pred             cCceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHHH
Confidence            44567899999999999999999998765 89999999998887  6777777776322212122221111      112


Q ss_pred             HHHHH-hCCCeEEEEEeCCC
Q 042806          246 LRNRL-KKEKTILVILDNIW  264 (390)
Q Consensus       246 l~~~l-~~~~~~LlVlDdv~  264 (390)
                      ..+++ ..++.+||++|++.
T Consensus       247 ~Ae~~~e~G~dVlL~iDsIt  266 (416)
T PRK09376        247 KAKRLVEHGKDVVILLDSIT  266 (416)
T ss_pred             HHHHHHHcCCCEEEEEEChH
Confidence            22222 34566999999996

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.51  E-value=4.7e-06  Score=83.59  Aligned_cols=199  Identities=15%  Similarity=0.116  Sum_probs=111.0

Q ss_pred             CcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          152 DYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ....++|.+..++.|..++..++. ..+.++|+.|+||||+|+.+.....-....+   +-.++.+.    ..+.+...-
T Consensus        11 ~f~eivGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~---~~pCg~C~----~C~~i~~~~   83 (584)
T PRK14952         11 TFAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPT---ATPCGVCE----SCVALAPNG   83 (584)
T ss_pred             cHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCC---CCcccccH----HHHHhhccc
Confidence            355789999999999999988764 4578999999999999999998764211110   00001000    011110000


Q ss_pred             C-------CCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEe-cchhhhh
Q 042806          231 G-------LTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTA-RSLDVLS  296 (390)
Q Consensus       231 ~-------~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTt-r~~~v~~  296 (390)
                      +       .+.......+.+..+.+.+.    ..+.-++|+|+++..  ...+.|...+..-...+.+|++| ....+..
T Consensus        84 ~~~~dvieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll~  163 (584)
T PRK14952         84 PGSIDVVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLP  163 (584)
T ss_pred             CCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhHH
Confidence            0       00000001111222222221    123358999999754  34555544443334455555544 4444433


Q ss_pred             hcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH-HHHHHHHHhc
Q 042806          297 RKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV-SIVTVARALG  358 (390)
Q Consensus       297 ~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL-ai~~l~~~L~  358 (390)
                      ....-...+++.+++.++..+.+.+.+.......+ ++....|++.++|-+- ++..+-.++.
T Consensus       164 TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi~i~-~~al~~Ia~~s~GdlR~aln~Ldql~~  225 (584)
T PRK14952        164 TIRSRTHHYPFRLLPPRTMRALIARICEQEGVVVD-DAVYPLVIRAGGGSPRDTLSVLDQLLA  225 (584)
T ss_pred             HHHHhceEEEeeCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            23333568999999999999888887652222121 3456788999999774 5555444443

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.50  E-value=7.1e-06  Score=80.98  Aligned_cols=180  Identities=16%  Similarity=0.132  Sum_probs=106.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcC-------------------CCCeEEEEE
Q 042806          153 YEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEK-------------------LFDQVIFVE  212 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~-------------------~f~~~~wv~  212 (390)
                      ...++|.+..+..|.+++..++. +.+.++|+.|+||||+|+.++.......                   .|....++.
T Consensus        15 f~diiGq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~~~d~~eid   94 (486)
T PRK14953         15 FKEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFPDLIEID   94 (486)
T ss_pred             HHHccChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCCCCcEEEEe
Confidence            45688999999999999987664 4567899999999999999988753110                   011112221


Q ss_pred             eCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEE
Q 042806          213 VSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVL  286 (390)
Q Consensus       213 v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~Ii  286 (390)
                      .+.....                     ..+..+.+.+.    .+++-++|+|+++..  ...+.+...+..-.+...+|
T Consensus        95 aas~~gv---------------------d~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v~I  153 (486)
T PRK14953         95 AASNRGI---------------------DDIRALRDAVSYTPIKGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFI  153 (486)
T ss_pred             CccCCCH---------------------HHHHHHHHHHHhCcccCCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEE
Confidence            1111111                     11222332221    123369999999754  23444443343333345555


Q ss_pred             EEe-cchhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          287 LTA-RSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       287 vTt-r~~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      ++| +...+..........+++.+++.++....+...+....... ..+.+..|++.++|.+..+..+.
T Consensus       154 l~tt~~~kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi~i-d~~al~~La~~s~G~lr~al~~L  221 (486)
T PRK14953        154 LCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIEY-EEKALDLLAQASEGGMRDAASLL  221 (486)
T ss_pred             EEECCHHHHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHH
Confidence            555 33333222222345899999999999988888764222111 23456789999999776555554

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=98.50  E-value=1.8e-06  Score=83.21  Aligned_cols=173  Identities=17%  Similarity=0.254  Sum_probs=100.0

Q ss_pred             cccccchhHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALKN-------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ...+.|++..++++.+.+..             ..++-|.++|++|+|||++|+.+++.....       |+.++.    
T Consensus       130 ~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~~~-------~i~v~~----  198 (389)
T PRK03992        130 YEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNAT-------FIRVVG----  198 (389)
T ss_pred             HHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhCCC-------EEEeeh----
Confidence            45688999888888776531             235668899999999999999999876421       222221    


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc------------c-cccccC---CCC--CCCC
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL------------D-FQAVGI---PHG--DDRK  281 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~------------~-~~~l~~---~l~--~~~~  281 (390)
                      .++....   .+      .....+..+.+......+.+|+||+++...            . ...+..   .+.  ....
T Consensus       199 ~~l~~~~---~g------~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~  269 (389)
T PRK03992        199 SELVQKF---IG------EGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRG  269 (389)
T ss_pred             HHHhHhh---cc------chHHHHHHHHHHHHhcCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCCCC
Confidence            1221110   01      112233444444444556899999997431            0 011111   111  1123


Q ss_pred             CcEEEEEecchhhhhh-cC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh
Q 042806          282 GCKVLLTARSLDVLSR-KM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       282 ~s~IivTtr~~~v~~~-~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      +..||.||........ ..   .....+++.+.+.++-.++|+.++.......+.  ....+++.+.|.-
T Consensus       270 ~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~--~~~~la~~t~g~s  337 (389)
T PRK03992        270 NVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDV--DLEELAELTEGAS  337 (389)
T ss_pred             CEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCcC--CHHHHHHHcCCCC
Confidence            5677777775432211 11   123579999999999999999887532222211  1346777777654

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.48  E-value=2e-06  Score=80.75  Aligned_cols=176  Identities=17%  Similarity=0.133  Sum_probs=96.6

Q ss_pred             ccCcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          150 IKDYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       150 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      |.....++|.+...+.+..++..++. .++.++|++|+||||+++.+++.....     ..+++.+. .... ..+..+.
T Consensus        17 P~~~~~~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~~~~-----~~~i~~~~-~~~~-~i~~~l~   89 (316)
T PHA02544         17 PSTIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAE-----VLFVNGSD-CRID-FVRNRLT   89 (316)
T ss_pred             CCcHHHhcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHhCcc-----ceEeccCc-ccHH-HHHHHHH
Confidence            34456789999999999999887654 567779999999999999998876321     23444443 2221 1111111


Q ss_pred             HhCCCCCCCCchHHHHHHHHHHh-CCCeEEEEEeCCCCC--ccc-ccccCCCCCCCCCcEEEEEecchhh-hhhcCCCcc
Q 042806          229 KLGLTLHEESDSGRARSLRNRLK-KEKTILVILDNIWGN--LDF-QAVGIPHGDDRKGCKVLLTARSLDV-LSRKMDSQQ  303 (390)
Q Consensus       229 ~l~~~~~~~~~~~~~~~l~~~l~-~~~~~LlVlDdv~~~--~~~-~~l~~~l~~~~~~s~IivTtr~~~v-~~~~~~~~~  303 (390)
                      .+                ..... .+.+-++|+|+++..  ... ..+...+.....++++|+||..... .........
T Consensus        90 ~~----------------~~~~~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~~~l~sR~~  153 (316)
T PHA02544         90 RF----------------ASTVSLTGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCR  153 (316)
T ss_pred             HH----------------HHhhcccCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhchHHHHhhce
Confidence            11                00000 012368999999754  111 2232223223456788888875321 111122234


Q ss_pred             eEecCCCCHHHHHHHHHHhhC------CCCCCCchHHHHHHHHHHcCCChH
Q 042806          304 NFSVGVLKEDEAWSLFKKMAG------DYIEGSEFKWVAKDVARECAGLPV  348 (390)
Q Consensus       304 ~~~l~~L~~~ea~~lf~~~~~------~~~~~~~~~~~~~~i~~~~~GlPL  348 (390)
                      .+.+...+.++..+++.....      .....+-.++....+++..+|---
T Consensus       154 ~i~~~~p~~~~~~~il~~~~~~~~~~~~~~~~~i~~~al~~l~~~~~~d~r  204 (316)
T PHA02544        154 VIDFGVPTKEEQIEMMKQMIVRCKGILEAEGVEVDMKVLAALVKKNFPDFR  204 (316)
T ss_pred             EEEeCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhcCCCHH
Confidence            677878888887766543221      011111123345667776665433

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=98.48  E-value=7.2e-06  Score=81.16  Aligned_cols=185  Identities=16%  Similarity=0.131  Sum_probs=109.1

Q ss_pred             CcccccchhHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcCCCC-------------------eEEEE
Q 042806          152 DYEACESRMSTLNDILDALKNPDVN-MLGIYGMGGIVKTTLAKEVARKAETEKLFD-------------------QVIFV  211 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~-------------------~~~wv  211 (390)
                      ....++|-+.....|...+..++.+ ++.++|+.|+||||+|+.+.+..-.....+                   ..+.+
T Consensus        12 ~fdeiiGqe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv~el   91 (535)
T PRK08451         12 HFDELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDIIEM   91 (535)
T ss_pred             CHHHccCcHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeEEEe
Confidence            3557899888889999988877654 678999999999999999988763211110                   11122


Q ss_pred             EeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEe
Q 042806          212 EVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTA  289 (390)
Q Consensus       212 ~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTt  289 (390)
                      ..+......++. ++.......+                ..++.-++|+|+++..  ...+.+...+-.-.+.+++|++|
T Consensus        92 daas~~gId~IR-elie~~~~~P----------------~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~t  154 (535)
T PRK08451         92 DAASNRGIDDIR-ELIEQTKYKP----------------SMARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILAT  154 (535)
T ss_pred             ccccccCHHHHH-HHHHHHhhCc----------------ccCCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEEE
Confidence            111111121111 1111110000                0123359999999755  33444443443334456666666


Q ss_pred             cch-hhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          290 RSL-DVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       290 r~~-~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      .+. .+......-...+++.+++.++....+.+.+....... .++.+..|++.++|.+--+..+.
T Consensus       155 td~~kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi~i-~~~Al~~Ia~~s~GdlR~alnlL  219 (535)
T PRK08451        155 TDPLKLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGVSY-EPEALEILARSGNGSLRDTLTLL  219 (535)
T ss_pred             CChhhCchHHHhhceeEEcCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCcHHHHHHHH
Confidence            552 32222223346999999999999999888775222222 24567889999999986555543

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.47  E-value=2.1e-06  Score=90.36  Aligned_cols=179  Identities=12%  Similarity=0.099  Sum_probs=99.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCC----CCeEEE-EEeCCCCCHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKL----FDQVIF-VEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~----f~~~~w-v~v~~~~~~~~l~~~i~  227 (390)
                      .++++||+.++.++++.|......-+.++|++|+||||+|+.+++.......    .+..+| +..+.-..         
T Consensus       186 ld~~iGr~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l~a---------  256 (852)
T TIGR03345       186 IDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQA---------  256 (852)
T ss_pred             CCcccCCHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEeehhhhhc---------
Confidence            5689999999999999988776667779999999999999999998643211    122222 22221000         


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHh-CCCeEEEEEeCCCCCc------cccc---ccCCCCCCCCCcEEEEEecchhhhh-
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLK-KEKTILVILDNIWGNL------DFQA---VGIPHGDDRKGCKVLLTARSLDVLS-  296 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~-~~~~~LlVlDdv~~~~------~~~~---l~~~l~~~~~~s~IivTtr~~~v~~-  296 (390)
                          .......-...+..+.+.+. .+.+.+|++|+++...      .-.+   +..+... ....++|-||....... 
T Consensus       257 ----g~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~-~G~l~~IgaTT~~e~~~~  331 (852)
T TIGR03345       257 ----GASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAGQGDAANLLKPALA-RGELRTIAATTWAEYKKY  331 (852)
T ss_pred             ----ccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCccccccHHHHhhHHhh-CCCeEEEEecCHHHHhhh
Confidence                00000001112223333332 2345999999997542      1111   2222212 22356666666532210 


Q ss_pred             -----hcCCCcceEecCCCCHHHHHHHHHHhhC---CCCCCCchHHHHHHHHHHcCC
Q 042806          297 -----RKMDSQQNFSVGVLKEDEAWSLFKKMAG---DYIEGSEFKWVAKDVARECAG  345 (390)
Q Consensus       297 -----~~~~~~~~~~l~~L~~~ea~~lf~~~~~---~~~~~~~~~~~~~~i~~~~~G  345 (390)
                           ....-...+.+.+++.++..++++....   ....-.-.++....+++.+.+
T Consensus       332 ~~~d~AL~rRf~~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~r  388 (852)
T TIGR03345       332 FEKDPALTRRFQVVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHR  388 (852)
T ss_pred             hhccHHHHHhCeEEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHccc
Confidence                 0111235899999999999999765442   111111123455566666654

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.

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

Probab=98.46  E-value=1.8e-06  Score=89.93  Aligned_cols=157  Identities=16%  Similarity=0.190  Sum_probs=91.3

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCC---C-CeEEEEEeCCCCCHHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKL---F-DQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~---f-~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      .++++||+.++..+++.|......-+.++|++|+|||++++.+++.......   + +..+|. +    +...+...   
T Consensus       181 l~~~igr~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~-~----~~~~l~a~---  252 (731)
T TIGR02639       181 IDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYS-L----DMGSLLAG---  252 (731)
T ss_pred             CCcccCcHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEE-e----cHHHHhhh---
Confidence            4689999999999999988766666789999999999999999998743221   1 233331 1    11111110   


Q ss_pred             HhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc----------cccc-ccCCCCCCCCCcEEEEEecchhhh--
Q 042806          229 KLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL----------DFQA-VGIPHGDDRKGCKVLLTARSLDVL--  295 (390)
Q Consensus       229 ~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~----------~~~~-l~~~l~~~~~~s~IivTtr~~~v~--  295 (390)
                          ..........+..+.+.+....+.+|++|+++...          +... +...+ . ....++|-+|...+..  
T Consensus       253 ----~~~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l-~-~g~i~~IgaTt~~e~~~~  326 (731)
T TIGR02639       253 ----TKYRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGATSGGSMDASNLLKPAL-S-SGKLRCIGSTTYEEYKNH  326 (731)
T ss_pred             ----ccccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHH-h-CCCeEEEEecCHHHHHHH
Confidence                00000112233444444443345899999997331          1112 22222 2 2234555555532210  


Q ss_pred             ----hhcCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          296 ----SRKMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       296 ----~~~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                          .....-...+++.+++.++..++++...
T Consensus       327 ~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~  358 (731)
T TIGR02639       327 FEKDRALSRRFQKIDVGEPSIEETVKILKGLK  358 (731)
T ss_pred             hhhhHHHHHhCceEEeCCCCHHHHHHHHHHHH
Confidence                0011122479999999999999998655

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.44  E-value=7.5e-06  Score=82.75  Aligned_cols=197  Identities=14%  Similarity=0.149  Sum_probs=108.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEE-----EeCCCCCHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFV-----EVSKIQDIRKIQGEI  226 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv-----~v~~~~~~~~l~~~i  226 (390)
                      ...++|.+..+..|..++..++. ..+.++|+.|+||||+|+.+.+...-....+...|.     .++.+    ...+.+
T Consensus        15 f~eivGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C----~sC~~~   90 (620)
T PRK14954         15 FADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGEC----ESCRDF   90 (620)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccC----HHHHHH
Confidence            45788999999999998887665 458899999999999999999886432111100111     11111    011111


Q ss_pred             HHHhCCC-----CCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEe-cchhh
Q 042806          227 ADKLGLT-----LHEESDSGRARSLRNRLK----KEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTA-RSLDV  294 (390)
Q Consensus       227 ~~~l~~~-----~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTt-r~~~v  294 (390)
                      ...-..+     .......+.+..+.+.+.    .+++-++|+|+++...  ..+.|...+-.-...+.+|++| +...+
T Consensus        91 ~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~kL  170 (620)
T PRK14954         91 DAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKI  170 (620)
T ss_pred             hccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhh
Confidence            0000000     000011122223333331    1223588999987553  3444444443323345555444 43444


Q ss_pred             hhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH-HHHHHH
Q 042806          295 LSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV-SIVTVA  354 (390)
Q Consensus       295 ~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL-ai~~l~  354 (390)
                      ..........+++.+++.++....+...+....... ..+.+..|++.++|..- ++..+-
T Consensus       171 l~TI~SRc~~vef~~l~~~ei~~~L~~i~~~egi~I-~~eal~~La~~s~Gdlr~al~eLe  230 (620)
T PRK14954        171 PATIASRCQRFNFKRIPLDEIQSQLQMICRAEGIQI-DADALQLIARKAQGSMRDAQSILD  230 (620)
T ss_pred             hHHHHhhceEEecCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHhCCCHHHHHHHHH
Confidence            332334457899999999999888887664211111 13467889999999555 444443

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=98.44  E-value=8.3e-06  Score=83.02  Aligned_cols=187  Identities=17%  Similarity=0.152  Sum_probs=106.1

Q ss_pred             cccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 042806          153 YEACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLG  231 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~  231 (390)
                      ...++|.+..+..|..++..++ .+.+.++|+.|+||||+|+.++...-.....+  .+-.+..+       ..   ..+
T Consensus        17 f~dIiGQe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~--~~~pC~~C-------~~---~~~   84 (725)
T PRK07133         17 FDDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTD--LLEPCQEC-------IE---NVN   84 (725)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCC--CCCchhHH-------HH---hhc
Confidence            4578899998999999998766 45678999999999999999988753211000  00000000       00   000


Q ss_pred             CCCC-------CCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEE-EEecchhhhhh
Q 042806          232 LTLH-------EESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVL-LTARSLDVLSR  297 (390)
Q Consensus       232 ~~~~-------~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~Ii-vTtr~~~v~~~  297 (390)
                      ...+       .......+..+.+.+.    .+++-++|+|+++..  ..+..+...+-.-...+.+| +|+....+...
T Consensus        85 ~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl~T  164 (725)
T PRK07133         85 NSLDIIEMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPLT  164 (725)
T ss_pred             CCCcEEEEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhhHH
Confidence            0000       0000112233333332    133359999999754  34555544332323344444 55444554433


Q ss_pred             cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHH
Q 042806          298 KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVT  352 (390)
Q Consensus       298 ~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~  352 (390)
                      ...-...+++.+++.++....+...+.......+ .+.+..|++.++|-+--+..
T Consensus       165 I~SRcq~ieF~~L~~eeI~~~L~~il~kegI~id-~eAl~~LA~lS~GslR~Als  218 (725)
T PRK07133        165 ILSRVQRFNFRRISEDEIVSRLEFILEKENISYE-KNALKLIAKLSSGSLRDALS  218 (725)
T ss_pred             HHhhceeEEccCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHH
Confidence            3333468999999999999888876642212121 34577899999997654433

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.42  E-value=1.7e-06  Score=78.94  Aligned_cols=135  Identities=17%  Similarity=0.208  Sum_probs=71.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      ...-+.++|++|+||||+|+.+++.....+......++.++.    .++...   ..+      .   ....+.+.+...
T Consensus        41 ~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~----~~l~~~---~~g------~---~~~~~~~~~~~a  104 (261)
T TIGR02881        41 QVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVER----ADLVGE---YIG------H---TAQKTREVIKKA  104 (261)
T ss_pred             CcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecH----HHhhhh---hcc------c---hHHHHHHHHHhc
Confidence            345678999999999999999988753322111122333322    122111   001      0   111222333222


Q ss_pred             CeEEEEEeCCCCCc----------ccccccCCCCCCCCCcEEEEEecchhhh------hh-cCCCcceEecCCCCHHHHH
Q 042806          254 KTILVILDNIWGNL----------DFQAVGIPHGDDRKGCKVLLTARSLDVL------SR-KMDSQQNFSVGVLKEDEAW  316 (390)
Q Consensus       254 ~~~LlVlDdv~~~~----------~~~~l~~~l~~~~~~s~IivTtr~~~v~------~~-~~~~~~~~~l~~L~~~ea~  316 (390)
                      ...+|++|+++...          ..+.+...+........+|+++......      +. .......+++++++.++-.
T Consensus       105 ~~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~vila~~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el~  184 (261)
T TIGR02881       105 LGGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVLILAGYSDEMDYFLSLNPGLRSRFPISIDFPDYTVEELM  184 (261)
T ss_pred             cCCEEEEechhhhccCCccchHHHHHHHHHHHHhccCCCEEEEecCCcchhHHHHhcChHHHhccceEEEECCCCHHHHH
Confidence            23589999997531          2223333332333334566665443220      00 1112347899999999999


Q ss_pred             HHHHHhhC
Q 042806          317 SLFKKMAG  324 (390)
Q Consensus       317 ~lf~~~~~  324 (390)
                      +++.+.+.
T Consensus       185 ~Il~~~~~  192 (261)
T TIGR02881       185 EIAERMVK  192 (261)
T ss_pred             HHHHHHHH
Confidence            99988875

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.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.42  E-value=1.2e-05  Score=81.52  Aligned_cols=182  Identities=13%  Similarity=0.155  Sum_probs=109.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhh---------------------cCCCCeEEE
Q 042806          153 YEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAET---------------------EKLFDQVIF  210 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~---------------------~~~f~~~~w  210 (390)
                      ...++|.+...+.|..++..++. ..+.++|+.|+||||+|+.+......                     ..+|+. ..
T Consensus        16 f~~viGq~~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n~-~~   94 (614)
T PRK14971         16 FESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYNI-HE   94 (614)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCce-EE
Confidence            45789999999999999988765 45889999999999999998887531                     112332 22


Q ss_pred             EEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEE
Q 042806          211 VEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLT  288 (390)
Q Consensus       211 v~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivT  288 (390)
                      +..+......++ +.+...+.....                .+++=++|+|+++..  ..++.+...+..-..++.+|++
T Consensus        95 ld~~~~~~vd~I-r~li~~~~~~P~----------------~~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~tifIL~  157 (614)
T PRK14971         95 LDAASNNSVDDI-RNLIEQVRIPPQ----------------IGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILA  157 (614)
T ss_pred             ecccccCCHHHH-HHHHHHHhhCcc----------------cCCcEEEEEECcccCCHHHHHHHHHHHhCCCCCeEEEEE
Confidence            222222222222 122222211100                112248899998755  3355554444333345565554


Q ss_pred             e-cchhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          289 A-RSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       289 t-r~~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      | ....+......-...+++.+++.++....+...+.......+ .+.+..|++.++|-.--+..+
T Consensus       158 tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi~i~-~~al~~La~~s~gdlr~al~~  222 (614)
T PRK14971        158 TTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGITAE-PEALNVIAQKADGGMRDALSI  222 (614)
T ss_pred             eCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHHH
Confidence            4 444443333344568999999999999999887752222221 345788999999977544443

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

Probab=98.41  E-value=3e-05  Score=73.66  Aligned_cols=204  Identities=11%  Similarity=0.109  Sum_probs=125.7

Q ss_pred             cCcccccchhHHHHHHHHHhcC----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 042806          151 KDYEACESRMSTLNDILDALKN----PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~----~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      .++...+||+.++..+.+++..    +....+-|.|-+|.|||.+...++.+......--.++++++..-.....++..|
T Consensus       147 ~~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~kI  226 (529)
T KOG2227|consen  147 APPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKKI  226 (529)
T ss_pred             CCCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHHH
Confidence            3466789999999999888764    456788899999999999999999987653212246888887767788888888


Q ss_pred             HHHh-CCCCCCCCchHHHHHHHHHHhC-CCeEEEEEeCCCCCc--ccccccC-CCCCCCCCcEEEEEecchhh------h
Q 042806          227 ADKL-GLTLHEESDSGRARSLRNRLKK-EKTILVILDNIWGNL--DFQAVGI-PHGDDRKGCKVLLTARSLDV------L  295 (390)
Q Consensus       227 ~~~l-~~~~~~~~~~~~~~~l~~~l~~-~~~~LlVlDdv~~~~--~~~~l~~-~l~~~~~~s~IivTtr~~~v------~  295 (390)
                      ...+ ..........+....+...... +..+|+|+|.++...  .-..+.. .....-+++++|+..--..+      .
T Consensus       227 ~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslDlTdR~L  306 (529)
T KOG2227|consen  227 FSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLDLTDRFL  306 (529)
T ss_pred             HHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhhHHHHHh
Confidence            8877 2111111224455566666654 447999999986431  1111111 01112345555544332111      1


Q ss_pred             hh----cCCCcceEecCCCCHHHHHHHHHHhhCCCCCC----CchHHHHHHHHHHcCCChHHHHHHH
Q 042806          296 SR----KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEG----SEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       296 ~~----~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~----~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      ..    ..-....+...|.+.++..++|..........    ..++-+|++++...|.+--|+...-
T Consensus       307 prL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~SGDlRkaLdv~R  373 (529)
T KOG2227|consen  307 PRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAPSGDLRKALDVCR  373 (529)
T ss_pred             hhhhhccCCCCceeeecCCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccCchhHHHHHHHHH
Confidence            11    12234688899999999999999887532222    2334445555555555555554443

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=98.41  E-value=4.5e-06  Score=80.49  Aligned_cols=194  Identities=18%  Similarity=0.160  Sum_probs=112.9

Q ss_pred             cchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCCCC
Q 042806          157 ESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLTLH  235 (390)
Q Consensus       157 ~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~~~  235 (390)
                      ..|..-+.++.+.+..... ++.|.|+.++||||+++.+.......     .+++...... +..++ .+.         
T Consensus        20 ~~~~~~~~~l~~~~~~~~~-i~~i~GpR~~GKTtll~~l~~~~~~~-----~iy~~~~d~~~~~~~l-~d~---------   83 (398)
T COG1373          20 IERRKLLPRLIKKLDLRPF-IILILGPRQVGKTTLLKLLIKGLLEE-----IIYINFDDLRLDRIEL-LDL---------   83 (398)
T ss_pred             hhHHhhhHHHHhhcccCCc-EEEEECCccccHHHHHHHHHhhCCcc-----eEEEEecchhcchhhH-HHH---------
Confidence            3444555666666554433 99999999999999997666554332     5555543322 11111 111         


Q ss_pred             CCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhhh-----hcCCCcceEecCCC
Q 042806          236 EESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLS-----RKMDSQQNFSVGVL  310 (390)
Q Consensus       236 ~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~~-----~~~~~~~~~~l~~L  310 (390)
                             ...+.+.-.. ++.+++||.|+...+|......+.+..+. +|++|+-+.....     ...+-...+++.||
T Consensus        84 -------~~~~~~~~~~-~~~yifLDEIq~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~Pl  154 (398)
T COG1373          84 -------LRAYIELKER-EKSYIFLDEIQNVPDWERALKYLYDRGNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPL  154 (398)
T ss_pred             -------HHHHHHhhcc-CCceEEEecccCchhHHHHHHHHHccccc-eEEEECCchhhhccchhhhcCCCceeEEECCC
Confidence                   1111111112 33899999999999999877777666666 8888888765432     22344569999999


Q ss_pred             CHHHHHH-------------HHHHhhC-CCCC----CCc---------hHHHHHHHHHHcCC-ChHHHHHHHHHhcCCCC
Q 042806          311 KEDEAWS-------------LFKKMAG-DYIE----GSE---------FKWVAKDVARECAG-LPVSIVTVARALGTRDY  362 (390)
Q Consensus       311 ~~~ea~~-------------lf~~~~~-~~~~----~~~---------~~~~~~~i~~~~~G-lPLai~~l~~~L~~~~~  362 (390)
                      |..|-..             +|..... +..+    ...         ..-+.++|.+.++= -+-.+..+..++..+..
T Consensus       155 SF~Efl~~~~~~~~~~~~~~~f~~Yl~~GGfP~~v~~~~~~~~~~~~~~~~~~~Di~~~~~~~~~~~~k~i~~~l~~~~g  234 (398)
T COG1373         155 SFREFLKLKGEEIEPSKLELLFEKYLETGGFPESVKADLSEKKLKEYLDTILKRDIIERGKIENADLMKRILRFLASNIG  234 (398)
T ss_pred             CHHHHHhhcccccchhHHHHHHHHHHHhCCCcHHHhCcchhhHHHHHHHHHHHHHHHHHcCcccHHHHHHHHHHHHhhcC
Confidence            9999865             4665542 1110    111         12234567777752 33444555554444332


Q ss_pred             CCCcccchhHHHHHh
Q 042806          363 LNGRTHWNSWGGLLQ  377 (390)
Q Consensus       363 ~~~~~~w~~~~~~l~  377 (390)
                        ..--|.++...+.
T Consensus       235 --~~~s~~~la~~l~  247 (398)
T COG1373         235 --SPISYSSLARELK  247 (398)
T ss_pred             --CccCHHHHHHHHh
Confidence              2556666666663

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.41  E-value=1.1e-05  Score=73.29  Aligned_cols=192  Identities=16%  Similarity=0.149  Sum_probs=115.4

Q ss_pred             HHHHHHHHHhcCC---CccEEEEEcCCCCcHHHHHHHHHHHhhhcCC----CCeEEEEEeCCCCCHHHHHHHHHHHhCCC
Q 042806          161 STLNDILDALKNP---DVNMLGIYGMGGIVKTTLAKEVARKAETEKL----FDQVIFVEVSKIQDIRKIQGEIADKLGLT  233 (390)
Q Consensus       161 ~~~~~l~~~L~~~---~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~~l~~~i~~~l~~~  233 (390)
                      ..++.|.+.+..+   ..+-+.|+|.+|.|||++++.+.........    --.++.|.....++...++..|+..++.+
T Consensus        44 ~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP  123 (302)
T PF05621_consen   44 EALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAP  123 (302)
T ss_pred             HHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCcc
Confidence            3344455545443   4577999999999999999999987543211    11467788888999999999999999987


Q ss_pred             CCCCC-chHHHHHHHHHHhCCCeEEEEEeCCCCCc---------ccccccCCCCCCCCCcEEEEEecchhhhhhc----C
Q 042806          234 LHEES-DSGRARSLRNRLKKEKTILVILDNIWGNL---------DFQAVGIPHGDDRKGCKVLLTARSLDVLSRK----M  299 (390)
Q Consensus       234 ~~~~~-~~~~~~~l~~~l~~~~~~LlVlDdv~~~~---------~~~~l~~~l~~~~~~s~IivTtr~~~v~~~~----~  299 (390)
                      ..... ...........++.-+.=+||+|++++..         .++.++ .+.+.-.-+-|.+-|+....+-..    .
T Consensus       124 ~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK-~L~NeL~ipiV~vGt~~A~~al~~D~QLa  202 (302)
T PF05621_consen  124 YRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALK-FLGNELQIPIVGVGTREAYRALRTDPQLA  202 (302)
T ss_pred             cCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHH-HHhhccCCCeEEeccHHHHHHhccCHHHH
Confidence            75443 33334445566665444699999997641         112221 121112233455555543222110    0


Q ss_pred             CCcceEecCCCCH-HHHHHHHHHhh---C-CCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          300 DSQQNFSVGVLKE-DEAWSLFKKMA---G-DYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       300 ~~~~~~~l~~L~~-~ea~~lf~~~~---~-~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      +-...+.+.+-.. ++...|+...-   . .....-...+++..|...++|+.=-+..+
T Consensus       203 ~RF~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~l~~l  261 (302)
T PF05621_consen  203 SRFEPFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIGELSRL  261 (302)
T ss_pred             hccCCccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchHHHHHH
Confidence            1123555555443 34455554332   1 33333445778999999999998665554

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.39  E-value=7.1e-06  Score=79.78  Aligned_cols=160  Identities=14%  Similarity=0.145  Sum_probs=95.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      ...+.|+|++|+|||+|++.+++.......=..++|++      ..++...+...+...        ....+.+.+..- 
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~------~~~~~~~~~~~~~~~--------~~~~~~~~~~~~-  200 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVS------SEKFTNDFVNALRNN--------KMEEFKEKYRSV-  200 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEE------HHHHHHHHHHHHHcC--------CHHHHHHHHHhC-
Confidence            34688999999999999999999876531112345554      334444555444321        123344445432 


Q ss_pred             eEEEEEeCCCCCcc---c-ccccCCCCC-CCCCcEEEEEecch--hhh------hhcCCCcceEecCCCCHHHHHHHHHH
Q 042806          255 TILVILDNIWGNLD---F-QAVGIPHGD-DRKGCKVLLTARSL--DVL------SRKMDSQQNFSVGVLKEDEAWSLFKK  321 (390)
Q Consensus       255 ~~LlVlDdv~~~~~---~-~~l~~~l~~-~~~~s~IivTtr~~--~v~------~~~~~~~~~~~l~~L~~~ea~~lf~~  321 (390)
                       -+|+|||++....   + +.+...+.. ...+..+|+|+...  .+.      ...+..+..+++.+.+.++-..++.+
T Consensus       201 -dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~  279 (405)
T TIGR00362       201 -DLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQK  279 (405)
T ss_pred             -CEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHHH
Confidence             3899999975321   1 112221111 12345677777641  110      11233445899999999999999999


Q ss_pred             hhCCCCCCCchHHHHHHHHHHcCCChHHHH
Q 042806          322 MAGDYIEGSEFKWVAKDVARECAGLPVSIV  351 (390)
Q Consensus       322 ~~~~~~~~~~~~~~~~~i~~~~~GlPLai~  351 (390)
                      .+......- .+++...|++.+.|.+-.+.
T Consensus       280 ~~~~~~~~l-~~e~l~~ia~~~~~~~r~l~  308 (405)
T TIGR00362       280 KAEEEGLEL-PDEVLEFIAKNIRSNVRELE  308 (405)
T ss_pred             HHHHcCCCC-CHHHHHHHHHhcCCCHHHHH
Confidence            886322222 25677889999888766433

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).

>COG3903 Predicted ATPase [General function prediction only]

Probab=98.39  E-value=3.7e-07  Score=85.27  Aligned_cols=179  Identities=25%  Similarity=0.295  Sum_probs=119.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFD-QVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKK  252 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  252 (390)
                      ..+.+.++|+|||||||++-++.. ....  |. .+.++...+..+...+.-.+...++.....  -......+...+.+
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~-~~~~--~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~~--g~~~~~~~~~~~~~   87 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH-AASE--YADGVAFVDLAPITDPALVFPTLAGALGLHVQP--GDSAVDTLVRRIGD   87 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh-Hhhh--cccceeeeeccccCchhHhHHHHHhhccccccc--chHHHHHHHHHHhh
Confidence            467899999999999999999988 4433  65 566666666667766667777777765432  12234455555655


Q ss_pred             CCeEEEEEeCCCCCcc-cccccCCCCCCCCCcEEEEEecchhhhhhcCCCcceEecCCCCHH-HHHHHHHHhhC----CC
Q 042806          253 EKTILVILDNIWGNLD-FQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKED-EAWSLFKKMAG----DY  326 (390)
Q Consensus       253 ~~~~LlVlDdv~~~~~-~~~l~~~l~~~~~~s~IivTtr~~~v~~~~~~~~~~~~l~~L~~~-ea~~lf~~~~~----~~  326 (390)
                      . +.++|+||.....+ -..+...+..+.+.-.|+.|+|....    ........+.+|+.. ++.++|...+.    .-
T Consensus        88 r-r~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~~l----~~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~f  162 (414)
T COG3903          88 R-RALLVLDNCEHLLDACAALIVALLGACPRLAILATSREAIL----VAGEVHRRVPSLSLFDEAIELFVCRAVLVALSF  162 (414)
T ss_pred             h-hHHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhhhc----ccccccccCCccccCCchhHHHHHHHHHhccce
Confidence            4 49999999865421 11122223334556678889987543    234456777777754 78888876663    11


Q ss_pred             CCCCchHHHHHHHHHHcCCChHHHHHHHHHhcCCCC
Q 042806          327 IEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDY  362 (390)
Q Consensus       327 ~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~~~  362 (390)
                      ...........+|.++.+|.||+|...++..++-..
T Consensus       163 ~l~~~~~a~v~~icr~ldg~~laielaaarv~sl~~  198 (414)
T COG3903         163 WLTDDNAAAVAEICRRLDGIPLAIELAAARVRSLSP  198 (414)
T ss_pred             eecCCchHHHHHHHHHhhcchHHHHHHHHHHHhcCH
Confidence            112223456789999999999999999998887665

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.38  E-value=4.9e-06  Score=87.76  Aligned_cols=180  Identities=14%  Similarity=0.165  Sum_probs=100.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCC---C-CeEEEEEeCCCCCHHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKL---F-DQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~---f-~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      .++++||+.+++.+++.|......-+.++|++|+|||++|..++........   . +..+|. +    +...++.    
T Consensus       178 ~~~~igr~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~-l----~~~~l~a----  248 (821)
T CHL00095        178 LDPVIGREKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVIT-L----DIGLLLA----  248 (821)
T ss_pred             CCCCCCcHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEE-e----eHHHHhc----
Confidence            4679999999999999998766666779999999999999999988643211   1 233442 1    2222111    


Q ss_pred             HhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc---------ccccccCCCCCCCCCcEEEEEecchhhhh---
Q 042806          229 KLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL---------DFQAVGIPHGDDRKGCKVLLTARSLDVLS---  296 (390)
Q Consensus       229 ~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~---------~~~~l~~~l~~~~~~s~IivTtr~~~v~~---  296 (390)
                        + ......-...+..+.+.+...++++|++|+++...         +...+..+... ....++|.+|.......   
T Consensus       249 --g-~~~~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~-rg~l~~IgaTt~~ey~~~ie  324 (821)
T CHL00095        249 --G-TKYRGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEGAIDAANILKPALA-RGELQCIGATTLDEYRKHIE  324 (821)
T ss_pred             --c-CCCccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHh-CCCcEEEEeCCHHHHHHHHh
Confidence              1 11111122234444444444455999999996321         11112112111 22345666665543211   


Q ss_pred             ---hcCCCcceEecCCCCHHHHHHHHHHhhC---CCCCCCchHHHHHHHHHHcCC
Q 042806          297 ---RKMDSQQNFSVGVLKEDEAWSLFKKMAG---DYIEGSEFKWVAKDVARECAG  345 (390)
Q Consensus       297 ---~~~~~~~~~~l~~L~~~ea~~lf~~~~~---~~~~~~~~~~~~~~i~~~~~G  345 (390)
                         ........+++...+.++...+++....   ......-.+++...+++.++|
T Consensus       325 ~D~aL~rRf~~I~v~ep~~~e~~aILr~l~~~~e~~~~v~i~deal~~i~~ls~~  379 (821)
T CHL00095        325 KDPALERRFQPVYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQ  379 (821)
T ss_pred             cCHHHHhcceEEecCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhc
Confidence               1122335788999999999888875431   111111123455666666653

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=98.38  E-value=1.3e-05  Score=78.52  Aligned_cols=178  Identities=15%  Similarity=0.148  Sum_probs=105.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcC---------------------CCCeEEE
Q 042806          153 YEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEK---------------------LFDQVIF  210 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~---------------------~f~~~~w  210 (390)
                      ...++|.+..+..|.+++..++. ..+.++|+.|+||||+|+.+.+......                     +++ .++
T Consensus        16 ~~diiGq~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~~~~d-~~~   94 (451)
T PRK06305         16 FSEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTSLD-VLE   94 (451)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcCCCCc-eEE
Confidence            55789999999999999987664 5688999999999999999988764211                     111 111


Q ss_pred             EEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcE
Q 042806          211 VEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCK  284 (390)
Q Consensus       211 v~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~  284 (390)
                      +........++                     +..+.+.+.    ..++-++|+|+++..  ...+.+...+......+.
T Consensus        95 i~g~~~~gid~---------------------ir~i~~~l~~~~~~~~~kvvIIdead~lt~~~~n~LLk~lEep~~~~~  153 (451)
T PRK06305         95 IDGASHRGIED---------------------IRQINETVLFTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVK  153 (451)
T ss_pred             eeccccCCHHH---------------------HHHHHHHHHhhhhcCCCEEEEEecHHhhCHHHHHHHHHHhhcCCCCce
Confidence            11111111111                     111222221    123368999998644  233344333333334556


Q ss_pred             EEEEecc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH-HHHHH
Q 042806          285 VLLTARS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV-SIVTV  353 (390)
Q Consensus       285 IivTtr~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL-ai~~l  353 (390)
                      +|++|.. ..+..........+++.+++.++....+...+....... .++.+..|++.++|.+- |+..+
T Consensus       154 ~Il~t~~~~kl~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~~i-~~~al~~L~~~s~gdlr~a~~~L  223 (451)
T PRK06305        154 FFLATTEIHKIPGTILSRCQKMHLKRIPEETIIDKLALIAKQEGIET-SREALLPIARAAQGSLRDAESLY  223 (451)
T ss_pred             EEEEeCChHhcchHHHHhceEEeCCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHH
Confidence            6666643 333222223345899999999999988887764221111 23467789999999764 44444

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=98.38  E-value=3.6e-06  Score=77.52  Aligned_cols=132  Identities=16%  Similarity=0.128  Sum_probs=73.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeE
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTI  256 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~  256 (390)
                      -+.++|++|+|||++|+.++......+......|+.++.    .++...+   .+.     .. .   .+.+.+..-..-
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~----~~l~~~~---~g~-----~~-~---~~~~~~~~a~~g  123 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTR----DDLVGQY---IGH-----TA-P---KTKEILKRAMGG  123 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecH----HHHhHhh---ccc-----ch-H---HHHHHHHHccCc
Confidence            477999999999999988887765433222223554442    2222211   111     11 1   122222221226


Q ss_pred             EEEEeCCCCC-----------cccccccCCCCCCCCCcEEEEEecchhhhhh-------cCCCcceEecCCCCHHHHHHH
Q 042806          257 LVILDNIWGN-----------LDFQAVGIPHGDDRKGCKVLLTARSLDVLSR-------KMDSQQNFSVGVLKEDEAWSL  318 (390)
Q Consensus       257 LlVlDdv~~~-----------~~~~~l~~~l~~~~~~s~IivTtr~~~v~~~-------~~~~~~~~~l~~L~~~ea~~l  318 (390)
                      +|+||++...           ..++.+...+.....+.+||+++.....-..       .......+++.+++.+|..++
T Consensus       124 vL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~l~~edl~~I  203 (284)
T TIGR02880       124 VLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMDSFFESNPGFSSRVAHHVDFPDYSEAELLVI  203 (284)
T ss_pred             EEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHHHHHH
Confidence            8999999632           1122333333334456677777654322110       011235799999999999999


Q ss_pred             HHHhhC
Q 042806          319 FKKMAG  324 (390)
Q Consensus       319 f~~~~~  324 (390)
                      +.+.+.
T Consensus       204 ~~~~l~  209 (284)
T TIGR02880       204 AGLMLK  209 (284)
T ss_pred             HHHHHH
Confidence            988874

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.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=98.38  E-value=1e-05  Score=80.79  Aligned_cols=159  Identities=16%  Similarity=0.120  Sum_probs=95.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      ..+.|+|..|+|||.|++.+++.......-..++|+.      ..++...+...+...        ....+.+.+.+-  
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yit------aeef~~el~~al~~~--------~~~~f~~~y~~~--  378 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVS------SEEFTNEFINSIRDG--------KGDSFRRRYREM--  378 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEee------HHHHHHHHHHHHHhc--------cHHHHHHHhhcC--
Confidence            4589999999999999999999875421112345543      344555554443211        123344444442  


Q ss_pred             EEEEEeCCCCC---ccccc-ccCCCCC-CCCCcEEEEEecch--hh------hhhcCCCcceEecCCCCHHHHHHHHHHh
Q 042806          256 ILVILDNIWGN---LDFQA-VGIPHGD-DRKGCKVLLTARSL--DV------LSRKMDSQQNFSVGVLKEDEAWSLFKKM  322 (390)
Q Consensus       256 ~LlVlDdv~~~---~~~~~-l~~~l~~-~~~~s~IivTtr~~--~v------~~~~~~~~~~~~l~~L~~~ea~~lf~~~  322 (390)
                      =+|+|||+...   ..|+. +...+.. ...+..||+||...  .+      ....+..+-.++|.+.+.+.-..++++.
T Consensus       379 DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~kk  458 (617)
T PRK14086        379 DILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAILRKK  458 (617)
T ss_pred             CEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHHHH
Confidence            38999999754   22221 2222211 13355688888752  11      1124556679999999999999999988


Q ss_pred             hCCCCCCCchHHHHHHHHHHcCCChHHHH
Q 042806          323 AGDYIEGSEFKWVAKDVARECAGLPVSIV  351 (390)
Q Consensus       323 ~~~~~~~~~~~~~~~~i~~~~~GlPLai~  351 (390)
                      +....... -++++..|++.+.+..-.|.
T Consensus       459 a~~r~l~l-~~eVi~yLa~r~~rnvR~Le  486 (617)
T PRK14086        459 AVQEQLNA-PPEVLEFIASRISRNIRELE  486 (617)
T ss_pred             HHhcCCCC-CHHHHHHHHHhccCCHHHHH
Confidence            86332222 24577788888776544433

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.37  E-value=1.9e-05  Score=80.12  Aligned_cols=197  Identities=14%  Similarity=0.071  Sum_probs=109.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 042806          153 YEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLG  231 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~  231 (390)
                      ...++|.+..+..|..++..++. +.+.++|+.|+||||+|+.++.......... ...    ..+..-+..+.+.....
T Consensus        15 f~~liGq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~-~~~----~~Cg~C~~C~~i~~g~h   89 (620)
T PRK14948         15 FDELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDK-PTP----EPCGKCELCRAIAAGNA   89 (620)
T ss_pred             HhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCC-CCC----CCCcccHHHHHHhcCCC
Confidence            45688999999999998887653 6788999999999999999999874321110 000    00111122222221111


Q ss_pred             CCC-----CCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecc-hhhhhhcC
Q 042806          232 LTL-----HEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARS-LDVLSRKM  299 (390)
Q Consensus       232 ~~~-----~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~-~~v~~~~~  299 (390)
                      .+.     ........+..+.+.+.    .+++-++|+|+++..  ..++.|...+-.-...+.+|++|.+ ..+.....
T Consensus        90 ~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~llpTIr  169 (620)
T PRK14948         90 LDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTII  169 (620)
T ss_pred             ccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhhhHHHH
Confidence            100     00011112222322221    123358999999754  3455554444333334555555543 33322223


Q ss_pred             CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHH
Q 042806          300 DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVAR  355 (390)
Q Consensus       300 ~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~  355 (390)
                      .-...+++.+++.++....+...+.......+ .+.+..|++.++|.+..+..+..
T Consensus       170 SRc~~~~f~~l~~~ei~~~L~~ia~kegi~is-~~al~~La~~s~G~lr~A~~lLe  224 (620)
T PRK14948        170 SRCQRFDFRRIPLEAMVQHLSEIAEKESIEIE-PEALTLVAQRSQGGLRDAESLLD  224 (620)
T ss_pred             hheeEEEecCCCHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHcCCCHHHHHHHHH
Confidence            33467888999999988888776642111111 34577899999998865555443

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.36  E-value=9.8e-06  Score=81.90  Aligned_cols=197  Identities=15%  Similarity=0.142  Sum_probs=108.7

Q ss_pred             CcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          152 DYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ....++|.+..+..|.+++..++. +.+.++|+.|+||||+|+.+.+..........       ..+..-.....|...-
T Consensus        14 ~f~~iiGq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~-------~~c~~c~~c~~i~~g~   86 (576)
T PRK14965         14 TFSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTA-------EPCNVCPPCVEITEGR   86 (576)
T ss_pred             CHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCC-------CCCCccHHHHHHhcCC
Confidence            355789999999999999887765 56789999999999999999888642211100       0000000000100000


Q ss_pred             CC-----CCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEe-cchhhhhhc
Q 042806          231 GL-----TLHEESDSGRARSLRNRLK----KEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTA-RSLDVLSRK  298 (390)
Q Consensus       231 ~~-----~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTt-r~~~v~~~~  298 (390)
                      ..     +.......+.+..+.+.+.    ..+.-++|+|+++...  ..+.|...+-.-...+.+|++| ....+....
T Consensus        87 ~~d~~eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~tI  166 (576)
T PRK14965         87 SVDVFEIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITI  166 (576)
T ss_pred             CCCeeeeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHHH
Confidence            00     0000000111222333221    1233589999997542  3444444443333455555544 445454333


Q ss_pred             CCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh-HHHHHHHHH
Q 042806          299 MDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP-VSIVTVARA  356 (390)
Q Consensus       299 ~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP-Lai~~l~~~  356 (390)
                      ..-...+++.+++.++....+...+.......+ ++....|++.++|.. .++..+-.+
T Consensus       167 ~SRc~~~~f~~l~~~~i~~~L~~i~~~egi~i~-~~al~~la~~a~G~lr~al~~Ldql  224 (576)
T PRK14965        167 LSRCQRFDFRRIPLQKIVDRLRYIADQEGISIS-DAALALVARKGDGSMRDSLSTLDQV  224 (576)
T ss_pred             HHhhhhhhcCCCCHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            334468889999999998888876642222121 345678999999865 555555443

>TIGR00767 rho transcription termination factor Rho

Probab=98.36  E-value=2.4e-06  Score=80.74  Aligned_cols=90  Identities=14%  Similarity=0.165  Sum_probs=62.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC--CCHHHHHHHHHHHhCCCCCCCCc---hHHHHHH--
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI--QDIRKIQGEIADKLGLTLHEESD---SGRARSL--  246 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~--~~~~~l~~~i~~~l~~~~~~~~~---~~~~~~l--  246 (390)
                      ....++|+|++|+|||||++.+++..... +|+..+|+.+.+.  .++.++++.+...+-....+.+.   ......+  
T Consensus       167 ~Gq~~~IvG~~g~GKTtL~~~i~~~I~~n-hfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e  245 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVLLQKIAQAITRN-HPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIE  245 (415)
T ss_pred             CCCEEEEECCCCCChhHHHHHHHHhhccc-CCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHH
Confidence            45678999999999999999999988654 7999999999865  68899999885433222111111   1122222  


Q ss_pred             --HHHHhCCCeEEEEEeCCC
Q 042806          247 --RNRLKKEKTILVILDNIW  264 (390)
Q Consensus       247 --~~~l~~~~~~LlVlDdv~  264 (390)
                        ......+++.+|++|++.
T Consensus       246 ~Ae~~~~~GkdVVLlIDEit  265 (415)
T TIGR00767       246 KAKRLVEHKKDVVILLDSIT  265 (415)
T ss_pred             HHHHHHHcCCCeEEEEEChh
Confidence              222234667999999996

Members of this family differ in the specificity of RNA binding.

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

Probab=98.33  E-value=4.5e-06  Score=75.00  Aligned_cols=183  Identities=19%  Similarity=0.155  Sum_probs=114.9

Q ss_pred             cccCcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeE-EEEEeCCCCCHHHHHHHHH
Q 042806          149 SIKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQV-IFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       149 ~~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~-~wv~v~~~~~~~~l~~~i~  227 (390)
                      .|...+.+.|-+..+.-|.+.+.....+....|||+|.|||+-|+.+....-..+.|.+. .-.++|...-.. +.+.=.
T Consensus        31 rPkt~de~~gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGis-vvr~Ki  109 (346)
T KOG0989|consen   31 RPKTFDELAGQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGIS-VVREKI  109 (346)
T ss_pred             CCCcHHhhcchHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhccccccccc-chhhhh
Confidence            344467789999999999999988778899999999999999999998887554556543 334554432221 111000


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHH----h-CCCe-EEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecc-hhhhhhc
Q 042806          228 DKLGLTLHEESDSGRARSLRNRL----K-KEKT-ILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARS-LDVLSRK  298 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l----~-~~~~-~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~-~~v~~~~  298 (390)
                      +.+             ..+.-..    . .-.+ -++|||+++..  +.|..+...+-+....++.|+.+.. ..+....
T Consensus       110 k~f-------------akl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi  176 (346)
T KOG0989|consen  110 KNF-------------AKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPL  176 (346)
T ss_pred             cCH-------------HHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHH
Confidence            000             0000000    0 0122 38899999865  6788877666554556665555544 3322112


Q ss_pred             CCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCC
Q 042806          299 MDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGL  346 (390)
Q Consensus       299 ~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~Gl  346 (390)
                      ..-...+..++|.+++...-++..+......-+ .+..+.|++.++|-
T Consensus       177 ~SRC~KfrFk~L~d~~iv~rL~~Ia~~E~v~~d-~~al~~I~~~S~Gd  223 (346)
T KOG0989|consen  177 VSRCQKFRFKKLKDEDIVDRLEKIASKEGVDID-DDALKLIAKISDGD  223 (346)
T ss_pred             HhhHHHhcCCCcchHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHcCCc
Confidence            223357889999999999888888863333333 34567899999874

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=98.33  E-value=2.9e-05  Score=78.20  Aligned_cols=194  Identities=15%  Similarity=0.131  Sum_probs=108.0

Q ss_pred             CcccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          152 DYEACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ....++|.+.....|.+++..++ .+.+.++|+.|+||||+|+.+..........+..   .++.+    .....+....
T Consensus        14 ~f~~viGq~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~---pC~~C----~~C~~i~~g~   86 (559)
T PRK05563         14 TFEDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGE---PCNEC----EICKAITNGS   86 (559)
T ss_pred             cHHhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCC---CCCcc----HHHHHHhcCC
Confidence            35678999999999999988765 4567789999999999999998875322110000   00000    1111111110


Q ss_pred             CCC-----CCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEe-cchhhhhhc
Q 042806          231 GLT-----LHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTA-RSLDVLSRK  298 (390)
Q Consensus       231 ~~~-----~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTt-r~~~v~~~~  298 (390)
                      ..+     .........+..+.+.+.    .++.-++|+|+++..  ..+..+...+..-.....+|++| ....+....
T Consensus        87 ~~dv~eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~tI  166 (559)
T PRK05563         87 LMDVIEIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPATI  166 (559)
T ss_pred             CCCeEEeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcHHH
Confidence            000     000011112223333322    233368899999754  34555544443323344455444 444443222


Q ss_pred             CCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          299 MDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       299 ~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      ..-...+++.+++.++....+...+.......+ .+.+..|++.++|-+.-+..+
T Consensus       167 ~SRc~~~~f~~~~~~ei~~~L~~i~~~egi~i~-~~al~~ia~~s~G~~R~al~~  220 (559)
T PRK05563        167 LSRCQRFDFKRISVEDIVERLKYILDKEGIEYE-DEALRLIARAAEGGMRDALSI  220 (559)
T ss_pred             HhHheEEecCCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHHH
Confidence            333468889999999999988887742221122 346778899998877654433

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=98.32  E-value=1e-05  Score=79.78  Aligned_cols=159  Identities=14%  Similarity=0.146  Sum_probs=94.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      ...+.|+|++|+|||+|++.+.+.......-..++|++.      .++...+...+...        ....+.+.+..  
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~------~~~~~~~~~~~~~~--------~~~~~~~~~~~--  211 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTS------EKFTNDFVNALRNN--------TMEEFKEKYRS--  211 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEH------HHHHHHHHHHHHcC--------cHHHHHHHHhc--
Confidence            356889999999999999999999865421223455543      33444444444211        12344455543  


Q ss_pred             eEEEEEeCCCCCcc---c-ccccCCCCC-CCCCcEEEEEecch--hhh------hhcCCCcceEecCCCCHHHHHHHHHH
Q 042806          255 TILVILDNIWGNLD---F-QAVGIPHGD-DRKGCKVLLTARSL--DVL------SRKMDSQQNFSVGVLKEDEAWSLFKK  321 (390)
Q Consensus       255 ~~LlVlDdv~~~~~---~-~~l~~~l~~-~~~~s~IivTtr~~--~v~------~~~~~~~~~~~l~~L~~~ea~~lf~~  321 (390)
                      .-+|+|||++....   + +.+...+.. ...|..||+|+...  .+.      ...+..+..+++++.+.++-..+++.
T Consensus       212 ~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~il~~  291 (450)
T PRK00149        212 VDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIAILKK  291 (450)
T ss_pred             CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHHHHHH
Confidence            24899999974311   1 222221111 12344577777642  111      11334556899999999999999999


Q ss_pred             hhCCCCCCCchHHHHHHHHHHcCCChHHH
Q 042806          322 MAGDYIEGSEFKWVAKDVARECAGLPVSI  350 (390)
Q Consensus       322 ~~~~~~~~~~~~~~~~~i~~~~~GlPLai  350 (390)
                      .+..... .-.+++...|++.++|..-.+
T Consensus       292 ~~~~~~~-~l~~e~l~~ia~~~~~~~R~l  319 (450)
T PRK00149        292 KAEEEGI-DLPDEVLEFIAKNITSNVREL  319 (450)
T ss_pred             HHHHcCC-CCCHHHHHHHHcCcCCCHHHH
Confidence            8853211 112457788999888876643

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=98.30  E-value=1.1e-05  Score=74.74  Aligned_cols=196  Identities=15%  Similarity=0.140  Sum_probs=116.7

Q ss_pred             ccccchhHHHHHHHHHhcCCC---ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          154 EACESRMSTLNDILDALKNPD---VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~~~---~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      +.+.+|+.++..+...+.++.   +..+.|+|.+|.|||.+++++++.....     .+|+++-.+++..-++..|+...
T Consensus         6 ~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~~-----~vw~n~~ecft~~~lle~IL~~~   80 (438)
T KOG2543|consen    6 PNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNLE-----NVWLNCVECFTYAILLEKILNKS   80 (438)
T ss_pred             cCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCCc-----ceeeehHHhccHHHHHHHHHHHh
Confidence            468899999999999887654   3456899999999999999999988433     68999999999999999999998


Q ss_pred             CCC-CCCCCch---HHHHHHHHHHh------C-CCeEEEEEeCCCCCcccccccCC----CC--CCCCCcEEEEEecc-h
Q 042806          231 GLT-LHEESDS---GRARSLRNRLK------K-EKTILVILDNIWGNLDFQAVGIP----HG--DDRKGCKVLLTARS-L  292 (390)
Q Consensus       231 ~~~-~~~~~~~---~~~~~l~~~l~------~-~~~~LlVlDdv~~~~~~~~l~~~----l~--~~~~~s~IivTtr~-~  292 (390)
                      +.. .+.....   .....+...+.      + +..++||||+++...+.+....+    ++  -+.+...|++..-. +
T Consensus        81 ~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i~iils~~~~e  160 (438)
T KOG2543|consen   81 QLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMDAILLQCLFRLYELLNEPTIVIILSAPSCE  160 (438)
T ss_pred             ccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCceEEEEeccccH
Confidence            622 2211111   11222222221      1 23599999999766544432110    00  12334434433332 2


Q ss_pred             hhhhhcCCCc--ceEecCCCCHHHHHHHHHHhhCCCCC----CCchHHHHHHHHHHcCCChHHHHHHHH
Q 042806          293 DVLSRKMDSQ--QNFSVGVLKEDEAWSLFKKMAGDYIE----GSEFKWVAKDVARECAGLPVSIVTVAR  355 (390)
Q Consensus       293 ~v~~~~~~~~--~~~~l~~L~~~ea~~lf~~~~~~~~~----~~~~~~~~~~i~~~~~GlPLai~~l~~  355 (390)
                      ......++..  .++....-+.+|..++|.+.-.+...    ..-+.-+..-....|+ -+-.+..++.
T Consensus       161 ~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~~~p~~r~~~~ya~fl~v~l~vF~~~cr-d~~eL~~~~~  228 (438)
T KOG2543|consen  161 KQYLINTGTLEIVVLHFPQYSVEETQVILSRDNPGKRKLDVYAQFLHVLLQVFYMACR-DVNELRSLIS  228 (438)
T ss_pred             HHhhcccCCCCceEEecCCCCHHHHHHHHhcCCccccchHHHHHHHHHHHHHHHHHhC-CHHHHHHHHH
Confidence            2211112332  46777888899998888664421111    0111122344555666 5555555543

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=98.30  E-value=3.5e-05  Score=77.38  Aligned_cols=194  Identities=13%  Similarity=0.129  Sum_probs=109.1

Q ss_pred             CcccccchhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          152 DYEACESRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ....++|-+..+..|..++..++. +.+.++|+.|+||||+|+.+++..........   ..+..+.+-    +.+...-
T Consensus        14 ~f~diiGqe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~---~pC~~C~~C----~~i~~~~   86 (563)
T PRK06647         14 DFNSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTP---MPCGECSSC----KSIDNDN   86 (563)
T ss_pred             CHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCC---CCCccchHH----HHHHcCC
Confidence            345789999999999999987664 46889999999999999999988643211100   001111111    0110000


Q ss_pred             CC-----CCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecc-hhhhhhc
Q 042806          231 GL-----TLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARS-LDVLSRK  298 (390)
Q Consensus       231 ~~-----~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~-~~v~~~~  298 (390)
                      ..     ..........+..+.+.+.    .+++-++|+|+++..  ..++.+...+..-.+.+.+|++|.. ..+....
T Consensus        87 ~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~~tI  166 (563)
T PRK06647         87 SLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATI  166 (563)
T ss_pred             CCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhHHHH
Confidence            00     0000001112222222111    123358999999755  3355555454433445566555543 3333222


Q ss_pred             CCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          299 MDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       299 ~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      ..-...+++.+++.++..+.+...+....... .++.+..|++.++|.+-.+..+
T Consensus       167 ~SRc~~~~f~~l~~~el~~~L~~i~~~egi~i-d~eAl~lLa~~s~GdlR~alsl  220 (563)
T PRK06647        167 KSRCQHFNFRLLSLEKIYNMLKKVCLEDQIKY-EDEALKWIAYKSTGSVRDAYTL  220 (563)
T ss_pred             HHhceEEEecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHH
Confidence            33345789999999999888888774222211 2456778999999988654444

>PRK06620 hypothetical protein; Validated

Probab=98.28  E-value=5.5e-06  Score=72.98  Aligned_cols=141  Identities=15%  Similarity=0.009  Sum_probs=84.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      +.+.|+|++|+|||+|++.+++....       .++.  ..+...                           +.... . 
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~~~-------~~~~--~~~~~~---------------------------~~~~~-~-   86 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLSNA-------YIIK--DIFFNE---------------------------EILEK-Y-   86 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhccCC-------EEcc--hhhhch---------------------------hHHhc-C-
Confidence            56899999999999999988776421       1111  000000                           01112 2 


Q ss_pred             EEEEEeCCCCCcc--cccccCCCCCCCCCcEEEEEecchhhh------hhcCCCcceEecCCCCHHHHHHHHHHhhCCCC
Q 042806          256 ILVILDNIWGNLD--FQAVGIPHGDDRKGCKVLLTARSLDVL------SRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYI  327 (390)
Q Consensus       256 ~LlVlDdv~~~~~--~~~l~~~l~~~~~~s~IivTtr~~~v~------~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~  327 (390)
                      -++++||++...+  +-.+...+  ...|..||+|++.....      ...+..+..+++++++.++-..++.+.+....
T Consensus        87 d~lliDdi~~~~~~~lf~l~N~~--~e~g~~ilits~~~p~~l~l~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~~~  164 (214)
T PRK06620         87 NAFIIEDIENWQEPALLHIFNII--NEKQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLNSPDDELIKILIFKHFSISS  164 (214)
T ss_pred             CEEEEeccccchHHHHHHHHHHH--HhcCCEEEEEcCCCccccchHHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcC
Confidence            4788899974321  11111111  13466889998843211      11234556899999999998888888775221


Q ss_pred             CCCchHHHHHHHHHHcCCChHHHHHHHHHh
Q 042806          328 EGSEFKWVAKDVARECAGLPVSIVTVARAL  357 (390)
Q Consensus       328 ~~~~~~~~~~~i~~~~~GlPLai~~l~~~L  357 (390)
                      . .--+++.+.|++.+.|---.+.-+-..|
T Consensus       165 l-~l~~ev~~~L~~~~~~d~r~l~~~l~~l  193 (214)
T PRK06620        165 V-TISRQIIDFLLVNLPREYSKIIEILENI  193 (214)
T ss_pred             C-CCCHHHHHHHHHHccCCHHHHHHHHHHH
Confidence            1 1225678899999988776665554433

>TIGR03689 pup_AAA proteasome ATPase

Probab=98.26  E-value=1.9e-05  Score=77.81  Aligned_cols=160  Identities=18%  Similarity=0.215  Sum_probs=90.0

Q ss_pred             cccccchhHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcC---CCCeEEEEEeCCC
Q 042806          153 YEACESRMSTLNDILDALKN-------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEK---LFDQVIFVEVSKI  216 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~---~f~~~~wv~v~~~  216 (390)
                      ...+.|.+..++++.+.+.-             ..++-+.++|++|+|||++|+.+++.....-   ......|+.++..
T Consensus       181 ~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl~v~~~  260 (512)
T TIGR03689       181 YADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFLNIKGP  260 (512)
T ss_pred             HHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEEeccch
Confidence            45677888888877776531             2345688999999999999999999875321   0123445554432


Q ss_pred             CCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHH----HhCCCeEEEEEeCCCCCc---------c-----cccccCCCCC
Q 042806          217 QDIRKIQGEIADKLGLTLHEESDSGRARSLRNR----LKKEKTILVILDNIWGNL---------D-----FQAVGIPHGD  278 (390)
Q Consensus       217 ~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~----l~~~~~~LlVlDdv~~~~---------~-----~~~l~~~l~~  278 (390)
                          +++...   .+      .....+..+.+.    ...+++++|+||+++...         +     ...+...+..
T Consensus       261 ----eLl~ky---vG------ete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~LDg  327 (512)
T TIGR03689       261 ----ELLNKY---VG------ETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSELDG  327 (512)
T ss_pred             ----hhcccc---cc------hHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHhcc
Confidence                111100   00      011112222222    223467999999997431         1     1122222211


Q ss_pred             --CCCCcEEEEEecchhhhh-hcC---CCcceEecCCCCHHHHHHHHHHhhCC
Q 042806          279 --DRKGCKVLLTARSLDVLS-RKM---DSQQNFSVGVLKEDEAWSLFKKMAGD  325 (390)
Q Consensus       279 --~~~~s~IivTtr~~~v~~-~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~  325 (390)
                        ...+..||.||....... ...   .....|++.+.+.++..++|..++..
T Consensus       328 l~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~  380 (512)
T TIGR03689       328 VESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTD  380 (512)
T ss_pred             cccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhc
Confidence              123455666665543321 112   22346999999999999999998753

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.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.25  E-value=1.8e-05  Score=77.48  Aligned_cols=157  Identities=16%  Similarity=0.164  Sum_probs=93.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFD-QVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      ..-+.|+|++|+|||+|++.+++..... +.. .+.|++.      .++...+...+...        ....+.+.+.. 
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l~~~-~~~~~v~yi~~------~~f~~~~~~~~~~~--------~~~~f~~~~~~-  193 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYVVQN-EPDLRVMYITS------EKFLNDLVDSMKEG--------KLNEFREKYRK-  193 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHHHh-CCCCeEEEEEH------HHHHHHHHHHHhcc--------cHHHHHHHHHh-
Confidence            3458899999999999999999987643 222 4556543      45566665555321        12233344332 


Q ss_pred             CeEEEEEeCCCCCc---cc-ccccCCCCC-CCCCcEEEEEec-chhh----hhh---cCCCcceEecCCCCHHHHHHHHH
Q 042806          254 KTILVILDNIWGNL---DF-QAVGIPHGD-DRKGCKVLLTAR-SLDV----LSR---KMDSQQNFSVGVLKEDEAWSLFK  320 (390)
Q Consensus       254 ~~~LlVlDdv~~~~---~~-~~l~~~l~~-~~~~s~IivTtr-~~~v----~~~---~~~~~~~~~l~~L~~~ea~~lf~  320 (390)
                      +.-+|++||++...   .+ ..+...+.. ...|..||+||. ...-    ...   .+..+..+++++.+.+.-..+++
T Consensus       194 ~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~  273 (440)
T PRK14088        194 KVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIAR  273 (440)
T ss_pred             cCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHH
Confidence            22589999997431   11 122222211 123456888875 2211    111   23455688999999999999999


Q ss_pred             HhhCCCCCCCchHHHHHHHHHHcCCChH
Q 042806          321 KMAGDYIEGSEFKWVAKDVARECAGLPV  348 (390)
Q Consensus       321 ~~~~~~~~~~~~~~~~~~i~~~~~GlPL  348 (390)
                      +.+......- -+++...|++.+.|..-
T Consensus       274 ~~~~~~~~~l-~~ev~~~Ia~~~~~~~R  300 (440)
T PRK14088        274 KMLEIEHGEL-PEEVLNFVAENVDDNLR  300 (440)
T ss_pred             HHHHhcCCCC-CHHHHHHHHhccccCHH
Confidence            8875221111 24567788888877533

>CHL00181 cbbX CbbX; Provisional

Probab=98.25  E-value=1.3e-05  Score=73.81  Aligned_cols=132  Identities=15%  Similarity=0.127  Sum_probs=73.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeE
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTI  256 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~  256 (390)
                      .+.++|++|+||||+|+.++......+.-....|+.++.    .++....   .+..     .    ......+.....-
T Consensus        61 ~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~----~~l~~~~---~g~~-----~----~~~~~~l~~a~gg  124 (287)
T CHL00181         61 HMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTR----DDLVGQY---IGHT-----A----PKTKEVLKKAMGG  124 (287)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecH----HHHHHHH---hccc-----h----HHHHHHHHHccCC
Confidence            477899999999999999988764322222222555542    2222221   1110     0    1112222221225


Q ss_pred             EEEEeCCCCC-----------cccccccCCCCCCCCCcEEEEEecchhhhh-------hcCCCcceEecCCCCHHHHHHH
Q 042806          257 LVILDNIWGN-----------LDFQAVGIPHGDDRKGCKVLLTARSLDVLS-------RKMDSQQNFSVGVLKEDEAWSL  318 (390)
Q Consensus       257 LlVlDdv~~~-----------~~~~~l~~~l~~~~~~s~IivTtr~~~v~~-------~~~~~~~~~~l~~L~~~ea~~l  318 (390)
                      +|++|++...           ...+.+...+.+...+.+||+++.......       ........+++.+++.+|..++
T Consensus       125 VLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~~~~~~vI~ag~~~~~~~~~~~np~L~sR~~~~i~F~~~t~~el~~I  204 (287)
T CHL00181        125 VLFIDEAYYLYKPDNERDYGSEAIEILLQVMENQRDDLVVIFAGYKDRMDKFYESNPGLSSRIANHVDFPDYTPEELLQI  204 (287)
T ss_pred             EEEEEccchhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhcCHHHHHhCCceEEcCCcCHHHHHHH
Confidence            9999999642           112223233333345567777776433210       0112345899999999999999


Q ss_pred             HHHhhC
Q 042806          319 FKKMAG  324 (390)
Q Consensus       319 f~~~~~  324 (390)
                      +...+.
T Consensus       205 ~~~~l~  210 (287)
T CHL00181        205 AKIMLE  210 (287)
T ss_pred             HHHHHH
Confidence            988874

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=98.24  E-value=0.00014  Score=64.04  Aligned_cols=178  Identities=15%  Similarity=0.134  Sum_probs=106.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC-CCCCHHHHHHHHHHHhCCCCCCCCchHHH----HHHH
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS-KIQDIRKIQGEIADKLGLTLHEESDSGRA----RSLR  247 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~-~~~~~~~l~~~i~~~l~~~~~~~~~~~~~----~~l~  247 (390)
                      ++..++.++|.-|+|||++++.........   +... +.++ +..+...+...++..+..+.. .......    ..+.
T Consensus        49 d~qg~~~vtGevGsGKTv~~Ral~~s~~~d---~~~~-v~i~~~~~s~~~~~~ai~~~l~~~p~-~~~~~~~e~~~~~L~  123 (269)
T COG3267          49 DGQGILAVTGEVGSGKTVLRRALLASLNED---QVAV-VVIDKPTLSDATLLEAIVADLESQPK-VNVNAVLEQIDRELA  123 (269)
T ss_pred             cCCceEEEEecCCCchhHHHHHHHHhcCCC---ceEE-EEecCcchhHHHHHHHHHHHhccCcc-chhHHHHHHHHHHHH
Confidence            456799999999999999999555554322   1222 4443 455778888888888877322 2222222    2333


Q ss_pred             HHHhC-CCeEEEEEeCCCCC--cccccccCCC---CCCCCCcEEEEEecchhhhh------hcC-CCcce-EecCCCCHH
Q 042806          248 NRLKK-EKTILVILDNIWGN--LDFQAVGIPH---GDDRKGCKVLLTARSLDVLS------RKM-DSQQN-FSVGVLKED  313 (390)
Q Consensus       248 ~~l~~-~~~~LlVlDdv~~~--~~~~~l~~~l---~~~~~~s~IivTtr~~~v~~------~~~-~~~~~-~~l~~L~~~  313 (390)
                      ...+. +++..+++|+.++.  +.++.++...   .+....-+|+.....+-...      ... .-... |++.|++.+
T Consensus       124 al~~~g~r~v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~~~~  203 (269)
T COG3267         124 ALVKKGKRPVVLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLTEA  203 (269)
T ss_pred             HHHHhCCCCeEEeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecCCcChH
Confidence            33344 45599999999755  3333332211   11111234555554321110      000 11123 999999999


Q ss_pred             HHHHHHHHhhCCC--CCCCchHHHHHHHHHHcCCChHHHHHHHH
Q 042806          314 EAWSLFKKMAGDY--IEGSEFKWVAKDVARECAGLPVSIVTVAR  355 (390)
Q Consensus       314 ea~~lf~~~~~~~--~~~~~~~~~~~~i~~~~~GlPLai~~l~~  355 (390)
                      +...++++++...  ..+--.++....|.....|.|.+|..++.
T Consensus       204 ~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~  247 (269)
T COG3267         204 ETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLAT  247 (269)
T ss_pred             HHHHHHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHHH
Confidence            9999999888622  22222245677899999999999988763

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.22  E-value=2.1e-05  Score=83.34  Aligned_cols=158  Identities=13%  Similarity=0.152  Sum_probs=89.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCC----CeEEEEEeCCCCCHHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLF----DQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f----~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      .++++||+.++.++++.|.......+.++|++|+|||+++..+..........    ...+|. +    +...++.    
T Consensus       172 ~~~~igr~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~-l----~~~~l~a----  242 (852)
T TIGR03346       172 LDPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLA-L----DMGALIA----  242 (852)
T ss_pred             CCcCCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEE-e----eHHHHhh----
Confidence            46799999999999999987666667799999999999999999886432111    222221 1    1111110    


Q ss_pred             HhCCCCCCCCchHHHHHHHHHHh-CCCeEEEEEeCCCCCcc---------cccccCCCCCCCCCcEEEEEecchhhh---
Q 042806          229 KLGLTLHEESDSGRARSLRNRLK-KEKTILVILDNIWGNLD---------FQAVGIPHGDDRKGCKVLLTARSLDVL---  295 (390)
Q Consensus       229 ~l~~~~~~~~~~~~~~~l~~~l~-~~~~~LlVlDdv~~~~~---------~~~l~~~l~~~~~~s~IivTtr~~~v~---  295 (390)
                        + ..........+..+.+.+. .+++.+|++|+++....         ...+..+... ....++|.+|.....-   
T Consensus       243 --~-~~~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l~-~g~i~~IgaTt~~e~r~~~  318 (852)
T TIGR03346       243 --G-AKYRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALA-RGELHCIGATTLDEYRKYI  318 (852)
T ss_pred             --c-chhhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcchhHHHHHhchhhh-cCceEEEEeCcHHHHHHHh
Confidence              0 0000011223334444443 23459999999974321         1112222212 2234555555543321   


Q ss_pred             ---hhcCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          296 ---SRKMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       296 ---~~~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                         .....-...+.+...+.++..++++...
T Consensus       319 ~~d~al~rRf~~i~v~~p~~~~~~~iL~~~~  349 (852)
T TIGR03346       319 EKDAALERRFQPVFVDEPTVEDTISILRGLK  349 (852)
T ss_pred             hcCHHHHhcCCEEEeCCCCHHHHHHHHHHHH
Confidence               0011122468899999999999988664

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.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=98.20  E-value=4e-05  Score=74.93  Aligned_cols=153  Identities=8%  Similarity=0.070  Sum_probs=89.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      ..+.|+|+.|+|||+|++.+++.....  -..++|++      ..++...+...+...        ....+.+.+...  
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~--~~~v~yi~------~~~f~~~~~~~l~~~--------~~~~f~~~~~~~--  203 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRES--GGKILYVR------SELFTEHLVSAIRSG--------EMQRFRQFYRNV--  203 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHc--CCCEEEee------HHHHHHHHHHHHhcc--------hHHHHHHHcccC--
Confidence            568899999999999999999987543  22345543      344555555554321        122344444332  


Q ss_pred             EEEEEeCCCCCcc----cccccCCCCC-CCCCcEEEEEecch-h----hh---hhcCCCcceEecCCCCHHHHHHHHHHh
Q 042806          256 ILVILDNIWGNLD----FQAVGIPHGD-DRKGCKVLLTARSL-D----VL---SRKMDSQQNFSVGVLKEDEAWSLFKKM  322 (390)
Q Consensus       256 ~LlVlDdv~~~~~----~~~l~~~l~~-~~~~s~IivTtr~~-~----v~---~~~~~~~~~~~l~~L~~~ea~~lf~~~  322 (390)
                      -+|++||++....    .+.+...+.. ...|..||+||... .    +.   ...+..+..+++.+++.++-..++.+.
T Consensus       204 dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k  283 (445)
T PRK12422        204 DALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERK  283 (445)
T ss_pred             CEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHH
Confidence            4889999975422    1122222210 12345688888542 1    11   112445679999999999999999888


Q ss_pred             hCCCCCCCchHHHHHHHHHHcCCCh
Q 042806          323 AGDYIEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       323 ~~~~~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      +...... --+++...|+..+.|.-
T Consensus       284 ~~~~~~~-l~~evl~~la~~~~~di  307 (445)
T PRK12422        284 AEALSIR-IEETALDFLIEALSSNV  307 (445)
T ss_pred             HHHcCCC-CCHHHHHHHHHhcCCCH
Confidence            7522111 12456666777776443

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.19  E-value=3e-05  Score=81.96  Aligned_cols=157  Identities=13%  Similarity=0.159  Sum_probs=88.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCC----CCe-EEEEEeCCCCCHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKL----FDQ-VIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~----f~~-~~wv~v~~~~~~~~l~~~i~  227 (390)
                      .++++||+.++.++++.|.......+.++|++|+|||++|..+.........    ... .+++.++.      ++..  
T Consensus       177 l~~vigr~~ei~~~i~iL~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~------l~ag--  248 (857)
T PRK10865        177 LDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGA------LVAG--  248 (857)
T ss_pred             CCcCCCCHHHHHHHHHHHhcCCcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEehhh------hhhc--
Confidence            5689999999999999998766667779999999999999999998643211    122 22222221      1100  


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHH-hCCCeEEEEEeCCCCCc---------ccccccCCCCCCCCCcEEEEEecchhhh--
Q 042806          228 DKLGLTLHEESDSGRARSLRNRL-KKEKTILVILDNIWGNL---------DFQAVGIPHGDDRKGCKVLLTARSLDVL--  295 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l-~~~~~~LlVlDdv~~~~---------~~~~l~~~l~~~~~~s~IivTtr~~~v~--  295 (390)
                           ..........+..+.+.+ ..+++.+|++|+++...         +...+..+... ....++|-+|.....-  
T Consensus       249 -----~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l~-~g~l~~IgaTt~~e~r~~  322 (857)
T PRK10865        249 -----AKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALA-RGELHCVGATTLDEYRQY  322 (857)
T ss_pred             -----cchhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCccchhHHHHhcchhh-cCCCeEEEcCCCHHHHHH
Confidence                 000001112233333333 22345999999997442         11222222222 2234566555544320  


Q ss_pred             ----hhcCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          296 ----SRKMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       296 ----~~~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                          .....-...+.+...+.++...+++...
T Consensus       323 ~~~d~al~rRf~~i~v~eP~~~~~~~iL~~l~  354 (857)
T PRK10865        323 IEKDAALERRFQKVFVAEPSVEDTIAILRGLK  354 (857)
T ss_pred             hhhcHHHHhhCCEEEeCCCCHHHHHHHHHHHh
Confidence                0011122356677778899999887655

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

Probab=98.19  E-value=4e-06  Score=67.65  Aligned_cols=23  Identities=35%  Similarity=0.338  Sum_probs=21.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.|+|++|+|||++++.+++...
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~   23 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLG   23 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTT
T ss_pred             CEEECcCCCCeeHHHHHHHhhcc
Confidence            57999999999999999999975

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 ....

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=98.19  E-value=7.9e-05  Score=69.56  Aligned_cols=195  Identities=13%  Similarity=0.109  Sum_probs=109.7

Q ss_pred             ccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhc--------------CCCCeEEEEEeCCCCC
Q 042806          154 EACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETE--------------KLFDQVIFVEVSKIQD  218 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~--------------~~f~~~~wv~v~~~~~  218 (390)
                      ..++|.+...+.+...+..++ .+...++|+.|+||+++|..+.+..-..              .|.| ..|+.-.....
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPD-l~~i~p~~~~~   82 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPD-LLWVEPTYQHQ   82 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCC-EEEEecccccc
Confidence            367899999999999998877 4789999999999999999998875322              1222 23332110000


Q ss_pred             HHHHHHHHHHHhCC--CCCCCCchHHHHHHHHHHhC----CCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEec
Q 042806          219 IRKIQGEIADKLGL--TLHEESDSGRARSLRNRLKK----EKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTAR  290 (390)
Q Consensus       219 ~~~l~~~i~~~l~~--~~~~~~~~~~~~~l~~~l~~----~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr  290 (390)
                      -..+-..-+...+.  .....-..+.+..+.+.+..    +++-++|+|+++..  ...+.+...+-.-. .+.+|++|.
T Consensus        83 g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEPp-~~~fILi~~  161 (314)
T PRK07399         83 GKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEPG-NGTLILIAP  161 (314)
T ss_pred             ccccchhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCCC-CCeEEEEEC
Confidence            00000000111110  00000011223445554431    23369999998654  23344433332222 344555554


Q ss_pred             -chhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          291 -SLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       291 -~~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                       ...+......-...+++.+++.++..+.+.+.......    ......++..++|.|..+..+.
T Consensus       162 ~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~~~----~~~~~~l~~~a~Gs~~~al~~l  222 (314)
T PRK07399        162 SPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEIL----NINFPELLALAQGSPGAAIANI  222 (314)
T ss_pred             ChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhccccc----hhHHHHHHHHcCCCHHHHHHHH
Confidence             44444434445579999999999999999887532111    1113578999999997665543

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

Probab=98.19  E-value=2e-05  Score=75.91  Aligned_cols=175  Identities=15%  Similarity=0.215  Sum_probs=96.7

Q ss_pred             cccccchhHHHHHHHHHhc----C---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALK----N---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~----~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ..++.|-+..+++|.+.+.    .         +.++-+.++|++|+|||+||+.+++.....  |     +.+..    
T Consensus       144 ~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~~--f-----i~i~~----  212 (398)
T PTZ00454        144 YSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTAT--F-----IRVVG----  212 (398)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCC--E-----EEEeh----
Confidence            4457777776666655442    1         235778999999999999999999876432  2     22211    


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc------------c----cccccCCCC--CCCC
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL------------D----FQAVGIPHG--DDRK  281 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~------------~----~~~l~~~l~--~~~~  281 (390)
                      .++...   .++      .....+..+........+.+|+||+++...            .    +..+...+.  ....
T Consensus       213 s~l~~k---~~g------e~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~  283 (398)
T PTZ00454        213 SEFVQK---YLG------EGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTT  283 (398)
T ss_pred             HHHHHH---hcc------hhHHHHHHHHHHHHhcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCCCC
Confidence            111111   111      111233444455555567999999986321            0    111111111  1224


Q ss_pred             CcEEEEEecchhhh-hhcC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHH
Q 042806          282 GCKVLLTARSLDVL-SRKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVS  349 (390)
Q Consensus       282 ~s~IivTtr~~~v~-~~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLa  349 (390)
                      +..||+||...... ....   .....+++...+.++-.++|+.+.......++..  ...+++.+.|+.-|
T Consensus       284 ~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~dvd--~~~la~~t~g~sga  353 (398)
T PTZ00454        284 NVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVD--LEDFVSRPEKISAA  353 (398)
T ss_pred             CEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCcccC--HHHHHHHcCCCCHH
Confidence            56788888754332 1112   2235788999999998888887764222222111  34667777666433

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.17  E-value=9.1e-06  Score=65.85  Aligned_cols=90  Identities=29%  Similarity=0.200  Sum_probs=51.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      ..+.|+|++|+||||+++.++.......  ...+++..+........... ...................+.+.....+.
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPG--GGVIYIDGEDILEEVLDQLL-LIIVGGKKASGSGELRLRLALALARKLKP   79 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCC--CCEEEECCEEccccCHHHHH-hhhhhccCCCCCHHHHHHHHHHHHHhcCC
Confidence            5788999999999999999999876432  23555555443221111111 11111122222333344455555554445


Q ss_pred             EEEEEeCCCCCcc
Q 042806          256 ILVILDNIWGNLD  268 (390)
Q Consensus       256 ~LlVlDdv~~~~~  268 (390)
                      .++++|++.....
T Consensus        80 ~viiiDei~~~~~   92 (148)
T smart00382       80 DVLILDEITSLLD   92 (148)
T ss_pred             CEEEEECCcccCC
Confidence            8999999986643

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.

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

Probab=98.14  E-value=1.9e-05  Score=76.02  Aligned_cols=69  Identities=20%  Similarity=0.145  Sum_probs=56.3

Q ss_pred             ccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 042806          154 EACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQG  224 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~  224 (390)
                      ..++..+..++.++..|..  .+.+.++|++|+|||++|+.+++.......|+.+.||.+++..+..+++.
T Consensus       175 ~d~~i~e~~le~l~~~L~~--~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~  243 (459)
T PRK11331        175 NDLFIPETTIETILKRLTI--KKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQ  243 (459)
T ss_pred             hcccCCHHHHHHHHHHHhc--CCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhc
Confidence            3466778888889888874  34677899999999999999999886655688899999999888777654

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=98.14  E-value=0.0001  Score=73.61  Aligned_cols=179  Identities=21%  Similarity=0.230  Sum_probs=95.2

Q ss_pred             cccccchhHHHHH---HHHHhcC---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 042806          153 YEACESRMSTLND---ILDALKN---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       153 ~~~~~gR~~~~~~---l~~~L~~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  220 (390)
                      ..++.|-+...++   +++++..         ..++-+.++|++|+|||+||+.+++.....       ++.++.    .
T Consensus        54 ~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~-------~~~i~~----~  122 (495)
T TIGR01241        54 FKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVP-------FFSISG----S  122 (495)
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCC-------eeeccH----H
Confidence            4456676554444   4444332         224568899999999999999998876432       222321    1


Q ss_pred             HHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc------------c----ccccCCCC--CCCCC
Q 042806          221 KIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD------------F----QAVGIPHG--DDRKG  282 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~------------~----~~l~~~l~--~~~~~  282 (390)
                      ++....   .+      .....+..+.+......+++|+||+++....            +    ..+...+.  ....+
T Consensus       123 ~~~~~~---~g------~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~  193 (495)
T TIGR01241       123 DFVEMF---VG------VGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTG  193 (495)
T ss_pred             HHHHHH---hc------ccHHHHHHHHHHHHhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCC
Confidence            111110   01      0112233444444445569999999964310            0    11111111  12334


Q ss_pred             cEEEEEecchhhh-hhcC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh-HHHHHH
Q 042806          283 CKVLLTARSLDVL-SRKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP-VSIVTV  353 (390)
Q Consensus       283 s~IivTtr~~~v~-~~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP-Lai~~l  353 (390)
                      ..||.||...... ....   .....+++...+.++-.++|..++.......+  .....+++.+.|.- --|..+
T Consensus       194 v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~~~--~~l~~la~~t~G~sgadl~~l  267 (495)
T TIGR01241       194 VIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPD--VDLKAVARRTPGFSGADLANL  267 (495)
T ss_pred             eEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCCcc--hhHHHHHHhCCCCCHHHHHHH
Confidence            5666667653321 1111   23358889999999889999887753222222  12457888887743 344443

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.

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

Probab=98.09  E-value=7.9e-05  Score=66.51  Aligned_cols=178  Identities=14%  Similarity=0.100  Sum_probs=104.4

Q ss_pred             cCcccccchhHHHHHHHHHhc-----CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          151 KDYEACESRMSTLNDILDALK-----NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~-----~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      .....|+|.++-.++|-=.+.     +..+--+.++||+|.||||||..+++...+.  +.    +..++-         
T Consensus        23 ~~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn--~k----~tsGp~---------   87 (332)
T COG2255          23 KTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELGVN--LK----ITSGPA---------   87 (332)
T ss_pred             ccHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhcCC--eE----eccccc---------
Confidence            335679998887777755443     2345668899999999999999999998764  21    111111         


Q ss_pred             HHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc---------ccccccCCC-CCCC-----------CCcE
Q 042806          226 IADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL---------DFQAVGIPH-GDDR-----------KGCK  284 (390)
Q Consensus       226 i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~---------~~~~l~~~l-~~~~-----------~~s~  284 (390)
                                 ......+..+...|..+.  ++.+|.++...         ..+++..-. -..+           +-.-
T Consensus        88 -----------leK~gDlaaiLt~Le~~D--VLFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTL  154 (332)
T COG2255          88 -----------LEKPGDLAAILTNLEEGD--VLFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTL  154 (332)
T ss_pred             -----------ccChhhHHHHHhcCCcCC--eEEEehhhhcChhHHHHhhhhhhheeEEEEEccCCccceEeccCCCeeE
Confidence                       111112222333344434  66677776331         111111100 0112           2234


Q ss_pred             EEEEecchhhhhh-cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHh
Q 042806          285 VLLTARSLDVLSR-KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARAL  357 (390)
Q Consensus       285 IivTtr~~~v~~~-~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L  357 (390)
                      |=.|||.-.+..- ....+.+.+++..+.+|-.++..+.+..-.. .-.++.+.+|+++..|-|--..-+-+-.
T Consensus       155 IGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i-~i~~~~a~eIA~rSRGTPRIAnRLLrRV  227 (332)
T COG2255         155 IGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGI-EIDEEAALEIARRSRGTPRIANRLLRRV  227 (332)
T ss_pred             eeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCC-CCChHHHHHHHHhccCCcHHHHHHHHHH
Confidence            5578886544211 1223458889999999999999888751111 1113467899999999998766555433

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

Probab=98.09  E-value=1.1e-05  Score=83.56  Aligned_cols=158  Identities=16%  Similarity=0.163  Sum_probs=91.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC-C---CCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEK-L---FDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~-~---f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      .++++||+.++.++++.|......-+.++|++|+|||++|+.+++.....+ .   .++.+|. .    +...++.    
T Consensus       185 ~~~liGR~~ei~~~i~iL~r~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~-l----~~~~lla----  255 (758)
T PRK11034        185 IDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYS-L----DIGSLLA----  255 (758)
T ss_pred             CCcCcCCCHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEe-c----cHHHHhc----
Confidence            467999999999999988875555567899999999999999998753321 1   1334441 1    1111110    


Q ss_pred             HhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--------c--ccccccCCCCCCCCCcEEEEEecchhhh---
Q 042806          229 KLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--------L--DFQAVGIPHGDDRKGCKVLLTARSLDVL---  295 (390)
Q Consensus       229 ~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--------~--~~~~l~~~l~~~~~~s~IivTtr~~~v~---  295 (390)
                        + .............+.+.+....+.+|++|+++..        .  +...+..++.. ....++|-+|......   
T Consensus       256 --G-~~~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~-~g~i~vIgATt~~E~~~~~  331 (758)
T PRK11034        256 --G-TKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS-SGKIRVIGSTTYQEFSNIF  331 (758)
T ss_pred             --c-cchhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHh-CCCeEEEecCChHHHHHHh
Confidence              0 0001112223344444454444589999999732        1  11111222212 2334566665543321   


Q ss_pred             ---hhcCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          296 ---SRKMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       296 ---~~~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                         .....-...+++.+++.++..++++...
T Consensus       332 ~~D~AL~rRFq~I~v~ePs~~~~~~IL~~~~  362 (758)
T PRK11034        332 EKDRALARRFQKIDITEPSIEETVQIINGLK  362 (758)
T ss_pred             hccHHHHhhCcEEEeCCCCHHHHHHHHHHHH
Confidence               0011122589999999999999998764

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=98.09  E-value=9.9e-05  Score=69.29  Aligned_cols=151  Identities=15%  Similarity=0.119  Sum_probs=89.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcC--------------------CCCeEEEEEeC---CCCCHHHHHHHHHHHhC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEK--------------------LFDQVIFVEVS---KIQDIRKIQGEIADKLG  231 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~--------------------~f~~~~wv~v~---~~~~~~~l~~~i~~~l~  231 (390)
                      ...+.++|+.|+|||++|+.+....--..                    |.| ..|+.-.   ....+            
T Consensus        22 ~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD-~~~i~~~~~~~~i~i------------   88 (328)
T PRK05707         22 PHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPD-NFVLEPEEADKTIKV------------   88 (328)
T ss_pred             ceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCC-EEEEeccCCCCCCCH------------
Confidence            56788999999999999999988864221                    112 1122110   01111            


Q ss_pred             CCCCCCCchHHHHHHHHHHh-----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecch-hhhhhcCCCcc
Q 042806          232 LTLHEESDSGRARSLRNRLK-----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSL-DVLSRKMDSQQ  303 (390)
Q Consensus       232 ~~~~~~~~~~~~~~l~~~l~-----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~-~v~~~~~~~~~  303 (390)
                               +.+..+.+.+.     +++ -++|+|+++..  ...+.+...+-.-..++.+|++|.+. .+.....+-..
T Consensus        89 ---------d~iR~l~~~~~~~~~~~~~-kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~  158 (328)
T PRK05707         89 ---------DQVRELVSFVVQTAQLGGR-KVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQ  158 (328)
T ss_pred             ---------HHHHHHHHHHhhccccCCC-eEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhce
Confidence                     12222333321     234 45678999754  34444544443333567777777764 44333334456


Q ss_pred             eEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          304 NFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       304 ~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      .+++.+++.+++.+.+...... .    .++.+..++..++|.|+....+
T Consensus       159 ~~~~~~~~~~~~~~~L~~~~~~-~----~~~~~~~~l~la~Gsp~~A~~l  203 (328)
T PRK05707        159 QQACPLPSNEESLQWLQQALPE-S----DERERIELLTLAGGSPLRALQL  203 (328)
T ss_pred             eeeCCCcCHHHHHHHHHHhccc-C----ChHHHHHHHHHcCCCHHHHHHH
Confidence            8999999999999988776421 1    1233557889999999865544

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

Probab=98.08  E-value=2.1e-05  Score=74.83  Aligned_cols=132  Identities=16%  Similarity=0.162  Sum_probs=82.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      ...+.|||+.|.|||.|++.+.+.....  ......+.+    +.++....++..+..        .....+.+.. +- 
T Consensus       113 ~nplfi~G~~GlGKTHLl~Aign~~~~~--~~~a~v~y~----~se~f~~~~v~a~~~--------~~~~~Fk~~y-~~-  176 (408)
T COG0593         113 YNPLFIYGGVGLGKTHLLQAIGNEALAN--GPNARVVYL----TSEDFTNDFVKALRD--------NEMEKFKEKY-SL-  176 (408)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHhh--CCCceEEec----cHHHHHHHHHHHHHh--------hhHHHHHHhh-cc-
Confidence            6789999999999999999999998754  332233333    334444444444322        1234455554 32 


Q ss_pred             eEEEEEeCCCCCc---ccc-cccCCCCC-CCCCcEEEEEecch---------hhhhhcCCCcceEecCCCCHHHHHHHHH
Q 042806          255 TILVILDNIWGNL---DFQ-AVGIPHGD-DRKGCKVLLTARSL---------DVLSRKMDSQQNFSVGVLKEDEAWSLFK  320 (390)
Q Consensus       255 ~~LlVlDdv~~~~---~~~-~l~~~l~~-~~~~s~IivTtr~~---------~v~~~~~~~~~~~~l~~L~~~ea~~lf~  320 (390)
                       =++++||++-..   .|+ .+...|.. ...|-.||+|++..         .+. ..+..+-.+++.+.+.+....+++
T Consensus       177 -dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~-SR~~~Gl~~~I~~Pd~e~r~aiL~  254 (408)
T COG0593         177 -DLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLR-SRLEWGLVVEIEPPDDETRLAILR  254 (408)
T ss_pred             -CeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHH-HHHhceeEEeeCCCCHHHHHHHHH
Confidence             389999997532   222 23222221 12334899999642         221 235566899999999999999999


Q ss_pred             HhhC
Q 042806          321 KMAG  324 (390)
Q Consensus       321 ~~~~  324 (390)
                      +.+.
T Consensus       255 kka~  258 (408)
T COG0593         255 KKAE  258 (408)
T ss_pred             HHHH
Confidence            8775

>CHL00176 ftsH cell division protein; Validated

Probab=98.06  E-value=6.2e-05  Score=76.61  Aligned_cols=169  Identities=20%  Similarity=0.265  Sum_probs=93.9

Q ss_pred             cccchhH---HHHHHHHHhcCC---------CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHH
Q 042806          155 ACESRMS---TLNDILDALKNP---------DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKI  222 (390)
Q Consensus       155 ~~~gR~~---~~~~l~~~L~~~---------~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l  222 (390)
                      ++.|.++   ++.++++.+..+         .++-+.++|++|+|||+||+.++......       |+.++..    ++
T Consensus       184 dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~p-------~i~is~s----~f  252 (638)
T CHL00176        184 DIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVP-------FFSISGS----EF  252 (638)
T ss_pred             hccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCC-------eeeccHH----HH
Confidence            4555543   445555555542         24568899999999999999998876432       2333221    11


Q ss_pred             HHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc------------c----cccccCCCC--CCCCCcE
Q 042806          223 QGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL------------D----FQAVGIPHG--DDRKGCK  284 (390)
Q Consensus       223 ~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~------------~----~~~l~~~l~--~~~~~s~  284 (390)
                      ....   .+      .....+..+.+......+++|+|||++...            .    +..+...+.  ....+..
T Consensus       253 ~~~~---~g------~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~Vi  323 (638)
T CHL00176        253 VEMF---VG------VGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVI  323 (638)
T ss_pred             HHHh---hh------hhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCee
Confidence            1100   01      011123334444445567999999996331            1    111211111  1234566


Q ss_pred             EEEEecchhhhh-hcC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC
Q 042806          285 VLLTARSLDVLS-RKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAG  345 (390)
Q Consensus       285 IivTtr~~~v~~-~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~G  345 (390)
                      ||.||....... ...   .....+.+...+.++-.++|+.++......+  ......+++.+.|
T Consensus       324 VIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~~~--d~~l~~lA~~t~G  386 (638)
T CHL00176        324 VIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSP--DVSLELIARRTPG  386 (638)
T ss_pred             EEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhcccch--hHHHHHHHhcCCC
Confidence            777776643321 111   1235888999999999999988875322222  2235678888887

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

Probab=98.05  E-value=0.00027  Score=62.46  Aligned_cols=53  Identities=13%  Similarity=0.172  Sum_probs=40.2

Q ss_pred             ccCcccccchhHHHHHHHHH----hcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          150 IKDYEACESRMSTLNDILDA----LKNPDVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       150 ~~~~~~~~gR~~~~~~l~~~----L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      +.+.+.++|-+...+.|++.    +.+....-+.+||..|.|||+|++.+.+....+
T Consensus        23 ~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~   79 (249)
T PF05673_consen   23 PIRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQ   79 (249)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhc
Confidence            34456788888888777654    333444567789999999999999999987654

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

Probab=98.05  E-value=0.00024  Score=65.55  Aligned_cols=184  Identities=18%  Similarity=0.245  Sum_probs=110.2

Q ss_pred             CcccccchhHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 042806          152 DYEACESRMSTLNDILDALKN-------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD  218 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  218 (390)
                      .+..+.|-++.+.+|.+.+.-             +.++=|.+|||+|.|||-||+.|++....       .|+.+...  
T Consensus       149 tY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~A-------tFIrvvgS--  219 (406)
T COG1222         149 TYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDA-------TFIRVVGS--  219 (406)
T ss_pred             ChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccCc-------eEEEeccH--
Confidence            355677778878777776542             35677889999999999999999998753       34444332  


Q ss_pred             HHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC-------------cc---cccccCCCC--CCC
Q 042806          219 IRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN-------------LD---FQAVGIPHG--DDR  280 (390)
Q Consensus       219 ~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~-------------~~---~~~l~~~l~--~~~  280 (390)
                        ++.+..   +|      .-..++..+.+.-+.+.++.|.+|.++..             +.   .-.|...+.  +..
T Consensus       220 --ElVqKY---iG------EGaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~  288 (406)
T COG1222         220 --ELVQKY---IG------EGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPR  288 (406)
T ss_pred             --HHHHHH---hc------cchHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCC
Confidence              222221   12      23456778888888889999999999632             00   111111111  123


Q ss_pred             CCcEEEEEecchhhhh-hcCC---CcceEecCCCCHHHHHHHHHHhhC--CCCCCCchHHHHHHHHHHcCCChH----HH
Q 042806          281 KGCKVLLTARSLDVLS-RKMD---SQQNFSVGVLKEDEAWSLFKKMAG--DYIEGSEFKWVAKDVARECAGLPV----SI  350 (390)
Q Consensus       281 ~~s~IivTtr~~~v~~-~~~~---~~~~~~l~~L~~~ea~~lf~~~~~--~~~~~~~~~~~~~~i~~~~~GlPL----ai  350 (390)
                      ...|||..|...++.. ..+.   -.+.+++..-+.+.=.++|+-+..  .-....+++    .+++.|.|.-=    ||
T Consensus       289 ~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e----~la~~~~g~sGAdlkai  364 (406)
T COG1222         289 GNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLE----LLARLTEGFSGADLKAI  364 (406)
T ss_pred             CCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcCHH----HHHHhcCCCchHHHHHH
Confidence            4568888887655432 1122   235777775555555677776664  233334444    56667766542    34


Q ss_pred             HHHHHHhcC
Q 042806          351 VTVARALGT  359 (390)
Q Consensus       351 ~~l~~~L~~  359 (390)
                      -+=|+++.-
T Consensus       365 ctEAGm~Ai  373 (406)
T COG1222         365 CTEAGMFAI  373 (406)
T ss_pred             HHHHhHHHH
Confidence            444666543

>TIGR00602 rad24 checkpoint protein rad24

Probab=98.02  E-value=2.7e-05  Score=78.71  Aligned_cols=51  Identities=18%  Similarity=0.154  Sum_probs=41.8

Q ss_pred             ccCcccccchhHHHHHHHHHhcCC-----CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          150 IKDYEACESRMSTLNDILDALKNP-----DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       150 ~~~~~~~~gR~~~~~~l~~~L~~~-----~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.....+++.+..+.++..++...     ..+++.|+|++|+||||+++.++....
T Consensus        80 P~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~  135 (637)
T TIGR00602        80 PETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELG  135 (637)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhh
Confidence            444677899999999998888652     345799999999999999999998764

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

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

Probab=98.01  E-value=4e-05  Score=74.36  Aligned_cols=172  Identities=18%  Similarity=0.219  Sum_probs=96.0

Q ss_pred             cccccchhHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALKN-------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ..++.|.+..+++|.+.+.-             ..++-+.++|++|+|||++|+.+++.....  |     +.+...   
T Consensus       182 ~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~--f-----i~V~~s---  251 (438)
T PTZ00361        182 YADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSAT--F-----LRVVGS---  251 (438)
T ss_pred             HHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCCC--E-----EEEecc---
Confidence            34567888777777665531             234568899999999999999999976432  3     222211   


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--------c--------cccccCCCC--CCCC
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--------D--------FQAVGIPHG--DDRK  281 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--------~--------~~~l~~~l~--~~~~  281 (390)
                       ++....   .+      .....+..+.+......+++|+||+++...        .        +..+...+.  ....
T Consensus       252 -eL~~k~---~G------e~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~  321 (438)
T PTZ00361        252 -ELIQKY---LG------DGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRG  321 (438)
T ss_pred             -hhhhhh---cc------hHHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhcccC
Confidence             111110   00      111223444444444566899999985321        0        001111111  1233


Q ss_pred             CcEEEEEecchhhhhh-cC---CCcceEecCCCCHHHHHHHHHHhhCCCC--CCCchHHHHHHHHHHcCCChH
Q 042806          282 GCKVLLTARSLDVLSR-KM---DSQQNFSVGVLKEDEAWSLFKKMAGDYI--EGSEFKWVAKDVARECAGLPV  348 (390)
Q Consensus       282 ~s~IivTtr~~~v~~~-~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~--~~~~~~~~~~~i~~~~~GlPL  348 (390)
                      +..||.||........ ..   .....+++.+.+.++-.++|..++....  ...++    ..++..+.|+-=
T Consensus       322 ~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dvdl----~~la~~t~g~sg  390 (438)
T PTZ00361        322 DVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDL----EEFIMAKDELSG  390 (438)
T ss_pred             CeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCcCH----HHHHHhcCCCCH
Confidence            5678888876433222 11   2235889999999999999998774222  12232    356666655543

>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=97.98  E-value=0.00044  Score=65.84  Aligned_cols=197  Identities=13%  Similarity=0.179  Sum_probs=122.9

Q ss_pred             hhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHH-HHHHHHhhhcCCCCeEEEEEeCCC---CCHHHHHHHHHHHhCCCC
Q 042806          159 RMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLA-KEVARKAETEKLFDQVIFVEVSKI---QDIRKIQGEIADKLGLTL  234 (390)
Q Consensus       159 R~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa-~~v~~~~~~~~~f~~~~wv~v~~~---~~~~~l~~~i~~~l~~~~  234 (390)
                      |.+..++|-.||.+..-.+|.|.||.|+||+.|+ .++..+.+      .+..+.+.+-   .+-..++..++.++|.-+
T Consensus         1 R~e~~~~L~~wL~e~~~TFIvV~GPrGSGK~elV~d~~L~~r~------~vL~IDC~~i~~ar~D~~~I~~lA~qvGY~P   74 (431)
T PF10443_consen    1 RKEAIEQLKSWLNENPNTFIVVQGPRGSGKRELVMDHVLKDRK------NVLVIDCDQIVKARGDAAFIKNLASQVGYFP   74 (431)
T ss_pred             CchHHHHHHHHHhcCCCeEEEEECCCCCCccHHHHHHHHhCCC------CEEEEEChHhhhccChHHHHHHHHHhcCCCc
Confidence            5677899999999988889999999999999999 77766533      2677777542   345566677777765321


Q ss_pred             C-----------------------C--CCchHHH--------HHHHHH-------------------Hh--CCCeEEEEE
Q 042806          235 H-----------------------E--ESDSGRA--------RSLRNR-------------------LK--KEKTILVIL  260 (390)
Q Consensus       235 ~-----------------------~--~~~~~~~--------~~l~~~-------------------l~--~~~~~LlVl  260 (390)
                      -                       .  .+....+        ..|+..                   |.  ..++-+||+
T Consensus        75 vFsw~nSiss~IDLa~qGltGqKaGfSes~e~Ql~~IL~~t~~ALr~ial~~~~~~~~~~~l~e~~yl~~hPe~~PVVVI  154 (431)
T PF10443_consen   75 VFSWMNSISSFIDLAVQGLTGQKAGFSESLETQLKKILQTTATALRDIALSNRKKDDKDANLKEEDYLEAHPERRPVVVI  154 (431)
T ss_pred             chHHHHHHHHHHHHHHhhccccccCCCCChHHHHHHHHHHHHHHHHHHHHHhhhccccccccCchhhhhhCCccCCEEEE
Confidence            0                       0  0111111        111110                   10  011368999


Q ss_pred             eCCCCCcc-----ccccc---CCCCCCCCCcEEEEEecchhhhh---hcC--CCcceEecCCCCHHHHHHHHHHhhCCCC
Q 042806          261 DNIWGNLD-----FQAVG---IPHGDDRKGCKVLLTARSLDVLS---RKM--DSQQNFSVGVLKEDEAWSLFKKMAGDYI  327 (390)
Q Consensus       261 Ddv~~~~~-----~~~l~---~~l~~~~~~s~IivTtr~~~v~~---~~~--~~~~~~~l~~L~~~ea~~lf~~~~~~~~  327 (390)
                      |++.....     |+.+.   ..+. .++-.+||++|-+.....   ..+  ...+.+.|.-.+++.|.++...++....
T Consensus       155 dnF~~k~~~~~~iy~~laeWAa~Lv-~~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak~yV~~~L~~~~  233 (431)
T PF10443_consen  155 DNFLHKAEENDFIYDKLAEWAASLV-QNNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAKQYVLSQLDEDT  233 (431)
T ss_pred             cchhccCcccchHHHHHHHHHHHHH-hcCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHHHHHHHHhcccc
Confidence            99864421     12110   1121 234557887777643322   122  2336889999999999999999885321


Q ss_pred             CC-------------------CchHHHHHHHHHHcCCChHHHHHHHHHhcCCCC
Q 042806          328 EG-------------------SEFKWVAKDVARECAGLPVSIVTVARALGTRDY  362 (390)
Q Consensus       328 ~~-------------------~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~~~  362 (390)
                      ..                   .....-....+..+||-=.=+..+++.++.-..
T Consensus       234 ~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRltDLe~lvrRiksGe~  287 (431)
T PF10443_consen  234 EDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLTDLEFLVRRIKSGES  287 (431)
T ss_pred             cccccccccccccccccccccccchHHHHHHHHHcCCcHHHHHHHHHHHHcCCC
Confidence            10                   123344678899999999999999998887543

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 [].

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.98  E-value=0.00023  Score=64.91  Aligned_cols=56  Identities=27%  Similarity=0.274  Sum_probs=36.9

Q ss_pred             HHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHH
Q 042806          161 STLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQ  223 (390)
Q Consensus       161 ~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~  223 (390)
                      .-++++..++..+  .-+.|.|++|+|||+||+.+.+....     ....++++...+..+++
T Consensus         9 ~l~~~~l~~l~~g--~~vLL~G~~GtGKT~lA~~la~~lg~-----~~~~i~~~~~~~~~dll   64 (262)
T TIGR02640         9 RVTSRALRYLKSG--YPVHLRGPAGTGKTTLAMHVARKRDR-----PVMLINGDAELTTSDLV   64 (262)
T ss_pred             HHHHHHHHHHhcC--CeEEEEcCCCCCHHHHHHHHHHHhCC-----CEEEEeCCccCCHHHHh
Confidence            3345555655543  34668999999999999999875421     24556666655555554

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).

>TIGR00763 lon ATP-dependent protease La

Probab=97.96  E-value=0.00043  Score=72.77  Aligned_cols=157  Identities=21%  Similarity=0.223  Sum_probs=82.4

Q ss_pred             cccchhHHHHHHHHHhc------CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          155 ACESRMSTLNDILDALK------NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~------~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      ..+|.+.-.+.+.+++.      ..+.+++.++|++|+|||++|+.+.+.....  |   .-++++...+..++...   
T Consensus       321 ~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l~~~--~---~~i~~~~~~~~~~i~g~---  392 (775)
T TIGR00763       321 DHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALNRK--F---VRFSLGGVRDEAEIRGH---  392 (775)
T ss_pred             hcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHhcCC--e---EEEeCCCcccHHHHcCC---
Confidence            46677777777776553      1244689999999999999999999987532  3   22233333333332211   


Q ss_pred             HhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc------cccccC--------CCCCC-------CCCcEEEE
Q 042806          229 KLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD------FQAVGI--------PHGDD-------RKGCKVLL  287 (390)
Q Consensus       229 ~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~------~~~l~~--------~l~~~-------~~~s~Iiv  287 (390)
                        .............+.+... ...+ -+++||+++....      ...+..        .|.+.       ..+..+|.
T Consensus       393 --~~~~~g~~~g~i~~~l~~~-~~~~-~villDEidk~~~~~~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I~  468 (775)
T TIGR00763       393 --RRTYVGAMPGRIIQGLKKA-KTKN-PLFLLDEIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIA  468 (775)
T ss_pred             --CCceeCCCCchHHHHHHHh-CcCC-CEEEEechhhcCCccCCCHHHHHHHhcCHHhcCccccccCCceeccCCEEEEE
Confidence              0001111112222222222 2233 4789999964411      011111        11111       12344555


Q ss_pred             Eecchh-hhhhcCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          288 TARSLD-VLSRKMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       288 Ttr~~~-v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                      ||.... +......-...+++.+++.++-.+++..+.
T Consensus       469 TtN~~~~i~~~L~~R~~vi~~~~~~~~e~~~I~~~~l  505 (775)
T TIGR00763       469 TANSIDTIPRPLLDRMEVIELSGYTEEEKLEIAKKYL  505 (775)
T ss_pred             ecCCchhCCHHHhCCeeEEecCCCCHHHHHHHHHHHH
Confidence            555432 222222333589999999998888886654

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.

>PRK08116 hypothetical protein; Validated

Probab=97.95  E-value=3.4e-05  Score=70.39  Aligned_cols=101  Identities=23%  Similarity=0.216  Sum_probs=60.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      ..+.++|++|+|||+||..+++.....  -..++|++      ..+++..+...+....     ......+.+.+.+.. 
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~~~--~~~v~~~~------~~~ll~~i~~~~~~~~-----~~~~~~~~~~l~~~d-  180 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELIEK--GVPVIFVN------FPQLLNRIKSTYKSSG-----KEDENEIIRSLVNAD-  180 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEE------HHHHHHHHHHHHhccc-----cccHHHHHHHhcCCC-
Confidence            458899999999999999999998654  23345554      4556666655543211     111233445555444 


Q ss_pred             EEEEEeCCC--CCccccc--ccCCCCC-CCCCcEEEEEecc
Q 042806          256 ILVILDNIW--GNLDFQA--VGIPHGD-DRKGCKVLLTARS  291 (390)
Q Consensus       256 ~LlVlDdv~--~~~~~~~--l~~~l~~-~~~~s~IivTtr~  291 (390)
                       ||||||+.  ...+|..  +...+.. ..++..+|+||..
T Consensus       181 -lLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~  220 (268)
T PRK08116        181 -LLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNL  220 (268)
T ss_pred             -EEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence             89999994  3344432  2222211 1345568888874

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=97.95  E-value=0.00034  Score=65.98  Aligned_cols=145  Identities=10%  Similarity=0.052  Sum_probs=85.6

Q ss_pred             ccc-hhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcC--------------------CCCeEEEEEe
Q 042806          156 CES-RMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEK--------------------LFDQVIFVEV  213 (390)
Q Consensus       156 ~~g-R~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~--------------------~f~~~~wv~v  213 (390)
                      ++| .+..++.+...+..++ .....++|+.|+||||+|+.+.+..--.+                    |.|.. ++..
T Consensus         7 i~~~q~~~~~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~-~i~~   85 (329)
T PRK08058          7 LTALQPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVH-LVAP   85 (329)
T ss_pred             HHhhHHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEE-Eecc
Confidence            455 5666777777777666 45678999999999999999988753221                    22211 1111


Q ss_pred             -CCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEE
Q 042806          214 -SKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVL  286 (390)
Q Consensus       214 -~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~Ii  286 (390)
                       +.....                     +.+..+.+.+.    .+++=++|+|+++..  ...+.+...+-.-..++.+|
T Consensus        86 ~~~~i~i---------------------d~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~I  144 (329)
T PRK08058         86 DGQSIKK---------------------DQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAI  144 (329)
T ss_pred             ccccCCH---------------------HHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEE
Confidence             111111                     12222333222    122248999998654  23444544443334566677


Q ss_pred             EEecc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHh
Q 042806          287 LTARS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKM  322 (390)
Q Consensus       287 vTtr~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~  322 (390)
                      ++|.+ ..+......-...+++.+++.++..+.+...
T Consensus       145 l~t~~~~~ll~TIrSRc~~i~~~~~~~~~~~~~L~~~  181 (329)
T PRK08058        145 LLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQEE  181 (329)
T ss_pred             EEeCChHhCcHHHHhhceeeeCCCCCHHHHHHHHHHc
Confidence            77765 3333333444579999999999998888653

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

Probab=97.95  E-value=4.2e-05  Score=75.02  Aligned_cols=188  Identities=15%  Similarity=0.142  Sum_probs=112.4

Q ss_pred             CcccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH-
Q 042806          152 DYEACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADK-  229 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~-  229 (390)
                      ...+++|-+.-...|.+.+..++ ..-....|+.|+||||+|+.++...--...-       ...++..=...+.|... 
T Consensus        14 ~F~evvGQe~v~~~L~nal~~~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~-------~~ePC~~C~~Ck~I~~g~   86 (515)
T COG2812          14 TFDDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENGP-------TAEPCGKCISCKEINEGS   86 (515)
T ss_pred             cHHHhcccHHHHHHHHHHHHhCcchhhhhhcCCCCcCchhHHHHHHHHhcCCCCC-------CCCcchhhhhhHhhhcCC
Confidence            34578999999999999988765 4556788999999999999998876432110       00011111111222111 


Q ss_pred             ----hCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCC--CcccccccCCCCCCCCCcEEE-EEecchhhhhhc
Q 042806          230 ----LGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWG--NLDFQAVGIPHGDDRKGCKVL-LTARSLDVLSRK  298 (390)
Q Consensus       230 ----l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~--~~~~~~l~~~l~~~~~~s~Ii-vTtr~~~v~~~~  298 (390)
                          +..+.......+.++.|.+...    .++.=+.|+|.|+-  ...|..+...+-.-..+...| .||-...++...
T Consensus        87 ~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip~TI  166 (515)
T COG2812          87 LIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTI  166 (515)
T ss_pred             cccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCchhh
Confidence                0000000111223444554443    23424999999974  367777766664444455555 455556665555


Q ss_pred             CCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh
Q 042806          299 MDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       299 ~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      ..-...|.++.++.++....+...+.......+ ++....|++..+|..
T Consensus       167 lSRcq~f~fkri~~~~I~~~L~~i~~~E~I~~e-~~aL~~ia~~a~Gs~  214 (515)
T COG2812         167 LSRCQRFDFKRLDLEEIAKHLAAILDKEGINIE-EDALSLIARAAEGSL  214 (515)
T ss_pred             hhccccccccCCCHHHHHHHHHHHHHhcCCccC-HHHHHHHHHHcCCCh
Confidence            566689999999999998888888863333222 345567777777643

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.94  E-value=0.00064  Score=63.51  Aligned_cols=177  Identities=12%  Similarity=0.049  Sum_probs=96.9

Q ss_pred             HHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC-----CC-C
Q 042806          163 LNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGL-----TL-H  235 (390)
Q Consensus       163 ~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~-----~~-~  235 (390)
                      ...|.+.+..++ ...+.++|+.|+||+++|+.+....--.......   .++.+    ...+.+...-..     .. .
T Consensus        11 ~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~---~Cg~C----~sC~~~~~g~HPD~~~i~p~~   83 (325)
T PRK06871         11 YQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQ---PCGQC----HSCHLFQAGNHPDFHILEPID   83 (325)
T ss_pred             HHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCC---CCCCC----HHHHHHhcCCCCCEEEEcccc
Confidence            455666666655 4678899999999999999998875322111000   00000    000000000000     00 0


Q ss_pred             C-CCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecch-hhhhhcCCCcceEec
Q 042806          236 E-ESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSL-DVLSRKMDSQQNFSV  307 (390)
Q Consensus       236 ~-~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~-~v~~~~~~~~~~~~l  307 (390)
                      . .-..+.+..+.+.+.    .++.=++|+|+++..  ...+.+...+-.-.+++.+|++|.+. .+.....+-...+.+
T Consensus        84 ~~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~~  163 (325)
T PRK06871         84 NKDIGVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWLI  163 (325)
T ss_pred             CCCCCHHHHHHHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceEEeC
Confidence            0 001122333333332    133358889999754  34455544444444566777777653 444333344569999


Q ss_pred             CCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHH
Q 042806          308 GVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVT  352 (390)
Q Consensus       308 ~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~  352 (390)
                      .+++.++..+.+......    +  ...+...+..++|.|+.+..
T Consensus       164 ~~~~~~~~~~~L~~~~~~----~--~~~~~~~~~l~~g~p~~A~~  202 (325)
T PRK06871        164 HPPEEQQALDWLQAQSSA----E--ISEILTALRINYGRPLLALT  202 (325)
T ss_pred             CCCCHHHHHHHHHHHhcc----C--hHHHHHHHHHcCCCHHHHHH
Confidence            999999999888876421    1  11245678899999974433

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

Probab=97.92  E-value=0.0014  Score=65.75  Aligned_cols=156  Identities=20%  Similarity=0.219  Sum_probs=88.3

Q ss_pred             ccchhHHHHHHHHHhc------CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 042806          156 CESRMSTLNDILDALK------NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       156 ~~gR~~~~~~l~~~L~------~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      =+|-++-.++|++.|.      .-+.+++.++||+|+|||+|++.++.....+  |   +-+++++-.+..+|-.+=-..
T Consensus       325 HYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al~Rk--f---vR~sLGGvrDEAEIRGHRRTY  399 (782)
T COG0466         325 HYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKALGRK--F---VRISLGGVRDEAEIRGHRRTY  399 (782)
T ss_pred             ccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHhCCC--E---EEEecCccccHHHhccccccc
Confidence            4566677777877764      2245799999999999999999999998644  4   445666666666643221111


Q ss_pred             hCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc---------cccc---------ccCCC---CCCCCCcEEEEE
Q 042806          230 LGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL---------DFQA---------VGIPH---GDDRKGCKVLLT  288 (390)
Q Consensus       230 l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~---------~~~~---------l~~~l---~~~~~~s~IivT  288 (390)
                      +|     .-+...++.+.+.  +.++-|++||.++...         .+-.         +...+   +-.-...-.|.|
T Consensus       400 IG-----amPGrIiQ~mkka--~~~NPv~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaT  472 (782)
T COG0466         400 IG-----AMPGKIIQGMKKA--GVKNPVFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIAT  472 (782)
T ss_pred             cc-----cCChHHHHHHHHh--CCcCCeEEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccchhheEEEee
Confidence            11     1222333333332  2233799999986321         0100         11111   111112223334


Q ss_pred             ecchh-hhhhcCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          289 ARSLD-VLSRKMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       289 tr~~~-v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                      +.+-+ ++...++--.+|++.+.+.+|=.++-.+++
T Consensus       473 ANsl~tIP~PLlDRMEiI~lsgYt~~EKl~IAk~~L  508 (782)
T COG0466         473 ANSLDTIPAPLLDRMEVIRLSGYTEDEKLEIAKRHL  508 (782)
T ss_pred             cCccccCChHHhcceeeeeecCCChHHHHHHHHHhc
Confidence            44333 333234455799999999998777766655

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.92  E-value=0.00087  Score=62.51  Aligned_cols=174  Identities=16%  Similarity=0.115  Sum_probs=97.1

Q ss_pred             HHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcC-----------------CCCeEEEEEeCCCCCHHHH
Q 042806          161 STLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEK-----------------LFDQVIFVEVSKIQDIRKI  222 (390)
Q Consensus       161 ~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~-----------------~f~~~~wv~v~~~~~~~~l  222 (390)
                      .....+...+..++. ..+.++|+.|+||+++|..+.+..--.+                 |.| ..|+.......    
T Consensus        11 ~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD-~~~i~~~p~~~----   85 (319)
T PRK08769         11 RAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPD-LQLVSFIPNRT----   85 (319)
T ss_pred             HHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCC-EEEEecCCCcc----
Confidence            345667777766664 5688999999999999999988753221                 111 11221000000    


Q ss_pred             HHHHHHHhCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecc-hhhh
Q 042806          223 QGEIADKLGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARS-LDVL  295 (390)
Q Consensus       223 ~~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~-~~v~  295 (390)
                              +......-..+.+..+.+.+.    .++.=++|+|+++..  ..-+.+...+-.-..++.+|++|.+ ..+.
T Consensus        86 --------~~k~~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lL  157 (319)
T PRK08769         86 --------GDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLP  157 (319)
T ss_pred             --------cccccccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCc
Confidence                    000000000112223333332    123359999999754  2333343334333446667777765 4444


Q ss_pred             hhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          296 SRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       296 ~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      ....+-...+.+.+++.+++.+.+....    .+   +..+..++..++|.|+....+.
T Consensus       158 pTIrSRCq~i~~~~~~~~~~~~~L~~~~----~~---~~~a~~~~~l~~G~p~~A~~~~  209 (319)
T PRK08769        158 ATIRSRCQRLEFKLPPAHEALAWLLAQG----VS---ERAAQEALDAARGHPGLAAQWL  209 (319)
T ss_pred             hHHHhhheEeeCCCcCHHHHHHHHHHcC----CC---hHHHHHHHHHcCCCHHHHHHHh
Confidence            3334445688999999999988886531    11   1225678999999998765543

>PRK08181 transposase; Validated

Probab=97.92  E-value=0.00019  Score=65.32  Aligned_cols=104  Identities=19%  Similarity=0.115  Sum_probs=57.5

Q ss_pred             HHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHH
Q 042806          168 DALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLR  247 (390)
Q Consensus       168 ~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~  247 (390)
                      +|+.  +..-+.++|++|+|||.|+..+.+..... .+ .+.|+      +..+++..+.....    .    .....+.
T Consensus       101 ~~~~--~~~nlll~Gp~GtGKTHLa~Aia~~a~~~-g~-~v~f~------~~~~L~~~l~~a~~----~----~~~~~~l  162 (269)
T PRK08181        101 SWLA--KGANLLLFGPPGGGKSHLAAAIGLALIEN-GW-RVLFT------RTTDLVQKLQVARR----E----LQLESAI  162 (269)
T ss_pred             HHHh--cCceEEEEecCCCcHHHHHHHHHHHHHHc-CC-ceeee------eHHHHHHHHHHHHh----C----CcHHHHH
Confidence            4554  33458899999999999999999876543 23 34444      34566666543321    1    1122334


Q ss_pred             HHHhCCCeEEEEEeCCCCC--cccc--cccCCCCCCCCCcEEEEEecc
Q 042806          248 NRLKKEKTILVILDNIWGN--LDFQ--AVGIPHGDDRKGCKVLLTARS  291 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~~--~~~~--~l~~~l~~~~~~s~IivTtr~  291 (390)
                      +.+..-  =||||||+...  ..+.  .+...+.....+..+||||..
T Consensus       163 ~~l~~~--dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~  208 (269)
T PRK08181        163 AKLDKF--DLLILDDLAYVTKDQAETSVLFELISARYERRSILITANQ  208 (269)
T ss_pred             HHHhcC--CEEEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCC
Confidence            444432  49999999533  1221  122222111112358888875

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

Probab=97.92  E-value=0.0006  Score=71.31  Aligned_cols=158  Identities=17%  Similarity=0.199  Sum_probs=89.3

Q ss_pred             ccccchhHHHHHHHHHhcC------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          154 EACESRMSTLNDILDALKN------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      ...+|.+.-.+.|+++|..      ....++.++|++|+||||+++.++......  |   .-+.++...+..++...-.
T Consensus       322 ~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l~~~--~---~~i~~~~~~d~~~i~g~~~  396 (784)
T PRK10787        322 TDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKATGRK--Y---VRMALGGVRDEAEIRGHRR  396 (784)
T ss_pred             hhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHhCCC--E---EEEEcCCCCCHHHhccchh
Confidence            4578888888888877752      245689999999999999999999876422  3   2233444444433322211


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc------cccccCCC---------------CCCCCCcEEE
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD------FQAVGIPH---------------GDDRKGCKVL  286 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~------~~~l~~~l---------------~~~~~~s~Ii  286 (390)
                      ...+     .......+.+.. ..... -+++||.++....      ...+...+               +-.-.+.-+|
T Consensus       397 ~~~g-----~~~G~~~~~l~~-~~~~~-~villDEidk~~~~~~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i  469 (784)
T PRK10787        397 TYIG-----SMPGKLIQKMAK-VGVKN-PLFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFV  469 (784)
T ss_pred             ccCC-----CCCcHHHHHHHh-cCCCC-CEEEEEChhhcccccCCCHHHHHHHHhccccEEEEecccccccccCCceEEE
Confidence            1111     111222222322 11223 4788999964311      11111111               1112345566


Q ss_pred             EEecchhhhhhcCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          287 LTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       287 vTtr~~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                      .|+.+..+.....+-...+++.+++.++-.++.+++.
T Consensus       470 ~TaN~~~i~~aLl~R~~ii~~~~~t~eek~~Ia~~~L  506 (784)
T PRK10787        470 ATSNSMNIPAPLLDRMEVIRLSGYTEDEKLNIAKRHL  506 (784)
T ss_pred             EcCCCCCCCHHHhcceeeeecCCCCHHHHHHHHHHhh
Confidence            6665544433333444689999999999888877666

>PHA00729 NTP-binding motif containing protein

Probab=97.89  E-value=0.00014  Score=63.85  Aligned_cols=36  Identities=36%  Similarity=0.341  Sum_probs=29.3

Q ss_pred             HHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          165 DILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       165 ~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+++.+.......|.|+|.+|+||||||..+.+...
T Consensus         7 ~~~~~l~~~~f~nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729          7 KIVSAYNNNGFVSAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             HHHHHHhcCCeEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            455556666667799999999999999999998753

>CHL00195 ycf46 Ycf46; Provisional

Probab=97.87  E-value=0.0001  Score=72.66  Aligned_cols=154  Identities=16%  Similarity=0.166  Sum_probs=82.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      .++-|.++|++|+|||.+|+.+.+.....  |   +-+..+      .++.        .... .....+..+.+.....
T Consensus       258 ~pkGILL~GPpGTGKTllAkaiA~e~~~~--~---~~l~~~------~l~~--------~~vG-ese~~l~~~f~~A~~~  317 (489)
T CHL00195        258 TPRGLLLVGIQGTGKSLTAKAIANDWQLP--L---LRLDVG------KLFG--------GIVG-ESESRMRQMIRIAEAL  317 (489)
T ss_pred             CCceEEEECCCCCcHHHHHHHHHHHhCCC--E---EEEEhH------Hhcc--------cccC-hHHHHHHHHHHHHHhc
Confidence            35678999999999999999999987532  2   222221      1110        0000 1112233344444445


Q ss_pred             CeEEEEEeCCCCCcc--------------cccccCCCCCCCCCcEEEEEecchhh-hhhcC---CCcceEecCCCCHHHH
Q 042806          254 KTILVILDNIWGNLD--------------FQAVGIPHGDDRKGCKVLLTARSLDV-LSRKM---DSQQNFSVGVLKEDEA  315 (390)
Q Consensus       254 ~~~LlVlDdv~~~~~--------------~~~l~~~l~~~~~~s~IivTtr~~~v-~~~~~---~~~~~~~l~~L~~~ea  315 (390)
                      .+++|++|+++....              ...+...+.....+.-||.||..... .....   .....+.+..-+.++-
T Consensus       318 ~P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR  397 (489)
T CHL00195        318 SPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEER  397 (489)
T ss_pred             CCcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceEEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHH
Confidence            679999999963210              00011111122334456667765432 11111   2335788998899999


Q ss_pred             HHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh
Q 042806          316 WSLFKKMAGDYIEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       316 ~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      .++|+.+............-...+++.+.|.-
T Consensus       398 ~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfS  429 (489)
T CHL00195        398 EKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFS  429 (489)
T ss_pred             HHHHHHHHhhcCCCcccccCHHHHHhhcCCCC
Confidence            99998887532111000111346777776654

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=97.83  E-value=0.00012  Score=73.36  Aligned_cols=47  Identities=26%  Similarity=0.355  Sum_probs=39.4

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...++|.+..+..+...+..+...-+.|+|++|+|||++|+.+++..
T Consensus        64 f~~iiGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lAr~i~~~~  110 (531)
T TIGR02902        64 FDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAARLVLEEA  110 (531)
T ss_pred             HHHeeCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            44688999888888888776666667899999999999999998754

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.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=97.81  E-value=0.00017  Score=65.22  Aligned_cols=82  Identities=21%  Similarity=0.280  Sum_probs=54.9

Q ss_pred             HHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHH
Q 042806          165 DILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRAR  244 (390)
Q Consensus       165 ~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~  244 (390)
                      .+.+++.  +..-+.++|++|+|||.||..+.+..- +..+. +.|+      +..+++..+......       .....
T Consensus        97 ~~~~~~~--~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g~s-v~f~------~~~el~~~Lk~~~~~-------~~~~~  159 (254)
T COG1484          97 SLVEFFE--RGENLVLLGPPGVGKTHLAIAIGNELL-KAGIS-VLFI------TAPDLLSKLKAAFDE-------GRLEE  159 (254)
T ss_pred             HHHHHhc--cCCcEEEECCCCCcHHHHHHHHHHHHH-HcCCe-EEEE------EHHHHHHHHHHHHhc-------CchHH
Confidence            3444444  566788999999999999999999987 43344 3333      556777777666543       12233


Q ss_pred             HHHHHHhCCCeEEEEEeCCCC
Q 042806          245 SLRNRLKKEKTILVILDNIWG  265 (390)
Q Consensus       245 ~l~~~l~~~~~~LlVlDdv~~  265 (390)
                      .|.+.+..-.  ||||||+-.
T Consensus       160 ~l~~~l~~~d--lLIiDDlG~  178 (254)
T COG1484         160 KLLRELKKVD--LLIIDDIGY  178 (254)
T ss_pred             HHHHHhhcCC--EEEEecccC
Confidence            4455454434  999999964

>PRK10536 hypothetical protein; Provisional

Probab=97.78  E-value=0.00038  Score=62.25  Aligned_cols=55  Identities=22%  Similarity=0.201  Sum_probs=41.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEE
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVI  209 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~  209 (390)
                      ...+.+|......++.++.+.  .++.+.|++|+|||+||..+..+.-..+.|+.++
T Consensus        54 ~~~i~p~n~~Q~~~l~al~~~--~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIi  108 (262)
T PRK10536         54 TSPILARNEAQAHYLKAIESK--QLIFATGEAGCGKTWISAAKAAEALIHKDVDRII  108 (262)
T ss_pred             CccccCCCHHHHHHHHHHhcC--CeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEE
Confidence            345677888888888888763  4899999999999999999988643223355333

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

Probab=97.78  E-value=0.0013  Score=58.75  Aligned_cols=208  Identities=14%  Similarity=0.090  Sum_probs=115.5

Q ss_pred             cccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC----CCCeEEEEEeCCC----------C---
Q 042806          155 ACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEK----LFDQVIFVEVSKI----------Q---  217 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~----------~---  217 (390)
                      .+.++.+..+.+.......+.+-+.++||+|.||.|.+..+.+..-..+    .-+...|.+-+..          +   
T Consensus        14 ~l~~~~e~~~~Lksl~~~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEistvsS~yHlE   93 (351)
T KOG2035|consen   14 ELIYHEELANLLKSLSSTGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEISTVSSNYHLE   93 (351)
T ss_pred             hcccHHHHHHHHHHhcccCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEEecccceEE
Confidence            4666766677777766656678888999999999999998888764311    1233444433322          1   


Q ss_pred             -C-------HHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeE-EEEEeCCCCC--cccccccCCCCCCCCCcEEE
Q 042806          218 -D-------IRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTI-LVILDNIWGN--LDFQAVGIPHGDDRKGCKVL  286 (390)
Q Consensus       218 -~-------~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~-LlVlDdv~~~--~~~~~l~~~l~~~~~~s~Ii  286 (390)
                       +       -+-+.+++++......+-.            ...+++| ++|+-.+++.  +....+....-...+.+|+|
T Consensus        94 itPSDaG~~DRvViQellKevAQt~qie------------~~~qr~fKvvvi~ead~LT~dAQ~aLRRTMEkYs~~~RlI  161 (351)
T KOG2035|consen   94 ITPSDAGNYDRVVIQELLKEVAQTQQIE------------TQGQRPFKVVVINEADELTRDAQHALRRTMEKYSSNCRLI  161 (351)
T ss_pred             eChhhcCcccHHHHHHHHHHHHhhcchh------------hccccceEEEEEechHhhhHHHHHHHHHHHHHHhcCceEE
Confidence             0       1112233333322111100            1134445 5666666433  22222332222234567777


Q ss_pred             EEecchhhh-hhcCCCcceEecCCCCHHHHHHHHHHhhCC-CCCCCchHHHHHHHHHHcCCChHHHHHHHHHhcCCCCCC
Q 042806          287 LTARSLDVL-SRKMDSQQNFSVGVLKEDEAWSLFKKMAGD-YIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLN  364 (390)
Q Consensus       287 vTtr~~~v~-~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~-~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~~~~~  364 (390)
                      +...+-+-. .....-.-.+.+...+++|....+...+.. ...-|  .+++.+|+++++|.---..++-..++.+....
T Consensus       162 l~cns~SriIepIrSRCl~iRvpaps~eeI~~vl~~v~~kE~l~lp--~~~l~rIa~kS~~nLRrAllmlE~~~~~n~~~  239 (351)
T KOG2035|consen  162 LVCNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQLP--KELLKRIAEKSNRNLRRALLMLEAVRVNNEPF  239 (351)
T ss_pred             EEecCcccchhHHhhheeEEeCCCCCHHHHHHHHHHHHHHhcccCc--HHHHHHHHHHhcccHHHHHHHHHHHHhccccc
Confidence            766542211 111122237788899999999999988852 22223  57899999999987665555555554443322


Q ss_pred             Cc-------ccchhHHHHH
Q 042806          365 GR-------THWNSWGGLL  376 (390)
Q Consensus       365 ~~-------~~w~~~~~~l  376 (390)
                      +.       -+|+-+...+
T Consensus       240 ~a~~~~i~~~dWe~~i~e~  258 (351)
T KOG2035|consen  240 TANSQVIPKPDWEIYIQEI  258 (351)
T ss_pred             cccCCCCCCccHHHHHHHH
Confidence            22       3676655443

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=97.78  E-value=0.0016  Score=60.71  Aligned_cols=160  Identities=13%  Similarity=0.095  Sum_probs=96.0

Q ss_pred             HHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcC-------------------CCCeEEEEEeC---CCCCH
Q 042806          163 LNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEK-------------------LFDQVIFVEVS---KIQDI  219 (390)
Q Consensus       163 ~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~-------------------~f~~~~wv~v~---~~~~~  219 (390)
                      ...+...+..++ ...+.++|+.|+||+++|..+....--.+                   |.| ..|+.-.   ....+
T Consensus        12 ~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD-~~~i~p~~~~~~I~v   90 (319)
T PRK06090         12 WQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPD-LHVIKPEKEGKSITV   90 (319)
T ss_pred             HHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCC-EEEEecCcCCCcCCH
Confidence            455666666655 45788999999999999999988753211                   122 1122110   01111


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecc-h
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARS-L  292 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~-~  292 (390)
                      +                     .+..+.+.+.    .++.=++|+|+++..  ...+.+...+-.-.+++.+|++|.+ .
T Consensus        91 d---------------------qiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~  149 (319)
T PRK06090         91 E---------------------QIRQCNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQK  149 (319)
T ss_pred             H---------------------HHHHHHHHHhhCcccCCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChh
Confidence            1                     2223333331    123258899999754  3455554444333455666666655 4


Q ss_pred             hhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          293 DVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       293 ~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      .+.....+-...+.+.+++.+++.+.+.....   .      ....++..++|.|+....+
T Consensus       150 ~lLpTI~SRCq~~~~~~~~~~~~~~~L~~~~~---~------~~~~~l~l~~G~p~~A~~~  201 (319)
T PRK06090        150 RLLPTIVSRCQQWVVTPPSTAQAMQWLKGQGI---T------VPAYALKLNMGSPLKTLAM  201 (319)
T ss_pred             hChHHHHhcceeEeCCCCCHHHHHHHHHHcCC---c------hHHHHHHHcCCCHHHHHHH
Confidence            45444445556999999999999988865421   1      1346789999999977655

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.75  E-value=0.00035  Score=65.88  Aligned_cols=99  Identities=11%  Similarity=0.168  Sum_probs=65.7

Q ss_pred             HHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCe-EEEEEeCC-CCCHHHHHHHHHHHhCCCCCCCCchH
Q 042806          165 DILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQ-VIFVEVSK-IQDIRKIQGEIADKLGLTLHEESDSG  241 (390)
Q Consensus       165 ~l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~-~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~~~~~~  241 (390)
                      ++++.+.. ++..-+.|+|++|+|||||++.+.+..... +-+. ++|+.+.. ..++.++++.+...+.....+.+...
T Consensus       122 RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~~i~~~-~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de~~~~  200 (380)
T PRK12608        122 RVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAAAVAAN-HPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDRPPDE  200 (380)
T ss_pred             hhhhheeecCCCceEEEECCCCCCHHHHHHHHHHHHHhc-CCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCCCHHH
Confidence            46666653 344556899999999999999999987543 3344 46766664 45788999998887765443332221


Q ss_pred             ------HHHHHHHHH-hCCCeEEEEEeCCC
Q 042806          242 ------RARSLRNRL-KKEKTILVILDNIW  264 (390)
Q Consensus       242 ------~~~~l~~~l-~~~~~~LlVlDdv~  264 (390)
                            .+..+.+++ ..+++.+||+|++.
T Consensus       201 ~~~v~~~~~~~Ae~f~~~GkdVVLvlDslt  230 (380)
T PRK12608        201 HIRVAELVLERAKRLVEQGKDVVILLDSLT  230 (380)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCEEEEEeCcH
Confidence                  122333333 34677999999985

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.75  E-value=0.00033  Score=73.98  Aligned_cols=106  Identities=18%  Similarity=0.239  Sum_probs=58.3

Q ss_pred             ccccchhHHHHHHHHHhcC-------C-C-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 042806          154 EACESRMSTLNDILDALKN-------P-D-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQG  224 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~-------~-~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~  224 (390)
                      ..++|.+..+..+.+.+..       + + ..++.++||+|+|||.||+.+.......  ....+-++.+.....    .
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~--~~~~~~~dmse~~~~----~  639 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGG--EQNLITINMSEFQEA----H  639 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhCC--CcceEEEeHHHhhhh----h
Confidence            4577888888888777631       2 2 3468899999999999999998876322  122222222221111    1


Q ss_pred             HHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 042806          225 EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       225 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~  266 (390)
                      .+.+-+|........ .....+.+.++.+...+|+||++...
T Consensus       640 ~~~~l~g~~~gyvg~-~~~g~L~~~v~~~p~svvllDEieka  680 (852)
T TIGR03345       640 TVSRLKGSPPGYVGY-GEGGVLTEAVRRKPYSVVLLDEVEKA  680 (852)
T ss_pred             hhccccCCCCCcccc-cccchHHHHHHhCCCcEEEEechhhc
Confidence            111122222111111 01123445555555579999999743

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.

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

Probab=97.73  E-value=0.00035  Score=73.07  Aligned_cols=102  Identities=18%  Similarity=0.235  Sum_probs=57.4

Q ss_pred             cccchhHHHHHHHHHhcC-------C-C-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          155 ACESRMSTLNDILDALKN-------P-D-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~-------~-~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      .++|.+..++.+.+.+..       + + ..++.++||+|+|||+||+.++....     ...+.++.+......    .
T Consensus       455 ~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~-----~~~~~~d~se~~~~~----~  525 (731)
T TIGR02639       455 KIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALG-----VHLERFDMSEYMEKH----T  525 (731)
T ss_pred             ceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhc-----CCeEEEeCchhhhcc----c
Confidence            456666666666666542       1 1 23578999999999999999988763     223445544422211    1


Q ss_pred             HHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 042806          226 IADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       226 i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~  266 (390)
                      +.+.++....... ......+.+.++.+...+++||+++..
T Consensus       526 ~~~lig~~~gyvg-~~~~~~l~~~~~~~p~~VvllDEieka  565 (731)
T TIGR02639       526 VSRLIGAPPGYVG-FEQGGLLTEAVRKHPHCVLLLDEIEKA  565 (731)
T ss_pred             HHHHhcCCCCCcc-cchhhHHHHHHHhCCCeEEEEechhhc
Confidence            1222222211111 111234555555555479999999744

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

Probab=97.73  E-value=0.00071  Score=66.50  Aligned_cols=93  Identities=22%  Similarity=0.294  Sum_probs=59.3

Q ss_pred             cccccchhHHHHHHHHHhc---CC---------CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 042806          153 YEACESRMSTLNDILDALK---NP---------DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~---~~---------~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  220 (390)
                      ..++.|-+..+.+|.+.+.   .+         .++=+.+|||+|+|||.||+.+.++..+.       |+.++.+    
T Consensus       189 f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vP-------f~~isAp----  257 (802)
T KOG0733|consen  189 FSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVP-------FLSISAP----  257 (802)
T ss_pred             hhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCc-------eEeecch----
Confidence            3456777777777766553   22         35678899999999999999999998754       3333322    


Q ss_pred             HHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCC
Q 042806          221 KIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWG  265 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~  265 (390)
                          +|.+...    . .....+..+...-.+.-+|++++|+++-
T Consensus       258 ----eivSGvS----G-ESEkkiRelF~~A~~~aPcivFiDeIDA  293 (802)
T KOG0733|consen  258 ----EIVSGVS----G-ESEKKIRELFDQAKSNAPCIVFIDEIDA  293 (802)
T ss_pred             ----hhhcccC----c-ccHHHHHHHHHHHhccCCeEEEeecccc
Confidence                1111111    1 1223444555555555679999999963

>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=97.69  E-value=0.0004  Score=58.38  Aligned_cols=137  Identities=19%  Similarity=0.149  Sum_probs=73.8

Q ss_pred             chhHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHhhhcCCC------------------CeEEEEEeCCC--
Q 042806          158 SRMSTLNDILDALKNPDV-NMLGIYGMGGIVKTTLAKEVARKAETEKLF------------------DQVIFVEVSKI--  216 (390)
Q Consensus       158 gR~~~~~~l~~~L~~~~~-~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f------------------~~~~wv~v~~~--  216 (390)
                      |-+...+.|.+.+..++. ..+.++|+.|+||+++|..+.+..-.....                  ....|+.-...  
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            344566777777777664 568999999999999999998875432211                  12333332221  


Q ss_pred             -CCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecchh
Q 042806          217 -QDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSLD  293 (390)
Q Consensus       217 -~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~~  293 (390)
                       ...+++- .+...+.....                .++.=++|+|+++..  .....+...+-.-..++.+|++|.+..
T Consensus        81 ~i~i~~ir-~i~~~~~~~~~----------------~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~  143 (162)
T PF13177_consen   81 SIKIDQIR-EIIEFLSLSPS----------------EGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPS  143 (162)
T ss_dssp             SBSHHHHH-HHHHHCTSS-T----------------TSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GG
T ss_pred             hhhHHHHH-HHHHHHHHHHh----------------cCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChH
Confidence             2232222 33333322211                122359999999754  445555544434456788888888744


Q ss_pred             -hhhhcCCCcceEecCCCC
Q 042806          294 -VLSRKMDSQQNFSVGVLK  311 (390)
Q Consensus       294 -v~~~~~~~~~~~~l~~L~  311 (390)
                       +......-...+.+.++|
T Consensus       144 ~il~TI~SRc~~i~~~~ls  162 (162)
T PF13177_consen  144 KILPTIRSRCQVIRFRPLS  162 (162)
T ss_dssp             GS-HHHHTTSEEEEE----
T ss_pred             HChHHHHhhceEEecCCCC
Confidence             333333334566666654

...

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

Probab=97.69  E-value=7.4e-05  Score=63.84  Aligned_cols=75  Identities=28%  Similarity=0.383  Sum_probs=45.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      +..-+.++|++|+|||.||..+.+..-.. .+. +.|+      +..+++..+-..    ....    ....+.+.+..-
T Consensus        46 ~~~~l~l~G~~G~GKThLa~ai~~~~~~~-g~~-v~f~------~~~~L~~~l~~~----~~~~----~~~~~~~~l~~~  109 (178)
T PF01695_consen   46 NGENLILYGPPGTGKTHLAVAIANEAIRK-GYS-VLFI------TASDLLDELKQS----RSDG----SYEELLKRLKRV  109 (178)
T ss_dssp             C--EEEEEESTTSSHHHHHHHHHHHHHHT-T---EEEE------EHHHHHHHHHCC----HCCT----THCHHHHHHHTS
T ss_pred             cCeEEEEEhhHhHHHHHHHHHHHHHhccC-Ccc-eeEe------ecCceecccccc----cccc----chhhhcCccccc
Confidence            34568999999999999999999987653 343 4454      345566655322    1111    122344555554


Q ss_pred             CeEEEEEeCCCCC
Q 042806          254 KTILVILDNIWGN  266 (390)
Q Consensus       254 ~~~LlVlDdv~~~  266 (390)
                      .  ||||||+-..
T Consensus       110 d--lLilDDlG~~  120 (178)
T PF01695_consen  110 D--LLILDDLGYE  120 (178)
T ss_dssp             S--CEEEETCTSS
T ss_pred             c--Eeccccccee
Confidence            4  8899999543

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.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=97.67  E-value=0.0022  Score=60.49  Aligned_cols=165  Identities=13%  Similarity=0.051  Sum_probs=96.0

Q ss_pred             HHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhc--------------------CCCCeEEEEEeCCCCCHH
Q 042806          162 TLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETE--------------------KLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       162 ~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~--------------------~~f~~~~wv~v~~~~~~~  220 (390)
                      .-+++.+.+..++ ...+.++|+.|+||+++|..+....--.                    .|.|. .++.-....   
T Consensus        10 ~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~-~~i~p~~~~---   85 (334)
T PRK07993         10 DYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDY-YTLTPEKGK---   85 (334)
T ss_pred             HHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCE-EEEeccccc---
Confidence            3456777776655 5678899999999999999988875321                    12221 111100000   


Q ss_pred             HHHHHHHHHhCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecc-hh
Q 042806          221 KIQGEIADKLGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARS-LD  293 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~-~~  293 (390)
                                    ... ..+.+..+.+.+.    .+++=++|+|+++..  ..-+.+...+-.-.+++.+|++|.+ ..
T Consensus        86 --------------~~I-~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~  150 (334)
T PRK07993         86 --------------SSL-GVDAVREVTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPAR  150 (334)
T ss_pred             --------------ccC-CHHHHHHHHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhh
Confidence                          000 1112333333332    133358999998754  3344454444333456666666665 44


Q ss_pred             hhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHH
Q 042806          294 VLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIV  351 (390)
Q Consensus       294 v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~  351 (390)
                      +.....+-...+.+.+++.+++.+.+....+   . +  .+.+..++..++|.|....
T Consensus       151 lLpTIrSRCq~~~~~~~~~~~~~~~L~~~~~---~-~--~~~a~~~~~la~G~~~~Al  202 (334)
T PRK07993        151 LLATLRSRCRLHYLAPPPEQYALTWLSREVT---M-S--QDALLAALRLSAGAPGAAL  202 (334)
T ss_pred             ChHHHHhccccccCCCCCHHHHHHHHHHccC---C-C--HHHHHHHHHHcCCCHHHHH
Confidence            4443344446889999999999888865431   1 1  2235678999999997543

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.65  E-value=0.00072  Score=71.86  Aligned_cols=106  Identities=18%  Similarity=0.261  Sum_probs=60.5

Q ss_pred             ccccchhHHHHHHHHHhcC-------C-C-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 042806          154 EACESRMSTLNDILDALKN-------P-D-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQG  224 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~-------~-~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~  224 (390)
                      ..++|.+..++.+...+..       + + ..++.++|++|+|||++|+.+.......  -...+.++.+.......   
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~--~~~~i~~d~s~~~~~~~---  639 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDD--EDAMVRIDMSEYMEKHS---  639 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCC--CCcEEEEechhhcccch---
Confidence            3578888888888777753       1 1 3467899999999999999999876432  22334444443322111   


Q ss_pred             HHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 042806          225 EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       225 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~  266 (390)
                       +.+.+|..+..... .....+.+.+......+|+||++...
T Consensus       640 -~~~l~g~~~g~~g~-~~~g~l~~~v~~~p~~vlllDeieka  679 (852)
T TIGR03346       640 -VARLIGAPPGYVGY-EEGGQLTEAVRRKPYSVVLFDEVEKA  679 (852)
T ss_pred             -HHHhcCCCCCccCc-ccccHHHHHHHcCCCcEEEEeccccC
Confidence             11222222111111 01123445554444369999999754

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.65  E-value=0.00063  Score=71.27  Aligned_cols=172  Identities=15%  Similarity=0.167  Sum_probs=93.4

Q ss_pred             ccccchhHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 042806          154 EACESRMSTLNDILDALK-------------NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  220 (390)
                      ..+.|.+...+.|.+.+.             -..++-+.++|++|+|||+||+.+++.....  |     +.++.    .
T Consensus       453 ~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~--f-----i~v~~----~  521 (733)
T TIGR01243       453 SDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGAN--F-----IAVRG----P  521 (733)
T ss_pred             hhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCC--E-----EEEeh----H
Confidence            445666655555554432             1234568899999999999999999986532  2     23322    1


Q ss_pred             HHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc---------c-----cccccCCCCC--CCCCcE
Q 042806          221 KIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL---------D-----FQAVGIPHGD--DRKGCK  284 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~---------~-----~~~l~~~l~~--~~~~s~  284 (390)
                      +++.    ..    .. .....+..+........+++|+||+++...         .     ...+...+..  ...+..
T Consensus       522 ~l~~----~~----vG-ese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v~  592 (733)
T TIGR01243       522 EILS----KW----VG-ESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVV  592 (733)
T ss_pred             HHhh----cc----cC-cHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCCEE
Confidence            1111    10    00 112234455555555566999999986321         0     1111111211  123455


Q ss_pred             EEEEecchhhh-hhcC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh
Q 042806          285 VLLTARSLDVL-SRKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       285 IivTtr~~~v~-~~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      ||.||...... ....   .....+.+...+.++-.++|..+........+.  -...+++.|.|.-
T Consensus       593 vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~--~l~~la~~t~g~s  657 (733)
T TIGR01243       593 VIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDV--DLEELAEMTEGYT  657 (733)
T ss_pred             EEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCccC--CHHHHHHHcCCCC
Confidence            66666554322 1111   234688899999998889997766422221211  1346777777654

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.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.64  E-value=0.00028  Score=62.04  Aligned_cols=87  Identities=16%  Similarity=0.206  Sum_probs=54.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh-CC---C---CCCCCc---hHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL-GL---T---LHEESD---SGRA  243 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l-~~---~---~~~~~~---~~~~  243 (390)
                      ...++.|+|++|+|||+++.++.......  -..++|++... ++...+.+ ++... ..   .   ....+.   ...+
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~~~--g~~v~yi~~e~-~~~~rl~~-~~~~~~~~~~~~i~~~~~~~~~~~~~~~   86 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAARQ--GKKVVYIDTEG-LSPERFKQ-IAEDRPERALSNFIVFEVFDFDEQGVAI   86 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCC-CCHHHHHH-HHHhChHHHhcCEEEEECCCHHHHHHHH
Confidence            45789999999999999999998876432  45689998876 66655444 33321 00   0   000111   1224


Q ss_pred             HHHHHHHhCCCeEEEEEeCCC
Q 042806          244 RSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       244 ~~l~~~l~~~~~~LlVlDdv~  264 (390)
                      ..+.+.+...+.-+||+|.+.
T Consensus        87 ~~l~~~~~~~~~~lvVIDSis  107 (209)
T TIGR02237        87 QKTSKFIDRDSASLVVVDSFT  107 (209)
T ss_pred             HHHHHHHhhcCccEEEEeCcH
Confidence            445555555455699999985

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

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.64  E-value=0.00033  Score=65.14  Aligned_cols=115  Identities=17%  Similarity=0.202  Sum_probs=67.0

Q ss_pred             chhHHHHHHHHHhcC----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCC
Q 042806          158 SRMSTLNDILDALKN----PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLT  233 (390)
Q Consensus       158 gR~~~~~~l~~~L~~----~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~  233 (390)
                      +|........+++..    ...+-+.|+|+.|+|||.|+..+++..... .+. +.|+++      .+++..+....+..
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~~~-g~~-v~~~~~------~~l~~~lk~~~~~~  206 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELAKK-GVS-STLLHF------PEFIRELKNSISDG  206 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHHHc-CCC-EEEEEH------HHHHHHHHHHHhcC
Confidence            444444444455442    235678899999999999999999998643 344 344443      45666666555321


Q ss_pred             CCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--ccccc--ccCCC-CCC-CCCcEEEEEec
Q 042806          234 LHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQA--VGIPH-GDD-RKGCKVLLTAR  290 (390)
Q Consensus       234 ~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~--l~~~l-~~~-~~~s~IivTtr  290 (390)
                              ......+.+..-  =||||||+-..  ..|..  +...+ ... ..+..+|+||.
T Consensus       207 --------~~~~~l~~l~~~--dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSN  259 (306)
T PRK08939        207 --------SVKEKIDAVKEA--PVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSN  259 (306)
T ss_pred             --------cHHHHHHHhcCC--CEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECC
Confidence                    123344445443  49999999533  45543  32222 111 23445777776

>PRK08118 topology modulation protein; Reviewed

Probab=97.63  E-value=3.2e-05  Score=65.36  Aligned_cols=34  Identities=26%  Similarity=0.456  Sum_probs=27.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhc-CCCCeEEE
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETE-KLFDQVIF  210 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~-~~f~~~~w  210 (390)
                      -|.|+|++|+||||||+.+++..... -+||..+|
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            58899999999999999999997654 34666665

>PRK07261 topology modulation protein; Provisional

Probab=97.63  E-value=0.00027  Score=60.00  Aligned_cols=34  Identities=26%  Similarity=0.423  Sum_probs=25.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhc-CCCCeEEE
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETE-KLFDQVIF  210 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~-~~f~~~~w  210 (390)
                      -|.|+|++|+||||||+.+....... -+.|...|
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~   36 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHF   36 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEe
Confidence            47899999999999999998775432 12454555

>PRK04132 replication factor C small subunit; Provisional

Probab=97.61  E-value=0.0019  Score=67.53  Aligned_cols=158  Identities=13%  Similarity=0.031  Sum_probs=95.3

Q ss_pred             c--CCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEE
Q 042806          182 G--MGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVI  259 (390)
Q Consensus       182 G--~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlV  259 (390)
                      |  |.++||||+|..++++.-..+.-...+-++++....... ++.+.+.+....+.              .+.+.-++|
T Consensus       571 G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~rgid~-IR~iIk~~a~~~~~--------------~~~~~KVvI  635 (846)
T PRK04132        571 GNLPTVLHNTTAALALARELFGENWRHNFLELNASDERGINV-IREKVKEFARTKPI--------------GGASFKIIF  635 (846)
T ss_pred             CCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcccHHH-HHHHHHHHHhcCCc--------------CCCCCEEEE
Confidence            7  889999999999999873321112466777776555543 33333332211110              011236999


Q ss_pred             EeCCCCCc--ccccccCCCCCCCCCcEEEEEecch-hhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHH
Q 042806          260 LDNIWGNL--DFQAVGIPHGDDRKGCKVLLTARSL-DVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVA  336 (390)
Q Consensus       260 lDdv~~~~--~~~~l~~~l~~~~~~s~IivTtr~~-~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~  336 (390)
                      +|+++...  ..+.+...+-.-...+++|+++.+. .+.....+-...+.+.+++.++..+.+...+......- .++..
T Consensus       636 IDEaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi~i-~~e~L  714 (846)
T PRK04132        636 LDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLEL-TEEGL  714 (846)
T ss_pred             EECcccCCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCCCC-CHHHH
Confidence            99998653  4445544443333466777766653 33222233456999999999999888887764211111 14567


Q ss_pred             HHHHHHcCCChHHHHHHHH
Q 042806          337 KDVARECAGLPVSIVTVAR  355 (390)
Q Consensus       337 ~~i~~~~~GlPLai~~l~~  355 (390)
                      ..|++.|+|-+-....+-.
T Consensus       715 ~~Ia~~s~GDlR~AIn~Lq  733 (846)
T PRK04132        715 QAILYIAEGDMRRAINILQ  733 (846)
T ss_pred             HHHHHHcCCCHHHHHHHHH
Confidence            8999999998855544433

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.61  E-value=0.00074  Score=70.77  Aligned_cols=174  Identities=15%  Similarity=0.149  Sum_probs=91.4

Q ss_pred             cccccchhHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALKN-------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ...+.|.+..++.+.+.+.-             ...+-+.++|++|+|||+|++.+++.....       ++.++..   
T Consensus       177 ~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~-------~i~i~~~---  246 (733)
T TIGR01243       177 YEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAY-------FISINGP---  246 (733)
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCe-------EEEEecH---
Confidence            34577888888777666531             234678899999999999999998876421       2222211   


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc-------------ccccccCCCCC-CCCCcEE
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL-------------DFQAVGIPHGD-DRKGCKV  285 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~-------------~~~~l~~~l~~-~~~~s~I  285 (390)
                       ++...    .    .. .....+..+.+......+.+|+||+++...             ....+...+.. ...+..+
T Consensus       247 -~i~~~----~----~g-~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~vi  316 (733)
T TIGR01243       247 -EIMSK----Y----YG-ESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVI  316 (733)
T ss_pred             -HHhcc----c----cc-HHHHHHHHHHHHHHhcCCcEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhccccCCCEE
Confidence             11100    0    00 111223333443334455899999985421             01112111111 1223334


Q ss_pred             EE-Eecchh-hhhhcC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH
Q 042806          286 LL-TARSLD-VLSRKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV  348 (390)
Q Consensus       286 iv-Ttr~~~-v~~~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL  348 (390)
                      ++ ||.... +.....   .....+.+...+.++-.+++...........+  .....+++.+.|..-
T Consensus       317 vI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~~d--~~l~~la~~t~G~~g  382 (733)
T TIGR01243       317 VIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAED--VDLDKLAEVTHGFVG  382 (733)
T ss_pred             EEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCccc--cCHHHHHHhCCCCCH
Confidence            44 454322 211111   12347888888888888888866532211111  124567888877653

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

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

Probab=97.60  E-value=0.00067  Score=67.76  Aligned_cols=153  Identities=15%  Similarity=0.079  Sum_probs=83.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC--CCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI--QDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKK  252 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~--~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  252 (390)
                      ..-|.|.|+.|+|||+|++.+++... +++.-.+.+++++.-  ...+.+.+.+...                +.+.+..
T Consensus       431 ~~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~v----------------fse~~~~  493 (952)
T KOG0735|consen  431 HGNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQKFLNNV----------------FSEALWY  493 (952)
T ss_pred             cccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHHHHHHHH----------------HHHHHhh
Confidence            46788999999999999999999987 344555666666542  2233333332222                2233333


Q ss_pred             CCeEEEEEeCCCCC--------cccc-----------cccCCCCCCCCCcEEEEEecchhhhhh----cCCCcceEecCC
Q 042806          253 EKTILVILDNIWGN--------LDFQ-----------AVGIPHGDDRKGCKVLLTARSLDVLSR----KMDSQQNFSVGV  309 (390)
Q Consensus       253 ~~~~LlVlDdv~~~--------~~~~-----------~l~~~l~~~~~~s~IivTtr~~~v~~~----~~~~~~~~~l~~  309 (390)
                       .|-+|||||++..        ..|.           ++...+...+....+|.|..+..-...    ..-......|..
T Consensus       494 -~PSiIvLDdld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~a  572 (952)
T KOG0735|consen  494 -APSIIVLDDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPA  572 (952)
T ss_pred             -CCcEEEEcchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCC
Confidence             3489999999632        1111           111112122222345555554322111    111234778888


Q ss_pred             CCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCC
Q 042806          310 LKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGL  346 (390)
Q Consensus       310 L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~Gl  346 (390)
                      +...+-.++++........... ......+..+|+|.
T Consensus       573 p~~~~R~~IL~~~~s~~~~~~~-~~dLd~ls~~TEGy  608 (952)
T KOG0735|consen  573 PAVTRRKEILTTIFSKNLSDIT-MDDLDFLSVKTEGY  608 (952)
T ss_pred             cchhHHHHHHHHHHHhhhhhhh-hHHHHHHHHhcCCc
Confidence            8888877877776642221111 11223367777653

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

Probab=97.59  E-value=0.0074  Score=60.65  Aligned_cols=156  Identities=20%  Similarity=0.199  Sum_probs=87.5

Q ss_pred             ccccchhHHHHHHHHHhcC------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          154 EACESRMSTLNDILDALKN------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      .+=+|.++-.+++++.+.-      -+.+++..+||+|||||++++.++.....+  |   +-++++.-.+..+|-..=-
T Consensus       411 eDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRk--F---fRfSvGG~tDvAeIkGHRR  485 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARALNRK--F---FRFSVGGMTDVAEIKGHRR  485 (906)
T ss_pred             ccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHhCCc--e---EEEeccccccHHhhcccce
Confidence            3446777778888887642      357899999999999999999999988643  3   3346677666665432211


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHhC--CCeEEEEEeCCCCCc---------ccccccCC---------CCCCC-CCcEEE
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLKK--EKTILVILDNIWGNL---------DFQAVGIP---------HGDDR-KGCKVL  286 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~~--~~~~LlVlDdv~~~~---------~~~~l~~~---------l~~~~-~~s~Ii  286 (390)
                      ...         ..+-.++.++|+.  ..+-|+.+|.|+...         .+-.+..|         +.+.. -=|+|+
T Consensus       486 TYV---------GAMPGkiIq~LK~v~t~NPliLiDEvDKlG~g~qGDPasALLElLDPEQNanFlDHYLdVp~DLSkVL  556 (906)
T KOG2004|consen  486 TYV---------GAMPGKIIQCLKKVKTENPLILIDEVDKLGSGHQGDPASALLELLDPEQNANFLDHYLDVPVDLSKVL  556 (906)
T ss_pred             eee---------ccCChHHHHHHHhhCCCCceEEeehhhhhCCCCCCChHHHHHHhcChhhccchhhhccccccchhheE
Confidence            111         1112244455542  223688999986431         01111111         10100 113443


Q ss_pred             --EEecc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          287 --LTARS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       287 --vTtr~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                        .|... ..++....+--..|++.+...+|=.++-++++
T Consensus       557 FicTAN~idtIP~pLlDRMEvIelsGYv~eEKv~IA~~yL  596 (906)
T KOG2004|consen  557 FICTANVIDTIPPPLLDRMEVIELSGYVAEEKVKIAERYL  596 (906)
T ss_pred             EEEeccccccCChhhhhhhheeeccCccHHHHHHHHHHhh
Confidence              33332 12222123334688899988888777766655

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.56  E-value=0.00076  Score=71.50  Aligned_cols=106  Identities=14%  Similarity=0.246  Sum_probs=58.2

Q ss_pred             ccccchhHHHHHHHHHhcC-------CC--ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 042806          154 EACESRMSTLNDILDALKN-------PD--VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQG  224 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~-------~~--~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~  224 (390)
                      ..++|.+..+..+...+..       ++  ..++.++|+.|+|||+||+.+.+.....  -...+.+..+.... ..   
T Consensus       568 ~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~--~~~~i~id~se~~~-~~---  641 (857)
T PRK10865        568 HRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMFDS--DDAMVRIDMSEFME-KH---  641 (857)
T ss_pred             CeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHhhcC--CCcEEEEEhHHhhh-hh---
Confidence            3577888877777766642       12  2468899999999999999999876322  12234444433211 11   


Q ss_pred             HHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 042806          225 EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       225 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~  266 (390)
                      .+.+-+|.+...... .....+.+.++....-+|+||++...
T Consensus       642 ~~~~LiG~~pgy~g~-~~~g~l~~~v~~~p~~vLllDEieka  682 (857)
T PRK10865        642 SVSRLVGAPPGYVGY-EEGGYLTEAVRRRPYSVILLDEVEKA  682 (857)
T ss_pred             hHHHHhCCCCccccc-chhHHHHHHHHhCCCCeEEEeehhhC
Confidence            112223322111111 11123444444433369999999743

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

Probab=97.55  E-value=0.00061  Score=70.80  Aligned_cols=102  Identities=14%  Similarity=0.186  Sum_probs=57.1

Q ss_pred             cccchhHHHHHHHHHhcC--------CC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          155 ACESRMSTLNDILDALKN--------PD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~--------~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      .++|-+..++.|.+.+..        ++ ...+.++|++|+|||++|+.+......     ..+.++.+......    .
T Consensus       459 ~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~~-----~~i~id~se~~~~~----~  529 (758)
T PRK11034        459 LVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGI-----ELLRFDMSEYMERH----T  529 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHhCC-----CcEEeechhhcccc----c
Confidence            456777777777776651        12 346889999999999999999887732     12334443322211    1


Q ss_pred             HHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 042806          226 IADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       226 i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~  266 (390)
                      +.+-+|.+..... ......+.+.+..+...+|+||+++..
T Consensus       530 ~~~LiG~~~gyvg-~~~~g~L~~~v~~~p~sVlllDEieka  569 (758)
T PRK11034        530 VSRLIGAPPGYVG-FDQGGLLTDAVIKHPHAVLLLDEIEKA  569 (758)
T ss_pred             HHHHcCCCCCccc-ccccchHHHHHHhCCCcEEEeccHhhh
Confidence            2222332211111 011123444454444479999999754

>PRK06526 transposase; Provisional

Probab=97.55  E-value=0.00011  Score=66.34  Aligned_cols=74  Identities=20%  Similarity=0.143  Sum_probs=43.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      ...+.|+|++|+|||+||..+.+..... .+. +.|      .+..+++..+......       . ........+.  +
T Consensus        98 ~~nlll~Gp~GtGKThLa~al~~~a~~~-g~~-v~f------~t~~~l~~~l~~~~~~-------~-~~~~~l~~l~--~  159 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIGLGIRACQA-GHR-VLF------ATAAQWVARLAAAHHA-------G-RLQAELVKLG--R  159 (254)
T ss_pred             CceEEEEeCCCCchHHHHHHHHHHHHHC-CCc-hhh------hhHHHHHHHHHHHHhc-------C-cHHHHHHHhc--c
Confidence            4568899999999999999998876543 233 233      2445555555433210       1 1111222332  2


Q ss_pred             eEEEEEeCCCCC
Q 042806          255 TILVILDNIWGN  266 (390)
Q Consensus       255 ~~LlVlDdv~~~  266 (390)
                      .-|||+||+...
T Consensus       160 ~dlLIIDD~g~~  171 (254)
T PRK06526        160 YPLLIVDEVGYI  171 (254)
T ss_pred             CCEEEEcccccC
Confidence            258999999643

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=97.55  E-value=0.0058  Score=57.58  Aligned_cols=89  Identities=16%  Similarity=0.191  Sum_probs=57.0

Q ss_pred             EEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecc-hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCch
Q 042806          256 ILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARS-LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEF  332 (390)
Q Consensus       256 ~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~-~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~  332 (390)
                      =++|+|+++..  ...+.+...+-.-.+++.+|++|.+ ..+.....+-...+.+.+++.++..+.+...-   .  ++ 
T Consensus       134 kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~~~---~--~~-  207 (342)
T PRK06964        134 RVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAAQG---V--AD-  207 (342)
T ss_pred             eEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHHcC---C--Ch-
Confidence            58889999754  4455555555444456656655555 55544334444699999999999998887652   1  11 


Q ss_pred             HHHHHHHHHHcCCChHHHHHH
Q 042806          333 KWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       333 ~~~~~~i~~~~~GlPLai~~l  353 (390)
                         ...++..++|.|+....+
T Consensus       208 ---~~~~l~~~~Gsp~~Al~~  225 (342)
T PRK06964        208 ---ADALLAEAGGAPLAALAL  225 (342)
T ss_pred             ---HHHHHHHcCCCHHHHHHH
Confidence               123678889999755433

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.54  E-value=0.00071  Score=62.33  Aligned_cols=87  Identities=20%  Similarity=0.262  Sum_probs=49.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc-CCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE-KLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK  251 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~  251 (390)
                      +.+++.++|++|+||||++..+......+ +.+ .+..++..... ...+-+......++...........+....+.+.
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~-~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~~~~  271 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNK-KVALITTDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALDRLR  271 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCC-eEEEEECCccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHHHcc
Confidence            45799999999999999999998877543 223 35555554321 2233334445555554433222223334444443


Q ss_pred             CCCeEEEEEeCC
Q 042806          252 KEKTILVILDNI  263 (390)
Q Consensus       252 ~~~~~LlVlDdv  263 (390)
                      +.  =+|++|..
T Consensus       272 ~~--d~vliDt~  281 (282)
T TIGR03499       272 DK--DLILIDTA  281 (282)
T ss_pred             CC--CEEEEeCC
Confidence            32  37777753

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=97.54  E-value=0.001  Score=60.92  Aligned_cols=168  Identities=18%  Similarity=0.156  Sum_probs=99.8

Q ss_pred             ccccchhHHHHHHHHHhcC----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCH-HHHHHHHH
Q 042806          154 EACESRMSTLNDILDALKN----PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFD-QVIFVEVSKIQDI-RKIQGEIA  227 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~----~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~-~~l~~~i~  227 (390)
                      ..++|-.++...+-+++..    +...-+.|+||.|+|||+|......+.+.   |. ...-|...+.... .-.++.|.
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~q~---~~E~~l~v~Lng~~~~dk~al~~I~  100 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDIQE---NGENFLLVRLNGELQTDKIALKGIT  100 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhHHh---cCCeEEEEEECccchhhHHHHHHHH
Confidence            3578888888888777763    44556779999999999999988888221   32 3445555554433 22455565


Q ss_pred             HHhCCCCC-----CCCchHHHHHHHHHHhC-----CCeEEEEEeCCCCCcc-------cccccCCCCCCCCCcEEEEEec
Q 042806          228 DKLGLTLH-----EESDSGRARSLRNRLKK-----EKTILVILDNIWGNLD-------FQAVGIPHGDDRKGCKVLLTAR  290 (390)
Q Consensus       228 ~~l~~~~~-----~~~~~~~~~~l~~~l~~-----~~~~LlVlDdv~~~~~-------~~~l~~~l~~~~~~s~IivTtr  290 (390)
                      +++.....     ..+-.+....+...|..     +-++++|+|.++-...       +..+-..-....|-|-|-+|||
T Consensus       101 rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttr  180 (408)
T KOG2228|consen  101 RQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTR  180 (408)
T ss_pred             HHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeecc
Confidence            55543221     12334455566666653     3348999998853311       1111111112456677889999


Q ss_pred             chhhh------hhcCCCcceEecCCCCHHHHHHHHHHhhC
Q 042806          291 SLDVL------SRKMDSQQNFSVGVLKEDEAWSLFKKMAG  324 (390)
Q Consensus       291 ~~~v~------~~~~~~~~~~~l~~L~~~ea~~lf~~~~~  324 (390)
                      -....      ...+.-..++-+.+++.++-..++++...
T Consensus       181 ld~lE~LEKRVKSRFshr~I~m~~~~~l~~yv~l~r~ll~  220 (408)
T KOG2228|consen  181 LDILELLEKRVKSRFSHRVIFMLPSLPLGDYVDLYRKLLS  220 (408)
T ss_pred             ccHHHHHHHHHHhhcccceeeccCCCChHHHHHHHHHHhc
Confidence            53221      11222223555677888999999998873

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

Probab=97.54  E-value=0.004  Score=58.44  Aligned_cols=29  Identities=28%  Similarity=0.243  Sum_probs=25.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ..+..+.|||++|.|||.+|+.+++....
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~elg~  174 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKMGI  174 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHcCC
Confidence            34678999999999999999999999865

>PRK12377 putative replication protein; Provisional

Probab=97.52  E-value=0.00046  Score=62.02  Aligned_cols=73  Identities=21%  Similarity=0.213  Sum_probs=47.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      ...+.++|++|+|||+||..+++.....  ...++++++      .+++..+-......       .....+.+.+..- 
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~l~~~--g~~v~~i~~------~~l~~~l~~~~~~~-------~~~~~~l~~l~~~-  164 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNRLLAK--GRSVIVVTV------PDVMSRLHESYDNG-------QSGEKFLQELCKV-  164 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEEEH------HHHHHHHHHHHhcc-------chHHHHHHHhcCC-
Confidence            4678899999999999999999998653  223455543      45666554443211       0122344555443 


Q ss_pred             eEEEEEeCCC
Q 042806          255 TILVILDNIW  264 (390)
Q Consensus       255 ~~LlVlDdv~  264 (390)
                       =||||||+.
T Consensus       165 -dLLiIDDlg  173 (248)
T PRK12377        165 -DLLVLDEIG  173 (248)
T ss_pred             -CEEEEcCCC
Confidence             499999994

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.52  E-value=0.00062  Score=60.96  Aligned_cols=90  Identities=20%  Similarity=0.258  Sum_probs=57.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCC----CCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC----------CCc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKL----FDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE----------ESD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~----------~~~  239 (390)
                      ...++.|+|++|+|||+|+.+++........    -..++|++....++...+ .++++.++.....          .+.
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl-~~~~~~~~~~~~~~~~~i~~~~~~~~   96 (235)
T cd01123          18 TGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERL-VQIAERFGLDPEEVLDNIYVARAYNS   96 (235)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHH-HHHHHHhccChHhHhcCEEEEecCCH
Confidence            4578999999999999999999865332211    257899988887766544 3344444332111          011


Q ss_pred             ---hHHHHHHHHHHhCC-CeEEEEEeCCC
Q 042806          240 ---SGRARSLRNRLKKE-KTILVILDNIW  264 (390)
Q Consensus       240 ---~~~~~~l~~~l~~~-~~~LlVlDdv~  264 (390)
                         ......+.+.+... +.-+||+|.+.
T Consensus        97 ~~l~~~l~~l~~~l~~~~~~~liVIDSis  125 (235)
T cd01123          97 DHQLQLLEELEAILIESSRIKLVIVDSVT  125 (235)
T ss_pred             HHHHHHHHHHHHHHhhcCCeeEEEEeCcH
Confidence               12334455555555 66899999985

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

>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=97.52  E-value=0.00014  Score=64.64  Aligned_cols=36  Identities=28%  Similarity=0.313  Sum_probs=28.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEV  213 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v  213 (390)
                      -.++|.|.+|+|||||+..+......  .|.++++++-
T Consensus        14 fr~viIG~sGSGKT~li~~lL~~~~~--~f~~I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLYYLRH--KFDHIFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhhcc--cCCEEEEEec
Confidence            35779999999999999999988764  4877766543

This is thought to be an ATPase involved in viral DNA packaging [].

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

Probab=97.50  E-value=0.00035  Score=69.92  Aligned_cols=75  Identities=21%  Similarity=0.330  Sum_probs=55.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      ..+++.++|++|.||||||..++...+    |. ++=|++|...+...+-..|...+.......             .+.
T Consensus       325 ~kKilLL~GppGlGKTTLAHViAkqaG----Ys-VvEINASDeRt~~~v~~kI~~avq~~s~l~-------------ads  386 (877)
T KOG1969|consen  325 PKKILLLCGPPGLGKTTLAHVIAKQAG----YS-VVEINASDERTAPMVKEKIENAVQNHSVLD-------------ADS  386 (877)
T ss_pred             ccceEEeecCCCCChhHHHHHHHHhcC----ce-EEEecccccccHHHHHHHHHHHHhhccccc-------------cCC
Confidence            468999999999999999999998875    42 778899998888777766655553221110             135


Q ss_pred             CeEEEEEeCCCCC
Q 042806          254 KTILVILDNIWGN  266 (390)
Q Consensus       254 ~~~LlVlDdv~~~  266 (390)
                      +|.-||+|.++..
T Consensus       387 rP~CLViDEIDGa  399 (877)
T KOG1969|consen  387 RPVCLVIDEIDGA  399 (877)
T ss_pred             CcceEEEecccCC
Confidence            7788999999754

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

Probab=97.47  E-value=0.01  Score=61.11  Aligned_cols=103  Identities=17%  Similarity=0.244  Sum_probs=63.1

Q ss_pred             cccchhHHHHHHHHHhcC-------CC--ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          155 ACESRMSTLNDILDALKN-------PD--VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~-------~~--~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      .++|-+..+..+.+.+..       ++  ..+....||.|||||-||+.++...-..+  +..+-+      ++.+....
T Consensus       492 rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e--~aliR~------DMSEy~Ek  563 (786)
T COG0542         492 RVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDE--QALIRI------DMSEYMEK  563 (786)
T ss_pred             ceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCC--ccceee------chHHHHHH
Confidence            577888888888777652       22  34677799999999999999999874321  222222      55554432


Q ss_pred             -HHHHhCCCCCC-CCchHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 042806          226 -IADKLGLTLHE-ESDSGRARSLRNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       226 -i~~~l~~~~~~-~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~  266 (390)
                       -.+.|-..++. ....+ -..|.+.++.+...+|.||+|...
T Consensus       564 HsVSrLIGaPPGYVGyee-GG~LTEaVRr~PySViLlDEIEKA  605 (786)
T COG0542         564 HSVSRLIGAPPGYVGYEE-GGQLTEAVRRKPYSVILLDEIEKA  605 (786)
T ss_pred             HHHHHHhCCCCCCceecc-ccchhHhhhcCCCeEEEechhhhc
Confidence             23344333222 22111 345667776654359999999743

>PRK06921 hypothetical protein; Provisional

Probab=97.47  E-value=0.00082  Score=61.26  Aligned_cols=72  Identities=22%  Similarity=0.328  Sum_probs=44.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      ....+.++|+.|+|||+|+..+++....+..+ .++|+..      .+++..+...+          .......+.+..-
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l~~~~g~-~v~y~~~------~~l~~~l~~~~----------~~~~~~~~~~~~~  178 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANELMRKKGV-PVLYFPF------VEGFGDLKDDF----------DLLEAKLNRMKKV  178 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHhhhcCc-eEEEEEH------HHHHHHHHHHH----------HHHHHHHHHhcCC
Confidence            45678999999999999999999987543123 3455553      34444443322          0112233344332


Q ss_pred             CeEEEEEeCCC
Q 042806          254 KTILVILDNIW  264 (390)
Q Consensus       254 ~~~LlVlDdv~  264 (390)
                        =||||||+.
T Consensus       179 --dlLiIDDl~  187 (266)
T PRK06921        179 --EVLFIDDLF  187 (266)
T ss_pred             --CEEEEeccc
Confidence              499999993

>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=97.46  E-value=0.00085  Score=58.23  Aligned_cols=87  Identities=18%  Similarity=0.242  Sum_probs=53.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCCCCC----CCchHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGLTLHE----ESDSGRARSLRNR  249 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~~~~~----~~~~~~~~~l~~~  249 (390)
                      +++|.++|+.|+||||.+..++.....+  -..+..++.... ....+-++..++.++.+...    .+.........+.
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~~~~--~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~~~~~l~~   78 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARLKLK--GKKVALISADTYRIGAVEQLKTYAEILGVPFYVARTESDPAEIAREALEK   78 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHHHHT--T--EEEEEESTSSTHHHHHHHHHHHHHTEEEEESSTTSCHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHHhhc--cccceeecCCCCCccHHHHHHHHHHHhccccchhhcchhhHHHHHHHHHH
Confidence            4789999999999999999888887654  334666666533 34555677778888865321    1233334333344


Q ss_pred             HhCCCeEEEEEeCC
Q 042806          250 LKKEKTILVILDNI  263 (390)
Q Consensus       250 l~~~~~~LlVlDdv  263 (390)
                      +..++.=++++|-.
T Consensus        79 ~~~~~~D~vlIDT~   92 (196)
T PF00448_consen   79 FRKKGYDLVLIDTA   92 (196)
T ss_dssp             HHHTTSSEEEEEE-
T ss_pred             HhhcCCCEEEEecC
Confidence            43323137777765

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 ....

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

Probab=97.44  E-value=0.0016  Score=61.28  Aligned_cols=140  Identities=17%  Similarity=0.117  Sum_probs=79.1

Q ss_pred             ccchhHHHHHHHHHhc-CCCcc-EEEEEcCCCCcHHHHHHHHHHHhhhcC-------------------CCCeEEEEEeC
Q 042806          156 CESRMSTLNDILDALK-NPDVN-MLGIYGMGGIVKTTLAKEVARKAETEK-------------------LFDQVIFVEVS  214 (390)
Q Consensus       156 ~~gR~~~~~~l~~~L~-~~~~~-vi~I~G~~GvGKTtLa~~v~~~~~~~~-------------------~f~~~~wv~v~  214 (390)
                      +++-+....++..+.. .++.+ .+.++|++|+||||+|..+.+......                   .......++.+
T Consensus         3 ~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s   82 (325)
T COG0470           3 LVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPS   82 (325)
T ss_pred             cccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEeccc
Confidence            3455566667777766 34444 499999999999999999999875322                   11234444444


Q ss_pred             CCCC---HHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEe
Q 042806          215 KIQD---IRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTA  289 (390)
Q Consensus       215 ~~~~---~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTt  289 (390)
                      ....   ..+..+++.+.......                .++.-++++|+++...  .-..+...+-.-...+.+|++|
T Consensus        83 ~~~~~~i~~~~vr~~~~~~~~~~~----------------~~~~kviiidead~mt~~A~nallk~lEep~~~~~~il~~  146 (325)
T COG0470          83 DLRKIDIIVEQVRELAEFLSESPL----------------EGGYKVVIIDEADKLTEDAANALLKTLEEPPKNTRFILIT  146 (325)
T ss_pred             ccCCCcchHHHHHHHHHHhccCCC----------------CCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCeEEEEEc
Confidence            4433   34444444444433221                1233699999997542  2333333333344566777777


Q ss_pred             cc-hhhhhhcCCCcceEecCCCC
Q 042806          290 RS-LDVLSRKMDSQQNFSVGVLK  311 (390)
Q Consensus       290 r~-~~v~~~~~~~~~~~~l~~L~  311 (390)
                      .. ..+......-...+++.+.+
T Consensus       147 n~~~~il~tI~SRc~~i~f~~~~  169 (325)
T COG0470         147 NDPSKILPTIRSRCQRIRFKPPS  169 (325)
T ss_pred             CChhhccchhhhcceeeecCCch
Confidence            74 33333223334566676633

>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=97.43  E-value=0.013  Score=55.13  Aligned_cols=40  Identities=20%  Similarity=0.391  Sum_probs=32.1

Q ss_pred             HHHHHHHhcC---CCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          163 LNDILDALKN---PDVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       163 ~~~l~~~L~~---~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      .+.|.+.+.+   +.+.+|+|.|+=|+||||+.+.+.+.....
T Consensus         5 a~~la~~I~~~~~~~~~~IgL~G~WGsGKSs~l~~l~~~L~~~   47 (325)
T PF07693_consen    5 AKALAEIIKNPDSDDPFVIGLYGEWGSGKSSFLNMLKEELKED   47 (325)
T ss_pred             HHHHHHHHhccCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcc
Confidence            4455555554   457899999999999999999999998765

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 [].

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

Probab=97.42  E-value=0.0022  Score=65.45  Aligned_cols=172  Identities=20%  Similarity=0.196  Sum_probs=104.4

Q ss_pred             hHHHHHHHHHhcCCC---------ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          160 MSTLNDILDALKNPD---------VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       160 ~~~~~~l~~~L~~~~---------~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ..|+.++++.|.++.         ++=+.++||+|.|||-||+.++-...+.       |++++..    ++.    ..+
T Consensus       320 K~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgVP-------F~svSGS----EFv----E~~  384 (774)
T KOG0731|consen  320 KEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGVP-------FFSVSGS----EFV----EMF  384 (774)
T ss_pred             HHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCCc-------eeeechH----HHH----HHh
Confidence            467778888888742         5668899999999999999998887653       4555542    111    111


Q ss_pred             CCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc-----------------ccccccCCCCC--CCCCcEEEEEecc
Q 042806          231 GLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL-----------------DFQAVGIPHGD--DRKGCKVLLTARS  291 (390)
Q Consensus       231 ~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~-----------------~~~~l~~~l~~--~~~~s~IivTtr~  291 (390)
                      ..     .....+..+....+...|+++.+|+++...                 .++.+...+..  ...+.-++.+|+.
T Consensus       385 ~g-----~~asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr  459 (774)
T KOG0731|consen  385 VG-----VGASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLAATNR  459 (774)
T ss_pred             cc-----cchHHHHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCC
Confidence            11     112345556666666667999999886331                 12222211111  1233445555555


Q ss_pred             hhhhhh-cC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHH
Q 042806          292 LDVLSR-KM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVT  352 (390)
Q Consensus       292 ~~v~~~-~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~  352 (390)
                      .++... .+   ...+.+.++.-+.....++|..++.......+..++.+ |+..+-|++=|...
T Consensus       460 ~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~-~a~~t~gf~gadl~  523 (774)
T KOG0731|consen  460 PDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSK-LASLTPGFSGADLA  523 (774)
T ss_pred             ccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHH-HHhcCCCCcHHHHH
Confidence            544321 11   23357888888888899999988864333344455666 88888888866543

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.42  E-value=0.0016  Score=58.43  Aligned_cols=76  Identities=20%  Similarity=0.240  Sum_probs=48.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      ...+.++|.+|+|||+|+..+++.....  -..++++      +..+++..+...+..  ..    .....+.+.+..- 
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~l~~~--g~~v~~i------t~~~l~~~l~~~~~~--~~----~~~~~~l~~l~~~-  163 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNELLLR--GKSVLII------TVADIMSAMKDTFSN--SE----TSEEQLLNDLSNV-  163 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEE------EHHHHHHHHHHHHhh--cc----ccHHHHHHHhccC-
Confidence            3578899999999999999999998653  2344555      345666655544421  11    1122344555532 


Q ss_pred             eEEEEEeCCCCC
Q 042806          255 TILVILDNIWGN  266 (390)
Q Consensus       255 ~~LlVlDdv~~~  266 (390)
                       =||||||+...
T Consensus       164 -dlLvIDDig~~  174 (244)
T PRK07952        164 -DLLVIDEIGVQ  174 (244)
T ss_pred             -CEEEEeCCCCC
Confidence             48899999643

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.42  E-value=0.0012  Score=62.73  Aligned_cols=89  Identities=18%  Similarity=0.223  Sum_probs=53.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-IQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKK  252 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  252 (390)
                      +..++.++|+.|+||||++..+......+.....+.++.... .....+-++...+.++..................+.+
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~l~~  215 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLALAELRN  215 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHHHHHHhcC
Confidence            357899999999999999999998764331223455555433 2344555666666776654333222222333344444


Q ss_pred             CCeEEEEEeCCC
Q 042806          253 EKTILVILDNIW  264 (390)
Q Consensus       253 ~~~~LlVlDdv~  264 (390)
                      .  -++++|..-
T Consensus       216 ~--DlVLIDTaG  225 (374)
T PRK14722        216 K--HMVLIDTIG  225 (374)
T ss_pred             C--CEEEEcCCC
Confidence            3  366788874

>TIGR02012 tigrfam_recA protein RecA

Probab=97.41  E-value=0.00051  Score=63.89  Aligned_cols=85  Identities=19%  Similarity=0.268  Sum_probs=54.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------CCCchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLH------EESDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~  247 (390)
                      ..+++.|+|++|+|||||+.++.......  -..++|++....++..     .+..++.+.+      ..........+.
T Consensus        54 ~G~iteI~G~~GsGKTtLaL~~~~~~~~~--g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~~  126 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLALHAIAEAQKA--GGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIAE  126 (321)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHH
Confidence            56799999999999999999988776543  2456788776655542     3455554321      112233344444


Q ss_pred             HHHhCCCeEEEEEeCCCC
Q 042806          248 NRLKKEKTILVILDNIWG  265 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~  265 (390)
                      ..++.+..-++|+|.+..
T Consensus       127 ~li~~~~~~lIVIDSv~a  144 (321)
T TIGR02012       127 TLVRSGAVDIIVVDSVAA  144 (321)
T ss_pred             HHhhccCCcEEEEcchhh
Confidence            445555557999999853

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

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

Probab=97.41  E-value=0.0012  Score=58.36  Aligned_cols=170  Identities=18%  Similarity=0.273  Sum_probs=99.5

Q ss_pred             ccccchhHHH---HHHHHHhcCC------CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 042806          154 EACESRMSTL---NDILDALKNP------DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQG  224 (390)
Q Consensus       154 ~~~~gR~~~~---~~l~~~L~~~------~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~  224 (390)
                      ++++|.+...   .-|++.|.++      .++-|..+|++|.|||-+|+.+.+..++.  |     +.+..    .+++.
T Consensus       121 ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~kvp--~-----l~vka----t~liG  189 (368)
T COG1223         121 DDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKVP--L-----LLVKA----TELIG  189 (368)
T ss_pred             hhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccCCc--e-----EEech----HHHHH
Confidence            4566765443   3456667664      37889999999999999999999988753  2     22211    12221


Q ss_pred             HHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--------------cccccccCCCC--CCCCCcEEEEE
Q 042806          225 EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--------------LDFQAVGIPHG--DDRKGCKVLLT  288 (390)
Q Consensus       225 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--------------~~~~~l~~~l~--~~~~~s~IivT  288 (390)
                      +   ..|      +....+..+.+....--+|++.+|.++..              +..+.+.-.+.  ..+.|...|..
T Consensus       190 e---hVG------dgar~Ihely~rA~~~aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGVvtIaa  260 (368)
T COG1223         190 E---HVG------DGARRIHELYERARKAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAA  260 (368)
T ss_pred             H---Hhh------hHHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCceEEEee
Confidence            1   111      22234455555555556799999998532              11122211111  13456666777


Q ss_pred             ecchhhhhhcC--CCcceEecCCCCHHHHHHHHHHhhC--CCCCCCchHHHHHHHHHHcCCCh
Q 042806          289 ARSLDVLSRKM--DSQQNFSVGVLKEDEAWSLFKKMAG--DYIEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       289 tr~~~v~~~~~--~~~~~~~l~~L~~~ea~~lf~~~~~--~~~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      |.+........  .....|+...-+++|-.++++..+.  .-.....    .+.++++.+|+.
T Consensus       261 TN~p~~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~----~~~~~~~t~g~S  319 (368)
T COG1223         261 TNRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLPVDAD----LRYLAAKTKGMS  319 (368)
T ss_pred             cCChhhcCHHHHhhhhheeeeeCCChHHHHHHHHHHHHhCCCccccC----HHHHHHHhCCCC
Confidence            76655432211  2234777778888999999998884  2222222    346777777653

>PRK09183 transposase/IS protein; Provisional

Probab=97.40  E-value=0.00044  Score=62.85  Aligned_cols=27  Identities=26%  Similarity=0.267  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...+.|+|++|+|||+|+..+.+....
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~~a~~  128 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGYEAVR  128 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            456779999999999999999877543

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

Probab=97.39  E-value=0.012  Score=56.24  Aligned_cols=154  Identities=13%  Similarity=0.125  Sum_probs=83.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      |=-.++||+|.||||++..++|.+.    |+..- +..+...+-.+ ++.++                    ..-  ..+
T Consensus       236 RGYLLYGPPGTGKSS~IaAmAn~L~----ydIyd-LeLt~v~~n~d-Lr~LL--------------------~~t--~~k  287 (457)
T KOG0743|consen  236 RGYLLYGPPGTGKSSFIAAMANYLN----YDIYD-LELTEVKLDSD-LRHLL--------------------LAT--PNK  287 (457)
T ss_pred             ccceeeCCCCCCHHHHHHHHHhhcC----CceEE-eeeccccCcHH-HHHHH--------------------HhC--CCC
Confidence            5577999999999999999999885    55321 22222111111 22221                    111  223


Q ss_pred             EEEEEeCCCCCcc-----------cc---------cccCC---CCCCCCCcEEE-EEecchhhh-hhcCC---CcceEec
Q 042806          256 ILVILDNIWGNLD-----------FQ---------AVGIP---HGDDRKGCKVL-LTARSLDVL-SRKMD---SQQNFSV  307 (390)
Q Consensus       256 ~LlVlDdv~~~~~-----------~~---------~l~~~---l~~~~~~s~Ii-vTtr~~~v~-~~~~~---~~~~~~l  307 (390)
                      -+||+.|++...+           .+         -|...   +.+++.+-||| .||...+-. +..+.   ....+++
T Consensus       288 SIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmhI~m  367 (457)
T KOG0743|consen  288 SILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMHIYM  367 (457)
T ss_pred             cEEEEeecccccccccccccccccccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeEEEc
Confidence            7888888863211           11         01111   11222233555 555543321 11222   2247888


Q ss_pred             CCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhcCCC
Q 042806          308 GVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRD  361 (390)
Q Consensus       308 ~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~~  361 (390)
                      .--+++....|+.+..+...+.    .+..+|.+.-.|.-+.=..++..|-.+.
T Consensus       368 gyCtf~~fK~La~nYL~~~~~h----~L~~eie~l~~~~~~tPA~V~e~lm~~~  417 (457)
T KOG0743|consen  368 GYCTFEAFKTLASNYLGIEEDH----RLFDEIERLIEETEVTPAQVAEELMKNK  417 (457)
T ss_pred             CCCCHHHHHHHHHHhcCCCCCc----chhHHHHHHhhcCccCHHHHHHHHhhcc
Confidence            8999999999999988643322    2445566666666666666766554443

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

Probab=97.37  E-value=0.00058  Score=63.58  Aligned_cols=84  Identities=23%  Similarity=0.285  Sum_probs=54.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------CCCchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLH------EESDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~  247 (390)
                      ..+++-|+|++|+|||||+.+++......  -..++|++....+++.     .+..++.+.+      ..+..+....+.
T Consensus        54 ~G~iteI~Gp~GsGKTtLal~~~~~~~~~--g~~~vyId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~i~~  126 (325)
T cd00983          54 KGRIIEIYGPESSGKTTLALHAIAEAQKL--GGTVAFIDAEHALDPV-----YAKKLGVDLDNLLISQPDTGEQALEIAD  126 (325)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc--CCCEEEECccccHHHH-----HHHHcCCCHHHheecCCCCHHHHHHHHH
Confidence            46789999999999999999988776433  3457888887766643     3444443211      112233344444


Q ss_pred             HHHhCCCeEEEEEeCCC
Q 042806          248 NRLKKEKTILVILDNIW  264 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~  264 (390)
                      ..+..+..-++|+|.+.
T Consensus       127 ~li~s~~~~lIVIDSva  143 (325)
T cd00983         127 SLVRSGAVDLIVVDSVA  143 (325)
T ss_pred             HHHhccCCCEEEEcchH
Confidence            44455555799999985

RecA couples ATP hydrolysis to DNA strand exchange.

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

Probab=97.36  E-value=0.00062  Score=65.86  Aligned_cols=88  Identities=25%  Similarity=0.253  Sum_probs=60.1

Q ss_pred             hhHHHHHHHHHhcCCC---------ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 042806          159 RMSTLNDILDALKNPD---------VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       159 R~~~~~~l~~~L~~~~---------~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      -..|++++++.|.++.         ++=|.++||+|.|||-||+.++-...+.      +|.+.+..|+.-  +    -.
T Consensus       312 AK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VP------FF~~sGSEFdEm--~----VG  379 (752)
T KOG0734|consen  312 AKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVP------FFYASGSEFDEM--F----VG  379 (752)
T ss_pred             HHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCC------eEeccccchhhh--h----hc
Confidence            4578899999998742         5678899999999999999998877653      344444444321  1    11


Q ss_pred             hCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 042806          230 LGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       230 l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~  266 (390)
                              --...+..|...-+..-||+|.+|.++..
T Consensus       380 --------vGArRVRdLF~aAk~~APcIIFIDEiDav  408 (752)
T KOG0734|consen  380 --------VGARRVRDLFAAAKARAPCIIFIDEIDAV  408 (752)
T ss_pred             --------ccHHHHHHHHHHHHhcCCeEEEEechhhh
Confidence                    11234455555556666899999999743

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

Probab=97.35  E-value=0.0075  Score=58.59  Aligned_cols=143  Identities=20%  Similarity=0.298  Sum_probs=80.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHH----HHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLR----NRL  250 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~----~~l  250 (390)
                      ...+.+.|++|+|||+||..++....    |..+--+  |    ++++.       |.     +.......+.    ..-
T Consensus       538 lvSvLl~Gp~~sGKTaLAA~iA~~S~----FPFvKii--S----pe~mi-------G~-----sEsaKc~~i~k~F~DAY  595 (744)
T KOG0741|consen  538 LVSVLLEGPPGSGKTALAAKIALSSD----FPFVKII--S----PEDMI-------GL-----SESAKCAHIKKIFEDAY  595 (744)
T ss_pred             ceEEEEecCCCCChHHHHHHHHhhcC----CCeEEEe--C----hHHcc-------Cc-----cHHHHHHHHHHHHHHhh
Confidence            55677899999999999999987653    6432221  1    12110       00     1111111222    222


Q ss_pred             hCCCeEEEEEeCCCCCcccccccCCCC---------------CCCCCcEEEEEecchhhhhhcCC----CcceEecCCCC
Q 042806          251 KKEKTILVILDNIWGNLDFQAVGIPHG---------------DDRKGCKVLLTARSLDVLSRKMD----SQQNFSVGVLK  311 (390)
Q Consensus       251 ~~~~~~LlVlDdv~~~~~~~~l~~~l~---------------~~~~~s~IivTtr~~~v~~~~~~----~~~~~~l~~L~  311 (390)
                      ++.- -.||+||+....+|-.++..|.               ..+...-|+-||....+... ++    ....|++..++
T Consensus       596 kS~l-siivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~-m~i~~~F~~~i~Vpnl~  673 (744)
T KOG0741|consen  596 KSPL-SIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQE-MGILDCFSSTIHVPNLT  673 (744)
T ss_pred             cCcc-eEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHH-cCHHHhhhheeecCccC
Confidence            3333 6999999987777666554331               12223345556665666432 22    23588898888


Q ss_pred             H-HHHHHHHHHhhCCCCCCCchHHHHHHHHHHc
Q 042806          312 E-DEAWSLFKKMAGDYIEGSEFKWVAKDVAREC  343 (390)
Q Consensus       312 ~-~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~  343 (390)
                      . ++..+.++..-  ...+.+.+.++.+...+|
T Consensus       674 ~~~~~~~vl~~~n--~fsd~~~~~~~~~~~~~~  704 (744)
T KOG0741|consen  674 TGEQLLEVLEELN--IFSDDEVRAIAEQLLSKK  704 (744)
T ss_pred             chHHHHHHHHHcc--CCCcchhHHHHHHHhccc
Confidence            7 77777776543  112334455566666666

>PRK09354 recA recombinase A; Provisional

Probab=97.35  E-value=0.00072  Score=63.46  Aligned_cols=85  Identities=20%  Similarity=0.269  Sum_probs=56.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------CCCchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLH------EESDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~  247 (390)
                      .-+++-|+|++|+|||||+.+++......  =..++|+.....++..     .++.++.+.+      ..+.......+.
T Consensus        59 ~G~IteI~G~~GsGKTtLal~~~~~~~~~--G~~~~yId~E~s~~~~-----~a~~lGvdld~lli~qp~~~Eq~l~i~~  131 (349)
T PRK09354         59 RGRIVEIYGPESSGKTTLALHAIAEAQKA--GGTAAFIDAEHALDPV-----YAKKLGVDIDNLLVSQPDTGEQALEIAD  131 (349)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEECCccchHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHH
Confidence            46789999999999999999998776543  3457898887766652     3455554321      112233344444


Q ss_pred             HHHhCCCeEEEEEeCCCC
Q 042806          248 NRLKKEKTILVILDNIWG  265 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~  265 (390)
                      ..++.+..-+||+|.|..
T Consensus       132 ~li~s~~~~lIVIDSvaa  149 (349)
T PRK09354        132 TLVRSGAVDLIVVDSVAA  149 (349)
T ss_pred             HHhhcCCCCEEEEeChhh
Confidence            455555657999999853

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=97.34  E-value=0.0025  Score=60.32  Aligned_cols=99  Identities=21%  Similarity=0.225  Sum_probs=55.8

Q ss_pred             HHHHHHHhcCC----CccEEEEEcCCCCcHH-HHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCCCCC
Q 042806          163 LNDILDALKNP----DVNMLGIYGMGGIVKT-TLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGLTLHE  236 (390)
Q Consensus       163 ~~~l~~~L~~~----~~~vi~I~G~~GvGKT-tLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~~~~~  236 (390)
                      ...+..++.++    +.++|+++||.||||| |||+..+......+.. .+..|+.... .-..+=++.-++.++.+...
T Consensus       187 l~~~~~~~~~~~~~~~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~-kVaiITtDtYRIGA~EQLk~Ya~im~vp~~v  265 (407)
T COG1419         187 LRKLLLSLIENLIVEQKRVIALVGPTGVGKTTTLAKLAARYVMLKKKK-KVAIITTDTYRIGAVEQLKTYADIMGVPLEV  265 (407)
T ss_pred             HHHHHHhhccccccccCcEEEEECCCCCcHHHHHHHHHHHHHhhccCc-ceEEEEeccchhhHHHHHHHHHHHhCCceEE
Confidence            33444444443    4799999999999999 5566555554222223 3555555433 23344455667777776554


Q ss_pred             CCchHHHHHHHHHHhCCCeEEEEEeCCC
Q 042806          237 ESDSGRARSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       237 ~~~~~~~~~l~~~l~~~~~~LlVlDdv~  264 (390)
                      .........-...+.+..  +|.+|-+-
T Consensus       266 v~~~~el~~ai~~l~~~d--~ILVDTaG  291 (407)
T COG1419         266 VYSPKELAEAIEALRDCD--VILVDTAG  291 (407)
T ss_pred             ecCHHHHHHHHHHhhcCC--EEEEeCCC
Confidence            433334444444454433  66667653

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=97.32  E-value=0.014  Score=58.67  Aligned_cols=203  Identities=18%  Similarity=0.158  Sum_probs=125.2

Q ss_pred             cccccchhHHHHHHHHHhcC-----CCccEEEEEcCCCCcHHHHHHHHHHHhhh---cCCCCe--EEEEEeCCCCCHHHH
Q 042806          153 YEACESRMSTLNDILDALKN-----PDVNMLGIYGMGGIVKTTLAKEVARKAET---EKLFDQ--VIFVEVSKIQDIRKI  222 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-----~~~~vi~I~G~~GvGKTtLa~~v~~~~~~---~~~f~~--~~wv~v~~~~~~~~l  222 (390)
                      +..+.+|+.+..+|-..+..     +....+-|.|.+|+|||..+..|.+.+..   ++.-..  .+.|+.-.-..+.++
T Consensus       395 p~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~  474 (767)
T KOG1514|consen  395 PESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREI  474 (767)
T ss_pred             cccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHH
Confidence            34578899999988877653     23458889999999999999999997652   222222  334444455679999


Q ss_pred             HHHHHHHhCCCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCCcc--cccccCCCC-CCCCCcEEEEEe-cc-hh
Q 042806          223 QGEIADKLGLTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGNLD--FQAVGIPHG-DDRKGCKVLLTA-RS-LD  293 (390)
Q Consensus       223 ~~~i~~~l~~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~~~--~~~l~~~l~-~~~~~s~IivTt-r~-~~  293 (390)
                      +..|...+......  ....+..|..++.    .++++++++|+++..-.  -+-+...|. ...++|+++|-+ -+ -.
T Consensus       475 Y~~I~~~lsg~~~~--~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~IaNTmd  552 (767)
T KOG1514|consen  475 YEKIWEALSGERVT--WDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIAIANTMD  552 (767)
T ss_pred             HHHHHHhcccCccc--HHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEEeccccc
Confidence            99999998754332  2223445555554    24558999998853311  111111111 134556544433 22 11


Q ss_pred             hhhhc-------CCCcceEecCCCCHHHHHHHHHHhhC--CCCCCCchHHHHHHHHHHcCCChHHHHHHHHHh
Q 042806          294 VLSRK-------MDSQQNFSVGVLKEDEAWSLFKKMAG--DYIEGSEFKWVAKDVARECAGLPVSIVTVARAL  357 (390)
Q Consensus       294 v~~~~-------~~~~~~~~l~~L~~~ea~~lf~~~~~--~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L  357 (390)
                      .+...       .-+...+...|.+.++-.++...++.  ........+-++++++...|-.-.|+...-+..
T Consensus       553 lPEr~l~nrvsSRlg~tRi~F~pYth~qLq~Ii~~RL~~~~~f~~~aielvarkVAavSGDaRraldic~RA~  625 (767)
T KOG1514|consen  553 LPERLLMNRVSSRLGLTRICFQPYTHEQLQEIISARLKGLDAFENKAIELVARKVAAVSGDARRALDICRRAA  625 (767)
T ss_pred             CHHHHhccchhhhccceeeecCCCCHHHHHHHHHHhhcchhhcchhHHHHHHHHHHhccccHHHHHHHHHHHH
Confidence            11111       12346888999999999999888775  233344455577888888887777777664443

>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=97.31  E-value=0.00022  Score=56.67  Aligned_cols=24  Identities=42%  Similarity=0.443  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +|.|.|++|+||||+|+.+.+...
T Consensus         1 vI~I~G~~gsGKST~a~~La~~~~   24 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAERLG   24 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHC
Confidence            689999999999999999998763

...

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=97.31  E-value=0.0013  Score=61.98  Aligned_cols=90  Identities=17%  Similarity=0.192  Sum_probs=58.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc---CC-CCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC----------Cc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE---KL-FDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE----------SD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~---~~-f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~----------~~  239 (390)
                      ...++-|+|++|+|||+|+.+++-.....   +. -..++||+....|+++.+.. +++.++.+....          +.
T Consensus       125 ~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~d~~~~l~~I~~~~~~~~  203 (344)
T PLN03187        125 TRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGMDADAVLDNIIYARAYTY  203 (344)
T ss_pred             CCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCCChhhhcCeEEEecCCCH
Confidence            45788899999999999999987543221   11 24689999999989887654 566676543211          11


Q ss_pred             h---HHHHHHHHHHhCCCeEEEEEeCCC
Q 042806          240 S---GRARSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       240 ~---~~~~~l~~~l~~~~~~LlVlDdv~  264 (390)
                      .   ..+..+...+...+.-|||+|.+.
T Consensus       204 e~~~~~l~~l~~~i~~~~~~LvVIDSit  231 (344)
T PLN03187        204 EHQYNLLLGLAAKMAEEPFRLLIVDSVI  231 (344)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEeCcH
Confidence            1   122333344444454699999985

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=97.29  E-value=0.0024  Score=65.65  Aligned_cols=149  Identities=20%  Similarity=0.237  Sum_probs=78.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      .+-+.|+|++|+|||++++.+.......  |     +.++..    ++.. +  ..+      ........+........
T Consensus       185 ~~gill~G~~G~GKt~~~~~~a~~~~~~--f-----~~is~~----~~~~-~--~~g------~~~~~~~~~f~~a~~~~  244 (644)
T PRK10733        185 PKGVLMVGPPGTGKTLLAKAIAGEAKVP--F-----FTISGS----DFVE-M--FVG------VGASRVRDMFEQAKKAA  244 (644)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHcCCC--E-----EEEehH----HhHH-h--hhc------ccHHHHHHHHHHHHhcC
Confidence            3458899999999999999998876532  2     222211    1111 0  000      01112233333344456


Q ss_pred             eEEEEEeCCCCCcc----------------cccccCCCC--CCCCCcEEEEEecchhhhh-hcC---CCcceEecCCCCH
Q 042806          255 TILVILDNIWGNLD----------------FQAVGIPHG--DDRKGCKVLLTARSLDVLS-RKM---DSQQNFSVGVLKE  312 (390)
Q Consensus       255 ~~LlVlDdv~~~~~----------------~~~l~~~l~--~~~~~s~IivTtr~~~v~~-~~~---~~~~~~~l~~L~~  312 (390)
                      +++|++|+++....                ...+...+.  ..+.+.-+|.||....... ...   ...+.+.+...+.
T Consensus       245 P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~  324 (644)
T PRK10733        245 PCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDV  324 (644)
T ss_pred             CcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCH
Confidence            69999999964310                111111111  1233455666776544321 111   2346788888888


Q ss_pred             HHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC
Q 042806          313 DEAWSLFKKMAGDYIEGSEFKWVAKDVARECAG  345 (390)
Q Consensus       313 ~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~G  345 (390)
                      ++-.+++..+.......++..  ...+++.+.|
T Consensus       325 ~~R~~Il~~~~~~~~l~~~~d--~~~la~~t~G  355 (644)
T PRK10733        325 RGREQILKVHMRRVPLAPDID--AAIIARGTPG  355 (644)
T ss_pred             HHHHHHHHHHhhcCCCCCcCC--HHHHHhhCCC
Confidence            888888887775322212111  2346666655

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.27  E-value=0.00085  Score=71.06  Aligned_cols=131  Identities=17%  Similarity=0.182  Sum_probs=69.9

Q ss_pred             ccccchhHHHHHHHHHhcC-------CC--ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 042806          154 EACESRMSTLNDILDALKN-------PD--VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQG  224 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~-------~~--~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~  224 (390)
                      ..++|.+..+..+...+..       ++  ...+.++||.|+|||+||+.+.+..-..  -...+-++.+.......+  
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~--~~~~~~~d~s~~~~~~~~--  584 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGS--EDAMIRLDMSEYMEKHTV--  584 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCC--ccceEEEEchhccccccH--
Confidence            4577877777777776642       22  2356789999999999999999876321  122334444432221111  


Q ss_pred             HHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCC-----------CCCcEEEEEecc
Q 042806          225 EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDD-----------RKGCKVLLTARS  291 (390)
Q Consensus       225 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~-----------~~~s~IivTtr~  291 (390)
                        .+-+|.+..... ......+.+.+..+...+++||+++..  ..++.+...+..+           ...+.||+||..
T Consensus       585 --~~l~g~~~gyvg-~~~~~~l~~~~~~~p~~VvllDeieka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~  661 (821)
T CHL00095        585 --SKLIGSPPGYVG-YNEGGQLTEAVRKKPYTVVLFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNL  661 (821)
T ss_pred             --HHhcCCCCcccC-cCccchHHHHHHhCCCeEEEECChhhCCHHHHHHHHHHhccCceecCCCcEEecCceEEEEeCCc
Confidence              111222111111 111224556665555469999999744  2333333222211           245667777764

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

Probab=97.27  E-value=0.0028  Score=56.32  Aligned_cols=91  Identities=18%  Similarity=0.242  Sum_probs=54.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcC----CCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC----------CCCc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEK----LFDQVIFVEVSKIQDIRKIQGEIADKLGLTLH----------EESD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~----------~~~~  239 (390)
                      ...++.|+|++|+|||+|+.+++......+    .=..++|+.....++...+. .++...+....          ..+.
T Consensus        18 ~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~rl~-~~~~~~~~~~~~~~~~i~~~~~~~~   96 (226)
T cd01393          18 TGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERLV-QLAVRFGLDPEEVLDNIYVARPYNG   96 (226)
T ss_pred             CCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHHHH-HHHHHhccchhhhhccEEEEeCCCH
Confidence            457899999999999999999987653221    01457898887776665443 33343322111          0122


Q ss_pred             hHHHHHHHHHH---hCCCeEEEEEeCCCC
Q 042806          240 SGRARSLRNRL---KKEKTILVILDNIWG  265 (390)
Q Consensus       240 ~~~~~~l~~~l---~~~~~~LlVlDdv~~  265 (390)
                      ......+....   ...+.-|+|+|.+..
T Consensus        97 ~~~~~~l~~~~~~~~~~~~~lvVIDsis~  125 (226)
T cd01393          97 EQQLEIVEELERIMSSGRVDLVVVDSVAA  125 (226)
T ss_pred             HHHHHHHHHHHHHhhcCCeeEEEEcCcch
Confidence            22333333332   244556999999853

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

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=97.27  E-value=0.0013  Score=61.25  Aligned_cols=90  Identities=18%  Similarity=0.257  Sum_probs=58.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc----CCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC----------Cc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE----KLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE----------SD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~----~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~----------~~  239 (390)
                      ..+++-|+|++|+|||+|+.+++-.....    ..=..++|++....++++.+. +++..++.+.+..          +.
T Consensus        95 ~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~-~~a~~~g~d~~~~l~~i~~~~~~~~  173 (313)
T TIGR02238        95 SMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIR-AIAERFGVDPDAVLDNILYARAYTS  173 (313)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHH-HHHHHcCCChHHhcCcEEEecCCCH
Confidence            45788899999999999999987543211    112368999999888887764 4567776543211          11


Q ss_pred             h---HHHHHHHHHHhCCCeEEEEEeCCC
Q 042806          240 S---GRARSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       240 ~---~~~~~l~~~l~~~~~~LlVlDdv~  264 (390)
                      .   ..+..+...+...+.-|||+|.+.
T Consensus       174 e~~~~~l~~l~~~i~~~~~~LvVIDSis  201 (313)
T TIGR02238       174 EHQMELLDYLAAKFSEEPFRLLIVDSIM  201 (313)
T ss_pred             HHHHHHHHHHHHHhhccCCCEEEEEcch
Confidence            1   223334444544454689999985

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.

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

Probab=97.26  E-value=0.0034  Score=61.91  Aligned_cols=131  Identities=19%  Similarity=0.265  Sum_probs=81.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      .+.=|.+|||+|+|||-||+.|+|..+..       |+++..+    +++..-   .|      .....+..+.++-+..
T Consensus       544 ~PsGvLL~GPPGCGKTLlAKAVANEag~N-------FisVKGP----ELlNkY---VG------ESErAVR~vFqRAR~s  603 (802)
T KOG0733|consen  544 APSGVLLCGPPGCGKTLLAKAVANEAGAN-------FISVKGP----ELLNKY---VG------ESERAVRQVFQRARAS  603 (802)
T ss_pred             CCCceEEeCCCCccHHHHHHHHhhhccCc-------eEeecCH----HHHHHH---hh------hHHHHHHHHHHHhhcC
Confidence            35668899999999999999999988643       4555543    332221   11      2334566777777777


Q ss_pred             CeEEEEEeCCCCC-------c------ccccccCCCCC--CCCCcEEEEEecchhhh-hhcCC---CcceEecCCCCHHH
Q 042806          254 KTILVILDNIWGN-------L------DFQAVGIPHGD--DRKGCKVLLTARSLDVL-SRKMD---SQQNFSVGVLKEDE  314 (390)
Q Consensus       254 ~~~LlVlDdv~~~-------~------~~~~l~~~l~~--~~~~s~IivTtr~~~v~-~~~~~---~~~~~~l~~L~~~e  314 (390)
                      -+|+|.||.++..       .      ....+.-.+..  ...|.-||-.|...++- .....   -...+.++.-+.+|
T Consensus       604 aPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~e  683 (802)
T KOG0733|consen  604 APCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEE  683 (802)
T ss_pred             CCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHH
Confidence            7899999999643       1      12222222222  23455566555543331 21222   23577788888888


Q ss_pred             HHHHHHHhhC
Q 042806          315 AWSLFKKMAG  324 (390)
Q Consensus       315 a~~lf~~~~~  324 (390)
                      -.+++.....
T Consensus       684 R~~ILK~~tk  693 (802)
T KOG0733|consen  684 RVAILKTITK  693 (802)
T ss_pred             HHHHHHHHhc
Confidence            8899988875

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

Probab=97.26  E-value=0.0029  Score=62.92  Aligned_cols=152  Identities=14%  Similarity=0.118  Sum_probs=81.9

Q ss_pred             cccccchhHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALKN-------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ..++.|-++...+|-+.+.-             ..++-|.++||+|+|||++|+.+.+.....  |     +.++.+   
T Consensus       433 W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~n--F-----lsvkgp---  502 (693)
T KOG0730|consen  433 WDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMN--F-----LSVKGP---  502 (693)
T ss_pred             hhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCC--e-----eeccCH---
Confidence            44555665555555443321             356788999999999999999999987643  3     344332   


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc-------------cccccCCCCCC--CCCcE
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD-------------FQAVGIPHGDD--RKGCK  284 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~-------------~~~l~~~l~~~--~~~s~  284 (390)
                       +++    +..-.     .....+..+...-+.--++++.||.++....             +..+...+...  ..+.-
T Consensus       503 -EL~----sk~vG-----eSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~  572 (693)
T KOG0730|consen  503 -ELF----SKYVG-----ESERAIREVFRKARQVAPCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVL  572 (693)
T ss_pred             -HHH----HHhcC-----chHHHHHHHHHHHhhcCCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCcEE
Confidence             111    11100     1122334444444444569999999864311             11111112111  12233


Q ss_pred             EEEEecc-hhhhhhcCC---CcceEecCCCCHHHHHHHHHHhhC
Q 042806          285 VLLTARS-LDVLSRKMD---SQQNFSVGVLKEDEAWSLFKKMAG  324 (390)
Q Consensus       285 IivTtr~-~~v~~~~~~---~~~~~~l~~L~~~ea~~lf~~~~~  324 (390)
                      ||..|.. ..+-...+.   ....+.+.+-+.+--.++|..++.
T Consensus       573 ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~k  616 (693)
T KOG0730|consen  573 VIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAK  616 (693)
T ss_pred             EEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHh
Confidence            3333332 333222333   335777777777778899998885

>PRK04296 thymidine kinase; Provisional

Probab=97.24  E-value=0.00049  Score=59.53  Aligned_cols=110  Identities=21%  Similarity=0.149  Sum_probs=61.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC---CCchHHHHHHHHHHhC
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE---ESDSGRARSLRNRLKK  252 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~---~~~~~~~~~l~~~l~~  252 (390)
                      .++.|+|+.|.||||++..+.......  -..++.+  .+.++.......+++.++.....   .........+.+  ..
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~--g~~v~i~--k~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~--~~   76 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEER--GMKVLVF--KPAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE--EG   76 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHc--CCeEEEE--eccccccccCCcEecCCCCcccceEeCChHHHHHHHHh--hC
Confidence            467899999999999999999887543  2223333  12222222234455666543322   112223333333  33


Q ss_pred             CCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecchh
Q 042806          253 EKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSLD  293 (390)
Q Consensus       253 ~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~~  293 (390)
                      ++.-+||+|.++-.  ++...+...+  ...|..||+|.+...
T Consensus        77 ~~~dvviIDEaq~l~~~~v~~l~~~l--~~~g~~vi~tgl~~~  117 (190)
T PRK04296         77 EKIDCVLIDEAQFLDKEQVVQLAEVL--DDLGIPVICYGLDTD  117 (190)
T ss_pred             CCCCEEEEEccccCCHHHHHHHHHHH--HHcCCeEEEEecCcc
Confidence            34348999999643  1122222221  345788999999743

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=97.22  E-value=0.0047  Score=57.96  Aligned_cols=86  Identities=9%  Similarity=0.062  Sum_probs=47.4

Q ss_pred             EEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEecch-hhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCch
Q 042806          256 ILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTARSL-DVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEF  332 (390)
Q Consensus       256 ~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTtr~~-~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~  332 (390)
                      =++|+|++...+  .-+.+...+..-..++.+|++|.+. .+......-...+.+.+++.+++.+.+....    .... 
T Consensus       115 kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~~~L~~~~----~~~~-  189 (325)
T PRK08699        115 RVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLRERG----VAEP-  189 (325)
T ss_pred             eEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHHHHHHhcC----CCcH-
Confidence            355668876542  2222222221112346677777764 3433333445689999999999988886541    1111 


Q ss_pred             HHHHHHHHHHcCCChHHH
Q 042806          333 KWVAKDVARECAGLPVSI  350 (390)
Q Consensus       333 ~~~~~~i~~~~~GlPLai  350 (390)
                      .    ..+..++|-|+..
T Consensus       190 ~----~~l~~~~g~p~~~  203 (325)
T PRK08699        190 E----ERLAFHSGAPLFD  203 (325)
T ss_pred             H----HHHHHhCCChhhh
Confidence            1    1235688888643

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.20  E-value=0.002  Score=57.31  Aligned_cols=46  Identities=22%  Similarity=0.292  Sum_probs=35.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKI  222 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l  222 (390)
                      ...++.|+|++|+|||+++.+++......  -..++|++.. .++.+.+
T Consensus        22 ~g~i~~i~G~~GsGKT~l~~~la~~~~~~--~~~v~yi~~e-~~~~~r~   67 (225)
T PRK09361         22 RGTITQIYGPPGSGKTNICLQLAVEAAKN--GKKVIYIDTE-GLSPERF   67 (225)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEECC-CCCHHHH
Confidence            45789999999999999999998876533  3568898887 4554443

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

Probab=97.20  E-value=0.0011  Score=57.66  Aligned_cols=65  Identities=20%  Similarity=0.116  Sum_probs=50.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ  217 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  217 (390)
                      ..++||-++.++.+.-...+++.+-+.|.||+|+||||-+..+++.+-....-+.+.-.++|...
T Consensus        26 l~dIVGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeR   90 (333)
T KOG0991|consen   26 LQDIVGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDER   90 (333)
T ss_pred             HHHhhCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCcccc
Confidence            45789999999988888888899999999999999999999998887543222344445555443

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

Probab=97.20  E-value=0.0014  Score=67.22  Aligned_cols=158  Identities=12%  Similarity=0.134  Sum_probs=91.6

Q ss_pred             CcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC----eEEEEEeCCCCCHHHHHHHHH
Q 042806          152 DYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFD----QVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~----~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      ..++++||+.++.++++.|....-.--.++|++|||||+++--++...-..+-..    ..++ +.    ++       .
T Consensus       168 klDPvIGRd~EI~r~iqIL~RR~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~-sL----D~-------g  235 (786)
T COG0542         168 KLDPVIGRDEEIRRTIQILSRRTKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIY-SL----DL-------G  235 (786)
T ss_pred             CCCCCcChHHHHHHHHHHHhccCCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEE-Ee----cH-------H
Confidence            3678999999999999999763222234679999999999999988865432111    1111 00    11       1


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--------cccc---ccCCCCCCCCCcEEEEEecchhhhh
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--------DFQA---VGIPHGDDRKGCKVLLTARSLDVLS  296 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--------~~~~---l~~~l~~~~~~s~IivTtr~~~v~~  296 (390)
                      .-.........-...+..+.+.+....+.+|.+|.++..-        ..+.   +++.+ ..+.--.|-.||-++.- .
T Consensus       236 ~LvAGakyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaL-ARGeL~~IGATT~~EYR-k  313 (786)
T COG0542         236 SLVAGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPAL-ARGELRCIGATTLDEYR-K  313 (786)
T ss_pred             HHhccccccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcccccccchhhhhHHHH-hcCCeEEEEeccHHHHH-H
Confidence            1111122222334455556666654446999999997541        1222   23333 11222235566654322 1


Q ss_pred             h------cCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          297 R------KMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       297 ~------~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                      +      ...-...+.+...+.+++..+++-..
T Consensus       314 ~iEKD~AL~RRFQ~V~V~EPs~e~ti~ILrGlk  346 (786)
T COG0542         314 YIEKDAALERRFQKVLVDEPSVEDTIAILRGLK  346 (786)
T ss_pred             HhhhchHHHhcCceeeCCCCCHHHHHHHHHHHH
Confidence            1      11233688899999999999987654

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.19  E-value=0.003  Score=52.51  Aligned_cols=39  Identities=28%  Similarity=0.411  Sum_probs=29.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ  217 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  217 (390)
                      ++.|+|++|+||||++..+.......  -..++|+......
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~~~--~~~v~~~~~e~~~   39 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIATK--GGKVVYVDIEEEI   39 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHHhc--CCEEEEEECCcch
Confidence            36799999999999999998887542  3457777776543

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=97.18  E-value=0.0032  Score=56.47  Aligned_cols=49  Identities=12%  Similarity=0.184  Sum_probs=35.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      ...++.|.|++|+|||+|+.++....-.+  =...+|++...  ++.++.+.+
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~~--ge~~lyvs~ee--~~~~i~~~~   68 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM--GEPGIYVALEE--HPVQVRRNM   68 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHc--CCcEEEEEeeC--CHHHHHHHH
Confidence            46789999999999999999987664322  34577777654  566666654

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.

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=97.17  E-value=0.0023  Score=60.32  Aligned_cols=86  Identities=29%  Similarity=0.353  Sum_probs=60.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC--CchHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE--SDSGRARSLRNRLK  251 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~--~~~~~~~~l~~~l~  251 (390)
                      .-.+|.|-|.+|+|||||..++..+...+.   .+.||  +..-+..++ +--++.|+...+..  -....++.+...+.
T Consensus        92 ~Gs~iLIgGdPGIGKSTLLLQva~~lA~~~---~vLYV--sGEES~~Qi-klRA~RL~~~~~~l~l~aEt~~e~I~~~l~  165 (456)
T COG1066          92 PGSVILIGGDPGIGKSTLLLQVAARLAKRG---KVLYV--SGEESLQQI-KLRADRLGLPTNNLYLLAETNLEDIIAELE  165 (456)
T ss_pred             cccEEEEccCCCCCHHHHHHHHHHHHHhcC---cEEEE--eCCcCHHHH-HHHHHHhCCCccceEEehhcCHHHHHHHHH
Confidence            357899999999999999999999987542   45555  444455443 33356676544332  22334567777777


Q ss_pred             CCCeEEEEEeCCCC
Q 042806          252 KEKTILVILDNIWG  265 (390)
Q Consensus       252 ~~~~~LlVlDdv~~  265 (390)
                      ..++-++|+|-++.
T Consensus       166 ~~~p~lvVIDSIQT  179 (456)
T COG1066         166 QEKPDLVVIDSIQT  179 (456)
T ss_pred             hcCCCEEEEeccce
Confidence            78889999999863

>PRK06696 uridine kinase; Validated

Probab=97.16  E-value=0.00072  Score=60.09  Aligned_cols=44  Identities=23%  Similarity=0.268  Sum_probs=35.9

Q ss_pred             chhHHHHHHHHHhc---CCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          158 SRMSTLNDILDALK---NPDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       158 gR~~~~~~l~~~L~---~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .|...+.+|.+.+.   .+++.+|+|.|.+|+||||||+.+......
T Consensus         2 ~~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~~l~~   48 (223)
T PRK06696          2 SRKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEEIKK   48 (223)
T ss_pred             cHHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            46666777777764   356789999999999999999999998754

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=97.16  E-value=0.002  Score=58.46  Aligned_cols=89  Identities=24%  Similarity=0.317  Sum_probs=56.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcC----CCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC----------Cc-
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEK----LFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE----------SD-  239 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~----------~~-  239 (390)
                      ..+.=|+|++|+|||.|+.+++-......    .=..++|++-...++.+.+. +|++..+......          +. 
T Consensus        38 g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~~~~~~~l~~I~v~~~~~~~  116 (256)
T PF08423_consen   38 GSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFGLDPEEILDNIFVIRVFDLE  116 (256)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTTS-HHHHHHTEEEEE-SSHH
T ss_pred             CcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccccccchhhhceeeeecCCHH
Confidence            46788999999999999999876643221    12469999999988887764 5666654322100          11 


Q ss_pred             --hHHHHHHHHHHhCCCeEEEEEeCCC
Q 042806          240 --SGRARSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       240 --~~~~~~l~~~l~~~~~~LlVlDdv~  264 (390)
                        ...+..+...+.+.+--|||+|.+-
T Consensus       117 ~l~~~L~~l~~~l~~~~ikLIVIDSIa  143 (256)
T PF08423_consen  117 ELLELLEQLPKLLSESKIKLIVIDSIA  143 (256)
T ss_dssp             HHHHHHHHHHHHHHHSCEEEEEEETSS
T ss_pred             HHHHHHHHHHhhccccceEEEEecchH
Confidence              1223344444545565699999984

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=97.13  E-value=0.0031  Score=59.04  Aligned_cols=91  Identities=16%  Similarity=0.248  Sum_probs=57.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcC----CCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC----------CC-
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEK----LFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE----------ES-  238 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~----------~~-  238 (390)
                      ...++-|+|++|+|||+|+.+++.......    .-..++||+....++.+.+. +++..++.....          .+ 
T Consensus        94 ~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~gl~~~~~~~~i~i~~~~~~  172 (310)
T TIGR02236        94 TQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARGLDPDEVLKNIYVARAYNS  172 (310)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcCCCHHHHhhceEEEecCCH
Confidence            467889999999999999999987753210    01268999998888877654 445555443210          01 


Q ss_pred             --chHHHHHHHHHHhCC--CeEEEEEeCCCC
Q 042806          239 --DSGRARSLRNRLKKE--KTILVILDNIWG  265 (390)
Q Consensus       239 --~~~~~~~l~~~l~~~--~~~LlVlDdv~~  265 (390)
                        .......+.+.+...  ..-+||+|.+..
T Consensus       173 ~~~~~lld~l~~~i~~~~~~~~lVVIDSisa  203 (310)
T TIGR02236       173 NHQMLLVEKAEDLIKELNNPVKLLIVDSLTS  203 (310)
T ss_pred             HHHHHHHHHHHHHHHhcCCCceEEEEecchH
Confidence              111233455555443  235899998853

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

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.12  E-value=0.0029  Score=62.37  Aligned_cols=89  Identities=21%  Similarity=0.265  Sum_probs=47.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKK  252 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  252 (390)
                      ...+|+|+|++|+||||++..+......+.....+..++.... ....+-+......++...........+..+.+.+.+
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v~~a~d~~~L~~aL~~l~~  428 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVHEADSAESLLDLLERLRD  428 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhcccCceeEecCcHHHHHHHHHHhcc
Confidence            3578999999999999999998876543321233455544321 122233333344444433222222223333344433


Q ss_pred             CCeEEEEEeCCC
Q 042806          253 EKTILVILDNIW  264 (390)
Q Consensus       253 ~~~~LlVlDdv~  264 (390)
                      .  =+|++|..-
T Consensus       429 ~--DLVLIDTaG  438 (559)
T PRK12727        429 Y--KLVLIDTAG  438 (559)
T ss_pred             C--CEEEecCCC
Confidence            2  377888764

>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=97.10  E-value=0.0012  Score=53.80  Aligned_cols=43  Identities=30%  Similarity=0.286  Sum_probs=33.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      |.|+|++|+|||+||+.++......     ...+.++...+..+++..
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~~~~-----~~~i~~~~~~~~~dl~g~   44 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALLGRP-----VIRINCSSDTTEEDLIGS   44 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHHTCE-----EEEEE-TTTSTHHHHHCE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhhcc-----eEEEEeccccccccceee
Confidence            5799999999999999999988332     455678888888877643

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.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.10  E-value=0.00065  Score=63.80  Aligned_cols=47  Identities=17%  Similarity=0.171  Sum_probs=40.4

Q ss_pred             cccchhHHHHHHHHHhcC------CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          155 ACESRMSTLNDILDALKN------PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .++|-++.++++++++..      .+.+++.|+|++|+||||||..+.+....
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~~  104 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEE  104 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            588898999999988853      24688999999999999999999998754

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

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=97.10  E-value=0.0036  Score=58.74  Aligned_cols=91  Identities=21%  Similarity=0.298  Sum_probs=58.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCC----CCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC----------Cc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKL----FDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE----------SD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~----------~~  239 (390)
                      ...++-|+|++|+|||+++.+++........    =..++||+....+++..+. +++..++...+..          +.
T Consensus       101 ~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~-~~~~~~g~~~~~~l~~i~~~~~~~~  179 (317)
T PRK04301        101 TQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIE-QMAEALGLDPDEVLDNIHVARAYNS  179 (317)
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHH-HHHHHcCCChHhhhccEEEEeCCCH
Confidence            4678899999999999999999876432211    1368999998888877654 4445555432110          11


Q ss_pred             ---hHHHHHHHHHHhC-CCeEEEEEeCCCC
Q 042806          240 ---SGRARSLRNRLKK-EKTILVILDNIWG  265 (390)
Q Consensus       240 ---~~~~~~l~~~l~~-~~~~LlVlDdv~~  265 (390)
                         ......+...+.. .+.-|||+|.+..
T Consensus       180 ~~~~~~~~~l~~~i~~~~~~~lvVIDSisa  209 (317)
T PRK04301        180 DHQMLLAEKAEELIKEGENIKLVIVDSLTA  209 (317)
T ss_pred             HHHHHHHHHHHHHHhccCceeEEEEECchH
Confidence               1123344444544 4445999999853

>PHA02244 ATPase-like protein

Probab=97.10  E-value=0.0042  Score=58.52  Aligned_cols=34  Identities=21%  Similarity=0.230  Sum_probs=25.5

Q ss_pred             HHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          165 DILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       165 ~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+..++..+.  -|.|+|++|+|||+||+.++....
T Consensus       111 ri~r~l~~~~--PVLL~GppGtGKTtLA~aLA~~lg  144 (383)
T PHA02244        111 DIAKIVNANI--PVFLKGGAGSGKNHIAEQIAEALD  144 (383)
T ss_pred             HHHHHHhcCC--CEEEECCCCCCHHHHHHHHHHHhC
Confidence            4445554332  366899999999999999998854

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.10  E-value=0.0039  Score=55.64  Aligned_cols=54  Identities=17%  Similarity=0.110  Sum_probs=36.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGL  232 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~  232 (390)
                      ...++.|.|++|+|||||+.+++.....+ . ...+|++  ...+..++++.+ ..++.
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~~~~-g-~~~~yi~--~e~~~~~~~~~~-~~~g~   76 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGFLQN-G-YSVSYVS--TQLTTTEFIKQM-MSLGY   76 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhC-C-CcEEEEe--CCCCHHHHHHHH-HHhCC
Confidence            45689999999999999987777665322 2 2356665  333567777776 34443

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

Probab=97.09  E-value=0.014  Score=51.51  Aligned_cols=147  Identities=18%  Similarity=0.252  Sum_probs=82.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhC
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKK  252 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  252 (390)
                      .+++-+.++|++|.|||-||+.++++.       ++-|+.+|..    ++.+..+.         .-...+..+.-..+.
T Consensus       179 aQPKGvlLygppgtGktLlaraVahht-------~c~firvsgs----elvqk~ig---------egsrmvrelfvmare  238 (404)
T KOG0728|consen  179 AQPKGVLLYGPPGTGKTLLARAVAHHT-------DCTFIRVSGS----ELVQKYIG---------EGSRMVRELFVMARE  238 (404)
T ss_pred             CCCcceEEecCCCCchhHHHHHHHhhc-------ceEEEEechH----HHHHHHhh---------hhHHHHHHHHHHHHh
Confidence            467888999999999999999997754       4567777763    33322211         112244445544555


Q ss_pred             CCeEEEEEeCCCCCcc------------cc----cccCCCC--CCCCCcEEEEEecchhhhhh-cCC---CcceEecCCC
Q 042806          253 EKTILVILDNIWGNLD------------FQ----AVGIPHG--DDRKGCKVLLTARSLDVLSR-KMD---SQQNFSVGVL  310 (390)
Q Consensus       253 ~~~~LlVlDdv~~~~~------------~~----~l~~~l~--~~~~~s~IivTtr~~~v~~~-~~~---~~~~~~l~~L  310 (390)
                      .-+-+|.+|.+++...            .+    .+...+.  ...++.+||..|...++... ...   ..+.++..+-
T Consensus       239 hapsiifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfeatknikvimatnridild~allrpgridrkiefp~p  318 (404)
T KOG0728|consen  239 HAPSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPP  318 (404)
T ss_pred             cCCceEeeecccccccccccCCCCccHHHHHHHHHHHHhccccccccceEEEEeccccccccHhhcCCCcccccccCCCC
Confidence            6678999998864310            00    1111111  12456678877776554321 111   2346777777


Q ss_pred             CHHHHHHHHHHhhC--CCCCCCchHHHHHHH
Q 042806          311 KEDEAWSLFKKMAG--DYIEGSEFKWVAKDV  339 (390)
Q Consensus       311 ~~~ea~~lf~~~~~--~~~~~~~~~~~~~~i  339 (390)
                      +.+.-.+++.-+..  .-....++..++.++
T Consensus       319 ~e~ar~~ilkihsrkmnl~rgi~l~kiaekm  349 (404)
T KOG0728|consen  319 NEEARLDILKIHSRKMNLTRGINLRKIAEKM  349 (404)
T ss_pred             CHHHHHHHHHHhhhhhchhcccCHHHHHHhC
Confidence            76666667665443  222334445444443

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.09  E-value=0.0031  Score=59.18  Aligned_cols=100  Identities=17%  Similarity=0.154  Sum_probs=55.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      ..+.++|++|+|||+|+..+++....++ + .++|+++      .+++..+...-. ..    .... ....+.+.+-. 
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g-~-~V~y~t~------~~l~~~l~~~~~-~~----~~~~-~~~~~~l~~~D-  248 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRG-K-SVIYRTA------DELIEILREIRF-NN----DKEL-EEVYDLLINCD-  248 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCC-C-eEEEEEH------HHHHHHHHHHHh-cc----chhH-HHHHHHhccCC-
Confidence            6789999999999999999999886542 3 3555543      445554433211 10    0011 11134444433 


Q ss_pred             EEEEEeCCCCC--cccc--cccCCCCC-CCCCcEEEEEecc
Q 042806          256 ILVILDNIWGN--LDFQ--AVGIPHGD-DRKGCKVLLTARS  291 (390)
Q Consensus       256 ~LlVlDdv~~~--~~~~--~l~~~l~~-~~~~s~IivTtr~  291 (390)
                       ||||||+...  ..|.  .+...+.. ...+..+||||..
T Consensus       249 -LLIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~tIiTSNl  288 (329)
T PRK06835        249 -LLIIDDLGTEKITEFSKSELFNLINKRLLRQKKMIISTNL  288 (329)
T ss_pred             -EEEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence             8999999543  2232  22222211 1224457888874

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

Probab=97.07  E-value=0.0046  Score=62.58  Aligned_cols=98  Identities=19%  Similarity=0.272  Sum_probs=67.5

Q ss_pred             cccCcccccchhHHHHHHHHHhcC---------C---CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 042806          149 SIKDYEACESRMSTLNDILDALKN---------P---DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI  216 (390)
Q Consensus       149 ~~~~~~~~~gR~~~~~~l~~~L~~---------~---~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  216 (390)
                      +....+++.|-++-..+|.+-+.-         .   +.+=|.+||++|.|||-||+.|+.+..       ..|++|.++
T Consensus       667 PnV~WdDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEcs-------L~FlSVKGP  739 (953)
T KOG0736|consen  667 PNVSWDDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATECS-------LNFLSVKGP  739 (953)
T ss_pred             CccchhcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhce-------eeEEeecCH
Confidence            344466788888888888876642         1   234688999999999999999998875       345666553


Q ss_pred             CCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 042806          217 QDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       217 ~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~  266 (390)
                          +++.-   ..|      ..+.-+..+.+.-+.-.||+|.||.+++.
T Consensus       740 ----ELLNM---YVG------qSE~NVR~VFerAR~A~PCVIFFDELDSl  776 (953)
T KOG0736|consen  740 ----ELLNM---YVG------QSEENVREVFERARSAAPCVIFFDELDSL  776 (953)
T ss_pred             ----HHHHH---Hhc------chHHHHHHHHHHhhccCCeEEEecccccc
Confidence                22211   111      22335667777777778899999999754

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.04  E-value=0.0018  Score=55.22  Aligned_cols=36  Identities=28%  Similarity=0.475  Sum_probs=29.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEE
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFV  211 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv  211 (390)
                      +..+|.+.|+.|+||||+++.++......  +...+++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l~~~--~~~~~~~   41 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERLKLK--YSNVIYL   41 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHc--CCcEEEE
Confidence            45689999999999999999999988643  5545554

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

Probab=97.03  E-value=0.0015  Score=59.61  Aligned_cols=133  Identities=15%  Similarity=0.232  Sum_probs=71.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc--CCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETE--KLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKK  252 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~--~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  252 (390)
                      .++|.++||+|.|||+|++.++++...+  +.|....-+.++.    ..++..=+++-|     .....+.+.+.+.+..
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEins----hsLFSKWFsESg-----KlV~kmF~kI~ELv~d  247 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINS----HSLFSKWFSESG-----KLVAKMFQKIQELVED  247 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEeh----hHHHHHHHhhhh-----hHHHHHHHHHHHHHhC
Confidence            5899999999999999999999998764  3344333343322    222222111111     0112233344444544


Q ss_pred             CCe-EEEEEeCCCCCc------------------------ccccccCCCCCCCCCcEEEEEecch----hhhhhcCCCcc
Q 042806          253 EKT-ILVILDNIWGNL------------------------DFQAVGIPHGDDRKGCKVLLTARSL----DVLSRKMDSQQ  303 (390)
Q Consensus       253 ~~~-~LlVlDdv~~~~------------------------~~~~l~~~l~~~~~~s~IivTtr~~----~v~~~~~~~~~  303 (390)
                      .+. +.+.+|.|.+..                        +++.++     ..++ .+|+||.+-    ++|. ...+.-
T Consensus       248 ~~~lVfvLIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDrlK-----~~~N-vliL~TSNl~~siD~Af-VDRADi  320 (423)
T KOG0744|consen  248 RGNLVFVLIDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDRLK-----RYPN-VLILATSNLTDSIDVAF-VDRADI  320 (423)
T ss_pred             CCcEEEEEeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHhc-----cCCC-EEEEeccchHHHHHHHh-hhHhhh
Confidence            443 455578886331                        112221     1223 355555542    2221 122334


Q ss_pred             eEecCCCCHHHHHHHHHHhh
Q 042806          304 NFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       304 ~~~l~~L~~~ea~~lf~~~~  323 (390)
                      ...+++-+.+...+++..+.
T Consensus       321 ~~yVG~Pt~~ai~~Ilksci  340 (423)
T KOG0744|consen  321 VFYVGPPTAEAIYEILKSCI  340 (423)
T ss_pred             eeecCCccHHHHHHHHHHHH
Confidence            67788888888888887665

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=97.01  E-value=0.0031  Score=59.46  Aligned_cols=91  Identities=14%  Similarity=0.190  Sum_probs=57.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc---C-CCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC----------Cc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE---K-LFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE----------SD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~---~-~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~----------~~  239 (390)
                      ...++-|+|++|+|||+|+..++-.....   + .-..++|++....++++.+ .++++.++......          +.
T Consensus       122 ~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl-~qia~~~~~~~~~~l~~i~~~~~~~~  200 (342)
T PLN03186        122 TGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRL-IQIAERFGLNGADVLENVAYARAYNT  200 (342)
T ss_pred             CceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHH-HHHHHHcCCChhhhccceEEEecCCH
Confidence            45788899999999999999887553211   1 1136899999998888775 45677766543211          11


Q ss_pred             hHH---HHHHHHHHhCCCeEEEEEeCCCC
Q 042806          240 SGR---ARSLRNRLKKEKTILVILDNIWG  265 (390)
Q Consensus       240 ~~~---~~~l~~~l~~~~~~LlVlDdv~~  265 (390)
                      ...   +..+...+...+.-|||+|.+..
T Consensus       201 e~~~~ll~~~~~~~~~~~~~LIVIDSI~a  229 (342)
T PLN03186        201 DHQSELLLEAASMMAETRFALMIVDSATA  229 (342)
T ss_pred             HHHHHHHHHHHHHhhccCCCEEEEeCcHH
Confidence            111   22222334444556999999853

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=97.01  E-value=0.0038  Score=56.86  Aligned_cols=121  Identities=21%  Similarity=0.168  Sum_probs=67.6

Q ss_pred             HHHHHHhc-CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEE---eCCCCCHHHHHHHHHHHhCC-CCC---
Q 042806          164 NDILDALK-NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVE---VSKIQDIRKIQGEIADKLGL-TLH---  235 (390)
Q Consensus       164 ~~l~~~L~-~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~---v~~~~~~~~l~~~i~~~l~~-~~~---  235 (390)
                      +.++..+. ..+..-++|.|+.|+|||||.+.+......   ..+.+++.   +.......++    +..... ...   
T Consensus        99 ~~~l~~l~~~~~~~~~~i~g~~g~GKttl~~~l~~~~~~---~~G~i~~~g~~v~~~d~~~ei----~~~~~~~~q~~~~  171 (270)
T TIGR02858        99 DKLLPYLVRNNRVLNTLIISPPQCGKTTLLRDLARILST---GISQLGLRGKKVGIVDERSEI----AGCVNGVPQHDVG  171 (270)
T ss_pred             HHHHHHHHhCCCeeEEEEEcCCCCCHHHHHHHHhCccCC---CCceEEECCEEeecchhHHHH----HHHhccccccccc
Confidence            33444443 334567899999999999999999887643   22333331   1111112233    222211 111   


Q ss_pred             ----CCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhh
Q 042806          236 ----EESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDV  294 (390)
Q Consensus       236 ----~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v  294 (390)
                          ..+.......+...+....+=++++|.+.....+..+...+   ..|..+|+||....+
T Consensus       172 ~r~~v~~~~~k~~~~~~~i~~~~P~villDE~~~~e~~~~l~~~~---~~G~~vI~ttH~~~~  231 (270)
T TIGR02858       172 IRTDVLDGCPKAEGMMMLIRSMSPDVIVVDEIGREEDVEALLEAL---HAGVSIIATAHGRDV  231 (270)
T ss_pred             ccccccccchHHHHHHHHHHhCCCCEEEEeCCCcHHHHHHHHHHH---hCCCEEEEEechhHH
Confidence                11111223344555554456799999997666555554443   247789999997655

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.

>PTZ00035 Rad51 protein; Provisional

Probab=97.00  E-value=0.0051  Score=58.04  Aligned_cols=91  Identities=14%  Similarity=0.199  Sum_probs=56.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc---C-CCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC----------CCc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE---K-LFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE----------ESD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~---~-~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~----------~~~  239 (390)
                      ...++.|+|++|+|||+|+.+++-.....   + .-..++|++....++.+. +.++++.++.....          .+.
T Consensus       117 ~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~er-i~~ia~~~g~~~~~~l~nI~~~~~~~~  195 (337)
T PTZ00035        117 TGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPER-IVQIAERFGLDPEDVLDNIAYARAYNH  195 (337)
T ss_pred             CCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHH-HHHHHHHhCCChHhHhhceEEEccCCH
Confidence            46789999999999999999987654310   1 123567998887777766 44556666543211          011


Q ss_pred             hH---HHHHHHHHHhCCCeEEEEEeCCCC
Q 042806          240 SG---RARSLRNRLKKEKTILVILDNIWG  265 (390)
Q Consensus       240 ~~---~~~~l~~~l~~~~~~LlVlDdv~~  265 (390)
                      ..   .+..+...+...+.-|||+|.+..
T Consensus       196 e~~~~~l~~~~~~l~~~~~~lvVIDSita  224 (337)
T PTZ00035        196 EHQMQLLSQAAAKMAEERFALLIVDSATA  224 (337)
T ss_pred             HHHHHHHHHHHHHhhccCccEEEEECcHH
Confidence            12   222233344445556999999853

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=97.00  E-value=0.0052  Score=54.81  Aligned_cols=30  Identities=27%  Similarity=0.324  Sum_probs=26.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      ++..+++|.|+.|+|||||++.+.......
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~~l~~~   60 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEALLQQD   60 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhhhc
Confidence            457799999999999999999999887653

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=96.99  E-value=0.0036  Score=58.56  Aligned_cols=90  Identities=14%  Similarity=0.171  Sum_probs=56.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh---cC-CCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC----------CCc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET---EK-LFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE----------ESD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~---~~-~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~----------~~~  239 (390)
                      ...++.|+|++|+|||+|+..++.....   .+ .-..++|++....++... +.++++.++.....          .+.
T Consensus        95 ~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~R-l~~ia~~~~~~~~~~l~~i~~~~~~~~  173 (316)
T TIGR02239        95 TGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPER-LLAIAERYGLNPEDVLDNVAYARAYNT  173 (316)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHH-HHHHHHHcCCChHHhhccEEEEecCCh
Confidence            4678999999999999999998764321   11 123578998888777765 44455665543221          011


Q ss_pred             hH---HHHHHHHHHhCCCeEEEEEeCCC
Q 042806          240 SG---RARSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       240 ~~---~~~~l~~~l~~~~~~LlVlDdv~  264 (390)
                      ..   .+..+...+...+.-|||+|.+.
T Consensus       174 ~~~~~~l~~~~~~~~~~~~~LvVIDSI~  201 (316)
T TIGR02239       174 DHQLQLLQQAAAMMSESRFALLIVDSAT  201 (316)
T ss_pred             HHHHHHHHHHHHhhccCCccEEEEECcH
Confidence            11   22333333444555699999985

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

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=96.99  E-value=0.0038  Score=56.65  Aligned_cols=91  Identities=18%  Similarity=0.280  Sum_probs=56.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCC-------CCCCCch-----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLT-------LHEESDS-----  240 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~-------~~~~~~~-----  240 (390)
                      +-.-++|.|.+|+|||||++.+++....+ +-+.++++.++... ...++...+...-...       ..+.+..     
T Consensus        68 ~GQr~~If~~~G~GKTtLa~~i~~~i~~~-~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~  146 (274)
T cd01133          68 KGGKIGLFGGAGVGKTVLIMELINNIAKA-HGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARARV  146 (274)
T ss_pred             cCCEEEEecCCCCChhHHHHHHHHHHHhc-CCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHH
Confidence            34568899999999999999999987653 22456666776543 4556666654432111       1111111     


Q ss_pred             -HHHHHHHHHHh-C-CCeEEEEEeCCCC
Q 042806          241 -GRARSLRNRLK-K-EKTILVILDNIWG  265 (390)
Q Consensus       241 -~~~~~l~~~l~-~-~~~~LlVlDdv~~  265 (390)
                       ...-.+.+++. . ++.+|+++||+..
T Consensus       147 ~~~a~~~AEyfr~~~g~~Vl~~~Dsltr  174 (274)
T cd01133         147 ALTGLTMAEYFRDEEGQDVLLFIDNIFR  174 (274)
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEeChhH
Confidence             12234556664 2 5669999999853

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>cd01394 radB RadB

Probab=96.99  E-value=0.0039  Score=55.06  Aligned_cols=43  Identities=19%  Similarity=0.319  Sum_probs=32.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD  218 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  218 (390)
                      ...++.|+|++|+||||++.+++......  -..++|++....+.
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~~a~~~~~~--g~~v~yi~~e~~~~   60 (218)
T cd01394          18 RGTVTQVYGPPGTGKTNIAIQLAVETAGQ--GKKVAYIDTEGLSS   60 (218)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEECCCCCH
Confidence            46789999999999999999998876432  23567877655443

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

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.99  E-value=0.0072  Score=58.89  Aligned_cols=57  Identities=23%  Similarity=0.276  Sum_probs=37.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGL  232 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~  232 (390)
                      .+.+|.++|++|+||||++..++...... .+ .+..+++... ....+-+..++..++.
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~~~-g~-kV~lV~~D~~R~aa~eQL~~la~~~gv  151 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFKKK-GL-KVGLVAADTYRPAAYDQLKQLAEKIGV  151 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHHc-CC-eEEEecCCCCCHHHHHHHHHHHHHcCC
Confidence            46789999999999999999999887643 23 2333444322 1234445555666554

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.99  E-value=0.0011  Score=54.44  Aligned_cols=31  Identities=29%  Similarity=0.308  Sum_probs=26.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeE
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQV  208 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~  208 (390)
                      -|.|.|++|+||||+++.+.+.++.++ |...
T Consensus         7 ki~ITG~PGvGKtTl~~ki~e~L~~~g-~kvg   37 (179)
T COG1618           7 KIFITGRPGVGKTTLVLKIAEKLREKG-YKVG   37 (179)
T ss_pred             EEEEeCCCCccHHHHHHHHHHHHHhcC-ceee
Confidence            488999999999999999999988753 6543

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.98  E-value=0.004  Score=59.51  Aligned_cols=87  Identities=25%  Similarity=0.276  Sum_probs=55.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC--CchHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE--SDSGRARSLRNRLK  251 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~--~~~~~~~~l~~~l~  251 (390)
                      ...++.|.|++|+|||||+.+++......  -..++|++...  +..++.. -+..++...+..  ........+.+.+.
T Consensus        81 ~GslvLI~G~pG~GKStLllq~a~~~a~~--g~~VlYvs~EE--s~~qi~~-Ra~rlg~~~~~l~l~~e~~le~I~~~i~  155 (372)
T cd01121          81 PGSVILIGGDPGIGKSTLLLQVAARLAKR--GGKVLYVSGEE--SPEQIKL-RADRLGISTENLYLLAETNLEDILASIE  155 (372)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhc--CCeEEEEECCc--CHHHHHH-HHHHcCCCcccEEEEccCcHHHHHHHHH
Confidence            35689999999999999999998876543  23567776543  3444332 245565433221  11122445566665


Q ss_pred             CCCeEEEEEeCCCC
Q 042806          252 KEKTILVILDNIWG  265 (390)
Q Consensus       252 ~~~~~LlVlDdv~~  265 (390)
                      ..++-++|+|.+..
T Consensus       156 ~~~~~lVVIDSIq~  169 (372)
T cd01121         156 ELKPDLVIIDSIQT  169 (372)
T ss_pred             hcCCcEEEEcchHH
Confidence            55667999999853

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.

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

Probab=96.98  E-value=0.006  Score=55.52  Aligned_cols=51  Identities=20%  Similarity=0.234  Sum_probs=40.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      +..+++.|+|.+|+|||+++.++.......  ...++||+...  +..++...+.
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~--ge~vlyvs~~e--~~~~l~~~~~   71 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYEGARE--GEPVLYVSTEE--SPEELLENAR   71 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHHHHhc--CCcEEEEEecC--CHHHHHHHHH
Confidence            467899999999999999999999987654  67789998876  4555555543

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=96.98  E-value=0.0021  Score=55.05  Aligned_cols=24  Identities=17%  Similarity=0.140  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +|.|+|++|+||||+++.+.....
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~~~   24 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVENFG   24 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHcC
Confidence            578999999999999999988653

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.

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

Probab=96.94  E-value=0.0098  Score=59.51  Aligned_cols=131  Identities=20%  Similarity=0.202  Sum_probs=74.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      ..+.+.++|++|.|||.||+.+++..+..  |     +.+...    +++..   .+|      .....+..+...-...
T Consensus       275 ~~~giLl~GpPGtGKT~lAkava~~~~~~--f-----i~v~~~----~l~sk---~vG------esek~ir~~F~~A~~~  334 (494)
T COG0464         275 PPKGVLLYGPPGTGKTLLAKAVALESRSR--F-----ISVKGS----ELLSK---WVG------ESEKNIRELFEKARKL  334 (494)
T ss_pred             CCCeeEEECCCCCCHHHHHHHHHhhCCCe--E-----EEeeCH----HHhcc---ccc------hHHHHHHHHHHHHHcC
Confidence            45689999999999999999999966532  3     222221    11100   000      1222344444444445


Q ss_pred             CeEEEEEeCCCCCccc-------------ccccCCCC--CCCCCcEEEEEecchhhhh-hc-C--CCcceEecCCCCHHH
Q 042806          254 KTILVILDNIWGNLDF-------------QAVGIPHG--DDRKGCKVLLTARSLDVLS-RK-M--DSQQNFSVGVLKEDE  314 (390)
Q Consensus       254 ~~~LlVlDdv~~~~~~-------------~~l~~~l~--~~~~~s~IivTtr~~~v~~-~~-~--~~~~~~~l~~L~~~e  314 (390)
                      .+++|.+|+++....+             ..+...+.  ....+..||-||....... .. .  .-...+.+.+-+.++
T Consensus       335 ~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~  414 (494)
T COG0464         335 APSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEE  414 (494)
T ss_pred             CCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCCCHHH
Confidence            6699999999643211             11222221  1223344555555433221 11 1  234588899999999


Q ss_pred             HHHHHHHhhC
Q 042806          315 AWSLFKKMAG  324 (390)
Q Consensus       315 a~~lf~~~~~  324 (390)
                      ..++|..+..
T Consensus       415 r~~i~~~~~~  424 (494)
T COG0464         415 RLEIFKIHLR  424 (494)
T ss_pred             HHHHHHHHhc
Confidence            9999999986

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.94  E-value=0.0044  Score=60.39  Aligned_cols=86  Identities=14%  Similarity=0.169  Sum_probs=46.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh-hcCCCCeEEEEEeCCCCC-HHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE-TEKLFDQVIFVEVSKIQD-IRKIQGEIADKLGLTLHEESDSGRARSLRNRLKK  252 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~-~~~~f~~~~wv~v~~~~~-~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  252 (390)
                      .++++++|++|+||||++..++.... ... -..+..++...... ..+-+....+.++..................+.+
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~-g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~~~~  299 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYG-KKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQLRD  299 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcC-CCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHHhCC
Confidence            46899999999999999999887764 222 23455666543211 1222333344455443222222222222223332


Q ss_pred             CCeEEEEEeCC
Q 042806          253 EKTILVILDNI  263 (390)
Q Consensus       253 ~~~~LlVlDdv  263 (390)
                      .  =+|++|..
T Consensus       300 ~--DlVlIDt~  308 (424)
T PRK05703        300 C--DVILIDTA  308 (424)
T ss_pred             C--CEEEEeCC
Confidence            2  48888865

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=96.93  E-value=0.016  Score=60.39  Aligned_cols=59  Identities=12%  Similarity=0.172  Sum_probs=40.0

Q ss_pred             cccchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 042806          155 ACESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK  215 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  215 (390)
                      .++|+...+..+.+.+..  ....-|.|+|+.|+|||++|+.+.+.....  -...+.+++..
T Consensus       377 ~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s~r~--~~~~v~i~c~~  437 (686)
T PRK15429        377 EIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGRN--NRRMVKMNCAA  437 (686)
T ss_pred             ceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcCCC--CCCeEEEeccc
Confidence            578888777777655542  233467799999999999999998865322  12344555544

>TIGR00959 ffh signal recognition particle protein

Probab=96.93  E-value=0.0071  Score=58.78  Aligned_cols=27  Identities=22%  Similarity=0.213  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+.++.++|++|+||||.+..++....
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~l~  124 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYYLK  124 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHH
Confidence            467899999999999999998887754

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>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=96.92  E-value=0.0038  Score=53.54  Aligned_cols=45  Identities=16%  Similarity=0.110  Sum_probs=31.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      ++.|.|++|+|||+|+.++....-..  =..++|++...  +..++...
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~~~--g~~v~~~s~e~--~~~~~~~~   45 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGLAR--GEPGLYVTLEE--SPEELIEN   45 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHC--CCcEEEEECCC--CHHHHHHH
Confidence            36799999999999999987775432  13466776543  45555554

A related protein is found in archaea.

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=96.92  E-value=0.0051  Score=57.19  Aligned_cols=85  Identities=21%  Similarity=0.277  Sum_probs=53.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC------CCchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE------ESDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~------~~~~~~~~~l~  247 (390)
                      ..+++-|+|+.|+|||||+..+.......  -..++|+...+.+++.-     +..+|.+.+.      ....+....+.
T Consensus        52 ~G~ivEi~G~~ssGKttLaL~~ia~~q~~--g~~~a~ID~e~~ld~~~-----a~~lGvdl~rllv~~P~~~E~al~~~e  124 (322)
T PF00154_consen   52 RGRIVEIYGPESSGKTTLALHAIAEAQKQ--GGICAFIDAEHALDPEY-----AESLGVDLDRLLVVQPDTGEQALWIAE  124 (322)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT--T-EEEEEESSS---HHH-----HHHTT--GGGEEEEE-SSHHHHHHHHH
T ss_pred             cCceEEEeCCCCCchhhhHHHHHHhhhcc--cceeEEecCcccchhhH-----HHhcCccccceEEecCCcHHHHHHHHH
Confidence            46799999999999999999999876543  34689999988776533     4455554321      12233444455


Q ss_pred             HHHhCCCeEEEEEeCCCC
Q 042806          248 NRLKKEKTILVILDNIWG  265 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~  265 (390)
                      ..++.+.--++|+|-|-.
T Consensus       125 ~lirsg~~~lVVvDSv~a  142 (322)
T PF00154_consen  125 QLIRSGAVDLVVVDSVAA  142 (322)
T ss_dssp             HHHHTTSESEEEEE-CTT
T ss_pred             HHhhcccccEEEEecCcc
Confidence            556666645899999853

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.92  E-value=0.0076  Score=53.92  Aligned_cols=86  Identities=12%  Similarity=0.171  Sum_probs=55.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-----------------
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE-----------------  236 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~-----------------  236 (390)
                      ...++.|+|++|+|||+|+.++....-..  =..++|++...  +..++.+.+ ..++.....                 
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~~~--g~~~~y~~~e~--~~~~~~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~~   98 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGALKQ--GKKVYVITTEN--TSKSYLKQM-ESVKIDISDFFLWGYLRIFPLNTEGF   98 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHHhC--CCEEEEEEcCC--CHHHHHHHH-HHCCCChhHHHhCCCceEEecccccc
Confidence            46789999999999999999997654222  23578888765  455666654 334322110                 


Q ss_pred             ----CCchHHHHHHHHHHhCCCeEEEEEeCCC
Q 042806          237 ----ESDSGRARSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       237 ----~~~~~~~~~l~~~l~~~~~~LlVlDdv~  264 (390)
                          .........+.+.+...++-++|+|.+.
T Consensus        99 ~~~~~~~~~ll~~l~~~i~~~~~~~iviDs~t  130 (234)
T PRK06067         99 EWNSTLANKLLELIIEFIKSKREDVIIIDSLT  130 (234)
T ss_pred             ccCcchHHHHHHHHHHHHHhcCCCEEEEecHH
Confidence                1113445566666655454689999985

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.92  E-value=0.063  Score=50.14  Aligned_cols=47  Identities=21%  Similarity=0.177  Sum_probs=34.1

Q ss_pred             eEecCCCCHHHHHHHHHHhhCCCCCC--CchHHHHHHHHHHcCCChHHH
Q 042806          304 NFSVGVLKEDEAWSLFKKMAGDYIEG--SEFKWVAKDVARECAGLPVSI  350 (390)
Q Consensus       304 ~~~l~~L~~~ea~~lf~~~~~~~~~~--~~~~~~~~~i~~~~~GlPLai  350 (390)
                      ++++.+++.+|+..++..........  ...+...+++.--.+|+|--+
T Consensus       258 ~i~v~~~s~~E~~~ll~yy~~~~~l~~~~~~~~~~e~~~~~s~GNp~el  306 (309)
T PF10236_consen  258 PIEVPRLSKEEARSLLEYYADSGWLRSRVDEELVLEKLFLSSNGNPREL  306 (309)
T ss_pred             eEEeCCCCHHHHHHHHHHHHHCCccccCCCCHHHHHHHHHhcCCCHHHh
Confidence            78999999999999998877522211  333445667777789999754

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>cd01131 PilT Pilus retraction ATPase PilT

Probab=96.90  E-value=0.002  Score=56.14  Aligned_cols=110  Identities=9%  Similarity=0.059  Sum_probs=57.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-IQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      .+|.|.|+.|+||||++..+.......  ....++..-.+ .+.... ...+..+-..   ..........+...+... 
T Consensus         2 GlilI~GptGSGKTTll~~ll~~~~~~--~~~~i~t~e~~~E~~~~~-~~~~i~q~~v---g~~~~~~~~~i~~aLr~~-   74 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYINKN--KTHHILTIEDPIEFVHES-KRSLINQREV---GLDTLSFENALKAALRQD-   74 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhhhc--CCcEEEEEcCCccccccC-ccceeeeccc---CCCccCHHHHHHHHhcCC-
Confidence            468899999999999999888776432  23333322211 110000 0001100000   001122344555666543 


Q ss_pred             eEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhh
Q 042806          255 TILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVL  295 (390)
Q Consensus       255 ~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~  295 (390)
                      +=++++|++.+.+....+...   ...|..++.|+...+..
T Consensus        75 pd~ii~gEird~e~~~~~l~~---a~~G~~v~~t~Ha~~~~  112 (198)
T cd01131          75 PDVILVGEMRDLETIRLALTA---AETGHLVMSTLHTNSAA  112 (198)
T ss_pred             cCEEEEcCCCCHHHHHHHHHH---HHcCCEEEEEecCCcHH
Confidence            469999999766554443222   23455688888866543

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.

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

Probab=96.90  E-value=0.0063  Score=54.04  Aligned_cols=92  Identities=18%  Similarity=0.293  Sum_probs=61.4

Q ss_pred             cccccchhHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALKN-------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      +.++.|-.+.+++|-+...-             +.++-|.++|++|.|||-+|+.|+|....       +|+.|-.    
T Consensus       176 y~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtda-------cfirvig----  244 (435)
T KOG0729|consen  176 YSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTDA-------CFIRVIG----  244 (435)
T ss_pred             cccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccCc-------eEEeehh----
Confidence            44566777777777664432             34677889999999999999999987642       3333322    


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCC
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~  264 (390)
                      .++.+.-.   |      .-...+..|.+..+.++-|+|.||.+.
T Consensus       245 selvqkyv---g------egarmvrelf~martkkaciiffdeid  280 (435)
T KOG0729|consen  245 SELVQKYV---G------EGARMVRELFEMARTKKACIIFFDEID  280 (435)
T ss_pred             HHHHHHHh---h------hhHHHHHHHHHHhcccceEEEEeeccc
Confidence            12222211   1      223466777787888888999999985

>PRK04328 hypothetical protein; Provisional

Probab=96.90  E-value=0.0056  Score=55.33  Aligned_cols=53  Identities=11%  Similarity=0.206  Sum_probs=36.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLG  231 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~  231 (390)
                      ...++.|.|++|+|||+|+.++....-.+  -...+|++...  ++.++.+. ++.++
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~~--ge~~lyis~ee--~~~~i~~~-~~~~g   74 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM--GEPGVYVALEE--HPVQVRRN-MRQFG   74 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhc--CCcEEEEEeeC--CHHHHHHH-HHHcC
Confidence            56789999999999999999987764322  24467777755  44454433 34443

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

Probab=96.88  E-value=0.0081  Score=51.85  Aligned_cols=88  Identities=23%  Similarity=0.188  Sum_probs=48.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCC--------CeEEEEEeCCCCCHHHHHHHHHHHhCCCC------------
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLF--------DQVIFVEVSKIQDIRKIQGEIADKLGLTL------------  234 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f--------~~~~wv~v~~~~~~~~l~~~i~~~l~~~~------------  234 (390)
                      ..+..|.|++|+||||++.++.........|        ..++|++....  ..++.+.+........            
T Consensus        32 g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~--~~~~~~rl~~~~~~~~~~~~~~~~~~~~  109 (193)
T PF13481_consen   32 GELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS--ESQIARRLRALLQDYDDDANLFFVDLSN  109 (193)
T ss_dssp             TSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS---HHHHHHHHHHHHTTS-HHHHHHHHHH--
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC--HHHHHHHHHHHhcccCCccceEEeeccc
Confidence            3578899999999999999999887643223        24667766554  4444444433332110            


Q ss_pred             -----------CCCCchHHHHHHHHHHhC-CCeEEEEEeCCC
Q 042806          235 -----------HEESDSGRARSLRNRLKK-EKTILVILDNIW  264 (390)
Q Consensus       235 -----------~~~~~~~~~~~l~~~l~~-~~~~LlVlDdv~  264 (390)
                                 ...........+.+.+.. .+.-++|+|.+.
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~lvviD~l~  151 (193)
T PF13481_consen  110 WGCIRLFEPDSGGPLLDEDLEELEAALKELYGPDLVVIDPLQ  151 (193)
T ss_dssp             E-EE---TTS---TTSHHHHHHHHHHHTT----SEEEEE-GG
T ss_pred             cccceeeecccccccchHHHHHHHHHHhhcCCCcEEEEcCHH
Confidence                       000112334566666665 455688888774

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.87  E-value=0.0077  Score=59.94  Aligned_cols=86  Identities=13%  Similarity=0.181  Sum_probs=59.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC----------------C
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE----------------E  237 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~----------------~  237 (390)
                      ...++.|.|++|+|||||+.++......+  =..++|++..  -+..++...+ +.++.+...                .
T Consensus       262 ~gs~~li~G~~G~GKt~l~~~f~~~~~~~--ge~~~y~s~e--Es~~~i~~~~-~~lg~~~~~~~~~g~l~~~~~~p~~~  336 (484)
T TIGR02655       262 KDSIILATGATGTGKTLLVSKFLENACAN--KERAILFAYE--ESRAQLLRNA-YSWGIDFEEMEQQGLLKIICAYPESA  336 (484)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEEee--CCHHHHHHHH-HHcCCChHHHhhCCcEEEEEcccccC
Confidence            56789999999999999999999886433  2345665544  3666777664 555543211                1


Q ss_pred             CchHHHHHHHHHHhCCCeEEEEEeCCC
Q 042806          238 SDSGRARSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       238 ~~~~~~~~l~~~l~~~~~~LlVlDdv~  264 (390)
                      .....+..+.+.+...++-++|+|.+.
T Consensus       337 ~~~~~~~~i~~~i~~~~~~~vvIDsi~  363 (484)
T TIGR02655       337 GLEDHLQIIKSEIADFKPARIAIDSLS  363 (484)
T ss_pred             ChHHHHHHHHHHHHHcCCCEEEEcCHH
Confidence            224566777777776565789999986

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

>PRK10867 signal recognition particle protein; Provisional

Probab=96.86  E-value=0.0069  Score=58.89  Aligned_cols=28  Identities=25%  Similarity=0.305  Sum_probs=23.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+.+|.++|++|+||||++..++.....
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~l~~  126 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKYLKK  126 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHH
Confidence            4679999999999999988888876654

>PTZ00494 tuzin-like protein; Provisional

Probab=96.86  E-value=0.11  Score=50.01  Aligned_cols=161  Identities=10%  Similarity=0.128  Sum_probs=97.5

Q ss_pred             cccccchhHHHHHHHHHh---cCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDAL---KNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L---~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      ...++.|+.+-.-+-+.|   ....++++++.|..|.||++|++.........     .++|.+...   ++-++.+.+.
T Consensus       370 ~~~~V~R~~eE~~vRqvL~qld~aHPRIvV~TG~~GcGKSslcRsAvrkE~~p-----aV~VDVRg~---EDtLrsVVKA  441 (664)
T PTZ00494        370 EAFEVRREDEEALVRSVLTQMAPSHPRIVALAGGSGGGRCVPCRRAVRVEGVA-----LVHVDVGGT---EDTLRSVVRA  441 (664)
T ss_pred             cccccchhhHHHHHHHHHhhccCCCCcEEEEecCCCCCchHHHHHHHHHcCCC-----eEEEEecCC---cchHHHHHHH
Confidence            446788877755444444   44578999999999999999999988776543     678888765   4557888888


Q ss_pred             hCCCCCCCCchHHHHHHHHHH------hCCCeEEEEEeCCCCCccccccc---CCCCCCCCCcEEEEEecchhhhh--hc
Q 042806          230 LGLTLHEESDSGRARSLRNRL------KKEKTILVILDNIWGNLDFQAVG---IPHGDDRKGCKVLLTARSLDVLS--RK  298 (390)
Q Consensus       230 l~~~~~~~~~~~~~~~l~~~l------~~~~~~LlVlDdv~~~~~~~~l~---~~l~~~~~~s~IivTtr~~~v~~--~~  298 (390)
                      ++.+.-+. ..+++.-+.+..      .+++.-+||+- +.+-..+..+.   ..+.....-|.|++----+.+-.  ..
T Consensus       442 LgV~nve~-CGDlLdFI~ea~~~A~~~~~g~~P~lVlk-LREGssL~RVYnE~vaLacDrRlCHvv~EVplESLT~~n~~  519 (664)
T PTZ00494        442 LGVSNVEV-CGDLLGFVEEAMRGATVKASDGVPFLVMR-LREGSDLGRVYGEVVSLVSDCQACHIVLAVPMKALTPLNVS  519 (664)
T ss_pred             hCCCChhh-hccHHHHHHHHHHHHHHhcCCCCCEEEEE-eccCCcHHHHHHHHHHHHccchhheeeeechHhhhchhhcc
Confidence            98765442 122222222221      12333455542 21222222111   12223445577776655444321  12


Q ss_pred             CCCcceEecCCCCHHHHHHHHHHhh
Q 042806          299 MDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       299 ~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                      .+-...|-+.+|+.++|.++-++..
T Consensus       520 LPRLDFy~VPnFSr~QAf~YtqH~l  544 (664)
T PTZ00494        520 SRRLDFYCIPPFSRRQAFAYAEHTL  544 (664)
T ss_pred             CccceeEecCCcCHHHHHHHHhccc
Confidence            3344688999999999999888765

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.85  E-value=0.0061  Score=58.44  Aligned_cols=89  Identities=16%  Similarity=0.147  Sum_probs=50.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcC--CCCeEEEEEeCCCC-CHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEK--LFDQVIFVEVSKIQ-DIRKIQGEIADKLGLTLHEESDSGRARSLRNRL  250 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~--~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l  250 (390)
                      .++++.++|+.|+||||.+..++.......  .-..+..+++.... ...+-++..++.++.+................+
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~~  252 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQS  252 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHHh
Confidence            457899999999999999999987765321  12245555555321 222235566666666433322222222222233


Q ss_pred             hCCCeEEEEEeCCC
Q 042806          251 KKEKTILVILDNIW  264 (390)
Q Consensus       251 ~~~~~~LlVlDdv~  264 (390)
                      .+ . -++++|..-
T Consensus       253 ~~-~-DlVLIDTaG  264 (388)
T PRK12723        253 KD-F-DLVLVDTIG  264 (388)
T ss_pred             CC-C-CEEEEcCCC
Confidence            22 2 478888774

>PRK06547 hypothetical protein; Provisional

Probab=96.84  E-value=0.0018  Score=54.96  Aligned_cols=35  Identities=31%  Similarity=0.242  Sum_probs=28.7

Q ss_pred             HHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          166 ILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       166 l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +...+......+|.|.|++|+||||+++.+.....
T Consensus         6 ~~~~~~~~~~~~i~i~G~~GsGKTt~a~~l~~~~~   40 (172)
T PRK06547          6 IAARLCGGGMITVLIDGRSGSGKTTLAGALAARTG   40 (172)
T ss_pred             HHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            44445566788999999999999999999988754

>TIGR01817 nifA Nif-specific regulatory protein

Probab=96.83  E-value=0.0088  Score=60.44  Aligned_cols=48  Identities=13%  Similarity=0.176  Sum_probs=37.2

Q ss_pred             cccccchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          153 YEACESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...++|....+.++.+.+..  .....|.|+|+.|+|||++|+.+.+...
T Consensus       195 ~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s~  244 (534)
T TIGR01817       195 EDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSP  244 (534)
T ss_pred             cCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhCC
Confidence            45788988888887776643  2334567999999999999999988753

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.

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

Probab=96.82  E-value=0.018  Score=52.14  Aligned_cols=71  Identities=25%  Similarity=0.342  Sum_probs=50.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      -+-|.++||+|.||+.||+.|+.....       -|+++|..    ++..   +-+|      ....++..|.+..+..+
T Consensus       166 wrgiLLyGPPGTGKSYLAKAVATEAnS-------TFFSvSSS----DLvS---KWmG------ESEkLVknLFemARe~k  225 (439)
T KOG0739|consen  166 WRGILLYGPPGTGKSYLAKAVATEANS-------TFFSVSSS----DLVS---KWMG------ESEKLVKNLFEMARENK  225 (439)
T ss_pred             ceeEEEeCCCCCcHHHHHHHHHhhcCC-------ceEEeehH----HHHH---HHhc------cHHHHHHHHHHHHHhcC
Confidence            467999999999999999999887642       23445442    2211   1222      23457778888888888


Q ss_pred             eEEEEEeCCCC
Q 042806          255 TILVILDNIWG  265 (390)
Q Consensus       255 ~~LlVlDdv~~  265 (390)
                      +-+|.+|.|+.
T Consensus       226 PSIIFiDEiDs  236 (439)
T KOG0739|consen  226 PSIIFIDEIDS  236 (439)
T ss_pred             CcEEEeehhhh
Confidence            89999999964

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=96.82  E-value=0.0085  Score=55.11  Aligned_cols=28  Identities=18%  Similarity=0.101  Sum_probs=23.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+.+|+|.|+.|+||||+++.+..-..
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~ll~   87 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQALLS   87 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4567999999999999999988765553

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.80  E-value=0.0049  Score=59.17  Aligned_cols=84  Identities=17%  Similarity=0.155  Sum_probs=44.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-IQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      ..+++++|++|+||||++..++........+. +..++... .....+.+...+..++.+....   .....+.+.+...
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~-V~Lit~Dt~R~aA~eQLk~yAe~lgvp~~~~---~~~~~l~~~l~~~  298 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKS-VSLYTTDNYRIAAIEQLKRYADTMGMPFYPV---KDIKKFKETLARD  298 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCCe-EEEecccchhhhHHHHHHHHHHhcCCCeeeh---HHHHHHHHHHHhC
Confidence            46899999999999999999987653222232 33333322 1122333444445555432211   1123344444322


Q ss_pred             CeEEEEEeC
Q 042806          254 KTILVILDN  262 (390)
Q Consensus       254 ~~~LlVlDd  262 (390)
                      ..=++++|-
T Consensus       299 ~~D~VLIDT  307 (432)
T PRK12724        299 GSELILIDT  307 (432)
T ss_pred             CCCEEEEeC
Confidence            213688883

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=96.80  E-value=0.0061  Score=55.22  Aligned_cols=92  Identities=22%  Similarity=0.261  Sum_probs=59.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh--hcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCCC-------CCCCchH--
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE--TEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLTL-------HEESDSG--  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~--~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~~-------~~~~~~~--  241 (390)
                      +-.-++|.|.+|+|||+|+..+.+...  .+++-+.++++.++... ...+++..+...-....       .+.+...  
T Consensus        68 ~GQR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~  147 (276)
T cd01135          68 RGQKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIERI  147 (276)
T ss_pred             cCCEEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHH
Confidence            345688999999999999999887754  12235678899887654 56667766655422211       1111111  


Q ss_pred             ----HHHHHHHHHhC--CCeEEEEEeCCCC
Q 042806          242 ----RARSLRNRLKK--EKTILVILDNIWG  265 (390)
Q Consensus       242 ----~~~~l~~~l~~--~~~~LlVlDdv~~  265 (390)
                          ..-.+.+++.+  ++++|+++||+..
T Consensus       148 ~a~~~a~aiAEyfrd~~g~~VLl~~D~ltr  177 (276)
T cd01135         148 ITPRMALTTAEYLAYEKGKHVLVILTDMTN  177 (276)
T ss_pred             HHHHHHHHHHHHHHhccCCeEEEEEcChhH
Confidence                23356667654  4779999999953

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=96.79  E-value=0.081  Score=49.00  Aligned_cols=143  Identities=13%  Similarity=0.066  Sum_probs=81.4

Q ss_pred             HHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHh--------hhcCCCCeEEEEEe-CCCCCHHHHHHHHHHHhCCC
Q 042806          164 NDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKA--------ETEKLFDQVIFVEV-SKIQDIRKIQGEIADKLGLT  233 (390)
Q Consensus       164 ~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~--------~~~~~f~~~~wv~v-~~~~~~~~l~~~i~~~l~~~  233 (390)
                      ..+.+.+..++ .++..++|+.|.||++++..+.+..        ....|-+...++.. +.....+++. ++...+...
T Consensus         6 ~~l~~~i~~~~l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~i~vd~Ir-~l~~~~~~~   84 (299)
T PRK07132          6 KFLDNSATQNKISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKDLSKSEFL-SAINKLYFS   84 (299)
T ss_pred             HHHHHHHHhCCCCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCcCCHHHHH-HHHHHhccC
Confidence            34445555544 5677899999999999999998886        22222222333322 1223333322 333333222


Q ss_pred             CCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEecc-hhhhhhcCCCcceEecCCC
Q 042806          234 LHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTARS-LDVLSRKMDSQQNFSVGVL  310 (390)
Q Consensus       234 ~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTtr~-~~v~~~~~~~~~~~~l~~L  310 (390)
                      .-               ..+.+=++|+|++....  ..+.+...+-.-.+++.+|++|.+ ..+......-...+++.++
T Consensus        85 ~~---------------~~~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~f~~l  149 (299)
T PRK07132         85 SF---------------VQSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEP  149 (299)
T ss_pred             Cc---------------ccCCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEEECCCC
Confidence            10               11233688899986542  344444444444456666665544 4443333445679999999


Q ss_pred             CHHHHHHHHHHh
Q 042806          311 KEDEAWSLFKKM  322 (390)
Q Consensus       311 ~~~ea~~lf~~~  322 (390)
                      +.++..+.+...
T Consensus       150 ~~~~l~~~l~~~  161 (299)
T PRK07132        150 DQQKILAKLLSK  161 (299)
T ss_pred             CHHHHHHHHHHc
Confidence            999988777654

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

Probab=96.79  E-value=0.00049  Score=56.20  Aligned_cols=44  Identities=18%  Similarity=0.228  Sum_probs=28.8

Q ss_pred             chhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          158 SRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       158 gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      |+...+.++.+.+..  .....|.|+|+.|+||+++|+.++.....
T Consensus         2 G~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~~~   47 (138)
T PF14532_consen    2 GKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYSGR   47 (138)
T ss_dssp             -SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTTTT
T ss_pred             CCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhcCc
Confidence            444444445444432  23445779999999999999999887543

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=96.78  E-value=0.013  Score=55.24  Aligned_cols=44  Identities=16%  Similarity=0.181  Sum_probs=29.4

Q ss_pred             cchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          157 ESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       157 ~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +|+...+.++.+.+..  ....-|.|+|+.|+||+++|+.+.+...
T Consensus         2 iG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~s~   47 (329)
T TIGR02974         2 IGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSK   47 (329)
T ss_pred             CcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHhcC
Confidence            3444445555444432  2234477999999999999999987653

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

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=96.78  E-value=0.0088  Score=52.96  Aligned_cols=24  Identities=25%  Similarity=0.320  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +|+|.|++|+||||||+.+.....
T Consensus         1 IigI~G~sGSGKTTla~~L~~~l~   24 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQALLS   24 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHHHh
Confidence            578999999999999999998875

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.75  E-value=0.0068  Score=59.55  Aligned_cols=87  Identities=25%  Similarity=0.299  Sum_probs=54.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC--CchHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE--SDSGRARSLRNRLK  251 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~--~~~~~~~~l~~~l~  251 (390)
                      ...++.|.|++|+|||||+.+++......  -..++|++...  +..++... ++.++...+..  ........+.+.+.
T Consensus        79 ~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~--g~~vlYvs~Ee--s~~qi~~r-a~rlg~~~~~l~~~~e~~l~~i~~~i~  153 (446)
T PRK11823         79 PGSVVLIGGDPGIGKSTLLLQVAARLAAA--GGKVLYVSGEE--SASQIKLR-AERLGLPSDNLYLLAETNLEAILATIE  153 (446)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEEccc--cHHHHHHH-HHHcCCChhcEEEeCCCCHHHHHHHHH
Confidence            35689999999999999999998876532  23467776543  44454333 45565432211  01112345555665


Q ss_pred             CCCeEEEEEeCCCC
Q 042806          252 KEKTILVILDNIWG  265 (390)
Q Consensus       252 ~~~~~LlVlDdv~~  265 (390)
                      ..++-++|+|.+..
T Consensus       154 ~~~~~lVVIDSIq~  167 (446)
T PRK11823        154 EEKPDLVVIDSIQT  167 (446)
T ss_pred             hhCCCEEEEechhh
Confidence            55556999999863

>PRK14527 adenylate kinase; Provisional

Probab=96.74  E-value=0.0078  Score=52.02  Aligned_cols=27  Identities=22%  Similarity=0.199  Sum_probs=24.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+|.|+|++|+||||+++.+.+...
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~~~   31 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQELG   31 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            567899999999999999999987764

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.74  E-value=0.0023  Score=54.54  Aligned_cols=24  Identities=42%  Similarity=0.444  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .|.|.|++|+||||+|+.+.+...
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~   25 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLG   25 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            377999999999999999999854

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=96.73  E-value=0.0081  Score=50.75  Aligned_cols=81  Identities=17%  Similarity=0.133  Sum_probs=48.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC-CeE
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE-KTI  256 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~-~~~  256 (390)
                      +.|.|.+|+|||++|.++....     ....+|+.-...++. ++...|.+.-...+......+....+.+.+... +.-
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~-----~~~~~y~at~~~~d~-em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~~~~   75 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAEL-----GGPVTYIATAEAFDD-EMAERIARHRKRRPAHWRTIETPRDLVSALKELDPGD   75 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhc-----CCCeEEEEccCcCCH-HHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcCCCC
Confidence            6799999999999999997652     234666666655544 455555443333333333333344555555321 224


Q ss_pred             EEEEeCCC
Q 042806          257 LVILDNIW  264 (390)
Q Consensus       257 LlVlDdv~  264 (390)
                      .+++|.+.
T Consensus        76 ~VLIDclt   83 (169)
T cd00544          76 VVLIDCLT   83 (169)
T ss_pred             EEEEEcHh
Confidence            79999973

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.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.73  E-value=0.011  Score=56.40  Aligned_cols=39  Identities=23%  Similarity=0.290  Sum_probs=28.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS  214 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~  214 (390)
                      ++++|+|+|++|+||||++..++.....+ .+. +..+...
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~L~~~-Gkk-VglI~aD  278 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQFHGK-KKT-VGFITTD  278 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHHHHHc-CCc-EEEEecC
Confidence            45799999999999999999998876532 232 3445543

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.72  E-value=0.0023  Score=52.56  Aligned_cols=45  Identities=33%  Similarity=0.469  Sum_probs=35.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCC
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTL  234 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~  234 (390)
                      +|.|.|++|+||||+++.+.+...-.  |  +         +...+++++++..|...
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~gl~--~--v---------saG~iFR~~A~e~gmsl   46 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLGLK--L--V---------SAGTIFREMARERGMSL   46 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhCCc--e--e---------eccHHHHHHHHHcCCCH
Confidence            68899999999999999999987643  1  1         34568888888887653

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=96.72  E-value=0.013  Score=53.44  Aligned_cols=88  Identities=19%  Similarity=0.244  Sum_probs=55.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH-hC---CCCCCC--CchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADK-LG---LTLHEE--SDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~-l~---~~~~~~--~~~~~~~~l~  247 (390)
                      ..+++=|+|+.|+||||+|.+++-.....  -..++|++..+.++++.+. +++.. +.   ...+..  .....+..+.
T Consensus        59 ~g~ItEiyG~~gsGKT~lal~~~~~aq~~--g~~a~fIDtE~~l~p~r~~-~l~~~~~d~l~v~~~~~~e~q~~i~~~~~  135 (279)
T COG0468          59 RGRITEIYGPESSGKTTLALQLVANAQKP--GGKAAFIDTEHALDPERAK-QLGVDLLDNLLVSQPDTGEQQLEIAEKLA  135 (279)
T ss_pred             cceEEEEecCCCcchhhHHHHHHHHhhcC--CCeEEEEeCCCCCCHHHHH-HHHHhhhcceeEecCCCHHHHHHHHHHHH
Confidence            45788899999999999999988876543  3378999999999886643 34443 21   111111  1122233333


Q ss_pred             HHHhCCCeEEEEEeCCCC
Q 042806          248 NRLKKEKTILVILDNIWG  265 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~  265 (390)
                      ..... +--|+|+|.+-.
T Consensus       136 ~~~~~-~i~LvVVDSvaa  152 (279)
T COG0468         136 RSGAE-KIDLLVVDSVAA  152 (279)
T ss_pred             HhccC-CCCEEEEecCcc
Confidence            33333 336999999853

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

Probab=96.71  E-value=0.0047  Score=54.94  Aligned_cols=87  Identities=18%  Similarity=0.211  Sum_probs=53.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------------------
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLH------------------  235 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------------------  235 (390)
                      ...++.|.|++|+|||+|+.++....-.+. =..++|++...  +..++...+. .++.+..                  
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~-ge~vlyvs~ee--~~~~l~~~~~-s~g~d~~~~~~~g~l~~~d~~~~~~   93 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNF-GEKVLYVSFEE--PPEELIENMK-SFGWDLEEYEDSGKLKIIDAFPERI   93 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHH-T--EEEEESSS---HHHHHHHHH-TTTS-HHHHHHTTSEEEEESSGGGS
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhc-CCcEEEEEecC--CHHHHHHHHH-HcCCcHHHHhhcCCEEEEecccccc
Confidence            567999999999999999999876543220 12367777654  4455555543 3432110                  


Q ss_pred             ---CCCchHHHHHHHHHHhCCCeEEEEEeCCC
Q 042806          236 ---EESDSGRARSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       236 ---~~~~~~~~~~l~~~l~~~~~~LlVlDdv~  264 (390)
                         ..+.......+.+.+...+...+|+|.+.
T Consensus        94 ~~~~~~~~~l~~~i~~~i~~~~~~~vVIDsls  125 (226)
T PF06745_consen   94 GWSPNDLEELLSKIREAIEELKPDRVVIDSLS  125 (226)
T ss_dssp             T-TSCCHHHHHHHHHHHHHHHTSSEEEEETHH
T ss_pred             cccccCHHHHHHHHHHHHHhcCCCEEEEECHH
Confidence               12334455666666665444799999874

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

>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=96.71  E-value=0.0016  Score=53.32  Aligned_cols=24  Identities=33%  Similarity=0.450  Sum_probs=21.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +|.+.|++|+||||+|+.+.....
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~~~   24 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKRLG   24 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHST
T ss_pred             CEEEECCCCCCHHHHHHHHHHHCC
Confidence            578999999999999999987654

...

>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=96.71  E-value=0.0015  Score=52.24  Aligned_cols=22  Identities=50%  Similarity=0.709  Sum_probs=20.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |.|.|.+|+||||+|+.+....
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            6899999999999999998885

...

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.68  E-value=0.12  Score=50.26  Aligned_cols=28  Identities=25%  Similarity=0.261  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+.+|.++|+.|+||||++..++.....
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~l~~  126 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYYYQR  126 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4679999999999999999999877654

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.67  E-value=0.0024  Score=56.27  Aligned_cols=24  Identities=25%  Similarity=0.182  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .+++.|+|+.|.|||||.+.+...
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~~   52 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVALI   52 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHHH
Confidence            488999999999999999999743

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

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=96.66  E-value=0.0077  Score=62.36  Aligned_cols=84  Identities=19%  Similarity=0.253  Sum_probs=56.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC------CCchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE------ESDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~------~~~~~~~~~l~  247 (390)
                      ..+++-|+|++|+|||||+.+++......  =..++|+.....++.     ..+..++.+.+.      .+.......+.
T Consensus        59 ~GsiteI~G~~GsGKTtLal~~~~~a~~~--G~~v~yId~E~t~~~-----~~A~~lGvDl~~llv~~~~~~E~~l~~i~  131 (790)
T PRK09519         59 RGRVIEIYGPESSGKTTVALHAVANAQAA--GGVAAFIDAEHALDP-----DYAKKLGVDTDSLLVSQPDTGEQALEIAD  131 (790)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEECCccchhH-----HHHHHcCCChhHeEEecCCCHHHHHHHHH
Confidence            46788999999999999998877654332  245788887776663     356667664331      12233444455


Q ss_pred             HHHhCCCeEEEEEeCCC
Q 042806          248 NRLKKEKTILVILDNIW  264 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~  264 (390)
                      ..+..+..-|||+|.+.
T Consensus       132 ~lv~~~~~~LVVIDSI~  148 (790)
T PRK09519        132 MLIRSGALDIVVIDSVA  148 (790)
T ss_pred             HHhhcCCCeEEEEcchh
Confidence            55566666799999985

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.65  E-value=0.0091  Score=54.29  Aligned_cols=40  Identities=20%  Similarity=0.332  Sum_probs=30.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK  215 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  215 (390)
                      ..+++.|.|++|+|||+++.+++......  =..++|++...
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~~--Ge~vlyis~Ee   74 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQASR--GNPVLFVTVES   74 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhC--CCcEEEEEecC
Confidence            46789999999999999999987764322  23567777764

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

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.65  E-value=0.022  Score=58.92  Aligned_cols=39  Identities=23%  Similarity=0.302  Sum_probs=27.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEe
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEV  213 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v  213 (390)
                      ..++.++|+.|+||||++..+............+..+..
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~  223 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTT  223 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecC
Confidence            469999999999999999999877643221223444444

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.64  E-value=0.016  Score=50.93  Aligned_cols=50  Identities=14%  Similarity=0.149  Sum_probs=35.9

Q ss_pred             cccccchhHHHHHHHHH----hcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          153 YEACESRMSTLNDILDA----LKNPDVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~----L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      ...++|-+...+.|++.    +.+-.-.-+.+||..|.||++|++.+.+....+
T Consensus        59 L~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~~  112 (287)
T COG2607          59 LADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYADE  112 (287)
T ss_pred             HHHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHHhc
Confidence            34567766666666543    333333457799999999999999999998754

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=96.64  E-value=0.009  Score=50.65  Aligned_cols=26  Identities=27%  Similarity=0.358  Sum_probs=22.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      ++.+.|++|+||||++..+.......
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~   27 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKK   27 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            67899999999999999999887543

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.64  E-value=0.0027  Score=62.95  Aligned_cols=47  Identities=17%  Similarity=0.203  Sum_probs=40.7

Q ss_pred             cccchhHHHHHHHHHhc------CCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          155 ACESRMSTLNDILDALK------NPDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~------~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +++|-++.++++++.|.      +...+++.++||+|+||||||+.+.+....
T Consensus        77 d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le~  129 (644)
T PRK15455         77 EFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLMER  129 (644)
T ss_pred             cccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHHHh
Confidence            57899999999999883      356689999999999999999999998754

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.64  E-value=0.016  Score=54.90  Aligned_cols=89  Identities=15%  Similarity=0.187  Sum_probs=52.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC-HHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD-IRKIQGEIADKLGLTLHEESDSGRARSLRNRLKK  252 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  252 (390)
                      +.++++++|+.|+||||++..+......++  ..+.+++...... ..+-++..++.++.+.........+....+.+..
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~~~g--~~V~lItaDtyR~gAveQLk~yae~lgvpv~~~~dp~dL~~al~~l~~  282 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLLKQN--RTVGFITTDTFRSGAVEQFQGYADKLDVELIVATSPAELEEAVQYMTY  282 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcC--CeEEEEeCCccCccHHHHHHHHhhcCCCCEEecCCHHHHHHHHHHHHh
Confidence            467999999999999999999987764432  3466666654322 3344555566666543322222223333344431


Q ss_pred             -CCeEEEEEeCCC
Q 042806          253 -EKTILVILDNIW  264 (390)
Q Consensus       253 -~~~~LlVlDdv~  264 (390)
                       +..=+|++|-.-
T Consensus       283 ~~~~D~VLIDTAG  295 (407)
T PRK12726        283 VNCVDHILIDTVG  295 (407)
T ss_pred             cCCCCEEEEECCC
Confidence             121478888774

>PRK05439 pantothenate kinase; Provisional

Probab=96.63  E-value=0.018  Score=53.49  Aligned_cols=28  Identities=21%  Similarity=0.164  Sum_probs=24.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+-+|+|.|.+|+||||+|+.+.....
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~~l~  111 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQALLS  111 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3567899999999999999999988664

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.63  E-value=0.02  Score=55.33  Aligned_cols=60  Identities=18%  Similarity=0.187  Sum_probs=34.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGLT  233 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~~  233 (390)
                      +..+++++|+.|+||||++..+............+..+..... ....+-+...++.++..
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rigalEQL~~~a~ilGvp  250 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLRIYGKLLGVS  250 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchhHHHHHHHHHHHcCCc
Confidence            3578999999999999999988775422212233444443321 12223344445555543

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=96.63  E-value=0.0019  Score=56.06  Aligned_cols=26  Identities=42%  Similarity=0.537  Sum_probs=23.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      +|+|.|++|+||||+|+.+.......
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L~~~   26 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQILNKR   26 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTTC
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCcc
Confidence            68999999999999999999998753

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.62  E-value=0.015  Score=48.03  Aligned_cols=24  Identities=25%  Similarity=0.390  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ++.|+|.+|+|||||++.+.....
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~l~   24 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEKLF   24 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHH
Confidence            578999999999999999998875

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=96.61  E-value=0.014  Score=54.25  Aligned_cols=43  Identities=26%  Similarity=0.309  Sum_probs=34.9

Q ss_pred             ccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          156 CESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       156 ~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      +-+|..+..--++.|.++....+.+.|.+|.|||-||....-.
T Consensus       226 i~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgle  268 (436)
T COG1875         226 IRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLE  268 (436)
T ss_pred             cCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHH
Confidence            4456677777788899999999999999999999887765433

>PRK14974 cell division protein FtsY; Provisional

Probab=96.61  E-value=0.023  Score=53.46  Aligned_cols=89  Identities=18%  Similarity=0.186  Sum_probs=49.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCCCCCC----CchHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGLTLHEE----SDSGRARSLRN  248 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~~~~~~----~~~~~~~~l~~  248 (390)
                      ++.+|.++|++|+||||++..++...... .+. ++.+..... ....+-+...+..++......    +....+....+
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~~~-g~~-V~li~~Dt~R~~a~eqL~~~a~~lgv~v~~~~~g~dp~~v~~~ai~  216 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLKKN-GFS-VVIAAGDTFRAGAIEQLEEHAERLGVKVIKHKYGADPAAVAYDAIE  216 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHc-CCe-EEEecCCcCcHHHHHHHHHHHHHcCCceecccCCCCHHHHHHHHHH
Confidence            46899999999999999999988876543 343 333433211 122334555666776543211    11122222222


Q ss_pred             HHh-CCCeEEEEEeCCCC
Q 042806          249 RLK-KEKTILVILDNIWG  265 (390)
Q Consensus       249 ~l~-~~~~~LlVlDdv~~  265 (390)
                      ... .+. =++++|-.-.
T Consensus       217 ~~~~~~~-DvVLIDTaGr  233 (336)
T PRK14974        217 HAKARGI-DVVLIDTAGR  233 (336)
T ss_pred             HHHhCCC-CEEEEECCCc
Confidence            222 223 3888998743

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=96.60  E-value=0.0072  Score=53.10  Aligned_cols=86  Identities=22%  Similarity=0.434  Sum_probs=53.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCC-------CCCCCCchH-----
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGL-------TLHEESDSG-----  241 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~-------~~~~~~~~~-----  241 (390)
                      -.-+.|.|.+|+|||+|+..+.+...    -+..+++.++.. ....++..++...-..       ...+.+...     
T Consensus        15 Gqr~~I~g~~g~GKt~Ll~~i~~~~~----~d~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~~   90 (215)
T PF00006_consen   15 GQRIGIFGGAGVGKTVLLQEIANNQD----ADVVVYALIGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRAP   90 (215)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHCT----TTEEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHHH
T ss_pred             CCEEEEEcCcccccchhhHHHHhccc----ccceeeeeccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhhh
Confidence            45688999999999999999999874    345588888754 4556666665333111       111111111     


Q ss_pred             -HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          242 -RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       242 -~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                       ..-.+.+++. .++.+|+++||+.
T Consensus        91 ~~a~t~AEyfrd~G~dVlli~Dslt  115 (215)
T PF00006_consen   91 YTALTIAEYFRDQGKDVLLIIDSLT  115 (215)
T ss_dssp             HHHHHHHHHHHHTTSEEEEEEETHH
T ss_pred             ccchhhhHHHhhcCCceeehhhhhH
Confidence             1123444443 3667999999984

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=96.58  E-value=0.0048  Score=50.44  Aligned_cols=39  Identities=13%  Similarity=0.197  Sum_probs=29.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK  215 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  215 (390)
                      ++|.|+|+.|+|||||++.+.+....+ .+...++.+...
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l~~~-g~~v~~ik~~~~   39 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINELKRR-GYRVAVIKHTDH   39 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEE-ST
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhHc-CCceEEEEEccC
Confidence            579999999999999999999998753 477666776665

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

Probab=96.58  E-value=0.067  Score=54.04  Aligned_cols=150  Identities=16%  Similarity=0.188  Sum_probs=86.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      .-|.++|++|.|||.||..+......       -||++.++    +++..   .+|      ...+.+..+.++.+.-+|
T Consensus       702 ~giLLyGppGcGKT~la~a~a~~~~~-------~fisvKGP----ElL~K---yIG------aSEq~vR~lF~rA~~a~P  761 (952)
T KOG0735|consen  702 TGILLYGPPGCGKTLLASAIASNSNL-------RFISVKGP----ELLSK---YIG------ASEQNVRDLFERAQSAKP  761 (952)
T ss_pred             cceEEECCCCCcHHHHHHHHHhhCCe-------eEEEecCH----HHHHH---Hhc------ccHHHHHHHHHHhhccCC
Confidence            45889999999999999999887653       45667654    33322   122      223456677777777788


Q ss_pred             EEEEEeCCCCCc-------------ccccccCCCCC--CCCCcEEE-EEecchhhhhhcCCCc---ceEecCCCCHHHHH
Q 042806          256 ILVILDNIWGNL-------------DFQAVGIPHGD--DRKGCKVL-LTARSLDVLSRKMDSQ---QNFSVGVLKEDEAW  316 (390)
Q Consensus       256 ~LlVlDdv~~~~-------------~~~~l~~~l~~--~~~~s~Ii-vTtr~~~v~~~~~~~~---~~~~l~~L~~~ea~  316 (390)
                      |++.||.+++..             ..+.+.-.+..  +-.|.-|+ .|||..-+-+.....+   +.+.-..-+..+-.
T Consensus       762 CiLFFDEfdSiAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl  841 (952)
T KOG0735|consen  762 CILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGVYILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPERL  841 (952)
T ss_pred             eEEEeccccccCcccCCCCCCchHHHHHHHHHhhccccccceEEEEEecCCccccCHhhcCCCccceeeeCCCCCcHHHH
Confidence            999999987431             12222222211  22344444 4566543322222222   23333444566677


Q ss_pred             HHHHHhhCC--CCCCCchHHHHHHHHHHcCCChHH
Q 042806          317 SLFKKMAGD--YIEGSEFKWVAKDVARECAGLPVS  349 (390)
Q Consensus       317 ~lf~~~~~~--~~~~~~~~~~~~~i~~~~~GlPLa  349 (390)
                      ++|......  .....+    .+.++.+++|..-|
T Consensus       842 ~il~~ls~s~~~~~~vd----l~~~a~~T~g~tgA  872 (952)
T KOG0735|consen  842 EILQVLSNSLLKDTDVD----LECLAQKTDGFTGA  872 (952)
T ss_pred             HHHHHHhhccCCccccc----hHHHhhhcCCCchh
Confidence            888776642  222233    34677888877644

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=96.56  E-value=0.012  Score=49.78  Aligned_cols=25  Identities=24%  Similarity=0.316  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..++.|.||+|+|||||++.++.+.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            4678999999999999999999876

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.55  E-value=0.0016  Score=55.56  Aligned_cols=27  Identities=37%  Similarity=0.466  Sum_probs=24.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      +.|.+.|.+|+||||+|+++...++.+
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L~~~   28 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKELRQE   28 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHHHHh
Confidence            568899999999999999999998765

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.55  E-value=0.019  Score=56.56  Aligned_cols=58  Identities=16%  Similarity=0.149  Sum_probs=36.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-IQDIRKIQGEIADKLGL  232 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~l~~~i~~~l~~  232 (390)
                      ..+++++|+.|+||||++..++.....+.....+..+.... .....+-++..++.++.
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQLr~~AeilGV  314 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRIYGKILGV  314 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHHHHHHHHhCC
Confidence            47999999999999999999998764332222344554433 12333334444555544

>PRK07667 uridine kinase; Provisional

Probab=96.54  E-value=0.0037  Score=54.20  Aligned_cols=38  Identities=24%  Similarity=0.429  Sum_probs=29.3

Q ss_pred             HHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          164 NDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       164 ~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +.+.+.+..  ++..+|+|.|.+|+||||+++.+......
T Consensus         4 ~~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~~l~~   43 (193)
T PRK07667          4 NELINIMKKHKENRFILGIDGLSRSGKTTFVANLKENMKQ   43 (193)
T ss_pred             HHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            344454443  34579999999999999999999998754

>PRK08233 hypothetical protein; Provisional

Probab=96.53  E-value=0.0022  Score=54.75  Aligned_cols=26  Identities=27%  Similarity=0.369  Sum_probs=23.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+|+|.|++|+||||||..+.....
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhCC
Confidence            46899999999999999999998764

>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=96.51  E-value=0.0024  Score=45.18  Aligned_cols=23  Identities=35%  Similarity=0.488  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +|.|.|+.|+||||+++.+.+..
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999885

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.

>PTZ00301 uridine kinase; Provisional

Probab=96.50  E-value=0.0069  Score=53.09  Aligned_cols=26  Identities=23%  Similarity=0.446  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+|+|.|++|+||||||+.+.+...
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~l~   28 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSELM   28 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHHHH
Confidence            46899999999999999999987764

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=96.49  E-value=0.0037  Score=62.27  Aligned_cols=57  Identities=18%  Similarity=0.243  Sum_probs=43.6

Q ss_pred             cccccchhHHHHHHHHHhcC-----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEe
Q 042806          153 YEACESRMSTLNDILDALKN-----PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEV  213 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-----~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v  213 (390)
                      ..++.-..+.++++..||..     ...+++.++||+|+||||.++.+++...    |+..=|.+-
T Consensus        18 ~~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~elg----~~v~Ew~np   79 (519)
T PF03215_consen   18 LDELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKELG----FEVQEWINP   79 (519)
T ss_pred             HHHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHhC----CeeEEecCC
Confidence            44555566777888888764     2357899999999999999999999874    666677643

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.48  E-value=0.0027  Score=55.73  Aligned_cols=27  Identities=30%  Similarity=0.343  Sum_probs=24.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .+..+|+|.|++|+|||||++.+....
T Consensus         4 ~~~~iI~I~G~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480          4 KKPIIIGIAGGSGSGKTTVASTIYEEL   30 (209)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            356799999999999999999999876

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=96.47  E-value=0.006  Score=57.47  Aligned_cols=45  Identities=16%  Similarity=0.174  Sum_probs=33.8

Q ss_pred             cccchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          155 ACESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .++|+...+.++.+.+..  ....-|.|+|+.|+||+++|+.+....
T Consensus         7 ~liG~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~s   53 (326)
T PRK11608          7 NLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLS   53 (326)
T ss_pred             ccEECCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhC
Confidence            477887777777766543  233457799999999999999997654

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=96.46  E-value=0.01  Score=58.00  Aligned_cols=90  Identities=19%  Similarity=0.292  Sum_probs=58.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCC-------CCCCCch-----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLT-------LHEESDS-----  240 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~-------~~~~~~~-----  240 (390)
                      +-.-++|.|.+|+|||||+..+.+..... +-+.++++.++... ...+++..+...-...       ..+.+..     
T Consensus       142 kGQR~gIfa~~G~GKt~Ll~~~~~~~~~~-~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a  220 (461)
T PRK12597        142 KGGKTGLFGGAGVGKTVLMMELIFNISKQ-HSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRV  220 (461)
T ss_pred             cCCEEEeecCCCCChhHHHHHHHHHHHhh-CCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHH
Confidence            44678899999999999999998887543 56788888776543 4566666665432211       1111111     


Q ss_pred             -HHHHHHHHHHhC--CCeEEEEEeCCC
Q 042806          241 -GRARSLRNRLKK--EKTILVILDNIW  264 (390)
Q Consensus       241 -~~~~~l~~~l~~--~~~~LlVlDdv~  264 (390)
                       .....+.+++++  ++.+|+++|++.
T Consensus       221 ~~~a~tiAEyfrd~~G~~VLl~~DslT  247 (461)
T PRK12597        221 VLTGLTIAEYLRDEEKEDVLLFIDNIF  247 (461)
T ss_pred             HHHHHHHHHHHHHhcCCceEEEeccch
Confidence             123356666643  466999999994

>PRK06762 hypothetical protein; Provisional

Probab=96.46  E-value=0.0027  Score=53.45  Aligned_cols=25  Identities=32%  Similarity=0.426  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +.+|.|.|++|+||||+|+.+.+..
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3678999999999999999998876

>CHL00206 ycf2 Ycf2; Provisional

Probab=96.46  E-value=0.026  Score=63.13  Aligned_cols=28  Identities=18%  Similarity=0.114  Sum_probs=24.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .++-|.++||+|.|||.||+.++.+..+
T Consensus      1629 pPKGILLiGPPGTGKTlLAKALA~es~V 1656 (2281)
T CHL00206       1629 PSRGILVIGSIGTGRSYLVKYLATNSYV 1656 (2281)
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHhcCC
Confidence            3567889999999999999999998754

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=96.45  E-value=0.022  Score=48.33  Aligned_cols=28  Identities=21%  Similarity=0.196  Sum_probs=24.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...++.|+|++|.|||||.+.+|...+.
T Consensus        27 ~Gef~fl~GpSGAGKSTllkLi~~~e~p   54 (223)
T COG2884          27 KGEFVFLTGPSGAGKSTLLKLIYGEERP   54 (223)
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhhhcC
Confidence            4568899999999999999999988754

>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=96.44  E-value=0.012  Score=53.60  Aligned_cols=26  Identities=31%  Similarity=0.293  Sum_probs=21.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +.|.|+|.+|+||||+|+++......
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~~~~   27 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKYLEE   27 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHHHh
Confidence            57899999999999999999998765

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>TIGR00235 udk uridine kinase

Probab=96.44  E-value=0.0029  Score=55.49  Aligned_cols=28  Identities=32%  Similarity=0.430  Sum_probs=24.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +...+|+|.|++|+|||||++.+.....
T Consensus         4 ~~g~vi~I~G~sGsGKSTl~~~l~~~l~   31 (207)
T TIGR00235         4 PKGIIIGIGGGSGSGKTTVARKIYEQLG   31 (207)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3567899999999999999999988754

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

>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=96.42  E-value=0.0029  Score=57.90  Aligned_cols=55  Identities=20%  Similarity=0.271  Sum_probs=34.2

Q ss_pred             HHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHH
Q 042806          165 DILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKI  222 (390)
Q Consensus       165 ~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l  222 (390)
                      .+++.+...+ +-+.++|+.|+|||++++......... .| ...-++.+...+...+
T Consensus        24 ~ll~~l~~~~-~pvLl~G~~GtGKT~li~~~l~~l~~~-~~-~~~~~~~s~~Tts~~~   78 (272)
T PF12775_consen   24 YLLDLLLSNG-RPVLLVGPSGTGKTSLIQNFLSSLDSD-KY-LVITINFSAQTTSNQL   78 (272)
T ss_dssp             HHHHHHHHCT-EEEEEESSTTSSHHHHHHHHHHCSTTC-CE-EEEEEES-TTHHHHHH
T ss_pred             HHHHHHHHcC-CcEEEECCCCCchhHHHHhhhccCCcc-cc-ceeEeeccCCCCHHHH
Confidence            4445444433 445799999999999999998765432 12 2445566665444444

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=96.42  E-value=0.0039  Score=51.66  Aligned_cols=28  Identities=29%  Similarity=0.342  Sum_probs=24.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      ..+|.|+|.+|+||||||+.+...+...
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~~L~~~   29 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALERRLFAR   29 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            4689999999999999999999998765

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>TIGR00416 sms DNA repair protein RadA

Probab=96.42  E-value=0.014  Score=57.49  Aligned_cols=87  Identities=22%  Similarity=0.260  Sum_probs=53.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC--CchHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE--SDSGRARSLRNRLK  251 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~--~~~~~~~~l~~~l~  251 (390)
                      ...++.|.|.+|+|||||+.++.......+  ..++|++...  +..++... +..++...+..  ........+.+.+.
T Consensus        93 ~GsvilI~G~pGsGKTTL~lq~a~~~a~~g--~kvlYvs~EE--s~~qi~~r-a~rlg~~~~~l~~~~e~~~~~I~~~i~  167 (454)
T TIGR00416        93 PGSLILIGGDPGIGKSTLLLQVACQLAKNQ--MKVLYVSGEE--SLQQIKMR-AIRLGLPEPNLYVLSETNWEQICANIE  167 (454)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHhcC--CcEEEEECcC--CHHHHHHH-HHHcCCChHHeEEcCCCCHHHHHHHHH
Confidence            457899999999999999999987764321  2467776543  44444332 33444432211  01112345556665


Q ss_pred             CCCeEEEEEeCCCC
Q 042806          252 KEKTILVILDNIWG  265 (390)
Q Consensus       252 ~~~~~LlVlDdv~~  265 (390)
                      ..++-++|+|.+..
T Consensus       168 ~~~~~~vVIDSIq~  181 (454)
T TIGR00416       168 EENPQACVIDSIQT  181 (454)
T ss_pred             hcCCcEEEEecchh
Confidence            55557899999864

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

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.41  E-value=0.0057  Score=59.74  Aligned_cols=45  Identities=18%  Similarity=0.150  Sum_probs=38.0

Q ss_pred             cccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          155 ACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .++||++.++.+...+..+.  -+.|.|++|+|||+||+.+......
T Consensus        21 ~i~gre~vI~lll~aalag~--hVLL~GpPGTGKT~LAraLa~~~~~   65 (498)
T PRK13531         21 GLYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAFQN   65 (498)
T ss_pred             hccCcHHHHHHHHHHHccCC--CEEEECCCChhHHHHHHHHHHHhcc
Confidence            58999999999988887543  4778999999999999999987643

>PRK05973 replicative DNA helicase; Provisional

Probab=96.40  E-value=0.026  Score=50.32  Aligned_cols=49  Identities=16%  Similarity=0.133  Sum_probs=34.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      ...++.|.|.+|+|||+++.++....... . ..++|++...  +..++...+
T Consensus        63 ~Gsl~LIaG~PG~GKT~lalqfa~~~a~~-G-e~vlyfSlEe--s~~~i~~R~  111 (237)
T PRK05973         63 PGDLVLLGARPGHGKTLLGLELAVEAMKS-G-RTGVFFTLEY--TEQDVRDRL  111 (237)
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHHhc-C-CeEEEEEEeC--CHHHHHHHH
Confidence            45688899999999999999998766432 2 2355665544  456666654

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.39  E-value=0.0032  Score=54.08  Aligned_cols=26  Identities=23%  Similarity=0.230  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +.++|.|.|++|+||||+++.+....
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999998765

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=96.39  E-value=0.011  Score=51.51  Aligned_cols=119  Identities=21%  Similarity=0.181  Sum_probs=67.4

Q ss_pred             HHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhc-CCCCeEEEEEeCCCCCHHHHHHHHHHHh--------CCCCCC
Q 042806          166 ILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETE-KLFDQVIFVEVSKIQDIRKIQGEIADKL--------GLTLHE  236 (390)
Q Consensus       166 l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~~~~~~l~~~i~~~l--------~~~~~~  236 (390)
                      ++..|-+..-.-..|.|++|+|||||.+.+..-.... +.|-..--.-+...   .    +|+..+        +...+-
T Consensus       128 li~~ly~~g~lntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDer---s----EIag~~~gvpq~~~g~R~dV  200 (308)
T COG3854         128 LIKDLYQNGWLNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDER---S----EIAGCLNGVPQHGRGRRMDV  200 (308)
T ss_pred             HHHHHHhcCceeeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEecc---c----hhhccccCCchhhhhhhhhh
Confidence            5555555444457789999999999999998876543 23432221112111   1    111111        111111


Q ss_pred             CCchHHHHHHHHHHhCCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhh
Q 042806          237 ESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDV  294 (390)
Q Consensus       237 ~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v  294 (390)
                      .+.....+-+...+++--|=++|+|.+-..++-..+...   .+.|.+++.|..-..+
T Consensus       201 ld~cpk~~gmmmaIrsm~PEViIvDEIGt~~d~~A~~ta---~~~GVkli~TaHG~~i  255 (308)
T COG3854         201 LDPCPKAEGMMMAIRSMSPEVIIVDEIGTEEDALAILTA---LHAGVKLITTAHGNGI  255 (308)
T ss_pred             cccchHHHHHHHHHHhcCCcEEEEeccccHHHHHHHHHH---HhcCcEEEEeeccccH
Confidence            122223344555566656679999999766555444333   3668899988875444

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=96.39  E-value=0.0026  Score=49.41  Aligned_cols=24  Identities=50%  Similarity=0.617  Sum_probs=21.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      |.|+|++|+|||+||+.++.+...
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~   24 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLK   24 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHH
Confidence            468999999999999999888754

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

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=96.37  E-value=0.013  Score=57.03  Aligned_cols=90  Identities=19%  Similarity=0.297  Sum_probs=59.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCC-------CCCCCch-----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLT-------LHEESDS-----  240 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~-------~~~~~~~-----  240 (390)
                      +-.-++|.|.+|+|||+|+..+...... .+-+.++|+.++... ...+++..+...-...       ..+.+..     
T Consensus       137 kGQr~~Ifg~~G~GKt~l~~~~~~~~~~-~~~~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~~  215 (449)
T TIGR03305       137 RGGKAGLFGGAGVGKTVLLTEMIHNMVG-QHQGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRV  215 (449)
T ss_pred             cCCEEEeecCCCCChhHHHHHHHHHHHh-cCCCEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHHH
Confidence            3456889999999999999999887542 234678888887654 4566666655432211       1111111     


Q ss_pred             -HHHHHHHHHHhC--CCeEEEEEeCCC
Q 042806          241 -GRARSLRNRLKK--EKTILVILDNIW  264 (390)
Q Consensus       241 -~~~~~l~~~l~~--~~~~LlVlDdv~  264 (390)
                       .....+.++++.  ++.+|+++||+.
T Consensus       216 ~~~a~tiAEyfrd~~G~~VLl~~DslT  242 (449)
T TIGR03305       216 GHTALTMAEYFRDDEKQDVLLLIDNIF  242 (449)
T ss_pred             HHHHHHHHHHHHHhcCCceEEEecChH
Confidence             123466677764  577999999984

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>TIGR01069 mutS2 MutS2 family protein

Probab=96.37  E-value=0.0037  Score=65.41  Aligned_cols=189  Identities=21%  Similarity=0.152  Sum_probs=88.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh-hhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC----CCchHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA-ETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE----ESDSGRARSLRN  248 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~-~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~----~~~~~~~~~l~~  248 (390)
                      ...++.|+|+.|.|||||.+.+.-.. ....    .++|.+...... ..+.++...++....-    ..-......+..
T Consensus       321 ~~~~liItGpNg~GKSTlLK~i~~~~l~aq~----G~~Vpa~~~~~~-~~~d~i~~~i~~~~si~~~LStfS~~m~~~~~  395 (771)
T TIGR01069       321 EKRVLAITGPNTGGKTVTLKTLGLLALMFQS----GIPIPANEHSEI-PYFEEIFADIGDEQSIEQNLSTFSGHMKNISA  395 (771)
T ss_pred             CceEEEEECCCCCCchHHHHHHHHHHHHHHh----CCCccCCccccc-cchhheeeecChHhHHhhhhhHHHHHHHHHHH
Confidence            34789999999999999999997662 1111    112211110000 0011111111110000    000111122223


Q ss_pred             HHhC-CCeEEEEEeCCCCCcccc---cc----cCCCCCCCCCcEEEEEecchhhhhhcCCCcc--eEecCCCCHHHHHHH
Q 042806          249 RLKK-EKTILVILDNIWGNLDFQ---AV----GIPHGDDRKGCKVLLTARSLDVLSRKMDSQQ--NFSVGVLKEDEAWSL  318 (390)
Q Consensus       249 ~l~~-~~~~LlVlDdv~~~~~~~---~l----~~~l~~~~~~s~IivTtr~~~v~~~~~~~~~--~~~l~~L~~~ea~~l  318 (390)
                      .+.. ..+-|+++|..-...+..   .+    ...+  ...|+.+|+||....+.........  ...+. ++. +... 
T Consensus       396 il~~~~~~sLvLlDE~g~GtD~~eg~ala~aiLe~l--~~~g~~viitTH~~eL~~~~~~~~~v~~~~~~-~d~-~~l~-  470 (771)
T TIGR01069       396 ILSKTTENSLVLFDELGAGTDPDEGSALAISILEYL--LKQNAQVLITTHYKELKALMYNNEGVENASVL-FDE-ETLS-  470 (771)
T ss_pred             HHHhcCCCcEEEecCCCCCCCHHHHHHHHHHHHHHH--HhcCCEEEEECChHHHHHHhcCCCCeEEeEEE-EcC-CCCc-
Confidence            3322 234899999987543211   12    1122  2357889999998766432221111  11111 111 1111 


Q ss_pred             HHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhcCCCCCCCcccchhHHHHHhhhh
Q 042806          319 FKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQLTL  380 (390)
Q Consensus       319 f~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~~~~~~~~~w~~~~~~l~~~~  380 (390)
                      |...+-...+.   ...+-+|++++ |+|-.|..-|..+....    ...++++...|....
T Consensus       471 p~Ykl~~G~~g---~S~a~~iA~~~-Glp~~ii~~A~~~~~~~----~~~~~~li~~L~~~~  524 (771)
T TIGR01069       471 PTYKLLKGIPG---ESYAFEIAQRY-GIPHFIIEQAKTFYGEF----KEEINVLIEKLSALE  524 (771)
T ss_pred             eEEEECCCCCC---CcHHHHHHHHh-CcCHHHHHHHHHHHHhh----HHHHHHHHHHHHHHH
Confidence            11111111111   23466788777 79998888888776543    456666666665543

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=96.36  E-value=0.013  Score=56.76  Aligned_cols=87  Identities=16%  Similarity=0.278  Sum_probs=53.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCC-------CCCCCchH----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLT-------LHEESDSG----  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~-------~~~~~~~~----  241 (390)
                      ....++|.|+.|+|||||++.+.....    .+.+++..++... ...++...+...-+..       ..+.+...    
T Consensus       161 ~GqrigI~G~sG~GKSTLL~~I~~~~~----~dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a  236 (444)
T PRK08972        161 KGQRMGLFAGSGVGKSVLLGMMTRGTT----ADVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKG  236 (444)
T ss_pred             CCCEEEEECCCCCChhHHHHHhccCCC----CCEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHH
Confidence            456789999999999999999986432    4566667776543 3455666654432211       11111111    


Q ss_pred             --HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          242 --RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       242 --~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                        ....+.+++. .++.+|+++||+.
T Consensus       237 ~~~A~tiAEyfrd~G~~VLl~~DslT  262 (444)
T PRK08972        237 CETATTIAEYFRDQGLNVLLLMDSLT  262 (444)
T ss_pred             HHHHHHHHHHHHHcCCCEEEEEcChH
Confidence              2234555553 3566999999985

>PF13245 AAA_19: Part of AAA domain

Probab=96.36  E-value=0.011  Score=42.62  Aligned_cols=26  Identities=19%  Similarity=0.109  Sum_probs=18.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +.+++.|.|++|.|||+++.......
T Consensus         9 ~~~~~vv~g~pGtGKT~~~~~~i~~l   34 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTTLAARIAEL   34 (76)
T ss_pred             hCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            45678889999999995555544443

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.35  E-value=0.04  Score=49.03  Aligned_cols=48  Identities=23%  Similarity=0.224  Sum_probs=33.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      ...++.|.|++|+|||||+.++....-.+  -...+|++...  +.+++...
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~~--g~~~~~is~e~--~~~~i~~~   66 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLRD--GDPVIYVTTEE--SRESIIRQ   66 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHhc--CCeEEEEEccC--CHHHHHHH
Confidence            45789999999999999999987654322  34567777643  44454433

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

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.29  E-value=0.036  Score=50.68  Aligned_cols=39  Identities=23%  Similarity=0.306  Sum_probs=29.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS  214 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~  214 (390)
                      +.+++.++|++|+||||++..++...... . ..+..++..
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~~l~~~-g-~~V~li~~D  109 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLANKLKKQ-G-KSVLLAAGD  109 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhc-C-CEEEEEeCC
Confidence            46789999999999999999998877543 2 245555554

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=96.29  E-value=0.0021  Score=67.36  Aligned_cols=190  Identities=22%  Similarity=0.177  Sum_probs=89.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC----CchHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE----SDSGRARSLRNR  249 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~----~~~~~~~~l~~~  249 (390)
                      +.+++.|+|+.+.||||+.+.+.-..--   ..+.++|.+.... .-.++..|+..++....-.    .-......+...
T Consensus       326 ~~~~~iITGpN~gGKTt~lktigl~~~m---aq~G~~vpa~~~~-~i~~~~~i~~~ig~~~si~~~lStfS~~m~~~~~I  401 (782)
T PRK00409        326 DKTVLVITGPNTGGKTVTLKTLGLAALM---AKSGLPIPANEPS-EIPVFKEIFADIGDEQSIEQSLSTFSGHMTNIVRI  401 (782)
T ss_pred             CceEEEEECCCCCCcHHHHHHHHHHHHH---HHhCCCcccCCCc-cccccceEEEecCCccchhhchhHHHHHHHHHHHH
Confidence            4578899999999999999998654210   1111222222110 0001111111111110000    001111222222


Q ss_pred             HhC-CCeEEEEEeCCCCCcccc---cc----cCCCCCCCCCcEEEEEecchhhhhhcCCCcc--eEecCCCCHHHHHHHH
Q 042806          250 LKK-EKTILVILDNIWGNLDFQ---AV----GIPHGDDRKGCKVLLTARSLDVLSRKMDSQQ--NFSVGVLKEDEAWSLF  319 (390)
Q Consensus       250 l~~-~~~~LlVlDdv~~~~~~~---~l----~~~l~~~~~~s~IivTtr~~~v~~~~~~~~~--~~~l~~L~~~ea~~lf  319 (390)
                      +.. ..+-|+++|..-...+..   .+    ...+  ...|+.+|+||....+.........  ...+. ++. +.....
T Consensus       402 l~~~~~~sLvLlDE~~~GtDp~eg~ala~aile~l--~~~~~~vIitTH~~el~~~~~~~~~v~~~~~~-~d~-~~l~~~  477 (782)
T PRK00409        402 LEKADKNSLVLFDELGAGTDPDEGAALAISILEYL--RKRGAKIIATTHYKELKALMYNREGVENASVE-FDE-ETLRPT  477 (782)
T ss_pred             HHhCCcCcEEEecCCCCCCCHHHHHHHHHHHHHHH--HHCCCEEEEECChHHHHHHHhcCCCeEEEEEE-Eec-CcCcEE
Confidence            221 234799999987543321   12    1122  2347889999998776543222111  11111 111 111110


Q ss_pred             HHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhcCCCCCCCcccchhHHHHHhhhh
Q 042806          320 KKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQLTL  380 (390)
Q Consensus       320 ~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~~~~~~~~~w~~~~~~l~~~~  380 (390)
                      .+...+...    ...|-+|++++ |+|-.|..-|.-+-...    ....+++...|....
T Consensus       478 Ykl~~G~~g----~S~a~~iA~~~-Glp~~ii~~A~~~~~~~----~~~~~~li~~l~~~~  529 (782)
T PRK00409        478 YRLLIGIPG----KSNAFEIAKRL-GLPENIIEEAKKLIGED----KEKLNELIASLEELE  529 (782)
T ss_pred             EEEeeCCCC----CcHHHHHHHHh-CcCHHHHHHHHHHHhhh----hhHHHHHHHHHHHHH
Confidence            111112111    23466788877 78988888887776554    456666666666543

>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=96.28  E-value=0.0046  Score=49.12  Aligned_cols=40  Identities=30%  Similarity=0.346  Sum_probs=22.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKI  222 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l  222 (390)
                      +.|+|.+|+||||+|+.+.......  |..   |.+.....+.++
T Consensus         2 vLleg~PG~GKT~la~~lA~~~~~~--f~R---Iq~tpdllPsDi   41 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARSLGLS--FKR---IQFTPDLLPSDI   41 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHHTT----EEE---EE--TT--HHHH
T ss_pred             EeeECCCccHHHHHHHHHHHHcCCc--eeE---EEecCCCCcccc
Confidence            5789999999999999999987643  643   333444444443

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.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=96.27  E-value=0.012  Score=56.46  Aligned_cols=39  Identities=18%  Similarity=0.272  Sum_probs=31.8

Q ss_pred             HHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          163 LNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       163 ~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ++.+++.+...+...+.|.|+||.|||+|.+.+.+..+.
T Consensus        10 ~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~~   48 (364)
T PF05970_consen   10 FDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYLRS   48 (364)
T ss_pred             HHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHhcc
Confidence            455566666667788999999999999999999988765

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.27  E-value=0.0079  Score=48.45  Aligned_cols=29  Identities=21%  Similarity=0.085  Sum_probs=25.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      ...+|.+.|.-|+|||||++.++......
T Consensus        21 ~~~~i~l~G~lGaGKTtl~~~l~~~lg~~   49 (133)
T TIGR00150        21 FGTVVLLKGDLGAGKTTLVQGLLQGLGIQ   49 (133)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHcCCC
Confidence            34689999999999999999999987643

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.

>PF05659 RPW8: Arabidopsis broad-spectrum mildew resistance protein RPW8; InterPro: IPR008808 This entry represents the RPW8 domain found in several broad-spectrum mildew resistance proteins from Arabidopsis thaliana and other dicots

Probab=96.27  E-value=0.06  Score=44.16  Aligned_cols=110  Identities=11%  Similarity=0.117  Sum_probs=73.1

Q ss_pred             hhhH-HHHHHHHHhhhhhhhhhhhchhhhhhhhHhHHHHHHHHhchHHHHHHHHHHHHHHHhccccchHHHHHHHHHHHH
Q 042806            2 ADII-LSVVVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRGEEIEEYVEKWLTSVNG   80 (390)
Q Consensus         2 a~~~-~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~i~~~l~~a~~~~~~~~~~~~~wl~~l~~   80 (390)
                      ||.+ .+|+|.+++.++..+........  .++.-++.+...++.|.....+|..+-       ...+...+.=++++.+
T Consensus         3 ~eL~~gaalG~~~~eLlk~v~~~~~k~~--~fk~~l~~L~sTl~~i~P~i~eI~~~~-------~eld~~~~ee~e~L~~   73 (147)
T PF05659_consen    3 AELVGGAALGAVFGELLKAVIDASKKSL--SFKSILKRLESTLESIIPIIKEIDKLN-------VELDRPRQEEIERLKE   73 (147)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH--hhhhHHHHHHHHHHHhhhHHHHHHHHh-------hhcCCchhHHHHHHHH
Confidence            4444 44777777888777777776666  667666677777777766655555542       2333333555678888


Q ss_pred             HHHHHHHhhhhhhhhccccccCcCCChhHHhhHHHHHHHHHHHHHHH
Q 042806           81 IIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQKEAIVKV  127 (390)
Q Consensus        81 ~~~d~ed~ld~~~~~~~~~~~~~~~~~~~r~~~~~~i~~~~~~l~~~  127 (390)
                      ...+++++++.+....       +.++...++++++|+++...+...
T Consensus        74 ~L~~g~~LV~k~sk~~-------r~n~~kk~~y~~Ki~~le~~l~~f  113 (147)
T PF05659_consen   74 LLEKGKELVEKCSKVR-------RWNLYKKPRYARKIEELEESLRRF  113 (147)
T ss_pred             HHHHHHHHHHHhcccc-------HHHHHhhHhHHHHHHHHHHHHHHH
Confidence            8888888887653322       234666777899999998887665

Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The R protein-mediated defences typically involve a rapid, localized necrosis, or hypersensitive response (HR), at the site of infection, and the localised formation of antimicrobial chemicals and proteins that restrict growth of the pathogen. The A. thaliana locus Resistance to Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes: RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance [, ]. RPW8.1 and RPW8.2 share similarity with an ~150 amino acid module forming the N terminus of a group of disease resistance proteins, which have a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) [, ]. The RPW8 domain sequences contain a predicted N-terminal transmembrane (TM) region or possibly a signal peptide, and a coiled-coil (CC) motif [].

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=96.26  E-value=0.019  Score=53.51  Aligned_cols=63  Identities=16%  Similarity=0.125  Sum_probs=43.2

Q ss_pred             cccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 042806          155 ACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQG  224 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~  224 (390)
                      .|+=.......++.++..+  +-|.|.|++|+||||+++.++......     .+.|.++...+..+++.
T Consensus        46 ~y~f~~~~~~~vl~~l~~~--~~ilL~G~pGtGKTtla~~lA~~l~~~-----~~rV~~~~~l~~~DliG  108 (327)
T TIGR01650        46 AYLFDKATTKAICAGFAYD--RRVMVQGYHGTGKSTHIEQIAARLNWP-----CVRVNLDSHVSRIDLVG  108 (327)
T ss_pred             CccCCHHHHHHHHHHHhcC--CcEEEEeCCCChHHHHHHHHHHHHCCC-----eEEEEecCCCChhhcCC
Confidence            4444445556677777543  458899999999999999999988632     34566666555555443

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.

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=96.25  E-value=0.11  Score=47.74  Aligned_cols=131  Identities=11%  Similarity=0.009  Sum_probs=69.0

Q ss_pred             HHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhc------------CCCCeEEEEEeCCC--CCHHHHHHHHH
Q 042806          163 LNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETE------------KLFDQVIFVEVSKI--QDIRKIQGEIA  227 (390)
Q Consensus       163 ~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~------------~~f~~~~wv~v~~~--~~~~~l~~~i~  227 (390)
                      -..|...+..++ .....++|+.|+||+++|..+....--.            .|.|..........  ..++++ +++.
T Consensus         6 ~~~L~~~i~~~rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~~~~I~idqi-R~l~   84 (290)
T PRK05917          6 WEALIQRVRDQKVPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGKGRLHSIETP-RAIK   84 (290)
T ss_pred             HHHHHHHHHcCCcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCCCCcCcHHHH-HHHH
Confidence            356667776665 4678899999999999999988775321            13332211111110  122221 2222


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecc-hhhhhhcCCCcce
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARS-LDVLSRKMDSQQN  304 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~-~~v~~~~~~~~~~  304 (390)
                      +.+...+.                .++.=++|+|+++..  ..++.+...+-.-.+++.+|++|.+ ..+.+...+-...
T Consensus        85 ~~~~~~p~----------------e~~~kv~ii~~ad~mt~~AaNaLLK~LEEPp~~~~fiL~~~~~~~ll~TI~SRcq~  148 (290)
T PRK05917         85 KQIWIHPY----------------ESPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTIRSRSLS  148 (290)
T ss_pred             HHHhhCcc----------------CCCceEEEEechhhcCHHHHHHHHHHhhcCCCCeEEEEEeCChhhCcHHHHhcceE
Confidence            22221111                123258899999754  4556665555444456666666665 4443332333345


Q ss_pred             EecCCC
Q 042806          305 FSVGVL  310 (390)
Q Consensus       305 ~~l~~L  310 (390)
                      +.+.++
T Consensus       149 ~~~~~~  154 (290)
T PRK05917        149 IHIPME  154 (290)
T ss_pred             EEccch
Confidence            556544

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=96.25  E-value=0.0095  Score=60.76  Aligned_cols=78  Identities=14%  Similarity=0.095  Sum_probs=57.9

Q ss_pred             cCcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          151 KDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ...+.++|.+..+..|...+...  +.+.++|++|+||||+++.+.+.... ..++..+|+.- ...+..++++.+...+
T Consensus        28 ~~~~~vigq~~a~~~L~~~~~~~--~~~l~~G~~G~GKttla~~l~~~l~~-~~~~~~~~~~n-p~~~~~~~~~~v~~~~  103 (637)
T PRK13765         28 RLIDQVIGQEHAVEVIKKAAKQR--RHVMMIGSPGTGKSMLAKAMAELLPK-EELQDILVYPN-PEDPNNPKIRTVPAGK  103 (637)
T ss_pred             ccHHHcCChHHHHHHHHHHHHhC--CeEEEECCCCCcHHHHHHHHHHHcCh-HhHHHheEeeC-CCcchHHHHHHHHHhc
Confidence            34567889888888887777654  46889999999999999999987643 33566777655 4446777777777666


Q ss_pred             CC
Q 042806          231 GL  232 (390)
Q Consensus       231 ~~  232 (390)
                      |.
T Consensus       104 G~  105 (637)
T PRK13765        104 GK  105 (637)
T ss_pred             CH
Confidence            53

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

Probab=96.25  E-value=0.031  Score=56.04  Aligned_cols=173  Identities=22%  Similarity=0.239  Sum_probs=90.7

Q ss_pred             cccchh---HHHHHHHHHhcCCC---------ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHH
Q 042806          155 ACESRM---STLNDILDALKNPD---------VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKI  222 (390)
Q Consensus       155 ~~~gR~---~~~~~l~~~L~~~~---------~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l  222 (390)
                      +.-|.+   +++.++++.|.++.         ++=+.++||+|.|||.||+.+..+..+.  |     .+.|...-+   
T Consensus       151 DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~VP--F-----f~iSGS~FV---  220 (596)
T COG0465         151 DVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVP--F-----FSISGSDFV---  220 (596)
T ss_pred             hhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCCC--c-----eeccchhhh---
Confidence            455654   45667777777653         4668899999999999999999988764  2     222222111   


Q ss_pred             HHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc------------c----cccccCCCCC--CCCCcE
Q 042806          223 QGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL------------D----FQAVGIPHGD--DRKGCK  284 (390)
Q Consensus       223 ~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~------------~----~~~l~~~l~~--~~~~s~  284 (390)
                        ++.-.        -....+..+...-+..-||++++|.++...            .    +..+......  .+.|..
T Consensus       221 --emfVG--------vGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~~~gvi  290 (596)
T COG0465         221 --EMFVG--------VGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNEGVI  290 (596)
T ss_pred             --hhhcC--------CCcHHHHHHHHHhhccCCCeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhccCCCCCceE
Confidence              01000        011233344443334446999999986331            1    2222222211  123444


Q ss_pred             EEEEecchhhh-hhc---CCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHH
Q 042806          285 VLLTARSLDVL-SRK---MDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVS  349 (390)
Q Consensus       285 IivTtr~~~v~-~~~---~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLa  349 (390)
                      |+..|...++. +..   -.-.+.+.++.-+-..-.+++.-++......+...  ...|++.+-|.-.|
T Consensus       291 viaaTNRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~~~Vd--l~~iAr~tpGfsGA  357 (596)
T COG0465         291 VIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVD--LKKIARGTPGFSGA  357 (596)
T ss_pred             EEecCCCcccchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCCCcCC--HHHHhhhCCCcccc
Confidence            44444444443 111   12224666666665666677776664222222211  12488888777654

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

Probab=96.24  E-value=0.044  Score=50.11  Aligned_cols=51  Identities=16%  Similarity=0.118  Sum_probs=35.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      ..++.|.|++|+||||++.++........ =..++|++...  +..++...+..
T Consensus        30 g~~~~i~g~~G~GKT~l~~~~~~~~~~~~-g~~vl~iS~E~--~~~~~~~r~~~   80 (271)
T cd01122          30 GELIILTAGTGVGKTTFLREYALDLITQH-GVRVGTISLEE--PVVRTARRLLG   80 (271)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHHhc-CceEEEEEccc--CHHHHHHHHHH
Confidence            45888999999999999999987764321 13477776654  44555555543

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

>PTZ00088 adenylate kinase 1; Provisional

Probab=96.24  E-value=0.0039  Score=55.41  Aligned_cols=23  Identities=26%  Similarity=0.512  Sum_probs=21.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.|.|++|+||||+|+.+.+...
T Consensus         9 Ivl~G~PGsGK~T~a~~La~~~g   31 (229)
T PTZ00088          9 IVLFGAPGVGKGTFAEILSKKEN   31 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            88999999999999999988764

>PRK04040 adenylate kinase; Provisional

Probab=96.24  E-value=0.0042  Score=53.51  Aligned_cols=47  Identities=23%  Similarity=0.370  Sum_probs=32.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGL  232 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~  232 (390)
                      ..+|+|+|++|+||||+++.+......  .+..   +      +..+++..++...+.
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~~l~~--~~~~---~------~~g~~~~~~a~~~g~   48 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALEKLKE--DYKI---V------NFGDVMLEVAKEEGL   48 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHhcc--CCeE---E------ecchHHHHHHHHcCC
Confidence            357999999999999999999988741  1332   2      224555666666554

>PRK06217 hypothetical protein; Validated

Probab=96.24  E-value=0.023  Score=48.73  Aligned_cols=25  Identities=28%  Similarity=0.361  Sum_probs=22.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      -|.|.|.+|+||||+++.+......
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~   27 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDI   27 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCC
Confidence            4889999999999999999988753

>PRK00131 aroK shikimate kinase; Reviewed

Probab=96.24  E-value=0.0047  Score=52.27  Aligned_cols=27  Identities=19%  Similarity=0.260  Sum_probs=23.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +...|.|+|++|+||||+++.+.....
T Consensus         3 ~~~~i~l~G~~GsGKstla~~La~~l~   29 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGRLLAKRLG   29 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHHHHHHHhC
Confidence            456899999999999999999999874

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.24  E-value=0.015  Score=49.59  Aligned_cols=26  Identities=19%  Similarity=0.250  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+|||||++.+.-..
T Consensus        27 ~Ge~~~i~G~nGsGKStLl~~l~G~~   52 (178)
T cd03247          27 QGEKIALLGRSGSGKSTLLQLLTGDL   52 (178)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccC
Confidence            45689999999999999999997764

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.

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=96.23  E-value=0.011  Score=53.34  Aligned_cols=25  Identities=32%  Similarity=0.565  Sum_probs=22.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +|.+.|.+|+||||+|+.+......
T Consensus         1 LIvl~G~pGSGKST~a~~La~~l~~   25 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKKLSE   25 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            3789999999999999999988754

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>PRK03839 putative kinase; Provisional

Probab=96.21  E-value=0.0043  Score=53.03  Aligned_cols=24  Identities=38%  Similarity=0.501  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .|.|.|++|+||||+++.+++...
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~~   25 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKLG   25 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            488999999999999999999874

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=96.21  E-value=0.73  Score=44.31  Aligned_cols=58  Identities=19%  Similarity=0.207  Sum_probs=38.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC-CCCCHHHHHHHHHHHhCCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS-KIQDIRKIQGEIADKLGLT  233 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~-~~~~~~~l~~~i~~~l~~~  233 (390)
                      .+.+|..+|.-|+||||.+..+++..+. ..+... -|++. ..+..-+=++.++.+.+.+
T Consensus        99 ~P~vImmvGLQGsGKTTt~~KLA~~lkk-~~~kvl-lVaaD~~RpAA~eQL~~La~q~~v~  157 (451)
T COG0541          99 PPTVILMVGLQGSGKTTTAGKLAKYLKK-KGKKVL-LVAADTYRPAAIEQLKQLAEQVGVP  157 (451)
T ss_pred             CCeEEEEEeccCCChHhHHHHHHHHHHH-cCCceE-EEecccCChHHHHHHHHHHHHcCCc
Confidence            4678999999999999999999998876 334332 22222 2333444456666666543

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=96.21  E-value=0.05  Score=48.75  Aligned_cols=51  Identities=14%  Similarity=0.164  Sum_probs=34.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      ...++.|.|++|+|||+++.+++...-..... .++|++...  +..++...+.
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~-~vly~s~E~--~~~~~~~r~~   62 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALNIAENIAKKQGK-PVLFFSLEM--SKEQLLQRLL   62 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCC-ceEEEeCCC--CHHHHHHHHH
Confidence            34688999999999999999998776543122 356655543  4555555553

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

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=96.20  E-value=0.0062  Score=54.31  Aligned_cols=60  Identities=20%  Similarity=0.235  Sum_probs=40.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC---------CCCCHHHH--HHHHHHHhCCCCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS---------KIQDIRKI--QGEIADKLGLTLH  235 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~---------~~~~~~~l--~~~i~~~l~~~~~  235 (390)
                      ++..|.++||+|+||||.++.++.....+...  ..-|+..         ...++++.  +++++++.+..+.
T Consensus        18 ~p~~ilVvGMAGSGKTTF~QrL~~hl~~~~~p--pYviNLDPAv~~vpy~aniDIRDtVkYkEvMkqY~LGPN   88 (366)
T KOG1532|consen   18 RPVIILVVGMAGSGKTTFMQRLNSHLHAKKTP--PYVINLDPAVRNVPYPANIDIRDTVKYKEVMKQYQLGPN   88 (366)
T ss_pred             CCcEEEEEecCCCCchhHHHHHHHHHhhccCC--CeEEeCCHHHhcCCCccCCchhhhhhHHHHHHHhCCCCC
Confidence            46678899999999999999999998765322  2222222         22345554  4577887765544

>PLN02924 thymidylate kinase

Probab=96.18  E-value=0.029  Score=49.61  Aligned_cols=53  Identities=6%  Similarity=0.014  Sum_probs=34.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      ...|+|-|..|+||||+++.+.+..... ++....+-.-+......+.++.++.
T Consensus        16 g~~IviEGiDGsGKsTq~~~L~~~l~~~-g~~v~~~~ep~~~~~~g~~ir~~l~   68 (220)
T PLN02924         16 GALIVLEGLDRSGKSTQCAKLVSFLKGL-GVAAELWRFPDRTTSVGQMISAYLS   68 (220)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc-CCCceeeeCCCCCChHHHHHHHHHh
Confidence            4689999999999999999999998764 3544333222222334444555443

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=96.17  E-value=0.011  Score=52.65  Aligned_cols=61  Identities=21%  Similarity=0.196  Sum_probs=37.8

Q ss_pred             HHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHH
Q 042806          163 LNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQ  223 (390)
Q Consensus       163 ~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~  223 (390)
                      ..++++.+..  ++..+|+|.|++|+||+||+-.+......+++=-.++-|.-|.+++--.++
T Consensus        15 ~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~~~~~~g~~VaVlAVDPSSp~tGGAlL   77 (266)
T PF03308_consen   15 ARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIRELRERGKRVAVLAVDPSSPFTGGALL   77 (266)
T ss_dssp             HHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHHHHHHTT--EEEEEE-GGGGCC---SS
T ss_pred             HHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHHHHhhcCCceEEEEECCCCCCCCCccc
Confidence            3455555543  467899999999999999999999988765333345555555566554443

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=96.17  E-value=0.023  Score=55.17  Aligned_cols=87  Identities=17%  Similarity=0.286  Sum_probs=53.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCC-------CCCCCchH----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLT-------LHEESDSG----  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~-------~~~~~~~~----  241 (390)
                      +...++|+|..|+|||||++.+.....    .+..++..++... ...++....+..-+..       ..+.+...    
T Consensus       157 ~Gqri~I~G~sG~GKTtLL~~I~~~~~----~d~~v~~~iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~a  232 (442)
T PRK08927        157 RGQRMGIFAGSGVGKSVLLSMLARNAD----ADVSVIGLIGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQA  232 (442)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhccC----CCEEEEEEEecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHHH
Confidence            457889999999999999999887653    3456666666543 3445554444332211       11111111    


Q ss_pred             --HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          242 --RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       242 --~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                        ....+.+++. .++.+|+++||+.
T Consensus       233 ~~~a~tiAEyfrd~G~~Vll~~DslT  258 (442)
T PRK08927        233 AYLTLAIAEYFRDQGKDVLCLMDSVT  258 (442)
T ss_pred             HHHHHHHHHHHHHCCCcEEEEEeCcH
Confidence              2234556663 3566999999984

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=96.16  E-value=0.014  Score=55.48  Aligned_cols=112  Identities=11%  Similarity=0.046  Sum_probs=58.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      ....+.|.|+.|+||||+++.+......  +....++. +..+.  +-........+...............+...|+. 
T Consensus       121 ~~g~ili~G~tGSGKTT~l~al~~~i~~--~~~~~i~t-iEdp~--E~~~~~~~~~i~q~evg~~~~~~~~~l~~~lr~-  194 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLASMIDYINK--NAAGHIIT-IEDPI--EYVHRNKRSLINQREVGLDTLSFANALRAALRE-  194 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHhhCc--CCCCEEEE-EcCCh--hhhccCccceEEccccCCCCcCHHHHHHHhhcc-
Confidence            3578999999999999999998876542  23334433 22211  111000000000000011112234445555654 


Q ss_pred             CeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhh
Q 042806          254 KTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDV  294 (390)
Q Consensus       254 ~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v  294 (390)
                      .+=+|++|.+.+.+.+......   ...|..++.|....+.
T Consensus       195 ~pd~i~vgEird~~~~~~~l~a---a~tGh~v~~T~Ha~~~  232 (343)
T TIGR01420       195 DPDVILIGEMRDLETVELALTA---AETGHLVFGTLHTNSA  232 (343)
T ss_pred             CCCEEEEeCCCCHHHHHHHHHH---HHcCCcEEEEEcCCCH
Confidence            4479999999876655442222   2345567777776444

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.

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=96.16  E-value=0.017  Score=58.98  Aligned_cols=76  Identities=17%  Similarity=0.134  Sum_probs=52.0

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGL  232 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~  232 (390)
                      ...++|+++.+..+...+...  +.+.++|++|+||||+++.+.+..... .|...+++. ....+..++++.++..++.
T Consensus        17 ~~~viG~~~a~~~l~~a~~~~--~~~ll~G~pG~GKT~la~~la~~l~~~-~~~~~~~~~-n~~~~~~~~~~~v~~~~g~   92 (608)
T TIGR00764        17 IDQVIGQEEAVEIIKKAAKQK--RNVLLIGEPGVGKSMLAKAMAELLPDE-ELEDILVYP-NPEDPNMPRIVEVPAGEGR   92 (608)
T ss_pred             HhhccCHHHHHHHHHHHHHcC--CCEEEECCCCCCHHHHHHHHHHHcCch-hheeEEEEe-CCCCCchHHHHHHHHhhch
Confidence            456788888887777766654  356699999999999999999887543 333333332 3333556667777666653

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

>PRK00279 adk adenylate kinase; Reviewed

Probab=96.15  E-value=0.02  Score=50.52  Aligned_cols=24  Identities=38%  Similarity=0.231  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .|.|+|++|+||||+++.+.....
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~~   25 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKYG   25 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            378999999999999999987653

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.15  E-value=0.02  Score=51.39  Aligned_cols=120  Identities=23%  Similarity=0.246  Sum_probs=64.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-----CCCHHHHHHHHHHHhCCCCCC-------CCchH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-----IQDIRKIQGEIADKLGLTLHE-------ESDSG  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-----~~~~~~l~~~i~~~l~~~~~~-------~~~~~  241 (390)
                      +..+++|+|++|+|||||++.+..-...   -.+.+++.-.+     .....+-..+++..++...+.       .+-.+
T Consensus        38 ~ge~~glVGESG~GKSTlgr~i~~L~~p---t~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQ  114 (268)
T COG4608          38 EGETLGLVGESGCGKSTLGRLILGLEEP---TSGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQ  114 (268)
T ss_pred             CCCEEEEEecCCCCHHHHHHHHHcCcCC---CCceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchh
Confidence            4678999999999999999999876542   22334433221     112334455666666643221       12222


Q ss_pred             HHHH-HHHHHhCCCeEEEEEeCCCCCccc---ccccCCCC--CCCCCcEEEEEecchhhhhh
Q 042806          242 RARS-LRNRLKKEKTILVILDNIWGNLDF---QAVGIPHG--DDRKGCKVLLTARSLDVLSR  297 (390)
Q Consensus       242 ~~~~-l~~~l~~~~~~LlVlDdv~~~~~~---~~l~~~l~--~~~~~s~IivTtr~~~v~~~  297 (390)
                      ...- +...|. .++=++|.|..-+..+.   ..+...+.  ....|...+..|.+-.+..+
T Consensus       115 rQRi~IARALa-l~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~~~~lt~lFIsHDL~vv~~  175 (268)
T COG4608         115 RQRIGIARALA-LNPKLIVADEPVSALDVSVQAQILNLLKDLQEELGLTYLFISHDLSVVRY  175 (268)
T ss_pred             hhhHHHHHHHh-hCCcEEEecCchhhcchhHHHHHHHHHHHHHHHhCCeEEEEEEEHHhhhh
Confidence            2222 223333 34579999987654221   11111110  11235567777777666543

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=96.15  E-value=0.0088  Score=54.21  Aligned_cols=62  Identities=26%  Similarity=0.317  Sum_probs=46.5

Q ss_pred             HHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          164 NDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       164 ~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      .+|+..+..  ++..+|+|.|.+|+||+||.-.+......+++--.++-|.-|.+++--.++..
T Consensus        38 ~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~rVaVlAVDPSSp~TGGsiLGD  101 (323)
T COG1703          38 RELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSSPFTGGSILGD  101 (323)
T ss_pred             HHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHHHHCCcEEEEEEECCCCCCCCcccccc
Confidence            345555543  56789999999999999999999999877665556666777777776666543

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=96.15  E-value=0.0075  Score=51.73  Aligned_cols=37  Identities=24%  Similarity=0.296  Sum_probs=29.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEe
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEV  213 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v  213 (390)
                      .++|.|+|+.|+|||||++.+.......  |...+..+-
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~~~~~--~~~~v~~TT   38 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQEFPDK--FGRVVSHTT   38 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHHSTTT--EEEEEEEES
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcccc--cccceeecc
Confidence            4789999999999999999999987643  754444433

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>PRK14531 adenylate kinase; Provisional

Probab=96.14  E-value=0.015  Score=49.80  Aligned_cols=24  Identities=25%  Similarity=0.128  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .|.|+|++|+||||+++.+.....
T Consensus         4 ~i~i~G~pGsGKsT~~~~la~~~g   27 (183)
T PRK14531          4 RLLFLGPPGAGKGTQAARLCAAHG   27 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            488999999999999999988764

>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=96.13  E-value=0.009  Score=51.90  Aligned_cols=125  Identities=19%  Similarity=0.193  Sum_probs=61.5

Q ss_pred             hhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC------CCHHH-------HHHH
Q 042806          159 RMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI------QDIRK-------IQGE  225 (390)
Q Consensus       159 R~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~------~~~~~-------l~~~  225 (390)
                      +..+....++.|.  +..++.+.|++|.|||.||....-+.-..+.|+.++++.-.-.      +-+.+       .+.-
T Consensus         5 ~~~~Q~~~~~al~--~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~p   82 (205)
T PF02562_consen    5 KNEEQKFALDALL--NNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLRP   82 (205)
T ss_dssp             -SHHHHHHHHHHH--H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHH
T ss_pred             CCHHHHHHHHHHH--hCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHHHH
Confidence            4445556666666  4568999999999999999999887655577888777632211      00111       1122


Q ss_pred             HHHHhCCCCCCCCchHHHHHHHH----------HHhCCC---eEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEec
Q 042806          226 IADKLGLTLHEESDSGRARSLRN----------RLKKEK---TILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTAR  290 (390)
Q Consensus       226 i~~~l~~~~~~~~~~~~~~~l~~----------~l~~~~---~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr  290 (390)
                      +.+.+..-....    ....+.+          +++ ++   ..+||+|++++.  ..+..+.-.   .+.+|++|++.-
T Consensus        83 ~~d~l~~~~~~~----~~~~~~~~~~Ie~~~~~~iR-Grt~~~~~iIvDEaQN~t~~~~k~ilTR---~g~~skii~~GD  154 (205)
T PF02562_consen   83 IYDALEELFGKE----KLEELIQNGKIEIEPLAFIR-GRTFDNAFIIVDEAQNLTPEELKMILTR---IGEGSKIIITGD  154 (205)
T ss_dssp             HHHHHTTTS-TT----CHHHHHHTTSEEEEEGGGGT-T--B-SEEEEE-SGGG--HHHHHHHHTT---B-TT-EEEEEE-
T ss_pred             HHHHHHHHhChH----hHHHHhhcCeEEEEehhhhc-CccccceEEEEecccCCCHHHHHHHHcc---cCCCcEEEEecC
Confidence            222222211111    1111111          111 22   369999999765  345555333   467999999987


Q ss_pred             chh
Q 042806          291 SLD  293 (390)
Q Consensus       291 ~~~  293 (390)
                      ...
T Consensus       155 ~~Q  157 (205)
T PF02562_consen  155 PSQ  157 (205)
T ss_dssp             ---
T ss_pred             cee
Confidence            543

; GO: 0005524 ATP binding; PDB: 3B85_A.

>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=96.11  E-value=0.035  Score=47.46  Aligned_cols=117  Identities=22%  Similarity=0.262  Sum_probs=59.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC--CCCHHHHH------HHHHHHhCCCC------CCCCc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK--IQDIRKIQ------GEIADKLGLTL------HEESD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~--~~~~~~l~------~~i~~~l~~~~------~~~~~  239 (390)
                      +..+++|.|+.|+|||||++.+.-....   ..+.+++.-..  ..+.....      .+++..++...      ...+.
T Consensus        24 ~G~~~~l~G~nGsGKStLl~~i~G~~~~---~~G~v~~~g~~~~~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~  100 (180)
T cd03214          24 AGEIVGILGPNGAGKSTLLKTLAGLLKP---SSGEILLDGKDLASLSPKELARKIAYVPQALELLGLAHLADRPFNELSG  100 (180)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCCC---CCcEEEECCEECCcCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCH
Confidence            4568999999999999999999775432   34444442111  11222211      12344444321      11121


Q ss_pred             hHH-HHHHHHHHhCCCeEEEEEeCCCCCcc---cccccCCCCC-CCC-CcEEEEEecchhh
Q 042806          240 SGR-ARSLRNRLKKEKTILVILDNIWGNLD---FQAVGIPHGD-DRK-GCKVLLTARSLDV  294 (390)
Q Consensus       240 ~~~-~~~l~~~l~~~~~~LlVlDdv~~~~~---~~~l~~~l~~-~~~-~s~IivTtr~~~v  294 (390)
                      ... .-.+...+.. ++-++++|+-...-+   .+.+...+.. ... +..||++|.....
T Consensus       101 G~~qrl~laral~~-~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~~  160 (180)
T cd03214         101 GERQRVLLARALAQ-EPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLNL  160 (180)
T ss_pred             HHHHHHHHHHHHhc-CCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHH
Confidence            111 1223333433 336999998764422   2222222211 112 5678888887554

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.

>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=96.11  E-value=0.0053  Score=51.85  Aligned_cols=24  Identities=38%  Similarity=0.396  Sum_probs=20.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      |.|+|++|+|||||++.+++..+.
T Consensus         2 i~iTG~pG~GKTTll~k~i~~l~~   25 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEELKK   25 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHhhc
Confidence            679999999999999999998854

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.

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=96.11  E-value=0.018  Score=55.27  Aligned_cols=47  Identities=21%  Similarity=0.228  Sum_probs=35.3

Q ss_pred             cccchhHHHHHHHHHhcC--------------CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          155 ACESRMSTLNDILDALKN--------------PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~--------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .++|.++.+..+...+..              ..++-|.++|++|+|||++|+.+......
T Consensus        13 ~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~   73 (441)
T TIGR00390        13 YIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANA   73 (441)
T ss_pred             hccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            567777776666554442              12467889999999999999999998754

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.

>PRK01184 hypothetical protein; Provisional

Probab=96.10  E-value=0.039  Score=47.26  Aligned_cols=21  Identities=38%  Similarity=0.699  Sum_probs=17.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      .+|+|+|++|+||||+++ ++.
T Consensus         2 ~~i~l~G~~GsGKsT~a~-~~~   22 (184)
T PRK01184          2 KIIGVVGMPGSGKGEFSK-IAR   22 (184)
T ss_pred             cEEEEECCCCCCHHHHHH-HHH
Confidence            478999999999999987 444

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=96.10  E-value=0.0057  Score=53.24  Aligned_cols=28  Identities=39%  Similarity=0.499  Sum_probs=25.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ++.+|+|.|.+|+||||+|+.++...+.
T Consensus         7 ~~iiIgIaG~SgSGKTTva~~l~~~~~~   34 (218)
T COG0572           7 KVIIIGIAGGSGSGKTTVAKELSEQLGV   34 (218)
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHhCc
Confidence            4578999999999999999999998864

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=96.09  E-value=0.0039  Score=52.84  Aligned_cols=43  Identities=23%  Similarity=0.210  Sum_probs=32.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD  218 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  218 (390)
                      ..++.+.||.|+|||.||+.+...... +.....+-++.+....
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~~l~~-~~~~~~~~~d~s~~~~   45 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAELLFV-GSERPLIRIDMSEYSE   45 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHHHHT--SSCCEEEEEEGGGHCS
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHhcc-CCccchHHHhhhcccc
Confidence            357889999999999999999998863 1245566666665544

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 ....

>PRK14532 adenylate kinase; Provisional

Probab=96.09  E-value=0.024  Score=48.71  Aligned_cols=22  Identities=27%  Similarity=0.279  Sum_probs=19.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |.|.|++|+||||+++.+....
T Consensus         3 i~~~G~pGsGKsT~a~~la~~~   24 (188)
T PRK14532          3 LILFGPPAAGKGTQAKRLVEER   24 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7789999999999999998765

>PRK08149 ATP synthase SpaL; Validated

Probab=96.09  E-value=0.023  Score=54.99  Aligned_cols=87  Identities=14%  Similarity=0.202  Sum_probs=52.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCC-------CCCCCch-----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-IQDIRKIQGEIADKLGLT-------LHEESDS-----  240 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~l~~~i~~~l~~~-------~~~~~~~-----  240 (390)
                      +...++|+|++|+|||||++.++....    .+.+++..+.. .....++...........       ..+.+..     
T Consensus       150 ~Gq~i~I~G~sG~GKTTLl~~i~~~~~----~dv~v~g~Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~a  225 (428)
T PRK08149        150 VGQRMGIFASAGCGKTSLMNMLIEHSE----ADVFVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCNA  225 (428)
T ss_pred             cCCEEEEECCCCCChhHHHHHHhcCCC----CCeEEEEEEeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHhH
Confidence            456789999999999999998876542    34444444543 335556666665543211       1111111     


Q ss_pred             -HHHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          241 -GRARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       241 -~~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                       .....+.+++. .++++||++||+.
T Consensus       226 ~~~a~tiAE~fr~~G~~Vll~~DslT  251 (428)
T PRK08149        226 ALVATTVAEYFRDQGKRVVLFIDSMT  251 (428)
T ss_pred             HHHHHHHHHHHHHcCCCEEEEccchH
Confidence             12334555553 3566999999985

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=96.08  E-value=0.0055  Score=48.21  Aligned_cols=24  Identities=21%  Similarity=0.320  Sum_probs=20.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      |.|+|..|+|||||++.+......
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~~~   25 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGEFP   25 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS--
T ss_pred             EEEECcCCCCHHHHHHHHhcCCCc
Confidence            679999999999999999987543

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=96.07  E-value=0.0061  Score=51.86  Aligned_cols=26  Identities=12%  Similarity=0.151  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|.+.|++|+||||+|+.+.....
T Consensus         2 ~~~i~l~G~~gsGKst~a~~l~~~~~   27 (175)
T cd00227           2 GRIIILNGGSSAGKSSIARALQSVLA   27 (175)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhhC
Confidence            35899999999999999999988753

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=96.07  E-value=0.0055  Score=52.28  Aligned_cols=25  Identities=20%  Similarity=0.238  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+++|.|++|+|||||++.+.....
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~~   26 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARLA   26 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcC
Confidence            4789999999999999999988754

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=96.05  E-value=0.08  Score=54.78  Aligned_cols=47  Identities=13%  Similarity=0.194  Sum_probs=33.6

Q ss_pred             ccccchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          154 EACESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.++|....+.++.+.+..  ....-|.|+|+.|+||+++|+.+.+...
T Consensus       325 ~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~s~  373 (638)
T PRK11388        325 DHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNESE  373 (638)
T ss_pred             cceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHhCC
Confidence            3567777666666655542  2233477999999999999999988653

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

Probab=96.04  E-value=0.017  Score=51.09  Aligned_cols=52  Identities=17%  Similarity=0.089  Sum_probs=32.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh-----hcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE-----TEKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~-----~~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      +..|+|++|.||||++..+.....     ........+-++.........++..+..
T Consensus        19 ~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen   19 ITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             -EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            688999999999987777777761     1122444555566655566677766665

>PRK14528 adenylate kinase; Provisional

Probab=96.04  E-value=0.023  Score=48.83  Aligned_cols=25  Identities=24%  Similarity=0.177  Sum_probs=21.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.|.|.|++|+||||+++.+.....
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~~~   26 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCERLS   26 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4588999999999999999977653

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=96.04  E-value=0.016  Score=58.14  Aligned_cols=61  Identities=8%  Similarity=0.171  Sum_probs=43.0

Q ss_pred             ccccchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 042806          154 EACESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI  216 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  216 (390)
                      ..++|+...+.++.+.+..  ....-|.|+|+.|+|||++|+.+.+.....  -...+.|++...
T Consensus       187 ~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~--~~p~v~v~c~~~  249 (509)
T PRK05022        187 GEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRA--DKPLVYLNCAAL  249 (509)
T ss_pred             CceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCCcC--CCCeEEEEcccC
Confidence            4688888888777776653  334567799999999999999998875422  223455555543

>TIGR01351 adk adenylate kinases

Probab=96.03  E-value=0.027  Score=49.43  Aligned_cols=23  Identities=39%  Similarity=0.330  Sum_probs=20.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.|.|++|+||||+|+.+.....
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~g   24 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKYG   24 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcC
Confidence            67899999999999999987653

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=96.02  E-value=0.015  Score=50.92  Aligned_cols=41  Identities=24%  Similarity=0.407  Sum_probs=29.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD  218 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  218 (390)
                      .|+|+|-||+||||++..+....-.++.|+ +.-|....+++
T Consensus         2 kIaI~GKGG~GKTtiaalll~~l~~~~~~~-VLvVDaDpd~n   42 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKRLLSKGGYN-VLVVDADPDSN   42 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHHHHhcCCce-EEEEeCCCCCC
Confidence            589999999999999999777665544344 44455555544

>COG4240 Predicted kinase [General function prediction only]

Probab=96.02  E-value=0.05  Score=47.41  Aligned_cols=81  Identities=16%  Similarity=0.166  Sum_probs=51.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC-----CCCCCCCchHHHHHHH
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLG-----LTLHEESDSGRARSLR  247 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~-----~~~~~~~~~~~~~~l~  247 (390)
                      +++-+++|.|+.|+||||++..+++....++. ..+...++..-+-...-.-.++++..     ...+...+..+...+.
T Consensus        48 grPli~gisGpQGSGKStls~~i~~~L~~kg~-ert~~lSLDDlYlthadrl~La~q~npllq~RGlpGTHD~tlglnVL  126 (300)
T COG4240          48 GRPLIVGISGPQGSGKSTLSALIVRLLAAKGL-ERTATLSLDDLYLTHADRLRLARQVNPLLQTRGLPGTHDPTLGLNVL  126 (300)
T ss_pred             CCceEEEeecCCCCchhhHHHHHHHHHHHhcc-cceEEeehhhhhcchHHHHHHHHhcCchhcccCCCCCCchHHHHHHH
Confidence            56778999999999999999999999887643 46666666554433333334444432     1223334555556666


Q ss_pred             HHHhCCC
Q 042806          248 NRLKKEK  254 (390)
Q Consensus       248 ~~l~~~~  254 (390)
                      +.+.+++
T Consensus       127 nai~~g~  133 (300)
T COG4240         127 NAIARGG  133 (300)
T ss_pred             HHHhcCC
Confidence            6665443

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

Probab=96.02  E-value=0.43  Score=42.61  Aligned_cols=95  Identities=14%  Similarity=0.192  Sum_probs=58.9

Q ss_pred             ccCcccccchhHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 042806          150 IKDYEACESRMSTLNDILDALKN-------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI  216 (390)
Q Consensus       150 ~~~~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  216 (390)
                      ...+.++.|-+..+++|++.+.-             ..++-+..|||+|.|||-+|+..+......  |-..+     . 
T Consensus       167 tE~YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT~aT--FLKLA-----g-  238 (424)
T KOG0652|consen  167 TEQYSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQTNAT--FLKLA-----G-  238 (424)
T ss_pred             cccccccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhccch--HHHhc-----c-
Confidence            33456778888999999887642             135668899999999999999887654322  31100     0 


Q ss_pred             CCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCC
Q 042806          217 QDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       217 ~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~  264 (390)
                             -++.+-+-.     +-..++.......+.+.+.+|.+|.+.
T Consensus       239 -------PQLVQMfIG-----dGAkLVRDAFaLAKEkaP~IIFIDElD  274 (424)
T KOG0652|consen  239 -------PQLVQMFIG-----DGAKLVRDAFALAKEKAPTIIFIDELD  274 (424)
T ss_pred             -------hHHHhhhhc-----chHHHHHHHHHHhhccCCeEEEEechh
Confidence                   011111110     223344444445566788999999885

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=96.02  E-value=0.067  Score=53.69  Aligned_cols=45  Identities=13%  Similarity=0.124  Sum_probs=35.4

Q ss_pred             ccccchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          154 EACESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..++|....+.++.+.+..  ....-|.|+|+.|+||+++|+.+.+.
T Consensus       219 ~~iiG~S~~m~~~~~~i~~~A~s~~pVLI~GE~GTGKe~~A~~IH~~  265 (538)
T PRK15424        219 GDLLGQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHRE  265 (538)
T ss_pred             hheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCCCHHHHHHHHHHh
Confidence            3578888777777776542  33456789999999999999999886

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=96.01  E-value=0.023  Score=48.12  Aligned_cols=80  Identities=16%  Similarity=0.125  Sum_probs=43.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---C-chHHHHHHHHHHhC
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE---S-DSGRARSLRNRLKK  252 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~---~-~~~~~~~l~~~l~~  252 (390)
                      .+.|.|.+|+||||+|..+......     ..+|+.-... .-.+....|..........-   . ...+...+.....+
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~-----~~~~iat~~~-~~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~~~   76 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGL-----QVLYIATAQP-FDDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRADAAP   76 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCC-----CcEeCcCCCC-ChHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhhcCC
Confidence            6889999999999999999876432     1334443333 33445555544443222211   1 11222223222332


Q ss_pred             CCeEEEEEeCCC
Q 042806          253 EKTILVILDNIW  264 (390)
Q Consensus       253 ~~~~LlVlDdv~  264 (390)
                      .  -++++|.+.
T Consensus        77 ~--~~VlID~Lt   86 (170)
T PRK05800         77 G--RCVLVDCLT   86 (170)
T ss_pred             C--CEEEehhHH
Confidence            2  378999873

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=96.01  E-value=0.029  Score=54.76  Aligned_cols=90  Identities=19%  Similarity=0.332  Sum_probs=56.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCC-------CCCCCchH----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLT-------LHEESDSG----  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~-------~~~~~~~~----  241 (390)
                      +-.-++|.|.+|+|||||+..+........ -+.++++.++... ...+++..+...-...       ..+.+...    
T Consensus       143 kGQR~gIfa~~GvGKt~Ll~~i~~~~~~~~-~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a  221 (463)
T PRK09280        143 KGGKIGLFGGAGVGKTVLIQELINNIAKEH-GGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRV  221 (463)
T ss_pred             cCCEEEeecCCCCChhHHHHHHHHHHHhcC-CCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHH
Confidence            446788999999999999999877765321 2467777776543 4566666665432221       11111111    


Q ss_pred             --HHHHHHHHHh--CCCeEEEEEeCCC
Q 042806          242 --RARSLRNRLK--KEKTILVILDNIW  264 (390)
Q Consensus       242 --~~~~l~~~l~--~~~~~LlVlDdv~  264 (390)
                        ..-.+.++++  .++++||++|++.
T Consensus       222 ~~~a~tiAEyfrd~~G~~VLll~DslT  248 (463)
T PRK09280        222 ALTGLTMAEYFRDVEGQDVLLFIDNIF  248 (463)
T ss_pred             HHHHHHHHHHHHHhcCCceEEEecchH
Confidence              2335666663  3566999999984

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=96.00  E-value=0.0051  Score=53.50  Aligned_cols=23  Identities=39%  Similarity=0.564  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +|+|.|++|+|||||++.+....
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999998875

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.00  E-value=0.023  Score=47.31  Aligned_cols=114  Identities=24%  Similarity=0.186  Sum_probs=60.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC---CCCHHHHHHHHHHHh-----CCC--CCCCCchH----
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK---IQDIRKIQGEIADKL-----GLT--LHEESDSG----  241 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~---~~~~~~l~~~i~~~l-----~~~--~~~~~~~~----  241 (390)
                      ..|-|++..|.||||+|....-..-.. .+. +.++.+-.   ......+++.+- .+     +..  ....+...    
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~ra~~~-g~~-v~~vQFlKg~~~~gE~~~l~~l~-~v~~~~~g~~~~~~~~~~~~~~~~   79 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALRALGH-GYR-VGVVQFLKGGWKYGELKALERLP-NIEIHRMGRGFFWTTENDEEDIAA   79 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHC-CCe-EEEEEEeCCCCccCHHHHHHhCC-CcEEEECCCCCccCCCChHHHHHH
Confidence            467899999999999999888776543 233 33333322   233444443330 01     110  00011111    


Q ss_pred             ---HHHHHHHHHhCCCeEEEEEeCCCCC-----cccccccCCCCCCCCCcEEEEEecch
Q 042806          242 ---RARSLRNRLKKEKTILVILDNIWGN-----LDFQAVGIPHGDDRKGCKVLLTARSL  292 (390)
Q Consensus       242 ---~~~~l~~~l~~~~~~LlVlDdv~~~-----~~~~~l~~~l~~~~~~s~IivTtr~~  292 (390)
                         ......+.+..+.-=|+|||++-..     ...+.+...+....++.-+|+|.|+.
T Consensus        80 a~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~  138 (159)
T cd00561          80 AAEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNA  138 (159)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCC
Confidence               1123334444555349999998432     23333434444445567899999984

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.

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=95.99  E-value=0.034  Score=54.14  Aligned_cols=90  Identities=18%  Similarity=0.321  Sum_probs=58.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCC-------CCCCCchH----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGLT-------LHEESDSG----  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~~-------~~~~~~~~----  241 (390)
                      +-.-++|.|.+|+|||||+..+....... +-..++++-++.. ....+++..+...-...       ..+.+...    
T Consensus       142 ~GQr~~If~~~G~GKt~L~~~~~~~~~~~-~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~a  220 (461)
T TIGR01039       142 KGGKIGLFGGAGVGKTVLIQELINNIAKE-HGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMRV  220 (461)
T ss_pred             cCCEEEeecCCCCChHHHHHHHHHHHHhc-CCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHH
Confidence            44678899999999999999998776432 2346778877654 34566777665432211       11111111    


Q ss_pred             --HHHHHHHHHhC--CCeEEEEEeCCC
Q 042806          242 --RARSLRNRLKK--EKTILVILDNIW  264 (390)
Q Consensus       242 --~~~~l~~~l~~--~~~~LlVlDdv~  264 (390)
                        ..-.+.++++.  ++.+||++||+.
T Consensus       221 ~~~a~tiAEyfrd~~G~~VLll~DslT  247 (461)
T TIGR01039       221 ALTGLTMAEYFRDEQGQDVLLFIDNIF  247 (461)
T ss_pred             HHHHHHHHHHHHHhcCCeeEEEecchh
Confidence              23456677754  567999999985

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=95.99  E-value=0.02  Score=47.35  Aligned_cols=21  Identities=38%  Similarity=0.377  Sum_probs=19.1

Q ss_pred             EEcCCCCcHHHHHHHHHHHhh
Q 042806          180 IYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       180 I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.|++|+||||+++.+.....
T Consensus         1 i~G~PgsGK~t~~~~la~~~~   21 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRYG   21 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHHT
T ss_pred             CcCCCCCChHHHHHHHHHhcC
Confidence            689999999999999999763

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.99  E-value=0.043  Score=54.66  Aligned_cols=48  Identities=17%  Similarity=0.154  Sum_probs=34.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCC-CeEEEEEeCCCCCHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLF-DQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f-~~~~wv~v~~~~~~~~l~~~  225 (390)
                      ..+++.|.|++|+|||||+.++....-.+  + ...+||+...  +.+++.+.
T Consensus        20 ~g~~~Li~G~pGsGKT~la~qfl~~g~~~--~ge~~lyvs~eE--~~~~l~~~   68 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSIQFLYNGIIH--FDEPGVFVTFEE--SPQDIIKN   68 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHh--CCCCEEEEEEec--CHHHHHHH
Confidence            56899999999999999999997653221  2 3577887753  45555544

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

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=95.98  E-value=0.026  Score=54.86  Aligned_cols=88  Identities=19%  Similarity=0.273  Sum_probs=48.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh-----CCC-CCCCCchH------
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL-----GLT-LHEESDSG------  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l-----~~~-~~~~~~~~------  241 (390)
                      ....++|+|+.|+|||||++.+......   ..++++..-....+..++........     +.- ..+.+...      
T Consensus       164 ~Gqri~I~G~SGsGKTTLL~~Ia~l~~p---d~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~  240 (450)
T PRK06002        164 AGQRIGIFAGSGVGKSTLLAMLARADAF---DTVVIALVGERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPL  240 (450)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCCCC---CeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHH
Confidence            3457999999999999999888654321   22333333223344555444333322     111 11111111      


Q ss_pred             HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          242 RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       242 ~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                      ..-.+.+++. .++.+|+++||+.
T Consensus       241 ~a~~iAEyfrd~G~~Vll~~DslT  264 (450)
T PRK06002        241 TATAIAEYFRDRGENVLLIVDSVT  264 (450)
T ss_pred             HHHHHHHHHHHcCCCEEEeccchH
Confidence            2234555553 3566999999984

>PRK00625 shikimate kinase; Provisional

Probab=95.98  E-value=0.0063  Score=51.67  Aligned_cols=24  Identities=21%  Similarity=0.292  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .|.|+|++|+||||+++.+.+...
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~   25 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLS   25 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999988764

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

Probab=95.98  E-value=0.02  Score=54.03  Aligned_cols=64  Identities=19%  Similarity=0.123  Sum_probs=47.4

Q ss_pred             cccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          155 ACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      .++|++.....+...+..+  +-+.+.|++|+|||+||+.+.......     ...|.+.......++...
T Consensus        25 ~~~g~~~~~~~~l~a~~~~--~~vll~G~PG~gKT~la~~lA~~l~~~-----~~~i~~t~~l~p~d~~G~   88 (329)
T COG0714          25 VVVGDEEVIELALLALLAG--GHVLLEGPPGVGKTLLARALARALGLP-----FVRIQCTPDLLPSDLLGT   88 (329)
T ss_pred             eeeccHHHHHHHHHHHHcC--CCEEEECCCCccHHHHHHHHHHHhCCC-----eEEEecCCCCCHHHhcCc
Confidence            4777777777776666543  346789999999999999999988632     466677777777776544

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=95.94  E-value=0.056  Score=45.60  Aligned_cols=115  Identities=19%  Similarity=0.101  Sum_probs=62.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeE--EEEEeCCCCCHHHHHHHHHHHh-----CC--CCCCCCch---H-
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQV--IFVEVSKIQDIRKIQGEIADKL-----GL--TLHEESDS---G-  241 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~--~wv~v~~~~~~~~l~~~i~~~l-----~~--~~~~~~~~---~-  241 (390)
                      ...|-|++..|.||||.|..+.-.....+ +.+.  -|+--........++..+  .+     +.  .+...+..   . 
T Consensus         5 ~Gli~v~~g~GkGKtt~a~g~a~ra~~~g-~~v~ivQFlKg~~~~GE~~~l~~~--~~~~~~~g~g~~~~~~~~~~~~~~   81 (173)
T TIGR00708         5 RGIIIVHTGNGKGKTTAAFGMALRALGHG-KKVGVIQFIKGAWPNGERAAFEPH--GVEFQVMGTGFTWETQNREADTAI   81 (173)
T ss_pred             ccEEEEECCCCCChHHHHHHHHHHHHHCC-CeEEEEEEecCCcccChHHHHHhc--CcEEEECCCCCeecCCCcHHHHHH
Confidence            35788899999999999999888765432 4321  133322223333444332  11     11  11111111   1 


Q ss_pred             ---HHHHHHHHHhCCCeEEEEEeCCCC-----CcccccccCCCCCCCCCcEEEEEecch
Q 042806          242 ---RARSLRNRLKKEKTILVILDNIWG-----NLDFQAVGIPHGDDRKGCKVLLTARSL  292 (390)
Q Consensus       242 ---~~~~l~~~l~~~~~~LlVlDdv~~-----~~~~~~l~~~l~~~~~~s~IivTtr~~  292 (390)
                         ......+.+..++-=|+|||.+-.     .-..+.+...+....++..||+|.|+.
T Consensus        82 ~~~~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~  140 (173)
T TIGR00708        82 AKAAWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGC  140 (173)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCC
Confidence               122344445555534999999842     223334444444455677899999974

Alternate name: corrinoid adenosyltransferase.

>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=95.94  E-value=0.028  Score=47.43  Aligned_cols=44  Identities=16%  Similarity=0.151  Sum_probs=28.9

Q ss_pred             cchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          157 ESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       157 ~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +|....+.++++.+..  ....-|.|+|+.|+||+.+|+.+.+...
T Consensus         2 iG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s~   47 (168)
T PF00158_consen    2 IGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNSP   47 (168)
T ss_dssp             S--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCST
T ss_pred             EeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhhh
Confidence            4555555555555432  2234566999999999999999988643

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 ....

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=95.93  E-value=0.0085  Score=50.63  Aligned_cols=28  Identities=29%  Similarity=0.268  Sum_probs=25.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ..++++|+|..|+|||||++.+......
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~l~~   32 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPALCA   32 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHHHhh
Confidence            4678999999999999999999988764

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=95.93  E-value=0.006  Score=50.39  Aligned_cols=23  Identities=26%  Similarity=0.491  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ++.|.|++|+||||+|+.+....
T Consensus         1 li~l~G~~GsGKST~a~~l~~~~   23 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAERL   23 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhhc
Confidence            47899999999999999998764

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=95.93  E-value=0.011  Score=49.31  Aligned_cols=36  Identities=19%  Similarity=0.361  Sum_probs=29.8

Q ss_pred             HHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          161 STLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       161 ~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..+++|.+.|.+   +++++.|+.|+|||||+..+....
T Consensus        24 ~g~~~l~~~l~~---k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen   24 EGIEELKELLKG---KTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             TTHHHHHHHHTT---SEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             cCHHHHHHHhcC---CEEEEECCCCCCHHHHHHHHHhhc
Confidence            446777777764   789999999999999999998764

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>PRK06936 type III secretion system ATPase; Provisional

Probab=95.92  E-value=0.026  Score=54.75  Aligned_cols=87  Identities=21%  Similarity=0.349  Sum_probs=53.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCC-------CCCCCchH----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLT-------LHEESDSG----  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~-------~~~~~~~~----  241 (390)
                      +...++|.|..|+|||||++.+++...    .+.++++.++... ...++....+..-+..       ..+.+...    
T Consensus       161 ~Gq~~~I~G~sG~GKStLl~~Ia~~~~----~dv~V~~liGERgrEv~ef~~~~l~~~~l~rtvvv~atsd~p~~~R~~a  236 (439)
T PRK06936        161 EGQRMGIFAAAGGGKSTLLASLIRSAE----VDVTVLALIGERGREVREFIESDLGEEGLRKAVLVVATSDRPSMERAKA  236 (439)
T ss_pred             CCCEEEEECCCCCChHHHHHHHhcCCC----CCEEEEEEEccCcHHHHHHHHHHhcccccceeEEEEECCCCCHHHHHHH
Confidence            456789999999999999999988653    4567788776543 4455554433322111       11111111    


Q ss_pred             --HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          242 --RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       242 --~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                        ....+.++++ .++++|+++||+.
T Consensus       237 ~~~a~tiAEyfrd~G~~Vll~~DslT  262 (439)
T PRK06936        237 GFVATSIAEYFRDQGKRVLLLMDSVT  262 (439)
T ss_pred             HHHHHHHHHHHHHcCCCEEEeccchh
Confidence              1234555553 3566999999985

>PLN02165 adenylate isopentenyltransferase

Probab=95.91  E-value=0.011  Score=55.21  Aligned_cols=31  Identities=23%  Similarity=0.244  Sum_probs=26.2

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          170 LKNPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       170 L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.+....+++|+|+.|+|||||+..++....
T Consensus        38 ~~~~~g~iivIiGPTGSGKStLA~~LA~~l~   68 (334)
T PLN02165         38 EQNCKDKVVVIMGATGSGKSRLSVDLATRFP   68 (334)
T ss_pred             ccCCCCCEEEEECCCCCcHHHHHHHHHHHcC
Confidence            3455667999999999999999999988854

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=95.91  E-value=0.042  Score=46.26  Aligned_cols=27  Identities=26%  Similarity=0.164  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+++|.|+.|+|||||++.+.-...
T Consensus        26 ~Ge~~~i~G~nGsGKSTLl~~l~G~~~   52 (166)
T cd03223          26 PGDRLLITGPSGTGKSSLFRALAGLWP   52 (166)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            456899999999999999999987653

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>TIGR00750 lao LAO/AO transport system ATPase

Probab=95.90  E-value=0.033  Score=51.83  Aligned_cols=39  Identities=23%  Similarity=0.382  Sum_probs=29.6

Q ss_pred             HHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          164 NDILDALK--NPDVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       164 ~~l~~~L~--~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      ..+++.+.  .+...+|.|.|++|+|||||+..+.......
T Consensus        21 ~~~~~~~~~~~~~~~~i~i~G~~G~GKttl~~~l~~~~~~~   61 (300)
T TIGR00750        21 KQLLDRIMPYTGNAHRVGITGTPGAGKSTLLEALGMELRRR   61 (300)
T ss_pred             HHHHHhCCcccCCceEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            33444443  2467899999999999999999998876543

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>PRK14529 adenylate kinase; Provisional

Probab=95.89  E-value=0.031  Score=49.35  Aligned_cols=84  Identities=19%  Similarity=0.148  Sum_probs=46.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhhcCCCCe--EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAETEKLFDQ--VIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~~~~~f~~--~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      |.|.|++|+||||+++.+....... ++..  .+.-.+..........+.++..    ....++.-....+.+.+.....
T Consensus         3 I~l~G~PGsGK~T~a~~La~~~~~~-~is~gdllr~~i~~~t~lg~~i~~~i~~----G~lvpdei~~~lv~~~l~~~~~   77 (223)
T PRK14529          3 ILIFGPNGSGKGTQGALVKKKYDLA-HIESGAIFREHIGGGTELGKKAKEYIDR----GDLVPDDITIPMILETLKQDGK   77 (223)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCC-CcccchhhhhhccCCChHHHHHHHHHhc----cCcchHHHHHHHHHHHHhccCC
Confidence            7789999999999999998887532 2221  1111122222222333333322    2222444455556666654223


Q ss_pred             EEEEEeCCCCC
Q 042806          256 ILVILDNIWGN  266 (390)
Q Consensus       256 ~LlVlDdv~~~  266 (390)
                      --+|||+.-..
T Consensus        78 ~g~iLDGfPRt   88 (223)
T PRK14529         78 NGWLLDGFPRN   88 (223)
T ss_pred             CcEEEeCCCCC
Confidence            56999999644

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=95.89  E-value=0.029  Score=58.73  Aligned_cols=126  Identities=21%  Similarity=0.193  Sum_probs=72.3

Q ss_pred             HHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC----
Q 042806          162 TLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE----  237 (390)
Q Consensus       162 ~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~----  237 (390)
                      ...+|++.+.  +..++.|.|+.|+||||-.-+++.+..-  .....+-+.=........+...++.+++....+.    
T Consensus        54 ~~~~i~~ai~--~~~vvii~getGsGKTTqlP~~lle~g~--~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY~  129 (845)
T COG1643          54 VRDEILKAIE--QNQVVIIVGETGSGKTTQLPQFLLEEGL--GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGYS  129 (845)
T ss_pred             HHHHHHHHHH--hCCEEEEeCCCCCChHHHHHHHHHhhhc--ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeEE
Confidence            3456666665  3468899999999999999999887642  1222333322333456677888888887642211    


Q ss_pred             ----------------CchHHHHHHHH-HHhCCCeEEEEEeCCCCCccccc-----ccCCCCCCCCCcEEEEEecch
Q 042806          238 ----------------SDSGRARSLRN-RLKKEKTILVILDNIWGNLDFQA-----VGIPHGDDRKGCKVLLTARSL  292 (390)
Q Consensus       238 ----------------~~~~~~~~l~~-~l~~~~~~LlVlDdv~~~~~~~~-----l~~~l~~~~~~s~IivTtr~~  292 (390)
                                      .+.-++..+.+ .+.++- -.+|+|.++...--.+     ++..+....+..||||+|-.-
T Consensus       130 iRfe~~~s~~Trik~mTdGiLlrei~~D~~Ls~y-s~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIimSATl  205 (845)
T COG1643         130 IRFESKVSPRTRIKVMTDGILLREIQNDPLLSGY-SVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMSATL  205 (845)
T ss_pred             EEeeccCCCCceeEEeccHHHHHHHhhCcccccC-CEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEEeccc
Confidence                            11222233331 222333 4899999986632111     111122223348999999863

>PHA02774 E1; Provisional

Probab=95.87  E-value=0.015  Score=57.74  Aligned_cols=49  Identities=27%  Similarity=0.305  Sum_probs=35.2

Q ss_pred             HHHHHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 042806          162 TLNDILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS  214 (390)
Q Consensus       162 ~~~~l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~  214 (390)
                      -+..|..+|.+ ++...+.|+||+|.|||.+|..+.+-..    -..+.|++..
T Consensus       420 fl~~lk~~l~~~PKknciv~~GPP~TGKS~fa~sL~~~L~----G~vi~fvN~~  469 (613)
T PHA02774        420 FLTALKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFLK----GKVISFVNSK  469 (613)
T ss_pred             HHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhC----CCEEEEEECc
Confidence            34555556554 3346899999999999999999998864    2345677653

>PRK14737 gmk guanylate kinase; Provisional

Probab=95.86  E-value=0.0076  Score=51.83  Aligned_cols=26  Identities=15%  Similarity=0.198  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..++|.|+|++|+|||||++.+....
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhcC
Confidence            45789999999999999999998764

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=95.86  E-value=0.037  Score=54.15  Aligned_cols=91  Identities=20%  Similarity=0.247  Sum_probs=57.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCC--CeEEEEEeCCC-CCHHHHHHHHHHHhCCCC-------CCCCch---
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLF--DQVIFVEVSKI-QDIRKIQGEIADKLGLTL-------HEESDS---  240 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f--~~~~wv~v~~~-~~~~~l~~~i~~~l~~~~-------~~~~~~---  240 (390)
                      .-.-++|.|..|+|||||+..+.+.....+.+  ..++++.++.. ....+++..+...-....       .+.+..   
T Consensus       140 ~GQR~gIfgg~G~GKs~L~~~ia~~~~ad~~~~~~v~V~~~iGERgrEv~efi~~~~~~~~l~rtvvv~atsd~p~~~R~  219 (458)
T TIGR01041       140 RGQKLPIFSGSGLPHNELAAQIARQATVRGEESEFAVVFAAMGITYEEANFFMKDFEETGALERAVVFLNLADDPAVERI  219 (458)
T ss_pred             cCCEEEeeCCCCCCHHHHHHHHHHhhcccCCCCceEEEEEEccccchHHHHHHHHHHhcCCcceEEEEEECCCCCHHHHH
Confidence            34568899999999999999998876432111  15677777654 356666666654332211       111111   


Q ss_pred             ---HHHHHHHHHHh--CCCeEEEEEeCCC
Q 042806          241 ---GRARSLRNRLK--KEKTILVILDNIW  264 (390)
Q Consensus       241 ---~~~~~l~~~l~--~~~~~LlVlDdv~  264 (390)
                         .....+.+++.  .++++||++||+.
T Consensus       220 ~a~~~a~tiAEyfr~d~G~~VLli~DslT  248 (458)
T TIGR01041       220 VTPRMALTAAEYLAFEKDMHVLVILTDMT  248 (458)
T ss_pred             HHHHHHHHHHHHHHHccCCcEEEEEcChh
Confidence               12345777776  4677999999984

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>PRK12678 transcription termination factor Rho; Provisional

Probab=95.85  E-value=0.033  Score=55.39  Aligned_cols=90  Identities=19%  Similarity=0.140  Sum_probs=49.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEE-EEEeCCCC-CHHHHHHHHHHHhCCCCCCCCc------hHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVI-FVEVSKIQ-DIRKIQGEIADKLGLTLHEESD------SGRARS  245 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~-wv~v~~~~-~~~~l~~~i~~~l~~~~~~~~~------~~~~~~  245 (390)
                      .-.-..|+|++|+|||||++.+.+.... .+-++.+ ++-|.... .+.++.+.+-..+-....+.+.      ..+...
T Consensus       415 kGQR~LIvgpp~aGKTtLL~~IAn~i~~-n~~~~~~ivvLIgERpeEVtdm~rsVkgeVVasT~D~p~~~~~~~a~~ai~  493 (672)
T PRK12678        415 KGQRGLIVSPPKAGKTTILQNIANAITT-NNPECHLMVVLVDERPEEVTDMQRSVKGEVIASTFDRPPSDHTTVAELAIE  493 (672)
T ss_pred             cCCEeEEeCCCCCCHHHHHHHHHHHHhh-cCCCeEEEEEEEeCchhhHHHHHHhccceEEEECCCCCHHHHHHHHHHHHH
Confidence            3456789999999999999999987643 2334433 44555433 2333322221111111111111      112334


Q ss_pred             HHHHHh-CCCeEEEEEeCCC
Q 042806          246 LRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       246 l~~~l~-~~~~~LlVlDdv~  264 (390)
                      +.+++. .++.+||++|++.
T Consensus       494 ~Ae~fre~G~dVlillDSlT  513 (672)
T PRK12678        494 RAKRLVELGKDVVVLLDSIT  513 (672)
T ss_pred             HHHHHHHcCCCEEEEEeCch
Confidence            445553 4566999999985

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.83  E-value=0.0069  Score=51.68  Aligned_cols=24  Identities=29%  Similarity=0.401  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ++|+|+|+.|+|||||++.+....
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~~   25 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEED   25 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHccC
Confidence            578999999999999999998854

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>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=95.83  E-value=0.0074  Score=49.44  Aligned_cols=24  Identities=38%  Similarity=0.461  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +|.|.|++|+||||+|+.+.....
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~~~   24 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKKLG   24 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhC
Confidence            588999999999999999998764

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=95.82  E-value=0.0062  Score=49.30  Aligned_cols=71  Identities=17%  Similarity=0.206  Sum_probs=41.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      .+-|.|.|.+|+|||||+.++.....       .-|+++|.....++++..--..  ......+.......|-..+..+.
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~~-------~~~i~isd~vkEn~l~~gyDE~--y~c~i~DEdkv~D~Le~~m~~Gg   77 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKTG-------LEYIEISDLVKENNLYEGYDEE--YKCHILDEDKVLDELEPLMIEGG   77 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHhC-------CceEehhhHHhhhcchhccccc--ccCccccHHHHHHHHHHHHhcCC
Confidence            35588999999999999999986553       3467776643333332211100  01112244555666666665555

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=95.82  E-value=0.056  Score=48.46  Aligned_cols=24  Identities=21%  Similarity=0.210  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +..|+|++|+|||+|+.+++-...
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~va   26 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALAMA   26 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHHHh
Confidence            567899999999999999987653

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PRK05922 type III secretion system ATPase; Validated

Probab=95.82  E-value=0.034  Score=53.93  Aligned_cols=87  Identities=14%  Similarity=0.263  Sum_probs=51.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCC-------CCCCchH----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-IQDIRKIQGEIADKLGLTL-------HEESDSG----  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~l~~~i~~~l~~~~-------~~~~~~~----  241 (390)
                      +...++|+|+.|+|||||++.+.....    .+...++.++. .....+.+.+....+....       .+.+...    
T Consensus       156 ~GqrigI~G~nG~GKSTLL~~Ia~~~~----~d~gvi~liGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~a  231 (434)
T PRK05922        156 KGQRIGVFSEPGSGKSSLLSTIAKGSK----STINVIALIGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVIA  231 (434)
T ss_pred             CCcEEEEECCCCCChHHHHHHHhccCC----CCceEEEEeCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHHHH
Confidence            445689999999999999999886543    34445444443 2344555555544332211       1111111    


Q ss_pred             --HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          242 --RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       242 --~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                        ....+.+++. .++++|+++||+.
T Consensus       232 ~~~a~tiAEyfrd~G~~VLl~~DslT  257 (434)
T PRK05922        232 GRAAMTIAEYFRDQGHRVLFIMDSLS  257 (434)
T ss_pred             HHHHHHHHHHHHHcCCCEEEeccchh
Confidence              2334556663 3566999999985

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=95.82  E-value=0.043  Score=47.02  Aligned_cols=29  Identities=24%  Similarity=0.352  Sum_probs=25.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ....++.|.|.+|+||||+++.+......
T Consensus        16 ~~~~~i~i~G~~GsGKstla~~l~~~l~~   44 (184)
T TIGR00455        16 HRGVVIWLTGLSGSGKSTIANALEKKLES   44 (184)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            45679999999999999999999988753

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>CHL00060 atpB ATP synthase CF1 beta subunit

Probab=95.81  E-value=0.041  Score=53.99  Aligned_cols=90  Identities=18%  Similarity=0.263  Sum_probs=57.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCCC--------------CCCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLTL--------------HEES  238 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~~--------------~~~~  238 (390)
                      +-.-++|.|.+|+|||||+..+....... +=+.++++-++... ...+++..+...-....              .+.+
T Consensus       160 kGQR~gIfgg~GvGKs~L~~~~~~~~~~~-~~dv~V~~lIGERgrEv~efi~~~~~~~~~~~~~~~~~rsvvv~atsd~p  238 (494)
T CHL00060        160 RGGKIGLFGGAGVGKTVLIMELINNIAKA-HGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMNEP  238 (494)
T ss_pred             cCCEEeeecCCCCChhHHHHHHHHHHHHh-cCCeEEEEEeccCchHHHHHHHHHHhcCccccCcccccceEEEEECCCCC
Confidence            44678899999999999999888773321 12678888887654 45667766655211110              1111


Q ss_pred             ch------HHHHHHHHHHhC--CCeEEEEEeCCC
Q 042806          239 DS------GRARSLRNRLKK--EKTILVILDNIW  264 (390)
Q Consensus       239 ~~------~~~~~l~~~l~~--~~~~LlVlDdv~  264 (390)
                      ..      .....+.+++++  ++.+||++||+.
T Consensus       239 ~~~R~~a~~~A~tiAEyfrd~g~~~VLll~DslT  272 (494)
T CHL00060        239 PGARMRVGLTALTMAEYFRDVNKQDVLLFIDNIF  272 (494)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCCEEEEcccch
Confidence            11      123457777754  436999999985

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=95.79  E-value=0.0079  Score=51.41  Aligned_cols=25  Identities=36%  Similarity=0.518  Sum_probs=22.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +|+|.|.+|+|||||++.+......
T Consensus         1 ii~i~G~sgsGKttla~~l~~~l~~   25 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQLRV   25 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHH
Confidence            5889999999999999999988753

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=95.79  E-value=0.015  Score=54.94  Aligned_cols=51  Identities=14%  Similarity=0.124  Sum_probs=43.4

Q ss_pred             cCcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          151 KDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .|...++|-++.+..|+..+.++...-+.|.|+.|+||||+|+.+++-...
T Consensus        14 ~pf~~ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~ar~~~~~l~~   64 (350)
T CHL00081         14 FPFTAIVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTTIRALVDLLPE   64 (350)
T ss_pred             CCHHHHhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHHHHHHHHHHhh
Confidence            345578999998888988888888888889999999999999999887653

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=95.79  E-value=0.0075  Score=51.80  Aligned_cols=23  Identities=43%  Similarity=0.485  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +|+|.|.+|+||||||+.+....
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~~   23 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRIL   23 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            58899999999999999998875

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.77  E-value=0.0092  Score=52.12  Aligned_cols=26  Identities=23%  Similarity=0.279  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+|+|+|++|+|||||++.+....
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l~~~~   29 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKALLERD   29 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            35689999999999999999998875

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

Probab=95.77  E-value=0.069  Score=49.88  Aligned_cols=29  Identities=34%  Similarity=0.418  Sum_probs=24.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      .++-|.++||+|.|||-||+.+..+....
T Consensus       126 p~kGiLL~GPpG~GKTmlAKA~Akeaga~  154 (386)
T KOG0737|consen  126 PPKGILLYGPPGTGKTMLAKAIAKEAGAN  154 (386)
T ss_pred             CCccceecCCCCchHHHHHHHHHHHcCCC
Confidence            35678899999999999999999987643

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=95.76  E-value=0.059  Score=54.15  Aligned_cols=86  Identities=15%  Similarity=0.170  Sum_probs=55.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC----------------CC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLH----------------EE  237 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~----------------~~  237 (390)
                      ...++.|.|++|+|||+|+.++.......  -..++|++...  +..++...+ ..++.+..                ..
T Consensus       272 ~g~~~li~G~~G~GKT~l~~~~~~~~~~~--g~~~~yis~e~--~~~~i~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~~  346 (509)
T PRK09302        272 RGSIILVSGATGTGKTLLASKFAEAACRR--GERCLLFAFEE--SRAQLIRNA-RSWGIDLEKMEEKGLLKIICARPESY  346 (509)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhC--CCcEEEEEecC--CHHHHHHHH-HHcCCChHHHhhcCCceeecCCcccC
Confidence            45788999999999999999998775432  34577877655  455555544 34443211                11


Q ss_pred             CchHHHHHHHHHHhCCCeEEEEEeCCC
Q 042806          238 SDSGRARSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       238 ~~~~~~~~l~~~l~~~~~~LlVlDdv~  264 (390)
                      ........+...+...+.-++|+|.+.
T Consensus       347 ~~~~~~~~i~~~i~~~~~~~vVIDslt  373 (509)
T PRK09302        347 GLEDHLIIIKREIEEFKPSRVAIDPLS  373 (509)
T ss_pred             CHHHHHHHHHHHHHHcCCCEEEEcCHH
Confidence            123344556666655455689999984

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=95.76  E-value=0.043  Score=49.80  Aligned_cols=95  Identities=12%  Similarity=0.162  Sum_probs=53.9

Q ss_pred             CccEEEEEcCCCCcHHHHH-HHHHHHhhhcCCCCeE-EEEEeCCCC-CHHHHHHHHHHHhCCC-------CCCCCchH--
Q 042806          174 DVNMLGIYGMGGIVKTTLA-KEVARKAETEKLFDQV-IFVEVSKIQ-DIRKIQGEIADKLGLT-------LHEESDSG--  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa-~~v~~~~~~~~~f~~~-~wv~v~~~~-~~~~l~~~i~~~l~~~-------~~~~~~~~--  241 (390)
                      +-.-++|.|.+|+|||+|+ ..+.+..    .-+.. +++.+.... ...++...+...-...       ..+.+...  
T Consensus        68 rGQr~~Ifg~~g~GKt~L~l~~i~~~~----~~~v~~V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~  143 (274)
T cd01132          68 RGQRELIIGDRQTGKTAIAIDTIINQK----GKKVYCIYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQY  143 (274)
T ss_pred             cCCEEEeeCCCCCCccHHHHHHHHHhc----CCCeEEEEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHH
Confidence            3456889999999999995 5555442    13434 666776543 4566666665432111       11111111  


Q ss_pred             ----HHHHHHHHHhC-CCeEEEEEeCCCCC-cccccc
Q 042806          242 ----RARSLRNRLKK-EKTILVILDNIWGN-LDFQAV  272 (390)
Q Consensus       242 ----~~~~l~~~l~~-~~~~LlVlDdv~~~-~~~~~l  272 (390)
                          ..-.+.+++.. ++.+|+++||+... ..++++
T Consensus       144 ~a~~~a~aiAE~fr~~G~~Vlvl~DslTr~A~A~rEi  180 (274)
T cd01132         144 LAPYTGCAMGEYFMDNGKHALIIYDDLSKQAVAYRQM  180 (274)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEcChHHHHHHHHHH
Confidence                12344555543 46699999999544 344444

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.

>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit

Probab=95.76  E-value=0.042  Score=53.40  Aligned_cols=91  Identities=16%  Similarity=0.224  Sum_probs=57.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh-----------cCCCCeEEEEEeCCCCCHHHHHHHHHHHhC-CCC-------
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET-----------EKLFDQVIFVEVSKIQDIRKIQGEIADKLG-LTL-------  234 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~-----------~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~-~~~-------  234 (390)
                      +-.-++|.|.+|+|||||+..+.+....           ++.-..+++..++......+.+...+..-+ ...       
T Consensus       140 ~GQRigIfagsGvGKs~L~~~i~~~~~~~~~~~aD~~~~~~~~~v~V~a~IGerre~~efi~~~l~~~g~l~rtvvv~at  219 (466)
T TIGR01040       140 RGQKIPIFSAAGLPHNEIAAQICRQAGLVKLPTKDVHDGHEDNFAIVFAAMGVNMETARFFKQDFEENGSMERVCLFLNL  219 (466)
T ss_pred             cCCeeeeecCCCCCHHHHHHHHHHhhccccccccccccccCCceEEEEEEeeeehHHHHHHHHHHHhcCCcceEEEEEEC
Confidence            3456889999999999999999887641           001116677788777665565555555544 211       


Q ss_pred             CCCCchH------HHHHHHHHHh--CCCeEEEEEeCCC
Q 042806          235 HEESDSG------RARSLRNRLK--KEKTILVILDNIW  264 (390)
Q Consensus       235 ~~~~~~~------~~~~l~~~l~--~~~~~LlVlDdv~  264 (390)
                      .+.+...      ..-.+.+++.  .++++|+++||+.
T Consensus       220 sd~p~~~R~~a~~~a~tiAEyfr~~~G~~VLl~~DslT  257 (466)
T TIGR01040       220 ANDPTIERIITPRLALTTAEYLAYQCEKHVLVILTDMS  257 (466)
T ss_pred             CCCCHHHHHHHHhhhHHHHHHHHHhcCCcEEEeccChH
Confidence            1111111      2335667776  3567999999984

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=95.75  E-value=0.065  Score=53.85  Aligned_cols=50  Identities=16%  Similarity=0.133  Sum_probs=35.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      ..+++.|.|.+|+|||+|+.++......+ +=..++|++...  +.+++...+
T Consensus        30 ~Gs~~li~G~pGsGKT~l~~qf~~~~~~~-~ge~~lyis~ee--~~~~i~~~~   79 (509)
T PRK09302         30 KGRPTLVSGTAGTGKTLFALQFLVNGIKR-FDEPGVFVTFEE--SPEDIIRNV   79 (509)
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHh-cCCCEEEEEccC--CHHHHHHHH
Confidence            56899999999999999999997664432 113467776655  455655554

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=95.74  E-value=0.082  Score=49.59  Aligned_cols=49  Identities=20%  Similarity=0.265  Sum_probs=36.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEI  226 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i  226 (390)
                      +-..++|.|..|+|||+|++++.+...    -+.++++.++... .+.+++.++
T Consensus       156 kGqr~~I~G~~G~GKT~L~~~Iak~~~----~dvvVyv~iGERg~Ev~e~l~ef  205 (369)
T cd01134         156 KGGTAAIPGPFGCGKTVIQQSLSKYSN----SDIVIYVGCGERGNEMTEVLEEF  205 (369)
T ss_pred             CCCEEEEECCCCCChHHHHHHHHhCCC----CCEEEEEEeCCChHHHHHHHHHH
Confidence            345788999999999999999988643    4578888887643 455555554

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.

>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]

Probab=95.73  E-value=0.037  Score=50.67  Aligned_cols=88  Identities=23%  Similarity=0.367  Sum_probs=51.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh-cCCCC-------eEEEEEeCCC-CCHHHHHHHHHHHhCCCCCCCC---------
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAET-EKLFD-------QVIFVEVSKI-QDIRKIQGEIADKLGLTLHEES---------  238 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~-~~~f~-------~~~wv~v~~~-~~~~~l~~~i~~~l~~~~~~~~---------  238 (390)
                      +..|+|.+|+|||||+...+-.... ++.|.       .+++|++... .++-.-++.+...++..+.+..         
T Consensus        91 ~~~~~gdsg~GKttllL~l~IalaaG~~lfG~~v~epGkvlyvslEl~re~~L~Rl~~v~a~mgLsPadvrn~dltd~~G  170 (402)
T COG3598          91 VSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSLELYREDILERLEPVRARMGLSPADVRNMDLTDVSG  170 (402)
T ss_pred             eEEEecCCcccHhHHHHHHHHHHHhhHHHhcccccCCCeEEEEEeccChHHHHHHHHHHHHHcCCChHhhhheecccccc
Confidence            4457799999999999988776533 23343       4566665432 2333334456666665432210         


Q ss_pred             --c------hHHHHHHHHHHhCCCeEEEEEeCCC
Q 042806          239 --D------SGRARSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       239 --~------~~~~~~l~~~l~~~~~~LlVlDdv~  264 (390)
                        .      ..+..+....+...++-++|+|-+-
T Consensus       171 aa~~~d~l~pkl~rRfek~~~Q~rp~~vViDp~v  204 (402)
T COG3598         171 AADESDVLSPKLYRRFEKILEQKRPDFVVIDPFV  204 (402)
T ss_pred             CCCccccccHHHHHHHHHHHHHhCCCeEEEcchh
Confidence              0      0223444445556777899999764

>PTZ00185 ATPase alpha subunit; Provisional

Probab=95.73  E-value=0.085  Score=51.90  Aligned_cols=90  Identities=14%  Similarity=0.157  Sum_probs=52.6

Q ss_pred             CccEEEEEcCCCCcHHHHH-HHHHHHhhh-----cCCCCeEEEEEeCCCCC-HHHHHHHHHHHhC-CCC-------CCCC
Q 042806          174 DVNMLGIYGMGGIVKTTLA-KEVARKAET-----EKLFDQVIFVEVSKIQD-IRKIQGEIADKLG-LTL-------HEES  238 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa-~~v~~~~~~-----~~~f~~~~wv~v~~~~~-~~~l~~~i~~~l~-~~~-------~~~~  238 (390)
                      +-.-++|.|..|+|||+|| -.+.+....     .++-..++|+.+++..+ ..+ +...+.+-+ ...       .+.+
T Consensus       188 RGQR~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGeR~rEV~e-i~~~L~e~GaL~~TvVV~AtAdep  266 (574)
T PTZ00185        188 RGQRELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQRCSNVAR-IHRLLRSYGALRYTTVMAATAAEP  266 (574)
T ss_pred             CCCEEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEeccchHHHHH-HHHHHHhcCCccceEEEEECCCCC
Confidence            3456889999999999996 566666422     12345788999987654 344 333333333 111       1111


Q ss_pred             chH------HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          239 DSG------RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       239 ~~~------~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                      ...      ..-.+.+++. .++.+|+|+||+.
T Consensus       267 ~~~r~~Apy~a~tiAEYFrd~GkdVLiv~DDLT  299 (574)
T PTZ00185        267 AGLQYLAPYSGVTMGEYFMNRGRHCLCVYDDLS  299 (574)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCEEEEEcCch
Confidence            111      1234555553 3566999999995

>PRK14738 gmk guanylate kinase; Provisional

Probab=95.71  E-value=0.0095  Score=52.17  Aligned_cols=25  Identities=16%  Similarity=0.250  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..++|.|+|++|+|||||++.+...
T Consensus        12 ~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738         12 KPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHhc
Confidence            5678999999999999999999754

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

Probab=95.71  E-value=0.054  Score=47.90  Aligned_cols=72  Identities=25%  Similarity=0.279  Sum_probs=46.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhC
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKK  252 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  252 (390)
                      +.++-+.++|++|.|||-|++.++++...       .|+.+...    ++.   -+.+|..      -..+..+....+.
T Consensus       187 dpprgvllygppg~gktml~kava~~t~a-------~firvvgs----efv---qkylgeg------prmvrdvfrlake  246 (408)
T KOG0727|consen  187 DPPRGVLLYGPPGTGKTMLAKAVANHTTA-------AFIRVVGS----EFV---QKYLGEG------PRMVRDVFRLAKE  246 (408)
T ss_pred             CCCcceEEeCCCCCcHHHHHHHHhhccch-------heeeeccH----HHH---HHHhccC------cHHHHHHHHHHhc
Confidence            45778889999999999999999987653       33433321    111   1223321      1244555555556


Q ss_pred             CCeEEEEEeCCC
Q 042806          253 EKTILVILDNIW  264 (390)
Q Consensus       253 ~~~~LlVlDdv~  264 (390)
                      +-+-++.+|.+.
T Consensus       247 napsiifideid  258 (408)
T KOG0727|consen  247 NAPSIIFIDEID  258 (408)
T ss_pred             cCCcEEEeehhh
Confidence            667899999885

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

Probab=95.71  E-value=0.027  Score=51.38  Aligned_cols=117  Identities=21%  Similarity=0.166  Sum_probs=59.4

Q ss_pred             HHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHH
Q 042806          164 NDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRA  243 (390)
Q Consensus       164 ~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~  243 (390)
                      +.+..++ .....++.|.|+.|+||||+++.+.+.....  -..++.+.-+..+....+     .++...  ........
T Consensus        70 ~~l~~~~-~~~~GlilisG~tGSGKTT~l~all~~i~~~--~~~iitiEdp~E~~~~~~-----~q~~v~--~~~~~~~~  139 (264)
T cd01129          70 EIFRKLL-EKPHGIILVTGPTGSGKTTTLYSALSELNTP--EKNIITVEDPVEYQIPGI-----NQVQVN--EKAGLTFA  139 (264)
T ss_pred             HHHHHHH-hcCCCEEEEECCCCCcHHHHHHHHHhhhCCC--CCeEEEECCCceecCCCc-----eEEEeC--CcCCcCHH
Confidence            3343333 3445689999999999999999887765321  112333221111111100     011111  11112234


Q ss_pred             HHHHHHHhCCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhh
Q 042806          244 RSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDV  294 (390)
Q Consensus       244 ~~l~~~l~~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v  294 (390)
                      ..+...++. .+=.++++++.+.+....+...   ...|..++.|....+.
T Consensus       140 ~~l~~~lR~-~PD~i~vgEiR~~e~a~~~~~a---a~tGh~v~tTlHa~~~  186 (264)
T cd01129         140 RGLRAILRQ-DPDIIMVGEIRDAETAEIAVQA---ALTGHLVLSTLHTNDA  186 (264)
T ss_pred             HHHHHHhcc-CCCEEEeccCCCHHHHHHHHHH---HHcCCcEEEEeccCCH
Confidence            445555544 4478999999887654433222   1234446666665443

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

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=95.70  E-value=0.035  Score=47.89  Aligned_cols=25  Identities=32%  Similarity=0.417  Sum_probs=22.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +|+|.|+.|+||||+++.+.+....
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~l~~   26 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAERLEA   26 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            6899999999999999999998753

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=95.70  E-value=0.066  Score=50.08  Aligned_cols=87  Identities=22%  Similarity=0.335  Sum_probs=51.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC-CCCCHHHHHHHHHHHhCCC-------CCCCCchH----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS-KIQDIRKIQGEIADKLGLT-------LHEESDSG----  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~-~~~~~~~l~~~i~~~l~~~-------~~~~~~~~----  241 (390)
                      ....++|.|+.|+|||||++.+.....    .+..++..+. ......++.......-+..       ..+.+...    
T Consensus        68 ~Gqri~I~G~sG~GKTtLl~~Ia~~~~----~~~~vi~~iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~~  143 (326)
T cd01136          68 KGQRLGIFAGSGVGKSTLLGMIARGTT----ADVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVKA  143 (326)
T ss_pred             CCcEEEEECCCCCChHHHHHHHhCCCC----CCEEEEEEEecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHHH
Confidence            446789999999999999998886543    3344444444 3335555555554433221       11111111    


Q ss_pred             --HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          242 --RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       242 --~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                        ....+.+++. .++.+|+++||+.
T Consensus       144 ~~~a~~~AEyfr~~g~~Vll~~Dslt  169 (326)
T cd01136         144 AYTATAIAEYFRDQGKDVLLLMDSLT  169 (326)
T ss_pred             HHHHHHHHHHHHHcCCCeEEEeccch
Confidence              2234445553 3556999999984

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.70  E-value=0.0082  Score=48.88  Aligned_cols=24  Identities=25%  Similarity=0.423  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +|+|+|+.|+|||||++.+.....
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~~~   24 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEEFD   24 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhcCC
Confidence            378999999999999999988653

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>PRK07933 thymidylate kinase; Validated

Probab=95.70  E-value=0.058  Score=47.49  Aligned_cols=26  Identities=27%  Similarity=0.426  Sum_probs=23.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      +|+|-|+-|+||||+++.+.+....+
T Consensus         2 ~IviEG~dGsGKST~~~~L~~~L~~~   27 (213)
T PRK07933          2 LIAIEGVDGAGKRTLTEALRAALEAR   27 (213)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHC
Confidence            68999999999999999999998764

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=95.70  E-value=0.04  Score=53.28  Aligned_cols=87  Identities=23%  Similarity=0.364  Sum_probs=50.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCC-------CCCCCchH----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGLT-------LHEESDSG----  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~~-------~~~~~~~~----  241 (390)
                      +...++|.|..|+|||||++.+.....    .+..++..+... ....++...+...-...       ..+.+...    
T Consensus       136 ~Gq~~~I~G~sG~GKTtLl~~I~~~~~----~~~~vi~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~tsd~~~~~r~~a  211 (411)
T TIGR03496       136 RGQRMGIFAGSGVGKSTLLGMMARYTE----ADVVVVGLIGERGREVKEFIEDILGEEGLARSVVVAATADESPLMRLRA  211 (411)
T ss_pred             cCcEEEEECCCCCCHHHHHHHHhcCCC----CCEEEEEEEecChHHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHHH
Confidence            456789999999999999988876543    344455555543 23444444443332111       11111111    


Q ss_pred             --HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          242 --RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       242 --~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                        ....+.+++. .++.+|+++||+.
T Consensus       212 ~~~a~tiAEyfr~~G~~Vll~~Dslt  237 (411)
T TIGR03496       212 AFYATAIAEYFRDQGKDVLLLMDSLT  237 (411)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEeChH
Confidence              2234555553 3556999999984

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=95.69  E-value=0.037  Score=49.91  Aligned_cols=25  Identities=16%  Similarity=0.262  Sum_probs=22.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +|+|.|.+|+||||+++.+....+.
T Consensus         1 IIgItG~SGSGKTTv~~~l~~~l~~   25 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEHIFAR   25 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHh
Confidence            5899999999999999999887754

PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=95.69  E-value=0.012  Score=50.06  Aligned_cols=28  Identities=29%  Similarity=0.309  Sum_probs=24.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...+|.|.|++|+||||+++.+......
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~l~~   30 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEKLRE   30 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3568999999999999999999998754

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=95.69  E-value=0.017  Score=48.11  Aligned_cols=35  Identities=20%  Similarity=0.213  Sum_probs=27.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEE
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVE  212 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~  212 (390)
                      ++.|+|+.|+|||||+..+......+ .+...+.-+
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~l~~~-G~~V~viK~   35 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKALKAR-GYRVATIKH   35 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHhc-CCeEEEEec
Confidence            57899999999999999999988653 465554443

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=95.68  E-value=0.012  Score=51.58  Aligned_cols=31  Identities=23%  Similarity=0.269  Sum_probs=26.8

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          170 LKNPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       170 L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +...++++|+++|..|+|||||...+.+...
T Consensus        17 ~~~~~~~~i~~~G~~gsGKTTli~~l~~~~~   47 (207)
T TIGR00073        17 LDKHGLVVLNFMSSPGSGKTTLIEKLIDNLK   47 (207)
T ss_pred             hhhcCcEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3445789999999999999999999988754

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=95.66  E-value=0.03  Score=57.03  Aligned_cols=53  Identities=13%  Similarity=-0.024  Sum_probs=34.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcC-CCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEK-LFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~-~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      .++..|.|.+|.||||+++.+........ .-...+.+.....-....+...+.
T Consensus       167 ~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~  220 (615)
T PRK10875        167 RRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLG  220 (615)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHH
Confidence            46888999999999999999988764321 112355555555444444444443

>PRK14530 adenylate kinase; Provisional

Probab=95.66  E-value=0.01  Score=52.27  Aligned_cols=25  Identities=20%  Similarity=0.178  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.|.|.|++|+||||+++.+.....
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~~   28 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEFG   28 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3588999999999999999987763

>PRK05748 replicative DNA helicase; Provisional

Probab=95.65  E-value=0.45  Score=46.99  Aligned_cols=54  Identities=13%  Similarity=0.041  Sum_probs=37.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ...++.|-|.+|+|||+++.++......+.+. .++|+  |-.-+..++...++...
T Consensus       202 ~G~livIaarpg~GKT~~al~ia~~~a~~~g~-~v~~f--SlEms~~~l~~R~l~~~  255 (448)
T PRK05748        202 PNDLIIVAARPSVGKTAFALNIAQNVATKTDK-NVAIF--SLEMGAESLVMRMLCAE  255 (448)
T ss_pred             CCceEEEEeCCCCCchHHHHHHHHHHHHhCCC-eEEEE--eCCCCHHHHHHHHHHHh
Confidence            34678899999999999999998875433223 34444  44456677777775444

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=95.65  E-value=0.013  Score=51.88  Aligned_cols=24  Identities=21%  Similarity=-0.036  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      ..+++.|.|+.|.||||+.+.+.-
T Consensus        30 ~g~~~~itG~N~~GKStll~~i~~   53 (222)
T cd03287          30 GGYCQIITGPNMGGKSSYIRQVAL   53 (222)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            456889999999999999999977

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

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=95.63  E-value=0.0092  Score=49.70  Aligned_cols=20  Identities=35%  Similarity=0.519  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVA  196 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~  196 (390)
                      .|.|.|.+|+||||++..+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58899999999999999997

>PRK13975 thymidylate kinase; Provisional

Probab=95.63  E-value=0.011  Score=51.20  Aligned_cols=26  Identities=35%  Similarity=0.366  Sum_probs=23.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+|+|.|+.|+||||+++.+......
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~l~~   28 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEKLNA   28 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            47999999999999999999998753

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=95.63  E-value=0.0083  Score=50.32  Aligned_cols=22  Identities=27%  Similarity=0.460  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |.|+|++|+||||+++.+....
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRL   22 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999998876

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=95.62  E-value=0.0096  Score=51.49  Aligned_cols=36  Identities=25%  Similarity=0.199  Sum_probs=26.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEE
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVE  212 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~  212 (390)
                      ...+++|.||+|+|||||.+.+..-...   -.+.+|+.
T Consensus        27 ~Gevv~iiGpSGSGKSTlLRclN~LE~~---~~G~I~i~   62 (240)
T COG1126          27 KGEVVVIIGPSGSGKSTLLRCLNGLEEP---DSGSITVD   62 (240)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCcCC---CCceEEEC
Confidence            4568999999999999999988543321   23456653

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=95.60  E-value=0.063  Score=56.27  Aligned_cols=101  Identities=17%  Similarity=0.199  Sum_probs=60.4

Q ss_pred             ccchhHHHHHHHHHhcC------C--CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          156 CESRMSTLNDILDALKN------P--DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       156 ~~gR~~~~~~l~~~L~~------~--~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      ++|-++.+..|.+.+..      +  ....+.+.||.|+|||-||+.+....-..  .+..+-++.      .+... +.
T Consensus       564 V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgs--e~~~IriDm------se~~e-vs  634 (898)
T KOG1051|consen  564 VIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYVFGS--EENFIRLDM------SEFQE-VS  634 (898)
T ss_pred             ccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHHHcCC--ccceEEech------hhhhh-hh
Confidence            44555555666665543      1  24567789999999999999998887322  333333333      33333 33


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~  266 (390)
                      +..+.+ +..--......|.+.++.+...+|.||||+..
T Consensus       635 kligsp-~gyvG~e~gg~LteavrrrP~sVVLfdeIEkA  672 (898)
T KOG1051|consen  635 KLIGSP-PGYVGKEEGGQLTEAVKRRPYSVVLFEEIEKA  672 (898)
T ss_pred             hccCCC-cccccchhHHHHHHHHhcCCceEEEEechhhc
Confidence            333332 22222234457888888766578899999744

>PRK00698 tmk thymidylate kinase; Validated

Probab=95.60  E-value=0.037  Score=48.14  Aligned_cols=28  Identities=21%  Similarity=0.214  Sum_probs=24.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      ..+|+|.|+.|+||||+++.+.+.....
T Consensus         3 ~~~I~ieG~~gsGKsT~~~~L~~~l~~~   30 (205)
T PRK00698          3 GMFITIEGIDGAGKSTQIELLKELLEQQ   30 (205)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            3689999999999999999999987543

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=95.59  E-value=0.033  Score=53.96  Aligned_cols=87  Identities=24%  Similarity=0.375  Sum_probs=50.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCC-------CCCCchH----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-IQDIRKIQGEIADKLGLTL-------HEESDSG----  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~l~~~i~~~l~~~~-------~~~~~~~----  241 (390)
                      +...++|+|..|+|||||++.+.....    .+......+.. .....++....+..-+...       .+.+...    
T Consensus       139 ~Gq~i~I~G~sG~GKTtLl~~I~~~~~----~~~gvi~~iGer~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a  214 (418)
T TIGR03498       139 RGQRLGIFAGSGVGKSTLLSMLARNTD----ADVVVIALVGERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQA  214 (418)
T ss_pred             CCcEEEEECCCCCChHHHHHHHhCCCC----CCEEEEEEEeeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHH
Confidence            446789999999999999988876543    23333333333 3345555555443322211       1111111    


Q ss_pred             --HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          242 --RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       242 --~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                        ....+.+++. .++.+|+++||+.
T Consensus       215 ~~~a~~iAEyfrd~G~~Vll~~DslT  240 (418)
T TIGR03498       215 AYTATAIAEYFRDQGKDVLLLMDSVT  240 (418)
T ss_pred             HHHHHHHHHHHHHcCCCEEEeccchh
Confidence              2234556663 3556999999985

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK13949 shikimate kinase; Provisional

Probab=95.59  E-value=0.011  Score=50.08  Aligned_cols=24  Identities=38%  Similarity=0.376  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      -|.|+|++|+||||+++.+.....
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l~   26 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARELG   26 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            488999999999999999998875

>PRK13947 shikimate kinase; Provisional

Probab=95.59  E-value=0.011  Score=50.00  Aligned_cols=25  Identities=32%  Similarity=0.314  Sum_probs=22.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      -|.|+|++|+||||+++.+.+....
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~   27 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSF   27 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCC
Confidence            4889999999999999999988753

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=95.57  E-value=2.6  Score=41.26  Aligned_cols=53  Identities=17%  Similarity=0.132  Sum_probs=37.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ..++.|-|.+|+|||+++..+......+..+ .++|++  -.-+..++...++...
T Consensus       194 g~liviag~pg~GKT~~al~ia~~~a~~~g~-~v~~fS--lEm~~~~l~~Rl~~~~  246 (421)
T TIGR03600       194 GDLIVIGARPSMGKTTLALNIAENVALREGK-PVLFFS--LEMSAEQLGERLLASK  246 (421)
T ss_pred             CceEEEEeCCCCCHHHHHHHHHHHHHHhCCC-cEEEEE--CCCCHHHHHHHHHHHH
Confidence            4578899999999999999998765432223 345554  4457777777766543

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=95.56  E-value=0.02  Score=47.94  Aligned_cols=33  Identities=24%  Similarity=0.309  Sum_probs=27.9

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          170 LKNPDVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       170 L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      +...+..+|-+.|.+|+||||+|..+...+...
T Consensus        18 ~~~~~~~viW~TGLSGsGKSTiA~ale~~L~~~   50 (197)
T COG0529          18 LKGQKGAVIWFTGLSGSGKSTIANALEEKLFAK   50 (197)
T ss_pred             HhCCCCeEEEeecCCCCCHHHHHHHHHHHHHHc
Confidence            334567899999999999999999999998654

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=95.56  E-value=0.031  Score=51.19  Aligned_cols=34  Identities=21%  Similarity=0.165  Sum_probs=28.3

Q ss_pred             HHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          168 DALKNPDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       168 ~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +.+...+..++.|.|.+|+|||||+..+.+....
T Consensus        97 ~~~~~~~~~~v~l~G~pGsGKTTLl~~l~~~l~~  130 (290)
T PRK10463         97 ARFAARKQLVLNLVSSPGSGKTTLLTETLMRLKD  130 (290)
T ss_pred             HHHHhcCCeEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            3344456889999999999999999999998754

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=95.55  E-value=0.0067  Score=52.15  Aligned_cols=22  Identities=23%  Similarity=0.067  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ++.|+|+.|.||||+++.+...
T Consensus         1 ~~~ltG~N~~GKst~l~~i~~~   22 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVGLI   22 (185)
T ss_pred             CEEEECCCCCcHHHHHHHHHHH
Confidence            4679999999999999999843

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=95.55  E-value=0.016  Score=51.91  Aligned_cols=34  Identities=26%  Similarity=0.349  Sum_probs=23.4

Q ss_pred             EEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 042806          180 IYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK  215 (390)
Q Consensus       180 I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  215 (390)
                      |.||+|+||||+++.+.+.....+  ..++-|+..+
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~~~~--~~~~~vNLDP   34 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLESNG--RDVYIVNLDP   34 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHTTT---S-EEEEE--T
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcc--CCceEEEcch
Confidence            689999999999999999886542  3355555543

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PRK15453 phosphoribulokinase; Provisional

Probab=95.55  E-value=0.11  Score=47.40  Aligned_cols=28  Identities=14%  Similarity=0.252  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+..+|+|.|.+|+||||+++.+.+..+
T Consensus         3 ~k~piI~ItG~SGsGKTTva~~l~~if~   30 (290)
T PRK15453          3 AKHPIIAVTGSSGAGTTTVKRAFEKIFR   30 (290)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3567999999999999999999987664

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=95.55  E-value=0.042  Score=53.32  Aligned_cols=88  Identities=14%  Similarity=0.245  Sum_probs=52.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCC-------CCCCCCchH---
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGL-------TLHEESDSG---  241 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~-------~~~~~~~~~---  241 (390)
                      .....++|.|..|+|||||++.+.+...    .+..++..++.. ....+++.+....-..       ...+.+...   
T Consensus       153 ~~GqrigI~G~sG~GKSTLL~~I~~~~~----~d~~vi~~iGeRgrEv~efl~~~~~~~~~~rtv~vv~tsd~p~~~r~~  228 (433)
T PRK07594        153 GEGQRVGIFSAPGVGKSTLLAMLCNAPD----ADSNVLVLIGERGREVREFIDFTLSEETRKRCVIVVATSDRPALERVR  228 (433)
T ss_pred             CCCCEEEEECCCCCCccHHHHHhcCCCC----CCEEEEEEECCCchHHHHHHHHhhccCCcceEEEEEECCCCCHHHHHH
Confidence            3456889999999999999998876543    455566666543 3444555554321110       011111111   


Q ss_pred             ---HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          242 ---RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       242 ---~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                         ....+.+++. .++.+||++||+.
T Consensus       229 a~~~a~tiAEyfrd~G~~VLl~~Dslt  255 (433)
T PRK07594        229 ALFVATTIAEFFRDNGKRVVLLADSLT  255 (433)
T ss_pred             HHHHHHHHHHHHHHCCCcEEEEEeCHH
Confidence               1234556664 3556999999985

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

Probab=95.54  E-value=0.02  Score=53.67  Aligned_cols=26  Identities=38%  Similarity=0.314  Sum_probs=23.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +-+.++||+|.|||-||+.|+.....
T Consensus       246 kgvLm~GPPGTGKTlLAKAvATEc~t  271 (491)
T KOG0738|consen  246 KGVLMVGPPGTGKTLLAKAVATECGT  271 (491)
T ss_pred             ceeeeeCCCCCcHHHHHHHHHHhhcC
Confidence            56789999999999999999999874

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=95.53  E-value=0.071  Score=47.24  Aligned_cols=48  Identities=15%  Similarity=0.246  Sum_probs=34.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      ...++.|.|++|+|||+++.+++...-.+  =..++|++...  +..++...
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~~~~~--g~~~~y~s~e~--~~~~l~~~   62 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQGLKN--GEKAMYISLEE--REERILGY   62 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCC--CHHHHHHH
Confidence            45789999999999999999998764332  23467777655  45555444

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

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=95.53  E-value=0.011  Score=50.91  Aligned_cols=24  Identities=17%  Similarity=0.329  Sum_probs=21.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .+++|+|+.|+|||||++.+....
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~   26 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQRE   26 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccC
Confidence            468899999999999999997654

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

Probab=95.52  E-value=0.028  Score=48.80  Aligned_cols=37  Identities=27%  Similarity=0.257  Sum_probs=28.1

Q ss_pred             HHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          166 ILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       166 l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      .+..+..+.-++..|.|++|+||||+++.+.......
T Consensus         9 a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~   45 (196)
T PF13604_consen    9 AVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALEAA   45 (196)
T ss_dssp             HHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHHhC
Confidence            3344433455788899999999999999998877654

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

Probab=95.50  E-value=0.024  Score=44.91  Aligned_cols=37  Identities=24%  Similarity=0.275  Sum_probs=27.5

Q ss_pred             HHHHHHHhcC---CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          163 LNDILDALKN---PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       163 ~~~l~~~L~~---~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ++.|...+.+   +++-|++.+|.+|+|||.+++.+++..
T Consensus        38 ~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   38 VNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence            3344444443   346688999999999999999998884

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

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=95.50  E-value=0.065  Score=51.11  Aligned_cols=41  Identities=22%  Similarity=0.247  Sum_probs=31.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI  216 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  216 (390)
                      +++.|.|.+|.|||.||..++.............+++.+..
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~~   42 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKELQNSEEGKKVLYLCGNHP   42 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHhhccccCCceEEEEecch
Confidence            47899999999999999999999822223555677777664

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=95.50  E-value=0.014  Score=50.71  Aligned_cols=25  Identities=28%  Similarity=0.352  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..+|.|.|.+|+||||+++.+....
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~   27 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHR   27 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999999998875

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=95.49  E-value=0.013  Score=48.50  Aligned_cols=23  Identities=30%  Similarity=0.384  Sum_probs=20.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.|+|++|+||||+++.+.....
T Consensus         2 i~l~G~~GsGKstla~~la~~l~   24 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKALG   24 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhC
Confidence            67999999999999999988764

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>PRK04196 V-type ATP synthase subunit B; Provisional

Probab=95.48  E-value=0.052  Score=53.25  Aligned_cols=90  Identities=21%  Similarity=0.292  Sum_probs=57.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc---CCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCCC-------CCCCch--
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE---KLFDQVIFVEVSKI-QDIRKIQGEIADKLGLTL-------HEESDS--  240 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~---~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~~~-------~~~~~~--  240 (390)
                      .-.-++|.|..|+|||+|+..+.+.....   ..+ .++++.++.. ....+++..+...-....       .+.+..  
T Consensus       142 ~GQR~gIfgg~G~GKs~L~~~ia~~~~~d~~~~~~-v~V~~~iGeRgrEv~e~~~~~~~~~~l~rtvvV~atsd~p~~~R  220 (460)
T PRK04196        142 RGQKLPIFSGSGLPHNELAAQIARQAKVLGEEENF-AVVFAAMGITFEEANFFMEDFEETGALERSVVFLNLADDPAIER  220 (460)
T ss_pred             CCCEEEeeCCCCCCccHHHHHHHHhhhhccCCCce-EEEEEEeccccHHHHHHHHHHHhcCCcceEEEEEEcCCCCHHHH
Confidence            34568899999999999999998876432   111 6777878654 356667766655422211       111111  


Q ss_pred             ----HHHHHHHHHHh--CCCeEEEEEeCCC
Q 042806          241 ----GRARSLRNRLK--KEKTILVILDNIW  264 (390)
Q Consensus       241 ----~~~~~l~~~l~--~~~~~LlVlDdv~  264 (390)
                          .....+.++++  .++++||++||+.
T Consensus       221 ~~a~~~a~tiAEyfr~d~G~~VLli~DslT  250 (460)
T PRK04196        221 ILTPRMALTAAEYLAFEKGMHVLVILTDMT  250 (460)
T ss_pred             HHHHHHHHHHHHHHHHhcCCcEEEEEcChH
Confidence                12346777776  4677999999984

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.48  E-value=0.11  Score=47.34  Aligned_cols=89  Identities=16%  Similarity=0.236  Sum_probs=47.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKK  252 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  252 (390)
                      +...++++|++|+||||++..+......+.  ..+.+++..... ...+-+...+..++.+.........+....+.+..
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~l~~~l~~~~--~~v~~i~~D~~ri~~~~ql~~~~~~~~~~~~~~~~~~~l~~~l~~l~~  151 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQFHGKK--KTVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKE  151 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHHHcC--CeEEEEecCCCCHHHHHHHHHHhhhcCceEEecCCHHHHHHHHHHHHh
Confidence            457899999999999999999987764321  235555554322 11111223333344332221222222333333432


Q ss_pred             -CCeEEEEEeCCC
Q 042806          253 -EKTILVILDNIW  264 (390)
Q Consensus       253 -~~~~LlVlDdv~  264 (390)
                       .+.=++++|..-
T Consensus       152 ~~~~D~ViIDt~G  164 (270)
T PRK06731        152 EARVDYILIDTAG  164 (270)
T ss_pred             cCCCCEEEEECCC
Confidence             222478888774

>PRK03846 adenylylsulfate kinase; Provisional

Probab=95.48  E-value=0.022  Score=49.56  Aligned_cols=29  Identities=21%  Similarity=0.198  Sum_probs=25.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+..+|.|+|++|+|||||++.+......
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~~l~~   50 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEEALHE   50 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            46789999999999999999999887643

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=95.47  E-value=0.013  Score=45.29  Aligned_cols=22  Identities=41%  Similarity=0.273  Sum_probs=19.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVA  196 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~  196 (390)
                      ...++|.|++|+|||||++.+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            4678999999999999999986

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=95.47  E-value=0.026  Score=53.22  Aligned_cols=47  Identities=17%  Similarity=0.183  Sum_probs=38.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...++|.+..+..|+-.+.++...-+.|.|+.|+|||||++.+..-.
T Consensus         3 f~~ivgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~r~~~~~~   49 (337)
T TIGR02030         3 FTAIVGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAVRALAALL   49 (337)
T ss_pred             ccccccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHHHHHHHhh
Confidence            34678888888888777777666667899999999999999998765

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.

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=95.46  E-value=0.012  Score=52.07  Aligned_cols=25  Identities=28%  Similarity=0.336  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..-+++|+|++|+|||||.+.+.--
T Consensus        28 ~GEfvsilGpSGcGKSTLLriiAGL   52 (248)
T COG1116          28 KGEFVAILGPSGCGKSTLLRLIAGL   52 (248)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4568999999999999999999654

>PRK13695 putative NTPase; Provisional

Probab=95.46  E-value=0.022  Score=48.32  Aligned_cols=34  Identities=32%  Similarity=0.350  Sum_probs=25.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEE
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFV  211 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv  211 (390)
                      -++|.|++|+|||||++.+++..... .+...-|+
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l~~~-G~~~~g~~   35 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELLKEE-GYKVGGFY   35 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-CCeEEEEE
Confidence            37899999999999999998876542 34433343

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=95.45  E-value=0.015  Score=48.11  Aligned_cols=47  Identities=30%  Similarity=0.346  Sum_probs=34.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLT  233 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~  233 (390)
                      .++++|+|.+|+||||+.+.+.... ..  +..+         +..++.-+++...+..
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~l-~~--~~iv---------NyG~~Mle~A~k~glv   50 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKEL-VK--HKIV---------NYGDLMLEIAKKKGLV   50 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHHH-hh--ceee---------eHhHHHHHHHHHhCCc
Confidence            5789999999999999999888776 21  2111         3456777777777654

>PRK09099 type III secretion system ATPase; Provisional

Probab=95.45  E-value=0.047  Score=53.20  Aligned_cols=87  Identities=18%  Similarity=0.324  Sum_probs=51.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC-CCCCHHHHHHHHHHHhCCC-------CCCCCch-----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS-KIQDIRKIQGEIADKLGLT-------LHEESDS-----  240 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~-~~~~~~~l~~~i~~~l~~~-------~~~~~~~-----  240 (390)
                      +...++|.|+.|+|||||++.+.....    .+..+++.+. ......++...+...-+..       ..+.+..     
T Consensus       162 ~Gq~~~I~G~sG~GKTtLl~~ia~~~~----~d~~vi~~iGer~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~~a  237 (441)
T PRK09099        162 EGQRMGIFAPAGVGKSTLMGMFARGTQ----CDVNVIALIGERGREVREFIELILGEDGMARSVVVCATSDRSSIERAKA  237 (441)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCC----CCeEEEEEEccChHHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHHHH
Confidence            456889999999999999999976543    2333444444 3345555555554432221       1111111     


Q ss_pred             -HHHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          241 -GRARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       241 -~~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                       .....+.+++. .++.+|+++||+.
T Consensus       238 ~~~a~tiAEyfrd~G~~VLl~~DslT  263 (441)
T PRK09099        238 AYVATAIAEYFRDRGLRVLLMMDSLT  263 (441)
T ss_pred             HHHHHHHHHHHHHcCCCEEEeccchh
Confidence             12234555663 3566999999985

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=95.43  E-value=0.047  Score=47.15  Aligned_cols=26  Identities=27%  Similarity=0.275  Sum_probs=23.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+|+|.|+.|+||||+++.+.+....
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~l~~   29 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKLLQE   29 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            57999999999999999999998765

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=95.43  E-value=0.026  Score=56.72  Aligned_cols=60  Identities=12%  Similarity=0.062  Sum_probs=38.3

Q ss_pred             ccccchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 042806          154 EACESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK  215 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  215 (390)
                      +.++|....+.++++.+..  ....-|.|+|+.|+||+++|+.+.+.....  -...+.+++..
T Consensus       204 ~~~ig~s~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~lA~aiH~~s~r~--~~pfv~inca~  265 (520)
T PRK10820        204 SQIVAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLRSPRG--KKPFLALNCAS  265 (520)
T ss_pred             cceeECCHHHHHHHHHHHHHhCCCCCEEEECCCCccHHHHHHHHHHhCCCC--CCCeEEecccc
Confidence            3577777766666665532  223347799999999999999986654211  12234555544

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

Probab=95.43  E-value=0.038  Score=53.14  Aligned_cols=48  Identities=21%  Similarity=0.220  Sum_probs=36.5

Q ss_pred             ccccchhHHHHHHHHHhcC--------------CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          154 EACESRMSTLNDILDALKN--------------PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~--------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ..++|.+..+..+..++..              ..++-|.++|++|+|||+||+.+......
T Consensus        15 ~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~   76 (443)
T PRK05201         15 KYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLANA   76 (443)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            3577887777777666632              01467899999999999999999988753

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=95.38  E-value=0.066  Score=52.19  Aligned_cols=87  Identities=17%  Similarity=0.319  Sum_probs=50.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCCC-------CCCCch-H---
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGLTL-------HEESDS-G---  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~~~-------~~~~~~-~---  241 (390)
                      ....++|+|..|+|||||++.+.....    .+..++..+... ....++...+...-+...       .+.+.. .   
T Consensus       167 ~GqrigI~G~sG~GKSTLl~~I~g~~~----~dv~V~g~Ig~rg~ev~~~~~~~~~~~~l~rsvvv~atsd~~p~~r~~a  242 (451)
T PRK05688        167 RGQRLGLFAGTGVGKSVLLGMMTRFTE----ADIIVVGLIGERGREVKEFIEHILGEEGLKRSVVVASPADDAPLMRLRA  242 (451)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCCC----CCEEEEEEeCcCcHhHHHHHHHHhhcCCccEEEEEEECCCCCHHHHHHH
Confidence            446789999999999999998876432    344444444433 244555555544332211       111111 1   


Q ss_pred             --HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          242 --RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       242 --~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                        ....+.+++. .++++||++||+.
T Consensus       243 ~~~a~aiAEyfrd~G~~VLl~~DslT  268 (451)
T PRK05688        243 AMYCTRIAEYFRDKGKNVLLLMDSLT  268 (451)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEecchh
Confidence              1234556663 3566999999985

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=95.37  E-value=0.016  Score=49.13  Aligned_cols=26  Identities=19%  Similarity=0.267  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...|+|+|+.|+||||+++.+.....
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l~   29 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQLN   29 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHcC
Confidence            34689999999999999999998764

>PRK06851 hypothetical protein; Provisional

Probab=95.37  E-value=0.028  Score=53.37  Aligned_cols=44  Identities=25%  Similarity=0.188  Sum_probs=34.8

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 042806          172 NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI  216 (390)
Q Consensus       172 ~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  216 (390)
                      .+-.+.+.|.|++|+|||||++.++.....+ .++..++-|.+.+
T Consensus       211 ~~~~~~~~i~G~pG~GKstl~~~i~~~a~~~-G~~v~~~hC~~dP  254 (367)
T PRK06851        211 EGVKNRYFLKGRPGTGKSTMLKKIAKAAEER-GFDVEVYHCGFDP  254 (367)
T ss_pred             cccceEEEEeCCCCCcHHHHHHHHHHHHHhC-CCeEEEEeCCCCC
Confidence            3446789999999999999999999998654 4777776665554

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=95.36  E-value=0.014  Score=49.05  Aligned_cols=21  Identities=33%  Similarity=0.295  Sum_probs=17.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+|.|..|+|||||++.+...
T Consensus         2 I~i~G~~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR   22 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHc
Confidence            789999999999999999877

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=95.36  E-value=0.033  Score=51.84  Aligned_cols=27  Identities=33%  Similarity=0.364  Sum_probs=22.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      +++.+.|-||+||||+|....-....+
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~~A~~   28 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALALARR   28 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             eEEEEecCCCCCcHHHHHHHHHHHhhC
Confidence            689999999999999998887776543

...

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=95.36  E-value=0.023  Score=53.12  Aligned_cols=48  Identities=21%  Similarity=0.234  Sum_probs=41.9

Q ss_pred             ccccchhHHHHHHHHHhcC------CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          154 EACESRMSTLNDILDALKN------PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ..|+|-++.++++++.+..      ..-+++.++||.|.|||||+..+.+..+.
T Consensus        61 ~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~le~  114 (358)
T PF08298_consen   61 DEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRGLEE  114 (358)
T ss_pred             ccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHHhhe
Confidence            4689999999999998863      45789999999999999999999888754

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PLN02200 adenylate kinase family protein

Probab=95.35  E-value=0.016  Score=51.74  Aligned_cols=27  Identities=15%  Similarity=0.048  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+.+|.|.|++|+||||+++.+.....
T Consensus        42 ~~~ii~I~G~PGSGKsT~a~~La~~~g   68 (234)
T PLN02200         42 TPFITFVLGGPGSGKGTQCEKIVETFG   68 (234)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            356789999999999999999987653

>PRK06851 hypothetical protein; Provisional

Probab=95.35  E-value=0.031  Score=53.02  Aligned_cols=44  Identities=18%  Similarity=0.141  Sum_probs=33.2

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 042806          172 NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI  216 (390)
Q Consensus       172 ~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~  216 (390)
                      .+..+++.|.|.+|+|||||++.+.+..... .|+...+.+.+.+
T Consensus        27 ~~~~~~~il~G~pGtGKStl~~~i~~~~~~~-g~~Ve~~~~~~d~   70 (367)
T PRK06851         27 DGANRIFILKGGPGTGKSTLMKKIGEEFLEK-GYDVEFLHCSSDN   70 (367)
T ss_pred             cccceEEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEEEcCCCC
Confidence            3456889999999999999999999988653 3665555544443

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=95.35  E-value=0.024  Score=53.27  Aligned_cols=47  Identities=15%  Similarity=0.215  Sum_probs=36.8

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...++|.+..+..+.-.+.+....-+.+.|++|+||||+|+.+..-.
T Consensus         7 f~~i~Gq~~~~~~l~~~~~~~~~~~vLl~G~pG~gKT~lar~la~ll   53 (334)
T PRK13407          7 FSAIVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKSTAVRALAALL   53 (334)
T ss_pred             HHHhCCHHHHHHHHHHHHhccCCCcEEEEcCCCCCHHHHHHHHHHHC
Confidence            45678998888877765544444457899999999999999997775

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=95.34  E-value=0.036  Score=47.86  Aligned_cols=27  Identities=33%  Similarity=0.314  Sum_probs=24.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ..+|+|-||=|+||||||+.+.++.+.
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l~~   30 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHLGF   30 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHhCC
Confidence            468999999999999999999999864

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

Probab=95.33  E-value=0.2  Score=51.25  Aligned_cols=168  Identities=15%  Similarity=0.120  Sum_probs=86.5

Q ss_pred             cccchhHHHHHHHHHhcCC---------CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC--eEEEEEeCCCCCHHHHH
Q 042806          155 ACESRMSTLNDILDALKNP---------DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFD--QVIFVEVSKIQDIRKIQ  223 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~~---------~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~--~~~wv~v~~~~~~~~l~  223 (390)
                      ...+++..+..+.+.+...         -..++.++|++|+||||+++.++...... -|.  |.-.++-+...+     
T Consensus       402 ~~~~~~~~~~~l~~vl~p~~~~s~~~~~~~~~vLLhG~~g~GK~t~V~~vas~lg~h-~~evdc~el~~~s~~~~-----  475 (953)
T KOG0736|consen  402 SPPGLEAKVLELVAVLSPQKQPSGALLTLNPSVLLHGPPGSGKTTVVRAVASELGLH-LLEVDCYELVAESASHT-----  475 (953)
T ss_pred             CCccchHHHHHHHHHhCcccCcchhccccceEEEEeCCCCCChHHHHHHHHHHhCCc-eEeccHHHHhhcccchh-----
Confidence            3455666666677766542         24678899999999999999999987532 121  111111111111     


Q ss_pred             HHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC-------cc------ccccc--CCCCCCCCCcEEEEE
Q 042806          224 GEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN-------LD------FQAVG--IPHGDDRKGCKVLLT  288 (390)
Q Consensus       224 ~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~-------~~------~~~l~--~~l~~~~~~s~IivT  288 (390)
                                     .. ......+..+.-.+.+|.|-+++-.       .+      .+.+.  .-++...++.-++.|
T Consensus       476 ---------------et-kl~~~f~~a~~~~pavifl~~~dvl~id~dgged~rl~~~i~~~ls~e~~~~~~~~~ivv~t  539 (953)
T KOG0736|consen  476 ---------------ET-KLQAIFSRARRCSPAVLFLRNLDVLGIDQDGGEDARLLKVIRHLLSNEDFKFSCPPVIVVAT  539 (953)
T ss_pred             ---------------HH-HHHHHHHHHhhcCceEEEEeccceeeecCCCchhHHHHHHHHHHHhcccccCCCCceEEEEe
Confidence                           11 1112222222223456665555311       11      11111  112223445555666


Q ss_pred             ecc-hhhhhh-cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCC
Q 042806          289 ARS-LDVLSR-KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGL  346 (390)
Q Consensus       289 tr~-~~v~~~-~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~Gl  346 (390)
                      +.+ +.+... .....+.+++..+++++=.++|+-.........  +.-.+..+.+|.|.
T Consensus       540 ~~s~~~lp~~i~~~f~~ei~~~~lse~qRl~iLq~y~~~~~~n~--~v~~k~~a~~t~gf  597 (953)
T KOG0736|consen  540 TSSIEDLPADIQSLFLHEIEVPALSEEQRLEILQWYLNHLPLNQ--DVNLKQLARKTSGF  597 (953)
T ss_pred             ccccccCCHHHHHhhhhhccCCCCCHHHHHHHHHHHHhccccch--HHHHHHHHHhcCCC
Confidence            554 333221 112346888999999999999987775322221  12234566666654

>COG3910 Predicted ATPase [General function prediction only]

Probab=95.33  E-value=0.12  Score=43.94  Aligned_cols=26  Identities=27%  Similarity=0.230  Sum_probs=22.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +.++-.|+|..|+||+||.-.+.-..
T Consensus        36 ~apIT~i~GENGsGKSTLLEaiA~~~   61 (233)
T COG3910          36 RAPITFITGENGSGKSTLLEAIAAGM   61 (233)
T ss_pred             cCceEEEEcCCCccHHHHHHHHHhhc
Confidence            56889999999999999999887654

>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]

Probab=95.32  E-value=0.062  Score=50.21  Aligned_cols=90  Identities=17%  Similarity=0.278  Sum_probs=58.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCCC----------CCCCc---h
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGLTL----------HEESD---S  240 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~~~----------~~~~~---~  240 (390)
                      -.-|++.|-+|+|||.|.+.+.+.... .|=...+|.-++.. ..-.+++.++...--.+.          +....   .
T Consensus       147 GgKiGLFGGAGVGKTVl~~ELI~Nia~-~h~g~SVFaGvGERtREGndLy~Em~es~vl~ktalv~gQMNEpPGaR~RVa  225 (468)
T COG0055         147 GGKIGLFGGAGVGKTVLIQELINNIAK-EHGGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARMRVA  225 (468)
T ss_pred             CceeeeeccCCccceeeHHHHHHHHHH-HcCCeEEEEeccccccchHHHHHHHHhcCCCCceeEEEeecCCCCcceeeeh
Confidence            456889999999999999999998764 34456788877654 356778888765532211          11111   1


Q ss_pred             HHHHHHHHHHhC--CCeEEEEEeCCCC
Q 042806          241 GRARSLRNRLKK--EKTILVILDNIWG  265 (390)
Q Consensus       241 ~~~~~l~~~l~~--~~~~LlVlDdv~~  265 (390)
                      -.-....+++++  ++.+|+.+||+..
T Consensus       226 ltGlT~AEyfRD~~gqdVLlFIDNIfR  252 (468)
T COG0055         226 LTGLTMAEYFRDEEGQDVLLFIDNIFR  252 (468)
T ss_pred             hhhhhHHHHhhcccCCeEEEEehhhhH
Confidence            112244555653  5669999999963

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=95.31  E-value=0.015  Score=51.29  Aligned_cols=26  Identities=38%  Similarity=0.403  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-+++|+|++|+|||||++.+.--.
T Consensus        32 ~Ge~lgivGeSGsGKSTL~r~l~Gl~   57 (252)
T COG1124          32 RGETLGIVGESGSGKSTLARLLAGLE   57 (252)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhccc
Confidence            45689999999999999999997544

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=95.29  E-value=0.051  Score=51.02  Aligned_cols=38  Identities=26%  Similarity=0.422  Sum_probs=29.6

Q ss_pred             HHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          165 DILDALK--NPDVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       165 ~l~~~L~--~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      .+++.+.  .++..+|.|.|++|+|||||+..+.......
T Consensus        44 ~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~l~~~l~~~   83 (332)
T PRK09435         44 ELLDALLPHTGNALRIGITGVPGVGKSTFIEALGMHLIEQ   83 (332)
T ss_pred             HHHHHHhhcCCCcEEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            4444443  3567899999999999999999998887653

>TIGR01287 nifH nitrogenase iron protein

Probab=95.27  E-value=0.018  Score=52.92  Aligned_cols=27  Identities=33%  Similarity=0.539  Sum_probs=23.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      +.|+|+|-||+||||++..+......+
T Consensus         1 ~~ia~~gKGGVGKTT~a~nLA~~La~~   27 (275)
T TIGR01287         1 RQIAIYGKGGIGKSTTTQNIAAALAEM   27 (275)
T ss_pred             CeeEEeCCCcCcHHHHHHHHHHHHHHC
Confidence            468999999999999999999887654

This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=95.25  E-value=0.025  Score=44.87  Aligned_cols=29  Identities=24%  Similarity=0.250  Sum_probs=24.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      ...+|.+.|.=|+||||+++.++......
T Consensus        14 ~g~vi~L~GdLGaGKTtf~r~l~~~lg~~   42 (123)
T PF02367_consen   14 PGDVILLSGDLGAGKTTFVRGLARALGID   42 (123)
T ss_dssp             S-EEEEEEESTTSSHHHHHHHHHHHTT--
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            45789999999999999999999988654

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=95.23  E-value=0.02  Score=47.75  Aligned_cols=29  Identities=34%  Similarity=0.489  Sum_probs=26.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEK  203 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~  203 (390)
                      .+++.|+|..|+|||||+..+....+.++
T Consensus         2 ~~Il~ivG~k~SGKTTLie~lv~~L~~~G   30 (161)
T COG1763           2 MKILGIVGYKNSGKTTLIEKLVRKLKARG   30 (161)
T ss_pred             CcEEEEEecCCCChhhHHHHHHHHHHhCC
Confidence            47899999999999999999999988753

>PRK13974 thymidylate kinase; Provisional

Probab=95.23  E-value=0.16  Score=44.63  Aligned_cols=28  Identities=18%  Similarity=0.253  Sum_probs=24.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcC
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEK  203 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~  203 (390)
                      .+|++.|+.|+||||+++.++......+
T Consensus         4 ~~i~~eG~dGsGKsT~~~~l~~~l~~~g   31 (212)
T PRK13974          4 KFIVLEGIDGCGKTTQIDHLSKWLPSSG   31 (212)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence            5799999999999999999999886543

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=95.22  E-value=0.016  Score=50.96  Aligned_cols=25  Identities=24%  Similarity=0.234  Sum_probs=21.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .--+++|+|++|+|||||...+.--
T Consensus        30 ~Ge~vaI~GpSGSGKSTLLniig~l   54 (226)
T COG1136          30 AGEFVAIVGPSGSGKSTLLNLLGGL   54 (226)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcc
Confidence            4568999999999999999988654

>PLN02674 adenylate kinase

Probab=95.20  E-value=0.1  Score=46.71  Aligned_cols=26  Identities=19%  Similarity=0.017  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...|.|.|++|+||||+++.+.....
T Consensus        31 ~~~i~l~G~PGsGKgT~a~~La~~~~   56 (244)
T PLN02674         31 DKRLILIGPPGSGKGTQSPIIKDEYC   56 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHcC
Confidence            35578999999999999999988753

>PRK07721 fliI flagellum-specific ATP synthase; Validated

Probab=95.19  E-value=0.079  Score=51.74  Aligned_cols=89  Identities=15%  Similarity=0.201  Sum_probs=48.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh------CC-CCCCCCch-----
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL------GL-TLHEESDS-----  240 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l------~~-~~~~~~~~-----  240 (390)
                      .....++|+|..|+|||||++.+......   -.+.+++.-.......++.......-      .. ...+.+..     
T Consensus       156 ~~Gq~i~I~G~sG~GKStLl~~I~~~~~~---~~gvI~~~Gerg~ev~e~~~~~l~~~~l~r~v~vv~~~~~~~~~r~~~  232 (438)
T PRK07721        156 GKGQRVGIFAGSGVGKSTLMGMIARNTSA---DLNVIALIGERGREVREFIERDLGPEGLKRSIVVVATSDQPALMRIKG  232 (438)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhcccCC---CeEEEEEEecCCccHHHHHHhhcChhhhcCeEEEEECCCCCHHHHHHH
Confidence            45678999999999999999988775432   12333332223334555444322211      10 11111111     


Q ss_pred             -HHHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          241 -GRARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       241 -~~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                       .....+.+++. .++.+||++||+.
T Consensus       233 ~~~a~~iAEyfr~~g~~Vll~~Dslt  258 (438)
T PRK07721        233 AYTATAIAEYFRDQGLNVMLMMDSVT  258 (438)
T ss_pred             HHHHHHHHHHHHHCCCcEEEEEeChH
Confidence             12234555663 3566999999984

>PRK06761 hypothetical protein; Provisional

Probab=95.17  E-value=0.038  Score=50.57  Aligned_cols=33  Identities=21%  Similarity=0.229  Sum_probs=26.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEE
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVI  209 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~  209 (390)
                      ++|.|.|++|+||||+++.+.+..... .++...
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L~~~-g~~v~~   36 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDILSQN-GIEVEL   36 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCcC-ceEEEE
Confidence            579999999999999999999987642 344433

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=95.17  E-value=0.07  Score=51.85  Aligned_cols=85  Identities=20%  Similarity=0.222  Sum_probs=49.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC-HHHHHHHHHHHhCCC---------CCCCCch--
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD-IRKIQGEIADKLGLT---------LHEESDS--  240 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~l~~~i~~~l~~~---------~~~~~~~--  240 (390)
                      .+...++|.|..|+|||||++.+.....    .+..++..++.... ..++...   .++..         ..+.+..  
T Consensus       155 ~~Gq~~~i~G~sG~GKStLl~~i~~~~~----~~v~vi~~iGergrev~e~~~~---~l~~~l~~tvvV~atsddsp~~R  227 (434)
T PRK08472        155 GKGQKLGIFAGSGVGKSTLMGMIVKGCL----APIKVVALIGERGREIPEFIEK---NLGGDLENTVIVVATSDDSPLMR  227 (434)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhhccC----CCEEEEEeeCccchhHHHHHHH---HhcCcccceEEEEECCCCCHHHh
Confidence            3456889999999999999999986542    34445555544432 2333332   22221         0011111  


Q ss_pred             ----HHHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          241 ----GRARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       241 ----~~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                          .....+.+++. .++.+|+++||+.
T Consensus       228 ~~~~~~a~~iAEyFrd~G~~Vll~~DslT  256 (434)
T PRK08472        228 KYGAFCAMSVAEYFKNQGLDVLFIMDSVT  256 (434)
T ss_pred             hHHHHHHHHHHHHHHHcCCCEEEecccch
Confidence                12334556663 3566999999985

>PRK08760 replicative DNA helicase; Provisional

Probab=95.17  E-value=0.88  Score=45.23  Aligned_cols=54  Identities=15%  Similarity=0.083  Sum_probs=36.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ...++.|-|.+|+|||+++..++.....+.... ++++  |-.-+..++...+....
T Consensus       228 ~G~LivIaarPg~GKTafal~iA~~~a~~~g~~-V~~f--SlEMs~~ql~~Rl~a~~  281 (476)
T PRK08760        228 PTDLIILAARPAMGKTTFALNIAEYAAIKSKKG-VAVF--SMEMSASQLAMRLISSN  281 (476)
T ss_pred             CCceEEEEeCCCCChhHHHHHHHHHHHHhcCCc-eEEE--eccCCHHHHHHHHHHhh
Confidence            346788999999999999999988764332333 3333  44456667777665543

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=95.15  E-value=0.089  Score=51.09  Aligned_cols=89  Identities=19%  Similarity=0.292  Sum_probs=52.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC-CCCCHHHHHHHHHHHhCCCC-------CCCCchH----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS-KIQDIRKIQGEIADKLGLTL-------HEESDSG----  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~-~~~~~~~l~~~i~~~l~~~~-------~~~~~~~----  241 (390)
                      ....++|+|..|+|||||++.++.....    +......+. ......+++...+..-+...       .+.+...    
T Consensus       155 ~Gqri~I~G~sG~GKTtLl~~Ia~~~~~----~~gvI~~iGerg~ev~e~~~~~l~~~gl~~tvvv~~tsd~s~~~r~ra  230 (432)
T PRK06793        155 IGQKIGIFAGSGVGKSTLLGMIAKNAKA----DINVISLVGERGREVKDFIRKELGEEGMRKSVVVVATSDESHLMQLRA  230 (432)
T ss_pred             CCcEEEEECCCCCChHHHHHHHhccCCC----CeEEEEeCCCCcccHHHHHHHHhhhcccceeEEEEECCCCCHHHHHHH
Confidence            4568899999999999999998876532    222222333 33566677666555533221       1111111    


Q ss_pred             --HHHHHHHHHh-CCCeEEEEEeCCCCC
Q 042806          242 --RARSLRNRLK-KEKTILVILDNIWGN  266 (390)
Q Consensus       242 --~~~~l~~~l~-~~~~~LlVlDdv~~~  266 (390)
                        ....+.+++. .+++.||++||+...
T Consensus       231 ~~~a~~iAEyfr~~G~~VLlilDslTr~  258 (432)
T PRK06793        231 AKLATSIAEYFRDQGNNVLLMMDSVTRF  258 (432)
T ss_pred             HHHHHHHHHHHHHcCCcEEEEecchHHH
Confidence              1224445553 356699999999644

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=95.15  E-value=0.065  Score=52.06  Aligned_cols=26  Identities=19%  Similarity=0.288  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +...++|.|+.|+|||||++.+....
T Consensus       154 ~GQ~igI~G~sGaGKSTLl~~I~g~~  179 (434)
T PRK07196        154 KGQRVGLMAGSGVGKSVLLGMITRYT  179 (434)
T ss_pred             cceEEEEECCCCCCccHHHHHHhccc
Confidence            45789999999999999999887644

>PLN02459 probable adenylate kinase

Probab=95.15  E-value=0.12  Score=46.60  Aligned_cols=24  Identities=21%  Similarity=0.201  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .|.|.|++|+||||++..+.....
T Consensus        31 ~ii~~G~PGsGK~T~a~~la~~~~   54 (261)
T PLN02459         31 NWVFLGCPGVGKGTYASRLSKLLG   54 (261)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            477789999999999999988653

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=95.14  E-value=0.018  Score=49.71  Aligned_cols=22  Identities=32%  Similarity=0.308  Sum_probs=20.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |.|.|++|+||||+++.+....
T Consensus         2 I~i~G~pGsGKst~a~~La~~~   23 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKY   23 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7899999999999999998874

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

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

Probab=95.13  E-value=0.049  Score=50.65  Aligned_cols=54  Identities=22%  Similarity=0.164  Sum_probs=41.3

Q ss_pred             cccccchhHHHH---HHHHHhcCCC--ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC
Q 042806          153 YEACESRMSTLN---DILDALKNPD--VNMLGIYGMGGIVKTTLAKEVARKAETEKLFD  206 (390)
Q Consensus       153 ~~~~~gR~~~~~---~l~~~L~~~~--~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~  206 (390)
                      .++++|..+..+   -+++++.+++  .+.|.+.|++|.|||.||..+.+.+...-+|.
T Consensus        38 ~dG~VGQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dvPF~   96 (450)
T COG1224          38 GDGLVGQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIARELGEDVPFV   96 (450)
T ss_pred             CCcccchHHHHHhhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHHHHHHhCCCCCce
Confidence            467888665443   4566666653  57899999999999999999999998665563

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=95.12  E-value=0.026  Score=49.81  Aligned_cols=22  Identities=32%  Similarity=0.243  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      ++++|.|+.|.||||+.+.+..
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~   52 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVAL   52 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            7899999999999999999864

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

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

Probab=95.12  E-value=0.017  Score=46.81  Aligned_cols=26  Identities=31%  Similarity=0.309  Sum_probs=22.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+++|+|+.|+|||||.+.++....
T Consensus        11 g~~~~i~G~nGsGKStLl~~l~g~~~   36 (137)
T PF00005_consen   11 GEIVAIVGPNGSGKSTLLKALAGLLP   36 (137)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHTTSSH
T ss_pred             CCEEEEEccCCCccccceeeeccccc
Confidence            45789999999999999998876653

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

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=95.10  E-value=0.07  Score=53.53  Aligned_cols=120  Identities=18%  Similarity=0.257  Sum_probs=64.4

Q ss_pred             HHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC--HHHHHHHHHHHhCCCCCC-----
Q 042806          164 NDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD--IRKIQGEIADKLGLTLHE-----  236 (390)
Q Consensus       164 ~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~--~~~l~~~i~~~l~~~~~~-----  236 (390)
                      .+|++.+.+  ..||.|+|..|+||||-..++.....    |...--|.+.++.-  .-.+.+.+...++.....     
T Consensus       362 ~~ll~~ir~--n~vvvivgETGSGKTTQl~QyL~edG----Y~~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VGYs  435 (1042)
T KOG0924|consen  362 DQLLSVIRE--NQVVVIVGETGSGKTTQLAQYLYEDG----YADNGMIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGYS  435 (1042)
T ss_pred             HHHHHHHhh--CcEEEEEecCCCCchhhhHHHHHhcc----cccCCeeeecCchHHHHHHHHHHHHHHhCCccccccceE
Confidence            344444443  46899999999999976555544432    43223455555543  344566777777442111     


Q ss_pred             -----C-Cc------hHHHHHHHHHHh----CCCeEEEEEeCCCCCcc----c-ccccCCCCCCCCCcEEEEEecc
Q 042806          237 -----E-SD------SGRARSLRNRLK----KEKTILVILDNIWGNLD----F-QAVGIPHGDDRKGCKVLLTARS  291 (390)
Q Consensus       237 -----~-~~------~~~~~~l~~~l~----~~~~~LlVlDdv~~~~~----~-~~l~~~l~~~~~~s~IivTtr~  291 (390)
                           . +.      ...-..|++.|.    .+. -+||+|..+....    + .-++..+ ......++||||-.
T Consensus       436 IRFEdvT~~~T~IkymTDGiLLrEsL~d~~L~kY-SviImDEAHERslNtDilfGllk~~l-arRrdlKliVtSAT  509 (1042)
T KOG0924|consen  436 IRFEDVTSEDTKIKYMTDGILLRESLKDRDLDKY-SVIIMDEAHERSLNTDILFGLLKKVL-ARRRDLKLIVTSAT  509 (1042)
T ss_pred             EEeeecCCCceeEEEeccchHHHHHhhhhhhhhe-eEEEechhhhcccchHHHHHHHHHHH-HhhccceEEEeecc
Confidence                 0 11      111123444443    333 6899999975522    1 1111111 23346799999875

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=95.09  E-value=0.088  Score=51.01  Aligned_cols=87  Identities=20%  Similarity=0.328  Sum_probs=49.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCC-------CCCCCch-----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGLT-------LHEESDS-----  240 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~~-------~~~~~~~-----  240 (390)
                      ....++|+|..|+|||||++.+.....    .+..+...++.. ....++....+..-+..       ..+.+..     
T Consensus       136 ~Gqri~I~G~sG~GKTtLl~~i~~~~~----~~~gvi~~~Ger~~ev~e~~~~~l~~~~~~~~v~v~~tsd~~~~~r~~~  211 (413)
T TIGR03497       136 KGQRVGIFAGSGVGKSTLLGMIARNAK----ADINVIALIGERGREVRDFIEKDLGEEGLKRSVVVVATSDQPALMRLKA  211 (413)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCC----CCeEEEEEEccchHHHHHHHHHHhcccccceEEEEEECCCCCHHHHHHH
Confidence            456899999999999999998876543    233333334432 24445554443322111       1111111     


Q ss_pred             -HHHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          241 -GRARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       241 -~~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                       .....+.+++. .++.+||++||+.
T Consensus       212 ~~~a~tiAEyfr~~G~~Vll~~Dslt  237 (413)
T TIGR03497       212 AFTATAIAEYFRDQGKDVLLMMDSVT  237 (413)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEcCcH
Confidence             12234555553 3566999999984

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=95.07  E-value=0.1  Score=45.54  Aligned_cols=25  Identities=24%  Similarity=0.072  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..+++.|.|+.|.||||+.+.+..-
T Consensus        28 ~~~~~~l~G~n~~GKstll~~i~~~   52 (204)
T cd03282          28 SSRFHIITGPNMSGKSTYLKQIALL   52 (204)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3478999999999999999988654

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

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=95.07  E-value=0.021  Score=48.07  Aligned_cols=24  Identities=42%  Similarity=0.419  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +|.|.|+.|+||||+|+.+.+...
T Consensus         2 iI~i~G~~GSGKstia~~la~~lg   25 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEKLS   25 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            689999999999999999988653

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>smart00072 GuKc Guanylate kinase homologues

Probab=95.06  E-value=0.023  Score=48.79  Aligned_cols=25  Identities=24%  Similarity=0.279  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .+.|.|+|++|+||+||+..+....
T Consensus         2 ~r~ivl~Gpsg~GK~tl~~~L~~~~   26 (184)
T smart00072        2 RRPIVLSGPSGVGKGTLLAELIQEI   26 (184)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHhcC
Confidence            4678999999999999999998875

Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.

>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=95.06  E-value=0.025  Score=53.83  Aligned_cols=77  Identities=16%  Similarity=0.106  Sum_probs=45.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      .++=+-|||+.|.|||-|+-.+|+....+..-          .....+.+..+-+.+.....   ....+..+.+.+.++
T Consensus        61 ~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~----------R~HFh~Fm~~vh~~l~~~~~---~~~~l~~va~~l~~~  127 (362)
T PF03969_consen   61 PPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKR----------RVHFHEFMLDVHSRLHQLRG---QDDPLPQVADELAKE  127 (362)
T ss_pred             CCceEEEECCCCCchhHHHHHHHHhCCccccc----------cccccHHHHHHHHHHHHHhC---CCccHHHHHHHHHhc
Confidence            45678899999999999999999997653110          01112444444333322111   111233444555444


Q ss_pred             CeEEEEEeCCC
Q 042806          254 KTILVILDNIW  264 (390)
Q Consensus       254 ~~~LlVlDdv~  264 (390)
                      . .||.||.+.
T Consensus       128 ~-~lLcfDEF~  137 (362)
T PF03969_consen  128 S-RLLCFDEFQ  137 (362)
T ss_pred             C-CEEEEeeee
Confidence            4 699999985

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

>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase

Probab=95.06  E-value=0.15  Score=49.62  Aligned_cols=88  Identities=18%  Similarity=0.297  Sum_probs=51.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCC-------CCCCCch----
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-IQDIRKIQGEIADKLGLT-------LHEESDS----  240 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~l~~~i~~~l~~~-------~~~~~~~----  240 (390)
                      .+...++|.|+.|+|||||++.+.....    .+...+..+.. .....++..+........       ....+..    
T Consensus       143 ~~Gq~~~I~G~sG~GKStLl~~I~~~~~----~~~~vi~~iG~~~~ev~~~~~~~~~~~~~~~tvvv~~~s~~p~~~r~~  218 (422)
T TIGR02546       143 GEGQRIGIFAGAGVGKSTLLGMIARGAS----ADVNVIALIGERGREVREFIEHHLGEEGRKRSVLVVSTSDRPSLERLK  218 (422)
T ss_pred             cCCCEEEEECCCCCChHHHHHHHhCCCC----CCEEEEEEEccCCcCHHHHHHHHhccccccceEEEeccccCCHHHHHH
Confidence            3456789999999999999998887543    34444445543 334555554443332111       1111111    


Q ss_pred             --HHHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          241 --GRARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       241 --~~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                        .....+.+++. .+++.|+++|++.
T Consensus       219 ~~~~a~~~AE~f~~~g~~Vl~~~Dslt  245 (422)
T TIGR02546       219 AAYTATAIAEYFRDQGKRVLLMMDSLT  245 (422)
T ss_pred             HHHHHHHHHHHHHHCCCcEEEEEeCch
Confidence              12223445553 3566999999995

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=95.05  E-value=0.074  Score=45.55  Aligned_cols=117  Identities=21%  Similarity=0.112  Sum_probs=63.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC---CCCHHHHHHHHH--HH--hCCC--CCCCCchH---
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK---IQDIRKIQGEIA--DK--LGLT--LHEESDSG---  241 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~---~~~~~~l~~~i~--~~--l~~~--~~~~~~~~---  241 (390)
                      ....|.|+|..|-||||.|.-+.-+.-..+ +. +..+.+-.   ......++..+-  ..  .+..  ....+...   
T Consensus        21 ~~g~v~v~~g~GkGKtt~a~g~a~ra~g~G-~~-V~ivQFlKg~~~~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~   98 (191)
T PRK05986         21 EKGLLIVHTGNGKGKSTAAFGMALRAVGHG-KK-VGVVQFIKGAWSTGERNLLEFGGGVEFHVMGTGFTWETQDRERDIA   98 (191)
T ss_pred             cCCeEEEECCCCCChHHHHHHHHHHHHHCC-Ce-EEEEEEecCCCccCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHH
Confidence            346788999999999999999888765432 33 22333321   234444443320  00  0111  11111111   


Q ss_pred             ----HHHHHHHHHhCCCeEEEEEeCCCCC-----cccccccCCCCCCCCCcEEEEEecch
Q 042806          242 ----RARSLRNRLKKEKTILVILDNIWGN-----LDFQAVGIPHGDDRKGCKVLLTARSL  292 (390)
Q Consensus       242 ----~~~~l~~~l~~~~~~LlVlDdv~~~-----~~~~~l~~~l~~~~~~s~IivTtr~~  292 (390)
                          ......+.+.+++-=|||||.+-..     -..+++...+....++..||+|-|+.
T Consensus        99 ~~~~~~~~a~~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~  158 (191)
T PRK05986         99 AAREGWEEAKRMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGA  158 (191)
T ss_pred             HHHHHHHHHHHHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCC
Confidence                1223444555555349999998432     23344444444445667899999974

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	390
3sfz_A	1249	Crystal Structure Of Full-Length Murine Apaf-1 Leng		3e-04
1z6t_A	591	Structure Of The Apoptotic Protease-activating Fact		8e-04

>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1 Length = 1249

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 59/212 (27%), Positives = 87/212 (41%), Gaps = 38/212 (17%)
Query: 172 NPDVNMLGIYGMGGIVKTTLAKEVAR-KAETEKLFD-QVIFVEVSKIQD----IRKIQG- 224
           N +   + IYGM G  K+ LA E  R  +  E  F   V +V + K QD    + K+Q  
Sbjct: 144 NGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGK-QDKSGLLMKLQNL 202
Query: 225 --------EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPH 276
                     + +L L + E  D  R   LR    K    L+ILD++W     +A     
Sbjct: 203 CMRLDQEESFSQRLPLNIEEAKDRLRVLMLR----KHPRSLLILDDVWDPWVLKAF---- 254
Query: 277 GDDRKGCKVLLTARSLDVLSRKMDSQQNFSV----GVLKEDEAWSLFKKMAGDYIEGSEF 332
            D++  C++LLT R   V    M  +    V    G  K  E  SLF  M  + +     
Sbjct: 255 -DNQ--CQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAE-- 309
Query: 333 KWVAKDVARECAGLPVSIVTVARALGTRDYLN 364
              A  + +EC G P+ +  +   L  RD+ N
Sbjct: 310 ---AHSIIKECKGSPLVVSLIGALL--RDFPN 336

>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1 Bound To Adp Length = 591

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 84/204 (41%), Gaps = 38/204 (18%)
Query: 180 IYGMGGIVKTTLAKEVAR-KAETEKLFD-QVIFVEVSKIQD----IRKIQG--------- 224
           I+GM G  K+ LA E  R  +  E  F   V +V V K QD    + K+Q          
Sbjct: 152 IHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGK-QDKSGLLMKLQNLCTRLDQDE 210
Query: 225 EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCK 284
             + +L L + E  D  R   LR    K    L+ILD++W +   +A           C+
Sbjct: 211 SFSQRLPLNIEEAKDRLRILMLR----KHPRSLLILDDVWDSWVLKAFD-------SQCQ 259
Query: 285 VLLTARSLDVLSRKMDSQQ----NFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVA 340
           +LLT R   V    M  +       S+G  K  E  SLF  M     + ++    A  + 
Sbjct: 260 ILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNM-----KKADLPEQAHSII 314
Query: 341 RECAGLPVSIVTVARALGTRDYLN 364
           +EC G P+ +  +   L  RD+ N
Sbjct: 315 KECKGSPLVVSLIGALL--RDFPN 336

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	390
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	9e-37
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-36
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	4e-24
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	3e-14

>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* Length = 549

 Score =  139 bits (351), Expect = 9e-37
 Identities = 48/341 (14%), Positives = 108/341 (31%), Gaps = 27/341 (7%)

Query: 65  EEIEEYVEKWLTSVNGIIDEAEKFTGVDARANK---RCFKGLCPNLKT-RRRLSKEAERQ 120
           E+  E + K  T +  I +    +    +               +L          A  +
Sbjct: 38  EDHSELISKMSTRLERIANFLRIYRRQASELGPLIDFFNYNNQSHLADFLEDYIDFAINE 97

Query: 121 KEAIVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDVNMLGI 180
            + +  V    +F R   +       +         E  +  +   LD + + D   L +
Sbjct: 98  PDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFL 157

Query: 181 YGMGGIVKTTLAKEVARKAE--TEKLFDQVIFVEVS---------KIQDIRKIQGEIADK 229
           +G  G  K+ +A +   K++      +D +++++ S            DI  +     D 
Sbjct: 158 HGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDL 217

Query: 230 LGLTLHEESDSGRARSLR-NRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLT 288
           L     E   S   + +  N L      L + D++      +             + L+T
Sbjct: 218 LNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWA------QELRLRCLVT 271

Query: 289 ARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV 348
            R +++ +    + +   V  L+ DE +   +        G + + V        +G P 
Sbjct: 272 TRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPA 331

Query: 349 SIVTVARALGTRD-----YLNGRTHWNSWGGLLQLTLKIYN 384
           +++   ++   +       LN +       G+  +T   Y 
Sbjct: 332 TLMMFFKSCEPKTFEKMAQLNNKLESRGLVGVECITPYSYK 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 =  140 bits (354), Expect = 1e-36
 Identities = 73/379 (19%), Positives = 131/379 (34%), Gaps = 73/379 (19%)

Query: 23  QMSYLRKSKYTSNLQNLKTEVG---IPEAER-VSKQREVDKAKRRGEEIEE-YVEKWLTS 77
           +  Y  K   +              + +  + +  + E+D      + +       W   
Sbjct: 13  EHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLL 72

Query: 78  VNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQKEAIVKVREVGRFDRIS 137
                +  +KF     R N   +K L   +KT        +RQ   + ++    R DR+ 
Sbjct: 73  SKQE-EMVQKFVEEVLRIN---YKFLMSPIKTE-------QRQPSMMTRMYIEQR-DRL- 119

Query: 138 YNIIPDDTLLLSIKDYEACESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEV 195
           YN             Y    SR+     +  AL    P  N + I G+ G  KT +A +V
Sbjct: 120 YNDNQ------VFAKYNV--SRLQPYLKLRQALLELRPAKN-VLIDGVLGSGKTWVALDV 170

Query: 196 ARKAETEKLFDQVIF----VEVSKIQDIRKIQGEIADKLGLTLHEESDSG-----RARSL 246
               + +   D  IF       +  + + ++  ++  ++       SD       R  S+
Sbjct: 171 CLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSI 230

Query: 247 RNRL------KKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTAR------SLDV 294
           +  L      K  +  L++L N+     + A  +        CK+LLT R       L  
Sbjct: 231 QAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNL-------SCKILLTTRFKQVTDFLSA 283

Query: 295 LSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARE-CAGLPVSIVTV 353
            +    S  + S+  L  DE  SL  K    Y++        +D+ RE     P  +  +
Sbjct: 284 ATTTHISLDHHSMT-LTPDEVKSLLLK----YLDCR-----PQDLPREVLTTNPRRLSII 333

Query: 354 ARALGTRDYLNGRTHWNSW 372
           A ++  RD L     W++W
Sbjct: 334 AESI--RDGLA---TWDNW 347

>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 = 42.9 bits (100), Expect = 1e-04
 Identities = 67/420 (15%), Positives = 122/420 (29%), Gaps = 140/420 (33%)

Query: 18  PPIYCQMSYLRKSKYT---SNLQNLKTEVGIPE-----------AERVSKQREVDKAKRR 63
             ++ + +  R   Y      L  L+    +             A  V    +V    + 
Sbjct: 123 NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQC--KM 180

Query: 64  GEEIEEYVEKWLTSVNGIIDEAEKFTGVDARANKRCFKGLCPNLKTRRRLSKEAERQKEA 123
             +I  +   WL   N    E      V     K  ++ + PN  +R   S   + +  +
Sbjct: 181 DFKI--F---WLNLKNCNSPET-----VLEMLQKLLYQ-IDPNWTSRSDHSSNIKLRIHS 229

Query: 124 IVKVREVGRFDRISYNIIPDDTLLLSIKDYEACESRMSTLNDILDALKNPDV-NMLGIYG 182
           I           +          LL  K YE C      L  +L  ++N    N   +  
Sbjct: 230 IQ--------AELRR--------LLKSKPYENC------L-LVLLNVQNAKAWNAFNL-- 264

Query: 183 MGG--IVKTTLAKEVAR--------------------KAETEKLFDQVIFVEVSKIQDIR 220
                I+ TT  K+V                        E + L  + +     + QD+ 
Sbjct: 265 --SCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDC---RPQDLP 319

Query: 221 KIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDR 280
           +   E+       L     S  A S+R+ L             W N  ++ V        
Sbjct: 320 R---EVLTTNPRRL-----SIIAESIRDGL-----------ATWDN--WKHVNC------ 352

Query: 281 KGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMA----GDYIEGS--EFKW 334
                       D L+  ++S    S+ VL+  E   +F +++      +I        W
Sbjct: 353 ------------DKLTTIIES----SLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIW 396

Query: 335 VAKDVARECAGLPVSIVT--VARALGTRDYLNGRTHWNSWGGLLQLTLKIYNQR--HIKL 390
              DV +      + +V      +L  +               L+L +K+ N+   H  +
Sbjct: 397 --FDVIKSD---VMVVVNKLHKYSLVEKQPKESTISIP--SIYLELKVKLENEYALHRSI 449

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score =  102 bits (257), Expect = 4e-24
 Identities = 45/227 (19%), Positives = 78/227 (34%), Gaps = 27/227 (11%)

Query: 164 NDILDALK--NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLF--DQVIFVEVS---KI 216
           N I   L     +   + I+GM G  K+ LA E  R     +      V +V V    K 
Sbjct: 134 NAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKS 193

Query: 217 QDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK-----KEKTILVILDNIWGNLDFQA 271
             + K+Q             +         ++RL+     K    L+ILD++W +   +A
Sbjct: 194 GLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKA 253

Query: 272 VGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSV-GVLKEDEAWSLFKKMAGDYIEGS 330
                      C++LLT R   V    M  +    V   L +++   +         + +
Sbjct: 254 FD-------SQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNM--KKA 304

Query: 331 EFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQ 377
           +    A  + +EC G P+ +  +   L           W  +   LQ
Sbjct: 305 DLPEQAHSIIKECKGSPLVVSLIGALLRDF-----PNRWEYYLKQLQ 346

>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* Length = 1249

 Score = 73.7 bits (181), Expect = 3e-14
 Identities = 44/212 (20%), Positives = 73/212 (34%), Gaps = 22/212 (10%)

Query: 159 RMSTLNDILDALKNPDV--NMLGIYGMGGIVKTTLAKEVARKAET-EKLF-DQVIFVEVS 214
           R   ++ I   L   +     + IYGM G  K+ LA E  R     E  F   V +V + 
Sbjct: 129 RKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIG 188

Query: 215 K---IQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK-----KEKTILVILDNIWGN 266
           K      + K+Q             +         ++RL+     K    L+ILD++W  
Sbjct: 189 KQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDP 248

Query: 267 LDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSV-GVLKEDEAWSLFKKMAGD 325
              +A           C++LLT R   V    M  +    V   L  ++   +       
Sbjct: 249 WVLKAFDNQ-------CQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNM 301

Query: 326 YIEGSEFKWVAKDVARECAGLPVSIVTVARAL 357
             E    +     + +EC G P+ +  +   L
Sbjct: 302 KKEDLPAEA--HSIIKECKGSPLVVSLIGALL 331

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	390
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.95
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.94
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.94
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.68
2fna_A	357	Conserved hypothetical protein; structural genomic	99.65
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.59
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.49
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.47
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.47
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.44
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.39
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.39
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.36
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.28
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.15
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.12
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.08
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.99
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.98
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.93
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.87
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.82
3bos_A	242	Putative DNA replication factor; P-loop containing	98.8
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.79
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.75
3pvs_A	447	Replication-associated recombination protein A; ma	98.75
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.73
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	98.7
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.69
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.69
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.69
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.67
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.64
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.63
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	98.62
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.61
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.59
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.58
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	98.58
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.57
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.56
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.53
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	98.51
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	98.46
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.43
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.42
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	98.41
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.41
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	98.32
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.31
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	98.31
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.29
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	98.28
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.28
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	98.24
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	98.2
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	98.17
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	98.17
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.15
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	98.11
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	98.1
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	98.07
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	98.04
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	98.01
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.92
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	97.89
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.84
3co5_A	143	Putative two-component system transcriptional RES	97.83
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.81
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.78
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.77
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	97.72
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.69
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.57
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	97.48
3io5_A	333	Recombination and repair protein; storage dimer, i	97.44
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	97.43
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	97.42
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.4
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.39
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.35
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	97.35
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	97.33
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.32
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.32
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	97.28
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.28
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.28
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.27
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	97.27
2qgz_A	308	Helicase loader, putative primosome component; str	97.21
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.18
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	97.18
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.18
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.13
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	97.08
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	97.02
1u94_A	356	RECA protein, recombinase A; homologous recombinat	96.98
4a74_A	231	DNA repair and recombination protein RADA; hydrola	96.8
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.74
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.71
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.68
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.68
2r44_A	331	Uncharacterized protein; putative ATPase, structur	96.61
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.6
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	96.57
3ice_A	422	Transcription termination factor RHO; transcriptio	96.55
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	96.52
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	96.48
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.48
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	96.47
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.47
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	96.46
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.45
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.43
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.42
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.4
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.35
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.35
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	96.32
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.29
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.29
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.27
2xxa_A	433	Signal recognition particle protein; protein trans	96.26
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.25
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	96.23
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.23
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.2
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.19
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.18
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	96.17
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.17
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	96.17
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.16
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	96.14
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	96.13
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.12
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	96.11
2hf9_A	226	Probable hydrogenase nickel incorporation protein	96.1
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.06
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	96.05
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	96.05
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	96.04
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	96.02
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	95.97
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	95.96
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	95.94
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.93
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	95.93
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	95.92
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	95.91
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	95.91
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	95.9
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.9
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	95.9
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.9
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	95.9
1via_A	175	Shikimate kinase; structural genomics, transferase	95.89
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	95.89
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	95.89
1tue_A	212	Replication protein E1; helicase, replication, E1E	95.88
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	95.87
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.87
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	95.87
2r6a_A	454	DNAB helicase, replicative helicase; replication,	95.86
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	95.85
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	95.85
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	95.84
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.83
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	95.82
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	95.82
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	95.81
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	95.81
2vli_A	183	Antibiotic resistance protein; transferase, tunica	95.81
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	95.8
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	95.8
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.79
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	95.79
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	95.77
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	95.75
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	95.74
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	95.72
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	95.71
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	95.71
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	95.7
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	95.69
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	95.68
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	95.68
3l0o_A	427	Transcription termination factor RHO; helicase, RH	95.67
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	95.66
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.66
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	95.65
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	95.65
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	95.64
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	95.64
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.64
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.62
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	95.61
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	95.6
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	95.6
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.59
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	95.57
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	95.56
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.52
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	95.51
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.51
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	95.51
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	95.5
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.5
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	95.49
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	95.48
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	95.48
3fwy_A	314	Light-independent protochlorophyllide reductase I	95.48
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	95.42
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	95.42
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	95.4
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	95.39
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	95.39
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	95.37
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.36
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	95.35
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	95.35
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.35
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	95.35
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	95.3
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	95.29
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.28
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	95.24
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	95.22
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	95.21
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	95.15
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	95.13
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	95.11
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	95.1
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	95.1
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	95.09
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	95.08
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	95.07
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.07
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	95.06
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	95.04
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	95.01
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	95.0
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	94.99
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	94.97
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	94.96
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.96
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	94.96
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	94.94
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	94.93
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	94.92
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.92
2eyu_A	261	Twitching motility protein PILT; pilus retraction	94.9
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	94.9
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	94.9
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	94.9
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	94.89
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	94.87
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	94.86
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	94.84
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	94.84
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	94.81
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	94.81
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.8
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	94.8
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	94.77
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	94.76
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	94.76
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	94.75
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.75
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	94.74
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	94.73
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	94.71
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	94.69
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	94.68
1ji0_A	240	ABC transporter; ATP binding protein, structural g	94.68
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.68
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	94.68
2og2_A	359	Putative signal recognition particle receptor; nuc	94.67
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	94.67
1g6h_A	257	High-affinity branched-chain amino acid transport	94.64
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	94.64
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	94.62
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.61
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	94.59
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	94.58
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.56
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	94.56
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	94.56
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	94.55
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	94.54
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	94.53
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	94.53
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	94.5
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	94.5
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	94.48
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	94.47
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.46
3end_A	307	Light-independent protochlorophyllide reductase ir	94.45
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	94.43
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	94.42
2wji_A	165	Ferrous iron transport protein B homolog; membrane	94.42
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	94.4
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	94.4
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	94.39
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	94.37
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	94.35
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	94.35
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	94.35
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	94.35
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	94.34
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	94.32
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	94.31
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	94.31
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	94.29
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	94.29
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	94.29
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	94.27
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	94.18
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	94.12
2ged_A	193	SR-beta, signal recognition particle receptor beta	94.1
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	94.1
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	94.09
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	94.06
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	94.05
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	94.04
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	93.99
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	93.98
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	93.97
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	93.97
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	93.96
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	93.96
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	93.96
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	93.95
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	93.94
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	93.93
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	93.92
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	93.91
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	93.9
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	93.89
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	93.88
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	93.84
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	93.83
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	93.83
1nrj_B	218	SR-beta, signal recognition particle receptor beta	93.82
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	93.81
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	93.81
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	93.8
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	93.8
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	93.8
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	93.77
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	93.76
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	93.76
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	93.75
3kta_A	182	Chromosome segregation protein SMC; structural mai	93.75
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	93.74
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	93.73
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	93.73
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	93.7
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	93.7
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	93.69
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	93.68
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	93.68
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	93.68
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	93.67
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	93.66
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	93.66
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	93.65
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	93.64
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	93.62
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	93.6
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	93.58
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	93.58
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	93.58
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	93.57
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	93.57
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	93.56
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	93.55
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	93.55
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	93.54
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	93.54
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	93.53
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	93.53
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	93.53
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	93.52
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	93.49
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	93.47
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	93.46
1p9r_A	418	General secretion pathway protein E; bacterial typ	93.46
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	93.45
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	93.45
2ewv_A	372	Twitching motility protein PILT; pilus retraction	93.44
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	93.43
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	93.42
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	93.42
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	93.39
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	93.39
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	93.39
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	93.35
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	93.34
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	93.34
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	93.31
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	93.31
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	93.29
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	93.26
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	93.26
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	93.25
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	93.25
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	93.25
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	93.23
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	93.22
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	93.21
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	93.21
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	93.19
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	93.18
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	93.15
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	93.14
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	93.12
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	93.12
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	93.11
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	93.11
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	93.1
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	93.09
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	93.08
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	93.08
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	93.07
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	93.06
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	93.05
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	93.04
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	93.03
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	93.03
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	93.03
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	93.01
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	93.01
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	92.99
2fh5_B	214	SR-beta, signal recognition particle receptor beta	92.99
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	92.95
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	92.91
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	92.9
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	92.9
3llu_A	196	RAS-related GTP-binding protein C; structural geno	92.89
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	92.88
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	92.86
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	92.86
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	92.83
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	92.82
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	92.81
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	92.8
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	92.8
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	92.78
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	92.77
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	92.71
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	92.6
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	92.6
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	92.59
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	92.56
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	92.55
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	92.49
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	92.45
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	92.42
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	92.41
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	92.38
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	92.35
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	92.34
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	92.29
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	92.28
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	92.26
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	92.26
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	92.24
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	92.24
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	92.23
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	92.18
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	92.17
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	92.17
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	92.16
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	92.16
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	92.1
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	92.08
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	92.02
3cwq_A	209	Para family chromosome partitioning protein; alpha	91.98
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	91.97
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	91.96
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	91.94
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	91.72
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	91.7
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	91.69
3k9g_A	267	PF-32 protein; ssgcid, SBRI, decode biostructures,	91.69
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	91.65
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	91.64
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	91.6
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	91.55
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	91.52
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	91.32
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	91.29
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	91.22
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	91.16
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	91.13
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	91.12
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	91.1

>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=100.00  E-value=3.7e-33  Score=279.60  Aligned_cols=198  Identities=14%  Similarity=0.167  Sum_probs=161.5

Q ss_pred             cchhHHHHHHHHHhcCC---CccEEEEEcCCCCcHHHHHHHHHH--HhhhcCCCCeEEEEEeCCCC--CHHHHHHHHHHH
Q 042806          157 ESRMSTLNDILDALKNP---DVNMLGIYGMGGIVKTTLAKEVAR--KAETEKLFDQVIFVEVSKIQ--DIRKIQGEIADK  229 (390)
Q Consensus       157 ~gR~~~~~~l~~~L~~~---~~~vi~I~G~~GvGKTtLa~~v~~--~~~~~~~f~~~~wv~v~~~~--~~~~l~~~i~~~  229 (390)
                      +||+.++++|.++|..+   +.++|+|+||||+||||||+++|+  +.+.+.+|++++||++++.+  +...++..|+..
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~  210 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLM  210 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHH
Confidence            59999999999999653   579999999999999999999998  45666789999999999875  789999999999


Q ss_pred             hCCCCC--------CCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhhhhcCCC
Q 042806          230 LGLTLH--------EESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDS  301 (390)
Q Consensus       230 l~~~~~--------~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~~~~~~~  301 (390)
                      ++....        ..+...+...+.+.|.++++|||||||||+...+ .+.     ..+||+||||||+..++......
T Consensus       211 l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~-~~~-----~~~gs~ilvTTR~~~v~~~~~~~  284 (549)
T 2a5y_B          211 LKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETI-RWA-----QELRLRCLVTTRDVEISNAASQT  284 (549)
T ss_dssp             HTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHH-HHH-----HHTTCEEEEEESBGGGGGGCCSC
T ss_pred             HhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhh-ccc-----ccCCCEEEEEcCCHHHHHHcCCC
Confidence            986522        1122335678888888863599999999997654 111     12799999999999987632224


Q ss_pred             cceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhcCC
Q 042806          302 QQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTR  360 (390)
Q Consensus       302 ~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~  360 (390)
                      ...|+|++|+.++||+||.+.++.....+++++++++|+++|+|+||||..+|+.|+.+
T Consensus       285 ~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~  343 (549)
T 2a5y_B          285 CEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPK  343 (549)
T ss_dssp             EEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSS
T ss_pred             CeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHhCCChHHHHHHHHHhccc
Confidence            46899999999999999999988554457788899999999999999999999998754

>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=99.95  E-value=8.2e-28  Score=262.55  Aligned_cols=216  Identities=21%  Similarity=0.298  Sum_probs=166.0

Q ss_pred             ccCcccccchhHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHhhh-cC-CCCeEEEEEeCCCCC--HHHHH
Q 042806          150 IKDYEACESRMSTLNDILDALK--NPDVNMLGIYGMGGIVKTTLAKEVARKAET-EK-LFDQVIFVEVSKIQD--IRKIQ  223 (390)
Q Consensus       150 ~~~~~~~~gR~~~~~~l~~~L~--~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~-~~-~f~~~~wv~v~~~~~--~~~l~  223 (390)
                      |.+...|+||+.++++|.+.|.  ++..++|+|+||||+||||||++++++... .. .|+.++|++++...+  ....+
T Consensus       120 p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~  199 (1249)
T 3sfz_A          120 PQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKL  199 (1249)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHHH
T ss_pred             CCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHHH
Confidence            3445679999999999999995  356899999999999999999999998643 23 356888999988543  34446


Q ss_pred             HHHHHHhCCCCC-----CCCchHHHHHHHHHHhCC-CeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhhhh
Q 042806          224 GEIADKLGLTLH-----EESDSGRARSLRNRLKKE-KTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSR  297 (390)
Q Consensus       224 ~~i~~~l~~~~~-----~~~~~~~~~~l~~~l~~~-~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~~~  297 (390)
                      ..++..+.....     ..........+...+..+ ++|||||||+|+...|..+       .+||+||||||+..++..
T Consensus       200 ~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~~~~~~-------~~~~~ilvTtR~~~~~~~  272 (1249)
T 3sfz_A          200 QNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAF-------DNQCQILLTTRDKSVTDS  272 (1249)
T ss_dssp             HHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHHHHTTT-------CSSCEEEEEESSTTTTTT
T ss_pred             HHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHHHHHhh-------cCCCEEEEEcCCHHHHHh
Confidence            667777765332     123344556677777654 3599999999988776654       468999999999988754


Q ss_pred             cCCCcceEecCC-CCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhcCCCCCCCcccchhHHHHH
Q 042806          298 KMDSQQNFSVGV-LKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLL  376 (390)
Q Consensus       298 ~~~~~~~~~l~~-L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~~~~~~~~~w~~~~~~l  376 (390)
                      .......+++.+ |+.++|++||...++..  .+++++++++|+++|+|+||||.++|++|+.++     ..|+++...|
T Consensus       273 ~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~--~~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~-----~~~~~~l~~l  345 (1249)
T 3sfz_A          273 VMGPKHVVPVESGLGREKGLEILSLFVNMK--KEDLPAEAHSIIKECKGSPLVVSLIGALLRDFP-----NRWAYYLRQL  345 (1249)
T ss_dssp             CCSCBCCEECCSSCCHHHHHHHHHHHHTSC--STTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSS-----SCHHHHHHHH
T ss_pred             hcCCceEEEecCCCCHHHHHHHHHHhhCCC--hhhCcHHHHHHHHHhCCCHHHHHHHHHHhhcCh-----hHHHHHHHHH
Confidence            556668999996 99999999999988632  233445789999999999999999999999765     3577777666


Q ss_pred             hhh
Q 042806          377 QLT  379 (390)
Q Consensus       377 ~~~  379 (390)
                      +..
T Consensus       346 ~~~  348 (1249)
T 3sfz_A          346 QNK  348 (1249)
T ss_dssp             HSC
T ss_pred             hhh
Confidence            543

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.94  E-value=3.3e-27  Score=242.66  Aligned_cols=197  Identities=19%  Similarity=0.186  Sum_probs=147.5

Q ss_pred             ccchhHHHHHHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCe-EEEEEeCCCCCHHHHHHHHHHHhCCC
Q 042806          156 CESRMSTLNDILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQ-VIFVEVSKIQDIRKIQGEIADKLGLT  233 (390)
Q Consensus       156 ~~gR~~~~~~l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~-~~wv~v~~~~~~~~l~~~i~~~l~~~  233 (390)
                      .+||+.++++|.++|.. +..++|+|+||||+||||||++++++.+...+|+. ++|+++++.++...++..+...++..
T Consensus       130 ~VGRe~eLeeL~elL~~~d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~~i  209 (1221)
T 1vt4_I          130 NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI  209 (1221)
T ss_dssp             CCCCHHHHHHHHHHHHHCCSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHhccCCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHhhc
Confidence            49999999999999875 45789999999999999999999998766667986 99999999999888888887754321


Q ss_pred             C---CCC---------CchHHHHHHHHHHh--CCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhhhhcC
Q 042806          234 L---HEE---------SDSGRARSLRNRLK--KEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKM  299 (390)
Q Consensus       234 ~---~~~---------~~~~~~~~l~~~l~--~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~~~~~  299 (390)
                      .   ...         +.......+.+.|.  .++++||||||+|+...|+.+.       +||+||||||+..++.. .
T Consensus       210 ~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f~-------pGSRILVTTRd~~Va~~-l  281 (1221)
T 1vt4_I          210 DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN-------LSCKILLTTRFKQVTDF-L  281 (1221)
T ss_dssp             CSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHHH-------SSCCEEEECSCSHHHHH-H
T ss_pred             CcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhhC-------CCeEEEEeccChHHHHh-c
Confidence            1   100         11223445666552  3455999999999988887652       68999999999888642 1


Q ss_pred             CCcceEecC------CCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhcCCCCCCCcccch
Q 042806          300 DSQQNFSVG------VLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWN  370 (390)
Q Consensus       300 ~~~~~~~l~------~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~~~~~~~~~w~  370 (390)
                      .....++++      +|+.+|||+||.+.++..  .   .++..+   .|+|+||||.++|+.|+.+..  +.++|+
T Consensus       282 ~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g~~--~---eeL~~e---ICgGLPLALkLaGs~Lr~k~~--s~eeW~  348 (1221)
T 1vt4_I          282 SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR--P---QDLPRE---VLTTNPRRLSIIAESIRDGLA--TWDNWK  348 (1221)
T ss_dssp             HHHSSCEEEECSSSSCCCHHHHHHHHHHHHCCC--T---TTHHHH---HCCCCHHHHHHHHHHHHHSCS--SHHHHH
T ss_pred             CCCeEEEecCccccCCcCHHHHHHHHHHHcCCC--H---HHHHHH---HhCCCHHHHHHHHHHHhCCCC--CHHHHh
Confidence            222356666      999999999999986432  1   122333   499999999999999998742  245664

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.94  E-value=3.4e-26  Score=231.50  Aligned_cols=210  Identities=22%  Similarity=0.326  Sum_probs=154.5

Q ss_pred             CcccccchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhhh-cCCC-CeEEEEEeCCCCCHHHHHHHH-
Q 042806          152 DYEACESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAET-EKLF-DQVIFVEVSKIQDIRKIQGEI-  226 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~~-~~~f-~~~~wv~v~~~~~~~~l~~~i-  226 (390)
                      ....|+||+.++++|.++|..  +..++++|+|+||+||||||.+++++... ..+| +.++|++++.. +...++..+ 
T Consensus       122 ~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~~l~  200 (591)
T 1z6t_A          122 RPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKLQ  200 (591)
T ss_dssp             CCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHHHHH
T ss_pred             CCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHHHHH
Confidence            345799999999999999974  46789999999999999999999987643 4558 58999999875 344444444 


Q ss_pred             --HHHhCCC-----CCCCCchHHHHHHHHHHhCC-CeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhhhhc
Q 042806          227 --ADKLGLT-----LHEESDSGRARSLRNRLKKE-KTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRK  298 (390)
Q Consensus       227 --~~~l~~~-----~~~~~~~~~~~~l~~~l~~~-~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~~~~  298 (390)
                        +..++..     ....+.......+.+.+.+. +++||||||+|+...+..+       .++++||+|||+..++...
T Consensus       201 ~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~l-------~~~~~ilvTsR~~~~~~~~  273 (591)
T 1z6t_A          201 NLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF-------DSQCQILLTTRDKSVTDSV  273 (591)
T ss_dssp             HHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHHHHHTT-------CSSCEEEEEESCGGGGTTC
T ss_pred             HHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHHHHHHh-------cCCCeEEEECCCcHHHHhc
Confidence              4455421     11123344556677777652 4599999999986655433       4689999999998875432


Q ss_pred             CCCcceEec---CCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhcCCCCCCCcccchhHHHH
Q 042806          299 MDSQQNFSV---GVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGL  375 (390)
Q Consensus       299 ~~~~~~~~l---~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~~~~~~~~~w~~~~~~  375 (390)
                      .  ...+++   ++|+.+++++||...++...  ....+.+.+|+++|+|+||||..+|+.|+.++     ..|+.+...
T Consensus       274 ~--~~~~~v~~l~~L~~~ea~~L~~~~~~~~~--~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~~-----~~w~~~l~~  344 (591)
T 1z6t_A          274 M--GPKYVVPVESSLGKEKGLEILSLFVNMKK--ADLPEQAHSIIKECKGSPLVVSLIGALLRDFP-----NRWEYYLKQ  344 (591)
T ss_dssp             C--SCEEEEECCSSCCHHHHHHHHHHHHTSCG--GGSCTHHHHHHHHHTTCHHHHHHHHHHHHHST-----TCHHHHHHH
T ss_pred             C--CCceEeecCCCCCHHHHHHHHHHHhCCCc--ccccHHHHHHHHHhCCCcHHHHHHHHHHhcCc-----hhHHHHHHH
Confidence            2  334444   58999999999999987421  22234678999999999999999999998753     368777666


Q ss_pred             Hhh
Q 042806          376 LQL  378 (390)
Q Consensus       376 l~~  378 (390)
                      |..
T Consensus       345 l~~  347 (591)
T 1z6t_A          345 LQN  347 (591)
T ss_dssp             HHS
T ss_pred             HHH
Confidence            654

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.68  E-value=3.3e-16  Score=147.41  Aligned_cols=196  Identities=14%  Similarity=0.127  Sum_probs=129.2

Q ss_pred             cCcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC------CHHHHHH
Q 042806          151 KDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ------DIRKIQG  224 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~------~~~~l~~  224 (390)
                      .....|+||+.+++.|.+++..+  +++.|+|++|+|||||++.+++...       .+|+++....      +...++.
T Consensus         9 ~~~~~~~gR~~el~~L~~~l~~~--~~v~i~G~~G~GKT~Ll~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~   79 (350)
T 2qen_A            9 TRREDIFDREEESRKLEESLENY--PLTLLLGIRRVGKSSLLRAFLNERP-------GILIDCRELYAERGHITREELIK   79 (350)
T ss_dssp             CSGGGSCSCHHHHHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHHHHSS-------EEEEEHHHHHHTTTCBCHHHHHH
T ss_pred             CChHhcCChHHHHHHHHHHHhcC--CeEEEECCCcCCHHHHHHHHHHHcC-------cEEEEeecccccccCCCHHHHHH
Confidence            34567999999999999988754  7899999999999999999987751       6777775432      5667777


Q ss_pred             HHHHHhCC-----------------CCC--CCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc---------cccccCCC
Q 042806          225 EIADKLGL-----------------TLH--EESDSGRARSLRNRLKKEKTILVILDNIWGNLD---------FQAVGIPH  276 (390)
Q Consensus       225 ~i~~~l~~-----------------~~~--~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~---------~~~l~~~l  276 (390)
                      .+...+..                 ..+  ..........+.+....+++++|||||++....         +..+....
T Consensus        80 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~L~~~~  159 (350)
T 2qen_A           80 ELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLALFAYAY  159 (350)
T ss_dssp             HHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHHHHHHH
Confidence            77666542                 000  011222333444444322259999999976432         12222111


Q ss_pred             CCCCCCcEEEEEecchhhhhh---------cC--CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC
Q 042806          277 GDDRKGCKVLLTARSLDVLSR---------KM--DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAG  345 (390)
Q Consensus       277 ~~~~~~s~IivTtr~~~v~~~---------~~--~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~G  345 (390)
                       +..++.++|+|++.......         ..  .....+++.+|+.+|+.+++...+....... ..+.+..|++.|+|
T Consensus       160 -~~~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~-~~~~~~~i~~~tgG  237 (350)
T 2qen_A          160 -DSLPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNLDV-PENEIEEAVELLDG  237 (350)
T ss_dssp             -HHCTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTTCCC-CHHHHHHHHHHHTT
T ss_pred             -HhcCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHhCC
Confidence             11247889999887542111         01  1124899999999999999987653211111 23467899999999


Q ss_pred             ChHHHHHHHHHh
Q 042806          346 LPVSIVTVARAL  357 (390)
Q Consensus       346 lPLai~~l~~~L  357 (390)
                      +|+++..++..+
T Consensus       238 ~P~~l~~~~~~~  249 (350)
T 2qen_A          238 IPGWLVVFGVEY  249 (350)
T ss_dssp             CHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHH
Confidence            999999998764

>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=99.65  E-value=1.7e-15  Score=142.85  Aligned_cols=194  Identities=11%  Similarity=0.172  Sum_probs=124.8

Q ss_pred             CcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-----CCHHHHHHHH
Q 042806          152 DYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-----QDIRKIQGEI  226 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-----~~~~~l~~~i  226 (390)
                      ....|+||+.+++.|.+ +..   +++.|+|++|+|||||++.+.+....     ..+|+.+...     .+...++..+
T Consensus        11 ~~~~~~gR~~el~~L~~-l~~---~~v~i~G~~G~GKT~L~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~l   81 (357)
T 2fna_A           11 NRKDFFDREKEIEKLKG-LRA---PITLVLGLRRTGKSSIIKIGINELNL-----PYIYLDLRKFEERNYISYKDFLLEL   81 (357)
T ss_dssp             SGGGSCCCHHHHHHHHH-TCS---SEEEEEESTTSSHHHHHHHHHHHHTC-----CEEEEEGGGGTTCSCCCHHHHHHHH
T ss_pred             CHHHhcChHHHHHHHHH-hcC---CcEEEECCCCCCHHHHHHHHHHhcCC-----CEEEEEchhhccccCCCHHHHHHHH
Confidence            34579999999999999 765   69999999999999999999987642     2578887643     3555666555


Q ss_pred             HHHhCC------------------CCCCC--C------chHHHHHHHHHHhCC--CeEEEEEeCCCCCc-----cccccc
Q 042806          227 ADKLGL------------------TLHEE--S------DSGRARSLRNRLKKE--KTILVILDNIWGNL-----DFQAVG  273 (390)
Q Consensus       227 ~~~l~~------------------~~~~~--~------~~~~~~~l~~~l~~~--~~~LlVlDdv~~~~-----~~~~l~  273 (390)
                      .+.+..                  ..+..  +      .......+.+.+...  ++++|||||++...     .+..+.
T Consensus        82 ~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~vlvlDe~~~~~~~~~~~~~~~l  161 (357)
T 2fna_A           82 QKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPAL  161 (357)
T ss_dssp             HHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHHH
T ss_pred             HHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCCCCeEEEEECHHHhhccCchhHHHHH
Confidence            544310                  00000  0      011233444444321  36999999997532     222221


Q ss_pred             CCCCCCCCCcEEEEEecchhhhhh---------cCC-C-cceEecCCCCHHHHHHHHHHhhCC-CCCCCchHHHHHHHHH
Q 042806          274 IPHGDDRKGCKVLLTARSLDVLSR---------KMD-S-QQNFSVGVLKEDEAWSLFKKMAGD-YIEGSEFKWVAKDVAR  341 (390)
Q Consensus       274 ~~l~~~~~~s~IivTtr~~~v~~~---------~~~-~-~~~~~l~~L~~~ea~~lf~~~~~~-~~~~~~~~~~~~~i~~  341 (390)
                      ..+.+..++.++|+|++.......         ... . ...+++.+|+.+++.+++...+.. .......    ..|++
T Consensus       162 ~~~~~~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~----~~i~~  237 (357)
T 2fna_A          162 AYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDY----EVVYE  237 (357)
T ss_dssp             HHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCCH----HHHHH
T ss_pred             HHHHHcCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCCCCcH----HHHHH
Confidence            111122246789999997543111         111 1 258999999999999999876531 1112221    68999


Q ss_pred             HcCCChHHHHHHHHHhc
Q 042806          342 ECAGLPVSIVTVARALG  358 (390)
Q Consensus       342 ~~~GlPLai~~l~~~L~  358 (390)
                      .|+|+|+++..++..+.
T Consensus       238 ~t~G~P~~l~~~~~~~~  254 (357)
T 2fna_A          238 KIGGIPGWLTYFGFIYL  254 (357)
T ss_dssp             HHCSCHHHHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHHHHc
Confidence            99999999999987764

>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=99.59  E-value=2.6e-14  Score=137.70  Aligned_cols=199  Identities=17%  Similarity=0.147  Sum_probs=132.7

Q ss_pred             ccccchhHHHHHHHHHh-c----C--CCccEEEE--EcCCCCcHHHHHHHHHHHhhhc---CCCC-eEEEEEeCCCCCHH
Q 042806          154 EACESRMSTLNDILDAL-K----N--PDVNMLGI--YGMGGIVKTTLAKEVARKAETE---KLFD-QVIFVEVSKIQDIR  220 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L-~----~--~~~~vi~I--~G~~GvGKTtLa~~v~~~~~~~---~~f~-~~~wv~v~~~~~~~  220 (390)
                      ..++||+.+++.|.+.+ .    .  ...+.+.|  +|++|+|||||++.+++.....   ..+. ..+|+.+....+..
T Consensus        22 ~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (412)
T 1w5s_A           22 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLY  101 (412)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHH
T ss_pred             CCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHH
Confidence            57999999999998888 3    2  34567777  9999999999999999886542   1133 36788877777889


Q ss_pred             HHHHHHHHHhCCCCCC--CCchHHHHHHHHHHh-CCCeEEEEEeCCCCCc--------ccccccCCC---CCCC--CCcE
Q 042806          221 KIQGEIADKLGLTLHE--ESDSGRARSLRNRLK-KEKTILVILDNIWGNL--------DFQAVGIPH---GDDR--KGCK  284 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~--~~~~~~~~~l~~~l~-~~~~~LlVlDdv~~~~--------~~~~l~~~l---~~~~--~~s~  284 (390)
                      +++..++..++...+.  .+.......+.+.+. .+++++|||||++...        .+..+...+   +..+  .+..
T Consensus       102 ~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~~v~  181 (412)
T 1w5s_A          102 TILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIG  181 (412)
T ss_dssp             HHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEE
T ss_pred             HHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCceEE
Confidence            9999999999765332  223344556666664 2457999999997532        222221111   1112  4456


Q ss_pred             EEEEecchhhhh--------hcCCCcceEecCCCCHHHHHHHHHHhhC---CCCCCCchHHHHHHHHHHcC------CCh
Q 042806          285 VLLTARSLDVLS--------RKMDSQQNFSVGVLKEDEAWSLFKKMAG---DYIEGSEFKWVAKDVARECA------GLP  347 (390)
Q Consensus       285 IivTtr~~~v~~--------~~~~~~~~~~l~~L~~~ea~~lf~~~~~---~~~~~~~~~~~~~~i~~~~~------GlP  347 (390)
                      +|+||+...+..        ........+++.+|+.++++++|.+.+.   ..  ..-.++....|++.|+      |.|
T Consensus       182 lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~--~~~~~~~~~~i~~~~~~~~~~~G~p  259 (412)
T 1w5s_A          182 FLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRD--TVWEPRHLELISDVYGEDKGGDGSA  259 (412)
T ss_dssp             EEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCT--TSCCHHHHHHHHHHHCGGGTSCCCH
T ss_pred             EEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcCCC--CCCChHHHHHHHHHHHHhccCCCcH
Confidence            888887544211        0111123499999999999999986643   21  1122456789999999      999


Q ss_pred             HHHHHHH
Q 042806          348 VSIVTVA  354 (390)
Q Consensus       348 Lai~~l~  354 (390)
                      ..+..+.
T Consensus       260 ~~~~~l~  266 (412)
T 1w5s_A          260 RRAIVAL  266 (412)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7665554

>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=99.49  E-value=3.8e-13  Score=119.28  Aligned_cols=199  Identities=12%  Similarity=0.111  Sum_probs=118.3

Q ss_pred             CcccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          152 DYEACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ....++||+..++.+..++..+. .+.+.|+|++|+|||||++.+++.......+..      ......... ..+....
T Consensus        21 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~------~~~~~~~~~-~~~~~~~   93 (250)
T 1njg_A           21 TFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITA------TPCGVCDNC-REIEQGR   93 (250)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCS------SCCSCSHHH-HHHHTTC
T ss_pred             cHHHHhCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC------CCCcccHHH-HHHhccC
Confidence            34579999999999999987654 457899999999999999999988753211100      000000000 0000000


Q ss_pred             C-----CCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecchhh-hhhc
Q 042806          231 G-----LTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSLDV-LSRK  298 (390)
Q Consensus       231 ~-----~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~~v-~~~~  298 (390)
                      .     ..............+.+.+.    .+++.+||+||++..  ..++.+...+.....+..+|+||+.... ....
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~~~l  173 (250)
T 1njg_A           94 FVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTI  173 (250)
T ss_dssp             CSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHH
T ss_pred             CcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCCHHH
Confidence            0     00000001111222222221    234589999999753  3344444333333457788888876432 1111


Q ss_pred             CCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhc
Q 042806          299 MDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALG  358 (390)
Q Consensus       299 ~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~  358 (390)
                      ......+++.+++.++..+++.+.+....... .++....|++.|+|.|..+..+...+.
T Consensus       174 ~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~~~-~~~~~~~l~~~~~G~~~~~~~~~~~~~  232 (250)
T 1njg_A          174 LSRCLQFHLKALDVEQIRHQLEHILNEEHIAH-EPRALQLLARAAEGSLRDALSLTDQAI  232 (250)
T ss_dssp             HTTSEEEECCCCCHHHHHHHHHHHHHHTTCCB-CHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHhhhccCCCCCHHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            22246899999999999999998875221111 245678999999999999988876554

>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=99.47  E-value=4.1e-13  Score=127.84  Aligned_cols=200  Identities=16%  Similarity=0.176  Sum_probs=130.6

Q ss_pred             ccccchhHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCC-CCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          154 EACESRMSTLNDILDALK----NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKL-FDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~----~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~-f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      ..++||+.+++.+.+++.    ....+.+.|+|++|+|||||++.+++....... -...+|+++....+...++..++.
T Consensus        20 ~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~   99 (386)
T 2qby_A           20 DELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLLE   99 (386)
T ss_dssp             SCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHHTT
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHHHH
Confidence            579999999999999887    345678999999999999999999998754311 124678887776777888888888


Q ss_pred             HhCCCCCCC--CchHHHHHHHHHHhC-CCeEEEEEeCCCCCc------ccccccCCCCC-CCCCcEEEEEecchhhhhh-
Q 042806          229 KLGLTLHEE--SDSGRARSLRNRLKK-EKTILVILDNIWGNL------DFQAVGIPHGD-DRKGCKVLLTARSLDVLSR-  297 (390)
Q Consensus       229 ~l~~~~~~~--~~~~~~~~l~~~l~~-~~~~LlVlDdv~~~~------~~~~l~~~l~~-~~~~s~IivTtr~~~v~~~-  297 (390)
                      .++......  +.......+.+.+.. +++.+||||+++...      .+..+...+.. ...+..+|+||+....... 
T Consensus       100 ~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~~~~~  179 (386)
T 2qby_A          100 SLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDLL  179 (386)
T ss_dssp             TTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGGGGGGC
T ss_pred             HhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCChHhhh
Confidence            776543321  233445566666654 336999999996432      22222111111 2335677888876532111 


Q ss_pred             -----cCCCcceEecCCCCHHHHHHHHHHhhCC-CCCCCchHHHHHHHHHHcC---CChHHHHHH
Q 042806          298 -----KMDSQQNFSVGVLKEDEAWSLFKKMAGD-YIEGSEFKWVAKDVARECA---GLPVSIVTV  353 (390)
Q Consensus       298 -----~~~~~~~~~l~~L~~~ea~~lf~~~~~~-~~~~~~~~~~~~~i~~~~~---GlPLai~~l  353 (390)
                           ..-....+++.+++.++..++|.+.+.. .....-..++...+++.++   |.|..+..+
T Consensus       180 ~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~l  244 (386)
T 2qby_A          180 DPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDL  244 (386)
T ss_dssp             TTHHHHTTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             CHHHhccCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCCHHHHHHH
Confidence                 1111258999999999999999886531 0011122456677888887   999854433

>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=99.47  E-value=9.3e-13  Score=115.22  Aligned_cols=188  Identities=12%  Similarity=0.052  Sum_probs=118.3

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGL  232 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~  232 (390)
                      ...++||+..++.+.+++.....+.+.|+|++|+|||+|++.+++.......-...+.+..+.......+...+......
T Consensus        16 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (226)
T 2chg_A           16 LDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVRHKIKEFART   95 (226)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETTCTTCHHHHHHHHHHHHTS
T ss_pred             HHHHcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccccccChHHHHHHHHHHhcc
Confidence            45789999999999999987766669999999999999999999876432111224444544444433332222211111


Q ss_pred             CCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEecchhhh-hhcCCCcceEecCC
Q 042806          233 TLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTARSLDVL-SRKMDSQQNFSVGV  309 (390)
Q Consensus       233 ~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTtr~~~v~-~~~~~~~~~~~l~~  309 (390)
                      ..               ....++.+||+||++...  ..+.+...+.....++++|+||+..... .........+++.+
T Consensus        96 ~~---------------~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i~~~~  160 (226)
T 2chg_A           96 AP---------------IGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKP  160 (226)
T ss_dssp             CC---------------STTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCC
T ss_pred             cC---------------CCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCceeecCC
Confidence            00               012345899999997652  2333333332234567888888764321 11112234899999


Q ss_pred             CCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHH
Q 042806          310 LKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARA  356 (390)
Q Consensus       310 L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~  356 (390)
                      ++.++..+++.+.+...... -.++....+++.++|.|..+..+...
T Consensus       161 ~~~~~~~~~l~~~~~~~~~~-~~~~~~~~l~~~~~g~~r~l~~~l~~  206 (226)
T 2chg_A          161 VPKEAMKKRLLEICEKEGVK-ITEDGLEALIYISGGDFRKAINALQG  206 (226)
T ss_dssp             CCHHHHHHHHHHHHHHHTCC-BCHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            99999999999877411111 12356778999999999976555433

>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=99.44  E-value=1.2e-12  Score=124.87  Aligned_cols=195  Identities=14%  Similarity=0.096  Sum_probs=130.4

Q ss_pred             ccccchhHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC----C--CCeEEEEEeCCCC-CHHHH
Q 042806          154 EACESRMSTLNDILDALK----NPDVNMLGIYGMGGIVKTTLAKEVARKAETEK----L--FDQVIFVEVSKIQ-DIRKI  222 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~----~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~----~--f~~~~wv~v~~~~-~~~~l  222 (390)
                      ..++||+.+++.+.+++.    ....+.+.|+|++|+||||||+.+++......    .  ....+|++++... +...+
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~   99 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAV   99 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHH
Confidence            579999999998887664    34567899999999999999999999864321    1  2356788877766 88889


Q ss_pred             HHHHHHHh-CCCCC--CCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc---ccc-ccCCCCCCCCCcEEEEEecchhh-
Q 042806          223 QGEIADKL-GLTLH--EESDSGRARSLRNRLKKEKTILVILDNIWGNLD---FQA-VGIPHGDDRKGCKVLLTARSLDV-  294 (390)
Q Consensus       223 ~~~i~~~l-~~~~~--~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~---~~~-l~~~l~~~~~~s~IivTtr~~~v-  294 (390)
                      +..++..+ +....  ..+.......+.+.+...+ .+|||||++....   .+. +. .+.....+..+|+||+.... 
T Consensus       100 ~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~-~vlilDEi~~l~~~~~~~~~l~-~l~~~~~~~~iI~~t~~~~~~  177 (384)
T 2qby_B          100 LSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIR-AIIYLDEVDTLVKRRGGDIVLY-QLLRSDANISVIMISNDINVR  177 (384)
T ss_dssp             HHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSC-EEEEEETTHHHHHSTTSHHHHH-HHHTSSSCEEEEEECSSTTTT
T ss_pred             HHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCC-CEEEEECHHHhccCCCCceeHH-HHhcCCcceEEEEEECCCchH
Confidence            99988887 32221  1233455667777777766 4999999975421   111 11 11111167789999886521 


Q ss_pred             ---hhhc-CCCcceEecCCCCHHHHHHHHHHhhC---C-CCCCCchHHHHHHHHHHcC---CChH-HHHHH
Q 042806          295 ---LSRK-MDSQQNFSVGVLKEDEAWSLFKKMAG---D-YIEGSEFKWVAKDVARECA---GLPV-SIVTV  353 (390)
Q Consensus       295 ---~~~~-~~~~~~~~l~~L~~~ea~~lf~~~~~---~-~~~~~~~~~~~~~i~~~~~---GlPL-ai~~l  353 (390)
                         .... ......+++.+++.++..++|...+.   . ...+   ++....+++.|+   |.|. ++..+
T Consensus       178 ~~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~---~~~~~~i~~~~~~~~G~~r~a~~~l  245 (384)
T 2qby_B          178 DYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYD---DEILSYIAAISAKEHGDARKAVNLL  245 (384)
T ss_dssp             TTSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCC---SHHHHHHHHHHHTTCCCHHHHHHHH
T ss_pred             hhhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcC---HHHHHHHHHHHHhccCCHHHHHHHH
Confidence               1110 11123899999999999999998753   1 1122   245677888888   9887 44443

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

Probab=99.39  E-value=5e-12  Score=120.38  Aligned_cols=193  Identities=17%  Similarity=0.159  Sum_probs=128.8

Q ss_pred             ccccchhHHHHHHHHHhcC----CCccEEEEEcCCCCcHHHHHHHHHHHhhhc----CCCCeEEEEEeCCCCCHHHHHHH
Q 042806          154 EACESRMSTLNDILDALKN----PDVNMLGIYGMGGIVKTTLAKEVARKAETE----KLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~----~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~----~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      ..++||+.+++.+..++..    ...+.+.|+|++|+|||||++.+++.....    +.-...+|+++....+...++..
T Consensus        19 ~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~   98 (387)
T 2v1u_A           19 DVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASA   98 (387)
T ss_dssp             SCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHHHH
Confidence            5799999999999998843    456789999999999999999999887432    11124678888888889999999


Q ss_pred             HHHHhCCCCCCC--CchHHHHHHHHHHhC-CCeEEEEEeCCCCCcc----ccccc---CCCCCC--CCCcEEEEEecchh
Q 042806          226 IADKLGLTLHEE--SDSGRARSLRNRLKK-EKTILVILDNIWGNLD----FQAVG---IPHGDD--RKGCKVLLTARSLD  293 (390)
Q Consensus       226 i~~~l~~~~~~~--~~~~~~~~l~~~l~~-~~~~LlVlDdv~~~~~----~~~l~---~~l~~~--~~~s~IivTtr~~~  293 (390)
                      ++..++...+..  +.......+.+.+.. +++++|+||+++....    .+.+.   ......  ..+..+|+||+...
T Consensus        99 l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~  178 (387)
T 2v1u_A           99 IAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLG  178 (387)
T ss_dssp             HHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEECSCST
T ss_pred             HHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEECCCc
Confidence            999997654322  233445666667643 4579999999975421    12221   111111  34567888877642


Q ss_pred             hh----hh--cCCCcceEecCCCCHHHHHHHHHHhhC---C-CCCCCchHHHHHHHHHHcC---CChHH
Q 042806          294 VL----SR--KMDSQQNFSVGVLKEDEAWSLFKKMAG---D-YIEGSEFKWVAKDVARECA---GLPVS  349 (390)
Q Consensus       294 v~----~~--~~~~~~~~~l~~L~~~ea~~lf~~~~~---~-~~~~~~~~~~~~~i~~~~~---GlPLa  349 (390)
                      ..    ..  ..-....+++.+++.++..+++.+.+.   . ....+   +....+++.++   |.|-.
T Consensus       179 ~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~G~~r~  244 (387)
T 2v1u_A          179 FVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDP---DVVPLCAALAAREHGDARR  244 (387)
T ss_dssp             TSSSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCS---SHHHHHHHHHHSSSCCHHH
T ss_pred             hHhhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCH---HHHHHHHHHHHHhccCHHH
Confidence            21    11  111124899999999999999988753   1 12222   34667888888   99943

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.39  E-value=5.1e-13  Score=104.27  Aligned_cols=78  Identities=12%  Similarity=0.063  Sum_probs=58.5

Q ss_pred             HHHHHhhhhhhhhhhhchhhhhhhhHhHHHHHHHHhchHHHHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHHHHHHHHH
Q 042806            9 VVEVAKCLAPPIYCQMSYLRKSKYTSNLQNLKTEVGIPEAERVSKQREVDKAKRRG-EEIEEYVEKWLTSVNGIIDEAEK   87 (390)
Q Consensus         9 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~i~~~l~~a~~~~-~~~~~~~~~wl~~l~~~~~d~ed   87 (390)
                      ++.+++++.+.+.++...+.         +++++++.|+..|..|++|+.+++.+. ...++.++.|+.+||+++||+||
T Consensus         3 v~~ll~KL~~ll~~E~~l~~---------gv~~~i~~Lk~eL~~m~a~L~da~~~~~~~~d~~vk~W~~~vrdlaYD~ED   73 (115)
T 3qfl_A            3 ISNLIPKLGELLTEEFKLHK---------GVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYVIED   73 (115)
T ss_dssp             TCSHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHh---------chHHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHH
Confidence            44556777777777776666         455556666666666666888998763 34689999999999999999999


Q ss_pred             hhhhhhhh
Q 042806           88 FTGVDARA   95 (390)
Q Consensus        88 ~ld~~~~~   95 (390)
                      |||+|...
T Consensus        74 ~iD~f~~~   81 (115)
T 3qfl_A           74 VVDKFLVQ   81 (115)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99998654

>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=99.36  E-value=1.8e-11  Score=116.67  Aligned_cols=199  Identities=15%  Similarity=0.152  Sum_probs=133.1

Q ss_pred             ccccchhHHHHHHHHHhcC----CCcc--EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          154 EACESRMSTLNDILDALKN----PDVN--MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~----~~~~--vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      +.++||+.+++.+.+++..    ....  .+.|+|++|+|||||++.+++....... ...+|++++...+...++..++
T Consensus        17 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~-~~~~~i~~~~~~~~~~~~~~l~   95 (389)
T 1fnn_A           17 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTT-ARFVYINGFIYRNFTAIIGEIA   95 (389)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCC-CEEEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcC-eeEEEEeCccCCCHHHHHHHHH
Confidence            5799999999999888864    3334  8999999999999999999988754211 2467888888888889999999


Q ss_pred             HHhCCCCCCC--CchHHHHHHHHHHhC-CCeEEEEEeCCCCC--cccccccCCCCCC-C---CCcEEEEEecchhhhhhc
Q 042806          228 DKLGLTLHEE--SDSGRARSLRNRLKK-EKTILVILDNIWGN--LDFQAVGIPHGDD-R---KGCKVLLTARSLDVLSRK  298 (390)
Q Consensus       228 ~~l~~~~~~~--~~~~~~~~l~~~l~~-~~~~LlVlDdv~~~--~~~~~l~~~l~~~-~---~~s~IivTtr~~~v~~~~  298 (390)
                      ..++...+..  +.......+.+.+.. +++.+||||+++..  ..+..+...+... .   .+..||++|+........
T Consensus        96 ~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l  175 (389)
T 1fnn_A           96 RSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNL  175 (389)
T ss_dssp             HHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTS
T ss_pred             HHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHh
Confidence            9887643322  334445555555542 44699999999764  2233332222111 1   467788888765332110


Q ss_pred             C------CCcceEecCCCCHHHHHHHHHHhhCC-CCCCCchHHHHHHHHHHc---------CCChHHHHHH
Q 042806          299 M------DSQQNFSVGVLKEDEAWSLFKKMAGD-YIEGSEFKWVAKDVAREC---------AGLPVSIVTV  353 (390)
Q Consensus       299 ~------~~~~~~~l~~L~~~ea~~lf~~~~~~-~~~~~~~~~~~~~i~~~~---------~GlPLai~~l  353 (390)
                      .      -....+++.+++.++..+++.+.+.. .....-.++....+++.+         +|.|..+..+
T Consensus       176 ~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~  246 (389)
T 1fnn_A          176 DPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDI  246 (389)
T ss_dssp             CHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHH
T ss_pred             CHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHH
Confidence            0      01237999999999999999887641 001122245778899999         7887655444

>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=2.1e-11  Score=113.25  Aligned_cols=190  Identities=14%  Similarity=0.045  Sum_probs=115.9

Q ss_pred             CcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 042806          152 DYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLG  231 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~  231 (390)
                      ....++||+..++.+.+++..+..+.+.|+|++|+||||+|+.+++...........++++.+.......+ +.++..+.
T Consensus        19 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~i-~~~~~~~~   97 (323)
T 1sxj_B           19 VLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVV-RNQIKHFA   97 (323)
T ss_dssp             SGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHH-HTHHHHHH
T ss_pred             CHHHHHCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCccccChHHH-HHHHHHHH
Confidence            34678999999999999998776655999999999999999999988643211112344444333232222 22222211


Q ss_pred             CCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecchhh-hhhcCCCcceEecC
Q 042806          232 LTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSLDV-LSRKMDSQQNFSVG  308 (390)
Q Consensus       232 ~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~~v-~~~~~~~~~~~~l~  308 (390)
                      ....             .+..+++.++|+||++..  ..++.+...+.....++.+|+||+...- ..........+++.
T Consensus        98 ~~~~-------------~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~~i~~~  164 (323)
T 1sxj_B           98 QKKL-------------HLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYS  164 (323)
T ss_dssp             HBCC-------------CCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECC
T ss_pred             hccc-------------cCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhceEEeec
Confidence            0000             000233589999999764  2333333333223456788888876322 11122234589999


Q ss_pred             CCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHH-HHHHHHH
Q 042806          309 VLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVS-IVTVARA  356 (390)
Q Consensus       309 ~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLa-i~~l~~~  356 (390)
                      +++.++..+++...+....... .++....|++.|+|.|.. +..+...
T Consensus       165 ~~~~~~~~~~l~~~~~~~~~~~-~~~~~~~l~~~~~G~~r~a~~~l~~~  212 (323)
T 1sxj_B          165 KLSDEDVLKRLLQIIKLEDVKY-TNDGLEAIIFTAEGDMRQAINNLQST  212 (323)
T ss_dssp             CCCHHHHHHHHHHHHHHHTCCB-CHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            9999999999988764111111 134678899999999954 4444433

>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=99.15  E-value=9.3e-11  Score=108.98  Aligned_cols=190  Identities=13%  Similarity=0.047  Sum_probs=114.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGL  232 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~  232 (390)
                      ...++|++..++.+..++..+..+.+.|+|++|+||||+|+.+++.......-...+.+..+....... +......+..
T Consensus        24 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  102 (327)
T 1iqp_A           24 LDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINV-IREKVKEFAR  102 (327)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHHHT-THHHHHHHHH
T ss_pred             HHHhhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeeccccCchHH-HHHHHHHHHh
Confidence            456899999999999998877666699999999999999999998864321001233333332111111 1111111000


Q ss_pred             CCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecchhh-hhhcCCCcceEecCC
Q 042806          233 TLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSLDV-LSRKMDSQQNFSVGV  309 (390)
Q Consensus       233 ~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~~v-~~~~~~~~~~~~l~~  309 (390)
                      ..              .+..+++.++|+|+++..  ..+..+...+.....++++|+||..... ..........+++.+
T Consensus       103 ~~--------------~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~~~~~~  168 (327)
T 1iqp_A          103 TK--------------PIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRP  168 (327)
T ss_dssp             SC--------------CGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCC
T ss_pred             hC--------------CcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhCcEEEecC
Confidence            00              011134489999999754  2333343333223456788888876432 111111234789999


Q ss_pred             CCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhc
Q 042806          310 LKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALG  358 (390)
Q Consensus       310 L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~  358 (390)
                      ++.++..+++...+...... -.++....|++.++|.|..+..+...+.
T Consensus       169 l~~~~~~~~l~~~~~~~~~~-~~~~~~~~l~~~~~g~~r~~~~~l~~~~  216 (327)
T 1iqp_A          169 LRDEDIAKRLRYIAENEGLE-LTEEGLQAILYIAEGDMRRAINILQAAA  216 (327)
T ss_dssp             CCHHHHHHHHHHHHHTTTCE-ECHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence            99999999998877422211 1245678899999999997666554443

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.12  E-value=2.1e-09  Score=98.82  Aligned_cols=172  Identities=9%  Similarity=0.055  Sum_probs=107.9

Q ss_pred             cccccchhHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCC---C-C-eEEEEEeCCCCCHHHHH
Q 042806          153 YEACESRMSTLNDILDALK----NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKL---F-D-QVIFVEVSKIQDIRKIQ  223 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~----~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~---f-~-~~~wv~v~~~~~~~~l~  223 (390)
                      ...+.+|+.+++.|...|.    ++..+.+.|+|++|+|||++++.+++.......   . . ..+++++....+...++
T Consensus        19 ~~~L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~   98 (318)
T 3te6_A           19 RELLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALY   98 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHH
T ss_pred             ccccCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHH
Confidence            3448899999999887665    467788999999999999999999999864211   1 1 35677777778889999


Q ss_pred             HHHHHHhCCCCC-CCCchHHHHHHHHHH--hCCCeEEEEEeCCCCCcccccccCCC--C-CCCCCcEEEEEecchhhhhh
Q 042806          224 GEIADKLGLTLH-EESDSGRARSLRNRL--KKEKTILVILDNIWGNLDFQAVGIPH--G-DDRKGCKVLLTARSLDVLSR  297 (390)
Q Consensus       224 ~~i~~~l~~~~~-~~~~~~~~~~l~~~l--~~~~~~LlVlDdv~~~~~~~~l~~~l--~-~~~~~s~IivTtr~~~v~~~  297 (390)
                      ..|++++..... .......+..+...+  ..+++++++||+++....-+.+...+  + .......||.++...+....
T Consensus        99 ~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~~~  178 (318)
T 3te6_A           99 EKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSIICVGGHNVTIRE  178 (318)
T ss_dssp             HHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSCCTHHHHHHHHHHHCSSCCEEEEEECCSSCCCHH
T ss_pred             HHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhhcchHHHHHHhcccccCCcEEEEEEecCcccchh
Confidence            999999954321 112233344444443  23456999999997654222221111  1 11122334444443211110


Q ss_pred             -------cCCCcceEecCCCCHHHHHHHHHHhhC
Q 042806          298 -------KMDSQQNFSVGVLKEDEAWSLFKKMAG  324 (390)
Q Consensus       298 -------~~~~~~~~~l~~L~~~ea~~lf~~~~~  324 (390)
                             ..-....+.+.|++.+|-.+++.+++.
T Consensus       179 ~L~~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl~  212 (318)
T 3te6_A          179 QINIMPSLKAHFTEIKLNKVDKNELQQMIITRLK  212 (318)
T ss_dssp             HHHTCHHHHTTEEEEECCCCCHHHHHHHHHHHHH
T ss_pred             hcchhhhccCCceEEEeCCCCHHHHHHHHHHHHH
Confidence                   011225799999999999999988874

>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=99.08  E-value=1.2e-09  Score=101.14  Aligned_cols=187  Identities=11%  Similarity=0.071  Sum_probs=115.0

Q ss_pred             CcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          152 DYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFD-QVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ....++|++..+..+.+++..+..+.+.++|++|+|||++|+.+++...... +. ..+.++.+.......+        
T Consensus        15 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~-~~~~~~~~~~~~~~~~~~~--------   85 (319)
T 2chq_A           15 TLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGEN-WRDNFIEMNASDERGIDVV--------   85 (319)
T ss_dssp             SGGGSCSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHHHTTC-HHHHCEEEETTSTTCTTTS--------
T ss_pred             CHHHHhCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHhcCCc-ccCCeEEEeCccccChHHH--------
Confidence            3456899999999999998877665689999999999999999998863211 11 1233343332111100        


Q ss_pred             CCCCCCCCchHHHHHHHHH--HhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecchh-hhhhcCCCcceE
Q 042806          231 GLTLHEESDSGRARSLRNR--LKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSLD-VLSRKMDSQQNF  305 (390)
Q Consensus       231 ~~~~~~~~~~~~~~~l~~~--l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~~-v~~~~~~~~~~~  305 (390)
                               ......+...  +..+++.++|+|+++..  .....+...+.....++++|+||.... +..........+
T Consensus        86 ---------~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~i  156 (319)
T 2chq_A           86 ---------RHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVF  156 (319)
T ss_dssp             ---------SHHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCEEE
T ss_pred             ---------HHHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCeEE
Confidence                     0011111100  11234589999999754  233444444433445678888876543 211112233589


Q ss_pred             ecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHh
Q 042806          306 SVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARAL  357 (390)
Q Consensus       306 ~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L  357 (390)
                      ++.+++.++..+++...+....... .++....+++.++|.|..+..+...+
T Consensus       157 ~~~~~~~~~~~~~l~~~~~~~~~~i-~~~~l~~l~~~~~G~~r~~~~~l~~~  207 (319)
T 2chq_A          157 RFKPVPKEAMKKRLLEICEKEGVKI-TEDGLEALIYISGGDFRKAINALQGA  207 (319)
T ss_dssp             ECCCCCHHHHHHHHHHHHHTTCCCB-CHHHHHHHHHTTTTCHHHHHHHHHHH
T ss_pred             EecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            9999999999999988774222211 24467789999999998765554333

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=98.99  E-value=3.4e-09  Score=100.32  Aligned_cols=195  Identities=12%  Similarity=0.127  Sum_probs=112.5

Q ss_pred             cccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 042806          153 YEACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLG  231 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~  231 (390)
                      ...++||+..++.+...+..++ .+.+.|+|++|+||||+|+.+.+.......+..      ..+..... ...+.....
T Consensus        15 ~~~~vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~------~~~~~~~~-~~~~~~~~~   87 (373)
T 1jr3_A           15 FADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITA------TPCGVCDN-CREIEQGRF   87 (373)
T ss_dssp             TTTSCSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCS------SCCSSSHH-HHHHHTSCC
T ss_pred             hhhccCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCC------CCCcccHH-HHHHhccCC
Confidence            4569999999999999887654 457889999999999999999987643211100      00000000 111110000


Q ss_pred             -----CCCCCCCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecchh-hhhhcC
Q 042806          232 -----LTLHEESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSLD-VLSRKM  299 (390)
Q Consensus       232 -----~~~~~~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~~-v~~~~~  299 (390)
                           ..............+.+.+.    .+++.++|+||++..  ...+.+...+.....+..+|++|.... +.....
T Consensus        88 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~~~l~  167 (373)
T 1jr3_A           88 VDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTIL  167 (373)
T ss_dssp             SSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSCHHHH
T ss_pred             CceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCcHHHH
Confidence                 00000001112233334332    234489999999754  233334333322334567777776432 212122


Q ss_pred             CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHH
Q 042806          300 DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVAR  355 (390)
Q Consensus       300 ~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~  355 (390)
                      .....+++.+++.++..+++.+.+....... ..+....|++.++|.|..+..+..
T Consensus       168 sr~~~i~~~~l~~~~~~~~l~~~~~~~~~~~-~~~a~~~l~~~~~G~~r~~~~~l~  222 (373)
T 1jr3_A          168 SRCLQFHLKALDVEQIRHQLEHILNEEHIAH-EPRALQLLARAAEGSLRDALSLTD  222 (373)
T ss_dssp             TTSEEEECCCCCHHHHHHHHHHHHHHHTCCB-CHHHHHHHHHHSSSCHHHHHHHHH
T ss_pred             hheeEeeCCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHCCCCHHHHHHHHH
Confidence            2346899999999999999987764111111 134577899999999998876643

>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=98.98  E-value=3.4e-09  Score=98.42  Aligned_cols=176  Identities=12%  Similarity=0.042  Sum_probs=108.4

Q ss_pred             cccccchhHHHHHHHHHhcC-----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKN-----PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-----~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      ...++|++..+..+..++..     .....+.|+|++|+|||+||+.+++....     ...+++.+......++..   
T Consensus        11 ~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~~~-----~~~~~~~~~~~~~~~l~~---   82 (324)
T 1hqc_A           11 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGV-----NLRVTSGPAIEKPGDLAA---   82 (324)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHHTC-----CEEEECTTTCCSHHHHHH---
T ss_pred             HHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHhCC-----CEEEEeccccCChHHHHH---
Confidence            45789999888888777652     23467889999999999999999987642     134444443333332222   


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHhC--CCeEEEEEeCCCCCc--ccccccCCCC--------C----------CCCCcEE
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLKK--EKTILVILDNIWGNL--DFQAVGIPHG--------D----------DRKGCKV  285 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~~--~~~~LlVlDdv~~~~--~~~~l~~~l~--------~----------~~~~s~I  285 (390)
                                           .+..  .++.+|+||+++...  ....+...+.        .          ..++.++
T Consensus        83 ---------------------~l~~~~~~~~~l~lDEi~~l~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~  141 (324)
T 1hqc_A           83 ---------------------ILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTL  141 (324)
T ss_dssp             ---------------------HHTTTCCTTCEEEETTTTSCCHHHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEE
T ss_pred             ---------------------HHHHhccCCCEEEEECCcccccchHHHHHHHHHhhhhHHhccccccccccccCCCCEEE
Confidence                                 1211  233689999997542  1111110000        0          0124567


Q ss_pred             EEEecchhhh-hhcCC-CcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhc
Q 042806          286 LLTARSLDVL-SRKMD-SQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALG  358 (390)
Q Consensus       286 ivTtr~~~v~-~~~~~-~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~  358 (390)
                      |.||...... ..... ....+++.+++.++..+++.+.+....... .++....+++.|+|.|-.+..+...+.
T Consensus       142 i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~-~~~~~~~l~~~~~G~~r~l~~~l~~~~  215 (324)
T 1hqc_A          142 IGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRI-TEEAALEIGRRSRGTMRVAKRLFRRVR  215 (324)
T ss_dssp             EEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHHHHHHHTTTCCC-CHHHHHHHHHHSCSCHHHHHHHHHHHT
T ss_pred             EEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence            7777643221 11111 235899999999999999988774221111 245678899999999998887766553

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.93  E-value=2.3e-09  Score=91.12  Aligned_cols=152  Identities=13%  Similarity=0.136  Sum_probs=86.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCC-----CCeEEEEEeCCCCCHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKL-----FDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~-----f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      ...++||+.++..+.+.+.....+.+.|+|++|+|||+|++.+++.......     ....+++.++      .+.    
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~----   90 (195)
T 1jbk_A           21 LDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMG------ALV----   90 (195)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHH------HHH----
T ss_pred             ccccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeHH------HHh----
Confidence            4568999999999999998877778899999999999999999998643210     1223444321      111    


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHH-hCCCeEEEEEeCCCCCc---------c-cccccCCCCCCCCCcEEEEEecchhhh-
Q 042806          228 DKLGLTLHEESDSGRARSLRNRL-KKEKTILVILDNIWGNL---------D-FQAVGIPHGDDRKGCKVLLTARSLDVL-  295 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l-~~~~~~LlVlDdv~~~~---------~-~~~l~~~l~~~~~~s~IivTtr~~~v~-  295 (390)
                         ...............+.+.+ ...++.+|+|||++...         . ...+...+  ...+..+|+||...... 
T Consensus        91 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~l~~~~--~~~~~~~i~~~~~~~~~~  165 (195)
T 1jbk_A           91 ---AGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPAL--ARGELHCVGATTLDEYRQ  165 (195)
T ss_dssp             ---TTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHH--HTTSCCEEEEECHHHHHH
T ss_pred             ---ccCCccccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhccCcccchHHHHHHHHHhh--ccCCeEEEEeCCHHHHHH
Confidence               00000000011122222322 23445899999996531         1 11121111  12345577777654321 


Q ss_pred             -----hhcCCCcceEecCCCCHHHHHHHH
Q 042806          296 -----SRKMDSQQNFSVGVLKEDEAWSLF  319 (390)
Q Consensus       296 -----~~~~~~~~~~~l~~L~~~ea~~lf  319 (390)
                           .....-...+++.+++.++..+++
T Consensus       166 ~~~~~~~l~~r~~~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          166 YIEKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             HTTTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             HHhcCHHHHHHhceeecCCCCHHHHHHHh
Confidence                 111122236889999998877654

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.87  E-value=1.3e-08  Score=95.60  Aligned_cols=195  Identities=12%  Similarity=0.090  Sum_probs=111.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCC-CeEEEEEeCCCCCHHHHHHHHHHHhC
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLF-DQVIFVEVSKIQDIRKIQGEIADKLG  231 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f-~~~~wv~v~~~~~~~~l~~~i~~~l~  231 (390)
                      ...++|++..++.+..++..+..+.+.|+|++|+||||+|+.+.+.......+ .....++.+.......+ ......+.
T Consensus        36 ~~~i~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~  114 (353)
T 1sxj_D           36 LDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIV-REKVKNFA  114 (353)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHH-TTHHHHHH
T ss_pred             HHHhhCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHHH-HHHHHHHh
Confidence            45789999999999999987765558999999999999999999886421111 12333444332233222 22222111


Q ss_pred             CC-CCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEecchh-hhhhcCCCcceEec
Q 042806          232 LT-LHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTARSLD-VLSRKMDSQQNFSV  307 (390)
Q Consensus       232 ~~-~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTtr~~~-v~~~~~~~~~~~~l  307 (390)
                      .. .......     ........++-+|++|+++...  ....+...+.......++|++|.... +......-...+++
T Consensus       115 ~~~~~~~~~~-----~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~~i~~  189 (353)
T 1sxj_D          115 RLTVSKPSKH-----DLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRF  189 (353)
T ss_dssp             HSCCCCCCTT-----HHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEEC
T ss_pred             hhcccccchh-----hcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCceEEe
Confidence            10 0000000     0011112233699999986542  22233222222234567777775432 21111112248899


Q ss_pred             CCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          308 GVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       308 ~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      .+++.++...++.+.+......- .++....|++.++|.|-.+..+.
T Consensus       190 ~~~~~~~~~~~l~~~~~~~~~~i-~~~~l~~l~~~~~G~~r~~~~~l  235 (353)
T 1sxj_D          190 KALDASNAIDRLRFISEQENVKC-DDGVLERILDISAGDLRRGITLL  235 (353)
T ss_dssp             CCCCHHHHHHHHHHHHHTTTCCC-CHHHHHHHHHHTSSCHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHcCCCHHHHHHHH
Confidence            99999999999988764221111 24567899999999998755443

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

Probab=98.82  E-value=2.8e-08  Score=90.47  Aligned_cols=180  Identities=16%  Similarity=0.183  Sum_probs=103.9

Q ss_pred             CcccccchhHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 042806          152 DYEACESRMSTLNDILDALKN-------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD  218 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  218 (390)
                      ....++|.+..++.|.+.+..             ...+-+.|+|++|+|||+||+.+++.....     .+.+..+....
T Consensus        15 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~-----~~~v~~~~~~~   89 (285)
T 3h4m_A           15 RYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNAT-----FIRVVGSELVK   89 (285)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCE-----EEEEEGGGGCC
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC-----EEEEehHHHHH
Confidence            355788999888888777632             345678999999999999999999886432     23333322111


Q ss_pred             HHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc----------------ccccccCCCC--CCC
Q 042806          219 IRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL----------------DFQAVGIPHG--DDR  280 (390)
Q Consensus       219 ~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~----------------~~~~l~~~l~--~~~  280 (390)
                      .              . ..........+........+.+|+||+++...                .+..+...+.  ...
T Consensus        90 ~--------------~-~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~  154 (285)
T 3h4m_A           90 K--------------F-IGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDAR  154 (285)
T ss_dssp             C--------------S-TTHHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSS
T ss_pred             h--------------c-cchHHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCCC
Confidence            0              0 00111223333444444456899999996420                0111111110  123


Q ss_pred             CCcEEEEEecchhhhhh-c-C--CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC-ChHHHHHH
Q 042806          281 KGCKVLLTARSLDVLSR-K-M--DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAG-LPVSIVTV  353 (390)
Q Consensus       281 ~~s~IivTtr~~~v~~~-~-~--~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~G-lPLai~~l  353 (390)
                      .+..||.||........ . .  .....+.+.+.+.++..++|...+.......+.  ....++..+.| .|-.|..+
T Consensus       155 ~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~--~~~~l~~~~~g~~~~~i~~l  230 (285)
T 3h4m_A          155 GDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDV--NLEEIAKMTEGCVGAELKAI  230 (285)
T ss_dssp             SSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTTC--CHHHHHHHCTTCCHHHHHHH
T ss_pred             CCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCcC--CHHHHHHHcCCCCHHHHHHH
Confidence            45677888875432111 1 1  223479999999999999999887632221111  13578888877 45455443

>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=98.80  E-value=5.4e-09  Score=92.35  Aligned_cols=173  Identities=12%  Similarity=0.068  Sum_probs=101.9

Q ss_pred             ccccch---hHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          154 EACESR---MSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       154 ~~~~gR---~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      +.|+++   ...+..+..++..+..+.+.|+|++|+||||||+.+++.....  .....|+.++.....      +    
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~--~~~~~~~~~~~~~~~------~----   95 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANEL--ERRSFYIPLGIHASI------S----   95 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEEEGGGGGGS------C----
T ss_pred             hhccCCCCCHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEHHHHHHH------H----
Confidence            455653   3555666666665567889999999999999999999987653  234566665432110      0    


Q ss_pred             CCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc----cccccCCCCC-CCCC-cEEEEEecchhhh-----hh--
Q 042806          231 GLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD----FQAVGIPHGD-DRKG-CKVLLTARSLDVL-----SR--  297 (390)
Q Consensus       231 ~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~----~~~l~~~l~~-~~~~-s~IivTtr~~~v~-----~~--  297 (390)
                               ..    ..+.+.  ++.+||+||++....    .+.+...+.. ...+ .++|+||+...-.     ..  
T Consensus        96 ---------~~----~~~~~~--~~~vliiDe~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~  160 (242)
T 3bos_A           96 ---------TA----LLEGLE--QFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLV  160 (242)
T ss_dssp             ---------GG----GGTTGG--GSSEEEEETGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCCHHHH
T ss_pred             ---------HH----HHHhcc--CCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhhhhh
Confidence                     00    001111  236999999965421    1222211100 0112 2477777642210     00  


Q ss_pred             -cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          298 -KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       298 -~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                       .......+++.+++.++..+++...+...... -.++....+++.++|.+-.+..+.
T Consensus       161 ~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~~-~~~~~~~~l~~~~~g~~r~l~~~l  217 (242)
T 3bos_A          161 SRMHWGLTYQLQPMMDDEKLAALQRRAAMRGLQ-LPEDVGRFLLNRMARDLRTLFDVL  217 (242)
T ss_dssp             HHHHHSEEEECCCCCGGGHHHHHHHHHHHTTCC-CCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             hHhhcCceEEeCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHccCCHHHHHHHH
Confidence             11122689999999999999998877411111 124567889999999998776554

>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=98.79  E-value=3.2e-08  Score=97.86  Aligned_cols=191  Identities=12%  Similarity=0.094  Sum_probs=108.5

Q ss_pred             cCcccccchhHHHHHHHHHhcC-----------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEe
Q 042806          151 KDYEACESRMSTLNDILDALKN-----------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEV  213 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~-----------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v  213 (390)
                      .....++|++..++.+.+++..                 +..+.+.|+|++|+||||+|+.+++...    + ..+.+++
T Consensus        36 ~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~----~-~~i~in~  110 (516)
T 1sxj_A           36 TNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG----Y-DILEQNA  110 (516)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT----C-EEEEECT
T ss_pred             CCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcC----C-CEEEEeC
Confidence            3456799999999999999875                 1347899999999999999999999873    2 2444555


Q ss_pred             CCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHH-HhCCCeEEEEEeCCCCCcc-----cccccCCCCCCCCCcEEEE
Q 042806          214 SKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNR-LKKEKTILVILDNIWGNLD-----FQAVGIPHGDDRKGCKVLL  287 (390)
Q Consensus       214 ~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~-l~~~~~~LlVlDdv~~~~~-----~~~l~~~l~~~~~~s~Iiv  287 (390)
                      +...... ++...+...........   ......+. ...+++.+|++|+++....     +..+...+.  ..+..||+
T Consensus       111 s~~~~~~-~~~~~i~~~~~~~~~~~---~~~~~~~~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~--~~~~~iIl  184 (516)
T 1sxj_A          111 SDVRSKT-LLNAGVKNALDNMSVVG---YFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCR--KTSTPLIL  184 (516)
T ss_dssp             TSCCCHH-HHHHTGGGGTTBCCSTT---TTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHH--HCSSCEEE
T ss_pred             CCcchHH-HHHHHHHHHhccccHHH---HHhhhhhhhhccCCCeEEEEECCCccchhhHHHHHHHHHHHH--hcCCCEEE
Confidence            5444432 22222221111100000   00000000 1124558999999965421     122222211  12334555


Q ss_pred             Eecchhh--hhhcCCCcceEecCCCCHHHHHHHHHHhhC--CCCCCCchHHHHHHHHHHcCC-ChHHHHHHHH
Q 042806          288 TARSLDV--LSRKMDSQQNFSVGVLKEDEAWSLFKKMAG--DYIEGSEFKWVAKDVARECAG-LPVSIVTVAR  355 (390)
Q Consensus       288 Ttr~~~v--~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~--~~~~~~~~~~~~~~i~~~~~G-lPLai~~l~~  355 (390)
                      ++.....  ..........+++.+++.++..+++...+.  +...++   +....|++.++| ++.++..+..
T Consensus       185 i~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~---~~l~~la~~s~GdiR~~i~~L~~  254 (516)
T 1sxj_A          185 ICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDP---NVIDRLIQTTRGDIRQVINLLST  254 (516)
T ss_dssp             EESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCT---THHHHHHHHTTTCHHHHHHHHTH
T ss_pred             EEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCCCCH---HHHHHHHHHcCCcHHHHHHHHHH
Confidence            5554221  111223345899999999999999987764  211222   246789999999 5555665543

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

Probab=98.75  E-value=2.7e-07  Score=82.65  Aligned_cols=181  Identities=16%  Similarity=0.180  Sum_probs=98.1

Q ss_pred             ccccchhHHHHHHHHH---hcC---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHH
Q 042806          154 EACESRMSTLNDILDA---LKN---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRK  221 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~---L~~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~  221 (390)
                      ..++|.+..+..+.+.   +..         ...+.+.|+|++|+|||++|+.+++.....     .+.+..+...+.  
T Consensus         6 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~-----~~~~~~~~~~~~--   78 (262)
T 2qz4_A            6 KDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVP-----FLAMAGAEFVEV--   78 (262)
T ss_dssp             TSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCC-----EEEEETTTTSSS--
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCC-----EEEechHHHHhh--
Confidence            3567776665555443   322         234568899999999999999999976422     344444332110  


Q ss_pred             HHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc-------------c----cccccCCCC--CCCCC
Q 042806          222 IQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL-------------D----FQAVGIPHG--DDRKG  282 (390)
Q Consensus       222 l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~-------------~----~~~l~~~l~--~~~~~  282 (390)
                                  .. .........+........+.+|+||+++...             .    +..+...+.  ....+
T Consensus        79 ------------~~-~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~  145 (262)
T 2qz4_A           79 ------------IG-GLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDH  145 (262)
T ss_dssp             ------------ST-THHHHHHHHHHHHHHHTCSEEEEEECC-------------------CHHHHHHHHHHHTCCTTCC
T ss_pred             ------------cc-ChhHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCCCC
Confidence                        00 0011122233333333445999999997531             0    111111111  12235


Q ss_pred             cEEEEEecchhhhh-hcC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH-HHHHHH
Q 042806          283 CKVLLTARSLDVLS-RKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV-SIVTVA  354 (390)
Q Consensus       283 s~IivTtr~~~v~~-~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL-ai~~l~  354 (390)
                      ..||.||....... ...   .....+.+.+.+.++-.+++.+.+...............+++.+.|.+- .|..+.
T Consensus       146 ~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~  222 (262)
T 2qz4_A          146 VIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANIC  222 (262)
T ss_dssp             EEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHH
T ss_pred             EEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHH
Confidence            66777776543211 111   1235788999999999999988775222222223334788999988754 555443

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

Probab=98.75  E-value=1.1e-07  Score=92.05  Aligned_cols=179  Identities=14%  Similarity=0.153  Sum_probs=106.5

Q ss_pred             cCcccccchhHHH---HHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHH
Q 042806          151 KDYEACESRMSTL---NDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEI  226 (390)
Q Consensus       151 ~~~~~~~gR~~~~---~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i  226 (390)
                      .....++|.+..+   ..|...+..+..+.+.|+|++|+||||||+.+.+.....       ++.++.. ....++ +.+
T Consensus        23 ~~l~~ivGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~~~~-------f~~l~a~~~~~~~i-r~~   94 (447)
T 3pvs_A           23 ENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYANAD-------VERISAVTSGVKEI-REA   94 (447)
T ss_dssp             CSTTTCCSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHHHTTCE-------EEEEETTTCCHHHH-HHH
T ss_pred             CCHHHhCCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHHHhCCC-------eEEEEeccCCHHHH-HHH
Confidence            3456788988877   677777777777889999999999999999999886432       2222221 122221 111


Q ss_pred             HHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEE-Eecchh--hhhhcCCC
Q 042806          227 ADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLL-TARSLD--VLSRKMDS  301 (390)
Q Consensus       227 ~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~Iiv-Ttr~~~--v~~~~~~~  301 (390)
                      +.                ........+++.+|+||+++..  ...+.+...+..  ....+|. ||.+..  +......-
T Consensus        95 ~~----------------~a~~~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le~--~~v~lI~att~n~~~~l~~aL~sR  156 (447)
T 3pvs_A           95 IE----------------RARQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIED--GTITFIGATTENPSFELNSALLSR  156 (447)
T ss_dssp             HH----------------HHHHHHHTTCCEEEEEETTTCC------CCHHHHHT--TSCEEEEEESSCGGGSSCHHHHTT
T ss_pred             HH----------------HHHHhhhcCCCcEEEEeChhhhCHHHHHHHHHHHhc--CceEEEecCCCCcccccCHHHhCc
Confidence            11                1111111234589999999755  223333333322  2234444 444432  11112233


Q ss_pred             cceEecCCCCHHHHHHHHHHhhCCC------CCCCchHHHHHHHHHHcCCChHHHHHHHH
Q 042806          302 QQNFSVGVLKEDEAWSLFKKMAGDY------IEGSEFKWVAKDVARECAGLPVSIVTVAR  355 (390)
Q Consensus       302 ~~~~~l~~L~~~ea~~lf~~~~~~~------~~~~~~~~~~~~i~~~~~GlPLai~~l~~  355 (390)
                      ...+.+.+++.++...++.+.+...      ....-.++....|++.++|.+-.+..+..
T Consensus       157 ~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~Gd~R~lln~Le  216 (447)
T 3pvs_A          157 ARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTLE  216 (447)
T ss_dssp             EEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCSCHHHHHHHHH
T ss_pred             eeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCCCHHHHHHHHH
Confidence            4588999999999999998876421      11112245678899999998876665543

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

Probab=98.73  E-value=2e-07  Score=84.25  Aligned_cols=180  Identities=14%  Similarity=0.123  Sum_probs=96.1

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHh
Q 042806          172 NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLK  251 (390)
Q Consensus       172 ~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~  251 (390)
                      ....+.+.|+|++|+|||+||+.+++....    . .+.+..+...            ++.  ...........+.....
T Consensus        61 ~~~~~~vLl~G~~GtGKT~la~~ia~~~~~----~-~~~i~~~~~~------------~g~--~~~~~~~~~~~~~~~~~  121 (272)
T 1d2n_A           61 RTPLVSVLLEGPPHSGKTALAAKIAEESNF----P-FIKICSPDKM------------IGF--SETAKCQAMKKIFDDAY  121 (272)
T ss_dssp             SCSEEEEEEECSTTSSHHHHHHHHHHHHTC----S-EEEEECGGGC------------TTC--CHHHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCcHHHHHHHHHHHhCC----C-EEEEeCHHHh------------cCC--chHHHHHHHHHHHHHHH
Confidence            345678899999999999999999997532    2 2222222110            000  00000011222333333


Q ss_pred             CCCeEEEEEeCCCCC-----------c-ccccccCCCC---CCCCCcEEEEEecchhhhhh--cCC-CcceEecCCCCH-
Q 042806          252 KEKTILVILDNIWGN-----------L-DFQAVGIPHG---DDRKGCKVLLTARSLDVLSR--KMD-SQQNFSVGVLKE-  312 (390)
Q Consensus       252 ~~~~~LlVlDdv~~~-----------~-~~~~l~~~l~---~~~~~s~IivTtr~~~v~~~--~~~-~~~~~~l~~L~~-  312 (390)
                      ..++.+|+||+++..           . .++.+...+.   .......||.||........  ... ....+++.+++. 
T Consensus       122 ~~~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~~l~~~~l~~rf~~~i~~p~l~~r  201 (272)
T 1d2n_A          122 KSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATG  201 (272)
T ss_dssp             TSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTTTSSEEEECCCEEEH
T ss_pred             hcCCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCEEEEEecCChhhcchhhhhcccceEEcCCCccHH
Confidence            345689999998532           1 1122222221   12234456777776543221  111 245788999988 


Q ss_pred             HHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC------ChHHHHHHHHHhcCCCCCCCcccchhHHHHHhhhh
Q 042806          313 DEAWSLFKKMAGDYIEGSEFKWVAKDVARECAG------LPVSIVTVARALGTRDYLNGRTHWNSWGGLLQLTL  380 (390)
Q Consensus       313 ~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~G------lPLai~~l~~~L~~~~~~~~~~~w~~~~~~l~~~~  380 (390)
                      ++...++.+...  .    ..+....+++.+.|      ++-++..+-......+    ...++.+...|+...
T Consensus       202 ~~i~~i~~~~~~--~----~~~~~~~l~~~~~g~~~~g~ir~l~~~l~~a~~~~~----~~~~~~~~~~l~~~~  265 (272)
T 1d2n_A          202 EQLLEALELLGN--F----KDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQMDP----EYRVRKFLALLREEG  265 (272)
T ss_dssp             HHHHHHHHHHTC--S----CHHHHHHHHHHHTTSEEEECHHHHHHHHHHHTTSCG----GGHHHHHHHHHHHTS
T ss_pred             HHHHHHHHhcCC--C----CHHHHHHHHHHhcCCCccccHHHHHHHHHHHhhhch----HHHHHHHHHHHHHcC
Confidence            667777665321  1    13456788999887      5555555544433222    456666666665543

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

Probab=98.70  E-value=4.3e-07  Score=85.44  Aligned_cols=182  Identities=9%  Similarity=0.051  Sum_probs=104.6

Q ss_pred             cccccchhHHHHHHHHHhc------------CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 042806          153 YEACESRMSTLNDILDALK------------NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~------------~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  220 (390)
                      ...++|.+..++.|.+.+.            ....+.+.|+|++|+|||+||+.+++....     ..+.++.+..... 
T Consensus        83 ~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~-----~~~~i~~~~l~~~-  156 (357)
T 3d8b_A           83 WEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQSGA-----TFFSISASSLTSK-  156 (357)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHTTC-----EEEEEEGGGGCCS-
T ss_pred             HHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHcCC-----eEEEEehHHhhcc-
Confidence            4568899888888877663            124567899999999999999999887632     2344444322110 


Q ss_pred             HHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc-------------ccccccCCCC----CCCCCc
Q 042806          221 KIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL-------------DFQAVGIPHG----DDRKGC  283 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~-------------~~~~l~~~l~----~~~~~s  283 (390)
                                   . ..........+.......++.+|+||+++...             ....+...+.    ....+.
T Consensus       157 -------------~-~g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~~v  222 (357)
T 3d8b_A          157 -------------W-VGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRI  222 (357)
T ss_dssp             -------------S-TTHHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC----CCCCE
T ss_pred             -------------c-cchHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccccCCCCE
Confidence                         0 00011122333333333455899999994320             0111211111    122355


Q ss_pred             EEEEEecchh-hhhh-cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC-ChHHHHHHHH
Q 042806          284 KVLLTARSLD-VLSR-KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAG-LPVSIVTVAR  355 (390)
Q Consensus       284 ~IivTtr~~~-v~~~-~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~G-lPLai~~l~~  355 (390)
                      .||.||.... +... .......+.+...+.++..+++...+......- .++....|++.+.| .|-.|..+..
T Consensus       223 ~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l-~~~~l~~la~~t~G~s~~dl~~l~~  296 (357)
T 3d8b_A          223 LVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMSKEQCCL-SEEEIEQIVQQSDAFSGADMTQLCR  296 (357)
T ss_dssp             EEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHHTSCBCC-CHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             EEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHhhcCCCc-cHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            6666776532 2111 112335788999999999999988774221111 13456789999988 5666666543

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

Probab=98.69  E-value=9.2e-08  Score=88.76  Aligned_cols=182  Identities=10%  Similarity=0.072  Sum_probs=103.9

Q ss_pred             cCcccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 042806          151 KDYEACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      ...+.++|++..+..+.+++..+. ..++.++|++|+|||++|+.+++....     ..+.++.+.. .... +...+..
T Consensus        23 ~~~~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l~~-----~~~~i~~~~~-~~~~-i~~~~~~   95 (324)
T 3u61_B           23 STIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNA-----DMMFVNGSDC-KIDF-VRGPLTN   95 (324)
T ss_dssp             CSTTTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHTTE-----EEEEEETTTC-CHHH-HHTHHHH
T ss_pred             CCHHHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHhCC-----CEEEEccccc-CHHH-HHHHHHH
Confidence            345678999999999999998765 467788899999999999999987642     2445554432 2222 2222211


Q ss_pred             hCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc---ccccccCCCCCCCCCcEEEEEecchhh-hhhcCCCcceE
Q 042806          230 LGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL---DFQAVGIPHGDDRKGCKVLLTARSLDV-LSRKMDSQQNF  305 (390)
Q Consensus       230 l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~---~~~~l~~~l~~~~~~s~IivTtr~~~v-~~~~~~~~~~~  305 (390)
                      +.....               ..+++.++++|+++...   ..+.+...+.....+.++|+||....- ......-...+
T Consensus        96 ~~~~~~---------------~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR~~~i  160 (324)
T 3u61_B           96 FASAAS---------------FDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVI  160 (324)
T ss_dssp             HHHBCC---------------CSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHHSEEE
T ss_pred             HHhhcc---------------cCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhhCcEE
Confidence            110000               01245899999997654   222232222112245678888876431 11111112479


Q ss_pred             ecCCCCHHHHHHHHH-------HhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          306 SVGVLKEDEAWSLFK-------KMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       306 ~l~~L~~~ea~~lf~-------~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      ++.+++.++-.+++.       ..+..........+....|++.++|.+-.+....
T Consensus       161 ~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~gd~R~a~~~L  216 (324)
T 3u61_B          161 TFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGEL  216 (324)
T ss_dssp             ECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCBSCHHHHHHHHHHTCSCTTHHHHHH
T ss_pred             EeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHhCCCCHHHHHHHH
Confidence            999999888443332       2222111111112567789999988776544433

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

Probab=98.69  E-value=1.4e-06  Score=80.68  Aligned_cols=182  Identities=15%  Similarity=0.153  Sum_probs=103.4

Q ss_pred             cccccchhHHHHHHHHHhc------------CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 042806          153 YEACESRMSTLNDILDALK------------NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~------------~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  220 (390)
                      ...++|-+..++.|.+.+.            ....+-+.|+|++|+|||+||+.+++.....    ..+.+..+.-.+  
T Consensus        11 ~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~~----~~~~i~~~~l~~--   84 (322)
T 1xwi_A           11 WSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNS----TFFSISSSDLVS--   84 (322)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHTTSC----EEEEEECCSSCC--
T ss_pred             HHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHcCCC----cEEEEEhHHHHh--
Confidence            4567787777776666542            1234678999999999999999999986211    123333332111  


Q ss_pred             HHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc-------------cccccC---CCCCCCCCcE
Q 042806          221 KIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD-------------FQAVGI---PHGDDRKGCK  284 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~-------------~~~l~~---~l~~~~~~s~  284 (390)
                                  ... .........+.......++.+|+||+++....             ...+..   .+.....+..
T Consensus        85 ------------~~~-g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~v~  151 (322)
T 1xwi_A           85 ------------KWL-GESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGIL  151 (322)
T ss_dssp             ------------SSC-CSCHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTTEE
T ss_pred             ------------hhh-hHHHHHHHHHHHHHHhcCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcccccCCCEE
Confidence                        000 11223344444444445569999999974310             011111   1111234556


Q ss_pred             EEEEecchhhhh-h-cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCC-hHHHHHHH
Q 042806          285 VLLTARSLDVLS-R-KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGL-PVSIVTVA  354 (390)
Q Consensus       285 IivTtr~~~v~~-~-~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~Gl-PLai~~l~  354 (390)
                      ||.||....... . .......+.+...+.++-.++|...+....... .+.....|++.+.|. +-.|..+.
T Consensus       152 vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l-~~~~l~~la~~t~G~sgadl~~l~  223 (322)
T 1xwi_A          152 VLGATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHLGTTQNSL-TEADFRELGRKTDGYSGADISIIV  223 (322)
T ss_dssp             EEEEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTCCBCC-CHHHHHHHHHTCTTCCHHHHHHHH
T ss_pred             EEEecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHHhcCCCCC-CHHHHHHHHHHcCCCCHHHHHHHH
Confidence            666665432211 0 112335788999999999999998875322211 134567899999887 44455443

>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=98.69  E-value=1e-07  Score=89.57  Aligned_cols=198  Identities=13%  Similarity=0.082  Sum_probs=106.4

Q ss_pred             CcccccchhHHHHHHHHHh-cCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCC----CCe-------------------
Q 042806          152 DYEACESRMSTLNDILDAL-KNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKL----FDQ-------------------  207 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L-~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~----f~~-------------------  207 (390)
                      ....++|++..++.+.+++ ..++.+.+.|+|++|+||||+++.+.........    ++.                   
T Consensus        12 ~~~~~vg~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~~~~~~~~~~~~~~~~~   91 (354)
T 1sxj_E           12 SLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSP   91 (354)
T ss_dssp             SGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------CCEECS
T ss_pred             CHHHhcCCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceeecccccccceeeeeccc
Confidence            3457899999999999988 6655444899999999999999999885421110    110                   


Q ss_pred             -EEEEEeCCCC-CHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCCCCCCCCCc
Q 042806          208 -VIFVEVSKIQ-DIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIPHGDDRKGC  283 (390)
Q Consensus       208 -~~wv~v~~~~-~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s  283 (390)
                       .+.+..+... ......+.++..+.........   . .+.. +. .++-++++|++...+  ..+.+...+.....++
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~---~-~ls~-l~-~~~~vlilDE~~~L~~~~~~~L~~~le~~~~~~  165 (354)
T 1sxj_E           92 YHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQ---D-SKDG-LA-HRYKCVIINEANSLTKDAQAALRRTMEKYSKNI  165 (354)
T ss_dssp             SEEEECCC----CCHHHHHHHHHHHTTTTC------------------CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTE
T ss_pred             ceEEecHhhcCCcchHHHHHHHHHHHHhcccccc---c-cccc-cC-CCCeEEEEeCccccCHHHHHHHHHHHHhhcCCC
Confidence             1111111100 0000122222222111000000   0 0000 11 234699999997642  1222322221123467


Q ss_pred             EEEEEecch-hhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHH
Q 042806          284 KVLLTARSL-DVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVAR  355 (390)
Q Consensus       284 ~IivTtr~~-~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~  355 (390)
                      .+|++|... .+......-...+++.+++.++..+++.+.+......-+.++....|++.++|.+-.+..+..
T Consensus       166 ~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~i~~~~~G~~r~a~~~l~  238 (354)
T 1sxj_E          166 RLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLE  238 (354)
T ss_dssp             EEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHHHHHT
T ss_pred             EEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCCHHHHHHHHH
Confidence            788887753 222212223368999999999999999887641111101023567899999999987766543

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

Probab=98.67  E-value=1.8e-07  Score=87.32  Aligned_cols=173  Identities=13%  Similarity=0.100  Sum_probs=103.0

Q ss_pred             CcccccchhHHHHHHHHHhcC-----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 042806          152 DYEACESRMSTLNDILDALKN-----PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~-----~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      ....++|++..+..+..++..     ...+.+.|+|++|+|||+||+.+++.....     .+.++.+......++    
T Consensus        27 ~~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~~~~-----~~~~~~~~~~~~~~~----   97 (338)
T 3pfi_A           27 NFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEMSAN-----IKTTAAPMIEKSGDL----   97 (338)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHTTCC-----EEEEEGGGCCSHHHH----
T ss_pred             CHHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHhCCC-----eEEecchhccchhHH----
Confidence            456799999988888887753     345578899999999999999998875422     233333322211111    


Q ss_pred             HHHhCCCCCCCCchHHHHHHHHHHh-CCCeEEEEEeCCCCCc--ccccccCCC------------------CCCCCCcEE
Q 042806          227 ADKLGLTLHEESDSGRARSLRNRLK-KEKTILVILDNIWGNL--DFQAVGIPH------------------GDDRKGCKV  285 (390)
Q Consensus       227 ~~~l~~~~~~~~~~~~~~~l~~~l~-~~~~~LlVlDdv~~~~--~~~~l~~~l------------------~~~~~~s~I  285 (390)
                                          ...+. ..+..+|+||+++...  ....+...+                  ....++..+
T Consensus        98 --------------------~~~~~~~~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (338)
T 3pfi_A           98 --------------------AAILTNLSEGDILFIDEIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTL  157 (338)
T ss_dssp             --------------------HHHHHTCCTTCEEEEETGGGCCHHHHHHHHHHHHTSCC---------CCCCCCCCCCCEE
T ss_pred             --------------------HHHHHhccCCCEEEEechhhcCHHHHHHHHHHHHhccchhhcccCccccceecCCCCeEE
Confidence                                11111 1233788999987541  111111100                  001123567


Q ss_pred             EEEecchhhh-hh-cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          286 LLTARSLDVL-SR-KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       286 ivTtr~~~v~-~~-~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      |.+|...... .. .......+++.+++.++...++.+.+..... .-.++....|++.+.|.|-.+..+.
T Consensus       158 i~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~~~~-~~~~~~~~~l~~~~~G~~r~l~~~l  227 (338)
T 3pfi_A          158 IGATTRAGMLSNPLRDRFGMQFRLEFYKDSELALILQKAALKLNK-TCEEKAALEIAKRSRSTPRIALRLL  227 (338)
T ss_dssp             EEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC-EECHHHHHHHHHTTTTCHHHHHHHH
T ss_pred             EEeCCCccccCHHHHhhcCEEeeCCCcCHHHHHHHHHHHHHhcCC-CCCHHHHHHHHHHHCcCHHHHHHHH
Confidence            7776653221 11 1122368999999999999999887742111 1224567789999999996655443

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

Probab=98.64  E-value=4.4e-08  Score=90.23  Aligned_cols=154  Identities=13%  Similarity=0.079  Sum_probs=85.3

Q ss_pred             cccchhHHHHHHHHHhc---------------CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          155 ACESRMSTLNDILDALK---------------NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~---------------~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      .++|.+..++.|.+.+.               ......+.|+|++|+|||+||+.+++............++.++..   
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~---  108 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRD---  108 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGG---
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHH---
Confidence            46777776666655432               233456889999999999999999888755332222223333311   


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC-----------cccccccCCCCCCCCCcEEEEE
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN-----------LDFQAVGIPHGDDRKGCKVLLT  288 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~-----------~~~~~l~~~l~~~~~~s~IivT  288 (390)
                       +        +...... ..   ...+...+...++.+|+||+++..           .....+...+.....+..||+|
T Consensus       109 -~--------l~~~~~g-~~---~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~~~i~~  175 (309)
T 3syl_A          109 -D--------LVGQYIG-HT---APKTKEVLKRAMGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLVVILA  175 (309)
T ss_dssp             -G--------TCCSSTT-CH---HHHHHHHHHHHTTSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTTCEEEEE
T ss_pred             -H--------hhhhccc-cc---HHHHHHHHHhcCCCEEEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCCEEEEEe
Confidence             0        0000000 11   111222222112369999999733           1223333333233456678888


Q ss_pred             ecchhhhh------h-cCCCcceEecCCCCHHHHHHHHHHhhC
Q 042806          289 ARSLDVLS------R-KMDSQQNFSVGVLKEDEAWSLFKKMAG  324 (390)
Q Consensus       289 tr~~~v~~------~-~~~~~~~~~l~~L~~~ea~~lf~~~~~  324 (390)
                      |.......      . .......+++.+++.++..+++.+.+.
T Consensus       176 ~~~~~~~~~~~~~~~l~~R~~~~i~~~~~~~~~~~~il~~~l~  218 (309)
T 3syl_A          176 GYADRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLD  218 (309)
T ss_dssp             ECHHHHHHHHHHSTTHHHHEEEEEEECCCCHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHhhCHHHHHhCCeEEEcCCcCHHHHHHHHHHHHH
Confidence            86432100      0 001226899999999999999988774

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

Probab=98.63  E-value=7.4e-07  Score=82.59  Aligned_cols=183  Identities=16%  Similarity=0.139  Sum_probs=106.3

Q ss_pred             cCcccccchhHHHHHHHHHhc----------C--CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 042806          151 KDYEACESRMSTLNDILDALK----------N--PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD  218 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~----------~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  218 (390)
                      .....++|.+..++.|.+.+.          .  ...+-+.|+|++|+|||+||+.+++.....     .+.++.     
T Consensus        15 ~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~~-----~~~v~~-----   84 (322)
T 3eie_A           15 VKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANST-----FFSVSS-----   84 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHTCE-----EEEEEH-----
T ss_pred             CCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHCCC-----EEEEch-----
Confidence            335678899888888887762          1  124568899999999999999999886432     233322     


Q ss_pred             HHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc-------------cccccC---CCCCCCCC
Q 042806          219 IRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD-------------FQAVGI---PHGDDRKG  282 (390)
Q Consensus       219 ~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~-------------~~~l~~---~l~~~~~~  282 (390)
                       .++...        .. .........+.......++.+|+||+++....             ...+..   .+.....+
T Consensus        85 -~~l~~~--------~~-g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~  154 (322)
T 3eie_A           85 -SDLVSK--------WM-GESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQG  154 (322)
T ss_dssp             -HHHHTT--------TG-GGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTSCCC
T ss_pred             -HHHhhc--------cc-chHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhccccccCCc
Confidence             111110        00 01122334444444445568999999964311             111111   11122345


Q ss_pred             cEEEEEecchhhhhh--cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC-ChHHHHHHH
Q 042806          283 CKVLLTARSLDVLSR--KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAG-LPVSIVTVA  354 (390)
Q Consensus       283 s~IivTtr~~~v~~~--~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~G-lPLai~~l~  354 (390)
                      ..||.||........  .......+.+...+.++-.++|...+........ +.....|++.+.| .+-.|..+.
T Consensus       155 v~vi~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~-~~~l~~la~~t~g~sg~di~~l~  228 (322)
T 3eie_A          155 VLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVLT-KEDYRTLGAMTEGYSGSDIAVVV  228 (322)
T ss_dssp             EEEEEEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHHHHHHTTCCCCCC-HHHHHHHHHTTTTCCHHHHHHHH
T ss_pred             eEEEEecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHHHHHhccCCCCCC-HHHHHHHHHHcCCCCHHHHHHHH
Confidence            667767765322110  0122357888999999999999998864322211 3356788899987 454454443

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

Probab=98.62  E-value=1.6e-06  Score=82.48  Aligned_cols=182  Identities=14%  Similarity=0.104  Sum_probs=103.4

Q ss_pred             CcccccchhHHHHHHHHHhcC------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          152 DYEACESRMSTLNDILDALKN------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ....++|.+..+..|.+.+..            ...+-+.|+|++|+|||+||+.+++....     ..+.++.+.... 
T Consensus       113 ~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~~~-----~~~~v~~~~l~~-  186 (389)
T 3vfd_A          113 KFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNA-----TFFNISAASLTS-  186 (389)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHTTC-----EEEEECSCCC---
T ss_pred             ChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhhcC-----cEEEeeHHHhhc-
Confidence            356789999998888887721            22467899999999999999999887532     123333322211 


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc-------------ccccccCCC---C-CCCCC
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL-------------DFQAVGIPH---G-DDRKG  282 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~-------------~~~~l~~~l---~-~~~~~  282 (390)
                       ...             .........+........+.+|+||+++...             ....+...+   . .....
T Consensus       187 -~~~-------------g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~  252 (389)
T 3vfd_A          187 -KYV-------------GEGEKLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDDR  252 (389)
T ss_dssp             -------------------CHHHHHHHHHHHHHSSSEEEEEETGGGGC--------CTHHHHHHHHHHHHHHHC-----C
T ss_pred             -ccc-------------chHHHHHHHHHHHHHhcCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhcccccCCCC
Confidence             000             0111223344444434445899999996430             001111111   0 11234


Q ss_pred             cEEEEEecchhhh-hh-cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH-HHHHHH
Q 042806          283 CKVLLTARSLDVL-SR-KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV-SIVTVA  354 (390)
Q Consensus       283 s~IivTtr~~~v~-~~-~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL-ai~~l~  354 (390)
                      ..||.||...... .. .......+.+...+.++-.+++...+....... .++....|++.+.|..- .|..+.
T Consensus       253 v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l-~~~~~~~la~~~~g~~~~~l~~L~  326 (389)
T 3vfd_A          253 VLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGSPL-TQKELAQLARMTDGYSGSDLTALA  326 (389)
T ss_dssp             EEEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCCCS-CHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             EEEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHcCCCCHHHHHHHH
Confidence            5666667653221 11 112234688999999999999998875322222 23456789999988554 665554

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

Probab=98.61  E-value=5.4e-07  Score=84.97  Aligned_cols=196  Identities=10%  Similarity=0.028  Sum_probs=104.5

Q ss_pred             cccccchhHHHHH---HHHHhcCCCc--cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEe----CCCCCHHHHH
Q 042806          153 YEACESRMSTLND---ILDALKNPDV--NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEV----SKIQDIRKIQ  223 (390)
Q Consensus       153 ~~~~~gR~~~~~~---l~~~L~~~~~--~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v----~~~~~~~~l~  223 (390)
                      ...++|++..+..   +.+.+..+..  +.+.|+|++|+|||+||+.+.+.......   .+.+..    +......+.+
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~~~~~---~~~~~~~~~~~~~~~~~~~~  119 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTP---FTAIAGSEIFSLEMSKTEAL  119 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHCSSCC---EEEEEGGGGSCSSSCHHHHH
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhcccCC---cccccchhhhhcccchhHHH
Confidence            4578999887655   5555555443  58999999999999999999998753211   122222    1223444444


Q ss_pred             HHHHHHhCC---------------------CC--------C--CCCchHHHHHHHHH----HhCCC----eEEEEEeCCC
Q 042806          224 GEIADKLGL---------------------TL--------H--EESDSGRARSLRNR----LKKEK----TILVILDNIW  264 (390)
Q Consensus       224 ~~i~~~l~~---------------------~~--------~--~~~~~~~~~~l~~~----l~~~~----~~LlVlDdv~  264 (390)
                      ...+.....                     ..        .  ..........+...    ...++    +.+|+||+++
T Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~~~vl~IDEi~  199 (368)
T 3uk6_A          120 TQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVH  199 (368)
T ss_dssp             HHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---CBCEEEEESGG
T ss_pred             HHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhccccccCceEEEhhcc
Confidence            444333110                     00        0  00011111111111    11222    3599999997


Q ss_pred             CC--cccccccCCCCCCCCCcEEEEEecc-------------hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCC
Q 042806          265 GN--LDFQAVGIPHGDDRKGCKVLLTARS-------------LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEG  329 (390)
Q Consensus       265 ~~--~~~~~l~~~l~~~~~~s~IivTtr~-------------~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~  329 (390)
                      ..  .....+...+...... .++++|..             ..+......-...+++.+++.++..+++...+......
T Consensus       200 ~l~~~~~~~L~~~le~~~~~-~~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~~~~~~~~~  278 (368)
T 3uk6_A          200 MLDIESFSFLNRALESDMAP-VLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVE  278 (368)
T ss_dssp             GSBHHHHHHHHHHTTCTTCC-EEEEEESCSEEECBTSSCEEETTCCHHHHTTEEEEEECCCCHHHHHHHHHHHHHHTTCC
T ss_pred             ccChHHHHHHHHHhhCcCCC-eeeeecccceeeeeccCCCCcccCCHHHHhhccEEEecCCCHHHHHHHHHHHHHHcCCC
Confidence            54  2223333223222222 34444431             11111111222458999999999999999877521111


Q ss_pred             CchHHHHHHHHHHcC-CChHHHHHH
Q 042806          330 SEFKWVAKDVARECA-GLPVSIVTV  353 (390)
Q Consensus       330 ~~~~~~~~~i~~~~~-GlPLai~~l  353 (390)
                       -.++....|++.+. |.|-.+..+
T Consensus       279 -~~~~~l~~l~~~~~~G~~r~~~~l  302 (368)
T 3uk6_A          279 -MSEDAYTVLTRIGLETSLRYAIQL  302 (368)
T ss_dssp             -BCHHHHHHHHHHHHHSCHHHHHHH
T ss_pred             -CCHHHHHHHHHHhcCCCHHHHHHH
Confidence             22456788999997 777665544

>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=98.59  E-value=4e-07  Score=85.10  Aligned_cols=185  Identities=13%  Similarity=0.076  Sum_probs=105.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCHHHHHHHHHHHhC
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFD-QVIFVEVSKIQDIRKIQGEIADKLG  231 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~l~~~i~~~l~  231 (390)
                      ...++|.+..++.|...+..++.+.+.++|++|+||||+++.++....... +. ....++.+.......+. .....+.
T Consensus        24 ~~~~~g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~~~~-~~~~~~~~~~~~~~~~~~ir-~~i~~~~  101 (340)
T 1sxj_C           24 LDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKN-YSNMVLELNASDDRGIDVVR-NQIKDFA  101 (340)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTS-HHHHEEEECTTSCCSHHHHH-THHHHHH
T ss_pred             HHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-ccceEEEEcCcccccHHHHH-HHHHHHH
Confidence            456788888888888888877655589999999999999999998864321 11 12223333222222221 1111111


Q ss_pred             CCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecchh-hhhhcCCCcceEecC
Q 042806          232 LTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSLD-VLSRKMDSQQNFSVG  308 (390)
Q Consensus       232 ~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~~-v~~~~~~~~~~~~l~  308 (390)
                      .....             + .+.+-++|+|+++..  ...+.+...+......+++|++|.... +......-...+++.
T Consensus       102 ~~~~~-------------~-~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~~~~~~~  167 (340)
T 1sxj_C          102 STRQI-------------F-SKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQ  167 (340)
T ss_dssp             HBCCS-------------S-SCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECC
T ss_pred             hhccc-------------C-CCCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhceeEecc
Confidence            00000             0 112378999998643  222223222211234566777765432 211112223478999


Q ss_pred             CCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          309 VLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       309 ~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      +++.++..+.+.+.+......- .++..+.+++.++|.+--+..+.
T Consensus       168 ~l~~~~~~~~l~~~~~~~~~~i-~~~~~~~i~~~s~G~~r~~~~~l  212 (340)
T 1sxj_C          168 PLPQEAIERRIANVLVHEKLKL-SPNAEKALIELSNGDMRRVLNVL  212 (340)
T ss_dssp             CCCHHHHHHHHHHHHHTTTCCB-CHHHHHHHHHHHTTCHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHH
Confidence            9999999998887763211111 13467789999999988554443

>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=98.58  E-value=5.3e-07  Score=87.21  Aligned_cols=171  Identities=16%  Similarity=0.182  Sum_probs=99.9

Q ss_pred             HHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHH
Q 042806          164 NDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGR  242 (390)
Q Consensus       164 ~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~  242 (390)
                      ..+......+. ...+.|+|++|+||||||+.+++.......-...++++.      .++...+...+...        .
T Consensus       118 ~~~~~~a~~~~~~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~------~~~~~~~~~~~~~~--------~  183 (440)
T 2z4s_A          118 HAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS------EKFLNDLVDSMKEG--------K  183 (440)
T ss_dssp             HHHHHHHHSTTSSCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEH------HHHHHHHHHHHHTT--------C
T ss_pred             HHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeH------HHHHHHHHHHHHcc--------c
Confidence            34444444433 567899999999999999999998754311112445443      33344444443221        1


Q ss_pred             HHHHHHHHhCCCeEEEEEeCCCCCcc----cccccCCCCC-CCCCcEEEEEecchh---------hhhhcCCCcceEecC
Q 042806          243 ARSLRNRLKKEKTILVILDNIWGNLD----FQAVGIPHGD-DRKGCKVLLTARSLD---------VLSRKMDSQQNFSVG  308 (390)
Q Consensus       243 ~~~l~~~l~~~~~~LlVlDdv~~~~~----~~~l~~~l~~-~~~~s~IivTtr~~~---------v~~~~~~~~~~~~l~  308 (390)
                      ...+...+.. ++-+|+|||++....    .+.+...+.. ...|..||+||....         +.. .+..+..+.+.
T Consensus       184 ~~~~~~~~~~-~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~s-R~~~g~~i~l~  261 (440)
T 2z4s_A          184 LNEFREKYRK-KVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVS-RFQMGLVAKLE  261 (440)
T ss_dssp             HHHHHHHHTT-TCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHH-HHHSSBCCBCC
T ss_pred             HHHHHHHhcC-CCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHh-hccCCeEEEeC
Confidence            1233344431 336999999975432    1222222110 134677888887621         111 12234688999


Q ss_pred             CCCHHHHHHHHHHhhC--CCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          309 VLKEDEAWSLFKKMAG--DYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       309 ~L~~~ea~~lf~~~~~--~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      +++.++..+++.+.+.  +...++   ++...|++.++|.+-.+..+
T Consensus       262 ~p~~e~r~~iL~~~~~~~~~~i~~---e~l~~la~~~~gn~R~l~~~  305 (440)
T 2z4s_A          262 PPDEETRKSIARKMLEIEHGELPE---EVLNFVAENVDDNLRRLRGA  305 (440)
T ss_dssp             CCCHHHHHHHHHHHHHHHTCCCCT---THHHHHHHHCCSCHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCCH---HHHHHHHHhcCCCHHHHHHH
Confidence            9999999999988774  211222   34678889999988765543

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

Probab=98.58  E-value=2.8e-06  Score=82.24  Aligned_cols=181  Identities=16%  Similarity=0.178  Sum_probs=103.3

Q ss_pred             cccccchhHHHHHHHHHhc------------CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 042806          153 YEACESRMSTLNDILDALK------------NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~------------~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  220 (390)
                      ...++|.+..+..|.+.+.            ....+-+.|+|++|+|||+||+.+++....      ..++.++..    
T Consensus       133 ~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~~~------~~~~~v~~~----  202 (444)
T 2zan_A          133 WSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANN------STFFSISSS----  202 (444)
T ss_dssp             GGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHCCS------SEEEEECCC----
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHcCC------CCEEEEeHH----
Confidence            4568888888888877652            123467899999999999999999998621      123334332    


Q ss_pred             HHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc-------------cccccCCCCC---CCCCcE
Q 042806          221 KIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD-------------FQAVGIPHGD---DRKGCK  284 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~-------------~~~l~~~l~~---~~~~s~  284 (390)
                      ++....   .+.      ....+..+........+.+|+||+++....             ...+...+..   ...+..
T Consensus       203 ~l~~~~---~g~------~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~v~  273 (444)
T 2zan_A          203 DLVSKW---LGE------SEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGIL  273 (444)
T ss_dssp             ------------------CCCTHHHHHHHHHHSCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCSSCE
T ss_pred             HHHhhh---cch------HHHHHHHHHHHHHHcCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccCCCCEE
Confidence            111110   110      111233444444444569999999975410             1112222211   234566


Q ss_pred             EEEEecchhhhh-h-cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCC-hHHHHHH
Q 042806          285 VLLTARSLDVLS-R-KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGL-PVSIVTV  353 (390)
Q Consensus       285 IivTtr~~~v~~-~-~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~Gl-PLai~~l  353 (390)
                      ||.||....... . .......+.+...+.++-..+|..++....... .+.....|++.+.|. +-.|..+
T Consensus       274 vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l-~~~~l~~la~~t~G~sgadl~~l  344 (444)
T 2zan_A          274 VLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSL-TEADFQELGRKTDGYSGADISII  344 (444)
T ss_dssp             EEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCEEC-CHHHHHHHHHHTTTCCHHHHHHH
T ss_pred             EEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhcCCCCC-CHHHHHHHHHHcCCCCHHHHHHH
Confidence            777776542211 1 112335788888899999999988875322111 134567899999884 4344443

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=98.57  E-value=1.2e-06  Score=81.61  Aligned_cols=171  Identities=12%  Similarity=0.037  Sum_probs=102.4

Q ss_pred             hhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcC--------------------CCCeEEEEEeC---
Q 042806          159 RMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEK--------------------LFDQVIFVEVS---  214 (390)
Q Consensus       159 R~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~--------------------~f~~~~wv~v~---  214 (390)
                      .+.....+...+..++ .+.+.++|++|+|||++|+.+.+......                    |++ ..++...   
T Consensus         7 ~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d-~~~~~~~~~~   85 (334)
T 1a5t_A            7 LRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPD-YYTLAPEKGK   85 (334)
T ss_dssp             GHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTT-EEEECCCTTC
T ss_pred             hHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCC-EEEEeccccC
Confidence            3455677777777665 45799999999999999999998864321                    122 2222221   


Q ss_pred             CCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecch
Q 042806          215 KIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSL  292 (390)
Q Consensus       215 ~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~  292 (390)
                      ......+ .+.+.+.+.....                .+++-++|+|+++..  ...+.+...+-.-..++.+|++|.+.
T Consensus        86 ~~~~i~~-ir~l~~~~~~~~~----------------~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~  148 (334)
T 1a5t_A           86 NTLGVDA-VREVTEKLNEHAR----------------LGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREP  148 (334)
T ss_dssp             SSBCHHH-HHHHHHHTTSCCT----------------TSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCG
T ss_pred             CCCCHHH-HHHHHHHHhhccc----------------cCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCCh
Confidence            1112221 1222222221110                123479999999754  22333433332333456777777654


Q ss_pred             -hhhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          293 -DVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       293 -~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                       .+......-...+++.+++.++..+++.+...   .   .++.+..+++.++|.|..+..+
T Consensus       149 ~~l~~ti~SRc~~~~~~~~~~~~~~~~L~~~~~---~---~~~~~~~l~~~s~G~~r~a~~~  204 (334)
T 1a5t_A          149 ERLLATLRSRCRLHYLAPPPEQYAVTWLSREVT---M---SQDALLAALRLSAGSPGAALAL  204 (334)
T ss_dssp             GGSCHHHHTTSEEEECCCCCHHHHHHHHHHHCC---C---CHHHHHHHHHHTTTCHHHHHHT
T ss_pred             HhCcHHHhhcceeeeCCCCCHHHHHHHHHHhcC---C---CHHHHHHHHHHcCCCHHHHHHH
Confidence             33332333446899999999999999988751   1   1345678999999999766543

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

Probab=98.56  E-value=3.5e-06  Score=76.89  Aligned_cols=182  Identities=12%  Similarity=0.086  Sum_probs=102.8

Q ss_pred             CcccccchhHHHHHHHHHhcC------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          152 DYEACESRMSTLNDILDALKN------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ....++|.+..+..+.+.+..            ...+.+.|+|++|+||||+|+.+++....     ..+.++.+.... 
T Consensus        19 ~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~~-----~~~~i~~~~l~~-   92 (297)
T 3b9p_A           19 EWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECSA-----TFLNISAASLTS-   92 (297)
T ss_dssp             CGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTTC-----EEEEEESTTTSS-
T ss_pred             CHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhCC-----CeEEeeHHHHhh-
Confidence            345788998888888777632            23567899999999999999999987642     123344432211 


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc-------------ccccc---CCCCCC--CC
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD-------------FQAVG---IPHGDD--RK  281 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~-------------~~~l~---~~l~~~--~~  281 (390)
                                   .. ..........+........+.+|+||++.....             ...+.   ..++..  +.
T Consensus        93 -------------~~-~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~  158 (297)
T 3b9p_A           93 -------------KY-VGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGD  158 (297)
T ss_dssp             -------------SS-CSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC------
T ss_pred             -------------cc-cchHHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhcccccCCCC
Confidence                         00 011122333334444344558999999964311             00011   111111  23


Q ss_pred             CcEEEEEecchhhh-hh-cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH-HHHHHH
Q 042806          282 GCKVLLTARSLDVL-SR-KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV-SIVTVA  354 (390)
Q Consensus       282 ~s~IivTtr~~~v~-~~-~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL-ai~~l~  354 (390)
                      +..||.||...... .. .......+.+...+.++-..++...+....... .......+++.+.|.+- .|..+.
T Consensus       159 ~v~vi~~tn~~~~l~~~l~~R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~-~~~~~~~la~~~~g~~~~~l~~l~  233 (297)
T 3b9p_A          159 RIVVLAATNRPQELDEAALRRFTKRVYVSLPDEQTRELLLNRLLQKQGSPL-DTEALRRLAKITDGYSGSDLTALA  233 (297)
T ss_dssp             CEEEEEEESCGGGBCHHHHHHCCEEEECCCCCHHHHHHHHHHHHGGGSCCS-CHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             cEEEEeecCChhhCCHHHHhhCCeEEEeCCcCHHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHcCCCCHHHHHHHH
Confidence            45677777653211 10 001235778888888888888887764211111 13456789999999876 554443

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

Probab=98.53  E-value=4.9e-07  Score=88.19  Aligned_cols=150  Identities=13%  Similarity=0.161  Sum_probs=85.5

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCC---CCe--EEEEEeCCCCCHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKL---FDQ--VIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~---f~~--~~wv~v~~~~~~~~l~~~i~  227 (390)
                      .++++||+.++..+++.|......-+.|+|++|+|||++|+.+++.......   ...  .+.++++.            
T Consensus       179 ld~iiGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~------------  246 (468)
T 3pxg_A          179 LDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMGT------------  246 (468)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC----------------
T ss_pred             CCCccCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeCCc------------
Confidence            4579999999999999997766666789999999999999999998643210   111  22222220            


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhh------hhhcCCC
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDV------LSRKMDS  301 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v------~~~~~~~  301 (390)
                       ...  .   ........+.+.+....+.+|++|  -..+....+...+.  ....++|.+|.....      ......-
T Consensus       247 -~~~--g---~~e~~~~~~~~~~~~~~~~iLfiD--~~~~a~~~L~~~L~--~g~v~vI~at~~~e~~~~~~~~~al~~R  316 (468)
T 3pxg_A          247 -KYR--G---EFEDRLKKVMDEIRQAGNIILFID--AAIDASNILKPSLA--RGELQCIGATTLDEYRKYIEKDAALERR  316 (468)
T ss_dssp             ------------CTTHHHHHHHHHTCCCCEEEEC--C--------CCCTT--SSSCEEEEECCTTTTHHHHTTCSHHHHS
T ss_pred             -ccc--c---hHHHHHHHHHHHHHhcCCeEEEEe--CchhHHHHHHHhhc--CCCEEEEecCCHHHHHHHhhcCHHHHHh
Confidence             000  0   001123344444444445899999  22222233433332  224566666654431      1111112


Q ss_pred             cceEecCCCCHHHHHHHHHHhhC
Q 042806          302 QQNFSVGVLKEDEAWSLFKKMAG  324 (390)
Q Consensus       302 ~~~~~l~~L~~~ea~~lf~~~~~  324 (390)
                      ...+.+.+.+.++..+++.....
T Consensus       317 f~~i~v~~p~~e~~~~iL~~~~~  339 (468)
T 3pxg_A          317 FQPIQVDQPSVDESIQILQGLRD  339 (468)
T ss_dssp             EEEEECCCCCHHHHHHHHHHTTT
T ss_pred             CccceeCCCCHHHHHHHHHHHHH
Confidence            24799999999999999997764

>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=98.51  E-value=4.2e-06  Score=78.59  Aligned_cols=180  Identities=17%  Similarity=0.156  Sum_probs=102.5

Q ss_pred             cccccchhHHHHHHHHHhcC------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 042806          153 YEACESRMSTLNDILDALKN------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  220 (390)
                      ...++|.+..+..|.+.+..            ...+-+.|+|++|+|||+||+.+++.....     .+.+..+      
T Consensus        50 ~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~~-----~~~v~~~------  118 (355)
T 2qp9_X           50 WEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANST-----FFSVSSS------  118 (355)
T ss_dssp             GGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHHTCE-----EEEEEHH------
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCC-----EEEeeHH------
Confidence            45688888888888776621            123458899999999999999999987422     2223221      


Q ss_pred             HHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc-------------cccccCC---CCCCCCCcE
Q 042806          221 KIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD-------------FQAVGIP---HGDDRKGCK  284 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~-------------~~~l~~~---l~~~~~~s~  284 (390)
                      ++...        .. .........+.......++.+|+||+++....             ...+...   +.....+..
T Consensus       119 ~l~~~--------~~-g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~  189 (355)
T 2qp9_X          119 DLVSK--------WM-GESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVL  189 (355)
T ss_dssp             HHHSC--------C----CHHHHHHHHHHHHHTSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC---CCEE
T ss_pred             HHhhh--------hc-chHHHHHHHHHHHHHHcCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhcccccCCCeE
Confidence            22110        00 01122334444444444569999999974321             1111111   111234566


Q ss_pred             EEEEecchhhh-hh-cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCC-hHHHHHH
Q 042806          285 VLLTARSLDVL-SR-KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGL-PVSIVTV  353 (390)
Q Consensus       285 IivTtr~~~v~-~~-~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~Gl-PLai~~l  353 (390)
                      ||.||...... .. .......+.+...+.++-.++|..++........ ......|++.+.|. |-.|..+
T Consensus       190 vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~-~~~l~~la~~t~G~sg~dl~~l  260 (355)
T 2qp9_X          190 VLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPSVLT-KEDYRTLGAMTEGYSGSDIAVV  260 (355)
T ss_dssp             EEEEESCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTSCBCCC-HHHHHHHHHHTTTCCHHHHHHH
T ss_pred             EEeecCCcccCCHHHHcccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCC-HHHHHHHHHHcCCCCHHHHHHH
Confidence            66677654211 10 1123457889999999999999988863221111 34567899999884 5444444

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

Probab=98.46  E-value=4.1e-06  Score=76.80  Aligned_cols=173  Identities=12%  Similarity=0.179  Sum_probs=98.6

Q ss_pred             cccccchhHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALKN-------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ...++|.+..+..|.+.+..             ...+.+.|+|++|+|||+||+.+++....       -++.++    .
T Consensus        14 ~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~-------~~i~v~----~   82 (301)
T 3cf0_A           14 WEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQA-------NFISIK----G   82 (301)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTC-------EEEEEC----H
T ss_pred             HHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCC-------CEEEEE----h
Confidence            44678877777766665531             34567899999999999999999987642       122332    2


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc------------c----cccccCCCC--CCCC
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL------------D----FQAVGIPHG--DDRK  281 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~------------~----~~~l~~~l~--~~~~  281 (390)
                      .++....   ++..      ......+.+......+.+|+||+++...            .    ...+...+.  ....
T Consensus        83 ~~l~~~~---~g~~------~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~  153 (301)
T 3cf0_A           83 PELLTMW---FGES------EANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKK  153 (301)
T ss_dssp             HHHHHHH---HTTC------TTHHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCTTS
T ss_pred             HHHHhhh---cCch------HHHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccCCC
Confidence            2333221   1211      1223344444444456999999996320            0    111111111  1234


Q ss_pred             CcEEEEEecchhhh-hhcC---CCcceEecCCCCHHHHHHHHHHhhCCCC--CCCchHHHHHHHHHHcCCChHH
Q 042806          282 GCKVLLTARSLDVL-SRKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYI--EGSEFKWVAKDVARECAGLPVS  349 (390)
Q Consensus       282 ~s~IivTtr~~~v~-~~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~--~~~~~~~~~~~i~~~~~GlPLa  349 (390)
                      +..||.||...... ....   .....+.+...+.++-.++|...+....  ...++    ..++..+.|.|-+
T Consensus       154 ~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~~~----~~la~~~~g~sg~  223 (301)
T 3cf0_A          154 NVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDL----EFLAKMTNGFSGA  223 (301)
T ss_dssp             SEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSCCH----HHHHHTCSSCCHH
T ss_pred             CEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccchH----HHHHHHcCCCCHH
Confidence            56777777754322 1111   1235789999999999999988875221  12222    3566677777643

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=98.43  E-value=2.3e-06  Score=79.22  Aligned_cols=166  Identities=15%  Similarity=0.124  Sum_probs=93.2

Q ss_pred             HHHHHHHhcCC--CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCch
Q 042806          163 LNDILDALKNP--DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDS  240 (390)
Q Consensus       163 ~~~l~~~L~~~--~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~  240 (390)
                      ...+...+..+  ....+.|+|++|+||||||+.+++..... .+ ..++++.      .++...+...+...       
T Consensus        23 ~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~~~~-~~-~~~~i~~------~~~~~~~~~~~~~~-------   87 (324)
T 1l8q_A           23 YEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKR-GY-RVIYSSA------DDFAQAMVEHLKKG-------   87 (324)
T ss_dssp             HHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHT-TC-CEEEEEH------HHHHHHHHHHHHHT-------
T ss_pred             HHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHHHHC-CC-EEEEEEH------HHHHHHHHHHHHcC-------
Confidence            34444444443  34678899999999999999999987543 12 2445443      33333333333210       


Q ss_pred             HHHHHHHHHHhCCCeEEEEEeCCCCCcc---c-ccccCCCCC-CCCCcEEEEEecchhh-----hh---hcCCCcceEec
Q 042806          241 GRARSLRNRLKKEKTILVILDNIWGNLD---F-QAVGIPHGD-DRKGCKVLLTARSLDV-----LS---RKMDSQQNFSV  307 (390)
Q Consensus       241 ~~~~~l~~~l~~~~~~LlVlDdv~~~~~---~-~~l~~~l~~-~~~~s~IivTtr~~~v-----~~---~~~~~~~~~~l  307 (390)
                       ....+...+..  +.+|+|||++....   + +.+...+.. ...+..||+||.....     ..   ........+++
T Consensus        88 -~~~~~~~~~~~--~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~sR~~~~~~i~l  164 (324)
T 1l8q_A           88 -TINEFRNMYKS--VDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEI  164 (324)
T ss_dssp             -CHHHHHHHHHT--CSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEEC
T ss_pred             -cHHHHHHHhcC--CCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhhcccCceEEEe
Confidence             11223333333  36999999975431   1 222222110 1235578888764211     00   11223357899


Q ss_pred             CCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHH
Q 042806          308 GVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVS  349 (390)
Q Consensus       308 ~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLa  349 (390)
                      .+ +.++..+++...+......- .+++...|++.+ |.+-.
T Consensus       165 ~~-~~~e~~~il~~~~~~~~~~l-~~~~l~~l~~~~-g~~r~  203 (324)
T 1l8q_A          165 EL-DNKTRFKIIKEKLKEFNLEL-RKEVIDYLLENT-KNVRE  203 (324)
T ss_dssp             CC-CHHHHHHHHHHHHHHTTCCC-CHHHHHHHHHHC-SSHHH
T ss_pred             CC-CHHHHHHHHHHHHHhcCCCC-CHHHHHHHHHhC-CCHHH
Confidence            99 99999999988774211111 145677888888 76654

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=98.42  E-value=8.1e-07  Score=93.17  Aligned_cols=157  Identities=10%  Similarity=0.159  Sum_probs=87.2

Q ss_pred             CcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCC---C-C-eEEEEEeCCCCCHHHHHHHH
Q 042806          152 DYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKL---F-D-QVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~---f-~-~~~wv~v~~~~~~~~l~~~i  226 (390)
                      ..++++||+.++..+++.|.....+.+.|+|++|+|||+||+.+++.......   . + ..++++++....        
T Consensus       168 ~ld~viGr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~--------  239 (854)
T 1qvr_A          168 KLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLA--------  239 (854)
T ss_dssp             CSCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-------------
T ss_pred             CCcccCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhc--------
Confidence            35679999999999999998766666789999999999999999998743211   1 1 233333322110        


Q ss_pred             HHHhCCCCCCCCchHHHHHHHHHHhC-CCeEEEEEeCCCCCc-------ccc---cccCCCCCCCCCcEEEEEecchhh-
Q 042806          227 ADKLGLTLHEESDSGRARSLRNRLKK-EKTILVILDNIWGNL-------DFQ---AVGIPHGDDRKGCKVLLTARSLDV-  294 (390)
Q Consensus       227 ~~~l~~~~~~~~~~~~~~~l~~~l~~-~~~~LlVlDdv~~~~-------~~~---~l~~~l~~~~~~s~IivTtr~~~v-  294 (390)
                          +.. ...........+.+.+.. .++.+|++|+++...       .++   .+...+  ...+..+|.+|..... 
T Consensus       240 ----g~~-~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l--~~~~i~~I~at~~~~~~  312 (854)
T 1qvr_A          240 ----GAK-YRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPAL--ARGELRLIGATTLDEYR  312 (854)
T ss_dssp             -----------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHH--HTTCCCEEEEECHHHHH
T ss_pred             ----cCc-cchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCccchHHHHHHHHHHH--hCCCeEEEEecCchHHh
Confidence                000 000112223344444433 345999999997542       011   122112  1223456655554321 


Q ss_pred             ----hhhcCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          295 ----LSRKMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       295 ----~~~~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                          ......-...+.+.+++.++..++++...
T Consensus       313 ~~~~d~aL~rRf~~i~l~~p~~~e~~~iL~~~~  345 (854)
T 1qvr_A          313 EIEKDPALERRFQPVYVDEPTVEETISILRGLK  345 (854)
T ss_dssp             HHTTCTTTCSCCCCEEECCCCHHHHHHHHHHHH
T ss_pred             hhccCHHHHhCCceEEeCCCCHHHHHHHHHhhh
Confidence                11111222468999999999999997554

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

Probab=98.41  E-value=5.5e-06  Score=78.13  Aligned_cols=175  Identities=15%  Similarity=0.174  Sum_probs=100.9

Q ss_pred             CcccccchhHHHHHHHHHhc----C---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 042806          152 DYEACESRMSTLNDILDALK----N---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD  218 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~----~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  218 (390)
                      ...++.|-+..+++|.+.+.    .         ..++-+.++||+|.|||.||+.+++.....     .+.+..+.-.+
T Consensus       146 ~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~-----f~~v~~s~l~s  220 (405)
T 4b4t_J          146 TYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCK-----FIRVSGAELVQ  220 (405)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCE-----EEEEEGGGGSC
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCC-----ceEEEhHHhhc
Confidence            35567777766666655442    1         235678899999999999999999987643     23444332211


Q ss_pred             HHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc----------------cccccCCCC--CCC
Q 042806          219 IRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD----------------FQAVGIPHG--DDR  280 (390)
Q Consensus       219 ~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~----------------~~~l~~~l~--~~~  280 (390)
                      .              +. ......+..+........+++|.||+++....                ...+...+.  ...
T Consensus       221 k--------------~v-Gese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~  285 (405)
T 4b4t_J          221 K--------------YI-GEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETS  285 (405)
T ss_dssp             S--------------ST-THHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTCC
T ss_pred             c--------------cc-chHHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCCC
Confidence            0              00 01122334444444455679999999974310                111111111  123


Q ss_pred             CCcEEEEEecchhhhh-h---cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH
Q 042806          281 KGCKVLLTARSLDVLS-R---KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV  348 (390)
Q Consensus       281 ~~s~IivTtr~~~v~~-~---~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL  348 (390)
                      .+..||.||....... .   .-.....+++...+.++-.++|+.+........+..  ...|++.|.|.-=
T Consensus       286 ~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvd--l~~lA~~t~G~SG  355 (405)
T 4b4t_J          286 KNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGIN--LRKVAEKMNGCSG  355 (405)
T ss_dssp             CCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCC--HHHHHHHCCSCCH
T ss_pred             CCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCC--HHHHHHHCCCCCH
Confidence            4556777776543211 1   113446899999999999999988875322222211  3568888887553

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.41  E-value=5e-07  Score=76.07  Aligned_cols=49  Identities=18%  Similarity=0.195  Sum_probs=43.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...++||+.++..+.+.+.....+.+.|+|++|+|||+||+.+++....
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~~~   69 (187)
T 2p65_A           21 LDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQ   69 (187)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHHHT
T ss_pred             cchhhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            4578999999999999998876778899999999999999999988643

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

Probab=98.32  E-value=1e-05  Score=77.39  Aligned_cols=173  Identities=14%  Similarity=0.165  Sum_probs=98.8

Q ss_pred             cccccchhHHHHHHHHHhc----C---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALK----N---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~----~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ..++.|-+..+++|.+.+.    .         ..++-|.++|++|+|||+||+.+++.....     .+.+..+.-.+ 
T Consensus       208 ~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~-----fi~vs~s~L~s-  281 (467)
T 4b4t_H          208 YSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDAT-----FIRVIGSELVQ-  281 (467)
T ss_dssp             CSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCE-----EEEEEGGGGCC-
T ss_pred             HHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCC-----eEEEEhHHhhc-
Confidence            3456777776666665432    1         346789999999999999999999987643     23333332111 


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc----------------cccccCCC--CCCCC
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD----------------FQAVGIPH--GDDRK  281 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~----------------~~~l~~~l--~~~~~  281 (390)
                                   .+. ......+..+........+++|++|+++....                ...+...+  .....
T Consensus       282 -------------k~v-Gesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~  347 (467)
T 4b4t_H          282 -------------KYV-GEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRG  347 (467)
T ss_dssp             -------------CSS-SHHHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCCTT
T ss_pred             -------------ccC-CHHHHHHHHHHHHHHhcCCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCCCC
Confidence                         000 01122334444444555679999999974310                00011111  01234


Q ss_pred             CcEEEEEecchhhh-hhc---CCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh
Q 042806          282 GCKVLLTARSLDVL-SRK---MDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       282 ~s~IivTtr~~~v~-~~~---~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      +..||.||...... ...   -.....+++...+.++-.++|+.++.......+..  ...|++.|.|.-
T Consensus       348 ~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvd--l~~LA~~T~GfS  415 (467)
T 4b4t_H          348 NIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIR--WELISRLCPNST  415 (467)
T ss_dssp             TEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCC--HHHHHHHCCSCC
T ss_pred             cEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCC--HHHHHHHCCCCC
Confidence            45566677643321 111   12446888998899988999988875322222211  346788888764

>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=98.31  E-value=7.1e-07  Score=75.23  Aligned_cols=116  Identities=16%  Similarity=0.121  Sum_probs=64.3

Q ss_pred             hhHHHHHHHHHhcC---CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC
Q 042806          159 RMSTLNDILDALKN---PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLH  235 (390)
Q Consensus       159 R~~~~~~l~~~L~~---~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~  235 (390)
                      ....++.+.+++.+   +....+.|+|++|+|||||++.+++.......+. ++++      +..++...+...+.....
T Consensus        19 ~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~-~~~~------~~~~~~~~~~~~~~~~~~   91 (180)
T 3ec2_A           19 QNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIR-GYFF------DTKDLIFRLKHLMDEGKD   91 (180)
T ss_dssp             HHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCC-CCEE------EHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCe-EEEE------EHHHHHHHHHHHhcCchH
Confidence            34444445444433   3457899999999999999999999875332232 2232      345555555444432111


Q ss_pred             CCCchHHHHHHHHHHhCCCeEEEEEeCCCC--Cccccc--ccCCCCC-CCCCcEEEEEecc
Q 042806          236 EESDSGRARSLRNRLKKEKTILVILDNIWG--NLDFQA--VGIPHGD-DRKGCKVLLTARS  291 (390)
Q Consensus       236 ~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~--~~~~~~--l~~~l~~-~~~~s~IivTtr~  291 (390)
                          .    .+.+.+.+  +-+|||||++.  .+.|..  +...+.. ...|..+|+||..
T Consensus        92 ----~----~~~~~~~~--~~llilDE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~  142 (180)
T 3ec2_A           92 ----T----KFLKTVLN--SPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNY  142 (180)
T ss_dssp             ----S----HHHHHHHT--CSEEEEETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCC
T ss_pred             ----H----HHHHHhcC--CCEEEEeCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCC
Confidence                1    23333433  35999999973  233321  2111111 1246678888874

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

Probab=98.31  E-value=1.5e-05  Score=75.45  Aligned_cols=174  Identities=14%  Similarity=0.147  Sum_probs=97.6

Q ss_pred             CcccccchhHHHHHHHHHhc----C---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 042806          152 DYEACESRMSTLNDILDALK----N---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD  218 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~----~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  218 (390)
                      ...++.|-+..+++|.+.+.    .         ..++-|.++||+|.|||.||+.+++.....     .+.+..+.-.+
T Consensus       180 ~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~-----fi~v~~s~l~s  254 (437)
T 4b4t_I          180 SYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSAT-----FLRIVGSELIQ  254 (437)
T ss_dssp             CGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCE-----EEEEESGGGCC
T ss_pred             cceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCC-----EEEEEHHHhhh
Confidence            34566777766666655432    2         235779999999999999999999987643     23333322111


Q ss_pred             HHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc----------------cccccCCC--CCCC
Q 042806          219 IRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD----------------FQAVGIPH--GDDR  280 (390)
Q Consensus       219 ~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~----------------~~~l~~~l--~~~~  280 (390)
                                    .+ .......+..+........+++|.+|+++....                ...+...+  ....
T Consensus       255 --------------k~-vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~~  319 (437)
T 4b4t_I          255 --------------KY-LGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDR  319 (437)
T ss_dssp             --------------SS-SSHHHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCCS
T ss_pred             --------------cc-CchHHHHHHHHHHHHHhcCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCCC
Confidence                          00 001122344444444455679999999863310                00111111  0223


Q ss_pred             CCcEEEEEecchhhhh-hcCC---CcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh
Q 042806          281 KGCKVLLTARSLDVLS-RKMD---SQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       281 ~~s~IivTtr~~~v~~-~~~~---~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      .+..||.||....... ....   ....+++..-+.++-.++|+.++.......+..  ...|++.+.|+-
T Consensus       320 ~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dvd--l~~LA~~T~GfS  388 (437)
T 4b4t_I          320 GDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVN--LETLVTTKDDLS  388 (437)
T ss_dssp             SSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCCC--HHHHHHHCCSCC
T ss_pred             CCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcCC--HHHHHHhCCCCC
Confidence            4556777776544322 1221   224688888888888899988875322222211  346778887764

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=98.29  E-value=9e-06  Score=84.20  Aligned_cols=156  Identities=14%  Similarity=0.159  Sum_probs=92.6

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCC----CCeEEEE-EeCCCCCHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKL----FDQVIFV-EVSKIQDIRKIQGEIA  227 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~----f~~~~wv-~v~~~~~~~~l~~~i~  227 (390)
                      .++++||+.++..+++.|......-+.|+|++|+|||++|+.+++.......    ..+.+|. ..+..           
T Consensus       185 ~d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l-----------  253 (758)
T 1r6b_X          185 IDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSL-----------  253 (758)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC-------------
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHH-----------
Confidence            4678999999999999998766677889999999999999999988643211    1233321 11110           


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--------c---cccccCCCCCCCCCcEEEEEecchhhhh
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--------D---FQAVGIPHGDDRKGCKVLLTARSLDVLS  296 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--------~---~~~l~~~l~~~~~~s~IivTtr~~~v~~  296 (390)
                        +...............+.+.+...++.+|++|+++...        .   ...+...+ . ..+..+|.+|.......
T Consensus       254 --~~~~~~~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l-~-~~~~~~I~at~~~~~~~  329 (758)
T 1r6b_X          254 --LAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLL-S-SGKIRVIGSTTYQEFSN  329 (758)
T ss_dssp             ---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCS-S-SCCCEEEEEECHHHHHC
T ss_pred             --hccccccchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHH-h-CCCeEEEEEeCchHHhh
Confidence              00000111222233444455544445899999997541        1   11233333 2 23456666666443210


Q ss_pred             h------cCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          297 R------KMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       297 ~------~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                      .      ...-...+.+.+.+.++..+++....
T Consensus       330 ~~~~d~aL~~Rf~~i~v~~p~~~e~~~il~~l~  362 (758)
T 1r6b_X          330 IFEKDRALARRFQKIDITEPSIEETVQIINGLK  362 (758)
T ss_dssp             CCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             hhhcCHHHHhCceEEEcCCCCHHHHHHHHHHHH
Confidence            0      01112368899999999988887654

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

Probab=98.28  E-value=4e-06  Score=80.21  Aligned_cols=171  Identities=13%  Similarity=0.170  Sum_probs=96.9

Q ss_pred             cccccchhHHHHHHHHHhc----C---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALK----N---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~----~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ..++.|-+..+++|.+.+.    .         ..++-|.+|||+|+|||.||+.+++.....     .+.+..+.-.+ 
T Consensus       180 ~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~-----f~~v~~s~l~~-  253 (434)
T 4b4t_M          180 YSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNAT-----FLKLAAPQLVQ-  253 (434)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCE-----EEEEEGGGGCS-
T ss_pred             hHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCC-----EEEEehhhhhh-
Confidence            5567787777777766532    2         236778999999999999999999987642     23333332111 


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC-------cc---------cccccCCCC--CCCC
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN-------LD---------FQAVGIPHG--DDRK  281 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~-------~~---------~~~l~~~l~--~~~~  281 (390)
                                   .+. ......+..+........+++|++|+++..       ..         ...+...+.  ....
T Consensus       254 -------------~~v-Gese~~ir~lF~~A~~~aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~~~~  319 (434)
T 4b4t_M          254 -------------MYI-GEGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDD  319 (434)
T ss_dssp             -------------SCS-SHHHHHHHHHHHHHHHHCSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTSCSSC
T ss_pred             -------------ccc-chHHHHHHHHHHHHHhcCCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhccCCCC
Confidence                         000 011223334444444445699999998521       00         011111111  1233


Q ss_pred             CcEEEEEecchhhhh-hcC---CCcceEecCCCCHHHHHHHHHHhhCCC--CCCCchHHHHHHHHHHcCCCh
Q 042806          282 GCKVLLTARSLDVLS-RKM---DSQQNFSVGVLKEDEAWSLFKKMAGDY--IEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       282 ~s~IivTtr~~~v~~-~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~--~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      +..||.||....... ...   .....+++...+.++-.++|+.++...  ....+    ...|++.|.|+-
T Consensus       320 ~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvd----l~~lA~~t~G~s  387 (434)
T 4b4t_M          320 RVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDIN----WQELARSTDEFN  387 (434)
T ss_dssp             SSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCC----HHHHHHHCSSCC
T ss_pred             CEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCC----HHHHHHhCCCCC
Confidence            456666776543321 111   123578888888888888887766421  12223    346788887754

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

Probab=98.28  E-value=3.8e-06  Score=87.02  Aligned_cols=152  Identities=12%  Similarity=0.157  Sum_probs=86.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC---CCCeEEEEEeCCCCCHHHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEK---LFDQVIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~---~f~~~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      .++++||+.++..++..|......-+.++|++|+|||++|+.+.+......   ......++.++.              
T Consensus       179 ld~iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~~~~--------------  244 (758)
T 3pxi_A          179 LDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDM--------------  244 (758)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC----------------
T ss_pred             CCCccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEEecc--------------
Confidence            467999999999999999876666688999999999999999999863211   011111121111              


Q ss_pred             hCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhh------hhhcCCCcc
Q 042806          230 LGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDV------LSRKMDSQQ  303 (390)
Q Consensus       230 l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v------~~~~~~~~~  303 (390)
                       +..... ........+.+.+....+.+|++|.  .......+...+ . ....++|.||.....      ......-..
T Consensus       245 -g~~~~G-~~e~~l~~~~~~~~~~~~~iLfiD~--~~~~~~~L~~~l-~-~~~v~~I~at~~~~~~~~~~~d~al~rRf~  318 (758)
T 3pxi_A          245 -GTKYRG-EFEDRLKKVMDEIRQAGNIILFIDA--AIDASNILKPSL-A-RGELQCIGATTLDEYRKYIEKDAALERRFQ  318 (758)
T ss_dssp             ----------CTTHHHHHHHHHTCCCCEEEECC----------CCCT-T-SSSCEEEEECCTTTTHHHHTTCSHHHHSEE
T ss_pred             -cccccc-hHHHHHHHHHHHHHhcCCEEEEEcC--chhHHHHHHHHH-h-cCCEEEEeCCChHHHHHHhhccHHHHhhCc
Confidence             000000 1111233344444444558999992  222222333333 2 334566766665431      010111124


Q ss_pred             eEecCCCCHHHHHHHHHHhhC
Q 042806          304 NFSVGVLKEDEAWSLFKKMAG  324 (390)
Q Consensus       304 ~~~l~~L~~~ea~~lf~~~~~  324 (390)
                      .+.+.+.+.++..+++.....
T Consensus       319 ~i~v~~p~~~~~~~il~~~~~  339 (758)
T 3pxi_A          319 PIQVDQPSVDESIQILQGLRD  339 (758)
T ss_dssp             EEECCCCCHHHHHHHHHHTTT
T ss_pred             EEEeCCCCHHHHHHHHHHHHH
Confidence            799999999999999997664

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

Probab=98.24  E-value=1.6e-05  Score=76.12  Aligned_cols=172  Identities=16%  Similarity=0.227  Sum_probs=98.3

Q ss_pred             cccccchhHHHHHHHHHhc----C---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALK----N---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~----~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ..++.|-+..+++|.+.+.    .         ..++-|.+|||+|+|||+||+.+++.....     .+.+..+.-.+ 
T Consensus       180 ~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~-----~~~v~~s~l~s-  253 (437)
T 4b4t_L          180 FDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGAN-----FIFSPASGIVD-  253 (437)
T ss_dssp             SGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCE-----EEEEEGGGTCC-
T ss_pred             hhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC-----EEEEehhhhcc-
Confidence            4566777666666555432    2         235779999999999999999999987643     33444333211 


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--------c--------cccccCCCC--CCCC
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--------D--------FQAVGIPHG--DDRK  281 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--------~--------~~~l~~~l~--~~~~  281 (390)
                                   .+. ......+..+........+++|.+|+++...        .        +..+...+.  ....
T Consensus       254 -------------k~~-Gese~~ir~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~  319 (437)
T 4b4t_L          254 -------------KYI-GESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLG  319 (437)
T ss_dssp             -------------SSS-SHHHHHHHHHHHHHHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSCTT
T ss_pred             -------------ccc-hHHHHHHHHHHHHHHhcCCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhcccCCC
Confidence                         000 0112233444444445567999999997431        0        111111111  2234


Q ss_pred             CcEEEEEecchhhhh-hcCC---CcceEecCCCCHHHHHHHHHHhhCCCC--CCCchHHHHHHHHHHcCCChH
Q 042806          282 GCKVLLTARSLDVLS-RKMD---SQQNFSVGVLKEDEAWSLFKKMAGDYI--EGSEFKWVAKDVARECAGLPV  348 (390)
Q Consensus       282 ~s~IivTtr~~~v~~-~~~~---~~~~~~l~~L~~~ea~~lf~~~~~~~~--~~~~~~~~~~~i~~~~~GlPL  348 (390)
                      +..||.||....... ....   ....+++...+.++-.++|+.++....  ...++    ..+++.+.|+-=
T Consensus       320 ~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl----~~lA~~t~G~sG  388 (437)
T 4b4t_L          320 QTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDF----EAAVKMSDGFNG  388 (437)
T ss_dssp             SSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCCH----HHHHHTCCSCCH
T ss_pred             CeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccCH----HHHHHhCCCCCH
Confidence            556777777543321 1121   235788888888888888887764222  22333    467888877543

>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=98.20  E-value=5.9e-06  Score=75.76  Aligned_cols=144  Identities=17%  Similarity=0.080  Sum_probs=87.9

Q ss_pred             hHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhc--CCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCC
Q 042806          160 MSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETE--KLFDQVIFVEVSK-IQDIRKIQGEIADKLGLTLHE  236 (390)
Q Consensus       160 ~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~--~~f~~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~  236 (390)
                      ++.++.|...+..++.+.+.++|++|+||||+|+.+.+.....  .+.+ ..++..+. ...+.+ .+++...+...+. 
T Consensus         3 ~~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d-~~~l~~~~~~~~id~-ir~li~~~~~~p~-   79 (305)
T 2gno_A            3 KDQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDD-IRTIKDFLNYSPE-   79 (305)
T ss_dssp             -CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEECCSSSCBCHHH-HHHHHHHHTSCCS-
T ss_pred             HHHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCC-EEEEcCCcCCCCHHH-HHHHHHHHhhccc-
Confidence            3456667777777677889999999999999999998863211  2334 34444433 333333 2334444432211 


Q ss_pred             CCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecch-hhhhhcCCCcceEecCCCCHH
Q 042806          237 ESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSL-DVLSRKMDSQQNFSVGVLKED  313 (390)
Q Consensus       237 ~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~-~v~~~~~~~~~~~~l~~L~~~  313 (390)
                                     .+++-++|+|+++..  ...+.+...+-.-.+.+.+|++|.+. .+.... ... .+++.+++.+
T Consensus        80 ---------------~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI-~SR-~~~f~~l~~~  142 (305)
T 2gno_A           80 ---------------LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTI-KSR-VFRVVVNVPK  142 (305)
T ss_dssp             ---------------SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHH-HTT-SEEEECCCCH
T ss_pred             ---------------cCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHH-Hce-eEeCCCCCHH
Confidence                           123369999999754  23344443332334567777776543 332222 222 9999999999


Q ss_pred             HHHHHHHHhh
Q 042806          314 EAWSLFKKMA  323 (390)
Q Consensus       314 ea~~lf~~~~  323 (390)
                      +..+.+.+.+
T Consensus       143 ~i~~~L~~~~  152 (305)
T 2gno_A          143 EFRDLVKEKI  152 (305)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999998876

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

Probab=98.17  E-value=0.00011  Score=65.47  Aligned_cols=179  Identities=16%  Similarity=0.191  Sum_probs=94.1

Q ss_pred             cccccchhHHHHHHH---HHhcC---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 042806          153 YEACESRMSTLNDIL---DALKN---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~---~~L~~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  220 (390)
                      ...++|.+..++.+.   .++..         ...+-+.|+|++|+||||||+.+++.....     .+.+..+.-.+. 
T Consensus        11 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~-----~~~i~~~~~~~~-   84 (257)
T 1lv7_A           11 FADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVP-----FFTISGSDFVEM-   84 (257)
T ss_dssp             GGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCC-----EEEECSCSSTTS-
T ss_pred             HHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCCC-----EEEEeHHHHHHH-
Confidence            446777766555444   33332         124458899999999999999999876421     233332221110 


Q ss_pred             HHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc----------------ccccccCCCC--CCCCC
Q 042806          221 KIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL----------------DFQAVGIPHG--DDRKG  282 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~----------------~~~~l~~~l~--~~~~~  282 (390)
                                   ... ........+.+......+.++++|+++...                ....+...+.  ....+
T Consensus        85 -------------~~~-~~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~  150 (257)
T 1lv7_A           85 -------------FVG-VGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEG  150 (257)
T ss_dssp             -------------CCC-CCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSC
T ss_pred             -------------hhh-hhHHHHHHHHHHHHHcCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCcccCCC
Confidence                         000 111223333444444455899999984210                0011111110  12345


Q ss_pred             cEEEEEecchhhh-hhcC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCC-ChHHHHHH
Q 042806          283 CKVLLTARSLDVL-SRKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAG-LPVSIVTV  353 (390)
Q Consensus       283 s~IivTtr~~~v~-~~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~G-lPLai~~l  353 (390)
                      ..||.||...... ....   .....+.+...+.++-.+++...+......++.  ....++..+.| .+--|..+
T Consensus       151 ~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~--~~~~la~~~~G~~~~dl~~l  224 (257)
T 1lv7_A          151 IIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDI--DAAIIARGTPGFSGADLANL  224 (257)
T ss_dssp             EEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTC--CHHHHHHTCTTCCHHHHHHH
T ss_pred             EEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCccc--cHHHHHHHcCCCCHHHHHHH
Confidence            5677777654321 1111   123478888888888888888776422111111  13457778888 66555543

>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=98.17  E-value=6.3e-07  Score=80.65  Aligned_cols=171  Identities=17%  Similarity=0.129  Sum_probs=88.0

Q ss_pred             ccccchhHHHHHHHHHhc---C---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHH
Q 042806          154 EACESRMSTLNDILDALK---N---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRK  221 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~---~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~  221 (390)
                      ..++|.+..++.+.+.+.   .         ...+-+.|+|++|+|||+||+.+++.....  |-   .+..+...+   
T Consensus        11 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~--~~---~v~~~~~~~---   82 (268)
T 2r62_A           11 KDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVP--FF---SMGGSSFIE---   82 (268)
T ss_dssp             TTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCC--CC---CCCSCTTTT---
T ss_pred             HHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCC--EE---EechHHHHH---
Confidence            456776665555544332   1         123447799999999999999999986432  21   111111100   


Q ss_pred             HHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc-----------------ccccccCCCCC---CCC
Q 042806          222 IQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL-----------------DFQAVGIPHGD---DRK  281 (390)
Q Consensus       222 l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~-----------------~~~~l~~~l~~---~~~  281 (390)
                             .+... ....    ...+.+......+.+|+||+++...                 .+..+...+..   ...
T Consensus        83 -------~~~~~-~~~~----~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~  150 (268)
T 2r62_A           83 -------MFVGL-GASR----VRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENA  150 (268)
T ss_dssp             -------SCSSS-CSSS----SSTTHHHHHHSCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCSCS
T ss_pred             -------hhcch-HHHH----HHHHHHHHHhcCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccCCC
Confidence                   00000 0000    1111222222345899999995331                 12222222211   122


Q ss_pred             CcEEEEEecchhhhh-hcC---CCcceEecCCCCHHHHHHHHHHhhCCCC--CCCchHHHHHHHHHHcCCChH
Q 042806          282 GCKVLLTARSLDVLS-RKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYI--EGSEFKWVAKDVARECAGLPV  348 (390)
Q Consensus       282 ~s~IivTtr~~~v~~-~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~--~~~~~~~~~~~i~~~~~GlPL  348 (390)
                      ...||.||....... ...   .....+.+.+.+.++-.+++...+....  ....+    ..+++.+.|.|-
T Consensus       151 ~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~----~~la~~~~g~~g  219 (268)
T 2r62_A          151 PVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNL----QEVAKLTAGLAG  219 (268)
T ss_dssp             CCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCCSSCCT----TTTTSSSCSSCH
T ss_pred             CEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCCCccCH----HHHHHHcCCCCH
Confidence            356777776543211 111   1235788999999999999988774221  11222    346677778754

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.15  E-value=6.2e-07  Score=72.87  Aligned_cols=46  Identities=17%  Similarity=0.127  Sum_probs=34.3

Q ss_pred             cccchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          155 ACESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|+...+.++.+.+..  ....-|.|+|++|+|||++|+.+++...
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~~   49 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGR   49 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSST
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhCC
Confidence            467888888888776642  2334577999999999999999988753

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

Probab=98.11  E-value=3.1e-05  Score=73.91  Aligned_cols=172  Identities=16%  Similarity=0.199  Sum_probs=92.4

Q ss_pred             CcccccchhHHHHHHHHHhc----C---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 042806          152 DYEACESRMSTLNDILDALK----N---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD  218 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~----~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  218 (390)
                      ...++.|-+..++.|.+.+.    .         ..++-+.++||+|+|||+||+.+++.....     .+.+..+...+
T Consensus       170 ~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~~-----~~~v~~~~l~~  244 (428)
T 4b4t_K          170 TYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAA-----FIRVNGSEFVH  244 (428)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTCE-----EEEEEGGGTCC
T ss_pred             CHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCCC-----eEEEecchhhc
Confidence            35567777777766665443    1         245678999999999999999999987532     33344332211


Q ss_pred             HHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--------cc--------cccccCCCC--CCC
Q 042806          219 IRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--------LD--------FQAVGIPHG--DDR  280 (390)
Q Consensus       219 ~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--------~~--------~~~l~~~l~--~~~  280 (390)
                      .              + .......+..+........++++++|+++..        ..        ...+...+.  ...
T Consensus       245 ~--------------~-~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~~  309 (428)
T 4b4t_K          245 K--------------Y-LGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQS  309 (428)
T ss_dssp             S--------------S-CSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCSS
T ss_pred             c--------------c-cchhHHHHHHHHHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCCC
Confidence            0              0 0011223344444444556799999999521        00        111111110  123


Q ss_pred             CCcEEEEEecchhhh-hhcC---CCcceEecCCCCH-HHHHHHHHHhhCCCC--CCCchHHHHHHHHHHcCCCh
Q 042806          281 KGCKVLLTARSLDVL-SRKM---DSQQNFSVGVLKE-DEAWSLFKKMAGDYI--EGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       281 ~~s~IivTtr~~~v~-~~~~---~~~~~~~l~~L~~-~ea~~lf~~~~~~~~--~~~~~~~~~~~i~~~~~GlP  347 (390)
                      .+..||.||...... ....   .....+++..++. ++-..+|..++....  ...++    ..+++.+.|+-
T Consensus       310 ~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~dl----~~lA~~t~G~s  379 (428)
T 4b4t_K          310 TNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADL----DSLIIRNDSLS  379 (428)
T ss_dssp             CSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTCCH----HHHHHHTTTCC
T ss_pred             CCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCcccCH----HHHHHHCCCCC
Confidence            455677777653321 1111   1224677765654 445566666653221  22233    46778887754

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

Probab=98.10  E-value=3.9e-06  Score=77.04  Aligned_cols=105  Identities=14%  Similarity=0.202  Sum_probs=58.6

Q ss_pred             cccchhHHHHHHHHHhcCC--------C-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          155 ACESRMSTLNDILDALKNP--------D-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~~--------~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      .++|....++.+...+...        . ...+.++|++|+|||++|+.+++.....  -...+.+.++....... .. 
T Consensus        18 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~--~~~~~~~~~~~~~~~~~-~~-   93 (311)
T 4fcw_A           18 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT--EEAMIRIDMTEYMEKHA-VS-   93 (311)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSC--GGGEEEEEGGGCCSTTH-HH-
T ss_pred             hcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCC--CcceEEeeccccccccc-HH-
Confidence            4667777777776665431        1 3478999999999999999999986432  12245555554332211 11 


Q ss_pred             HHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 042806          226 IADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       226 i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~  266 (390)
                        ..++......... ....+...+......+++||++...
T Consensus        94 --~l~g~~~~~~~~~-~~~~~~~~~~~~~~~vl~lDEi~~l  131 (311)
T 4fcw_A           94 --RLIGAPPGYVGYE-EGGQLTEAVRRRPYSVILFDAIEKA  131 (311)
T ss_dssp             --HHHCCCTTSTTTT-TCCHHHHHHHHCSSEEEEEETGGGS
T ss_pred             --HhcCCCCcccccc-ccchHHHHHHhCCCeEEEEeChhhc
Confidence              1223221111100 0023334444334479999999654

>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=98.07  E-value=1.7e-05  Score=72.63  Aligned_cols=46  Identities=22%  Similarity=0.243  Sum_probs=36.8

Q ss_pred             cccchhHHHHHHHHHhcC--------------CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          155 ACESRMSTLNDILDALKN--------------PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~--------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|++..+..+...+..              .....+.|+|++|+|||++|+.+.+...
T Consensus        16 ~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~   75 (310)
T 1ofh_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN   75 (310)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             hcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            578888888888776643              2345688999999999999999998873

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

Probab=98.04  E-value=3.1e-05  Score=75.12  Aligned_cols=173  Identities=16%  Similarity=0.214  Sum_probs=94.1

Q ss_pred             cccccchhHHHHHHH---HHhcCC---------CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 042806          153 YEACESRMSTLNDIL---DALKNP---------DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~---~~L~~~---------~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  220 (390)
                      ...++|.+..+.++.   ..+..+         -++-+.|+|++|+|||+||+.+++.....     .+.++.+..... 
T Consensus        15 f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~-----f~~is~~~~~~~-   88 (476)
T 2ce7_A           15 FKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVP-----FFHISGSDFVEL-   88 (476)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCC-----EEEEEGGGTTTC-
T ss_pred             HHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCC-----eeeCCHHHHHHH-
Confidence            345777766554444   444321         23458899999999999999999876432     233443322110 


Q ss_pred             HHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc----------------ccccccCCCC--CCCCC
Q 042806          221 KIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL----------------DFQAVGIPHG--DDRKG  282 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~----------------~~~~l~~~l~--~~~~~  282 (390)
                               +    .. ........+........+++|+||+++...                .+..+...+.  ....+
T Consensus        89 ---------~----~g-~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~  154 (476)
T 2ce7_A           89 ---------F----VG-VGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEG  154 (476)
T ss_dssp             ---------C----TT-HHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGGGT
T ss_pred             ---------H----hc-ccHHHHHHHHHHHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCCC
Confidence                     0    00 011122233333334456999999995421                1111211110  12345


Q ss_pred             cEEEEEecchhhhh-hcC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh
Q 042806          283 CKVLLTARSLDVLS-RKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       283 s~IivTtr~~~v~~-~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      ..||.||....... ...   .....+.+.+.+.++-.++|..++......++..  ...+++.+.|..
T Consensus       155 viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v~--l~~la~~t~G~s  221 (476)
T 2ce7_A          155 IIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVN--LEIIAKRTPGFV  221 (476)
T ss_dssp             EEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCC--HHHHHHTCTTCC
T ss_pred             EEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchhh--HHHHHHhcCCCc
Confidence            67777777654321 111   1234788888888888888887775322112111  345788888877

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

Probab=98.01  E-value=0.0001  Score=71.99  Aligned_cols=179  Identities=13%  Similarity=0.161  Sum_probs=99.9

Q ss_pred             cccccchhHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALKN-------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ...++|.+..+.+|.+.+..             ...+-+.|+|++|+|||+||+.+++....     ..+.++++     
T Consensus       203 ~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~-----~fv~vn~~-----  272 (489)
T 3hu3_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGA-----FFFLINGP-----  272 (489)
T ss_dssp             GGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSS-----EEEEEEHH-----
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCC-----CEEEEEch-----
Confidence            45688988888888776642             34566889999999999999999887632     12333321     


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc-------------ccccccCCCC--CCCCCcE
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL-------------DFQAVGIPHG--DDRKGCK  284 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~-------------~~~~l~~~l~--~~~~~s~  284 (390)
                       ++.    ..+    . .........+.......++.+|+||+++...             ....+...+.  ....+..
T Consensus       273 -~l~----~~~----~-g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~  342 (489)
T 3hu3_A          273 -EIM----SKL----A-GESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVI  342 (489)
T ss_dssp             -HHH----TSC----T-THHHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEE
T ss_pred             -Hhh----hhh----c-chhHHHHHHHHHHHHhcCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceE
Confidence             111    000    0 0011122233333334456899999994210             0111111111  1233556


Q ss_pred             EEEEecchhh-hhhcC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCC-hHHHHHH
Q 042806          285 VLLTARSLDV-LSRKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGL-PVSIVTV  353 (390)
Q Consensus       285 IivTtr~~~v-~~~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~Gl-PLai~~l  353 (390)
                      ||.||..... .....   .....+.+...+.++-.++|+.++.......+.  ....+++.+.|. +-.|..+
T Consensus       343 vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~~--~l~~la~~t~g~s~~dL~~L  414 (489)
T 3hu3_A          343 VMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDV--DLEQVANETHGHVGADLAAL  414 (489)
T ss_dssp             EEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCTTC--CHHHHHHTCTTCCHHHHHHH
T ss_pred             EEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcchh--hHHHHHHHccCCcHHHHHHH
Confidence            7777775432 11111   223478999999999999999887532211111  124677777774 5555544

>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=97.92  E-value=8.9e-05  Score=71.93  Aligned_cols=48  Identities=17%  Similarity=0.143  Sum_probs=36.2

Q ss_pred             cccccchhHHHHHH---HHHhcCCC--ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          153 YEACESRMSTLNDI---LDALKNPD--VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       153 ~~~~~gR~~~~~~l---~~~L~~~~--~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...++|.+..++.+   ++.+..+.  .+-+.++|++|+|||+||+.+.+...
T Consensus        36 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~l~   88 (456)
T 2c9o_A           36 ASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELG   88 (456)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHHhC
Confidence            35788988776644   44444432  35788999999999999999999875

>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=97.89  E-value=0.00018  Score=66.81  Aligned_cols=173  Identities=14%  Similarity=0.080  Sum_probs=92.1

Q ss_pred             cccccchhHHHHHHHHHhcC-----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKN-----PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-----~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      ...++|.+..++.+...+..     .....+.|+|++|+|||||++.+++.....  |   .....+-.....++     
T Consensus        24 l~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~--~---~~~sg~~~~~~~~l-----   93 (334)
T 1in4_A           24 LDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTN--I---HVTSGPVLVKQGDM-----   93 (334)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCC--E---EEEETTTCCSHHHH-----
T ss_pred             HHHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC--E---EEEechHhcCHHHH-----
Confidence            45677877766666555542     234678999999999999999999987432  1   11111111111111     


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCC---CC------CC---------CCCcEEE-
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIP---HG------DD---------RKGCKVL-  286 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~---l~------~~---------~~~s~Ii-  286 (390)
                                      ..+...+. .+ .++++|++....  ..+.+...   ..      ..         .+...++ 
T Consensus        94 ----------------~~~~~~~~-~~-~v~~iDE~~~l~~~~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l~~~~li~  155 (334)
T 1in4_A           94 ----------------AAILTSLE-RG-DVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVG  155 (334)
T ss_dssp             ----------------HHHHHHCC-TT-CEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEEEE
T ss_pred             ----------------HHHHHHcc-CC-CEEEEcchhhcCHHHHHHHHHHHHhcccceeeccCcccccccccCCCeEEEE
Confidence                            11111111 22 467778875431  11111100   00      00         0112233 


Q ss_pred             EEecchhhhhh-cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          287 LTARSLDVLSR-KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       287 vTtr~~~v~~~-~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      .|++...+... .......+.+++.+.++-.+++.+.+..... .-.++.+..|++.+.|.|-.+..+.
T Consensus       156 at~~~~~Ls~~l~sR~~l~~~Ld~~~~~~l~~iL~~~~~~~~~-~~~~~~~~~ia~~~~G~~R~a~~ll  223 (334)
T 1in4_A          156 ATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDV-EIEDAAAEMIAKRSRGTPRIAIRLT  223 (334)
T ss_dssp             EESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC-CBCHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             ecCCcccCCHHHHHhcCceeeCCCCCHHHHHHHHHHHHHHcCC-CcCHHHHHHHHHhcCCChHHHHHHH
Confidence            34443322111 1112236889999999999999887641111 1224568899999999997655443

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.84  E-value=3.9e-05  Score=65.63  Aligned_cols=113  Identities=15%  Similarity=0.068  Sum_probs=61.2

Q ss_pred             HHHHHHHHHhcCC----CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC
Q 042806          161 STLNDILDALKNP----DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE  236 (390)
Q Consensus       161 ~~~~~l~~~L~~~----~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~  236 (390)
                      ..++.+.+++...    ..+.+.|+|++|+|||+||+.+++.....  ...++|+++      .++...+...+..    
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~--~~~~~~~~~------~~~~~~~~~~~~~----  103 (202)
T 2w58_A           36 KAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKR--NVSSLIVYV------PELFRELKHSLQD----  103 (202)
T ss_dssp             HHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTT--TCCEEEEEH------HHHHHHHHHC-------
T ss_pred             HHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEh------HHHHHHHHHHhcc----
Confidence            3444555555432    12688999999999999999999987643  234556544      3444444332211    


Q ss_pred             CCchHHHHHHHHHHhCCCeEEEEEeCCCCC--ccccc--ccC-CCCCC-CCCcEEEEEecc
Q 042806          237 ESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQA--VGI-PHGDD-RKGCKVLLTARS  291 (390)
Q Consensus       237 ~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~--l~~-~l~~~-~~~s~IivTtr~  291 (390)
                      ...    ..+.+.+...  -+|||||++..  ..|..  +.. .+... ..+.++|+||..
T Consensus       104 ~~~----~~~~~~~~~~--~~lilDei~~~~~~~~~~~~ll~~~l~~~~~~~~~~i~tsn~  158 (202)
T 2w58_A          104 QTM----NEKLDYIKKV--PVLMLDDLGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNF  158 (202)
T ss_dssp             CCC----HHHHHHHHHS--SEEEEEEECCC---CCGGGTTHHHHHHHHHHTTCCEEEEESS
T ss_pred             chH----HHHHHHhcCC--CEEEEcCCCCCcCCHHHHHHHHHHHHHHHHhCCCCEEEEcCC
Confidence            111    2223334332  39999999643  33322  211 11111 235568888874

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.83  E-value=2.2e-06  Score=69.43  Aligned_cols=45  Identities=9%  Similarity=0.099  Sum_probs=31.8

Q ss_pred             cccchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          155 ACESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .++|+...+.++.+.+..  ....-|.|+|++|+|||++|+.+.+..
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~   51 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNG   51 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTT
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhC
Confidence            567887777777766542  233447799999999999999997754

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=97.81  E-value=1.5e-05  Score=71.39  Aligned_cols=60  Identities=13%  Similarity=0.138  Sum_probs=38.4

Q ss_pred             ccccchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 042806          154 EACESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK  215 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  215 (390)
                      +.++|+...+..+.+.+..  .....+.|+|++|+|||+||+.+++.....  -...+.++++.
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~~~~--~~~~~~v~~~~   67 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSRW--QGPFISLNCAA   67 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTSTTT--TSCEEEEEGGG
T ss_pred             ccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhcCcc--CCCeEEEecCC
Confidence            3577888777777665532  233567799999999999999999876432  12245555554

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.78  E-value=4.6e-05  Score=69.81  Aligned_cols=46  Identities=15%  Similarity=0.191  Sum_probs=35.4

Q ss_pred             cccchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          155 ACESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|+...+.++.+.+..  .....+.|+|++|+|||++|+.+.+...
T Consensus         3 ~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~~   50 (304)
T 1ojl_A            3 HMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSA   50 (304)
T ss_dssp             CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHSS
T ss_pred             CcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhCc
Confidence            477887777777766543  3345577999999999999999998653

>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=97.77  E-value=6.4e-05  Score=77.24  Aligned_cols=173  Identities=13%  Similarity=0.191  Sum_probs=94.3

Q ss_pred             cccccchhHHHHHHHHHh----cC---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDAL----KN---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L----~~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ..++.|-+..+++|.+.+    ..         ..++-|.++|++|+|||+||+.+++.....     .+.++.+     
T Consensus       203 ~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg~~-----~~~v~~~-----  272 (806)
T 3cf2_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAF-----FFLINGP-----  272 (806)
T ss_dssp             GGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTTCE-----EEEEEHH-----
T ss_pred             hhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCe-----EEEEEhH-----
Confidence            344566655555554433    22         235679999999999999999999887532     2333321     


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--------c-----cccccCCCC--CCCCCcE
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--------D-----FQAVGIPHG--DDRKGCK  284 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--------~-----~~~l~~~l~--~~~~~s~  284 (390)
                       ++.       + ... ......+..+.+......+++|+||+++...        .     ...+...+.  ....+..
T Consensus       273 -~l~-------s-k~~-gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~  342 (806)
T 3cf2_A          273 -EIM-------S-KLA-GESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVI  342 (806)
T ss_dssp             -HHH-------S-SCT-THHHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEE
T ss_pred             -Hhh-------c-ccc-hHHHHHHHHHHHHHHHcCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCEE
Confidence             111       0 000 0112233344444445567999999996431        0     011111110  1123445


Q ss_pred             EEEEecchhhh-hhcC---CCcceEecCCCCHHHHHHHHHHhhCCCC--CCCchHHHHHHHHHHcCCChHH
Q 042806          285 VLLTARSLDVL-SRKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYI--EGSEFKWVAKDVARECAGLPVS  349 (390)
Q Consensus       285 IivTtr~~~v~-~~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~--~~~~~~~~~~~i~~~~~GlPLa  349 (390)
                      ||.||...... ....   .....+++...+.++-.++|+.+.....  .+.+    ...|++++.|.--|
T Consensus       343 VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvd----l~~lA~~T~Gfsga  409 (806)
T 3cf2_A          343 VMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVD----LEQVANETHGHVGA  409 (806)
T ss_dssp             EEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTCC----HHHHHHHCCSCCHH
T ss_pred             EEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcccC----HHHHHHhcCCCCHH
Confidence            66666543321 1111   2335788999999888899988775221  2223    34688888877533

>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=97.72  E-value=0.00011  Score=72.79  Aligned_cols=138  Identities=20%  Similarity=0.195  Sum_probs=66.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      ....+.++|++|+||||||+.++......     ...+.++...+..++........+..      ..............
T Consensus       107 ~g~~vll~Gp~GtGKTtlar~ia~~l~~~-----~~~i~~~~~~~~~~~~g~~~~~ig~~------~~~~~~~~~~a~~~  175 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLAKSIAKSLGRK-----FVRISLGGVRDESEIRGHRRTYVGAM------PGRIIQGMKKAGKL  175 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHHHHHHHHHTCE-----EEEECCCC--------------------------CHHHHHHTTCSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhcCCC-----eEEEEecccchhhhhhhHHHHHhccC------chHHHHHHHHhhcc
Confidence            45689999999999999999999887422     22333333222222222111111110      00111111222223


Q ss_pred             CeEEEEEeCCCCCcc------cccccCCCCCC---------------CCCcEEEEEecchhhh-hhcCCCcceEecCCCC
Q 042806          254 KTILVILDNIWGNLD------FQAVGIPHGDD---------------RKGCKVLLTARSLDVL-SRKMDSQQNFSVGVLK  311 (390)
Q Consensus       254 ~~~LlVlDdv~~~~~------~~~l~~~l~~~---------------~~~s~IivTtr~~~v~-~~~~~~~~~~~l~~L~  311 (390)
                      . -+++||++.....      ...+...+...               .....||.||...... .....-...+++.+++
T Consensus       176 ~-~vl~lDEid~l~~~~~~~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~ttN~~~~l~~aL~~R~~vi~~~~~~  254 (543)
T 3m6a_A          176 N-PVFLLDEIDKMSSDFRGDPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATANNLATIPGPLRDRMEIINIAGYT  254 (543)
T ss_dssp             S-EEEEEEESSSCC---------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEECSSTTTSCHHHHHHEEEEECCCCC
T ss_pred             C-CEEEEhhhhhhhhhhccCHHHHHHHHHhhhhcceeecccCCeeecccceEEEeccCccccCCHHHHhhcceeeeCCCC
Confidence            4 4888999975421      12222222110               1345667666653211 1111111478999999


Q ss_pred             HHHHHHHHHHhh
Q 042806          312 EDEAWSLFKKMA  323 (390)
Q Consensus       312 ~~ea~~lf~~~~  323 (390)
                      .++-.+++..++
T Consensus       255 ~~e~~~Il~~~l  266 (543)
T 3m6a_A          255 EIEKLEIVKDHL  266 (543)
T ss_dssp             HHHHHHHHHHTH
T ss_pred             HHHHHHHHHHHH
Confidence            999888887765

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

Probab=97.69  E-value=2.4e-05  Score=81.03  Aligned_cols=149  Identities=15%  Similarity=0.188  Sum_probs=82.2

Q ss_pred             ccccchhHHHHHHHHHhcC-------CC--ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 042806          154 EACESRMSTLNDILDALKN-------PD--VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQG  224 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~-------~~--~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~  224 (390)
                      ..++|.+..+..+...+..       ++  ...+.++|++|+|||++|+.+++.....  -...+.++++........  
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~--~~~~i~i~~s~~~~~~~~--  566 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIFGD--EESMIRIDMSEYMEKHST--  566 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSC--TTCEEEEEGGGGCSSCCC--
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCC--CcceEEEechhccccccc--
Confidence            3578888877777766642       11  1268899999999999999999987322  223455665543211000  


Q ss_pred             HHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCC-----CCC------CCCCcEEEEEecc
Q 042806          225 EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIP-----HGD------DRKGCKVLLTARS  291 (390)
Q Consensus       225 ~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~-----l~~------~~~~s~IivTtr~  291 (390)
                                   .    ...+.+.+......+|+||++....  ....+...     +..      ...+.+||+||..
T Consensus       567 -------------~----~~~l~~~~~~~~~~vl~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~  629 (758)
T 3pxi_A          567 -------------S----GGQLTEKVRRKPYSVVLLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNV  629 (758)
T ss_dssp             -------------C-------CHHHHHHCSSSEEEEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESS
T ss_pred             -------------c----cchhhHHHHhCCCeEEEEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCC
Confidence                         0    1112223333333599999996541  11222111     100      1235688888873


Q ss_pred             hh-------------hhhh-cCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          292 LD-------------VLSR-KMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       292 ~~-------------v~~~-~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                      ..             .... .......+.+.+++.++..+++...+
T Consensus       630 ~~~~~~~~~~~~~~~f~p~l~~Rl~~~i~~~~l~~~~~~~i~~~~l  675 (758)
T 3pxi_A          630 GASEKDKVMGELKRAFRPEFINRIDEIIVFHSLEKKHLTEIVSLMS  675 (758)
T ss_dssp             STTCCHHHHHHHHHHSCHHHHTTSSEEEECC--CHHHHHHHHHHHH
T ss_pred             ChhhHHHHHHHHHhhCCHHHHhhCCeEEecCCCCHHHHHHHHHHHH
Confidence            10             0000 11123589999999999888887655

>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=97.57  E-value=9.6e-05  Score=76.47  Aligned_cols=159  Identities=12%  Similarity=0.124  Sum_probs=83.5

Q ss_pred             cccchhHHHHHHHHHhcC-------C--CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          155 ACESRMSTLNDILDALKN-------P--DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~-------~--~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      .++|.+..+..+...+..       +  ....+.++|++|+|||++|+.+.+...     ...+.++.+.......    
T Consensus       459 ~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l~-----~~~~~i~~s~~~~~~~----  529 (758)
T 1r6b_X          459 LVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG-----IELLRFDMSEYMERHT----  529 (758)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT-----CEEEEEEGGGCSSSSC----
T ss_pred             hccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHhc-----CCEEEEechhhcchhh----
Confidence            467777777766665542       1  123688999999999999999998873     2244455543321100    


Q ss_pred             HHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCC-----C------CCCcEEEEEecch
Q 042806          226 IADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGD-----D------RKGCKVLLTARSL  292 (390)
Q Consensus       226 i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~-----~------~~~s~IivTtr~~  292 (390)
                      +...++.. +..........+.+.+......+|+||++...  ..+..+...+..     .      ..+..||.||...
T Consensus       530 ~~~l~g~~-~g~~g~~~~~~l~~~~~~~~~~vl~lDEi~~~~~~~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~~  608 (758)
T 1r6b_X          530 VSRLIGAP-PGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAG  608 (758)
T ss_dssp             CSSSCCCC-SCSHHHHHTTHHHHHHHHCSSEEEEEETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSS
T ss_pred             HhhhcCCC-CCCcCccccchHHHHHHhCCCcEEEEeCccccCHHHHHHHHHHhcCcEEEcCCCCEEecCCeEEEEecCcc
Confidence            00001111 00000001112344444444489999999754  222222111110     0      1345677787641


Q ss_pred             h--------------------------hhhh-cCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          293 D--------------------------VLSR-KMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       293 ~--------------------------v~~~-~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                      .                          +... .......+.+.+++.++...++...+
T Consensus       609 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~l~~~~~~~i~~~~l  666 (758)
T 1r6b_X          609 VRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFI  666 (758)
T ss_dssp             CC-----------------CHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHHH
T ss_pred             hhhhhhcccCccccchHHHHHHHHHHhcCHHHHhhCCcceeeCCCCHHHHHHHHHHHH
Confidence            1                          0000 01122468899999998888887665

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

Probab=97.48  E-value=0.0012  Score=58.55  Aligned_cols=149  Identities=15%  Similarity=0.146  Sum_probs=77.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeE
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTI  256 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~  256 (390)
                      -+.|+|++|+|||||++.++.....     ..+.+..      .++..    ..    . ......+..+.+......+.
T Consensus        51 g~ll~G~~G~GKTtl~~~i~~~~~~-----~~i~~~~------~~~~~----~~----~-~~~~~~i~~~~~~~~~~~~~  110 (254)
T 1ixz_A           51 GVLLVGPPGVGKTHLARAVAGEARV-----PFITASG------SDFVE----MF----V-GVGAARVRDLFETAKRHAPC  110 (254)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHTTC-----CEEEEEH------HHHHH----SC----T-THHHHHHHHHHHHHTTSSSE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCC-----CEEEeeH------HHHHH----HH----h-hHHHHHHHHHHHHHHhcCCe
Confidence            3889999999999999999987642     1233322      11110    00    0 00011223333443333458


Q ss_pred             EEEEeCCCCCc------------c----cccccCCCCCC--CCCcEEEEEecchhhhhh-cC---CCcceEecCCCCHHH
Q 042806          257 LVILDNIWGNL------------D----FQAVGIPHGDD--RKGCKVLLTARSLDVLSR-KM---DSQQNFSVGVLKEDE  314 (390)
Q Consensus       257 LlVlDdv~~~~------------~----~~~l~~~l~~~--~~~s~IivTtr~~~v~~~-~~---~~~~~~~l~~L~~~e  314 (390)
                      ++++|+++...            .    ...+...+...  .....++.||........ ..   .....+++...+.++
T Consensus       111 i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~  190 (254)
T 1ixz_A          111 IVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKG  190 (254)
T ss_dssp             EEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHH
T ss_pred             EEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCCCCCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHH
Confidence            99999994210            0    11121111111  122345556665443221 11   234578899999988


Q ss_pred             HHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh
Q 042806          315 AWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       315 a~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      -.++++..+.......+.  ....+++.+.|.-
T Consensus       191 r~~il~~~~~~~~~~~~~--~~~~la~~~~G~~  221 (254)
T 1ixz_A          191 REQILRIHARGKPLAEDV--DLALLAKRTPGFV  221 (254)
T ss_dssp             HHHHHHHHHTTSCBCTTC--CHHHHHHTCTTCC
T ss_pred             HHHHHHHHHcCCCCCccc--CHHHHHHHcCCCC
Confidence            888888776422111111  1346788888764

>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=97.44  E-value=0.001  Score=60.46  Aligned_cols=85  Identities=9%  Similarity=0.101  Sum_probs=56.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-----CchHHH-HHHHHH-
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE-----SDSGRA-RSLRNR-  249 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~-----~~~~~~-~~l~~~-  249 (390)
                      ++.|+|++|+|||||+.+++........=..++|++....++..     .++.++.+.+..     ...+.+ ..+.+. 
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E~~~l~i~~~l  104 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPA-----YLRSMGVDPERVIHTPVQSLEQLRIDMVNQL  104 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHH-----HHHHTTCCGGGEEEEECSBHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHH-----HHHHhCCCHHHeEEEcCCCHHHHHHHHHHHH
Confidence            78999999999999999998876543112357898887777653     367777654421     122222 233333 


Q ss_pred             --HhCCCeEEEEEeCCCCC
Q 042806          250 --LKKEKTILVILDNIWGN  266 (390)
Q Consensus       250 --l~~~~~~LlVlDdv~~~  266 (390)
                        +...++-|+|+|-+...
T Consensus       105 ~~i~~~~~~lvVIDSI~aL  123 (333)
T 3io5_A          105 DAIERGEKVVVFIDSLGNL  123 (333)
T ss_dssp             HTCCTTCCEEEEEECSTTC
T ss_pred             HHhhccCceEEEEeccccc
Confidence              35566789999999654

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

Probab=97.43  E-value=0.00014  Score=66.11  Aligned_cols=27  Identities=33%  Similarity=0.300  Sum_probs=24.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++.+.++|++|+|||+||+.+++...
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~l~   61 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRKMG   61 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            356788999999999999999999885

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

Probab=97.42  E-value=0.0012  Score=64.29  Aligned_cols=170  Identities=15%  Similarity=0.172  Sum_probs=89.6

Q ss_pred             cccccchhHHHHHH---HHHhcCC---------CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 042806          153 YEACESRMSTLNDI---LDALKNP---------DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       153 ~~~~~gR~~~~~~l---~~~L~~~---------~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  220 (390)
                      ...++|.+..+.++   +..+..+         -.+-+.|+|++|+||||||+.++.....     ..+.++.+.-... 
T Consensus        30 f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~~-----~~i~i~g~~~~~~-  103 (499)
T 2dhr_A           30 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARV-----PFITASGSDFVEM-  103 (499)
T ss_dssp             TTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTTC-----CEEEEEGGGGTSS-
T ss_pred             HHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCC-----CEEEEehhHHHHh-
Confidence            34577776555444   4444321         1234889999999999999999987642     2344443321110 


Q ss_pred             HHHHHHHHHhCCCCCCCCchHHHHHHHHHHhC---CCeEEEEEeCCCCCcc----------------cccccCCCCC--C
Q 042806          221 KIQGEIADKLGLTLHEESDSGRARSLRNRLKK---EKTILVILDNIWGNLD----------------FQAVGIPHGD--D  279 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~---~~~~LlVlDdv~~~~~----------------~~~l~~~l~~--~  279 (390)
                                       ........+...+..   ..++++++|+++....                ...+...+..  .
T Consensus       104 -----------------~~g~~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~  166 (499)
T 2dhr_A          104 -----------------FVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEK  166 (499)
T ss_dssp             -----------------CTTHHHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCS
T ss_pred             -----------------hhhhHHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhccccc
Confidence                             000111222232322   2348999999953210                1112111111  1


Q ss_pred             CCCcEEEEEecchhhhhh-cC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh
Q 042806          280 RKGCKVLLTARSLDVLSR-KM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       280 ~~~s~IivTtr~~~v~~~-~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      .....++.||........ ..   .....+.+...+.++-.+++..++......++.  ....|+..+.|+.
T Consensus       167 ~~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~dv--~l~~lA~~t~G~~  236 (499)
T 2dhr_A          167 DTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDV--DLALLAKRTPGFV  236 (499)
T ss_dssp             SCCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCSS--TTHHHHTTSCSCC
T ss_pred             CccEEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChHH--HHHHHHHhcCCCC
Confidence            234456666666544221 11   233588899999998889998776422111111  1345777777765

>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=97.40  E-value=0.00068  Score=63.12  Aligned_cols=86  Identities=19%  Similarity=0.252  Sum_probs=56.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC------CCchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE------ESDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~------~~~~~~~~~l~  247 (390)
                      ...++.|+|++|+|||||+.+++......+  ..++|++....++..     .++.++.....      .+.......+.
T Consensus        60 ~G~i~~I~GppGsGKSTLal~la~~~~~~g--g~VlyId~E~s~~~~-----ra~rlgv~~~~l~i~~~~~~e~~l~~~~  132 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLALHAIAEAQKMG--GVAAFIDAEHALDPV-----YAKNLGVDLKSLLISQPDHGEQALEIVD  132 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhcC--CeEEEEecccccchH-----HHHHcCCchhhhhhhhccCHHHHHHHHH
Confidence            457999999999999999999998865421  246788777666543     45566654322      12233334444


Q ss_pred             HHHhCCCeEEEEEeCCCCC
Q 042806          248 NRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~~  266 (390)
                      ..+...+.-++|+|.+...
T Consensus       133 ~l~~~~~~dlvVIDSi~~l  151 (356)
T 3hr8_A          133 ELVRSGVVDLIVVDSVAAL  151 (356)
T ss_dssp             HHHHTSCCSEEEEECTTTC
T ss_pred             HHhhhcCCCeEEehHhhhh
Confidence            4444445469999998543

>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=97.39  E-value=0.0012  Score=57.76  Aligned_cols=92  Identities=11%  Similarity=0.123  Sum_probs=56.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcC----CCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC----------CCCc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEK----LFDQVIFVEVSKIQDIRKIQGEIADKLGLTLH----------EESD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~----------~~~~  239 (390)
                      ...++.|+|++|+|||||++.+........    .-..++|+.....++...+. .++..++....          ..+.
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~  101 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLL-AVAERYGLSGSDVLDNVAYARAFNT  101 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHH-HHHHHcCCCHHHHhhCeEEEecCCH
Confidence            456899999999999999999988532211    12468888877655555443 34455554321          1111


Q ss_pred             hH---HHHHHHHHHhCCCeEEEEEeCCCCC
Q 042806          240 SG---RARSLRNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       240 ~~---~~~~l~~~l~~~~~~LlVlDdv~~~  266 (390)
                      ..   ....+.+.+...++-+||+|.+...
T Consensus       102 ~~~~~~~~~~~~~~~~~~~~lliiD~~~~~  131 (243)
T 1n0w_A          102 DHQTQLLYQASAMMVESRYALLIVDSATAL  131 (243)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETSSGG
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEEeCchHH
Confidence            11   2233555555556689999998643

>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=97.35  E-value=0.00014  Score=76.15  Aligned_cols=46  Identities=24%  Similarity=0.353  Sum_probs=35.3

Q ss_pred             cccchhHHHHHHHHHhcC-------CC--ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          155 ACESRMSTLNDILDALKN-------PD--VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~-------~~--~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|.+..+..+...+..       ++  ...+.|+|++|+|||++|+.+.+...
T Consensus       559 ~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~  613 (854)
T 1qvr_A          559 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLF  613 (854)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHH
T ss_pred             ccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhc
Confidence            468888877777666542       11  24788999999999999999998874

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

Probab=97.35  E-value=0.0022  Score=57.64  Aligned_cols=126  Identities=16%  Similarity=0.192  Sum_probs=69.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC--HHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD--IRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~--~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      -+.|+|++|+|||||++.++.....     ..+++..+...+  ..+.                 ...+..+.+......
T Consensus        46 GvlL~Gp~GtGKTtLakala~~~~~-----~~i~i~g~~l~~~~~~~~-----------------~~~i~~vf~~a~~~~  103 (274)
T 2x8a_A           46 GVLLAGPPGCGKTLLAKAVANESGL-----NFISVKGPELLNMYVGES-----------------ERAVRQVFQRAKNSA  103 (274)
T ss_dssp             EEEEESSTTSCHHHHHHHHHHHTTC-----EEEEEETTTTCSSTTHHH-----------------HHHHHHHHHHHHHTC
T ss_pred             eEEEECCCCCcHHHHHHHHHHHcCC-----CEEEEEcHHHHhhhhhHH-----------------HHHHHHHHHHHHhcC
Confidence            3899999999999999999987642     234444322111  0110                 111223333322234


Q ss_pred             eEEEEEeCCCCCcc---------c----ccccCCCCC--CCCCcEEEEEecchhhhhhc--C--CCcceEecCCCCHHHH
Q 042806          255 TILVILDNIWGNLD---------F----QAVGIPHGD--DRKGCKVLLTARSLDVLSRK--M--DSQQNFSVGVLKEDEA  315 (390)
Q Consensus       255 ~~LlVlDdv~~~~~---------~----~~l~~~l~~--~~~~s~IivTtr~~~v~~~~--~--~~~~~~~l~~L~~~ea  315 (390)
                      ++++++|++.....         .    ..+...+..  .....-++.+|....+....  .  .....+.+...+.++-
T Consensus       104 p~i~~~Deid~~~~~r~~~~~~~~~~~~~~~l~~Lsgg~~~~~~i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r  183 (274)
T 2x8a_A          104 PCVIFFDEVDALCPRRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADR  183 (274)
T ss_dssp             SEEEEEETCTTTCC---------CTTHHHHHHHHHHTCCSTTCEEEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHH
T ss_pred             CCeEeeehhhhhhcccCCCcchHHHHHHHHHHHhhhcccccCCEEEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHH
Confidence            58999999964211         0    001111111  12234566666655442211  1  2345788999999999


Q ss_pred             HHHHHHhhC
Q 042806          316 WSLFKKMAG  324 (390)
Q Consensus       316 ~~lf~~~~~  324 (390)
                      .++|+....
T Consensus       184 ~~il~~~~~  192 (274)
T 2x8a_A          184 LAILKTITK  192 (274)
T ss_dssp             HHHHHHHTT
T ss_pred             HHHHHHHHh
Confidence            999988764

>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=97.33  E-value=0.0031  Score=58.49  Aligned_cols=165  Identities=7%  Similarity=-0.061  Sum_probs=101.2

Q ss_pred             HHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHH
Q 042806          168 DALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLR  247 (390)
Q Consensus       168 ~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~  247 (390)
                      +.+.+.-.++..++|+.|.||++.+..+.+..... .|+....+.+....++.++...+...                  
T Consensus        11 ~~l~~~~~~~yl~~G~e~~~~~~~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~------------------   71 (343)
T 1jr3_D           11 AQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQ-GFEEHHTFSIDPNTDWNAIFSLCQAM------------------   71 (343)
T ss_dssp             HHHHHCCCSEEEEEESCHHHHHHHHHHHHHHHHHH-TCCEEEEEECCTTCCHHHHHHHHHHH------------------
T ss_pred             HHHhcCCCcEEEEECCcHHHHHHHHHHHHHHHHhC-CCCeeEEEEecCCCCHHHHHHHhcCc------------------
Confidence            33332346789999999999999999998876533 25432223344445555544432111                  


Q ss_pred             HHHhCCCeEEEEEeCCCC-C--cccccccCCCCCCCCCcEEEEEecc-------hhhhhhcCCCcceEecCCCCHHHHHH
Q 042806          248 NRLKKEKTILVILDNIWG-N--LDFQAVGIPHGDDRKGCKVLLTARS-------LDVLSRKMDSQQNFSVGVLKEDEAWS  317 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~-~--~~~~~l~~~l~~~~~~s~IivTtr~-------~~v~~~~~~~~~~~~l~~L~~~ea~~  317 (390)
                       -+-+++ -++|+|+++. .  ..++.+...+..-.+++.+|+++..       ..+..........++..+++.++...
T Consensus        72 -plf~~~-kvvii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~~~~l~~  149 (343)
T 1jr3_D           72 -SLFASR-QTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPR  149 (343)
T ss_dssp             -HHCCSC-EEEEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTTHHHH
T ss_pred             -CCccCC-eEEEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCCHHHHHH
Confidence             011233 6889999865 3  3445554444333456777766643       12333334455789999999999998


Q ss_pred             HHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          318 LFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       318 lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      .+.+.+......- .++.+..+++.++|.+..+...-
T Consensus       150 ~l~~~~~~~g~~i-~~~a~~~l~~~~~gdl~~~~~el  185 (343)
T 1jr3_D          150 WVAARAKQLNLEL-DDAANQVLCYCYEGNLLALAQAL  185 (343)
T ss_dssp             HHHHHHHHTTCEE-CHHHHHHHHHSSTTCHHHHHHHH
T ss_pred             HHHHHHHHcCCCC-CHHHHHHHHHHhchHHHHHHHHH
Confidence            8887764221111 13567789999999888877643

>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=97.32  E-value=0.0004  Score=63.34  Aligned_cols=70  Identities=11%  Similarity=0.136  Sum_probs=44.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEe--CCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEV--SKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKK  252 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v--~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  252 (390)
                      .+++.|+|++|+|||+||.++......     .++|++.  ....+.             .  ..+.......+.+.+..
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~~G~-----~VlyIs~~~eE~v~~-------------~--~~~le~~l~~i~~~l~~  182 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEALGG-----KDKYATVRFGEPLSG-------------Y--NTDFNVFVDDIARAMLQ  182 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHHHHT-----TSCCEEEEBSCSSTT-------------C--BCCHHHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHhCCC-----CEEEEEecchhhhhh-------------h--hcCHHHHHHHHHHHHhh
Confidence            457789999999999999999887211     2356666  222110             0  02233344556666655


Q ss_pred             CCeEEEEEeCCCCC
Q 042806          253 EKTILVILDNIWGN  266 (390)
Q Consensus       253 ~~~~LlVlDdv~~~  266 (390)
                      .+  +||+|++...
T Consensus       183 ~~--LLVIDsI~aL  194 (331)
T 2vhj_A          183 HR--VIVIDSLKNV  194 (331)
T ss_dssp             CS--EEEEECCTTT
T ss_pred             CC--EEEEeccccc
Confidence            44  9999999653

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.32  E-value=0.00035  Score=60.70  Aligned_cols=49  Identities=18%  Similarity=0.218  Sum_probs=32.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      ...++.|.|++|+|||||++.++......+  ..+.|+....  +..++...+
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~--~~v~~~~~~~--~~~~~~~~~   70 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFSLHFIAKGLRDG--DPCIYVTTEE--SRDSIIRQA   70 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHHHHHT--CCEEEEESSS--CHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHCC--CeEEEEEccc--CHHHHHHHH
Confidence            346899999999999999999986654321  2355655433  445544443

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

Probab=97.28  E-value=0.0013  Score=59.20  Aligned_cols=149  Identities=16%  Similarity=0.139  Sum_probs=77.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeE
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTI  256 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~  256 (390)
                      -+.|+|++|+|||||++.++.....     ..+.+...      ++..    ...     ......+..+.+......+.
T Consensus        75 gvll~Gp~GtGKTtl~~~i~~~~~~-----~~i~~~~~------~~~~----~~~-----~~~~~~i~~~~~~~~~~~~~  134 (278)
T 1iy2_A           75 GVLLVGPPGVGKTHLARAVAGEARV-----PFITASGS------DFVE----MFV-----GVGAARVRDLFETAKRHAPC  134 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHTTC-----CEEEEEHH------HHHH----STT-----THHHHHHHHHHHHHHTSCSE
T ss_pred             eEEEECCCcChHHHHHHHHHHHcCC-----CEEEecHH------HHHH----HHh-----hHHHHHHHHHHHHHHhcCCc
Confidence            3889999999999999999987642     12333221      1111    000     00011222333433333458


Q ss_pred             EEEEeCCCCC------------cc----cccccCCCCCC--CCCcEEEEEecchhhhhh----cCCCcceEecCCCCHHH
Q 042806          257 LVILDNIWGN------------LD----FQAVGIPHGDD--RKGCKVLLTARSLDVLSR----KMDSQQNFSVGVLKEDE  314 (390)
Q Consensus       257 LlVlDdv~~~------------~~----~~~l~~~l~~~--~~~s~IivTtr~~~v~~~----~~~~~~~~~l~~L~~~e  314 (390)
                      ++++|++...            ..    ...+...+...  .....++.||........    .......+++...+.++
T Consensus       135 i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~  214 (278)
T 1iy2_A          135 IVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKG  214 (278)
T ss_dssp             EEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTCCTTCCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHH
T ss_pred             EEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCCCCCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHH
Confidence            9999999421            00    11111112111  122345556655433211    11234588999999998


Q ss_pred             HHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh
Q 042806          315 AWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP  347 (390)
Q Consensus       315 a~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP  347 (390)
                      -.+++...+.......+.  ....++..+.|..
T Consensus       215 r~~il~~~~~~~~~~~~~--~~~~la~~~~G~~  245 (278)
T 1iy2_A          215 REQILRIHARGKPLAEDV--DLALLAKRTPGFV  245 (278)
T ss_dssp             HHHHHHHHHTTSCBCTTC--CHHHHHHTCTTCC
T ss_pred             HHHHHHHHHccCCCCccc--CHHHHHHHcCCCC
Confidence            888888776422211111  1346788888865

>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=97.28  E-value=0.0014  Score=61.02  Aligned_cols=91  Identities=15%  Similarity=0.226  Sum_probs=58.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcC----CCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC----------CCCc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEK----LFDQVIFVEVSKIQDIRKIQGEIADKLGLTLH----------EESD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~----------~~~~  239 (390)
                      ...++.|+|++|+|||||+.+++.......    .-..++|++....++...+.. ++..++....          ..+.
T Consensus       121 ~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~-~~~~~g~~~~~~l~~l~~~~~~~~  199 (343)
T 1v5w_A          121 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRD-IADRFNVDHDAVLDNVLYARAYTS  199 (343)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHH-HHHHTTCCHHHHHHTEEEEECCST
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHcCCCHHHHHhceeEeecCCH
Confidence            457899999999999999999988743211    124688998888777766543 4455554321          0111


Q ss_pred             h---HHHHHHHHHHhC--CCeEEEEEeCCCC
Q 042806          240 S---GRARSLRNRLKK--EKTILVILDNIWG  265 (390)
Q Consensus       240 ~---~~~~~l~~~l~~--~~~~LlVlDdv~~  265 (390)
                      .   ..+..+...+..  .+.-+||+|.+..
T Consensus       200 e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~  230 (343)
T 1v5w_A          200 EHQMELLDYVAAKFHEEAGIFKLLIIDSIMA  230 (343)
T ss_dssp             THHHHHHHHHHHHHHHSCSSEEEEEEETSGG
T ss_pred             HHHHHHHHHHHHHHHhcCCCccEEEEechHH
Confidence            1   223344555554  5657999999853

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.28  E-value=0.00059  Score=55.31  Aligned_cols=47  Identities=13%  Similarity=0.220  Sum_probs=32.7

Q ss_pred             HHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 042806          167 LDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK  215 (390)
Q Consensus       167 ~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  215 (390)
                      +..|..-....+.|+|+.|+|||||++.++...... .+. .+++....
T Consensus        28 ~~~l~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~-g~~-~~~~~~~~   74 (149)
T 2kjq_A           28 VYVLRHKHGQFIYVWGEEGAGKSHLLQAWVAQALEA-GKN-AAYIDAAS   74 (149)
T ss_dssp             HHHCCCCCCSEEEEESSSTTTTCHHHHHHHHHHHTT-TCC-EEEEETTT
T ss_pred             HHHHHhcCCCEEEEECCCCCCHHHHHHHHHHHHHhc-CCc-EEEEcHHH
Confidence            334433355689999999999999999999987542 222 55665543

>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=97.27  E-value=0.0021  Score=55.24  Aligned_cols=86  Identities=21%  Similarity=0.227  Sum_probs=51.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCC-----------CCCCC-c-h
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLT-----------LHEES-D-S  240 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~-----------~~~~~-~-~  240 (390)
                      ...++.|+|++|+|||||+..+.. .  .  -..++|++.....+...+.. +...++..           ..... . .
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~-~--~--~~~v~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL-L--S--GKKVAYVDTEGGFSPERLVQ-MAETRGLNPEEALSRFILFTPSDFKEQR   92 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH-H--H--CSEEEEEESSCCCCHHHHHH-HHHTTTCCHHHHHHHEEEECCTTTSHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH-H--c--CCcEEEEECCCCCCHHHHHH-HHHhcCCChHHHhhcEEEEecCCHHHHH
Confidence            456899999999999999999988 2  1  24578888776556555443 33333221           11111 1 1


Q ss_pred             HHHHHHHHHHhCCCeEEEEEeCCCCC
Q 042806          241 GRARSLRNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       241 ~~~~~l~~~l~~~~~~LlVlDdv~~~  266 (390)
                      ..+..+...+.. ++-+||+|.+...
T Consensus        93 ~~~~~~~~l~~~-~~~lliiD~~~~~  117 (220)
T 2cvh_A           93 RVIGSLKKTVDS-NFALVVVDSITAH  117 (220)
T ss_dssp             HHHHHHHHHCCT-TEEEEEEECCCCC
T ss_pred             HHHHHHHHHhhc-CCCEEEEcCcHHH
Confidence            123333333333 4679999998654

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=97.21  E-value=0.00048  Score=63.11  Aligned_cols=53  Identities=25%  Similarity=0.323  Sum_probs=35.3

Q ss_pred             hhHHHHHHHHHhcCC---CccEEEEEcCCCCcHHHHHHHHHHHhh-hcCCCCeEEEEEe
Q 042806          159 RMSTLNDILDALKNP---DVNMLGIYGMGGIVKTTLAKEVARKAE-TEKLFDQVIFVEV  213 (390)
Q Consensus       159 R~~~~~~l~~~L~~~---~~~vi~I~G~~GvGKTtLa~~v~~~~~-~~~~f~~~~wv~v  213 (390)
                      +...+..+.+++...   ....+.|+|++|+|||+||..+++... .. .+. +.++.+
T Consensus       133 ~~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~-g~~-v~~~~~  189 (308)
T 2qgz_A          133 RMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKK-GVS-TTLLHF  189 (308)
T ss_dssp             HHHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHS-CCC-EEEEEH
T ss_pred             HHHHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHHHHhc-CCc-EEEEEH
Confidence            444444555555431   246788999999999999999999876 43 233 445443

>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=97.18  E-value=0.0015  Score=60.82  Aligned_cols=85  Identities=18%  Similarity=0.237  Sum_probs=54.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC------CCchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE------ESDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~------~~~~~~~~~l~  247 (390)
                      ...++.|+|++|+|||||+.++.......  =..++|++....++..     .++.++...+.      .+.......+.
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~~--g~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i~~~~~~e~~l~~~~  132 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQAA--GGIAAFIDAEHALDPE-----YAKKLGVDTDSLLVSQPDTGEQALEIAD  132 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCCCcCHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHH
Confidence            45789999999999999999998776432  2357888887766543     25556644321      12222233333


Q ss_pred             HHHhCCCeEEEEEeCCCC
Q 042806          248 NRLKKEKTILVILDNIWG  265 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~  265 (390)
                      ......++-+||+|.+..
T Consensus       133 ~l~~~~~~~lIVIDsl~~  150 (349)
T 2zr9_A          133 MLVRSGALDIIVIDSVAA  150 (349)
T ss_dssp             HHHTTTCCSEEEEECGGG
T ss_pred             HHHhcCCCCEEEEcChHh
Confidence            333444556999999854

>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=97.18  E-value=0.0013  Score=60.62  Aligned_cols=90  Identities=12%  Similarity=0.205  Sum_probs=58.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc------------CCC--CeEEEEEeCCCCCHHHHHHHHHHHhCCCCC----
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE------------KLF--DQVIFVEVSKIQDIRKIQGEIADKLGLTLH----  235 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~------------~~f--~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~----  235 (390)
                      ...++.|+|++|+|||+|+.+++......            +..  ..++|++....++.+++.. ++..++.+..    
T Consensus        97 ~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~-~~~~~g~~~~~~~~  175 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQ-MAEHAGIDGQTVLD  175 (322)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHH-HHHHHTCCHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHH-HHHHcCCCHHHHhc
Confidence            45789999999999999999998763211            111  4688988888777776654 3455654321    


Q ss_pred             -----C-CCch---HHHHHHHHHHhC-CCeEEEEEeCCC
Q 042806          236 -----E-ESDS---GRARSLRNRLKK-EKTILVILDNIW  264 (390)
Q Consensus       236 -----~-~~~~---~~~~~l~~~l~~-~~~~LlVlDdv~  264 (390)
                           . .+..   .....+...+.. .+.-+||+|.+.
T Consensus       176 ~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~  214 (322)
T 2i1q_A          176 NTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLT  214 (322)
T ss_dssp             TEEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSS
T ss_pred             CEEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECcH
Confidence                 0 1111   233445556655 555799999985

>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=97.18  E-value=0.0011  Score=61.11  Aligned_cols=91  Identities=16%  Similarity=0.282  Sum_probs=59.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcC---C-CCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC----------CCCc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEK---L-FDQVIFVEVSKIQDIRKIQGEIADKLGLTLH----------EESD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~---~-f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~----------~~~~  239 (390)
                      ...++.|+|++|+|||||+.+++.......   . -..++|++....++...+.. ++..++....          ..+.
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~-~~~~~g~~~~~~~~~l~~~~~~~~  184 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIEN-MAKALGLDIDNVMNNIYYIRAINT  184 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHH-HHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHhCCCHHHHhccEEEEeCCCH
Confidence            456899999999999999999987743210   0 23688998888777766553 4556655321          0111


Q ss_pred             h---HHHHHHHHHHhC-CCeEEEEEeCCCC
Q 042806          240 S---GRARSLRNRLKK-EKTILVILDNIWG  265 (390)
Q Consensus       240 ~---~~~~~l~~~l~~-~~~~LlVlDdv~~  265 (390)
                      .   ..+..+...+.. .+.-+||+|.+..
T Consensus       185 ~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~  214 (324)
T 2z43_A          185 DHQIAIVDDLQELVSKDPSIKLIVVDSVTS  214 (324)
T ss_dssp             HHHHHHHHHHHHHHHHCTTEEEEEETTTTH
T ss_pred             HHHHHHHHHHHHHHHhccCCCEEEEeCcHH
Confidence            1   234455555655 5667999999853

>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=97.13  E-value=0.0022  Score=60.04  Aligned_cols=85  Identities=20%  Similarity=0.238  Sum_probs=54.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC------CCchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE------ESDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~------~~~~~~~~~l~  247 (390)
                      ...++.|+|++|+||||||.++.......  -..++|++....++..     .+..++.+.+.      .+.......+.
T Consensus        73 ~G~li~I~G~pGsGKTtlal~la~~~~~~--g~~vlyi~~E~s~~~~-----~a~~~g~d~~~l~i~~~~~~e~~l~~l~  145 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALAIVAQAQKA--GGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIME  145 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHHHHC--CCeEEEEECCCChhHH-----HHHHcCCCHHHceeecCCcHHHHHHHHH
Confidence            45689999999999999999998876433  2358899888766543     24555553221      12223333444


Q ss_pred             HHHhCCCeEEEEEeCCCC
Q 042806          248 NRLKKEKTILVILDNIWG  265 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~  265 (390)
                      ..+.....-+||+|.+..
T Consensus       146 ~l~~~~~~~lVVIDsl~~  163 (366)
T 1xp8_A          146 LLVRSGAIDVVVVDSVAA  163 (366)
T ss_dssp             HHHTTTCCSEEEEECTTT
T ss_pred             HHHhcCCCCEEEEeChHH
Confidence            444444446999999854

>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=97.08  E-value=0.0034  Score=56.99  Aligned_cols=58  Identities=19%  Similarity=0.169  Sum_probs=36.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-IQDIRKIQGEIADKLGL  232 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~l~~~i~~~l~~  232 (390)
                      ...+++|+|++|+||||++..+.......... .+.++.... .....+-+.......+.
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~-~V~lv~~D~~r~~a~eqL~~~~~~~gl  162 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISMLEKHK-KIAFITTDTYRIAAVEQLKTYAELLQA  162 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHHTTCC-CEEEEECCCSSTTHHHHHHHHHTTTTC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCC-EEEEEecCcccchHHHHHHHHHHhcCC
Confidence            45799999999999999999999877642222 244454433 22333334444443443

>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=97.02  E-value=0.0019  Score=61.22  Aligned_cols=91  Identities=11%  Similarity=0.171  Sum_probs=56.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc---C-CCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC----------CCCc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE---K-LFDQVIFVEVSKIQDIRKIQGEIADKLGLTLH----------EESD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~---~-~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~----------~~~~  239 (390)
                      ...++.|+|++|+|||||+.+++-.....   + .-..++|++....++...+ ..+++.++....          ..+.
T Consensus       177 ~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl-~~~a~~~gl~~~~vleni~~~~~~~~  255 (400)
T 3lda_A          177 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRL-VSIAQRFGLDPDDALNNVAYARAYNA  255 (400)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHH-HHHHHHcCCChHhHhhcEEEeccCCh
Confidence            45789999999999999999886443221   1 2345888887766655443 446666665321          0011


Q ss_pred             ---hHHHHHHHHHHhCCCeEEEEEeCCCC
Q 042806          240 ---SGRARSLRNRLKKEKTILVILDNIWG  265 (390)
Q Consensus       240 ---~~~~~~l~~~l~~~~~~LlVlDdv~~  265 (390)
                         ......+...+...++-+||+|.+..
T Consensus       256 ~~~~~~l~~~~~~l~~~~~~llVIDs~t~  284 (400)
T 3lda_A          256 DHQLRLLDAAAQMMSESRFSLIVVDSVMA  284 (400)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETGGG
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEecchhh
Confidence               12233444455555668999999753

>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=96.98  E-value=0.0026  Score=59.31  Aligned_cols=85  Identities=20%  Similarity=0.248  Sum_probs=53.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC------CchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE------SDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~------~~~~~~~~l~  247 (390)
                      ..+++.|+|++|+||||||.+++......+  ..++|++....++..     .+..++...+..      +.......+.
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~~g--~~vlyid~E~s~~~~-----~a~~~g~~~~~l~i~~~~~~e~~~~~~~  134 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD  134 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCC--CeEEEEeCCCCccHH-----HHHHcCCChhheeeeCCCCHHHHHHHHH
Confidence            457899999999999999999988765432  358888887766643     245555433211      1122222232


Q ss_pred             HHHhCCCeEEEEEeCCCC
Q 042806          248 NRLKKEKTILVILDNIWG  265 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~  265 (390)
                      ......+.-+||+|.+..
T Consensus       135 ~l~~~~~~~lVVIDsl~~  152 (356)
T 1u94_A          135 ALARSGAVDVIVVDSVAA  152 (356)
T ss_dssp             HHHHHTCCSEEEEECGGG
T ss_pred             HHHhccCCCEEEEcCHHH
Confidence            233334445999999853

>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=96.80  E-value=0.0054  Score=52.95  Aligned_cols=91  Identities=21%  Similarity=0.250  Sum_probs=53.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc---C-CCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC----------CCCc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE---K-LFDQVIFVEVSKIQDIRKIQGEIADKLGLTLH----------EESD  239 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~---~-~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~----------~~~~  239 (390)
                      ...+++|+|++|+|||||++.++......   . .-...+|+.-........ +..+.+.++....          ....
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~~~-i~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER-IREIAQNRGLDPDEVLKHIYVARAFNS  102 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHH-HHHHHHHTTSCHHHHHHTEEEEECCSH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCHHH-HHHHHHHcCCCHHHHhhcEEEEecCCh
Confidence            35689999999999999999998743221   1 133577777655444333 3344444443211          0011


Q ss_pred             ---hHHHHHHHHHHh-----CCCeEEEEEeCCCC
Q 042806          240 ---SGRARSLRNRLK-----KEKTILVILDNIWG  265 (390)
Q Consensus       240 ---~~~~~~l~~~l~-----~~~~~LlVlDdv~~  265 (390)
                         ......+...+.     ..++-++|+|....
T Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~llilDe~~~  136 (231)
T 4a74_A          103 NHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTS  136 (231)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSSSCEEEEEEETSSH
T ss_pred             HHHHHHHHHHHHHHHHhcccCCceeEEEECChHH
Confidence               112334444444     55668999999854

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

Probab=96.74  E-value=0.0016  Score=66.92  Aligned_cols=172  Identities=12%  Similarity=0.176  Sum_probs=80.2

Q ss_pred             cccccchhHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALKN-------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ...+.|-+...++|.+.+.-             ...+-+.++|++|.|||.||+.+++....       .++.++.    
T Consensus       476 w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~-------~f~~v~~----  544 (806)
T 3cf2_A          476 WEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQA-------NFISIKG----  544 (806)
T ss_dssp             STTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTC-------EEEECCH----
T ss_pred             HHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCC-------ceEEecc----
Confidence            34556666666666554431             12455789999999999999999998753       2333322    


Q ss_pred             HHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--------c--------cccccCCCC--CCCC
Q 042806          220 RKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--------D--------FQAVGIPHG--DDRK  281 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--------~--------~~~l~~~l~--~~~~  281 (390)
                      .+++    .    .+-. .....+..+.+..+...+++|+||+++...        .        ...+...+.  ....
T Consensus       545 ~~l~----s----~~vG-ese~~vr~lF~~Ar~~~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~~  615 (806)
T 3cf2_A          545 PELL----T----MWFG-ESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKK  615 (806)
T ss_dssp             HHHH----T----TTCS-SCHHHHHHHHHHHHTTCSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCSSS
T ss_pred             chhh----c----cccc-hHHHHHHHHHHHHHHcCCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCCC
Confidence            2221    1    1111 223455666666666667999999986431        0        111111111  1223


Q ss_pred             CcEEEEEecchhhh-hhc-C--CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCC
Q 042806          282 GCKVLLTARSLDVL-SRK-M--DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGL  346 (390)
Q Consensus       282 ~s~IivTtr~~~v~-~~~-~--~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~Gl  346 (390)
                      +.-||.||...... ... .  .....+.+..-+.++-.++|+.++.......+.+  ...+++.+.|+
T Consensus       616 ~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~~~~d--l~~la~~t~g~  682 (806)
T 3cf2_A          616 NVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVD--LEFLAKMTNGF  682 (806)
T ss_dssp             SEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--CCC---------------
T ss_pred             CEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCCCCCC--HHHHHHhCCCC
Confidence            33444455433221 111 1  2345778877777777778876664222222111  23455666554

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.71  E-value=0.0017  Score=55.31  Aligned_cols=43  Identities=21%  Similarity=0.257  Sum_probs=33.6

Q ss_pred             hhHHHHHHHHHhcC---CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          159 RMSTLNDILDALKN---PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       159 R~~~~~~l~~~L~~---~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      |.+.++.|.+.+..   ....+|+|.|+.|+|||||++.+......
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~~~   48 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTLRE   48 (201)
T ss_dssp             HHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            55566777776654   34679999999999999999999887643

>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=96.68  E-value=0.0061  Score=58.54  Aligned_cols=88  Identities=19%  Similarity=0.313  Sum_probs=53.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCC-------CCCCCCc-hHH----
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGL-------TLHEESD-SGR----  242 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~-------~~~~~~~-~~~----  242 (390)
                      ..++|+|++|+|||||++.+........ -+..+++.++... ...+++.++...-..       .....+. ...    
T Consensus       152 q~~~i~G~sGvGKTtL~~~l~~~~~~~~-~~i~V~~~iGerttev~el~~~l~~~~~l~~tvvv~~~~~d~pg~r~~~~~  230 (473)
T 1sky_E          152 GKIGLFGGAGVGKTVLIQELIHNIAQEH-GGISVFAGVGERTREGNDLYHEMKDSGVISKTAMVFGQMNEPPGARMRVAL  230 (473)
T ss_dssp             CEEEEECCSSSCHHHHHHHHHHHHHHHT-CCCEEEEEESSCHHHHHHHHHHHHHTSGGGGEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEECCCCCCccHHHHHHHhhhhhcc-CcEEEEeeeccCchHHHHHHHHhhhcCCcceeEEEEEcCCCCHHHHHHHHH
Confidence            3588999999999999999988765432 2445677776543 445555555432110       0111111 111    


Q ss_pred             -HHHHHHHHh--CCCeEEEEEeCCC
Q 042806          243 -ARSLRNRLK--KEKTILVILDNIW  264 (390)
Q Consensus       243 -~~~l~~~l~--~~~~~LlVlDdv~  264 (390)
                       .-.+.+++.  .++..|+++||+.
T Consensus       231 ~~ltiAEyFrd~~G~~VLl~~D~it  255 (473)
T 1sky_E          231 TGLTMAEYFRDEQGQDGLLFIDNIF  255 (473)
T ss_dssp             HHHHHHHHHHHHSCCEEEEEEECTH
T ss_pred             HHHHHHHHHHHhcCCcEEEEeccHH
Confidence             224555554  3677999999994

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.68  E-value=0.013  Score=53.65  Aligned_cols=52  Identities=15%  Similarity=0.098  Sum_probs=37.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      ...++.|.|.+|+|||||+.+++.....++  ..++|++..  -+..++...+...
T Consensus        67 ~G~l~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~slE--~s~~~l~~R~~~~  118 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLE--MGKKENIKRLIVT  118 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEESS--SCHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEECC--CCHHHHHHHHHHH
Confidence            356899999999999999999987765432  467777654  4566666666543

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

Probab=96.61  E-value=0.0028  Score=58.39  Aligned_cols=150  Identities=11%  Similarity=0.136  Sum_probs=82.0

Q ss_pred             cccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCC
Q 042806          155 ACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTL  234 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~  234 (390)
                      .++|++..+..+...+..+  .-+.++|++|+|||+||+.+.+.....     ...+.++......++.....    ...
T Consensus        28 ~i~g~~~~~~~l~~~l~~~--~~vll~G~pGtGKT~la~~la~~~~~~-----~~~i~~~~~~~~~~l~g~~~----~~~   96 (331)
T 2r44_A           28 VVVGQKYMINRLLIGICTG--GHILLEGVPGLAKTLSVNTLAKTMDLD-----FHRIQFTPDLLPSDLIGTMI----YNQ   96 (331)
T ss_dssp             TCCSCHHHHHHHHHHHHHT--CCEEEESCCCHHHHHHHHHHHHHTTCC-----EEEEECCTTCCHHHHHEEEE----EET
T ss_pred             ceeCcHHHHHHHHHHHHcC--CeEEEECCCCCcHHHHHHHHHHHhCCC-----eEEEecCCCCChhhcCCcee----ecC
Confidence            5788888888888777653  357799999999999999998876421     23344444444444321110    000


Q ss_pred             CCCCchHHHHHHHHHHhCC--CeEEEEEeCCCCCc--ccccccCCC-------C----CCCCCcEEEEEecchh------
Q 042806          235 HEESDSGRARSLRNRLKKE--KTILVILDNIWGNL--DFQAVGIPH-------G----DDRKGCKVLLTARSLD------  293 (390)
Q Consensus       235 ~~~~~~~~~~~l~~~l~~~--~~~LlVlDdv~~~~--~~~~l~~~l-------~----~~~~~s~IivTtr~~~------  293 (390)
                       .....        .+..+  ...++++|+++...  ....+...+       .    .......|+.|+....      
T Consensus        97 -~~~~~--------~~~~g~l~~~vl~iDEi~~~~~~~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~~~~~~~~  167 (331)
T 2r44_A           97 -HKGNF--------EVKKGPVFSNFILADEVNRSPAKVQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPVEQEGTYP  167 (331)
T ss_dssp             -TTTEE--------EEEECTTCSSEEEEETGGGSCHHHHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTTCCSCCCC
T ss_pred             -CCCce--------EeccCcccccEEEEEccccCCHHHHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCCcccCccc
Confidence             00000        00001  01489999986441  111111100       0    0123455666665322      


Q ss_pred             hhhhcC-CCcceEecCCCCHHHHHHHHHHhhC
Q 042806          294 VLSRKM-DSQQNFSVGVLKEDEAWSLFKKMAG  324 (390)
Q Consensus       294 v~~~~~-~~~~~~~l~~L~~~ea~~lf~~~~~  324 (390)
                      +..... .....+.+.+.+.++-.+++.+...
T Consensus       168 l~~~l~~Rf~~~i~i~~p~~~~~~~il~~~~~  199 (331)
T 2r44_A          168 LPEAQVDRFMMKIHLTYLDKESELEVMRRVSN  199 (331)
T ss_dssp             CCHHHHTTSSEEEECCCCCHHHHHHHHHHHHC
T ss_pred             CCHHHHhheeEEEEcCCCCHHHHHHHHHhccc
Confidence            111111 1223688999999999999988775

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.60  E-value=0.0025  Score=54.62  Aligned_cols=41  Identities=22%  Similarity=0.371  Sum_probs=31.6

Q ss_pred             HHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          161 STLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       161 ~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .-+++|.+.+..  +...+++|.|+.|+|||||++.+......
T Consensus         6 ~~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~~~~~   48 (208)
T 3c8u_A            6 ALCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAAALSA   48 (208)
T ss_dssp             HHHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            345566666653  45679999999999999999999887653

>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=96.57  E-value=0.0051  Score=57.23  Aligned_cols=92  Identities=21%  Similarity=0.273  Sum_probs=54.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc---CCCC-eEEEEEeCCCCCHHHHHHHHHHHhCCCCC----------CCC-
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE---KLFD-QVIFVEVSKIQDIRKIQGEIADKLGLTLH----------EES-  238 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~---~~f~-~~~wv~v~~~~~~~~l~~~i~~~l~~~~~----------~~~-  238 (390)
                      ...++.|+|++|+|||||+++++......   +... .++|++....+....+ ..+++.++....          ... 
T Consensus       130 ~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i-~~i~q~~~~~~~~v~~ni~~~~~~~~  208 (349)
T 1pzn_A          130 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI-REIAQNRGLDPDEVLKHIYVARAFNS  208 (349)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH-HHHHHTTTCCHHHHGGGEEEEECCSH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHH-HHHHHHcCCCHHHHhhCEEEEecCCh
Confidence            46799999999999999999998875211   1112 3588887665444433 334544433211          001 


Q ss_pred             --chHHHHHHHHHHhC-----CCeEEEEEeCCCCC
Q 042806          239 --DSGRARSLRNRLKK-----EKTILVILDNIWGN  266 (390)
Q Consensus       239 --~~~~~~~l~~~l~~-----~~~~LlVlDdv~~~  266 (390)
                        ....+..+...+..     .++-+||+|.+...
T Consensus       209 ~~~~~~l~~~~~~~~~lS~G~~~~~llIlDs~ta~  243 (349)
T 1pzn_A          209 NHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSH  243 (349)
T ss_dssp             HHHHHHHHHHHHHHHHSSSSSSCEEEEEEETSSTT
T ss_pred             HHHHHHHHHHHHHHHHhccccCCCCEEEEeCchHh
Confidence              11123334444443     46689999998654

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=96.55  E-value=0.0038  Score=58.26  Aligned_cols=99  Identities=16%  Similarity=0.160  Sum_probs=53.2

Q ss_pred             HHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcC-CCCeEEEEEeCCCC-CHHHHHHHHHHHhCCCCCCCCchH
Q 042806          165 DILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETEK-LFDQVIFVEVSKIQ-DIRKIQGEIADKLGLTLHEESDSG  241 (390)
Q Consensus       165 ~l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~-~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~~~~~~~~~  241 (390)
                      +.++.+.. .....++|+|++|+|||||++.+.+...... .+. ++++.++... ...++.+.+-..+-....+.+...
T Consensus       163 raID~~~pi~rGQr~~IvG~sG~GKTtLl~~Iar~i~~~~~~v~-~I~~lIGER~~Ev~~~~~~~~~~vV~atadep~~~  241 (422)
T 3ice_A          163 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCV-LMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASR  241 (422)
T ss_dssp             HHHHHHSCCBTTCEEEEECCSSSSHHHHHHHHHHHHHHHCTTSE-EEEEEESSCHHHHHHHHTTCSSEEEEECTTSCHHH
T ss_pred             eeeeeeeeecCCcEEEEecCCCCChhHHHHHHHHHHhhcCCCee-EEEEEecCChHHHHHHHHHhCeEEEEeCCCCCHHH
Confidence            34454443 3456899999999999999999887654321 233 4467777543 223332222000000111111111


Q ss_pred             ------HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          242 ------RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       242 ------~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                            ..-.+.+++. .++.+||++||+.
T Consensus       242 r~~~a~~alt~AEyfrd~G~dVLil~DslT  271 (422)
T 3ice_A          242 HVQVAEMVIEKAKRLVEHKKDVIILLDSIT  271 (422)
T ss_dssp             HHHHHHHHHHHHHHHHHTSCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEEEEEeCch
Confidence                  1112334443 4677999999984

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=96.52  E-value=0.009  Score=57.50  Aligned_cols=98  Identities=18%  Similarity=0.277  Sum_probs=63.1

Q ss_pred             HHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCC-------C--
Q 042806          166 ILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLT-------L--  234 (390)
Q Consensus       166 l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~-------~--  234 (390)
                      .++.|.. .+-.-++|+|.+|+|||+|+..+.+.... .+-+.++|+.++... ...+++.++...-...       .  
T Consensus       155 vID~l~pigkGqr~gIfgg~GvGKT~L~~~l~~~~a~-~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~l~~~rtv  233 (498)
T 1fx0_B          155 VVNLLAPYRRGGKIGLFGGAGVGKTVLIMELINNIAK-AHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVA  233 (498)
T ss_dssp             THHHHSCCCTTCCEEEEECSSSSHHHHHHHHHHHTTT-TCSSCEEEEEESCCSHHHHHHHHHHHHTTSSCSSTTCCCCEE
T ss_pred             EeeeecccccCCeEEeecCCCCCchHHHHHHHHHHHh-hCCCEEEEEEcccCcHHHHHHHHhhhcccccccccccccceE
Confidence            3444432 23456889999999999999999887532 235678888888655 4567777766542221       0  


Q ss_pred             -----CCCCc------hHHHHHHHHHHhC--CCeEEEEEeCCC
Q 042806          235 -----HEESD------SGRARSLRNRLKK--EKTILVILDNIW  264 (390)
Q Consensus       235 -----~~~~~------~~~~~~l~~~l~~--~~~~LlVlDdv~  264 (390)
                           .+.+.      ....-.+.+++.+  ++.+||++||+.
T Consensus       234 vV~~t~d~p~~~R~~~~~~altiAEyfrd~~G~dVLl~~Dsit  276 (498)
T 1fx0_B          234 LVYGQMNEPPGARMRVGLTALTMAEYFRDVNEQDVLLFIDNIF  276 (498)
T ss_dssp             EEEECTTSCHHHHTTHHHHHHHTHHHHTTTSCCEEEEEEECSH
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHH
Confidence                 01111      1123456677766  677999999984

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=96.48  E-value=0.0015  Score=60.55  Aligned_cols=48  Identities=17%  Similarity=0.203  Sum_probs=35.1

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...++|.+..+..+...+..+...-+.|+|++|+|||+||+.+.+...
T Consensus        23 f~~i~G~~~~~~~l~~~~~~~~~~~vLl~G~~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           23 FSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALLP   70 (350)
T ss_dssp             GGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHSC
T ss_pred             chhccChHHHHHHHHHHhhCCCCceEEEECCCCccHHHHHHHHHHhCc
Confidence            456888877655554444333334488999999999999999998764

>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=96.48  E-value=0.019  Score=54.84  Aligned_cols=28  Identities=29%  Similarity=0.316  Sum_probs=24.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+.+|.++|++|+||||++..++.....
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l~~  126 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYFQK  126 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHHHH
Confidence            4689999999999999999999887764

>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=96.47  E-value=0.0017  Score=53.89  Aligned_cols=25  Identities=12%  Similarity=0.113  Sum_probs=22.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+|.|.|++|+||||+++.+.....
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l~   28 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcC
Confidence            5789999999999999999988764

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=96.46  E-value=0.024  Score=54.40  Aligned_cols=99  Identities=17%  Similarity=0.288  Sum_probs=62.7

Q ss_pred             HHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCC---------
Q 042806          165 DILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLT---------  233 (390)
Q Consensus       165 ~l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~---------  233 (390)
                      +.++.|.. .+-.-++|+|.+|+|||+|+..+.+.... .+-+.++++.++... ...+++.++...-...         
T Consensus       142 r~ID~l~pigkGQr~~Ifgg~G~GKT~L~~~i~~~~~~-~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~~~~rtv  220 (482)
T 2ck3_D          142 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAK-AHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVA  220 (482)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHTTT-TCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEE
T ss_pred             EEEecccccccCCeeeeecCCCCChHHHHHHHHHhhHh-hCCCEEEEEECCCcchHHHHHHHHhhhccccccccCCceEE
Confidence            34455543 24456889999999999999999887532 234667888887654 4566777776553222         


Q ss_pred             ----CCCCCch------HHHHHHHHHHhC--CCeEEEEEeCCC
Q 042806          234 ----LHEESDS------GRARSLRNRLKK--EKTILVILDNIW  264 (390)
Q Consensus       234 ----~~~~~~~------~~~~~l~~~l~~--~~~~LlVlDdv~  264 (390)
                          ..+.+..      ...-.+.+++.+  ++.+||++||+.
T Consensus       221 vV~~t~d~p~~~r~~~~~~a~tiAEyfrd~~G~dVLll~Dsit  263 (482)
T 2ck3_D          221 LVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIF  263 (482)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTH
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHH
Confidence                0111111      123355566654  677999999984

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.45  E-value=0.013  Score=51.12  Aligned_cols=49  Identities=14%  Similarity=0.192  Sum_probs=33.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      ...++.|.|++|+|||||+.+++......  =..++|++...  +..++...+
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~~~--~~~v~~~~~e~--~~~~~~~~~   70 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGLKM--GEPGIYVALEE--HPVQVRQNM   70 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHHHT--TCCEEEEESSS--CHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEEccC--CHHHHHHHH
Confidence            35689999999999999999887765432  23467766543  345554443

>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=96.43  E-value=0.0082  Score=51.34  Aligned_cols=75  Identities=23%  Similarity=0.131  Sum_probs=44.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh----------CCCCCCCCchHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL----------GLTLHEESDSGRARSL  246 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l----------~~~~~~~~~~~~~~~l  246 (390)
                      +|.|.|++|+||+|.|+.+.....    |.   .+      +..+++++.+..-          -......++.-....+
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~g----~~---~i------stGdllR~~i~~~t~lg~~~~~~~~~G~lvpd~iv~~lv   68 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEKG----FV---HI------STGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALI   68 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC----CE---EE------EHHHHHHHHHHHTCHHHHHHHHHHHHTCCCCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC----Ce---EE------cHHHHHHHHHHhcChhhhhHHHHHhcCCcCCHHHHHHHH
Confidence            578999999999999999998764    21   22      2345554432221          1111222344445566


Q ss_pred             HHHHhCCCeEEEEEeCCCCC
Q 042806          247 RNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       247 ~~~l~~~~~~LlVlDdv~~~  266 (390)
                      .+.+.... . +|||++-..
T Consensus        69 ~~~l~~~~-~-~ilDGfPRt   86 (206)
T 3sr0_A           69 EEVFPKHG-N-VIFDGFPRT   86 (206)
T ss_dssp             HHHCCSSS-C-EEEESCCCS
T ss_pred             HHhhccCC-c-eEecCCchh
Confidence            66776555 2 688998544

>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=96.42  E-value=0.0019  Score=53.07  Aligned_cols=25  Identities=16%  Similarity=0.295  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+|+|.|++|+||||+++.+.....
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~l~   26 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKELK   26 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4789999999999999999988764

>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=96.40  E-value=0.0019  Score=53.10  Aligned_cols=20  Identities=35%  Similarity=0.416  Sum_probs=18.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEV  195 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v  195 (390)
                      .+|+|.|++|+||||+++.+
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            47899999999999999999

>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=96.35  E-value=0.0015  Score=56.65  Aligned_cols=110  Identities=14%  Similarity=0.006  Sum_probs=59.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CchHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE---SDSGRARSLRNRL  250 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~l~~~l  250 (390)
                      ...++.++|+.|+||||++..+.+.....+ .. ++.+.....  .. ....+++.++...+..   ........+.+.+
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~~g-~k-Vli~~~~~d--~r-~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~   85 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEYAD-VK-YLVFKPKID--TR-SIRNIQSRTGTSLPSVEVESAPEILNYIMSNS   85 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHHTT-CC-EEEEEECCC--GG-GCSSCCCCCCCSSCCEEESSTHHHHHHHHSTT
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHhcC-CE-EEEEEeccC--ch-HHHHHHHhcCCCccccccCCHHHHHHHHHHHh
Confidence            356889999999999999999988876532 33 333333221  11 2223445555433221   1112222233223


Q ss_pred             hCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecc
Q 042806          251 KKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARS  291 (390)
Q Consensus       251 ~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~  291 (390)
                      ..++.-+||+|.++..  +.++.+.. +.  +.+..||+|.+.
T Consensus        86 ~~~~~dvViIDEaQ~l~~~~ve~l~~-L~--~~gi~Vil~Gl~  125 (223)
T 2b8t_A           86 FNDETKVIGIDEVQFFDDRICEVANI-LA--ENGFVVIISGLD  125 (223)
T ss_dssp             SCTTCCEEEECSGGGSCTHHHHHHHH-HH--HTTCEEEEECCS
T ss_pred             hCCCCCEEEEecCccCcHHHHHHHHH-HH--hCCCeEEEEecc
Confidence            3344359999999753  22222221 11  126789999983

>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=96.35  E-value=0.016  Score=55.22  Aligned_cols=29  Identities=24%  Similarity=0.132  Sum_probs=25.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      .+.+|.++|++|+||||++..++......
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l~~~  124 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFYKKR  124 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            36799999999999999999999877543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=96.32  E-value=0.0085  Score=67.07  Aligned_cols=84  Identities=20%  Similarity=0.265  Sum_probs=56.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC------CCchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE------ESDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~------~~~~~~~~~l~  247 (390)
                      ..+.+.|+|++|+|||+||.++.......+  ..++|+++...++...     ++.++.+.+.      .+.......+.
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~~G--~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~~ 1498 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICD 1498 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTTT--CCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcC--CcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHHHHHHHHH
Confidence            567899999999999999999988765431  2477888777666544     4555533211      12233444555


Q ss_pred             HHHhCCCeEEEEEeCCC
Q 042806          248 NRLKKEKTILVILDNIW  264 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~  264 (390)
                      ...+..++.+||+|.+.
T Consensus      1499 ~lvr~~~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1499 ALARSGAVDVIVVDSVA 1515 (2050)
T ss_dssp             HHHHHTCCSEEEESCGG
T ss_pred             HHHhcCCCCEEEEcChh
Confidence            55555666899999984

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.29  E-value=0.0023  Score=53.42  Aligned_cols=25  Identities=16%  Similarity=0.283  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .++++|+|++|+|||||++.+....
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLITKH   29 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3689999999999999999998765

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.29  E-value=0.0024  Score=52.93  Aligned_cols=22  Identities=27%  Similarity=0.303  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      .+|.|.|++|+||||+++.+..
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            4789999999999999999987

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=96.27  E-value=0.014  Score=49.55  Aligned_cols=84  Identities=19%  Similarity=0.135  Sum_probs=47.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC------CchHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE------SDSGRARSLRNRL  250 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~------~~~~~~~~l~~~l  250 (390)
                      .|+|-|.-|+||||.++.+.+.+...+ +. +++..-.......+..+.++..-.......      ........+...|
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~L~~~g-~~-v~~treP~~t~~~~~ir~~l~~~~~~~~~~~ll~~a~r~~~~~~I~~~L   79 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQYLEKRG-KK-VILKREPGGTETGEKIRKILLEEEVTPKAELFLFLASRNLLVTEIKQYL   79 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTT-CC-EEEEESSCSSHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCC-Cc-EEEEECCCCCcHHHHHHHHhhcccCChHHHHHHHHHHHHHHHHHHHHHH
Confidence            578899999999999999999987643 33 344444444444555555543322110000      1111233455556


Q ss_pred             hCCCeEEEEEeCCC
Q 042806          251 KKEKTILVILDNIW  264 (390)
Q Consensus       251 ~~~~~~LlVlDdv~  264 (390)
                      ..++  .+|.|-..
T Consensus        80 ~~g~--~Vi~DRy~   91 (197)
T 3hjn_A           80 SEGY--AVLLDRYT   91 (197)
T ss_dssp             TTTC--EEEEESCH
T ss_pred             HCCC--eEEecccc
Confidence            5554  67888653

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=96.26  E-value=0.024  Score=54.20  Aligned_cols=29  Identities=17%  Similarity=0.182  Sum_probs=25.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      .+++|.++|.+|+||||++..+......+
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~~~  127 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLREK  127 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            46799999999999999999999887654

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.25  E-value=0.0029  Score=53.73  Aligned_cols=27  Identities=37%  Similarity=0.338  Sum_probs=23.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+|.|+|++|+||||+++.+.....
T Consensus        24 ~~~~i~l~G~~GsGKsTl~~~La~~l~   50 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLGKAFARKLN   50 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            456899999999999999999998763

>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=96.23  E-value=0.0024  Score=53.74  Aligned_cols=25  Identities=28%  Similarity=0.250  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.|+|+||+|+|||||++.+.....
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~   26 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCC
Confidence            5688999999999999999987753

>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=96.23  E-value=0.0027  Score=53.26  Aligned_cols=25  Identities=32%  Similarity=0.332  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...+++|.|++|+|||||++.+...
T Consensus         8 ~g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            8 GGNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhc
Confidence            3568999999999999999999765

>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=96.20  E-value=0.0036  Score=53.15  Aligned_cols=29  Identities=21%  Similarity=0.218  Sum_probs=25.6

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          172 NPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       172 ~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .....+|+|.|++|+|||||++.+.....
T Consensus        22 ~~~g~~i~l~G~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           22 DQKGCVIWVTGLSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             TSCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            34568999999999999999999998875

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.19  E-value=0.0027  Score=52.39  Aligned_cols=25  Identities=20%  Similarity=0.300  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+|+|+|+.|+|||||++.+.....
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~   29 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLN   29 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            4799999999999999999988753

>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=96.18  E-value=0.0032  Score=53.89  Aligned_cols=27  Identities=22%  Similarity=0.283  Sum_probs=23.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+|+|+|+.|+|||||++.+.....
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~~~   33 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKDPE   33 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHSTT
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhCC
Confidence            467899999999999999999987753

>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=96.17  E-value=0.0035  Score=52.61  Aligned_cols=25  Identities=24%  Similarity=0.228  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..+|.|.|++|+||||+++.+....
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHc
Confidence            4689999999999999999998876

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.17  E-value=0.0031  Score=52.84  Aligned_cols=26  Identities=19%  Similarity=0.276  Sum_probs=23.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+|.|.|++|+||||+++.+......
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~l~~   27 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            47899999999999999999998753

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=96.17  E-value=0.0033  Score=52.50  Aligned_cols=26  Identities=19%  Similarity=0.351  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+.|.|+|++|+||||+++.+.....
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l~   30 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLTK   30 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45788999999999999999988763

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.16  E-value=0.0034  Score=53.30  Aligned_cols=27  Identities=30%  Similarity=0.369  Sum_probs=23.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ....+|+|.|+.|+|||||++.+....
T Consensus        27 ~~g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           27 EPTRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            456789999999999999999998765

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=96.14  E-value=0.014  Score=50.99  Aligned_cols=50  Identities=24%  Similarity=0.291  Sum_probs=32.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      ...++.|.|.+|+|||+||.+++.....+. -..++|++..  .+..++...+
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~-~~~v~~~s~E--~~~~~~~~~~   78 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYKGAEEY-GEPGVFVTLE--ERARDLRREM   78 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHHHH-CCCEEEEESS--SCHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhc-CCCceeeccc--CCHHHHHHHH
Confidence            356899999999999999999765532221 2235555544  3556665554

>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=96.13  E-value=0.0034  Score=52.54  Aligned_cols=26  Identities=15%  Similarity=0.221  Sum_probs=23.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+|.|.|++|+||||+++.+......
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~~   29 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLRK   29 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            57999999999999999999987653

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.12  E-value=0.003  Score=53.66  Aligned_cols=25  Identities=16%  Similarity=0.340  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..+|+|.|+.|+||||+++.+....
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999998876

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=96.11  E-value=0.12  Score=47.53  Aligned_cols=51  Identities=12%  Similarity=0.012  Sum_probs=36.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      ...++.|.|.+|+|||||+.+++......  =..++|++.  .-+..++...++.
T Consensus        45 ~G~LiiIaG~pG~GKTt~al~ia~~~a~~--g~~Vl~fSl--Ems~~ql~~Rlls   95 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLMMNMVLSALND--DRGVAVFSL--EMSAEQLALRALS   95 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHT--TCEEEEEES--SSCHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHc--CCeEEEEeC--CCCHHHHHHHHHH
Confidence            34688999999999999999998886542  134566554  4466677666644

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=96.10  E-value=0.0052  Score=53.04  Aligned_cols=37  Identities=19%  Similarity=0.177  Sum_probs=28.3

Q ss_pred             HHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          164 NDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       164 ~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.+...+.......|+|+|.+|+|||||+..+.....
T Consensus        27 ~~~r~~~~~~~~~~i~ivG~~gvGKTtl~~~l~~~~~   63 (226)
T 2hf9_A           27 DKNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDNLK   63 (226)
T ss_dssp             HHHHHHHHHTTCEEEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCCeEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            3344444445678899999999999999999998764

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.06  E-value=0.0033  Score=53.57  Aligned_cols=26  Identities=31%  Similarity=0.346  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..++|+|.|++|+|||||++.+....
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHHC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            35689999999999999999998876

>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=96.05  E-value=0.0037  Score=51.99  Aligned_cols=26  Identities=38%  Similarity=0.460  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|.|.|++|+||||+++.+.....
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~~   36 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKSG   36 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHhC
Confidence            46788999999999999999987763

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=96.04  E-value=0.0042  Score=52.74  Aligned_cols=25  Identities=24%  Similarity=0.325  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..+++|.|+.|+|||||++.+....
T Consensus         7 g~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            7 ANLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhhC
Confidence            4689999999999999999998764

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=96.02  E-value=0.069  Score=51.97  Aligned_cols=28  Identities=25%  Similarity=0.261  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+++|+|+|.+|+||||++..+......
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l~~  127 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYYQR  127 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            3568999999999999999999987654

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=95.97  E-value=0.0069  Score=54.70  Aligned_cols=26  Identities=19%  Similarity=0.183  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+|.|.|++|+||||+++.+....
T Consensus        32 ~~~livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           32 SPTAFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999998765

>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=95.96  E-value=0.0074  Score=56.41  Aligned_cols=46  Identities=20%  Similarity=0.096  Sum_probs=35.1

Q ss_pred             cccchhHHHHHHHHHhc-------------C--CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          155 ACESRMSTLNDILDALK-------------N--PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~-------------~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|.+..+..+...+.             .  .....+.++|++|+|||++|+.+++...
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~~   76 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLD   76 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHcC
Confidence            35777777777776662             1  1345688999999999999999998873

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=95.94  E-value=0.0051  Score=51.70  Aligned_cols=27  Identities=22%  Similarity=0.251  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+|+|.|++|+||||+++.+.....
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~La~~l~   34 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQCEKIVQKYG   34 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHHC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            356899999999999999999988763

>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=95.93  E-value=0.005  Score=52.19  Aligned_cols=27  Identities=11%  Similarity=0.273  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..++++|+|+.|+|||||++.+.....
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhhCC
Confidence            457899999999999999999987653

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=95.93  E-value=0.0058  Score=51.10  Aligned_cols=28  Identities=25%  Similarity=0.243  Sum_probs=24.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...+|.|.|++|+||||+++.+......
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~l~~   39 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADLLQK   39 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            4578999999999999999999988764

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=95.92  E-value=0.094  Score=48.10  Aligned_cols=29  Identities=21%  Similarity=0.187  Sum_probs=25.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +...+++|+|+.|+||||+++.+......
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~Lag~l~~  155 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLANWLKN  155 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            45679999999999999999999887654

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=95.91  E-value=0.0049  Score=51.69  Aligned_cols=26  Identities=19%  Similarity=0.102  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+|+|.|++|+||||+++.+.....
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~~~   28 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEKYG   28 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45799999999999999999987653

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=95.91  E-value=0.0046  Score=54.75  Aligned_cols=25  Identities=28%  Similarity=0.266  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ++|.|.|++|+||||||+.+.....
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~~~   26 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQETG   26 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCcCHHHHHHHHHhcCC
Confidence            4789999999999999999988753

>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=95.90  E-value=0.037  Score=50.30  Aligned_cols=39  Identities=21%  Similarity=0.217  Sum_probs=29.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS  214 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~  214 (390)
                      ...++.|+|++|+||||++..++......+ . .+.++...
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g-~-kV~lv~~D  141 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKMFVDEG-K-SVVLAAAD  141 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHTT-C-CEEEEEEC
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHHHHhcC-C-EEEEEccc
Confidence            457999999999999999999998876431 2 24445443

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.90  E-value=0.024  Score=51.82  Aligned_cols=27  Identities=19%  Similarity=0.191  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+.+|+|.|+.|+|||||++.+..-..
T Consensus        91 ~p~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           91 VPYIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            456899999999999999999877654

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=95.90  E-value=0.0054  Score=52.88  Aligned_cols=27  Identities=19%  Similarity=0.215  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.++|.|.|++|+||||.|+.+.....
T Consensus        28 k~kiI~llGpPGsGKgTqa~~L~~~~g   54 (217)
T 3umf_A           28 KAKVIFVLGGPGSGKGTQCEKLVQKFH   54 (217)
T ss_dssp             SCEEEEEECCTTCCHHHHHHHHHHHHC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHC
Confidence            578999999999999999999998764

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.90  E-value=0.0053  Score=52.13  Aligned_cols=26  Identities=19%  Similarity=0.255  Sum_probs=22.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+||||+++.+....
T Consensus         5 ~g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            5 KGLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            34689999999999999999998765

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=95.90  E-value=0.043  Score=52.72  Aligned_cols=52  Identities=13%  Similarity=-0.003  Sum_probs=36.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      ...++.|.|.+|+|||||+.+++........ ..++|++..  -+..++...+..
T Consensus       199 ~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g-~~vl~~slE--~~~~~l~~R~~~  250 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFALTIAQNAALKEG-VGVGIYSLE--MPAAQLTLRMMC  250 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHTTC-CCEEEEESS--SCHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHhCC-CeEEEEECC--CCHHHHHHHHHH
Confidence            3468999999999999999999987654211 246666554  456677766543

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=95.89  E-value=0.0045  Score=51.23  Aligned_cols=25  Identities=28%  Similarity=0.399  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.|.|.|++|+||||+++.+.....
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~~l~   29 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAKDLD   29 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            3588999999999999999988764

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=95.89  E-value=0.005  Score=52.13  Aligned_cols=24  Identities=29%  Similarity=0.537  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .|+|.|+.|+||||+++.+.....
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~   25 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLG   25 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcC
Confidence            689999999999999999998764

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=95.89  E-value=0.0055  Score=52.65  Aligned_cols=39  Identities=21%  Similarity=0.199  Sum_probs=29.4

Q ss_pred             HHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          162 TLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       162 ~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+.+...+.....++++|+|.+|+|||||+..+.....
T Consensus        17 ~~~~~~~~~~~~~~~~i~i~G~~g~GKTTl~~~l~~~~~   55 (221)
T 2wsm_A           17 LAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERIG   55 (221)
T ss_dssp             HHHHHHHHHHHHTCEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             HHHHHHHhhcccCceEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            334444444344678999999999999999999988764

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=95.88  E-value=0.0071  Score=51.35  Aligned_cols=37  Identities=19%  Similarity=0.181  Sum_probs=27.3

Q ss_pred             HHHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          164 NDILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       164 ~~l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+..++.+ ++...+.|+|++|+||||+|..+++...
T Consensus        46 ~~l~~~~~~iPkkn~ili~GPPGtGKTt~a~ala~~l~   83 (212)
T 1tue_A           46 GALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQ   83 (212)
T ss_dssp             HHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             HHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhC
Confidence            334444443 2334789999999999999999998864

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=95.87  E-value=0.0055  Score=51.99  Aligned_cols=26  Identities=19%  Similarity=0.262  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +..+|+|.|+.|+||||+++.+....
T Consensus        14 ~~~~I~l~G~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           14 QVSVIFVLGGPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            45789999999999999999998765

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.87  E-value=0.0041  Score=52.83  Aligned_cols=25  Identities=24%  Similarity=0.247  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .++++|+|+.|+|||||++.+....
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3578999999999999999998754

>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=95.87  E-value=0.0058  Score=50.49  Aligned_cols=25  Identities=28%  Similarity=0.414  Sum_probs=22.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..+|+|.|+.|+||||+++.+....
T Consensus         8 g~~i~l~G~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHhh
Confidence            4689999999999999999998765

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=95.86  E-value=0.048  Score=52.54  Aligned_cols=51  Identities=12%  Similarity=0.191  Sum_probs=35.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      ...++.|.|.+|+|||||+.+++........ ..++|++..  .+..++...+.
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g-~~Vl~~s~E--~s~~~l~~r~~  252 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVATKTN-ENVAIFSLE--MSAQQLVMRML  252 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHHHSS-CCEEEEESS--SCHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhCC-CcEEEEECC--CCHHHHHHHHH
Confidence            3468999999999999999999988654321 246666543  34556655543

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=95.85  E-value=0.0057  Score=51.01  Aligned_cols=24  Identities=33%  Similarity=0.410  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|+|+.|+|||||++.+.....
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~   25 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            578999999999999999988765

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=95.85  E-value=0.0058  Score=52.04  Aligned_cols=27  Identities=19%  Similarity=0.163  Sum_probs=23.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ..+|+|.|++|+||||+++.+......
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~~l~~   30 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKDWIEL   30 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHTT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHhh
Confidence            357999999999999999999988754

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=95.84  E-value=0.0056  Score=51.60  Aligned_cols=26  Identities=23%  Similarity=0.202  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+|+|.|++|+||||+++.+.....
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l~   37 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKYG   37 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999988764

>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=95.83  E-value=0.0077  Score=54.45  Aligned_cols=54  Identities=7%  Similarity=-0.063  Sum_probs=34.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcC-CCCeEEEEEeCCCCCHHHHHHHH
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEK-LFDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~-~f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      +...+|+|.|+.|+|||||++.+.......+ .......|+....+-.......+
T Consensus        29 ~~~~ii~I~G~sGsGKSTla~~L~~~l~~~g~~~~~~~iv~~D~f~~~~~~~~~l   83 (290)
T 1odf_A           29 KCPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKL   83 (290)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhhhcCCCCceEEEeccccccCChHHHHHH
Confidence            4567899999999999999999988765421 12334444554433333334444

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=95.82  E-value=0.037  Score=52.68  Aligned_cols=28  Identities=32%  Similarity=0.274  Sum_probs=24.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...++.++|++|+||||++..++.....
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~  124 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKG  124 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3568999999999999999999988764

>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=95.82  E-value=0.0067  Score=50.04  Aligned_cols=34  Identities=24%  Similarity=0.141  Sum_probs=26.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeE
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQV  208 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~  208 (390)
                      ..+++.|.|+.|+|||||+..+......+ .+...
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~~l~~~-g~~v~   36 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVAAAVRE-GWRVG   36 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhhHhc-CCeee
Confidence            35789999999999999999999887643 34433

>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=95.81  E-value=0.0053  Score=51.48  Aligned_cols=22  Identities=32%  Similarity=0.394  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      .+++|.|+.|+|||||++.+..
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhc
Confidence            4789999999999999999975

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=95.81  E-value=0.0039  Score=60.81  Aligned_cols=44  Identities=18%  Similarity=0.136  Sum_probs=36.2

Q ss_pred             cccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          155 ACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|++..++.+...+..+  .-+.|+|++|+|||+||+.+.+...
T Consensus        23 ~ivGq~~~i~~l~~al~~~--~~VLL~GpPGtGKT~LAraLa~~l~   66 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALSG--ESVFLLGPPGIAKSLIARRLKFAFQ   66 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHHT--CEEEEECCSSSSHHHHHHHGGGGBS
T ss_pred             hhHHHHHHHHHHHHHHhcC--CeeEeecCchHHHHHHHHHHHHHHh
Confidence            5788888888887776644  3578999999999999999988764

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=95.81  E-value=0.0041  Score=51.73  Aligned_cols=26  Identities=23%  Similarity=0.217  Sum_probs=19.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+|.|.|++|+||||+++.+.....
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l~   30 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERLP   30 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHST
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            46899999999999999999987754

>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=0.0059  Score=53.67  Aligned_cols=27  Identities=22%  Similarity=0.183  Sum_probs=23.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+.+|+|.|+.|+|||||++.+.....
T Consensus        26 ~~~~i~l~G~~GsGKSTl~k~La~~lg   52 (246)
T 2bbw_A           26 KLLRAVILGPPGSGKGTVCQRIAQNFG   52 (246)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            357899999999999999999997663

>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=95.80  E-value=0.0071  Score=50.56  Aligned_cols=25  Identities=28%  Similarity=0.235  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      +...|.|+|+.|+||||+++.+...
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHh
Confidence            4568999999999999999999886

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.79  E-value=0.0058  Score=52.21  Aligned_cols=27  Identities=37%  Similarity=0.358  Sum_probs=23.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+|+|.|+.|+|||||++.+.....
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHG
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            456899999999999999999988654

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=95.79  E-value=0.0063  Score=50.76  Aligned_cols=26  Identities=23%  Similarity=0.142  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...|+|.|++|+||||+++.+.....
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~~l~   29 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQELG   29 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            35789999999999999999987653

>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=95.77  E-value=0.0051  Score=51.28  Aligned_cols=25  Identities=20%  Similarity=0.299  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ++|.|.|++|+||||+++.+.....
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg   27 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKALG   27 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcC
Confidence            4689999999999999999988764

>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=95.75  E-value=0.0056  Score=50.38  Aligned_cols=25  Identities=28%  Similarity=0.312  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+|.|.|+.|+||||+++.+.....
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg   27 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARALG   27 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhC
Confidence            4689999999999999999988764

>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=95.74  E-value=0.017  Score=48.75  Aligned_cols=116  Identities=18%  Similarity=0.095  Sum_probs=60.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC---CCCHHHHHHHHH---HHhC--CCCCCCC-------c
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK---IQDIRKIQGEIA---DKLG--LTLHEES-------D  239 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~---~~~~~~l~~~i~---~~l~--~~~~~~~-------~  239 (390)
                      ...|.|++..|.||||+|--..-..-.. .+. +.++.+-.   ......++..+.   ..++  ..+....       .
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~-G~r-V~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a  105 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGH-GKN-VGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAAC  105 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHT-TCC-EEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHC-CCe-EEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHH
Confidence            3567777778899999999988876543 243 44444433   223333433331   0000  1111111       0


Q ss_pred             hHHHHHHHHHHhCCCeEEEEEeCCCC-----CcccccccCCCCCCCCCcEEEEEecch
Q 042806          240 SGRARSLRNRLKKEKTILVILDNIWG-----NLDFQAVGIPHGDDRKGCKVLLTARSL  292 (390)
Q Consensus       240 ~~~~~~l~~~l~~~~~~LlVlDdv~~-----~~~~~~l~~~l~~~~~~s~IivTtr~~  292 (390)
                      ......+.+.+.+++-=|||||++-.     ....+.+...+........||+|+|..
T Consensus       106 ~~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~a  163 (196)
T 1g5t_A          106 MAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGC  163 (196)
T ss_dssp             HHHHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSC
T ss_pred             HHHHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCC
Confidence            11223445555555534999999832     222233333333334566899999974

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=95.72  E-value=0.0068  Score=49.71  Aligned_cols=27  Identities=26%  Similarity=0.345  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+|.|.|+.|+||||+++.+.....
T Consensus         6 ~~~~i~l~G~~GsGKSTva~~La~~lg   32 (168)
T 1zuh_A            6 HMQHLVLIGFMGSGKSSLAQELGLALK   32 (168)
T ss_dssp             --CEEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ccceEEEECCCCCCHHHHHHHHHHHhC
Confidence            356899999999999999999988764

>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=95.71  E-value=0.0067  Score=50.74  Aligned_cols=26  Identities=23%  Similarity=0.202  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+|+|.|+.|+||||+++.+.....
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l~   31 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDFG   31 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999988753

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=95.71  E-value=0.011  Score=55.47  Aligned_cols=26  Identities=23%  Similarity=0.285  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+.++|++|+|||++|+.+++...
T Consensus        72 ~~~ill~Gp~GtGKT~la~~la~~l~   97 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQTLAKHLD   97 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHhC
Confidence            34688999999999999999998773

>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=95.70  E-value=0.0081  Score=50.89  Aligned_cols=27  Identities=26%  Similarity=0.133  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+|.|.|++|+||||+++.+.....
T Consensus        19 ~~~~I~l~G~~GsGKST~a~~La~~l~   45 (201)
T 2cdn_A           19 SHMRVLLLGPPGAGKGTQAVKLAEKLG   45 (201)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            345899999999999999999988763

>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=95.69  E-value=0.0068  Score=53.86  Aligned_cols=26  Identities=23%  Similarity=0.454  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+|.|.|++|+||||+++.+.....
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L~   29 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKILS   29 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            46899999999999999999998754

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=95.68  E-value=0.0051  Score=50.87  Aligned_cols=23  Identities=26%  Similarity=0.401  Sum_probs=19.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVA  196 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~  196 (390)
                      ...+++|+|+.|+|||||++.++
T Consensus         8 ~gei~~l~G~nGsGKSTl~~~~~   30 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAKKHF   30 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHS
T ss_pred             CCEEEEEECCCCCCHHHHHHHHc
Confidence            34689999999999999999643

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=95.68  E-value=0.068  Score=46.26  Aligned_cols=25  Identities=28%  Similarity=0.145  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .-++|.|++|+||||+++.+.....
T Consensus         9 ~~~~~~G~pGsGKsT~a~~L~~~~g   33 (230)
T 3gmt_A            9 MRLILLGAPGAGKGTQANFIKEKFG   33 (230)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             cceeeECCCCCCHHHHHHHHHHHhC
Confidence            3578999999999999999988764

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=95.67  E-value=0.0057  Score=57.02  Aligned_cols=51  Identities=18%  Similarity=0.038  Sum_probs=35.3

Q ss_pred             HHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhc-CCCCeEEEEEeCCC
Q 042806          165 DILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETE-KLFDQVIFVEVSKI  216 (390)
Q Consensus       165 ~l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~  216 (390)
                      +.++.+.. .+-.-++|+|.+|+|||+|+..+.+..... ..+. ++++.++..
T Consensus       164 raID~l~PigrGQR~lIfg~~g~GKT~Ll~~Ia~~i~~~~~dv~-~V~~lIGER  216 (427)
T 3l0o_A          164 RLIDLFAPIGKGQRGMIVAPPKAGKTTILKEIANGIAENHPDTI-RIILLIDER  216 (427)
T ss_dssp             HHHHHHSCCBTTCEEEEEECTTCCHHHHHHHHHHHHHHHCTTSE-EEEEECSCC
T ss_pred             hhhhhcccccCCceEEEecCCCCChhHHHHHHHHHHhhcCCCeE-EEEEEeccC
Confidence            45666654 345578899999999999999998876532 1233 356777654

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=95.66  E-value=0.0076  Score=51.39  Aligned_cols=32  Identities=13%  Similarity=0.078  Sum_probs=26.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCe
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQ  207 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~  207 (390)
                      ..+|+|.|+.|+||||+++.+....... +++.
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l~~~-~~~~   41 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYLKNN-NVEV   41 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHHHHT-TCCE
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHc-CCcE
Confidence            4689999999999999999999887542 4554

>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=95.66  E-value=0.008  Score=51.32  Aligned_cols=33  Identities=9%  Similarity=0.059  Sum_probs=26.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCe
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQ  207 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~  207 (390)
                      +..+|+|.|+.|+||||+++.+....... +++.
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~L~~~l~~~-~~~v   40 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSRKLVEALCAA-GHRA   40 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHHT-TCCE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHc-CCcE
Confidence            35689999999999999999999887543 3554

>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=95.65  E-value=0.0071  Score=52.21  Aligned_cols=24  Identities=33%  Similarity=0.360  Sum_probs=21.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .+|+|.|+.|+||||+++.+....
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~   29 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEAL   29 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            579999999999999999998765

>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=95.65  E-value=0.0075  Score=50.97  Aligned_cols=26  Identities=27%  Similarity=0.211  Sum_probs=23.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ++..+|+|.|+.|+||||+++.+...
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHC
Confidence            35678999999999999999999875

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=95.64  E-value=0.0068  Score=52.28  Aligned_cols=27  Identities=22%  Similarity=0.073  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ....|.|.|++|+||||+++.+.....
T Consensus         4 ~~~~I~l~G~~GsGKsT~~~~La~~l~   30 (222)
T 1zak_A            4 DPLKVMISGAPASGKGTQCELIKTKYQ   30 (222)
T ss_dssp             CSCCEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            346789999999999999999988764

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=95.64  E-value=0.013  Score=54.12  Aligned_cols=30  Identities=20%  Similarity=0.184  Sum_probs=25.1

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          172 NPDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       172 ~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+....|.|+|++|+||||+++.++.....
T Consensus        21 ~g~~~~i~l~G~~G~GKTTl~~~la~~l~~   50 (359)
T 2ga8_A           21 DNYRVCVILVGSPGSGKSTIAEELCQIINE   50 (359)
T ss_dssp             TCSCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             cCCeeEEEEECCCCCcHHHHHHHHHHHhCC
Confidence            455667999999999999999999887653

>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=95.64  E-value=0.0069  Score=52.35  Aligned_cols=27  Identities=11%  Similarity=0.153  Sum_probs=23.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+++|+|+.|+|||||++.+.....
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            456899999999999999999987654

>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=95.62  E-value=0.0071  Score=51.62  Aligned_cols=26  Identities=12%  Similarity=0.160  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+..-.
T Consensus        19 ~Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           19 VGRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            45689999999999999999998765

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=95.61  E-value=0.051  Score=49.19  Aligned_cols=87  Identities=21%  Similarity=0.261  Sum_probs=49.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----CCCchHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLTLH----EESDSGRARSLRNR  249 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~~~~l~~~  249 (390)
                      ..+++++|++|+||||++..+.......+ . .+.++...... ...+.+.......+...-    ..+.........+.
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g-~-~v~l~~~D~~r~~a~~ql~~~~~~~~v~v~~~~~~~~p~~~~~~~l~~  175 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKG-F-KVGLVGADVYRPAALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVEK  175 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTT-C-CEEEEECCCSSSHHHHHHHHHHHHHTCCEECCTTCCCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCC-C-eEEEEecCCCCHHHHHHHHHHhccCCeEEEecCCCCCHHHHHHHHHHH
Confidence            57899999999999999999998876432 2 35555554322 223333444555544211    12233333444455


Q ss_pred             HhCCCeEEEEEeCC
Q 042806          250 LKKEKTILVILDNI  263 (390)
Q Consensus       250 l~~~~~~LlVlDdv  263 (390)
                      +...+.=++++|-.
T Consensus       176 ~~~~~~D~ViIDTp  189 (297)
T 1j8m_F          176 FLSEKMEIIIVDTA  189 (297)
T ss_dssp             HHHTTCSEEEEECC
T ss_pred             HHhCCCCEEEEeCC
Confidence            54223127888865

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=95.60  E-value=0.0073  Score=52.34  Aligned_cols=26  Identities=19%  Similarity=0.152  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ....|.|.|++|+||||+++.+....
T Consensus         6 ~~~~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            6 RLLRAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             -CCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            34679999999999999999998865

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.59  E-value=0.0063  Score=52.54  Aligned_cols=26  Identities=31%  Similarity=0.369  Sum_probs=22.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+....
T Consensus        22 ~G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           22 NIYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            45689999999999999999998755

>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=95.56  E-value=0.0085  Score=51.59  Aligned_cols=26  Identities=19%  Similarity=0.126  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...|.|.|++|+||||+++.+.....
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~l~   29 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQERFH   29 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcC
Confidence            45789999999999999999988763

>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=95.52  E-value=0.0049  Score=52.67  Aligned_cols=26  Identities=23%  Similarity=0.363  Sum_probs=22.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+|+|.|+.|+||||+++.+......
T Consensus         1 ~~I~i~G~~GsGKsTl~~~L~~~l~~   26 (214)
T 1gtv_A            1 MLIAIEGVDGAGKRTLVEKLSGAFRA   26 (214)
T ss_dssp             CEEEEEEEEEEEHHHHHHHHHHHHHE
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            36899999999999999999887653

>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=95.51  E-value=0.009  Score=52.70  Aligned_cols=28  Identities=11%  Similarity=0.203  Sum_probs=24.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+.+|+|.|+.|+||||+++.+.....
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~~lg   47 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQLLG   47 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            3567899999999999999999988754

>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=95.51  E-value=0.008  Score=49.04  Aligned_cols=27  Identities=26%  Similarity=0.214  Sum_probs=23.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ....+++|.|+.|+|||||++.+..-.
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            345689999999999999999998876

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=95.51  E-value=0.0091  Score=48.82  Aligned_cols=24  Identities=17%  Similarity=0.155  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .|.|.|+.|+||||+++.+.....
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~   25 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLN   25 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            588999999999999999988764

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=95.50  E-value=0.0088  Score=50.08  Aligned_cols=24  Identities=29%  Similarity=0.368  Sum_probs=22.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +|+|.|+.|+||||+++.+.+...
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~   25 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLK   25 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            689999999999999999998764

>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=95.50  E-value=0.0082  Score=51.14  Aligned_cols=26  Identities=35%  Similarity=0.465  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+|+|.|++|+||||+++.+....
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTTS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            35689999999999999999997653

>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=95.49  E-value=0.0081  Score=50.98  Aligned_cols=22  Identities=27%  Similarity=0.339  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      .+|+|.|+.|+||||+++.+..
T Consensus         2 ~~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            2 KRIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            3689999999999999999987

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=95.48  E-value=0.069  Score=52.15  Aligned_cols=51  Identities=12%  Similarity=0.160  Sum_probs=36.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      ...++.|.|.+|+|||||+.+++........ ..++|++..  -+..++...++
T Consensus       241 ~G~l~li~G~pG~GKT~lal~~a~~~a~~~g-~~vl~~s~E--~s~~~l~~r~~  291 (503)
T 1q57_A          241 GGEVIMVTSGSGMVMSTFVRQQALQWGTAMG-KKVGLAMLE--ESVEETAEDLI  291 (503)
T ss_dssp             TTCEEEEEESSCHHHHHHHHHHHHHHTTTSC-CCEEEEESS--SCHHHHHHHHH
T ss_pred             CCeEEEEeecCCCCchHHHHHHHHHHHHhcC-CcEEEEecc--CCHHHHHHHHH
Confidence            3468899999999999999999988654311 246666553  35666666654

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=95.48  E-value=0.012  Score=52.06  Aligned_cols=27  Identities=19%  Similarity=0.161  Sum_probs=23.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+|.|.|++|+||||+++.+.....
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~L~~~l~   57 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRIKQKEFQ   57 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            357899999999999999999988753

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=95.48  E-value=0.01  Score=54.25  Aligned_cols=41  Identities=20%  Similarity=0.332  Sum_probs=31.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK  215 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  215 (390)
                      ++.++|+|+|-|||||||.+-.+...+...+ +. +.-|.+..
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~aLA~~G-kk-VllID~Dp   86 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSAAFSILG-KR-VLQIGCDP   86 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHHHHTT-CC-EEEEEESS
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHHHHHCC-Ce-EEEEecCC
Confidence            4678999999999999999999988876532 33 55566654

>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=95.42  E-value=0.012  Score=53.51  Aligned_cols=28  Identities=21%  Similarity=0.303  Sum_probs=24.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...+++|+|++|+|||||++.+......
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~~  128 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQN  128 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHh
Confidence            4679999999999999999999877653

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=95.42  E-value=0.011  Score=52.34  Aligned_cols=27  Identities=26%  Similarity=0.283  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+|+|.|+.|+||||+++.+.....
T Consensus        26 ~g~~I~I~G~~GsGKSTl~k~La~~Lg   52 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLCKALAESLN   52 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhcC
Confidence            456899999999999999999987653

>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=95.40  E-value=0.032  Score=61.69  Aligned_cols=84  Identities=20%  Similarity=0.227  Sum_probs=61.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC------CchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE------SDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~------~~~~~~~~l~  247 (390)
                      +-++|-|+|+.|+||||||.++.......  =...+|+.+.+..+..-     ++.+|.+.+..      .....+..+.
T Consensus      1430 rg~~iei~g~~~sGkttl~~~~~a~~~~~--g~~~~~i~~e~~~~~~~-----~~~~Gv~~~~l~~~~p~~~e~~l~~~~ 1502 (1706)
T 3cmw_A         1430 MGRIVEIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICD 1502 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEECTTSCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHhc--CCeEEEEecCCCCCHHH-----HHHcCCCHHHeEEeCCCcHHHHHHHHH
Confidence            45899999999999999999999775543  24578888887777542     77888765432      2234455566


Q ss_pred             HHHhCCCeEEEEEeCCC
Q 042806          248 NRLKKEKTILVILDNIW  264 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~  264 (390)
                      ..++.+..-+||+|-|-
T Consensus      1503 ~~~~s~~~~~vvvDsv~ 1519 (1706)
T 3cmw_A         1503 ALARSGAVDVIVVDSVA 1519 (1706)
T ss_dssp             HHHHHTCCSEEEESCST
T ss_pred             HHHHcCCCCEEEEccHH
Confidence            66677776799999884

>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=95.39  E-value=0.0093  Score=54.50  Aligned_cols=29  Identities=21%  Similarity=0.248  Sum_probs=24.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ....+++|.|+.|+|||||++.+..-...
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~gll~~  116 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQALLAR  116 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHhhccc
Confidence            35679999999999999999999887653

>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=95.39  E-value=0.043  Score=63.52  Aligned_cols=138  Identities=11%  Similarity=0.055  Sum_probs=75.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      +-+.++|++|+|||++|+.+.....   .+ ....++++...+...+...+...+...........      .--..+++
T Consensus      1268 ~~vLL~GPpGtGKT~la~~~l~~~~---~~-~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~~~------~P~~~gk~ 1337 (2695)
T 4akg_A         1268 RGIILCGPPGSGKTMIMNNALRNSS---LY-DVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTL------LPKSDIKN 1337 (2695)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSCS---SC-EEEEEECCTTCCHHHHHHHHHHHBCCEEETTTEEE------EEBSSSSC
T ss_pred             CeEEEECCCCCCHHHHHHHHHhcCC---CC-ceEEEEeecCCCHHHHHHHHHHHhhhccccCCccc------cCCCCCce
Confidence            4577999999999999988776542   23 35667888877877777766665532210000000      00002345


Q ss_pred             EEEEEeCCCCC--cc------cccccCCCC-----CCC-------CCcEEEEEecchh------hhhhcCCCcceEecCC
Q 042806          256 ILVILDNIWGN--LD------FQAVGIPHG-----DDR-------KGCKVLLTARSLD------VLSRKMDSQQNFSVGV  309 (390)
Q Consensus       256 ~LlVlDdv~~~--~~------~~~l~~~l~-----~~~-------~~s~IivTtr~~~------v~~~~~~~~~~~~l~~  309 (390)
                      +++.+||+.-.  +.      .+.+...+.     +..       .+..+|.++....      +..+...-...+.+..
T Consensus      1338 ~VlFiDEinmp~~d~yg~q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllRrf~vi~i~~ 1417 (2695)
T 4akg_A         1338 LVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYLGY 1417 (2695)
T ss_dssp             EEEEEETTTCSCCCSSSCCHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHTTEEEEECCC
T ss_pred             EEEEecccccccccccCchhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhheeeEEEeCC
Confidence            89999997421  11      111111110     001       1234555554331      1111122235788999


Q ss_pred             CCHHHHHHHHHHhh
Q 042806          310 LKEDEAWSLFKKMA  323 (390)
Q Consensus       310 L~~~ea~~lf~~~~  323 (390)
                      .+.++-..+|....
T Consensus      1418 P~~~~l~~I~~~il 1431 (2695)
T 4akg_A         1418 PSGKSLSQIYEIYY 1431 (2695)
T ss_dssp             CTTTHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            99998888887765

>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=95.37  E-value=0.011  Score=51.90  Aligned_cols=26  Identities=15%  Similarity=0.050  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .+..|+|.|++|+||||+++.+.+..
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            56689999999999999999998765

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.36  E-value=0.011  Score=52.02  Aligned_cols=26  Identities=15%  Similarity=0.220  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+|+|.|+.|+|||||++.+....
T Consensus        24 ~g~iigI~G~~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVCEKIMELL   49 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            45689999999999999999998765

>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=95.35  E-value=0.01  Score=50.28  Aligned_cols=25  Identities=16%  Similarity=0.122  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..+|+|.|+.|+||||+++.+....
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHTS
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4679999999999999999998876

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=95.35  E-value=0.01  Score=50.82  Aligned_cols=24  Identities=29%  Similarity=0.360  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .|+|.|++|+||||+++.+.....
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~   25 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKYE   25 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999987753

>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=95.35  E-value=0.073  Score=48.09  Aligned_cols=87  Identities=21%  Similarity=0.298  Sum_probs=47.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC-HHHHHHHHHHHhCCCCC----CCCchHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD-IRKIQGEIADKLGLTLH----EESDSGRARSLRN  248 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~l~~~i~~~l~~~~~----~~~~~~~~~~l~~  248 (390)
                      ...+++|+|++|+||||++..++......+  ..+.++....... ...-+.......+...-    ..+...+......
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~~~--~~v~l~~~d~~~~~~~~ql~~~~~~~~l~~~~~~~~~~p~~l~~~~l~  174 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKG--RRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEE  174 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHTT--CCEEEEECCSSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcC--CeEEEecCCcccHhHHHHHHHhcccCCeEEEEcCCCCCHHHHHHHHHH
Confidence            356899999999999999999998876431  2344444432211 11112334444443221    1123333333333


Q ss_pred             HHh-CCCeEEEEEeCC
Q 042806          249 RLK-KEKTILVILDNI  263 (390)
Q Consensus       249 ~l~-~~~~~LlVlDdv  263 (390)
                      .+. .+. =++++|--
T Consensus       175 ~~~~~~~-D~viiDtp  189 (295)
T 1ls1_A          175 KARLEAR-DLILVDTA  189 (295)
T ss_dssp             HHHHHTC-CEEEEECC
T ss_pred             HHHhCCC-CEEEEeCC
Confidence            332 323 47888976

>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=95.35  E-value=0.036  Score=61.30  Aligned_cols=86  Identities=20%  Similarity=0.217  Sum_probs=56.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC------CchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE------SDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~------~~~~~~~~l~  247 (390)
                      ..+++.|+|++|+||||||.+++......  =..++|++.....+..     .++.++.+.+..      +.......+.
T Consensus       382 ~G~lilI~G~pGsGKTtLaLq~a~~~~~~--G~~vlyis~E~s~~~~-----~a~~lGvd~~~L~i~~~~~~e~~l~~l~  454 (1706)
T 3cmw_A          382 MGRIVEIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD  454 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEECTTSCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHh--CCCeEEEEccCchHHH-----HHHHcCCCHHHeEEcCCCCHHHHHHHHH
Confidence            46789999999999999999998886543  2357888877766543     256666543321      2223333343


Q ss_pred             HHHhCCCeEEEEEeCCCCC
Q 042806          248 NRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~~  266 (390)
                      ..+...+.-+||+|-+...
T Consensus       455 ~lv~~~~~~lVVIDSL~al  473 (1706)
T 3cmw_A          455 ALARSGAVDVIVVDSVAAL  473 (1706)
T ss_dssp             HHHHHTCCSEEEESCSTTC
T ss_pred             HHHHhcCCCEEEECCHHHh
Confidence            3344445569999998643

>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=95.30  E-value=0.0092  Score=50.73  Aligned_cols=22  Identities=32%  Similarity=0.339  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      .+|+|.|+.|+||||+++.+..
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999999965

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=95.29  E-value=0.059  Score=51.73  Aligned_cols=51  Identities=16%  Similarity=0.099  Sum_probs=35.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      ...++.|.|.+|+|||||+.+++.....++  ..++|++..  -+..++...+..
T Consensus       196 ~G~liiIaG~pG~GKTtlal~ia~~~a~~g--~~vl~fSlE--ms~~ql~~R~~~  246 (444)
T 3bgw_A          196 RRNFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLE--MGKKENIKRLIV  246 (444)
T ss_dssp             SSCEEEEEECSSSSHHHHHHHHHHHHHHTT--CEEEEECSS--SCTTHHHHHHHH
T ss_pred             CCcEEEEEeCCCCChHHHHHHHHHHHHHcC--CEEEEEECC--CCHHHHHHHHHH
Confidence            346899999999999999999998875431  245665443  344555555443

>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=95.28  E-value=0.013  Score=50.18  Aligned_cols=28  Identities=21%  Similarity=0.166  Sum_probs=24.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ....+|.|.|+.|+||||+++.+.....
T Consensus        23 ~~~~~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           23 QRGLTIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3457899999999999999999988775

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=95.24  E-value=0.021  Score=54.39  Aligned_cols=99  Identities=18%  Similarity=0.254  Sum_probs=58.8

Q ss_pred             HHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhc-CCCC-eEEEEEeCCC-CCHHHHHHHHHHHhCC-------CC
Q 042806          166 ILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETE-KLFD-QVIFVEVSKI-QDIRKIQGEIADKLGL-------TL  234 (390)
Q Consensus       166 l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~-~~f~-~~~wv~v~~~-~~~~~l~~~i~~~l~~-------~~  234 (390)
                      .++.|.. .+-.-++|.|.+|+|||+|+.++.+..... ++-+ .++++.++.. ....+++..+...-..       ..
T Consensus       141 aID~l~pigrGQr~~Ifgg~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~~g~~~rtvvV~at  220 (465)
T 3vr4_D          141 AIDHLNTLVRGQKLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNL  220 (465)
T ss_dssp             HHHTTSCCBTTCBCCEEECTTSCHHHHHHHHHHHCBCSSCSSCEEEEEEEEEECHHHHHHHHHHHHHHTGGGGEEEEEEE
T ss_pred             EEecccccccCCEEEEeCCCCcChHHHHHHHHHHHHhccCCCceEEEEEEecCCcHHHHHHHHHHhhcCCccceEEEEEC
Confidence            4444432 223346789999999999999998876531 0111 6777777754 3556666665443111       11


Q ss_pred             CCCCchH------HHHHHHHHHhC--CCeEEEEEeCCC
Q 042806          235 HEESDSG------RARSLRNRLKK--EKTILVILDNIW  264 (390)
Q Consensus       235 ~~~~~~~------~~~~l~~~l~~--~~~~LlVlDdv~  264 (390)
                      .+.+...      ..-.+.+++.+  ++.+|+++||+.
T Consensus       221 sd~p~~~r~~a~~~a~tiAEyfrd~~G~~VLl~~DslT  258 (465)
T 3vr4_D          221 ANDPAIERIATPRMALTAAEYLAYEKGMHVLVIMTDMT  258 (465)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChH
Confidence            1112111      22356677763  677999999984

>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=95.22  E-value=0.013  Score=48.54  Aligned_cols=27  Identities=26%  Similarity=0.278  Sum_probs=23.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+++.|.|+.|+|||||+..+......
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l~~   32 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPALCA   32 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhccc
Confidence            578999999999999999999987653

>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=95.21  E-value=0.012  Score=50.51  Aligned_cols=23  Identities=26%  Similarity=0.307  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .|+|.|++|+||||+++.+....
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998765

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=95.15  E-value=0.031  Score=48.29  Aligned_cols=56  Identities=14%  Similarity=0.096  Sum_probs=35.9

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHhhh-cCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          172 NPDVNMLGIYGMGGIVKTTLAKEVARKAET-EKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       172 ~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~-~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      .....+|.|.|+.|+||||+++.+.+.... . .+.......-.......+.++.++.
T Consensus        18 ~~~~~~i~~~G~~g~GKst~~~~l~~~l~~~~-g~~v~~~treP~~t~~g~~ir~~l~   74 (223)
T 3ld9_A           18 GPGSMFITFEGIDGSGKTTQSHLLAEYLSEIY-GVNNVVLTREPGGTLLNESVRNLLF   74 (223)
T ss_dssp             -CCCEEEEEECSTTSSHHHHHHHHHHHHHHHH-CGGGEEEEESSCSSHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHhhcc-CceeeEeeeCCCCChHHHHHHHHHh
Confidence            345678999999999999999999998865 3 2444432323333233444444443

>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=95.13  E-value=0.044  Score=47.76  Aligned_cols=37  Identities=19%  Similarity=0.243  Sum_probs=29.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEE
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVE  212 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~  212 (390)
                      ..+|.|.|+.|+||||+++.+....... ++.......
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l~~~-~~~~~~~~r   63 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETLQQN-GIDHITRTR   63 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHHHHT-TCCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc-CCCeeeeec
Confidence            4689999999999999999999988653 465344443

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=95.11  E-value=0.012  Score=49.51  Aligned_cols=24  Identities=25%  Similarity=0.256  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +++|+|+.|+|||||++.+.....
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            688999999999999999988764

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=95.10  E-value=0.013  Score=51.38  Aligned_cols=26  Identities=15%  Similarity=0.132  Sum_probs=22.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .. .+++|+|+.|+|||||++.+.--.
T Consensus        23 ~~-e~~~liG~nGsGKSTLl~~l~Gl~   48 (240)
T 2onk_A           23 GR-DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             CS-SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CC-EEEEEECCCCCCHHHHHHHHhCCC
Confidence            35 789999999999999999997643

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=95.10  E-value=0.048  Score=61.18  Aligned_cols=85  Identities=20%  Similarity=0.269  Sum_probs=55.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCC------CCchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHE------ESDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~------~~~~~~~~~l~  247 (390)
                      ...++.|+|++|+|||||+.+++......+  ..++|++.....+..     .++.++.+.+.      .+.......+.
T Consensus       382 ~G~lilI~G~pGsGKTtLaLqia~~~a~~G--~~vlyis~E~s~~~~-----~a~~lGvd~~~L~I~~~~~~e~il~~~~  454 (2050)
T 3cmu_A          382 MGRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD  454 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTTT--CCEEEECTTSCCCHH-----HHHHTTCCTTTCEEECCSSHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHhcC--CeEEEEEcCCCHHHH-----HHHHcCCCHHHeEEeCCCCHHHHHHHHH
Confidence            457899999999999999999998875432  357888777665543     25666654321      12223333333


Q ss_pred             HHHhCCCeEEEEEeCCCC
Q 042806          248 NRLKKEKTILVILDNIWG  265 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~  265 (390)
                      ........-+||+|-+..
T Consensus       455 ~lv~~~~~~lIVIDSL~a  472 (2050)
T 3cmu_A          455 ALARSGAVDVIVVDSVAA  472 (2050)
T ss_dssp             HHHHHTCCSEEEESCGGG
T ss_pred             HHHHhcCCcEEEECCHHH
Confidence            333344556999999853

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=95.09  E-value=0.013  Score=48.48  Aligned_cols=26  Identities=27%  Similarity=0.221  Sum_probs=23.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ++++|+|+.|+|||||++.+......
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~~   28 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILRE   28 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            57999999999999999999887664

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=95.08  E-value=0.051  Score=46.58  Aligned_cols=53  Identities=17%  Similarity=0.128  Sum_probs=34.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      ..+|++.|+.|+||||+++.+.+..... ++..+.+..-.......+.++.++.
T Consensus         3 g~~i~~eG~~gsGKsT~~~~l~~~l~~~-~~~~v~~~rep~~t~~g~~ir~~l~   55 (213)
T 4tmk_A            3 SKYIVIEGLEGAGKTTARNVVVETLEQL-GIRDMVFTREPGGTQLAEKLRSLLL   55 (213)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHHHHT-TCCCEEEEESSCSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc-CCCcceeeeCCCCCHHHHHHHHHHh
Confidence            3579999999999999999999988754 3533343333333334444555443

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=95.07  E-value=0.05  Score=46.74  Aligned_cols=27  Identities=22%  Similarity=0.198  Sum_probs=24.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ..+|.+.|+.|+||||+++.+.+....
T Consensus         5 g~~i~~eG~~g~GKst~~~~l~~~l~~   31 (216)
T 3tmk_A            5 GKLILIEGLDRTGKTTQCNILYKKLQP   31 (216)
T ss_dssp             CCEEEEEECSSSSHHHHHHHHHHHHCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            468999999999999999999998763

>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=95.07  E-value=0.016  Score=48.02  Aligned_cols=28  Identities=18%  Similarity=0.135  Sum_probs=23.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...+|.|.|+.|+||||+++.+......
T Consensus         4 ~g~~i~l~G~~GsGKST~~~~L~~~l~~   31 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSMALEEYLVC   31 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            3467899999999999999999887643

>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=95.06  E-value=0.047  Score=49.20  Aligned_cols=39  Identities=15%  Similarity=0.072  Sum_probs=28.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEe
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEV  213 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v  213 (390)
                      ...+++|.|++|+|||||++.++......... .+.|+..
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~-~v~~~~~   72 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQQALQWGTAMGK-KVGLAML   72 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHHHHHHTSCC-CEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCC-eEEEEeC
Confidence            45689999999999999999998876543111 3556554

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=95.04  E-value=0.009  Score=51.89  Aligned_cols=25  Identities=24%  Similarity=0.242  Sum_probs=16.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH-HHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVA-RKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~-~~~  199 (390)
                      ..+++|+|+.|+|||||++.+. ...
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC---
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            4689999999999999999998 543

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=95.01  E-value=0.014  Score=50.97  Aligned_cols=25  Identities=20%  Similarity=0.271  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...+++|+|+.|+|||||++.+.--
T Consensus        30 ~Ge~~~iiG~nGsGKSTLl~~l~Gl   54 (235)
T 3tif_A           30 EGEFVSIMGPSGSGKSTMLNIIGCL   54 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcC
Confidence            4568999999999999999998654

>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=95.00  E-value=0.016  Score=50.43  Aligned_cols=26  Identities=19%  Similarity=0.323  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+|+|.|++|+||||+++.+.....
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~lg   34 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARALG   34 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999987764

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=94.99  E-value=0.016  Score=52.66  Aligned_cols=28  Identities=25%  Similarity=0.271  Sum_probs=24.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...+++|+|+.|+||||+++.++.....
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~l~~  126 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHRLKN  126 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            4568999999999999999999887653

>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=94.97  E-value=0.018  Score=50.05  Aligned_cols=26  Identities=23%  Similarity=0.061  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...|.|.|+.|+||||+++.+.....
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~l~   41 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKNFC   41 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999988764

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=94.96  E-value=0.035  Score=51.68  Aligned_cols=38  Identities=21%  Similarity=0.289  Sum_probs=29.1

Q ss_pred             HHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          163 LNDILDALK--NPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       163 ~~~l~~~L~--~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...++..+.  .++..+|+|+|.+|+|||||+..+.....
T Consensus        65 ~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~~l~  104 (355)
T 3p32_A           65 AQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLI  104 (355)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHHHHH
Confidence            334444443  35678999999999999999999987764

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.96  E-value=0.011  Score=51.13  Aligned_cols=25  Identities=24%  Similarity=0.218  Sum_probs=21.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...+++|+|+.|+|||||++.+.--
T Consensus        29 ~Ge~~~iiG~nGsGKSTLl~~l~Gl   53 (224)
T 2pcj_A           29 KGEFVSIIGASGSGKSTLLYILGLL   53 (224)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3468999999999999999998654

>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=94.96  E-value=0.015  Score=52.73  Aligned_cols=26  Identities=19%  Similarity=0.277  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|+|.||.|+|||||+..++....
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~~~~   28 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAKRLN   28 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHTTT
T ss_pred             CcEEEEECCCcCCHHHHHHHHHHhCc
Confidence            46889999999999999999987653

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

Probab=94.94  E-value=0.016  Score=55.45  Aligned_cols=46  Identities=22%  Similarity=0.243  Sum_probs=33.8

Q ss_pred             cccchhHHHHHHHHHhcC--------------CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          155 ACESRMSTLNDILDALKN--------------PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~~--------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|.+..+..+...+..              ...+-|.++|++|+||||+|+.++....
T Consensus        16 ~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~   75 (444)
T 1g41_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN   75 (444)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             HhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcC
Confidence            467766666666554421              1245688999999999999999998874

>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=94.93  E-value=0.072  Score=46.22  Aligned_cols=56  Identities=18%  Similarity=0.109  Sum_probs=30.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh-hhcCCC-CeEEEEEeCCCCCHHHHHHHHHHHhC
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA-ETEKLF-DQVIFVEVSKIQDIRKIQGEIADKLG  231 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~-~~~~~f-~~~~wv~v~~~~~~~~l~~~i~~~l~  231 (390)
                      +.+.|.|+.|+||||+...+.-.. ...... ...+.+.........++...+...++
T Consensus        77 ~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~  134 (235)
T 3llm_A           77 SVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERG  134 (235)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTT
T ss_pred             CEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhc
Confidence            578899999999998776665442 221111 22333333333333444455554443

>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=94.92  E-value=0.017  Score=49.48  Aligned_cols=23  Identities=26%  Similarity=0.245  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      ..+|+|.|+.|+||||+++.+..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999999965

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.92  E-value=0.012  Score=50.46  Aligned_cols=24  Identities=29%  Similarity=0.115  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..+++|.|+.|+|||||++.+.--
T Consensus        22 Ge~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           22 NTIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             CSEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            457999999999999999999866

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=94.90  E-value=0.038  Score=49.05  Aligned_cols=28  Identities=14%  Similarity=0.145  Sum_probs=24.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ....+++|+|+.|+|||||++.+.....
T Consensus        23 ~~g~~v~i~Gp~GsGKSTll~~l~g~~~   50 (261)
T 2eyu_A           23 RKMGLILVTGPTGSGKSTTIASMIDYIN   50 (261)
T ss_dssp             CSSEEEEEECSTTCSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCccHHHHHHHHHHhCC
Confidence            3456899999999999999999987654

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=94.90  E-value=0.021  Score=54.36  Aligned_cols=99  Identities=19%  Similarity=0.269  Sum_probs=58.1

Q ss_pred             HHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhc--------CCCC-eEEEEEeCCC-CCHHHHHHHHHHHhCC--
Q 042806          166 ILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETE--------KLFD-QVIFVEVSKI-QDIRKIQGEIADKLGL--  232 (390)
Q Consensus       166 l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~--------~~f~-~~~wv~v~~~-~~~~~l~~~i~~~l~~--  232 (390)
                      .++.|.. .+-.-++|.|.+|+|||+|+.++.+.....        ++-+ .++++.++.. ....++...+...-..  
T Consensus       137 aID~l~pigrGQr~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~l~~~g~~~r  216 (464)
T 3gqb_B          137 TIDVMNTLVRGQKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSR  216 (464)
T ss_dssp             HHHTTSCCBTTCBCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEECHHHHHHHHHHHHHTSGGGG
T ss_pred             eeecccccccCCEEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCchHHHHHHHHHhhhcccccc
Confidence            4444432 233456789999999999999998876431        1122 5677777754 3456666655432111  


Q ss_pred             -----CCCCCCchH------HHHHHHHHHhC--CCeEEEEEeCCC
Q 042806          233 -----TLHEESDSG------RARSLRNRLKK--EKTILVILDNIW  264 (390)
Q Consensus       233 -----~~~~~~~~~------~~~~l~~~l~~--~~~~LlVlDdv~  264 (390)
                           ...+.+...      ..-.+.+++..  ++.+|+++||+.
T Consensus       217 tvvv~~t~d~p~~~r~~~~~~a~tiAEyfrd~~G~~VLl~~DdlT  261 (464)
T 3gqb_B          217 SVLFLNKADDPTIERILTPRMALTVAEYLAFEHDYHVLVILTDMT  261 (464)
T ss_dssp             EEEEEEETTSCTHHHHHHHHHHHHHHHHHHHTTCCEEEEEEETHH
T ss_pred             eEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChH
Confidence                 111112111      22356677763  677999999984

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=94.90  E-value=0.017  Score=49.95  Aligned_cols=23  Identities=30%  Similarity=0.242  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .|.|.|++|+||||+++.+....
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999998876

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=94.90  E-value=0.017  Score=57.93  Aligned_cols=46  Identities=15%  Similarity=0.133  Sum_probs=38.3

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...++|.+..++.+...+..+  ..+.|+|++|+||||||+.+.....
T Consensus        40 l~~i~G~~~~l~~l~~~i~~g--~~vll~Gp~GtGKTtlar~ia~~l~   85 (604)
T 3k1j_A           40 IDQVIGQEHAVEVIKTAANQK--RHVLLIGEPGTGKSMLGQAMAELLP   85 (604)
T ss_dssp             HHHCCSCHHHHHHHHHHHHTT--CCEEEECCTTSSHHHHHHHHHHTSC
T ss_pred             cceEECchhhHhhccccccCC--CEEEEEeCCCCCHHHHHHHHhccCC
Confidence            456888888888877777655  4788999999999999999998764

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=94.89  E-value=0.016  Score=53.29  Aligned_cols=25  Identities=36%  Similarity=0.309  Sum_probs=22.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+|+|.|+.|+|||||+..++....
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~   32 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFN   32 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcC
Confidence            5899999999999999999988754

>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=94.87  E-value=0.018  Score=48.79  Aligned_cols=24  Identities=25%  Similarity=0.289  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +|+|.|+.|+||||+++.+.....
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~lg   27 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAALG   27 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcC
Confidence            899999999999999999988764

>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=94.86  E-value=0.018  Score=48.63  Aligned_cols=26  Identities=23%  Similarity=0.290  Sum_probs=22.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+|+|.|+.|+||||+++.+....
T Consensus        11 ~~~iIgltG~~GSGKSTva~~L~~~l   36 (192)
T 2grj_A           11 HHMVIGVTGKIGTGKSTVCEILKNKY   36 (192)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHhc
Confidence            35689999999999999999998764

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=94.84  E-value=0.017  Score=49.54  Aligned_cols=25  Identities=20%  Similarity=0.146  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..|.|.|++|+||||+++.+.....
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l~   30 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEYG   30 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4688999999999999999988763

>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=94.84  E-value=0.033  Score=48.35  Aligned_cols=28  Identities=25%  Similarity=0.208  Sum_probs=24.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...+|+|.|+.|+||||+++.+......
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l~~   52 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRLVK   52 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHTT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHhc
Confidence            4568999999999999999999998764

>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=94.81  E-value=0.057  Score=52.08  Aligned_cols=43  Identities=23%  Similarity=0.297  Sum_probs=32.2

Q ss_pred             hhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          159 RMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       159 R~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      ....+..+...+.+++ +.+.|.|++|+||||++..+.......
T Consensus        30 Q~~av~~~~~~i~~~~-~~~li~G~aGTGKT~ll~~~~~~l~~~   72 (459)
T 3upu_A           30 QKNAFNIVMKAIKEKK-HHVTINGPAGTGATTLTKFIIEALIST   72 (459)
T ss_dssp             HHHHHHHHHHHHHSSS-CEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhcCC-CEEEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            3344555666665544 388999999999999999999887654

>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=94.81  E-value=0.018  Score=49.25  Aligned_cols=23  Identities=22%  Similarity=0.047  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .|.|.|++|+||||+++.+....
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            47899999999999999998876

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=94.80  E-value=0.015  Score=50.82  Aligned_cols=26  Identities=15%  Similarity=0.262  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           30 EGALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45689999999999999999997654

>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=94.80  E-value=0.018  Score=52.22  Aligned_cols=27  Identities=22%  Similarity=0.092  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..++|+|.|+.|+|||||+..++....
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~~~~   35 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRKILP   35 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCcEEEEECCCccCHHHHHHHHHHhCC
Confidence            356899999999999999999988753

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=94.77  E-value=0.017  Score=52.75  Aligned_cols=25  Identities=24%  Similarity=0.143  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ++|.|+|+.|+|||||+..+.....
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l~   30 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADALP   30 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcC
Confidence            5799999999999999999988753

>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=94.76  E-value=0.018  Score=51.74  Aligned_cols=23  Identities=26%  Similarity=0.556  Sum_probs=21.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVA  196 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~  196 (390)
                      .+.+|+|.|+.|+||||+++.+.
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            45689999999999999999998

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=94.76  E-value=0.019  Score=52.33  Aligned_cols=28  Identities=18%  Similarity=0.107  Sum_probs=24.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ....+|+|.|+.|+|||||++.+.....
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3457899999999999999999987654

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=94.75  E-value=0.018  Score=48.22  Aligned_cols=25  Identities=20%  Similarity=0.308  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-.++|+|+.|+|||||++.+....
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcCC
Confidence            3468899999999999999998754

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.75  E-value=0.016  Score=51.57  Aligned_cols=26  Identities=19%  Similarity=0.245  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        31 ~Ge~~~liG~nGsGKSTLlk~l~Gl~   56 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTFLRCINFLE   56 (262)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45689999999999999999986543

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=94.74  E-value=0.017  Score=50.93  Aligned_cols=26  Identities=35%  Similarity=0.294  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+|+|+|+.|+||||+++.+.....
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~lg   73 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARSLG   73 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcC
Confidence            45799999999999999999988764

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=94.73  E-value=0.017  Score=50.94  Aligned_cols=25  Identities=28%  Similarity=0.320  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...+++|.|+.|+|||||++.+.--
T Consensus        28 ~Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           28 KGEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3468999999999999999999874

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=94.71  E-value=0.017  Score=53.12  Aligned_cols=27  Identities=22%  Similarity=0.305  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..++|+|.|+.|+|||||+..++....
T Consensus        39 ~~~lIvI~GPTgsGKTtLa~~LA~~l~   65 (339)
T 3a8t_A           39 KEKLLVLMGATGTGKSRLSIDLAAHFP   65 (339)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHTTSC
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHCC
Confidence            346899999999999999999988653

>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=94.69  E-value=0.017  Score=54.99  Aligned_cols=27  Identities=26%  Similarity=0.335  Sum_probs=23.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ....+|.|+|++|+||||+++.+....
T Consensus       256 ~~~~lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          256 PNPEVVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             SSCCEEEEESCTTSSHHHHHHHHTGGG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            457899999999999999999998765

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=94.68  E-value=0.027  Score=53.92  Aligned_cols=99  Identities=19%  Similarity=0.260  Sum_probs=59.6

Q ss_pred             HHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCC--CCeEEEEEeCCCC-CHHHHHHHHHHHhCCC-------C
Q 042806          166 ILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETEKL--FDQVIFVEVSKIQ-DIRKIQGEIADKLGLT-------L  234 (390)
Q Consensus       166 l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~--f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~-------~  234 (390)
                      .++.|.. .+-.-++|.|.+|+|||+|+.++++.......  =+.++++.++... ...+++..+...-...       .
T Consensus       142 ~ID~l~pigrGQr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~Ev~e~~~~~~~~g~m~rtvvV~~t  221 (469)
T 2c61_A          142 TIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNL  221 (469)
T ss_dssp             HHHTTSCCBTTCBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHHHHHHHHHHHHHSGGGGEEEEEEE
T ss_pred             eeeeeeccccCCEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHHHHHHHHHHHhccCccceEEEEEC
Confidence            4454443 23345678899999999999999988653211  1357777776543 4566666665442111       1


Q ss_pred             CCCCchH------HHHHHHHHHh--CCCeEEEEEeCCC
Q 042806          235 HEESDSG------RARSLRNRLK--KEKTILVILDNIW  264 (390)
Q Consensus       235 ~~~~~~~------~~~~l~~~l~--~~~~~LlVlDdv~  264 (390)
                      .+.+...      ..-.+.+++.  .++.+|+++||+.
T Consensus       222 sd~p~~~r~~~~~~a~tiAEyfrdd~G~dVLl~~Dslt  259 (469)
T 2c61_A          222 ADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDIT  259 (469)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEeCHH
Confidence            1111111      2335666666  4677999999973

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.68  E-value=0.015  Score=50.98  Aligned_cols=26  Identities=23%  Similarity=0.252  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.++--.
T Consensus        31 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~   56 (240)
T 1ji0_A           31 RGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            44689999999999999999997543

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.68  E-value=0.012  Score=53.08  Aligned_cols=27  Identities=11%  Similarity=0.198  Sum_probs=20.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +..+|+|.|+.|+||||+++.+.....
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~lg   30 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQIFR   30 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHh
Confidence            456899999999999999999988654

>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=94.68  E-value=0.07  Score=45.72  Aligned_cols=32  Identities=16%  Similarity=0.086  Sum_probs=26.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCe
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQ  207 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~  207 (390)
                      ..+|+|.|+.|+||||+++.+.+..... .+..
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l~~~-~~~v   37 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERLRER-GIEV   37 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHTT-TCCE
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHHHc-CCCc
Confidence            4689999999999999999999988653 3554

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=94.67  E-value=0.022  Score=52.93  Aligned_cols=28  Identities=25%  Similarity=0.271  Sum_probs=24.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...+++|+|+.|+||||+++.++.....
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l~~  183 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRLKN  183 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhccc
Confidence            3569999999999999999999887653

>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=94.67  E-value=0.017  Score=51.76  Aligned_cols=25  Identities=24%  Similarity=0.268  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...+++|+|+.|+|||||++.+.--
T Consensus        33 ~Ge~~~iiGpnGsGKSTLl~~l~Gl   57 (275)
T 3gfo_A           33 RGEVTAILGGNGVGKSTLFQNFNGI   57 (275)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcC
Confidence            4568999999999999999998654

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=94.64  E-value=0.015  Score=51.48  Aligned_cols=26  Identities=23%  Similarity=0.158  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        32 ~Ge~~~liG~nGsGKSTLlk~l~Gl~   57 (257)
T 1g6h_A           32 KGDVTLIIGPNGSGKSTLINVITGFL   57 (257)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            44689999999999999999986543

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=94.64  E-value=0.019  Score=48.43  Aligned_cols=24  Identities=21%  Similarity=0.296  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..++|+|+.|+|||||++.+....
T Consensus         6 ~kv~lvG~~g~GKSTLl~~l~~~~   29 (199)
T 2f9l_A            6 FKVVLIGDSGVGKSNLLSRFTRNE   29 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECcCCCCHHHHHHHHhcCC
Confidence            457899999999999999998753

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=94.62  E-value=0.021  Score=50.89  Aligned_cols=25  Identities=28%  Similarity=0.331  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...+++|+|+.|+|||||++.++--
T Consensus        45 ~Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           45 PGEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4568999999999999999999874

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=94.61  E-value=0.014  Score=50.22  Aligned_cols=26  Identities=35%  Similarity=0.390  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.++--.
T Consensus        34 ~Ge~~~iiG~NGsGKSTLlk~l~Gl~   59 (214)
T 1sgw_A           34 KGNVVNFHGPNGIGKTTLLKTISTYL   59 (214)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34579999999999999999987643

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=94.59  E-value=0.018  Score=51.19  Aligned_cols=26  Identities=15%  Similarity=0.179  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        49 ~Gei~~liG~NGsGKSTLlk~l~Gl~   74 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTFLRCLNLLE   74 (263)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEEcCCCCcHHHHHHHHHcCC
Confidence            45689999999999999999987543

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=94.58  E-value=0.028  Score=51.45  Aligned_cols=28  Identities=25%  Similarity=0.298  Sum_probs=24.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...+|+|+|++|+||||++..++.....
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~l~~  131 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANYYAE  131 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4679999999999999999999887764

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=94.56  E-value=0.017  Score=50.27  Aligned_cols=26  Identities=23%  Similarity=0.257  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        33 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   58 (229)
T 2pze_A           33 RGQLLAVAGSTGAGKTSLLMMIMGEL   58 (229)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            45689999999999999999997654

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=94.56  E-value=0.044  Score=52.84  Aligned_cols=95  Identities=18%  Similarity=0.177  Sum_probs=56.0

Q ss_pred             HHHHhcC-CCccEEEEEcCCCCcHHHHH-HHHHHHhhhcCCCC-eEEEEEeCCCC-CHHHHHHHHHHHhCCC-------C
Q 042806          166 ILDALKN-PDVNMLGIYGMGGIVKTTLA-KEVARKAETEKLFD-QVIFVEVSKIQ-DIRKIQGEIADKLGLT-------L  234 (390)
Q Consensus       166 l~~~L~~-~~~~vi~I~G~~GvGKTtLa-~~v~~~~~~~~~f~-~~~wv~v~~~~-~~~~l~~~i~~~l~~~-------~  234 (390)
                      .++.|.. .+-.-++|.|.+|+|||+|+ ..+.+...    .+ .++++.++... ...++...+...-...       .
T Consensus       152 aID~l~PigrGQR~~Ifg~~g~GKT~Lal~~I~~~~~----~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~tvvV~at  227 (502)
T 2qe7_A          152 AIDSMIPIGRGQRELIIGDRQTGKTTIAIDTIINQKG----QDVICIYVAIGQKQSTVAGVVETLRQHDALDYTIVVTAS  227 (502)
T ss_dssp             HHHHSSCCBTTCBCEEEECSSSCHHHHHHHHHHGGGS----CSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTEEEEEEC
T ss_pred             ecccccccccCCEEEEECCCCCCchHHHHHHHHHhhc----CCcEEEEEECCCcchHHHHHHHHHhhCCCcceeEEEEEC
Confidence            4455543 23456789999999999995 46666542    45 35778887654 4556666665432221       1


Q ss_pred             CCCCchH------HHHHHHHHHhC-CCeEEEEEeCCC
Q 042806          235 HEESDSG------RARSLRNRLKK-EKTILVILDNIW  264 (390)
Q Consensus       235 ~~~~~~~------~~~~l~~~l~~-~~~~LlVlDdv~  264 (390)
                      .+.+...      ..-.+.+++.+ ++.+|+++||+.
T Consensus       228 ad~p~~~r~~a~~~a~tiAEyfrd~G~dVLl~~Dslt  264 (502)
T 2qe7_A          228 ASEPAPLLYLAPYAGCAMGEYFMYKGKHALVVYDDLS  264 (502)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEECHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEecHH
Confidence            1111111      12245555543 567999999984

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=94.56  E-value=0.14  Score=49.84  Aligned_cols=96  Identities=14%  Similarity=0.188  Sum_probs=58.0

Q ss_pred             HHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC-HHHHHHHHHH----HhCC------
Q 042806          165 DILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD-IRKIQGEIAD----KLGL------  232 (390)
Q Consensus       165 ~l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~-~~~l~~~i~~----~l~~------  232 (390)
                      +.++.|.. .+-.-++|.|..|+|||+|+.++.+..    +-+.++++.++.... ..+++.++-.    ..+.      
T Consensus       216 rvID~l~PigkGqr~~I~g~~g~GKT~L~~~ia~~~----~~~~~V~~~iGER~~Ev~e~~~~~~el~d~~~g~~~m~rt  291 (588)
T 3mfy_A          216 RVIDTFFPQAKGGTAAIPGPAGSGKTVTQHQLAKWS----DAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTGKPLMERT  291 (588)
T ss_dssp             HHHHHHSCEETTCEEEECSCCSHHHHHHHHHHHHHS----SCSEEEEEECCSSSSHHHHHHHHTTTCEETTTTEEGGGGE
T ss_pred             chhhccCCcccCCeEEeecCCCCCHHHHHHHHHhcc----CCCEEEEEEecccHHHHHHHHHHHHHhcccccccccccce
Confidence            34555543 344568899999999999999987653    246788888887654 5555555422    1110      


Q ss_pred             ----CCCCCCchH------HHHHHHHHHhC-CCeEEEEEeCCC
Q 042806          233 ----TLHEESDSG------RARSLRNRLKK-EKTILVILDNIW  264 (390)
Q Consensus       233 ----~~~~~~~~~------~~~~l~~~l~~-~~~~LlVlDdv~  264 (390)
                          ...+.+...      ..-.+.+++.+ ++.+||++|++.
T Consensus       292 vvV~~tsd~p~~~r~~~~~~a~tiAEyfrd~G~dVLl~~Dslt  334 (588)
T 3mfy_A          292 VLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTS  334 (588)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTT
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCCCEEEeecchH
Confidence                111111111      12244455543 667999999995

>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=94.55  E-value=0.021  Score=51.68  Aligned_cols=23  Identities=30%  Similarity=0.336  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .+|.|.|++|+||||+++.+...
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~   25 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAK   25 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            57899999999999999999874

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=94.54  E-value=0.019  Score=50.41  Aligned_cols=25  Identities=20%  Similarity=0.191  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...+++|+|+.|+|||||++.+.--
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (243)
T 1mv5_A           27 PNSIIAFAGPSGGGKSTIFSLLERF   51 (243)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999999998754

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=94.53  E-value=0.017  Score=50.86  Aligned_cols=26  Identities=35%  Similarity=0.431  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        34 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   59 (247)
T 2ff7_A           34 QGEVIGIVGRSGSGKSTLTKLIQRFY   59 (247)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34689999999999999999986553

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=94.53  E-value=0.019  Score=51.16  Aligned_cols=26  Identities=27%  Similarity=0.298  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        36 ~Ge~~~liG~nGsGKSTLl~~l~Gl~   61 (266)
T 4g1u_C           36 SGEMVAIIGPNGAGKSTLLRLLTGYL   61 (266)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHTSSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            45689999999999999999997543

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=94.50  E-value=0.047  Score=52.68  Aligned_cols=95  Identities=15%  Similarity=0.169  Sum_probs=55.6

Q ss_pred             HHHHhcC-CCccEEEEEcCCCCcHHHHH-HHHHHHhhhcCCCC-eEEEEEeCCCC-CHHHHHHHHHHHhCC-------CC
Q 042806          166 ILDALKN-PDVNMLGIYGMGGIVKTTLA-KEVARKAETEKLFD-QVIFVEVSKIQ-DIRKIQGEIADKLGL-------TL  234 (390)
Q Consensus       166 l~~~L~~-~~~~vi~I~G~~GvGKTtLa-~~v~~~~~~~~~f~-~~~wv~v~~~~-~~~~l~~~i~~~l~~-------~~  234 (390)
                      .++.|.. .+-.-++|.|.+|+|||+|+ ..+.+...    .+ .++++.++... ...++...+...-..       ..
T Consensus       165 aID~l~PigrGQR~~I~g~~g~GKT~Lal~~I~~~~~----~dv~~V~~~IGeR~~Ev~e~~~~~~~~g~m~rtvvV~at  240 (515)
T 2r9v_A          165 AIDSMIPIGRGQRELIIGDRQTGKTAIAIDTIINQKG----QGVYCIYVAIGQKKSAIARIIDKLRQYGAMEYTTVVVAS  240 (515)
T ss_dssp             HHHHHSCEETTCBEEEEEETTSSHHHHHHHHHHTTTT----TTEEEEEEEESCCHHHHHHHHHHHHHTTGGGGEEEEEEC
T ss_pred             ccccccccccCCEEEEEcCCCCCccHHHHHHHHHhhc----CCcEEEEEEcCCCcHHHHHHHHHHHhCCCcceeEEEEEC
Confidence            4444443 23456789999999999995 46666542    55 35778887654 455666666542211       11


Q ss_pred             CCCCchH------HHHHHHHHHhC-CCeEEEEEeCCC
Q 042806          235 HEESDSG------RARSLRNRLKK-EKTILVILDNIW  264 (390)
Q Consensus       235 ~~~~~~~------~~~~l~~~l~~-~~~~LlVlDdv~  264 (390)
                      .+.+...      ..-.+.+++.+ ++.+|+++||+.
T Consensus       241 ad~p~~~r~~a~~~a~tiAEyfrd~G~dVLli~DslT  277 (515)
T 2r9v_A          241 ASDPASLQYIAPYAGCAMGEYFAYSGRDALVVYDDLS  277 (515)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEETHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEeccHH
Confidence            1111111      12245555543 567999999984

>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=94.50  E-value=0.023  Score=51.57  Aligned_cols=27  Identities=22%  Similarity=0.247  Sum_probs=23.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +...+++|+|+.|+|||||++.+..-.
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            456789999999999999999998654

>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=94.48  E-value=0.02  Score=50.70  Aligned_cols=26  Identities=23%  Similarity=0.353  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+|||||++.++--.
T Consensus        40 ~Gei~~l~G~NGsGKSTLlk~l~Gl~   65 (256)
T 1vpl_A           40 EGEIFGLIGPNGAGKTTTLRIISTLI   65 (256)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            45689999999999999999987543

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=94.47  E-value=0.04  Score=48.55  Aligned_cols=27  Identities=33%  Similarity=0.326  Sum_probs=23.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...++.+.|.+|+||||++..+.....
T Consensus        13 ~~~i~~~~GkgGvGKTTl~~~La~~l~   39 (262)
T 1yrb_A           13 ASMIVVFVGTAGSGKTTLTGEFGRYLE   39 (262)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            356788999999999999999998775

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.46  E-value=0.02  Score=50.78  Aligned_cols=25  Identities=28%  Similarity=0.232  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...+++|+|+.|+|||||++.+.--
T Consensus        45 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   69 (260)
T 2ghi_A           45 SGTTCALVGHTGSGKSTIAKLLYRF   69 (260)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcc
Confidence            4568999999999999999999654

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=94.43  E-value=0.021  Score=51.07  Aligned_cols=26  Identities=19%  Similarity=0.146  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        44 ~Ge~~~i~G~nGsGKSTLlk~l~Gl~   69 (271)
T 2ixe_A           44 PGKVTALVGPNGSGKSTVAALLQNLY   69 (271)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45689999999999999999987543

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=94.42  E-value=0.026  Score=45.27  Aligned_cols=24  Identities=21%  Similarity=0.275  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +-|+|+|.+|+|||||+..+....
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~~   25 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKKR   25 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            357899999999999999998753

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=94.42  E-value=0.022  Score=46.36  Aligned_cols=23  Identities=13%  Similarity=0.235  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..|+|+|.+|+|||||.+.+...
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            45889999999999999999764

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=94.40  E-value=0.02  Score=47.51  Aligned_cols=22  Identities=36%  Similarity=0.379  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      -|+|+|.+|+|||||++.+...
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3789999999999999999763

>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=94.40  E-value=0.022  Score=50.99  Aligned_cols=27  Identities=22%  Similarity=0.222  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...++.|+|++|+|||||+..+.....
T Consensus        29 ~G~i~~i~G~~GsGKTtl~~~l~~~~~   55 (279)
T 1nlf_A           29 AGTVGALVSPGGAGKSMLALQLAAQIA   55 (279)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            456899999999999999999987554

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=94.39  E-value=0.019  Score=50.61  Aligned_cols=26  Identities=27%  Similarity=0.301  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        25 ~Ge~~~liG~NGsGKSTLlk~l~Gl~   50 (249)
T 2qi9_C           25 AGEILHLVGPNGAGKSTLLARMAGMT   50 (249)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34689999999999999999986543

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=94.37  E-value=0.024  Score=50.61  Aligned_cols=23  Identities=22%  Similarity=0.368  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .++|+|+.|+|||||++.++...
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~   26 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQ   26 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            47899999999999999998765

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=94.35  E-value=0.092  Score=50.70  Aligned_cols=99  Identities=15%  Similarity=0.201  Sum_probs=57.0

Q ss_pred             HHHHhcC-CCccEEEEEcCCCCcHHHHH-HHHHHHhhh----cCCCC-eEEEEEeCCCC-CHHHHHHHHHHHhCCC----
Q 042806          166 ILDALKN-PDVNMLGIYGMGGIVKTTLA-KEVARKAET----EKLFD-QVIFVEVSKIQ-DIRKIQGEIADKLGLT----  233 (390)
Q Consensus       166 l~~~L~~-~~~~vi~I~G~~GvGKTtLa-~~v~~~~~~----~~~f~-~~~wv~v~~~~-~~~~l~~~i~~~l~~~----  233 (390)
                      .++.|.. .+-.-++|.|.+|+|||+|| ..+.+....    .++-+ .++++.++... ...++...+...-...    
T Consensus       152 aID~l~PigrGQR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~~~~~~~~~~g~m~~tvv  231 (510)
T 2ck3_A          152 AVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIV  231 (510)
T ss_dssp             HHHHHSCCBTTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEE
T ss_pred             eeccccccccCCEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHHHHHHHHHHHhcCCcccceE
Confidence            4444443 23455789999999999994 566666542    12244 47788887654 4566666665422111    


Q ss_pred             ---CCCCCchH------HHHHHHHHHhC-CCeEEEEEeCCC
Q 042806          234 ---LHEESDSG------RARSLRNRLKK-EKTILVILDNIW  264 (390)
Q Consensus       234 ---~~~~~~~~------~~~~l~~~l~~-~~~~LlVlDdv~  264 (390)
                         ..+.+...      ..-.+.+++.+ ++.+||++||+.
T Consensus       232 V~atad~p~~~r~~a~~~a~tiAEyfrd~G~dVLli~Dslt  272 (510)
T 2ck3_A          232 VSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLS  272 (510)
T ss_dssp             EEECTTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEETHH
T ss_pred             EEECCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEcCHH
Confidence               11111111      12245555543 567999999984

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=94.35  E-value=0.019  Score=50.68  Aligned_cols=26  Identities=23%  Similarity=0.285  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        30 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~   55 (253)
T 2nq2_C           30 KGDILAVLGQNGCGKSTLLDLLLGIH   55 (253)
T ss_dssp             TTCEEEEECCSSSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34689999999999999999997654

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=94.35  E-value=0.022  Score=50.72  Aligned_cols=26  Identities=31%  Similarity=0.199  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.++--.
T Consensus        32 ~Ge~~~liG~nGsGKSTLl~~i~Gl~   57 (266)
T 2yz2_A           32 EGECLLVAGNTGSGKSTLLQIVAGLI   57 (266)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            45689999999999999999986543

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=94.35  E-value=0.027  Score=46.38  Aligned_cols=34  Identities=24%  Similarity=0.255  Sum_probs=25.4

Q ss_pred             HHHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHH
Q 042806          164 NDILDALKN-PDVNMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       164 ~~l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      .++.+.+.. .+..-|+|+|.+|+|||||+..+..
T Consensus         6 ~~~~~~~~~~~~~~~i~v~G~~~~GKssli~~l~~   40 (183)
T 1moz_A            6 SSMFDKLWGSNKELRILILGLDGAGKTTILYRLQI   40 (183)
T ss_dssp             HHHHGGGTTCSSCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             HHHHHHhcCCCCccEEEEECCCCCCHHHHHHHHhc
Confidence            344454544 4556788999999999999998864

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=94.34  E-value=0.033  Score=53.83  Aligned_cols=28  Identities=29%  Similarity=0.348  Sum_probs=24.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...+++|+|+.|+|||||++.+......
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll~~  319 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQFEQ  319 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHhhh
Confidence            4579999999999999999999887653

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=94.32  E-value=0.02  Score=51.42  Aligned_cols=26  Identities=27%  Similarity=0.304  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        46 ~Ge~~~liG~NGsGKSTLlk~l~Gl~   71 (279)
T 2ihy_A           46 KGDKWILYGLNGAGKTTLLNILNAYE   71 (279)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            45689999999999999999987543

>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=94.31  E-value=0.18  Score=43.81  Aligned_cols=38  Identities=18%  Similarity=-0.043  Sum_probs=25.6

Q ss_pred             hhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          159 RMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       159 R~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |....+.+..++.. +  -+.|+|+.|.|||.++..+....
T Consensus        95 ~~~Q~~ai~~~~~~-~--~~ll~~~tG~GKT~~a~~~~~~~  132 (237)
T 2fz4_A           95 RDYQEKALERWLVD-K--RGCIVLPTGSGKTHVAMAAINEL  132 (237)
T ss_dssp             CHHHHHHHHHHTTT-S--EEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHhC-C--CEEEEeCCCCCHHHHHHHHHHHc
Confidence            33334444444433 2  27789999999999999887765

>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=94.31  E-value=0.025  Score=45.39  Aligned_cols=23  Identities=26%  Similarity=0.468  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+++|.+|+|||||+..+....
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            37899999999999999998764

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=94.29  E-value=0.028  Score=49.04  Aligned_cols=26  Identities=23%  Similarity=0.193  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...|+|.|..|+||||+++.+.....
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            46799999999999999999998863

>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=94.29  E-value=0.026  Score=45.61  Aligned_cols=24  Identities=13%  Similarity=0.264  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+....
T Consensus         6 ~~i~v~G~~~~GKssl~~~l~~~~   29 (168)
T 1z2a_A            6 IKMVVVGNGAVGKSSMIQRYCKGI   29 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEEEECcCCCCHHHHHHHHHcCC
Confidence            347899999999999999998753

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=94.29  E-value=0.034  Score=46.46  Aligned_cols=108  Identities=19%  Similarity=0.038  Sum_probs=50.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      .++.|+|+.|+||||++..++......+ .. +.++.....  .......+...++........ .....+.+.+. ++.
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~~~~g-~~-v~~~~~~~d--~r~~~~~i~s~~g~~~~~~~~-~~~~~~~~~~~-~~~   77 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIYKLGK-KK-VAVFKPKID--SRYHSTMIVSHSGNGVEAHVI-ERPEEMRKYIE-EDT   77 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTT-CE-EEEEEEC-------CCCEECC----CEECEEE-SSGGGGGGGCC-TTE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCC-Ce-EEEEeeccc--cccCcccEEecCCCceeeEEE-CCHHHHHHHhc-CCC
Confidence            5788999999999999977776654322 32 233322211  000000111111111110000 00111222222 244


Q ss_pred             EEEEEeCCCCC-cccccccCCCCCCCCCcEEEEEecc
Q 042806          256 ILVILDNIWGN-LDFQAVGIPHGDDRKGCKVLLTARS  291 (390)
Q Consensus       256 ~LlVlDdv~~~-~~~~~l~~~l~~~~~~s~IivTtr~  291 (390)
                      -+|++|.++.. .+|......+.+  .+..|++|.+.
T Consensus        78 dvviIDE~Q~~~~~~~~~l~~l~~--~~~~Vi~~Gl~  112 (184)
T 2orw_A           78 RGVFIDEVQFFNPSLFEVVKDLLD--RGIDVFCAGLD  112 (184)
T ss_dssp             EEEEECCGGGSCTTHHHHHHHHHH--TTCEEEEEEES
T ss_pred             CEEEEECcccCCHHHHHHHHHHHH--CCCCEEEEeec
Confidence            69999999765 344443322212  27789998884

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=94.27  E-value=0.038  Score=45.82  Aligned_cols=33  Identities=24%  Similarity=0.210  Sum_probs=25.4

Q ss_pred             HHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          165 DILDALKNPDVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       165 ~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .+.+ +...+..-|+|+|.+|+|||||+..+...
T Consensus         7 ~~~~-~~~~~~~~i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A            7 RIWR-LFNHQEHKVIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             HHHH-HHTTSCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHH-hcCCCccEEEEECCCCCCHHHHHHHHhcC
Confidence            4455 34445566889999999999999999854

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=94.18  E-value=0.04  Score=45.58  Aligned_cols=25  Identities=28%  Similarity=0.311  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...-|+|+|.+|+|||||+..+...
T Consensus        15 ~~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           15 QEVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CceEEEEECCCCCCHHHHHHHHhcC
Confidence            4456889999999999999998764

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=94.12  E-value=0.087  Score=45.57  Aligned_cols=29  Identities=17%  Similarity=0.193  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      ...+|+|.|+.|+||||+++.+.+.....
T Consensus        24 ~g~~I~~eG~~GsGKsT~~~~l~~~l~~~   52 (227)
T 3v9p_A           24 RGKFITFEGIDGAGKTTHLQWFCDRLQER   52 (227)
T ss_dssp             CCCEEEEECCC---CHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhh
Confidence            34689999999999999999999988653

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=94.10  E-value=0.036  Score=46.14  Aligned_cols=26  Identities=19%  Similarity=0.042  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ....|+|+|.+|+|||||+..+....
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34578899999999999999998753

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=94.10  E-value=0.026  Score=46.77  Aligned_cols=23  Identities=13%  Similarity=0.235  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..|+|+|.+|+|||||+..+...
T Consensus         8 ~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            8 YEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46889999999999999999874

>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=94.09  E-value=0.032  Score=52.26  Aligned_cols=27  Identities=26%  Similarity=0.108  Sum_probs=23.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +...+++|+|++|+|||||++.+....
T Consensus       167 ~~~~~i~l~G~~GsGKSTl~~~l~~~~  193 (377)
T 1svm_A          167 PKKRYWLFKGPIDSGKTTLAAALLELC  193 (377)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            456799999999999999999998754

>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=94.06  E-value=0.032  Score=44.91  Aligned_cols=22  Identities=18%  Similarity=0.194  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+....
T Consensus         3 i~~~G~~~~GKssl~~~l~~~~   24 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLGE   24 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            6799999999999999998654

>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=94.05  E-value=0.028  Score=45.27  Aligned_cols=23  Identities=22%  Similarity=0.336  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+....
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            47899999999999999998754

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=94.04  E-value=0.028  Score=52.18  Aligned_cols=26  Identities=35%  Similarity=0.266  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+|||||++.+.--.
T Consensus        29 ~Ge~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           29 PGEILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCchHHHHHHHHhcCC
Confidence            45689999999999999999997643

>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=93.99  E-value=0.033  Score=52.40  Aligned_cols=25  Identities=28%  Similarity=0.426  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ++|+|.|+.|+|||||+..++....
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~~   27 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKFN   27 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHHT
T ss_pred             cEEEEECcchhhHHHHHHHHHHHCC
Confidence            5789999999999999999988754

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=93.98  E-value=0.034  Score=45.47  Aligned_cols=25  Identities=24%  Similarity=0.194  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      +...|+|+|.+|+|||||+..+...
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567889999999999999999764

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=93.97  E-value=0.04  Score=47.90  Aligned_cols=27  Identities=26%  Similarity=0.233  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+|+|.|+.|+||||+++.+.....
T Consensus        15 ~~~~i~i~G~~gsGKst~~~~l~~~lg   41 (236)
T 1q3t_A           15 KTIQIAIDGPASSGKSTVAKIIAKDFG   41 (236)
T ss_dssp             CCCEEEEECSSCSSHHHHHHHHHHHHC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHcC
Confidence            456899999999999999999987653

>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=93.97  E-value=0.032  Score=44.83  Aligned_cols=23  Identities=22%  Similarity=0.404  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+....
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            47899999999999999988654

>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=93.96  E-value=0.027  Score=47.52  Aligned_cols=25  Identities=24%  Similarity=0.187  Sum_probs=22.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .+.|.|.|++|+||||||..+....
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhC
Confidence            4678899999999999999998764

>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=93.96  E-value=0.03  Score=45.25  Aligned_cols=23  Identities=13%  Similarity=0.225  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+.+..
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            37899999999999999998764

>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=93.96  E-value=0.03  Score=45.56  Aligned_cols=24  Identities=33%  Similarity=0.307  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+....
T Consensus         5 ~ki~i~G~~~vGKSsl~~~l~~~~   28 (175)
T 2nzj_A            5 YRVVLLGDPGVGKTSLASLFAGKQ   28 (175)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHCC-
T ss_pred             EEEEEECCCCccHHHHHHHHhcCC
Confidence            357899999999999999997653

>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=93.95  E-value=0.033  Score=44.89  Aligned_cols=23  Identities=26%  Similarity=0.440  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+.+..
T Consensus         5 ki~v~G~~~~GKssli~~l~~~~   27 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            47899999999999999998753

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=93.94  E-value=0.026  Score=50.12  Aligned_cols=24  Identities=29%  Similarity=0.257  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..+++|.|+.|+|||||++.+.--
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~Gl   53 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISGL   53 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999999754

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=93.93  E-value=0.04  Score=47.48  Aligned_cols=37  Identities=16%  Similarity=-0.008  Sum_probs=27.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK  215 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  215 (390)
                      .|.+.|.||+||||++..+....... .++ +.++.+..
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~-G~~-V~v~d~D~   44 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQ-GVR-VMAGVVET   44 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHT-TCC-EEEEECCC
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHC-CCC-EEEEEeCC
Confidence            37789999999999999999887653 354 34444443

>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=93.92  E-value=0.033  Score=46.24  Aligned_cols=23  Identities=26%  Similarity=0.468  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+....
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            47799999999999999998764

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=93.91  E-value=0.034  Score=45.04  Aligned_cols=24  Identities=21%  Similarity=0.219  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+....
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~~   30 (170)
T 1z08_A            7 FKVVLLGEGCVGKTSLVLRYCENK   30 (170)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            347899999999999999998653

>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=93.90  E-value=0.031  Score=45.22  Aligned_cols=23  Identities=13%  Similarity=0.255  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+....
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            47899999999999999998764

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=93.89  E-value=0.023  Score=49.31  Aligned_cols=25  Identities=24%  Similarity=0.061  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      +..+|+|.|+.|+|||||++.+...
T Consensus        19 ~g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           19 QPFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhc
Confidence            4578999999999999999998765

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=93.88  E-value=0.029  Score=51.36  Aligned_cols=26  Identities=23%  Similarity=0.290  Sum_probs=22.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +.++++|.|+.|+|||||++.+....
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~~~   28 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILNEQ   28 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHSC
T ss_pred             cccEEEEEecCCCCHHHHHHHHHhhc
Confidence            46789999999999999999998653

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=93.84  E-value=0.032  Score=45.72  Aligned_cols=25  Identities=24%  Similarity=0.286  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+....
T Consensus         8 ~~~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A            8 ILKVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhCc
Confidence            4458899999999999999998754

>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=93.83  E-value=0.035  Score=45.96  Aligned_cols=24  Identities=21%  Similarity=0.153  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+....
T Consensus         8 ~ki~v~G~~~vGKSsli~~l~~~~   31 (184)
T 1m7b_A            8 CKIVVVGDSQCGKTALLHVFAKDC   31 (184)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            347899999999999999998753

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=93.83  E-value=0.23  Score=48.57  Aligned_cols=95  Identities=13%  Similarity=0.246  Sum_probs=56.9

Q ss_pred             HHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHH----HhCCC------
Q 042806          166 ILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIAD----KLGLT------  233 (390)
Q Consensus       166 l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~----~l~~~------  233 (390)
                      .++.|.. .+-.-++|.|..|+|||+|+.++.+...    -+.++++.++.. ....+++.++-.    .++..      
T Consensus       222 vID~l~PigrGqr~~Ifgg~g~GKT~L~~~ia~~~~----~~v~V~~~iGER~~Ev~e~~~~~~el~d~~~G~~~m~rtv  297 (600)
T 3vr4_A          222 VIDTFFPVTKGGAAAVPGPFGAGKTVVQHQIAKWSD----VDLVVYVGCGERGNEMTDVVNEFPELIDPNTGESLMERTV  297 (600)
T ss_dssp             HHHHHSCCBTTCEEEEECCTTSCHHHHHHHHHHHSS----CSEEEEEEEEECHHHHHHHHHHTTTCBCTTTCSBGGGGEE
T ss_pred             hhhccCCccCCCEEeeecCCCccHHHHHHHHHhccC----CCEEEEEEecccHHHHHHHHHHHHhhcccccccccccceE
Confidence            4555543 3456788999999999999999987642    467888888765 344455444321    11110      


Q ss_pred             ----CCCCCchH------HHHHHHHHHhC-CCeEEEEEeCCC
Q 042806          234 ----LHEESDSG------RARSLRNRLKK-EKTILVILDNIW  264 (390)
Q Consensus       234 ----~~~~~~~~------~~~~l~~~l~~-~~~~LlVlDdv~  264 (390)
                          ..+.+...      ..-.+.+++.+ ++.+||++|++.
T Consensus       298 vV~~tsd~p~~~R~~~~~~altiAEyfrd~G~dVLl~~Ds~t  339 (600)
T 3vr4_A          298 LIANTSNMPVAAREASIYTGITIAEYFRDMGYDVAIMADSTS  339 (600)
T ss_dssp             EEEEETTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEECHH
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEecchH
Confidence                01111111      12345556654 567999999984

>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=93.82  E-value=0.043  Score=46.75  Aligned_cols=26  Identities=19%  Similarity=0.042  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...-|+|+|++|+|||||+..+....
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45678899999999999999998764

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=93.81  E-value=0.033  Score=51.66  Aligned_cols=26  Identities=31%  Similarity=0.437  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+|||||++.++--.
T Consensus        40 ~Ge~~~llGpnGsGKSTLLr~iaGl~   65 (355)
T 1z47_A           40 EGEMVGLLGPSGSGKTTILRLIAGLE   65 (355)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            45689999999999999999987543

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=93.81  E-value=0.032  Score=50.31  Aligned_cols=26  Identities=23%  Similarity=0.257  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        63 ~Ge~~~i~G~NGsGKSTLlk~l~Gl~   88 (290)
T 2bbs_A           63 RGQLLAVAGSTGAGKTSLLMMIMGEL   88 (290)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            45689999999999999999987654

>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=93.80  E-value=0.041  Score=45.84  Aligned_cols=26  Identities=8%  Similarity=0.263  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +..-|+|+|.+|+|||||+..+....
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~~   47 (195)
T 1svi_A           22 GLPEIALAGRSNVGKSSFINSLINRK   47 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC-
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            45678899999999999999998653

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=93.80  E-value=0.036  Score=46.07  Aligned_cols=23  Identities=22%  Similarity=0.185  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+.+..
T Consensus        22 ki~ivG~~~vGKSsL~~~~~~~~   44 (184)
T 3ihw_A           22 KVGIVGNLSSGKSALVHRYLTGT   44 (184)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            47899999999999999887754

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=93.80  E-value=0.032  Score=45.17  Aligned_cols=22  Identities=23%  Similarity=0.578  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      -|+|+|.+|+|||||+..+...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            5 RVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4789999999999999999864

>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=93.77  E-value=0.037  Score=45.22  Aligned_cols=24  Identities=21%  Similarity=0.308  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+....
T Consensus         8 ~~i~v~G~~~~GKSsli~~l~~~~   31 (177)
T 1wms_A            8 FKVILLGDGGVGKSSLMNRYVTNK   31 (177)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            357899999999999999998653

>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=93.76  E-value=0.037  Score=44.74  Aligned_cols=23  Identities=17%  Similarity=0.232  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+....
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1g16_A            5 KILLIGDSGVGKSCLLVRFVEDK   27 (170)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEEECcCCCCHHHHHHHHHhCC
Confidence            47899999999999999998653

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=93.76  E-value=0.097  Score=48.45  Aligned_cols=31  Identities=26%  Similarity=0.358  Sum_probs=26.1

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          170 LKNPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       170 L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +..+..+++.+.|.||+||||++..+.....
T Consensus        13 l~~~~~~i~~~~gkGGvGKTt~a~~lA~~la   43 (348)
T 3io3_A           13 VQHDSLKWIFVGGKGGVGKTTTSSSVAVQLA   43 (348)
T ss_dssp             HTCTTCSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             hcCCCcEEEEEeCCCCCcHHHHHHHHHHHHH
Confidence            3355678999999999999999999987765

>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=93.75  E-value=0.037  Score=46.80  Aligned_cols=27  Identities=22%  Similarity=0.144  Sum_probs=21.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .+.--|+|+|.+|+|||||+..+.+..
T Consensus        28 ~~~~ki~vvG~~~~GKSsLi~~l~~~~   54 (204)
T 4gzl_A           28 GQAIKCVVVGDGAVGKTCLLISYTTNA   54 (204)
T ss_dssp             --CEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             CCeEEEEEECcCCCCHHHHHHHHHhCC
Confidence            344457899999999999999998653

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=93.75  E-value=0.037  Score=45.77  Aligned_cols=24  Identities=17%  Similarity=0.234  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .+.+|+|+.|+|||||+..++--.
T Consensus        27 g~~~i~G~NGsGKStll~ai~~~l   50 (182)
T 3kta_A           27 GFTAIVGANGSGKSNIGDAILFVL   50 (182)
T ss_dssp             SEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHH
Confidence            488999999999999999987654

>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=93.74  E-value=0.033  Score=44.92  Aligned_cols=21  Identities=24%  Similarity=0.332  Sum_probs=18.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      -|+|+|.+|+|||||++.+.+
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            377999999999999998864

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=93.73  E-value=0.036  Score=45.27  Aligned_cols=23  Identities=26%  Similarity=0.313  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+.+..
T Consensus         8 ki~v~G~~~~GKssl~~~l~~~~   30 (178)
T 2hxs_A            8 KIVVLGDGASGKTSLTTCFAQET   30 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHGGG
T ss_pred             EEEEECcCCCCHHHHHHHHHhCc
Confidence            47899999999999999998653

>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=93.73  E-value=0.042  Score=51.07  Aligned_cols=112  Identities=11%  Similarity=0.054  Sum_probs=58.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCe-EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQ-VIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKK  252 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~-~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~  252 (390)
                      ...+++|.|+.|+|||||++.+.......  ... ++.+.-.-.+..... ..+   +...............+...|..
T Consensus       122 ~~g~i~I~GptGSGKTTlL~~l~g~~~~~--~~~~i~t~ed~~e~~~~~~-~~~---v~q~~~~~~~~~~~~~La~aL~~  195 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTLAAMLDYLNNT--KYHHILTIEDPIEFVHESK-KCL---VNQREVHRDTLGFSEALRSALRE  195 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHHHH--CCCEEEEEESSCCSCCCCS-SSE---EEEEEBTTTBSCHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcccCC--CCcEEEEccCcHHhhhhcc-ccc---eeeeeeccccCCHHHHHHHHhhh
Confidence            34589999999999999999998776432  112 222211111100000 000   00000000112233456666654


Q ss_pred             CCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhh
Q 042806          253 EKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVL  295 (390)
Q Consensus       253 ~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~  295 (390)
                       +|=+|++|+..+.+.++.+...   ...|..||+|+...+.+
T Consensus       196 -~PdvillDEp~d~e~~~~~~~~---~~~G~~vl~t~H~~~~~  234 (356)
T 3jvv_A          196 -DPDIILVGEMRDLETIRLALTA---AETGHLVFGTLHTTSAA  234 (356)
T ss_dssp             -CCSEEEESCCCSHHHHHHHHHH---HHTTCEEEEEESCSSHH
T ss_pred             -CcCEEecCCCCCHHHHHHHHHH---HhcCCEEEEEEccChHH
Confidence             3468899999866555443222   22356688888875543

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=93.70  E-value=0.038  Score=45.22  Aligned_cols=25  Identities=24%  Similarity=0.359  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+....
T Consensus         9 ~~~i~v~G~~~~GKssli~~l~~~~   33 (181)
T 2fn4_A            9 THKLVVVGGGGVGKSALTIQFIQSY   33 (181)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhCc
Confidence            3458899999999999999998763

>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=93.70  E-value=0.037  Score=44.81  Aligned_cols=21  Identities=29%  Similarity=0.351  Sum_probs=18.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      -|+|+|.+|+|||||+..+..
T Consensus         4 ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            378999999999999999864

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=93.69  E-value=0.036  Score=51.90  Aligned_cols=26  Identities=23%  Similarity=0.261  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+|||||++.+.--.
T Consensus        28 ~Ge~~~llGpsGsGKSTLLr~iaGl~   53 (381)
T 3rlf_A           28 EGEFVVFVGPSGCGKSTLLRMIAGLE   53 (381)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHHcCC
Confidence            45689999999999999999997644

>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=93.68  E-value=0.063  Score=52.30  Aligned_cols=46  Identities=4%  Similarity=-0.146  Sum_probs=32.9

Q ss_pred             ccchhHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          156 CESRMSTLNDILDALK--NPDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       156 ~~gR~~~~~~l~~~L~--~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      -+.|.+-.+.+.+...  ..+..+|.+.|+.|+||||+++.+...+..
T Consensus       374 ~f~rpeV~~vLr~~~~~~~~~~~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          374 WFSYPEVVKILRESNPPRPKQGFSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             TTSCHHHHHHHHHHSCCGGGCCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             cccChhhHHHHHHhcccccccceEEEecccCCCCHHHHHHHHHHHHHH
Confidence            4445444444445442  234578999999999999999999999864

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=93.68  E-value=0.14  Score=43.55  Aligned_cols=25  Identities=28%  Similarity=0.284  Sum_probs=22.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.|+|-|..|+||||+++.+.+.+.
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~L~   27 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHRLV   27 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHHH
Confidence            4789999999999999999999885

>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=93.68  E-value=0.032  Score=50.75  Aligned_cols=26  Identities=23%  Similarity=0.217  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+..-.
T Consensus        79 ~Ge~vaivG~sGsGKSTLl~ll~gl~  104 (306)
T 3nh6_A           79 PGQTLALVGPSGAGKSTILRLLFRFY  104 (306)
T ss_dssp             TTCEEEEESSSCHHHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCchHHHHHHHHHcCC
Confidence            45789999999999999999986543

>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=93.67  E-value=0.041  Score=51.14  Aligned_cols=26  Identities=27%  Similarity=0.211  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+|||||.+.+.--.
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (359)
T 2yyz_A           28 DGEFVALLGPSGCGKTTTLLMLAGIY   53 (359)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHHCCC
Confidence            45689999999999999999997643

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=93.66  E-value=0.041  Score=51.20  Aligned_cols=26  Identities=27%  Similarity=0.310  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+|||||.+.++--.
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (362)
T 2it1_A           28 DGEFMALLGPSGSGKSTLLYTIAGIY   53 (362)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCchHHHHHHHHhcCC
Confidence            45689999999999999999997643

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=93.66  E-value=0.035  Score=45.55  Aligned_cols=23  Identities=22%  Similarity=0.176  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .-|+|+|.+|+|||||.+.+...
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            35789999999999999999865

>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=93.65  E-value=0.04  Score=44.47  Aligned_cols=22  Identities=18%  Similarity=0.271  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      -|+|+|.+|+|||||+..+...
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            4789999999999999999875

>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=93.64  E-value=0.08  Score=46.88  Aligned_cols=36  Identities=19%  Similarity=0.239  Sum_probs=27.9

Q ss_pred             HHHHHHhcCC--CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          164 NDILDALKNP--DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       164 ~~l~~~L~~~--~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-+..|+...  ....+.++|++|.|||.+|..+.+..
T Consensus        91 ~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~~  128 (267)
T 1u0j_A           91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhhh
Confidence            3466666653  24579999999999999999998864

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=93.62  E-value=0.037  Score=46.07  Aligned_cols=24  Identities=29%  Similarity=0.296  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        22 ~ki~vvG~~~vGKTsLi~~l~~~~   45 (187)
T 3c5c_A           22 VNLAILGRRGAGKSALTVKFLTKR   45 (187)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCcHHHHHHHHHhCC
Confidence            357899999999999999988754

>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=93.60  E-value=0.034  Score=53.15  Aligned_cols=28  Identities=32%  Similarity=0.382  Sum_probs=24.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+.+|+|+|++|+||||++..+......
T Consensus        98 ~~~vI~ivG~~GvGKTTla~~La~~l~~  125 (432)
T 2v3c_C           98 KQNVILLVGIQGSGKTTTAAKLARYIQK  125 (432)
T ss_dssp             SCCCEEEECCSSSSTTHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3568999999999999999999887654

>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=93.58  E-value=0.042  Score=44.51  Aligned_cols=24  Identities=25%  Similarity=0.239  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+....
T Consensus         8 ~~i~v~G~~~~GKssl~~~l~~~~   31 (171)
T 1upt_A            8 MRILILGLDGAGKTTILYRLQVGE   31 (171)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCC
Confidence            457899999999999999997653

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=93.58  E-value=0.038  Score=51.65  Aligned_cols=26  Identities=27%  Similarity=0.266  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+|||||.+.++--.
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (372)
T 1g29_1           28 DGEFMILLGPSGCGKTTTLRMIAGLE   53 (372)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCcHHHHHHHHHHcCC
Confidence            34689999999999999999997543

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=93.58  E-value=0.1  Score=51.17  Aligned_cols=28  Identities=21%  Similarity=0.176  Sum_probs=24.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .-.++.|.|++|+|||||++.++.....
T Consensus       280 ~G~i~~i~G~~GsGKSTLl~~l~g~~~~  307 (525)
T 1tf7_A          280 KDSIILATGATGTGKTLLVSRFVENACA  307 (525)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            4568999999999999999999877543

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=93.57  E-value=0.065  Score=48.59  Aligned_cols=33  Identities=15%  Similarity=0.318  Sum_probs=26.4

Q ss_pred             HHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          163 LNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       163 ~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +++|.+.+.   ..+++|.|+.|+|||||++.+. ..
T Consensus       156 i~~L~~~l~---G~i~~l~G~sG~GKSTLln~l~-~~  188 (302)
T 2yv5_A          156 IDELVDYLE---GFICILAGPSGVGKSSILSRLT-GE  188 (302)
T ss_dssp             HHHHHHHTT---TCEEEEECSTTSSHHHHHHHHH-SC
T ss_pred             HHHHHhhcc---CcEEEEECCCCCCHHHHHHHHH-Hh
Confidence            456666654   3588999999999999999998 54

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=93.57  E-value=0.059  Score=45.28  Aligned_cols=24  Identities=25%  Similarity=0.248  Sum_probs=20.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      +..-|+|+|.+|+|||||+..+..
T Consensus        24 ~~~ki~lvG~~~vGKSsLi~~l~~   47 (198)
T 1f6b_A           24 KTGKLVFLGLDNAGKTTLLHMLKD   47 (198)
T ss_dssp             CCEEEEEEEETTSSHHHHHHHHSC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhc
Confidence            344578999999999999999865

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=93.56  E-value=0.041  Score=45.91  Aligned_cols=24  Identities=25%  Similarity=0.213  Sum_probs=20.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..-|+|+|.+|+|||||+..+.+.
T Consensus        23 ~~ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           23 HGKLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             -CEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            346789999999999999999874

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=93.55  E-value=0.09  Score=50.61  Aligned_cols=95  Identities=17%  Similarity=0.207  Sum_probs=55.0

Q ss_pred             HHHHhcC-CCccEEEEEcCCCCcHHHHH-HHHHHHhhhcCCCC-eEEEEEeCCCC-CHHHHHHHHHHHhCCC-------C
Q 042806          166 ILDALKN-PDVNMLGIYGMGGIVKTTLA-KEVARKAETEKLFD-QVIFVEVSKIQ-DIRKIQGEIADKLGLT-------L  234 (390)
Q Consensus       166 l~~~L~~-~~~~vi~I~G~~GvGKTtLa-~~v~~~~~~~~~f~-~~~wv~v~~~~-~~~~l~~~i~~~l~~~-------~  234 (390)
                      .++.|.. .+-.-++|.|.+|+|||+|+ ..+.+..    +-+ .++|+.++... ...++...+...-...       .
T Consensus       152 aID~l~PigrGQR~~Ifg~~g~GKT~l~l~~I~n~~----~~dv~~V~~~IGeR~~ev~e~~~~l~~~g~m~~tvvV~at  227 (513)
T 3oaa_A          152 AVDSMIPIGRGQRELIIGDRQTGKTALAIDAIINQR----DSGIKCIYVAIGQKASTISNVVRKLEEHGALANTIVVVAT  227 (513)
T ss_dssp             HHHHHSCCBTTCBCEEEESSSSSHHHHHHHHHHTTS----SSSCEEEEEEESCCHHHHHHHHHHHHHHSCSTTEEEEEEC
T ss_pred             eeccccccccCCEEEeecCCCCCcchHHHHHHHhhc----cCCceEEEEEecCChHHHHHHHHHHhhcCcccceEEEEEC
Confidence            4444442 23445789999999999996 4666542    233 46788888754 4566666654432221       1


Q ss_pred             CCCCchH------HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          235 HEESDSG------RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       235 ~~~~~~~------~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                      .+.+...      ..-.+.+++. .++.+||++||+.
T Consensus       228 ad~p~~~r~~a~~~a~tiAEyfrd~G~dVLli~Dslt  264 (513)
T 3oaa_A          228 ASESAALQYLAPYAGCAMGEYFRDRGEDALIIYDDLS  264 (513)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHHTTCEEEEEEETHH
T ss_pred             CCCChHHHHHHHHHHHHHHHHHHhcCCCEEEEecChH
Confidence            1111111      1223445554 3677999999984

>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=93.55  E-value=0.042  Score=44.81  Aligned_cols=25  Identities=24%  Similarity=0.230  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+....
T Consensus        15 ~~~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           15 IFKYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcCC
Confidence            3458899999999999999998764

>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=93.54  E-value=0.045  Score=50.93  Aligned_cols=26  Identities=27%  Similarity=0.339  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+|||||++.+.--.
T Consensus        53 ~Gei~~IiGpnGaGKSTLlr~i~GL~   78 (366)
T 3tui_C           53 AGQIYGVIGASGAGKSTLIRCVNLLE   78 (366)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHhcCC
Confidence            45789999999999999999987543

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=93.54  E-value=0.052  Score=48.07  Aligned_cols=38  Identities=24%  Similarity=0.359  Sum_probs=29.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK  215 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  215 (390)
                      ++|+|.|-||+||||++..+....... .+ .+.-|....
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~~la~~-G~-~VlliD~D~   39 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTSGLHAM-GK-TIMVVGCDP   39 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTT-TC-CEEEEEECT
T ss_pred             cEEEEecCCCCcHHHHHHHHHHHHHHC-CC-cEEEEcCCC
Confidence            578889999999999999999887643 23 355666653

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=93.53  E-value=0.034  Score=45.58  Aligned_cols=23  Identities=22%  Similarity=0.278  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+.+..
T Consensus         9 ki~~vG~~~vGKTsli~~l~~~~   31 (178)
T 2iwr_A            9 RLGVLGDARSGKSSLIHRFLTGS   31 (178)
T ss_dssp             EEEEECCGGGCHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            47899999999999999998753

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=93.53  E-value=0.045  Score=45.84  Aligned_cols=23  Identities=30%  Similarity=0.277  Sum_probs=19.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      --|+|+|.+|+|||||...+...
T Consensus         7 ~kv~lvG~~~vGKSsL~~~~~~~   29 (192)
T 2cjw_A            7 YRVVLIGEQGVGKSTLANIFAGV   29 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            34789999999999999998753

>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=93.53  E-value=0.039  Score=45.53  Aligned_cols=24  Identities=21%  Similarity=0.209  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+.+..
T Consensus        11 ~ki~v~G~~~~GKSsli~~l~~~~   34 (186)
T 2bme_A           11 FKFLVIGNAGTGKSCLLHQFIEKK   34 (186)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            457899999999999999998764

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=93.52  E-value=0.045  Score=51.15  Aligned_cols=25  Identities=32%  Similarity=0.308  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...+++|.|+.|+|||||++.+.--
T Consensus        36 ~Ge~~~llGpnGsGKSTLLr~iaGl   60 (372)
T 1v43_A           36 DGEFLVLLGPSGCGKTTTLRMIAGL   60 (372)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcC
Confidence            4568999999999999999999754

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=93.49  E-value=0.04  Score=44.98  Aligned_cols=23  Identities=22%  Similarity=0.208  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|..|+|||||+..+....
T Consensus        16 ~i~v~G~~~~GKssli~~l~~~~   38 (179)
T 2y8e_A           16 KLVFLGEQSVGKTSLITRFMYDS   38 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            47899999999999999998653

>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=93.47  E-value=0.038  Score=51.18  Aligned_cols=26  Identities=23%  Similarity=0.133  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+|||||++.+.--.
T Consensus        25 ~Ge~~~llGpnGsGKSTLLr~iaGl~   50 (348)
T 3d31_A           25 SGEYFVILGPTGAGKTLFLELIAGFH   50 (348)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCccHHHHHHHHHcCC
Confidence            44689999999999999999997543

>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=93.46  E-value=0.041  Score=45.30  Aligned_cols=24  Identities=29%  Similarity=0.386  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        19 ~ki~v~G~~~~GKSsl~~~l~~~~   42 (183)
T 3kkq_A           19 YKLVVVGDGGVGKSALTIQFFQKI   42 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhCC
Confidence            357899999999999999998753

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=93.46  E-value=0.069  Score=50.75  Aligned_cols=29  Identities=14%  Similarity=0.058  Sum_probs=24.6

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          172 NPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       172 ~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .....+++|.|+.|+|||||++.+.....
T Consensus       164 ~~~ggii~I~GpnGSGKTTlL~allg~l~  192 (418)
T 1p9r_A          164 KRPHGIILVTGPTGSGKSTTLYAGLQELN  192 (418)
T ss_dssp             TSSSEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             HhcCCeEEEECCCCCCHHHHHHHHHhhcC
Confidence            34556899999999999999999988764

>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=93.45  E-value=0.044  Score=45.21  Aligned_cols=23  Identities=22%  Similarity=0.374  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+.+..
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            47899999999999999998754

>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=93.45  E-value=0.044  Score=45.35  Aligned_cols=24  Identities=17%  Similarity=0.115  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+....
T Consensus        12 ~ki~v~G~~~~GKSsli~~l~~~~   35 (195)
T 3bc1_A           12 IKFLALGDSGVGKTSVLYQYTDGK   35 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            457899999999999999998753

>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=93.44  E-value=0.062  Score=50.32  Aligned_cols=108  Identities=14%  Similarity=0.094  Sum_probs=55.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEE-EEEeCCCCCHHHHHHHHHHHhCCCCC---CCCchHHHHHHHH
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVI-FVEVSKIQDIRKIQGEIADKLGLTLH---EESDSGRARSLRN  248 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~-wv~v~~~~~~~~l~~~i~~~l~~~~~---~~~~~~~~~~l~~  248 (390)
                      ....+++|+|+.|+|||||++.+.......  ....+ ++.-.-.....       ...+.-..   ..........+..
T Consensus       134 ~~g~~i~ivG~~GsGKTTll~~l~~~~~~~--~~g~I~~~e~~~e~~~~-------~~~~~v~Q~~~g~~~~~~~~~l~~  204 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTTIASMIDYINQT--KSYHIITIEDPIEYVFK-------HKKSIVNQREVGEDTKSFADALRA  204 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHHHHHHHHHHHHH--SCCEEEEEESSCCSCCC-------CSSSEEEEEEBTTTBSCSHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhhcCcC--CCcEEEEecccHhhhhc-------cCceEEEeeecCCCHHHHHHHHHH
Confidence            345689999999999999999998865432  12222 33211110000       00000000   0011122345666


Q ss_pred             HHhCCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchh
Q 042806          249 RLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLD  293 (390)
Q Consensus       249 ~l~~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~  293 (390)
                      .|.. ++=+|++|.+.+......+...   ...|..|+.|+...+
T Consensus       205 ~L~~-~pd~illdE~~d~e~~~~~l~~---~~~g~~vi~t~H~~~  245 (372)
T 2ewv_A          205 ALRE-DPDVIFVGEMRDLETVETALRA---AETGHLVFGTLHTNT  245 (372)
T ss_dssp             HTTS-CCSEEEESCCCSHHHHHHHHHH---HTTTCEEEECCCCCS
T ss_pred             Hhhh-CcCEEEECCCCCHHHHHHHHHH---HhcCCEEEEEECcch
Confidence            6655 3468889999755443332222   123556777777544

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=93.43  E-value=0.11  Score=47.74  Aligned_cols=32  Identities=25%  Similarity=0.297  Sum_probs=26.2

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          170 LKNPDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       170 L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +.++..+++.+.|.||+||||++..+......
T Consensus        11 l~~~~~~i~~~sgkGGvGKTt~a~~lA~~la~   42 (334)
T 3iqw_A           11 LDQRSLRWIFVGGKGGVGKTTTSCSLAIQLAK   42 (334)
T ss_dssp             HHCTTCCEEEEECSTTSSHHHHHHHHHHHHTT
T ss_pred             hcCCCeEEEEEeCCCCccHHHHHHHHHHHHHh
Confidence            33455678889999999999999999888754

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=93.42  E-value=0.048  Score=45.22  Aligned_cols=25  Identities=12%  Similarity=0.219  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+....
T Consensus        23 ~~~i~v~G~~~~GKSsli~~l~~~~   47 (195)
T 3pqc_A           23 KGEVAFVGRSNVGKSSLLNALFNRK   47 (195)
T ss_dssp             TCEEEEEEBTTSSHHHHHHHHHTSC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHcCc
Confidence            4568899999999999999998764

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=93.42  E-value=0.037  Score=45.78  Aligned_cols=23  Identities=22%  Similarity=0.218  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+....
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~~   25 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTGKK   25 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCcC
Confidence            37899999999999999998753

>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=93.39  E-value=0.048  Score=45.40  Aligned_cols=23  Identities=26%  Similarity=0.200  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+....
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            47799999999999999998764

>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=93.39  E-value=0.044  Score=45.53  Aligned_cols=23  Identities=35%  Similarity=0.196  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||++.+.+..
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            47899999999999997666543

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=93.39  E-value=0.05  Score=52.52  Aligned_cols=86  Identities=13%  Similarity=0.197  Sum_probs=49.7

Q ss_pred             ccEEEEEcCCCCcHHHHH-HHHHHHhhhcCCCC-eEEEEEeCCCC-CHHHHHHHHHHHhCC-------CCCCCCc-h---
Q 042806          175 VNMLGIYGMGGIVKTTLA-KEVARKAETEKLFD-QVIFVEVSKIQ-DIRKIQGEIADKLGL-------TLHEESD-S---  240 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa-~~v~~~~~~~~~f~-~~~wv~v~~~~-~~~~l~~~i~~~l~~-------~~~~~~~-~---  240 (390)
                      -.-++|.|.+|+|||+|+ ..+.+...    .+ .++++.++... ...++...+...-..       ...+.+. .   
T Consensus       163 GQR~~Ifg~~g~GKT~Lal~~I~~~~~----~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r~~  238 (507)
T 1fx0_A          163 GQRELIIGDRQTGKTAVATDTILNQQG----QNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYL  238 (507)
T ss_dssp             TCBCBEEESSSSSHHHHHHHHHHTCCT----TTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTH
T ss_pred             CCEEEEecCCCCCccHHHHHHHHHhhc----CCcEEEEEEcCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHHHH
Confidence            345779999999999995 46666542    44 46778887653 345555554332111       0111111 1   


Q ss_pred             --HHHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          241 --GRARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       241 --~~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                        ...-.+.+++. .++.+|+++||+.
T Consensus       239 a~~~a~tiAEyfrd~G~dVLli~Dslt  265 (507)
T 1fx0_A          239 APYTGAALAEYFMYRERHTLIIYDDLS  265 (507)
T ss_dssp             HHHHHHHHHHHHHHTTCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHHcCCcEEEEEecHH
Confidence              12234445554 3567999999973

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=93.35  E-value=0.025  Score=50.15  Aligned_cols=26  Identities=15%  Similarity=0.152  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +...|+|.|..|+||||+++.+....
T Consensus        23 ~~~~I~ieG~~GsGKST~~~~L~~~l   48 (263)
T 1p5z_B           23 RIKKISIEGNIAAGKSTFVNILKQLC   48 (263)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGGGC
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHhc
Confidence            56789999999999999999998765

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=93.34  E-value=0.047  Score=45.44  Aligned_cols=24  Identities=25%  Similarity=0.324  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+....
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~~~   49 (193)
T 2oil_A           26 FKVVLIGESGVGKTNLLSRFTRNE   49 (193)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            458899999999999999998754

>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=93.34  E-value=0.044  Score=45.09  Aligned_cols=24  Identities=21%  Similarity=0.339  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+....
T Consensus        19 ~ki~v~G~~~~GKSsli~~l~~~~   42 (187)
T 2a9k_A           19 HKVIMVGSGGVGKSALTLQFMYDE   42 (187)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHhhCC
Confidence            457899999999999999998754

>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=93.31  E-value=0.048  Score=44.82  Aligned_cols=23  Identities=26%  Similarity=0.218  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+.+..
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            47899999999999999998653

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=93.31  E-value=0.024  Score=56.57  Aligned_cols=23  Identities=26%  Similarity=0.320  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -+.++|++|+|||+||+.+.+..
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~~  351 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRVA  351 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTTC
T ss_pred             ceEEECCCchHHHHHHHHHHHhC
Confidence            47899999999999999997765

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=93.29  E-value=0.045  Score=44.95  Aligned_cols=25  Identities=16%  Similarity=0.275  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+.+..
T Consensus         6 ~~ki~~~G~~~~GKSsli~~l~~~~   30 (181)
T 3t5g_A            6 SRKIAILGYRSVGKSSLTIQFVEGQ   30 (181)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcCC
Confidence            3458899999999999999998653

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=93.26  E-value=0.045  Score=45.77  Aligned_cols=27  Identities=15%  Similarity=0.096  Sum_probs=21.7

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          172 NPDVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       172 ~~~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..+..-|+|+|.+|+|||||+..+...
T Consensus        26 ~~~~~ki~v~G~~~vGKSsLi~~l~~~   52 (192)
T 2b6h_A           26 GKKQMRILMVGLDAAGKTTILYKLKLG   52 (192)
T ss_dssp             TTSCEEEEEEESTTSSHHHHHHHHCSS
T ss_pred             cCCccEEEEECCCCCCHHHHHHHHHhC
Confidence            334456889999999999999998643

>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=93.26  E-value=0.045  Score=45.97  Aligned_cols=25  Identities=20%  Similarity=0.349  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+....
T Consensus        14 ~~ki~v~G~~~~GKSsli~~l~~~~   38 (206)
T 2bov_A           14 LHKVIMVGSGGVGKSALTLQFMYDE   38 (206)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhCC
Confidence            3458899999999999999998654

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=93.25  E-value=0.035  Score=51.52  Aligned_cols=25  Identities=32%  Similarity=0.397  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...+++|.|+.|+|||||++.++--
T Consensus        30 ~Ge~~~llGpnGsGKSTLLr~iaGl   54 (353)
T 1oxx_K           30 NGERFGILGPSGAGKTTFMRIIAGL   54 (353)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCC
Confidence            4568999999999999999999754

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=93.25  E-value=0.05  Score=44.58  Aligned_cols=24  Identities=21%  Similarity=0.094  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+....
T Consensus         9 ~ki~v~G~~~~GKssl~~~~~~~~   32 (182)
T 3bwd_D            9 IKCVTVGDGAVGKTCLLISYTSNT   32 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            457899999999999999988653

>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=93.25  E-value=0.05  Score=44.54  Aligned_cols=24  Identities=21%  Similarity=0.230  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+....
T Consensus        13 ~ki~v~G~~~~GKSsli~~l~~~~   36 (181)
T 2efe_B           13 AKLVLLGDVGAGKSSLVLRFVKDQ   36 (181)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            347899999999999999998763

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=93.23  E-value=0.04  Score=50.01  Aligned_cols=21  Identities=29%  Similarity=0.357  Sum_probs=18.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+|+|+.|+|||||++.++..
T Consensus        21 I~lvG~nG~GKSTLl~~L~g~   41 (301)
T 2qnr_A           21 LMVVGESGLGKSTLINSLFLT   41 (301)
T ss_dssp             EEEEEETTSSHHHHHHHHHC-
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            589999999999999997653

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=93.22  E-value=0.054  Score=51.32  Aligned_cols=24  Identities=17%  Similarity=0.217  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      ...+++|+|+.|+|||||.+.+..
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhC
Confidence            456899999999999999999987

>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=93.21  E-value=0.052  Score=44.42  Aligned_cols=24  Identities=25%  Similarity=0.187  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+....
T Consensus        11 ~~i~v~G~~~~GKssli~~l~~~~   34 (180)
T 2g6b_A           11 FKVMLVGDSGVGKTCLLVRFKDGA   34 (180)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhCC
Confidence            357899999999999999998754

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=93.21  E-value=0.06  Score=45.00  Aligned_cols=26  Identities=27%  Similarity=0.373  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..--|+|+|.+|+|||||+..+....
T Consensus        27 ~~~ki~v~G~~~vGKSsli~~l~~~~   52 (196)
T 2atv_A           27 AEVKLAIFGRAGVGKSALVVRFLTKR   52 (196)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhCC
Confidence            34458899999999999999998763

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=93.19  E-value=0.052  Score=46.37  Aligned_cols=24  Identities=29%  Similarity=0.293  Sum_probs=21.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .+|.|.|+.|+||||+++.+....
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~   27 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASEL   27 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            478999999999999999998765

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=93.18  E-value=0.038  Score=46.40  Aligned_cols=22  Identities=27%  Similarity=0.350  Sum_probs=19.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVA  196 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~  196 (390)
                      ..-|+|+|.+|+|||||+..+.
T Consensus        23 ~~ki~vvG~~~vGKSsLi~~l~   44 (195)
T 3cbq_A           23 IFKVMLVGESGVGKSTLAGTFG   44 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHTC
T ss_pred             EEEEEEECCCCCCHHHHHHHHH
Confidence            3458899999999999999985

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=93.15  E-value=0.047  Score=44.62  Aligned_cols=24  Identities=29%  Similarity=0.292  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..-|+|+|.+|+|||||+..+...
T Consensus         9 ~~~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B            9 LFKLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHCSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcC
Confidence            345789999999999999998765

>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=93.14  E-value=0.052  Score=45.86  Aligned_cols=25  Identities=20%  Similarity=0.302  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+....
T Consensus        26 ~~ki~lvG~~~vGKSsLi~~l~~~~   50 (201)
T 2ew1_A           26 LFKIVLIGNAGVGKTCLVRRFTQGL   50 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhCC
Confidence            3457899999999999999988653

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=93.12  E-value=0.059  Score=49.99  Aligned_cols=27  Identities=19%  Similarity=0.165  Sum_probs=23.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+|+|+|++|+|||||...+.....
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~~~~   99 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGKMLT   99 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHhh
Confidence            367899999999999999999987653

>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=93.12  E-value=0.049  Score=46.81  Aligned_cols=21  Identities=24%  Similarity=0.232  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+|+|.+|+|||+|+..+.+.
T Consensus        16 ivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           16 LVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCcCHHHHHHHHHhC
Confidence            678999999999999998764

>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=93.11  E-value=0.054  Score=44.97  Aligned_cols=24  Identities=25%  Similarity=0.181  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        23 ~ki~v~G~~~~GKSsli~~l~~~~   46 (188)
T 1zd9_A           23 MELTLVGLQYSGKTTFVNVIASGQ   46 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHHcCC
Confidence            347899999999999999998754

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=93.11  E-value=0.048  Score=45.86  Aligned_cols=25  Identities=28%  Similarity=0.324  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+....
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~~   32 (207)
T 1vg8_A            8 LLKVIILGDSGVGKTSLMNQYVNKK   32 (207)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcCC
Confidence            3458899999999999999998764

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=93.10  E-value=0.048  Score=45.07  Aligned_cols=27  Identities=22%  Similarity=0.180  Sum_probs=22.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .+..-|+|+|.+|+|||||+..+....
T Consensus        16 ~~~~~i~v~G~~~~GKssl~~~l~~~~   42 (186)
T 1ksh_A           16 ERELRLLMLGLDNAGKTTILKKFNGED   42 (186)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHTTCC
T ss_pred             CCeeEEEEECCCCCCHHHHHHHHhcCC
Confidence            345568899999999999999998654

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=93.09  E-value=0.054  Score=45.19  Aligned_cols=24  Identities=8%  Similarity=0.199  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+....
T Consensus         8 ~ki~v~G~~~~GKSsli~~l~~~~   31 (208)
T 3clv_A            8 YKTVLLGESSVGKSSIVLRLTKDT   31 (208)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhCc
Confidence            357899999999999999998764

>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=93.08  E-value=0.054  Score=45.16  Aligned_cols=24  Identities=13%  Similarity=0.213  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+....
T Consensus        24 ~ki~vvG~~~~GKSsli~~l~~~~   47 (192)
T 2fg5_A           24 LKVCLLGDTGVGKSSIVCRFVQDH   47 (192)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            358899999999999999998764

>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=93.08  E-value=0.054  Score=45.92  Aligned_cols=25  Identities=20%  Similarity=0.125  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .--|+|+|.+|+|||||+..+....
T Consensus        28 ~~ki~vvG~~~vGKSsLi~~l~~~~   52 (205)
T 1gwn_A           28 KCKIVVVGDSQCGKTALLHVFAKDC   52 (205)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcCC
Confidence            3457899999999999999998763

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=93.07  E-value=0.067  Score=48.00  Aligned_cols=39  Identities=26%  Similarity=0.347  Sum_probs=29.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK  215 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  215 (390)
                      .++|+|.|-||+||||++..+....... .+ .+.-|....
T Consensus         2 MkvIavs~KGGvGKTT~a~nLA~~La~~-G~-rVlliD~D~   40 (289)
T 2afh_E            2 MRQCAIYGKGGIGKSTTTQNLVAALAEM-GK-KVMIVGCDP   40 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHHHT-TC-CEEEEEECS
T ss_pred             ceEEEEeCCCcCcHHHHHHHHHHHHHHC-CC-eEEEEecCC
Confidence            3678889999999999999999887653 23 355566653

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=93.06  E-value=0.059  Score=49.70  Aligned_cols=28  Identities=21%  Similarity=0.258  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ....+++|+|++|+|||||.+.+.....
T Consensus        53 ~~g~~v~i~G~~GaGKSTLl~~l~g~~~   80 (337)
T 2qm8_A           53 GRAIRVGITGVPGVGKSTTIDALGSLLT   80 (337)
T ss_dssp             CCSEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHhhh
Confidence            4567999999999999999999987654

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=93.05  E-value=0.051  Score=45.08  Aligned_cols=24  Identities=21%  Similarity=0.140  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+....
T Consensus        23 ~ki~vvG~~~~GKSsli~~l~~~~   46 (189)
T 2gf9_A           23 FKLLLIGNSSVGKTSFLFRYADDS   46 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            358899999999999999998764

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=93.04  E-value=0.12  Score=44.96  Aligned_cols=39  Identities=26%  Similarity=0.343  Sum_probs=29.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD  218 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  218 (390)
                      |+|.|-||+||||++..+.......+  ..++-|......+
T Consensus         3 I~vs~kGGvGKTt~a~~LA~~la~~g--~~VlliD~D~~~~   41 (254)
T 3kjh_A            3 LAVAGKGGVGKTTVAAGLIKIMASDY--DKIYAVDGDPDSC   41 (254)
T ss_dssp             EEEECSSSHHHHHHHHHHHHHHTTTC--SCEEEEEECTTSC
T ss_pred             EEEecCCCCCHHHHHHHHHHHHHHCC--CeEEEEeCCCCcC
Confidence            66699999999999999999886542  3466666655443

>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=93.03  E-value=0.056  Score=44.96  Aligned_cols=23  Identities=26%  Similarity=0.232  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|.+|+|||||+..+.+..
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~~   45 (191)
T 2a5j_A           23 KYIIIGDTGVGKSCLLLQFTDKR   45 (191)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            47899999999999999998753

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=93.03  E-value=0.055  Score=45.46  Aligned_cols=25  Identities=24%  Similarity=0.254  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+....
T Consensus        24 ~~ki~vvG~~~~GKSsli~~l~~~~   48 (201)
T 3oes_A           24 YRKVVILGYRCVGKTSLAHQFVEGE   48 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             cEEEEEECCCCcCHHHHHHHHHhCC
Confidence            4458899999999999999998764

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=93.03  E-value=0.037  Score=46.84  Aligned_cols=26  Identities=8%  Similarity=0.036  Sum_probs=21.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .....++|+|+.|+|||||++.+...
T Consensus        24 ~~~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           24 DTGIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             SCSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            44567999999999999999988654

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=93.01  E-value=0.053  Score=51.02  Aligned_cols=25  Identities=28%  Similarity=0.310  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...+++|.|+.|+|||||++.+.--
T Consensus        46 ~Ge~~~llGpsGsGKSTLLr~iaGl   70 (390)
T 3gd7_A           46 PGQRVGLLGRTGSGKSTLLSAFLRL   70 (390)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCC
Confidence            4568999999999999999999753

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=93.01  E-value=0.077  Score=52.32  Aligned_cols=28  Identities=25%  Similarity=0.254  Sum_probs=24.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +..++.|.|+.|+|||||++.+......
T Consensus       368 ~G~iI~LiG~sGSGKSTLar~La~~L~~  395 (552)
T 3cr8_A          368 QGFTVFFTGLSGAGKSTLARALAARLME  395 (552)
T ss_dssp             SCEEEEEEESSCHHHHHHHHHHHHHHHT
T ss_pred             cceEEEEECCCCChHHHHHHHHHHhhcc
Confidence            4578999999999999999999988753

>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=92.99  E-value=0.057  Score=44.98  Aligned_cols=24  Identities=21%  Similarity=0.228  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+....
T Consensus        24 ~ki~~vG~~~~GKSsl~~~l~~~~   47 (194)
T 3reg_A           24 LKIVVVGDGAVGKTCLLLAFSKGE   47 (194)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            357899999999999999998764

>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=92.99  E-value=0.057  Score=45.83  Aligned_cols=25  Identities=16%  Similarity=0.025  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+....
T Consensus         7 ~~ki~vvG~~~~GKTsli~~l~~~~   31 (214)
T 2fh5_B            7 QRAVLFVGLCDSGKTLLFVRLLTGQ   31 (214)
T ss_dssp             -CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4568899999999999999998764

>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=92.95  E-value=0.057  Score=45.02  Aligned_cols=23  Identities=22%  Similarity=0.478  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .-|+|+|.+|+|||||+..+...
T Consensus         9 ~ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A            9 YRVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCcHHHHHHHHHcC
Confidence            45789999999999999999874

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=92.91  E-value=0.053  Score=50.61  Aligned_cols=26  Identities=19%  Similarity=0.201  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...++|+|+.|+|||||++.+.....
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~~  195 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVFN  195 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTT
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999987654

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=92.90  E-value=0.06  Score=44.77  Aligned_cols=24  Identities=25%  Similarity=0.227  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|..|+|||||+..+....
T Consensus        17 ~ki~v~G~~~~GKSsli~~l~~~~   40 (196)
T 3tkl_A           17 FKLLLIGDSGVGKSCLLLRFADDT   40 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            358899999999999999998754

>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=92.90  E-value=0.06  Score=44.65  Aligned_cols=25  Identities=16%  Similarity=0.134  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+....
T Consensus        20 ~~ki~v~G~~~~GKSsli~~l~~~~   44 (189)
T 1z06_A           20 IFKIIVIGDSNVGKTCLTYRFCAGR   44 (189)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHcCC
Confidence            3458899999999999999998653

>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=92.89  E-value=0.05  Score=45.54  Aligned_cols=23  Identities=22%  Similarity=0.229  Sum_probs=19.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .-|+|+|.+|+|||||++.+.+.
T Consensus        21 ~ki~~vG~~~vGKTsLi~~l~~~   43 (196)
T 3llu_A           21 PRILLMGLRRSGKSSIQKVVFHK   43 (196)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhc
Confidence            45779999999999999977664

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=92.88  E-value=0.049  Score=50.77  Aligned_cols=27  Identities=26%  Similarity=0.231  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+++|+|+.|+|||||++.+.....
T Consensus       174 ~G~~i~ivG~sGsGKSTll~~l~~~~~  200 (361)
T 2gza_A          174 LERVIVVAGETGSGKTTLMKALMQEIP  200 (361)
T ss_dssp             TTCCEEEEESSSSCHHHHHHHHHTTSC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            345799999999999999999987653

>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=92.86  E-value=0.054  Score=45.47  Aligned_cols=24  Identities=21%  Similarity=0.140  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+....
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~~   32 (203)
T 1zbd_A            9 FKILIIGNSSVGKTSFLFRYADDS   32 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTCC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcCC
Confidence            357899999999999999998754

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=92.86  E-value=0.091  Score=47.58  Aligned_cols=34  Identities=18%  Similarity=0.405  Sum_probs=26.6

Q ss_pred             HHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          163 LNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       163 ~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ++++...+..   .+++|.|++|+|||||.+.+....
T Consensus       160 v~~lf~~l~g---eiv~l~G~sG~GKSTll~~l~g~~  193 (301)
T 1u0l_A          160 IEELKEYLKG---KISTMAGLSGVGKSSLLNAINPGL  193 (301)
T ss_dssp             HHHHHHHHSS---SEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             HHHHHHHhcC---CeEEEECCCCCcHHHHHHHhcccc
Confidence            4566666543   588999999999999999996543

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=92.83  E-value=0.058  Score=46.12  Aligned_cols=22  Identities=32%  Similarity=0.315  Sum_probs=19.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      .-|+|+|.+|+|||||+..+..
T Consensus        38 ~kVvlvG~~~vGKSSLl~r~~~   59 (211)
T 2g3y_A           38 YRVVLIGEQGVGKSTLANIFAG   59 (211)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            3488999999999999999874

>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=92.82  E-value=0.062  Score=45.05  Aligned_cols=26  Identities=8%  Similarity=0.183  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...-|+|+|.+|+|||||+..+....
T Consensus        27 ~~~ki~v~G~~~~GKSsli~~l~~~~   52 (199)
T 2p5s_A           27 KAYKIVLAGDAAVGKSSFLMRLCKNE   52 (199)
T ss_dssp             -CEEEEEESSTTSSHHHHHHHHHHCC
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHhCC
Confidence            34568899999999999999997653

>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=92.81  E-value=0.062  Score=45.27  Aligned_cols=24  Identities=21%  Similarity=0.220  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+....
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~~   32 (206)
T 2bcg_Y            9 FKLLLIGNSGVGKSCLLLRFSDDT   32 (206)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcCC
Confidence            457899999999999999998754

>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=92.80  E-value=0.063  Score=44.53  Aligned_cols=24  Identities=21%  Similarity=0.245  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+.+..
T Consensus        16 ~~i~v~G~~~~GKssli~~l~~~~   39 (195)
T 1x3s_A           16 LKILIIGESGVGKSSLLLRFTDDT   39 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            357899999999999999998764

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=92.80  E-value=0.074  Score=45.06  Aligned_cols=26  Identities=19%  Similarity=0.061  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+|.|.|+.|+||||+++.+.....
T Consensus         6 ~~iI~i~g~~GsGk~ti~~~la~~lg   31 (201)
T 3fdi_A            6 QIIIAIGREFGSGGHLVAKKLAEHYN   31 (201)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHTT
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHhC
Confidence            35899999999999999999999875

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=92.78  E-value=0.052  Score=45.65  Aligned_cols=25  Identities=16%  Similarity=0.203  Sum_probs=20.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .--|+|+|.+|+|||||+..+....
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~~   49 (200)
T 2o52_A           25 LFKFLVIGSAGTGKSCLLHQFIENK   49 (200)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHC--
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhCC
Confidence            3457899999999999999997543

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=92.77  E-value=0.053  Score=45.46  Aligned_cols=24  Identities=21%  Similarity=0.199  Sum_probs=19.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        21 ~ki~~~G~~~~GKssl~~~l~~~~   44 (201)
T 2q3h_A           21 VKCVLVGDGAVGKTSLVVSYTTNG   44 (201)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC--
T ss_pred             eEEEEECCCCCCHHHHHHHHHhCC
Confidence            457799999999999999998653

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=92.71  E-value=0.051  Score=44.77  Aligned_cols=23  Identities=22%  Similarity=0.226  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      --|+|+|.+|+|||||+..+...
T Consensus        22 ~~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           22 HKVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             EEEEEEEETTSSHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            35789999999999999999865

>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=92.60  E-value=0.079  Score=51.94  Aligned_cols=28  Identities=18%  Similarity=0.211  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ...+|.++|++|+||||+++.+.....-
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~~L~~   61 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTRYLNW   61 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            4568999999999999999999887753

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=92.60  E-value=0.088  Score=43.70  Aligned_cols=34  Identities=21%  Similarity=0.229  Sum_probs=24.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ  217 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~  217 (390)
                      +.|+|.+|+||||+|.++... .    . .++|+.-...+
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~-~----~-~~~yiaT~~~~   35 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD-A----P-QVLYIATSQIL   35 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-C----S-SEEEEECCCC-
T ss_pred             EEEECCCCCcHHHHHHHHHhc-C----C-CeEEEecCCCC
Confidence            689999999999999999765 2    1 25565554443

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=92.59  E-value=0.069  Score=49.44  Aligned_cols=28  Identities=25%  Similarity=0.298  Sum_probs=24.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+-..++|+|+.|+|||||++.+.....
T Consensus        69 ~~Gq~~gIiG~nGaGKTTLl~~I~g~~~   96 (347)
T 2obl_A           69 GIGQRIGIFAGSGVGKSTLLGMICNGAS   96 (347)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHSC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            3556899999999999999999998864

>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=92.56  E-value=0.064  Score=44.62  Aligned_cols=24  Identities=29%  Similarity=0.205  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+.+..
T Consensus        19 ~ki~v~G~~~~GKssli~~l~~~~   42 (194)
T 2atx_A           19 LKCVVVGDGAVGKTCLLMSYANDA   42 (194)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            357899999999999999998763

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.55  E-value=0.07  Score=45.09  Aligned_cols=24  Identities=25%  Similarity=0.235  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+....
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~~~   49 (207)
T 2fv8_A           26 KKLVVVGDGACGKTCLLIVFSKDE   49 (207)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             cEEEEECcCCCCHHHHHHHHhcCC
Confidence            358899999999999999998753

>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=92.49  E-value=0.059  Score=45.89  Aligned_cols=23  Identities=30%  Similarity=0.245  Sum_probs=19.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      --|+|+|.+|+|||||+..+.+.
T Consensus        35 ~ki~vvG~~~vGKSsli~~l~~~   57 (214)
T 2j1l_A           35 VKVVLVGDGGCGKTSLLMVFADG   57 (214)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHC-
T ss_pred             EEEEEECcCCCCHHHHHHHHHcC
Confidence            45889999999999999999864

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=92.45  E-value=0.068  Score=46.01  Aligned_cols=25  Identities=16%  Similarity=0.228  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      +..-|+|+|.+|+|||||+..+...
T Consensus        28 ~~~kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           28 HKKTIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             TSEEEEEECSTTSSHHHHHHHHTTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3456889999999999999999765

>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=92.42  E-value=0.074  Score=44.75  Aligned_cols=25  Identities=20%  Similarity=0.186  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+.+..
T Consensus        29 ~~ki~vvG~~~vGKSsli~~l~~~~   53 (201)
T 2hup_A           29 LFKLVLVGDASVGKTCVVQRFKTGA   53 (201)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhhCC
Confidence            3458899999999999999997653

>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=92.41  E-value=0.075  Score=44.85  Aligned_cols=25  Identities=16%  Similarity=0.226  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+....
T Consensus        20 ~~~i~v~G~~~~GKSsli~~l~~~~   44 (213)
T 3cph_A           20 IMKILLIGDSGVGKSCLLVRFVEDK   44 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHCC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhCC
Confidence            3458899999999999999998653

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=92.38  E-value=0.076  Score=44.94  Aligned_cols=24  Identities=17%  Similarity=0.019  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+.+..
T Consensus        10 ~ki~i~G~~~~GKTsli~~l~~~~   33 (212)
T 2j0v_A           10 IKCVTVGDGAVGKTCMLICYTSNK   33 (212)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            347899999999999999998653

>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=92.35  E-value=0.042  Score=45.21  Aligned_cols=23  Identities=22%  Similarity=0.185  Sum_probs=9.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .-|+|+|.+|+|||||+..+.+.
T Consensus         9 ~ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C            9 FKLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEEECCCCC------------
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            45889999999999999998754

>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=92.34  E-value=0.078  Score=44.55  Aligned_cols=24  Identities=29%  Similarity=0.245  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+....
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~~~   49 (201)
T 2gco_A           26 KKLVIVGDGACGKTCLLIVFSKDQ   49 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhCc
Confidence            347899999999999999998754

>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=92.29  E-value=0.079  Score=45.12  Aligned_cols=24  Identities=21%  Similarity=0.134  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+....
T Consensus        28 ~ki~vvG~~~vGKSsL~~~l~~~~   51 (214)
T 3q3j_B           28 CKLVLVGDVQCGKTAMLQVLAKDC   51 (214)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECcCCCCHHHHHHHHhcCC
Confidence            347799999999999999998764

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=92.28  E-value=0.072  Score=44.41  Aligned_cols=25  Identities=20%  Similarity=0.186  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-|+|+|.+|+|||||+..+....
T Consensus        17 ~~ki~v~G~~~~GKSsl~~~l~~~~   41 (199)
T 4bas_A           17 KLQVVMCGLDNSGKTTIINQVKPAQ   41 (199)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHSCCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCC
Confidence            4568899999999999999997653

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=92.26  E-value=0.077  Score=49.21  Aligned_cols=24  Identities=17%  Similarity=0.203  Sum_probs=21.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .+++|+|++|+|||||++.+....
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g~~  239 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLGLQ  239 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHCCS
T ss_pred             CEEEEECCCCccHHHHHHHHhccc
Confidence            588999999999999999987544

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=92.26  E-value=0.068  Score=51.48  Aligned_cols=26  Identities=23%  Similarity=0.183  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.++.-.
T Consensus       137 ~Ge~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          137 EGPRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             SCCCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCcc
Confidence            45689999999999999999998764

>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=92.24  E-value=0.075  Score=46.16  Aligned_cols=26  Identities=12%  Similarity=0.141  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...-|+|+|.+|+|||||+..+....
T Consensus        28 ~~~~i~lvG~~g~GKStlin~l~g~~   53 (239)
T 3lxx_A           28 SQLRIVLVGKTGAGKSATGNSILGRK   53 (239)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHTSC
T ss_pred             CceEEEEECCCCCCHHHHHHHHcCCC
Confidence            44568899999999999999998653

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=92.24  E-value=0.066  Score=50.85  Aligned_cols=21  Identities=24%  Similarity=0.265  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ++|+|+.|+|||||++.++..
T Consensus        45 vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           45 ILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             EEEECSTTSSSHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCc
Confidence            999999999999999999764

>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=92.23  E-value=0.14  Score=50.66  Aligned_cols=28  Identities=11%  Similarity=0.023  Sum_probs=24.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +..+|.|.|++|+||||+++.+......
T Consensus       395 ~~~~I~l~GlsGSGKSTiA~~La~~L~~  422 (573)
T 1m8p_A          395 QGFTIFLTGYMNSGKDAIARALQVTLNQ  422 (573)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             cceEEEeecCCCCCHHHHHHHHHHHhcc
Confidence            4568999999999999999999988764

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=92.18  E-value=0.088  Score=48.60  Aligned_cols=28  Identities=21%  Similarity=0.201  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+..+++|+|.+|+|||||+..+.....
T Consensus        54 ~~~~~i~i~G~~g~GKSTl~~~l~~~~~   81 (341)
T 2p67_A           54 GNTLRLGVTGTPGAGKSTFLEAFGMLLI   81 (341)
T ss_dssp             SCSEEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            4678899999999999999999987654

>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X

Probab=92.17  E-value=0.081  Score=47.90  Aligned_cols=26  Identities=19%  Similarity=0.279  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +...|+|+|.+|+|||||+..+....
T Consensus         7 r~~~VaIvG~~nvGKSTLln~L~g~~   32 (301)
T 1ega_A            7 YCGFIAIVGRPNVGKSTLLNKLLGQK   32 (301)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTCS
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHCCC
Confidence            34679999999999999999998753

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=92.17  E-value=0.19  Score=42.21  Aligned_cols=42  Identities=17%  Similarity=0.279  Sum_probs=30.2

Q ss_pred             cEEEEE-cCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 042806          176 NMLGIY-GMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       176 ~vi~I~-G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~  219 (390)
                      ++|+|+ +-||+||||++..+.......+ . .+..+......+.
T Consensus         2 ~vi~v~s~kgG~GKTt~a~~la~~la~~g-~-~vlliD~D~~~~~   44 (206)
T 4dzz_A            2 KVISFLNPKGGSGKTTAVINIATALSRSG-Y-NIAVVDTDPQMSL   44 (206)
T ss_dssp             EEEEECCSSTTSSHHHHHHHHHHHHHHTT-C-CEEEEECCTTCHH
T ss_pred             eEEEEEeCCCCccHHHHHHHHHHHHHHCC-C-eEEEEECCCCCCH
Confidence            577787 6799999999999999876532 3 3566666654433

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=92.16  E-value=0.076  Score=44.24  Aligned_cols=23  Identities=26%  Similarity=0.346  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -|+|+|..|+|||||+..+....
T Consensus        28 ki~vvG~~~~GKSsLi~~l~~~~   50 (192)
T 2il1_A           28 QVIIIGSRGVGKTSLMERFTDDT   50 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHCC--
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            47899999999999999997653

>3fkq_A NTRC-like two-domain protein; RER070207001320, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: ATP 2PE; 2.10A {Eubacterium rectale}

Probab=92.16  E-value=0.21  Score=46.67  Aligned_cols=40  Identities=15%  Similarity=0.235  Sum_probs=30.1

Q ss_pred             CCccEEEEEc-CCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 042806          173 PDVNMLGIYG-MGGIVKTTLAKEVARKAETEKLFDQVIFVEVS  214 (390)
Q Consensus       173 ~~~~vi~I~G-~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~  214 (390)
                      .+.++|+|+| -||+||||++..++......+ . .++.+.+.
T Consensus       141 ~~~kvIav~s~KGGvGKTT~a~nLA~~La~~g-~-rVlliD~D  181 (373)
T 3fkq_A          141 DKSSVVIFTSPCGGVGTSTVAAACAIAHANMG-K-KVFYLNIE  181 (373)
T ss_dssp             TSCEEEEEECSSTTSSHHHHHHHHHHHHHHHT-C-CEEEEECC
T ss_pred             CCceEEEEECCCCCChHHHHHHHHHHHHHhCC-C-CEEEEECC
Confidence            3578899885 899999999999988876542 2 36667754

>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=92.10  E-value=0.054  Score=49.80  Aligned_cols=106  Identities=15%  Similarity=0.099  Sum_probs=54.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEK  254 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~  254 (390)
                      ..+++|+|+.|+|||||++.+......   -...+.+.-......... .   +.++.-..  ........+...|.. +
T Consensus       171 g~~v~i~G~~GsGKTTll~~l~g~~~~---~~g~i~i~~~~e~~~~~~-~---~~i~~~~g--gg~~~r~~la~aL~~-~  240 (330)
T 2pt7_A          171 GKNVIVCGGTGSGKTTYIKSIMEFIPK---EERIISIEDTEEIVFKHH-K---NYTQLFFG--GNITSADCLKSCLRM-R  240 (330)
T ss_dssp             TCCEEEEESTTSCHHHHHHHGGGGSCT---TSCEEEEESSCCCCCSSC-S---SEEEEECB--TTBCHHHHHHHHTTS-C
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCcC---CCcEEEECCeeccccccc-h---hEEEEEeC--CChhHHHHHHHHhhh-C
Confidence            357999999999999999999876532   234555543221110000 0   00000000  111223344455544 4


Q ss_pred             eEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchh
Q 042806          255 TILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLD  293 (390)
Q Consensus       255 ~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~  293 (390)
                      +=++++|+..+...++.+.. +.  ..+..+|+||...+
T Consensus       241 p~ilildE~~~~e~~~~l~~-~~--~g~~tvi~t~H~~~  276 (330)
T 2pt7_A          241 PDRIILGELRSSEAYDFYNV-LC--SGHKGTLTTLHAGS  276 (330)
T ss_dssp             CSEEEECCCCSTHHHHHHHH-HH--TTCCCEEEEEECSS
T ss_pred             CCEEEEcCCChHHHHHHHHH-Hh--cCCCEEEEEEcccH
Confidence            46889999977544443322 21  11223666666543

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=92.08  E-value=0.099  Score=41.93  Aligned_cols=25  Identities=20%  Similarity=0.155  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..+.+|+|+.|+||||+...++--.
T Consensus        23 ~g~~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           23 EGINLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            3578899999999999999987644

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=92.02  E-value=0.099  Score=50.56  Aligned_cols=27  Identities=19%  Similarity=0.231  Sum_probs=23.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+|.++|++|+||||+++.+.....
T Consensus        38 ~~~~IvlvGlpGsGKSTia~~La~~l~   64 (469)
T 1bif_A           38 CPTLIVMVGLPARGKTYISKKLTRYLN   64 (469)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            456789999999999999999988765

>3cwq_A Para family chromosome partitioning protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: ADP; 2.47A {Synechocystis SP}

Probab=91.98  E-value=0.26  Score=41.82  Aligned_cols=41  Identities=15%  Similarity=0.204  Sum_probs=30.2

Q ss_pred             EEEEE-cCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 042806          177 MLGIY-GMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       177 vi~I~-G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  220 (390)
                      +|+|+ +-||+||||++..+.......+   .+..+......+..
T Consensus         2 vI~v~s~KGGvGKTT~a~~LA~~la~~g---~VlliD~D~q~~~~   43 (209)
T 3cwq_A            2 IITVASFKGGVGKTTTAVHLSAYLALQG---ETLLIDGDPNRSAT   43 (209)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHTTS---CEEEEEECTTCHHH
T ss_pred             EEEEEcCCCCCcHHHHHHHHHHHHHhcC---CEEEEECCCCCCHH
Confidence            56664 7799999999999999887542   56777776654443

>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle, G-protein, prokaryote, GTP-BIND nucleotide-binding, metal transport; 2.70A {Pyrococcus furiosus}

Probab=91.97  E-value=0.096  Score=46.52  Aligned_cols=24  Identities=17%  Similarity=0.216  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..|+|+|.+|+|||||...+....
T Consensus         4 ~~i~lvG~~g~GKTTL~n~l~g~~   27 (271)
T 3k53_A            4 KTVALVGNPNVGKTTIFNALTGLR   27 (271)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHTTC
T ss_pred             eEEEEECCCCCCHHHHHHHHhCCC
Confidence            468899999999999999997653

>2h57_A ADP-ribosylation factor-like protein 6; GTP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GTP; 2.00A {Homo sapiens}

Probab=91.96  E-value=0.05  Score=45.19  Aligned_cols=24  Identities=17%  Similarity=0.142  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .-|+|+|.+|+|||||+..+....
T Consensus        22 ~ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           22 VHVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEEEECTTSSHHHHHHHTSCGG
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCC
Confidence            357899999999999999998765

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=91.94  E-value=0.097  Score=43.05  Aligned_cols=23  Identities=22%  Similarity=0.161  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      +-+.|.|++|+||||||..+...
T Consensus        17 ~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           17 MGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            56889999999999999999874

>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=91.72  E-value=0.095  Score=44.50  Aligned_cols=23  Identities=26%  Similarity=0.180  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      --|+|+|.+|+|||||+..+...
T Consensus        26 ~ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           26 IKLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEEECcCCCCHHHHHHHHhcC
Confidence            35789999999999999998764

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=91.70  E-value=0.1  Score=44.71  Aligned_cols=24  Identities=17%  Similarity=0.282  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      --|+|+|.+|+|||||+..+....
T Consensus        14 ~ki~v~G~~~vGKSsli~~l~~~~   37 (223)
T 3cpj_B           14 FKIVLIGDSGVGKSNLLSRFTKNE   37 (223)
T ss_dssp             EEEEEESCTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            357899999999999999998753

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=91.69  E-value=0.11  Score=51.79  Aligned_cols=27  Identities=19%  Similarity=0.146  Sum_probs=24.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +..+|.|.|++|+||||+++.+.....
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~L~   77 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEYLV   77 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            567899999999999999999998874

>3k9g_A PF-32 protein; ssgcid, SBRI, decode biostructures, UW, NIH, niaid, borellia burgdorferi, plasmid partition protein, iodide; 2.25A {Borrelia burgdorferi} PDB: 3k9h_A

Probab=91.69  E-value=0.48  Score=41.66  Aligned_cols=43  Identities=19%  Similarity=0.239  Sum_probs=31.3

Q ss_pred             CCccEEEEE-cCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 042806          173 PDVNMLGIY-GMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQD  218 (390)
Q Consensus       173 ~~~~vi~I~-G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~  218 (390)
                      ...++|+|+ |-||+||||++..+..... ++ + .+.-|......+
T Consensus        25 ~~~~vI~v~s~kGGvGKTT~a~~LA~~la-~g-~-~VlliD~D~~~~   68 (267)
T 3k9g_A           25 KKPKIITIASIKGGVGKSTSAIILATLLS-KN-N-KVLLIDMDTQAS   68 (267)
T ss_dssp             -CCEEEEECCSSSSSCHHHHHHHHHHHHT-TT-S-CEEEEEECTTCH
T ss_pred             CCCeEEEEEeCCCCchHHHHHHHHHHHHH-CC-C-CEEEEECCCCCC
Confidence            456788885 5699999999999999887 42 3 466667765443

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=91.65  E-value=0.19  Score=49.50  Aligned_cols=44  Identities=14%  Similarity=0.095  Sum_probs=30.6

Q ss_pred             chhHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          158 SRMSTLNDILDALK--NPDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       158 gR~~~~~~l~~~L~--~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .|.+-...+.+...  .....+|.+.|++|+||||+++.+......
T Consensus       353 ~r~eV~~~lr~~~~~~~~~~~~I~l~G~~GsGKSTia~~La~~L~~  398 (546)
T 2gks_A          353 TRPEVAEILAETYVPKHKQGFCVWLTGLPCAGKSTIAEILATMLQA  398 (546)
T ss_dssp             SCHHHHHHHHHHSCCGGGCCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHhhccccccceEEEccCCCCCCHHHHHHHHHHHhhh
Confidence            34333444444442  234578999999999999999999887654

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=91.64  E-value=0.1  Score=49.96  Aligned_cols=28  Identities=21%  Similarity=0.322  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..-..++|+|+.|+|||||++.+.....
T Consensus       155 ~~Gq~~~IvG~sGsGKSTLl~~Iag~~~  182 (438)
T 2dpy_A          155 GRGQRMGLFAGSGVGKSVLLGMMARYTR  182 (438)
T ss_dssp             BTTCEEEEEECTTSSHHHHHHHHHHHSC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcccC
Confidence            4557899999999999999999988764

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=91.60  E-value=0.077  Score=50.39  Aligned_cols=22  Identities=27%  Similarity=0.336  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|+.|+|||||++.++...
T Consensus        34 I~lvG~sGaGKSTLln~L~g~~   55 (418)
T 2qag_C           34 LMVVGESGLGKSTLINSLFLTD   55 (418)
T ss_dssp             EEEECCTTSSHHHHHHHHTTCC
T ss_pred             EEEECCCCCcHHHHHHHHhCCC
Confidence            5899999999999999998653

>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome condensation, condensin, SMC, N subunit, ABC-type ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus ducreyi} PDB: 3euk_A*

Probab=91.55  E-value=0.1  Score=50.47  Aligned_cols=25  Identities=16%  Similarity=0.040  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+++|+|+.|+|||||++.+.--..
T Consensus        30 e~~~liG~nGsGKSTLl~~l~Gl~~   54 (483)
T 3euj_A           30 LVTTLSGGNGAGKSTTMAGFVTALI   54 (483)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             ceEEEECCCCCcHHHHHHHHhcCCC
Confidence            7899999999999999999986543

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=91.52  E-value=0.31  Score=49.12  Aligned_cols=60  Identities=20%  Similarity=0.161  Sum_probs=36.3

Q ss_pred             HHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          163 LNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       163 ~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      .+.+...|..  ..+..|+||+|.|||+.+..+....-..   ...+.++........+++..+.
T Consensus       195 ~~AV~~al~~--~~~~lI~GPPGTGKT~ti~~~I~~l~~~---~~~ILv~a~TN~AvD~i~erL~  254 (646)
T 4b3f_X          195 KEAVLFALSQ--KELAIIHGPPGTGKTTTVVEIILQAVKQ---GLKVLCCAPSNIAVDNLVERLA  254 (646)
T ss_dssp             HHHHHHHHHC--SSEEEEECCTTSCHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHHHHHHHH
T ss_pred             HHHHHHHhcC--CCceEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEcCchHHHHHHHHHHH
Confidence            3445555543  2467899999999996655555444322   1246666666555666666553

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=91.32  E-value=0.076  Score=45.29  Aligned_cols=26  Identities=12%  Similarity=0.056  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +...|+|+|..|+|||||+..+....
T Consensus        28 ~~~~i~v~G~~~~GKSslin~l~~~~   53 (223)
T 4dhe_A           28 VQPEIAFAGRSNAGKSTAINVLCNQK   53 (223)
T ss_dssp             CSCEEEEEESCHHHHHHHHHHHTTCS
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhCCC
Confidence            45678899999999999999998764

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=91.29  E-value=0.14  Score=42.34  Aligned_cols=25  Identities=12%  Similarity=0.061  Sum_probs=20.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHH
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      .+..-|+|+|.+|+|||||+..+..
T Consensus        20 ~~~~~i~v~G~~~~GKssli~~l~~   44 (189)
T 2x77_A           20 DRKIRVLMLGLDNAGKTSILYRLHL   44 (189)
T ss_dssp             TSCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHc
Confidence            3445688999999999999999854

>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*

Probab=91.22  E-value=0.11  Score=47.22  Aligned_cols=25  Identities=24%  Similarity=0.328  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ....|+|+|.+|+|||||...+...
T Consensus         9 ~~g~v~ivG~~nvGKSTLin~l~g~   33 (308)
T 3iev_A            9 KVGYVAIVGKPNVGKSTLLNNLLGT   33 (308)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCC
Confidence            3568999999999999999999865

>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5 c.37.1.8

Probab=91.16  E-value=0.059  Score=48.92  Aligned_cols=24  Identities=17%  Similarity=0.255  Sum_probs=20.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..+++|.|++|+|||||++.+...
T Consensus       173 G~~~~lvG~sG~GKSTLln~L~g~  196 (307)
T 1t9h_A          173 DKTTVFAGQSGVGKSSLLNAISPE  196 (307)
T ss_dssp             TSEEEEEESHHHHHHHHHHHHCC-
T ss_pred             CCEEEEECCCCCCHHHHHHHhccc
Confidence            358999999999999999998644

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=91.13  E-value=0.37  Score=43.99  Aligned_cols=27  Identities=30%  Similarity=0.305  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      .++...|.||+||||+|..+.......
T Consensus        15 ~i~v~sgKGGvGKTTvA~~LA~~lA~~   41 (324)
T 3zq6_A           15 TFVFIGGKGGVGKTTISAATALWMARS   41 (324)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEEeCCCCchHHHHHHHHHHHHHHC
Confidence            566667999999999999998887543

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=91.12  E-value=0.11  Score=51.03  Aligned_cols=20  Identities=40%  Similarity=0.517  Sum_probs=0.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVA  196 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~  196 (390)
                      +++|+|+.|+|||||++.+.
T Consensus        49 ~~~LvG~NGaGKSTLlk~l~   68 (538)
T 1yqt_A           49 VVGIVGPNGTGKSTAVKILA   68 (538)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=91.10  E-value=0.25  Score=44.23  Aligned_cols=26  Identities=12%  Similarity=0.243  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...-|+|+|.+|+|||||...+....
T Consensus        25 ~~~~i~vvG~~~~GKSSLln~l~g~~   50 (299)
T 2aka_B           25 DLPQIAVVGGQSAGKSSVLENFVGRD   50 (299)
T ss_dssp             CCCEEEEEEBTTSCHHHHHHHHHTSC
T ss_pred             CCCeEEEEeCCCCCHHHHHHHHHCCC
Confidence            35679999999999999999997653

---

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	390
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	1e-26

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

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]

 Score =  105 bits (262), Expect = 1e-26
 Identities = 29/234 (12%), Positives = 75/234 (32%), Gaps = 24/234 (10%)

Query: 157 ESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAE--TEKLFDQVIFVEVS 214
           E  +  +   LD + + D   L ++G  G  K+ +A +   K++      +D +++++ S
Sbjct: 26  EYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDS 85

Query: 215 KIQDIRKIQGEIADKLGLTLHEE-----------SDSGRARSLRNRLKKEKTILVILDNI 263
                          L L   ++           S   +       +      L + D++
Sbjct: 86  GTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALID-RPNTLFVFDDV 144

Query: 264 WGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMA 323
                 +             + L+T R +++ +    + +   V  L+ DE +   +   
Sbjct: 145 VQEETIRW------AQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYG 198

Query: 324 GDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQ 377
                G + + V        +G P +++   ++   +               L+
Sbjct: 199 MPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKT----FEKMAQLNNKLE 248

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	390
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.43
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.16
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.11
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.06
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.03
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.02
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.01
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.97
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.88
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.88
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.8
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.71
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.68
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.65
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.64
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.62
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.56
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.53
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.52
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.45
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.32
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	98.32
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.54
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.51
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.39
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.37
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.36
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.3
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.27
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.27
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.24
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	97.24
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.21
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.16
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.15
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.14
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.13
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.13
d1okkd2	207	GTPase domain of the signal recognition particle r	97.11
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.1
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	97.05
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.04
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.04
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	97.03
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.02
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.94
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.93
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.91
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.89
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.89
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.86
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.85
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	96.83
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.79
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.72
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.7
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.69
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.69
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	96.66
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.65
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	96.65
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.62
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.6
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	96.6
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	96.55
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.51
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.5
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	96.47
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.46
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	96.37
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.37
d1xpua3	289	Transcription termination factor Rho, ATPase domai	96.36
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	96.33
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	96.33
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	96.29
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.29
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.28
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.26
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	96.25
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	96.19
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	96.18
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.14
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	96.13
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	96.03
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.02
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	96.0
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.96
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.95
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	95.91
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	95.89
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	95.89
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.83
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	95.82
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	95.77
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.74
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.72
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.68
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	95.63
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	95.57
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	95.56
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	95.54
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	95.47
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.47
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.43
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	95.38
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	95.36
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	95.24
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	95.18
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	95.11
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	95.08
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.08
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	95.06
d2awna2	232	Maltose transport protein MalK, N-terminal domain	95.02
d1g2912	240	Maltose transport protein MalK, N-terminal domain	94.99
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	94.98
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	94.94
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.92
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	94.88
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	94.87
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	94.86
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	94.86
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	94.81
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	94.81
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	94.81
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	94.78
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	94.78
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	94.77
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	94.76
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	94.75
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	94.68
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	94.66
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	94.65
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	94.62
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	94.59
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	94.58
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	94.58
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	94.57
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	94.55
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	94.55
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	94.54
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	94.54
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	94.54
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.53
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	94.53
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	94.52
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	94.5
d1nrjb_	209	Signal recognition particle receptor beta-subunit	94.48
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	94.48
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	94.46
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	94.46
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.43
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.43
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	94.43
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	94.42
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	94.41
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	94.41
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	94.39
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	94.36
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	94.35
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	94.33
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	94.31
d2fh5b1	207	Signal recognition particle receptor beta-subunit	94.3
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	94.29
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	94.23
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	94.21
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	94.16
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	94.16
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	94.14
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	94.13
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	94.1
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	94.09
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	94.05
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	94.03
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	94.02
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	94.01
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.0
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	93.99
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.98
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	93.96
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	93.95
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	93.9
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	93.9
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	93.89
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	93.88
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	93.86
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.8
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	93.79
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	93.76
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	93.73
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	93.69
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	93.69
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	93.64
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	93.63
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	93.6
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	93.6
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	93.56
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	93.55
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	93.54
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	93.52
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	93.49
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	93.49
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.38
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	93.34
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	93.31
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	93.28
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	93.28
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	93.28
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	93.21
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	93.07
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	92.88
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	92.84
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	92.81
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	92.66
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	92.46
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	92.23
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	92.11
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	91.75
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	91.62
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	91.57
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.96
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	90.8
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	90.58
d1tuea_	205	Replication protein E1 helicase domain {Human papi	90.23
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	90.1
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	89.59
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	89.39
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	89.27
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	88.95
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	88.94
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	88.93
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	88.0
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	87.71
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	86.69
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	86.65
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	86.61
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	85.88
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	85.65
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	84.94
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	84.16
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	82.47
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	81.67
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	80.62
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	80.6
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	80.07

>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=100.00  E-value=3.7e-37  Score=279.73  Aligned_cols=215  Identities=13%  Similarity=0.151  Sum_probs=167.9

Q ss_pred             ccccchhHHHHHHHHHhc---CCCccEEEEEcCCCCcHHHHHHHHHHHhh--hcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 042806          154 EACESRMSTLNDILDALK---NPDVNMLGIYGMGGIVKTTLAKEVARKAE--TEKLFDQVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~---~~~~~vi~I~G~~GvGKTtLa~~v~~~~~--~~~~f~~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      +.++||+.++++|+++|.   +.+.++|+|+||||+||||||+++|++..  ...+|++++|+++++.++...+...+..
T Consensus        20 ~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~~   99 (277)
T d2a5yb3          20 MTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDI   99 (277)
T ss_dssp             CCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHH
T ss_pred             CceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHHH
Confidence            457899999999999985   34578999999999999999999999854  4567999999999999888777766644


Q ss_pred             Hh---CCCCCC-----CC--chH-HHHHHHHHHhCCCeEEEEEeCCCCCcccccccCCCCCCCCCcEEEEEecchhhhhh
Q 042806          229 KL---GLTLHE-----ES--DSG-RARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCKVLLTARSLDVLSR  297 (390)
Q Consensus       229 ~l---~~~~~~-----~~--~~~-~~~~l~~~l~~~~~~LlVlDdv~~~~~~~~l~~~l~~~~~~s~IivTtr~~~v~~~  297 (390)
                      .+   +.....     ..  ... ....+.+.+..++ +|+||||+|+...|+.+.      ..||+||||||+..++..
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr-~LlVLDDv~~~~~~~~~~------~~~srilvTTR~~~v~~~  172 (277)
T d2a5yb3         100 LLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPN-TLFVFDDVVQEETIRWAQ------ELRLRCLVTTRDVEISNA  172 (277)
T ss_dssp             HHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTT-EEEEEEEECCHHHHHHHH------HTTCEEEEEESBGGGGGG
T ss_pred             HHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCC-eeEecchhhHHhhhhhhc------ccCceEEEEeehHHHHHh
Confidence            43   221111     11  111 1223445555555 999999999988887653      247899999999999765


Q ss_pred             cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHhcCCCCCCCcccchhHHHHHh
Q 042806          298 KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARALGTRDYLNGRTHWNSWGGLLQ  377 (390)
Q Consensus       298 ~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L~~~~~~~~~~~w~~~~~~l~  377 (390)
                      .....+.|++++|+.+|||+||...++.....+..++++++|+++|+|+||||+++|+.|+.++    .+.|..+...|+
T Consensus       173 ~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k~----~~~~~~~~~~L~  248 (277)
T d2a5yb3         173 ASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKT----FEKMAQLNNKLE  248 (277)
T ss_dssp             CCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSS----HHHHHHHHHHHH
T ss_pred             cCCCCceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHhCCCHHHHHHHHHHhccCC----HHHHHHHHHHHh
Confidence            4455578999999999999999999886555666788999999999999999999999998664    678888888786


Q ss_pred             hh
Q 042806          378 LT  379 (390)
Q Consensus       378 ~~  379 (390)
                      +.
T Consensus       249 ~~  250 (277)
T d2a5yb3         249 SR  250 (277)
T ss_dssp             HH
T ss_pred             cC
Confidence            53

>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=99.43  E-value=2.2e-12  Score=114.72  Aligned_cols=194  Identities=11%  Similarity=0.165  Sum_probs=114.0

Q ss_pred             CcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-----CCCHHHHHHHH
Q 042806          152 DYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-----IQDIRKIQGEI  226 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-----~~~~~~l~~~i  226 (390)
                      ..+.|+||++++++|.+.    ..+++.|+|++|+|||+|++++.+.....     ..|+.+..     ......+...+
T Consensus        10 ~~~~f~GR~~el~~l~~~----~~~~i~i~G~~G~GKTsLl~~~~~~~~~~-----~~~i~~~~~~~~~~~~~~~~~~~~   80 (283)
T d2fnaa2          10 NRKDFFDREKEIEKLKGL----RAPITLVLGLRRTGKSSIIKIGINELNLP-----YIYLDLRKFEERNYISYKDFLLEL   80 (283)
T ss_dssp             SGGGSCCCHHHHHHHHHT----CSSEEEEEESTTSSHHHHHHHHHHHHTCC-----EEEEEGGGGTTCSCCCHHHHHHHH
T ss_pred             ChhhCCChHHHHHHHHhc----cCCEEEEEcCCCCcHHHHHHHHHHHCCCC-----eEEEEeccccccccccHHHHHHHH
Confidence            357899999999998774    34689999999999999999998876432     45555432     22344444444


Q ss_pred             HHHhCC--------------CC------------CCCCchHHHHHHHHHH--hCCCeEEEEEeCCCCCcc-----c-ccc
Q 042806          227 ADKLGL--------------TL------------HEESDSGRARSLRNRL--KKEKTILVILDNIWGNLD-----F-QAV  272 (390)
Q Consensus       227 ~~~l~~--------------~~------------~~~~~~~~~~~l~~~l--~~~~~~LlVlDdv~~~~~-----~-~~l  272 (390)
                      ......              ..            ...........+.+.+  ..++++++|+|++.....     + ..+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~~~~~~~~~l  160 (283)
T d2fnaa2          81 QKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPAL  160 (283)
T ss_dssp             HHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHHH
T ss_pred             HHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhcccchHHHHHHH
Confidence            333210              00            0000111122233333  234559999999853311     1 111


Q ss_pred             cCCCCCCCCCcEEEEEecchhhhhhcC-----------CCcceEecCCCCHHHHHHHHHHhhCC-CCCCCchHHHHHHHH
Q 042806          273 GIPHGDDRKGCKVLLTARSLDVLSRKM-----------DSQQNFSVGVLKEDEAWSLFKKMAGD-YIEGSEFKWVAKDVA  340 (390)
Q Consensus       273 ~~~l~~~~~~s~IivTtr~~~v~~~~~-----------~~~~~~~l~~L~~~ea~~lf~~~~~~-~~~~~~~~~~~~~i~  340 (390)
                      .... ........+++++.........           .....+.|.+|+.+++.+++.+.+.. ....++    ..+|+
T Consensus       161 ~~~~-~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~~~~----~~~i~  235 (283)
T d2fnaa2         161 AYAY-DNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKD----YEVVY  235 (283)
T ss_dssp             HHHH-HHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCC----HHHHH
T ss_pred             HHHH-HhhhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCCCHHH----HHHHH
Confidence            1111 1233455566655433211110           12357899999999999999887641 122222    45899


Q ss_pred             HHcCCChHHHHHHHHHhcC
Q 042806          341 RECAGLPVSIVTVARALGT  359 (390)
Q Consensus       341 ~~~~GlPLai~~l~~~L~~  359 (390)
                      +.++|+|..+..++..+..
T Consensus       236 ~~~~G~P~~L~~~~~~~~~  254 (283)
T d2fnaa2         236 EKIGGIPGWLTYFGFIYLD  254 (283)
T ss_dssp             HHHCSCHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHh
Confidence            9999999999999876654

>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=99.16  E-value=1e-10  Score=100.90  Aligned_cols=189  Identities=14%  Similarity=0.065  Sum_probs=117.8

Q ss_pred             ccCcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 042806          150 IKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       150 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      |....+++|.+..++.|..++.+++.+-+.++|++|+||||+|+.+++....+..-.....++.+.......+...+...
T Consensus        11 P~~~~d~ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~~~~~~i~~~~~~~   90 (224)
T d1sxjb2          11 PQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHF   90 (224)
T ss_dssp             CSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHTHHHHH
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHhccccccccccccccccCCceehhhHHHHH
Confidence            44466899999999999999998877778899999999999999999886543211124444555544444433332222


Q ss_pred             hCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEecch-hhhhhcCCCcceEe
Q 042806          230 LGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTARSL-DVLSRKMDSQQNFS  306 (390)
Q Consensus       230 l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTtr~~-~v~~~~~~~~~~~~  306 (390)
                      .......              ...+.-++|+|++....  ....+...+......+++++++.+. .+..........++
T Consensus        91 ~~~~~~~--------------~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~  156 (224)
T d1sxjb2          91 AQKKLHL--------------PPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILR  156 (224)
T ss_dssp             HHBCCCC--------------CTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEE
T ss_pred             HHhhccC--------------CCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHHHhh
Confidence            1111000              01233688899997542  2222322222334456677776653 33222334456899


Q ss_pred             cCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHH
Q 042806          307 VGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTV  353 (390)
Q Consensus       307 l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l  353 (390)
                      +.+++.++...++...+.......+ ++....|++.|+|-+--+...
T Consensus       157 ~~~~~~~~i~~~l~~i~~~e~~~i~-~~~l~~I~~~s~Gd~R~ai~~  202 (224)
T d1sxjb2         157 YSKLSDEDVLKRLLQIIKLEDVKYT-NDGLEAIIFTAEGDMRQAINN  202 (224)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHTCCBC-HHHHHHHHHHHTTCHHHHHHH
T ss_pred             hcccchhhhHHHHHHHHHhcccCCC-HHHHHHHHHHcCCcHHHHHHH
Confidence            9999999999999887752111222 346789999999987654433

>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=99.11  E-value=1.8e-10  Score=99.40  Aligned_cols=182  Identities=13%  Similarity=0.064  Sum_probs=112.9

Q ss_pred             cCcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          151 KDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ....+++|.++.++.|..++..+..+.+.++|++|+||||+|+.+++............-.+.+................
T Consensus        11 ~~~~divg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~   90 (227)
T d1sxjc2          11 ETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFA   90 (227)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTHHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCeeeeecchhhcc
Confidence            34567999999999999999887777678999999999999999999865432112233333333333332222211111


Q ss_pred             CCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEecch-hhhhhcCCCcceEec
Q 042806          231 GLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTARSL-DVLSRKMDSQQNFSV  307 (390)
Q Consensus       231 ~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTtr~~-~v~~~~~~~~~~~~l  307 (390)
                      ....               +..++.-++|+|++....  ....+...+......+.++++|... .+..........+++
T Consensus        91 ~~~~---------------~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~  155 (227)
T d1sxjc2          91 STRQ---------------IFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRF  155 (227)
T ss_dssp             HBCC---------------SSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             cccc---------------ccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhhhcc
Confidence            1000               111233688999997552  2222333333334567777777753 332223344568999


Q ss_pred             CCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH
Q 042806          308 GVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV  348 (390)
Q Consensus       308 ~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL  348 (390)
                      .+++.++..+++.+.+......-+ ++....|++.++|-.-
T Consensus       156 ~~~~~~~i~~~l~~I~~~e~i~i~-~~~l~~i~~~s~Gd~R  195 (227)
T d1sxjc2         156 QPLPQEAIERRIANVLVHEKLKLS-PNAEKALIELSNGDMR  195 (227)
T ss_dssp             CCCCHHHHHHHHHHHHHTTTCCBC-HHHHHHHHHHHTTCHH
T ss_pred             ccccccccccccccccccccccCC-HHHHHHHHHHcCCcHH
Confidence            999999999999887753222222 3567889999999763

>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=99.06  E-value=4.5e-10  Score=97.35  Aligned_cols=197  Identities=14%  Similarity=0.137  Sum_probs=116.6

Q ss_pred             cCcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC-CCCeEEEEEeCCCCCHHHHHHHHHHH
Q 042806          151 KDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEK-LFDQVIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~-~f~~~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      ....+++|++..++.|..++.....+.+.++|++|+||||+++.+++...... .......++.+.......+...+-..
T Consensus         9 ~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (237)
T d1sxjd2           9 KNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNF   88 (237)
T ss_dssp             SSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHHHHH
Confidence            34567899999999999999988777788999999999999999998853321 12234445555554544433333222


Q ss_pred             hCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecch-hhhhhcCCCcceEe
Q 042806          230 LGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSL-DVLSRKMDSQQNFS  306 (390)
Q Consensus       230 l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~-~v~~~~~~~~~~~~  306 (390)
                      ..........    ..+.. ....+.-++|+|++...  ..+..+...+......+++++|+... ........-...++
T Consensus        89 ~~~~~~~~~~----~~~~~-~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i~  163 (237)
T d1sxjd2          89 ARLTVSKPSK----HDLEN-YPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFR  163 (237)
T ss_dssp             HHSCCCCCCT----THHHH-SCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEE
T ss_pred             hhhhhhhhhH----HHHhh-ccccCceEEEEecccccCHHHHHHHhhccccccccccccccccccccccccccchhhhhc
Confidence            2111111111    11111 12223247899998754  22233322222234456677666652 22211122235899


Q ss_pred             cCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCCh-HHHHHH
Q 042806          307 VGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLP-VSIVTV  353 (390)
Q Consensus       307 l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlP-Lai~~l  353 (390)
                      +.+++.++..+++.+.+.......+ ++....|++.++|-+ .||..+
T Consensus       164 f~~~~~~~~~~~L~~i~~~e~i~i~-~~~l~~ia~~s~gd~R~ai~~L  210 (237)
T d1sxjd2         164 FKALDASNAIDRLRFISEQENVKCD-DGVLERILDISAGDLRRGITLL  210 (237)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTTCCCC-HHHHHHHHHHTSSCHHHHHHHH
T ss_pred             cccccccccchhhhhhhhhhcCcCC-HHHHHHHHHHcCCCHHHHHHHH
Confidence            9999999999999888753222222 456789999997754 555544

>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=99.03  E-value=7.4e-09  Score=91.09  Aligned_cols=170  Identities=15%  Similarity=0.190  Sum_probs=110.6

Q ss_pred             ccccchhHHHHHHHHHhcC------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          154 EACESRMSTLNDILDALKN------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      ..++||+.+++.+.++|..      ..++.+.|+|++|+|||++++.+++.......+ ..+|+..........++..+.
T Consensus        16 ~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~   94 (276)
T d1fnna2          16 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTA-RFVYINGFIYRNFTAIIGEIA   94 (276)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCC-EEEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCC-cEEEecchhhhhhhhhhhhhH
Confidence            3589999999999988852      345789999999999999999999998654323 456777778888889999998


Q ss_pred             HHhCCCCCCC--CchHHHHHHHHHHhC-CCeEEEEEeCCCCCcc-----cccccCCCCC-CCCCcEEEEEecchhhhhh-
Q 042806          228 DKLGLTLHEE--SDSGRARSLRNRLKK-EKTILVILDNIWGNLD-----FQAVGIPHGD-DRKGCKVLLTARSLDVLSR-  297 (390)
Q Consensus       228 ~~l~~~~~~~--~~~~~~~~l~~~l~~-~~~~LlVlDdv~~~~~-----~~~l~~~l~~-~~~~s~IivTtr~~~v~~~-  297 (390)
                      ..++......  ........+.+.+.. ....++++|+++....     ...+...... ......+|.++........ 
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  174 (276)
T d1fnna2          95 RSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNL  174 (276)
T ss_dssp             HHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTS
T ss_pred             HhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchhhhhhc
Confidence            8887654432  333444455554433 3447888888765421     1111111111 2233455555554332111 


Q ss_pred             -----cCCCcceEecCCCCHHHHHHHHHHhhC
Q 042806          298 -----KMDSQQNFSVGVLKEDEAWSLFKKMAG  324 (390)
Q Consensus       298 -----~~~~~~~~~l~~L~~~ea~~lf~~~~~  324 (390)
                           .......+.+.+.+.++.++++.+++.
T Consensus       175 ~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~~  206 (276)
T d1fnna2         175 DPSTRGIMGKYVIRFSPYTKDQIFDILLDRAK  206 (276)
T ss_dssp             CHHHHHHHTTCEEECCCCBHHHHHHHHHHHHH
T ss_pred             chhhhhhhcchhccccchhHHHHHHHHHHHHH
Confidence                 111234688999999999999987663

>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=99.02  E-value=3.2e-09  Score=92.15  Aligned_cols=184  Identities=12%  Similarity=0.151  Sum_probs=111.6

Q ss_pred             CcccccchhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC-------------------eEEEE
Q 042806          152 DYEACESRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFD-------------------QVIFV  211 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~-------------------~~~wv  211 (390)
                      ...+++|.+..++.|..++..++ ++.+.++|++|+||||+|+.+++.........                   ....+
T Consensus        10 ~~~dlig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~   89 (239)
T d1njfa_          10 TFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEI   89 (239)
T ss_dssp             SGGGSCSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHTCCTTEEEE
T ss_pred             CHHHccChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchHHHHHHcCCCCeEEEe
Confidence            35678999999999999998766 45688999999999999999988764321111                   01222


Q ss_pred             EeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc--ccccccCCCCCCCCCcEEEEEe
Q 042806          212 EVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL--DFQAVGIPHGDDRKGCKVLLTA  289 (390)
Q Consensus       212 ~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IivTt  289 (390)
                      ..+......+ .+.+.+.+....                ..++.-++|+|+++...  ....|...+-....++++|++|
T Consensus        90 ~~~~~~~i~~-ir~~~~~~~~~~----------------~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~t  152 (239)
T d1njfa_          90 DAASRTKVED-TRDLLDNVQYAP----------------ARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLAT  152 (239)
T ss_dssp             ETTCSSSHHH-HHHHHHSCCCSC----------------SSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEE
T ss_pred             cchhcCCHHH-HHHHHHHHHhcc----------------ccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEc
Confidence            2222222211 112222211110                01333689999997652  2223333332334567788777


Q ss_pred             cchh-hhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChH-HHHHH
Q 042806          290 RSLD-VLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPV-SIVTV  353 (390)
Q Consensus       290 r~~~-v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPL-ai~~l  353 (390)
                      .+.. +......-...+.+.+++.++..+.+...+....... .++....|++.++|.+- ||..+
T Consensus       153 n~~~~i~~~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~~~-~~~~l~~i~~~s~Gd~R~ain~l  217 (239)
T d1njfa_         153 TDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAH-EPRALQLLARAAEGSLRDALSLT  217 (239)
T ss_dssp             SCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCB-CHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             CCccccChhHhhhhcccccccCcHHHhhhHHHHHHhhhccCC-CHHHHHHHHHHcCCCHHHHHHHH
Confidence            7632 2222233446899999999999998888774111112 23467889999999985 55555

>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=99.01  E-value=4.5e-10  Score=97.09  Aligned_cols=184  Identities=13%  Similarity=0.051  Sum_probs=110.7

Q ss_pred             ccCcccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCHHHHHHHHHH
Q 042806          150 IKDYEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFD-QVIFVEVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       150 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~~~~~l~~~i~~  228 (390)
                      |....+++|.+..++.|..++..++.+-+.++|++|+||||+|+.+++..... .+. ..+.++.+.......+...+..
T Consensus        20 P~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l~~~-~~~~~~~e~n~s~~~~~~~~~~~~~~   98 (231)
T d1iqpa2          20 PQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGE-NWRHNFLELNASDERGINVIREKVKE   98 (231)
T ss_dssp             CCSTTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGG-GHHHHEEEEETTCHHHHHTTHHHHHH
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHHhc-ccCCCeeEEecCcccchhHHHHHHHH
Confidence            33466899999999999999998888888999999999999999999876432 121 1233343332211111111111


Q ss_pred             HhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecch-hhhhhcCCCcceE
Q 042806          229 KLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSL-DVLSRKMDSQQNF  305 (390)
Q Consensus       229 ~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~-~v~~~~~~~~~~~  305 (390)
                      .....               .....+..++++|++...  ..+..+...+........+|+||... .+......-...+
T Consensus        99 ~~~~~---------------~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i  163 (231)
T d1iqpa2          99 FARTK---------------PIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIF  163 (231)
T ss_dssp             HHHSC---------------CGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEE
T ss_pred             HHhhh---------------hccCCCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccccc
Confidence            11000               011234479999999644  23333333322233445666666543 2222222234689


Q ss_pred             ecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHH
Q 042806          306 SVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSI  350 (390)
Q Consensus       306 ~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai  350 (390)
                      .+.+.+.++...++...+......- .++....|++.|+|-.--+
T Consensus       164 ~~~~~~~~~~~~~l~~~~~~e~i~i-~~~~l~~I~~~~~gdiR~a  207 (231)
T d1iqpa2         164 RFRPLRDEDIAKRLRYIAENEGLEL-TEEGLQAILYIAEGDMRRA  207 (231)
T ss_dssp             ECCCCCHHHHHHHHHHHHHTTTCEE-CHHHHHHHHHHHTTCHHHH
T ss_pred             cccccchhhHHHHHHHHHHHhCCCC-CHHHHHHHHHHcCCCHHHH
Confidence            9999999999999988875322211 2456788999999876543

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.97  E-value=1e-08  Score=89.63  Aligned_cols=156  Identities=15%  Similarity=0.171  Sum_probs=98.4

Q ss_pred             ccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC----CCCeEEEE-EeCCCCCHHHHHHHHHH
Q 042806          154 EACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEK----LFDQVIFV-EVSKIQDIRKIQGEIAD  228 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~----~f~~~~wv-~v~~~~~~~~l~~~i~~  228 (390)
                      ++++||+.+++++++.|......-+.++|++|+|||+++..++......+    ..+..+|. +.+.-            
T Consensus        18 d~~igRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~l------------   85 (268)
T d1r6bx2          18 DPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSL------------   85 (268)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC--------------
T ss_pred             CcccChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechH------------
Confidence            46899999999999999876666777999999999999999998864422    12234443 22110            


Q ss_pred             HhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc----------ccccccCCCCCCCCCcEEEEEecchhhhhhc
Q 042806          229 KLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL----------DFQAVGIPHGDDRKGCKVLLTARSLDVLSRK  298 (390)
Q Consensus       229 ~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~----------~~~~l~~~l~~~~~~s~IivTtr~~~v~~~~  298 (390)
                       +........-......+.+.+....+.++++|+++...          +...+..|+- .....++|.||..+......
T Consensus        86 -iag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L-~rg~i~vIgatT~eey~~~~  163 (268)
T d1r6bx2          86 -LAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLL-SSGKIRVIGSTTYQEFSNIF  163 (268)
T ss_dssp             --CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCS-SSCCCEEEEEECHHHHHCCC
T ss_pred             -hccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHH-hCCCCeEEEeCCHHHHHHHH
Confidence             00001111222233444455544445999999987541          1222333322 24456899999887664321


Q ss_pred             ------CCCcceEecCCCCHHHHHHHHHHhh
Q 042806          299 ------MDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       299 ------~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                            ......+++.+.+.+++.+++....
T Consensus       164 e~d~al~rrF~~I~V~Eps~e~t~~IL~~~~  194 (268)
T d1r6bx2         164 EKDRALARRFQKIDITEPSIEETVQIINGLK  194 (268)
T ss_dssp             CCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             hhcHHHHhhhcccccCCCCHHHHHHHHHHhh
Confidence                  1122589999999999999997654

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.88  E-value=3.6e-09  Score=92.37  Aligned_cols=197  Identities=14%  Similarity=0.088  Sum_probs=102.4

Q ss_pred             cCcccccchhHHHHHHHHHhcCC-CccEEEEEcCCCCcHHHHHHHHHHHhhhcC----CCCeEEEEEeCCC---------
Q 042806          151 KDYEACESRMSTLNDILDALKNP-DVNMLGIYGMGGIVKTTLAKEVARKAETEK----LFDQVIFVEVSKI---------  216 (390)
Q Consensus       151 ~~~~~~~gR~~~~~~l~~~L~~~-~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~---------  216 (390)
                      ...++++|++...+.|..++... ..+-+.|+|++|+||||+|+.+++......    .++...+...+..         
T Consensus         8 ~~~~diig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (252)
T d1sxje2           8 KSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSS   87 (252)
T ss_dssp             CSGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------CCEEC
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccccccccccchhhhhhccC
Confidence            34567999998888888887654 345577999999999999999999853211    1111111111000         


Q ss_pred             ------------CCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCC
Q 042806          217 ------------QDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKG  282 (390)
Q Consensus       217 ------------~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~  282 (390)
                                  .....................      ..........+.-++|||+++..  ..+..+...+......
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~iiiide~d~l~~~~~~~l~~~~e~~~~~  161 (252)
T d1sxje2          88 PYHLEITPSDMGNNDRIVIQELLKEVAQMEQVD------FQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKN  161 (252)
T ss_dssp             SSEEEECCC----CCHHHHHHHHHHHTTTTC------------------CCEEEEEECTTSSCHHHHHHHHHHHHHSTTT
T ss_pred             CccceeeecccccCCcceeeehhhhhhhhhhhh------hhhcccccCCCceEEEeccccccccccchhhhccccccccc
Confidence                        001111111111111000000      00000001123358899999764  2233333333223456


Q ss_pred             cEEEEEecchh-hhhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHH-HHHH
Q 042806          283 CKVLLTARSLD-VLSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVS-IVTV  353 (390)
Q Consensus       283 s~IivTtr~~~-v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLa-i~~l  353 (390)
                      +++|+||.+.. +......-...+++.+++.++..+++...+.........+++...|++.+.|-+-. |..+
T Consensus       162 ~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~~~~~~~~l~~i~~~s~Gd~R~ai~~L  234 (252)
T d1sxje2         162 IRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLML  234 (252)
T ss_dssp             EEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ccceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCcHHHHHHHH
Confidence            77787777532 21111122357899999999999999877641111111134667899999888754 4444

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.88  E-value=6.2e-08  Score=85.45  Aligned_cols=201  Identities=17%  Similarity=0.148  Sum_probs=118.2

Q ss_pred             cccccchhHHHHHHHHHhc----CC----C-ccEEEEEcCCCCcHHHHHHHHHHHhhhc----CCCCeEEEEEeCCCCCH
Q 042806          153 YEACESRMSTLNDILDALK----NP----D-VNMLGIYGMGGIVKTTLAKEVARKAETE----KLFDQVIFVEVSKIQDI  219 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~----~~----~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~----~~f~~~~wv~v~~~~~~  219 (390)
                      ++.+.+|+.+++.|.+.+.    .+    + ..++.|+|++|+|||++++.+++.....    .......++......+.
T Consensus        15 P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~   94 (287)
T d1w5sa2          15 PPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNL   94 (287)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccccch
Confidence            3468899999999988763    11    1 2245678999999999999999986432    11235667777777788


Q ss_pred             HHHHHHHHHHhCCCCCCC--CchHHHHHHHHHHh-CCCeEEEEEeCCCCCc--------c---ccccc---CCCCCCCCC
Q 042806          220 RKIQGEIADKLGLTLHEE--SDSGRARSLRNRLK-KEKTILVILDNIWGNL--------D---FQAVG---IPHGDDRKG  282 (390)
Q Consensus       220 ~~l~~~i~~~l~~~~~~~--~~~~~~~~l~~~l~-~~~~~LlVlDdv~~~~--------~---~~~l~---~~l~~~~~~  282 (390)
                      ...+......++......  ........+.+... .+...++++|.+....        .   +..+.   ........-
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~  174 (287)
T d1w5sa2          95 YTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRI  174 (287)
T ss_dssp             HHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBE
T ss_pred             hhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccchhHHHHHHHHHHhcchhhcccce
Confidence            888888888877644332  33334444554443 3455788888875221        0   11111   111112222


Q ss_pred             cEEEEEecchhhh-------hhcCCCcceEecCCCCHHHHHHHHHHhhCC-CCCCCchHHHHHHHHHHc------CCCh-
Q 042806          283 CKVLLTARSLDVL-------SRKMDSQQNFSVGVLKEDEAWSLFKKMAGD-YIEGSEFKWVAKDVAREC------AGLP-  347 (390)
Q Consensus       283 s~IivTtr~~~v~-------~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~-~~~~~~~~~~~~~i~~~~------~GlP-  347 (390)
                      ..|++++......       .........+++.+++.++..+++..++.. .....-.++..+.|++..      .|.| 
T Consensus       175 ~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~~~~~~~~~gd~R  254 (287)
T d1w5sa2         175 GFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSAR  254 (287)
T ss_dssp             EEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCHH
T ss_pred             eEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHHHhccccCCCCHH
Confidence            3444454443211       111223468899999999999999887631 011111234566677665      5766 


Q ss_pred             HHHHHH
Q 042806          348 VSIVTV  353 (390)
Q Consensus       348 Lai~~l  353 (390)
                      .|+..+
T Consensus       255 ~ai~~l  260 (287)
T d1w5sa2         255 RAIVAL  260 (287)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444443

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.80  E-value=1.2e-08  Score=88.90  Aligned_cols=189  Identities=13%  Similarity=0.068  Sum_probs=106.4

Q ss_pred             CcccccchhHHHHHHHHHhcC-----------------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 042806          152 DYEACESRMSTLNDILDALKN-----------------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS  214 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~-----------------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~  214 (390)
                      ....++|.+..+++|.+++..                 ...+.+.++||+|+||||+|+.+++....     ...++..+
T Consensus        12 ~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~-----~~~~~~~~   86 (253)
T d1sxja2          12 NLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGY-----DILEQNAS   86 (253)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTC-----EEEEECTT
T ss_pred             CHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHh-----hhhccccc
Confidence            356789999999999888743                 23467999999999999999999998642     24566666


Q ss_pred             CCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc-----ccccccCCCCCCCCCcEEEEEe
Q 042806          215 KIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL-----DFQAVGIPHGDDRKGCKVLLTA  289 (390)
Q Consensus       215 ~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~-----~~~~l~~~l~~~~~~s~IivTt  289 (390)
                      ...+...+... ................  ........++..++++|++....     .+..+.....  .....+++|+
T Consensus        87 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~--~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~~~--~~~~~ii~i~  161 (253)
T d1sxja2          87 DVRSKTLLNAG-VKNALDNMSVVGYFKH--NEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCR--KTSTPLILIC  161 (253)
T ss_dssp             SCCCHHHHHHT-GGGGTTBCCSTTTTTC------CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHH--HCSSCEEEEE
T ss_pred             cchhhHHHHHH-HHHHhhcchhhhhhhh--hhhcccccccceEEEeeeccccccchhhhhHHHhhhhc--cccccccccc
Confidence            55554443222 2222111110000000  00001112344889999986431     1222211110  1122344444


Q ss_pred             cc--hhhhhhcCCCcceEecCCCCHHHHHHHHHHhhC--CCCCCCchHHHHHHHHHHcCCCh-HHHHHH
Q 042806          290 RS--LDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAG--DYIEGSEFKWVAKDVARECAGLP-VSIVTV  353 (390)
Q Consensus       290 r~--~~v~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~--~~~~~~~~~~~~~~i~~~~~GlP-Lai~~l  353 (390)
                      ..  .............+++.+++.++....+...+.  +-..++   +....|++.++|-. .||..+
T Consensus       162 ~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~---~~l~~i~~~s~GDiR~ai~~L  227 (253)
T d1sxja2         162 NERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDP---NVIDRLIQTTRGDIRQVINLL  227 (253)
T ss_dssp             SCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCT---THHHHHHHHTTTCHHHHHHHH
T ss_pred             ccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCCH---HHHHHHHHhCCCcHHHHHHHH
Confidence            32  212122334456999999999999999888763  111122   24678999999976 555444

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.71  E-value=2.5e-08  Score=82.46  Aligned_cols=152  Identities=13%  Similarity=0.155  Sum_probs=90.4

Q ss_pred             ccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC----CCCeEEEEEeCCCCCHHHHHHHHHHH
Q 042806          154 EACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEK----LFDQVIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      ++.+||+.+++++++.|......-+.++|++|+|||+++..++......+    ..+..+|. +    +...++..    
T Consensus        22 d~~igRd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~-l----d~~~LiAg----   92 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLA-L----DMGALVAG----   92 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEE-E----CHHHHHTT----
T ss_pred             CCCcCcHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEE-e----eHHHHhcc----
Confidence            46889999999999999876666778999999999999999998765422    12334442 1    22221100    


Q ss_pred             hCCCCCCCCchHHHHHHHHHH-hCCCeEEEEEeCCCCCc---------cccc-ccCCCCCCCCCcEEEEEecchhhhhh-
Q 042806          230 LGLTLHEESDSGRARSLRNRL-KKEKTILVILDNIWGNL---------DFQA-VGIPHGDDRKGCKVLLTARSLDVLSR-  297 (390)
Q Consensus       230 l~~~~~~~~~~~~~~~l~~~l-~~~~~~LlVlDdv~~~~---------~~~~-l~~~l~~~~~~s~IivTtr~~~v~~~-  297 (390)
                         ......-......+.+.+ ....+.+|++|++...-         +... ++..+  .....++|.||..+..... 
T Consensus        93 ---~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L--~rg~l~~IgatT~eey~~~~  167 (195)
T d1jbka_          93 ---AKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPAL--ARGELHCVGATTLDEYRQYI  167 (195)
T ss_dssp             ---TCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHH--HTTSCCEEEEECHHHHHHHT
T ss_pred             ---CCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHH--hCCCceEEecCCHHHHHHHH
Confidence               000001112233344433 23334999999996431         1112 22222  1345678888887654322 


Q ss_pred             -----cCCCcceEecCCCCHHHHHHHH
Q 042806          298 -----KMDSQQNFSVGVLKEDEAWSLF  319 (390)
Q Consensus       298 -----~~~~~~~~~l~~L~~~ea~~lf  319 (390)
                           .......+++...+.+++..++
T Consensus       168 e~d~aL~rrF~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         168 EKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             TTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             HcCHHHHhcCCEeecCCCCHHHHHHHh
Confidence                 1223368899999999887653

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.68  E-value=2.6e-07  Score=77.85  Aligned_cols=181  Identities=10%  Similarity=0.008  Sum_probs=102.5

Q ss_pred             chhHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCC---
Q 042806          158 SRMSTLNDILDALKNPD-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLT---  233 (390)
Q Consensus       158 gR~~~~~~l~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~---  233 (390)
                      ..+...+++...+..++ +..+.++|++|+||||+|+.+++..-......   +-......+.    ..+.......   
T Consensus         6 w~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~---~~~~~~~~~~----~~i~~~~~~~~~~   78 (207)
T d1a5ta2           6 WLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQG---HKSCGHCRGC----QLMQAGTHPDYYT   78 (207)
T ss_dssp             GGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBT---TBCCSCSHHH----HHHHHTCCTTEEE
T ss_pred             ccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccccccc---cccccccchh----hhhhhccccccch
Confidence            33455777888887766 45689999999999999999988753111000   0000000000    0111100000   


Q ss_pred             --CCC---CCchHHHHHHHHHHh----CCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecchh-hhhhcCCC
Q 042806          234 --LHE---ESDSGRARSLRNRLK----KEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSLD-VLSRKMDS  301 (390)
Q Consensus       234 --~~~---~~~~~~~~~l~~~l~----~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~~-v~~~~~~~  301 (390)
                        ...   .-....+..+.+.+.    .+++-++|+|+++..  .....+...+-.-..++.+|+||++.. +......-
T Consensus        79 ~~~~~~~~~i~~~~ir~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~tI~SR  158 (207)
T d1a5ta2          79 LAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSR  158 (207)
T ss_dssp             ECCCTTCSSBCHHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTT
T ss_pred             hhhhhcccccccchhhHHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChhhhhhhhcce
Confidence              000   001112223333332    133469999999754  334444444433456778888887743 33322333


Q ss_pred             cceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHH
Q 042806          302 QQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIV  351 (390)
Q Consensus       302 ~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~  351 (390)
                      ...+.+.+++.++....+.....    .  .++.+..|++.++|.|-.+.
T Consensus       159 c~~i~~~~~~~~~~~~~L~~~~~----~--~~~~~~~i~~~s~Gs~r~al  202 (207)
T d1a5ta2         159 CRLHYLAPPPEQYAVTWLSREVT----M--SQDALLAALRLSAGSPGAAL  202 (207)
T ss_dssp             SEEEECCCCCHHHHHHHHHHHCC----C--CHHHHHHHHHHTTTCHHHHH
T ss_pred             eEEEecCCCCHHHHHHHHHHcCC----C--CHHHHHHHHHHcCCCHHHHH
Confidence            46999999999999999876542    1  13457789999999986654

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=98.65  E-value=3.1e-07  Score=79.88  Aligned_cols=174  Identities=17%  Similarity=0.189  Sum_probs=99.9

Q ss_pred             ccccchhHHHHHHH---HHhcC---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHH
Q 042806          154 EACESRMSTLNDIL---DALKN---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRK  221 (390)
Q Consensus       154 ~~~~gR~~~~~~l~---~~L~~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~  221 (390)
                      .+++|-+...++|.   .++..         ..++-+.++||+|+|||++|+.+++.....     .+.+..+.-.+.  
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~~-----~~~i~~~~l~~~--   84 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVP-----FFTISGSDFVEM--   84 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCC-----EEEECSCSSTTS--
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCCC-----EEEEEhHHhhhc--
Confidence            46777766655554   44332         235678899999999999999999887532     233333322110  


Q ss_pred             HHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC------------cc----cccccCCCC--CCCCCc
Q 042806          222 IQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN------------LD----FQAVGIPHG--DDRKGC  283 (390)
Q Consensus       222 l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~------------~~----~~~l~~~l~--~~~~~s  283 (390)
                                  ... .....+..+.+..+...|++|++||++..            ..    +..+...+.  ....+.
T Consensus        85 ------------~~g-~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v  151 (256)
T d1lv7a_          85 ------------FVG-VGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGI  151 (256)
T ss_dssp             ------------CCC-CCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCE
T ss_pred             ------------chh-HHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCE
Confidence                        001 11223445555555667799999999521            00    111111111  223455


Q ss_pred             EEEEEecchhhh-hhcC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHH
Q 042806          284 KVLLTARSLDVL-SRKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVS  349 (390)
Q Consensus       284 ~IivTtr~~~v~-~~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLa  349 (390)
                      -||.||...... ....   .-.+.+++.+.+.++-.++|+..........+.  ....+++.+.|+.-+
T Consensus       152 ~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~--~~~~la~~t~G~s~a  219 (256)
T d1lv7a_         152 IVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDI--DAAIIARGTPGFSGA  219 (256)
T ss_dssp             EEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTC--CHHHHHHTCTTCCHH
T ss_pred             EEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCccc--CHHHHHHhCCCCCHH
Confidence            666677754332 2122   234689999999999999998887532222221  135788888887544

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.64  E-value=9.6e-08  Score=88.00  Aligned_cols=156  Identities=12%  Similarity=0.139  Sum_probs=89.2

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcC----CCCeEEE-EEeCCCCCHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEK----LFDQVIF-VEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~----~f~~~~w-v~v~~~~~~~~l~~~i~  227 (390)
                      .++++||+.+++++++.|......-+.++|++|||||+++..++.......    -.+..+| ++++.-      +..  
T Consensus        21 ld~~~gr~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l------~ag--   92 (387)
T d1qvra2          21 LDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSL------LAG--   92 (387)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC--------------
T ss_pred             CCCCcCcHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhh------hcc--
Confidence            346899999999999999865544556789999999999988777653322    1234444 333221      100  


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHhC-CCeEEEEEeCCCCCc---------cc-ccccCCCCCCCCCcEEEEEecchhhhh
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLKK-EKTILVILDNIWGNL---------DF-QAVGIPHGDDRKGCKVLLTARSLDVLS  296 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~~-~~~~LlVlDdv~~~~---------~~-~~l~~~l~~~~~~s~IivTtr~~~v~~  296 (390)
                           ......-...+..+...+.. ..+++|++|+++..-         +. +-|+..+  .....++|.||..+....
T Consensus        93 -----~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L--~rg~~~~I~~tT~~ey~~  165 (387)
T d1qvra2          93 -----AKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPAL--ARGELRLIGATTLDEYRE  165 (387)
T ss_dssp             ----------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHH--HTTCCCEEEEECHHHHHH
T ss_pred             -----cCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHH--hCCCcceeeecCHHHHHH
Confidence                 00001122233344444433 335999999997541         11 1122222  233457787777655432


Q ss_pred             h-----cCCCcceEecCCCCHHHHHHHHHHhh
Q 042806          297 R-----KMDSQQNFSVGVLKEDEAWSLFKKMA  323 (390)
Q Consensus       297 ~-----~~~~~~~~~l~~L~~~ea~~lf~~~~  323 (390)
                      .     ...-...+++.+.+.+++..+++...
T Consensus       166 ~e~d~al~rrF~~v~v~ep~~~~~~~il~~~~  197 (387)
T d1qvra2         166 IEKDPALERRFQPVYVDEPTVEETISILRGLK  197 (387)
T ss_dssp             HTTCTTTCSCCCCEEECCCCHHHHHHHHHHHH
T ss_pred             hcccHHHHHhcccccCCCCcHHHHHHHHHHHH
Confidence            1     11233699999999999999998665

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=98.62  E-value=9.9e-08  Score=82.71  Aligned_cols=175  Identities=15%  Similarity=0.166  Sum_probs=95.9

Q ss_pred             cccccchhHHHHHH---HHHhcC---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 042806          153 YEACESRMSTLNDI---LDALKN---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       153 ~~~~~gR~~~~~~l---~~~L~~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  220 (390)
                      .++++|-+...+.|   +..+..         ..++-+.++|++|+|||+||+.+++.....     .+.+..      .
T Consensus         8 ~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~-----~~~i~~------~   76 (247)
T d1ixza_           8 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVP-----FITASG------S   76 (247)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCC-----EEEEEH------H
T ss_pred             HHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCC-----EEEEEh------H
Confidence            34566766554443   333332         235678999999999999999999876432     233322      2


Q ss_pred             HHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC--------c--------ccccccCCCC--CCCCC
Q 042806          221 KIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN--------L--------DFQAVGIPHG--DDRKG  282 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~--------~--------~~~~l~~~l~--~~~~~  282 (390)
                      ++...        ... .....+..+.+......|++|+|||++..        .        .+..+...+.  ....+
T Consensus        77 ~l~~~--------~~g-~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~  147 (247)
T d1ixza_          77 DFVEM--------FVG-VGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTA  147 (247)
T ss_dssp             HHHHS--------CTT-HHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCC
T ss_pred             Hhhhc--------ccc-HHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCC
Confidence            22110        000 11123344555555556799999998521        0        0111111111  12334


Q ss_pred             cEEEEEecchhhh-hhcC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHH
Q 042806          283 CKVLLTARSLDVL-SRKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVS  349 (390)
Q Consensus       283 s~IivTtr~~~v~-~~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLa  349 (390)
                      .-||.||...... ....   .....+++.+.+.++-.++|+..........+..  ...+++.|.|+.-+
T Consensus       148 vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~~--~~~la~~t~g~s~~  216 (247)
T d1ixza_         148 IVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVD--LALLAKRTPGFVGA  216 (247)
T ss_dssp             EEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCC--HHHHHHTCTTCCHH
T ss_pred             EEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCccccC--HHHHHHHCCCCCHH
Confidence            4445566653322 1111   2346899999999999999998886322222111  34678888886443

>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=98.56  E-value=2.5e-06  Score=73.09  Aligned_cols=174  Identities=14%  Similarity=0.097  Sum_probs=100.1

Q ss_pred             CcccccchhHHHHHHHHHhcC-----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 042806          152 DYEACESRMSTLNDILDALKN-----PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       152 ~~~~~~gR~~~~~~l~~~L~~-----~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      ..+.++|-+..+++|..++..     ...+-+.++||+|+||||+|+.+++....    + ...++.+......++.. +
T Consensus         7 ~~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~~~----~-~~~~~~~~~~~~~~~~~-~   80 (238)
T d1in4a2           7 SLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQT----N-IHVTSGPVLVKQGDMAA-I   80 (238)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTC----C-EEEEETTTCCSHHHHHH-H
T ss_pred             cHHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhccCC----C-cccccCcccccHHHHHH-H
Confidence            356789999888888887752     23456789999999999999999998753    2 23344444444433222 1


Q ss_pred             HHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc---------ccc-----------ccCCCCCCCCCcEEE
Q 042806          227 ADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD---------FQA-----------VGIPHGDDRKGCKVL  286 (390)
Q Consensus       227 ~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~---------~~~-----------l~~~l~~~~~~s~Ii  286 (390)
                      +...                      ++...+++|.+.....         .+.           .........+...+|
T Consensus        81 ~~~~----------------------~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I  138 (238)
T d1in4a2          81 LTSL----------------------ERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLV  138 (238)
T ss_dssp             HHHC----------------------CTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEEE
T ss_pred             HHhh----------------------ccCCchHHHHHHHhhhHHHhhcccceeeeeeeeeecCcccccccccCCCCeEEE
Confidence            1111                      1224555665543210         000           000000112344555


Q ss_pred             EEecch-hhhhh-cCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          287 LTARSL-DVLSR-KMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       287 vTtr~~-~v~~~-~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      ++|... ..... .......+.+++.+.++...++...+..... ...++....|++.++|-+-.+..+.
T Consensus       139 ~at~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~~~~l~~i~~~s~gd~R~ai~~l  207 (238)
T d1in4a2         139 GATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDV-EIEDAAAEMIAKRSRGTPRIAIRLT  207 (238)
T ss_dssp             EEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC-CBCHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             EecCCCccccccceeeeeEEEEecCCCHHHHHHHHHHhhhhccc-hhhHHHHHHHHHhCCCCHHHHHHHH
Confidence            555543 22111 2233457899999999999999887752222 2224567899999999887765443

>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=98.53  E-value=3.8e-07  Score=79.62  Aligned_cols=174  Identities=13%  Similarity=0.138  Sum_probs=99.0

Q ss_pred             ccccchhHHHHHHHHHh----cC---------CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 042806          154 EACESRMSTLNDILDAL----KN---------PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L----~~---------~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~  220 (390)
                      ..+.|-+..+++|.+.+    ..         ..++-+.++||+|+|||++++.+++.....     .+.+..+      
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~~-----~~~i~~~------   72 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAF-----FFLINGP------   72 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTCE-----EEEECHH------
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCCe-----EEEEEch------
Confidence            34666666666665543    22         235678999999999999999999986532     2222211      


Q ss_pred             HHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCc---------cc----ccccC--CCCCCCCCcEE
Q 042806          221 KIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNL---------DF----QAVGI--PHGDDRKGCKV  285 (390)
Q Consensus       221 ~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~---------~~----~~l~~--~l~~~~~~s~I  285 (390)
                      ++        ...... .....+..+.+......+++|++||++...         ..    ..+..  .......+.-|
T Consensus        73 ~l--------~~~~~g-~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlv  143 (258)
T d1e32a2          73 EI--------MSKLAG-ESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIV  143 (258)
T ss_dssp             HH--------TTSCTT-HHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEE
T ss_pred             hh--------cccccc-cHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccccCCccE
Confidence            11        100000 011223333444444566999999997431         01    11111  11123445566


Q ss_pred             EEEecchhhh-hhcC---CCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHH
Q 042806          286 LLTARSLDVL-SRKM---DSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVS  349 (390)
Q Consensus       286 ivTtr~~~v~-~~~~---~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLa  349 (390)
                      |.||...... ....   .....+++...+.++-..+|...........+..  ...|++.+.|+--|
T Consensus       144 i~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~--~~~la~~t~G~s~a  209 (258)
T d1e32a2         144 MAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVD--LEQVANETHGHVGA  209 (258)
T ss_dssp             EEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTCC--HHHHHHHCTTCCHH
T ss_pred             EEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccccccc--hhhhhhcccCCCHH
Confidence            7788764332 2122   2446999999999999999988875322222211  35799999886543

>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=98.52  E-value=2.7e-07  Score=78.06  Aligned_cols=148  Identities=17%  Similarity=0.158  Sum_probs=90.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      ..+.|+|++|+|||.|++.+++.....  ....+|++      ..++...+...+...        ....+.+.+..-. 
T Consensus        37 n~l~l~G~~G~GKTHLl~A~~~~~~~~--~~~~~~~~------~~~~~~~~~~~~~~~--------~~~~~~~~~~~~d-   99 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLLQAAGNEAKKR--GYRVIYSS------ADDFAQAMVEHLKKG--------TINEFRNMYKSVD-   99 (213)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHT--TCCEEEEE------HHHHHHHHHHHHHHT--------CHHHHHHHHHTCS-
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHhccC--ccceEEec------hHHHHHHHHHHHHcc--------chhhHHHHHhhcc-
Confidence            447899999999999999999998764  33455553      344555554444211        1234445555544 


Q ss_pred             EEEEEeCCCCC---ccccc-ccCCCCC-CCCCcEEEEEecchhh---------hhhcCCCcceEecCCCCHHHHHHHHHH
Q 042806          256 ILVILDNIWGN---LDFQA-VGIPHGD-DRKGCKVLLTARSLDV---------LSRKMDSQQNFSVGVLKEDEAWSLFKK  321 (390)
Q Consensus       256 ~LlVlDdv~~~---~~~~~-l~~~l~~-~~~~s~IivTtr~~~v---------~~~~~~~~~~~~l~~L~~~ea~~lf~~  321 (390)
                       +|++||++..   ..|+. +...+.. ...|.+||+||+....         .+ ....+..++++ +++++-.+++++
T Consensus       100 -ll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~S-RL~~g~~~~i~-p~d~~~~~iL~~  176 (213)
T d1l8qa2         100 -LLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVS-RFEGGILVEIE-LDNKTRFKIIKE  176 (213)
T ss_dssp             -EEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHH-HHHTSEEEECC-CCHHHHHHHHHH
T ss_pred             -chhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHH-HhhCceEEEEC-CCcHHHHHHHHH
Confidence             9999999743   34443 2221111 2356789999985321         11 23455688886 577778888888


Q ss_pred             hhCCCCCCCchHHHHHHHHHHcC
Q 042806          322 MAGDYIEGSEFKWVAKDVARECA  344 (390)
Q Consensus       322 ~~~~~~~~~~~~~~~~~i~~~~~  344 (390)
                      .+......-. +++...|++++.
T Consensus       177 ~a~~rgl~l~-~~v~~yl~~~~~  198 (213)
T d1l8qa2         177 KLKEFNLELR-KEVIDYLLENTK  198 (213)
T ss_dssp             HHHHTTCCCC-HHHHHHHHHHCS
T ss_pred             HHHHcCCCCC-HHHHHHHHHhcC
Confidence            8752222222 457778888774

>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=98.45  E-value=8.9e-06  Score=69.60  Aligned_cols=174  Identities=13%  Similarity=0.034  Sum_probs=98.8

Q ss_pred             cccccchhHHHHHHHHHhcC-----CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKN-----PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIA  227 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~-----~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~  227 (390)
                      .++++|-+..+++|..++..     ..++-+.++||+|+||||+|+.+++.....     ..+++.+...........+.
T Consensus         8 ~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~-----~~~~~~~~~~~~~~~~~~~~   82 (239)
T d1ixsb2           8 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVN-----LRVTSGPAIEKPGDLAAILA   82 (239)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHHTCC-----EEEEETTTCCSHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCC-----eEeccCCccccchhhHHHHH
Confidence            55788988877777766642     235667799999999999999999887532     34444444333322222221


Q ss_pred             HHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCcc---------ccc----ccCC-------CCCCCCCcEEEE
Q 042806          228 DKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLD---------FQA----VGIP-------HGDDRKGCKVLL  287 (390)
Q Consensus       228 ~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~~~---------~~~----l~~~-------l~~~~~~s~Iiv  287 (390)
                      .                    .+ ... .++++|++.....         .+.    ....       .....+...++.
T Consensus        83 ~--------------------~~-~~~-~i~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~i~  140 (239)
T d1ixsb2          83 N--------------------SL-EEG-DILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIG  140 (239)
T ss_dssp             T--------------------TC-CTT-CEEEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTTCCCEEEEECCCCEEEE
T ss_pred             h--------------------hc-cCC-CeeeeecccccchhHHHhhhhhhhhhhhhhhhccchhhhhcccCCCCEEEEe
Confidence            1                    11 112 3555676643310         000    0000       000123344554


Q ss_pred             Eecch-hh-hhhcCCCcceEecCCCCHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHH
Q 042806          288 TARSL-DV-LSRKMDSQQNFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVA  354 (390)
Q Consensus       288 Ttr~~-~v-~~~~~~~~~~~~l~~L~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~  354 (390)
                      +|.+. .. ..........+.+.+.+.++..+++...+....... ..+....|++.+.|.+-.+..+.
T Consensus       141 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~-~~~~l~~ia~~s~gd~R~a~~~l  208 (239)
T d1ixsb2         141 ATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRI-TEEAALEIGRRSRGTMRVAKRLF  208 (239)
T ss_dssp             EESCCSSCSCGGGGGCSEEEECCCCCHHHHHHHHHHHHGGGCCCB-CHHHHHHHHHHTTSSHHHHHHHH
T ss_pred             eccCcccccchhhcccceeeEeeccChhhhhHHHHHHHHHhCCcc-chHHHHHHHHHcCCCHHHHHHHH
Confidence            44432 21 111233456888999999999998887775222222 24578899999999876665443

>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=98.32  E-value=1.1e-06  Score=76.93  Aligned_cols=152  Identities=13%  Similarity=0.180  Sum_probs=86.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKE  253 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~  253 (390)
                      ..+-|.++|++|+|||+||+.+++.....       ++.++    ..++.       + .. .......+..+.......
T Consensus        40 ~~~giLL~Gp~GtGKT~l~~ala~~~~~~-------~~~~~----~~~l~-------~-~~-~~~~~~~l~~~f~~A~~~   99 (265)
T d1r7ra3          40 PSKGVLFYGPPGCGKTLLAKAIANECQAN-------FISIK----GPELL-------T-MW-FGESEANVREIFDKARQA   99 (265)
T ss_dssp             CCCEEEEBCCTTSSHHHHHHHHHHHTTCE-------EEEEC----HHHHH-------T-SC-TTTHHHHHHHHHHHHHHT
T ss_pred             CCCeEEEECCCCCcchhHHHHHHHHhCCc-------EEEEE----HHHhh-------h-cc-ccchHHHHHHHHHHHHhc
Confidence            35678899999999999999999987532       22222    11111       0 11 111222333444444445


Q ss_pred             CeEEEEEeCCCCCc--------c--------cccccCCCC--CCCCCcEEEEEecchhhh-hhcC---CCcceEecCCCC
Q 042806          254 KTILVILDNIWGNL--------D--------FQAVGIPHG--DDRKGCKVLLTARSLDVL-SRKM---DSQQNFSVGVLK  311 (390)
Q Consensus       254 ~~~LlVlDdv~~~~--------~--------~~~l~~~l~--~~~~~s~IivTtr~~~v~-~~~~---~~~~~~~l~~L~  311 (390)
                      .|++|+|||++...        .        ...+...+.  ...++.-||.||...... ....   .....+++.+.+
T Consensus       100 ~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~  179 (265)
T d1r7ra3         100 APCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPD  179 (265)
T ss_dssp             CSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCC
T ss_pred             CCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCchhCCHHHhCCCCccEEEEecchH
Confidence            67999999996331        0        112222221  123345677777754322 2111   234689999999


Q ss_pred             HHHHHHHHHHhhCCCCC--CCchHHHHHHHHHHcCCChHH
Q 042806          312 EDEAWSLFKKMAGDYIE--GSEFKWVAKDVARECAGLPVS  349 (390)
Q Consensus       312 ~~ea~~lf~~~~~~~~~--~~~~~~~~~~i~~~~~GlPLa  349 (390)
                      .++-.++|+..+.....  ..++    .++++++.|..-+
T Consensus       180 ~~~R~~il~~~l~~~~~~~~~~l----~~la~~t~g~s~~  215 (265)
T d1r7ra3         180 EKSRVAILKANLRKSPVAKDVDL----EFLAKMTNGFSGA  215 (265)
T ss_dssp             CHHHHHHHHHHTTCC----CCCC----HHHHHHHCSSCCH
T ss_pred             HHHHHHHHHHHhccCCchhhhhH----HHHHhcCCCCCHH
Confidence            99999999887753222  2232    4688888886644

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=98.32  E-value=6.2e-06  Score=71.03  Aligned_cols=26  Identities=23%  Similarity=0.187  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+-|.++|++|+|||++|+.+++...
T Consensus        40 ~~~vLL~GppGtGKT~la~alA~~~~   65 (246)
T d1d2na_          40 LVSVLLEGPPHSGKTALAAKIAEESN   65 (246)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECcCCCCHHHHHHHHhhccc
Confidence            45688999999999999999998865

>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=97.54  E-value=0.00025  Score=58.44  Aligned_cols=140  Identities=17%  Similarity=0.087  Sum_probs=78.1

Q ss_pred             HHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhc--CCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCCCCc
Q 042806          163 LNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETE--KLFDQVIFVEVSK-IQDIRKIQGEIADKLGLTLHEESD  239 (390)
Q Consensus       163 ~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~--~~f~~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~~~~  239 (390)
                      ++-+-.++..+..+.+.++|++|+|||++|..+.+.....  .|.| ..++.-.. ...++++ +.+.+.+......   
T Consensus         3 ~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D-~~~i~~~~~~I~Id~I-R~i~~~~~~~~~~---   77 (198)
T d2gnoa2           3 LETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDDI-RTIKDFLNYSPEL---   77 (198)
T ss_dssp             HHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEECCSSSCBCHHHH-HHHHHHHTSCCSS---
T ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCC-EEEEeCCcCCCCHHHH-HHHHHHHhhCccc---
Confidence            4445555666778899999999999999999999876432  2334 34443222 2233333 3344444332211   


Q ss_pred             hHHHHHHHHHHhCCCeEEEEEeCCCCC--cccccccCCCCCCCCCcEEEEEecch-hhhhhcCCCcceEecCCCCHHHHH
Q 042806          240 SGRARSLRNRLKKEKTILVILDNIWGN--LDFQAVGIPHGDDRKGCKVLLTARSL-DVLSRKMDSQQNFSVGVLKEDEAW  316 (390)
Q Consensus       240 ~~~~~~l~~~l~~~~~~LlVlDdv~~~--~~~~~l~~~l~~~~~~s~IivTtr~~-~v~~~~~~~~~~~~l~~L~~~ea~  316 (390)
                                  +++ =++|+|+++..  ...+.+...+-.-..++.+|++|.+. .+......-...+.+.+.  .+..
T Consensus        78 ------------~~~-KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~TI~SRC~~i~~~~p--~~~~  142 (198)
T d2gnoa2          78 ------------YTR-KYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVP--KEFR  142 (198)
T ss_dssp             ------------SSS-EEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCC--HHHH
T ss_pred             ------------CCC-EEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChhhCHHHHhcceEEEeCCCc--hHHH
Confidence                        223 49999999754  44555544443334567777777663 333322233346666543  3343


Q ss_pred             HHHHHh
Q 042806          317 SLFKKM  322 (390)
Q Consensus       317 ~lf~~~  322 (390)
                      .+....
T Consensus       143 ~~~~~~  148 (198)
T d2gnoa2         143 DLVKEK  148 (198)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444433

>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=97.51  E-value=0.0004  Score=59.87  Aligned_cols=86  Identities=19%  Similarity=0.215  Sum_probs=60.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC------CchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE------SDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~------~~~~~~~~l~  247 (390)
                      ..+++-|+|++|+||||||.+++......+  ..++|++....++.+.     ++.++.+.+..      ...+....+.
T Consensus        59 ~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g--~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~~~  131 (269)
T d1mo6a1          59 RGRVIEIYGPESSGKTTVALHAVANAQAAG--GVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALEIAD  131 (269)
T ss_dssp             SSSEEEEECSSSSSHHHHHHHHHHHHHHTT--CEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             cceeEEEecCCCcHHHHHHHHHHHHHhcCC--CEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHHHHHHHHH
Confidence            468999999999999999998888766543  3589999999888754     55667654431      2233333344


Q ss_pred             HHHhCCCeEEEEEeCCCCC
Q 042806          248 NRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~~  266 (390)
                      ..+..++.-|||+|.+-..
T Consensus       132 ~l~~~~~~~liIiDSi~al  150 (269)
T d1mo6a1         132 MLIRSGALDIVVIDSVAAL  150 (269)
T ss_dssp             HHHHTTCEEEEEEECSTTC
T ss_pred             HHHhcCCCCEEEEeccccc
Confidence            4445666789999998543

>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=97.39  E-value=0.0004  Score=59.90  Aligned_cols=85  Identities=20%  Similarity=0.232  Sum_probs=60.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC------CchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE------SDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~------~~~~~~~~l~  247 (390)
                      ..+++-|+|++|+|||+||.+++......+  ..++|++....++.+     +++.+|.+.+..      +.++....+.
T Consensus        56 ~g~itei~G~~~sGKT~l~l~~~~~aqk~g--~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~~  128 (268)
T d1xp8a1          56 RGRITEIYGPESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIME  128 (268)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CceEEEEecCCccchHHHHHHHHHHHHhCC--CEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHHHH
Confidence            467999999999999999999988876543  348899999888874     567777765432      2233333344


Q ss_pred             HHHhCCCeEEEEEeCCCC
Q 042806          248 NRLKKEKTILVILDNIWG  265 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~~  265 (390)
                      ..+..++.-|||+|-+-.
T Consensus       129 ~l~~~~~~~liIiDSi~a  146 (268)
T d1xp8a1         129 LLVRSGAIDVVVVDSVAA  146 (268)
T ss_dssp             HHHTTTCCSEEEEECTTT
T ss_pred             HHHhcCCCcEEEEecccc
Confidence            444455557999999853

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.37  E-value=0.00018  Score=63.85  Aligned_cols=46  Identities=15%  Similarity=0.224  Sum_probs=33.8

Q ss_pred             cccchhHHHHHHHHHhc-------C-CC-ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          155 ACESRMSTLNDILDALK-------N-PD-VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~-------~-~~-~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|-+..++.+...+.       + ++ ..++.++||+|+|||.||+.+.....
T Consensus        23 ~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~   77 (315)
T d1r6bx3          23 LVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG   77 (315)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             eecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhcc
Confidence            46677777776666552       2 22 34788999999999999999998763

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.36  E-value=0.00017  Score=64.06  Aligned_cols=105  Identities=15%  Similarity=0.244  Sum_probs=53.4

Q ss_pred             cccchhHHHHHHHHHhc-------CC-C-ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          155 ACESRMSTLNDILDALK-------NP-D-VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~-------~~-~-~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      .++|.+..++.+.+.+.       ++ + ..++.++|+.|+|||.||+.+....-..  -...+-++.+...+...+..-
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~--~~~~~~~~~~~~~~~~~~~~L  101 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT--EEAMIRIDMTEYMEKHAVSRL  101 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSS--GGGEEEECTTTCCSSGGGGGC
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCC--CcceEEEeccccccchhhhhh
Confidence            35566666665554432       22 2 2378899999999999999999886311  112333444433322221110


Q ss_pred             HHHHhCCCCCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC
Q 042806          226 IADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGN  266 (390)
Q Consensus       226 i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~LlVlDdv~~~  266 (390)
                          +|.+..... ......+.+.+......+++||+++..
T Consensus       102 ----~g~~~gyvG-~~~~~~l~~~~~~~p~~Vvl~DEieK~  137 (315)
T d1qvra3         102 ----IGAPPGYVG-YEEGGQLTEAVRRRPYSVILFDEIEKA  137 (315)
T ss_dssp             -------------------CHHHHHHHCSSEEEEESSGGGS
T ss_pred             ----cCCCCCCcC-cccCChHHHHHHhCCCcEEEEehHhhc
Confidence                011100000 001123455555555589999999744

>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=97.30  E-value=7.3e-05  Score=59.65  Aligned_cols=28  Identities=25%  Similarity=0.273  Sum_probs=24.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      .+++.|+|+.|+|||||++.+.+....+
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~l~~~   29 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPALCAR   29 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHC
Confidence            3689999999999999999999987654

>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=97.27  E-value=0.00023  Score=58.10  Aligned_cols=33  Identities=30%  Similarity=0.419  Sum_probs=27.4

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          170 LKNPDVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       170 L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      +....+-+|+|.|++|+||||||+.+.......
T Consensus        17 ~~~~~~~iIgI~G~~GSGKSTla~~L~~~l~~~   49 (198)
T d1rz3a_          17 IKTAGRLVLGIDGLSRSGKTTLANQLSQTLREQ   49 (198)
T ss_dssp             SCCSSSEEEEEEECTTSSHHHHHHHHHHHHHHT
T ss_pred             ccCCCCEEEEEECCCCCCHHHHHHHHHHHhccc
Confidence            444556689999999999999999999887653

>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=97.27  E-value=7e-05  Score=60.59  Aligned_cols=26  Identities=19%  Similarity=0.201  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ++.|+|.|++|+||||||+.+.+...
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~~   32 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVFN   32 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhC
Confidence            57899999999999999999998764

>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=97.24  E-value=7.1e-05  Score=59.17  Aligned_cols=25  Identities=20%  Similarity=0.300  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.|.|.|++|+||||+|+.+.....
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L~   27 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQLN   27 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            4688899999999999999999864

>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=97.24  E-value=0.00057  Score=58.76  Aligned_cols=84  Identities=20%  Similarity=0.249  Sum_probs=57.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC------CchHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEE------SDSGRARSLR  247 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~------~~~~~~~~l~  247 (390)
                      ..+++-|+|++|+|||||+.+++......+  ..++|++....++..     .++.++.+.+..      ........+.
T Consensus        53 ~g~itei~G~~gsGKTtl~l~~~~~~q~~g--~~~vyidtE~~~~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i~  125 (263)
T d1u94a1          53 MGRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD  125 (263)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHHcCC--CEEEEEccccccCHH-----HHHHhCCCHHHEEEecCCCHHHHHHHHH
Confidence            457999999999999999999999876543  347899988888764     356667654322      2222333333


Q ss_pred             HHHhCCCeEEEEEeCCC
Q 042806          248 NRLKKEKTILVILDNIW  264 (390)
Q Consensus       248 ~~l~~~~~~LlVlDdv~  264 (390)
                      ...+.++.-|+|+|-+.
T Consensus       126 ~l~~~~~~~liViDSi~  142 (263)
T d1u94a1         126 ALARSGAVDVIVVDSVA  142 (263)
T ss_dssp             HHHHHTCCSEEEEECGG
T ss_pred             HHHhcCCCCEEEEECcc
Confidence            33444554699999884

>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=97.21  E-value=0.00017  Score=57.87  Aligned_cols=37  Identities=11%  Similarity=-0.006  Sum_probs=29.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEE
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFV  211 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv  211 (390)
                      +..+|.|+|++|+||||+|+.+...+... +++...++
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~~L~~~-~~~~~~~~   41 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQVTLNQQ-GGRSVSLL   41 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHH-CSSCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhc-CCCchhhh
Confidence            45789999999999999999999988654 34444444

>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=97.16  E-value=0.00011  Score=57.50  Aligned_cols=24  Identities=29%  Similarity=0.318  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ++|.|+|++|+||||||+.+....
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            478899999999999999886643

>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=97.15  E-value=0.00014  Score=59.71  Aligned_cols=29  Identities=21%  Similarity=0.201  Sum_probs=25.4

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          172 NPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       172 ~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+.+|+|.|++|+||||+|+.+++...
T Consensus         3 ~~kp~iI~i~G~pGSGKsT~a~~La~~~g   31 (194)
T d1qf9a_           3 KSKPNVVFVLGGPGSGKGTQCANIVRDFG   31 (194)
T ss_dssp             CCCCEEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHC
Confidence            45678999999999999999999998763

>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=97.14  E-value=0.00088  Score=55.36  Aligned_cols=60  Identities=13%  Similarity=0.126  Sum_probs=40.2

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH--HHHHHHHHHHhCCCC
Q 042806          172 NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDI--RKIQGEIADKLGLTL  234 (390)
Q Consensus       172 ~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~--~~l~~~i~~~l~~~~  234 (390)
                      .+.+.||.++|+.|+||||.+..++.....+ ..  .+.+...+.+..  .+-++..++.++.+.
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~~~-g~--kV~lit~Dt~R~gA~eQL~~~a~~l~v~~   67 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFEQQ-GK--SVMLAAGDTFRAAAVEQLQVWGQRNNIPV   67 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHHTT-TC--CEEEECCCTTCHHHHHHHHHHHHHTTCCE
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHC-CC--cEEEEecccccccchhhhhhhhhhcCCcc
Confidence            3457899999999999998888888776532 22  333333344443  445666777777654

>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=97.13  E-value=0.00019  Score=57.79  Aligned_cols=27  Identities=22%  Similarity=0.252  Sum_probs=23.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      +.|.|+|++|+|||||++.++......
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~~   28 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKSS   28 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHC
Confidence            568999999999999999999987654

>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=97.13  E-value=0.00012  Score=58.44  Aligned_cols=24  Identities=29%  Similarity=0.365  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ++|.|.|++|+||||+|+.+....
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~   26 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQL   26 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            579999999999999999998765

>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=97.11  E-value=0.0014  Score=54.09  Aligned_cols=60  Identities=18%  Similarity=0.209  Sum_probs=43.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCC
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK-IQDIRKIQGEIADKLGLTL  234 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~-~~~~~~l~~~i~~~l~~~~  234 (390)
                      ++.++|.++|+.|+||||.+..++...... .. .+..+++.. .....+-++..++.++...
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaKLA~~~~~~-g~-kV~lit~Dt~R~gA~eQL~~~a~~l~i~~   64 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAKLGRYYQNL-GK-KVMFCAGDTFRAAGGTQLSEWGKRLSIPV   64 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHHHHHHHHTT-TC-CEEEECCCCSSTTHHHHHHHHHHHHTCCE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHC-CC-cEEEEEeccccccchhhHhhcccccCceE
Confidence            467899999999999999888888776543 23 466666654 3455566777777777653

>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=97.10  E-value=0.0009  Score=55.25  Aligned_cols=58  Identities=22%  Similarity=0.221  Sum_probs=39.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGLT  233 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~~  233 (390)
                      +.+||.++|+.|+||||.+..++.....+ ... +..+++... ....+-++..++.++.+
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~~~~~-g~k-V~lit~Dt~R~gA~eQL~~~a~~l~v~   67 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALYYKGK-GRR-PLLVAADTQRPAAREQLRLLGEKVGVP   67 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHT-TCC-EEEEECCSSCHHHHHHHHHHHHHHTCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHC-CCc-EEEEecccccchHHHHHHHHHHhcCCc
Confidence            46789999999999998888888777643 333 455555432 23445566667777664

>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=97.05  E-value=0.001  Score=56.12  Aligned_cols=86  Identities=13%  Similarity=0.185  Sum_probs=55.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCC----------------CCC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTL----------------HEE  237 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~----------------~~~  237 (390)
                      ...++.|+|++|+|||+|+.++.......  ...++|++...  +...+.+. +..++...                ...
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~~~~~--~~~~~~is~e~--~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVENACAN--KERAILFAYEE--SRAQLLRN-AYSWGMDFEEMERQNLLKIVCAYPESA   99 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHHTT--TCCEEEEESSS--CHHHHHHH-HHTTSCCHHHHHHTTSEEECCCCGGGS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHh--ccccceeeccC--CHHHHHHH-HHHcCCChHHHhhcCceEEEEeecchh
Confidence            56789999999999999999999986533  55577877654  33443333 23332211                111


Q ss_pred             CchHHHHHHHHHHhCCCeEEEEEeCCC
Q 042806          238 SDSGRARSLRNRLKKEKTILVILDNIW  264 (390)
Q Consensus       238 ~~~~~~~~l~~~l~~~~~~LlVlDdv~  264 (390)
                      ........+...+...+.-++|+|.+.
T Consensus       100 ~~~~~~~~i~~~i~~~~~~~vviDs~~  126 (242)
T d1tf7a2         100 GLEDHLQIIKSEINDFKPARIAIDSLS  126 (242)
T ss_dssp             CHHHHHHHHHHHHHTTCCSEEEEECHH
T ss_pred             hHHHHHHHHHHHHHhcCCceeeeecch
Confidence            233345566666666666789999864

>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=97.04  E-value=0.001  Score=54.97  Aligned_cols=60  Identities=17%  Similarity=0.180  Sum_probs=36.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCCC
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLTL  234 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~~  234 (390)
                      ..+.||.++|+.|+||||.+..++.....+ ... +..|++.... ...+-++..++.++.+.
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~~~~~~-g~k-V~lit~Dt~R~ga~eQL~~~a~~l~v~~   70 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAYFYKKK-GFK-VGLVGADVYRPAALEQLQQLGQQIGVPV   70 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHHHHHHT-TCC-EEEEECCCSSHHHHHHHHHHHHHHTCCE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHC-CCc-eEEEEeeccccchhHHHHHhccccCcce
Confidence            457899999999999998887777776543 333 5666665332 23444566677777653

>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=97.04  E-value=0.00015  Score=57.88  Aligned_cols=25  Identities=40%  Similarity=0.454  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.|.|.|++|+||||+|+.+.....
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~l~   29 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASKSG   29 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHC
Confidence            4577999999999999999988764

>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=97.03  E-value=0.00029  Score=60.69  Aligned_cols=27  Identities=19%  Similarity=0.197  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++.|.++|++|+||||||+.+++...
T Consensus        31 ~P~~ilL~GpPGtGKT~la~~la~~~~   57 (273)
T d1gvnb_          31 SPTAFLLGGQPGSGKTSLRSAIFEETQ   57 (273)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHTT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            467799999999999999999999875

>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=97.02  E-value=0.00019  Score=58.50  Aligned_cols=29  Identities=17%  Similarity=0.135  Sum_probs=25.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      +..+|.++|++|+||||+|+.+.......
T Consensus        18 ~g~vI~L~G~pGSGKTTiAk~La~~l~~~   46 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKTTVSMALEEYLVCH   46 (195)
T ss_dssp             CCEEEEEESSCHHHHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            35689999999999999999999887653

>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=96.94  E-value=0.00029  Score=56.10  Aligned_cols=28  Identities=29%  Similarity=0.418  Sum_probs=24.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ...+++.|.|++|+||||+|+.+.....
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~~l~   31 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAHQLH   31 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3578999999999999999999988764

>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=96.93  E-value=0.00028  Score=56.29  Aligned_cols=28  Identities=29%  Similarity=0.318  Sum_probs=23.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ++...|.|.|++|+||||+++.+.....
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~l~   30 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAELD   30 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHhC
Confidence            4456799999999999999999988753

>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=96.91  E-value=0.00026  Score=56.50  Aligned_cols=26  Identities=12%  Similarity=0.109  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|.|.|++|+||||+|+.+.....
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~   28 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcC
Confidence            47899999999999999999998864

>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=96.89  E-value=0.00026  Score=56.93  Aligned_cols=28  Identities=25%  Similarity=0.334  Sum_probs=23.6

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          172 NPDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       172 ~~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .+++.+|.++|++|+||||+|+.++...
T Consensus        11 ~~~p~liil~G~pGsGKST~a~~l~~~~   38 (172)
T d1yj5a2          11 SPNPEVVVAVGFPGAGKSTFIQEHLVSA   38 (172)
T ss_dssp             CSSCCEEEEECCTTSSHHHHHHHHTGGG
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            3567899999999999999999886543

>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=96.89  E-value=0.00029  Score=56.81  Aligned_cols=27  Identities=19%  Similarity=0.257  Sum_probs=24.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      ++|+|.|++|+||||+++.+.......
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~   28 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKE   28 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            689999999999999999999887643

>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=96.86  E-value=0.00031  Score=57.59  Aligned_cols=28  Identities=18%  Similarity=0.237  Sum_probs=24.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ++.++|.|.|++|+||||+|+.+++...
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~~~g   33 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVKDYS   33 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHHSS
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4678999999999999999999988763

>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=96.85  E-value=0.0035  Score=51.74  Aligned_cols=60  Identities=17%  Similarity=0.180  Sum_probs=41.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCCC
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKI-QDIRKIQGEIADKLGLTL  234 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~-~~~~~l~~~i~~~l~~~~  234 (390)
                      ..+.+|.++|+.|+||||.+..++.....+ + ..+..+++... ....+-++..++.++...
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLAa~~~~~-~-~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~   69 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLAKMFVDE-G-KSVVLAAADTFRAAAIEQLKIWGERVGATV   69 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHHHHHT-T-CCEEEEEECTTCHHHHHHHHHHHHHHTCEE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHC-C-CceEEEeecccccchhHHHHHHhhhcCccc
Confidence            357799999999999998888888777543 2 34666666543 234455666777777643

>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=96.83  E-value=0.003  Score=54.16  Aligned_cols=99  Identities=17%  Similarity=0.308  Sum_probs=61.7

Q ss_pred             HHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCC---------
Q 042806          165 DILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGLT---------  233 (390)
Q Consensus       165 ~l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~~---------  233 (390)
                      +.++.+.. .+-.-++|.|.+|+|||+|+..+.+.... .+-+.++++.+.... ...++..++...--..         
T Consensus        57 raID~l~pigkGQr~~If~~~g~GKt~l~~~i~~~~~~-~~~~v~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~~~~tv  135 (276)
T d2jdid3          57 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAK-AHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVA  135 (276)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHHTT-TCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEE
T ss_pred             eeeeeeccccCCCEEEeeCCCCCCHHHHHHHHHHHHHh-hCCCeEEEEEeccChHHHHHHHHHHHhcCccccccccceEE
Confidence            34455543 23345889999999999999999887532 235678888888653 4566666665532111         


Q ss_pred             ----CCCCCchH------HHHHHHHHHh-C-CCeEEEEEeCCC
Q 042806          234 ----LHEESDSG------RARSLRNRLK-K-EKTILVILDNIW  264 (390)
Q Consensus       234 ----~~~~~~~~------~~~~l~~~l~-~-~~~~LlVlDdv~  264 (390)
                          ..+.+...      ..-.+.+++. . ++.+|+++||+.
T Consensus       136 vv~~~s~~~~~~r~~~~~~a~~iAEyf~~~~G~~VLv~~Dslt  178 (276)
T d2jdid3         136 LVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIF  178 (276)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTH
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHhcCCCeEEEEEcchh
Confidence                01111111      2235667775 3 677999999984

>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=96.79  E-value=0.00054  Score=54.43  Aligned_cols=34  Identities=24%  Similarity=0.124  Sum_probs=27.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEE
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIF  210 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~w  210 (390)
                      +++.|+|..|+|||||+..+...+..+ .+...+-
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~L~~~-g~~v~vi   35 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAAAVRE-GWRVGTV   35 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEE
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHhC-CCeEEEE
Confidence            689999999999999999999998764 3554443

>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=96.72  E-value=0.00043  Score=55.04  Aligned_cols=23  Identities=22%  Similarity=0.358  Sum_probs=20.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.+.|++|+||||+++.++....
T Consensus         4 IvliG~~G~GKSTig~~La~~l~   26 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKALG   26 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            44569999999999999998875

>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=96.70  E-value=0.00048  Score=55.17  Aligned_cols=24  Identities=33%  Similarity=0.430  Sum_probs=21.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      |+|+|++|+|||||++.+......
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHGG
T ss_pred             EEEECCCCcHHHHHHHHHHhcCCC
Confidence            789999999999999999987754

>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=96.69  E-value=0.00047  Score=56.88  Aligned_cols=27  Identities=19%  Similarity=0.244  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +.+|.++|.+|+||||+|+.++.....
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~l~~   28 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRYLNF   28 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            457899999999999999999987754

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=96.69  E-value=0.00037  Score=55.61  Aligned_cols=26  Identities=31%  Similarity=0.323  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..++|.|.|++|+||||+|+.+....
T Consensus         3 ~g~iI~l~G~~GsGKSTia~~La~~l   28 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIAEALANLP   28 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTCS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            35789999999999999999997654

>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=96.66  E-value=0.0016  Score=53.88  Aligned_cols=32  Identities=9%  Similarity=0.064  Sum_probs=26.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCe
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQ  207 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~  207 (390)
                      ...|+|-|+.|+||||+++.+.+.+... .+.+
T Consensus         3 G~lI~ieG~dGsGKsT~~~~L~~~L~~~-g~~v   34 (209)
T d1nn5a_           3 GALIVLEGVDRAGKSTQSRKLVEALCAA-GHRA   34 (209)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHT-TCCE
T ss_pred             eeEEEEECCCCCCHHHHHHHHHHHHHHC-CCcE
Confidence            3679999999999999999999988664 3443

>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=96.65  E-value=0.00047  Score=55.09  Aligned_cols=24  Identities=29%  Similarity=0.313  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .|.+.|++|+||||+++.+++...
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~Lg   27 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARALG   27 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhC
Confidence            467889999999999999999875

>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=96.65  E-value=0.0029  Score=55.61  Aligned_cols=71  Identities=11%  Similarity=0.113  Sum_probs=42.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHhCCCe
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRLKKEKT  255 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~l~~~~~  255 (390)
                      .++.++|++|+|||.||+.++.....+..|   +-+..+.-.+               .........+..+.+..+.  +
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~~~~~~~~---~~~~~~~~~~---------------~~~G~~e~~~~~~f~~a~~--~  183 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEALGGKDKY---ATVRFGEPLS---------------GYNTDFNVFVDDIARAMLQ--H  183 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHHHHTTSCC---EEEEBSCSST---------------TCBCCHHHHHHHHHHHHHH--C
T ss_pred             ceEEEECCCCccHHHHHHHHHHHhcCCCCe---EEEEhhHhhh---------------cccchHHHHHHHHHHHHhh--c
Confidence            355668999999999999999987643233   2233333221               0111222233444444433  4


Q ss_pred             EEEEEeCCCCC
Q 042806          256 ILVILDNIWGN  266 (390)
Q Consensus       256 ~LlVlDdv~~~  266 (390)
                      ++|++|.++..
T Consensus       184 ~ilf~DEid~~  194 (321)
T d1w44a_         184 RVIVIDSLKNV  194 (321)
T ss_dssp             SEEEEECCTTT
T ss_pred             cEEEeehhhhh
Confidence            79999999754

>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=96.62  E-value=0.00056  Score=56.91  Aligned_cols=42  Identities=26%  Similarity=0.268  Sum_probs=32.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      .++|+|.||+|+||||+|+.+.++..    |.++         +..+++++++..
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~g----l~~i---------StGdLlR~~a~~   44 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEALQ----WHLL---------DSGAIYRVLALA   44 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHT----CEEE---------EHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC----CcEE---------CHHHHHHHHHHH
Confidence            36999999999999999999999985    3221         556788876654

>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=96.60  E-value=0.00059  Score=55.67  Aligned_cols=26  Identities=19%  Similarity=0.102  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.+|.|.|++|+||||+|+.+++...
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~~~g   26 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVEKYG   26 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999998763

>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=96.60  E-value=0.00058  Score=54.10  Aligned_cols=23  Identities=30%  Similarity=0.453  Sum_probs=21.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.|.|++|+||||+++.++....
T Consensus         3 I~liG~~GsGKsTi~k~La~~l~   25 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKDLD   25 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            67889999999999999999985

>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=96.55  E-value=0.0036  Score=52.45  Aligned_cols=89  Identities=11%  Similarity=0.178  Sum_probs=51.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCC----CCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC-------------C
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKL----FDQVIFVEVSKIQDIRKIQGEIADKLGLTLH-------------E  236 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~----f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~-------------~  236 (390)
                      ..+++.|+|++|+|||||+.++.........    -...+|+.....+.... .......++....             .
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  111 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVR-LVSIAQRFGLDPDDALNNVAYARAYNA  111 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGGG-GHHHHHHTCCCHHHHGGGEEEEECCST
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHHH-HHHHHHhcCCchhhhhcceEEEeccch
Confidence            4679999999999999999999766432211    23577887766655333 2333333332211             0


Q ss_pred             CCchHHHHHHHHHHhCCCeEEEEEeCC
Q 042806          237 ESDSGRARSLRNRLKKEKTILVILDNI  263 (390)
Q Consensus       237 ~~~~~~~~~l~~~l~~~~~~LlVlDdv  263 (390)
                      .........+...+......++++|.+
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~ds~  138 (251)
T d1szpa2         112 DHQLRLLDAAAQMMSESRFSLIVVDSV  138 (251)
T ss_dssp             TTHHHHHHHTHHHHHHSCEEEEEEETG
T ss_pred             hHHHHHHHHHHHHhhccccceeeehhh
Confidence            111222333444455556578888877

>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=96.51  E-value=0.0008  Score=54.27  Aligned_cols=30  Identities=17%  Similarity=0.245  Sum_probs=25.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFD  206 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~  206 (390)
                      ++|.|.|++|+||||+++.+...+..+ +|.
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~L~~~-~~~   31 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEILDNQ-GIN   31 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHTT-TCC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc-CCC
Confidence            688999999999999999999888643 344

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=96.50  E-value=0.00089  Score=59.10  Aligned_cols=46  Identities=20%  Similarity=0.222  Sum_probs=32.9

Q ss_pred             cccchhHHHHHHHHHhc--------------CCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          155 ACESRMSTLNDILDALK--------------NPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       155 ~~~gR~~~~~~l~~~L~--------------~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++|-++-++.+...+.              +..++.+.++||+|+|||.||+.+++...
T Consensus        15 ~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~   74 (309)
T d1ofha_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN   74 (309)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             cccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhccc
Confidence            35666666666654441              01346678999999999999999998764

>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=96.47  E-value=0.002  Score=55.65  Aligned_cols=50  Identities=26%  Similarity=0.458  Sum_probs=37.5

Q ss_pred             HHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 042806          163 LNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS  214 (390)
Q Consensus       163 ~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~  214 (390)
                      +..+.+.+..+..++|.+.|-||+||||++..+......++ +. +.-|...
T Consensus         8 ~~~~~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~~lA~~G-~r-VllvD~D   57 (279)
T d1ihua2           8 LSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMG-FD-VHLTTSD   57 (279)
T ss_dssp             HHHHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHHHTT-CC-EEEEESC
T ss_pred             HHHHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHHHHCC-Cc-EEEEeCC
Confidence            45567777788899999999999999999988888776542 22 4445444

>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=96.46  E-value=0.0014  Score=54.30  Aligned_cols=32  Identities=25%  Similarity=0.253  Sum_probs=26.9

Q ss_pred             hcCCCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          170 LKNPDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       170 L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ....+..+|.+.|++|+||||||+.+......
T Consensus        19 ~~~~kg~vIwltGlsGsGKTTia~~L~~~l~~   50 (208)
T d1m7ga_          19 LRNQRGLTIWLTGLSASGKSTLAVELEHQLVR   50 (208)
T ss_dssp             HHTSSCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             HhCCCCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            34567789999999999999999999887643

>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=96.37  E-value=0.00091  Score=54.32  Aligned_cols=26  Identities=19%  Similarity=0.015  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +..|.|.|++|+||||+|+.+.+...
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~~   28 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKYQ   28 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHC
Confidence            44578999999999999999988764

>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=96.37  E-value=0.0012  Score=54.69  Aligned_cols=27  Identities=11%  Similarity=0.197  Sum_probs=23.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +-+|+|.|+.|+||||+++.+......
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhch
Confidence            458999999999999999999888754

>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=96.36  E-value=0.0034  Score=54.13  Aligned_cols=96  Identities=20%  Similarity=0.167  Sum_probs=54.0

Q ss_pred             HHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEE-EeCCCCCHHHHHHHHHHHhCC----CCCCCC
Q 042806          165 DILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFV-EVSKIQDIRKIQGEIADKLGL----TLHEES  238 (390)
Q Consensus       165 ~l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv-~v~~~~~~~~l~~~i~~~l~~----~~~~~~  238 (390)
                      ++++.+.. .+-.-++|.|..|+|||+|+..+.+..... +-++++.+ .+...  .+++ .++......    ...+.+
T Consensus        32 r~ID~l~PigrGQr~~I~g~~g~GKT~l~~~i~~~~~~~-~~~~v~~~~~iger--~~ev-~~~~~~~~~~vv~~t~d~~  107 (289)
T d1xpua3          32 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYN-HPDCVLMVLLIDER--PEEV-TEMQRLVKGEVVASTFDEP  107 (289)
T ss_dssp             HHHHHHSCCBTTCEEEEEECSSSSHHHHHHHHHHHHHHH-CTTSEEEEEEEEEC--HHHH-HHHHHHCSSEEEEEETTSC
T ss_pred             eeeeecccccCCCeeeEeCCCCCCHHHHHHHHHHHHhhc-CCCeEEEEEeecee--HHHH-HhHHhhcceEEEeccCCCc
Confidence            46666654 345678899999999999999999887653 23434433 33322  2222 222222211    111111


Q ss_pred             ch------HHHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          239 DS------GRARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       239 ~~------~~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                      ..      ...-.+.+++. .++.+||++||+.
T Consensus       108 ~~~r~~~~~~a~~iAEyfrd~G~dVLli~Dslt  140 (289)
T d1xpua3         108 ASRHVQVAEMVIEKAKRLVEHKKDVIILLDSIT  140 (289)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTTCEEEEEESCHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHhccCceeecCcHH
Confidence            11      12334556664 3677999999984

>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=96.33  E-value=0.0011  Score=54.00  Aligned_cols=26  Identities=19%  Similarity=0.220  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +.++|.|.|++|+||||+|+.+....
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~~   32 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQKY   32 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            46789999999999999999998865

>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=96.33  E-value=0.0043  Score=51.32  Aligned_cols=28  Identities=21%  Similarity=0.188  Sum_probs=24.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +.+.|+|-|+-|+||||+++.+.+.+..
T Consensus         2 kGk~I~iEG~DGsGKST~~~~L~~~L~~   29 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQCNILYKKLQP   29 (214)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHTTT
T ss_pred             CeEEEEEECCCCCcHHHHHHHHHHHHHh
Confidence            4578999999999999999999988753

>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=96.29  E-value=0.0011  Score=55.15  Aligned_cols=43  Identities=21%  Similarity=0.140  Sum_probs=32.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLG  231 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~  231 (390)
                      -+|+|-||+|+||||+|+.+..+..    |.+.         +..++++.++....
T Consensus         4 i~IaIdGp~GsGKgT~ak~La~~lg----~~~i---------stGdl~R~~a~~~~   46 (223)
T d1q3ta_           4 IQIAIDGPASSGKSTVAKIIAKDFG----FTYL---------DTGAMYRAATYMAL   46 (223)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHHHC----CEEE---------EHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC----CcEE---------CHHHHHHHHHHHHH
Confidence            3688999999999999999999875    2211         45677777665443

>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=96.29  E-value=0.0032  Score=55.58  Aligned_cols=54  Identities=22%  Similarity=0.324  Sum_probs=36.4

Q ss_pred             HHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCC
Q 042806          163 LNDILDALK--NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFD-QVIFVEVSKIQ  217 (390)
Q Consensus       163 ~~~l~~~L~--~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~-~~~wv~v~~~~  217 (390)
                      ..++++.+.  ..+..+|+|.|++|+|||||...+.......+ +. .++-+..+..+
T Consensus        37 ~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~~~~~g-~~vaViavDpss~~   93 (323)
T d2qm8a1          37 VRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTAAG-HKVAVLAVDPSSTR   93 (323)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHHHHTT-CCEEEEEECGGGGS
T ss_pred             HHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHHHhhcC-CceeeeecccccHH
Confidence            445555553  35678999999999999999999998765432 33 34444444443

>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=96.28  E-value=0.001  Score=53.94  Aligned_cols=25  Identities=28%  Similarity=0.250  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.|+|+||+|+|||||++.+.+...
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~   26 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCC
Confidence            4588999999999999999988764

>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=96.26  E-value=0.0011  Score=54.01  Aligned_cols=24  Identities=25%  Similarity=0.281  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .|+|.||+|+|||||++.+.....
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~~   25 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEHS   25 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHhCC
Confidence            477999999999999999988764

>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=96.25  E-value=0.01  Score=48.66  Aligned_cols=36  Identities=25%  Similarity=0.273  Sum_probs=27.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEE
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFV  211 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv  211 (390)
                      .+.|+|-|+.|+||||+++.+.+.+... .+..+.+.
T Consensus         2 gkfIviEG~dGsGKsT~~~~L~~~L~~~-g~~~~~~~   37 (210)
T d4tmka_           2 SKYIVIEGLEGAGKTTARNVVVETLEQL-GIRDMVFT   37 (210)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHHHHT-TCCCEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhC-CCCeEEEe
Confidence            3679999999999999999999887653 34444443

>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=96.19  E-value=0.0014  Score=52.82  Aligned_cols=24  Identities=13%  Similarity=0.259  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ++|.|+||+|+|||||++.+....
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhC
Confidence            578999999999999999998765

>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=96.18  E-value=0.0013  Score=52.74  Aligned_cols=23  Identities=26%  Similarity=0.300  Sum_probs=20.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.|.|++|+||||+|+.++....
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~~   25 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAYG   25 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHC
Confidence            77999999999999999988763

>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=96.14  E-value=0.0041  Score=55.02  Aligned_cols=62  Identities=27%  Similarity=0.246  Sum_probs=34.5

Q ss_pred             HHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 042806          164 NDILDALK--NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGE  225 (390)
Q Consensus       164 ~~l~~~L~--~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~  225 (390)
                      .++++.+.  .++..+|+|.|++|+|||||...+......+++=-+++-+.-+.+++-..++..
T Consensus        41 ~~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss~~~ggailgd  104 (327)
T d2p67a1          41 TQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSPVTGGSILGD  104 (327)
T ss_dssp             HHHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC-----------
T ss_pred             HHHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCceeeeccccccc
Confidence            34555443  356889999999999999999999888765432112333333444444444443

>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=96.13  E-value=0.0015  Score=52.51  Aligned_cols=23  Identities=30%  Similarity=0.234  Sum_probs=21.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.|.|++|+||||+|+.+++...
T Consensus         3 I~i~G~pGsGKsT~a~~La~~~g   25 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLAEKLG   25 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHC
Confidence            67889999999999999998874

>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=96.03  E-value=0.0017  Score=52.18  Aligned_cols=23  Identities=26%  Similarity=0.328  Sum_probs=20.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.|.|++|+||||+|+.++....
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~g   25 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEKYG   25 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHC
Confidence            67899999999999999998874

>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=96.02  E-value=0.0071  Score=52.78  Aligned_cols=27  Identities=19%  Similarity=0.122  Sum_probs=24.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+-+|+|.|..|+||||+|+.+.....
T Consensus        79 ~P~iIGIaG~sgSGKSTla~~L~~lL~  105 (308)
T d1sq5a_          79 IPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEEeCCCCCCCcHHHHHHHHHHh
Confidence            466899999999999999999988775

>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=96.00  E-value=0.0051  Score=53.22  Aligned_cols=41  Identities=22%  Similarity=0.246  Sum_probs=31.0

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 042806          172 NPDVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS  214 (390)
Q Consensus       172 ~~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~  214 (390)
                      ++.+++|.+.|-||+||||++..+......++ . .+.-|+..
T Consensus         5 ~~~p~~i~~sGKGGVGKTTvaa~lA~~lA~~G-~-rVLlvD~D   45 (296)
T d1ihua1           5 QNIPPYLFFTGKGGVGKTSISCATAIRLAEQG-K-RVLLVSTD   45 (296)
T ss_dssp             SSCCSEEEEECSTTSSHHHHHHHHHHHHHHTT-C-CEEEEECC
T ss_pred             CCCCeEEEEECCCcChHHHHHHHHHHHHHHCC-C-CEEEEeCC
Confidence            45688999999999999999999988876543 2 24555544

>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=95.96  E-value=0.0019  Score=52.53  Aligned_cols=25  Identities=24%  Similarity=0.275  Sum_probs=21.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      --|.|.|++|+||||+++.+.....
T Consensus         7 mrIiliG~PGSGKtT~a~~La~~~g   31 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSRITKHFE   31 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHBC
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHHC
Confidence            3466889999999999999998753

>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=95.95  E-value=0.0021  Score=51.63  Aligned_cols=25  Identities=16%  Similarity=0.303  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.|.|+||+|+|||||++.+.....
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~~~   28 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITKHP   28 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhCC
Confidence            5788999999999999999987653

>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=95.91  E-value=0.0024  Score=54.79  Aligned_cols=37  Identities=24%  Similarity=0.374  Sum_probs=29.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS  214 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~  214 (390)
                      +.|+|+|-||+||||++..+....... .+. +.-|.+.
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~LA~~-G~r-VllID~D   38 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSGLHAM-GKT-IMVVGCD   38 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTT-TCC-EEEEEEC
T ss_pred             CEEEEECCCcCCHHHHHHHHHHHHHhC-CCc-EEEEecC
Confidence            689999999999999999999988754 343 5556664

>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=95.89  E-value=0.0025  Score=52.48  Aligned_cols=26  Identities=12%  Similarity=0.147  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+|.|+||+|+|||||.+.+.....
T Consensus         2 G~livi~GPSG~GK~tl~~~L~~~~p   27 (205)
T d1s96a_           2 GTLYIVSAPSGAGKSSLIQALLKTQP   27 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhhCC
Confidence            46789999999999999999988753

>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=95.89  E-value=0.0022  Score=51.52  Aligned_cols=23  Identities=22%  Similarity=0.222  Sum_probs=20.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.|.|++|+||||+++.+.....
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~g   27 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERFH   27 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            45779999999999999988763

>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=95.83  E-value=0.0031  Score=51.02  Aligned_cols=25  Identities=28%  Similarity=0.283  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .++| |.|++|+||||+|+.++....
T Consensus         4 ~rii-l~G~pGSGKsT~a~~La~~~g   28 (190)
T d1ak2a1           4 VRAV-LLGPPGAGKGTQAPKLAKNFC   28 (190)
T ss_dssp             CEEE-EECCTTSSHHHHHHHHHHHHT
T ss_pred             cEEE-EECCCCCCHHHHHHHHHHHhC
Confidence            3455 789999999999999988763

>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=95.82  E-value=0.0024  Score=51.11  Aligned_cols=23  Identities=22%  Similarity=0.060  Sum_probs=20.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |.|.|++|+||||+++.++....
T Consensus         3 I~i~G~pGSGKsT~~~~La~~~~   25 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEKYG   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            66899999999999999998763

>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=95.77  E-value=0.031  Score=47.47  Aligned_cols=25  Identities=24%  Similarity=0.287  Sum_probs=21.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+..|+|++|+|||||+.+++-...
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~ia   54 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQIA   54 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            5788999999999999999987654

>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=95.74  E-value=0.014  Score=50.28  Aligned_cols=77  Identities=9%  Similarity=0.022  Sum_probs=45.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCC-CeEEEEEeCCCC-CHHHHHHHHHHHhC-------CCCCCCCchHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLF-DQVIFVEVSKIQ-DIRKIQGEIADKLG-------LTLHEESDSGRARS  245 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f-~~~~wv~v~~~~-~~~~l~~~i~~~l~-------~~~~~~~~~~~~~~  245 (390)
                      +-+|+|.|+.|+|||||+..+.......... ..+..++...-+ +.++ ...+.....       ...+...+..+...
T Consensus        27 P~iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY~t~~~-r~~L~~~~~~~pl~~~RG~PgThD~~ll~~  105 (286)
T d1odfa_          27 PLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHED-QLKLNEQFKNNKLLQGRGLPGTHDMKLLQE  105 (286)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHH-HHHHHHHTTTCGGGSSSCSTTSBCHHHHHH
T ss_pred             CEEEEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCCCCHHH-HHHHhhhccccccceecCCCcchhHHHHHH
Confidence            4588999999999999999998876543212 245556665543 3332 333444331       12233344555566


Q ss_pred             HHHHHhC
Q 042806          246 LRNRLKK  252 (390)
Q Consensus       246 l~~~l~~  252 (390)
                      ..+.|..
T Consensus       106 ~l~~l~~  112 (286)
T d1odfa_         106 VLNTIFN  112 (286)
T ss_dssp             HHHHHTC
T ss_pred             HHHHHHh
Confidence            6666654

>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=95.72  E-value=0.012  Score=49.42  Aligned_cols=48  Identities=21%  Similarity=0.252  Sum_probs=35.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc----CCCCeEEEEEeCCCCCHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE----KLFDQVIFVEVSKIQDIRK  221 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~----~~f~~~~wv~v~~~~~~~~  221 (390)
                      ..+++.|+|++|+||||++.++.......    ......+|+......+...
T Consensus        35 ~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER   86 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHH
Confidence            46799999999999999999998875422    1234677887777666543

>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=95.68  E-value=0.0036  Score=52.49  Aligned_cols=24  Identities=38%  Similarity=0.415  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ||+|.|+.|+|||||...+.....
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~~   25 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYLE   25 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Confidence            789999999999999999987664

>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=95.63  E-value=0.035  Score=47.23  Aligned_cols=52  Identities=12%  Similarity=0.081  Sum_probs=34.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADK  229 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~  229 (390)
                      ..++.|.|.+|+|||+++.++..+......+. +.|++.  ..+..++...++..
T Consensus        35 G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~-v~~~s~--E~~~~~~~~r~~~~   86 (277)
T d1cr2a_          35 GEVIMVTSGSGMGKSTFVRQQALQWGTAMGKK-VGLAML--EESVEETAEDLIGL   86 (277)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHHTSCCC-EEEEES--SSCHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHhhhhhcccc-eeEeee--ccchhhHHhHHHHH
Confidence            35788999999999999999987654332343 444443  34556655555443

>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=95.57  E-value=0.0025  Score=51.80  Aligned_cols=27  Identities=22%  Similarity=0.053  Sum_probs=23.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .++.+|+|-|..|+||||+++.+....
T Consensus         7 ~kp~~I~ieG~~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1           7 TQPFTVLIEGNIGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGGT
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHh
Confidence            356689999999999999999987655

>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=95.56  E-value=0.0034  Score=55.73  Aligned_cols=46  Identities=17%  Similarity=0.224  Sum_probs=32.9

Q ss_pred             cccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          153 YEACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       153 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...++|.+..+..|.-.+......-+.|.|++|+||||||+.+..-
T Consensus         6 f~~I~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~lar~~~~i   51 (333)
T d1g8pa_           6 FSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAAL   51 (333)
T ss_dssp             GGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHH
T ss_pred             hhhccCcHHHHHHHHHHHhccCCCeEEEECCCCccHHHHHHHHHHh
Confidence            4467898876665544333323345789999999999999999753

>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=95.54  E-value=0.011  Score=49.01  Aligned_cols=40  Identities=18%  Similarity=0.063  Sum_probs=27.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS  214 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~  214 (390)
                      ...++.|+|++|+|||+|+.+++....... -....|++..
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~~~~-~~~~~~~s~e   64 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEF-DEPGVFVTFE   64 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHH-CCCEEEEESS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhc-CCCccccccc
Confidence            467899999999999999988765432221 2235565543

>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=95.47  E-value=0.004  Score=55.87  Aligned_cols=52  Identities=13%  Similarity=-0.017  Sum_probs=32.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhc-CCCCeEEEEEeCCCCCHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETE-KLFDQVIFVEVSKIQDIRKIQGEI  226 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~-~~f~~~~wv~v~~~~~~~~l~~~i  226 (390)
                      .++..|.|++|.||||++..+....... ..-...+.+..........+...+
T Consensus       163 ~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~  215 (359)
T d1w36d1         163 RRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESL  215 (359)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHH
T ss_pred             CCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHH
Confidence            4689999999999999987765554321 112235666665544444444443

>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=95.47  E-value=0.0038  Score=50.48  Aligned_cols=23  Identities=30%  Similarity=0.300  Sum_probs=19.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVA  196 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~  196 (390)
                      ++-+|+|+|+.|+||||+|..+-
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            35689999999999999998773

>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=95.43  E-value=0.0042  Score=48.16  Aligned_cols=22  Identities=18%  Similarity=0.194  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |.|+|++|+|||||...+..+.
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            5699999999999999987664

>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=95.38  E-value=0.013  Score=45.60  Aligned_cols=30  Identities=23%  Similarity=0.200  Sum_probs=26.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhhc
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAETE  202 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~  202 (390)
                      ...-+|.+.|.=|+||||+++.+++.....
T Consensus        31 ~~g~ii~L~G~LGaGKTtfvr~~~~~lg~~   60 (158)
T d1htwa_          31 EKAIMVYLNGDLGAGKTTLTRGMLQGIGHQ   60 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHTTCC
T ss_pred             CCCeEEEEecCCCccHHHHHHHHHhhcccc
Confidence            345589999999999999999999998764

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

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: Azotobacter vinelandii [TaxId: 354]

Probab=95.36  E-value=0.0051  Score=53.31  Aligned_cols=39  Identities=26%  Similarity=0.339  Sum_probs=29.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK  215 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  215 (390)
                      .+.|+|+|-||+||||++..+...+... .+. +.-|.+..
T Consensus         2 Mr~IaisgKGGVGKTT~a~NLA~~LA~~-G~r-VLlID~Dp   40 (289)
T d2afhe1           2 MRQCAIYGKGGIGKSTTTQNLVAALAEM-GKK-VMIVGCDP   40 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHHHT-TCC-EEEEEECS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHHHHHC-CCC-EEEEecCC
Confidence            3678899999999999999998887654 343 56666654

>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=95.24  E-value=0.0056  Score=51.37  Aligned_cols=26  Identities=23%  Similarity=0.193  Sum_probs=23.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ++.|+|-|+-|+||||+++.+.+...
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~l~   27 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHh
Confidence            67899999999999999999998764

>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=95.18  E-value=0.019  Score=49.05  Aligned_cols=87  Identities=13%  Similarity=0.167  Sum_probs=50.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCC-------CCCCCCch------H
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQ-DIRKIQGEIADKLGL-------TLHEESDS------G  241 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~-~~~~l~~~i~~~l~~-------~~~~~~~~------~  241 (390)
                      .-++|+|.+|+|||+|+.........  +...++++.+.... ...++..++...-..       ...+.+..      .
T Consensus        68 Qr~~Ifg~~g~GKt~l~~~~~~~~~~--~~~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a~~  145 (276)
T d1fx0a3          68 QRELIIGDRQTGKTAVATDTILNQQG--QNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAPY  145 (276)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHTCCT--TTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHHH
T ss_pred             ceEeeccCCCCChHHHHHHHHhhhcc--cCceeeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHHHH
Confidence            34778999999999999886555432  35677888877653 233333333222110       01111111      2


Q ss_pred             HHHHHHHHHhC-CCeEEEEEeCCC
Q 042806          242 RARSLRNRLKK-EKTILVILDNIW  264 (390)
Q Consensus       242 ~~~~l~~~l~~-~~~~LlVlDdv~  264 (390)
                      ..-.+.+++.+ ++..|+++||+.
T Consensus       146 ~a~tiAEyfrd~G~~Vlll~Dslt  169 (276)
T d1fx0a3         146 TGAALAEYFMYRERHTLIIYDDLS  169 (276)
T ss_dssp             HHHHHHHHHHHTTCEEEEEEECHH
T ss_pred             HHHHHHHHHHHcCCceeEEeeccH
Confidence            33455666643 567999999984

>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=95.11  E-value=0.011  Score=48.24  Aligned_cols=31  Identities=19%  Similarity=0.273  Sum_probs=25.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeE
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAETEKLFDQV  208 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~  208 (390)
                      .|+|-|.-|+||||+++.+.+....++ +...
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~l~~~g-~~v~   32 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGAFRAAG-RSVA   32 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTT-CCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCC-CCEE
Confidence            588999999999999999998876542 4433

>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=95.08  E-value=0.031  Score=46.65  Aligned_cols=47  Identities=15%  Similarity=0.155  Sum_probs=35.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhc----CCCCeEEEEEeCCCCCHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETE----KLFDQVIFVEVSKIQDIR  220 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~----~~f~~~~wv~v~~~~~~~  220 (390)
                      ..+++.|+|++|+|||+++.+++......    ..+....|+.....+...
T Consensus        36 ~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (258)
T d1v5wa_          36 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPD   86 (258)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHH
Confidence            46799999999999999999998764321    235567888877766644

>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=95.08  E-value=0.0054  Score=47.89  Aligned_cols=22  Identities=27%  Similarity=0.320  Sum_probs=19.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||.+.+.+..
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            6799999999999999997764

>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=95.06  E-value=0.0042  Score=50.80  Aligned_cols=26  Identities=35%  Similarity=0.390  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +..+++|+|+.|+|||||.+.++.-.
T Consensus        26 ~Gei~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhccc
Confidence            45689999999999999999997654

>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=95.02  E-value=0.0062  Score=50.83  Aligned_cols=25  Identities=24%  Similarity=0.271  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      +..+++|.|+.|+|||||++.+.--
T Consensus        25 ~Gei~~liGpsGsGKSTLl~~i~Gl   49 (232)
T d2awna2          25 EGEFVVFVGPSGCGKSTLLRMIAGL   49 (232)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcC
Confidence            4568999999999999999988654

>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=94.99  E-value=0.0064  Score=51.02  Aligned_cols=26  Identities=27%  Similarity=0.266  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +..+++|.|+.|+|||||++.++--.
T Consensus        28 ~Ge~~~liG~sGaGKSTll~~i~gl~   53 (240)
T d1g2912          28 DGEFMILLGPSGCGKTTTLRMIAGLE   53 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCC
Confidence            34689999999999999999996543

>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=94.98  E-value=0.0061  Score=50.84  Aligned_cols=25  Identities=20%  Similarity=0.271  Sum_probs=21.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...+++|.|+.|+|||||++.+.--
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~gl   54 (230)
T d1l2ta_          30 EGEFVSIMGPSGSGKSTMLNIIGCL   54 (230)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCcchhhHhccCC
Confidence            4568999999999999999977553

>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=94.94  E-value=0.0048  Score=53.22  Aligned_cols=28  Identities=11%  Similarity=0.189  Sum_probs=21.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      +.++|+|.|.+|+||||+++.+.+..+.
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~~~   30 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIFRR   30 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHhh
Confidence            4679999999999999999998887654

>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=94.92  E-value=0.011  Score=46.73  Aligned_cols=34  Identities=18%  Similarity=0.227  Sum_probs=25.3

Q ss_pred             HHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          164 NDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       164 ~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..+...+.....+ |.|+|.+|+|||||+..+...
T Consensus         5 ~~~~~~~~~k~~k-I~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1           5 TRIWRLFNHQEHK-VIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             HHHHHHHTTSCEE-EEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHHHHhCCCeEE-EEEECCCCCCHHHHHHHHhcC
Confidence            4556555544454 668999999999999998765

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=94.88  E-value=0.016  Score=48.88  Aligned_cols=45  Identities=18%  Similarity=0.246  Sum_probs=31.7

Q ss_pred             ccchhHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          156 CESRMSTLNDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       156 ~~gR~~~~~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      |||....+.++.+.+..  ....-|.|+|+.|+|||++|+.+.....
T Consensus         2 ~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~s~   48 (247)
T d1ny5a2           2 YVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSD   48 (247)
T ss_dssp             CCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHST
T ss_pred             eEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcC
Confidence            66666666666665542  1222367899999999999999987543

>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=94.87  E-value=0.0059  Score=51.23  Aligned_cols=26  Identities=27%  Similarity=0.339  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +..+++|.|+.|+|||||++.+.--.
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          30 AGQIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             SSCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcCCc
Confidence            45689999999999999999986543

>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=94.86  E-value=0.0079  Score=49.07  Aligned_cols=46  Identities=9%  Similarity=0.075  Sum_probs=31.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcC----CCCeEEEEEeCCCCCH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEK----LFDQVIFVEVSKIQDI  219 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~----~f~~~~wv~v~~~~~~  219 (390)
                      ...++.|.|++|+|||+|+.+++.+.....    .+....++........
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~~~~~~~~~~~~~~~~~~~~~~~~~~   71 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRP   71 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCH
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHHHHHhhccccccceehhhhhhhhhHH
Confidence            457899999999999999999987754322    1234455555544444

>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=94.86  E-value=0.0068  Score=47.66  Aligned_cols=22  Identities=27%  Similarity=0.282  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+.+..
T Consensus         7 ivlvG~~~vGKTsli~~~~~~~   28 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEKK   28 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999988753

>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=94.81  E-value=0.0076  Score=50.49  Aligned_cols=26  Identities=31%  Similarity=0.297  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+|||||++.+.--.
T Consensus        31 ~Ge~~~liGpsGaGKSTLl~~i~Gl~   56 (239)
T d1v43a3          31 DGEFLVLLGPSGCGKTTTLRMIAGLE   56 (239)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcCC
Confidence            45689999999999999999886543

>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=94.81  E-value=0.0089  Score=53.53  Aligned_cols=29  Identities=24%  Similarity=0.079  Sum_probs=25.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ++.+.+.++||+|+|||++|+.+++....
T Consensus       152 ~~~~~~~~~g~~~~gk~~~~~~~~~~~~~  180 (362)
T d1svma_         152 PKKRYWLFKGPIDSGKTTLAAALLELCGG  180 (362)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHHCC
T ss_pred             CCcCeEEEECCCCCCHHHHHHHHHHHcCC
Confidence            45678999999999999999999998864

>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=94.81  E-value=0.0076  Score=50.45  Aligned_cols=24  Identities=17%  Similarity=0.169  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      -+++|.|+.|+|||||++.+.--.
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl~   48 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEEECCCCChHHHHHHHHHcCC
Confidence            377899999999999999997754

>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=94.78  E-value=0.0072  Score=47.89  Aligned_cols=22  Identities=27%  Similarity=0.264  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+.+..
T Consensus         6 ivvvG~~~vGKTsli~r~~~~~   27 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDKR   27 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHhcCC
Confidence            6689999999999999987663

>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=94.78  E-value=0.0073  Score=50.80  Aligned_cols=26  Identities=35%  Similarity=0.431  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ....++|+|+.|+|||||++.+..-.
T Consensus        28 ~Ge~vaIvG~sGsGKSTLl~ll~gl~   53 (241)
T d2pmka1          28 QGEVIGIVGRSGSGKSTLTKLIQRFY   53 (241)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcC
Confidence            34689999999999999999997654

>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=94.77  E-value=0.0081  Score=47.08  Aligned_cols=21  Identities=14%  Similarity=0.381  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+++|.+|+|||||+..+.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            668999999999999998864

>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=94.76  E-value=0.0088  Score=48.32  Aligned_cols=26  Identities=8%  Similarity=0.248  Sum_probs=22.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ++.+.|+|+|.+|+|||||...+.+.
T Consensus        21 ~~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          21 GGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHhcCC
Confidence            34567999999999999999999853

>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=94.75  E-value=0.0074  Score=47.26  Aligned_cols=22  Identities=18%  Similarity=0.173  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |.++|.+|+|||||+..+.+..
T Consensus         5 v~liG~~~vGKTsLl~~~~~~~   26 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAGR   26 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6799999999999999998763

>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=94.68  E-value=0.0079  Score=47.28  Aligned_cols=22  Identities=23%  Similarity=0.444  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+.+..
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~~   27 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999998753

>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=94.66  E-value=0.0047  Score=51.70  Aligned_cols=26  Identities=19%  Similarity=0.202  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .+.|+|-|+.|+||||+++.+.+...
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~l~   27 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQLCE   27 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHh
Confidence            47899999999999999999988763

>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=94.65  E-value=0.0092  Score=50.60  Aligned_cols=26  Identities=23%  Similarity=0.258  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        40 ~Ge~iaivG~sGsGKSTLl~ll~gl~   65 (253)
T d3b60a1          40 AGKTVALVGRSGSGKSTIASLITRFY   65 (253)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHTTTT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhccc
Confidence            45689999999999999999996543

>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=94.62  E-value=0.0083  Score=47.28  Aligned_cols=22  Identities=32%  Similarity=0.528  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||+|+..+.+..
T Consensus         5 i~lvG~~~vGKTsli~r~~~~~   26 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTKR   26 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            5689999999999999998754

>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=94.59  E-value=0.0075  Score=50.19  Aligned_cols=26  Identities=23%  Similarity=0.133  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..-+++|.|+.|+|||||++.+.--.
T Consensus        25 ~Ge~~~liGpsGaGKSTll~~l~Gl~   50 (229)
T d3d31a2          25 SGEYFVILGPTGAGKTLFLELIAGFH   50 (229)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCc
Confidence            45689999999999999999997654

>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=94.58  E-value=0.029  Score=42.19  Aligned_cols=52  Identities=10%  Similarity=0.043  Sum_probs=34.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLG  231 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~~~~~~~l~~~i~~~l~  231 (390)
                      ..++..|+++.|+|||+++-.++...      ...+.+.+....-.++....+.+.++
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~~~~------~~~vli~~P~~~l~~q~~~~~~~~~~   58 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAHG   58 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHTT------TCCEEEEESCHHHHHHHHHHHHHHHS
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHc------CCcEEEEcChHHHHHHHHHHHHHHhh
Confidence            45678899999999999887665432      23466666655445555555555554

>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=94.58  E-value=0.0086  Score=47.27  Aligned_cols=22  Identities=23%  Similarity=0.383  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||++.+.+..
T Consensus         8 i~lvG~~~vGKTsLi~~l~~~~   29 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQGL   29 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6799999999999999998753

>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=94.57  E-value=0.25  Score=40.67  Aligned_cols=47  Identities=23%  Similarity=0.181  Sum_probs=38.2

Q ss_pred             ccccchhHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          154 EACESRMSTLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       154 ~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..........+++.+.+..+......|+|..|+|||-++.......-
T Consensus        55 ~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~  101 (233)
T d2eyqa3          55 ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAV  101 (233)
T ss_dssp             CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHH
T ss_pred             ccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHH
Confidence            33445667788888888888888899999999999999888877653

>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=94.55  E-value=0.0088  Score=46.77  Aligned_cols=22  Identities=23%  Similarity=0.238  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||++.+.+..
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~~   24 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYDS   24 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6788999999999999998653

>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=94.55  E-value=0.0089  Score=47.10  Aligned_cols=21  Identities=24%  Similarity=0.213  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+++|.+|+|||||+..+.+.
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            679999999999999998765

>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=94.54  E-value=0.0089  Score=46.98  Aligned_cols=22  Identities=14%  Similarity=0.288  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||++.+.+..
T Consensus         7 i~lvG~~~vGKTsli~rl~~~~   28 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVEDS   28 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6688999999999999998754

>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=94.54  E-value=0.01  Score=49.94  Aligned_cols=26  Identities=19%  Similarity=0.156  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ....++|+|+.|+|||||++.+.--.
T Consensus        27 ~Ge~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          27 PNSIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            45689999999999999999996543

>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=94.54  E-value=0.011  Score=51.03  Aligned_cols=26  Identities=31%  Similarity=0.275  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|+|+.|+|||||++.+.--.
T Consensus        61 ~Ge~vaivG~nGsGKSTLl~~i~Gl~   86 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTSLLMLILGEL   86 (281)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCCC
Confidence            45789999999999999999997654

>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=94.53  E-value=0.0078  Score=47.46  Aligned_cols=22  Identities=23%  Similarity=0.613  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+.+..
T Consensus         5 i~viG~~~vGKTsLi~r~~~~~   26 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKGT   26 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTCC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            5688999999999999988753

>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=94.53  E-value=0.01  Score=50.19  Aligned_cols=26  Identities=19%  Similarity=0.147  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ....++|+|+.|+|||||++.+..-.
T Consensus        39 ~Ge~vaivG~sGsGKSTLl~li~gl~   64 (251)
T d1jj7a_          39 PGEVTALVGPNGSGKSTVAALLQNLY   64 (251)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhccc
Confidence            45689999999999999999986543

>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=94.52  E-value=0.009  Score=46.94  Aligned_cols=22  Identities=23%  Similarity=0.306  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+.+..
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~~   27 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCENK   27 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999987653

>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=94.50  E-value=0.0095  Score=49.48  Aligned_cols=26  Identities=23%  Similarity=0.290  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..+|..|.|.-|+|||||.+.+....
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~~   27 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNEQ   27 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHSC
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhcC
Confidence            56889999999999999999998753

>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=94.48  E-value=0.011  Score=48.12  Aligned_cols=23  Identities=22%  Similarity=0.094  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      +.|+|+|.+|+|||||...+.+.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            47889999999999999999865

>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=94.48  E-value=0.0095  Score=46.97  Aligned_cols=22  Identities=18%  Similarity=0.290  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+.++.+..
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~~   30 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999998654

>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=94.46  E-value=0.0094  Score=47.19  Aligned_cols=22  Identities=27%  Similarity=0.410  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+.+..
T Consensus         9 v~lvG~~~vGKTsLi~r~~~~~   30 (173)
T d2fn4a1           9 LVVVGGGGVGKSALTIQFIQSY   30 (173)
T ss_dssp             EEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6799999999999999988653

>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=94.46  E-value=0.0081  Score=47.63  Aligned_cols=24  Identities=25%  Similarity=0.248  Sum_probs=19.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..-|+|+|.+|+|||||...+...
T Consensus        13 ~~kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          13 TGKLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            344779999999999999988554

>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=94.43  E-value=0.0096  Score=46.97  Aligned_cols=22  Identities=27%  Similarity=0.410  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+.+..
T Consensus         8 i~lvG~~~vGKTsLi~r~~~~~   29 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQSY   29 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            6789999999999999988753

>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=94.43  E-value=0.0095  Score=46.59  Aligned_cols=21  Identities=29%  Similarity=0.352  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+|+|.+|+|||||.+.+...
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            669999999999999998654

>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=94.43  E-value=0.0098  Score=46.69  Aligned_cols=23  Identities=17%  Similarity=0.309  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      =|+|+|.+|+|||||+..+.+..
T Consensus         6 Kv~liG~~~vGKTsLl~~~~~~~   28 (167)
T d1xtqa1           6 KIAILGYRSVGKSSLTIQFVEGQ   28 (167)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            36789999999999999987653

>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=94.42  E-value=0.0097  Score=47.04  Aligned_cols=22  Identities=27%  Similarity=0.344  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+.+..
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~~   26 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVNDK   26 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHcCC
Confidence            6799999999999999987643

>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=94.41  E-value=0.0099  Score=50.50  Aligned_cols=25  Identities=20%  Similarity=0.255  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...+++|.|+.|+|||||++.+.--
T Consensus        27 ~GEi~~iiG~sGsGKSTLl~~i~Gl   51 (258)
T d1b0ua_          27 AGDVISIIGSSGSGKSTFLRCINFL   51 (258)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcC
Confidence            4568999999999999999999643

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {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: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.41  E-value=0.026  Score=46.58  Aligned_cols=38  Identities=21%  Similarity=0.259  Sum_probs=29.8

Q ss_pred             cEEEEE-cCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 042806          176 NMLGIY-GMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK  215 (390)
Q Consensus       176 ~vi~I~-G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~~  215 (390)
                      ++|+|. |-||+||||++..++......  -..+..|....
T Consensus         2 kvIav~s~KGGvGKTtia~nlA~~la~~--g~~VlliD~D~   40 (232)
T d1hyqa_           2 RTITVASGKGGTGKTTITANLGVALAQL--GHDVTIVDADI   40 (232)
T ss_dssp             EEEEEEESSSCSCHHHHHHHHHHHHHHT--TCCEEEEECCC
T ss_pred             EEEEEECCCCCChHHHHHHHHHHHHHhC--CCCEEEEeCCC
Confidence            688887 789999999999999888754  23477777653

>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=94.39  E-value=0.01  Score=46.58  Aligned_cols=22  Identities=18%  Similarity=0.264  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+++|.+|+|||||+..+.+..
T Consensus         5 i~vvG~~~vGKTSli~~l~~~~   26 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVEDK   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6799999999999999988753

>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=94.36  E-value=0.011  Score=45.53  Aligned_cols=21  Identities=29%  Similarity=0.290  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+|+|.+|+|||||+..+.+.
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            679999999999999998765

>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=94.35  E-value=0.01  Score=46.51  Aligned_cols=22  Identities=27%  Similarity=0.510  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+.+..
T Consensus         6 i~viG~~~vGKTsli~~l~~~~   27 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            6789999999999999998753

>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=94.33  E-value=0.011  Score=46.52  Aligned_cols=22  Identities=27%  Similarity=0.481  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||+|+..+....
T Consensus         6 ivvvG~~~vGKTsli~r~~~~~   27 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            6789999999999999988764

>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=94.31  E-value=0.01  Score=46.65  Aligned_cols=21  Identities=24%  Similarity=0.327  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+|+|.+|+|||||++.+.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            678999999999999998664

>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=94.30  E-value=0.013  Score=47.85  Aligned_cols=24  Identities=17%  Similarity=0.047  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +-|+|+|.+|+|||||...+....
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~~   24 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTGQ   24 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHcCC
Confidence            458999999999999999998753

>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=94.29  E-value=0.011  Score=46.95  Aligned_cols=22  Identities=32%  Similarity=0.241  Sum_probs=19.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||+|+..+.+..
T Consensus         5 ivvvG~~~vGKTsLi~~~~~~~   26 (177)
T d1kmqa_           5 LVIVGDGACGKTCLLIVNSKDQ   26 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5688999999999999988764

>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=94.23  E-value=0.01  Score=47.53  Aligned_cols=21  Identities=29%  Similarity=0.264  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+|+|.+|+|||||+..+.+.
T Consensus         8 i~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            678999999999999998764

>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=94.21  E-value=0.012  Score=46.60  Aligned_cols=21  Identities=24%  Similarity=0.316  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+++|.+|+|||||+..+...
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            779999999999999998765

>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=94.16  E-value=0.014  Score=46.78  Aligned_cols=22  Identities=27%  Similarity=0.303  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+++|.+|+|||+|++++....
T Consensus         5 ivllG~~~vGKTsl~~r~~~~~   26 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKIIH   26 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhCC
Confidence            5689999999999999986654

>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=94.16  E-value=0.012  Score=46.60  Aligned_cols=21  Identities=24%  Similarity=0.409  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+|+|..|+|||||+..+.+.
T Consensus         7 i~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999998775

>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=94.14  E-value=0.012  Score=46.22  Aligned_cols=22  Identities=14%  Similarity=0.256  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|..|+|||+|+..+.+..
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~~   27 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5689999999999999988764

>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=94.13  E-value=0.0087  Score=50.17  Aligned_cols=26  Identities=31%  Similarity=0.378  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +..+++|.|+.|+|||||++.+.--.
T Consensus        30 ~Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          30 NGERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            45689999999999999999997643

>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=94.10  E-value=0.012  Score=47.50  Aligned_cols=22  Identities=23%  Similarity=0.308  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+.+..
T Consensus         9 ivvvG~~~vGKTsli~~l~~~~   30 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDDT   30 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHhhCC
Confidence            6789999999999999998754

>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=94.09  E-value=0.013  Score=46.85  Aligned_cols=22  Identities=27%  Similarity=0.249  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||+|+.++.+..
T Consensus         8 ivviG~~~vGKTsli~~~~~~~   29 (183)
T d1mh1a_           8 CVVVGDGAVGKTCLLISYTTNA   29 (183)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            7799999999999999988754

>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=94.05  E-value=0.015  Score=45.81  Aligned_cols=22  Identities=27%  Similarity=0.333  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .|+|.|.+|+|||||++.+...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5889999999999999999753

>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=94.03  E-value=0.068  Score=45.71  Aligned_cols=99  Identities=15%  Similarity=0.152  Sum_probs=53.8

Q ss_pred             HHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhhhcC-----CC-CeEEEEEeCCCC-CHHHHHHHHHHHhCCC----
Q 042806          166 ILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAETEK-----LF-DQVIFVEVSKIQ-DIRKIQGEIADKLGLT----  233 (390)
Q Consensus       166 l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~-----~f-~~~~wv~v~~~~-~~~~l~~~i~~~l~~~----  233 (390)
                      .++.|.. .+-.-++|.|.+|+|||+|+..+........     .- ..++++.+.... ...++...+...-...    
T Consensus        58 aID~l~pig~GQr~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~~e~~~~~~~~~~~~~tvv  137 (285)
T d2jdia3          58 AVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIV  137 (285)
T ss_dssp             HHHHHSCCBTTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEE
T ss_pred             EEecccCccCCCEEEeecCCCCChHHHHHHHHHhHHhhccccccccceEEEEeeeCccHHHHHHHHHHhcccccccceEE
Confidence            4444443 2334577899999999999988876643211     11 145676676543 3344555444332111    


Q ss_pred             ---CCCCCchH------HHHHHHHHHh-CCCeEEEEEeCCC
Q 042806          234 ---LHEESDSG------RARSLRNRLK-KEKTILVILDNIW  264 (390)
Q Consensus       234 ---~~~~~~~~------~~~~l~~~l~-~~~~~LlVlDdv~  264 (390)
                         ..+.+...      ..-.+.+++. .++.+|+++||+.
T Consensus       138 v~~ts~~~~~~r~~~~~~a~tiAEyfrd~G~~VLll~Dslt  178 (285)
T d2jdia3         138 VSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLS  178 (285)
T ss_dssp             EEECTTSCHHHHHHHHHHHHHHHHHHHHTTCEEEEEEETHH
T ss_pred             EEECCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEcChH
Confidence               11111111      1224455554 3567999999984

>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=94.02  E-value=0.015  Score=45.78  Aligned_cols=22  Identities=27%  Similarity=0.271  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||+|+.++.+..
T Consensus         9 i~vvG~~~vGKTsli~~~~~~~   30 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKDGA   30 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7799999999999999987753

>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=94.01  E-value=0.013  Score=46.88  Aligned_cols=22  Identities=32%  Similarity=0.289  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |.|+|.+|+|||+|+..+.+..
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~~   33 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYANDA   33 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHhhCC
Confidence            7799999999999999988754

>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=94.00  E-value=0.014  Score=45.66  Aligned_cols=22  Identities=27%  Similarity=0.261  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |++.|.+|+|||||+.++....
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            5688999999999999987653

>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=93.99  E-value=0.024  Score=50.60  Aligned_cols=25  Identities=24%  Similarity=0.260  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+...||.|+|||-||+.++...
T Consensus        68 ~~niLfiGPTGvGKTElAk~LA~~~   92 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLMAQTLAKHL   92 (364)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CcceeeeCCCCccHHHHHHHHHhhc
Confidence            4568889999999999999998764

>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=93.98  E-value=0.016  Score=45.69  Aligned_cols=31  Identities=16%  Similarity=0.209  Sum_probs=22.8

Q ss_pred             HHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          167 LDALKNPD-VNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       167 ~~~L~~~~-~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .+.+.+.+ .+ |.|+|.+|+|||||++.+.+.
T Consensus         4 ~~~~~~~k~~k-IvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_           4 LSKIFGNKEMR-ILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             HHHHHTTCCEE-EEEEEETTSSHHHHHHHTTCC
T ss_pred             hhhhhCCCeEE-EEEECCCCCCHHHHHHHHhcC
Confidence            34444433 44 668999999999999998654

>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=93.96  E-value=0.014  Score=48.95  Aligned_cols=26  Identities=23%  Similarity=0.252  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +-.+++|.|+.|+|||||.+.+.--.
T Consensus        31 ~Gei~~liGpnGaGKSTl~~~i~Gl~   56 (240)
T d1ji0a_          31 RGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            45689999999999999999997654

>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=93.95  E-value=0.016  Score=46.62  Aligned_cols=22  Identities=27%  Similarity=0.276  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |.+.|.+|+|||+|+.++....
T Consensus         5 iv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            5689999999999999986553

>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=93.90  E-value=0.014  Score=46.10  Aligned_cols=22  Identities=32%  Similarity=0.401  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      -|+|+|.+|+|||||+..+...
T Consensus        18 kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4779999999999999988553

>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=93.90  E-value=0.015  Score=45.77  Aligned_cols=22  Identities=23%  Similarity=0.373  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+.+..
T Consensus         7 ivlvG~~~vGKTsli~~~~~~~   28 (168)
T d1u8za_           7 VIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6799999999999999987643

>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=93.89  E-value=0.015  Score=48.76  Aligned_cols=26  Identities=23%  Similarity=0.353  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+|||||.+.+.--.
T Consensus        27 ~Gei~glvG~nGaGKSTLl~~l~G~~   52 (238)
T d1vpla_          27 EGEIFGLIGPNGAGKTTTLRIISTLI   52 (238)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45689999999999999999986654

>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=93.88  E-value=0.02  Score=45.46  Aligned_cols=35  Identities=23%  Similarity=0.249  Sum_probs=23.5

Q ss_pred             HHHHHHhcCC-CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          164 NDILDALKNP-DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       164 ~~l~~~L~~~-~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ..+.+.|... +.--|.++|.+|+|||||...+...
T Consensus         5 ~~~~~~l~~~~k~~KI~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_           5 SSMFDKLWGSNKELRILILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             HHHHGGGTTCSSCEEEEEEEETTSSHHHHHHHTCCS
T ss_pred             HHHHHHHhCCCceEEEEEECCCCCCHHHHHHHHhcC
Confidence            3444444332 2233669999999999999988544

>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=93.86  E-value=0.018  Score=47.97  Aligned_cols=56  Identities=9%  Similarity=0.111  Sum_probs=36.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhhhcC--------------CCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAETEK--------------LFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~~~~--------------~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      ...++.|.|++|+|||+++.+++......+              ....+.|+......+.. ....+...+
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~e~~~~~~-~~~~~~~~~  102 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPE-RIMQMAEHA  102 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHH-HHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCCceEEeecccchhcCceEEEEEecCCcCHH-HHHHHHhhc
Confidence            357899999999999999999987653321              11246777776554433 334444444

>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=93.80  E-value=0.017  Score=46.11  Aligned_cols=22  Identities=32%  Similarity=0.407  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+.+..
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~~   26 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNKK   26 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6799999999999999998753

>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=93.79  E-value=0.016  Score=45.82  Aligned_cols=21  Identities=24%  Similarity=0.430  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+|+|.+|+|||||+..+.+.
T Consensus         9 I~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            779999999999999988765

>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=93.76  E-value=0.017  Score=45.92  Aligned_cols=22  Identities=23%  Similarity=0.215  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |.++|..|+|||+|+..+.+..
T Consensus         5 ivliG~~~vGKTsli~r~~~~~   26 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKDC   26 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5689999999999999998764

>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=93.73  E-value=0.015  Score=46.78  Aligned_cols=18  Identities=28%  Similarity=0.414  Sum_probs=16.9

Q ss_pred             EEEEcCCCCcHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEV  195 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v  195 (390)
                      |.|.|.+|+|||||+.++
T Consensus         5 ivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            668999999999999998

>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=93.69  E-value=0.016  Score=46.54  Aligned_cols=22  Identities=23%  Similarity=0.206  Sum_probs=19.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+++|.+|+|||+|+..+.+..
T Consensus         6 vvllG~~~vGKTSli~r~~~~~   27 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTNK   27 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6688999999999999987654

>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=93.69  E-value=0.015  Score=49.29  Aligned_cols=26  Identities=23%  Similarity=0.158  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ...+++|.|+.|+|||||++.+.--.
T Consensus        29 ~Gei~~liG~nGaGKSTLl~~i~Gl~   54 (254)
T d1g6ha_          29 KGDVTLIIGPNGSGKSTLINVITGFL   54 (254)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHCCC
Confidence            34689999999999999999997654

>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=93.64  E-value=0.017  Score=45.38  Aligned_cols=22  Identities=32%  Similarity=0.463  Sum_probs=19.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |.++|.+|+|||||+..+.+..
T Consensus         7 i~lvG~~~vGKTsll~~~~~~~   28 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQKI   28 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5678999999999999998754

>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=93.63  E-value=0.018  Score=45.47  Aligned_cols=24  Identities=21%  Similarity=0.346  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...|+|.|.+|+|||||...+.+.
T Consensus         5 ~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           5 CGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhCC
Confidence            456899999999999999999864

>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=93.60  E-value=0.018  Score=45.40  Aligned_cols=21  Identities=33%  Similarity=0.352  Sum_probs=18.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |.++|.+|+|||||+..+...
T Consensus         6 v~lvG~~~vGKTsLi~~~~~~   26 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAGV   26 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999988754

>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=93.60  E-value=0.019  Score=45.52  Aligned_cols=24  Identities=21%  Similarity=0.274  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ...|+|+|.+|+|||||++.+...
T Consensus         5 ~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           5 SGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            357999999999999999999865

>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=93.56  E-value=0.032  Score=46.02  Aligned_cols=34  Identities=18%  Similarity=0.405  Sum_probs=26.0

Q ss_pred             HHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          163 LNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       163 ~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ++.|.+.|.+   +..++.|.+|+|||||...+..+.
T Consensus        86 ~~~L~~~l~~---kt~~~~G~SGVGKSTLiN~L~~~~  119 (225)
T d1u0la2          86 IEELKEYLKG---KISTMAGLSGVGKSSLLNAINPGL  119 (225)
T ss_dssp             HHHHHHHHSS---SEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             HhhHHHHhcC---CeEEEECCCCCCHHHHHHhhcchh
Confidence            4566666643   567789999999999999886543

>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=93.55  E-value=0.018  Score=45.58  Aligned_cols=22  Identities=23%  Similarity=0.333  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|+|.+|+|||||+..+.+..
T Consensus        10 i~vvG~~~vGKTsli~~l~~~~   31 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDDT   31 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7799999999999999987653

>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=93.54  E-value=0.019  Score=46.99  Aligned_cols=19  Identities=26%  Similarity=0.319  Sum_probs=17.5

Q ss_pred             EEEEEcCCCCcHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEV  195 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v  195 (390)
                      +|+|+|..|+||||+++.+
T Consensus         5 iIgitG~igSGKStv~~~l   23 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAF   23 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHH
Confidence            7999999999999999865

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {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: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=93.52  E-value=0.026  Score=46.72  Aligned_cols=37  Identities=24%  Similarity=0.312  Sum_probs=28.9

Q ss_pred             cEEEEE-cCCCCcHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 042806          176 NMLGIY-GMGGIVKTTLAKEVARKAETEKLFDQVIFVEVS  214 (390)
Q Consensus       176 ~vi~I~-G~~GvGKTtLa~~v~~~~~~~~~f~~~~wv~v~  214 (390)
                      ++|+|+ +-||+||||++..+....... .+ .++.+...
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~la~~-g~-~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVALGDR-GR-KVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHHHT-TC-CEEEEECC
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHhC-CC-CEEEEeCC
Confidence            689898 669999999999999988754 23 46666654

>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=93.49  E-value=0.019  Score=46.75  Aligned_cols=20  Identities=35%  Similarity=0.368  Sum_probs=17.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEV  195 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v  195 (390)
                      -+|+|+|..|+||||+++.+
T Consensus         3 ~iIgITG~igSGKStv~~~l   22 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLF   22 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            37899999999999999866

>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=93.49  E-value=0.015  Score=48.57  Aligned_cols=24  Identities=29%  Similarity=0.337  Sum_probs=21.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      ...+++|.|+.|+|||||.+.+.-
T Consensus        24 ~Gei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          24 AGEILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             TTCEEECBCCTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhC
Confidence            356899999999999999998865

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=93.38  E-value=0.018  Score=52.89  Aligned_cols=27  Identities=26%  Similarity=0.361  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .+-|.++||.|+|||.||+.++....+
T Consensus        49 ksNILliGPTGvGKTlLAr~LAk~l~V   75 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIARRLAKLANA   75 (443)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTTC
T ss_pred             cccEEEECCCCCCHHHHHHHHHHHhCC
Confidence            346889999999999999999987754

>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=93.34  E-value=0.02  Score=45.36  Aligned_cols=22  Identities=23%  Similarity=0.317  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |++.|.+|+|||||+..+.+..
T Consensus         8 i~vlG~~~vGKTsLi~~~~~~~   29 (175)
T d2bmja1           8 LGVLGDARSGKSSLIHRFLTGS   29 (175)
T ss_dssp             EEEECCTTTTHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            6789999999999999998764

>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=93.31  E-value=0.019  Score=45.60  Aligned_cols=22  Identities=23%  Similarity=0.234  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .|+|+|.+|+|||||...+.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999864

>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=93.28  E-value=0.014  Score=49.39  Aligned_cols=25  Identities=28%  Similarity=0.308  Sum_probs=21.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      ....++|+|+.|+|||||++.+..-
T Consensus        43 ~Ge~vaivG~sGsGKSTLl~ll~gl   67 (255)
T d2hyda1          43 KGETVAFVGMSGGGKSTLINLIPRF   67 (255)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHhc
Confidence            4568999999999999999988543

>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=93.28  E-value=0.011  Score=46.61  Aligned_cols=21  Identities=38%  Similarity=0.393  Sum_probs=17.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+|+|.+|+|||||+..+.+.
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            668899999999999988665

>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=93.28  E-value=0.03  Score=45.67  Aligned_cols=31  Identities=13%  Similarity=0.138  Sum_probs=25.5

Q ss_pred             cEEEEEcCC-CCcHHHHHHHHHHHhhhcCCCCe
Q 042806          176 NMLGIYGMG-GIVKTTLAKEVARKAETEKLFDQ  207 (390)
Q Consensus       176 ~vi~I~G~~-GvGKTtLa~~v~~~~~~~~~f~~  207 (390)
                      +-+.|.|-+ ||||||++..+......++ +..
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G-~rV   33 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAG-YRT   33 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTT-CCE
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCC-CeE
Confidence            457899998 9999999999999987653 553

>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=93.21  E-value=0.023  Score=43.94  Aligned_cols=21  Identities=24%  Similarity=0.249  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+|+|.+|+|||||...+...
T Consensus         4 I~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            679999999999999999754

>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=93.07  E-value=0.027  Score=46.51  Aligned_cols=22  Identities=27%  Similarity=0.286  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      =|.+.|.+|+|||||++++...
T Consensus         8 KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3679999999999999998654

>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=92.88  E-value=0.02  Score=45.64  Aligned_cols=22  Identities=27%  Similarity=0.395  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      -|+|+|.+++|||||...+...
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~~   24 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSSA   24 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEEE
T ss_pred             eEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999988543

>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=92.84  E-value=0.021  Score=45.31  Aligned_cols=21  Identities=24%  Similarity=0.419  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+|+|.+|+|||||+..+...
T Consensus         4 VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            889999999999999998654

>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=92.81  E-value=0.033  Score=46.36  Aligned_cols=24  Identities=17%  Similarity=0.104  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ++|+|+|..|+||||+|+.+.+..
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e~~   25 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMSNY   25 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            589999999999999999987653

>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=92.66  E-value=0.017  Score=45.55  Aligned_cols=21  Identities=24%  Similarity=0.273  Sum_probs=8.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 042806          178 LGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |+|+|.+|+|||||+..+.+.
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999887754

>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=92.46  E-value=0.019  Score=45.39  Aligned_cols=25  Identities=8%  Similarity=0.017  Sum_probs=21.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHH
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      ++..-|+|+|.+++|||||.+.+..
T Consensus        14 ~~~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          14 DTGIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             SCSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             ccCCEEEEECCCCCCHHHHHHHHhC
Confidence            4456799999999999999988754

>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=92.23  E-value=0.04  Score=43.58  Aligned_cols=23  Identities=26%  Similarity=0.244  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      +-|.|.|++|+||||||..+...
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            46789999999999999988765

>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=92.11  E-value=0.037  Score=43.91  Aligned_cols=22  Identities=27%  Similarity=0.362  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|.|..|+|||||+..+.+..
T Consensus        11 V~iiG~~~~GKSTLin~l~~~~   32 (186)
T d1mkya2          11 VAIVGRPNVGKSTLFNAILNKE   32 (186)
T ss_dssp             EEEECSTTSSHHHHHHHHHTST
T ss_pred             EEEECCCCCCHHHHHHHHHCCC
Confidence            7889999999999999988653

>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=91.75  E-value=0.043  Score=43.40  Aligned_cols=23  Identities=26%  Similarity=0.231  Sum_probs=19.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .-+.|.|++|+||||||..+...
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            45789999999999999988764

>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=91.62  E-value=0.019  Score=44.38  Aligned_cols=22  Identities=23%  Similarity=0.292  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |++.|.+|+|||||+..+....
T Consensus         3 I~liG~~n~GKSSLin~l~g~~   24 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNED   24 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            6899999999999999998654

>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=91.57  E-value=0.052  Score=42.59  Aligned_cols=23  Identities=30%  Similarity=0.273  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .-+.|.|.+|+||||||..+...
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            45789999999999999888766

>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=90.80  E-value=0.052  Score=47.54  Aligned_cols=24  Identities=25%  Similarity=0.144  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      .|.|.|+.|+||||+++.++....
T Consensus       168 nili~G~tgSGKTT~l~al~~~i~  191 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIMEFIP  191 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGGSC
T ss_pred             CEEEEeeccccchHHHHHHhhhcc
Confidence            478999999999999999987653

>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=90.58  E-value=0.09  Score=44.27  Aligned_cols=37  Identities=22%  Similarity=0.392  Sum_probs=26.4

Q ss_pred             HHHHHHHHhcCC--CccEEEEEcCCCCcHHHHHHHHHHH
Q 042806          162 TLNDILDALKNP--DVNMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       162 ~~~~l~~~L~~~--~~~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      .+.++...+.+.  ..--|+|+|.+|+|||||...++..
T Consensus        17 ~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          17 KLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            344444444432  3345889999999999999999875

>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=90.23  E-value=0.13  Score=41.34  Aligned_cols=38  Identities=21%  Similarity=0.211  Sum_probs=29.5

Q ss_pred             HHHHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          163 LNDILDALKN-PDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       163 ~~~l~~~L~~-~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +..+..+|.+ ++...+.++|+++.|||+++..+..-..
T Consensus        40 l~~l~~~l~~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~   78 (205)
T d1tuea_          40 LGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQ   78 (205)
T ss_dssp             HHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCCCceEEEEECCCCccHHHHHHHHHHHhC
Confidence            4455555643 5667899999999999999999888764

>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=90.10  E-value=0.14  Score=46.07  Aligned_cols=38  Identities=13%  Similarity=0.074  Sum_probs=28.8

Q ss_pred             HHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          162 TLNDILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       162 ~~~~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..+.+.+ +......+|.|.|+.|+||||.+..+.+...
T Consensus       146 ~~~~l~~-l~~~~~GliLvtGpTGSGKSTTl~~~l~~~~  183 (401)
T d1p9ra_         146 NHDNFRR-LIKRPHGIILVTGPTGSGKSTTLYAGLQELN  183 (401)
T ss_dssp             HHHHHHH-HHTSSSEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             HHHHHHH-HHhhhhceEEEEcCCCCCccHHHHHHhhhhc
Confidence            3344444 4445668899999999999999999988763

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=89.59  E-value=0.2  Score=42.69  Aligned_cols=53  Identities=13%  Similarity=0.113  Sum_probs=27.1

Q ss_pred             EEEEEcCCCCcHHHHHH-HHHHHhhhcC-CCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAK-EVARKAETEK-LFDQVIFVEVSKIQDIRKIQGEIADKL  230 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~-~v~~~~~~~~-~f~~~~wv~v~~~~~~~~l~~~i~~~l  230 (390)
                      .+.|.|++|+||||.+. .+.+-..... .-..+..++.+.. ...++...+....
T Consensus        16 ~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~-a~~~i~~~~~~~~   70 (306)
T d1uaaa1          16 PCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNK-AAREMKERVGQTL   70 (306)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHH-HHHHHHHHHHHHS
T ss_pred             CEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHH-HHHHHHHHHHHhc
Confidence            36788999999997543 3333322211 1234555554432 2334444444433

>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=89.39  E-value=0.16  Score=43.68  Aligned_cols=38  Identities=16%  Similarity=0.100  Sum_probs=21.6

Q ss_pred             EEEEcCCCCcHHHHHHH-HHHHhhhcC-CCCeEEEEEeCC
Q 042806          178 LGIYGMGGIVKTTLAKE-VARKAETEK-LFDQVIFVEVSK  215 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~-v~~~~~~~~-~f~~~~wv~v~~  215 (390)
                      +.|.|.+|+||||.+.+ +.+-..... .-..+++++.+.
T Consensus        27 ~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~   66 (318)
T d1pjra1          27 LLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTN   66 (318)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSH
T ss_pred             EEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccH
Confidence            66889999999976544 333322211 123455555544

>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=89.27  E-value=0.13  Score=42.27  Aligned_cols=25  Identities=24%  Similarity=0.247  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          175 VNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       175 ~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      .++|+|.|-.++|||||+..+....
T Consensus         5 ~p~IaIiGh~d~GKSTL~~~L~~~~   29 (227)
T d1g7sa4           5 SPIVSVLGHVDHGKTTLLDHIRGSA   29 (227)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCccHHHHHHHHHhhc
Confidence            4679999999999999999887653

>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=88.95  E-value=0.12  Score=45.33  Aligned_cols=26  Identities=27%  Similarity=0.239  Sum_probs=22.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      ..|.|-|+-|+||||+++.+.+....
T Consensus         7 ~rI~iEG~iGsGKSTl~~~L~~~l~~   32 (333)
T d1p6xa_           7 VRIYLDGVYGIGKSTTGRVMASAASG   32 (333)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHSGGGC
T ss_pred             EEEEEECCccCCHHHHHHHHHHHhcc
Confidence            45788899999999999999998754

>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=88.94  E-value=0.056  Score=44.67  Aligned_cols=23  Identities=17%  Similarity=0.307  Sum_probs=18.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      +..++.|.+|+|||||...+..+
T Consensus        98 ~~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          98 KTTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC-
T ss_pred             ceEEEECCCCccHHHHHHhhccH
Confidence            34568899999999999988644

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), 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 G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=88.93  E-value=0.11  Score=44.04  Aligned_cols=27  Identities=19%  Similarity=0.106  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      +.|-|+|+|..|.|||||+-.+.....
T Consensus         5 ~iRni~i~gh~~~GKTtL~e~ll~~~g   31 (276)
T d2bv3a2           5 RLRNIGIAAHIDAGKTTTTERILYYTG   31 (276)
T ss_dssp             GEEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             hceEEEEEeCCCCCHHHHHHHHHHhcC
Confidence            467899999999999999999977654

>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=87.71  E-value=0.17  Score=42.67  Aligned_cols=23  Identities=30%  Similarity=0.392  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARK  198 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~  198 (390)
                      |.|+|.|..|.|||||+-.+...
T Consensus         3 RNv~iiGh~~~GKTtL~e~ll~~   25 (267)
T d2dy1a2           3 RTVALVGHAGSGKTTLTEALLYK   25 (267)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCcHHHHHHHHHHH
Confidence            67899999999999999998654

>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=86.69  E-value=0.18  Score=39.53  Aligned_cols=21  Identities=43%  Similarity=0.482  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 042806          177 MLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      -|+|+|..++|||||...+..
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            489999999999999999874

>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=86.65  E-value=0.16  Score=44.36  Aligned_cols=25  Identities=32%  Similarity=0.238  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhhh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKAET  201 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~~~  201 (390)
                      .|+|-|.-|+||||+++.+.+....
T Consensus         7 rI~IEG~iGsGKSTl~~~L~~~l~~   31 (331)
T d1osna_           7 RIYLDGAYGIGKTTAAEEFLHHFAI   31 (331)
T ss_dssp             EEEEEESSSSCTTHHHHHHHHTTTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhh
Confidence            4788899999999999999887653

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), 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: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.61  E-value=0.24  Score=42.04  Aligned_cols=34  Identities=26%  Similarity=0.341  Sum_probs=27.0

Q ss_pred             HHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          165 DILDALKNPDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       165 ~l~~~L~~~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ++++.+ +..+.||+|.|+.+.|||+|+..++...
T Consensus        23 ~~l~~~-~~~v~vvsi~G~~~sGKS~llN~l~~~~   56 (277)
T d1f5na2          23 KILSAI-TQPMVVVAIVGLYRTGKSYLMNKLAGKK   56 (277)
T ss_dssp             HHHHTC-CSBEEEEEEEEBTTSSHHHHHHHHTTCS
T ss_pred             HHHHcC-CCCEEEEEEECCCCCCHHHHHHHHcCCC
Confidence            344544 3458899999999999999999998754

>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=85.65  E-value=0.078  Score=42.11  Aligned_cols=23  Identities=17%  Similarity=0.137  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 042806          177 MLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       177 vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      +.+|+|+.|+||||+...+.--.
T Consensus        26 ~tvi~G~NGsGKStil~Ai~~~L   48 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFVTAL   48 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            45578999999999999997665

>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=84.94  E-value=0.19  Score=43.76  Aligned_cols=25  Identities=24%  Similarity=0.122  Sum_probs=19.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhh
Q 042806          176 NMLGIYGMGGIVKTTLAKEVARKAE  200 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~~~~  200 (390)
                      ..|.|-|.-|+||||+++.+.+...
T Consensus         5 lrI~IEG~iGsGKTTl~~~La~~l~   29 (329)
T d1e2ka_           5 LRVYIDGPHGMGKTTTTQLLVALGS   29 (329)
T ss_dssp             EEEEECSCTTSSHHHHHHHHTC---
T ss_pred             eEEEEECCcCCCHHHHHHHHHHHhC
Confidence            3588899999999999999976553

>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=84.16  E-value=0.59  Score=39.21  Aligned_cols=36  Identities=19%  Similarity=0.230  Sum_probs=27.9

Q ss_pred             HHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          164 NDILDALKN--PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       164 ~~l~~~L~~--~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ..+..+|..  +....+.++|+|+.|||+++..+..-.
T Consensus        91 ~~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l  128 (267)
T d1u0ja_          91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            344555643  456788999999999999999998876

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {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: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.47  E-value=0.33  Score=43.54  Aligned_cols=22  Identities=14%  Similarity=0.178  Sum_probs=19.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVAR  197 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~~  197 (390)
                      --|+|+|.+|+|||||...+..
T Consensus        57 l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          57 LNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            3489999999999999999974

>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=81.67  E-value=0.47  Score=38.05  Aligned_cols=22  Identities=32%  Similarity=0.265  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 042806          178 LGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       178 i~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      |+|.|-.+.|||||+.++....
T Consensus         6 i~iiGhvd~GKSTL~~~Ll~~~   27 (204)
T d2c78a3           6 VGTIGHVDHGKTTLTAALTYVA   27 (204)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEeCCCCcHHHHHHHHHHHh
Confidence            8899999999999999987553

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=80.62  E-value=0.36  Score=41.14  Aligned_cols=21  Identities=19%  Similarity=0.327  Sum_probs=18.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHH
Q 042806          176 NMLGIYGMGGIVKTTLAKEVA  196 (390)
Q Consensus       176 ~vi~I~G~~GvGKTtLa~~v~  196 (390)
                      ++-+|+|+.|+|||++...+.
T Consensus        25 ~lnvlvG~NgsGKS~iL~Ai~   45 (308)
T d1e69a_          25 RVTAIVGPNGSGKSNIIDAIK   45 (308)
T ss_dssp             SEEEEECCTTTCSTHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHH
Confidence            477899999999999987773

>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=80.60  E-value=0.58  Score=38.41  Aligned_cols=164  Identities=18%  Similarity=0.151  Sum_probs=78.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHhh--hcC-----------CCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCch
Q 042806          174 DVNMLGIYGMGGIVKTTLAKEVARKAE--TEK-----------LFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDS  240 (390)
Q Consensus       174 ~~~vi~I~G~~GvGKTtLa~~v~~~~~--~~~-----------~f~~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~  240 (390)
                      +.+++.|+|+.+.||||+++.+.-..-  .-+           .|+ .++..+....+..+-..             .-.
T Consensus        40 ~~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d-~I~~~~~~~d~~~~~~S-------------~F~  105 (234)
T d1wb9a2          40 QRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPID-RIFTRVGAADDLASGRS-------------TFM  105 (234)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCC-EEEEEEC------------------------CH
T ss_pred             CceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccch-hheeEEccCcccccchh-------------HHH
Confidence            457899999999999999999976531  111           222 23333333222211110             111


Q ss_pred             HHHHHHHHHHh-CCCeEEEEEeCCCCCccccc-------ccCCCCCCCCCcEEEEEecchhhhhh--cCCCcceEecCCC
Q 042806          241 GRARSLRNRLK-KEKTILVILDNIWGNLDFQA-------VGIPHGDDRKGCKVLLTARSLDVLSR--KMDSQQNFSVGVL  310 (390)
Q Consensus       241 ~~~~~l~~~l~-~~~~~LlVlDdv~~~~~~~~-------l~~~l~~~~~~s~IivTtr~~~v~~~--~~~~~~~~~l~~L  310 (390)
                      ....++.+.+. .+++.|+++|.+-....-.+       +...+ ....++.+++||....+...  .......+++...
T Consensus       106 ~E~~~~~~il~~~~~~sLvliDE~~~gT~~~eg~~l~~a~l~~l-~~~~~~~~i~tTH~~~l~~~~~~~~~v~~~~~~~~  184 (234)
T d1wb9a2         106 VEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENL-ANKIKALTLFATHYFELTQLPEKMEGVANVHLDAL  184 (234)
T ss_dssp             HHHHHHHHHHHHCCTTEEEEEESCCCCSSSSHHHHHHHHHHHHH-HHTTCCEEEEECSCGGGGGHHHHSTTEEEEEEEEE
T ss_pred             HHHHHHHHHHHhcccccEEeecccccCCChhhhhHHHHHhhhhh-hccccceEEEecchHHHhhhhhcccceEEEEEEEe
Confidence            22333444442 23448999999965422111       11111 12346789999997665432  2233334555444


Q ss_pred             CHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHcCCChHHHHHHHHHh
Q 042806          311 KEDEAWSLFKKMAGDYIEGSEFKWVAKDVARECAGLPVSIVTVARAL  357 (390)
Q Consensus       311 ~~~ea~~lf~~~~~~~~~~~~~~~~~~~i~~~~~GlPLai~~l~~~L  357 (390)
                      ..++...+..+...+. ...   ..+-++++.+| +|-.+..-|..+
T Consensus       185 ~~~~~i~f~YkL~~G~-~~~---s~ai~iA~~~G-lp~~ii~~A~~i  226 (234)
T d1wb9a2         185 EHGDTIAFMHSVQDGA-ASK---SYGLAVAALAG-VPKEVIKRARQK  226 (234)
T ss_dssp             EETTEEEEEEEEEESC-CSS---CCHHHHHHHTT-CCHHHHHHHHHH
T ss_pred             eccCcceEEEEecCCC-CCC---cHHHHHHHHhC-cCHHHHHHHHHH
Confidence            3332211111111111 111   23556777664 887777666433

>d1n0ua2 c.37.1.8 (A:3-343) Elongation factor 2 (eEF-2), N-terminal (G) 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: G proteins
domain: Elongation factor 2 (eEF-2), N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.07  E-value=0.59  Score=40.74  Aligned_cols=27  Identities=19%  Similarity=0.260  Sum_probs=23.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHh
Q 042806          173 PDVNMLGIYGMGGIVKTTLAKEVARKA  199 (390)
Q Consensus       173 ~~~~vi~I~G~~GvGKTtLa~~v~~~~  199 (390)
                      ++.|-|+|.|..|.|||||+-.+....
T Consensus        15 ~~IRNI~iiGhvd~GKTTL~d~Ll~~~   41 (341)
T d1n0ua2          15 TNVRNMSVIAHVDHGKSTLTDSLVQRA   41 (341)
T ss_dssp             GGEEEEEEECCGGGTHHHHHHHHHHHH
T ss_pred             ccCcEEEEEeCCCCcHHHHHHHHHHHC
Confidence            357889999999999999999887543