Citrus Sinensis ID: 022641

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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----
Protein Sequence
MRANFGKIHKSGKNKSPNFTQKFSTTQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTGGSGGAFRGVQKW
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHccccccEEEEccccccHHHHHHHHHHHHcccccccccEEEEcccccccHHHHHHHHHHHHHHccccccccccccccccEEEEEEccccccHHHHHHHHHHHHHcccccEEEEEccccccccHHHHHccccEEEccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHccccHHHHHHHHHHHHHHcccccccccHHHcccccccccHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHcccccccccccccccHHHHccHHccccccccccccccccccHccccHHHHcccccHHHHHcHHHHHHHHHHHHHcccccEEEEEccccccHHHHHHHHHHHHcccHHccccEEEEcccccccHHHHHHHHHHHHHHccccccccccccccccEEEEEccHHHHcHHHHHHHHHHHHcccccEEEEEEEcccccccHHHHHHccEEEcccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccHHHHHHHHccccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mranfgkihksgknkspnftqkfsttqsspeksedeVKRKmapvlqssqpwvekyrpkqvkdvaHQEEVVRVLTNTletancphmlfygppgtgktTTALAIAHQLFGPELYKSRVLElnasddrgiNVVRTKIKTFAAVAVgsgqrrggypcppykiiiLDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASrcakfrfkplseeVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLfgssitskdlisvsgyptggsggafrgvqkw
Flexible Loop (DISEMBL)
mranfgkihksgknkspnftqkfsttqsspeksedevkrkmapvlqssqpwvekyrpkQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAavavgsgqrrggypcpPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLIsvsgyptggsggafrgvqkw
Low Complexity Region (SEG)
MRANFGKIHKSGKNKSPNFTQKFSTTQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTGGSGGAFRGVQKW
Disordered region (IsUnstruct)
***********************************************************VKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEAD********ALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGY***************
Disordered Region (DISOPRED)
*************************************************PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAV*************PPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTGGSGGAFRGVQKW
Disordered Region (DISEMBL)
************KNKSPNFTQ*******************MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTGGSGGAFRGVQKW
Disordered Region (DISPRO)
**********************************************SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTGGSGGAFRGVQKW
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRANFGKIHKSGKNKSPNFTQKFSTTQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTGGSGGAFRGVQKW
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	294	2.2.26 [Sep-21-2011]
P35249	363	Replication factor C subu	yes	no	0.843	0.683	0.585	5e-81
Q99J62	364	Replication factor C subu	yes	no	0.829	0.670	0.591	1e-80
P0C7N7	411	Replication factor C subu	N/A	no	0.755	0.540	0.570	6e-76
Q54MD4	347	Probable replication fact	yes	no	0.792	0.671	0.566	1e-74
Q09843	340	Replication factor C subu	yes	no	0.809	0.7	0.538	3e-74
P40348	353	Replication factor C subu	yes	no	0.734	0.611	0.600	4e-74
O28219	319	Replication factor C smal	yes	no	0.707	0.652	0.539	4e-62
Q9YBS7	325	Replication factor C smal	yes	no	0.721	0.652	0.524	2e-60
P53016	334	Replication factor C subu	yes	no	0.761	0.670	0.497	5e-60
A3DNV9	329	Replication factor C smal	yes	no	0.717	0.641	0.513	1e-59

>sp|P35249|RFC4_HUMAN Replication factor C subunit 4 OS=Homo sapiens GN=RFC4 PE=1 SV=2

 Score =  301 bits (770), Expect = 5e-81,   Method: Compositional matrix adjust.
 Identities = 150/256 (58%), Positives = 183/256 (71%), Gaps = 8/256 (3%)

Query: 39  RKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTT 98
           +K  PV     PWVEKYRPK V +VA QEEVV VL  +LE A+ P++LFYGPPGTGKT+T
Sbjct: 33  KKAKPV-----PWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPNLLFYGPPGTGKTST 87

Query: 99  ALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKI 158
            LA A +LFGPEL++ RVLELNASD+RGI VVR K+K FA + V SG R  G PCPP+KI
Sbjct: 88  ILAAARELFGPELFRLRVLELNASDERGIQVVREKVKNFAQLTV-SGSRSDGKPCPPFKI 146

Query: 159 IILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEV 218
           +ILDEADSMT  AQ ALRRTME  SK TRF  ICNY+SRIIEPL SRC+KFRFKPLS+++
Sbjct: 147 VILDEADSMTSAAQAALRRTMEKESKTTRFCLICNYVSRIIEPLTSRCSKFRFKPLSDKI 206

Query: 219 MSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF-GSSITSKDLISVS 277
              R+L I  +E + +  E ++ L  +S+GDLR+AIT+LQ A RL  G  IT K +  ++
Sbjct: 207 QQQRLLDIAKKENVKISDEGIAYLVKVSEGDLRKAITFLQSATRLTGGKEITEKVITDIA 266

Query: 278 GY-PTGGSGGAFRGVQ 292
           G  P     G F   Q
Sbjct: 267 GVIPAEKIDGVFAACQ 282

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. This subunit may be involved in the elongation of the multiprimed DNA template.
Homo sapiens (taxid: 9606)

>sp|Q99J62|RFC4_MOUSE Replication factor C subunit 4 OS=Mus musculus GN=Rfc4 PE=1 SV=1

 Score =  299 bits (766), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 149/252 (59%), Positives = 185/252 (73%), Gaps = 8/252 (3%)

Query: 39  RKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTT 98
           +K+ PV     PWVEKYRPK V +VA Q+EVV VL  +LE A+ P++LFYGPPGTGKT+T
Sbjct: 33  KKVKPV-----PWVEKYRPKCVDEVAFQDEVVAVLRKSLEGADLPNLLFYGPPGTGKTST 87

Query: 99  ALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKI 158
            LA A +LFGPEL++ RVLELNASD+RGI VVR K+K FA + V SG R  G PCPP+KI
Sbjct: 88  ILAAARELFGPELFRLRVLELNASDERGIQVVREKVKNFAQLTV-SGSRSDGKPCPPFKI 146

Query: 159 IILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEV 218
           +ILDEADSMT  AQ ALRRTME  SK TRF  ICNY+SRIIEPL SRC+KFRFKPLS+++
Sbjct: 147 VILDEADSMTSAAQAALRRTMEKESKTTRFCLICNYVSRIIEPLTSRCSKFRFKPLSDKI 206

Query: 219 MSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLIS-VS 277
              R+L I  +E + +  E ++ L  IS+GDLR+AIT+LQ A RL G    S+D+I+ ++
Sbjct: 207 QQERLLDIAEKENVKIGNEEIAYLVKISEGDLRKAITFLQSATRLTGGKEVSEDVITDIA 266

Query: 278 GY-PTGGSGGAF 288
           G  P     G F
Sbjct: 267 GVIPAATIDGIF 278

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. This subunit may be involved in the elongation of the multiprimed DNA template.

Mus musculus (taxid: 10090)

>sp|P0C7N7|RFC2_PHANO Replication factor C subunit 2 OS=Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) GN=RFC2 PE=3 SV=1

 Score =  284 bits (726), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 137/240 (57%), Positives = 177/240 (73%), Gaps = 18/240 (7%)

Query: 49  QPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFG 108
           QPWVEKYRPK + +V  Q+  +++L+ TL+++N PHMLFYGPPGTGKT+T LA+A QL+G
Sbjct: 33  QPWVEKYRPKTLSEVTAQDNTIQILSRTLQSSNLPHMLFYGPPGTGKTSTILALAKQLYG 92

Query: 109 PELYKSRVLELNASDDRGINVVRTKIKTFA----AVA----VGSGQRRGG---------- 150
           PEL KSRVLELNASD+RGI++VR K+K FA    +VA    V +  + GG          
Sbjct: 93  PELMKSRVLELNASDERGISIVRQKVKDFARQQLSVAPTYNVMTEDKDGGEAKMVRYRDK 152

Query: 151 YPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFR 210
           Y CPP+KII+LDEADSMT+DAQ+ALRRTMETYS++TRF  +CNY++RII+PLASRC+KFR
Sbjct: 153 YSCPPFKIIVLDEADSMTQDAQSALRRTMETYSRMTRFCLVCNYVTRIIDPLASRCSKFR 212

Query: 211 FKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITS 270
           FK L +     RV  I   E + LDA     L  ++ GDLR+AIT+LQ AARL G++ T+
Sbjct: 213 FKSLDQGNAVRRVDDIAKLEDVKLDAGVSEELVRVADGDLRKAITFLQSAARLVGATQTA 272

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. Subunit 2 binds ATP and single-stranded DNA.

Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) (taxid: 321614)

>sp|Q54MD4|RFC4_DICDI Probable replication factor C subunit 4 OS=Dictyostelium discoideum GN=rfc4 PE=3 SV=1

 Score =  280 bits (715), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 132/233 (56%), Positives = 164/233 (70%)

Query: 46  QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQ 105
           + ++PWV KYRPK V DV++QE+V+  L  +L T N PH+LFYGPPGTGKT+T LAIA  
Sbjct: 7   KDTEPWVAKYRPKTVDDVSYQEDVISALKKSLNTGNLPHLLFYGPPGTGKTSTILAIAMD 66

Query: 106 LFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEAD 165
           ++GPEL K RVLELNASD+RGI VVRTKIK FA  AV         P   +K+IILDEAD
Sbjct: 67  IYGPELMKQRVLELNASDERGIEVVRTKIKNFAGYAVNKTTTGTSNPGATFKLIILDEAD 126

Query: 166 SMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLH 225
           SMT DAQ ALRRT+ET SK TRF  +CNYISRII+PLASRCAKFRFKPL       R+  
Sbjct: 127 SMTTDAQAALRRTIETTSKTTRFCLLCNYISRIIDPLASRCAKFRFKPLDTVATIERLKF 186

Query: 226 ICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
           I  +EG+  +      +  +S GD+R+AITYLQ A R F + I+   + +++G
Sbjct: 187 ISQQEGIKCEESVYQAIQVVSNGDMRKAITYLQSAFRFFANKISEDVIYNIAG 239

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins PCNA and activator 1. This subunit may be involved in the elongation of the multiprimed DNA template.

Dictyostelium discoideum (taxid: 44689)

>sp|Q09843|RFC2_SCHPO Replication factor C subunit 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rfc2 PE=1 SV=1

 Score =  278 bits (711), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 134/249 (53%), Positives = 182/249 (73%), Gaps = 11/249 (4%)

Query: 31  EKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGP 90
           +K+E E K+        S PWVE YRPK +  V+ QE  V+VL  TL + N PHMLFYG 
Sbjct: 9   KKTEQEAKK--------SIPWVELYRPKTLDQVSSQESTVQVLKKTLLSNNLPHMLFYGS 60

Query: 91  PGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGG 150
           PGTGKT+T LA++ +LFGP+L KSRVLELNASD+RGI+++R K+K+FA   V +  +  G
Sbjct: 61  PGTGKTSTILALSRELFGPQLMKSRVLELNASDERGISIIREKVKSFAKTTVTN--KVDG 118

Query: 151 YPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFR 210
           YPCPP+KIIILDEADSMT+DAQ ALRRTME+Y+++TRF  ICNY++RII+PL+SRC+K+R
Sbjct: 119 YPCPPFKIIILDEADSMTQDAQAALRRTMESYARITRFCLICNYMTRIIDPLSSRCSKYR 178

Query: 211 FKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF-GSSIT 269
           FKPL  E M  R+  I  ++ ++++   ++ L   S GD+R+AIT+LQ AA L  G+ IT
Sbjct: 179 FKPLDNENMVKRLEFIAADQAVSMEPGVVNALVECSGGDMRKAITFLQSAANLHQGTPIT 238

Query: 270 SKDLISVSG 278
              +  ++G
Sbjct: 239 ISSVEELAG 247

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins PCNA and activator 1. Subunit 2 binds ATP and single-stranded DNA.

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

>sp|P40348|RFC2_YEAST Replication factor C subunit 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RFC2 PE=1 SV=1

 Score =  278 bits (711), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 131/218 (60%), Positives = 160/218 (73%), Gaps = 2/218 (0%)

Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL 106
           + QPWVEKYRPK + +V  Q+  V VL  TL++AN PHMLFYGPPGTGKT+T LA+  +L
Sbjct: 23  AQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKEL 82

Query: 107 FGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRG--GYPCPPYKIIILDEA 164
           +GP+L KSR+LELNASD+RGI++VR K+K FA + V    +     YPCPPYKIIILDEA
Sbjct: 83  YGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEA 142

Query: 165 DSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVL 224
           DSMT DAQ+ALRRTMETYS VTRF  ICNY++RII+PLASRC+KFRFK L       R+ 
Sbjct: 143 DSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASRCSKFRFKALDASNAIDRLR 202

Query: 225 HICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAAR 262
            I  +E +  D   L  +  IS GDLRR IT LQ A++
Sbjct: 203 FISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK 240

Component of ATP-dependent clamp loader (RFC and RFC-like) complexes for DNA clamps, such as the POL30/PCNA homotrimer and the checkpoint clamp DDC1:MEC3:RAD17 complex. During a clamp loading circle, the RFC:clamp complex binds to DNA and the recognition of the double-stranded/single-stranded junction stimulates ATP hydrolysis by RFC. The complex presumably provides bipartite ATP sites in which one subunit supplies a catalytic site for hydrolysis of ATP bound to the neighboring subunit. Dissociation of RFC from the clamp leaves the clamp encircling DNA. Component of the replication factor C (RFC or activator 1) complex which loads POL30/PCNA and acts during elongation of primed DNA templates by DNA polymerase delta and epsilon. RFC has an essential but redundant activity in sister chromatid cohesion establishment. Component of the RFC-like complex CTF18-RFC which is required for efficient establishment of chromosome cohesion during S-phase and may load or unload POL30/PCNA. Component of the RFC-like RAD24-RFC complex which loads the checkpoint clamp DDC1:MEC3:RAD17 complex and is involved in DNA repair pathways. Component of the RFC-like ELG1-RFC complex which appears to have a role in DNA replication, replication fork re-start, recombination and repair. RFC2 binds ATP and single-stranded DNA.

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

>sp|O28219|RFCS_ARCFU Replication factor C small subunit OS=Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) GN=rfcS PE=1 SV=1

 Score =  238 bits (607), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 117/217 (53%), Positives = 150/217 (69%), Gaps = 9/217 (4%)

Query: 45  LQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAH 104
           +++ + WVEKYRP+ + +V  Q+EV++ L   +E  N PH+LF GPPGTGKT TA+A+A 
Sbjct: 1   MENFEIWVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALAR 60

Query: 105 QLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEA 164
            LFG E ++   +E+NASD+RGI+VVR KIK FA  A   G         P+KII LDEA
Sbjct: 61  DLFG-ENWRDNFIEMNASDERGIDVVRHKIKEFARTAPIGG--------APFKIIFLDEA 111

Query: 165 DSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVL 224
           D++T DAQ ALRRTME YSK  RF   CNY+SRIIEP+ SRCA FRFKP+ +E M  R+L
Sbjct: 112 DALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLL 171

Query: 225 HICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA 261
            IC +EG+ +  + L  L  IS GD R+AI  LQGAA
Sbjct: 172 EICEKEGVKITEDGLEALIYISGGDFRKAINALQGAA 208

Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA. The complex possesses DNA-dependent ATPase activity which is further stimulated by PCNA.

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

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

 Score =  233 bits (593), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 117/223 (52%), Positives = 153/223 (68%), Gaps = 11/223 (4%)

Query: 41  MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 100
           M+ VL+    WVEKYRP+ + D+  Q+ VV  L   ++  N PH+LF GPPGTGKTT A 
Sbjct: 1   MSSVLE--MLWVEKYRPRSLDDIVDQKHVVERLKQFVKQRNMPHLLFAGPPGTGKTTAAH 58

Query: 101 AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII 160
           A+AH LFG E Y+  +LELNASD+RGINV+R K+K FA        R    P  P+KI++
Sbjct: 59  ALAHDLFG-ENYRQYMLELNASDERGINVIREKVKEFA--------RSRTPPEIPFKIVL 109

Query: 161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 220
           LDEAD+MT DAQ ALRR ME YS VTRF  I NY S+II+P+ SRCA FRF+PLS++ + 
Sbjct: 110 LDEADNMTSDAQQALRRLMELYSSVTRFILIANYPSKIIDPIQSRCAFFRFQPLSKQDVI 169

Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARL 263
            R+ +I   EG++ + EAL  +  IS+GD+R+AI  LQ A+ L
Sbjct: 170 ERLRYIAENEGVDYEEEALDAIYEISEGDMRKAINVLQAASYL 212

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

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

>sp|P53016|RFC4_CAEEL Replication factor C subunit 4 OS=Caenorhabditis elegans GN=rfc-4 PE=1 SV=1

 Score =  231 bits (589), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 115/231 (49%), Positives = 150/231 (64%), Gaps = 7/231 (3%)

Query: 36  EVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGK 95
           EV  K   VL     W EKYRPK + D+A+Q+EVV +L   L+  + PH+LFYGPPGTGK
Sbjct: 6   EVDNKRPKVLT----WTEKYRPKTLDDIAYQDEVVTMLKGALQGRDLPHLLFYGPPGTGK 61

Query: 96  TTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPP 155
           T+ ALA   QLF   ++  RVL+LNASD+RGI VVR KI++F+  ++G   R        
Sbjct: 62  TSAALAFCRQLFPKNIFHDRVLDLNASDERGIAVVRQKIQSFSKSSLGHSHREDVLK--- 118

Query: 156 YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLS 215
            KIIILDE D+MT +AQ A+RR +E +SK TRF  ICNY+SR+I P+ SRCAKFRFK L 
Sbjct: 119 LKIIILDEVDAMTREAQAAMRRVIEDFSKTTRFILICNYVSRLIPPVVSRCAKFRFKSLP 178

Query: 216 EEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGS 266
            E+   R+  IC+ EG  +  + L  +   S+GDLRRA+  LQ  A +  S
Sbjct: 179 AEIQVQRLRTICDAEGTPMSDDELKQVMEYSEGDLRRAVCTLQSLAPILKS 229

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins PCNA and activator 1. This subunit may be involved in the elongation of the multiprimed DNA template.

Caenorhabditis elegans (taxid: 6239)

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

 Score =  230 bits (586), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 113/220 (51%), Positives = 148/220 (67%), Gaps = 9/220 (4%)

Query: 51  WVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE 110
           W EKYRPK + ++  QEE+V  L   ++  N PH+LF GPPGTGKTT A  +AH LFG E
Sbjct: 13  WAEKYRPKTLDEIVDQEEIVSRLKQFVKERNMPHLLFAGPPGTGKTTAAHCLAHDLFG-E 71

Query: 111 LYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED 170
            Y+  +LELNASD+RGI+V+R+K+K FA   V +          P+KI++LDEAD+MT D
Sbjct: 72  NYRQYMLELNASDERGIDVIRSKVKEFARTRVAAN--------IPFKIVLLDEADNMTAD 123

Query: 171 AQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEE 230
           AQ ALRR ME Y+  TRF  I NY S+IIEP+ SRCA FRF PL +E + SR+  I  +E
Sbjct: 124 AQQALRRLMEMYTATTRFILIANYPSKIIEPIQSRCAVFRFAPLKKEDVISRLKWIAEQE 183

Query: 231 GLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITS 270
            + +D EAL  +  +S+GD+RRAI  LQ AA L   ++ S
Sbjct: 184 KVEIDEEALEAIHDLSEGDMRRAINILQAAAALGKVTVDS 223

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

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

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	294
255558610	342	replication factor C / DNA polymerase II	0.843	0.725	0.919	1e-133
225459625	341	PREDICTED: replication factor C subunit	0.809	0.697	0.949	1e-132
147858312	341	hypothetical protein VITISV_019805 [Viti	0.809	0.697	0.945	1e-131
224084964	342	predicted protein [Populus trichocarpa]	0.809	0.695	0.932	1e-131
449449767	336	PREDICTED: replication factor C subunit	0.809	0.708	0.928	1e-129
18395021	339	replication factor C subunit 2/4 [Arabid	0.809	0.702	0.920	1e-129
334182756	341	replication factor C subunit 2/4 [Arabid	0.809	0.697	0.920	1e-128
297845144	339	EMB1968 [Arabidopsis lyrata subsp. lyrat	0.809	0.702	0.915	1e-128
388505532	342	unknown [Lotus japonicus]	0.809	0.695	0.907	1e-127
356509379	342	PREDICTED: replication factor C subunit	0.809	0.695	0.899	1e-126

>gi|255558610|ref|XP_002520330.1| replication factor C / DNA polymerase III gamma-tau subunit, putative [Ricinus communis] gi|223540549|gb|EEF42116.1| replication factor C / DNA polymerase III gamma-tau subunit, putative [Ricinus communis]

 Score =  481 bits (1237), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 228/248 (91%), Positives = 237/248 (95%)

Query: 41  MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 100
           MAP+LQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLET+NCPHMLFYGPPGTGKTTTAL
Sbjct: 1   MAPILQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETSNCPHMLFYGPPGTGKTTTAL 60

Query: 101 AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII 160
           AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK FAAVAVGSGQR GGYPCPPYKIII
Sbjct: 61  AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKNFAAVAVGSGQRAGGYPCPPYKIII 120

Query: 161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 220
           LDEADSMTEDAQNALRRTMETYSKVTRFFF+CNYISRIIEPLASRCAKFRFKPLSEE+MS
Sbjct: 121 LDEADSMTEDAQNALRRTMETYSKVTRFFFLCNYISRIIEPLASRCAKFRFKPLSEEIMS 180

Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYP 280
           SRVLHIC EEGLNLDAEALSTLS +SQGDLRRAITYLQGAARL+GS+I+SKDLISVSG  
Sbjct: 181 SRVLHICREEGLNLDAEALSTLSYVSQGDLRRAITYLQGAARLYGSTISSKDLISVSGVI 240

Query: 281 TGGSGGAF 288
              + GA 
Sbjct: 241 PQEAVGAL 248

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225459625|ref|XP_002285874.1| PREDICTED: replication factor C subunit 4 isoform 1 [Vitis vinifera] gi|302141781|emb|CBI18984.3| unnamed protein product [Vitis vinifera]

 Score =  477 bits (1227), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 226/238 (94%), Positives = 232/238 (97%)

Query: 41  MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 100
           MAPVLQSSQPWVEKYRPKQVKDVAHQ+EVVRVLTNTLET NCPHMLFYGPPGTGKTTTAL
Sbjct: 1   MAPVLQSSQPWVEKYRPKQVKDVAHQDEVVRVLTNTLETTNCPHMLFYGPPGTGKTTTAL 60

Query: 101 AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII 160
           AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK FAAVAVGSG R+GGYPCPPYKIII
Sbjct: 61  AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKDFAAVAVGSGHRQGGYPCPPYKIII 120

Query: 161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 220
           LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEE+MS
Sbjct: 121 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEIMS 180

Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
           SR+LHIC EE LNLD+EALSTLSSISQGDLRRAITYLQGAARLFGS I+SKDLISVSG
Sbjct: 181 SRILHICKEEELNLDSEALSTLSSISQGDLRRAITYLQGAARLFGSIISSKDLISVSG 238

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147858312|emb|CAN83520.1| hypothetical protein VITISV_019805 [Vitis vinifera]

 Score =  475 bits (1223), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 225/238 (94%), Positives = 231/238 (97%)

Query: 41  MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 100
           MAPVLQSSQPWVEKYRPKQVKDVAHQ+EVVRVLTNTLET NCPHMLFYGPPGTGKTTTAL
Sbjct: 1   MAPVLQSSQPWVEKYRPKQVKDVAHQDEVVRVLTNTLETTNCPHMLFYGPPGTGKTTTAL 60

Query: 101 AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII 160
           AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK FA VAVGSG R+GGYPCPPYKIII
Sbjct: 61  AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKDFAXVAVGSGHRQGGYPCPPYKIII 120

Query: 161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 220
           LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEE+MS
Sbjct: 121 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEIMS 180

Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
           SR+LHIC EE LNLD+EALSTLSSISQGDLRRAITYLQGAARLFGS I+SKDLISVSG
Sbjct: 181 SRILHICKEEELNLDSEALSTLSSISQGDLRRAITYLQGAARLFGSIISSKDLISVSG 238

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224084964|ref|XP_002307456.1| predicted protein [Populus trichocarpa] gi|222856905|gb|EEE94452.1| predicted protein [Populus trichocarpa]

 Score =  473 bits (1217), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 222/238 (93%), Positives = 232/238 (97%)

Query: 41  MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 100
           MAP+LQSSQ WVEKYRPKQ+KDVAHQ+EVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL
Sbjct: 1   MAPLLQSSQQWVEKYRPKQIKDVAHQDEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 60

Query: 101 AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII 160
           AIAHQL+GPELYKSRVLELNASDDRGINVVRTKIK FAAVAVGSGQR+G YPCPPYKIII
Sbjct: 61  AIAHQLYGPELYKSRVLELNASDDRGINVVRTKIKDFAAVAVGSGQRQGVYPCPPYKIII 120

Query: 161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 220
           LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPL EE+MS
Sbjct: 121 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLPEEIMS 180

Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
           +R+LHICNEEGL LD EALSTLSS+SQGDLRRAITYLQGAARLFGSSI+SKDLISVSG
Sbjct: 181 NRILHICNEEGLTLDTEALSTLSSVSQGDLRRAITYLQGAARLFGSSISSKDLISVSG 238

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449449767|ref|XP_004142636.1| PREDICTED: replication factor C subunit 4-like [Cucumis sativus]

 Score =  468 bits (1205), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 221/238 (92%), Positives = 231/238 (97%)

Query: 41  MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 100
           MAP+LQSSQPWVEKYRPKQVKDVAHQ+EVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL
Sbjct: 1   MAPLLQSSQPWVEKYRPKQVKDVAHQDEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 60

Query: 101 AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII 160
           AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK FA VAV SGQR+GGYPCPP+KIII
Sbjct: 61  AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKDFAGVAVSSGQRQGGYPCPPFKIII 120

Query: 161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 220
           LDEADSMTEDAQNALRRTMET+SKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS
Sbjct: 121 LDEADSMTEDAQNALRRTMETHSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 180

Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
            R+LHI NEEGL+LD EALSTLSSISQGDLRRAITYLQ AARLFGSSI+SKDL++VSG
Sbjct: 181 KRILHIGNEEGLSLDGEALSTLSSISQGDLRRAITYLQSAARLFGSSISSKDLVNVSG 238

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18395021|ref|NP_564148.1| replication factor C subunit 2/4 [Arabidopsis thaliana] gi|15810343|gb|AAL07059.1| putative replication factor [Arabidopsis thaliana] gi|17065122|gb|AAL32715.1| Similar replication factor C, 37-kDa subunit [Arabidopsis thaliana] gi|21536935|gb|AAM61276.1| putative replication factor [Arabidopsis thaliana] gi|34098857|gb|AAQ56811.1| At1g21690 [Arabidopsis thaliana] gi|332192018|gb|AEE30139.1| replication factor C subunit 2/4 [Arabidopsis thaliana]

 Score =  466 bits (1199), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 219/238 (92%), Positives = 229/238 (96%)

Query: 41  MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 100
           MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTL+TA+CPHMLFYGPPGTGKTTTAL
Sbjct: 1   MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLQTADCPHMLFYGPPGTGKTTTAL 60

Query: 101 AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII 160
           AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK FAAVAVGS  R+ GYPCP +KIII
Sbjct: 61  AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKDFAAVAVGSNHRQSGYPCPSFKIII 120

Query: 161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 220
           LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS
Sbjct: 121 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 180

Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
           +R+LHICNEEGL+LD EALSTLSSISQGDLRRAITYLQ A RLFGS+ITS DL++VSG
Sbjct: 181 NRILHICNEEGLSLDGEALSTLSSISQGDLRRAITYLQSATRLFGSTITSTDLLNVSG 238

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334182756|ref|NP_001185061.1| replication factor C subunit 2/4 [Arabidopsis thaliana] gi|332192021|gb|AEE30142.1| replication factor C subunit 2/4 [Arabidopsis thaliana]

 Score =  464 bits (1195), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 219/238 (92%), Positives = 229/238 (96%)

Query: 41  MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 100
           MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTL+TA+CPHMLFYGPPGTGKTTTAL
Sbjct: 1   MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLQTADCPHMLFYGPPGTGKTTTAL 60

Query: 101 AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII 160
           AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK FAAVAVGS  R+ GYPCP +KIII
Sbjct: 61  AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKDFAAVAVGSNHRQSGYPCPSFKIII 120

Query: 161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 220
           LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS
Sbjct: 121 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 180

Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
           +R+LHICNEEGL+LD EALSTLSSISQGDLRRAITYLQ A RLFGS+ITS DL++VSG
Sbjct: 181 NRILHICNEEGLSLDGEALSTLSSISQGDLRRAITYLQSATRLFGSTITSTDLLNVSG 238

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297845144|ref|XP_002890453.1| EMB1968 [Arabidopsis lyrata subsp. lyrata] gi|297336295|gb|EFH66712.1| EMB1968 [Arabidopsis lyrata subsp. lyrata]

 Score =  462 bits (1189), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 218/238 (91%), Positives = 227/238 (95%)

Query: 41  MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 100
           MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTL+TA+CPHMLFYGPPGTGKTTTAL
Sbjct: 1   MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLQTADCPHMLFYGPPGTGKTTTAL 60

Query: 101 AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII 160
           AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK FAAVAVGS  R+ GYPCP +KIII
Sbjct: 61  AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKDFAAVAVGSNHRQSGYPCPSFKIII 120

Query: 161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 220
           LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS
Sbjct: 121 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 180

Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
           +R+LHICNEEGL+L  EALSTLSSISQGDLRRAITYLQ A RLFGS+ITS DL+ VSG
Sbjct: 181 NRILHICNEEGLSLGGEALSTLSSISQGDLRRAITYLQSATRLFGSTITSTDLLDVSG 238

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388505532|gb|AFK40832.1| unknown [Lotus japonicus]

 Score =  461 bits (1187), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 216/238 (90%), Positives = 231/238 (97%)

Query: 41  MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 100
           MAP++QSSQPWVEKYRPKQVKDVA+Q+EVVRVLTNTLET +CPHMLFYGPPGTGKTTTAL
Sbjct: 1   MAPIVQSSQPWVEKYRPKQVKDVAYQDEVVRVLTNTLETGSCPHMLFYGPPGTGKTTTAL 60

Query: 101 AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII 160
           AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK FAAVAVG+  ++GGYPCPPYKII+
Sbjct: 61  AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKDFAAVAVGTNPKKGGYPCPPYKIIV 120

Query: 161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 220
           LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEE+MS
Sbjct: 121 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEIMS 180

Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
           SR+L+ICNEEGL+LDAE LSTLSSISQGDLRRAITYLQ +ARLFGS I+SKDLISVSG
Sbjct: 181 SRILYICNEEGLHLDAEGLSTLSSISQGDLRRAITYLQSSARLFGSHISSKDLISVSG 238

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509379|ref|XP_003523427.1| PREDICTED: replication factor C subunit 4-like isoform 1 [Glycine max]

 Score =  457 bits (1177), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 214/238 (89%), Positives = 229/238 (96%)

Query: 41  MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 100
           MAP+LQS+QPWVEKYRPKQVKDVAHQ+EVVRVLTNTLET +CPHMLFYGPPGTGKTTTAL
Sbjct: 1   MAPILQSTQPWVEKYRPKQVKDVAHQDEVVRVLTNTLETGSCPHMLFYGPPGTGKTTTAL 60

Query: 101 AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII 160
           AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK FAAVAVG+ QR+ GYPCPP+KII+
Sbjct: 61  AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKDFAAVAVGTNQRKSGYPCPPFKIIV 120

Query: 161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 220
           LDEADSMTEDAQNALRRTMETYSKVTRFFFICNY+SRIIEPLASRCAKFRFKPLSEE+MS
Sbjct: 121 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYVSRIIEPLASRCAKFRFKPLSEEIMS 180

Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
           SR+L+I  EEGL LDAEALSTLSSIS GDLRRAITYLQ AARLFGSSI+S++LISVSG
Sbjct: 181 SRILYISQEEGLCLDAEALSTLSSISHGDLRRAITYLQSAARLFGSSISSENLISVSG 238

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	294
UNIPROTKB|E2R2M6	363	RFC4 "Uncharacterized protein"	0.823	0.666	0.604	3.6e-73
UNIPROTKB|P35249	363	RFC4 "Replication factor C sub	0.908	0.735	0.553	9.6e-73
RGD|1310142	364	Rfc4 "replication factor C (ac	0.829	0.670	0.603	9.6e-73
MGI|MGI:2146571	364	Rfc4 "replication factor C (ac	0.846	0.684	0.589	1.6e-72
UNIPROTKB|F1NEW1	362	RFC4 "Uncharacterized protein"	0.795	0.646	0.601	2.5e-72
UNIPROTKB|F1NIY0	359	RFC4 "Uncharacterized protein"	0.795	0.651	0.601	2.5e-72
UNIPROTKB|C9JZI1	336	RFC4 "Replication factor C sub	0.860	0.752	0.570	3.2e-72
ASPGD|ASPL0000039105	387	AN2969 [Emericella nidulans (t	0.823	0.625	0.572	5.3e-72
UNIPROTKB|Q29RS9	337	RFC4 "Uncharacterized protein"	0.775	0.676	0.617	6.7e-72
UNIPROTKB|F1SFI3	366	RFC4 "Uncharacterized protein"	0.826	0.663	0.589	1.8e-71

UNIPROTKB|E2R2M6 RFC4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 739 (265.2 bits), Expect = 3.6e-73, P = 3.6e-73
 Identities = 148/245 (60%), Positives = 181/245 (73%)

Query:    50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP 109
             PWVEKYRPK V +VA QEEVV VL  +LE A+ P++LFYGPPGTGKT+T LA A +LFGP
Sbjct:    38 PWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAARELFGP 97

Query:   110 ELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE 169
             EL++ RVLELNASD+RGI VVR K+K FA + V SG R  G PCPP+KI+ILDEADSMT 
Sbjct:    98 ELFRLRVLELNASDERGIQVVREKVKNFAQLTV-SGSRSDGKPCPPFKIVILDEADSMTS 156

Query:   170 DAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE 229
              AQ ALRRTME  SK TRF  ICNY+SRIIEPL SRC+KFRFKPLS+++   R+L I ++
Sbjct:   157 AAQAALRRTMEKESKTTRFCLICNYVSRIIEPLTSRCSKFRFKPLSDKIQQQRLLDIADK 216

Query:   230 EGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS-ITSKDLISVSGY-PTGGSGGA 287
             E + +  E ++ L  +S+GDLR+AIT+LQ A RL G   IT K +  ++G  P G   G 
Sbjct:   217 EHVKVSNEGIAYLVKVSEGDLRKAITFLQSATRLTGGKEITEKVITDIAGVIPAGTIDGI 276

Query:   288 FRGVQ 292
             F   Q
Sbjct:   277 FAACQ 281

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

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P35249 RFC4 "Replication factor C subunit 4" [Homo sapiens (taxid:9606)]

 Score = 735 (263.8 bits), Expect = 9.6e-73, P = 9.6e-73
 Identities = 154/278 (55%), Positives = 190/278 (68%)

Query:    17 PNFTQKFSTTQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNT 76
             P  T+      S+    E+   +K  PV     PWVEKYRPK V +VA QEEVV VL  +
Sbjct:    14 PPLTKDRGVAASAGSSGEN---KKAKPV-----PWVEKYRPKCVDEVAFQEEVVAVLKKS 65

Query:    77 LETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKT 136
             LE A+ P++LFYGPPGTGKT+T LA A +LFGPEL++ RVLELNASD+RGI VVR K+K 
Sbjct:    66 LEGADLPNLLFYGPPGTGKTSTILAAARELFGPELFRLRVLELNASDERGIQVVREKVKN 125

Query:   137 FAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYIS 196
             FA + V SG R  G PCPP+KI+ILDEADSMT  AQ ALRRTME  SK TRF  ICNY+S
Sbjct:   126 FAQLTV-SGSRSDGKPCPPFKIVILDEADSMTSAAQAALRRTMEKESKTTRFCLICNYVS 184

Query:   197 RIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITY 256
             RIIEPL SRC+KFRFKPLS+++   R+L I  +E + +  E ++ L  +S+GDLR+AIT+
Sbjct:   185 RIIEPLTSRCSKFRFKPLSDKIQQQRLLDIAKKENVKISDEGIAYLVKVSEGDLRKAITF 244

Query:   257 LQGAARLFGSS-ITSKDLISVSGY-PTGGSGGAFRGVQ 292
             LQ A RL G   IT K +  ++G  P     G F   Q
Sbjct:   245 LQSATRLTGGKEITEKVITDIAGVIPAEKIDGVFAACQ 282

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

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

GO:0048015 "phosphatidylinositol-mediated signaling" evidence=NAS

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005654 "nucleoplasm" evidence=TAS

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

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

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

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

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

GO:0000075 "cell cycle checkpoint" evidence=TAS

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

GO:0000278 "mitotic cell cycle" evidence=TAS

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

GO:0000723 "telomere maintenance" evidence=TAS

RGD|1310142 Rfc4 "replication factor C (activator 1) 4" [Rattus norvegicus (taxid:10116)]

 Score = 735 (263.8 bits), Expect = 9.6e-73, P = 9.6e-73
 Identities = 152/252 (60%), Positives = 186/252 (73%)

Query:    28 SSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLF 87
             SS   S  E K K+ PV     PWVEKYRPK V +VA QEEVV VL  +LE A+ P++LF
Sbjct:    23 SSSAGSSGETK-KVKPV-----PWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPNLLF 76

Query:    88 YGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQR 147
             YGPPGTGKT+T LA A +LFGPEL++ RVLELNASD+RGI VVR K+K FA + V SG R
Sbjct:    77 YGPPGTGKTSTILAAARELFGPELFRLRVLELNASDERGIQVVREKVKNFAQLTV-SGSR 135

Query:   148 RGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA 207
               G PCPP+KI+ILDEADSMT  AQ ALRRTME  SK TRF  ICNY+SRIIEPL SRC+
Sbjct:   136 SDGKPCPPFKIVILDEADSMTSAAQAALRRTMEKESKTTRFCLICNYVSRIIEPLTSRCS 195

Query:   208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS 267
             KFRFKPLS+++   R+L I  +E + +  E ++ L  IS+GDLR+AIT+LQ A RL G  
Sbjct:   196 KFRFKPLSDKIQQKRLLDIAEKENVKIGDEEIAYLVRISEGDLRKAITFLQSATRLTGGK 255

Query:   268 ITSKDLIS-VSG 278
               S+D+I+ ++G
Sbjct:   256 EISEDVITDIAG 267

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

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

GO:0006260 "DNA replication" evidence=IEA

GO:0008150 "biological_process" evidence=ND

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

MGI|MGI:2146571 Rfc4 "replication factor C (activator 1) 4" [Mus musculus (taxid:10090)]

 Score = 733 (263.1 bits), Expect = 1.6e-72, P = 1.6e-72
 Identities = 152/258 (58%), Positives = 187/258 (72%)

Query:    33 SEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPG 92
             S  E K K+ PV     PWVEKYRPK V +VA Q+EVV VL  +LE A+ P++LFYGPPG
Sbjct:    28 SSGETK-KVKPV-----PWVEKYRPKCVDEVAFQDEVVAVLRKSLEGADLPNLLFYGPPG 81

Query:    93 TGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYP 152
             TGKT+T LA A +LFGPEL++ RVLELNASD+RGI VVR K+K FA + V SG R  G P
Sbjct:    82 TGKTSTILAAARELFGPELFRLRVLELNASDERGIQVVREKVKNFAQLTV-SGSRSDGKP 140

Query:   153 CPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFK 212
             CPP+KI+ILDEADSMT  AQ ALRRTME  SK TRF  ICNY+SRIIEPL SRC+KFRFK
Sbjct:   141 CPPFKIVILDEADSMTSAAQAALRRTMEKESKTTRFCLICNYVSRIIEPLTSRCSKFRFK 200

Query:   213 PLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKD 272
             PLS+++   R+L I  +E + +  E ++ L  IS+GDLR+AIT+LQ A RL G    S+D
Sbjct:   201 PLSDKIQQERLLDIAEKENVKIGNEEIAYLVKISEGDLRKAITFLQSATRLTGGKEVSED 260

Query:   273 LIS-VSGY-PTGGSGGAF 288
             +I+ ++G  P     G F
Sbjct:   261 VITDIAGVIPAATIDGIF 278

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0006260 "DNA replication" evidence=IEA

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

UNIPROTKB|F1NEW1 RFC4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 731 (262.4 bits), Expect = 2.5e-72, P = 2.5e-72
 Identities = 145/241 (60%), Positives = 179/241 (74%)

Query:    39 RKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTT 98
             +K+ PV     PWVEKYRPK V +VA Q+EVV VL  +LE A+ P++LFYGPPGTGKT+T
Sbjct:    31 KKLKPV-----PWVEKYRPKNVDEVAFQDEVVAVLKKSLEGADLPNLLFYGPPGTGKTST 85

Query:    99 ALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKI 158
              LA A +LFGPEL++ RVLELNASD+RGI V+R K+K FA +   SG R  G  CPP+KI
Sbjct:    86 ILAAARELFGPELFRQRVLELNASDERGIQVIREKVKAFAQLTA-SGSRADGKVCPPFKI 144

Query:   159 IILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEV 218
             +ILDEADSMT  AQ ALRRTME  SK TRF  ICNYISRIIEPL SRC+KFRFKPLS+++
Sbjct:   145 VILDEADSMTSAAQAALRRTMEKESKTTRFCLICNYISRIIEPLTSRCSKFRFKPLSDKI 204

Query:   219 MSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS-ITSKDLISVS 277
                R+L +  +E + + +EA+S L  +S GDLR+AITYLQ A RL G   IT K +  ++
Sbjct:   205 QQQRLLDVSEKENVKITSEAVSYLVKVSDGDLRKAITYLQSATRLMGGKEITEKTVTEIA 264

Query:   278 G 278
             G
Sbjct:   265 G 265

GO:0003677 "DNA binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|F1NIY0 RFC4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 731 (262.4 bits), Expect = 2.5e-72, P = 2.5e-72
 Identities = 145/241 (60%), Positives = 179/241 (74%)

Query:    39 RKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTT 98
             +K+ PV     PWVEKYRPK V +VA Q+EVV VL  +LE A+ P++LFYGPPGTGKT+T
Sbjct:    31 KKLKPV-----PWVEKYRPKNVDEVAFQDEVVAVLKKSLEGADLPNLLFYGPPGTGKTST 85

Query:    99 ALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKI 158
              LA A +LFGPEL++ RVLELNASD+RGI V+R K+K FA +   SG R  G  CPP+KI
Sbjct:    86 ILAAARELFGPELFRQRVLELNASDERGIQVIREKVKAFAQLTA-SGSRADGKVCPPFKI 144

Query:   159 IILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEV 218
             +ILDEADSMT  AQ ALRRTME  SK TRF  ICNYISRIIEPL SRC+KFRFKPLS+++
Sbjct:   145 VILDEADSMTSAAQAALRRTMEKESKTTRFCLICNYISRIIEPLTSRCSKFRFKPLSDKI 204

Query:   219 MSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS-ITSKDLISVS 277
                R+L +  +E + + +EA+S L  +S GDLR+AITYLQ A RL G   IT K +  ++
Sbjct:   205 QQQRLLDVSEKENVKITSEAVSYLVKVSDGDLRKAITYLQSATRLMGGKEITEKTVTEIA 264

Query:   278 G 278
             G
Sbjct:   265 G 265

GO:0003677 "DNA binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|C9JZI1 RFC4 "Replication factor C subunit 4" [Homo sapiens (taxid:9606)]

 Score = 730 (262.0 bits), Expect = 3.2e-72, P = 3.2e-72
 Identities = 150/263 (57%), Positives = 186/263 (70%)

Query:    17 PNFTQKFSTTQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNT 76
             P  T+      S+    E+   +K  PV     PWVEKYRPK V +VA QEEVV VL  +
Sbjct:    14 PPLTKDRGVAASAGSSGEN---KKAKPV-----PWVEKYRPKCVDEVAFQEEVVAVLKKS 65

Query:    77 LETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKT 136
             LE A+ P++LFYGPPGTGKT+T LA A +LFGPEL++ RVLELNASD+RGI VVR K+K 
Sbjct:    66 LEGADLPNLLFYGPPGTGKTSTILAAARELFGPELFRLRVLELNASDERGIQVVREKVKN 125

Query:   137 FAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYIS 196
             FA + V SG R  G PCPP+KI+ILDEADSMT  AQ ALRRTME  SK TRF  ICNY+S
Sbjct:   126 FAQLTV-SGSRSDGKPCPPFKIVILDEADSMTSAAQAALRRTMEKESKTTRFCLICNYVS 184

Query:   197 RIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITY 256
             RIIEPL SRC+KFRFKPLS+++   R+L I  +E + +  E ++ L  +S+GDLR+AIT+
Sbjct:   185 RIIEPLTSRCSKFRFKPLSDKIQQQRLLDIAKKENVKISDEGIAYLVKVSEGDLRKAITF 244

Query:   257 LQGAARLFGSS-ITSKDLISVSG 278
             LQ A RL G   IT K +  ++G
Sbjct:   245 LQSATRLTGGKEITEKVITDIAG 267

GO:0003677 "DNA binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

ASPGD|ASPL0000039105 AN2969 [Emericella nidulans (taxid:162425)]

 Score = 728 (261.3 bits), Expect = 5.3e-72, P = 5.3e-72
 Identities = 146/255 (57%), Positives = 183/255 (71%)

Query:    23 FSTTQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANC 82
             FS+++  P + ++E  R         QPWVEKYRPK + DVA Q+   +VL  TL+ +N 
Sbjct:    16 FSSSKQKPTEGKEEQSRL--------QPWVEKYRPKTLDDVAAQDHTTKVLQRTLQASNL 67

Query:    83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAV 142
             PHMLFYGPPGTGKT+T LA+A  LFGP LY+SR+LELNASD+RGI +VR K+K FA V +
Sbjct:    68 PHMLFYGPPGTGKTSTILALAKSLFGPALYRSRILELNASDERGIGIVREKVKGFARVQL 127

Query:   143 G--SG---QRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISR 197
                +G   +    YPCPP+KIIILDEADSMT+DAQ+ALRRTME YS++TRF  +CNY++R
Sbjct:   128 SHPTGLDAEYFEKYPCPPFKIIILDEADSMTQDAQSALRRTMEQYSRITRFCLVCNYVTR 187

Query:   198 IIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYL 257
             IIEPLASRC+KFRFKPL       R+  I   E L+L+   +  L S S GDLRRAITYL
Sbjct:   188 IIEPLASRCSKFRFKPLDNSAAGDRLAQIAQLEKLSLENGVVDKLISCSDGDLRRAITYL 247

Query:   258 QGAARLFGSSITSKD 272
             Q AARL G++  +KD
Sbjct:   248 QSAARLVGAAKAAKD 262

GO:0005524 "ATP binding" evidence=IEA

GO:0033314 "mitotic DNA replication checkpoint" evidence=IEA

GO:0006272 "leading strand elongation" evidence=IEA

GO:0007062 "sister chromatid cohesion" evidence=IEA

GO:0006270 "DNA replication initiation" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0031390 "Ctf18 RFC-like complex" evidence=IEA

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

GO:0005829 "cytosol" evidence=IEA

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

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

UNIPROTKB|Q29RS9 RFC4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 727 (261.0 bits), Expect = 6.7e-72, P = 6.7e-72
 Identities = 142/230 (61%), Positives = 176/230 (76%)

Query:    50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP 109
             PWVEKYRPK V +VA QEEVV VL  +LE A+ P++LFYGPPGTGKT+T LA A +LFGP
Sbjct:    39 PWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAARELFGP 98

Query:   110 ELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE 169
             EL++ RVLELNASD+RGI VVR K+K FA + V SG R  G PCPP+KI+ILDEADSMT 
Sbjct:    99 ELFRLRVLELNASDERGIQVVREKVKNFAQLTV-SGSRSDGKPCPPFKIVILDEADSMTS 157

Query:   170 DAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE 229
              AQ ALRRTME  SK TRF  ICNY+SRIIEPL SRC+KFRFKPLS+++   R+L I ++
Sbjct:   158 AAQAALRRTMEKESKTTRFCLICNYVSRIIEPLTSRCSKFRFKPLSDKIQQQRLLDIADK 217

Query:   230 EGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS-ITSKDLISVSG 278
             E + +  E ++ L  +S+GDLR+AIT+LQ A RL G   +T K +  ++G
Sbjct:   218 EHVKISNEGIAYLVQVSEGDLRKAITFLQSATRLTGGKEVTEKVITDIAG 267

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

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1SFI3 RFC4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 723 (259.6 bits), Expect = 1.8e-71, P = 1.8e-71
 Identities = 145/246 (58%), Positives = 179/246 (72%)

Query:    50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP 109
             PWVEKYRPK V +VA QEEVV VL  +LE A+ P++LFYGPPGTGKT+T LA A +LFGP
Sbjct:    39 PWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAARELFGP 98

Query:   110 ELYKSRVLELNASDDRGINVVRTKIKTFAAVAV-GSGQRRGGYPCPPYKIIILDEADSMT 168
             EL++ RVLELNASD+RGI VVR K+K FA + V GS     G PCPP+KI+ILDEADSMT
Sbjct:    99 ELFRLRVLELNASDERGIQVVREKVKNFAQLTVSGSRSEISGKPCPPFKIVILDEADSMT 158

Query:   169 EDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICN 228
               AQ ALRRTME  SK TRF  ICNY+SRIIEPL SRC+KFRFKPLS+++   R+L I +
Sbjct:   159 SAAQAALRRTMEKESKTTRFCLICNYVSRIIEPLTSRCSKFRFKPLSDKIQQQRLLDIAD 218

Query:   229 EEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS-ITSKDLISVSGY-PTGGSGG 286
             +E + +  E ++ L  +S+GDLR+AIT+LQ A RL G   +T K +  ++G  PT    G
Sbjct:   219 KEHVKISDEGIAYLVKVSEGDLRKAITFLQSATRLTGGKEVTEKMITDIAGVVPTETIDG 278

Query:   287 AFRGVQ 292
                  Q
Sbjct:   279 VLAACQ 284

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

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q09843	RFC2_SCHPO	No assigned EC number	0.5381	0.8095	0.7	yes	no
P40348	RFC2_YEAST	No assigned EC number	0.6009	0.7346	0.6118	yes	no
P35249	RFC4_HUMAN	No assigned EC number	0.5859	0.8435	0.6831	yes	no
O28219	RFCS_ARCFU	No assigned EC number	0.5391	0.7074	0.6520	yes	no
Q99J62	RFC4_MOUSE	No assigned EC number	0.5912	0.8299	0.6703	yes	no
Q54MD4	RFC4_DICDI	No assigned EC number	0.5665	0.7925	0.6714	yes	no
A4WGV2	RFCS1_PYRAR	No assigned EC number	0.5047	0.6836	0.6109	yes	no
Q9YBS7	RFCS_AERPE	No assigned EC number	0.5246	0.7210	0.6523	yes	no
A3DNV9	RFCS_STAMF	No assigned EC number	0.5136	0.7176	0.6413	yes	no
A1RWU7	RFCS_THEPD	No assigned EC number	0.5092	0.6972	0.6307	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00015431001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (341 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00024178001	RecName- Full=Proliferating cell nuclear antigen;; This protein is an auxiliary protein of DNA [...] (266 aa)			•	•	•	•	•		0.975
	GSVIVG00027060001	SubName- Full=Chromosome chr8 scaffold_41, whole genome shotgun sequence; (354 aa)			•	•	•	•	•	•	0.905
	GSVIVG00006013001	RecName- Full=DNA polymerase; EC=2.7.7.7; (1126 aa)				•	•	•	•		0.879
	GSVIVG00022496001	SubName- Full=Chromosome chr14 scaffold_27, whole genome shotgun sequence; (330 aa)				•			•		0.852
	GSVIVG00022150001	RecName- Full=DNA ligase; EC=6.5.1.1; (783 aa)				•	•		•		0.826
	GSVIVG00001122001	SubName- Full=Chromosome chr2 scaffold_112, whole genome shotgun sequence; (326 aa)			•	•	•	•	•	•	0.818
	GSVIVG00015413001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (360 aa)			•	•	•	•	•	•	0.811
	GSVIVG00002439001	RecName- Full=DNA primase; EC=2.7.7.-; (457 aa)				•		•	•		0.766
	GSVIVG00017275001	SubName- Full=Chromosome chr6 scaffold_15, whole genome shotgun sequence; (854 aa)					•	•	•	•	0.741
	GSVIVG00022048001	RecName- Full=DNA polymerase; EC=2.7.7.7; (2224 aa)				•	•	•	•		0.724

---

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	294
PRK00440	319	PRK00440, rfc, replication factor C small subunit;	1e-106
PLN03025	319	PLN03025, PLN03025, replication factor C subunit;	2e-77
PRK12402	337	PRK12402, PRK12402, replication factor C small sub	4e-57
PRK04132	846	PRK04132, PRK04132, replication factor C small sub	7e-56
PHA02544	316	PHA02544, 44, clamp loader, small subunit; Provisi	1e-39
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	4e-34
PRK14953	486	PRK14953, PRK14953, DNA polymerase III subunits ga	1e-32
TIGR02397	355	TIGR02397, dnaX_nterm, DNA polymerase III, subunit	1e-30
PRK14962	472	PRK14962, PRK14962, DNA polymerase III subunits ga	2e-29
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	2e-27
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	5e-27
COG2812	515	COG2812, DnaX, DNA polymerase III, gamma/tau subun	1e-26
PRK07133	725	PRK07133, PRK07133, DNA polymerase III subunits ga	4e-25
COG2256	436	COG2256, MGS1, ATPase related to the helicase subu	2e-23
PRK06305	451	PRK06305, PRK06305, DNA polymerase III subunits ga	5e-22
TIGR00678	188	TIGR00678, holB, DNA polymerase III, delta' subuni	4e-21
PRK14956	484	PRK14956, PRK14956, DNA polymerase III subunits ga	4e-21
PRK14963	504	PRK14963, PRK14963, DNA polymerase III subunits ga	3e-20
pfam13177	161	pfam13177, DNA_pol3_delta2, DNA polymerase III, de	2e-19
PRK14970	367	PRK14970, PRK14970, DNA polymerase III subunits ga	1e-18
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	1e-18
PRK14961	363	PRK14961, PRK14961, DNA polymerase III subunits ga	2e-18
PRK05563	559	PRK05563, PRK05563, DNA polymerase III subunits ga	3e-18
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	5e-18
PRK14955	397	PRK14955, PRK14955, DNA polymerase III subunits ga	3e-17
PRK06645	507	PRK06645, PRK06645, DNA polymerase III subunits ga	4e-17
PRK14969	527	PRK14969, PRK14969, DNA polymerase III subunits ga	7e-17
PRK14964	491	PRK14964, PRK14964, DNA polymerase III subunits ga	9e-17
PRK06647	563	PRK06647, PRK06647, DNA polymerase III subunits ga	3e-16
PRK08691	709	PRK08691, PRK08691, DNA polymerase III subunits ga	3e-16
PRK14954	620	PRK14954, PRK14954, DNA polymerase III subunits ga	6e-16
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	6e-16
PRK05896	605	PRK05896, PRK05896, DNA polymerase III subunits ga	1e-15
PRK08451	535	PRK08451, PRK08451, DNA polymerase III subunits ga	1e-15
PRK14959	624	PRK14959, PRK14959, DNA polymerase III subunits ga	9e-15
PRK14960	702	PRK14960, PRK14960, DNA polymerase III subunits ga	2e-14
smart00382	148	smart00382, AAA, ATPases associated with a variety	5e-14
COG0470	230	COG0470, HolB, ATPase involved in DNA replication	1e-13
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	2e-13
PRK04132	846	PRK04132, PRK04132, replication factor C small sub	4e-13
PRK05564	313	PRK05564, PRK05564, DNA polymerase III subunit del	5e-13
PRK07399	314	PRK07399, PRK07399, DNA polymerase III subunit del	7e-13
PRK09112	351	PRK09112, PRK09112, DNA polymerase III subunit del	1e-12
PRK14957	546	PRK14957, PRK14957, DNA polymerase III subunits ga	2e-12
PRK09111	598	PRK09111, PRK09111, DNA polymerase III subunits ga	4e-12
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	8e-12
PRK14952	584	PRK14952, PRK14952, DNA polymerase III subunits ga	8e-12
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	2e-11
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	2e-10
PRK13341	725	PRK13341, PRK13341, recombination factor protein R	3e-10
PRK07471	365	PRK07471, PRK07471, DNA polymerase III subunit del	5e-10
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	6e-10
PRK14958	509	PRK14958, PRK14958, DNA polymerase III subunits ga	1e-09
TIGR02902	531	TIGR02902, spore_lonB, ATP-dependent protease LonB	1e-09
TIGR00602	637	TIGR00602, rad24, checkpoint protein rad24	1e-08
pfam03215	490	pfam03215, Rad17, Rad17 cell cycle checkpoint prot	2e-08
COG2255	332	COG2255, RuvB, Holliday junction resolvasome, heli	7e-08
pfam13401	124	pfam13401, AAA_22, AAA domain	9e-08
PRK08058	329	PRK08058, PRK08058, DNA polymerase III subunit del	1e-07
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	2e-07
PRK06090	319	PRK06090, PRK06090, DNA polymerase III subunit del	4e-07
pfam05496	231	pfam05496, RuvB_N, Holliday junction DNA helicase	7e-07
PRK00080	328	PRK00080, ruvB, Holliday junction DNA helicase Ruv	1e-06
COG1474	366	COG1474, CDC6, Cdc6-related protein, AAA superfami	2e-06
TIGR03922	557	TIGR03922, T7SS_EccA, type VII secretion AAA-ATPas	2e-05
pfam13086	220	pfam13086, AAA_11, AAA domain	3e-05
TIGR00635	305	TIGR00635, ruvB, Holliday junction DNA helicase, R	8e-05
TIGR02903	615	TIGR02903, spore_lon_C, ATP-dependent protease, Lo	1e-04
PRK05707	328	PRK05707, PRK05707, DNA polymerase III subunit del	1e-04
pfam09848	348	pfam09848, DUF2075, Uncharacterized conserved prot	2e-04
PRK06964	342	PRK06964, PRK06964, DNA polymerase III subunit del	2e-04
PRK08699	325	PRK08699, PRK08699, DNA polymerase III subunit del	2e-04
PRK07993	334	PRK07993, PRK07993, DNA polymerase III subunit del	2e-04
TIGR03345	852	TIGR03345, VI_ClpV1, type VI secretion ATPase, Clp	3e-04
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	5e-04
pfam07728	135	pfam07728, AAA_5, AAA domain (dynein-related subfa	5e-04
COG0714	329	COG0714, COG0714, MoxR-like ATPases [General funct	6e-04
PRK07940	394	PRK07940, PRK07940, DNA polymerase III subunit del	7e-04
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	0.001
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	0.001
TIGR02881	261	TIGR02881, spore_V_K, stage V sporulation protein	0.001
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	0.002
PRK07132	299	PRK07132, PRK07132, DNA polymerase III subunit del	0.002
pfam13173	127	pfam13173, AAA_14, AAA domain	0.002
CHL00181	287	CHL00181, cbbX, CbbX; Provisional	0.002
PRK14949	944	PRK14949, PRK14949, DNA polymerase III subunits ga	0.002
PRK00411	394	PRK00411, cdc6, cell division control protein 6; R	0.002
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	0.002
pfam01078	207	pfam01078, Mg_chelatase, Magnesium chelatase, subu	0.003
pfam07724	168	pfam07724, AAA_2, AAA domain (Cdc48 subfamily)	0.004
TIGR00368	499	TIGR00368, TIGR00368, Mg chelatase-related protein	0.004
PRK08769	319	PRK08769, PRK08769, DNA polymerase III subunit del	0.004

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

 Score =  310 bits (797), Expect = e-106
 Identities = 114/230 (49%), Positives = 156/230 (67%), Gaps = 10/230 (4%)

Query: 50  PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP 109
            WVEKYRP+ + ++  QEE+V  L + ++  N PH+LF GPPGTGKTT ALA+A +L+G 
Sbjct: 6   IWVEKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYG- 64

Query: 110 ELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE 169
           E ++   LELNASD+RGI+V+R KIK FA  A       GG P   +KII LDEAD++T 
Sbjct: 65  EDWRENFLELNASDERGIDVIRNKIKEFARTAPV-----GGAP---FKIIFLDEADNLTS 116

Query: 170 DAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE 229
           DAQ ALRRTME YS+ TRF   CNY S+II+P+ SRCA FRF PL +E ++ R+ +I   
Sbjct: 117 DAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAEN 176

Query: 230 EGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGY 279
           EG+ +  +AL  +  +S+GD+R+AI  LQ AA   G  +T + +  ++G 
Sbjct: 177 EGIEITDDALEAIYYVSEGDMRKAINALQAAAAT-GKEVTEEAVYKITGT 225

Length = 319

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

 Score =  238 bits (608), Expect = 2e-77
 Identities = 106/216 (49%), Positives = 135/216 (62%), Gaps = 8/216 (3%)

Query: 50  PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP 109
           PWVEKYRP ++ D+   E+ V  L       N P+++  GPPGTGKTT+ LA+AH+L GP
Sbjct: 2   PWVEKYRPTKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGP 61

Query: 110 ELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE 169
             YK  VLELNASDDRGI+VVR KIK FA       Q++   P   +KI+ILDEADSMT 
Sbjct: 62  -NYKEAVLELNASDDRGIDVVRNKIKMFA-------QKKVTLPPGRHKIVILDEADSMTS 113

Query: 170 DAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE 229
            AQ ALRRTME YS  TRF   CN  S+IIEP+ SRCA  RF  LS++ +  R++ +   
Sbjct: 114 GAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEA 173

Query: 230 EGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFG 265
           E +    E L  +   + GD+R+A+  LQ     FG
Sbjct: 174 EKVPYVPEGLEAIIFTADGDMRQALNNLQATHSGFG 209

Length = 319

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

 Score =  186 bits (474), Expect = 4e-57
 Identities = 82/238 (34%), Positives = 124/238 (52%), Gaps = 23/238 (9%)

Query: 51  WVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE 110
           W EKYRP  ++D+  Q+EVV  L+  +++ N PH+L  GPPG+GKT    A+A +L+G +
Sbjct: 5   WTEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYG-D 63

Query: 111 LYKSRVLELNASD--DRGINVVRTKIKTFAAVAVGSGQRR--------------GGYPCP 154
            +++   E N +D  D+G   +      FA       + R                Y  P
Sbjct: 64  PWENNFTEFNVADFFDQGKKYLVED-PRFAHFLGTDKRIRSSKIDNFKHVLKEYASYR-P 121

Query: 155 ---PYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRF 211
               YK I+LD A+++ EDAQ ALRR ME YS+  RF       S++I P+ SRC    F
Sbjct: 122 LSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFF 181

Query: 212 KPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSIT 269
           +  +++ +   +  I   EG++ D + L  ++  + GDLR+AI  LQ AA L    IT
Sbjct: 182 RAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAA-LAAGEIT 238

Length = 337

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

 Score =  192 bits (490), Expect = 7e-56
 Identities = 91/182 (50%), Positives = 119/182 (65%), Gaps = 10/182 (5%)

Query: 96  TTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPP 155
           TT ALA+A +LFG E ++   LELNASD+RGINV+R K+K FA      G          
Sbjct: 580 TTAALALARELFG-ENWRHNFLELNASDERGINVIREKVKEFARTKPIGGA--------S 630

Query: 156 YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLS 215
           +KII LDEAD++T+DAQ ALRRTME +S   RF   CNY S+IIEP+ SRCA FRF+PL 
Sbjct: 631 FKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLR 690

Query: 216 EEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLIS 275
           +E ++ R+ +I   EGL L  E L  +  I++GD+RRAI  LQ AA L    IT +++  
Sbjct: 691 DEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAAL-DDKITDENVFL 749

Query: 276 VS 277
           V+
Sbjct: 750 VA 751

Length = 846

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

 Score =  140 bits (355), Expect = 1e-39
 Identities = 74/218 (33%), Positives = 103/218 (47%), Gaps = 27/218 (12%)

Query: 51  WVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGP-PGTGKTTTALAIAHQLFGP 109
           W +KYRP  + +            + ++    P+ML + P PGTGKTT A A+ +++   
Sbjct: 11  WEQKYRPSTIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV--- 67

Query: 110 ELYKSRVLELNASDDRGINVVRTKIKTFAA-VAVGSGQRRGGYPCPPYKIIILDEAD-SM 167
               + VL +N SD R I+ VR ++  FA+ V++              K+II+DE D   
Sbjct: 68  ---GAEVLFVNGSDCR-IDFVRNRLTRFASTVSL----------TGGGKVIIIDEFDRLG 113

Query: 168 TEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRF-KPLSEE---VMSS-- 221
             DAQ  LR  ME YSK   F    N  + IIEPL SRC    F  P  EE   +M    
Sbjct: 114 LADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQMI 173

Query: 222 -RVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQ 258
            R   I   EG+ +D + L+ L   +  D RR I  LQ
Sbjct: 174 VRCKGILEAEGVEVDMKVLAALVKKNFPDFRRTINELQ 211

Length = 316

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

 Score =  128 bits (325), Expect = 4e-34
 Identities = 77/240 (32%), Positives = 105/240 (43%), Gaps = 31/240 (12%)

Query: 50  PWVEKYRPKQVKDVAHQEEVVRVLTNTLET--ANCPH--MLFYGPPGTGKTTTALAIAHQ 105
           PWVEKYRPK + DV   E+    L   +E+     P   +L YGPPG GKT+ A A+A+ 
Sbjct: 3   PWVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALAND 62

Query: 106 LFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEAD 165
                 Y   V+ELNASD R        I+  A    G     G       K+I+LDE D
Sbjct: 63  ------YGWEVIELNASDQRT----ADVIERVA----GEAATSGSLFGARRKLILLDEVD 108

Query: 166 SM--TEDA--QNALRRTMETYSKVTRFFFIC---NYISRIIEPLASRCAKFRFKPLSEEV 218
            +   ED     A+   +    K  +   I    +     +  L + C    FK LS   
Sbjct: 109 GIHGNEDRGGARAILELI----KKAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRS 164

Query: 219 MSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
           +   +  IC +EG+  D EAL  ++  S GDLR AI  LQ  A   G    + + +   G
Sbjct: 165 IVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAE--GYGKLTLEDVKTLG 222

Length = 482

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

 Score =  124 bits (314), Expect = 1e-32
 Identities = 78/254 (30%), Positives = 119/254 (46%), Gaps = 41/254 (16%)

Query: 50  PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTA--------- 99
           P+  KYRPK  K+V  QE VVR+L N ++     H  +F GP GTGKTT A         
Sbjct: 5   PFARKYRPKFFKEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNC 64

Query: 100 ---------------LAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGS 144
                          + I    F P+L      E++A+ +RGI+ +R  ++     AV  
Sbjct: 65  LNPQEGEPCGKCENCVEIDKGSF-PDLI-----EIDAASNRGIDDIRA-LRD----AVSY 113

Query: 145 GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLAS 204
              +G      YK+ I+DEA  +T++A NAL +T+E     T F        +I   + S
Sbjct: 114 TPIKG-----KYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILS 168

Query: 205 RCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF 264
           RC +F F   ++E +   +  ICNEE +  + +AL  L+  S+G +R A + L  A+   
Sbjct: 169 RCQRFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQASEGGMRDAASLLDQASTYG 228

Query: 265 GSSITSKDLISVSG 278
              +T K +    G
Sbjct: 229 EGKVTIKVVEEFLG 242

Length = 486

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

 Score =  117 bits (295), Expect = 1e-30
 Identities = 68/247 (27%), Positives = 114/247 (46%), Gaps = 33/247 (13%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY 112
           KYRP+  +DV  QE +V+ L N ++     H  LF GP GTGKT+ A   A  L      
Sbjct: 7   KYRPQTFEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGP 66

Query: 113 KSR------------------VLELNASDDRGINVVRTKIKT--FAAVAVGSGQRRGGYP 152
                                V+E++A+ + G++ +R  +    +A     SG+      
Sbjct: 67  DGEPCNECESCKEINSGSSLDVIEIDAASNNGVDDIREILDNVKYAPS---SGK------ 117

Query: 153 CPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFK 212
              YK+ I+DE   +++ A NAL +T+E   +   F        +I   + SRC +F FK
Sbjct: 118 ---YKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKIPATILSRCQRFDFK 174

Query: 213 PLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKD 272
            +  E +  R+  I ++EG+ ++ EAL  ++  + G LR A++ L         +IT +D
Sbjct: 175 RIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLLDQLISFGNGNITYED 234

Query: 273 LISVSGY 279
           +  + G 
Sbjct: 235 VNELLGL 241

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis [DNA metabolism, DNA replication, recombination, and repair]. Length = 355

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

 Score =  116 bits (291), Expect = 2e-29
 Identities = 73/239 (30%), Positives = 118/239 (49%), Gaps = 29/239 (12%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQL------ 106
           KYRPK   +V  Q+ V +++ N L+  +  H  +F GP GTGKTT A  +A  L      
Sbjct: 7   KYRPKTFSEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRK 66

Query: 107 FGPELYKSR------------VLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCP 154
                 + R            V+EL+A+ +RGI+ +R KI+     AVG     G Y   
Sbjct: 67  GVEPCNECRACRSIDEGTFMDVIELDAASNRGIDEIR-KIRD----AVGYRPMEGKY--- 118

Query: 155 PYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPL 214
             K+ I+DE   +T++A NAL +T+E       F      + ++   + SRC    F+ +
Sbjct: 119 --KVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPPTIISRCQVIEFRNI 176

Query: 215 SEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDL 273
           S+E++  R+  +   EG+ +D EALS ++  + G LR A+T L+   +     IT + +
Sbjct: 177 SDELIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLEQVWKFSEGKITLETV 235

Length = 472

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

 Score =  109 bits (276), Expect = 2e-27
 Identities = 70/237 (29%), Positives = 101/237 (42%), Gaps = 34/237 (14%)

Query: 53  EKYRPKQVKDVAHQEEVV---RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP 109
           E+ RPK + +V  QE ++   + L   +E      M+ +GPPGTGKTT A  IA      
Sbjct: 4   ERMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGAT--- 60

Query: 110 ELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE 169
               +    L+A    G+  +R  I+  A     +G+R          I+ +DE     +
Sbjct: 61  ---DAPFEALSAVTS-GVKDLREVIEE-ARQRRSAGRR---------TILFIDEIHRFNK 106

Query: 170 DAQNALRRTMETYSKVTRFFFIC----N-YISRIIEPLASRCAKFRFKPLSEEVMSS--- 221
             Q+AL   +E    +T    I     N     +   L SR   F  KPLSEE +     
Sbjct: 107 AQQDALLPHVEDG-TIT---LIGATTENPSFE-VNPALLSRAQVFELKPLSEEDIEQLLK 161

Query: 222 RVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
           R L       + LD EAL  L+ ++ GD RRA+  L+ AA     SIT + L     
Sbjct: 162 RALEDKERGLVELDDEALDALARLANGDARRALNLLELAALG-VDSITLELLEEALQ 217

Length = 413

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

 Score =  102 bits (256), Expect = 5e-27
 Identities = 49/149 (32%), Positives = 66/149 (44%), Gaps = 16/149 (10%)

Query: 66  QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR 125
           QEE +  L   LE     ++L YGPPGTGKTT A AIA++LF P    +  L LNASD  
Sbjct: 3   QEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP---GAPFLYLNASDLL 59

Query: 126 GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKV 185
              VV      F    +     +         ++ +DE DS++  AQNAL R +ET + +
Sbjct: 60  EGLVVAELFGHFLVRLLFELAEKA-----KPGVLFIDEIDSLSRGAQNALLRVLETLNDL 114

Query: 186 T------RFFFICNYIS--RIIEPLASRC 206
                  R     N      +   L  R 
Sbjct: 115 RIDRENVRVIGATNRPLLGDLDRALYDRL 143

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

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

 Score =  108 bits (271), Expect = 1e-26
 Identities = 73/253 (28%), Positives = 117/253 (46%), Gaps = 33/253 (13%)

Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIA-- 103
           S Q    KYRPK   DV  QE VV+ L+N LE     H  LF GP G GKTT A  +A  
Sbjct: 2   SYQVLARKYRPKTFDDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKA 61

Query: 104 -------HQLFGPELYKSR---------VLELNASDDRGINVVRTKIKT--FAAVAVGSG 145
                        +    +         V+E++A+ + G++ +R  I+   +A       
Sbjct: 62  LNCENGPTAEPCGKCISCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGR-- 119

Query: 146 QRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASR 205
                     YK+ I+DE   +++ A NAL +T+E      +F        +I   + SR
Sbjct: 120 ----------YKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTILSR 169

Query: 206 CAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFG 265
           C +F FK L  E ++  +  I ++EG+N++ +ALS ++  ++G LR A++ L  A     
Sbjct: 170 CQRFDFKRLDLEEIAKHLAAILDKEGINIEEDALSLIARAAEGSLRDALSLLDQAIAFGE 229

Query: 266 SSITSKDLISVSG 278
             IT + +  + G
Sbjct: 230 GEITLESVRDMLG 242

Length = 515

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

 Score =  104 bits (261), Expect = 4e-25
 Identities = 68/244 (27%), Positives = 119/244 (48%), Gaps = 26/244 (10%)

Query: 51  WVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIA------ 103
              KYRPK   D+  Q+ +V+ L N +++    H  LF GP GTGKT+ A   A      
Sbjct: 8   LYRKYRPKTFDDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCS 67

Query: 104 HQ--LFGP------ELYKS-RVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCP 154
           H+  L  P       +  S  ++E++A+ + G++ +R  I+    +   S          
Sbjct: 68  HKTDLLEPCQECIENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQS---------- 117

Query: 155 PYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPL 214
            YKI I+DE   +++ A NAL +T+E   K   F      + +I   + SR  +F F+ +
Sbjct: 118 KYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPLTILSRVQRFNFRRI 177

Query: 215 SEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLI 274
           SE+ + SR+  I  +E ++ +  AL  ++ +S G LR A++  +  +    + IT K++ 
Sbjct: 178 SEDEIVSRLEFILEKENISYEKNALKLIAKLSSGSLRDALSIAEQVSIFGNNKITLKNVE 237

Query: 275 SVSG 278
            + G
Sbjct: 238 ELFG 241

Length = 725

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

 Score = 98.8 bits (247), Expect = 2e-23
 Identities = 68/235 (28%), Positives = 94/235 (40%), Gaps = 41/235 (17%)

Query: 47  SSQPWVEKYRPKQVKDVAHQEEVV---RVLTNTLETANCPHMLFYGPPGTGKTTTALAIA 103
              P  E+ RPK + +V  QE ++   + L   +E  +   M+ +GPPGTGKTT A  IA
Sbjct: 10  FRMPLAERLRPKSLDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTLARLIA 69

Query: 104 HQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDE 163
                     +    L+A    G+  +R  I+  A      G+R          I+ LDE
Sbjct: 70  GTT------NAAFEALSAVTS-GVKDLREIIEE-ARKNRLLGRR---------TILFLDE 112

Query: 164 ADSMTEDAQNALRRTMETYSKVTRF-------FFICNYISRIIEPLASRCAKFRFKPLSE 216
                +  Q+AL   +E    +           F  N        L SR   F  KPLS 
Sbjct: 113 IHRFNKAQQDALLPHVENG-TIILIGATTENPSFELN------PALLSRARVFELKPLSS 165

Query: 217 EVMSSRVLHICN--EEGL-----NLDAEALSTLSSISQGDLRRAITYLQGAARLF 264
           E +   +       E GL      LD EAL  L  +S GD RRA+  L+ AA   
Sbjct: 166 EDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRALNLLELAALSA 220

Length = 436

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

 Score = 94.8 bits (236), Expect = 5e-22
 Identities = 72/254 (28%), Positives = 108/254 (42%), Gaps = 30/254 (11%)

Query: 45  LQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIA 103
           + S Q    KYRP+   ++  Q+ VV VL N L      H  LF G  GTGKTT A   A
Sbjct: 1   MTSYQVSSRKYRPQTFSEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFA 60

Query: 104 HQLFGPELYKSR-------------------VLELNASDDRGINVVRTKIKTFAAVAVGS 144
             L      + +                   VLE++ +  RGI  +R   +T        
Sbjct: 61  KALNCQNPTEDQEPCNQCASCKEISSGTSLDVLEIDGASHRGIEDIRQINETVLFTPS-K 119

Query: 145 GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLAS 204
            +         YKI I+DE   +T++A N+L +T+E   +  +FF     I +I   + S
Sbjct: 120 SR---------YKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPGTILS 170

Query: 205 RCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF 264
           RC K   K + EE +  ++  I  +EG+    EAL  ++  +QG LR A +       LF
Sbjct: 171 RCQKMHLKRIPEETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDAESLYDYVVGLF 230

Query: 265 GSSITSKDLISVSG 278
             S+    +    G
Sbjct: 231 PKSLDPDSVAKALG 244

Length = 451

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

 Score = 88.1 bits (219), Expect = 4e-21
 Identities = 50/203 (24%), Positives = 78/203 (38%), Gaps = 36/203 (17%)

Query: 71  RVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYKS----------RVLEL 119
           + L   LE     H  LF GP G GK   ALA+A  L   +               +   
Sbjct: 2   QQLKRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAG 61

Query: 120 NASDDR---------GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED 170
           N  D            ++ VR  ++  +     SG           +++I+++A+ M E 
Sbjct: 62  NHPDLHRLEPEGQSIKVDQVRELVEFLSRTPQESG----------RRVVIIEDAERMNEA 111

Query: 171 AQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEE 230
           A NAL +T+E     T F  I     +++  + SRC    F PLSEE +  + L      
Sbjct: 112 AANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEAL-LQWL-----I 165

Query: 231 GLNLDAEALSTLSSISQGDLRRA 253
              +  EA   L +++ G    A
Sbjct: 166 RQGISEEAAELLLALAGGSPGAA 188

This model describes the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tighly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classisified as delta'. The noise cutoff is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau [DNA metabolism, DNA replication, recombination, and repair]. Length = 188

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

 Score = 92.3 bits (229), Expect = 4e-21
 Identities = 68/245 (27%), Positives = 109/245 (44%), Gaps = 29/245 (11%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQL------ 106
           KYRP+  +DV HQ+  +  L N L++    H  +F+GP G GKTT A  +A +L      
Sbjct: 11  KYRPQFFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPI 70

Query: 107 ---------FGPELYK---SRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCP 154
                       E+ K   S VLE++A+ +RGI  +R          +G           
Sbjct: 71  GNEPCNECTSCLEITKGISSDVLEIDAASNRGIENIRELRDNVKFAPMGG---------- 120

Query: 155 PYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPL 214
            YK+ I+DE   +T+ + NAL +T+E       F        +I E + SRC  F FK +
Sbjct: 121 KYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRCQDFIFKKV 180

Query: 215 SEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLI 274
              V+      +C  E +  D E L  ++    G +R  +++++ A     S +T   + 
Sbjct: 181 PLSVLQDYSEKLCKIENVQYDQEGLFWIAKKGDGSVRDMLSFMEQAIVFTDSKLTGVKIR 240

Query: 275 SVSGY 279
            + GY
Sbjct: 241 KMIGY 245

Length = 484

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

 Score = 89.9 bits (223), Expect = 3e-20
 Identities = 71/250 (28%), Positives = 111/250 (44%), Gaps = 33/250 (13%)

Query: 53  EKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTA--LAIAHQLFGP 109
           ++ RP    +V  QE V  VL   L      H  LF GP G GKTTTA  +A+A    G 
Sbjct: 6   QRARPITFDEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGE 65

Query: 110 ---------------ELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCP 154
                                VLE++A+ +  +  VR  ++    +A   G R       
Sbjct: 66  DPKPCGECESCLAVRRGAHPDVLEIDAASNNSVEDVR-DLREKVLLAPLRGGR------- 117

Query: 155 PYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPL 214
             K+ ILDEA  M++ A NAL +T+E   +   F        ++   + SR   FRF+ L
Sbjct: 118 --KVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQHFRFRRL 175

Query: 215 SEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF--GSSITSKD 272
           +EE ++ ++  +   EG   + EAL  ++ ++ G +R A + L+   RL   G+ +T K 
Sbjct: 176 TEEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDAESLLE---RLLALGTPVTRKQ 232

Query: 273 LISVSGYPTG 282
           +    G P  
Sbjct: 233 VEEALGLPPQ 242

Length = 504

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

 Score = 83.0 bits (206), Expect = 2e-19
 Identities = 46/170 (27%), Positives = 75/170 (44%), Gaps = 30/170 (17%)

Query: 66  QEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLF----------GPELYKS 114
           Q +V+++L N+++     H  LF GP G GK   AL  A  LF          G      
Sbjct: 2   QPKVIKLLKNSIKKNKLSHAYLFSGPDGVGKLELALEFAKALFCENPQDDEPCGECKSCK 61

Query: 115 RVLELN-------ASDDRGINV--VRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEAD 165
           R+   N         + + I +  +R  I+ F+                  K+ I+++A+
Sbjct: 62  RIENGNHPDVIIIEPEGKSIKIDQIRELIEEFSKKPFEGK----------KKVYIIEDAE 111

Query: 166 SMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLS 215
            MTE A NAL +T+E   + T F  + +  ++++  + SRC    FKPLS
Sbjct: 112 KMTESAANALLKTLEEPPENTYFILLTSNPNKLLPTIRSRCQVINFKPLS 161

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

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

 Score = 84.5 bits (209), Expect = 1e-18
 Identities = 64/234 (27%), Positives = 104/234 (44%), Gaps = 25/234 (10%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGP--- 109
           KYRP+   DV  Q  +   L N +E  +    +LF GP G GKTT A  +A ++  P   
Sbjct: 10  KYRPQTFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYD 69

Query: 110 ---ELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPP----YKIIILD 162
              E +   + EL+A+ +  ++ +R  I           Q R     PP    YKI I+D
Sbjct: 70  DPNEDFSFNIFELDAASNNSVDDIRNLID----------QVR----IPPQTGKYKIYIID 115

Query: 163 EADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSR 222
           E   ++  A NA  +T+E       F        +II  + SRC  F FK ++ + +   
Sbjct: 116 EVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEH 175

Query: 223 VLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISV 276
           +  I  +EG+  + +AL  ++  + G LR A++         G +IT + +   
Sbjct: 176 LAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFDRVVTFCGKNITRQAVTEN 229

Length = 367

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

 Score = 79.6 bits (197), Expect = 1e-18
 Identities = 36/151 (23%), Positives = 61/151 (40%), Gaps = 41/151 (27%)

Query: 85  MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINV------VRTKIKTFA 138
           +L YGPPGTGKTT A A+A +L       +  +E++ S+     V      +R   + F 
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKEL------GAPFIEISGSELVSKYVGESEKRLR---ELFE 51

Query: 139 AVAVGSGQRRGGYPCPPYKIIILDEADSM-----------TEDAQNALRRTMETY-SKVT 186
           A    +       PC    +I +DE D++           +    N L   ++ + S ++
Sbjct: 52  AAKKLA-------PC----VIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLS 100

Query: 187 RFFFIC--NYISRIIEPL-ASRCAKFRFKPL 214
           +   I   N   ++   L   R  +    PL
Sbjct: 101 KVIVIAATNRPDKLDPALLRGRFDRIIEFPL 131

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

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

 Score = 84.1 bits (208), Expect = 2e-18
 Identities = 61/246 (24%), Positives = 109/246 (44%), Gaps = 29/246 (11%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQL------ 106
           K+RP+  +D+  Q+ +V  ++N L      H  L  G  G GKTT A  +A  L      
Sbjct: 9   KWRPQYFRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGI 68

Query: 107 ---------FGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPY- 156
                       E+ K   L+L   D       RTK++    +          Y  P   
Sbjct: 69  TSNPCRKCIICKEIEKGLCLDLIEID----AASRTKVEEMREIL------DNIYYSPSKS 118

Query: 157 --KIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPL 214
             K+ ++DE   ++  + NAL +T+E   +  +F      + +I + + SRC +F+ K +
Sbjct: 119 RFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFKLKII 178

Query: 215 SEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLI 274
           SEE + + + +I  +E ++ D  AL  ++  + G +R A+  L+ A  L   +I  K++ 
Sbjct: 179 SEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLEHAINLGKGNINIKNVT 238

Query: 275 SVSGYP 280
            + G  
Sbjct: 239 DMLGLL 244

Length = 363

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

 Score = 84.2 bits (209), Expect = 3e-18
 Identities = 73/269 (27%), Positives = 121/269 (44%), Gaps = 73/269 (27%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTA--LAIA----HQL 106
           K+RP+  +DV  QE + + L N ++     H  LF GP GTGKT+ A   A A    +  
Sbjct: 9   KWRPQTFEDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPP 68

Query: 107 FG-P----ELYKS-------RVLELNASDDRGINVVRT---KIKTFAAVAVGSGQRRGGY 151
            G P    E+ K+        V+E++A+ + G++ +R    K+K +A             
Sbjct: 69  DGEPCNECEICKAITNGSLMDVIEIDAASNNGVDEIRDIRDKVK-YAPSEA--------- 118

Query: 152 PCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEP-------LA- 203
               YK+ I+DE   ++  A NAL +T+E                   EP       LA 
Sbjct: 119 ---KYKVYIIDEVHMLSTGAFNALLKTLE-------------------EPPAHVIFILAT 156

Query: 204 -----------SRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRR 252
                      SRC +F FK +S E +  R+ +I ++EG+  + EAL  ++  ++G +R 
Sbjct: 157 TEPHKIPATILSRCQRFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAAEGGMRD 216

Query: 253 AITYLQGAARLFGSSITSKDLISVSGYPT 281
           A++ L  A       +T +D + V+G  +
Sbjct: 217 ALSILDQAISFGDGKVTYEDALEVTGSVS 245

Length = 559

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

 Score = 83.6 bits (207), Expect = 5e-18
 Identities = 64/244 (26%), Positives = 114/244 (46%), Gaps = 29/244 (11%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQL---FGP 109
           KYRP+   D+  QE V R L N ++T    H  LF G  G GKT+TA  +A  L    G 
Sbjct: 9   KYRPQTFSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGL 68

Query: 110 ------------ELYKSR---VLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCP 154
                       E+ + R   V E++ + + G++ +R   +      + S  R       
Sbjct: 69  TAEPCNVCPPCVEITEGRSVDVFEIDGASNTGVDDIRELRE--NVKYLPSRSR------- 119

Query: 155 PYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPL 214
            YKI I+DE   ++ +A NAL +T+E      +F F      ++   + SRC +F F+ +
Sbjct: 120 -YKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITILSRCQRFDFRRI 178

Query: 215 SEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLI 274
             + +  R+ +I ++EG+++   AL+ ++    G +R +++ L       G ++   D+ 
Sbjct: 179 PLQKIVDRLRYIADQEGISISDAALALVARKGDGSMRDSLSTLDQVLAFCGDAVGDDDVA 238

Query: 275 SVSG 278
            + G
Sbjct: 239 ELLG 242

Length = 576

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

 Score = 80.7 bits (199), Expect = 3e-17
 Identities = 68/234 (29%), Positives = 103/234 (44%), Gaps = 29/234 (12%)

Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQ 105
           S Q    KYRPK+  D+  QE + R + N+L      H  +F G  G GKTT A   A  
Sbjct: 2   SYQVIARKYRPKKFADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKA 61

Query: 106 LFGPEL-----YKSRVLE----------------LNASD-DRGINVVRTKIKTFAAVAVG 143
           +    +     Y   V E                LN S+ D   N     I+      V 
Sbjct: 62  VNCQRMIDDADYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRLLRE-NVR 120

Query: 144 SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLA 203
            G ++G      Y++ I+DE   ++  A NA  +T+E       F F    + +I   +A
Sbjct: 121 YGPQKG-----RYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIA 175

Query: 204 SRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYL 257
           SRC +F FK +  E +  ++  IC  EG+++DA+AL  +   +QG +R A + L
Sbjct: 176 SRCQRFNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDAQSIL 229

Length = 397

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

 Score = 81.1 bits (200), Expect = 4e-17
 Identities = 64/249 (25%), Positives = 109/249 (43%), Gaps = 36/249 (14%)

Query: 50  PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFG 108
           P+  KYRP    ++  QE +V+VL+ T+         L  G  G GKTT+A  IA  +  
Sbjct: 10  PFARKYRPSNFAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNC 69

Query: 109 PELY----------------------KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQ 146
             L                          ++E++A+    ++ +R  I++     +    
Sbjct: 70  SALITENTTIKTCEQCTNCISFNNHNHPDIIEIDAASKTSVDDIRRIIESAEYKPLQG-- 127

Query: 147 RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRC 206
                    +KI I+DE   +++ A NAL +T+E       F F    + +I   + SRC
Sbjct: 128 --------KHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIISRC 179

Query: 207 AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGS 266
            ++  + LS E +   + +I  +E L  D EAL  ++  S+G  R A++ L  AA +   
Sbjct: 180 QRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSILDQAASM--- 236

Query: 267 SITSKDLIS 275
           S  S ++IS
Sbjct: 237 SAKSDNIIS 245

Length = 507

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

 Score = 80.2 bits (198), Expect = 7e-17
 Identities = 68/245 (27%), Positives = 112/245 (45%), Gaps = 29/245 (11%)

Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQ 105
           S Q    K+RPK   ++  QE VVR LTN LE     H  LF G  G GKTT A  +A  
Sbjct: 2   SYQVLARKWRPKSFSELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKS 61

Query: 106 L-------FGP--------ELYKSR---VLELNASDDRGINVVRTKIKTFAAVAVGSGQR 147
           L         P        E+   R   ++E++A+ +  ++ +R  +   A  A   G+ 
Sbjct: 62  LNCETGVTATPCGVCSACLEIDSGRFVDLIEVDAASNTQVDAMRELLDN-AQYAPTRGR- 119

Query: 148 RGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA 207
                   +K+ I+DE   +++ A NA+ +T+E   +  +F        +I   + SRC 
Sbjct: 120 --------FKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCL 171

Query: 208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS 267
           +F  K +   ++ S + HI  +E +  DA AL  L+  + G +R A++ L  A    G +
Sbjct: 172 QFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAAAGSMRDALSLLDQAIAYGGGT 231

Query: 268 ITSKD 272
           +   +
Sbjct: 232 VNESE 236

Length = 527

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

 Score = 79.8 bits (197), Expect = 9e-17
 Identities = 60/243 (24%), Positives = 107/243 (44%), Gaps = 35/243 (14%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQL---FGP 109
           KYRP   KD+  Q+ +VR+L N       P  +L  G  G GKTT A  I+  L    GP
Sbjct: 6   KYRPSSFKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGP 65

Query: 110 ---------------ELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCP 154
                                V+E++A+ +  ++ ++  ++    + + S          
Sbjct: 66  TSDPCGTCHNCISIKNSNHPDVIEIDAASNTSVDDIKVILENSCYLPISS---------- 115

Query: 155 PYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPL 214
            +K+ I+DE   ++  A NAL +T+E  +   +F      + +I   + SRC +F  + +
Sbjct: 116 KFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQKI 175

Query: 215 SEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLI 274
             + +   ++ I  +E +  D E+L  ++  S G +R A+  L+ AA      I S + I
Sbjct: 176 PTDKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNALFLLEQAA------IYSNNKI 229

Query: 275 SVS 277
           S  
Sbjct: 230 SEK 232

Length = 491

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

 Score = 78.3 bits (193), Expect = 3e-16
 Identities = 63/242 (26%), Positives = 106/242 (43%), Gaps = 29/242 (11%)

Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQ 105
           S +    K RP+    +  Q+ VV  L +++E+    +  +F GP G GKT++A A A  
Sbjct: 2   SYRGTATKRRPRDFNSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARC 61

Query: 106 L---FGP------ELYKSR---------VLELNASDDRGINVVRTKIKTFAAVAVGSGQR 147
           L    GP      E    +         V+E++ + +  +  VR +IK        S + 
Sbjct: 62  LNCVNGPTPMPCGECSSCKSIDNDNSLDVIEIDGASNTSVQDVR-QIKEEIMFPPASSR- 119

Query: 148 RGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA 207
                   Y++ I+DE   ++  A NAL +T+E       F F    + ++   + SRC 
Sbjct: 120 --------YRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIKSRCQ 171

Query: 208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS 267
            F F+ LS E + + +  +C E+ +  + EAL  ++  S G +R A T          S 
Sbjct: 172 HFNFRLLSLEKIYNMLKKVCLEDQIKYEDEALKWIAYKSTGSVRDAYTLFDQVVSFSDSD 231

Query: 268 IT 269
           IT
Sbjct: 232 IT 233

Length = 563

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

 Score = 78.2 bits (192), Expect = 3e-16
 Identities = 62/251 (24%), Positives = 113/251 (45%), Gaps = 29/251 (11%)

Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQ 105
           + Q    K+RPK   D+  QE VV+ L N L+     H  L  G  G GKTT A  +A  
Sbjct: 2   AYQVLARKWRPKTFADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKS 61

Query: 106 L---------------FGPELYKSR---VLELNASDDRGINVVRTKIKTFAAVAVGSGQR 147
           L                  ++   R   +LE++A+ + GI+ +R  ++  A  A  +G+ 
Sbjct: 62  LNCENAQHGEPCGVCQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLEN-AQYAPTAGK- 119

Query: 148 RGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA 207
                   YK+ I+DE   +++ A NA+ +T+E   +  +F        ++   + SRC 
Sbjct: 120 --------YKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVTVLSRCL 171

Query: 208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS 267
           +F  + ++ + ++  + H+ + E +  +  AL  L   + G +R A++ L  A  L    
Sbjct: 172 QFVLRNMTAQQVADHLAHVLDSEKIAYEPPALQLLGRAAAGSMRDALSLLDQAIALGSGK 231

Query: 268 ITSKDLISVSG 278
           +   D+  + G
Sbjct: 232 VAENDVRQMIG 242

Length = 709

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

 Score = 77.7 bits (191), Expect = 6e-16
 Identities = 66/234 (28%), Positives = 103/234 (44%), Gaps = 29/234 (12%)

Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIA-- 103
           S Q    KYRP +  D+  QE +   + N+L      H  +F G  G GKTT A   A  
Sbjct: 2   SYQVIARKYRPSKFADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKA 61

Query: 104 ---HQLFGPELYKSRVLE----------------LNASD-DRGINVVRTKIKTFAAVAVG 143
               ++    +Y   V E                LN S+ D   N     I+      V 
Sbjct: 62  VNCQRMIDDPVYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRQLRE-NVR 120

Query: 144 SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLA 203
            G ++G      Y++ I+DE   ++  A NA  +T+E       F F    + +I   +A
Sbjct: 121 YGPQKG-----RYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIA 175

Query: 204 SRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYL 257
           SRC +F FK +  + + S++  IC  EG+ +DA+AL  ++  +QG +R A + L
Sbjct: 176 SRCQRFNFKRIPLDEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDAQSIL 229

Length = 620

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

 Score = 77.5 bits (191), Expect = 6e-16
 Identities = 64/243 (26%), Positives = 104/243 (42%), Gaps = 30/243 (12%)

Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTA--LAIA 103
           + Q    K+R +   ++  QE VV+ L N +      H  LF GP G GKT+TA  LA A
Sbjct: 2   TVQVLYRKWRSQTFAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKA 61

Query: 104 HQLFGPE--------------LYKSR---VLELNASDDRGINVVRTKIKTFAAVAVGSGQ 146
                 +              + +     V+E++A+    ++  R  I+    V      
Sbjct: 62  VNCTTNDPKGRPCGTCEMCRAIAEGSAVDVIEMDAASHTSVDDAREIIER---VQFRPAL 118

Query: 147 RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRC 206
            R       YK+ I+DE   ++  A NAL +T+E       F      + ++   + SRC
Sbjct: 119 AR-------YKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILSRC 171

Query: 207 AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGS 266
            +F F   S   M++ +  I   EG+NL+  AL  ++  + G +R A   LQ  A  +G 
Sbjct: 172 QRFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDAENLLQQLATTYGG 231

Query: 267 SIT 269
            I+
Sbjct: 232 EIS 234

Length = 585

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

 Score = 76.8 bits (189), Expect = 1e-15
 Identities = 58/246 (23%), Positives = 100/246 (40%), Gaps = 31/246 (12%)

Query: 53  EKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL 111
            KYRP   K +  QE + ++L N +      H  +F GP G GKT+ A   A  +     
Sbjct: 8   RKYRPHNFKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNP 67

Query: 112 YKSRV------------------LELNASDDRGINVVRTKIKT-FAAVAVGSGQRRGGYP 152
                                  +EL+A+ + G++ +R  I                   
Sbjct: 68  KDGDCCNSCSVCESINTNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTFK-------- 119

Query: 153 CPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFK 212
              YK+ I+DEA  ++  A NAL +T+E   K   F F      +I   + SRC ++ FK
Sbjct: 120 ---YKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTIISRCQRYNFK 176

Query: 213 PLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKD 272
            L+   +   +  I  +E + ++  A+  ++ ++ G LR  ++ L   +    S I  +D
Sbjct: 177 KLNNSELQELLKSIAKKEKIKIEDNAIDKIADLADGSLRDGLSILDQLSTFKNSEIDIED 236

Query: 273 LISVSG 278
           +    G
Sbjct: 237 INKTFG 242

Length = 605

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

 Score = 76.6 bits (189), Expect = 1e-15
 Identities = 71/244 (29%), Positives = 108/244 (44%), Gaps = 65/244 (26%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQLF---GP 109
           KYRPK   ++  QE V + L+  L+     H  LF G  G+GKT++A   A  L    GP
Sbjct: 7   KYRPKHFDELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGP 66

Query: 110 ELYKSR------------------VLELNASDDRGINVVR-----TKIK-TFAAVAVGSG 145
               S                   ++E++A+ +RGI+ +R     TK K + A       
Sbjct: 67  ---SSTPCDTCIQCQSALENRHIDIIEMDAASNRGIDDIRELIEQTKYKPSMAR------ 117

Query: 146 QRRGGYPCPPYKIIILDEADSMTEDAQNALRRTME---TYSKVTRFFFICNYISRIIEPL 202
                     +KI I+DE   +T++A NAL +T+E   +Y K         +I    +PL
Sbjct: 118 ----------FKIFIIDEVHMLTKEAFNALLKTLEEPPSYVK---------FILATTDPL 158

Query: 203 A------SRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITY 256
                  SR   FRFK + +  + S +  I  +EG++ + EAL  L+    G LR  +T 
Sbjct: 159 KLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGVSYEPEALEILARSGNGSLRDTLTL 218

Query: 257 LQGA 260
           L  A
Sbjct: 219 LDQA 222

Length = 535

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

 Score = 73.9 bits (181), Expect = 9e-15
 Identities = 64/242 (26%), Positives = 102/242 (42%), Gaps = 29/242 (11%)

Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTL-ETANCPHMLFYGPPGTGKTTTALAIAHQ 105
           S      +YRP+   +VA QE V  +L+    E    P  LF G  G GKTT A   A  
Sbjct: 2   SHASLTARYRPQTFAEVAGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKA 61

Query: 106 LFGPELYKSR------------------VLELNASDDRGINVVRTKIKTFAAVAVGSGQR 147
           L                           V+E++ + +RGI+  + ++K     A+G    
Sbjct: 62  LNCETAPTGEPCNTCEQCRKVTQGMHVDVVEIDGASNRGIDDAK-RLKE----AIGYAPM 116

Query: 148 RGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA 207
            G      YK+ I+DEA  +T +A NAL +T+E       F        +    + SRC 
Sbjct: 117 EG-----RYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIVSRCQ 171

Query: 208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS 267
            F F  LSE  + + +  +   EG++ D  A+  ++  + G +R +++ L     L  S 
Sbjct: 172 HFTFTRLSEAGLEAHLTKVLGREGVDYDPAAVRLIARRAAGSVRDSMSLLGQVLALGESR 231

Query: 268 IT 269
           +T
Sbjct: 232 LT 233

Length = 624

>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau; Provisional

 Score = 73.2 bits (179), Expect = 2e-14
 Identities = 64/235 (27%), Positives = 107/235 (45%), Gaps = 30/235 (12%)

Query: 49  QPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQLF 107
           Q    KYRP+   ++  Q  V R L++ LE     H  LF G  G GKTT A  +A  L 
Sbjct: 3   QVLARKYRPRNFNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLN 62

Query: 108 GPELYKSRVLELNAS-----DDRGINVV------RTKIKT----FAAVAVGSGQRRGGYP 152
                 S   E+ A+     + R I+++      RTK++        V     Q R    
Sbjct: 63  CETGVTSTPCEVCATCKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGR---- 118

Query: 153 CPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFK 212
              +K+ ++DE   ++  + NAL +T+E   +  +F F      ++   + SRC +F  +
Sbjct: 119 ---FKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVISRCLQFTLR 175

Query: 213 PLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLR-------RAITYLQGA 260
           PL+ + ++  +  I  +E +  D +A+  ++  +QG LR       +AI Y QGA
Sbjct: 176 PLAVDEITKHLGAILEKEQIAADQDAIWQIAESAQGSLRDALSLTDQAIAYGQGA 230

Length = 702

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

 Score = 67.8 bits (165), Expect = 5e-14
 Identities = 30/144 (20%), Positives = 47/144 (32%), Gaps = 21/144 (14%)

Query: 84  HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVG 143
            +L  GPPG+GKTT A A+A +L  P      V+ ++  D     + +  +         
Sbjct: 4   VILIVGPPGSGKTTLARALARELGPPG---GGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60

Query: 144 SGQRRGG--------YPCPPYKIIILDEADSMTEDAQNALRRTMETYSKV--------TR 187
                             P   ++ILDE  S+ +  Q AL   +E    +          
Sbjct: 61  GSGELRLRLALALARKLKP--DVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLT 118

Query: 188 FFFICNYISRIIEPLASRCAKFRF 211
                N    +   L  R    R 
Sbjct: 119 VILTTNDEKDLGPALLRRRFDRRI 142

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

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

 Score = 68.5 bits (167), Expect = 1e-13
 Identities = 28/84 (33%), Positives = 40/84 (47%), Gaps = 11/84 (13%)

Query: 180 ETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEAL 239
               K TRF  I N  S+I+  + SRC + RFKP S          I   E      + L
Sbjct: 39  TAPPKNTRFILITNDPSKILPTIRSRCQRIRFKPPSRL------EAIAWLE-----DQGL 87

Query: 240 STLSSISQGDLRRAITYLQGAARL 263
             ++++++GD R+AI  LQ  A L
Sbjct: 88  EEIAAVAEGDARKAINPLQALAAL 111

Length = 230

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

 Score = 70.3 bits (172), Expect = 2e-13
 Identities = 63/233 (27%), Positives = 105/233 (45%), Gaps = 34/233 (14%)

Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTA--LAIA 103
           S Q    K+RP+    +  QE VVR LT+ LE     H  LF G  G GKTT +  LA +
Sbjct: 2   SYQVLARKWRPRDFTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKS 61

Query: 104 HQLFGP------------------ELYKSRV---LELNASDDRGINVVRTKIKTFAAVAV 142
               G                   E+   R    +E++A+ +RG++ +  ++   A  A 
Sbjct: 62  LNCTGADGEGGITAQPCGQCRACTEIDAGRFVDYIEMDAASNRGVDEM-AQLLDKAVYAP 120

Query: 143 GSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPL 202
            +G+         +K+ ++DE   +T  A NA+ +T+E   +  +F        +I   +
Sbjct: 121 TAGR---------FKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVTV 171

Query: 203 ASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAIT 255
            SRC +F  K +    + S +  I  EEG+  +  AL  L+  +QG +R A++
Sbjct: 172 LSRCLQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALRLLAQAAQGSMRDALS 224

Length = 700

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

 Score = 69.1 bits (169), Expect = 4e-13
 Identities = 25/50 (50%), Positives = 37/50 (74%)

Query: 49 QPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTT 98
          +PWVEKYRP+++ D+  QE +V+ L + ++T + PH+LF GPPG GK  T
Sbjct: 7  KPWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKCLT 56

Length = 846

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

 Score = 67.8 bits (166), Expect = 5e-13
 Identities = 43/191 (22%), Positives = 80/191 (41%), Gaps = 27/191 (14%)

Query: 67  EEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQLFGPELYKSRV--LELNASD 123
           E +   + N++      H  +  G  G GK+  A  IA ++ G    +  V  +E    +
Sbjct: 10  ENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPIN 69

Query: 124 DRGINV--VRTKIKTFAAVAVGSGQRRGGYPCPPY----KIIILDEADSMTEDAQNALRR 177
            + I V  +R  I+                   PY    K+II+  ++ MTE AQNA  +
Sbjct: 70  KKSIGVDDIRNIIEEVNK--------------KPYEGDKKVIIIYNSEKMTEQAQNAFLK 115

Query: 178 TMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAE 237
           T+E   K      +C  + +I++ + SRC  ++   LS+E +   +    + +  ++  E
Sbjct: 116 TIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEIEKFI----SYKYNDIKEE 171

Query: 238 ALSTLSSISQG 248
              +  + S G
Sbjct: 172 EKKSAIAFSDG 182

Length = 313

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

 Score = 67.2 bits (165), Expect = 7e-13
 Identities = 59/224 (26%), Positives = 92/224 (41%), Gaps = 35/224 (15%)

Query: 66  QEEVVRVLTNTLET---ANCPHMLFYGPPGTGKTTTALAIAHQLF----GPELYKSRVLE 118
           Q   + +LT  ++    A  P  LF GP G G+   AL     L       +  + R+ E
Sbjct: 9   QPLAIELLTAAIKQNRIA--PAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEE 66

Query: 119 LNASDDRGIN---VVRTKIKTFAAVAVGSGQRRGGYPC---------------PPY---- 156
            N  D   +      + K+ T A+ A  +G +R   P                PP     
Sbjct: 67  GNHPDLLWVEPTYQHQGKLIT-ASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPR 125

Query: 157 KIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSE 216
           K++++++A++M E A NAL +T+E     T    I      ++  + SRC    F  LS+
Sbjct: 126 KVVVIEDAETMNEAAANALLKTLEEPGNGT-LILIAPSPESLLPTIVSRCQIIPFYRLSD 184

Query: 217 EVMSSRVLHIC-NEEGLNLDAEALSTLSSISQGDLRRAITYLQG 259
           E +   VL    +EE LN++   L  L+  S G     I  LQ 
Sbjct: 185 EQLEQ-VLKRLGDEEILNINFPELLALAQGSPGAAIANIEQLQS 227

Length = 314

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

 Score = 67.4 bits (165), Expect = 1e-12
 Identities = 52/222 (23%), Positives = 84/222 (37%), Gaps = 26/222 (11%)

Query: 57  PKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLF---GPELY 112
           P +   +   EE    L          H +LF GP G GK T A  +A+ +     P   
Sbjct: 19  PSENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEA 78

Query: 113 KSRVL--ELNASDDRGI------NV------VRTKIKTFAAVAVGSGQRRGGY------P 152
              +   +  +   R I      N+         K   F         RR G+       
Sbjct: 79  PETLADPDPASPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSG 138

Query: 153 CPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFK 212
              ++I+I+D AD M  +A NA+ +T+E       F  I +   R++  + SRC     K
Sbjct: 139 DGNWRIVIIDPADDMNRNAANAILKTLEEPPARALFILISHSSGRLLPTIRSRCQPISLK 198

Query: 213 PLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAI 254
           PL ++ +   + H+        D E    L   S+G +R+A+
Sbjct: 199 PLDDDELKKALSHL--GSSQGSDGEITEALLQRSKGSVRKAL 238

Length = 351

>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau; Provisional

 Score = 67.0 bits (163), Expect = 2e-12
 Identities = 57/241 (23%), Positives = 103/241 (42%), Gaps = 29/241 (12%)

Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQ 105
           S Q    KYRP+   +VA Q+  +  L + LET    H  LF G  G GKTT    +A  
Sbjct: 2   SYQALARKYRPQSFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKC 61

Query: 106 LFGPELYKSR------------------VLELNASDDRGINVVRTKIKTFAAVAVGSGQR 147
           L       +                   ++E++A+   G+   +   +    +     Q 
Sbjct: 62  LNCKTGVTAEPCNKCENCVAINNNSFIDLIEIDAASRTGVEETK---EILDNIQYMPSQG 118

Query: 148 RGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA 207
           R       YK+ ++DE   +++ + NAL +T+E   +  +F        +I   + SRC 
Sbjct: 119 R-------YKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIPVTILSRCI 171

Query: 208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS 267
           +   K +S+  +  ++  I  +E +N D ++L  ++  ++G LR A++ L  A    G  
Sbjct: 172 QLHLKHISQADIKDQLKIILAKENINSDEQSLEYIAYHAKGSLRDALSLLDQAISFCGGE 231

Query: 268 I 268
           +
Sbjct: 232 L 232

Length = 546

>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau; Validated

 Score = 66.1 bits (162), Expect = 4e-12
 Identities = 63/214 (29%), Positives = 101/214 (47%), Gaps = 40/214 (18%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPH--MLFYGPPGTGKTTTALAIAHQL----- 106
           KYRP+   D+  QE +VR LTN  ET       ML  G  G GKTTTA  +A  L     
Sbjct: 17  KYRPQTFDDLIGQEAMVRTLTNAFETGRIAQAFML-TGVRGVGKTTTARILARALNYEGP 75

Query: 107 ---FGPEL------------YKSR---VLELNASDDRGINVVRTKIKT--FAAVAVGSGQ 146
               GP +             + R   VLE++A+   G++ +R  I++  +  V      
Sbjct: 76  DGDGGPTIDLCGVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPV-----S 130

Query: 147 RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRC 206
            R       YK+ I+DE   ++  A NAL +T+E      +F F    I ++   + SRC
Sbjct: 131 AR-------YKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKVPVTVLSRC 183

Query: 207 AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALS 240
            +F  + +  +V+++ +  I  +EG+ ++ EAL+
Sbjct: 184 QRFDLRRIEADVLAAHLSRIAAKEGVEVEDEALA 217

Length = 598

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

 Score = 65.2 bits (159), Expect = 8e-12
 Identities = 64/244 (26%), Positives = 105/244 (43%), Gaps = 36/244 (14%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAH----QLFG 108
           KYRP   + V  QE +   L N + T    H  LF GP G GKTT A   A     Q   
Sbjct: 10  KYRPSTFESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLT 69

Query: 109 PE------------LYKSR---VLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPC 153
            +              + R   + EL+A+ +  ++ +R  I+          Q R   P 
Sbjct: 70  ADGEACNECESCVAFNEQRSYNIHELDAASNNSVDDIRNLIE----------QVR--IP- 116

Query: 154 PP---YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFR 210
           P    YKI I+DE   +++ A NA  +T+E       F        +I+  + SRC  F 
Sbjct: 117 PQIGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFD 176

Query: 211 FKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITS 270
           F  +    + + + ++ ++EG+  + EAL+ ++  + G +R A++         G +IT 
Sbjct: 177 FNRIQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGNITY 236

Query: 271 KDLI 274
           K +I
Sbjct: 237 KSVI 240

Length = 614

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

 Score = 65.3 bits (159), Expect = 8e-12
 Identities = 58/204 (28%), Positives = 89/204 (43%), Gaps = 33/204 (16%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQL------ 106
           KYRP    +V  QE V   L++ L+     H  LF GP G GKT++A  +A  L      
Sbjct: 6   KYRPATFAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGP 65

Query: 107 -------------FGPELYKS-RVLELNASDDRGINVVRT-KIKTFAAVAVGSGQRRGGY 151
                          P    S  V+EL+A+   G++  R  + + F A A    Q R   
Sbjct: 66  TATPCGVCESCVALAPNGPGSIDVVELDAASHGGVDDTRELRDRAFYAPA----QSR--- 118

Query: 152 PCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRF 211
               Y+I I+DEA  +T    NAL + +E   +   F F      +++  + SR   + F
Sbjct: 119 ----YRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRSRTHHYPF 174

Query: 212 KPLSEEVMSSRVLHICNEEGLNLD 235
           + L    M + +  IC +EG+ +D
Sbjct: 175 RLLPPRTMRALIARICEQEGVVVD 198

Length = 584

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 64.2 bits (157), Expect = 2e-11
 Identities = 66/231 (28%), Positives = 110/231 (47%), Gaps = 35/231 (15%)

Query: 46  QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETAN-CPHMLFYGPPGTGKTTTALAIAH 104
            + +P   KYRP++  ++  QE +   L N L +    P  LF GP GTGKT++A  +A 
Sbjct: 1   MAYEPLHHKYRPQRFDELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAK 60

Query: 105 QLF-----GP--------ELYKS-------RVLELNASDDRGINVVRTKIK--TFAAVAV 142
            L       P        EL ++        V+E++A+ + G++ +R  I+   FA V  
Sbjct: 61  SLNCLNSDKPTPEPCGKCELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAPV-- 118

Query: 143 GSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPL 202
              Q R       +K+ ++DE   ++  A NAL +T+E       F        R++  +
Sbjct: 119 ---QAR-------WKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTI 168

Query: 203 ASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRA 253
            SRC +F F+ +  E M   +  I  +E + ++ EAL+ ++  SQG LR A
Sbjct: 169 ISRCQRFDFRRIPLEAMVQHLSEIAEKESIEIEPEALTLVAQRSQGGLRDA 219

Length = 620

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 60.9 bits (148), Expect = 2e-10
 Identities = 63/237 (26%), Positives = 109/237 (45%), Gaps = 35/237 (14%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQL--FGP- 109
           KYRP+   ++  QE VV+ LTN L      H  LF G  G GKTT +  +A  L   GP 
Sbjct: 9   KYRPRSFSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPD 68

Query: 110 -----------------ELYKSRVL---ELNASDDRGINVVRTKIKTFAAVAVGSGQRRG 149
                            ++   R +   EL+A+ +RG++ V+  ++   AV      R  
Sbjct: 69  GQGGITATPCGVCQACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQ--AVYKPVQGR-- 124

Query: 150 GYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKF 209
                 +K+ ++DE   +T  A NA+ +T+E   +  +F        ++   + SRC +F
Sbjct: 125 ------FKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPVTVLSRCLQF 178

Query: 210 RFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGS 266
             +P++ E +   +  +   E +  + +AL  L+  ++G +R A++ L   A  FGS
Sbjct: 179 NLRPMAPETVLEHLTQVLAAENVPAEPQALRLLARAARGSMRDALS-LTDQAIAFGS 234

Length = 618

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

 Score = 60.5 bits (147), Expect = 3e-10
 Identities = 57/234 (24%), Positives = 98/234 (41%), Gaps = 42/234 (17%)

Query: 45  LQSSQPWVEKYRPKQVKDVAHQEEVV---RVLTNTLETANCPHMLFYGPPGTGKTTTALA 101
            QS  P  ++ RP+ +++   Q+ ++   R+L   ++      ++ YGPPG GKTT A  
Sbjct: 12  SQSEAPLADRLRPRTLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARI 71

Query: 102 IAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIIL 161
           IA+        ++    LNA    G+  +R ++         + +R   +      I+ +
Sbjct: 72  IANH------TRAHFSSLNAV-LAGVKDLRAEVDR-------AKERLERH--GKRTILFI 115

Query: 162 DEADSMTEDAQNAL-----RRTMETYSKVTR--FFFICNYISRIIEPLASRCAKFRFKPL 214
           DE     +  Q+AL       T+      T   +F        + + L SR   FR K L
Sbjct: 116 DEVHRFNKAQQDALLPWVENGTITLIGATTENPYF-------EVNKALVSRSRLFRLKSL 168

Query: 215 SEEVMSS---RVLHICNEEG-----LNLDAEALSTLSSISQGDLRRAITYLQGA 260
           S+E +     R L    E G     ++L+ EA   L  ++ GD R  +  L+ A
Sbjct: 169 SDEDLHQLLKRALQDK-ERGYGDRKVDLEPEAEKHLVDVANGDARSLLNALELA 221

Length = 725

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

 Score = 59.3 bits (144), Expect = 5e-10
 Identities = 50/243 (20%), Positives = 89/243 (36%), Gaps = 50/243 (20%)

Query: 56  RPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIA-----HQLFGP 109
            P++   +         L +   +    H  L  GP G GK T A  +A         G 
Sbjct: 14  HPRETTALFGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGG 73

Query: 110 ELYKSRV--LELNASD-----------------DRGIN----VVRTKI--------KTFA 138
           +        L ++                    +R  N     +RT I         +F 
Sbjct: 74  DGAVPPPTSLAIDPDHPVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFF 133

Query: 139 AVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRI 198
            +    G  R         ++I+D AD M  +A NAL + +E     + F  + +  +R+
Sbjct: 134 GLTAAEGGWR---------VVIVDTADEMNANAANALLKVLEEPPARSLFLLVSHAPARL 184

Query: 199 IEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQ 258
           +  + SRC K R +PL+ E +    L      G +L  +  + L+++++G + RA+    
Sbjct: 185 LPTIRSRCRKLRLRPLAPEDVID-ALA---AAGPDLPDDPRAALAALAEGSVGRALRLAG 240

Query: 259 GAA 261
           G  
Sbjct: 241 GDG 243

Length = 365

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

 Score = 59.5 bits (144), Expect = 6e-10
 Identities = 60/221 (27%), Positives = 100/221 (45%), Gaps = 29/221 (13%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQL------ 106
           K+RPK    +  QE VVR LT+ L+     H  LF G  G GKTT +   A  L      
Sbjct: 9   KWRPKDFASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGV 68

Query: 107 -FGP--------ELYKSRVL---ELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCP 154
              P        E+ + R +   E++A+ +RG++ +   ++   AV      R       
Sbjct: 69  TSQPCGVCRACREIDEGRFVDYVEMDAASNRGVDEMAALLER--AVYAPVDAR------- 119

Query: 155 PYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPL 214
            +K+ ++DE   +T  A NA+ +T+E      +F        +I   + SRC +F  K +
Sbjct: 120 -FKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVLSRCLQFNLKQM 178

Query: 215 SEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAIT 255
               + S +  I  EE +  + +AL  L+  +QG +R A++
Sbjct: 179 PAGHIVSHLERILGEERIAFEPQALRLLARAAQGSMRDALS 219

Length = 830

>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau; Provisional

 Score = 58.6 bits (141), Expect = 1e-09
 Identities = 57/231 (24%), Positives = 98/231 (42%), Gaps = 31/231 (13%)

Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQ 105
           + Q    K+RP+  ++V  Q  VVR L+N L+     H  LF G  G GKTT +  +A  
Sbjct: 2   AHQVLARKWRPRCFQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKC 61

Query: 106 L-------FGP--------ELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGG 150
           L         P        E+ + R  +L   D       RTK++        + +    
Sbjct: 62  LNCEKGVSANPCNDCENCREIDEGRFPDLFEVD----AASRTKVED-------TRELLDN 110

Query: 151 YPCPP----YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRC 206
            P  P    +K+ ++DE   ++  + NAL +T+E      +F        ++   + SRC
Sbjct: 111 IPYAPTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRC 170

Query: 207 AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYL 257
            +F    L    +++   H+  EE +  +  AL  L+  + G +R A++ L
Sbjct: 171 LQFHLAQLPPLQIAAHCQHLLKEENVEFENAALDLLARAANGSVRDALSLL 221

Length = 509

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

 Score = 58.6 bits (142), Expect = 1e-09
 Identities = 73/294 (24%), Positives = 117/294 (39%), Gaps = 63/294 (21%)

Query: 20  TQKFSTTQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLET 79
           T K +  + S  K E E   KM  + + ++P  EK RPK   ++  QEE ++ L   L  
Sbjct: 27  TNKITIDKES--KKELEKLNKMRAI-RLTEPLSEKTRPKSFDEIIGQEEGIKALKAALCG 83

Query: 80  ANCPHMLFYGPPGTGKTTTA-----LAIAHQLFGPELYKSRVLELNAS----DDRGI--- 127
            N  H++ YGPPG GKT  A      A  +    P    +  +E++A+    D+RGI   
Sbjct: 84  PNPQHVIIYGPPGVGKTAAARLVLEEAKKNP-ASPFKEGAAFVEIDATTARFDERGIADP 142

Query: 128 --NVVRTKIKTFAAVAVGSGQRRGGYPCPPY--------KIIILDEADSMTEDAQNALRR 177
               V   I   A   +G      G P P           ++ +DE   +     N L +
Sbjct: 143 LIGSVHDPIYQGAG-PLGI----AGIPQPKPGAVTRAHGGVLFIDEIGELHPVQMNKLLK 197

Query: 178 TMETYSKV---TRFFF-----ICNYISRIIE----------------------PLASRCA 207
            +E   KV   + ++      I ++I  I +                       L SRC 
Sbjct: 198 VLED-RKVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRNPEEIPPALRSRCV 256

Query: 208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA 261
           +  F+PL +E +     +   + G+NL+  AL  +   +    R A+  +Q AA
Sbjct: 257 EIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYASNG-REAVNIVQLAA 309

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis [Protein fate, Degradation of proteins, peptides, and glycopeptides, Cellular processes, Sporulation and germination]. Length = 531

>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24

 Score = 55.3 bits (133), Expect = 1e-08
 Identities = 52/255 (20%), Positives = 92/255 (36%), Gaps = 46/255 (18%)

Query: 49  QPWVEKYRPKQVKDVA-HQEEVVRV----LTNTLETANCPHMLFYGPPGTGKTTTALAIA 103
           +PWVEKY+P+   ++A H++++  V        LE A    +L  GP G GK+TT   ++
Sbjct: 72  EPWVEKYKPETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILS 131

Query: 104 HQL-------FGPELYKSRVLELNASDDRGINVVR--TKIKTFAAV---AVGSGQRRGGY 151
            +L         P L   +  +   +           ++I+ F+     A    Q  G  
Sbjct: 132 KELGIQVQEWSNPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDD 191

Query: 152 PCPPYKIIILDEADSMTEDAQNALRRTMET-YSKVTRFFFICNYISRIIEPLAS------ 204
                KII++++  +       AL   +   Y  + R   +   I+  +E   +      
Sbjct: 192 LMTDKKIILVEDLPNQFYRDTRALHEILRWKYVSIGRCPLVF-IITESLEGDNNQRRLLF 250

Query: 205 --------------RCAKFRFKPLSEEVMSSRVLHICNEEGLNL-------DAEALSTLS 243
                         R +   F P++  +M   +  I   E              ++  L 
Sbjct: 251 PAETIMNKEILEEPRVSNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVELLC 310

Query: 244 SISQGDLRRAITYLQ 258
               GD+R AI  LQ
Sbjct: 311 QGCSGDIRSAINSLQ 325

All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 637

>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein

 Score = 55.0 bits (132), Expect = 2e-08
 Identities = 55/252 (21%), Positives = 93/252 (36%), Gaps = 44/252 (17%)

Query: 49  QPWVEKYRPKQVKDVA-HQEEVVRV----LTNTLETANCPHMLFYGPPGTGKTTTALAIA 103
           + W EKY+P++  ++A H++++  V        LE+     +L  GP G GK+TT   ++
Sbjct: 7   ELWTEKYKPRRRDELAIHKKKIAEVDHWLKAVFLESNKQLILLLTGPSGCGKSTTVKVLS 66

Query: 104 HQL-------FGPELYKSRVLELNASDDRGINVVR-----TKIKTFAAVAVGSGQRRGGY 151
            +L         PE   +   E    D RG  +V       + + F       G  +GG 
Sbjct: 67  KELGIEIIEWSNPEYLHNPDNECQKPDFRGDCIVNSLSQMEQFREFLLRGARYGSLQGGG 126

Query: 152 PCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFI------CNYISRIIEP---- 201
                K+I+++E  +         R  +    +      +      CN +          
Sbjct: 127 --LKKKLILVEELPNQFYSDAEKFREVIREVLQSIWHLPLIFCLTECNSLEGDNNQDRFG 184

Query: 202 ------------LASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQ-- 247
                       +  R     F P++   M   ++ I  +EG     ++ S L  I Q  
Sbjct: 185 IDAETIMTKDILIMPRIDTITFNPIAPTFMKKALVRISVQEGKLKSPKSDSKLEVICQEA 244

Query: 248 -GDLRRAITYLQ 258
            GDLR AI  LQ
Sbjct: 245 GGDLRSAINSLQ 256

Length = 490

>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

 Score = 52.6 bits (127), Expect = 7e-08
 Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 17/83 (20%)

Query: 29  SPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETA----NCP- 83
           SPEK E+E+K + +             RPK + +   QE+V   L   ++ A        
Sbjct: 6   SPEKQEEEMKIERSL------------RPKTLDEFIGQEKVKEQLQIFIKAAKKRGEALD 53

Query: 84  HMLFYGPPGTGKTTTALAIAHQL 106
           H+L +GPPG GKTT A  IA++L
Sbjct: 54  HVLLFGPPGLGKTTLAHIIANEL 76

Length = 332

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

 Score = 49.6 bits (119), Expect = 9e-08
 Identities = 25/120 (20%), Positives = 41/120 (34%), Gaps = 22/120 (18%)

Query: 84  HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVG 143
             +  G  G+GKTT    +A Q     L   RV+ + A        +  KI      A+G
Sbjct: 6   IGVLTGESGSGKTTLLRRLARQ-----LPNRRVVYVEAPSLGTPKDLLRKI----LRALG 56

Query: 144 SGQRRGGYP------------CPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFI 191
                G                    ++I+DEA  ++ +A   LR   +   K  +   +
Sbjct: 57  LPLSGGTTAELLEAILDALKRR-GRPLLIIDEAQHLSLEALEELRDLYDLSEKGIQVILV 115

Length = 124

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

 Score = 51.8 bits (125), Expect = 1e-07
 Identities = 57/197 (28%), Positives = 85/197 (43%), Gaps = 37/197 (18%)

Query: 66  QEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYKS---------- 114
           Q  VV++L N++      H  LF G  GTGK  TAL +A  LF  E              
Sbjct: 11  QPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCK 70

Query: 115 RVLELN-------ASDDRGINV--VRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEAD 165
           R+   N       A D + I    +R   + F+   V S +          K+ I++ AD
Sbjct: 71  RIDSGNHPDVHLVAPDGQSIKKDQIRYLKEEFSKSGVESNK----------KVYIIEHAD 120

Query: 166 SMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLH 225
            MT  A N+L + +E  S  T    +     +I+  + SRC    F+PL  E +  R+  
Sbjct: 121 KMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQ- 179

Query: 226 ICNEEGLNLDAEALSTL 242
              EEG+   +E+L+TL
Sbjct: 180 ---EEGI---SESLATL 190

Length = 329

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

 Score = 51.7 bits (124), Expect = 2e-07
 Identities = 46/221 (20%), Positives = 74/221 (33%), Gaps = 47/221 (21%)

Query: 82  CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRT--KIKTFAA 139
              +L YGPPGTGKT  A A+A +       +SR + +  S+     V  +   I+    
Sbjct: 276 PKGVLLYGPPGTGKTLLAKAVALES------RSRFISVKGSELLSKWVGESEKNIRELFE 329

Query: 140 VAVGSGQRRGGYPCPPYKIIILDEADSM-----------TEDAQNALRRTMETYSKVTRF 188
            A      R   P     II +DE DS+                  L   ++   K    
Sbjct: 330 KA------RKLAPS----IIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGV 379

Query: 189 FFIC--NYISRIIEPLASRCAKFRFK---PLSEEVMSSRVLHICNEEGL-----NLDAEA 238
             I   N     ++P   R  +F      PL +      +  I   +       ++D E 
Sbjct: 380 LVIAATNRP-DDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEE 438

Query: 239 LSTLSSISQG-----DLRRAITYLQGAARLFGSSITSKDLI 274
           L+ ++    G      +R A   L+         +T  D +
Sbjct: 439 LAEITEGYSGADIAALVREAA--LEALREARRREVTLDDFL 477

Length = 494

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

 Score = 50.2 bits (120), Expect = 4e-07
 Identities = 26/103 (25%), Positives = 49/103 (47%), Gaps = 12/103 (11%)

Query: 156 YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLS 215
           Y++ +++ AD+M E A NAL +T+E  +    F  + +   R++  + SRC ++   P S
Sbjct: 109 YRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWVVTPPS 168

Query: 216 EEVMSSRVLHICNEEGLNLDAEAL--------STLSSISQGDL 250
                  +      +G+ + A AL         TL+ + +G L
Sbjct: 169 TAQAMQWL----KGQGITVPAYALKLNMGSPLKTLAMMKEGGL 207

Length = 319

>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus

 Score = 48.6 bits (117), Expect = 7e-07
 Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 5/56 (8%)

Query: 56  RPKQVKDVAHQEEVVRVLTNTLETA---NCP--HMLFYGPPGTGKTTTALAIAHQL 106
           RP+++ +   QE+V   L   +E A        H+L YGPPG GKTT A  IA+++
Sbjct: 19  RPRRLDEYIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEM 74

The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein. Length = 231

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

 Score = 48.6 bits (117), Expect = 1e-06
 Identities = 23/56 (41%), Positives = 31/56 (55%), Gaps = 5/56 (8%)

Query: 56  RPKQVKDVAHQEEVVRVLTNTLETAN-----CPHMLFYGPPGTGKTTTALAIAHQL 106
           RPK + +   QE+V   L   +E A        H+L YGPPG GKTT A  IA+++
Sbjct: 20  RPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEM 75

Length = 328

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

 Score = 48.1 bits (115), Expect = 2e-06
 Identities = 50/236 (21%), Positives = 84/236 (35%), Gaps = 41/236 (17%)

Query: 61  KDVAHQEEVVRVLTNTLETA---NCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYKSRV 116
           +++ H+EE +  L + L  A     P  ++ YGP GTGKT T   +  +L         V
Sbjct: 17  EELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEES-SANVEV 75

Query: 117 LELNASDDRGINVVRTKIKTFAAVA--VGSGQRRGGYPCPPYK-------------IIIL 161
           + +N         +RT  +  + +   +G     G       K             I+IL
Sbjct: 76  VYINC------LELRTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVIL 129

Query: 162 DEADSMTEDAQNALR---RTMETYSKVTRFFFICN---YISRIIEPLASRCAKFR--FKP 213
           DE D++ +     L    R             + N   ++  +   + S        F P
Sbjct: 130 DEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPRVKSSLGPSEIVFPP 189

Query: 214 LSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQ------GDLRRAITYLQGAARL 263
            + E +   +L    EEG +        L  I+       GD R+AI  L+ A  +
Sbjct: 190 YTAEELYD-ILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEI 244

Length = 366

>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA

 Score = 45.6 bits (108), Expect = 2e-05
 Identities = 30/87 (34%), Positives = 42/87 (48%), Gaps = 12/87 (13%)

Query: 84  HMLFYGPPGTGKTTTALAIAHQLFGPE-LYKSRVLELNASDDRGINVVRTKIKTFAAVAV 142
           HMLF GPPGTGKTT A  +A    G   L K  V E++ +D  G  +  ++ KT   +  
Sbjct: 314 HMLFAGPPGTGKTTIARVVAKIYCGLGVLRKPLVREVSRADLIGQYIGESEAKTNEIIDS 373

Query: 143 GSGQRRGGYPCPPYKIIILDEADSMTE 169
             G            ++ LDEA ++ E
Sbjct: 374 ALG-----------GVLFLDEAYTLVE 389

This model represents the AAA family ATPase, EccA, of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccA1, EccA2, etc [Protein fate, Protein and peptide secretion and trafficking]. Length = 557

>gnl|CDD|221912 pfam13086, AAA_11, AAA domain

 Score = 43.9 bits (104), Expect = 3e-05
 Identities = 35/186 (18%), Positives = 58/186 (31%), Gaps = 44/186 (23%)

Query: 86  LFYGPPGTGKTTTALAIAHQLFGPELYKSRVL-------------ELNASDDRGINVVRT 132
           L  GPPGTGKTTT + I  QL        +VL             E       G+ +VR 
Sbjct: 21  LIQGPPGTGKTTTIVEIIKQLLSN-APGKKVLVCAPSNSAVDNILERLLEQKFGLKIVR- 78

Query: 133 KIKTFAAVAVGSGQRRGGYPCPPYKI--IILDEADSMTEDAQNALRRTMETYSKVTRFFF 190
                    +GS  R        Y +  ++  + + + +  +       E          
Sbjct: 79  ---------IGSPAREIHEDVLQYSLEYLLEAKFEQLLKRIRKLKSLLEEKSKLKRERRK 129

Query: 191 ICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDL 250
           + + I ++ + L       R     E +  + V  +C            +TLS      L
Sbjct: 130 LRSEIKKLKKELERL----RKSIRKEILDEADV--VC------------TTLSGAGSSLL 171

Query: 251 RRAITY 256
                +
Sbjct: 172 EGLKKF 177

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. Length = 220

>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit

 Score = 43.1 bits (102), Expect = 8e-05
 Identities = 14/23 (60%), Positives = 18/23 (78%)

Query: 84  HMLFYGPPGTGKTTTALAIAHQL 106
           H+L YGPPG GKTT A  IA+++
Sbjct: 32  HLLLYGPPGLGKTTLAHIIANEM 54

All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 305

>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family

 Score = 43.3 bits (102), Expect = 1e-04
 Identities = 16/44 (36%), Positives = 25/44 (56%)

Query: 56  RPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTA 99
           RP+   ++  QE  ++ L   + +    H++ YGPPG GKTT A
Sbjct: 149 RPRAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAA 192

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 [Protein fate, Degradation of proteins, peptides, and glycopeptides, Cellular processes, Sporulation and germination]. Length = 615

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

 Score = 42.8 bits (101), Expect = 1e-04
 Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 1/89 (1%)

Query: 156 YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLS 215
            K+++++ A++M  +A NAL +++E  S  T    I +  SR++  + SRC +    PL 
Sbjct: 107 RKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQAC-PLP 165

Query: 216 EEVMSSRVLHICNEEGLNLDAEALSTLSS 244
               S + L     E    +   L TL+ 
Sbjct: 166 SNEESLQWLQQALPESDERERIELLTLAG 194

Length = 328

>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075)

 Score = 42.2 bits (100), Expect = 2e-04
 Identities = 26/127 (20%), Positives = 43/127 (33%), Gaps = 25/127 (19%)

Query: 83  PHMLF-YGPPGTGKTTTALAIAHQLFGPELYKSRVLEL-NASDDRGINVVRTKIK----- 135
             +    G PGTGKT  AL +  +L   +L ++ V    N      + V+   +      
Sbjct: 1   KAVFLVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHPL---VLVLYEALAGDLKV 57

Query: 136 TFAAVAVGSGQRRGGY--PCPPYKIIILDEA----------DSMTEDAQNALRRTMETYS 183
               +               P   ++I+DEA           + +   Q  L   M+  +
Sbjct: 58  RKKKLFRKPTSFINNLHKAPPHEDVVIVDEAHRLWTKSDLYFNFSGPNQ--LDEIMKR-A 114

Query: 184 KVTRFFF 190
           KV  FF 
Sbjct: 115 KVVVFFI 121

This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function. Length = 348

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

 Score = 42.1 bits (99), Expect = 2e-04
 Identities = 41/171 (23%), Positives = 62/171 (36%), Gaps = 49/171 (28%)

Query: 83  PH-MLFYGPPGTGKTTTALAIAHQL--------------------FG----PELYKSR-- 115
           PH +L +G  G GK   A  +A  L                    F     P+    R  
Sbjct: 21  PHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRPE 80

Query: 116 VLELNAS----------DDRGINVVRT-----KIKTFAAV--AVGSGQRRGGYPCPPYKI 158
            L   A            D G    +      KI+   A+    G G  RGG      ++
Sbjct: 81  ALAAEAPGAADEAKEADADEGGKKTKAPSKEIKIEQVRALLDFCGVGTHRGGA-----RV 135

Query: 159 IILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKF 209
           ++L  A+++   A NAL +T+E     T F  +   I R++  + SRC +F
Sbjct: 136 VVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQF 186

Length = 342

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

 Score = 42.2 bits (99), Expect = 2e-04
 Identities = 35/162 (21%), Positives = 56/162 (34%), Gaps = 41/162 (25%)

Query: 86  LFYGPPGTGKTTTALAIAHQL--------------------FG----PELYKSRVLELNA 121
           LF G  G GKT  A   A  L                    FG    P+ Y   +  L+ 
Sbjct: 25  LFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFY--EITPLSD 82

Query: 122 SDDRGINVVRTKIKT------FAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNAL 175
             + G  +++ KI           +    G  R         +I++  A+SM   A N+L
Sbjct: 83  EPENGRKLLQIKIDAVREIIDNVYLTSVRGGLR---------VILIHPAESMNLQAANSL 133

Query: 176 RRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEE 217
            + +E       F  + +   +++  + SRC K      S E
Sbjct: 134 LKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHE 175

Length = 325

>gnl|CDD|181190 PRK07993, PRK07993, DNA polymerase III subunit delta'; Validated

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 19/50 (38%), Positives = 30/50 (60%)

Query: 157 KIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRC 206
           K++ L +A  +T+ A NAL +T+E   + T FF  C   +R++  L SRC
Sbjct: 110 KVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRC 159

Length = 334

>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family

 Score = 41.9 bits (99), Expect = 3e-04
 Identities = 15/25 (60%), Positives = 17/25 (68%)

Query: 86  LFYGPPGTGKTTTALAIAHQLFGPE 110
           L  GP G GKT TALA+A  L+G E
Sbjct: 600 LLVGPSGVGKTETALALAELLYGGE 624

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 [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis]. Length = 852

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

 Score = 41.0 bits (97), Expect = 5e-04
 Identities = 14/20 (70%), Positives = 16/20 (80%)

Query: 86  LFYGPPGTGKTTTALAIAHQ 105
           L YGPPGTGKT  A A+AH+
Sbjct: 169 LLYGPPGTGKTLLAKAVAHE 188

Length = 389

>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily)

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 24/93 (25%), Positives = 37/93 (39%), Gaps = 8/93 (8%)

Query: 84  HMLFYGPPGTGKTTTALAIAHQLFG-PELYKSRVLELNASDDRGINVVRTKIKTFAAVAV 142
            +L  GPPGTGK+  A  +A  L   P  Y     +    D +G   +     ++    +
Sbjct: 1   GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPL 60

Query: 143 GSGQRRGGYPCPPYKIIILDEADSMTEDAQNAL 175
               R G       +I +LDE +    D  N+L
Sbjct: 61  VRAAREG-------EIAVLDEINRANPDVLNSL 86

This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 135

>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction only]

 Score = 40.5 bits (95), Expect = 6e-04
 Identities = 30/103 (29%), Positives = 42/103 (40%), Gaps = 16/103 (15%)

Query: 84  HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVL---ELNASDDRGINVVRTKIKTFAAV 140
           H+L  GPPG GKT  A A+A +  G      R+    +L  SD  G       +      
Sbjct: 45  HVLLEGPPGVGKTLLARALA-RALGLPF--VRIQCTPDLLPSDLLGTYAYAALLL----- 96

Query: 141 AVGSGQRR---GGYPCPPYKIIILDEADSMTEDAQNALRRTME 180
               G+ R   G        I++LDE +    + QNAL   +E
Sbjct: 97  --EPGEFRFVPGPLFAAVRVILLLDEINRAPPEVQNALLEALE 137

Length = 329

>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated

 Score = 40.3 bits (95), Expect = 7e-04
 Identities = 39/147 (26%), Positives = 59/147 (40%), Gaps = 38/147 (25%)

Query: 62  DVAHQEEVVRVLTN------TLETANCPHM----LFYGPPGTGKTTTALAIAHQLFGPEL 111
           D+  QE VV  L            A    M    LF GPPG+G++  A A A  L   + 
Sbjct: 6   DLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDP 65

Query: 112 YK---------SRVLELNASDDR---------GINVVRTKIKTFAAVAVGSGQRRGGYPC 153
            +           VL     D R         G++ VR  +   AA    +G        
Sbjct: 66  DEPGCGECRACRTVLAGTHPDVRVVAPEGLSIGVDEVRELVTI-AARRPSTG-------- 116

Query: 154 PPYKIIILDEADSMTEDAQNALRRTME 180
             ++I+++++AD +TE A NAL + +E
Sbjct: 117 -RWRIVVIEDADRLTERAANALLKAVE 142

Length = 394

>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 23/134 (17%), Positives = 35/134 (26%), Gaps = 32/134 (23%)

Query: 89  GPPGTGKTTTALAIAHQLFGPELYK-------SRVL------ELNASDDRGINVV----- 130
            P G+GKT  AL    +L              +R L       L      GI V      
Sbjct: 7   APTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGG 66

Query: 131 ------RTKIKTFAAVAVGS------GQRRGGYPCPPYKIIILDEADSMTE--DAQNALR 176
                    +     + VG+         R         ++ILDEA  +         L+
Sbjct: 67  TSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLK 126

Query: 177 RTMETYSKVTRFFF 190
             ++          
Sbjct: 127 ILLKLPKDRQVLLL 140

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Length = 144

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

 Score = 39.6 bits (93), Expect = 0.001
 Identities = 17/33 (51%), Positives = 20/33 (60%), Gaps = 7/33 (21%)

Query: 86  LFYGPPGTGKTTTALAIAHQ-------LFGPEL 111
           L YGPPGTGKT  A A+A+Q       + G EL
Sbjct: 189 LLYGPPGTGKTLLAKAVANQTDATFIRVVGSEL 221

Length = 406

>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K

 Score = 38.9 bits (91), Expect = 0.001
 Identities = 30/109 (27%), Positives = 47/109 (43%), Gaps = 20/109 (18%)

Query: 84  HMLFYGPPGTGKTTTALAIAHQLFGPE-LYKSRVLELNASDDRGINVVRTKIKTFAAVAV 142
           HM+F G PGTGKTT A  +         L K  ++E+  +D  G  +  T  KT   +  
Sbjct: 44  HMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERADLVGEYIGHTAQKTREVIK- 102

Query: 143 GSGQRRGGYPCPPYKIIILDEADSMT--------EDAQNALRRTMETYS 183
              +  GG       ++ +DEA S+         ++A + L + ME   
Sbjct: 103 ---KALGG-------VLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNR 141

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 [Cellular processes, Sporulation and germination]. Length = 261

>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain

 Score = 37.9 bits (88), Expect = 0.002
 Identities = 19/122 (15%), Positives = 34/122 (27%), Gaps = 9/122 (7%)

Query: 67  EEVVRVLTNTLETAN---CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD 123
           EE +  L + L  A     P +L  GP GTGKT+    +   L        +  +   + 
Sbjct: 6   EEELERLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAG---KCDQAERNP 62

Query: 124 DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS 183
                     ++      +                 +  E     +D    L R +    
Sbjct: 63  PYAF---SQALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLARAR 119

Query: 184 KV 185
            +
Sbjct: 120 PL 121

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Length = 154

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

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 17/57 (29%), Positives = 28/57 (49%)

Query: 156 YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFK 212
            KI+I+   +  +    NAL +T+E   K T F      I++++  + SRC  F  K
Sbjct: 91  KKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVK 147

Length = 299

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

 Score = 37.5 bits (88), Expect = 0.002
 Identities = 32/134 (23%), Positives = 45/134 (33%), Gaps = 21/134 (15%)

Query: 86  LFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSG 145
           +  GP   GKTT  L      F  EL    +L +N  D R            A + +   
Sbjct: 6   VITGPRQVGKTTLLL-----QFLKELLSENILYINLDDPR--------FLRLALLDLLEE 52

Query: 146 QRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFF----ICNYISRIIEP 201
             +   P   Y  + LDE      D ++AL+R  +    + R              I   
Sbjct: 53  FLKLLLPGKKY--LFLDEI-QKVPDWEDALKRLYDDGRNL-RIILTGSSSLLLSKEIATS 108

Query: 202 LASRCAKFRFKPLS 215
           LA R  +    PLS
Sbjct: 109 LAGRAEELELYPLS 122

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

>gnl|CDD|177083 CHL00181, cbbX, CbbX; Provisional

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 15/24 (62%), Positives = 17/24 (70%)

Query: 84  HMLFYGPPGTGKTTTALAIAHQLF 107
           HM F G PGTGKTT AL +A  L+
Sbjct: 61  HMSFTGSPGTGKTTVALKMADILY 84

Length = 287

>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau; Provisional

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 31/111 (27%), Positives = 61/111 (54%), Gaps = 1/111 (0%)

Query: 156 YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLS 215
           +K+ ++DE   ++  + NAL +T+E   +  +F        ++   + SRC +F  K L+
Sbjct: 120 FKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPVTVLSRCLQFNLKSLT 179

Query: 216 EEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGS 266
           ++ + +++ HI  +E L  +AEAL+ L+  + G +R A++ L   A  FG 
Sbjct: 180 QDEIGTQLNHILTQEQLPFEAEALTLLAKAANGSMRDALS-LTDQAIAFGG 229

Length = 944

>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed

 Score = 38.7 bits (91), Expect = 0.002
 Identities = 54/222 (24%), Positives = 82/222 (36%), Gaps = 67/222 (30%)

Query: 86  LFYGPPGTGKTTTALAIAHQLFGPEL----YKSRVLELNASDDRGINVVRTKIKTFAAVA 141
           L YGPPGTGKTTT      +    EL     K   + +N        + RT+   F+ +A
Sbjct: 59  LIYGPPGTGKTTTV-----KKVFEELEEIAVKVVYVYIN------CQIDRTRYAIFSEIA 107

Query: 142 VGSGQRRGGYPCPP---------------------YKIIILDEADSMTEDAQN----ALR 176
               ++  G+P P                        I+ LD+ + + E   N    +L 
Sbjct: 108 ----RQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLL 163

Query: 177 RTMETYSKV-TRFFFICNYISRIIEPLASRCAK-FR-----FKPLSEE----VMSSRVLH 225
           R  E Y         I + ++  +  L  R    FR     F P + +    ++  RV  
Sbjct: 164 RAHEEYPGARIGVIGISSDLT-FLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRV-- 220

Query: 226 ICNEEGLN---LDAEALSTLSSI---SQGDLRRAITYLQGAA 261
              EEG     +D E L  ++ +     GD R AI  L+ A 
Sbjct: 221 ---EEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAG 259

Length = 394

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 39.1 bits (92), Expect = 0.002
 Identities = 20/47 (42%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 54 KYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTA 99
          K+RP+   +V  QE V+  L N L+     H  LF G  G GKTT A
Sbjct: 9  KWRPQTFAEVVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIA 55

Length = 647

>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI

 Score = 37.9 bits (89), Expect = 0.003
 Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 2/39 (5%)

Query: 61 KDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTA 99
           DV  QE+  R L   +  A   ++L  GPPG+GKT  A
Sbjct: 3  ADVKGQEQAKRALE--IAAAGGHNLLMIGPPGSGKTMLA 39

Magnesium-chelatase is a three-component enzyme that catalyzes the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa. Length = 207

>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily)

 Score = 36.8 bits (86), Expect = 0.004
 Identities = 30/92 (32%), Positives = 39/92 (42%), Gaps = 5/92 (5%)

Query: 86  LFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVV-RTKIKTFAAVAVG- 143
           LF GP G GKT  A A+A  LFG E    R+   + S+    + V R        V    
Sbjct: 7   LFLGPTGVGKTELAKALAELLFGDERALIRI---DMSEYMEEHSVSRLIGAPPGYVGYEE 63

Query: 144 SGQRRGGYPCPPYKIIILDEADSMTEDAQNAL 175
            GQ        PY I+++DE +      QN L
Sbjct: 64  GGQLTEAVRRKPYSIVLIDEIEKAHPGVQNDL 95

This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 168

>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein

 Score = 37.9 bits (88), Expect = 0.004
 Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 7/89 (7%)

Query: 36  EVKRKMAPVL-QSSQPWVEKYRPKQ--VKDVAHQEEVVRVLTNTLETANCPHMLFYGPPG 92
           E   K+ P      +  + K       +KD+  Q+   R L   +  A   ++L +GPPG
Sbjct: 164 EGSEKLPPRTNTKPKSIINKSYIIDLDLKDIKGQQHAKRALE--IAAAGGHNLLLFGPPG 221

Query: 93  TGKTTTALAIAHQLFGPELYKSRVLELNA 121
           +GKT  A  +   L  P L     +E   
Sbjct: 222 SGKTMLASRLQGIL--PPLTNEEAIETAR 248

The N-terminal end matches very strongly a pfam Mg_chelatase domain [Unknown function, General]. Length = 499

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

 Score = 37.6 bits (87), Expect = 0.004
 Identities = 40/151 (26%), Positives = 69/151 (45%), Gaps = 15/151 (9%)

Query: 85  MLFYGPPGTGKTTTALAIAHQLFGP---ELYKSRVLELNAS----DDRGINVV--RT--K 133
           +L  GP G GK   ALA+A  +           R  +L A+    D + ++ +  RT  K
Sbjct: 29  LLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGDK 88

Query: 134 IKTFAAVAVGSGQRRGGYPCPPY---KIIILDEADSMTEDAQNALRRTMETYSKVTRFFF 190
           ++T   +       +     P Y   +++I+D AD++   A NAL +T+E  S     + 
Sbjct: 89  LRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWL 148

Query: 191 ICNYISRIIEPLASRCAKFRFK-PLSEEVMS 220
           I    +R+   + SRC +  FK P + E ++
Sbjct: 149 ISAQPARLPATIRSRCQRLEFKLPPAHEALA 179

Length = 319

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	294
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	100.0
PLN03025	319	replication factor C subunit; Provisional	100.0
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	100.0
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	100.0
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	100.0
COG2256	436	MGS1 ATPase related to the helicase subunit of the	100.0
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	100.0
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	100.0
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.98
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.98
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.97
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.97
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.97
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.97
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.97
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.97
PRK12402	337	replication factor C small subunit 2; Reviewed	99.97
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.97
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.97
PRK04195	482	replication factor C large subunit; Provisional	99.97
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.97
PRK13342	413	recombination factor protein RarA; Reviewed	99.96
PHA02544	316	44 clamp loader, small subunit; Provisional	99.96
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	99.95
KOG2028	554	consensus ATPase related to the helicase subunit o	99.95
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.95
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	99.95
PRK13341	725	recombination factor protein RarA/unknown domain f	99.95
KOG1969	877	consensus DNA replication checkpoint protein CHL12	99.94
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.94
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.94
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.94
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.93
PRK04132	846	replication factor C small subunit; Provisional	99.92
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.92
PRK08084	235	DNA replication initiation factor; Provisional	99.91
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.91
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.9
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.9
PRK06893	229	DNA replication initiation factor; Validated	99.9
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.9
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.9
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	99.89
PRK08727	233	hypothetical protein; Validated	99.89
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.89
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.89
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.89
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	99.88
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.88
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.87
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.87
PRK06620	214	hypothetical protein; Validated	99.87
PRK05642	234	DNA replication initiation factor; Validated	99.87
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.86
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.86
PRK07993	334	DNA polymerase III subunit delta'; Validated	99.86
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	99.86
PRK05707	328	DNA polymerase III subunit delta'; Validated	99.86
CHL00195	489	ycf46 Ycf46; Provisional	99.86
CHL00181	287	cbbX CbbX; Provisional	99.86
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.85
PRK06871	325	DNA polymerase III subunit delta'; Validated	99.85
PRK09087	226	hypothetical protein; Validated	99.85
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.85
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.85
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.85
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.85
PRK08769	319	DNA polymerase III subunit delta'; Validated	99.85
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	99.84
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.84
PRK06090	319	DNA polymerase III subunit delta'; Validated	99.84
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.83
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.83
CHL00176	638	ftsH cell division protein; Validated	99.83
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.82
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.82
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.82
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	99.82
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.82
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	99.81
PRK12422	445	chromosomal replication initiation protein; Provis	99.81
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	99.81
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.81
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.81
PRK06526	254	transposase; Provisional	99.81
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.81
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.81
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.8
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.8
PRK06964	342	DNA polymerase III subunit delta'; Validated	99.8
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.79
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.78
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	99.78
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.78
COG0593	408	DnaA ATPase involved in DNA replication initiation	99.77
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.77
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	99.77
PRK08181	269	transposase; Validated	99.77
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.77
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.77
PRK05917	290	DNA polymerase III subunit delta'; Validated	99.77
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.75
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.75
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.75
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	99.75
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	99.74
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	99.74
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.74
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.74
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.73
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.73
PRK10865	857	protein disaggregation chaperone; Provisional	99.73
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	99.72
PRK07276	290	DNA polymerase III subunit delta'; Validated	99.72
CHL00206	2281	ycf2 Ycf2; Provisional	99.72
PRK07132	299	DNA polymerase III subunit delta'; Validated	99.72
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.71
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	99.71
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	99.71
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.71
CHL00095	821	clpC Clp protease ATP binding subunit	99.71
PRK08699	325	DNA polymerase III subunit delta'; Validated	99.7
PRK09183	259	transposase/IS protein; Provisional	99.7
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.7
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.7
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.7
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.69
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	99.69
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	99.69
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.69
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	99.68
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.68
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.67
COG2204	464	AtoC Response regulator containing CheY-like recei	99.67
COG1221	403	PspF Transcriptional regulators containing an AAA-	99.67
PF00004	132	AAA: ATPase family associated with various cellula	99.66
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.66
PRK11608	326	pspF phage shock protein operon transcriptional ac	99.66
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.66
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	99.65
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.65
PRK13531	498	regulatory ATPase RavA; Provisional	99.65
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.65
PRK05818	261	DNA polymerase III subunit delta'; Validated	99.64
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.64
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	99.64
PRK15424	538	propionate catabolism operon regulatory protein Pr	99.64
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.64
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	99.64
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	99.64
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.63
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	99.62
CHL00095	821	clpC Clp protease ATP binding subunit	99.62
PRK05022	509	anaerobic nitric oxide reductase transcription reg	99.62
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	99.61
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	99.61
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.6
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	99.6
PRK10865	857	protein disaggregation chaperone; Provisional	99.59
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	99.59
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	99.59
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	99.58
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.58
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.57
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.57
KOG2680	454	consensus DNA helicase TIP49, TBP-interacting prot	99.57
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.57
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	99.57
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.56
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.55
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.55
COG0714	329	MoxR-like ATPases [General function prediction onl	99.55
smart00350	509	MCM minichromosome maintenance proteins.	99.54
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	99.53
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.53
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.53
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.52
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.52
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	99.52
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	99.51
PHA02244	383	ATPase-like protein	99.51
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.5
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	99.49
COG1484	254	DnaC DNA replication protein [DNA replication, rec	99.49
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.48
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	99.47
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	99.47
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	99.46
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	99.46
PRK15115	444	response regulator GlrR; Provisional	99.46
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.45
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	99.44
PRK06581	263	DNA polymerase III subunit delta'; Validated	99.43
PRK13765	637	ATP-dependent protease Lon; Provisional	99.42
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	99.42
KOG1514	767	consensus Origin recognition complex, subunit 1, a	99.4
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	99.39
PRK12377	248	putative replication protein; Provisional	99.39
PF07726	131	AAA_3: ATPase family associated with various cellu	99.39
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	99.39
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	99.38
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.37
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	99.36
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	99.35
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	99.35
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	99.33
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.32
PRK10365	441	transcriptional regulatory protein ZraR; Provision	99.31
PRK08116	268	hypothetical protein; Validated	99.3
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	99.29
PRK09862	506	putative ATP-dependent protease; Provisional	99.29
PRK07952	244	DNA replication protein DnaC; Validated	99.27
PRK08485	206	DNA polymerase III subunit delta'; Validated	99.27
PF13173	128	AAA_14: AAA domain	99.26
KOG0482	721	consensus DNA replication licensing factor, MCM7 c	99.26
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	99.25
PRK08939	306	primosomal protein DnaI; Reviewed	99.25
COG0606	490	Predicted ATPase with chaperone activity [Posttran	99.24
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	99.24
PRK06835	329	DNA replication protein DnaC; Validated	99.21
COG1241	682	MCM2 Predicted ATPase involved in replication cont	99.19
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	99.19
KOG0480	764	consensus DNA replication licensing factor, MCM6 c	99.19
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	99.18
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	99.17
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	99.16
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	99.15
PRK06921	266	hypothetical protein; Provisional	99.15
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	99.14
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	99.13
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	99.11
smart00382	148	AAA ATPases associated with a variety of cellular	99.1
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	99.1
PF05729	166	NACHT: NACHT domain	99.1
TIGR01128	302	holA DNA polymerase III, delta subunit. subunit ar	99.1
PRK05629	318	hypothetical protein; Validated	99.09
PRK07452	326	DNA polymerase III subunit delta; Validated	99.08
PRK14700	300	recombination factor protein RarA; Provisional	99.02
PRK04841	903	transcriptional regulator MalT; Provisional	99.01
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.0
PRK06585	343	holA DNA polymerase III subunit delta; Reviewed	99.0
PRK07914	320	hypothetical protein; Reviewed	98.98
PRK05574	340	holA DNA polymerase III subunit delta; Reviewed	98.96
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	98.96
KOG0477	854	consensus DNA replication licensing factor, MCM2 c	98.93
PLN03210	1153	Resistant to P. syringae 6; Provisional	98.93
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.91
PRK05907	311	hypothetical protein; Provisional	98.88
PRK08487	328	DNA polymerase III subunit delta; Validated	98.85
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	98.84
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.8
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	98.79
PHA00729	226	NTP-binding motif containing protein	98.77
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	98.74
PF14516	331	AAA_35: AAA-like domain	98.73
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	98.73
KOG0481	729	consensus DNA replication licensing factor, MCM5 c	98.73
PRK10536	262	hypothetical protein; Provisional	98.72
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	98.71
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	98.68
COG4650	531	RtcR Sigma54-dependent transcription regulator con	98.68
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	98.67
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.64
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	98.61
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	98.6
PF06144	172	DNA_pol3_delta: DNA polymerase III, delta subunit;	98.57
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.55
PHA02774	613	E1; Provisional	98.54
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	98.53
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	98.53
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	98.5
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	98.48
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	98.46
PRK10875	615	recD exonuclease V subunit alpha; Provisional	98.44
PHA02624	647	large T antigen; Provisional	98.4
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	98.39
PRK04296	190	thymidine kinase; Provisional	98.38
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	98.38
KOG0479	818	consensus DNA replication licensing factor, MCM3 c	98.37
COG1466	334	HolA DNA polymerase III, delta subunit [DNA replic	98.37
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	98.32
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	98.32
PRK13695	174	putative NTPase; Provisional	98.32
PRK04132	846	replication factor C small subunit; Provisional	98.31
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	98.28
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	98.28
COG3899	849	Predicted ATPase [General function prediction only	98.27
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	98.25
PTZ00202	550	tuzin; Provisional	98.25
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	98.24
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	98.22
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	98.21
) 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	98.19
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	98.18
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	98.17
PRK15455	644	PrkA family serine protein kinase; Provisional	98.17
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	98.16
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	98.15
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	98.15
PRK14532	188	adenylate kinase; Provisional	98.15
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.14
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.13
PRK08118	167	topology modulation protein; Reviewed	98.13
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	98.11
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	98.1
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	98.1
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	98.09
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	98.09
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.08
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.08
PRK14974	336	cell division protein FtsY; Provisional	98.07
cd01128	249	rho_factor Transcription termination factor rho is	98.07
PRK07261	171	topology modulation protein; Provisional	98.06
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	98.05
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	98.05
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	98.04
PRK13889	988	conjugal transfer relaxase TraA; Provisional	98.02
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	98.02
PRK13826	1102	Dtr system oriT relaxase; Provisional	98.0
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.98
PRK14528	186	adenylate kinase; Provisional	97.98
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	97.97
COG2884	223	FtsE Predicted ATPase involved in cell division [C	97.96
PF13245	76	AAA_19: Part of AAA domain	97.94
TIGR00767	415	rho transcription termination factor Rho. Members	97.92
cd03216	163	ABC_Carb_Monos_I This family represents the domain	97.92
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	97.91
PF08303	168	tRNA_lig_kinase: tRNA ligase kinase domain; InterP	97.91
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.91
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	97.89
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	97.88
PRK09376	416	rho transcription termination factor Rho; Provisio	97.88
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	97.87
PRK00625	173	shikimate kinase; Provisional	97.86
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.86
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	97.85
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	97.85
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	97.85
PF13337	457	Lon_2: Putative ATP-dependent Lon protease	97.85
PRK00131	175	aroK shikimate kinase; Reviewed	97.84
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	97.84
PRK06547	172	hypothetical protein; Provisional	97.83
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	97.83
PF00519	432	PPV_E1_C: Papillomavirus helicase; InterPro: IPR00	97.83
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	97.83
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	97.83
PRK03839	180	putative kinase; Provisional	97.83
COG4178	604	ABC-type uncharacterized transport system, permeas	97.83
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	97.83
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.82
PRK13947	171	shikimate kinase; Provisional	97.82
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	97.81
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	97.81
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	97.81
PRK13808	333	adenylate kinase; Provisional	97.8
PRK06762	166	hypothetical protein; Provisional	97.8
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	97.8
PRK02496	184	adk adenylate kinase; Provisional	97.79
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	97.79
smart00487	201	DEXDc DEAD-like helicases superfamily.	97.78
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	97.78
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	97.77
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	97.76
cd03246	173	ABCC_Protease_Secretion This family represents the	97.76
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.76
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	97.75
PLN02674	244	adenylate kinase	97.75
PRK13949	169	shikimate kinase; Provisional	97.75
PHA02530	300	pseT polynucleotide kinase; Provisional	97.75
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	97.75
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	97.75
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	97.75
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	97.74
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	97.73
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	97.73
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	97.73
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	97.73
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	97.72
PRK14530	215	adenylate kinase; Provisional	97.7
COG1485	367	Predicted ATPase [General function prediction only	97.7
cd03215	182	ABC_Carb_Monos_II This family represents domain II	97.7
PRK06217	183	hypothetical protein; Validated	97.69
PRK00279	215	adk adenylate kinase; Reviewed	97.69
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.69
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	97.69
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	97.68
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	97.67
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	97.66
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	97.65
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	97.65
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	97.65
KOG1808	1856	consensus AAA ATPase containing von Willebrand fac	97.65
COG1119	257	ModF ABC-type molybdenum transport system, ATPase	97.63
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	97.63
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	97.63
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.62
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.62
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	97.62
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	97.62
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	97.61
PRK13948	182	shikimate kinase; Provisional	97.61
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	97.61
PRK06696	223	uridine kinase; Validated	97.61
TIGR01613	304	primase_Cterm phage/plasmid primase, P4 family, C-	97.61
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.6
cd03115	173	SRP The signal recognition particle (SRP) mediates	97.6
PRK14531	183	adenylate kinase; Provisional	97.6
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	97.59
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	97.59
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	97.59
PRK13851	344	type IV secretion system protein VirB11; Provision	97.59
PRK12608	380	transcription termination factor Rho; Provisional	97.58
PRK05057	172	aroK shikimate kinase I; Reviewed	97.58
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	97.56
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	97.55
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	97.55
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.55
PTZ00088	229	adenylate kinase 1; Provisional	97.55
TIGR00174	287	miaA tRNA isopentenyltransferase (miaA). Catalyzes	97.54
KOG3928	461	consensus Mitochondrial ribosome small subunit com	97.54
TIGR00064	272	ftsY signal recognition particle-docking protein F	97.54
PRK05973	237	replicative DNA helicase; Provisional	97.54
PRK13946	184	shikimate kinase; Provisional	97.53
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	97.53
PF13479	213	AAA_24: AAA domain	97.52
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	97.52
PRK06067	234	flagellar accessory protein FlaH; Validated	97.51
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	97.51
PRK11823	446	DNA repair protein RadA; Provisional	97.49
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.49
PRK03731	171	aroL shikimate kinase II; Reviewed	97.48
KOG3354	191	consensus Gluconate kinase [Carbohydrate transport	97.48
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	97.47
PRK10867	433	signal recognition particle protein; Provisional	97.46
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	97.45
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	97.44
cd03239	178	ABC_SMC_head The structural maintenance of chromos	97.44
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.44
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	97.43
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	97.42
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	97.42
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	97.42
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	97.42
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	97.41
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	97.41
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	97.4
PRK14529	223	adenylate kinase; Provisional	97.4
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	97.4
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	97.4
PRK08233	182	hypothetical protein; Provisional	97.4
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	97.39
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	97.39
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	97.39
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	97.38
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.38
PRK14527	191	adenylate kinase; Provisional	97.37
PLN02200	234	adenylate kinase family protein	97.37
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	97.37
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.37
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	97.37
PTZ00293	211	thymidine kinase; Provisional	97.37
PRK05541	176	adenylylsulfate kinase; Provisional	97.36
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	97.36
TIGR02533	486	type_II_gspE general secretory pathway protein E.	97.36
COG4619	223	ABC-type uncharacterized transport system, ATPase	97.36
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	97.36
KOG2383	467	consensus Predicted ATPase [General function predi	97.36
PRK04040	188	adenylate kinase; Provisional	97.35
cd03240	204	ABC_Rad50 The catalytic domains of Rad50 are simil	97.35
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	97.35
COG1067	647	LonB Predicted ATP-dependent protease [Posttransla	97.34
PRK13833	323	conjugal transfer protein TrbB; Provisional	97.34
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	97.34
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	97.33
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	97.33
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	97.32
TIGR00376	637	DNA helicase, putative. The gene product may repre	97.32

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

Probab=100.00  E-value=4.8e-40  Score=261.53  Aligned_cols=229  Identities=57%  Similarity=0.910  Sum_probs=207.7

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcch
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGI  127 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~  127 (294)
                      .+.|+++|+|+.++++.|++.++..|...+.....|+++|+||||||||+.|.+++++++|++...+.+.+.++++.++.
T Consensus        23 ~~swteKYrPkt~de~~gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGi  102 (346)
T KOG0989|consen   23 HRSWTEKYRPKTFDELAGQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGI  102 (346)
T ss_pred             ccchHHHhCCCcHHhhcchHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccc
Confidence            34599999999999999999999999999999888999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhcccc
Q 022641          128 NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      ...+..+..+........ .........+.++||||+|.|+.++++.|++.|+.++...++|++||....+.+.+.+||.
T Consensus       103 svvr~Kik~fakl~~~~~-~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~  181 (346)
T KOG0989|consen  103 SVVREKIKNFAKLTVLLK-RSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQ  181 (346)
T ss_pred             cchhhhhcCHHHHhhccc-cccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHH
Confidence            999988888877655443 3334455667899999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhcc
Q 022641          208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG  278 (294)
Q Consensus       208 ~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~  278 (294)
                      .+.|+++..+.+...|+.++.++|+.++++++..|++.++||+|.|+++||.++. .++.||...+.+.++
T Consensus       182 KfrFk~L~d~~iv~rL~~Ia~~E~v~~d~~al~~I~~~S~GdLR~Ait~Lqsls~-~gk~It~~~~~e~~~  251 (346)
T KOG0989|consen  182 KFRFKKLKDEDIVDRLEKIASKEGVDIDDDALKLIAKISDGDLRRAITTLQSLSL-LGKRITTSLVNEELA  251 (346)
T ss_pred             HhcCCCcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHhhc-cCcccchHHHHHHHh
Confidence            9999999999999999999999999999999999999999999999999999998 477788544444444

>PLN03025 replication factor C subunit; Provisional

Probab=100.00  E-value=2.3e-35  Score=249.92  Aligned_cols=226  Identities=46%  Similarity=0.719  Sum_probs=196.0

Q ss_pred             chhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchh
Q 022641           49 QPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGIN  128 (294)
Q Consensus        49 ~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~  128 (294)
                      .||.++|+|..+++++|+++++..|..++..+..++++|+||||||||++|++++++++|+.+ ...++++++++..+.+
T Consensus         1 ~~w~~kyrP~~l~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~~~~-~~~~~eln~sd~~~~~   79 (319)
T PLN03025          1 LPWVEKYRPTKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGPNY-KEAVLELNASDDRGID   79 (319)
T ss_pred             CChhhhcCCCCHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhcccC-ccceeeecccccccHH
Confidence            489999999999999999999999999999988899999999999999999999999977542 3457788888888888


Q ss_pred             HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccE
Q 022641          129 VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAK  208 (294)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~  208 (294)
                      .++..+..+.......       ..++..+++|||+|.++...++.|++.++.++....+|++||....+.+++.+||..
T Consensus        80 ~vr~~i~~~~~~~~~~-------~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~  152 (319)
T PLN03025         80 VVRNKIKMFAQKKVTL-------PPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAI  152 (319)
T ss_pred             HHHHHHHHHHhccccC-------CCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhc
Confidence            7777766654332111       113467999999999999999999999998888888999999999999999999999


Q ss_pred             EEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhcccccCC
Q 022641          209 FRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       209 i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~~~~~  283 (294)
                      +.|.+++.+++..++.++++++|+.+++++++.+++.++||+|.+++.||.+.. ....||.+++.++++...++
T Consensus       153 i~f~~l~~~~l~~~L~~i~~~egi~i~~~~l~~i~~~~~gDlR~aln~Lq~~~~-~~~~i~~~~v~~~~~~~~~~  226 (319)
T PLN03025        153 VRFSRLSDQEILGRLMKVVEAEKVPYVPEGLEAIIFTADGDMRQALNNLQATHS-GFGFVNQENVFKVCDQPHPL  226 (319)
T ss_pred             ccCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHh-cCCCCCHHHHHHHcCCCCHH
Confidence            999999999999999999999999999999999999999999999999995543 24579999999887765544

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=3e-35  Score=253.84  Aligned_cols=228  Identities=29%  Similarity=0.464  Sum_probs=197.1

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc-------------
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL-------------  111 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~-------------  111 (294)
                      ....||.++|+|..|++++|+++++..|..++..++.++ ++|+||+|||||++|+.+++.+.|...             
T Consensus         3 ~~~~~L~~KyRP~~f~dvVGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C~sC~   82 (484)
T PRK14956          3 GTHEVLSRKYRPQFFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTSCL   82 (484)
T ss_pred             CCcchhHHHhCCCCHHHHhChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCCcHHH
Confidence            346799999999999999999999999999999998776 899999999999999999999987531             


Q ss_pred             -----cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcc
Q 022641          112 -----YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVT  186 (294)
Q Consensus       112 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~  186 (294)
                           ....++++++....+.+.++.....+.....          .+++.|+||||+|+++...++.|++.+++++.++
T Consensus        83 ~i~~g~~~dviEIdaas~~gVd~IReL~e~l~~~p~----------~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~v  152 (484)
T PRK14956         83 EITKGISSDVLEIDAASNRGIENIRELRDNVKFAPM----------GGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHI  152 (484)
T ss_pred             HHHccCCccceeechhhcccHHHHHHHHHHHHhhhh----------cCCCEEEEEechhhcCHHHHHHHHHHhhcCCCce
Confidence                 1224666776666667777766555443221          1345799999999999999999999999999999


Q ss_pred             eEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCC
Q 022641          187 RFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGS  266 (294)
Q Consensus       187 ~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~  266 (294)
                      .+|++|+.+..+.+++++||+.+.|.+++.+++..++++++..+|+.++++++..|++.++|++|.++++|+.+..+.+.
T Consensus       153 iFILaTte~~kI~~TI~SRCq~~~f~~ls~~~i~~~L~~i~~~Egi~~e~eAL~~Ia~~S~Gd~RdAL~lLeq~i~~~~~  232 (484)
T PRK14956        153 VFILATTEFHKIPETILSRCQDFIFKKVPLSVLQDYSEKLCKIENVQYDQEGLFWIAKKGDGSVRDMLSFMEQAIVFTDS  232 (484)
T ss_pred             EEEeecCChhhccHHHHhhhheeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCChHHHHHHHHHHHHHhCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999987766666


Q ss_pred             CCChhhhhhhcccccCC
Q 022641          267 SITSKDLISVSGYPTGG  283 (294)
Q Consensus       267 ~it~~~v~~~~~~~~~~  283 (294)
                      .||.+.|.++++....+
T Consensus       233 ~it~~~V~~~lg~~~~~  249 (484)
T PRK14956        233 KLTGVKIRKMIGYHGIE  249 (484)
T ss_pred             CcCHHHHHHHhCCCCHH
Confidence            79999999988765433

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

Probab=100.00  E-value=2.3e-35  Score=226.09  Aligned_cols=229  Identities=45%  Similarity=0.711  Sum_probs=207.9

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      ....||+++|+|..+.+++|+++.+..|.-....+.-||++|.|||||||||.+.++|+++.++. +...+.++|+++.+
T Consensus        12 ~~~l~wVeKYrP~~l~dIVGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~-~ke~vLELNASdeR   90 (333)
T KOG0991|consen   12 KYQLPWVEKYRPSVLQDIVGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDS-YKEAVLELNASDER   90 (333)
T ss_pred             cccchHHHhhCchHHHHhhCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChh-hhhHhhhccCcccc
Confidence            45678999999999999999999999999999999999999999999999999999999996543 34578899999999


Q ss_pred             chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhcc
Q 022641          126 GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASR  205 (294)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r  205 (294)
                      +.+.++..++.+......       .+.++..+||+||+|.+...+++.|.+.|+-+....+++++||....+..++.+|
T Consensus        91 GIDvVRn~IK~FAQ~kv~-------lp~grhKIiILDEADSMT~gAQQAlRRtMEiyS~ttRFalaCN~s~KIiEPIQSR  163 (333)
T KOG0991|consen   91 GIDVVRNKIKMFAQKKVT-------LPPGRHKIIILDEADSMTAGAQQALRRTMEIYSNTTRFALACNQSEKIIEPIQSR  163 (333)
T ss_pred             ccHHHHHHHHHHHHhhcc-------CCCCceeEEEeeccchhhhHHHHHHHHHHHHHcccchhhhhhcchhhhhhhHHhh
Confidence            999999999998876544       3345677999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhcccccCC
Q 022641          206 CAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       206 ~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~~~~~  283 (294)
                      |.++.|..+++.++...+..+++.+++.++++.++.+.--+.||.|+++|.||..... -.-++.+.|.++++.+.+.
T Consensus       164 CAiLRysklsd~qiL~Rl~~v~k~Ekv~yt~dgLeaiifta~GDMRQalNnLQst~~g-~g~Vn~enVfKv~d~PhP~  240 (333)
T KOG0991|consen  164 CAILRYSKLSDQQILKRLLEVAKAEKVNYTDDGLEAIIFTAQGDMRQALNNLQSTVNG-FGLVNQENVFKVCDEPHPL  240 (333)
T ss_pred             hHhhhhcccCHHHHHHHHHHHHHHhCCCCCcchHHHhhhhccchHHHHHHHHHHHhcc-ccccchhhhhhccCCCChH
Confidence            9999999999999999999999999999999999999999999999999999966543 3458888998888887664

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=1.5e-34  Score=258.28  Aligned_cols=226  Identities=26%  Similarity=0.381  Sum_probs=198.1

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--------------  112 (294)
                      ++.|.+||+|.+|++++||+++++.|.+++..++.++ +||+||+|||||++++.+++.++|....              
T Consensus         3 Y~vLarKYRPqtFdEVIGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~sCr~I   82 (830)
T PRK07003          3 YQVLARKWRPKDFASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREI   82 (830)
T ss_pred             cHhHHHHhCCCcHHHHcCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHHHHHH
Confidence            5689999999999999999999999999999988777 5999999999999999999999875321              


Q ss_pred             ----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          113 ----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       113 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                          ...+++++..+..+.+.++..+........          .+++.|+||||+|+|+...++.|++.|++.+.++.|
T Consensus        83 ~~G~h~DviEIDAas~rgVDdIReLIe~a~~~P~----------~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~F  152 (830)
T PRK07003         83 DEGRFVDYVEMDAASNRGVDEMAALLERAVYAPV----------DARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKF  152 (830)
T ss_pred             hcCCCceEEEecccccccHHHHHHHHHHHHhccc----------cCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEE
Confidence                124677777777777777777765443221          234679999999999999999999999999999999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++||+...+.+.+++||..+.|.+++.+++..+|++++..+++.++++.+..|++.++|++|.++++++.+..+....|
T Consensus       153 ILaTtd~~KIp~TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI~id~eAL~lIA~~A~GsmRdALsLLdQAia~~~~~I  232 (830)
T PRK07003        153 ILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERILGEERIAFEPQALRLLARAAQGSMRDALSLTDQAIAYSANEV  232 (830)
T ss_pred             EEEECChhhccchhhhheEEEecCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999988887777789


Q ss_pred             ChhhhhhhcccccCC
Q 022641          269 TSKDLISVSGYPTGG  283 (294)
Q Consensus       269 t~~~v~~~~~~~~~~  283 (294)
                      +.+.|..+++.....
T Consensus       233 t~~~V~~~LG~~d~~  247 (830)
T PRK07003        233 TETAVSGMLGALDQT  247 (830)
T ss_pred             CHHHHHHHhCCCCHH
Confidence            999999888776443

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=3.3e-34  Score=253.89  Aligned_cols=228  Identities=23%  Similarity=0.346  Sum_probs=201.2

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc-------------
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY-------------  112 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~-------------  112 (294)
                      ..++|.++|+|..|++++|++.++..|..++..++.++ ++|+||+|||||++|+++++.+.|....             
T Consensus         2 ~y~~l~~kyRP~~f~divGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~   81 (509)
T PRK14958          2 AHQVLARKWRPRCFQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCRE   81 (509)
T ss_pred             CchhHHHHHCCCCHHHhcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHH
Confidence            35689999999999999999999999999999998888 7999999999999999999999875422             


Q ss_pred             -----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcce
Q 022641          113 -----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTR  187 (294)
Q Consensus       113 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~  187 (294)
                           ...++++++.+..+.+.++..+......+.          .+++.|+||||+|+++...++.|++.+++++.++.
T Consensus        82 i~~g~~~d~~eidaas~~~v~~iR~l~~~~~~~p~----------~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~  151 (509)
T PRK14958         82 IDEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPT----------KGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVK  151 (509)
T ss_pred             HhcCCCceEEEEcccccCCHHHHHHHHHHHhhccc----------cCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeE
Confidence                 224677787777788888877665443321          23567999999999999999999999999999999


Q ss_pred             EEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCC
Q 022641          188 FFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS  267 (294)
Q Consensus       188 ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~  267 (294)
                      +|++|+++..+++.+.+||..+.|.+++.+++..++.++++.+|+.++++++..+++.++|++|.+++.++.++.+.++.
T Consensus       152 fIlattd~~kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi~~~~~al~~ia~~s~GslR~al~lLdq~ia~~~~~  231 (509)
T PRK14958        152 FILATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEENVEFENAALDLLARAANGSVRDALSLLDQSIAYGNGK  231 (509)
T ss_pred             EEEEECChHhchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhcCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999888776678


Q ss_pred             CChhhhhhhcccccCCC
Q 022641          268 ITSKDLISVSGYPTGGS  284 (294)
Q Consensus       268 it~~~v~~~~~~~~~~~  284 (294)
                      ||.++|..+++...++.
T Consensus       232 It~~~V~~~lg~~~~~~  248 (509)
T PRK14958        232 VLIADVKTMLGTIEPLL  248 (509)
T ss_pred             cCHHHHHHHHCCCCHHH
Confidence            99999999998876553

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=5e-34  Score=251.93  Aligned_cols=224  Identities=26%  Similarity=0.395  Sum_probs=197.7

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc---------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL---------------  111 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~---------------  111 (294)
                      +++|.+||+|..|++++|++++++.|.+++..++.+| +||+||+|+|||++|+.+++.++|...               
T Consensus         3 y~vLarKYRPqtFddVIGQe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~   82 (700)
T PRK12323          3 YQVLARKWRPRDFTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCR   82 (700)
T ss_pred             chhHHHHhCCCcHHHHcCcHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccH
Confidence            5689999999999999999999999999999999888 699999999999999999999988321               


Q ss_pred             --------cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc
Q 022641          112 --------YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS  183 (294)
Q Consensus       112 --------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~  183 (294)
                              ....+++++..+..+++.+++.+........          .+++.|+||||+|+|+...+|.|++.||+.+
T Consensus        83 sC~~I~aG~hpDviEIdAas~~gVDdIReLie~~~~~P~----------~gr~KViIIDEah~Ls~~AaNALLKTLEEPP  152 (700)
T PRK12323         83 ACTEIDAGRFVDYIEMDAASNRGVDEMAQLLDKAVYAPT----------AGRFKVYMIDEVHMLTNHAFNAMLKTLEEPP  152 (700)
T ss_pred             HHHHHHcCCCCcceEecccccCCHHHHHHHHHHHHhchh----------cCCceEEEEEChHhcCHHHHHHHHHhhccCC
Confidence                    1125667777777778888877766544321          2346799999999999999999999999999


Q ss_pred             CcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHH
Q 022641          184 KVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARL  263 (294)
Q Consensus       184 ~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~  263 (294)
                      .++.||++|+.+..+++.+++||..+.|.+++.+++..++.+++..+++.++++++..|++.++|++|.++++++.+..+
T Consensus       153 ~~v~FILaTtep~kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~Egi~~d~eAL~~IA~~A~Gs~RdALsLLdQaia~  232 (700)
T PRK12323        153 EHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALRLLAQAAQGSMRDALSLTDQAIAY  232 (700)
T ss_pred             CCceEEEEeCChHhhhhHHHHHHHhcccCCCChHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999887777


Q ss_pred             hCCCCChhhhhhhccccc
Q 022641          264 FGSSITSKDLISVSGYPT  281 (294)
Q Consensus       264 ~~~~it~~~v~~~~~~~~  281 (294)
                      ....||.+.|..+++...
T Consensus       233 ~~~~It~~~V~~~LG~~d  250 (700)
T PRK12323        233 SAGNVSEEAVRGMLGAID  250 (700)
T ss_pred             ccCCcCHHHHHHHhCCCC
Confidence            667799998888887765

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.2e-33  Score=250.10  Aligned_cols=226  Identities=24%  Similarity=0.373  Sum_probs=197.1

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc---------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL---------------  111 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~---------------  111 (294)
                      ..++.++|+|..|++++|++.+++.|..++..++.++ ++|+||+|+|||++|+++|+.+.|...               
T Consensus         2 Y~~LarKyRPktFddVIGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I   81 (702)
T PRK14960          2 YQVLARKYRPRNFNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAV   81 (702)
T ss_pred             chhHHHHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHH
Confidence            4689999999999999999999999999999988766 699999999999999999999977431               


Q ss_pred             ---cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          112 ---YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       112 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                         ....++.+++.+..+.+.++..+......+.          .+++.++||||+|+|+....+.|++.+++.+..+.+
T Consensus        82 ~~g~hpDviEIDAAs~~~VddIReli~~~~y~P~----------~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~F  151 (702)
T PRK14960         82 NEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPT----------QGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKF  151 (702)
T ss_pred             hcCCCCceEEecccccCCHHHHHHHHHHHhhhhh----------cCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEE
Confidence               2235667777766677777777665443321          134679999999999999999999999999999999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++|+.+..++..+++||..+.|.+++.+++..++.+++..+++.++++++..|++.++|++|.+++++..+..+.++.|
T Consensus       152 ILaTtd~~kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~kEgI~id~eAL~~IA~~S~GdLRdALnLLDQaIayg~g~I  231 (702)
T PRK14960        152 LFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQIAADQDAIWQIAESAQGSLRDALSLTDQAIAYGQGAV  231 (702)
T ss_pred             EEEECChHhhhHHHHHhhheeeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCc
Confidence            99999998899999999999999999999999999999999999999999999999999999999999988777767789


Q ss_pred             ChhhhhhhcccccCC
Q 022641          269 TSKDLISVSGYPTGG  283 (294)
Q Consensus       269 t~~~v~~~~~~~~~~  283 (294)
                      |.++|..+++.....
T Consensus       232 T~edV~~lLG~~d~e  246 (702)
T PRK14960        232 HHQDVKEMLGLIDRT  246 (702)
T ss_pred             CHHHHHHHhccCCHH
Confidence            999999998865443

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.7e-33  Score=245.70  Aligned_cols=224  Identities=25%  Similarity=0.433  Sum_probs=200.1

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc-----------------
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL-----------------  111 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~-----------------  111 (294)
                      .|..+|+|..|++++||+.+++.|.+++..++.++ ++|+||+|+||||+|+.+|+.+.|...                 
T Consensus         2 ~la~KyRP~~f~dliGQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~   81 (491)
T PRK14964          2 NLALKYRPSSFKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKN   81 (491)
T ss_pred             ChhHHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhc
Confidence            47889999999999999999999999999988875 999999999999999999999876432                 


Q ss_pred             -cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEE
Q 022641          112 -YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFF  190 (294)
Q Consensus       112 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~  190 (294)
                       ....++++++.+..+.+.++..+......+.          .+++.++||||+|.++...++.|++.+++++.++.+|+
T Consensus        82 ~~~~Dv~eidaas~~~vddIR~Iie~~~~~P~----------~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIl  151 (491)
T PRK14964         82 SNHPDVIEIDAASNTSVDDIKVILENSCYLPI----------SSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFIL  151 (491)
T ss_pred             cCCCCEEEEecccCCCHHHHHHHHHHHHhccc----------cCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEE
Confidence             3456788888888888888887766544332          24567999999999999999999999999999999999


Q ss_pred             EecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCCh
Q 022641          191 ICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITS  270 (294)
Q Consensus       191 ~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~  270 (294)
                      +|+....+.+.+.+||..+.|.+++.+++..++.++++++|+.+++++++.|++.++|++|.+++.++.++.+.++.||.
T Consensus       152 atte~~Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~Egi~i~~eAL~lIa~~s~GslR~alslLdqli~y~~~~It~  231 (491)
T PRK14964        152 ATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNALFLLEQAAIYSNNKISE  231 (491)
T ss_pred             EeCChHHHHHHHHHhheeeecccccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCCCH
Confidence            99998899999999999999999999999999999999999999999999999999999999999999999888788999


Q ss_pred             hhhhhhcccccCC
Q 022641          271 KDLISVSGYPTGG  283 (294)
Q Consensus       271 ~~v~~~~~~~~~~  283 (294)
                      ++|..+++....+
T Consensus       232 e~V~~llg~~~~~  244 (491)
T PRK14964        232 KSVRDLLGCVDKH  244 (491)
T ss_pred             HHHHHHHccCCHH
Confidence            9999988765443

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=5.8e-33  Score=252.49  Aligned_cols=224  Identities=24%  Similarity=0.378  Sum_probs=192.8

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--------------  112 (294)
                      ..+|.++|+|..|++++|+++++..|.+++..++.++ ++|+||+|||||++|+.+++.+.|....              
T Consensus         3 Y~~LaeKyRP~tFddIIGQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i   82 (944)
T PRK14949          3 YQVLARKWRPATFEQMVGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEI   82 (944)
T ss_pred             chhHHHHhCCCCHHHhcCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHH
Confidence            5789999999999999999999999999999998888 4899999999999999999999885321              


Q ss_pred             ----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          113 ----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       113 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                          ...++++++.+....+.++..+..+.....          .+++.|+||||+|+|+...++.|++.|++++.++++
T Consensus        83 ~~g~~~DviEidAas~~kVDdIReLie~v~~~P~----------~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrF  152 (944)
T PRK14949         83 AQGRFVDLIEVDAASRTKVDDTRELLDNVQYRPS----------RGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKF  152 (944)
T ss_pred             hcCCCceEEEeccccccCHHHHHHHHHHHHhhhh----------cCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEE
Confidence                112344555544566777776655433221          235679999999999999999999999999999999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++|+.+..+.+.+++||..+.|.+++.+++..+|.+++..+++.++++++..|++.++|++|.+++++..+..+..+.+
T Consensus       153 ILaTTe~~kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il~~EgI~~edeAL~lIA~~S~Gd~R~ALnLLdQala~~~~~I  232 (944)
T PRK14949        153 LLATTDPQKLPVTVLSRCLQFNLKSLTQDEIGTQLNHILTQEQLPFEAEALTLLAKAANGSMRDALSLTDQAIAFGGGQV  232 (944)
T ss_pred             EEECCCchhchHHHHHhheEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999988776666778


Q ss_pred             Chhhhhhhccccc
Q 022641          269 TSKDLISVSGYPT  281 (294)
Q Consensus       269 t~~~v~~~~~~~~  281 (294)
                      +.+.+..+++...
T Consensus       233 t~~~V~~llG~iD  245 (944)
T PRK14949        233 MLTQVQTMLGSID  245 (944)
T ss_pred             cHHHHHHHhCCCC
Confidence            8888888776653

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=1e-32  Score=247.43  Aligned_cols=223  Identities=25%  Similarity=0.379  Sum_probs=194.1

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--------------  112 (294)
                      ++++.++|+|..|++++|++.++..|.+.+..++.++ ++|+||+|||||++|+.+++.+.|....              
T Consensus         3 y~~La~KyRP~~f~divGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~~C~~i   82 (647)
T PRK07994          3 YQVLARKWRPQTFAEVVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGECDNCREI   82 (647)
T ss_pred             chhHHHHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCCHHHHHH
Confidence            5789999999999999999999999999999998888 6899999999999999999999885321              


Q ss_pred             ----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          113 ----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       113 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                          ...++++++.+....+.++..+..+.....          .+++.|+||||+|+|+...++.|++.|++++.++.+
T Consensus        83 ~~g~~~D~ieidaas~~~VddiR~li~~~~~~p~----------~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~F  152 (647)
T PRK07994         83 EQGRFVDLIEIDAASRTKVEDTRELLDNVQYAPA----------RGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKF  152 (647)
T ss_pred             HcCCCCCceeecccccCCHHHHHHHHHHHHhhhh----------cCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEE
Confidence                124456666655567777776665443322          235679999999999999999999999999999999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++|+.+..+++.+++||..+.|.+++.+++..+|.+++..+++.++++++..|+..++|++|.++++++.+....+..|
T Consensus       153 IL~Tt~~~kLl~TI~SRC~~~~f~~Ls~~ei~~~L~~il~~e~i~~e~~aL~~Ia~~s~Gs~R~Al~lldqaia~~~~~i  232 (647)
T PRK07994        153 LLATTDPQKLPVTILSRCLQFHLKALDVEQIRQQLEHILQAEQIPFEPRALQLLARAADGSMRDALSLTDQAIASGNGQV  232 (647)
T ss_pred             EEecCCccccchHHHhhheEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999988776656679


Q ss_pred             Chhhhhhhcccc
Q 022641          269 TSKDLISVSGYP  280 (294)
Q Consensus       269 t~~~v~~~~~~~  280 (294)
                      +.+++..+++..
T Consensus       233 t~~~v~~~lg~~  244 (647)
T PRK07994        233 TTDDVSAMLGTL  244 (647)
T ss_pred             CHHHHHHHHccC
Confidence            999998887753

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.4e-32  Score=243.14  Aligned_cols=223  Identities=25%  Similarity=0.399  Sum_probs=194.0

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--------------  112 (294)
                      .+||.++|+|..|++++|++.++..|..++..++.++ ++|+||+|+|||++|+.+++.+.|....              
T Consensus         3 y~~La~KyRP~~f~diiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i   82 (546)
T PRK14957          3 YQALARKYRPQSFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAI   82 (546)
T ss_pred             chhHHHHHCcCcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHH
Confidence            5799999999999999999999999999999988777 7899999999999999999999874221              


Q ss_pred             ----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          113 ----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       113 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                          ...++++++....+.+.++..+..+...+.          .+++.|+||||+|+++...++.|++.+++++..+.+
T Consensus        83 ~~~~~~dlieidaas~~gvd~ir~ii~~~~~~p~----------~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~f  152 (546)
T PRK14957         83 NNNSFIDLIEIDAASRTGVEETKEILDNIQYMPS----------QGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKF  152 (546)
T ss_pred             hcCCCCceEEeecccccCHHHHHHHHHHHHhhhh----------cCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceE
Confidence                124455555555566666666655443321          235679999999999999999999999999999999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++|++...+++.+.+||..+.|.+++.+++..++.++++.+|+.++++++..+++.++||+|.++++++.++.+.++.|
T Consensus       153 IL~Ttd~~kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~egi~~e~~Al~~Ia~~s~GdlR~alnlLek~i~~~~~~I  232 (546)
T PRK14957        153 ILATTDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENINSDEQSLEYIAYHAKGSLRDALSLLDQAISFCGGEL  232 (546)
T ss_pred             EEEECChhhhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCC
Confidence            99999999899899999999999999999999999999999999999999999999999999999999999988877889


Q ss_pred             Chhhhhhhcccc
Q 022641          269 TSKDLISVSGYP  280 (294)
Q Consensus       269 t~~~v~~~~~~~  280 (294)
                      +.++++++++..
T Consensus       233 t~~~V~~~l~~~  244 (546)
T PRK14957        233 KQAQIKQMLGII  244 (546)
T ss_pred             CHHHHHHHHccC
Confidence            999999988764

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.6e-32  Score=235.99  Aligned_cols=226  Identities=24%  Similarity=0.367  Sum_probs=190.0

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--------------  112 (294)
                      .+++.++|+|..|++++||++.++.+..++..++.++ ++|+||+|+|||++|+.+++.+.|....              
T Consensus         3 ~~~l~~kyrP~~~~~iiGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~~c~~~   82 (363)
T PRK14961          3 YQILARKWRPQYFRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCIICKEI   82 (363)
T ss_pred             cHHHHHHhCCCchhhccChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHH
Confidence            5689999999999999999999999999999988777 6899999999999999999999764321              


Q ss_pred             ----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          113 ----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       113 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                          ...++.+++......+.++..+......+          ..+++.++||||+|.++...++.|++.+++++....+
T Consensus        83 ~~~~~~d~~~~~~~~~~~v~~ir~i~~~~~~~p----------~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~f  152 (363)
T PRK14961         83 EKGLCLDLIEIDAASRTKVEEMREILDNIYYSP----------SKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKF  152 (363)
T ss_pred             hcCCCCceEEecccccCCHHHHHHHHHHHhcCc----------ccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEE
Confidence                11334444443344555554444332211          1234579999999999999999999999999889999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++|+....+.+++.+||..+.|.|++.+++.+++.++++.+|..+++++++.+++.++||+|.+++.++.++.+....|
T Consensus       153 Il~t~~~~~l~~tI~SRc~~~~~~~l~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s~G~~R~al~~l~~~~~~~~~~I  232 (363)
T PRK14961        153 ILATTDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLEHAINLGKGNI  232 (363)
T ss_pred             EEEcCChHhhhHHHHhhceEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCC
Confidence            99998888899999999999999999999999999999999999999999999999999999999999999887777789


Q ss_pred             ChhhhhhhcccccCC
Q 022641          269 TSKDLISVSGYPTGG  283 (294)
Q Consensus       269 t~~~v~~~~~~~~~~  283 (294)
                      |.++|.++++...++
T Consensus       233 t~~~v~~~l~~~~~~  247 (363)
T PRK14961        233 NIKNVTDMLGLLNEK  247 (363)
T ss_pred             CHHHHHHHHCCCCHH
Confidence            999999988865443

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=2.1e-32  Score=240.75  Aligned_cols=229  Identities=27%  Similarity=0.384  Sum_probs=199.0

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCC-cEEEECCCCCCHHHHHHHHHHHhcCCCc-------------
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCP-HMLFYGPPGTGKTTTALAIAHQLFGPEL-------------  111 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~-~ill~Gp~G~GKT~la~~la~~~~~~~~-------------  111 (294)
                      ....||.++|+|..|++++|++.++..|...+..++.+ .++|+||+|||||++|+.+++.+.|...             
T Consensus         6 ~~y~~la~kyRP~~f~dliGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C   85 (507)
T PRK06645          6 NQYIPFARKYRPSNFAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQC   85 (507)
T ss_pred             ccccchhhhhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCC
Confidence            56789999999999999999999999999988887764 5999999999999999999999987532             


Q ss_pred             ---------cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh
Q 022641          112 ---------YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY  182 (294)
Q Consensus       112 ---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~  182 (294)
                               ....++++++.+..+.+.++..+......+          ..+++.++||||+|.++...++.|++.++++
T Consensus        86 ~~C~~i~~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P----------~~~~~KVvIIDEa~~Ls~~a~naLLk~LEep  155 (507)
T PRK06645         86 TNCISFNNHNHPDIIEIDAASKTSVDDIRRIIESAEYKP----------LQGKHKIFIIDEVHMLSKGAFNALLKTLEEP  155 (507)
T ss_pred             hHHHHHhcCCCCcEEEeeccCCCCHHHHHHHHHHHHhcc----------ccCCcEEEEEEChhhcCHHHHHHHHHHHhhc
Confidence                     123566677766677888887776644332          2245679999999999999999999999999


Q ss_pred             cCcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHH
Q 022641          183 SKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAAR  262 (294)
Q Consensus       183 ~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~  262 (294)
                      +..+.+|++|+....+++.+.+||..+.|.+++.+++..++.++++.+|+.++++++..|++.++|++|.+++.++.++.
T Consensus       156 p~~~vfI~aTte~~kI~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~GslR~al~~Ldkai~  235 (507)
T PRK06645        156 PPHIIFIFATTEVQKIPATIISRCQRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSILDQAAS  235 (507)
T ss_pred             CCCEEEEEEeCChHHhhHHHHhcceEEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            99999999999888899999999999999999999999999999999999999999999999999999999999999877


Q ss_pred             HhC---CCCChhhhhhhcccccCCC
Q 022641          263 LFG---SSITSKDLISVSGYPTGGS  284 (294)
Q Consensus       263 ~~~---~~it~~~v~~~~~~~~~~~  284 (294)
                      +.+   ..||.++|..+++......
T Consensus       236 ~~~~~~~~It~~~V~~llg~~~~~~  260 (507)
T PRK06645        236 MSAKSDNIISPQVINQMLGLVDSSV  260 (507)
T ss_pred             hhccCCCCcCHHHHHHHHCCCCHHH
Confidence            653   3699999999998866553

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=2.2e-32  Score=244.16  Aligned_cols=223  Identities=25%  Similarity=0.372  Sum_probs=195.3

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc-----------------
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL-----------------  111 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~-----------------  111 (294)
                      .|.++|+|..|++++||+++++.|..++..++.+| ++|+||+|||||++|+.+++.++|...                 
T Consensus         2 al~~kyRP~~f~eivGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~   81 (584)
T PRK14952          2 ALYRKYRPATFAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAP   81 (584)
T ss_pred             cHHHHhCCCcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccHHHHHhhc
Confidence            46799999999999999999999999999999888 699999999999999999999987431                 


Q ss_pred             ---cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          112 ---YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       112 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                         ....++++++....+.+.+++........+.          .+++.|+||||+|+++...++.|++.|++.+.++.+
T Consensus        82 ~~~~~~dvieidaas~~gvd~iRel~~~~~~~P~----------~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~f  151 (584)
T PRK14952         82 NGPGSIDVVELDAASHGGVDDTRELRDRAFYAPA----------QSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIF  151 (584)
T ss_pred             ccCCCceEEEeccccccCHHHHHHHHHHHHhhhh----------cCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEE
Confidence               1235666777666677777776555433321          235679999999999999999999999999999999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh-CCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF-GSS  267 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~-~~~  267 (294)
                      |++|+.+..+.+.+.+||..+.|.+++.+++..++.++++.+|+.++++++..+++.++|++|.++++|+.++.+. +..
T Consensus       152 IL~tte~~kll~TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi~i~~~al~~Ia~~s~GdlR~aln~Ldql~~~~~~~~  231 (584)
T PRK14952        152 IFATTEPEKVLPTIRSRTHHYPFRLLPPRTMRALIARICEQEGVVVDDAVYPLVIRAGGGSPRDTLSVLDQLLAGAADTH  231 (584)
T ss_pred             EEEeCChHhhHHHHHHhceEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhccCCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999988776 567


Q ss_pred             CChhhhhhhcccccC
Q 022641          268 ITSKDLISVSGYPTG  282 (294)
Q Consensus       268 it~~~v~~~~~~~~~  282 (294)
                      ||.+++..+++....
T Consensus       232 It~~~v~~llg~~~~  246 (584)
T PRK14952        232 VTYQRALGLLGATDV  246 (584)
T ss_pred             cCHHHHHHHHCCCCH
Confidence            999999999887543

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.5e-32  Score=246.02  Aligned_cols=226  Identities=24%  Similarity=0.383  Sum_probs=197.7

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc---------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL---------------  111 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~---------------  111 (294)
                      ++.|.+||+|..|++++|++.++..|.+++..++.++ ++|+||+|+|||++|+.+++.++|...               
T Consensus         3 y~vla~KyRP~~f~dviGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~   82 (618)
T PRK14951          3 YLVLARKYRPRSFSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVCQ   82 (618)
T ss_pred             hHHHHHHHCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCccH
Confidence            5689999999999999999999999999999998877 599999999999999999999987431               


Q ss_pred             --------cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc
Q 022641          112 --------YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS  183 (294)
Q Consensus       112 --------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~  183 (294)
                              ....++++++....+.+.+++.+........          .+++.|+||||+|+|+...++.|++.+++.+
T Consensus        83 ~C~~i~~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~----------~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP  152 (618)
T PRK14951         83 ACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQAVYKPV----------QGRFKVFMIDEVHMLTNTAFNAMLKTLEEPP  152 (618)
T ss_pred             HHHHHHcCCCCceeecCcccccCHHHHHHHHHHHHhCcc----------cCCceEEEEEChhhCCHHHHHHHHHhcccCC
Confidence                    1224666777666777778777765433221          2356799999999999999999999999999


Q ss_pred             CcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHH
Q 022641          184 KVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARL  263 (294)
Q Consensus       184 ~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~  263 (294)
                      .++.+|++|+++..++..+++||..+.|.+++.+++..++++++..+|+.++++++..|++.++|++|.++++++.+..+
T Consensus       153 ~~~~fIL~Ttd~~kil~TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi~ie~~AL~~La~~s~GslR~al~lLdq~ia~  232 (618)
T PRK14951        153 EYLKFVLATTDPQKVPVTVLSRCLQFNLRPMAPETVLEHLTQVLAAENVPAEPQALRLLARAARGSMRDALSLTDQAIAF  232 (618)
T ss_pred             CCeEEEEEECCchhhhHHHHHhceeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence            99999999999989999999999999999999999999999999999999999999999999999999999999888877


Q ss_pred             hCCCCChhhhhhhcccccCC
Q 022641          264 FGSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       264 ~~~~it~~~v~~~~~~~~~~  283 (294)
                      ..+.||.++|.++++....+
T Consensus       233 ~~~~It~~~V~~~Lg~~~~~  252 (618)
T PRK14951        233 GSGQLQEAAVRQMLGSVDRS  252 (618)
T ss_pred             cCCCcCHHHHHHHHcCCCHH
Confidence            77789999999998875443

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=3e-32  Score=239.85  Aligned_cols=225  Identities=29%  Similarity=0.443  Sum_probs=196.7

Q ss_pred             chhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc----------------
Q 022641           49 QPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL----------------  111 (294)
Q Consensus        49 ~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~----------------  111 (294)
                      ++|.++|+|..|++++|++.++..|..++..++.++ ++|+||+|+|||++|+.+++.+.|...                
T Consensus         2 ~~l~~KyRP~~fdeiiGqe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~   81 (535)
T PRK08451          2 QALALKYRPKHFDELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSAL   81 (535)
T ss_pred             ccHHHHHCCCCHHHccCcHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHh
Confidence            478999999999999999999999999999998887 589999999999999999999987543                


Q ss_pred             --cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEE
Q 022641          112 --YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFF  189 (294)
Q Consensus       112 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii  189 (294)
                        .+..++.+++.+..+.+.++..+......+          ..+++.|+||||+|.++...++.|++.+++++..+.+|
T Consensus        82 ~~~h~dv~eldaas~~gId~IRelie~~~~~P----------~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FI  151 (535)
T PRK08451         82 ENRHIDIIEMDAASNRGIDDIRELIEQTKYKP----------SMARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFI  151 (535)
T ss_pred             hcCCCeEEEeccccccCHHHHHHHHHHHhhCc----------ccCCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEE
Confidence              233566666666567777777765533221          12356799999999999999999999999999999999


Q ss_pred             EEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCC
Q 022641          190 FICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSIT  269 (294)
Q Consensus       190 ~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it  269 (294)
                      ++|+.+..+.+++.+||..+.|.|++.+++..++.+++..+|+.++++++..+++.++||+|.+++.++.+..+....||
T Consensus       152 L~ttd~~kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi~i~~~Al~~Ia~~s~GdlR~alnlLdqai~~~~~~It  231 (535)
T PRK08451        152 LATTDPLKLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGVSYEPEALEILARSGNGSLRDTLTLLDQAIIYCKNAIT  231 (535)
T ss_pred             EEECChhhCchHHHhhceeEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998888777899


Q ss_pred             hhhhhhhcccccCC
Q 022641          270 SKDLISVSGYPTGG  283 (294)
Q Consensus       270 ~~~v~~~~~~~~~~  283 (294)
                      .++|..+++...+.
T Consensus       232 ~~~V~~~lg~~~~~  245 (535)
T PRK08451        232 ESKVADMLGLLDPS  245 (535)
T ss_pred             HHHHHHHhCCCCHH
Confidence            99999988765443

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=2.3e-32  Score=244.09  Aligned_cols=226  Identities=26%  Similarity=0.416  Sum_probs=196.2

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--------------  112 (294)
                      +++|.+||+|..|++++|++++++.|..++..++.++ ++|+||+|||||++|+.+++.+.|....              
T Consensus         3 y~vLarKYRP~tFddIIGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i   82 (709)
T PRK08691          3 YQVLARKWRPKTFADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQI   82 (709)
T ss_pred             chhHHHHhCCCCHHHHcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHH
Confidence            5689999999999999999999999999999988776 7999999999999999999999875321              


Q ss_pred             ----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          113 ----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       113 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                          ...+++++.....+.+.++..+........          .+++.|+||||+|.++...++.|++.|++.+..+.+
T Consensus        83 ~~g~~~DvlEidaAs~~gVd~IRelle~a~~~P~----------~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~f  152 (709)
T PRK08691         83 DAGRYVDLLEIDAASNTGIDNIREVLENAQYAPT----------AGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKF  152 (709)
T ss_pred             hccCccceEEEeccccCCHHHHHHHHHHHHhhhh----------hCCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEE
Confidence                123456666666777777777665433221          134579999999999999999999999999999999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++|+++..++..+++||..+.|.+++.+++..+|.+++..+|+.++++++..|++.++||+|.++++|+.+..+....|
T Consensus       153 ILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A~GslRdAlnLLDqaia~g~g~I  232 (709)
T PRK08691        153 ILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIAYEPPALQLLGRAAAGSMRDALSLLDQAIALGSGKV  232 (709)
T ss_pred             EEEeCCccccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998887766679


Q ss_pred             ChhhhhhhcccccCC
Q 022641          269 TSKDLISVSGYPTGG  283 (294)
Q Consensus       269 t~~~v~~~~~~~~~~  283 (294)
                      +.++|..+++....+
T Consensus       233 t~e~V~~lLG~~d~~  247 (709)
T PRK08691        233 AENDVRQMIGAVDKQ  247 (709)
T ss_pred             CHHHHHHHHcccCHH
Confidence            999999998876543

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.4e-32  Score=241.16  Aligned_cols=226  Identities=30%  Similarity=0.449  Sum_probs=193.6

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc-----------------
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL-----------------  111 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~-----------------  111 (294)
                      .|.++|+|..|++++|+++++..|..++..+..++ ++|+|||||||||+|+++++.+.|...                 
T Consensus         3 ~l~~kyRP~~~~divGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~   82 (472)
T PRK14962          3 ALYRKYRPKTFSEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDE   82 (472)
T ss_pred             hhHHHHCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhc
Confidence            58899999999999999999999999999988876 899999999999999999999976432                 


Q ss_pred             -cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEE
Q 022641          112 -YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFF  190 (294)
Q Consensus       112 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~  190 (294)
                       ....++.+++....+.+.++.........+          ..+++.+|||||+|.++...++.|+..++..+..+.+|+
T Consensus        83 g~~~dv~el~aa~~~gid~iR~i~~~~~~~p----------~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Il  152 (472)
T PRK14962         83 GTFMDVIELDAASNRGIDEIRKIRDAVGYRP----------MEGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVL  152 (472)
T ss_pred             CCCCccEEEeCcccCCHHHHHHHHHHHhhCh----------hcCCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEEEE
Confidence             122567777776667777765443332211          123467999999999999999999999999888888888


Q ss_pred             EecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCCh
Q 022641          191 ICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITS  270 (294)
Q Consensus       191 ~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~  270 (294)
                      +|+.+..+.+++.+||..+.|.|++.+++..+++++++.+++.++++++..|++.++||+|.+++.|+.++.+.+..||.
T Consensus       153 attn~~kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi~i~~eal~~Ia~~s~GdlR~aln~Le~l~~~~~~~It~  232 (472)
T PRK14962        153 ATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLEQVWKFSEGKITL  232 (472)
T ss_pred             EeCChHhhhHHHhcCcEEEEECCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCH
Confidence            88888889999999999999999999999999999999999999999999999999999999999999988776667999


Q ss_pred             hhhhhhcccccCCCC
Q 022641          271 KDLISVSGYPTGGSG  285 (294)
Q Consensus       271 ~~v~~~~~~~~~~~~  285 (294)
                      +++..+++...++..
T Consensus       233 e~V~~~l~~~~~~~i  247 (472)
T PRK14962        233 ETVHEALGLIPIEVV  247 (472)
T ss_pred             HHHHHHHcCCCHHHH
Confidence            999999987765433

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

Probab=100.00  E-value=2.8e-32  Score=225.10  Aligned_cols=214  Identities=30%  Similarity=0.378  Sum_probs=182.5

Q ss_pred             chhhhhcCCCcchhhcccHHHH---HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           49 QPWVEKYRPKQVKDVAHQEEVV---RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        49 ~~~~~~~~~~~~~~~~g~~~~~---~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      .|+..+++|.++++++||++++   ..|.+++..+..++++|||||||||||+|+.++...      +..|..+++... 
T Consensus        12 ~PLA~rmRP~~lde~vGQ~HLlg~~~~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~------~~~f~~~sAv~~-   84 (436)
T COG2256          12 MPLAERLRPKSLDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTT------NAAFEALSAVTS-   84 (436)
T ss_pred             cChHHHhCCCCHHHhcChHhhhCCCchHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhh------CCceEEeccccc-
Confidence            4999999999999999999999   688999999999999999999999999999999998      888888887764 


Q ss_pred             chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEe--cCCcccchHhh
Q 022641          126 GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFIC--NYISRIIEPLA  203 (294)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~--~~~~~~~~~l~  203 (294)
                      ++..++..+.........          +++-||||||+|++++.+|+.|+..+++  ..+.+|.+|  |+.+.+.++++
T Consensus        85 gvkdlr~i~e~a~~~~~~----------gr~tiLflDEIHRfnK~QQD~lLp~vE~--G~iilIGATTENPsF~ln~ALl  152 (436)
T COG2256          85 GVKDLREIIEEARKNRLL----------GRRTILFLDEIHRFNKAQQDALLPHVEN--GTIILIGATTENPSFELNPALL  152 (436)
T ss_pred             cHHHHHHHHHHHHHHHhc----------CCceEEEEehhhhcChhhhhhhhhhhcC--CeEEEEeccCCCCCeeecHHHh
Confidence            677788777776444321          3346999999999999999999999987  444455554  67788999999


Q ss_pred             ccccEEEecCCCHHHHHHHHHHHHHH--hCCC-----CCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCC--CCChhhhh
Q 022641          204 SRCAKFRFKPLSEEVMSSRVLHICNE--EGLN-----LDAEALSTLSSISQGDLRRAITYLQGAARLFGS--SITSKDLI  274 (294)
Q Consensus       204 ~r~~~i~~~~~~~~~~~~~l~~~~~~--~~~~-----~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~--~it~~~v~  274 (294)
                      +||.++.|.|++.+++..++.+.+..  .++.     +++++++.++..++||.|.++|.|+.+....+.  .++.+.+.
T Consensus       153 SR~~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~GD~R~aLN~LE~~~~~~~~~~~~~~~~l~  232 (436)
T COG2256         153 SRARVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRALNLLELAALSAEPDEVLILELLE  232 (436)
T ss_pred             hhhheeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCchHHHHHHHHHHHHHhcCCCcccCHHHHH
Confidence            99999999999999999999995543  3444     789999999999999999999999999988733  45688888


Q ss_pred             hhccccc
Q 022641          275 SVSGYPT  281 (294)
Q Consensus       275 ~~~~~~~  281 (294)
                      ++++...
T Consensus       233 ~~l~~~~  239 (436)
T COG2256         233 EILQRRS  239 (436)
T ss_pred             HHHhhhh
Confidence            8888744

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=8.4e-32  Score=238.33  Aligned_cols=225  Identities=26%  Similarity=0.451  Sum_probs=193.7

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--------------  112 (294)
                      ..+|.++|+|..|++++|++..+..|.+++..++.++ ++|+||+|+|||++|+.+++.+.|....              
T Consensus         3 ~~~~~~KyRP~~F~dIIGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C~sCr~i   82 (605)
T PRK05896          3 EITFYRKYRPHNFKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSVCESI   82 (605)
T ss_pred             chhHHHHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHH
Confidence            4689999999999999999999999999998887776 8899999999999999999999875432              


Q ss_pred             ----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          113 ----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       113 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                          ...++.+++....+.+.++..+......+.          .+++.++||||+|.++...++.|++.+++++....+
T Consensus        83 ~~~~h~DiieIdaas~igVd~IReIi~~~~~~P~----------~~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvf  152 (605)
T PRK05896         83 NTNQSVDIVELDAASNNGVDEIRNIIDNINYLPT----------TFKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVF  152 (605)
T ss_pred             HcCCCCceEEeccccccCHHHHHHHHHHHHhchh----------hCCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEE
Confidence                124455665555667777776655443322          134679999999999999999999999999999999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++|+.+..+.+.+++||..+.|.+++.+++..++..++..+|+.+++++++.+++.++|++|.+++.++.++.+.+..|
T Consensus       153 IL~Tt~~~KLl~TI~SRcq~ieF~~Ls~~eL~~~L~~il~kegi~Is~eal~~La~lS~GdlR~AlnlLekL~~y~~~~I  232 (605)
T PRK05896        153 IFATTEFQKIPLTIISRCQRYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKIADLADGSLRDGLSILDQLSTFKNSEI  232 (605)
T ss_pred             EEECCChHhhhHHHHhhhhhcccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhhcCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999888876669


Q ss_pred             ChhhhhhhcccccC
Q 022641          269 TSKDLISVSGYPTG  282 (294)
Q Consensus       269 t~~~v~~~~~~~~~  282 (294)
                      +.+++..+++....
T Consensus       233 t~e~V~ellg~~~~  246 (605)
T PRK05896        233 DIEDINKTFGLVDN  246 (605)
T ss_pred             CHHHHHHHhccCCH
Confidence            99999887765443

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=1.3e-31  Score=247.53  Aligned_cols=224  Identities=26%  Similarity=0.389  Sum_probs=193.8

Q ss_pred             chhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc----------------
Q 022641           49 QPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL----------------  111 (294)
Q Consensus        49 ~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~----------------  111 (294)
                      ..|.+||+|..|++++||+.+++.|..++..++.+| +||+||+|||||++|+.|++.++|...                
T Consensus         3 ~~l~~KyRP~~f~eiiGqe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~   82 (824)
T PRK07764          3 LALYRRYRPATFAEVIGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALA   82 (824)
T ss_pred             hhHHHHhCCCCHHHhcCcHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHH
Confidence            457899999999999999999999999999998888 799999999999999999999987532                


Q ss_pred             ----cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcce
Q 022641          112 ----YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTR  187 (294)
Q Consensus       112 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~  187 (294)
                          ....+++++..+..+++.++++........          ...+++|+||||+|+|+...++.|+++|++.+.+++
T Consensus        83 ~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~~~p----------~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~  152 (824)
T PRK07764         83 PGGPGSLDVTEIDAASHGGVDDARELRERAFFAP----------AESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLK  152 (824)
T ss_pred             cCCCCCCcEEEecccccCCHHHHHHHHHHHHhch----------hcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeE
Confidence                123456666656566777776554433221          124567999999999999999999999999999999


Q ss_pred             EEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh-CC
Q 022641          188 FFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF-GS  266 (294)
Q Consensus       188 ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~-~~  266 (294)
                      ||++|+....+.+.|++||..+.|.+++.+++..+|.++++.+++.++++++..++..++||+|.++++|+.+..+. .+
T Consensus       153 fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~EGv~id~eal~lLa~~sgGdlR~Al~eLEKLia~~~~~  232 (824)
T PRK07764        153 FIFATTEPDKVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQEGVPVEPGVLPLVIRAGGGSVRDSLSVLDQLLAGAGPE  232 (824)
T ss_pred             EEEEeCChhhhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCC
Confidence            99999988889999999999999999999999999999999999999999999999999999999999999988764 46


Q ss_pred             CCChhhhhhhcccccC
Q 022641          267 SITSKDLISVSGYPTG  282 (294)
Q Consensus       267 ~it~~~v~~~~~~~~~  282 (294)
                      .||.+++..+++....
T Consensus       233 ~IT~e~V~allg~~~~  248 (824)
T PRK07764        233 GVTYERAVALLGVTDS  248 (824)
T ss_pred             CCCHHHHHHHhcCCCH
Confidence            7999999988876543

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=3.2e-31  Score=237.94  Aligned_cols=226  Identities=28%  Similarity=0.447  Sum_probs=197.8

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc---------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL---------------  111 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~---------------  111 (294)
                      .+.|.++|+|..|++++|+++++..|.+++..++.++ ++|+||+|||||++|+.+++.+.|...               
T Consensus         3 y~al~~k~rP~~f~~viGq~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C~~C~~i   82 (559)
T PRK05563          3 YQALYRKWRPQTFEDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNECEICKAI   82 (559)
T ss_pred             cHHHHHHhCCCcHHhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccHHHHHH
Confidence            4678899999999999999999999999999988777 788999999999999999999987542               


Q ss_pred             ---cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          112 ---YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       112 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                         ....++++++....+.+.++.........+          ..+++.++||||+|.|+...++.|++.+++++.++.+
T Consensus        83 ~~g~~~dv~eidaas~~~vd~ir~i~~~v~~~p----------~~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~if  152 (559)
T PRK05563         83 TNGSLMDVIEIDAASNNGVDEIRDIRDKVKYAP----------SEAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIF  152 (559)
T ss_pred             hcCCCCCeEEeeccccCCHHHHHHHHHHHhhCc----------ccCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEE
Confidence               234566777766667777776665544322          1345679999999999999999999999999999999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++|+.+..+++.+.+||..+.|.+++..++..++..+++++|+.+++++++.++..++|++|.+++.|+.+..+.+..|
T Consensus       153 Ilatt~~~ki~~tI~SRc~~~~f~~~~~~ei~~~L~~i~~~egi~i~~~al~~ia~~s~G~~R~al~~Ldq~~~~~~~~I  232 (559)
T PRK05563        153 ILATTEPHKIPATILSRCQRFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAAEGGMRDALSILDQAISFGDGKV  232 (559)
T ss_pred             EEEeCChhhCcHHHHhHheEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998887777789


Q ss_pred             ChhhhhhhcccccCC
Q 022641          269 TSKDLISVSGYPTGG  283 (294)
Q Consensus       269 t~~~v~~~~~~~~~~  283 (294)
                      |.++|..+++.....
T Consensus       233 t~~~V~~vlg~~~~~  247 (559)
T PRK05563        233 TYEDALEVTGSVSQE  247 (559)
T ss_pred             CHHHHHHHhCCCCHH
Confidence            999999988876554

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.9e-31  Score=240.55  Aligned_cols=226  Identities=26%  Similarity=0.457  Sum_probs=197.6

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--------------  112 (294)
                      ++-+.++|+|..|++++|+++++..|.+++..++.++ ++|+||+|+|||++|+.+++.+.|....              
T Consensus         3 y~~l~~k~RP~~f~~iiGq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~~c~~i   82 (576)
T PRK14965          3 YLVLARKYRPQTFSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPCVEI   82 (576)
T ss_pred             cHHHHHHhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccHHHHHH
Confidence            4568899999999999999999999999999988877 6999999999999999999999876432              


Q ss_pred             ----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          113 ----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       113 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                          ...++++++....+.+.++.........+          ..+++.++||||+|+++...++.|++.|++++.++.+
T Consensus        83 ~~g~~~d~~eid~~s~~~v~~ir~l~~~~~~~p----------~~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~f  152 (576)
T PRK14965         83 TEGRSVDVFEIDGASNTGVDDIRELRENVKYLP----------SRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKF  152 (576)
T ss_pred             hcCCCCCeeeeeccCccCHHHHHHHHHHHHhcc----------ccCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEE
Confidence                23456666666667777777665543322          1245679999999999999999999999999999999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++|+.+..+++.+++||..+.|.+++.+++..++..+++++|+.++++++..+++.++||+|.+++.++.+..+.++.|
T Consensus       153 Il~t~~~~kl~~tI~SRc~~~~f~~l~~~~i~~~L~~i~~~egi~i~~~al~~la~~a~G~lr~al~~Ldqliay~g~~I  232 (576)
T PRK14965        153 IFATTEPHKVPITILSRCQRFDFRRIPLQKIVDRLRYIADQEGISISDAALALVARKGDGSMRDSLSTLDQVLAFCGDAV  232 (576)
T ss_pred             EEEeCChhhhhHHHHHhhhhhhcCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999988887789


Q ss_pred             ChhhhhhhcccccCC
Q 022641          269 TSKDLISVSGYPTGG  283 (294)
Q Consensus       269 t~~~v~~~~~~~~~~  283 (294)
                      |.+++..+++.....
T Consensus       233 t~edV~~llG~~~~~  247 (576)
T PRK14965        233 GDDDVAELLGVVDRR  247 (576)
T ss_pred             CHHHHHHHhCCCCHH
Confidence            999999987765443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.8e-31  Score=237.96  Aligned_cols=224  Identities=28%  Similarity=0.424  Sum_probs=193.9

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--------------  112 (294)
                      .+++.++|+|..|++++|++++++.|..++..++.++ ++|+||+|+|||++|+.+++.+.|....              
T Consensus         3 ~~~l~~k~rP~~f~divGq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i   82 (527)
T PRK14969          3 YQVLARKWRPKSFSELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEI   82 (527)
T ss_pred             cHHHHHHhCCCcHHHhcCcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHH
Confidence            5689999999999999999999999999999988887 6899999999999999999999875321              


Q ss_pred             ----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          113 ----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       113 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                          ...++++++......+.++..+......+          ..+++.|+||||+|.++...++.|++.+++++..+.+
T Consensus        83 ~~~~~~d~~ei~~~~~~~vd~ir~l~~~~~~~p----------~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~f  152 (527)
T PRK14969         83 DSGRFVDLIEVDAASNTQVDAMRELLDNAQYAP----------TRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKF  152 (527)
T ss_pred             hcCCCCceeEeeccccCCHHHHHHHHHHHhhCc----------ccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEE
Confidence                11345555555556677776665543222          1245679999999999999999999999999999999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++|+++..+++.+++||..+.|.+++.+++..++.++++.+|+.++++++..+++.++|++|.++++++.+..+..+.|
T Consensus       153 IL~t~d~~kil~tI~SRc~~~~f~~l~~~~i~~~L~~il~~egi~~~~~al~~la~~s~Gslr~al~lldqai~~~~~~I  232 (527)
T PRK14969        153 ILATTDPQKIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAAAGSMRDALSLLDQAIAYGGGTV  232 (527)
T ss_pred             EEEeCChhhCchhHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCc
Confidence            99999988888899999999999999999999999999999999999999999999999999999999999888877789


Q ss_pred             Chhhhhhhccccc
Q 022641          269 TSKDLISVSGYPT  281 (294)
Q Consensus       269 t~~~v~~~~~~~~  281 (294)
                      +.+++..+++...
T Consensus       233 ~~~~v~~~~~~~~  245 (527)
T PRK14969        233 NESEVRAMLGAID  245 (527)
T ss_pred             CHHHHHHHHCCCC
Confidence            9999999887653

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=3.2e-31  Score=237.97  Aligned_cols=227  Identities=28%  Similarity=0.457  Sum_probs=197.6

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc------------
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY------------  112 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~------------  112 (294)
                      ...++|.++|+|..|++++|++.+++.|.+++..++.++ ++|+||+|+|||++|+.+++.+.|....            
T Consensus         9 ~~y~~la~KyRP~~f~dliGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~   88 (598)
T PRK09111          9 TPYRVLARKYRPQTFDDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGV   88 (598)
T ss_pred             ccchhHHhhhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCcc
Confidence            456789999999999999999999999999999998876 9999999999999999999999875321            


Q ss_pred             -----------CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh
Q 022641          113 -----------KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMET  181 (294)
Q Consensus       113 -----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~  181 (294)
                                 +..++++++....+.+.+++.+......+.          .+++.|+||||+|.++....+.|++.|++
T Consensus        89 c~~C~~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~----------~a~~KVvIIDEad~Ls~~a~naLLKtLEe  158 (598)
T PRK09111         89 GEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPV----------SARYKVYIIDEVHMLSTAAFNALLKTLEE  158 (598)
T ss_pred             cHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHHhchh----------cCCcEEEEEEChHhCCHHHHHHHHHHHHh
Confidence                       123455665666677788777665543322          24567999999999999999999999999


Q ss_pred             hcCcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHH
Q 022641          182 YSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA  261 (294)
Q Consensus       182 ~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~  261 (294)
                      ++..+.+|++++....+.+.+.+||..+.|.+++.+++..++.++++++++.++++++..|++.++|++|.+++.++.++
T Consensus       159 Pp~~~~fIl~tte~~kll~tI~SRcq~~~f~~l~~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~Gdlr~al~~Ldkli  238 (598)
T PRK09111        159 PPPHVKFIFATTEIRKVPVTVLSRCQRFDLRRIEADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLLDQAI  238 (598)
T ss_pred             CCCCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            99999999999988888899999999999999999999999999999999999999999999999999999999998887


Q ss_pred             HHhCCCCChhhhhhhcccccC
Q 022641          262 RLFGSSITSKDLISVSGYPTG  282 (294)
Q Consensus       262 ~~~~~~it~~~v~~~~~~~~~  282 (294)
                      .+..+.||.++|..+++....
T Consensus       239 ~~g~g~It~e~V~~llg~~~~  259 (598)
T PRK09111        239 AHGAGEVTAEAVRDMLGLADR  259 (598)
T ss_pred             hhcCCCcCHHHHHHHhCCCCH
Confidence            776678999999999886443

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=3.3e-31  Score=238.94  Aligned_cols=227  Identities=28%  Similarity=0.463  Sum_probs=193.9

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc------------
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY------------  112 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~------------  112 (294)
                      ....+|.++|+|..|++++|++.+++.|..++..++.++ ++|+||+|+|||++|+.+++.+.|....            
T Consensus         3 m~y~~l~~KyRP~~f~dIiGQe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~   82 (725)
T PRK07133          3 MKYKALYRKYRPKTFDDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIEN   82 (725)
T ss_pred             cchhhHHHHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHh
Confidence            456799999999999999999999999999999988777 6899999999999999999999885421            


Q ss_pred             ---CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEE
Q 022641          113 ---KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFF  189 (294)
Q Consensus       113 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii  189 (294)
                         ...++.+++....+.+.++.....+...+.          .+++.|+||||+|.++...++.|++.|++++..+.+|
T Consensus        83 ~~~~~Dvieidaasn~~vd~IReLie~~~~~P~----------~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifI  152 (725)
T PRK07133         83 VNNSLDIIEMDAASNNGVDEIRELIENVKNLPT----------QSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFI  152 (725)
T ss_pred             hcCCCcEEEEeccccCCHHHHHHHHHHHHhchh----------cCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEE
Confidence               112334444444456667666655443322          2456799999999999999999999999999999999


Q ss_pred             EEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCC
Q 022641          190 FICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSIT  269 (294)
Q Consensus       190 ~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it  269 (294)
                      ++|+.+..+++.+++||..+.|.+++.+++..++..++.++|+.+++++++.++..++|++|.++++++.++.+....|+
T Consensus       153 LaTte~~KLl~TI~SRcq~ieF~~L~~eeI~~~L~~il~kegI~id~eAl~~LA~lS~GslR~AlslLekl~~y~~~~It  232 (725)
T PRK07133        153 LATTEVHKIPLTILSRVQRFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLSSGSLRDALSIAEQVSIFGNNKIT  232 (725)
T ss_pred             EEcCChhhhhHHHHhhceeEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998877666699


Q ss_pred             hhhhhhhcccccC
Q 022641          270 SKDLISVSGYPTG  282 (294)
Q Consensus       270 ~~~v~~~~~~~~~  282 (294)
                      .+++..+++....
T Consensus       233 ~e~V~ellg~~~~  245 (725)
T PRK07133        233 LKNVEELFGLVSN  245 (725)
T ss_pred             HHHHHHHHcCCCH
Confidence            9999888776444

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=3.1e-31  Score=235.91  Aligned_cols=227  Identities=27%  Similarity=0.405  Sum_probs=191.2

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCC-CcEEEECCCCCCHHHHHHHHHHHhcCCCc--------------
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANC-PHMLFYGPPGTGKTTTALAIAHQLFGPEL--------------  111 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~-~~ill~Gp~G~GKT~la~~la~~~~~~~~--------------  111 (294)
                      ...||.++|+|..|++++|++.++..|.+++..++. +.++|+||+|||||++|+.+++.+.|...              
T Consensus         2 s~~~la~KyRP~sf~dIiGQe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C~sC~~   81 (624)
T PRK14959          2 SHASLTARYRPQTFAEVAGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQCRK   81 (624)
T ss_pred             CcchHHHHhCCCCHHHhcCCHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCcccHHHHH
Confidence            356999999999999999999999999999998874 55889999999999999999999987521              


Q ss_pred             ----cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcce
Q 022641          112 ----YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTR  187 (294)
Q Consensus       112 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~  187 (294)
                          ....++++++......+.++.....+.....          .+++.||||||+|.++...++.|++.+++.+....
T Consensus        82 i~~g~hpDv~eId~a~~~~Id~iR~L~~~~~~~p~----------~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~i  151 (624)
T PRK14959         82 VTQGMHVDVVEIDGASNRGIDDAKRLKEAIGYAPM----------EGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVT  151 (624)
T ss_pred             HhcCCCCceEEEecccccCHHHHHHHHHHHHhhhh----------cCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEE
Confidence                1234566666555566666654443332221          23457999999999999999999999999888899


Q ss_pred             EEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCC
Q 022641          188 FFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS  267 (294)
Q Consensus       188 ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~  267 (294)
                      +|++|+.+..+...+.+||..+.|.+++.+++..+|..++..+++.++++++..|++.++||+|.++++|+.++...+..
T Consensus       152 fILaTt~~~kll~TI~SRcq~i~F~pLs~~eL~~~L~~il~~egi~id~eal~lIA~~s~GdlR~Al~lLeqll~~g~~~  231 (624)
T PRK14959        152 FVLATTEPHKFPVTIVSRCQHFTFTRLSEAGLEAHLTKVLGREGVDYDPAAVRLIARRAAGSVRDSMSLLGQVLALGESR  231 (624)
T ss_pred             EEEecCChhhhhHHHHhhhhccccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCC
Confidence            99999998888899999999999999999999999999999999999999999999999999999999999876554667


Q ss_pred             CChhhhhhhcccccCC
Q 022641          268 ITSKDLISVSGYPTGG  283 (294)
Q Consensus       268 it~~~v~~~~~~~~~~  283 (294)
                      ||.++|..+++.....
T Consensus       232 It~d~V~~~lg~~~~e  247 (624)
T PRK14959        232 LTIDGARGVLGLAGQE  247 (624)
T ss_pred             cCHHHHHHHhCCCCHH
Confidence            9999998888765433

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

Probab=100.00  E-value=7.1e-32  Score=234.63  Aligned_cols=226  Identities=32%  Similarity=0.477  Sum_probs=204.2

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc-c-------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL-Y-------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~-~-------------  112 (294)
                      .+++..+|+|..|++++|++.+...|...+..++..| .+|+||.|||||++|+.+|+.+.|... .             
T Consensus         3 yq~L~rKyRP~~F~evvGQe~v~~~L~nal~~~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C~~Ck~I   82 (515)
T COG2812           3 YQVLARKYRPKTFDDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISCKEI   82 (515)
T ss_pred             hHHHHHHhCcccHHHhcccHHHHHHHHHHHHhCcchhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCCcchhhhhhHhh
Confidence            4578899999999999999999999999999988766 999999999999999999999988641 1             


Q ss_pred             ----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          113 ----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       113 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                          ...++++++.+..+++.++.........+.          .+++.|.||||+|+|+....+.|++.+++++.++.+
T Consensus        83 ~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~----------~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~F  152 (515)
T COG2812          83 NEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPS----------EGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKF  152 (515)
T ss_pred             hcCCcccchhhhhhhccChHHHHHHHHHhccCCc----------cccceEEEEecHHhhhHHHHHHHhcccccCccCeEE
Confidence                235566677777788888887777655543          356789999999999999999999999999999999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++|..+.+++..+++||+.+.|..++.+++...|..++.++++.++++++..+++.++|++|.++.+|+.+..+.++.|
T Consensus       153 IlATTe~~Kip~TIlSRcq~f~fkri~~~~I~~~L~~i~~~E~I~~e~~aL~~ia~~a~Gs~RDalslLDq~i~~~~~~I  232 (515)
T COG2812         153 ILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAAILDKEGINIEEDALSLIARAAEGSLRDALSLLDQAIAFGEGEI  232 (515)
T ss_pred             EEecCCcCcCchhhhhccccccccCCCHHHHHHHHHHHHHhcCCccCHHHHHHHHHHcCCChhhHHHHHHHHHHccCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999878889


Q ss_pred             ChhhhhhhcccccCC
Q 022641          269 TSKDLISVSGYPTGG  283 (294)
Q Consensus       269 t~~~v~~~~~~~~~~  283 (294)
                      |.+.+..+++.....
T Consensus       233 t~~~v~~~lG~~~~~  247 (515)
T COG2812         233 TLESVRDMLGLTDIE  247 (515)
T ss_pred             cHHHHHHHhCCCCHH
Confidence            999999999987654

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=8.2e-31  Score=231.09  Aligned_cols=227  Identities=32%  Similarity=0.460  Sum_probs=193.3

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc-------------
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY-------------  112 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~-------------  112 (294)
                      +..||.++|+|..|.+++|++.++..|..++..+..++ ++|+||+|+|||++|+.+++.+.|....             
T Consensus         2 ~y~~~~~kyRP~~f~diiGq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~   81 (486)
T PRK14953          2 MYIPFARKYRPKFFKEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVE   81 (486)
T ss_pred             CchHHHHhhCCCcHHHccChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHH
Confidence            35699999999999999999999999999999988777 6789999999999999999999763211             


Q ss_pred             -----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcce
Q 022641          113 -----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTR  187 (294)
Q Consensus       113 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~  187 (294)
                           ...++.+++....+.+.++.........+          ..+++.++||||+|.++...++.|++.+++++....
T Consensus        82 i~~g~~~d~~eidaas~~gvd~ir~I~~~~~~~P----------~~~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v  151 (486)
T PRK14953         82 IDKGSFPDLIEIDAASNRGIDDIRALRDAVSYTP----------IKGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTI  151 (486)
T ss_pred             HhcCCCCcEEEEeCccCCCHHHHHHHHHHHHhCc----------ccCCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeE
Confidence                 12344455555556666665544433222          124567999999999999999999999999988999


Q ss_pred             EEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCC
Q 022641          188 FFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS  267 (294)
Q Consensus       188 ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~  267 (294)
                      +|++++....+++++.+||..+.|.|++.+++..++..+++.+|+.+++++++.+++.++||+|.+++.++.++.+.+..
T Consensus       152 ~Il~tt~~~kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi~id~~al~~La~~s~G~lr~al~~Ldkl~~~~~~~  231 (486)
T PRK14953        152 FILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQASEGGMRDAASLLDQASTYGEGK  231 (486)
T ss_pred             EEEEECCHHHHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCC
Confidence            99999888888899999999999999999999999999999999999999999999999999999999999998877778


Q ss_pred             CChhhhhhhcccccCC
Q 022641          268 ITSKDLISVSGYPTGG  283 (294)
Q Consensus       268 it~~~v~~~~~~~~~~  283 (294)
                      ||.++|..+++.....
T Consensus       232 It~~~V~~~lg~~~~~  247 (486)
T PRK14953        232 VTIKVVEEFLGIVSQE  247 (486)
T ss_pred             cCHHHHHHHhCCCCHH
Confidence            9999999988876554

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1e-30  Score=231.12  Aligned_cols=222  Identities=30%  Similarity=0.409  Sum_probs=190.8

Q ss_pred             hhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcE-EEECCCCCCHHHHHHHHHHHhcCCC-----------------cc
Q 022641           51 WVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQLFGPE-----------------LY  112 (294)
Q Consensus        51 ~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~i-ll~Gp~G~GKT~la~~la~~~~~~~-----------------~~  112 (294)
                      +.++|+|..|++++||++++..|..++..+..++. +|+||||||||++|+++++.+.|..                 ..
T Consensus         4 l~~KyRP~~~~dvvGq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~   83 (504)
T PRK14963          4 LYQRARPITFDEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGA   83 (504)
T ss_pred             HHHhhCCCCHHHhcChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCC
Confidence            44899999999999999999999999999988875 9999999999999999999997643                 12


Q ss_pred             CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEe
Q 022641          113 KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFIC  192 (294)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~  192 (294)
                      ...++.+++.+..+.+.++.........+          ..+++.++||||+|.++...++.|++.+++.+..+.+|+++
T Consensus        84 h~dv~el~~~~~~~vd~iR~l~~~~~~~p----------~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t  153 (504)
T PRK14963         84 HPDVLEIDAASNNSVEDVRDLREKVLLAP----------LRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILAT  153 (504)
T ss_pred             CCceEEecccccCCHHHHHHHHHHHhhcc----------ccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEc
Confidence            33566777766666666666544333221          12345799999999999999999999999988888899999


Q ss_pred             cCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhh
Q 022641          193 NYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKD  272 (294)
Q Consensus       193 ~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~  272 (294)
                      +.+..+.+.+.+||..+.|.+++.+++..++.++++.+|+.+++++++.|++.++||+|.+++.|+.+..+ +..||.++
T Consensus       154 ~~~~kl~~~I~SRc~~~~f~~ls~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~GdlR~aln~Lekl~~~-~~~It~~~  232 (504)
T PRK14963        154 TEPEKMPPTILSRTQHFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDAESLLERLLAL-GTPVTRKQ  232 (504)
T ss_pred             CChhhCChHHhcceEEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhc-CCCCCHHH
Confidence            98888999999999999999999999999999999999999999999999999999999999999998765 66799999


Q ss_pred             hhhhcccccCC
Q 022641          273 LISVSGYPTGG  283 (294)
Q Consensus       273 v~~~~~~~~~~  283 (294)
                      |..+++.....
T Consensus       233 V~~~l~~~~~~  243 (504)
T PRK14963        233 VEEALGLPPQE  243 (504)
T ss_pred             HHHHHCCCcHH
Confidence            99998876654

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.98  E-value=3.5e-30  Score=219.64  Aligned_cols=227  Identities=49%  Similarity=0.834  Sum_probs=191.7

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG  126 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~  126 (294)
                      ...||.++|+|..+++++|++.++..+..++..+..++++|+||+|+|||++++.+++++.+... ...++.++.++...
T Consensus         3 ~~~~w~~kyrP~~~~~~~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~-~~~~i~~~~~~~~~   81 (319)
T PRK00440          3 MEEIWVEKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGEDW-RENFLELNASDERG   81 (319)
T ss_pred             ccCccchhhCCCcHHHhcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCcc-ccceEEeccccccc
Confidence            45799999999999999999999999999999888888999999999999999999999866543 34566676666555


Q ss_pred             hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccc
Q 022641          127 INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRC  206 (294)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~  206 (294)
                      ...+...+..+......        ......+|+|||++.++...++.|+..++..+....+|++++....+.+++.+||
T Consensus        82 ~~~~~~~i~~~~~~~~~--------~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~  153 (319)
T PRK00440         82 IDVIRNKIKEFARTAPV--------GGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRC  153 (319)
T ss_pred             hHHHHHHHHHHHhcCCC--------CCCCceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHh
Confidence            54444444443322111        0123569999999999998889999999988888889999998888889999999


Q ss_pred             cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhcccccCC
Q 022641          207 AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       207 ~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~~~~~  283 (294)
                      ..+.|.|++.+++..++..+++.+++.+++++++.+++.++||+|.+++.++.++.. ++.||.++|..++....+.
T Consensus       154 ~~~~~~~l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~-~~~it~~~v~~~~~~~~~~  229 (319)
T PRK00440        154 AVFRFSPLKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAAT-GKEVTEEAVYKITGTARPE  229 (319)
T ss_pred             heeeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc-CCCCCHHHHHHHhCCCCHH
Confidence            999999999999999999999999999999999999999999999999999988775 6679999999998776544

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.98  E-value=2.6e-30  Score=223.52  Aligned_cols=224  Identities=29%  Similarity=0.472  Sum_probs=189.8

Q ss_pred             chhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc---------------
Q 022641           49 QPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY---------------  112 (294)
Q Consensus        49 ~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~---------------  112 (294)
                      +||.++|+|..|++++|++..+..|..++..+..++ ++|+||||+|||++|+.+++.+.|....               
T Consensus         2 ~~~~~~~rp~~~~~iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~   81 (355)
T TIGR02397         2 QVLARKYRPQTFEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEIN   81 (355)
T ss_pred             ccHHHHhCCCcHhhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHh
Confidence            599999999999999999999999999999888776 7899999999999999999999765321               


Q ss_pred             ---CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEE
Q 022641          113 ---KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFF  189 (294)
Q Consensus       113 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii  189 (294)
                         ...++.+++......+.++..+......+          ..+++.+++|||++.++...++.|++.+++.+..+.+|
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p----------~~~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~lI  151 (355)
T TIGR02397        82 SGSSLDVIEIDAASNNGVDDIREILDNVKYAP----------SSGKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFI  151 (355)
T ss_pred             cCCCCCEEEeeccccCCHHHHHHHHHHHhcCc----------ccCCceEEEEeChhhcCHHHHHHHHHHHhCCccceeEE
Confidence               23455555554445555555555433221          12345799999999999999999999999988888889


Q ss_pred             EEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCC
Q 022641          190 FICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSIT  269 (294)
Q Consensus       190 ~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it  269 (294)
                      ++++.+..+.+.+.+||..+.|.|++.+++..++..+++.+|+.+++++++.+++.++||+|.+++.++.++.+.++.||
T Consensus       152 l~~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~~~~it  231 (355)
T TIGR02397       152 LATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLLDQLISFGNGNIT  231 (355)
T ss_pred             EEeCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCChHHHHHHHHHHHhhcCCCCC
Confidence            99988888889999999999999999999999999999999999999999999999999999999999999888777799


Q ss_pred             hhhhhhhcccccC
Q 022641          270 SKDLISVSGYPTG  282 (294)
Q Consensus       270 ~~~v~~~~~~~~~  282 (294)
                      .++|++++.....
T Consensus       232 ~~~v~~~~~~~~~  244 (355)
T TIGR02397       232 YEDVNELLGLVDD  244 (355)
T ss_pred             HHHHHHHhCCCCH
Confidence            9999888765443

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.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.97  E-value=3.4e-30  Score=225.98  Aligned_cols=226  Identities=31%  Similarity=0.449  Sum_probs=191.4

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--------------  112 (294)
                      .+++.++|+|..|++++|++.++..|..++..++.++ ++|+||+|+|||++|+.+++.+.|....              
T Consensus         4 ~~~~~~kyRP~~~~diiGq~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~   83 (451)
T PRK06305          4 YQVSSRKYRPQTFSEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKE   83 (451)
T ss_pred             hHHHHHHhCCCCHHHhcCcHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHH
Confidence            5689999999999999999999999999999888766 8999999999999999999999875311              


Q ss_pred             -----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcce
Q 022641          113 -----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTR  187 (294)
Q Consensus       113 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~  187 (294)
                           ...++.+++....+.+.++..........          ..+++.++||||+|.++...++.|++.+++.+..+.
T Consensus        84 i~~~~~~d~~~i~g~~~~gid~ir~i~~~l~~~~----------~~~~~kvvIIdead~lt~~~~n~LLk~lEep~~~~~  153 (451)
T PRK06305         84 ISSGTSLDVLEIDGASHRGIEDIRQINETVLFTP----------SKSRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVK  153 (451)
T ss_pred             HhcCCCCceEEeeccccCCHHHHHHHHHHHHhhh----------hcCCCEEEEEecHHhhCHHHHHHHHHHhhcCCCCce
Confidence                 22455565555555666665443332221          123467999999999999999999999999888999


Q ss_pred             EEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCC
Q 022641          188 FFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS  267 (294)
Q Consensus       188 ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~  267 (294)
                      +|++++....+.+.+.+||..+.|.+++.+++..++..+++.+|+.+++++++.|+..++||+|.+++.++.++.+.+..
T Consensus       154 ~Il~t~~~~kl~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~~i~~~al~~L~~~s~gdlr~a~~~Lekl~~~~~~~  233 (451)
T PRK06305        154 FFLATTEIHKIPGTILSRCQKMHLKRIPEETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDAESLYDYVVGLFPKS  233 (451)
T ss_pred             EEEEeCChHhcchHHHHhceEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC
Confidence            99999988899999999999999999999999999999999999999999999999999999999999999988776667


Q ss_pred             CChhhhhhhcccccCC
Q 022641          268 ITSKDLISVSGYPTGG  283 (294)
Q Consensus       268 it~~~v~~~~~~~~~~  283 (294)
                      |+.++|..+++....+
T Consensus       234 It~~~V~~l~~~~~~~  249 (451)
T PRK06305        234 LDPDSVAKALGLLSQD  249 (451)
T ss_pred             cCHHHHHHHHCCCCHH
Confidence            9999998887764433

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.97  E-value=7e-30  Score=229.58  Aligned_cols=226  Identities=26%  Similarity=0.429  Sum_probs=192.1

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--------------  112 (294)
                      .+...++|+|..|++++||+.++..|.+++..++.++ ++|+||+|||||++|+.+++.+.|....              
T Consensus         3 ~~~l~~kyRP~~f~eivGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg   82 (620)
T PRK14954          3 YQVIARKYRPSKFADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCG   82 (620)
T ss_pred             cHHHHHHHCCCCHHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCc
Confidence            4567899999999999999999999999999988877 8999999999999999999999885321              


Q ss_pred             ------------CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHH
Q 022641          113 ------------KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTME  180 (294)
Q Consensus       113 ------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~  180 (294)
                                  +..+..+++....+.+.++.....+...+          ..+++.++||||+|.++...++.|++.++
T Consensus        83 ~C~sC~~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P----------~~~~~KVvIIdEad~Lt~~a~naLLK~LE  152 (620)
T PRK14954         83 ECESCRDFDAGTSLNISEFDAASNNSVDDIRQLRENVRYGP----------QKGRYRVYIIDEVHMLSTAAFNAFLKTLE  152 (620)
T ss_pred             cCHHHHHHhccCCCCeEEecccccCCHHHHHHHHHHHHhhh----------hcCCCEEEEEeChhhcCHHHHHHHHHHHh
Confidence                        12344454444455667766655543222          12356799999999999999999999999


Q ss_pred             hhcCcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHH
Q 022641          181 TYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGA  260 (294)
Q Consensus       181 ~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~  260 (294)
                      +++....+|++++....+.+.+.+||..+.|.+++.+++..++.++++.+|+.+++++++.+++.++||+|.+++.++.+
T Consensus       153 ePp~~tv~IL~t~~~~kLl~TI~SRc~~vef~~l~~~ei~~~L~~i~~~egi~I~~eal~~La~~s~Gdlr~al~eLeKL  232 (620)
T PRK14954        153 EPPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLDEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDAQSILDQV  232 (620)
T ss_pred             CCCCCeEEEEEeCChhhhhHHHHhhceEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            99999999999988888999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHh-----CCCCChhhhhhhcccccCC
Q 022641          261 ARLF-----GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       261 ~~~~-----~~~it~~~v~~~~~~~~~~  283 (294)
                      +.+.     ++.||.++|.+++....++
T Consensus       233 ~~y~~~~~~~~~It~~~V~~lv~~~~e~  260 (620)
T PRK14954        233 IAFSVGSEAEKVIAYQGVAELLNYIDDE  260 (620)
T ss_pred             HHhccccccCCccCHHHHHHHHcCCCHH
Confidence            8886     5679999998888665443

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.97  E-value=7.2e-30  Score=228.33  Aligned_cols=226  Identities=26%  Similarity=0.388  Sum_probs=192.4

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--------------  112 (294)
                      ...+..+|+|..|++++||+.++..|..++..++.++ ++|+||+|+|||++|+++++.+.|....              
T Consensus         3 y~~l~~kyRP~~f~diiGqe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C~~C~~i   82 (563)
T PRK06647          3 YRGTATKRRPRDFNSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSSCKSI   82 (563)
T ss_pred             cHHHHHHhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccchHHHHH
Confidence            4568899999999999999999999999999988877 8999999999999999999999875211              


Q ss_pred             ----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          113 ----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       113 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                          ...++.+++....+.+.++.........+          ..+++.++||||+|.++...++.|++.+++++..+.+
T Consensus        83 ~~~~~~dv~~idgas~~~vddIr~l~e~~~~~p----------~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vf  152 (563)
T PRK06647         83 DNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPP----------ASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVF  152 (563)
T ss_pred             HcCCCCCeEEecCcccCCHHHHHHHHHHHHhch----------hcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEE
Confidence                22445555544455566665544433322          1245679999999999999999999999999999999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++++.+..+.+++.+||..+.|.+++.+++..++..++..+++.++++++..|++.++||+|.++++++.++.+.+..|
T Consensus       153 I~~tte~~kL~~tI~SRc~~~~f~~l~~~el~~~L~~i~~~egi~id~eAl~lLa~~s~GdlR~alslLdklis~~~~~I  232 (563)
T PRK06647        153 IFATTEVHKLPATIKSRCQHFNFRLLSLEKIYNMLKKVCLEDQIKYEDEALKWIAYKSTGSVRDAYTLFDQVVSFSDSDI  232 (563)
T ss_pred             EEecCChHHhHHHHHHhceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCC
Confidence            99998888899999999999999999999999999999999999999999999999999999999999998888777789


Q ss_pred             ChhhhhhhcccccCC
Q 022641          269 TSKDLISVSGYPTGG  283 (294)
Q Consensus       269 t~~~v~~~~~~~~~~  283 (294)
                      |.+++..+++.....
T Consensus       233 t~e~V~~llg~~~~~  247 (563)
T PRK06647        233 TLEQIRSKMGLTGDE  247 (563)
T ss_pred             CHHHHHHHhCCCCHH
Confidence            999999988765443

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

Probab=99.97  E-value=2.3e-30  Score=200.67  Aligned_cols=196  Identities=24%  Similarity=0.314  Sum_probs=144.3

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHc-----CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLET-----ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~-----~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      ....|+.+.++|..+++++||++++..+.-++..     ...++++|+||||+||||||..+|+++      +..+..++
T Consensus         9 ~~~~~l~~~lRP~~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~------~~~~~~~s   82 (233)
T PF05496_consen    9 EEEAPLAERLRPKSLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANEL------GVNFKITS   82 (233)
T ss_dssp             ---S-HHHHTS-SSCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHC------T--EEEEE
T ss_pred             CcchhhHHhcCCCCHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhcc------CCCeEecc
Confidence            3455888999999999999999999887666542     345689999999999999999999999      77777787


Q ss_pred             CCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------------
Q 022641          121 ASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------------  183 (294)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------------  183 (294)
                      ++.......+...+..+.                ++.||||||+|++++.+++.|+..||++.                 
T Consensus        83 g~~i~k~~dl~~il~~l~----------------~~~ILFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~  146 (233)
T PF05496_consen   83 GPAIEKAGDLAAILTNLK----------------EGDILFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRIN  146 (233)
T ss_dssp             CCC--SCHHHHHHHHT------------------TT-EEEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE
T ss_pred             chhhhhHHHHHHHHHhcC----------------CCcEEEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeecc
Confidence            765444444544443321                24599999999999999999999999643                 


Q ss_pred             -CcceEEEEecCCcccchHhhccccE-EEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHH
Q 022641          184 -KVTRFFFICNYISRIIEPLASRCAK-FRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA  261 (294)
Q Consensus       184 -~~~~ii~~~~~~~~~~~~l~~r~~~-i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~  261 (294)
                       .++.+|.+|+....+..++++||.+ ..+..++.+++..++.+.+...++.++++...+|+..|.|.||-+.++|+.+.
T Consensus       147 l~~FTligATTr~g~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~i~~~~~~~Ia~rsrGtPRiAnrll~rvr  226 (233)
T PF05496_consen  147 LPPFTLIGATTRAGLLSSPLRDRFGIVLRLEFYSEEELAKIVKRSARILNIEIDEDAAEEIARRSRGTPRIANRLLRRVR  226 (233)
T ss_dssp             ----EEEEEESSGCCTSHCCCTTSSEEEE----THHHHHHHHHHCCHCTT-EE-HHHHHHHHHCTTTSHHHHHHHHHHHC
T ss_pred             CCCceEeeeeccccccchhHHhhcceecchhcCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence             2355777788888889999999996 58999999999999999998899999999999999999999999999999775


Q ss_pred             HH
Q 022641          262 RL  263 (294)
Q Consensus       262 ~~  263 (294)
                      .+
T Consensus       227 D~  228 (233)
T PF05496_consen  227 DF  228 (233)
T ss_dssp             CC
T ss_pred             HH
Confidence            44

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.97  E-value=9.1e-30  Score=221.27  Aligned_cols=225  Identities=27%  Similarity=0.440  Sum_probs=189.2

Q ss_pred             chhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc---------------
Q 022641           49 QPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY---------------  112 (294)
Q Consensus        49 ~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~---------------  112 (294)
                      ..+.++|+|..|++++||+.++..|..++..++.++ ++|+||+|+|||++|+++++.+.|....               
T Consensus         4 ~~l~~k~RP~~~~eiiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~   83 (397)
T PRK14955          4 QVIARKYRPKKFADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGE   83 (397)
T ss_pred             HHHHHhcCCCcHhhccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCC
Confidence            467899999999999999999999999999998887 8999999999999999999999885311               


Q ss_pred             -----------CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh
Q 022641          113 -----------KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMET  181 (294)
Q Consensus       113 -----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~  181 (294)
                                 +..++.+++....+.+.++.....+...+          ..+++.++||||+|.++...++.|++.+++
T Consensus        84 c~~c~~~~~~~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p----------~~~~~kvvIIdea~~l~~~~~~~LLk~LEe  153 (397)
T PRK14955         84 CESCRDFDAGTSLNISEFDAASNNSVDDIRLLRENVRYGP----------QKGRYRVYIIDEVHMLSIAAFNAFLKTLEE  153 (397)
T ss_pred             CHHHHHHhcCCCCCeEeecccccCCHHHHHHHHHHHhhch----------hcCCeEEEEEeChhhCCHHHHHHHHHHHhc
Confidence                       11334444444445666665544443222          123567999999999999999999999999


Q ss_pred             hcCcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHH
Q 022641          182 YSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA  261 (294)
Q Consensus       182 ~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~  261 (294)
                      ++....+|++++....+.+.+.+||..+.|.|++.+++..++...++.++..+++++++.+++.++||+|.+++.++.+.
T Consensus       154 p~~~t~~Il~t~~~~kl~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~~i~~~al~~l~~~s~g~lr~a~~~L~kl~  233 (397)
T PRK14955        154 PPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDAQSILDQVI  233 (397)
T ss_pred             CCCCeEEEEEeCChHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            88888899999888888899999999999999999999999999999999999999999999999999999999999988


Q ss_pred             HHh-----CCCCChhhhhhhcccccCC
Q 022641          262 RLF-----GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       262 ~~~-----~~~it~~~v~~~~~~~~~~  283 (294)
                      .+.     ++.||.++|..+++...+.
T Consensus       234 ~~~~~~~~~~~It~~~v~~~v~~~~~~  260 (397)
T PRK14955        234 AFSVESEGEGSIRYDKVAELLNYIDDE  260 (397)
T ss_pred             HhccccCCCCccCHHHHHHHHCCCCHH
Confidence            774     3479999998887665443

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.97  E-value=1.6e-29  Score=228.62  Aligned_cols=223  Identities=26%  Similarity=0.424  Sum_probs=193.6

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc--------------
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL--------------  111 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~--------------  111 (294)
                      ....|.++|+|..|++++|+++++..|..++..++.++ ++|+||+|+|||++|+.+++.+.|...              
T Consensus         3 ~~~~~~~kyRP~~f~~viGq~~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~   82 (614)
T PRK14971          3 NYIVSARKYRPSTFESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCV   82 (614)
T ss_pred             hhHHHHHHHCCCCHHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHH
Confidence            35689999999999999999999999999999998888 899999999999999999999976432              


Q ss_pred             -----cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcc
Q 022641          112 -----YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVT  186 (294)
Q Consensus       112 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~  186 (294)
                           ....++.+++.+..+.+.++..+......+.          .+++.++||||+|.++...++.|++.|++++...
T Consensus        83 ~~~~~~~~n~~~ld~~~~~~vd~Ir~li~~~~~~P~----------~~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~t  152 (614)
T PRK14971         83 AFNEQRSYNIHELDAASNNSVDDIRNLIEQVRIPPQ----------IGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYA  152 (614)
T ss_pred             HHhcCCCCceEEecccccCCHHHHHHHHHHHhhCcc----------cCCcEEEEEECcccCCHHHHHHHHHHHhCCCCCe
Confidence                 1345566666655566777766655433322          2356799999999999999999999999999999


Q ss_pred             eEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCC
Q 022641          187 RFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGS  266 (294)
Q Consensus       187 ~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~  266 (294)
                      .+|++++....+.+.+++||..+.|.+++.+++..++.+++..+|+.+++++++.|++.++||+|.+++.++.++.+.+.
T Consensus       153 ifIL~tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~  232 (614)
T PRK14971        153 IFILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGG  232 (614)
T ss_pred             EEEEEeCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccC
Confidence            99999998899999999999999999999999999999999999999999999999999999999999999998888766


Q ss_pred             CCChhhhhhhccc
Q 022641          267 SITSKDLISVSGY  279 (294)
Q Consensus       267 ~it~~~v~~~~~~  279 (294)
                      .|+.+++.+.+..
T Consensus       233 ~It~~~V~~~l~~  245 (614)
T PRK14971        233 NITYKSVIENLNI  245 (614)
T ss_pred             CccHHHHHHHhCC
Confidence            6999888777654

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.97  E-value=4.7e-29  Score=214.26  Aligned_cols=224  Identities=34%  Similarity=0.542  Sum_probs=178.3

Q ss_pred             chhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcch-
Q 022641           49 QPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGI-  127 (294)
Q Consensus        49 ~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~-  127 (294)
                      .+|.++|+|..+++++|++..+..|..++..+..++++|+||||||||++|+++++.+.+... ...++.+++.+.... 
T Consensus         3 ~~w~~ky~P~~~~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~~~~-~~~~~~i~~~~~~~~~   81 (337)
T PRK12402          3 PLWTEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDPW-ENNFTEFNVADFFDQG   81 (337)
T ss_pred             CchHHhhCCCcHHHhcCCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcCccc-ccceEEechhhhhhcc
Confidence            489999999999999999999999999999988788999999999999999999999865431 223455554432100 


Q ss_pred             -hH--------------------HHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcc
Q 022641          128 -NV--------------------VRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVT  186 (294)
Q Consensus       128 -~~--------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~  186 (294)
                       ..                    ....+..........     ........+|||||++.++...++.|+.+++..+...
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~  156 (337)
T PRK12402         82 KKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASY-----RPLSADYKTILLDNAEALREDAQQALRRIMEQYSRTC  156 (337)
T ss_pred             hhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhc-----CCCCCCCcEEEEeCcccCCHHHHHHHHHHHHhccCCC
Confidence             00                    001111111000000     0011335699999999999988999999999888778


Q ss_pred             eEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCC
Q 022641          187 RFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGS  266 (294)
Q Consensus       187 ~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~  266 (294)
                      .+|++++.+..+.+.+.+||..+.|.|++.+++..++.+++..+++.+++++++.+++.++||+|.+++.++.++. ..+
T Consensus       157 ~~Il~~~~~~~~~~~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~-~~~  235 (337)
T PRK12402        157 RFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL-AAG  235 (337)
T ss_pred             eEEEEeCChhhCchhhcCCceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH-cCC
Confidence            8999988877888899999999999999999999999999999999999999999999999999999999998773 345


Q ss_pred             CCChhhhhhhccc
Q 022641          267 SITSKDLISVSGY  279 (294)
Q Consensus       267 ~it~~~v~~~~~~  279 (294)
                      .||.+++.+++..
T Consensus       236 ~It~~~v~~~~~~  248 (337)
T PRK12402        236 EITMEAAYEALGD  248 (337)
T ss_pred             CCCHHHHHHHhCC
Confidence            7999999998886

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.97  E-value=4.9e-29  Score=215.81  Aligned_cols=226  Identities=26%  Similarity=0.433  Sum_probs=190.0

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCC-cEEEECCCCCCHHHHHHHHHHHhcCCCc------cCCcceee
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCP-HMLFYGPPGTGKTTTALAIAHQLFGPEL------YKSRVLEL  119 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~-~ill~Gp~G~GKT~la~~la~~~~~~~~------~~~~~~~~  119 (294)
                      .+.+|.++|+|..|++++|++..++.+.+++..+..+ +++|+||||+|||++++++++.+.|...      ....++++
T Consensus         3 ~~~~~~~k~rP~~~~~iig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l   82 (367)
T PRK14970          3 NFVVSARKYRPQTFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFEL   82 (367)
T ss_pred             chHHHHHHHCCCcHHhcCCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEe
Confidence            4578999999999999999999999999999988765 5999999999999999999999876421      22334445


Q ss_pred             cCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccc
Q 022641          120 NASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRII  199 (294)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~  199 (294)
                      +.........++..+......+          ..+++.+|+|||++.++...++.|++.+++++....+|++++....+.
T Consensus        83 ~~~~~~~~~~i~~l~~~~~~~p----------~~~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~  152 (367)
T PRK14970         83 DAASNNSVDDIRNLIDQVRIPP----------QTGKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKII  152 (367)
T ss_pred             ccccCCCHHHHHHHHHHHhhcc----------ccCCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCC
Confidence            5444444556655555432221          123467999999999999889999999998878888889998888999


Q ss_pred             hHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhccc
Q 022641          200 EPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGY  279 (294)
Q Consensus       200 ~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~  279 (294)
                      +++.+||..+.|.+++.+++..++...+.++|+.+++++++.+++.++||+|.+++.++.++.+.+..||.+++..++..
T Consensus       153 ~~l~sr~~~v~~~~~~~~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~gdlr~~~~~lekl~~y~~~~it~~~v~~~~~~  232 (367)
T PRK14970        153 PTILSRCQIFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFDRVVTFCGKNITRQAVTENLNI  232 (367)
T ss_pred             HHHHhcceeEecCCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHhCC
Confidence            99999999999999999999999999999999999999999999999999999999999999887666999999988876


Q ss_pred             ccC
Q 022641          280 PTG  282 (294)
Q Consensus       280 ~~~  282 (294)
                      ..+
T Consensus       233 ~~~  235 (367)
T PRK14970        233 LDY  235 (367)
T ss_pred             CCH
Confidence            543

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.97  E-value=4.1e-29  Score=225.86  Aligned_cols=224  Identities=29%  Similarity=0.457  Sum_probs=190.2

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCC-CcEEEECCCCCCHHHHHHHHHHHhcCCCcc-------------
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANC-PHMLFYGPPGTGKTTTALAIAHQLFGPELY-------------  112 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~-~~ill~Gp~G~GKT~la~~la~~~~~~~~~-------------  112 (294)
                      ...||.++|+|..|.+++|++.++..|..++..++. +.++|+||+|+|||++|+++++.+.|....             
T Consensus         2 ~~~pl~~kyRP~~f~~liGq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg~C~~C   81 (620)
T PRK14948          2 AYEPLHHKYRPQRFDELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCGKCELC   81 (620)
T ss_pred             CcchHHHHhCCCcHhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCcccHHH
Confidence            356999999999999999999999999999998865 569999999999999999999999875321             


Q ss_pred             -------CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCc
Q 022641          113 -------KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKV  185 (294)
Q Consensus       113 -------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~  185 (294)
                             +..+++++.......+.+++.+........          .+++.|+||||+|.|+...++.|++.+++.+..
T Consensus        82 ~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~----------~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~  151 (620)
T PRK14948         82 RAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAPV----------QARWKVYVIDECHMLSTAAFNALLKTLEEPPPR  151 (620)
T ss_pred             HHHhcCCCccEEEEeccccCCHHHHHHHHHHHhhChh----------cCCceEEEEECccccCHHHHHHHHHHHhcCCcC
Confidence                   123445555555566777776655433221          234579999999999999999999999999899


Q ss_pred             ceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhC
Q 022641          186 TRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFG  265 (294)
Q Consensus       186 ~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~  265 (294)
                      +.+|++++++..+.+.+++||..+.|.+++.+++..++..++.++++.++++++..+++.++|++|.++++++..+.+. 
T Consensus       152 tvfIL~t~~~~~llpTIrSRc~~~~f~~l~~~ei~~~L~~ia~kegi~is~~al~~La~~s~G~lr~A~~lLeklsL~~-  230 (620)
T PRK14948        152 VVFVLATTDPQRVLPTIISRCQRFDFRRIPLEAMVQHLSEIAEKESIEIEPEALTLVAQRSQGGLRDAESLLDQLSLLP-  230 (620)
T ss_pred             eEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhcc-
Confidence            9999999988889999999999999999999999999999999999999999999999999999999999999887764 


Q ss_pred             CCCChhhhhhhccccc
Q 022641          266 SSITSKDLISVSGYPT  281 (294)
Q Consensus       266 ~~it~~~v~~~~~~~~  281 (294)
                      ..||.+++..+++...
T Consensus       231 ~~It~e~V~~lvg~~~  246 (620)
T PRK14948        231 GPITPEAVWDLLGAVP  246 (620)
T ss_pred             CCCCHHHHHHHhcCCC
Confidence            4699988887776543

>PRK04195 replication factor C large subunit; Provisional

Probab=99.97  E-value=3.6e-29  Score=222.93  Aligned_cols=214  Identities=33%  Similarity=0.451  Sum_probs=177.6

Q ss_pred             chhhhhcCCCcchhhcccHHHHHHHHHHHHcCC----CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC
Q 022641           49 QPWVEKYRPKQVKDVAHQEEVVRVLTNTLETAN----CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD  124 (294)
Q Consensus        49 ~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~----~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~  124 (294)
                      .+|+++|+|..+++++|++..+..|..|+....    .++++|+||||||||++|+++++++      +..++++++++.
T Consensus         2 ~~W~eKyrP~~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el------~~~~ielnasd~   75 (482)
T PRK04195          2 MPWVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDY------GWEVIELNASDQ   75 (482)
T ss_pred             CCchhhcCCCCHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHc------CCCEEEEccccc
Confidence            489999999999999999999999999986432    4569999999999999999999998      788999999887


Q ss_pred             cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH----HHHHHHHHHHHhhcCcceEEEEecCCcccch
Q 022641          125 RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE----DAQNALRRTMETYSKVTRFFFICNYISRIIE  200 (294)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~----~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~  200 (294)
                      .....+...+........-.        ..++.+|||||+|.++.    ...+.|+..++.  ....+|+++|.+..+..
T Consensus        76 r~~~~i~~~i~~~~~~~sl~--------~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~--~~~~iIli~n~~~~~~~  145 (482)
T PRK04195         76 RTADVIERVAGEAATSGSLF--------GARRKLILLDEVDGIHGNEDRGGARAILELIKK--AKQPIILTANDPYDPSL  145 (482)
T ss_pred             ccHHHHHHHHHHhhccCccc--------CCCCeEEEEecCcccccccchhHHHHHHHHHHc--CCCCEEEeccCccccch
Confidence            77666665555433221100        02467999999999975    557788888875  44568889998877766


Q ss_pred             -HhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhccc
Q 022641          201 -PLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGY  279 (294)
Q Consensus       201 -~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~  279 (294)
                       .+.++|..+.|++|+..++..++..++..+++.+++++++.|++.++||+|.+++.|+.++. ....|+.+++..+...
T Consensus       146 k~Lrsr~~~I~f~~~~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~~s~GDlR~ain~Lq~~a~-~~~~it~~~v~~~~~~  224 (482)
T PRK04195        146 RELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAE-GYGKLTLEDVKTLGRR  224 (482)
T ss_pred             hhHhccceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHhc-CCCCCcHHHHHHhhcC
Confidence             88999999999999999999999999999999999999999999999999999999998443 2456999999877643

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.97  E-value=8.1e-29  Score=224.60  Aligned_cols=225  Identities=28%  Similarity=0.428  Sum_probs=190.4

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--------------  112 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--------------  112 (294)
                      ++-|.++|+|..|++++|+++++..|..++..++.++ ++|+||+|+|||++|+.+++.+.|....              
T Consensus         3 ~~~l~~kyRP~~~~eiiGq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~~c~~c~~   82 (585)
T PRK14950          3 VQVLYRKWRSQTFAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCEMCRA   82 (585)
T ss_pred             cHHHHHHhCCCCHHHhcCCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccCHHHHH
Confidence            4568899999999999999999999999999887766 6999999999999999999999764321              


Q ss_pred             -----CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcce
Q 022641          113 -----KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTR  187 (294)
Q Consensus       113 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~  187 (294)
                           +..++.++.......+.++..+..+....          ..+++.|+||||+|.++...++.|++.+++.+....
T Consensus        83 i~~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p----------~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv  152 (585)
T PRK14950         83 IAEGSAVDVIEMDAASHTSVDDAREIIERVQFRP----------ALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAI  152 (585)
T ss_pred             HhcCCCCeEEEEeccccCCHHHHHHHHHHHhhCc----------ccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeE
Confidence                 12344555545556666666554432221          124567999999999999999999999999888889


Q ss_pred             EEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCC
Q 022641          188 FFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS  267 (294)
Q Consensus       188 ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~  267 (294)
                      +|++++....+.+.+.+||..+.|.+++..++..++..++..+|+.++++++..|++.++||+|.+++.++.++.+.+..
T Consensus       153 ~Il~t~~~~kll~tI~SR~~~i~f~~l~~~el~~~L~~~a~~egl~i~~eal~~La~~s~Gdlr~al~~LekL~~y~~~~  232 (585)
T PRK14950        153 FILATTEVHKVPATILSRCQRFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDAENLLQQLATTYGGE  232 (585)
T ss_pred             EEEEeCChhhhhHHHHhccceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCC
Confidence            99999888888899999999999999999999999999999999999999999999999999999999999988877778


Q ss_pred             CChhhhhhhcccccC
Q 022641          268 ITSKDLISVSGYPTG  282 (294)
Q Consensus       268 it~~~v~~~~~~~~~  282 (294)
                      ||.+++..+++...+
T Consensus       233 It~e~V~~ll~~s~~  247 (585)
T PRK14950        233 ISLSQVQSLLGISGD  247 (585)
T ss_pred             CCHHHHHHHhcCCCH
Confidence            999999988876543

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.96  E-value=9.3e-28  Score=210.09  Aligned_cols=211  Identities=31%  Similarity=0.404  Sum_probs=173.7

Q ss_pred             hhhhhcCCCcchhhcccHHHHHH---HHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRV---LTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG  126 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~---l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~  126 (294)
                      ||.++|+|..+++++|+++.+..   +..++..+..++++|+||||||||++|+.+++..      +..++.+++... +
T Consensus         1 pla~~~RP~~l~d~vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~------~~~~~~l~a~~~-~   73 (413)
T PRK13342          1 PLAERMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGAT------DAPFEALSAVTS-G   73 (413)
T ss_pred             ChhhhhCCCCHHHhcCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHh------CCCEEEEecccc-c
Confidence            79999999999999999999766   9999998888899999999999999999999988      667777776643 4


Q ss_pred             hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEe--cCCcccchHhhc
Q 022641          127 INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFIC--NYISRIIEPLAS  204 (294)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~--~~~~~~~~~l~~  204 (294)
                      ...++..+........          .+++.+|+|||+|.++...++.|+..++.  ....+|.++  |....+.+++.+
T Consensus        74 ~~~ir~ii~~~~~~~~----------~g~~~vL~IDEi~~l~~~~q~~LL~~le~--~~iilI~att~n~~~~l~~aL~S  141 (413)
T PRK13342         74 VKDLREVIEEARQRRS----------AGRRTILFIDEIHRFNKAQQDALLPHVED--GTITLIGATTENPSFEVNPALLS  141 (413)
T ss_pred             HHHHHHHHHHHHHhhh----------cCCceEEEEechhhhCHHHHHHHHHHhhc--CcEEEEEeCCCChhhhccHHHhc
Confidence            4445555444332211          12456999999999999999999999986  334444444  334578899999


Q ss_pred             cccEEEecCCCHHHHHHHHHHHHHHh--CC-CCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhcccc
Q 022641          205 RCAKFRFKPLSEEVMSSRVLHICNEE--GL-NLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYP  280 (294)
Q Consensus       205 r~~~i~~~~~~~~~~~~~l~~~~~~~--~~-~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~~  280 (294)
                      ||..+.|.|++.+++..++.+.+...  ++ .+++++++.+++.++||+|.++++++.++.. +..|+.+++..+++..
T Consensus       142 R~~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~Le~~~~~-~~~It~~~v~~~~~~~  219 (413)
T PRK13342        142 RAQVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLLELAALG-VDSITLELLEEALQKR  219 (413)
T ss_pred             cceeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHc-cCCCCHHHHHHHHhhh
Confidence            99999999999999999999988653  44 7999999999999999999999999998876 6779999999988763

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.96  E-value=1.1e-26  Score=197.56  Aligned_cols=214  Identities=33%  Similarity=0.459  Sum_probs=171.3

Q ss_pred             ccCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEE-ECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           45 LQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLF-YGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        45 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill-~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      .....+|.++|+|..+++++|++.....+..++..+..++++| +||||+|||++++++++++      +..+..+++.+
T Consensus         5 ~~~~~~w~~kyrP~~~~~~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~------~~~~~~i~~~~   78 (316)
T PHA02544          5 NPNEFMWEQKYRPSTIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV------GAEVLFVNGSD   78 (316)
T ss_pred             CCCCCcceeccCCCcHHHhcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHh------CccceEeccCc
Confidence            3556799999999999999999999999999999888777655 8999999999999999987      55677788776


Q ss_pred             CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCC-CHHHHHHHHHHHHhhcCcceEEEEecCCcccchHh
Q 022641          124 DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSM-TEDAQNALRRTMETYSKVTRFFFICNYISRIIEPL  202 (294)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l-~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l  202 (294)
                      . ....++..+..+.....         ....+++|+|||+|.+ ....++.|...++..+..+.+|+++|....+.+++
T Consensus        79 ~-~~~~i~~~l~~~~~~~~---------~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~~~l  148 (316)
T PHA02544         79 C-RIDFVRNRLTRFASTVS---------LTGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPL  148 (316)
T ss_pred             c-cHHHHHHHHHHHHHhhc---------ccCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhchHHH
Confidence            3 24444443433322211         1124579999999999 66677888888999888889999999998999999


Q ss_pred             hccccEEEecCCCHHHHHHHHH-------HHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhh
Q 022641          203 ASRCAKFRFKPLSEEVMSSRVL-------HICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLIS  275 (294)
Q Consensus       203 ~~r~~~i~~~~~~~~~~~~~l~-------~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~  275 (294)
                      .+||..+.|++|+.++...++.       .++..+++.++++++..+++.+.||.|.+++.++..+.  ...++.+++..
T Consensus       149 ~sR~~~i~~~~p~~~~~~~il~~~~~~~~~~~~~~~~~i~~~al~~l~~~~~~d~r~~l~~l~~~~~--~~~i~~~~l~~  226 (316)
T PHA02544        149 RSRCRVIDFGVPTKEEQIEMMKQMIVRCKGILEAEGVEVDMKVLAALVKKNFPDFRRTINELQRYAS--TGKIDAGILSE  226 (316)
T ss_pred             HhhceEEEeCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHc--cCCCCHHHHHH
Confidence            9999999999999888775544       34556789999999999999999999999999996653  34577666554


Q ss_pred             h
Q 022641          276 V  276 (294)
Q Consensus       276 ~  276 (294)
                      .
T Consensus       227 ~  227 (316)
T PHA02544        227 V  227 (316)
T ss_pred             h
Confidence            3

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

Probab=99.95  E-value=1e-27  Score=192.39  Aligned_cols=236  Identities=42%  Similarity=0.614  Sum_probs=206.8

Q ss_pred             cccCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           44 VLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        44 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      .....+||+++|+|..+.++++++..+..+.+....++.++++++||||+|||+...+.++.+.++......+.++++++
T Consensus        24 ~~~~~~pwvekyrP~~l~dv~~~~ei~st~~~~~~~~~lPh~L~YgPPGtGktsti~a~a~~ly~~~~~~~m~lelnaSd  103 (360)
T KOG0990|consen   24 SPQYPQPWVEKYRPPFLGIVIKQEPIWSTENRYSGMPGLPHLLFYGPPGTGKTSTILANARDFYSPHPTTSMLLELNASD  103 (360)
T ss_pred             CcccCCCCccCCCCchhhhHhcCCchhhHHHHhccCCCCCcccccCCCCCCCCCchhhhhhhhcCCCCchhHHHHhhccC
Confidence            34678899999999999999999999999999988899999999999999999999999999988877777789999999


Q ss_pred             CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhh
Q 022641          124 DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLA  203 (294)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~  203 (294)
                      .++.+..+..+..+.........+.    .....++|+||+|.+...+++.|.+.++.+..+.+|++++|.+..+.++++
T Consensus       104 ~rgid~vr~qi~~fast~~~~~fst----~~~fKlvILDEADaMT~~AQnALRRviek~t~n~rF~ii~n~~~ki~pa~q  179 (360)
T KOG0990|consen  104 DRGIDPVRQQIHLFASTQQPTTYST----HAAFKLVILDEADAMTRDAQNALRRVIEKYTANTRFATISNPPQKIHPAQQ  179 (360)
T ss_pred             ccCCcchHHHHHHHHhhccceeccc----cCceeEEEecchhHhhHHHHHHHHHHHHHhccceEEEEeccChhhcCchhh
Confidence            9999998888887766543211111    124569999999999999999999999999999999999999999999999


Q ss_pred             ccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh----CCCCChhhhhhhccc
Q 022641          204 SRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF----GSSITSKDLISVSGY  279 (294)
Q Consensus       204 ~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~  279 (294)
                      +||..+.|.|++..+....+.+++..+....+++....++..+.||.|.++|.|+-...+.    ...++-+.+..+.+.
T Consensus       180 sRctrfrf~pl~~~~~~~r~shi~e~e~~~~~~~~~~a~~r~s~gDmr~a~n~Lqs~~~~~~~~~e~~~~~~~vy~c~g~  259 (360)
T KOG0990|consen  180 SRCTRFRFAPLTMAQQTERQSHIRESEQKETNPEGYSALGRLSVGDMRVALNYLQSILKKVMERKELNNPNDLVYQCKGA  259 (360)
T ss_pred             cccccCCCCCCChhhhhhHHHHHHhcchhhcCHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCCCCCCCCchhhHHHhcCC
Confidence            9999999999999999999999999999999999999999999999999999999877665    233556667887777


Q ss_pred             ccCC
Q 022641          280 PTGG  283 (294)
Q Consensus       280 ~~~~  283 (294)
                      +.+.
T Consensus       260 p~~~  263 (360)
T KOG0990|consen  260 PQPS  263 (360)
T ss_pred             CChh
Confidence            6655

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

Probab=99.95  E-value=1.4e-26  Score=188.86  Aligned_cols=218  Identities=24%  Similarity=0.344  Sum_probs=173.1

Q ss_pred             CCchhhhhcCCCcchhhcccHHHH---HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVV---RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~---~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ...|+.++++|+.+++++||++++   ..|+..++.++.+.++||||||||||+||+.++.....+   ...|+++++..
T Consensus       124 qh~PLaermRPktL~dyvGQ~hlv~q~gllrs~ieq~~ipSmIlWGppG~GKTtlArlia~tsk~~---SyrfvelSAt~  200 (554)
T KOG2028|consen  124 QHKPLAERMRPKTLDDYVGQSHLVGQDGLLRSLIEQNRIPSMILWGPPGTGKTTLARLIASTSKKH---SYRFVELSATN  200 (554)
T ss_pred             ccCChhhhcCcchHHHhcchhhhcCcchHHHHHHHcCCCCceEEecCCCCchHHHHHHHHhhcCCC---ceEEEEEeccc
Confidence            466999999999999999999988   467888899999999999999999999999999876221   24577777665


Q ss_pred             CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEe--cCCcccchH
Q 022641          124 DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFIC--NYISRIIEP  201 (294)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~--~~~~~~~~~  201 (294)
                      . ....+++.+........         ...++-||||||+|+++..+++.++..++.  ..+.+|.+|  |..+.+..+
T Consensus       201 a-~t~dvR~ife~aq~~~~---------l~krkTilFiDEiHRFNksQQD~fLP~VE~--G~I~lIGATTENPSFqln~a  268 (554)
T KOG2028|consen  201 A-KTNDVRDIFEQAQNEKS---------LTKRKTILFIDEIHRFNKSQQDTFLPHVEN--GDITLIGATTENPSFQLNAA  268 (554)
T ss_pred             c-chHHHHHHHHHHHHHHh---------hhcceeEEEeHHhhhhhhhhhhcccceecc--CceEEEecccCCCccchhHH
Confidence            4 44556666666544322         223456999999999999999999999986  444455554  667889999


Q ss_pred             hhccccEEEecCCCHHHHHHHHHHHHHH----h----C-----CCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh----
Q 022641          202 LASRCAKFRFKPLSEEVMSSRVLHICNE----E----G-----LNLDAEALSTLSSISQGDLRRAITYLQGAARLF----  264 (294)
Q Consensus       202 l~~r~~~i~~~~~~~~~~~~~l~~~~~~----~----~-----~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~----  264 (294)
                      +++||.++.+.+++.+.+..+|.+....    +    +     +.+++.++++++..|.||-|.++|.|+......    
T Consensus       269 LlSRC~VfvLekL~~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyla~lsdGDaR~aLN~Lems~~m~~tr~  348 (554)
T KOG2028|consen  269 LLSRCRVFVLEKLPVNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDGDARAALNALEMSLSMFCTRS  348 (554)
T ss_pred             HHhccceeEeccCCHHHHHHHHHHHHHhhccccccCCCCCCcchhhhHHHHHHHHHhcCchHHHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999999985541    1    1     236788999999999999999999999774333    


Q ss_pred             ----CCCCChhhhhhhccc
Q 022641          265 ----GSSITSKDLISVSGY  279 (294)
Q Consensus       265 ----~~~it~~~v~~~~~~  279 (294)
                          +..++.+++++.+..
T Consensus       349 g~~~~~~lSidDvke~lq~  367 (554)
T KOG2028|consen  349 GQSSRVLLSIDDVKEGLQR  367 (554)
T ss_pred             CCcccceecHHHHHHHHhh
Confidence                235899999887754

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.95  E-value=5.9e-26  Score=193.36  Aligned_cols=210  Identities=20%  Similarity=0.242  Sum_probs=167.4

Q ss_pred             chhhhhcCCCcchhhcccHHHHHHHHHHHHc-----CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           49 QPWVEKYRPKQVKDVAHQEEVVRVLTNTLET-----ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        49 ~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~-----~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ..|..+|+|..|++++|+++.+..+..++..     ...++++|+||||||||++|+++++++      +..+...+...
T Consensus        13 ~~~~~~~rP~~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l------~~~~~~~~~~~   86 (328)
T PRK00080         13 DEIERSLRPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEM------GVNIRITSGPA   86 (328)
T ss_pred             chhhhhcCcCCHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHh------CCCeEEEeccc
Confidence            4567899999999999999999988877753     233579999999999999999999998      44444444433


Q ss_pred             CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc------------------Cc
Q 022641          124 DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS------------------KV  185 (294)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~------------------~~  185 (294)
                      ......+...+..+                ...++|+|||+|.++....+.|+..++.+.                  ..
T Consensus        87 ~~~~~~l~~~l~~l----------------~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~~~~~l~~~~~~~~~~~~l~~  150 (328)
T PRK00080         87 LEKPGDLAAILTNL----------------EEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARSIRLDLPP  150 (328)
T ss_pred             ccChHHHHHHHHhc----------------ccCCEEEEecHhhcchHHHHHHHHHHHhcceeeeeccCccccceeecCCC
Confidence            22222222222211                124599999999999888888888887643                  23


Q ss_pred             ceEEEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh
Q 022641          186 TRFFFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF  264 (294)
Q Consensus       186 ~~ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~  264 (294)
                      ..+|++|+....+.+++++||. .+.|.+++.+++.+++++.+...++.++++++..|++.|+|++|.+.++++.+..++
T Consensus       151 ~~li~at~~~~~l~~~L~sRf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a  230 (328)
T PRK00080        151 FTLIGATTRAGLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFA  230 (328)
T ss_pred             ceEEeecCCcccCCHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHH
Confidence            5678888888888899999995 799999999999999999999999999999999999999999999999999766554


Q ss_pred             ----CCCCChhhhhhhcccc
Q 022641          265 ----GSSITSKDLISVSGYP  280 (294)
Q Consensus       265 ----~~~it~~~v~~~~~~~  280 (294)
                          ...|+.+++..++...
T Consensus       231 ~~~~~~~I~~~~v~~~l~~~  250 (328)
T PRK00080        231 QVKGDGVITKEIADKALDML  250 (328)
T ss_pred             HHcCCCCCCHHHHHHHHHHh
Confidence                4579999999888664

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

Probab=99.95  E-value=5.8e-26  Score=178.65  Aligned_cols=208  Identities=37%  Similarity=0.619  Sum_probs=174.8

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCcc-----------------
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELY-----------------  112 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~-----------------  112 (294)
                      .|.++|+|+.+..+.++++....+......+..||++++||+|+||.|.+.++.+++++....                 
T Consensus         2 LWvdkyrpksl~~l~~~~e~~~~Lksl~~~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kkl   81 (351)
T KOG2035|consen    2 LWVDKYRPKSLDELIYHEELANLLKSLSSTGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKL   81 (351)
T ss_pred             cchhhcCcchhhhcccHHHHHHHHHHhcccCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceE
Confidence            599999999999999999999999888887778999999999999999999999999763211                 


Q ss_pred             ------CCcceeecCCCCcc--hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcC
Q 022641          113 ------KSRVLELNASDDRG--INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSK  184 (294)
Q Consensus       113 ------~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~  184 (294)
                            ....+++++++.-.  ...+.+.++.......-..     .......+++|.|+|.|+.+++..|...|+.+..
T Consensus        82 EistvsS~yHlEitPSDaG~~DRvViQellKevAQt~qie~-----~~qr~fKvvvi~ead~LT~dAQ~aLRRTMEkYs~  156 (351)
T KOG2035|consen   82 EISTVSSNYHLEITPSDAGNYDRVVIQELLKEVAQTQQIET-----QGQRPFKVVVINEADELTRDAQHALRRTMEKYSS  156 (351)
T ss_pred             EEEEecccceEEeChhhcCcccHHHHHHHHHHHHhhcchhh-----ccccceEEEEEechHhhhHHHHHHHHHHHHHHhc
Confidence                  22344555555433  2345555555544322111     1112457999999999999999999999999999


Q ss_pred             cceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHH
Q 022641          185 VTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAAR  262 (294)
Q Consensus       185 ~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~  262 (294)
                      .+++|++||..+.+.+++++||..+.++.|+++++..++..+++++++.++.+.+..|++.++||+|.++.+++.+..
T Consensus       157 ~~RlIl~cns~SriIepIrSRCl~iRvpaps~eeI~~vl~~v~~kE~l~lp~~~l~rIa~kS~~nLRrAllmlE~~~~  234 (351)
T KOG2035|consen  157 NCRLILVCNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQLPKELLKRIAEKSNRNLRRALLMLEAVRV  234 (351)
T ss_pred             CceEEEEecCcccchhHHhhheeEEeCCCCCHHHHHHHHHHHHHHhcccCcHHHHHHHHHHhcccHHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999996654

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

Probab=99.95  E-value=1.8e-26  Score=211.26  Aligned_cols=215  Identities=24%  Similarity=0.348  Sum_probs=167.1

Q ss_pred             CCchhhhhcCCCcchhhcccHHHH---HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVV---RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~---~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ...||.++|+|.++++++|+++.+   ..+.+.+..+..++++|+|||||||||+|+++++..      ...++.+++..
T Consensus        14 ~~~PLaek~RP~tldd~vGQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~------~~~f~~lna~~   87 (725)
T PRK13341         14 SEAPLADRLRPRTLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHT------RAHFSSLNAVL   87 (725)
T ss_pred             ccCChHHhcCCCcHHHhcCcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHh------cCcceeehhhh
Confidence            345999999999999999999988   468888888888899999999999999999999987      45566666653


Q ss_pred             CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEe--cCCcccchH
Q 022641          124 DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFIC--NYISRIIEP  201 (294)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~--~~~~~~~~~  201 (294)
                      . +...++..+........         ...+..+|||||+|.++...++.|+..++.  ....+|.++  |..+.+.++
T Consensus        88 ~-~i~dir~~i~~a~~~l~---------~~~~~~IL~IDEIh~Ln~~qQdaLL~~lE~--g~IiLI~aTTenp~~~l~~a  155 (725)
T PRK13341         88 A-GVKDLRAEVDRAKERLE---------RHGKRTILFIDEVHRFNKAQQDALLPWVEN--GTITLIGATTENPYFEVNKA  155 (725)
T ss_pred             h-hhHHHHHHHHHHHHHhh---------hcCCceEEEEeChhhCCHHHHHHHHHHhcC--ceEEEEEecCCChHhhhhhH
Confidence            2 33333333333221111         012346999999999999999999998875  233344433  334568899


Q ss_pred             hhccccEEEecCCCHHHHHHHHHHHHH-------HhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhC------CCC
Q 022641          202 LASRCAKFRFKPLSEEVMSSRVLHICN-------EEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFG------SSI  268 (294)
Q Consensus       202 l~~r~~~i~~~~~~~~~~~~~l~~~~~-------~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~------~~i  268 (294)
                      +.+||..+.|+|++.+++..++++.+.       .+++.+++++++.|++.++||+|.+++.|+.++....      ..|
T Consensus       156 L~SR~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD~R~lln~Le~a~~~~~~~~~~~i~I  235 (725)
T PRK13341        156 LVSRSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDARSLLNALELAVESTPPDEDGLIDI  235 (725)
T ss_pred             hhccccceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccCCCCceec
Confidence            999999999999999999999999987       4567899999999999999999999999998775431      127


Q ss_pred             Chhhhhhhccc
Q 022641          269 TSKDLISVSGY  279 (294)
Q Consensus       269 t~~~v~~~~~~  279 (294)
                      |.+.+.+++..
T Consensus       236 t~~~~~e~l~~  246 (725)
T PRK13341        236 TLAIAEESIQQ  246 (725)
T ss_pred             cHHHHHHHHHH
Confidence            77777776654

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

Probab=99.94  E-value=1.7e-25  Score=196.65  Aligned_cols=225  Identities=29%  Similarity=0.399  Sum_probs=182.8

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHc--------------------------------CC--CCcEEEECCCCCCH
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLET--------------------------------AN--CPHMLFYGPPGTGK   95 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~--------------------------------~~--~~~ill~Gp~G~GK   95 (294)
                      .|+++|+|..|.++.|.+..-+.+..||..                                ++  ...++|+||||.||
T Consensus       260 LWVdky~Pk~FtdLLsDe~tNR~~L~WLK~WD~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~GppGlGK  339 (877)
T KOG1969|consen  260 LWVDKYRPKKFTDLLSDEKTNRRMLGWLKQWDPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPPGLGK  339 (877)
T ss_pred             eeecccChhHHHHHhcchhHHHHHHHHHHhhcHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCCCCCh
Confidence            899999999999999999999999999853                                01  12399999999999


Q ss_pred             HHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHH
Q 022641           96 TTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNAL  175 (294)
Q Consensus        96 T~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L  175 (294)
                      ||||+.+|++.      ++.++++|+++.++...+.+.+..........+      ...++.+|||||||..+....+.+
T Consensus       340 TTLAHViAkqa------GYsVvEINASDeRt~~~v~~kI~~avq~~s~l~------adsrP~CLViDEIDGa~~~~Vdvi  407 (877)
T KOG1969|consen  340 TTLAHVIAKQA------GYSVVEINASDERTAPMVKEKIENAVQNHSVLD------ADSRPVCLVIDEIDGAPRAAVDVI  407 (877)
T ss_pred             hHHHHHHHHhc------CceEEEecccccccHHHHHHHHHHHHhhccccc------cCCCcceEEEecccCCcHHHHHHH
Confidence            99999999999      999999999999999999988888766543221      113456999999999998889999


Q ss_pred             HHHHHh------hc---------------CcceEEEEecCCc-ccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCC
Q 022641          176 RRTMET------YS---------------KVTRFFFICNYIS-RIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLN  233 (294)
Q Consensus       176 ~~~l~~------~~---------------~~~~ii~~~~~~~-~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~  233 (294)
                      +.++..      ++               -...||++||+.. .-+..|+..+.++.|.||+..-+.+.|+.+|..+++.
T Consensus       408 lslv~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNdLYaPaLR~Lr~~A~ii~f~~p~~s~Lv~RL~~IC~rE~mr  487 (877)
T KOG1969|consen  408 LSLVKATNKQATGKQAKKDKKRKKKRSKLLTRPIICICNDLYAPALRPLRPFAEIIAFVPPSQSRLVERLNEICHRENMR  487 (877)
T ss_pred             HHHHHhhcchhhcCcccchhhhhhhccccccCCEEEEecCccchhhhhcccceEEEEecCCChhHHHHHHHHHHhhhcCC
Confidence            888861      11               1234899998754 4456677788899999999999999999999999999


Q ss_pred             CCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCC---CCChhhhhhhcccccCCCCC
Q 022641          234 LDAEALSTLSSISQGDLRRAITYLQGAARLFGS---SITSKDLISVSGYPTGGSGG  286 (294)
Q Consensus       234 ~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~---~it~~~v~~~~~~~~~~~~~  286 (294)
                      .+..++..|++++.+|+|.++|.||+++.-..+   .|++.++-+......++..+
T Consensus       488 ~d~~aL~~L~el~~~DIRsCINtLQfLa~~~~r~ds~i~~~~i~a~~~~~k~~~~s  543 (877)
T KOG1969|consen  488 ADSKALNALCELTQNDIRSCINTLQFLASNVDRRDSSISVKLICAKNVGAKSNSDS  543 (877)
T ss_pred             CCHHHHHHHHHHhcchHHHHHHHHHHHHHhcccccccchhhhhhhhhhcccccccc
Confidence            999999999999999999999999999976533   36666654444433444333

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

Probab=99.94  E-value=1.5e-25  Score=177.19  Aligned_cols=206  Identities=21%  Similarity=0.260  Sum_probs=168.8

Q ss_pred             hhhcCCCcchhhcccHHHHHHHHHHHHcCC-----CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc
Q 022641           52 VEKYRPKQVKDVAHQEEVVRVLTNTLETAN-----CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG  126 (294)
Q Consensus        52 ~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~-----~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~  126 (294)
                      ...++|+.+.+++||+++++.|.-.+...+     ..|++|+||||.||||||..+|+++      +..+...++.....
T Consensus        17 e~~lRP~~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Em------gvn~k~tsGp~leK   90 (332)
T COG2255          17 ERSLRPKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANEL------GVNLKITSGPALEK   90 (332)
T ss_pred             hcccCcccHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHh------cCCeEecccccccC
Confidence            346789999999999999999988776533     3469999999999999999999999      66666665555444


Q ss_pred             hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc------------------CcceE
Q 022641          127 INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS------------------KVTRF  188 (294)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~------------------~~~~i  188 (294)
                      ...+...+..+                ..++|+||||||++++...+.|+..|+++.                  .++.+
T Consensus        91 ~gDlaaiLt~L----------------e~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTL  154 (332)
T COG2255          91 PGDLAAILTNL----------------EEGDVLFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTL  154 (332)
T ss_pred             hhhHHHHHhcC----------------CcCCeEEEehhhhcChhHHHHhhhhhhheeEEEEEccCCccceEeccCCCeeE
Confidence            44444444432                234799999999999999999999999654                  34446


Q ss_pred             EEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---
Q 022641          189 FFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---  264 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---  264 (294)
                      |.+|.....+...+++||. ..++..++.+++..++.+.+...++.++++....|++.+.|.||-+.++|....-++   
T Consensus       155 IGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~~~a~eIA~rSRGTPRIAnRLLrRVRDfa~V~  234 (332)
T COG2255         155 IGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGIEIDEEAALEIARRSRGTPRIANRLLRRVRDFAQVK  234 (332)
T ss_pred             eeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCCCCChHHHHHHHHhccCCcHHHHHHHHHHHHHHHHh
Confidence            7777777778899999998 789999999999999999999999999999999999999999999999999887776   


Q ss_pred             -CCCCChhhhhhhccc
Q 022641          265 -GSSITSKDLISVSGY  279 (294)
Q Consensus       265 -~~~it~~~v~~~~~~  279 (294)
                       ...|+.+-...++..
T Consensus       235 ~~~~I~~~ia~~aL~~  250 (332)
T COG2255         235 GDGDIDRDIADKALKM  250 (332)
T ss_pred             cCCcccHHHHHHHHHH
Confidence             455777766666654

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.94  E-value=2.9e-25  Score=198.89  Aligned_cols=247  Identities=24%  Similarity=0.331  Sum_probs=183.0

Q ss_pred             chHHHHhhccccccCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCC---
Q 022641           33 SEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP---  109 (294)
Q Consensus        33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~---  109 (294)
                      .+.+..++++.. .-..||.++|+|..|++++|++..++.+...+......+++|+||||||||++|+++.+.+...   
T Consensus        38 ~~~~~~~~~~~~-~~~~~~~~~~rp~~f~~iiGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s  116 (531)
T TIGR02902        38 KELEKLNKMRAI-RLTEPLSEKTRPKSFDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAARLVLEEAKKNPAS  116 (531)
T ss_pred             HHHHHHHHhhhh-hhcchHHHhhCcCCHHHeeCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhhhccCC
Confidence            334444555532 3367999999999999999999999999988887777889999999999999999998765321   


Q ss_pred             -CccCCcceeecCCCCc-chhHHH-HHHHHHHhh------hcc----cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHH
Q 022641          110 -ELYKSRVLELNASDDR-GINVVR-TKIKTFAAV------AVG----SGQRRGGYPCPPYKIIILDEADSMTEDAQNALR  176 (294)
Q Consensus       110 -~~~~~~~~~~~~~~~~-~~~~~~-~~~~~~~~~------~~~----~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~  176 (294)
                       .....+++.+++.... ....+. ..+......      ..+    ...+.+....+.+++|+|||++.|++..++.|+
T Consensus       117 ~~~~~~~fi~id~~~~~~~~~~~~~~li~~~~~p~~~~~~~~g~~g~~~~~~G~l~~a~gG~L~IdEI~~L~~~~q~~LL  196 (531)
T TIGR02902       117 PFKEGAAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGELHPVQMNKLL  196 (531)
T ss_pred             CcCCCCCEEEEccccccCCccccchhhcCCcccchhccccccccCCcccccCchhhccCCcEEEEechhhCCHHHHHHHH
Confidence             1124577888875321 111111 111100000      000    001222333556789999999999999999999


Q ss_pred             HHHHhhc----------------------------CcceEEEEe-cCCcccchHhhccccEEEecCCCHHHHHHHHHHHH
Q 022641          177 RTMETYS----------------------------KVTRFFFIC-NYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHIC  227 (294)
Q Consensus       177 ~~l~~~~----------------------------~~~~ii~~~-~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~  227 (294)
                      +.+++..                            ..+++|++| +.+..+++++++||..+.|+|++.+++..++++.+
T Consensus       197 ~~Le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~rlI~ATt~~p~~L~paLrsR~~~I~f~pL~~eei~~Il~~~a  276 (531)
T TIGR02902       197 KVLEDRKVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRNPEEIPPALRSRCVEIFFRPLLDEEIKEIAKNAA  276 (531)
T ss_pred             HHHHhCeeeeccccccccCcccccchhhhcccCcccceEEEEEecCCcccCChHHhhhhheeeCCCCCHHHHHHHHHHHH
Confidence            9997531                            123555554 56788999999999999999999999999999999


Q ss_pred             HHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh----CCCCChhhhhhhccccc
Q 022641          228 NEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF----GSSITSKDLISVSGYPT  281 (294)
Q Consensus       228 ~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~  281 (294)
                      ++.++.+++++++.|..++. |.|.+.++++.++..+    ...|+.+++..++....
T Consensus       277 ~k~~i~is~~al~~I~~y~~-n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~~~  333 (531)
T TIGR02902       277 EKIGINLEKHALELIVKYAS-NGREAVNIVQLAAGIALGEGRKRILAEDIEWVAENGN  333 (531)
T ss_pred             HHcCCCcCHHHHHHHHHhhh-hHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCCcc
Confidence            99999999999999888765 8999999999988766    23699999999987543

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.94  E-value=3.6e-25  Score=187.38  Aligned_cols=200  Identities=20%  Similarity=0.242  Sum_probs=158.0

Q ss_pred             CcchhhcccHHHHHHHHHHHHc-----CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHH
Q 022641           58 KQVKDVAHQEEVVRVLTNTLET-----ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRT  132 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~-----~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (294)
                      ++|++++|+++.+..|..++..     ...++++|+||||||||++|+++++++      ...+.............+..
T Consensus         1 ~~~~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~------~~~~~~~~~~~~~~~~~l~~   74 (305)
T TIGR00635         1 KLLAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEM------GVNLKITSGPALEKPGDLAA   74 (305)
T ss_pred             CCHHHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHh------CCCEEEeccchhcCchhHHH
Confidence            3688999999999999988863     344579999999999999999999998      44444444333222233322


Q ss_pred             HHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc------------------CcceEEEEecC
Q 022641          133 KIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS------------------KVTRFFFICNY  194 (294)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~------------------~~~~ii~~~~~  194 (294)
                      .+...                ....+|+|||++.++...++.|+.+++...                  .+..+|.+++.
T Consensus        75 ~l~~~----------------~~~~vl~iDEi~~l~~~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li~~t~~  138 (305)
T TIGR00635        75 ILTNL----------------EEGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTR  138 (305)
T ss_pred             HHHhc----------------ccCCEEEEehHhhhCHHHHHHhhHHHhhhheeeeeccCccccceeecCCCeEEEEecCC
Confidence            22221                123599999999999988888988887544                  22567777788


Q ss_pred             CcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh----CCCCC
Q 022641          195 ISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF----GSSIT  269 (294)
Q Consensus       195 ~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~----~~~it  269 (294)
                      +..+.+++++||. .+.|.+++.+++.+++++.+...++.++++++..|++.++|++|.+.+++..+..++    ...|+
T Consensus       139 ~~~l~~~l~sR~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it  218 (305)
T TIGR00635       139 AGMLTSPLRDRFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIIN  218 (305)
T ss_pred             ccccCHHHHhhcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcC
Confidence            8888899999996 689999999999999999999999999999999999999999999999998776554    34599


Q ss_pred             hhhhhhhccc
Q 022641          270 SKDLISVSGY  279 (294)
Q Consensus       270 ~~~v~~~~~~  279 (294)
                      .+.+..++..
T Consensus       219 ~~~v~~~l~~  228 (305)
T TIGR00635       219 RDIALKALEM  228 (305)
T ss_pred             HHHHHHHHHH
Confidence            9999888876

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.

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.93  E-value=1.3e-23  Score=178.40  Aligned_cols=194  Identities=25%  Similarity=0.414  Sum_probs=153.5

Q ss_pred             hcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc-----c--C-----C------
Q 022641           54 KYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL-----Y--K-----S------  114 (294)
Q Consensus        54 ~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~-----~--~-----~------  114 (294)
                      ...|..+.+++|++++...|...+..++.++ ++|+||+|+|||++|..+++.+.|...     .  .     +      
T Consensus        16 ~~~P~~~~~l~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~~~~~c~~c~~i   95 (351)
T PRK09112         16 VPSPSENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLADPDPASPVWRQI   95 (351)
T ss_pred             CCCCCchhhccCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCCCCCCCHHHHHH
Confidence            3679999999999999999999999999887 999999999999999999999987310     0  0     0      


Q ss_pred             ------cceeecCC---------CCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHH
Q 022641          115 ------RVLELNAS---------DDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTM  179 (294)
Q Consensus       115 ------~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l  179 (294)
                            .+..+...         ...+.+.++.....+....          ..+++.|+||||+|.++....+.|++.+
T Consensus        96 ~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~----------~~g~~rVviIDeAd~l~~~aanaLLk~L  165 (351)
T PRK09112         96 AQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTS----------GDGNWRIVIIDPADDMNRNAANAILKTL  165 (351)
T ss_pred             HcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhcc----------ccCCceEEEEEchhhcCHHHHHHHHHHH
Confidence                  11112111         0112344443333222211          2245679999999999999999999999


Q ss_pred             HhhcCcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHH
Q 022641          180 ETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQG  259 (294)
Q Consensus       180 ~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~  259 (294)
                      ++++....+|++++.+..+.+.+++||..+.|.|++.+++..++.+.....+  ++++.+..+++.++|++|.++++++.
T Consensus       166 EEpp~~~~fiLit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~~~--~~~~~~~~i~~~s~G~pr~Al~ll~~  243 (351)
T PRK09112        166 EEPPARALFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSSQG--SDGEITEALLQRSKGSVRKALLLLNY  243 (351)
T ss_pred             hcCCCCceEEEEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcccC--CCHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            9998999999999999999999999999999999999999999987543322  77999999999999999999999864

>PRK04132 replication factor C small subunit; Provisional

Probab=99.92  E-value=7.2e-24  Score=195.18  Aligned_cols=188  Identities=48%  Similarity=0.750  Sum_probs=164.3

Q ss_pred             EEEEC--CCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEe
Q 022641           85 MLFYG--PPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILD  162 (294)
Q Consensus        85 ill~G--p~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiD  162 (294)
                      -+..|  |.+.||||+|.++++++++. ..+..++++|+++.++.+.++..+..+.....-.        ..++.++|||
T Consensus       567 ~~~~G~lPh~lGKTT~A~ala~~l~g~-~~~~~~lElNASd~rgid~IR~iIk~~a~~~~~~--------~~~~KVvIID  637 (846)
T PRK04132        567 NFIGGNLPTVLHNTTAALALARELFGE-NWRHNFLELNASDERGINVIREKVKEFARTKPIG--------GASFKIIFLD  637 (846)
T ss_pred             hhhcCCCCCcccHHHHHHHHHHhhhcc-cccCeEEEEeCCCcccHHHHHHHHHHHHhcCCcC--------CCCCEEEEEE
Confidence            45668  99999999999999998764 3456899999999999999998887765432211        1235799999


Q ss_pred             CCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHH
Q 022641          163 EADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTL  242 (294)
Q Consensus       163 ei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l  242 (294)
                      |+|.|+..+++.|++.|+.++..+.+|++||++..+.+++++||..+.|.|++.+++...+.+++..+++.++++++..+
T Consensus       638 EaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi~i~~e~L~~I  717 (846)
T PRK04132        638 EADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAI  717 (846)
T ss_pred             CcccCCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhcccccC
Q 022641          243 SSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTG  282 (294)
Q Consensus       243 ~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~~~~  282 (294)
                      +..++||+|.++++|+.++.. ...||.+++..+.+.+.+
T Consensus       718 a~~s~GDlR~AIn~Lq~~~~~-~~~It~~~V~~~~~~~~~  756 (846)
T PRK04132        718 LYIAEGDMRRAINILQAAAAL-DDKITDENVFLVASRARP  756 (846)
T ss_pred             HHHcCCCHHHHHHHHHHHHHh-cCCCCHHHHHHHhCCCCH
Confidence            999999999999999987754 456999998887766544

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.92  E-value=2e-23  Score=179.47  Aligned_cols=184  Identities=26%  Similarity=0.377  Sum_probs=146.4

Q ss_pred             cchhhcccHHHHHHHHHHHHcCC---------CCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc----------------
Q 022641           59 QVKDVAHQEEVVRVLTNTLETAN---------CPH-MLFYGPPGTGKTTTALAIAHQLFGPELY----------------  112 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~~---------~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~----------------  112 (294)
                      .|++++|++.++..|.+++..+.         .++ ++|+||+|+|||++|+.+++.+.|....                
T Consensus         3 ~f~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~   82 (394)
T PRK07940          3 VWDDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAG   82 (394)
T ss_pred             hhhhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcC
Confidence            57899999999999999998875         444 9999999999999999999999886421                


Q ss_pred             -CCcceeecCC-CCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEE
Q 022641          113 -KSRVLELNAS-DDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFF  190 (294)
Q Consensus       113 -~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~  190 (294)
                       ...+..+... .....+.++..+......+          ..+++.|+||||+|.++...++.|++.+++++....+|+
T Consensus        83 ~hpD~~~i~~~~~~i~i~~iR~l~~~~~~~p----------~~~~~kViiIDead~m~~~aanaLLk~LEep~~~~~fIL  152 (394)
T PRK07940         83 THPDVRVVAPEGLSIGVDEVRELVTIAARRP----------STGRWRIVVIEDADRLTERAANALLKAVEEPPPRTVWLL  152 (394)
T ss_pred             CCCCEEEeccccccCCHHHHHHHHHHHHhCc----------ccCCcEEEEEechhhcCHHHHHHHHHHhhcCCCCCeEEE
Confidence             1122222222 2234556665555443322          123567999999999999999999999999999999999


Q ss_pred             EecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHH
Q 022641          191 ICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYL  257 (294)
Q Consensus       191 ~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l  257 (294)
                      +|+.+..+++.+++||..+.|.+|+.+++..++.+   ..  .++++.+..++..++|+++.++.++
T Consensus       153 ~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~---~~--~~~~~~a~~la~~s~G~~~~A~~l~  214 (394)
T PRK07940        153 CAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVR---RD--GVDPETARRAARASQGHIGRARRLA  214 (394)
T ss_pred             EECChHHChHHHHhhCeEEECCCCCHHHHHHHHHH---hc--CCCHHHHHHHHHHcCCCHHHHHHHh
Confidence            99999999999999999999999999999888852   22  3678889999999999999887664

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.91  E-value=6.6e-23  Score=166.07  Aligned_cols=199  Identities=15%  Similarity=0.161  Sum_probs=146.2

Q ss_pred             cchhhc--ccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHH
Q 022641           59 QVKDVA--HQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKT  136 (294)
Q Consensus        59 ~~~~~~--g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  136 (294)
                      +|++++  ++..++..+.++......++++|+||+||||||+++++++++...   +..+..+.......  ...+....
T Consensus        20 ~fd~f~~~~n~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~---~~~v~y~~~~~~~~--~~~~~~~~   94 (235)
T PRK08084         20 TFASFYPGDNDSLLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAELSQR---GRAVGYVPLDKRAW--FVPEVLEG   94 (235)
T ss_pred             CccccccCccHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEEHHHHhh--hhHHHHHH
Confidence            455555  467788888888877766789999999999999999999987422   12223332221100  01111111


Q ss_pred             HHhhhcccCccCCCCCCCCcEEEEEeCCCCCC--HHHHHHHHHHHHhhcC--cceEEEEecCCc-c---cchHhhccc--
Q 022641          137 FAAVAVGSGQRRGGYPCPPYKIIILDEADSMT--EDAQNALRRTMETYSK--VTRFFFICNYIS-R---IIEPLASRC--  206 (294)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--~~~~~~L~~~l~~~~~--~~~ii~~~~~~~-~---~~~~l~~r~--  206 (294)
                      +.                +.++|+|||++.+.  +..+..|+.+++....  ...+|++++.+. .   +.+.+.+|+  
T Consensus        95 ~~----------------~~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~  158 (235)
T PRK08084         95 ME----------------QLSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDW  158 (235)
T ss_pred             hh----------------hCCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHHHhC
Confidence            11                12499999999985  3445667777765543  346788876542 2   578999999  


Q ss_pred             -cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHH---hCCCCChhhhhhhcc
Q 022641          207 -AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARL---FGSSITSKDLISVSG  278 (294)
Q Consensus       207 -~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~---~~~~it~~~v~~~~~  278 (294)
                       .++.+.||+.+++..++++.+...|+.++++++++|++.++||+|.+++.++.+...   .+..||.+.++++++
T Consensus       159 g~~~~l~~~~~~~~~~~l~~~a~~~~~~l~~~v~~~L~~~~~~d~r~l~~~l~~l~~~~l~~~~~it~~~~k~~l~  234 (235)
T PRK08084        159 GQIYKLQPLSDEEKLQALQLRARLRGFELPEDVGRFLLKRLDREMRTLFMTLDQLDRASITAQRKLTIPFVKEILK  234 (235)
T ss_pred             CceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHc
Confidence             599999999999999999989889999999999999999999999999999986533   257799999988764

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.91  E-value=1.3e-22  Score=173.21  Aligned_cols=190  Identities=24%  Similarity=0.403  Sum_probs=150.6

Q ss_pred             cCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCccCC-------------------
Q 022641           55 YRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYKS-------------------  114 (294)
Q Consensus        55 ~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~~~-------------------  114 (294)
                      ..|..+.+++|++.++..|.+.+..++.++ ++|+||+|+||+++|.++++.++|......                   
T Consensus        13 ~~P~~~~~iiGq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~~~~c~~c   92 (365)
T PRK07471         13 PHPRETTALFGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDHPVA   92 (365)
T ss_pred             CCCCchhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccCCCCChHH
Confidence            679999999999999999999999999888 999999999999999999999987542110                   


Q ss_pred             ---------cceeecCC--C-------CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHH
Q 022641          115 ---------RVLELNAS--D-------DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALR  176 (294)
Q Consensus       115 ---------~~~~~~~~--~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~  176 (294)
                               .+..+...  .       ...++.++.....+...          ...+.+.|+||||+|.++....+.|+
T Consensus        93 ~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~----------~~~~~~kVviIDead~m~~~aanaLL  162 (365)
T PRK07471         93 RRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLT----------AAEGGWRVVIVDTADEMNANAANALL  162 (365)
T ss_pred             HHHHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcC----------cccCCCEEEEEechHhcCHHHHHHHH
Confidence                     11222110  1       11234444433332211          12245679999999999999999999


Q ss_pred             HHHHhhcCcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHH
Q 022641          177 RTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITY  256 (294)
Q Consensus       177 ~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~  256 (294)
                      +.+++.+....+|++|+.+..+.+.+++||..+.|.|++.+++..++...    +...+++.+..++..++|+++.++.+
T Consensus       163 K~LEepp~~~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~----~~~~~~~~~~~l~~~s~Gsp~~Al~l  238 (365)
T PRK07471        163 KVLEEPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAA----GPDLPDDPRAALAALAEGSVGRALRL  238 (365)
T ss_pred             HHHhcCCCCeEEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHh----cccCCHHHHHHHHHHcCCCHHHHHHH
Confidence            99999888899999999998999999999999999999999999998653    34456666688899999999999988


Q ss_pred             HH
Q 022641          257 LQ  258 (294)
Q Consensus       257 l~  258 (294)
                      ++
T Consensus       239 l~  240 (365)
T PRK07471        239 AG  240 (365)
T ss_pred             hc
Confidence            86

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

Probab=99.90  E-value=1.2e-22  Score=165.73  Aligned_cols=205  Identities=20%  Similarity=0.231  Sum_probs=150.9

Q ss_pred             CcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC
Q 022641           58 KQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD  124 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~  124 (294)
                      .+++++-|.+..++.+++.+.-             ..+..++||||||||||.||+++|++.      +..|+.+.++..
T Consensus       148 vtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T------~AtFIrvvgSEl  221 (406)
T COG1222         148 VTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQT------DATFIRVVGSEL  221 (406)
T ss_pred             CChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhcc------CceEEEeccHHH
Confidence            4678889999999999998754             233459999999999999999999998      888998887764


Q ss_pred             cc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHh-----h
Q 022641          125 RG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMET-----Y  182 (294)
Q Consensus       125 ~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~-----~  182 (294)
                      ..      ...+++.+.-....              .+.+|||||+|.+.           .+.|..+++++.+     .
T Consensus       222 VqKYiGEGaRlVRelF~lArek--------------aPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~  287 (406)
T COG1222         222 VQKYIGEGARLVRELFELAREK--------------APSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDP  287 (406)
T ss_pred             HHHHhccchHHHHHHHHHHhhc--------------CCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCC
Confidence            32      22333433332222              24599999999873           3456666666653     2


Q ss_pred             cCcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCc-HHHHHHHHH
Q 022641          183 SKVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGD-LRRAITYLQ  258 (294)
Q Consensus       183 ~~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~-~r~~~~~l~  258 (294)
                      ..++.+|++||.+..++|++++  |+. .|+|+.|+.+...++++-+.++..+. ++-.++.|++.+.|- --.+..++.
T Consensus       288 ~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~-~dvd~e~la~~~~g~sGAdlkaict  366 (406)
T COG1222         288 RGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLA-DDVDLELLARLTEGFSGADLKAICT  366 (406)
T ss_pred             CCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCc-cCcCHHHHHHhcCCCchHHHHHHHH
Confidence            3578899999999999999987  887 89999999999999998888764432 223377777776552 233344555


Q ss_pred             HHHHHh----CCCCChhhhhhhcccccCC
Q 022641          259 GAARLF----GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       259 ~~~~~~----~~~it~~~v~~~~~~~~~~  283 (294)
                      .|..++    +..+|++|+.++...+...
T Consensus       367 EAGm~AiR~~R~~Vt~~DF~~Av~KV~~~  395 (406)
T COG1222         367 EAGMFAIRERRDEVTMEDFLKAVEKVVKK  395 (406)
T ss_pred             HHhHHHHHhccCeecHHHHHHHHHHHHhc
Confidence            555555    5679999999998886654

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

Probab=99.90  E-value=2e-22  Score=157.64  Aligned_cols=215  Identities=25%  Similarity=0.265  Sum_probs=156.3

Q ss_pred             hhcCCCcchhhcccHHHHH---HHHHHHHcC------CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           53 EKYRPKQVKDVAHQEEVVR---VLTNTLETA------NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        53 ~~~~~~~~~~~~g~~~~~~---~l~~~l~~~------~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      +......+++++||+.+++   .+...|.+.      .+.|++|+||||||||++|+++++++      ..+++.+.+..
T Consensus       113 e~~~~it~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~------kvp~l~vkat~  186 (368)
T COG1223         113 EIISDITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEA------KVPLLLVKATE  186 (368)
T ss_pred             hhhccccHhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhccc------CCceEEechHH
Confidence            4455668899999998885   455555542      45689999999999999999999998      78888887766


Q ss_pred             Ccchh--HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH------------HHHHHHHHHHHhhc--Ccce
Q 022641          124 DRGIN--VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE------------DAQNALRRTMETYS--KVTR  187 (294)
Q Consensus       124 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~------------~~~~~L~~~l~~~~--~~~~  187 (294)
                      ..+.+  .....+..+.....          ...++++||||+|.+..            ...|.|+.-|+...  ..++
T Consensus       187 liGehVGdgar~Ihely~rA~----------~~aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGVv  256 (368)
T COG1223         187 LIGEHVGDGARRIHELYERAR----------KAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVV  256 (368)
T ss_pred             HHHHHhhhHHHHHHHHHHHHH----------hcCCeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCceE
Confidence            44332  22222333322211          12246999999998732            35677887777544  4567


Q ss_pred             EEEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC----cHHH--HHHHHHHH
Q 022641          188 FFFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG----DLRR--AITYLQGA  260 (294)
Q Consensus       188 ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G----~~r~--~~~~l~~~  260 (294)
                      .|.+||.+..+++++++||. .|+|.-|+.+++.++++++++..-++++.. ++++++.++|    |+..  +-..|..+
T Consensus       257 tIaaTN~p~~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~-~~~~~~~t~g~SgRdikekvlK~aLh~A  335 (368)
T COG1223         257 TIAATNRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLPVDAD-LRYLAAKTKGMSGRDIKEKVLKTALHRA  335 (368)
T ss_pred             EEeecCChhhcCHHHHhhhhheeeeeCCChHHHHHHHHHHHHhCCCccccC-HHHHHHHhCCCCchhHHHHHHHHHHHHH
Confidence            88889999999999999998 899999999999999999998876666555 7788877655    4332  22345555


Q ss_pred             HHHhCCCCChhhhhhhcccccCCC
Q 022641          261 ARLFGSSITSKDLISVSGYPTGGS  284 (294)
Q Consensus       261 ~~~~~~~it~~~v~~~~~~~~~~~  284 (294)
                      ..-..+.|+.+|+..++.....+.
T Consensus       336 i~ed~e~v~~edie~al~k~r~~r  359 (368)
T COG1223         336 IAEDREKVEREDIEKALKKERKRR  359 (368)
T ss_pred             HHhchhhhhHHHHHHHHHhhcccc
Confidence            555577899999999998644443

>PRK06893 DNA replication initiation factor; Validated

Probab=99.90  E-value=3.6e-22  Score=161.29  Aligned_cols=202  Identities=13%  Similarity=0.182  Sum_probs=139.1

Q ss_pred             CCCcchhhcccHHHH--HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHH
Q 022641           56 RPKQVKDVAHQEEVV--RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTK  133 (294)
Q Consensus        56 ~~~~~~~~~g~~~~~--~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  133 (294)
                      .+.+|+++++.+...  ..+.+.......+.++|+||||||||||++++++++.... ....++.++......    ...
T Consensus        11 ~~~~fd~f~~~~~~~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~-~~~~y~~~~~~~~~~----~~~   85 (229)
T PRK06893         11 DDETLDNFYADNNLLLLDSLRKNFIDLQQPFFYIWGGKSSGKSHLLKAVSNHYLLNQ-RTAIYIPLSKSQYFS----PAV   85 (229)
T ss_pred             CcccccccccCChHHHHHHHHHHhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHcC-CCeEEeeHHHhhhhh----HHH
Confidence            456788888554332  2333333333445689999999999999999999974322 122222222111111    111


Q ss_pred             HHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC--HHHHHHHHHHHHhhcCc--ceEEEEecCCc-c---cchHhhcc
Q 022641          134 IKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT--EDAQNALRRTMETYSKV--TRFFFICNYIS-R---IIEPLASR  205 (294)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--~~~~~~L~~~l~~~~~~--~~ii~~~~~~~-~---~~~~l~~r  205 (294)
                      +..                ..+.++|+|||++.+.  ......|+.+++.....  ..++++++... .   ..+.+.+|
T Consensus        86 ~~~----------------~~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sR  149 (229)
T PRK06893         86 LEN----------------LEQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASR  149 (229)
T ss_pred             Hhh----------------cccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHH
Confidence            111                1133599999999874  33445688888766543  23455565432 2   34789999


Q ss_pred             cc---EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---CCCCChhhhhhhcc
Q 022641          206 CA---KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---GSSITSKDLISVSG  278 (294)
Q Consensus       206 ~~---~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---~~~it~~~v~~~~~  278 (294)
                      +.   .+.+.+|+.+++..++++.+..+++.++++++++|++.++||+|.+.+.++......   ++.||.+.++++++
T Consensus       150 l~~g~~~~l~~pd~e~~~~iL~~~a~~~~l~l~~~v~~~L~~~~~~d~r~l~~~l~~l~~~~~~~~~~it~~~v~~~L~  228 (229)
T PRK06893        150 LTWGEIYQLNDLTDEQKIIVLQRNAYQRGIELSDEVANFLLKRLDRDMHTLFDALDLLDKASLQAQRKLTIPFVKEILG  228 (229)
T ss_pred             HhcCCeeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhc
Confidence            86   899999999999999999999999999999999999999999999999988664322   56799999988765

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=99.90  E-value=8.7e-22  Score=165.14  Aligned_cols=188  Identities=22%  Similarity=0.340  Sum_probs=143.9

Q ss_pred             cchhhcccHHHHHHHHHHHHcCCCC-cEEEECCCCCCHHHHHHHHHHHhcCCCc------------cCCcceeecCCC--
Q 022641           59 QVKDVAHQEEVVRVLTNTLETANCP-HMLFYGPPGTGKTTTALAIAHQLFGPEL------------YKSRVLELNASD--  123 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~~~~-~ill~Gp~G~GKT~la~~la~~~~~~~~------------~~~~~~~~~~~~--  123 (294)
                      .|++++|++.++..|...+..++.+ .++|+||+|+||+++|.++++.+.|...            ....+..+.+..  
T Consensus         2 ~f~~iiGq~~~~~~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~~~~   81 (314)
T PRK07399          2 LFANLIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQH   81 (314)
T ss_pred             cHHHhCCHHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEeccccc
Confidence            4789999999999999999998864 5999999999999999999999987641            111222222110  


Q ss_pred             ---------------------CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh
Q 022641          124 ---------------------DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY  182 (294)
Q Consensus       124 ---------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~  182 (294)
                                           ....+.+++....+...          ...+.+.|+|||+++.++....+.|++.++++
T Consensus        82 ~g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~----------p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEP  151 (314)
T PRK07399         82 QGKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRP----------PLEAPRKVVVIEDAETMNEAAANALLKTLEEP  151 (314)
T ss_pred             cccccchhhhhhccccccccccCcHHHHHHHHHHHccC----------cccCCceEEEEEchhhcCHHHHHHHHHHHhCC
Confidence                                 01122333322222211          12345779999999999999999999999998


Q ss_pred             cCcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHH
Q 022641          183 SKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGA  260 (294)
Q Consensus       183 ~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~  260 (294)
                      + +..+|++++.+..+.+.+++||..+.|.|++.+++..+|.+....++.   +.....++..++|+++.+++.++..
T Consensus       152 p-~~~fILi~~~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~~~---~~~~~~l~~~a~Gs~~~al~~l~~~  225 (314)
T PRK07399        152 G-NGTLILIAPSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEIL---NINFPELLALAQGSPGAAIANIEQL  225 (314)
T ss_pred             C-CCeEEEEECChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhccccc---hhHHHHHHHHcCCCHHHHHHHHHHH
Confidence            8 788999999999999999999999999999999999999876532221   2235678899999999999988754

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.90  E-value=9.2e-22  Score=166.60  Aligned_cols=185  Identities=22%  Similarity=0.371  Sum_probs=149.8

Q ss_pred             cchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc--cCCcceeecC--CCCcchhHHHHH
Q 022641           59 QVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL--YKSRVLELNA--SDDRGINVVRTK  133 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~--~~~~~~~~~~--~~~~~~~~~~~~  133 (294)
                      .|++++|++.+++.+..++..++.++ ++|+||+|+|||++|+.+++.+.|...  ....+..+..  ......+.+++.
T Consensus         2 ~~~~i~g~~~~~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~ir~~   81 (313)
T PRK05564          2 SFHTIIGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDDIRNI   81 (313)
T ss_pred             ChhhccCcHHHHHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHHHHHH
Confidence            57899999999999999999988877 689999999999999999999987532  2233434433  223345566665


Q ss_pred             HHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEEecC
Q 022641          134 IKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKP  213 (294)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~  213 (294)
                      ...+...+          ..+++.++|||++|.++....+.|++.+++++..+.+|++|+.+..+.+.+++||..+.|.+
T Consensus        82 ~~~~~~~p----------~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~~~~~~  151 (313)
T PRK05564         82 IEEVNKKP----------YEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNR  151 (313)
T ss_pred             HHHHhcCc----------ccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhceeeeCCC
Confidence            55433322          12456799999999999999999999999999999999999989999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHH
Q 022641          214 LSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYL  257 (294)
Q Consensus       214 ~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l  257 (294)
                      ++.+++..++.+.+.    .++++.+..++.+++|++..+...+
T Consensus       152 ~~~~~~~~~l~~~~~----~~~~~~~~~l~~~~~g~~~~a~~~~  191 (313)
T PRK05564        152 LSKEEIEKFISYKYN----DIKEEEKKSAIAFSDGIPGKVEKFI  191 (313)
T ss_pred             cCHHHHHHHHHHHhc----CCCHHHHHHHHHHcCCCHHHHHHHh
Confidence            999999998865442    5788889999999999888776543

>TIGR00602 rad24 checkpoint protein rad24

Probab=99.89  E-value=9.2e-22  Score=177.14  Aligned_cols=205  Identities=22%  Similarity=0.324  Sum_probs=136.6

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCC-----cEEEECCCCCCHHHHHHHHHHHhcCCCccCCccee-e
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCP-----HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLE-L  119 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~-----~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~-~  119 (294)
                      ....||.++|+|..+++++|+++.+..+..|+......     .++|+||+|||||++++.+++.+.      ..+.+ .
T Consensus        69 ~~~~pW~eKyrP~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~------~~~~Ew~  142 (637)
T TIGR00602        69 DGNEPWVEKYKPETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELG------IQVQEWS  142 (637)
T ss_pred             cccCchHHHhCCCCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhh------hHHHHHh
Confidence            45679999999999999999999999999998764332     299999999999999999999872      22211 1


Q ss_pred             cCC------C---------------CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH---HHHHH
Q 022641          120 NAS------D---------------DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED---AQNAL  175 (294)
Q Consensus       120 ~~~------~---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~---~~~~L  175 (294)
                      +..      +               ..........+....    ......+.....+..||+|||++.+...   .+..+
T Consensus       143 npv~~~~~~~~~~~~~s~~~~~~~~~s~~~~F~~fl~~a~----~~~~~~g~~~~~~~~IILIDEiPn~~~r~~~~lq~l  218 (637)
T TIGR00602       143 NPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRAT----NKLQMLGDDLMTDKKIILVEDLPNQFYRDTRALHEI  218 (637)
T ss_pred             hhhhhcccccccccchhhhhccccccchHHHHHHHHHHHH----hhhcccccccCCceeEEEeecchhhchhhHHHHHHH
Confidence            100      0               001111222222211    0000001111245679999999766432   23333


Q ss_pred             HH--HHHhhcCcceEEEEecCC-----------cc----cchHhhc--cccEEEecCCCHHHHHHHHHHHHHHhCCC---
Q 022641          176 RR--TMETYSKVTRFFFICNYI-----------SR----IIEPLAS--RCAKFRFKPLSEEVMSSRVLHICNEEGLN---  233 (294)
Q Consensus       176 ~~--~l~~~~~~~~ii~~~~~~-----------~~----~~~~l~~--r~~~i~~~~~~~~~~~~~l~~~~~~~~~~---  233 (294)
                      +.  ..+  ...+.+|++++..           +.    +.+++++  |+..|.|+|++..++.+.|.+++..++..   
T Consensus       219 Lr~~~~e--~~~~pLI~I~TE~~~~~~~~~~~~f~~~~lL~~eLls~~rv~~I~FnPia~t~l~K~L~rIl~~E~~~~~~  296 (637)
T TIGR00602       219 LRWKYVS--IGRCPLVFIITESLEGDNNQRRLLFPAETIMNKEILEEPRVSNISFNPIAPTIMKKFLNRIVTIEAKKNGE  296 (637)
T ss_pred             HHHHhhc--CCCceEEEEecCCccccccccccccchhcccCHhHhcccceeEEEeCCCCHHHHHHHHHHHHHhhhhcccc
Confidence            33  222  2344555555421           11    3368887  55689999999999999999999876432   


Q ss_pred             ---C-CHHHHHHHHhhccCcHHHHHHHHHHHHH
Q 022641          234 ---L-DAEALSTLSSISQGDLRRAITYLQGAAR  262 (294)
Q Consensus       234 ---~-~~~~l~~l~~~~~G~~r~~~~~l~~~~~  262 (294)
                         + +++++..|+..++||+|.|+++|++++.
T Consensus       297 ~~~~p~~~~l~~I~~~s~GDiRsAIn~LQf~~~  329 (637)
T TIGR00602       297 KIKVPKKTSVELLCQGCSGDIRSAINSLQFSSS  329 (637)
T ss_pred             ccccCCHHHHHHHHHhCCChHHHHHHHHHHHHh
Confidence               2 5689999999999999999999999864

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

>PRK08727 hypothetical protein; Validated

Probab=99.89  E-value=2.4e-21  Score=156.76  Aligned_cols=200  Identities=18%  Similarity=0.228  Sum_probs=142.1

Q ss_pred             cchhhcc-cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHH
Q 022641           59 QVKDVAH-QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTF  137 (294)
Q Consensus        59 ~~~~~~g-~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  137 (294)
                      +|+++++ .......+...........++|+||+||||||+++++++++....   ..+..++.....  ..+...+..+
T Consensus        17 ~f~~f~~~~~n~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~a~~~~~~~~~---~~~~y~~~~~~~--~~~~~~~~~l   91 (233)
T PRK08727         17 RFDSYIAAPDGLLAQLQALAAGQSSDWLYLSGPAGTGKTHLALALCAAAEQAG---RSSAYLPLQAAA--GRLRDALEAL   91 (233)
T ss_pred             ChhhccCCcHHHHHHHHHHHhccCCCeEEEECCCCCCHHHHHHHHHHHHHHcC---CcEEEEeHHHhh--hhHHHHHHHH
Confidence            5666654 444444444443333333499999999999999999999874332   233333322211  1111111111


Q ss_pred             HhhhcccCccCCCCCCCCcEEEEEeCCCCCC--HHHHHHHHHHHHhhcC-cceEEEEecCCcc----cchHhhcc---cc
Q 022641          138 AAVAVGSGQRRGGYPCPPYKIIILDEADSMT--EDAQNALRRTMETYSK-VTRFFFICNYISR----IIEPLASR---CA  207 (294)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--~~~~~~L~~~l~~~~~-~~~ii~~~~~~~~----~~~~l~~r---~~  207 (294)
                                      .+.++|+|||++.+.  ...+..++.+++.... ...+|++++.+..    +.+.+.+|   +.
T Consensus        92 ----------------~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~SRl~~~~  155 (233)
T PRK08727         92 ----------------EGRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSRLAQCI  155 (233)
T ss_pred             ----------------hcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHHHHhcCc
Confidence                            123599999999985  3455678888776544 3458888875432    46899999   56


Q ss_pred             EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHH---HhCCCCChhhhhhhccc
Q 022641          208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAAR---LFGSSITSKDLISVSGY  279 (294)
Q Consensus       208 ~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~---~~~~~it~~~v~~~~~~  279 (294)
                      .+.++||+.+++..++++++...++.++++++++|++.++||+|.++++++.+..   ..++.||.+.+++++..
T Consensus       156 ~~~l~~~~~e~~~~iL~~~a~~~~l~l~~e~~~~La~~~~rd~r~~l~~L~~l~~~~~~~~~~it~~~~~~~l~~  230 (233)
T PRK08727        156 RIGLPVLDDVARAAVLRERAQRRGLALDEAAIDWLLTHGERELAGLVALLDRLDRESLAAKRRVTVPFLRRVLEE  230 (233)
T ss_pred             eEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhh
Confidence            8999999999999999999999999999999999999999999999988886643   33677999999988764

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.89  E-value=2.4e-21  Score=156.92  Aligned_cols=200  Identities=17%  Similarity=0.192  Sum_probs=147.6

Q ss_pred             CCCcchhhc--ccHHHHHHHHHHHHc-CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHH
Q 022641           56 RPKQVKDVA--HQEEVVRVLTNTLET-ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRT  132 (294)
Q Consensus        56 ~~~~~~~~~--g~~~~~~~l~~~l~~-~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (294)
                      .|.+|++++  ++...+..+..+... ...++++|+||+||||||+|+++++++...   +..++.+++.....      
T Consensus        13 ~~~~~d~f~~~~~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~---~~~~~~i~~~~~~~------   83 (227)
T PRK08903         13 PPPTFDNFVAGENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASYG---GRNARYLDAASPLL------   83 (227)
T ss_pred             ChhhhcccccCCcHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHHHhC---CCcEEEEehHHhHH------
Confidence            345667666  346677777777653 234569999999999999999999987332   33445554433211      


Q ss_pred             HHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcc--eEEEEecCCc---ccchHhhccc-
Q 022641          133 KIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVT--RFFFICNYIS---RIIEPLASRC-  206 (294)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~--~ii~~~~~~~---~~~~~l~~r~-  206 (294)
                      .+    .            .....++|+|||++.++...+..|+.+++......  .++++++...   .+.+.+.+|+ 
T Consensus        84 ~~----~------------~~~~~~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~  147 (227)
T PRK08903         84 AF----D------------FDPEAELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRTRLG  147 (227)
T ss_pred             HH----h------------hcccCCEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHHHHh
Confidence            00    0            01123599999999999888888988887654332  3555554322   2456778786 


Q ss_pred             --cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---CCCCChhhhhhhcccc
Q 022641          207 --AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---GSSITSKDLISVSGYP  280 (294)
Q Consensus       207 --~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---~~~it~~~v~~~~~~~  280 (294)
                        ..+.++||+.++...++...+...++.+++++++.|++.++||+|.+.++++....++   +..||.+.++++++.+
T Consensus       148 ~~~~i~l~pl~~~~~~~~l~~~~~~~~v~l~~~al~~L~~~~~gn~~~l~~~l~~l~~~~~~~~~~i~~~~~~~~l~~~  226 (227)
T PRK08903        148 WGLVYELKPLSDADKIAALKAAAAERGLQLADEVPDYLLTHFRRDMPSLMALLDALDRYSLEQKRPVTLPLLREMLAQP  226 (227)
T ss_pred             cCeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcc
Confidence              5899999999999999999998999999999999999999999999999888876544   6779999999998753

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.89  E-value=3.4e-21  Score=158.94  Aligned_cols=193  Identities=21%  Similarity=0.235  Sum_probs=134.7

Q ss_pred             cchhhcccHHHHHHHHHHHHc---------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCc-cCCcceeecCC
Q 022641           59 QVKDVAHQEEVVRVLTNTLET---------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPEL-YKSRVLELNAS  122 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~---------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~-~~~~~~~~~~~  122 (294)
                      .+.+++|.+.++..+.+....               +...+++|+||||||||++|+++++.+..... ....++.++++
T Consensus         4 ~l~~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~   83 (261)
T TIGR02881         4 ELSRMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERA   83 (261)
T ss_pred             HHHHhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecHH
Confidence            356788998888776544311               13346999999999999999999998743221 22345555544


Q ss_pred             CCcchhH--HHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC--------HHHHHHHHHHHHhhcCcceEEEEe
Q 022641          123 DDRGINV--VRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT--------EDAQNALRRTMETYSKVTRFFFIC  192 (294)
Q Consensus       123 ~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--------~~~~~~L~~~l~~~~~~~~ii~~~  192 (294)
                      +..+...  ....+......             ...++|||||+|.+.        ...++.|++.++.......+|+++
T Consensus        84 ~l~~~~~g~~~~~~~~~~~~-------------a~~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~vila~  150 (261)
T TIGR02881        84 DLVGEYIGHTAQKTREVIKK-------------ALGGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVLILAG  150 (261)
T ss_pred             HhhhhhccchHHHHHHHHHh-------------ccCCEEEEechhhhccCCccchHHHHHHHHHHHHhccCCCEEEEecC
Confidence            3222110  01111111111             112499999999875        346788888988876676666665


Q ss_pred             cCC-----cccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhh----------ccCcHHHHHHH
Q 022641          193 NYI-----SRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSI----------SQGDLRRAITY  256 (294)
Q Consensus       193 ~~~-----~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~----------~~G~~r~~~~~  256 (294)
                      ...     ..+.+++.+||. .+.|++++.+++.+++++++...+..++++++..+++.          +.||.|.+.|+
T Consensus       151 ~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~~~~gn~R~~~n~  230 (261)
T TIGR02881       151 YSDEMDYFLSLNPGLRSRFPISIDFPDYTVEELMEIAERMVKEREYKLTEEAKWKLREHLYKVDQLSSREFSNARYVRNI  230 (261)
T ss_pred             CcchhHHHHhcChHHHhccceEEEECCCCHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHHHHHhccCCCCchHHHHHHH
Confidence            432     235789999995 79999999999999999999998889999998888543          46999999999


Q ss_pred             HHHHHHHh
Q 022641          257 LQGAARLF  264 (294)
Q Consensus       257 l~~~~~~~  264 (294)
                      ++.+....
T Consensus       231 ~e~a~~~~  238 (261)
T TIGR02881       231 IEKAIRRQ  238 (261)
T ss_pred             HHHHHHHH
Confidence            99876543

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.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.89  E-value=1.5e-21  Score=153.53  Aligned_cols=166  Identities=28%  Similarity=0.444  Sum_probs=128.5

Q ss_pred             HHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc------------------CCcceeecCC-CCcchhHHH
Q 022641           72 VLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY------------------KSRVLELNAS-DDRGINVVR  131 (294)
Q Consensus        72 ~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~------------------~~~~~~~~~~-~~~~~~~~~  131 (294)
                      .|.+.+..++.++ ++|+||+|+|||++++.+++.+.|....                  ...+..+... ...+.+.++
T Consensus         3 ~l~~~i~~~~~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i~   82 (188)
T TIGR00678         3 QLKRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQVR   82 (188)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHHH
Confidence            4667777777655 9999999999999999999999774111                  1112222221 123445555


Q ss_pred             HHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEEe
Q 022641          132 TKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRF  211 (294)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~  211 (294)
                      ..+..+...+          ..+.+.++||||+|.++...++.|++.+++.+....+|++++....+.+++.+||..+.|
T Consensus        83 ~i~~~~~~~~----------~~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~~~~~~  152 (188)
T TIGR00678        83 ELVEFLSRTP----------QESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPF  152 (188)
T ss_pred             HHHHHHccCc----------ccCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhcEEeeC
Confidence            5444433222          124567999999999999999999999999888899999998888899999999999999


Q ss_pred             cCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHH
Q 022641          212 KPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRA  253 (294)
Q Consensus       212 ~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~  253 (294)
                      .|++.+++..++.+.    |  +++++++.+++.++|++|.+
T Consensus       153 ~~~~~~~~~~~l~~~----g--i~~~~~~~i~~~~~g~~r~~  188 (188)
T TIGR00678       153 PPLSEEALLQWLIRQ----G--ISEEAAELLLALAGGSPGAA  188 (188)
T ss_pred             CCCCHHHHHHHHHHc----C--CCHHHHHHHHHHcCCCcccC
Confidence            999999999999654    4  78999999999999999864

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.

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=99.88  E-value=4.8e-21  Score=169.60  Aligned_cols=211  Identities=23%  Similarity=0.363  Sum_probs=140.0

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCC-----CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETAN-----CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~-----~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      ....||.++|+|...+++..+++.+.+++.|+....     .+.++|+||+||||||+++.+++++      +..+.+-.
T Consensus         4 ~~~~~W~~ky~P~~~~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~el------g~~v~Ew~   77 (519)
T PF03215_consen    4 DESEPWVEKYAPKTLDELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKEL------GFEVQEWI   77 (519)
T ss_pred             cccCccchhcCCCCHHHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHh------CCeeEEec
Confidence            467799999999999999999999999999997632     2348999999999999999999998      33333321


Q ss_pred             CCCC-----------cc----hhHHHHHHHHHHhhhcccCc-----cCCCCCCCCcEEEEEeCCCCCCHH----HHHHHH
Q 022641          121 ASDD-----------RG----INVVRTKIKTFAAVAVGSGQ-----RRGGYPCPPYKIIILDEADSMTED----AQNALR  176 (294)
Q Consensus       121 ~~~~-----------~~----~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~lliiDei~~l~~~----~~~~L~  176 (294)
                      .+..           .+    ..........+.........     ..+.....+..||+|||+..+...    ..+.|.
T Consensus        78 np~~~~~~~~~~~d~~s~~~~~~~f~sq~~~F~~f~l~~s~y~~l~~~g~~~~~~~kvILVEDlPN~~~~~~~~f~~~L~  157 (519)
T PF03215_consen   78 NPVSFRESDNQEDDFESDFNKFDEFLSQSDKFSEFLLRASKYSSLSMSGSNSSSNKKVILVEDLPNVFHRDTSRFREALR  157 (519)
T ss_pred             CCCCccccccccccccccccccccccchhhhhccccccccccccccccCCCcCCCceEEEeeccccccchhHHHHHHHHH
Confidence            1110           00    00001111222222111111     112223356789999999876432    334455


Q ss_pred             HHHHhhcC-cceEEEEe-c------CCc--------ccchHhhcc--ccEEEecCCCHHHHHHHHHHHHHHh-----CC-
Q 022641          177 RTMETYSK-VTRFFFIC-N------YIS--------RIIEPLASR--CAKFRFKPLSEEVMSSRVLHICNEE-----GL-  232 (294)
Q Consensus       177 ~~l~~~~~-~~~ii~~~-~------~~~--------~~~~~l~~r--~~~i~~~~~~~~~~~~~l~~~~~~~-----~~-  232 (294)
                      +++..... +.++|++- .      ...        .+.+.+...  +..|.|+|.....+++.|.+++..+     +. 
T Consensus       158 ~~l~~~~~~PlV~iiSe~~~~~~~~~~~~~~~t~~~L~~~~il~~~~i~~I~FNpIa~T~mkKaL~rI~~~E~~~~~~~~  237 (519)
T PF03215_consen  158 QYLRSSRCLPLVFIISETESLSGDNSYRSNSFTAERLFPKEILNHPGITRIKFNPIAPTFMKKALKRILKKEARSSSGKN  237 (519)
T ss_pred             HHHHcCCCCCEEEEEecccccCCCCcccccchhhhhccCHHHHhCCCceEEEecCCCHHHHHHHHHHHHHHHhhhhcCCc
Confidence            55554334 44444441 1      111        245666664  4589999999999999999999987     22 


Q ss_pred             CCC--HHHHHHHHhhccCcHHHHHHHHHHHHH
Q 022641          233 NLD--AEALSTLSSISQGDLRRAITYLQGAAR  262 (294)
Q Consensus       233 ~~~--~~~l~~l~~~~~G~~r~~~~~l~~~~~  262 (294)
                      ..+  .+.++.|++.++||||.|++.||+++.
T Consensus       238 ~~p~~~~~l~~I~~~s~GDIRsAIn~LQf~~~  269 (519)
T PF03215_consen  238 KVPDKQSVLDSIAESSNGDIRSAINNLQFWCL  269 (519)
T ss_pred             cCCChHHHHHHHHHhcCchHHHHHHHHHHHhc
Confidence            222  346999999999999999999999997

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.88  E-value=2.4e-21  Score=157.11  Aligned_cols=199  Identities=17%  Similarity=0.177  Sum_probs=145.0

Q ss_pred             Ccchhhc--ccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHH
Q 022641           58 KQVKDVA--HQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK  135 (294)
Q Consensus        58 ~~~~~~~--g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (294)
                      .+|++++  ++...+..+.+++......+++|+||+|||||++|+.+++.+...   +..++.+++......  ....+.
T Consensus        12 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~~~---~~~~~~i~~~~~~~~--~~~~~~   86 (226)
T TIGR03420        12 PTFDNFYAGGNAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEER---GKSAIYLPLAELAQA--DPEVLE   86 (226)
T ss_pred             hhhcCcCcCCcHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHHhc---CCcEEEEeHHHHHHh--HHHHHh
Confidence            3455554  467788999998877666789999999999999999999987422   234444544332211  011111


Q ss_pred             HHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH--HHHHHHHHHHhhc-CcceEEEEecCCc-c--cc-hHhhcccc-
Q 022641          136 TFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED--AQNALRRTMETYS-KVTRFFFICNYIS-R--II-EPLASRCA-  207 (294)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~--~~~~L~~~l~~~~-~~~~ii~~~~~~~-~--~~-~~l~~r~~-  207 (294)
                      .                ..+.++|+|||++.++..  .++.|+.+++... ....+|++++... .  .. +.+.+|+. 
T Consensus        87 ~----------------~~~~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~  150 (226)
T TIGR03420        87 G----------------LEQADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAW  150 (226)
T ss_pred             h----------------cccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhc
Confidence            1                012349999999999763  3777887776533 2346777776432 2  22 67777763 


Q ss_pred             --EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---CCCCChhhhhhhc
Q 022641          208 --KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---GSSITSKDLISVS  277 (294)
Q Consensus       208 --~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---~~~it~~~v~~~~  277 (294)
                        .+.++|++.++...+++.++...++.+++++++.|++.++||+|.+.+.++.+...+   ++.||.+.+.+++
T Consensus       151 ~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~l~~L~~~~~gn~r~L~~~l~~~~~~~~~~~~~i~~~~~~~~~  225 (226)
T TIGR03420       151 GLVFQLPPLSDEEKIAALQSRAARRGLQLPDEVADYLLRHGSRDMGSLMALLDALDRASLAAKRKITIPFVKEVL  225 (226)
T ss_pred             CeeEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence              799999999999999999988889999999999999999999999999988766433   6779999988775

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.

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

Probab=99.87  E-value=2.4e-21  Score=165.72  Aligned_cols=185  Identities=40%  Similarity=0.607  Sum_probs=149.9

Q ss_pred             hhcccHHHHHHHHHHHH-cCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc------------------cCCcceeecC
Q 022641           62 DVAHQEEVVRVLTNTLE-TANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL------------------YKSRVLELNA  121 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~-~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~------------------~~~~~~~~~~  121 (294)
                      ++++++.....+..+.. .++.++ ++|+||||+|||++|.++++.+.|...                  ....++++++
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~   81 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNP   81 (325)
T ss_pred             CcccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecc
Confidence            46778888888888887 566777 999999999999999999999987553                  3468888999


Q ss_pred             CCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchH
Q 022641          122 SDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEP  201 (294)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~  201 (294)
                      ++....+...+.+..+.......+.      .++..+++|||+|.++.+.++.|++.+++++....+|++||.+..+.+.
T Consensus        82 s~~~~~~i~~~~vr~~~~~~~~~~~------~~~~kviiidead~mt~~A~nallk~lEep~~~~~~il~~n~~~~il~t  155 (325)
T COG0470          82 SDLRKIDIIVEQVRELAEFLSESPL------EGGYKVVIIDEADKLTEDAANALLKTLEEPPKNTRFILITNDPSKILPT  155 (325)
T ss_pred             cccCCCcchHHHHHHHHHHhccCCC------CCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCeEEEEEcCChhhccch
Confidence            9887755445555555544332221      2456799999999999999999999999999999999999999999999


Q ss_pred             hhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHH
Q 022641          202 LASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARL  263 (294)
Q Consensus       202 l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~  263 (294)
                      +.+||..+.|.|++........      +     ++.+..+...+.||.|.+++.++..+..
T Consensus       156 I~SRc~~i~f~~~~~~~~i~~~------e-----~~~l~~i~~~~~gd~r~~i~~lq~~~~~  206 (325)
T COG0470         156 IRSRCQRIRFKPPSRLEAIAWL------E-----DQGLEEIAAVAEGDARKAINPLQALAAL  206 (325)
T ss_pred             hhhcceeeecCCchHHHHHHHh------h-----ccchhHHHHHHHHHHHcCCCHHHHHHHh
Confidence            9999999999995544433333      2     6778899999999999999999988875

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.87  E-value=1.3e-20  Score=160.02  Aligned_cols=183  Identities=27%  Similarity=0.394  Sum_probs=141.9

Q ss_pred             cchhhcc-cHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc------------------CCccee
Q 022641           59 QVKDVAH-QEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY------------------KSRVLE  118 (294)
Q Consensus        59 ~~~~~~g-~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~------------------~~~~~~  118 (294)
                      .|+.+.| ++.+++.|...+..++.++ ++|+||+|+||+++|+.+++.+.|....                  ...+..
T Consensus         3 ~~~~i~~~q~~~~~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~   82 (329)
T PRK08058          3 TWEQLTALQPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHL   82 (329)
T ss_pred             cHHHHHhhHHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEE
Confidence            3677888 8999999999999998888 5999999999999999999999886421                  112222


Q ss_pred             ecCC-CCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcc
Q 022641          119 LNAS-DDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISR  197 (294)
Q Consensus       119 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~  197 (294)
                      +... .....+.+++....+...+          ..+.+.++||||++.++...++.|++.+++++..+.+|++|+.+..
T Consensus        83 i~~~~~~i~id~ir~l~~~~~~~~----------~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~  152 (329)
T PRK08058         83 VAPDGQSIKKDQIRYLKEEFSKSG----------VESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQ  152 (329)
T ss_pred             eccccccCCHHHHHHHHHHHhhCC----------cccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHh
Confidence            2221 1233455555554433222          1234579999999999999999999999999999999999999999


Q ss_pred             cchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHH
Q 022641          198 IIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQ  258 (294)
Q Consensus       198 ~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~  258 (294)
                      +.+.+++||..+.|.+++.+++..++.    .+|  ++++....++..+ |+++.++.++.
T Consensus       153 ll~TIrSRc~~i~~~~~~~~~~~~~L~----~~g--i~~~~~~~l~~~~-g~~~~A~~l~~  206 (329)
T PRK08058        153 ILPTILSRCQVVEFRPLPPESLIQRLQ----EEG--ISESLATLLAGLT-NSVEEALALSE  206 (329)
T ss_pred             CcHHHHhhceeeeCCCCCHHHHHHHHH----HcC--CChHHHHHHHHHc-CCHHHHHHHhc
Confidence            999999999999999999999988774    445  5666666666654 68888887654

>PRK06620 hypothetical protein; Validated

Probab=99.87  E-value=1.4e-20  Score=149.81  Aligned_cols=192  Identities=13%  Similarity=0.154  Sum_probs=131.2

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHcC-C-C--CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLETA-N-C--PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~-~-~--~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      ++..+|...+|-.-..+..+...+..|.... . .  +.++|+||||+|||||++++++..      +..+  +..... 
T Consensus         8 ~~~~~~tfd~Fvvg~~N~~a~~~~~~~~~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~------~~~~--~~~~~~-   78 (214)
T PRK06620          8 TTSSKYHPDEFIVSSSNDQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYLTKIWQNLS------NAYI--IKDIFF-   78 (214)
T ss_pred             CCCCCCCchhhEecccHHHHHHHHHHHHHccccCCCcceEEEECCCCCCHHHHHHHHHhcc------CCEE--cchhhh-
Confidence            4444444333322223566777777776532 1 1  459999999999999999988765      2111  110000 


Q ss_pred             chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcC-cceEEEEecCC---cccchH
Q 022641          126 GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSK-VTRFFFICNYI---SRIIEP  201 (294)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~---~~~~~~  201 (294)
                      .        ...               ....++|+|||+|.+...   .|+.+++.... ...++++++.+   ..+ ++
T Consensus        79 ~--------~~~---------------~~~~d~lliDdi~~~~~~---~lf~l~N~~~e~g~~ilits~~~p~~l~l-~~  131 (214)
T PRK06620         79 N--------EEI---------------LEKYNAFIIEDIENWQEP---ALLHIFNIINEKQKYLLLTSSDKSRNFTL-PD  131 (214)
T ss_pred             c--------hhH---------------HhcCCEEEEeccccchHH---HHHHHHHHHHhcCCEEEEEcCCCccccch-HH
Confidence            0        000               012359999999977432   34444433222 23455555422   234 88


Q ss_pred             hhcccc---EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---CCCCChhhhhh
Q 022641          202 LASRCA---KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---GSSITSKDLIS  275 (294)
Q Consensus       202 l~~r~~---~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---~~~it~~~v~~  275 (294)
                      +++|+.   ++.+.+|+.+++..++++.+...++.++++++++|++.++||+|.+++.++.+...+   ++.||.+.+++
T Consensus       132 L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~~~l~l~~ev~~~L~~~~~~d~r~l~~~l~~l~~~~~~~~~~it~~~~~~  211 (214)
T PRK06620        132 LSSRIKSVLSILLNSPDDELIKILIFKHFSISSVTISRQIIDFLLVNLPREYSKIIEILENINYFALISKRKITISLVKE  211 (214)
T ss_pred             HHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            999998   899999999999999999999889999999999999999999999999999865432   56699999887


Q ss_pred             hc
Q 022641          276 VS  277 (294)
Q Consensus       276 ~~  277 (294)
                      ++
T Consensus       212 ~l  213 (214)
T PRK06620        212 VL  213 (214)
T ss_pred             Hh
Confidence            75

>PRK05642 DNA replication initiation factor; Validated

Probab=99.87  E-value=3e-20  Score=150.35  Aligned_cols=199  Identities=15%  Similarity=0.161  Sum_probs=139.8

Q ss_pred             cchhhc-c-cHHHHHHHHHHHHcC---CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHH
Q 022641           59 QVKDVA-H-QEEVVRVLTNTLETA---NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTK  133 (294)
Q Consensus        59 ~~~~~~-g-~~~~~~~l~~~l~~~---~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  133 (294)
                      +|++++ | +..++..+.++....   ..++++|+||+|+|||||++++++++...   +..++.++..+....  ....
T Consensus        17 tfdnF~~~~~~~a~~~~~~~~~~~~~~~~~~l~l~G~~G~GKTHLl~a~~~~~~~~---~~~v~y~~~~~~~~~--~~~~   91 (234)
T PRK05642         17 TFANYYPGANAAALGYVERLCEADAGWTESLIYLWGKDGVGRSHLLQAACLRFEQR---GEPAVYLPLAELLDR--GPEL   91 (234)
T ss_pred             cccccCcCChHHHHHHHHHHhhccccCCCCeEEEECCCCCCHHHHHHHHHHHHHhC---CCcEEEeeHHHHHhh--hHHH
Confidence            555555 3 234444555444321   12458999999999999999999887322   234444443321110  0111


Q ss_pred             HHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC--HHHHHHHHHHHHhhcC-cceEEEEecCCc----ccchHhhccc
Q 022641          134 IKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT--EDAQNALRRTMETYSK-VTRFFFICNYIS----RIIEPLASRC  206 (294)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--~~~~~~L~~~l~~~~~-~~~ii~~~~~~~----~~~~~l~~r~  206 (294)
                      ...+                .+.++|+|||++.+.  +...+.|+.+++.... ...++++++...    ...+.+.+|+
T Consensus        92 ~~~~----------------~~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl  155 (234)
T PRK05642         92 LDNL----------------EQYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRL  155 (234)
T ss_pred             HHhh----------------hhCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHH
Confidence            1111                122599999999875  3446778888887655 456777776432    2368899999


Q ss_pred             ---cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---CCCCChhhhhhhcc
Q 022641          207 ---AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---GSSITSKDLISVSG  278 (294)
Q Consensus       207 ---~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---~~~it~~~v~~~~~  278 (294)
                         ..+.+.+|+.+++..+++..+...++.++++++++|++.++||+|.+.+.++.....+   ++.||.+.++++++
T Consensus       156 ~~gl~~~l~~~~~e~~~~il~~ka~~~~~~l~~ev~~~L~~~~~~d~r~l~~~l~~l~~~~l~~~~~it~~~~~~~L~  233 (234)
T PRK05642        156 TLALVFQMRGLSDEDKLRALQLRASRRGLHLTDEVGHFILTRGTRSMSALFDLLERLDQASLQAQRKLTIPFLKETLG  233 (234)
T ss_pred             hcCeeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHcCCcCCHHHHHHHhc
Confidence               5899999999999999998888889999999999999999999999999888775433   57799999998875

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.86  E-value=7.4e-20  Score=166.59  Aligned_cols=233  Identities=21%  Similarity=0.240  Sum_probs=166.7

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCC----ccCCcceeecCCC
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE----LYKSRVLELNASD  123 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~----~~~~~~~~~~~~~  123 (294)
                      ..|..+.++|..|++++|+...+..+...+.....++++|+||+|||||++|+.+.+......    .....++.+++..
T Consensus       141 ~~~~~~~~rp~~~~~iiGqs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~  220 (615)
T TIGR02903       141 HKSAQSLLRPRAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTT  220 (615)
T ss_pred             hhHHhhhcCcCcHHhceeCcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechh
Confidence            457788899999999999999998888888777777899999999999999999987763211    1245677777654


Q ss_pred             Ccc-hhHHHH-HHH-----------HHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-------
Q 022641          124 DRG-INVVRT-KIK-----------TFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-------  183 (294)
Q Consensus       124 ~~~-~~~~~~-~~~-----------~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-------  183 (294)
                      ... ...+.. .+.           .............+.......++|||||++.|+...++.|+..+++..       
T Consensus       221 l~~d~~~i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~~Le~~~v~~~~~~  300 (615)
T TIGR02903       221 LRWDPREVTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLEDKRVEFSSSY  300 (615)
T ss_pred             ccCCHHHHhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCHHHHHHHHHHHhhCeEEeecce
Confidence            311 111100 000           000000000011111223345699999999999999999999997532       


Q ss_pred             -------------------Cc--ceEEEE-ecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHH
Q 022641          184 -------------------KV--TRFFFI-CNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALST  241 (294)
Q Consensus       184 -------------------~~--~~ii~~-~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~  241 (294)
                                         ..  +.+|.+ ++.+..+.+++++||..+.|.|++.+++..++++.+...++.+++++++.
T Consensus       301 ~~~~~~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~Il~~~a~~~~v~ls~eal~~  380 (615)
T TIGR02903       301 YDPDDPNVPKYIKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIALIVLNAAEKINVHLAAGVEEL  380 (615)
T ss_pred             eccCCcccchhhhhhcccCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence                               11  223333 34566788999999999999999999999999999998888899999999


Q ss_pred             HHhhccCcHHHHHHHHHHHHHHh------------CCCCChhhhhhhccccc
Q 022641          242 LSSISQGDLRRAITYLQGAARLF------------GSSITSKDLISVSGYPT  281 (294)
Q Consensus       242 l~~~~~G~~r~~~~~l~~~~~~~------------~~~it~~~v~~~~~~~~  281 (294)
                      |.+++. +.|.+++.|+.+..+.            ...|+.+++.++++...
T Consensus       381 L~~ys~-~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r  431 (615)
T TIGR02903       381 IARYTI-EGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQISR  431 (615)
T ss_pred             HHHCCC-cHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCCc
Confidence            998865 6699999998765442            12589999999998765

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.

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

Probab=99.86  E-value=9.3e-21  Score=165.73  Aligned_cols=209  Identities=21%  Similarity=0.220  Sum_probs=160.2

Q ss_pred             hcCCCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           54 KYRPKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        54 ~~~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      .....+|+++-|++++++.|.+.+.-             ..+..++|+||||||||++|+++|++.      +.+|+.+.
T Consensus       427 e~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~------~~nFlsvk  500 (693)
T KOG0730|consen  427 EMPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEA------GMNFLSVK  500 (693)
T ss_pred             cCCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhh------cCCeeecc
Confidence            44556899999999999999877632             233459999999999999999999999      78888886


Q ss_pred             CCCC------cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHhhc
Q 022641          121 ASDD------RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMETYS  183 (294)
Q Consensus       121 ~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~~~  183 (294)
                      +...      .+...++..+........              .|||+||+|.+.           ....+.|+.-|+...
T Consensus       501 gpEL~sk~vGeSEr~ir~iF~kAR~~aP--------------~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e  566 (693)
T KOG0730|consen  501 GPELFSKYVGESERAIREVFRKARQVAP--------------CIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLE  566 (693)
T ss_pred             CHHHHHHhcCchHHHHHHHHHHHhhcCC--------------eEEehhhHHhHhhccCCCccchHHHHHHHHHHHccccc
Confidence            6543      334456665555444332              499999999873           235677777777544


Q ss_pred             --CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHH-HHHHHHhhccC-cHHHHHHH
Q 022641          184 --KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAE-ALSTLSSISQG-DLRRAITY  256 (294)
Q Consensus       184 --~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~-~l~~l~~~~~G-~~r~~~~~  256 (294)
                        .++.+|.+||.+..+++++++  |+. .|++++|+.+-..++++..+++  ++++++ .++.|++.|.| +-..+..+
T Consensus       567 ~~k~V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kk--mp~~~~vdl~~La~~T~g~SGAel~~l  644 (693)
T KOG0730|consen  567 ALKNVLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKK--MPFSEDVDLEELAQATEGYSGAEIVAV  644 (693)
T ss_pred             ccCcEEEEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhc--CCCCccccHHHHHHHhccCChHHHHHH
Confidence              356678888999999999999  888 8999999999999999887754  666666 68899998765 45667778


Q ss_pred             HHHHHHHh------CCCCChhhhhhhcccccCCC
Q 022641          257 LQGAARLF------GSSITSKDLISVSGYPTGGS  284 (294)
Q Consensus       257 l~~~~~~~------~~~it~~~v~~~~~~~~~~~  284 (294)
                      ++.|+..+      ...|+.+|+.+++.......
T Consensus       645 Cq~A~~~a~~e~i~a~~i~~~hf~~al~~~r~s~  678 (693)
T KOG0730|consen  645 CQEAALLALRESIEATEITWQHFEEALKAVRPSL  678 (693)
T ss_pred             HHHHHHHHHHHhcccccccHHHHHHHHHhhcccC
Confidence            88888777      34688999988887766543

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=99.86  E-value=3.1e-20  Score=156.99  Aligned_cols=178  Identities=23%  Similarity=0.330  Sum_probs=144.1

Q ss_pred             cHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc------------------cCCcceeecCC---C
Q 022641           66 QEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL------------------YKSRVLELNAS---D  123 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~------------------~~~~~~~~~~~---~  123 (294)
                      +....+.+.+.+..++.++ ++|+||+|+||+++|.++|+.+.|...                  .+..+..+...   .
T Consensus         7 l~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~   86 (334)
T PRK07993          7 LRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTPEKGKS   86 (334)
T ss_pred             ChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccc
Confidence            4566778888888888877 889999999999999999999988532                  12233444332   2


Q ss_pred             CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhh
Q 022641          124 DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLA  203 (294)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~  203 (294)
                      ...++.++.....+...+.          .+++.|+|||++|.|+....|.|++.+|+++.+..+|++|+.+..+++.++
T Consensus        87 ~I~idqiR~l~~~~~~~~~----------~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIr  156 (334)
T PRK07993         87 SLGVDAVREVTEKLYEHAR----------LGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLR  156 (334)
T ss_pred             cCCHHHHHHHHHHHhhccc----------cCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHH
Confidence            3456677776665554432          245679999999999999999999999999999999999999999999999


Q ss_pred             ccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHH
Q 022641          204 SRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQ  258 (294)
Q Consensus       204 ~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~  258 (294)
                      |||+.+.|+|++.+++..+|..     ...++++....++..++|++..++.+++
T Consensus       157 SRCq~~~~~~~~~~~~~~~L~~-----~~~~~~~~a~~~~~la~G~~~~Al~l~~  206 (334)
T PRK07993        157 SRCRLHYLAPPPEQYALTWLSR-----EVTMSQDALLAALRLSAGAPGAALALLQ  206 (334)
T ss_pred             hccccccCCCCCHHHHHHHHHH-----ccCCCHHHHHHHHHHcCCCHHHHHHHhc
Confidence            9999999999999999998852     2346777788889999999999988764

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

Probab=99.86  E-value=4.4e-20  Score=158.30  Aligned_cols=211  Identities=22%  Similarity=0.315  Sum_probs=144.8

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHH-----cCCCC--cEEEECCCCCCHHHHHHHHHHHhcCCCccCCccee
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLE-----TANCP--HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLE  118 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~-----~~~~~--~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~  118 (294)
                      ....+|.++|+|...+++..+++.+.++..|+.     ..+.+  .++|+||+||||||+++.|++++      +..+++
T Consensus        67 d~~elW~eKy~P~t~eeLAVHkkKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkvLskel------g~~~~E  140 (634)
T KOG1970|consen   67 DEFELWVEKYKPRTLEELAVHKKKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKVLSKEL------GYQLIE  140 (634)
T ss_pred             cccchhHHhcCcccHHHHhhhHHhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHHHHHhh------Cceeee
Confidence            566799999999999999999999999999998     44433  49999999999999999999999      444444


Q ss_pred             ecCC-------C------Ccc--hhHHHHHHHHHHhhh--cccCccCCCCCCCCcEEEEEeCCCCCCHH-----HHHHHH
Q 022641          119 LNAS-------D------DRG--INVVRTKIKTFAAVA--VGSGQRRGGYPCPPYKIIILDEADSMTED-----AQNALR  176 (294)
Q Consensus       119 ~~~~-------~------~~~--~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~lliiDei~~l~~~-----~~~~L~  176 (294)
                      -..+       .      ...  ...--..+..+....  .+.-+..+.....++.+|+|||+......     .++.|.
T Consensus       141 w~Npi~~~~~~~~h~~t~~~~~~~~s~L~~fesFler~~kyg~l~~~g~~~~~~~~liLveDLPn~~~~d~~~~f~evL~  220 (634)
T KOG1970|consen  141 WSNPINLKEPENLHNETSFLMFPYQSQLAVFESFLLRATKYGSLQMSGDDLRTDKKLILVEDLPNQFYRDDSETFREVLR  220 (634)
T ss_pred             ecCCccccccccccccchhcccchhhHHHHHHHHHHHHHhhchhhhcccccccCceEEEeeccchhhhhhhHHHHHHHHH
Confidence            3311       0      001  111111222232222  22223344455566779999999876432     234444


Q ss_pred             HHHHhhcCcceEEEEecCC--------cccchH--hhccccEEEecCCCHHHHHHHHHHHHHHhCCCCC------HHHHH
Q 022641          177 RTMETYSKVTRFFFICNYI--------SRIIEP--LASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLD------AEALS  240 (294)
Q Consensus       177 ~~l~~~~~~~~ii~~~~~~--------~~~~~~--l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~------~~~l~  240 (294)
                      .+......+ .|+++|+..        ......  ...|...|.|+|....-+++.|.++|..++...+      ...++
T Consensus       221 ~y~s~g~~P-lIf~iTd~~~~g~nnq~rlf~~d~q~~~ri~~IsFNPIa~T~MKK~L~ric~~e~~~~s~~k~~~~~~v~  299 (634)
T KOG1970|consen  221 LYVSIGRCP-LIFIITDSLSNGNNNQDRLFPKDIQEEPRISNISFNPIAPTIMKKFLKRICRIEANKKSGIKVPDTAEVE  299 (634)
T ss_pred             HHHhcCCCc-EEEEEeccccCCCcchhhhchhhhhhccCcceEeecCCcHHHHHHHHHHHHHHhcccccCCcCchhHHHH
Confidence            333333334 445555221        112222  3346669999999999999999999998887666      67789


Q ss_pred             HHHhhccCcHHHHHHHHHHHHHH
Q 022641          241 TLSSISQGDLRRAITYLQGAARL  263 (294)
Q Consensus       241 ~l~~~~~G~~r~~~~~l~~~~~~  263 (294)
                      .++..++||+|.|++.||+.+..
T Consensus       300 ~i~~~s~GDIRsAInsLQlsssk  322 (634)
T KOG1970|consen  300 LICQGSGGDIRSAINSLQLSSSK  322 (634)
T ss_pred             HHHHhcCccHHHHHhHhhhhccc
Confidence            99999999999999999998743

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=99.86  E-value=3.9e-20  Score=155.97  Aligned_cols=170  Identities=22%  Similarity=0.288  Sum_probs=133.5

Q ss_pred             HHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc------------------CCcceeecCC---CCcchhHHHH
Q 022641           75 NTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY------------------KSRVLELNAS---DDRGINVVRT  132 (294)
Q Consensus        75 ~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~------------------~~~~~~~~~~---~~~~~~~~~~  132 (294)
                      +++..++.++ ++|+||+|+|||++|..+++.+.|....                  +..+..+...   ....++.++.
T Consensus        14 ~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~~~i~id~iR~   93 (328)
T PRK05707         14 QLAGRGRHPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEADKTIKVDQVRE   93 (328)
T ss_pred             HHHHCCCcceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCCCCCCCHHHHHH
Confidence            3444566666 8999999999999999999999885321                  2233444332   2346677777


Q ss_pred             HHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEEec
Q 022641          133 KIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFK  212 (294)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~  212 (294)
                      ....+...+.          .+++.|+|||++|.++....+.|++.+|+++.++.+|++|+.+..+++.+++||..+.|.
T Consensus        94 l~~~~~~~~~----------~~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~  163 (328)
T PRK05707         94 LVSFVVQTAQ----------LGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACP  163 (328)
T ss_pred             HHHHHhhccc----------cCCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCC
Confidence            6655544332          234679999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHH
Q 022641          213 PLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQ  258 (294)
Q Consensus       213 ~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~  258 (294)
                      |++.+++..++....    ...+++....++..++|++..++.+++
T Consensus       164 ~~~~~~~~~~L~~~~----~~~~~~~~~~~l~la~Gsp~~A~~l~~  205 (328)
T PRK05707        164 LPSNEESLQWLQQAL----PESDERERIELLTLAGGSPLRALQLHE  205 (328)
T ss_pred             CcCHHHHHHHHHHhc----ccCChHHHHHHHHHcCCCHHHHHHHHC
Confidence            999999999986432    135667777888999999998887654

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.86  E-value=3.2e-20  Score=163.45  Aligned_cols=209  Identities=17%  Similarity=0.106  Sum_probs=150.2

Q ss_pred             CCcchhhcccHHHHHHHHHHHHc----------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc-
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLET----------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR-  125 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~----------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~-  125 (294)
                      +..|+++.|.+.++..+......          ..+..++|+||||||||.+|++++.++      +.+++.++.+... 
T Consensus       224 ~~~~~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~------~~~~~~l~~~~l~~  297 (489)
T CHL00195        224 NEKISDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDW------QLPLLRLDVGKLFG  297 (489)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHh------CCCEEEEEhHHhcc
Confidence            45688999998888766553211          123459999999999999999999998      7778877765422 


Q ss_pred             -----chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH------------HHHHHHHHHHHhhcCcceE
Q 022641          126 -----GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE------------DAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       126 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~------------~~~~~L~~~l~~~~~~~~i  188 (294)
                           +...++..+......              .+.||+|||+|.+..            .....++..+++....+.+
T Consensus       298 ~~vGese~~l~~~f~~A~~~--------------~P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~v  363 (489)
T CHL00195        298 GIVGESESRMRQMIRIAEAL--------------SPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFV  363 (489)
T ss_pred             cccChHHHHHHHHHHHHHhc--------------CCcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceEE
Confidence                 222333333322221              235999999997632            1344566777766667778


Q ss_pred             EEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCC-CCHHHHHHHHhhccC----cHHHHHHHHHHH
Q 022641          189 FFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLN-LDAEALSTLSSISQG----DLRRAITYLQGA  260 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~-~~~~~l~~l~~~~~G----~~r~~~~~l~~~  260 (294)
                      |.|||.+..+++++.+  ||. .+.++.|+.+++.++++.++.+.+.. .++..+..+++.+.|    +++.++......
T Consensus       364 IaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfSGAdI~~lv~eA~~~  443 (489)
T CHL00195        364 VATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSGAEIEQSIIEAMYI  443 (489)
T ss_pred             EEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCCHHHHHHHHHHHHHH
Confidence            8999999999999986  887 79999999999999999999875543 345567788877544    666665554444


Q ss_pred             HHHhCCCCChhhhhhhcccccCCCC
Q 022641          261 ARLFGSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       261 ~~~~~~~it~~~v~~~~~~~~~~~~  285 (294)
                      +...+..++.+++..++....+...
T Consensus       444 A~~~~~~lt~~dl~~a~~~~~Pls~  468 (489)
T CHL00195        444 AFYEKREFTTDDILLALKQFIPLAQ  468 (489)
T ss_pred             HHHcCCCcCHHHHHHHHHhcCCCcc
Confidence            4444778999999999998887654

>CHL00181 cbbX CbbX; Provisional

Probab=99.86  E-value=5.3e-20  Score=152.72  Aligned_cols=191  Identities=23%  Similarity=0.208  Sum_probs=132.7

Q ss_pred             hhhcccHHHHHHHHHHHH--------c-------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCcc-CCcceeecCCCC
Q 022641           61 KDVAHQEEVVRVLTNTLE--------T-------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELY-KSRVLELNASDD  124 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~--------~-------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~-~~~~~~~~~~~~  124 (294)
                      .+++|.+.+++.+.++..        .       ....+++|+||||||||++|+++++.+...... ...++.++..+.
T Consensus        23 ~~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~~~l  102 (287)
T CHL00181         23 EELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDDL  102 (287)
T ss_pred             HhcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecHHHH
Confidence            478899888876665531        0       123359999999999999999999987432221 223555553321


Q ss_pred             cchhHH--HHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCC---------CHHHHHHHHHHHHhhcCcceEEEEec
Q 022641          125 RGINVV--RTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSM---------TEDAQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       125 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l---------~~~~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      .+....  ..........             ..+++|||||++.+         ....++.|+..|+.....+++|++++
T Consensus       103 ~~~~~g~~~~~~~~~l~~-------------a~ggVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~~~~~~vI~ag~  169 (287)
T CHL00181        103 VGQYIGHTAPKTKEVLKK-------------AMGGVLFIDEAYYLYKPDNERDYGSEAIEILLQVMENQRDDLVVIFAGY  169 (287)
T ss_pred             HHHHhccchHHHHHHHHH-------------ccCCEEEEEccchhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCC
Confidence            111100  0000111110             12359999999987         35578889999988777777777765


Q ss_pred             CCc-----ccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhh--------ccCcHHHHHHHHHH
Q 022641          194 YIS-----RIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSI--------SQGDLRRAITYLQG  259 (294)
Q Consensus       194 ~~~-----~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~--------~~G~~r~~~~~l~~  259 (294)
                      ...     ...+++.+||. .+.|+|++.+++..++..++++.+..++++....+.+.        ..||.|.+.++++.
T Consensus       170 ~~~~~~~~~~np~L~sR~~~~i~F~~~t~~el~~I~~~~l~~~~~~l~~~~~~~L~~~i~~~~~~~~~GNaR~vrn~ve~  249 (287)
T CHL00181        170 KDRMDKFYESNPGLSSRIANHVDFPDYTPEELLQIAKIMLEEQQYQLTPEAEKALLDYIKKRMEQPLFANARSVRNALDR  249 (287)
T ss_pred             cHHHHHHHhcCHHHHHhCCceEEcCCcCHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHhCCCCCCccHHHHHHHHHH
Confidence            321     23589999998 89999999999999999999999999998887766664        34899999999998


Q ss_pred             HHHHh
Q 022641          260 AARLF  264 (294)
Q Consensus       260 ~~~~~  264 (294)
                      +....
T Consensus       250 ~~~~~  254 (287)
T CHL00181        250 ARMRQ  254 (287)
T ss_pred             HHHHH
Confidence            77554

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.85  E-value=6.7e-20  Score=158.94  Aligned_cols=209  Identities=21%  Similarity=0.248  Sum_probs=142.8

Q ss_pred             CCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ...++++.|.+..++.+...+..             ..+.+++|+||||||||++|+++++++      +..++.++++.
T Consensus       127 ~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~------~~~~i~v~~~~  200 (389)
T PRK03992        127 NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET------NATFIRVVGSE  200 (389)
T ss_pred             CCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHh------CCCEEEeehHH
Confidence            34678999999999888877632             233469999999999999999999998      56677776554


Q ss_pred             Ccc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHhh----
Q 022641          124 DRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMETY----  182 (294)
Q Consensus       124 ~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~~----  182 (294)
                      ...      ...++..+.....              ..+.+|+|||+|.+.           ...+..+.+++...    
T Consensus       201 l~~~~~g~~~~~i~~~f~~a~~--------------~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~  266 (389)
T PRK03992        201 LVQKFIGEGARLVRELFELARE--------------KAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFD  266 (389)
T ss_pred             HhHhhccchHHHHHHHHHHHHh--------------cCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccC
Confidence            321      1112222221111              123599999999872           33444555555332    


Q ss_pred             -cCcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHHH
Q 022641          183 -SKVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITYL  257 (294)
Q Consensus       183 -~~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~l  257 (294)
                       ...+.+|++||.+..+++++++  ||. .|.+++|+.+++.++++.++....+. .+..+..+++.+.| +.+.+..++
T Consensus       267 ~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~-~~~~~~~la~~t~g~sgadl~~l~  345 (389)
T PRK03992        267 PRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLA-DDVDLEELAELTEGASGADLKAIC  345 (389)
T ss_pred             CCCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCC-CcCCHHHHHHHcCCCCHHHHHHHH
Confidence             2367789999999999999986  776 79999999999999999887654332 12346667776654 233344444


Q ss_pred             HHHHHHh----CCCCChhhhhhhcccccCCCCC
Q 022641          258 QGAARLF----GSSITSKDLISVSGYPTGGSGG  286 (294)
Q Consensus       258 ~~~~~~~----~~~it~~~v~~~~~~~~~~~~~  286 (294)
                      ..++..+    ...|+.+++.+++....+....
T Consensus       346 ~eA~~~a~~~~~~~i~~~d~~~A~~~~~~~~~~  378 (389)
T PRK03992        346 TEAGMFAIRDDRTEVTMEDFLKAIEKVMGKEEK  378 (389)
T ss_pred             HHHHHHHHHcCCCCcCHHHHHHHHHHHhccccc
Confidence            4444443    4579999999999988776543

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=99.85  E-value=1.7e-19  Score=150.90  Aligned_cols=178  Identities=21%  Similarity=0.286  Sum_probs=140.0

Q ss_pred             cHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc------------------CCcceeecC--CCC
Q 022641           66 QEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY------------------KSRVLELNA--SDD  124 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~------------------~~~~~~~~~--~~~  124 (294)
                      +......+.+.+..++.+| ++|+||+|+||+++|..+++.+.|....                  +..+..+.+  ...
T Consensus         7 ~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~   86 (325)
T PRK06871          7 LQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPIDNKD   86 (325)
T ss_pred             hHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccccCCC
Confidence            4566778888898888777 7899999999999999999999885421                  223333433  223


Q ss_pred             cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhc
Q 022641          125 RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLAS  204 (294)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~  204 (294)
                      .+++.+++....+...+.          .+++.|+|||++|.|+....|.|++.+|+++.++.+|++|+.+..+++.++|
T Consensus        87 I~id~iR~l~~~~~~~~~----------~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~S  156 (325)
T PRK06871         87 IGVDQVREINEKVSQHAQ----------QGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYS  156 (325)
T ss_pred             CCHHHHHHHHHHHhhccc----------cCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHh
Confidence            456677766555444332          2346799999999999999999999999999999999999999999999999


Q ss_pred             cccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHH
Q 022641          205 RCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQ  258 (294)
Q Consensus       205 r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~  258 (294)
                      ||..+.|.|++.+++..+|....     ..++..+..++..++|++..++.++.
T Consensus       157 RC~~~~~~~~~~~~~~~~L~~~~-----~~~~~~~~~~~~l~~g~p~~A~~~~~  205 (325)
T PRK06871        157 RCQTWLIHPPEEQQALDWLQAQS-----SAEISEILTALRINYGRPLLALTFLE  205 (325)
T ss_pred             hceEEeCCCCCHHHHHHHHHHHh-----ccChHHHHHHHHHcCCCHHHHHHHhh
Confidence            99999999999999999986532     23444566778889999988777654

>PRK09087 hypothetical protein; Validated

Probab=99.85  E-value=4.6e-20  Score=148.07  Aligned_cols=190  Identities=16%  Similarity=0.163  Sum_probs=136.7

Q ss_pred             cchhhcc---cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHH
Q 022641           59 QVKDVAH---QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK  135 (294)
Q Consensus        59 ~~~~~~g---~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (294)
                      +|++++.   +..+...+.++. ....+.++|+||+|+|||||++++++..      +..+  ++... ....    .+.
T Consensus        19 ~~~~Fi~~~~N~~a~~~l~~~~-~~~~~~l~l~G~~GsGKThLl~~~~~~~------~~~~--i~~~~-~~~~----~~~   84 (226)
T PRK09087         19 GRDDLLVTESNRAAVSLVDHWP-NWPSPVVVLAGPVGSGKTHLASIWREKS------DALL--IHPNE-IGSD----AAN   84 (226)
T ss_pred             ChhceeecCchHHHHHHHHhcc-cCCCCeEEEECCCCCCHHHHHHHHHHhc------CCEE--ecHHH-cchH----HHH
Confidence            5666663   445555555544 2233459999999999999999998765      2222  22211 1111    111


Q ss_pred             HHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcC-cceEEEEecCCc---c-cchHhhccc---c
Q 022641          136 TFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSK-VTRFFFICNYIS---R-IIEPLASRC---A  207 (294)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~---~-~~~~l~~r~---~  207 (294)
                      ...                 .++|+|||++.+.. .+..|+.+++.... ...++++++...   . ..+.+++|+   .
T Consensus        85 ~~~-----------------~~~l~iDDi~~~~~-~~~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl  146 (226)
T PRK09087         85 AAA-----------------EGPVLIEDIDAGGF-DETGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAAT  146 (226)
T ss_pred             hhh-----------------cCeEEEECCCCCCC-CHHHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHHHHhCCc
Confidence            100                 13899999998853 35668888876555 455777776432   2 368899999   5


Q ss_pred             EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHH---HHhCCCCChhhhhhhcccc
Q 022641          208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA---RLFGSSITSKDLISVSGYP  280 (294)
Q Consensus       208 ~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~---~~~~~~it~~~v~~~~~~~  280 (294)
                      .+.+.+|+.+++..++++.++..++.++++++++|++.+.|++|.++..+..+.   ...++.||.+.+++++...
T Consensus       147 ~~~l~~pd~e~~~~iL~~~~~~~~~~l~~ev~~~La~~~~r~~~~l~~~l~~L~~~~~~~~~~it~~~~~~~l~~~  222 (226)
T PRK09087        147 VVEIGEPDDALLSQVIFKLFADRQLYVDPHVVYYLVSRMERSLFAAQTIVDRLDRLALERKSRITRALAAEVLNEM  222 (226)
T ss_pred             eeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHhh
Confidence            999999999999999999999999999999999999999999999998666554   3337789999999998765

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.85  E-value=1.3e-19  Score=150.65  Aligned_cols=191  Identities=21%  Similarity=0.186  Sum_probs=134.4

Q ss_pred             hhhcccHHHHHHHHHHHH----------cC-----CCCcEEEECCCCCCHHHHHHHHHHHhcCCCcc-CCcceeecCCCC
Q 022641           61 KDVAHQEEVVRVLTNTLE----------TA-----NCPHMLFYGPPGTGKTTTALAIAHQLFGPELY-KSRVLELNASDD  124 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~----------~~-----~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~-~~~~~~~~~~~~  124 (294)
                      .+++|.+.+++.+..+..          .+     ...+++|+||||||||++|+++++.+...... ..+++.+++++.
T Consensus        22 ~~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~~~l  101 (284)
T TIGR02880        22 RELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDDL  101 (284)
T ss_pred             HhccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecHHHH
Confidence            468888888877655431          11     12369999999999999999999988433221 224565554322


Q ss_pred             cchhHH--HHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCC---------CHHHHHHHHHHHHhhcCcceEEEEec
Q 022641          125 RGINVV--RTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSM---------TEDAQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       125 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l---------~~~~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      ......  ...+......             ...++|||||++.+         +...++.|++.|+......++|++++
T Consensus       102 ~~~~~g~~~~~~~~~~~~-------------a~~gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~  168 (284)
T TIGR02880       102 VGQYIGHTAPKTKEILKR-------------AMGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGY  168 (284)
T ss_pred             hHhhcccchHHHHHHHHH-------------ccCcEEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCC
Confidence            110000  0001111110             12359999999987         24567889999998777777777765


Q ss_pred             CC-----cccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhh--------ccCcHHHHHHHHHH
Q 022641          194 YI-----SRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSI--------SQGDLRRAITYLQG  259 (294)
Q Consensus       194 ~~-----~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~--------~~G~~r~~~~~l~~  259 (294)
                      ..     ..+.+++.+||. .|.|++++.+++..++.+++++.+..+++++++.+.++        +.||.|.+.|+++.
T Consensus       169 ~~~~~~~~~~np~L~sR~~~~i~fp~l~~edl~~I~~~~l~~~~~~l~~~a~~~L~~~l~~~~~~~~~GN~R~lrn~ve~  248 (284)
T TIGR02880       169 KDRMDSFFESNPGFSSRVAHHVDFPDYSEAELLVIAGLMLKEQQYRFSAEAEEAFADYIALRRTQPHFANARSIRNAIDR  248 (284)
T ss_pred             cHHHHHHHhhCHHHHhhCCcEEEeCCcCHHHHHHHHHHHHHHhccccCHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHH
Confidence            32     124689999997 89999999999999999999998888999998888775        46999999999998


Q ss_pred             HHHHh
Q 022641          260 AARLF  264 (294)
Q Consensus       260 ~~~~~  264 (294)
                      +....
T Consensus       249 ~~~~~  253 (284)
T TIGR02880       249 ARLRQ  253 (284)
T ss_pred             HHHHH
Confidence            77554

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.

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

Probab=99.85  E-value=3e-20  Score=173.30  Aligned_cols=223  Identities=19%  Similarity=0.210  Sum_probs=166.9

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCC----ccCCcceeecC
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE----LYKSRVLELNA  121 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~----~~~~~~~~~~~  121 (294)
                      ....|+.++.+|..++.++|+++.+..+.+.+......|++|+||||||||++++++++.+....    ..+..++.++.
T Consensus       167 ~~~~~l~~~~r~~~l~~~igr~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~~~  246 (731)
T TIGR02639       167 KYTVDLTEKAKNGKIDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDM  246 (731)
T ss_pred             HHhhhHHHHHhcCCCCcccCcHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEecH
Confidence            46679999999999999999999999999999998888999999999999999999999974322    22455666654


Q ss_pred             CCCc----chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC---------HHHHHHHHHHHHhhcCcceE
Q 022641          122 SDDR----GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT---------EDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       122 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~---------~~~~~~L~~~l~~~~~~~~i  188 (294)
                      +...    ....+...+..+......          ..+.||||||+|.+.         .+..+.|+..++.  ....+
T Consensus       247 ~~l~a~~~~~g~~e~~l~~i~~~~~~----------~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l~~--g~i~~  314 (731)
T TIGR02639       247 GSLLAGTKYRGDFEERLKAVVSEIEK----------EPNAILFIDEIHTIVGAGATSGGSMDASNLLKPALSS--GKLRC  314 (731)
T ss_pred             HHHhhhccccchHHHHHHHHHHHHhc----------cCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHHhC--CCeEE
Confidence            3321    112233333333322111          113599999999884         2356778888764  55678


Q ss_pred             EEEecC-----CcccchHhhccccEEEecCCCHHHHHHHHHHHHHH----hCCCCCHHHHHHHHhhccC------cHHHH
Q 022641          189 FFICNY-----ISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE----EGLNLDAEALSTLSSISQG------DLRRA  253 (294)
Q Consensus       189 i~~~~~-----~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~----~~~~~~~~~l~~l~~~~~G------~~r~~  253 (294)
                      |.+|+.     ....++++.+||..+.+++|+.++...+++.....    +++.++++++..+++.+..      -|+.+
T Consensus       315 IgaTt~~e~~~~~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~ls~ryi~~r~~P~ka  394 (731)
T TIGR02639       315 IGSTTYEEYKNHFEKDRALSRRFQKIDVGEPSIEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSARYINDRFLPDKA  394 (731)
T ss_pred             EEecCHHHHHHHhhhhHHHHHhCceEEeCCCCHHHHHHHHHHHHHHHHhccCcccCHHHHHHHHHhhhcccccccCCHHH
Confidence            888875     24568899999999999999999999999987754    4578999999999988753      38889


Q ss_pred             HHHHHHHHHHh--------CCCCChhhhhhhcccc
Q 022641          254 ITYLQGAARLF--------GSSITSKDLISVSGYP  280 (294)
Q Consensus       254 ~~~l~~~~~~~--------~~~it~~~v~~~~~~~  280 (294)
                      +.+++.++...        ...++.+++..++...
T Consensus       395 i~lld~a~a~~~~~~~~~~~~~v~~~~i~~~i~~~  429 (731)
T TIGR02639       395 IDVIDEAGASFRLRPKAKKKANVSVKDIENVVAKM  429 (731)
T ss_pred             HHHHHHhhhhhhcCcccccccccCHHHHHHHHHHH
Confidence            99999877533        1238888888887664

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.85  E-value=4.4e-20  Score=167.15  Aligned_cols=222  Identities=20%  Similarity=0.218  Sum_probs=154.5

Q ss_pred             hhhcccHHHHHHHHHHHHc----CCCCc-EEEECCCCCCHHHHHHHHHHHhcCC----CccCCcceeecCCCCcchhHHH
Q 022641           61 KDVAHQEEVVRVLTNTLET----ANCPH-MLFYGPPGTGKTTTALAIAHQLFGP----ELYKSRVLELNASDDRGINVVR  131 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~----~~~~~-ill~Gp~G~GKT~la~~la~~~~~~----~~~~~~~~~~~~~~~~~~~~~~  131 (294)
                      +.+++++..++.|...+..    ....+ ++|+|+||||||++++.+.+++...    ......++.++|........+.
T Consensus       755 D~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIY  834 (1164)
T PTZ00112        755 KYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAY  834 (1164)
T ss_pred             CcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHH
Confidence            5788999988887776643    23334 5699999999999999999887321    1223567888887655444333


Q ss_pred             HHHHHHH-hhhcccCcc----------CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh---cCcceEEEEecC---
Q 022641          132 TKIKTFA-AVAVGSGQR----------RGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY---SKVTRFFFICNY---  194 (294)
Q Consensus       132 ~~~~~~~-~~~~~~~~~----------~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~---~~~~~ii~~~~~---  194 (294)
                      ..+.... ......+..          ..........||||||+|.|....++.|+.+++..   ...+.+|+++|.   
T Consensus       835 qvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLIGISNdlDL  914 (1164)
T PTZ00112        835 QVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLIAISNTMDL  914 (1164)
T ss_pred             HHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEEEecCchhc
Confidence            3322111 111100000          00011123459999999999876677777777642   234567777775   


Q ss_pred             CcccchHhhcccc--EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHh---hccCcHHHHHHHHHHHHHHh-CCCC
Q 022641          195 ISRIIEPLASRCA--KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSS---ISQGDLRRAITYLQGAARLF-GSSI  268 (294)
Q Consensus       195 ~~~~~~~l~~r~~--~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~---~~~G~~r~~~~~l~~~~~~~-~~~i  268 (294)
                      +..+.+++.+|+.  .+.|+|++.+++.+||..++......+++++++.+++   ...||.|.|+++|..++... +..|
T Consensus       915 perLdPRLRSRLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIArkVAq~SGDARKALDILRrAgEikegskV  994 (1164)
T PTZ00112        915 PERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCARKVANVSGDIRKALQICRKAFENKRGQKI  994 (1164)
T ss_pred             chhhhhhhhhccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhhcCCHHHHHHHHHHHHHhhcCCCcc
Confidence            3456678888886  5899999999999999999976545589999999998   67899999999999998765 4469


Q ss_pred             ChhhhhhhcccccC
Q 022641          269 TSKDLISVSGYPTG  282 (294)
Q Consensus       269 t~~~v~~~~~~~~~  282 (294)
                      +.++|.++......
T Consensus       995 T~eHVrkAleeiE~ 1008 (1164)
T PTZ00112        995 VPRDITEATNQLFD 1008 (1164)
T ss_pred             CHHHHHHHHHHHHh
Confidence            99999988866533

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.85  E-value=8e-20  Score=163.78  Aligned_cols=206  Identities=21%  Similarity=0.182  Sum_probs=142.4

Q ss_pred             cCCCcchhhcccHHHHHHHHHHHH------------cCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           55 YRPKQVKDVAHQEEVVRVLTNTLE------------TANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        55 ~~~~~~~~~~g~~~~~~~l~~~l~------------~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      .....|+++.|.+..+..+.+++.            ...+.+++|+||||||||++|++++.++      +.+++.++++
T Consensus        49 ~~~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~------~~~~~~i~~~  122 (495)
T TIGR01241        49 KPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA------GVPFFSISGS  122 (495)
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHc------CCCeeeccHH
Confidence            345689999999988877766553            1223469999999999999999999998      6677776654


Q ss_pred             CCc------chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhh
Q 022641          123 DDR------GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTMETY  182 (294)
Q Consensus       123 ~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~~~  182 (294)
                      +..      +...++..+......              .+.+|+|||+|.+..              ...+.|+..++..
T Consensus       123 ~~~~~~~g~~~~~l~~~f~~a~~~--------------~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~  188 (495)
T TIGR01241       123 DFVEMFVGVGASRVRDLFEQAKKN--------------APCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGF  188 (495)
T ss_pred             HHHHHHhcccHHHHHHHHHHHHhc--------------CCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccc
Confidence            321      222333333332211              235999999998742              2334555555543


Q ss_pred             c--CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHH
Q 022641          183 S--KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITY  256 (294)
Q Consensus       183 ~--~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~  256 (294)
                      .  ..+.+|++||.+..+++++.+  ||. .+.+++|+.+++.++++.++...... ++..+..+++.+.| +.+.+.++
T Consensus       189 ~~~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgadl~~l  267 (495)
T TIGR01241       189 GTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLA-PDVDLKAVARRTPGFSGADLANL  267 (495)
T ss_pred             cCCCCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCC-cchhHHHHHHhCCCCCHHHHHHH
Confidence            3  346688889999999999987  776 79999999999999999888654433 34557788887655 34444455


Q ss_pred             HHHHHHHh----CCCCChhhhhhhccccc
Q 022641          257 LQGAARLF----GSSITSKDLISVSGYPT  281 (294)
Q Consensus       257 l~~~~~~~----~~~it~~~v~~~~~~~~  281 (294)
                      ++.++..+    ...|+.+++..++....
T Consensus       268 ~~eA~~~a~~~~~~~i~~~~l~~a~~~~~  296 (495)
T TIGR01241       268 LNEAALLAARKNKTEITMNDIEEAIDRVI  296 (495)
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHHh
Confidence            55444332    45699999999888653

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.

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=99.85  E-value=2e-19  Score=150.26  Aligned_cols=178  Identities=23%  Similarity=0.325  Sum_probs=138.6

Q ss_pred             ccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCccC---------------Ccceee--cCCC---
Q 022641           65 HQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYK---------------SRVLEL--NASD---  123 (294)
Q Consensus        65 g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~~---------------~~~~~~--~~~~---  123 (294)
                      -+......+...+..++.++ ++|+||+|+||+++|.++++.+.|.....               ..+..+  .+..   
T Consensus         8 W~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~~~   87 (319)
T PRK08769          8 WQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGD   87 (319)
T ss_pred             cHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCcccc
Confidence            45677888999999998888 99999999999999999999998864221               122222  1111   


Q ss_pred             ----CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccc
Q 022641          124 ----DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRII  199 (294)
Q Consensus       124 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~  199 (294)
                          ...++.+++....+...+          ..+++.|+|||++|.|+....|.|++.+|+++.++.+|++++.+..++
T Consensus        88 k~~~~I~idqIR~l~~~~~~~p----------~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lL  157 (319)
T PRK08769         88 KLRTEIVIEQVREISQKLALTP----------QYGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLP  157 (319)
T ss_pred             cccccccHHHHHHHHHHHhhCc----------ccCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCc
Confidence                122444444444333222          123467999999999999999999999999999999999999999999


Q ss_pred             hHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHH
Q 022641          200 EPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQ  258 (294)
Q Consensus       200 ~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~  258 (294)
                      +.++|||..+.|.+|+.+++..+|.    ..+  ++++....++..++|+|..++..++
T Consensus       158 pTIrSRCq~i~~~~~~~~~~~~~L~----~~~--~~~~~a~~~~~l~~G~p~~A~~~~~  210 (319)
T PRK08769        158 ATIRSRCQRLEFKLPPAHEALAWLL----AQG--VSERAAQEALDAARGHPGLAAQWLR  210 (319)
T ss_pred             hHHHhhheEeeCCCcCHHHHHHHHH----HcC--CChHHHHHHHHHcCCCHHHHHHHhc
Confidence            9999999999999999999999885    233  5666677788999999998887764

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

Probab=99.84  E-value=1e-19  Score=138.75  Aligned_cols=141  Identities=38%  Similarity=0.612  Sum_probs=107.8

Q ss_pred             ccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc-----------------CCcceeecCCCC--
Q 022641           65 HQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY-----------------KSRVLELNASDD--  124 (294)
Q Consensus        65 g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~-----------------~~~~~~~~~~~~--  124 (294)
                      ||+..++.|...+..++.++ ++|+||+|+||+++|.++++.++|....                 ...+..+.....  
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            78999999999999999888 7999999999999999999999887644                 445555555443  


Q ss_pred             -cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhh
Q 022641          125 -RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLA  203 (294)
Q Consensus       125 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~  203 (294)
                       ...+.++.....+.....          .+.+.++||||+|.|+..+++.|++.||+++..+.+|++|+.+..+.+.++
T Consensus        81 ~i~i~~ir~i~~~~~~~~~----------~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~~il~TI~  150 (162)
T PF13177_consen   81 SIKIDQIREIIEFLSLSPS----------EGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPSKILPTIR  150 (162)
T ss_dssp             SBSHHHHHHHHHHCTSS-T----------TSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GGGS-HHHH
T ss_pred             hhhHHHHHHHHHHHHHHHh----------cCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChHHChHHHH
Confidence             456666655554433322          245679999999999999999999999999999999999999999999999


Q ss_pred             ccccEEEecCCC
Q 022641          204 SRCAKFRFKPLS  215 (294)
Q Consensus       204 ~r~~~i~~~~~~  215 (294)
                      +||..+.|.|++
T Consensus       151 SRc~~i~~~~ls  162 (162)
T PF13177_consen  151 SRCQVIRFRPLS  162 (162)
T ss_dssp             TTSEEEEE----
T ss_pred             hhceEEecCCCC
Confidence            999999999875

...

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.84  E-value=4.3e-19  Score=154.06  Aligned_cols=228  Identities=18%  Similarity=0.219  Sum_probs=150.3

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHc----CCCCcEEEECCCCCCHHHHHHHHHHHhcCCC---ccCCcceeecCC
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLET----ANCPHMLFYGPPGTGKTTTALAIAHQLFGPE---LYKSRVLELNAS  122 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~----~~~~~ill~Gp~G~GKT~la~~la~~~~~~~---~~~~~~~~~~~~  122 (294)
                      .+...|.|.   .++|++..++.|..++..    ...++++|+||||||||++++.+++++....   .....++.+++.
T Consensus         7 ~l~~~~~p~---~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~   83 (365)
T TIGR02928         7 LLEPDYVPD---RIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQ   83 (365)
T ss_pred             hCCCCCCCC---CCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECC
Confidence            445566674   688999999888888753    3446799999999999999999999874211   111466777776


Q ss_pred             CCcchh-HHHHHHHHHHh--hhcc-cCccC---------CCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHH-----hhc-
Q 022641          123 DDRGIN-VVRTKIKTFAA--VAVG-SGQRR---------GGYPCPPYKIIILDEADSMTEDAQNALRRTME-----TYS-  183 (294)
Q Consensus       123 ~~~~~~-~~~~~~~~~~~--~~~~-~~~~~---------~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~-----~~~-  183 (294)
                      ...+.. .+......+..  .... .+...         ......+..+|+|||+|.+.......|..++.     ..+ 
T Consensus        84 ~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~  163 (365)
T TIGR02928        84 ILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDN  163 (365)
T ss_pred             CCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCC
Confidence            654432 22233332211  0000 00000         00012345699999999995222223333332     222 


Q ss_pred             CcceEEEEecCCc---ccchHhhcccc--EEEecCCCHHHHHHHHHHHHHH--hCCCCCHHHHHHHHh---hccCcHHHH
Q 022641          184 KVTRFFFICNYIS---RIIEPLASRCA--KFRFKPLSEEVMSSRVLHICNE--EGLNLDAEALSTLSS---ISQGDLRRA  253 (294)
Q Consensus       184 ~~~~ii~~~~~~~---~~~~~l~~r~~--~i~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~l~~l~~---~~~G~~r~~  253 (294)
                      .++.+|+++|.+.   .+.+.+.+|+.  .+.|+|++.+++.++++..++.  ....+++++++.+++   .+.||+|.+
T Consensus       164 ~~v~lI~i~n~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~a  243 (365)
T TIGR02928       164 AKVGVIGISNDLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKA  243 (365)
T ss_pred             CeEEEEEEECCcchHhhcCHHHhccCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHH
Confidence            4567888888764   46677788874  7999999999999999998863  223478887776555   457999999


Q ss_pred             HHHHHHHHHHh----CCCCChhhhhhhcccc
Q 022641          254 ITYLQGAARLF----GSSITSKDLISVSGYP  280 (294)
Q Consensus       254 ~~~l~~~~~~~----~~~it~~~v~~~~~~~  280 (294)
                      ++++..++..+    ...||.+++..++...
T Consensus       244 l~~l~~a~~~a~~~~~~~it~~~v~~a~~~~  274 (365)
T TIGR02928       244 IDLLRVAGEIAEREGAERVTEDHVEKAQEKI  274 (365)
T ss_pred             HHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            99999888665    3469999999877654

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.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=99.84  E-value=5.7e-19  Score=147.36  Aligned_cols=175  Identities=16%  Similarity=0.284  Sum_probs=136.9

Q ss_pred             cHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc-----------------CCcceeecCC---CC
Q 022641           66 QEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY-----------------KSRVLELNAS---DD  124 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~-----------------~~~~~~~~~~---~~  124 (294)
                      +....+.+...+..++.++ ++|+||.|+||+++|..+++.+.|....                 +..+..+...   ..
T Consensus         8 l~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~   87 (319)
T PRK06090          8 LVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPEKEGKS   87 (319)
T ss_pred             HHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecCcCCCc
Confidence            4566778888888888877 8999999999999999999999886421                 2234444332   22


Q ss_pred             cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhc
Q 022641          125 RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLAS  204 (294)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~  204 (294)
                      ..++.++..........          ..+.+.|+|||++|.++....|.|++.+|+++.++.+|++|+.+..+++.++|
T Consensus        88 I~vdqiR~l~~~~~~~~----------~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~S  157 (319)
T PRK06090         88 ITVEQIRQCNRLAQESS----------QLNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVS  157 (319)
T ss_pred             CCHHHHHHHHHHHhhCc----------ccCCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHh
Confidence            45566665544333222          22346799999999999999999999999999999999999999999999999


Q ss_pred             cccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHH
Q 022641          205 RCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQ  258 (294)
Q Consensus       205 r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~  258 (294)
                      ||..+.|++|+.+++..++.    .++..    ....++..++|+|..++.+++
T Consensus       158 RCq~~~~~~~~~~~~~~~L~----~~~~~----~~~~~l~l~~G~p~~A~~~~~  203 (319)
T PRK06090        158 RCQQWVVTPPSTAQAMQWLK----GQGIT----VPAYALKLNMGSPLKTLAMMK  203 (319)
T ss_pred             cceeEeCCCCCHHHHHHHHH----HcCCc----hHHHHHHHcCCCHHHHHHHhC
Confidence            99999999999999999884    34443    234667889999998888764

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

Probab=99.83  E-value=4.2e-19  Score=153.28  Aligned_cols=206  Identities=21%  Similarity=0.225  Sum_probs=140.2

Q ss_pred             CCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ...|.++.|.+..+..+.+.+..             ..+.+++|+||||||||++|+++++++      ...++.+.++.
T Consensus       141 ~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l------~~~fi~i~~s~  214 (398)
T PTZ00454        141 DVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHT------TATFIRVVGSE  214 (398)
T ss_pred             CCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhc------CCCEEEEehHH
Confidence            45788999999999888877632             123469999999999999999999988      55666654432


Q ss_pred             Cc------chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHH---HHhh-
Q 022641          124 DR------GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRT---METY-  182 (294)
Q Consensus       124 ~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~---l~~~-  182 (294)
                      ..      +...++..+....              ...+.+|+|||+|.+.           ...+..+..+   ++.. 
T Consensus       215 l~~k~~ge~~~~lr~lf~~A~--------------~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~  280 (398)
T PTZ00454        215 FVQKYLGEGPRMVRDVFRLAR--------------ENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFD  280 (398)
T ss_pred             HHHHhcchhHHHHHHHHHHHH--------------hcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccC
Confidence            21      1111222222111              1234699999999762           1223334444   4332 


Q ss_pred             -cCcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHHH
Q 022641          183 -SKVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITYL  257 (294)
Q Consensus       183 -~~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~l  257 (294)
                       ...+.+|++||.+..+++++++  |+. .|.|++|+.+++..+++.++...++. .+-.+..++..+.| +...+..++
T Consensus       281 ~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~-~dvd~~~la~~t~g~sgaDI~~l~  359 (398)
T PTZ00454        281 QTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLS-EEVDLEDFVSRPEKISAADIAAIC  359 (398)
T ss_pred             CCCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCC-cccCHHHHHHHcCCCCHHHHHHHH
Confidence             2456789999999999999887  776 79999999999999999888765543 22346677777644 455555666


Q ss_pred             HHHHHHh----CCCCChhhhhhhcccccCC
Q 022641          258 QGAARLF----GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       258 ~~~~~~~----~~~it~~~v~~~~~~~~~~  283 (294)
                      +.++..+    ...|+.+|+.+++......
T Consensus       360 ~eA~~~A~r~~~~~i~~~df~~A~~~v~~~  389 (398)
T PTZ00454        360 QEAGMQAVRKNRYVILPKDFEKGYKTVVRK  389 (398)
T ss_pred             HHHHHHHHHcCCCccCHHHHHHHHHHHHhc
Confidence            6665544    3569999999998876443

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.83  E-value=6.3e-19  Score=154.56  Aligned_cols=231  Identities=22%  Similarity=0.266  Sum_probs=155.2

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHc----CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecC
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLET----ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA  121 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~----~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~  121 (294)
                      ....++...+.|   +.++|++..++.|...+..    ...++++|+||||+|||++++.+++++.... ....++.+++
T Consensus        18 ~~~~~l~~~~~P---~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~-~~~~~v~in~   93 (394)
T PRK00411         18 KDEEVLEPDYVP---ENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIA-VKVVYVYINC   93 (394)
T ss_pred             CChhhCCCCCcC---CCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhc-CCcEEEEEEC
Confidence            334455555555   5678999888888777633    3446799999999999999999999874322 2356677777


Q ss_pred             CCCcchhH-HHHHHHHHHhhhc-ccCccCC---------CCCCCCcEEEEEeCCCCCC----HHHHHHHHHHHHhhcC-c
Q 022641          122 SDDRGINV-VRTKIKTFAAVAV-GSGQRRG---------GYPCPPYKIIILDEADSMT----EDAQNALRRTMETYSK-V  185 (294)
Q Consensus       122 ~~~~~~~~-~~~~~~~~~~~~~-~~~~~~~---------~~~~~~~~lliiDei~~l~----~~~~~~L~~~l~~~~~-~  185 (294)
                      ....+... +......+..... ..+....         .....++.+|+|||+|.+.    ......|+..++.... +
T Consensus        94 ~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~  173 (394)
T PRK00411         94 QIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEEYPGAR  173 (394)
T ss_pred             CcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhccCCCe
Confidence            65444322 2222222211000 0000000         0012345699999999985    3344555555544333 5


Q ss_pred             ceEEEEecCCc---ccchHhhcccc--EEEecCCCHHHHHHHHHHHHHHh--CCCCCHHHHHHHHhhc---cCcHHHHHH
Q 022641          186 TRFFFICNYIS---RIIEPLASRCA--KFRFKPLSEEVMSSRVLHICNEE--GLNLDAEALSTLSSIS---QGDLRRAIT  255 (294)
Q Consensus       186 ~~ii~~~~~~~---~~~~~l~~r~~--~i~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~l~~l~~~~---~G~~r~~~~  255 (294)
                      ..+|+++|...   .+.+.+.+++.  .+.|+|++.+++.++++..+...  ...+++++++.+++.+   .||+|.+++
T Consensus       174 v~vI~i~~~~~~~~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~  253 (394)
T PRK00411        174 IGVIGISSDLTFLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAID  253 (394)
T ss_pred             EEEEEEECCcchhhhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHH
Confidence            66888887653   35667777774  78999999999999999988643  2358999999999887   899999999


Q ss_pred             HHHHHHHHh----CCCCChhhhhhhcccc
Q 022641          256 YLQGAARLF----GSSITSKDLISVSGYP  280 (294)
Q Consensus       256 ~l~~~~~~~----~~~it~~~v~~~~~~~  280 (294)
                      ++..++..+    ...|+.+++..++...
T Consensus       254 ll~~a~~~a~~~~~~~I~~~~v~~a~~~~  282 (394)
T PRK00411        254 LLRRAGLIAEREGSRKVTEEDVRKAYEKS  282 (394)
T ss_pred             HHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence            999877665    3569999999888765

>CHL00176 ftsH cell division protein; Validated

Probab=99.83  E-value=5.7e-19  Score=160.32  Aligned_cols=203  Identities=21%  Similarity=0.203  Sum_probs=141.7

Q ss_pred             CCcchhhcccHHHHHHHHHHHH---c---------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLE---T---------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD  124 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~---~---------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~  124 (294)
                      ...|+++.|.++.+..+...+.   .         ..+.+++|+||||||||++|++++.++      +.+++.+++++.
T Consensus       179 ~~~f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~------~~p~i~is~s~f  252 (638)
T CHL00176        179 GITFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEA------EVPFFSISGSEF  252 (638)
T ss_pred             CCCHHhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHh------CCCeeeccHHHH
Confidence            3578899999888877766642   1         123459999999999999999999998      667777766542


Q ss_pred             cc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH-----------H---HHHHHHHHHHhhc-
Q 022641          125 RG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE-----------D---AQNALRRTMETYS-  183 (294)
Q Consensus       125 ~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~-----------~---~~~~L~~~l~~~~-  183 (294)
                      ..      ...++..+.....              ..+.+|+|||+|.+..           .   ..+.|+..++... 
T Consensus       253 ~~~~~g~~~~~vr~lF~~A~~--------------~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~  318 (638)
T CHL00176        253 VEMFVGVGAARVRDLFKKAKE--------------NSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKG  318 (638)
T ss_pred             HHHhhhhhHHHHHHHHHHHhc--------------CCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccC
Confidence            21      1122222222111              2245999999998731           2   2334444444322 


Q ss_pred             -CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHHHH
Q 022641          184 -KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITYLQ  258 (294)
Q Consensus       184 -~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~l~  258 (294)
                       ....+|++||.+..+++++++  ||. .+.+++|+.+++..+++.+++.... .++..+..+++.+.| +.+.+.+++.
T Consensus       319 ~~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~-~~d~~l~~lA~~t~G~sgaDL~~lvn  397 (638)
T CHL00176        319 NKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKL-SPDVSLELIARRTPGFSGADLANLLN  397 (638)
T ss_pred             CCCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhccc-chhHHHHHHHhcCCCCCHHHHHHHHH
Confidence             356788888999889999986  665 7999999999999999999876332 345678889998877 6666666666


Q ss_pred             HHHHHh----CCCCChhhhhhhcccc
Q 022641          259 GAARLF----GSSITSKDLISVSGYP  280 (294)
Q Consensus       259 ~~~~~~----~~~it~~~v~~~~~~~  280 (294)
                      .++..+    ...||.+++..++...
T Consensus       398 eAal~a~r~~~~~It~~dl~~Ai~rv  423 (638)
T CHL00176        398 EAAILTARRKKATITMKEIDTAIDRV  423 (638)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHHHH
Confidence            655433    4569999999998765

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

Probab=99.82  E-value=3.6e-19  Score=154.34  Aligned_cols=180  Identities=21%  Similarity=0.230  Sum_probs=137.9

Q ss_pred             cchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC---
Q 022641           59 QVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD---  123 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~---  123 (294)
                      .|.++-|.+..+.+|...+..            ..++.++|+||||||||.||+++|.++      +.+++.+++..   
T Consensus       188 ~f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel------~vPf~~isApeivS  261 (802)
T KOG0733|consen  188 SFSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGEL------GVPFLSISAPEIVS  261 (802)
T ss_pred             chhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhc------CCceEeecchhhhc
Confidence            488999999999888877632            122359999999999999999999999      88999887654   


Q ss_pred             ---CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH-----------HHHHHHHHHHhhc------
Q 022641          124 ---DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED-----------AQNALRRTMETYS------  183 (294)
Q Consensus       124 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~-----------~~~~L~~~l~~~~------  183 (294)
                         +.+...+++.+.......              +.++||||||.+.+.           ....|+..|++..      
T Consensus       262 GvSGESEkkiRelF~~A~~~a--------------PcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g  327 (802)
T KOG0733|consen  262 GVSGESEKKIRELFDQAKSNA--------------PCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTKG  327 (802)
T ss_pred             ccCcccHHHHHHHHHHHhccC--------------CeEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccccCC
Confidence               334556666666654433              359999999998642           3456777777543      


Q ss_pred             CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHH
Q 022641          184 KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQG  259 (294)
Q Consensus       184 ~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~  259 (294)
                      ..+.+|.+||.+..++++|++  ||. .|.+.-|+...+.+||+.+|+.-.+.. +=.+..|++++.|-+..-+..|-.
T Consensus       328 ~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g-~~d~~qlA~lTPGfVGADL~AL~~  405 (802)
T KOG0733|consen  328 DPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSG-DFDFKQLAKLTPGFVGADLMALCR  405 (802)
T ss_pred             CCeEEEecCCCCcccCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCC-CcCHHHHHhcCCCccchhHHHHHH
Confidence            456788889999999999987  787 799999999999999999997543332 233778899999977776655443

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.82  E-value=6.2e-19  Score=165.68  Aligned_cols=208  Identities=18%  Similarity=0.214  Sum_probs=154.6

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCC----CccCCcceeecC
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP----ELYKSRVLELNA  121 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~----~~~~~~~~~~~~  121 (294)
                      ....++.++.+|..++.++|+++.++.+...+.....+|++|+||||||||++++.+++.+...    ...+..++.++.
T Consensus       172 ~~~~~L~~~~r~~~ld~~iGr~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~l  251 (852)
T TIGR03345       172 QYTTDLTAQAREGKIDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDL  251 (852)
T ss_pred             HHhhhHHHHhcCCCCCcccCCHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEeeh
Confidence            5667899999999999999999999999999999988999999999999999999999987422    123344555544


Q ss_pred             CCCc----chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------HHHHHHHHHHHhhcCcceEE
Q 022641          122 SDDR----GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------DAQNALRRTMETYSKVTRFF  189 (294)
Q Consensus       122 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------~~~~~L~~~l~~~~~~~~ii  189 (294)
                      +...    ....+...+..+.......         ..+.||||||+|.+..        +..+.|+..++.  ....+|
T Consensus       252 ~~l~ag~~~~ge~e~~lk~ii~e~~~~---------~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~~--G~l~~I  320 (852)
T TIGR03345       252 GLLQAGASVKGEFENRLKSVIDEVKAS---------PQPIILFIDEAHTLIGAGGQAGQGDAANLLKPALAR--GELRTI  320 (852)
T ss_pred             hhhhcccccchHHHHHHHHHHHHHHhc---------CCCeEEEEeChHHhccCCCccccccHHHHhhHHhhC--CCeEEE
Confidence            3321    2222333333333322110         1245999999999853        233467777765  566688


Q ss_pred             EEecC-----CcccchHhhccccEEEecCCCHHHHHHHHHHHHHH----hCCCCCHHHHHHHHhhccC------cHHHHH
Q 022641          190 FICNY-----ISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE----EGLNLDAEALSTLSSISQG------DLRRAI  254 (294)
Q Consensus       190 ~~~~~-----~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~----~~~~~~~~~l~~l~~~~~G------~~r~~~  254 (294)
                      .+|+.     ....+++|.+||..|.+++|+.++...+|+.+...    +++.++++++..+++++.+      -|..++
T Consensus       321 gaTT~~e~~~~~~~d~AL~rRf~~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ryi~~r~LPDKAI  400 (852)
T TIGR03345       321 AATTWAEYKKYFEKDPALTRRFQVVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYIPGRQLPDKAV  400 (852)
T ss_pred             EecCHHHHhhhhhccHHHHHhCeEEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHcccccccccCccHHH
Confidence            88764     34578999999999999999999999997666543    5688999999999998764      478899


Q ss_pred             HHHHHHHHHh
Q 022641          255 TYLQGAARLF  264 (294)
Q Consensus       255 ~~l~~~~~~~  264 (294)
                      .++..++...
T Consensus       401 dlldea~a~~  410 (852)
T TIGR03345       401 SLLDTACARV  410 (852)
T ss_pred             HHHHHHHHHH
Confidence            9999876543

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.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.82  E-value=9.4e-19  Score=153.91  Aligned_cols=217  Identities=12%  Similarity=0.158  Sum_probs=146.3

Q ss_pred             CCCcchhhc-cc--HHHHHHHHHHHHcCC--CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHH
Q 022641           56 RPKQVKDVA-HQ--EEVVRVLTNTLETAN--CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVV  130 (294)
Q Consensus        56 ~~~~~~~~~-g~--~~~~~~l~~~l~~~~--~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~  130 (294)
                      .+.+|+.++ |.  ..+......+....+  ...++|+|++|+|||||++++++.+.... .+..++.+++.+.     .
T Consensus       110 ~~~tFdnFv~g~~n~~A~~aa~~~a~~~~~~~npl~i~G~~G~GKTHLl~Ai~~~l~~~~-~~~~v~yv~~~~f-----~  183 (450)
T PRK14087        110 NENTFENFVIGSSNEQAFIAVQTVSKNPGISYNPLFIYGESGMGKTHLLKAAKNYIESNF-SDLKVSYMSGDEF-----A  183 (450)
T ss_pred             cccchhcccCCCcHHHHHHHHHHHHhCcCcccCceEEECCCCCcHHHHHHHHHHHHHHhC-CCCeEEEEEHHHH-----H
Confidence            346777666 33  334444455544322  23499999999999999999999763211 1234444443321     1


Q ss_pred             HHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC--HHHHHHHHHHHHhhcCc-ceEEEEecCCc----ccchHhh
Q 022641          131 RTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT--EDAQNALRRTMETYSKV-TRFFFICNYIS----RIIEPLA  203 (294)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--~~~~~~L~~~l~~~~~~-~~ii~~~~~~~----~~~~~l~  203 (294)
                      ......+....  .............++|+|||++.+.  ...++.|+.+++..... ..+|++++.+.    .+.+++.
T Consensus       184 ~~~~~~l~~~~--~~~~~~~~~~~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~  261 (450)
T PRK14087        184 RKAVDILQKTH--KEIEQFKNEICQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLI  261 (450)
T ss_pred             HHHHHHHHHhh--hHHHHHHHHhccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHH
Confidence            11111110000  0000000011234699999999986  55678888888765543 35777776543    3568899


Q ss_pred             cccc---EEEecCCCHHHHHHHHHHHHHHhCC--CCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh--C---CCCChhhh
Q 022641          204 SRCA---KFRFKPLSEEVMSSRVLHICNEEGL--NLDAEALSTLSSISQGDLRRAITYLQGAARLF--G---SSITSKDL  273 (294)
Q Consensus       204 ~r~~---~i~~~~~~~~~~~~~l~~~~~~~~~--~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~--~---~~it~~~v  273 (294)
                      +|+.   .+.+.||+.+++..++++.++..|+  .++++++++|++.++||+|.+.+++..+...+  .   ..||.+.+
T Consensus       262 SR~~~Gl~~~L~~pd~e~r~~iL~~~~~~~gl~~~l~~evl~~Ia~~~~gd~R~L~gaL~~l~~~a~~~~~~~~it~~~v  341 (450)
T PRK14087        262 TRFNMGLSIAIQKLDNKTATAIIKKEIKNQNIKQEVTEEAINFISNYYSDDVRKIKGSVSRLNFWSQQNPEEKIITIEIV  341 (450)
T ss_pred             HHHhCCceeccCCcCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHccCCCHHHHHHHHHHHHHHHhcccCCCCCCHHHH
Confidence            9986   8999999999999999999998875  69999999999999999999999998775444  2   57999999


Q ss_pred             hhhcccc
Q 022641          274 ISVSGYP  280 (294)
Q Consensus       274 ~~~~~~~  280 (294)
                      ++++...
T Consensus       342 ~~~l~~~  348 (450)
T PRK14087        342 SDLFRDI  348 (450)
T ss_pred             HHHHhhc
Confidence            9998764

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

Probab=99.82  E-value=4.6e-19  Score=151.50  Aligned_cols=206  Identities=21%  Similarity=0.204  Sum_probs=147.5

Q ss_pred             hhhcCCCcchhhcccHHHHHHHHHHHH---c--------CCC-CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee
Q 022641           52 VEKYRPKQVKDVAHQEEVVRVLTNTLE---T--------ANC-PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL  119 (294)
Q Consensus        52 ~~~~~~~~~~~~~g~~~~~~~l~~~l~---~--------~~~-~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~  119 (294)
                      .+......|+++.|-++++.+|.+.+.   .        |+. ..++|+||||||||.||+++|-++      +.+|+..
T Consensus       295 p~~~~nv~F~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA------~VPFF~~  368 (752)
T KOG0734|consen  295 PEQMKNVTFEDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEA------GVPFFYA  368 (752)
T ss_pred             hhhhcccccccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhccc------CCCeEec
Confidence            344455679999999998887766653   2        222 349999999999999999999999      7888877


Q ss_pred             cCCC------CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH-----------HHHHHHHHHHHhh
Q 022641          120 NASD------DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE-----------DAQNALRRTMETY  182 (294)
Q Consensus       120 ~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~-----------~~~~~L~~~l~~~  182 (294)
                      .++.      ..+...+++++.......              ++||||||+|.+..           ...+.|+--|+.+
T Consensus       369 sGSEFdEm~VGvGArRVRdLF~aAk~~A--------------PcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF  434 (752)
T KOG0734|consen  369 SGSEFDEMFVGVGARRVRDLFAAAKARA--------------PCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGF  434 (752)
T ss_pred             cccchhhhhhcccHHHHHHHHHHHHhcC--------------CeEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCc
Confidence            7664      234455666665544433              35999999998731           2456666666665


Q ss_pred             cC--cceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHH-HHHHHHhhccC-cHHHHHH
Q 022641          183 SK--VTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAE-ALSTLSSISQG-DLRRAIT  255 (294)
Q Consensus       183 ~~--~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~-~l~~l~~~~~G-~~r~~~~  255 (294)
                      ..  .+.+|.+||.+..++++|.+  ||. .|.++.|+..-+.+||..++++  +.++++ .+..|++-+.| +--.+-|
T Consensus       435 ~qNeGiIvigATNfpe~LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~k--i~~~~~VD~~iiARGT~GFsGAdLaN  512 (752)
T KOG0734|consen  435 KQNEGIIVIGATNFPEALDKALTRPGRFDRHVTVPLPDVRGRTEILKLYLSK--IPLDEDVDPKIIARGTPGFSGADLAN  512 (752)
T ss_pred             CcCCceEEEeccCChhhhhHHhcCCCccceeEecCCCCcccHHHHHHHHHhc--CCcccCCCHhHhccCCCCCchHHHHH
Confidence            54  55667778999999999987  887 7899999999999999999864  545533 36667777655 3344455


Q ss_pred             HHHHHHHHh----CCCCChhhhhhhccc
Q 022641          256 YLQGAARLF----GSSITSKDLISVSGY  279 (294)
Q Consensus       256 ~l~~~~~~~----~~~it~~~v~~~~~~  279 (294)
                      +...++..+    .+.+|+.+++.+=..
T Consensus       513 lVNqAAlkAa~dga~~VtM~~LE~akDr  540 (752)
T KOG0734|consen  513 LVNQAALKAAVDGAEMVTMKHLEFAKDR  540 (752)
T ss_pred             HHHHHHHHHHhcCcccccHHHHhhhhhh
Confidence            666666555    566999888765443

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

Probab=99.82  E-value=8.6e-19  Score=152.27  Aligned_cols=208  Identities=19%  Similarity=0.247  Sum_probs=138.8

Q ss_pred             hhhcCCCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCccee
Q 022641           52 VEKYRPKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLE  118 (294)
Q Consensus        52 ~~~~~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~  118 (294)
                      .++.-+..|.++.|.+..++.+.+++..             ..+.+++|+||||||||++|+++++++      ...++.
T Consensus       174 ~~~~p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el------~~~fi~  247 (438)
T PTZ00361        174 VDKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANET------SATFLR  247 (438)
T ss_pred             cccCCCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhh------CCCEEE
Confidence            3445557889999999999988887742             123459999999999999999999998      556666


Q ss_pred             ecCCCCcc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHH--
Q 022641          119 LNASDDRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTM--  179 (294)
Q Consensus       119 ~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l--  179 (294)
                      +..+....      ...++..+.....              ..+.+|+|||+|.+.           ...+..++.++  
T Consensus       248 V~~seL~~k~~Ge~~~~vr~lF~~A~~--------------~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~  313 (438)
T PTZ00361        248 VVGSELIQKYLGDGPKLVRELFRVAEE--------------NAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQ  313 (438)
T ss_pred             EecchhhhhhcchHHHHHHHHHHHHHh--------------CCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHH
Confidence            66554322      1112222221111              123599999998763           12233344444  


Q ss_pred             -Hhh--cCcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhc----cCc
Q 022641          180 -ETY--SKVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSIS----QGD  249 (294)
Q Consensus       180 -~~~--~~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~----~G~  249 (294)
                       +..  ...+.+|++||....+++++.+  |+. .|.|++|+.+++.++++.++....+. ++-.+..++..+    +++
T Consensus       314 Ldg~~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~-~dvdl~~la~~t~g~sgAd  392 (438)
T PTZ00361        314 LDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLA-EDVDLEEFIMAKDELSGAD  392 (438)
T ss_pred             HhhhcccCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCC-cCcCHHHHHHhcCCCCHHH
Confidence             332  3467789999999999999875  776 89999999999999999887654432 122355555444    445


Q ss_pred             HHHHHHHHHHHHHHh----CCCCChhhhhhhcccccCC
Q 022641          250 LRRAITYLQGAARLF----GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       250 ~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~~~  283 (294)
                      ++.+   +..|+..+    ...|+.+++..+...+...
T Consensus       393 I~~i---~~eA~~~Alr~~r~~Vt~~D~~~A~~~v~~~  427 (438)
T PTZ00361        393 IKAI---CTEAGLLALRERRMKVTQADFRKAKEKVLYR  427 (438)
T ss_pred             HHHH---HHHHHHHHHHhcCCccCHHHHHHHHHHHHhh
Confidence            5544   44444443    4579999999998886443

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

Probab=99.81  E-value=4.6e-18  Score=138.90  Aligned_cols=125  Identities=20%  Similarity=0.235  Sum_probs=107.3

Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecC------------CcccchHhhccccEEEecCCCHHHHHHHH
Q 022641          156 YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNY------------ISRIIEPLASRCAKFRFKPLSEEVMSSRV  223 (294)
Q Consensus       156 ~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~------------~~~~~~~l~~r~~~i~~~~~~~~~~~~~l  223 (294)
                      +++|||||+|.|+-.+...|-+.+++-- ...+|++||.            |+.++..|++|..+|...|++.+++++++
T Consensus       292 pGVLFIDEvHmLDIE~FsFlnrAlEse~-aPIii~AtNRG~~kiRGTd~~sPhGIP~DlLDRllII~t~py~~~EireIi  370 (450)
T COG1224         292 PGVLFIDEVHMLDIECFSFLNRALESEL-APIIILATNRGMTKIRGTDIESPHGIPLDLLDRLLIISTRPYSREEIREII  370 (450)
T ss_pred             cceEEEechhhhhHHHHHHHHHHhhccc-CcEEEEEcCCceeeecccCCcCCCCCCHhhhhheeEEecCCCCHHHHHHHH
Confidence            5699999999999999999999998733 3446777763            56789999999999999999999999999


Q ss_pred             HHHHHHhCCCCCHHHHHHHHhhc-cCcHHHHHHHHHHHHHHh----CCCCChhhhhhhccccc
Q 022641          224 LHICNEEGLNLDAEALSTLSSIS-QGDLRRAITYLQGAARLF----GSSITSKDLISVSGYPT  281 (294)
Q Consensus       224 ~~~~~~~~~~~~~~~l~~l~~~~-~G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~  281 (294)
                      +..++.+++.++++++++|+... .-++|.++++|.-+...+    +..+..+||..+-..+.
T Consensus       371 ~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~lF~  433 (450)
T COG1224         371 RIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKELFL  433 (450)
T ss_pred             HHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHHHh
Confidence            99999999999999999999985 568999999999666555    55799999988766543

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.81  E-value=1.3e-18  Score=152.47  Aligned_cols=211  Identities=14%  Similarity=0.156  Sum_probs=144.5

Q ss_pred             Ccchhhc-cc--HHHHHHHHHHHHc-----CC-CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchh
Q 022641           58 KQVKDVA-HQ--EEVVRVLTNTLET-----AN-CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGIN  128 (294)
Q Consensus        58 ~~~~~~~-g~--~~~~~~l~~~l~~-----~~-~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~  128 (294)
                      .+|+.++ |.  ..+...+..+...     +. ...++|+||+|+|||||++++++++...   +..++.++....    
T Consensus       108 ~tFdnFv~g~~N~~a~~~a~~~a~~~~~~~~~~~npl~L~G~~G~GKTHLl~Ai~~~l~~~---~~~v~yi~~~~f----  180 (445)
T PRK12422        108 MTFANFLVTPENDLPHRILQEFTKVSEQGKGFPFNPIYLFGPEGSGKTHLMQAAVHALRES---GGKILYVRSELF----  180 (445)
T ss_pred             ccccceeeCCcHHHHHHHHHHHHhccccccCCCCceEEEEcCCCCCHHHHHHHHHHHHHHc---CCCEEEeeHHHH----
Confidence            3566665 43  3333455555432     11 2349999999999999999999998432   344444443221    


Q ss_pred             HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--HHHHHHHHHHHhhc-CcceEEEEecCC----cccchH
Q 022641          129 VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--DAQNALRRTMETYS-KVTRFFFICNYI----SRIIEP  201 (294)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--~~~~~L~~~l~~~~-~~~~ii~~~~~~----~~~~~~  201 (294)
                       .......+...    ............++|+|||++.+..  ..++.|+..++... ....+|++++.+    ..+.++
T Consensus       181 -~~~~~~~l~~~----~~~~f~~~~~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~r  255 (445)
T PRK12422        181 -TEHLVSAIRSG----EMQRFRQFYRNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEER  255 (445)
T ss_pred             -HHHHHHHHhcc----hHHHHHHHcccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHH
Confidence             00111111000    0000000123456999999999853  45677777776543 345677888654    246789


Q ss_pred             hhcccc---EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHH---HHh---CCCCChhh
Q 022641          202 LASRCA---KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA---RLF---GSSITSKD  272 (294)
Q Consensus       202 l~~r~~---~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~---~~~---~~~it~~~  272 (294)
                      +.+||.   .+.+.||+.+++..++++.+...++.++++++++|+....||+|.+.+.+..++   .+.   +..||.+.
T Consensus       256 L~SR~~~Gl~~~l~~pd~e~r~~iL~~k~~~~~~~l~~evl~~la~~~~~dir~L~g~l~~l~~~~a~~~~~~~~i~~~~  335 (445)
T PRK12422        256 LISRFEWGIAIPLHPLTKEGLRSFLERKAEALSIRIEETALDFLIEALSSNVKSLLHALTLLAKRVAYKKLSHQLLYVDD  335 (445)
T ss_pred             HHhhhcCCeEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHhhCCCCCHHH
Confidence            999994   899999999999999999999999999999999999999999999999999774   332   56799999


Q ss_pred             hhhhcccc
Q 022641          273 LISVSGYP  280 (294)
Q Consensus       273 v~~~~~~~  280 (294)
                      +++++...
T Consensus       336 ~~~~l~~~  343 (445)
T PRK12422        336 IKALLHDV  343 (445)
T ss_pred             HHHHHHHh
Confidence            99998764

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

Probab=99.81  E-value=3.8e-19  Score=146.61  Aligned_cols=203  Identities=22%  Similarity=0.239  Sum_probs=138.6

Q ss_pred             CcchhhcccHHHHHHHHHHHH---------cCCC---CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           58 KQVKDVAHQEEVVRVLTNTLE---------TANC---PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~---------~~~~---~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      ..|+++.|..++++-|.+++-         .+..   ..++++||||||||.||++++.+.      +..|+-++.+...
T Consensus       209 ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTlLAKAvATEc------~tTFFNVSsstlt  282 (491)
T KOG0738|consen  209 IKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTLLAKAVATEC------GTTFFNVSSSTLT  282 (491)
T ss_pred             cChHhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHHHHHHHHHhh------cCeEEEechhhhh
Confidence            467899999999988888752         2222   349999999999999999999998      7788888776654


Q ss_pred             chh------HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC------------HHHHHHHHHHHHhhcC---
Q 022641          126 GIN------VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT------------EDAQNALRRTMETYSK---  184 (294)
Q Consensus       126 ~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~------------~~~~~~L~~~l~~~~~---  184 (294)
                      ++.      .++-++.......              +..|||||||.|.            ...-..|+..|+....   
T Consensus       283 SKwRGeSEKlvRlLFemARfyA--------------PStIFiDEIDslcs~RG~s~EHEaSRRvKsELLvQmDG~~~t~e  348 (491)
T KOG0738|consen  283 SKWRGESEKLVRLLFEMARFYA--------------PSTIFIDEIDSLCSQRGGSSEHEASRRVKSELLVQMDGVQGTLE  348 (491)
T ss_pred             hhhccchHHHHHHHHHHHHHhC--------------CceeehhhHHHHHhcCCCccchhHHHHHHHHHHHHhhccccccc
Confidence            432      2222222222222              2499999999883            2355677777774331   


Q ss_pred             --c-ceEEEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCC-CHHHHHHHHhhccC----cHHHHHH
Q 022641          185 --V-TRFFFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNL-DAEALSTLSSISQG----DLRRAIT  255 (294)
Q Consensus       185 --~-~~ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~-~~~~l~~l~~~~~G----~~r~~~~  255 (294)
                        . +.|+.+||.++.++.+|++|+. .|.++-|+.+.+..+++..+..  +.. ++-.++.|++.+.|    ||+.++ 
T Consensus       349 ~~k~VmVLAATN~PWdiDEAlrRRlEKRIyIPLP~~~~R~~Li~~~l~~--~~~~~~~~~~~lae~~eGySGaDI~nvC-  425 (491)
T KOG0738|consen  349 NSKVVMVLAATNFPWDIDEALRRRLEKRIYIPLPDAEARSALIKILLRS--VELDDPVNLEDLAERSEGYSGADITNVC-  425 (491)
T ss_pred             cceeEEEEeccCCCcchHHHHHHHHhhheeeeCCCHHHHHHHHHHhhcc--ccCCCCccHHHHHHHhcCCChHHHHHHH-
Confidence              2 3355567999999999999999 7999888888888888766643  333 33346666666544    555444 


Q ss_pred             HHHHHHHHh---------------------CCCCChhhhhhhcccccCCCC
Q 022641          256 YLQGAARLF---------------------GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       256 ~l~~~~~~~---------------------~~~it~~~v~~~~~~~~~~~~  285 (294)
                        ..++...                     ...++.++++.++..+.+...
T Consensus       426 --reAsm~~mRR~i~g~~~~ei~~lakE~~~~pv~~~Dfe~Al~~v~pSvs  474 (491)
T KOG0738|consen  426 --REASMMAMRRKIAGLTPREIRQLAKEEPKMPVTNEDFEEALRKVRPSVS  474 (491)
T ss_pred             --HHHHHHHHHHHHhcCCcHHhhhhhhhccccccchhhHHHHHHHcCcCCC
Confidence              3333222                     123788888888888877765

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

Probab=99.81  E-value=1.3e-18  Score=150.94  Aligned_cols=206  Identities=18%  Similarity=0.145  Sum_probs=149.4

Q ss_pred             cchhhcccHHHHHHHHHHHHcC-------------CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           59 QVKDVAHQEEVVRVLTNTLETA-------------NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~-------------~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      +|+++-+.+++..+|..++...             .+..++|+||||||||.||+++|++.      +.+|+.+.+....
T Consensus       509 tW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANEa------g~NFisVKGPELl  582 (802)
T KOG0733|consen  509 TWDDIGALEEVRLELNMAILAPIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANEA------GANFISVKGPELL  582 (802)
T ss_pred             ChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhhc------cCceEeecCHHHH
Confidence            6778888888888877666432             23459999999999999999999999      8899988877654


Q ss_pred             chh------HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHhhc--Ccc
Q 022641          126 GIN------VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMETYS--KVT  186 (294)
Q Consensus       126 ~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~~~--~~~  186 (294)
                      +.+      .++..++.....              .+.|||+||+|.|.           ....+.|+.-|+...  ..+
T Consensus       583 NkYVGESErAVR~vFqRAR~s--------------aPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV  648 (802)
T KOG0733|consen  583 NKYVGESERAVRQVFQRARAS--------------APCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGV  648 (802)
T ss_pred             HHHhhhHHHHHHHHHHHhhcC--------------CCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccce
Confidence            433      344444443333              24699999999984           346788888887653  355


Q ss_pred             eEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHH-HHHHHhhc------cCcHHHHHHH
Q 022641          187 RFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEA-LSTLSSIS------QGDLRRAITY  256 (294)
Q Consensus       187 ~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-l~~l~~~~------~G~~r~~~~~  256 (294)
                      .+|.+||.+..+++++++  |+. .+.+.+|+.++..+||+.+.+..+..+++++ ++.|+..+      +.|+-.++.-
T Consensus       649 ~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVdl~eia~~~~c~gftGADLaaLvre  728 (802)
T KOG0733|consen  649 YVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEERVAILKTITKNTKPPLSSDVDLDEIARNTKCEGFTGADLAALVRE  728 (802)
T ss_pred             EEEeecCCCcccchhhcCCCccCceeeecCCCHHHHHHHHHHHhccCCCCCCcccCHHHHhhcccccCCchhhHHHHHHH
Confidence            678889999999999987  777 7889999999999999999987777776655 77777653      3455554443


Q ss_pred             HHHHHHHh-------C----------CCCChhhhhhhcccccCCC
Q 022641          257 LQGAARLF-------G----------SSITSKDLISVSGYPTGGS  284 (294)
Q Consensus       257 l~~~~~~~-------~----------~~it~~~v~~~~~~~~~~~  284 (294)
                      ...++.-.       +          ..+|..|+.+++....+..
T Consensus       729 Asi~AL~~~~~~~~~~~~~~~~~~~~~~~t~~hF~eA~~~i~pSv  773 (802)
T KOG0733|consen  729 ASILALRESLFEIDSSEDDVTVRSSTIIVTYKHFEEAFQRIRPSV  773 (802)
T ss_pred             HHHHHHHHHHhhccccCcccceeeeeeeecHHHHHHHHHhcCCCc
Confidence            33333221       0          1256678888888777664

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.81  E-value=1.5e-18  Score=154.61  Aligned_cols=213  Identities=15%  Similarity=0.097  Sum_probs=145.3

Q ss_pred             Ccchhhc-cc--HHHHHHHHHHHHcC-CC-CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHH
Q 022641           58 KQVKDVA-HQ--EEVVRVLTNTLETA-NC-PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRT  132 (294)
Q Consensus        58 ~~~~~~~-g~--~~~~~~l~~~l~~~-~~-~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (294)
                      .+|++++ |.  ..+...+..+.... .. ..++|+|++|+|||||++++++.+... ..+..+++++..+...     .
T Consensus       285 ~TFDnFvvG~sN~~A~aaa~avae~~~~~~NpL~LyG~sGsGKTHLL~AIa~~a~~~-~~g~~V~Yitaeef~~-----e  358 (617)
T PRK14086        285 YTFDTFVIGASNRFAHAAAVAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRL-YPGTRVRYVSSEEFTN-----E  358 (617)
T ss_pred             CCHhhhcCCCccHHHHHHHHHHHhCccccCCcEEEECCCCCCHHHHHHHHHHHHHHh-CCCCeEEEeeHHHHHH-----H
Confidence            4667665 33  22333444444432 22 239999999999999999999987321 1123444444332111     1


Q ss_pred             HHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--HHHHHHHHHHHhhcC-cceEEEEecCCc----ccchHhhcc
Q 022641          133 KIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--DAQNALRRTMETYSK-VTRFFFICNYIS----RIIEPLASR  205 (294)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--~~~~~L~~~l~~~~~-~~~ii~~~~~~~----~~~~~l~~r  205 (294)
                      ....+......    .......+.++|+|||++.+..  ..++.|+.+++.... ...+|++++...    .+.+.|.+|
T Consensus       359 l~~al~~~~~~----~f~~~y~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SR  434 (617)
T PRK14086        359 FINSIRDGKGD----SFRRRYREMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNR  434 (617)
T ss_pred             HHHHHHhccHH----HHHHHhhcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhh
Confidence            11110000000    0000112346999999999853  346778888887665 355778887642    467889999


Q ss_pred             cc---EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---CCCCChhhhhhhccc
Q 022641          206 CA---KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---GSSITSKDLISVSGY  279 (294)
Q Consensus       206 ~~---~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---~~~it~~~v~~~~~~  279 (294)
                      +.   .+.+.+|+.+.+..+|++.+...++.++++++++|++...+|+|.+...|..+..++   +..||.+.++.++..
T Consensus       435 f~~GLvv~I~~PD~EtR~aIL~kka~~r~l~l~~eVi~yLa~r~~rnvR~LegaL~rL~a~a~~~~~~itl~la~~vL~~  514 (617)
T PRK14086        435 FEWGLITDVQPPELETRIAILRKKAVQEQLNAPPEVLEFIASRISRNIRELEGALIRVTAFASLNRQPVDLGLTEIVLRD  514 (617)
T ss_pred             hhcCceEEcCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHH
Confidence            86   799999999999999999999999999999999999999999999998888766554   667999888888875


Q ss_pred             c
Q 022641          280 P  280 (294)
Q Consensus       280 ~  280 (294)
                      .
T Consensus       515 ~  515 (617)
T PRK14086        515 L  515 (617)
T ss_pred             h
Confidence            4

>PRK06526 transposase; Provisional

Probab=99.81  E-value=2e-20  Score=152.22  Aligned_cols=202  Identities=15%  Similarity=0.183  Sum_probs=134.5

Q ss_pred             CCcccccccccccCCCCCcccCCCC--cccCCCCchHHHHhhccccccCCchhhhhcCCCcchhhccc-HHHHHHHHHHH
Q 022641            1 MRANFGKIHKSGKNKSPNFTQKFST--TQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQ-EEVVRVLTNTL   77 (294)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~-~~~~~~l~~~l   77 (294)
                      |+++|++++..+...++++.+++..  +.|...|.++...++++   .+.+|+.+.+...++....+. +..+..+...-
T Consensus        17 ~~~~~~~~~~~a~~~~~~~~e~l~~ll~~E~~~R~~~~~~~~lk---~a~~p~~~~le~fd~~~~~~~~~~~~~~l~~~~   93 (254)
T PRK06526         17 LAGAVERLAERARAESWSHEEFLAACLQREVAARESHGGEGRIR---AARFPARKSLEEFDFDHQRSLKRDTIAHLGTLD   93 (254)
T ss_pred             HHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHH---hCCCCCCCChhhccCccCCCcchHHHHHHhcCc
Confidence            4577888899999999999999887  66777888888888877   788899888888888776653 44555554433


Q ss_pred             HcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcE
Q 022641           78 ETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYK  157 (294)
Q Consensus        78 ~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (294)
                      +....++++|+||||||||+++.+++.++....   ..+.....         ...+..+.................+.+
T Consensus        94 fi~~~~nlll~Gp~GtGKThLa~al~~~a~~~g---~~v~f~t~---------~~l~~~l~~~~~~~~~~~~l~~l~~~d  161 (254)
T PRK06526         94 FVTGKENVVFLGPPGTGKTHLAIGLGIRACQAG---HRVLFATA---------AQWVARLAAAHHAGRLQAELVKLGRYP  161 (254)
T ss_pred             hhhcCceEEEEeCCCCchHHHHHHHHHHHHHCC---CchhhhhH---------HHHHHHHHHHHhcCcHHHHHHHhccCC
Confidence            334556899999999999999999999884221   11111111         111111111100000000001123457


Q ss_pred             EEEEeCCCCCC--HHHHHHHHHHHHhhcCcceEEEEecCCcc--------------cchHhhccccEEEecCCCHH
Q 022641          158 IIILDEADSMT--EDAQNALRRTMETYSKVTRFFFICNYISR--------------IIEPLASRCAKFRFKPLSEE  217 (294)
Q Consensus       158 lliiDei~~l~--~~~~~~L~~~l~~~~~~~~ii~~~~~~~~--------------~~~~l~~r~~~i~~~~~~~~  217 (294)
                      +|||||++.++  ....+.|+++++..+....+|++||.+..              +.+++.+.+..+.|...+..
T Consensus       162 lLIIDD~g~~~~~~~~~~~L~~li~~r~~~~s~IitSn~~~~~w~~~~~d~~~a~ai~dRl~~~~~~i~~~g~s~R  237 (254)
T PRK06526        162 LLIVDEVGYIPFEPEAANLFFQLVSSRYERASLIVTSNKPFGRWGEVFGDDVVAAAMIDRLVHHAEVISLKGDSYR  237 (254)
T ss_pred             EEEEcccccCCCCHHHHHHHHHHHHHHHhcCCEEEEcCCCHHHHHHHcCChHHHHHHHHHHhcCceEEeecCCCcc
Confidence            99999999875  56677899999887777789999987643              23455566678888876644

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.81  E-value=8.4e-19  Score=153.77  Aligned_cols=212  Identities=15%  Similarity=0.151  Sum_probs=140.9

Q ss_pred             cchhhc-ccH--HHHHHHHHHHHcCC--CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHH
Q 022641           59 QVKDVA-HQE--EVVRVLTNTLETAN--CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTK  133 (294)
Q Consensus        59 ~~~~~~-g~~--~~~~~l~~~l~~~~--~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  133 (294)
                      +|++++ |..  .+...+..+.....  ...++|+||+|+|||||++++++++... ..+..++.+++.+..     ...
T Consensus       108 tfd~fi~g~~n~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKThL~~ai~~~l~~~-~~~~~v~yi~~~~~~-----~~~  181 (405)
T TIGR00362       108 TFDNFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNEILEN-NPNAKVVYVSSEKFT-----NDF  181 (405)
T ss_pred             cccccccCCcHHHHHHHHHHHHhCcCccCCeEEEECCCCCcHHHHHHHHHHHHHHh-CCCCcEEEEEHHHHH-----HHH
Confidence            455543 433  23444555544432  2348999999999999999999998432 113445555433211     111


Q ss_pred             HHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--HHHHHHHHHHHhhcC-cceEEEEecCCc----ccchHhhccc
Q 022641          134 IKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--DAQNALRRTMETYSK-VTRFFFICNYIS----RIIEPLASRC  206 (294)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--~~~~~L~~~l~~~~~-~~~ii~~~~~~~----~~~~~l~~r~  206 (294)
                      ...+...    ....-.......++|+|||+|.+..  ..++.|+..++.... ...+|++++...    .+.+++.+|+
T Consensus       182 ~~~~~~~----~~~~~~~~~~~~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl  257 (405)
T TIGR00362       182 VNALRNN----KMEEFKEKYRSVDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRF  257 (405)
T ss_pred             HHHHHcC----CHHHHHHHHHhCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhc
Confidence            1111000    0000000011235999999998853  356677777776543 345777776432    3567889998


Q ss_pred             c---EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---CCCCChhhhhhhcccc
Q 022641          207 A---KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---GSSITSKDLISVSGYP  280 (294)
Q Consensus       207 ~---~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---~~~it~~~v~~~~~~~  280 (294)
                      .   .+.+.+|+.+++..+++..++..++.++++++++|++.+.||+|.+...+..+..++   +..||.+.+.+++...
T Consensus       258 ~~g~~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~r~l~~~l~~l~~~a~~~~~~it~~~~~~~L~~~  337 (405)
T TIGR00362       258 EWGLVVDIEPPDLETRLAILQKKAEEEGLELPDEVLEFIAKNIRSNVRELEGALNRLLAYASLTGKPITLELAKEALKDL  337 (405)
T ss_pred             cCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHh
Confidence            5   799999999999999999999999999999999999999999999777776655444   6779999998888764

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).

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.81  E-value=1.1e-18  Score=154.74  Aligned_cols=207  Identities=15%  Similarity=0.190  Sum_probs=143.8

Q ss_pred             cchhhc-c--cHHHHHHHHHHHHcCC--CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHH
Q 022641           59 QVKDVA-H--QEEVVRVLTNTLETAN--CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTK  133 (294)
Q Consensus        59 ~~~~~~-g--~~~~~~~l~~~l~~~~--~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  133 (294)
                      +|++++ |  +..+...+..+.....  ...++|+||+|+|||||++++++++.... .+..++.+++.+...  .+...
T Consensus       120 tfd~fv~g~~n~~a~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~-~~~~v~yi~~~~~~~--~~~~~  196 (450)
T PRK00149        120 TFDNFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNYILEKN-PNAKVVYVTSEKFTN--DFVNA  196 (450)
T ss_pred             cccccccCCCcHHHHHHHHHHHhCcCccCCeEEEECCCCCCHHHHHHHHHHHHHHhC-CCCeEEEEEHHHHHH--HHHHH
Confidence            455544 3  4445556666655432  23499999999999999999999984321 123444444432211  11111


Q ss_pred             HH-----HHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--HHHHHHHHHHHhhcCc-ceEEEEecCCc----ccchH
Q 022641          134 IK-----TFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--DAQNALRRTMETYSKV-TRFFFICNYIS----RIIEP  201 (294)
Q Consensus       134 ~~-----~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--~~~~~L~~~l~~~~~~-~~ii~~~~~~~----~~~~~  201 (294)
                      +.     .+..            .....++|+|||+|.+..  ..++.|+.+++..... ..++++++.+.    .+.++
T Consensus       197 ~~~~~~~~~~~------------~~~~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~  264 (450)
T PRK00149        197 LRNNTMEEFKE------------KYRSVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEER  264 (450)
T ss_pred             HHcCcHHHHHH------------HHhcCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHH
Confidence            10     1110            011245999999999853  3466777777665433 34677776542    25678


Q ss_pred             hhcccc---EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---CCCCChhhhhh
Q 022641          202 LASRCA---KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---GSSITSKDLIS  275 (294)
Q Consensus       202 l~~r~~---~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---~~~it~~~v~~  275 (294)
                      +.+|+.   .+.+.+|+.+++..++++.+...++.++++++++|++.+.||+|.+...+..+..++   +..||.+.+++
T Consensus       265 l~SRl~~gl~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~R~l~~~l~~l~~~~~~~~~~it~~~~~~  344 (450)
T PRK00149        265 LRSRFEWGLTVDIEPPDLETRIAILKKKAEEEGIDLPDEVLEFIAKNITSNVRELEGALNRLIAYASLTGKPITLELAKE  344 (450)
T ss_pred             HHhHhcCCeeEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHcCcCCCHHHHHHHHHHHHHHHHhhCCCCCHHHHHH
Confidence            999995   799999999999999999999989999999999999999999999888777666544   67799999999


Q ss_pred             hcccc
Q 022641          276 VSGYP  280 (294)
Q Consensus       276 ~~~~~  280 (294)
                      ++...
T Consensus       345 ~l~~~  349 (450)
T PRK00149        345 ALKDL  349 (450)
T ss_pred             HHHHh
Confidence            98865

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

Probab=99.80  E-value=6e-19  Score=155.99  Aligned_cols=252  Identities=22%  Similarity=0.276  Sum_probs=179.9

Q ss_pred             cccCCCCchHHHHhhccccccCCchhhhhcCCC-cc--------hhhcccHHHHHHHHHHHHc------CCCCcEEEECC
Q 022641           26 TQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPK-QV--------KDVAHQEEVVRVLTNTLET------ANCPHMLFYGP   90 (294)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~--------~~~~g~~~~~~~l~~~l~~------~~~~~ill~Gp   90 (294)
                      ..-++.+++..+-|++-.+ .-..||.++-... ++        .+-.|.+++++++.+.+..      -+.+.+||+||
T Consensus       280 ~~m~~~SaE~~ViRnYlDw-ll~lPW~~~sk~~~Dl~~a~~iLd~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGP  358 (782)
T COG0466         280 ETMSPMSAEATVIRNYLDW-LLDLPWGKRSKDKLDLKKAEKILDKDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGP  358 (782)
T ss_pred             hcCCCCCchHHHHHHHHHH-HHhCCCccccchhhhHHHHHHHhcccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECC
Confidence            3456777788888887766 4567897654432 11        2445888888888887743      34467999999


Q ss_pred             CCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH
Q 022641           91 PGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED  170 (294)
Q Consensus        91 ~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~  170 (294)
                      ||+|||+|++.+|+.+      +..|+.++.+..+....++.--..+.....+...+........+.+++|||+|.++.+
T Consensus       359 PGVGKTSLgkSIA~al------~RkfvR~sLGGvrDEAEIRGHRRTYIGamPGrIiQ~mkka~~~NPv~LLDEIDKm~ss  432 (782)
T COG0466         359 PGVGKTSLGKSIAKAL------GRKFVRISLGGVRDEAEIRGHRRTYIGAMPGKIIQGMKKAGVKNPVFLLDEIDKMGSS  432 (782)
T ss_pred             CCCCchhHHHHHHHHh------CCCEEEEecCccccHHHhccccccccccCChHHHHHHHHhCCcCCeEEeechhhccCC
Confidence            9999999999999999      8899999988888877777655555554443332222223345569999999999643


Q ss_pred             ----HHHHHHHHHHh-------------hc--CcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHH----
Q 022641          171 ----AQNALRRTMET-------------YS--KVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHIC----  227 (294)
Q Consensus       171 ----~~~~L~~~l~~-------------~~--~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~----  227 (294)
                          -...|+.+++-             .+  +.+.||+|+|....++.+|++|+.+|++..++.+|-.++.++++    
T Consensus       433 ~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTANsl~tIP~PLlDRMEiI~lsgYt~~EKl~IAk~~LiPk~  512 (782)
T COG0466         433 FRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATANSLDTIPAPLLDRMEVIRLSGYTEDEKLEIAKRHLIPKQ  512 (782)
T ss_pred             CCCChHHHHHhhcCHhhcCchhhccccCccchhheEEEeecCccccCChHHhcceeeeeecCCChHHHHHHHHHhcchHH
Confidence                34567777641             11  35568888899999999999999999999999999999988865    


Q ss_pred             -HHhC-----CCCCHHHHHHHHhhc--cCcHHHHHHHHHHHHHHh---------CC--CCChhhhhhhcccccCCC
Q 022641          228 -NEEG-----LNLDAEALSTLSSIS--QGDLRRAITYLQGAARLF---------GS--SITSKDLISVSGYPTGGS  284 (294)
Q Consensus       228 -~~~~-----~~~~~~~l~~l~~~~--~G~~r~~~~~l~~~~~~~---------~~--~it~~~v~~~~~~~~~~~  284 (294)
                       +.+|     +.++++++..|++..  ...+|.+-..+...++-.         ..  .|+..++.+.++......
T Consensus       513 ~~~~gL~~~el~i~d~ai~~iI~~YTREAGVR~LeR~i~ki~RK~~~~i~~~~~k~~~~i~~~~l~~yLG~~~f~~  588 (782)
T COG0466         513 LKEHGLKKGELTITDEAIKDIIRYYTREAGVRNLEREIAKICRKAAKKILLKKEKSIVKIDEKNLKKYLGVPVFRY  588 (782)
T ss_pred             HHHcCCCccceeecHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHHHHHHhcCcccceeeCHHHHHHHhCCcccCc
Confidence             3444     458999999988764  233666555555444332         11  478888999998866553

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.80  E-value=4.6e-18  Score=146.99  Aligned_cols=206  Identities=19%  Similarity=0.202  Sum_probs=132.7

Q ss_pred             CCcchhhcccHHHHHHHHHHHHcC-------------CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLETA-------------NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~~-------------~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ...++++.|.+..++.+...+...             .+.+++|+||||||||++|+++++++      ...++.+....
T Consensus       118 ~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l------~~~~~~v~~~~  191 (364)
T TIGR01242       118 NVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET------NATFIRVVGSE  191 (364)
T ss_pred             CCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhC------CCCEEecchHH
Confidence            446789999999999888876421             23459999999999999999999998      45555554332


Q ss_pred             Ccch--hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHhh-----cCc
Q 022641          124 DRGI--NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMETY-----SKV  185 (294)
Q Consensus       124 ~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~~-----~~~  185 (294)
                      ....  ......+........          ...+.+|+|||+|.+.           ...+..+.+++...     ...
T Consensus       192 l~~~~~g~~~~~i~~~f~~a~----------~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~  261 (364)
T TIGR01242       192 LVRKYIGEGARLVREIFELAK----------EKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGN  261 (364)
T ss_pred             HHHHhhhHHHHHHHHHHHHHH----------hcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCCCCC
Confidence            1110  000111111111110          1123599999999873           22344455554332     246


Q ss_pred             ceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHHHHHHH
Q 022641          186 TRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITYLQGAA  261 (294)
Q Consensus       186 ~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~l~~~~  261 (294)
                      +.+|++||.+..+++++.+  ||. .+.+++|+.+++.++++.++....+. ++..+..+++.+.| +.+.+..++..++
T Consensus       262 v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~-~~~~~~~la~~t~g~sg~dl~~l~~~A~  340 (364)
T TIGR01242       262 VKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLA-EDVDLEAIAKMTEGASGADLKAICTEAG  340 (364)
T ss_pred             EEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCC-ccCCHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            7789999999999999886  776 79999999999999998877543332 11246667776654 2233334444444


Q ss_pred             HHh----CCCCChhhhhhhccc
Q 022641          262 RLF----GSSITSKDLISVSGY  279 (294)
Q Consensus       262 ~~~----~~~it~~~v~~~~~~  279 (294)
                      ..+    ...|+.+++.+++..
T Consensus       341 ~~a~~~~~~~i~~~d~~~a~~~  362 (364)
T TIGR01242       341 MFAIREERDYVTMDDFIKAVEK  362 (364)
T ss_pred             HHHHHhCCCccCHHHHHHHHHH
Confidence            333    467999999988765

Many proteins may score above the trusted cutoff because an internal

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=99.80  E-value=1.3e-17  Score=140.64  Aligned_cols=170  Identities=21%  Similarity=0.281  Sum_probs=122.9

Q ss_pred             HHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc--C-----------------CcceeecCC-----
Q 022641           68 EVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY--K-----------------SRVLELNAS-----  122 (294)
Q Consensus        68 ~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~--~-----------------~~~~~~~~~-----  122 (294)
                      .....+...  .++.++ ++|+||+|+||+++|..+++.+.|....  .                 ..+..+...     
T Consensus         8 ~~~~~l~~~--~~rl~ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~~~~~~~~Cg~C~~C~~~~~~~HPD~~~i~p~~~~~~   85 (342)
T PRK06964          8 DDWNRLQAL--RARLPHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRPEALAAE   85 (342)
T ss_pred             HHHHHHHHh--cCCcceEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEeccccccc
Confidence            334444443  334444 8899999999999999999999886421  1                 122222211     


Q ss_pred             ------------------------CCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHH
Q 022641          123 ------------------------DDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRT  178 (294)
Q Consensus       123 ------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~  178 (294)
                                              .....+.++.....+...          ...+++.|+|||++|.|+....|.|++.
T Consensus        86 ~~~~~~~~~~~~~~~~~~k~~~~~~~I~idqiR~l~~~~~~~----------~~~~~~kV~iI~~ae~m~~~AaNaLLKt  155 (342)
T PRK06964         86 APGAADEAKEADADEGGKKTKAPSKEIKIEQVRALLDFCGVG----------THRGGARVVVLYPAEALNVAAANALLKT  155 (342)
T ss_pred             ccccccccccchhhcccccccccccccCHHHHHHHHHHhccC----------CccCCceEEEEechhhcCHHHHHHHHHH
Confidence                                    112334444443332221          1234567999999999999999999999


Q ss_pred             HHhhcCcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHH
Q 022641          179 METYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYL  257 (294)
Q Consensus       179 l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l  257 (294)
                      +|+++..+.+|++|+.+..+++.++|||..+.|.||+.+++..+|..    .+  +++.  +.+...++|++..++.++
T Consensus       156 LEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~----~~--~~~~--~~~l~~~~Gsp~~Al~~~  226 (342)
T PRK06964        156 LEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAA----QG--VADA--DALLAEAGGAPLAALALA  226 (342)
T ss_pred             hcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHH----cC--CChH--HHHHHHcCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999853    23  3332  234677899998887765

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.79  E-value=3.8e-18  Score=150.00  Aligned_cols=213  Identities=14%  Similarity=0.145  Sum_probs=141.4

Q ss_pred             cchhhc-cc--HHHHHHHHHHHHcCC-CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHH
Q 022641           59 QVKDVA-HQ--EEVVRVLTNTLETAN-CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKI  134 (294)
Q Consensus        59 ~~~~~~-g~--~~~~~~l~~~l~~~~-~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  134 (294)
                      +|++++ |.  ..+......+..... ...++|+||+|+|||||++++++++.... .+..++.+++.+.     .....
T Consensus       103 tFdnFv~g~~n~~a~~~~~~~~~~~~~~n~l~lyG~~G~GKTHLl~ai~~~l~~~~-~~~~v~yi~~~~f-----~~~~~  176 (440)
T PRK14088        103 TFENFVVGPGNSFAYHAALEVAKNPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNE-PDLRVMYITSEKF-----LNDLV  176 (440)
T ss_pred             cccccccCCchHHHHHHHHHHHhCcCCCCeEEEEcCCCCcHHHHHHHHHHHHHHhC-CCCeEEEEEHHHH-----HHHHH
Confidence            566555 43  333345555554332 23599999999999999999999874221 1234444443321     11111


Q ss_pred             HHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC--HHHHHHHHHHHHhhcC-cceEEEEecCC-c---ccchHhhcccc
Q 022641          135 KTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT--EDAQNALRRTMETYSK-VTRFFFICNYI-S---RIIEPLASRCA  207 (294)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--~~~~~~L~~~l~~~~~-~~~ii~~~~~~-~---~~~~~l~~r~~  207 (294)
                      ..+......   ..........++|+|||++.+.  ...+..|+..++.... ...+|++++.. .   .+.+++.+|+.
T Consensus       177 ~~~~~~~~~---~f~~~~~~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~  253 (440)
T PRK14088        177 DSMKEGKLN---EFREKYRKKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQ  253 (440)
T ss_pred             HHHhcccHH---HHHHHHHhcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHh
Confidence            111000000   0000000124699999999874  2345667777765443 34566766533 2   35678899987


Q ss_pred             ---EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---CCCCChhhhhhhcccc
Q 022641          208 ---KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---GSSITSKDLISVSGYP  280 (294)
Q Consensus       208 ---~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---~~~it~~~v~~~~~~~  280 (294)
                         .+.+.||+.+.+..++++.+...++.++++++++|++.+.||+|.+...+..+..++   +..||.+.+.+++...
T Consensus       254 ~gl~v~i~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~~~~~R~L~g~l~~l~~~~~~~~~~it~~~a~~~L~~~  332 (440)
T PRK14088        254 MGLVAKLEPPDEETRKKIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGEEVDLKEAILLLKDF  332 (440)
T ss_pred             cCceEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhccccCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence               899999999999999999999999999999999999999999999998888765544   6779999998888754

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

Probab=99.78  E-value=5.6e-18  Score=135.55  Aligned_cols=191  Identities=18%  Similarity=0.230  Sum_probs=123.8

Q ss_pred             Ccchhhc-c--cHHHHHHHHHHHHcCCC--CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHH
Q 022641           58 KQVKDVA-H--QEEVVRVLTNTLETANC--PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRT  132 (294)
Q Consensus        58 ~~~~~~~-g--~~~~~~~l~~~l~~~~~--~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (294)
                      .+|+.++ |  ++.+.............  ..++|+||+|+|||||++++++++.... .+..++.+++.....  ....
T Consensus         5 ~tFdnfv~g~~N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~-~~~~v~y~~~~~f~~--~~~~   81 (219)
T PF00308_consen    5 YTFDNFVVGESNELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIANEAQKQH-PGKRVVYLSAEEFIR--EFAD   81 (219)
T ss_dssp             -SCCCS--TTTTHHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHHHHHHHC-TTS-EEEEEHHHHHH--HHHH
T ss_pred             CccccCCcCCcHHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHHHHHhcc-ccccceeecHHHHHH--HHHH
Confidence            3566664 4  45555555555544332  2489999999999999999999873211 133444443322100  0000


Q ss_pred             HH-----HHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH--HHHHHHHHHHhhcC-cceEEEEecCC----cccch
Q 022641          133 KI-----KTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED--AQNALRRTMETYSK-VTRFFFICNYI----SRIIE  200 (294)
Q Consensus       133 ~~-----~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~--~~~~L~~~l~~~~~-~~~ii~~~~~~----~~~~~  200 (294)
                      .+     ..+...            ....++|+|||++.+...  .++.|+.+++.... ...+|++++.+    ..+.+
T Consensus        82 ~~~~~~~~~~~~~------------~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~  149 (219)
T PF00308_consen   82 ALRDGEIEEFKDR------------LRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLP  149 (219)
T ss_dssp             HHHTTSHHHHHHH------------HCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-H
T ss_pred             HHHcccchhhhhh------------hhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccCh
Confidence            00     111111            112469999999999754  47888888876543 44677777543    23577


Q ss_pred             Hhhcccc---EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHH
Q 022641          201 PLASRCA---KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARL  263 (294)
Q Consensus       201 ~l~~r~~---~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~  263 (294)
                      .+.+|+.   .+.+.+|+.+.+..++++.+...++.++++++++|++...+|+|.+...+.....+
T Consensus       150 ~L~SRl~~Gl~~~l~~pd~~~r~~il~~~a~~~~~~l~~~v~~~l~~~~~~~~r~L~~~l~~l~~~  215 (219)
T PF00308_consen  150 DLRSRLSWGLVVELQPPDDEDRRRILQKKAKERGIELPEEVIEYLARRFRRDVRELEGALNRLDAY  215 (219)
T ss_dssp             HHHHHHHCSEEEEE----HHHHHHHHHHHHHHTT--S-HHHHHHHHHHTTSSHHHHHHHHHHHHHH
T ss_pred             hhhhhHhhcchhhcCCCCHHHHHHHHHHHHHHhCCCCcHHHHHHHHHhhcCCHHHHHHHHHHHHHH
Confidence            8999986   89999999999999999999999999999999999999999999999999877655

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.

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

Probab=99.78  E-value=8.8e-18  Score=151.35  Aligned_cols=207  Identities=24%  Similarity=0.205  Sum_probs=153.5

Q ss_pred             CCcchhhcccHHHHHHHHHHHH---c---------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLE---T---------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD  124 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~---~---------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~  124 (294)
                      +..|+++.|.++++++|.+.+.   +         .-++.++|+||||||||.||+++|.++      +.+|+.++++..
T Consensus       307 ~V~FkDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEA------gVPF~svSGSEF  380 (774)
T KOG0731|consen  307 GVKFKDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEA------GVPFFSVSGSEF  380 (774)
T ss_pred             CCccccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhccc------CCceeeechHHH
Confidence            3578999999999987776653   2         123459999999999999999999999      889998887763


Q ss_pred             ------cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH---------------HHHHHHHHHHHhhc
Q 022641          125 ------RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE---------------DAQNALRRTMETYS  183 (294)
Q Consensus       125 ------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~---------------~~~~~L~~~l~~~~  183 (294)
                            .....+++++......              .+.+++|||+|.+..               ...+.|+--|+.+.
T Consensus       381 vE~~~g~~asrvr~lf~~ar~~--------------aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~  446 (774)
T KOG0731|consen  381 VEMFVGVGASRVRDLFPLARKN--------------APSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFE  446 (774)
T ss_pred             HHHhcccchHHHHHHHHHhhcc--------------CCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCc
Confidence                  2233444444443332              345999999997632               23556666666544


Q ss_pred             --CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHH-HHHHH
Q 022641          184 --KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRR-AITYL  257 (294)
Q Consensus       184 --~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~-~~~~l  257 (294)
                        ..+.++.+||.+..+++++++  ||. .+++..|+...+..|++.+++.-....++..+..++..+.|.... +.|++
T Consensus       447 ~~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~a~~t~gf~gadl~n~~  526 (774)
T KOG0731|consen  447 TSKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKLASLTPGFSGADLANLC  526 (774)
T ss_pred             CCCcEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHHHHhcCCCCcHHHHHhhh
Confidence              345667778999999999987  887 799999999999999999998766665666777799998875444 44666


Q ss_pred             HHHHHHh----CCCCChhhhhhhcccccCC
Q 022641          258 QGAARLF----GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       258 ~~~~~~~----~~~it~~~v~~~~~~~~~~  283 (294)
                      ..++..+    ...|+..++..++......
T Consensus       527 neaa~~a~r~~~~~i~~~~~~~a~~Rvi~G  556 (774)
T KOG0731|consen  527 NEAALLAARKGLREIGTKDLEYAIERVIAG  556 (774)
T ss_pred             hHHHHHHHHhccCccchhhHHHHHHHHhcc
Confidence            6666665    4579999998888854444

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.78  E-value=1.2e-17  Score=156.53  Aligned_cols=207  Identities=19%  Similarity=0.202  Sum_probs=142.4

Q ss_pred             CCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ...|+++.|.+..+..|.+.+..             ..+.+++|+||||||||++|++++.++      +.+++.+.+++
T Consensus       449 ~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~------~~~fi~v~~~~  522 (733)
T TIGR01243       449 NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATES------GANFIAVRGPE  522 (733)
T ss_pred             ccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhc------CCCEEEEehHH
Confidence            44788999999999888777642             122359999999999999999999998      67788777654


Q ss_pred             Ccc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC------------HHHHHHHHHHHHh--hc
Q 022641          124 DRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT------------EDAQNALRRTMET--YS  183 (294)
Q Consensus       124 ~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~------------~~~~~~L~~~l~~--~~  183 (294)
                      ..+      ...++..+......              .+.+|+|||+|.+.            ....+.|+..++.  ..
T Consensus       523 l~~~~vGese~~i~~~f~~A~~~--------------~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~  588 (733)
T TIGR01243       523 ILSKWVGESEKAIREIFRKARQA--------------APAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQEL  588 (733)
T ss_pred             HhhcccCcHHHHHHHHHHHHHhc--------------CCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCC
Confidence            322      22333333332221              23599999999873            1245566777764  23


Q ss_pred             CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCH-HHHHHHHhhccC----cHHHHHH
Q 022641          184 KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDA-EALSTLSSISQG----DLRRAIT  255 (294)
Q Consensus       184 ~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~-~~l~~l~~~~~G----~~r~~~~  255 (294)
                      ....+|++||.+..+++++++  ||. .+.+++|+.+++.++++....  +..+++ ..+..+++.+.|    |+..+++
T Consensus       589 ~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~--~~~~~~~~~l~~la~~t~g~sgadi~~~~~  666 (733)
T TIGR01243       589 SNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTR--SMPLAEDVDLEELAEMTEGYTGADIEAVCR  666 (733)
T ss_pred             CCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhc--CCCCCccCCHHHHHHHcCCCCHHHHHHHHH
Confidence            467788899999999999986  897 899999999999999986654  344433 347777877654    4544443


Q ss_pred             HHHHHHHHh-------------------CCCCChhhhhhhcccccCCCC
Q 022641          256 YLQGAARLF-------------------GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       256 ~l~~~~~~~-------------------~~~it~~~v~~~~~~~~~~~~  285 (294)
                      .....+...                   ...|+.+|+..++....+...
T Consensus       667 ~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~f~~al~~~~ps~~  715 (733)
T TIGR01243       667 EAAMAALRESIGSPAKEKLEVGEEEFLKDLKVEMRHFLEALKKVKPSVS  715 (733)
T ss_pred             HHHHHHHHHHhhhccchhhhcccccccccCcccHHHHHHHHHHcCCCCC
Confidence            222222110                   125889999998888776644

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.

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

Probab=99.77  E-value=1.5e-17  Score=141.49  Aligned_cols=214  Identities=14%  Similarity=0.168  Sum_probs=147.7

Q ss_pred             cchhhc---ccHHHHHHHHHHHHcCC--CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHH
Q 022641           59 QVKDVA---HQEEVVRVLTNTLETAN--CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTK  133 (294)
Q Consensus        59 ~~~~~~---g~~~~~~~l~~~l~~~~--~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  133 (294)
                      +|+.++   ++.-+......+-...+  .+.++|+||+|.|||||++++++...... ....++.+...+.     ....
T Consensus        85 tFdnFv~g~~N~~A~aa~~~va~~~g~~~nplfi~G~~GlGKTHLl~Aign~~~~~~-~~a~v~y~~se~f-----~~~~  158 (408)
T COG0593          85 TFDNFVVGPSNRLAYAAAKAVAENPGGAYNPLFIYGGVGLGKTHLLQAIGNEALANG-PNARVVYLTSEDF-----TNDF  158 (408)
T ss_pred             chhheeeCCchHHHHHHHHHHHhccCCcCCcEEEECCCCCCHHHHHHHHHHHHHhhC-CCceEEeccHHHH-----HHHH
Confidence            455554   44555566666666543  33499999999999999999999984321 1222333322221     1111


Q ss_pred             HHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--HHHHHHHHHHHhhcCcc-eEEEEecCC-c---ccchHhhccc
Q 022641          134 IKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--DAQNALRRTMETYSKVT-RFFFICNYI-S---RIIEPLASRC  206 (294)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--~~~~~L~~~l~~~~~~~-~ii~~~~~~-~---~~~~~l~~r~  206 (294)
                      +......    ....-...+ ..++++|||++.+..  ..++.++..++...... .+++++..+ .   .+.+.+.+|+
T Consensus       159 v~a~~~~----~~~~Fk~~y-~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~  233 (408)
T COG0593         159 VKALRDN----EMEKFKEKY-SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRL  233 (408)
T ss_pred             HHHHHhh----hHHHHHHhh-ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHH
Confidence            1111110    000000112 346999999999864  45778888887665544 566666443 2   3568999998


Q ss_pred             c---EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---CCCCChhhhhhhcccc
Q 022641          207 A---KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---GSSITSKDLISVSGYP  280 (294)
Q Consensus       207 ~---~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---~~~it~~~v~~~~~~~  280 (294)
                      .   .+.+.||+.+.+..+|++.+...++.++++++.+++.....|+|++...+..+..++   +..||.+.+++++...
T Consensus       234 ~~Gl~~~I~~Pd~e~r~aiL~kka~~~~~~i~~ev~~~la~~~~~nvReLegaL~~l~~~a~~~~~~iTi~~v~e~L~~~  313 (408)
T COG0593         234 EWGLVVEIEPPDDETRLAILRKKAEDRGIEIPDEVLEFLAKRLDRNVRELEGALNRLDAFALFTKRAITIDLVKEILKDL  313 (408)
T ss_pred             hceeEEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccHHHHHHHHHHHHHHHHhcCccCcHHHHHHHHHHh
Confidence            6   899999999999999999999999999999999999999999999998888776666   6689999999988775


Q ss_pred             cCC
Q 022641          281 TGG  283 (294)
Q Consensus       281 ~~~  283 (294)
                      ...
T Consensus       314 ~~~  316 (408)
T COG0593         314 LRA  316 (408)
T ss_pred             hcc
Confidence            443

>TIGR00763 lon ATP-dependent protease La

Probab=99.77  E-value=1.8e-18  Score=162.28  Aligned_cols=216  Identities=22%  Similarity=0.252  Sum_probs=138.6

Q ss_pred             hhcccHHHHHHHHHHHHc------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHH
Q 022641           62 DVAHQEEVVRVLTNTLET------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK  135 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (294)
                      ++.|++.+++.+..++..      ...++++|+||||||||++|+++++.+      +..++.++.........+.....
T Consensus       321 ~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l------~~~~~~i~~~~~~~~~~i~g~~~  394 (775)
T TIGR00763       321 DHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKAL------NRKFVRFSLGGVRDEAEIRGHRR  394 (775)
T ss_pred             hcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHh------cCCeEEEeCCCcccHHHHcCCCC
Confidence            577899999888886642      234569999999999999999999998      56666665543222211110000


Q ss_pred             HHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH----HHHHHHHHHHhh--------c-------CcceEEEEecCCc
Q 022641          136 TFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED----AQNALRRTMETY--------S-------KVTRFFFICNYIS  196 (294)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~----~~~~L~~~l~~~--------~-------~~~~ii~~~~~~~  196 (294)
                      .+.....+..............+|+|||+|.+...    ..+.|+++++..        +       .++.+|+|+|...
T Consensus       395 ~~~g~~~g~i~~~l~~~~~~~~villDEidk~~~~~~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I~TtN~~~  474 (775)
T TIGR00763       395 TYVGAMPGRIIQGLKKAKTKNPLFLLDEIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSID  474 (775)
T ss_pred             ceeCCCCchHHHHHHHhCcCCCEEEEechhhcCCccCCCHHHHHHHhcCHHhcCccccccCCceeccCCEEEEEecCCch
Confidence            00000000000000000112349999999999653    246788877631        0       3466788999999


Q ss_pred             ccchHhhccccEEEecCCCHHHHHHHHHHHH-----HHhC-----CCCCHHHHHHHHhhcc--CcHHHHHHHHH----HH
Q 022641          197 RIIEPLASRCAKFRFKPLSEEVMSSRVLHIC-----NEEG-----LNLDAEALSTLSSISQ--GDLRRAITYLQ----GA  260 (294)
Q Consensus       197 ~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~-----~~~~-----~~~~~~~l~~l~~~~~--G~~r~~~~~l~----~~  260 (294)
                      .+++++++||.+|.|++++.++...++++++     +..+     +.++++++..|++.+.  ...|.+...++    .+
T Consensus       475 ~i~~~L~~R~~vi~~~~~~~~e~~~I~~~~l~~~~~~~~~l~~~~~~~~~~~l~~i~~~~~~e~g~R~l~r~i~~~~~~~  554 (775)
T TIGR00763       475 TIPRPLLDRMEVIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKITDEALLLLIKYYTREAGVRNLERQIEKICRKA  554 (775)
T ss_pred             hCCHHHhCCeeEEecCCCCHHHHHHHHHHHHHHHHHHHcCCCcceEEECHHHHHHHHHhcChhcCChHHHHHHHHHHHHH
Confidence            9999999999999999999999999998765     2233     4689999999987532  23444333333    22


Q ss_pred             HHH-h-----C------CCCChhhhhhhcccccCC
Q 022641          261 ARL-F-----G------SSITSKDLISVSGYPTGG  283 (294)
Q Consensus       261 ~~~-~-----~------~~it~~~v~~~~~~~~~~  283 (294)
                      +.- .     .      -.|+.+++...++.+...
T Consensus       555 ~~~~~~~~~~~~~~~~~v~i~~~~~~~~lg~~~~~  589 (775)
T TIGR00763       555 AVKLVEQGEKKKSEAESVVITPDNLKKYLGKPVFT  589 (775)
T ss_pred             HHHHHhccCcccCCcccccCCHHHHHHhcCccccc
Confidence            221 1     1      268888999998876544

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.

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

Probab=99.77  E-value=1.9e-17  Score=137.29  Aligned_cols=105  Identities=25%  Similarity=0.296  Sum_probs=81.2

Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecC------------CcccchHhhccccEEEecCCCHHHHHHHH
Q 022641          156 YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNY------------ISRIIEPLASRCAKFRFKPLSEEVMSSRV  223 (294)
Q Consensus       156 ~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~------------~~~~~~~l~~r~~~i~~~~~~~~~~~~~l  223 (294)
                      ++||||||+|.|+-++...|.+.++.. ....+|++||.            ++.++..|++||.+|...|++.+++++++
T Consensus       279 pGVLFIDEvHmLDiEcFsfLnralEs~-~sPiiIlATNRg~~~irGt~~~sphGiP~DlLDRllII~t~py~~~ei~~Il  357 (398)
T PF06068_consen  279 PGVLFIDEVHMLDIECFSFLNRALESE-LSPIIILATNRGITKIRGTDIISPHGIPLDLLDRLLIIRTKPYSEEEIKQIL  357 (398)
T ss_dssp             E-EEEEESGGGSBHHHHHHHHHHHTST-T--EEEEEES-SEEE-BTTS-EEETT--HHHHTTEEEEEE----HHHHHHHH
T ss_pred             cceEEecchhhccHHHHHHHHHHhcCC-CCcEEEEecCceeeeccCccCcCCCCCCcchHhhcEEEECCCCCHHHHHHHH
Confidence            569999999999999999999999873 34457777763            45688999999999999999999999999


Q ss_pred             HHHHHHhCCCCCHHHHHHHHhhc-cCcHHHHHHHHHHHH
Q 022641          224 LHICNEEGLNLDAEALSTLSSIS-QGDLRRAITYLQGAA  261 (294)
Q Consensus       224 ~~~~~~~~~~~~~~~l~~l~~~~-~G~~r~~~~~l~~~~  261 (294)
                      +-.|+.+++.+++++++.|.+.. ..++|.+++++.-+.
T Consensus       358 ~iR~~~E~v~i~~~al~~L~~ig~~~SLRYAiqLi~~a~  396 (398)
T PF06068_consen  358 KIRAKEEDVEISEDALDLLTKIGVETSLRYAIQLITPAS  396 (398)
T ss_dssp             HHHHHHCT--B-HHHHHHHHHHHHHS-HHHHHHCHHHHH
T ss_pred             HhhhhhhcCcCCHHHHHHHHHHhhhccHHHHHHhhhhhh
Confidence            99999999999999999999884 678999999988664

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

>PRK08181 transposase; Validated

Probab=99.77  E-value=1.7e-19  Score=147.43  Aligned_cols=199  Identities=16%  Similarity=0.231  Sum_probs=129.3

Q ss_pred             CCcccccccccccCCCCCcccCCCC--cccCCCCchHHHHhhccccccCCchhhhhcCCCcchhhcc-cHHHHHHHH---
Q 022641            1 MRANFGKIHKSGKNKSPNFTQKFST--TQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAH-QEEVVRVLT---   74 (294)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g-~~~~~~~l~---   74 (294)
                      |+++|+++...+...++++.+++..  +.|...|.++...+.++   .+.+|..+.+..+++....+ .+..+..+.   
T Consensus        24 ~~~~~~~~~~~a~~~~~~~~e~L~~ll~~E~~~R~~~~~~r~lk---~A~~p~~~tle~fd~~~~~~~~~~~~~~L~~~~  100 (269)
T PRK08181         24 IKTLWPQFAEQADKEGWPAARFLAAIAEHELAERARRRIERHLA---EAHLPPGKTLDSFDFEAVPMVSKAQVMAIAAGD  100 (269)
T ss_pred             HHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHH---HCCCCCCCCHhhCCccCCCCCCHHHHHHHHHHH
Confidence            4567888888888899999999987  56777777777777777   67778766666666665544 344444443   


Q ss_pred             HHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCC
Q 022641           75 NTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCP  154 (294)
Q Consensus        75 ~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (294)
                      .|+.  ...+++|+||||||||||+.++++++...   +..++.+...+      +...+..   ...............
T Consensus       101 ~~~~--~~~nlll~Gp~GtGKTHLa~Aia~~a~~~---g~~v~f~~~~~------L~~~l~~---a~~~~~~~~~l~~l~  166 (269)
T PRK08181        101 SWLA--KGANLLLFGPPGGGKSHLAAAIGLALIEN---GWRVLFTRTTD------LVQKLQV---ARRELQLESAIAKLD  166 (269)
T ss_pred             HHHh--cCceEEEEecCCCcHHHHHHHHHHHHHHc---CCceeeeeHHH------HHHHHHH---HHhCCcHHHHHHHHh
Confidence            4554  44589999999999999999999988432   22333332211      1111111   000000000000123


Q ss_pred             CcEEEEEeCCCCCC--HHHHHHHHHHHHhhcCcceEEEEecCCcc--------------cchHhhccccEEEecCCCH
Q 022641          155 PYKIIILDEADSMT--EDAQNALRRTMETYSKVTRFFFICNYISR--------------IIEPLASRCAKFRFKPLSE  216 (294)
Q Consensus       155 ~~~lliiDei~~l~--~~~~~~L~~~l~~~~~~~~ii~~~~~~~~--------------~~~~l~~r~~~i~~~~~~~  216 (294)
                      +.++|||||++..+  ....+.|+++++..+....+|++||.+..              +.+++.+++..+.|...+.
T Consensus       167 ~~dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~~~~w~~~~~D~~~a~aildRL~h~~~~i~~~g~s~  244 (269)
T PRK08181        167 KFDLLILDDLAYVTKDQAETSVLFELISARYERRSILITANQPFGEWNRVFPDPAMTLAAVDRLVHHATIFEMNVESY  244 (269)
T ss_pred             cCCEEEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCCHHHHHHhcCCccchhhHHHhhhcCceEEecCCccc
Confidence            45699999999875  44567899999988877789999986532              2345555666888877663

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.77  E-value=1.2e-16  Score=131.73  Aligned_cols=201  Identities=16%  Similarity=0.157  Sum_probs=135.2

Q ss_pred             HHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHH---------HHHHH
Q 022641           67 EEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRT---------KIKTF  137 (294)
Q Consensus        67 ~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~  137 (294)
                      +..++.+..++..+.  +++|+||||||||++|+++++.+      +.+++.+++........+..         ....+
T Consensus         8 ~~l~~~~l~~l~~g~--~vLL~G~~GtGKT~lA~~la~~l------g~~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~   79 (262)
T TIGR02640         8 KRVTSRALRYLKSGY--PVHLRGPAGTGKTTLAMHVARKR------DRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQF   79 (262)
T ss_pred             HHHHHHHHHHHhcCC--eEEEEcCCCCCHHHHHHHHHHHh------CCCEEEEeCCccCCHHHHhhhhcccchhhHHHHH
Confidence            345566666776654  79999999999999999999977      67777776655433222111         00111


Q ss_pred             Hhhhcc--------cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc----------------CcceEEEEec
Q 022641          138 AAVAVG--------SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS----------------KVTRFFFICN  193 (294)
Q Consensus       138 ~~~~~~--------~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~----------------~~~~ii~~~~  193 (294)
                      ......        ....+.......+.+|+|||++.++++.++.|+.++++..                ..+.+|+|+|
T Consensus        80 ~~~~~~~~~~~~~~~~~g~l~~A~~~g~~lllDEi~r~~~~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN  159 (262)
T TIGR02640        80 IHNVVKLEDIVRQNWVDNRLTLAVREGFTLVYDEFTRSKPETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSN  159 (262)
T ss_pred             HHHhhhhhcccceeecCchHHHHHHcCCEEEEcchhhCCHHHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeC
Confidence            000000        0000000001234699999999999999999999997532                2567888988


Q ss_pred             CC-----cccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhc------c----CcHHHHHHHHH
Q 022641          194 YI-----SRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSIS------Q----GDLRRAITYLQ  258 (294)
Q Consensus       194 ~~-----~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~------~----G~~r~~~~~l~  258 (294)
                      ..     ..+++++.+||..+.+..|+.++..+++...+     .++++.++.+++..      +    -.+|..+...+
T Consensus       160 ~~~~~g~~~l~~aL~~R~~~i~i~~P~~~~e~~Il~~~~-----~~~~~~~~~iv~~~~~~R~~~~~~~~~~r~~i~~~~  234 (262)
T TIGR02640       160 PVEYAGVHETQDALLDRLITIFMDYPDIDTETAILRAKT-----DVAEDSAATIVRLVREFRASGDEITSGLRASLMIAE  234 (262)
T ss_pred             CccccceecccHHHHhhcEEEECCCCCHHHHHHHHHHhh-----CCCHHHHHHHHHHHHHHHhhCCccCCcHHHHHHHHH
Confidence            65     24578999999999999999999999987643     35676666665441      1    13888888888


Q ss_pred             HHHHHh-CCCCChhhhhhhcccc
Q 022641          259 GAARLF-GSSITSKDLISVSGYP  280 (294)
Q Consensus       259 ~~~~~~-~~~it~~~v~~~~~~~  280 (294)
                      .++... ...++.+++.+++..+
T Consensus       235 ~~~~~~~~~~~~~~~~~~~~~~~  257 (262)
T TIGR02640       235 VATQQDIPVDVDDEDFVDLCIDI  257 (262)
T ss_pred             HHHHcCCCCCCCcHHHHHHHHHH
Confidence            877765 4468888888877554

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).

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

Probab=99.77  E-value=8e-18  Score=156.57  Aligned_cols=246  Identities=20%  Similarity=0.227  Sum_probs=158.2

Q ss_pred             CCCCchHHHHhhccccccCCchhhhhcCCCcc----------hhhcccHHHHHHHHHHHHc------CCCCcEEEECCCC
Q 022641           29 SPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQV----------KDVAHQEEVVRVLTNTLET------ANCPHMLFYGPPG   92 (294)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~g~~~~~~~l~~~l~~------~~~~~ill~Gp~G   92 (294)
                      .+.+.+..+-+.+..+ ..+.||.+.. +..+          ++..|.+.+++.+..++..      ...+.++|+||||
T Consensus       282 ~~~~~e~~~~~~yl~~-~~~~pw~~~~-~~~~~~~~~~~~l~~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG  359 (784)
T PRK10787        282 SPMSAEATVVRGYIDW-MVQVPWNARS-KVKKDLRQAQEILDTDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPG  359 (784)
T ss_pred             CCCCchHHHHHHHHHH-HHhCCCCCCC-cccccHHHHHHHhhhhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCC
Confidence            4445555555555554 3457895543 3222          2577999999999887763      3445699999999


Q ss_pred             CCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHH-
Q 022641           93 TGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDA-  171 (294)
Q Consensus        93 ~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~-  171 (294)
                      +|||++++.++..+      +..++.++.+.......+......+.....+..............+++|||+|.++... 
T Consensus       360 ~GKTtl~~~ia~~l------~~~~~~i~~~~~~d~~~i~g~~~~~~g~~~G~~~~~l~~~~~~~~villDEidk~~~~~~  433 (784)
T PRK10787        360 VGKTSLGQSIAKAT------GRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQKMAKVGVKNPLFLLDEIDKMSSDMR  433 (784)
T ss_pred             CCHHHHHHHHHHHh------CCCEEEEEcCCCCCHHHhccchhccCCCCCcHHHHHHHhcCCCCCEEEEEChhhcccccC
Confidence            99999999999988      66677676555444333322211111111000000000011123599999999998764 


Q ss_pred             ---HHHHHHHHHhhc---------------CcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHH----
Q 022641          172 ---QNALRRTMETYS---------------KVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE----  229 (294)
Q Consensus       172 ---~~~L~~~l~~~~---------------~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~----  229 (294)
                         .+.|+++++...               ..+.+|+|+|.. .++++|++||.++.|.+++.++..++.++++..    
T Consensus       434 g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~-~i~~aLl~R~~ii~~~~~t~eek~~Ia~~~L~~k~~~  512 (784)
T PRK10787        434 GDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSM-NIPAPLLDRMEVIRLSGYTEDEKLNIAKRHLLPKQIE  512 (784)
T ss_pred             CCHHHHHHHHhccccEEEEecccccccccCCceEEEEcCCCC-CCCHHHhcceeeeecCCCCHHHHHHHHHHhhhHHHHH
Confidence               578998887311               445566666665 699999999999999999999999999887741    


Q ss_pred             -h-----CCCCCHHHHHHHHhhcc--CcHHHHHHHHHHHHHHh------C-----CCCChhhhhhhcccccCC
Q 022641          230 -E-----GLNLDAEALSTLSSISQ--GDLRRAITYLQGAARLF------G-----SSITSKDLISVSGYPTGG  283 (294)
Q Consensus       230 -~-----~~~~~~~~l~~l~~~~~--G~~r~~~~~l~~~~~~~------~-----~~it~~~v~~~~~~~~~~  283 (294)
                       .     .+.++++++..|++.+.  -..|.+-..++..+...      +     -.|+.+++.+.++.....
T Consensus       513 ~~~l~~~~l~i~~~ai~~ii~~yt~e~GaR~LeR~I~~i~r~~l~~~~~~~~~~~v~v~~~~~~~~lg~~~~~  585 (784)
T PRK10787        513 RNALKKGELTVDDSAIIGIIRYYTREAGVRSLEREISKLCRKAVKQLLLDKSLKHIEINGDNLHDYLGVQRFD  585 (784)
T ss_pred             HhCCCCCeEEECHHHHHHHHHhCCcccCCcHHHHHHHHHHHHHHHHHHhcCCCceeeecHHHHHHHhCCCccc
Confidence             1     24589999999987542  11333333333322211      2     259999999999986543

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=99.77  E-value=6.5e-17  Score=132.47  Aligned_cols=158  Identities=19%  Similarity=0.229  Sum_probs=121.6

Q ss_pred             HHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCC----------ccCCcceeecCCC---CcchhHHHHHH
Q 022641           69 VVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPE----------LYKSRVLELNASD---DRGINVVRTKI  134 (294)
Q Consensus        69 ~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~----------~~~~~~~~~~~~~---~~~~~~~~~~~  134 (294)
                      ..+.|...+..++.+| ++|+||+|+||+++|..+++.+.|..          ..+..+..+.+..   ..+.+.++...
T Consensus         5 ~~~~L~~~i~~~rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~~~~I~idqiR~l~   84 (290)
T PRK05917          5 AWEALIQRVRDQKVPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGKGRLHSIETPRAIK   84 (290)
T ss_pred             HHHHHHHHHHcCCcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCCCCcCcHHHHHHHH
Confidence            4567888888888877 78999999999999999999998853          2233444443322   13566666655


Q ss_pred             HHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEEecCC
Q 022641          135 KTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPL  214 (294)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~  214 (294)
                      ..+...+.          .+.+.++|||++|.++....+.|++.+|+++.++.+|++|+.+..+++.++|||+.+.|+|+
T Consensus        85 ~~~~~~p~----------e~~~kv~ii~~ad~mt~~AaNaLLK~LEEPp~~~~fiL~~~~~~~ll~TI~SRcq~~~~~~~  154 (290)
T PRK05917         85 KQIWIHPY----------ESPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTIRSRSLSIHIPME  154 (290)
T ss_pred             HHHhhCcc----------CCCceEEEEechhhcCHHHHHHHHHHhhcCCCCeEEEEEeCChhhCcHHHHhcceEEEccch
Confidence            55444332          24567999999999999999999999999999999999999999999999999999999886


Q ss_pred             CHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHH
Q 022641          215 SEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLR  251 (294)
Q Consensus       215 ~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r  251 (294)
                      ..               ..++++.+..++..++|+++
T Consensus       155 ~~---------------~~i~~~~~~~l~~~~~g~~~  176 (290)
T PRK05917        155 EK---------------TLVSKEDIAYLIGYAQGKES  176 (290)
T ss_pred             hc---------------cCCCHHHHHHHHHHhCCChh
Confidence            21               13566666666666777663

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.75  E-value=1.1e-16  Score=134.83  Aligned_cols=229  Identities=16%  Similarity=0.110  Sum_probs=143.0

Q ss_pred             CCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccC-C--cceeecCC----------
Q 022641           56 RPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYK-S--RVLELNAS----------  122 (294)
Q Consensus        56 ~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~-~--~~~~~~~~----------  122 (294)
                      .|..|.+++|++..++.+.-.+...+..+++|.|+||+|||++|++++..+.+..... .  .+......          
T Consensus         3 ~~~~f~~i~Gq~~~~~~l~~~~~~~~~~~vLl~G~pG~gKT~lar~la~llP~~~~~e~~~~~~~~~~~~~~~~~~~~~~   82 (334)
T PRK13407          3 KPFPFSAIVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSARPEDCPEWAHVSSTT   82 (334)
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHhccCCCcEEEEcCCCCCHHHHHHHHHHHCCCcchhcccccccCcccCCcccccccCCc
Confidence            5788999999999999887655434445799999999999999999999983211100 0  00000000          


Q ss_pred             ------------CCcchhHHHHHHHHHHhh-hcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc------
Q 022641          123 ------------DDRGINVVRTKIKTFAAV-AVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS------  183 (294)
Q Consensus       123 ------------~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~------  183 (294)
                                  ...+.+.+...+.--... ........+....+.+++|++||++.+++..++.|++.+++..      
T Consensus        83 ~~~~~~p~~~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~l~~A~~GiL~lDEInrl~~~~q~~Lle~mee~~v~v~r~  162 (334)
T PRK13407         83 MIERPTPVVDLPLGVTEDRVVGALDIERALTRGEKAFEPGLLARANRGYLYIDEVNLLEDHIVDLLLDVAQSGENVVERE  162 (334)
T ss_pred             ccccCCccccCCCCCCcceeecchhhhhhhhcCCeeecCCceEEcCCCeEEecChHhCCHHHHHHHHHHHHcCCeEEEEC
Confidence                        000000000000000000 0011122333334566899999999999999999999998643      


Q ss_pred             -------CcceEEEEecCCc-ccchHhhcccc-EEEecCCCH-HHHHHHHHHHHHH------------------------
Q 022641          184 -------KVTRFFFICNYIS-RIIEPLASRCA-KFRFKPLSE-EVMSSRVLHICNE------------------------  229 (294)
Q Consensus       184 -------~~~~ii~~~~~~~-~~~~~l~~r~~-~i~~~~~~~-~~~~~~l~~~~~~------------------------  229 (294)
                             ..+.++.++|... .+.+++..||. .+.+.++.. ++..+++.+....                        
T Consensus       163 G~~~~~p~rfiviAt~NP~e~~l~~aLldRF~~~v~v~~~~~~~e~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~  242 (334)
T PRK13407        163 GLSIRHPARFVLVGSGNPEEGELRPQLLDRFGLSVEVRSPRDVETRVEVIRRRDAYDADHDAFMAKWGAEDMQLRGRILG  242 (334)
T ss_pred             CeEEecCCCEEEEecCCcccCCCCHHHHhhcceEEEcCCCCcHHHHHHHHHHhhcccccchhhhccccccccCCHHHHHH
Confidence                   2334444455433 47889999998 678877766 6666666653211                        


Q ss_pred             -----hCCCCCHHHHHHHHhhc---c-CcHHHHHHHHHHHHHHh----CCCCChhhhhhhcccccCCC
Q 022641          230 -----EGLNLDAEALSTLSSIS---Q-GDLRRAITYLQGAARLF----GSSITSKDLISVSGYPTGGS  284 (294)
Q Consensus       230 -----~~~~~~~~~l~~l~~~~---~-G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~~~~  284 (294)
                           ..+.++++.++++++.+   + ..+|..+.++..+...+    .+.++.++|..+...+-.+.
T Consensus       243 a~~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~~~vl~hR  310 (334)
T PRK13407        243 ARARLPQLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVATMALSHR  310 (334)
T ss_pred             HHHhcCCcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHHHHhhhhh
Confidence                 13558888888887763   2 36788777777666555    56799999988876655443

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

Probab=99.75  E-value=6.1e-17  Score=138.24  Aligned_cols=223  Identities=21%  Similarity=0.274  Sum_probs=152.2

Q ss_pred             hhcCCCcchhhcccHHHHHHHHHH----HHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchh
Q 022641           53 EKYRPKQVKDVAHQEEVVRVLTNT----LETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGIN  128 (294)
Q Consensus        53 ~~~~~~~~~~~~g~~~~~~~l~~~----l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~  128 (294)
                      +.|-|..   +.+++..+..+...    +..+.+.|++++||||||||++++.+.+++..+.. ...++.+||....+..
T Consensus        12 ~~~iP~~---l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~-~~~~~yINc~~~~t~~   87 (366)
T COG1474          12 EDYIPEE---LPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSA-NVEVVYINCLELRTPY   87 (366)
T ss_pred             CCCCccc---ccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhc-cCceEEEeeeeCCCHH
Confidence            3444533   77777777665544    45667778999999999999999999999953321 1127788887766655


Q ss_pred             HHHHHHHHHHhhhcccCccCC---------CCCCCCcEEEEEeCCCCCCHHHHHHHHHHHH---hhcCcceEEEEecCCc
Q 022641          129 VVRTKIKTFAAVAVGSGQRRG---------GYPCPPYKIIILDEADSMTEDAQNALRRTME---TYSKVTRFFFICNYIS  196 (294)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~lliiDei~~l~~~~~~~L~~~l~---~~~~~~~ii~~~~~~~  196 (294)
                      .+...+..........+....         .......-+|+|||+|.|.....+.|+.++.   .....+.+|+++|...
T Consensus        88 ~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~~~LY~L~r~~~~~~~~v~vi~i~n~~~  167 (366)
T COG1474          88 QVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDK  167 (366)
T ss_pred             HHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccchHHHHHHhhccccceeEEEEEEeccHH
Confidence            444333332211111111000         0113456799999999997654455555554   3333456777777653


Q ss_pred             ---ccchHhhcccc--EEEecCCCHHHHHHHHHHHHHHh--CCCCCHHHHHHHHhh---ccCcHHHHHHHHHHHHHHh--
Q 022641          197 ---RIIEPLASRCA--KFRFKPLSEEVMSSRVLHICNEE--GLNLDAEALSTLSSI---SQGDLRRAITYLQGAARLF--  264 (294)
Q Consensus       197 ---~~~~~l~~r~~--~i~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~l~~l~~~---~~G~~r~~~~~l~~~~~~~--  264 (294)
                         .+.+.+.+++.  .|.|+|++.+|+.+++...+...  .-.+++++++.++..   .+||.|.++.+|..++..+  
T Consensus       168 ~~~~ld~rv~s~l~~~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~  247 (366)
T COG1474         168 FLDYLDPRVKSSLGPSEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAER  247 (366)
T ss_pred             HHHHhhhhhhhccCcceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHh
Confidence               46777888775  68999999999999999988642  234788888877744   6789999999999999888  


Q ss_pred             --CCCCChhhhhhhccc
Q 022641          265 --GSSITSKDLISVSGY  279 (294)
Q Consensus       265 --~~~it~~~v~~~~~~  279 (294)
                        ...++.+++..+...
T Consensus       248 ~~~~~v~~~~v~~a~~~  264 (366)
T COG1474         248 EGSRKVSEDHVREAQEE  264 (366)
T ss_pred             hCCCCcCHHHHHHHHHH
Confidence              456999999888443

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.75  E-value=7.3e-17  Score=152.80  Aligned_cols=208  Identities=18%  Similarity=0.206  Sum_probs=152.0

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCC----CccCCcceeecC
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP----ELYKSRVLELNA  121 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~----~~~~~~~~~~~~  121 (294)
                      ....++.++.++..++.++|+++.++.+...+......|++|+||||||||+++++++..+...    ...+..++.++.
T Consensus       158 ~~~~~l~~~~~~~~~~~~igr~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l~~  237 (852)
T TIGR03346       158 KYARDLTERAREGKLDPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDM  237 (852)
T ss_pred             HHhhhHHHHhhCCCCCcCCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEeeH
Confidence            5567899999999999999999999999999999888899999999999999999999987421    112445555543


Q ss_pred             CCCc----chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------HHHHHHHHHHHhhcCcceEE
Q 022641          122 SDDR----GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------DAQNALRRTMETYSKVTRFF  189 (294)
Q Consensus       122 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------~~~~~L~~~l~~~~~~~~ii  189 (294)
                      ....    ........+..+......         ...+.||||||+|.+..        +..+.|...++.  ....+|
T Consensus       238 ~~l~a~~~~~g~~e~~l~~~l~~~~~---------~~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l~~--g~i~~I  306 (852)
T TIGR03346       238 GALIAGAKYRGEFEERLKAVLNEVTK---------SEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALAR--GELHCI  306 (852)
T ss_pred             HHHhhcchhhhhHHHHHHHHHHHHHh---------cCCCeEEEeccHHHhhcCCCCcchhHHHHHhchhhhc--CceEEE
Confidence            3221    111222222332222110         01245999999998852        245667666653  456777


Q ss_pred             EEecCC-----cccchHhhccccEEEecCCCHHHHHHHHHHHHHH----hCCCCCHHHHHHHHhhccC---c---HHHHH
Q 022641          190 FICNYI-----SRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE----EGLNLDAEALSTLSSISQG---D---LRRAI  254 (294)
Q Consensus       190 ~~~~~~-----~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~----~~~~~~~~~l~~l~~~~~G---~---~r~~~  254 (294)
                      .+|+..     ...++++.+||..+.+++|+.++...+++.+...    +++.++++++..++.++.+   +   |..++
T Consensus       307 gaTt~~e~r~~~~~d~al~rRf~~i~v~~p~~~~~~~iL~~~~~~~e~~~~v~~~d~~i~~~~~ls~~yi~~r~lPdkAi  386 (852)
T TIGR03346       307 GATTLDEYRKYIEKDAALERRFQPVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSHRYITDRFLPDKAI  386 (852)
T ss_pred             EeCcHHHHHHHhhcCHHHHhcCCEEEeCCCCHHHHHHHHHHHHHHhccccCCCCCHHHHHHHHHhccccccccCCchHHH
Confidence            777654     3578999999999999999999999999877654    4677899999998887653   3   88999


Q ss_pred             HHHHHHHHHh
Q 022641          255 TYLQGAARLF  264 (294)
Q Consensus       255 ~~l~~~~~~~  264 (294)
                      .+++.++...
T Consensus       387 dlld~a~a~~  396 (852)
T TIGR03346       387 DLIDEAAARI  396 (852)
T ss_pred             HHHHHHHHHH
Confidence            9999887644

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.

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

Probab=99.75  E-value=8.7e-17  Score=125.69  Aligned_cols=213  Identities=22%  Similarity=0.256  Sum_probs=144.2

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcc
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRV  116 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~  116 (294)
                      -.+++.-..+++-+-|.+..++.+.+.+.-             ..+..++|+||||+|||.+|+++++..      .+.|
T Consensus       136 MmVeKvPDStYeMiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht------~c~f  209 (404)
T KOG0728|consen  136 MMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHT------DCTF  209 (404)
T ss_pred             HhhhhCCccHHHHhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhc------ceEE
Confidence            344555555565566778888887777643             234469999999999999999999988      7788


Q ss_pred             eeecCCCCcch------hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHH
Q 022641          117 LELNASDDRGI------NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTM  179 (294)
Q Consensus       117 ~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l  179 (294)
                      +.++++.....      .-+++.+-......              +.+||+||+|.+.           .+.+...+.++
T Consensus       210 irvsgselvqk~igegsrmvrelfvmareha--------------psiifmdeidsigs~r~e~~~ggdsevqrtmlell  275 (404)
T KOG0728|consen  210 IRVSGSELVQKYIGEGSRMVRELFVMAREHA--------------PSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELL  275 (404)
T ss_pred             EEechHHHHHHHhhhhHHHHHHHHHHHHhcC--------------CceEeeecccccccccccCCCCccHHHHHHHHHHH
Confidence            88877654322      12222222222222              2499999999873           23455555555


Q ss_pred             Hh---h--cCcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHH-HHHHHHhhccC-c
Q 022641          180 ET---Y--SKVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAE-ALSTLSSISQG-D  249 (294)
Q Consensus       180 ~~---~--~~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~-~l~~l~~~~~G-~  249 (294)
                      +.   +  ..+..+|++||...-+++++++  |.. .|+|+||+.+...++++-...+.++  +.. .+..+++...| +
T Consensus       276 nqldgfeatknikvimatnridild~allrpgridrkiefp~p~e~ar~~ilkihsrkmnl--~rgi~l~kiaekm~gas  353 (404)
T KOG0728|consen  276 NQLDGFEATKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNL--TRGINLRKIAEKMPGAS  353 (404)
T ss_pred             HhccccccccceEEEEeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHHhhhhhch--hcccCHHHHHHhCCCCc
Confidence            43   2  3567899999999999999987  555 7999999999999999877665433  221 25666666443 2


Q ss_pred             HHHHHHHHHHHHHHh----CCCCChhhhhhhcccccCCC
Q 022641          250 LRRAITYLQGAARLF----GSSITSKDLISVSGYPTGGS  284 (294)
Q Consensus       250 ~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~~~~  284 (294)
                      -..+-..+..+..++    .-++|.++++-+++.+...+
T Consensus       354 gaevk~vcteagm~alrerrvhvtqedfemav~kvm~k~  392 (404)
T KOG0728|consen  354 GAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKD  392 (404)
T ss_pred             cchhhhhhhhhhHHHHHHhhccccHHHHHHHHHHHHhcc
Confidence            234445566666666    44699999999888765543

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

Probab=99.74  E-value=8.9e-18  Score=148.17  Aligned_cols=222  Identities=20%  Similarity=0.269  Sum_probs=150.2

Q ss_pred             CCCchHHHHhhccccccCCchhhhhcCCCcc----------hhhcccHHHHHHHHHHHHcCC------CCcEEEECCCCC
Q 022641           30 PEKSEDEVKRKMAPVLQSSQPWVEKYRPKQV----------KDVAHQEEVVRVLTNTLETAN------CPHMLFYGPPGT   93 (294)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~g~~~~~~~l~~~l~~~~------~~~ill~Gp~G~   93 (294)
                      +..++-..-|++..+ ..+.||-+ +....+          ++-.|-+++++.+.+.+.-++      ++.++|+||||+
T Consensus       372 ~~~sEfnvtrNYLdw-lt~LPWgk-~S~En~dl~~Ak~iLdeDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGV  449 (906)
T KOG2004|consen  372 PSSSEFNVTRNYLDW-LTSLPWGK-SSTENLDLARAKEILDEDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGV  449 (906)
T ss_pred             ccccchhHHHHHHHH-HHhCCCCC-CChhhhhHHHHHHhhcccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCC
Confidence            334444555555554 56778843 222233          244577888888888886543      345999999999


Q ss_pred             CHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH---
Q 022641           94 GKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED---  170 (294)
Q Consensus        94 GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~---  170 (294)
                      |||++++.+|+.+      +..|+.++.........++.--..+.....+............+.+++|||+|.+...   
T Consensus       450 GKTSI~kSIA~AL------nRkFfRfSvGG~tDvAeIkGHRRTYVGAMPGkiIq~LK~v~t~NPliLiDEvDKlG~g~qG  523 (906)
T KOG2004|consen  450 GKTSIAKSIARAL------NRKFFRFSVGGMTDVAEIKGHRRTYVGAMPGKIIQCLKKVKTENPLILIDEVDKLGSGHQG  523 (906)
T ss_pred             CcccHHHHHHHHh------CCceEEEeccccccHHhhcccceeeeccCChHHHHHHHhhCCCCceEEeehhhhhCCCCCC
Confidence            9999999999999      7888888777666666665444443333332222222222344569999999998532   


Q ss_pred             -HHHHHHHHHHh------------hc---CcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHH-----H
Q 022641          171 -AQNALRRTMET------------YS---KVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICN-----E  229 (294)
Q Consensus       171 -~~~~L~~~l~~------------~~---~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~-----~  229 (294)
                       -...|+.+++-            .+   ..+.||+|+|....++++|++|+.+|++..+..+|-.+|.++++-     .
T Consensus       524 DPasALLElLDPEQNanFlDHYLdVp~DLSkVLFicTAN~idtIP~pLlDRMEvIelsGYv~eEKv~IA~~yLip~a~~~  603 (906)
T KOG2004|consen  524 DPASALLELLDPEQNANFLDHYLDVPVDLSKVLFICTANVIDTIPPPLLDRMEVIELSGYVAEEKVKIAERYLIPQALKD  603 (906)
T ss_pred             ChHHHHHHhcChhhccchhhhccccccchhheEEEEeccccccCChhhhhhhheeeccCccHHHHHHHHHHhhhhHHHHH
Confidence             24566666641            11   345688888999999999999999999999999999999888763     2


Q ss_pred             -----hCCCCCHHHHHHHHhhcc--CcHHHHHHHHHH
Q 022641          230 -----EGLNLDAEALSTLSSISQ--GDLRRAITYLQG  259 (294)
Q Consensus       230 -----~~~~~~~~~l~~l~~~~~--G~~r~~~~~l~~  259 (294)
                           +.+.++++++..|++...  ..+|.+-..+..
T Consensus       604 ~gl~~e~v~is~~al~~lI~~YcrEaGVRnLqk~iek  640 (906)
T KOG2004|consen  604 CGLKPEQVKISDDALLALIERYCREAGVRNLQKQIEK  640 (906)
T ss_pred             cCCCHHhcCccHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence                 335689999888777632  235655554443

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

Probab=99.74  E-value=5.5e-17  Score=129.70  Aligned_cols=215  Identities=20%  Similarity=0.186  Sum_probs=141.1

Q ss_pred             CcchhhcccHHHHHHHHHHHH---------cCCC---CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           58 KQVKDVAHQEEVVRVLTNTLE---------TANC---PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~---------~~~~---~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      ..|.++.|.+.+++.|.+++-         .++.   +.++|+||||||||.||+++|.++      +..|+.++.++..
T Consensus       130 VkWsDVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATEA------nSTFFSvSSSDLv  203 (439)
T KOG0739|consen  130 VKWSDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATEA------NSTFFSVSSSDLV  203 (439)
T ss_pred             CchhhhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhhc------CCceEEeehHHHH
Confidence            368999999999999988752         2322   349999999999999999999999      7888888887755


Q ss_pred             chh--HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH-----------HH-HHHHHHHHH--hhcCcceEE
Q 022641          126 GIN--VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE-----------DA-QNALRRTME--TYSKVTRFF  189 (294)
Q Consensus       126 ~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~-----------~~-~~~L~~~l~--~~~~~~~ii  189 (294)
                      +..  .-..++..+....          +..++.||||||||.+..           .. -+.|.++--  .....+.++
T Consensus       204 SKWmGESEkLVknLFemA----------Re~kPSIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqGVG~d~~gvLVL  273 (439)
T KOG0739|consen  204 SKWMGESEKLVKNLFEMA----------RENKPSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGVGNDNDGVLVL  273 (439)
T ss_pred             HHHhccHHHHHHHHHHHH----------HhcCCcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhccccCCCceEEE
Confidence            432  1122333332222          123456999999998731           11 223333322  222456677


Q ss_pred             EEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCc--------HHHHHH----H
Q 022641          190 FICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGD--------LRRAIT----Y  256 (294)
Q Consensus       190 ~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~--------~r~~~~----~  256 (294)
                      .+||-++.++.++++||. .|+++-|...-+...++-.+..-...++++.+.+|+..+.|.        +|.++.    -
T Consensus       274 gATNiPw~LDsAIRRRFekRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d~~eL~~kTeGySGsDisivVrDalmePvRk  353 (439)
T KOG0739|consen  274 GATNIPWVLDSAIRRRFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEGYSGSDISIVVRDALMEPVRK  353 (439)
T ss_pred             ecCCCchhHHHHHHHHhhcceeccCCcHHHhhhhheeccCCCccccchhhHHHHHhhcCCCCcCceEEEehhhhhhhHHH
Confidence            788999999999999998 788877777766666655554444568999999999987662        233332    2


Q ss_pred             HHHHHHHhC--CCCChhhhhhhcccccCCCCCcc
Q 022641          257 LQGAARLFG--SSITSKDLISVSGYPTGGSGGAF  288 (294)
Q Consensus       257 l~~~~~~~~--~~it~~~v~~~~~~~~~~~~~~~  288 (294)
                      .|.+..+..  ..-...++..++...++.+.+++
T Consensus       354 vqsAthFk~v~~~s~~~~~~~lltpcspgd~ga~  387 (439)
T KOG0739|consen  354 VQSATHFKKVSGPSNPSEVDDLLTPCSPGDPGAI  387 (439)
T ss_pred             hhhhhhhhccCCCCChhhhccccCCCCCCCcchh
Confidence            333333321  11134446667776666655443

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

Probab=99.74  E-value=6.1e-17  Score=149.69  Aligned_cols=222  Identities=16%  Similarity=0.142  Sum_probs=153.8

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCC----ccCCcceeecC
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE----LYKSRVLELNA  121 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~----~~~~~~~~~~~  121 (294)
                      .....+.+.-+...++.++|++..+..+.+.+......|++|+||||||||++|+.++.......    ..+..++.++.
T Consensus       171 ~~~~~l~~~a~~g~~~~liGR~~ei~~~i~iL~r~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l~~  250 (758)
T PRK11034        171 NFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDI  250 (758)
T ss_pred             HHHHhHHHHHHcCCCCcCcCCCHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEeccH
Confidence            34456666667778889999999999999999998888999999999999999999998763221    12334444332


Q ss_pred             CCCc----chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC---------HHHHHHHHHHHHhhcCcceE
Q 022641          122 SDDR----GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT---------EDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       122 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~---------~~~~~~L~~~l~~~~~~~~i  188 (294)
                      ....    ........+..+......          ..+.+|||||+|.+-         .+..+.|..+++.  ....+
T Consensus       251 ~~llaG~~~~Ge~e~rl~~l~~~l~~----------~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~~--g~i~v  318 (758)
T PRK11034        251 GSLLAGTKYRGDFEKRFKALLKQLEQ----------DTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSS--GKIRV  318 (758)
T ss_pred             HHHhcccchhhhHHHHHHHHHHHHHh----------cCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHhC--CCeEE
Confidence            2211    111222222222211100          123599999999871         2234556666654  45667


Q ss_pred             EEEecCC-----cccchHhhccccEEEecCCCHHHHHHHHHHHHH----HhCCCCCHHHHHHHHhhccC------cHHHH
Q 022641          189 FFICNYI-----SRIIEPLASRCAKFRFKPLSEEVMSSRVLHICN----EEGLNLDAEALSTLSSISQG------DLRRA  253 (294)
Q Consensus       189 i~~~~~~-----~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~----~~~~~~~~~~l~~l~~~~~G------~~r~~  253 (294)
                      |.+|+..     ...+++|.+||..|.+++|+.++...+|+.+..    .+++.++++++..+++++..      -|..+
T Consensus       319 IgATt~~E~~~~~~~D~AL~rRFq~I~v~ePs~~~~~~IL~~~~~~ye~~h~v~i~~~al~~a~~ls~ryi~~r~lPdKa  398 (758)
T PRK11034        319 IGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKA  398 (758)
T ss_pred             EecCChHHHHHHhhccHHHHhhCcEEEeCCCCHHHHHHHHHHHHHHhhhccCCCcCHHHHHHHHHHhhccccCccChHHH
Confidence            7777754     346899999999999999999999999987654    46788999999988876432      47799


Q ss_pred             HHHHHHHHHHh--------CCCCChhhhhhhccc
Q 022641          254 ITYLQGAARLF--------GSSITSKDLISVSGY  279 (294)
Q Consensus       254 ~~~l~~~~~~~--------~~~it~~~v~~~~~~  279 (294)
                      +.+++.++...        ...++.+++..++..
T Consensus       399 idlldea~a~~~~~~~~~~~~~v~~~~i~~v~~~  432 (758)
T PRK11034        399 IDVIDEAGARARLMPVSKRKKTVNVADIESVVAR  432 (758)
T ss_pred             HHHHHHHHHhhccCcccccccccChhhHHHHHHH
Confidence            99999887533        223777777777654

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

Probab=99.74  E-value=2.3e-16  Score=141.94  Aligned_cols=208  Identities=20%  Similarity=0.185  Sum_probs=148.2

Q ss_pred             CCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ...|.++.|.+..+..+...+..             .....++|+||||||||++|++++.+.      +.+|+.+..++
T Consensus       238 ~v~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~~------~~~fi~v~~~~  311 (494)
T COG0464         238 DVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALES------RSRFISVKGSE  311 (494)
T ss_pred             CcceehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhhC------CCeEEEeeCHH
Confidence            34677887877777666665421             122359999999999999999999988      78888887764


Q ss_pred             Ccc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHh--hcC
Q 022641          124 DRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMET--YSK  184 (294)
Q Consensus       124 ~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~--~~~  184 (294)
                      ..+      ...++..+.....              ..+.+|+|||+|.+.           ....+.|+..++.  ...
T Consensus       312 l~sk~vGesek~ir~~F~~A~~--------------~~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~  377 (494)
T COG0464         312 LLSKWVGESEKNIRELFEKARK--------------LAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAE  377 (494)
T ss_pred             HhccccchHHHHHHHHHHHHHc--------------CCCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccC
Confidence            433      2233333333321              123599999999872           2466777777753  334


Q ss_pred             cceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCC-CCHHHHHHHHhhccCc-HHHHHHHHHH
Q 022641          185 VTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLN-LDAEALSTLSSISQGD-LRRAITYLQG  259 (294)
Q Consensus       185 ~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~-~~~~~l~~l~~~~~G~-~r~~~~~l~~  259 (294)
                      .+.+|.+||.+..+++++++  ||. .+.+++|+.++..++++..+...... ..+-.++.+++.+.|- ...+..+++.
T Consensus       378 ~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~~sgadi~~i~~e  457 (494)
T COG0464         378 GVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVRE  457 (494)
T ss_pred             ceEEEecCCCccccCHhhcccCccceEeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhcCCCHHHHHHHHHH
Confidence            56678889999999999999  998 89999999999999999999765554 3455677778766552 3444455555


Q ss_pred             HHHHh-----CCCCChhhhhhhcccccCCC
Q 022641          260 AARLF-----GSSITSKDLISVSGYPTGGS  284 (294)
Q Consensus       260 ~~~~~-----~~~it~~~v~~~~~~~~~~~  284 (294)
                      ++..+     ...+|.+++..+.....+..
T Consensus       458 a~~~~~~~~~~~~~~~~~~~~a~~~~~p~~  487 (494)
T COG0464         458 AALEALREARRREVTLDDFLDALKKIKPSV  487 (494)
T ss_pred             HHHHHHHHhccCCccHHHHHHHHHhcCCCC
Confidence            55444     33699999999998866553

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

Probab=99.73  E-value=9e-16  Score=127.73  Aligned_cols=230  Identities=15%  Similarity=0.157  Sum_probs=139.6

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG  126 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~  126 (294)
                      ...|+.....|..+-.-.++..+...+...+.. +.+.++|+||+|+|||++++.+++.+.+...   .+..+.... ..
T Consensus         9 ~~~pF~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~l~G~~G~GKTtl~~~l~~~l~~~~~---~~~~~~~~~-~~   83 (269)
T TIGR03015         9 TTKPFQLLPDPDFFYPSKGHKRAMAYLEYGLSQ-REGFILITGEVGAGKTTLIRNLLKRLDQERV---VAAKLVNTR-VD   83 (269)
T ss_pred             CCCCCCCCCCHHHhCCCHHHHHHHHHHHHHHhc-CCCEEEEEcCCCCCHHHHHHHHHHhcCCCCe---EEeeeeCCC-CC
Confidence            344666555555443334445555555555543 2346999999999999999999998742211   111111111 11


Q ss_pred             hhHHHHHHHHHHhhhcccCcc-----C------CCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh---cCcceEEEEe
Q 022641          127 INVVRTKIKTFAAVAVGSGQR-----R------GGYPCPPYKIIILDEADSMTEDAQNALRRTMETY---SKVTRFFFIC  192 (294)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~-----~------~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~---~~~~~ii~~~  192 (294)
                      .......+.............     .      .....+++.+|+|||++.++....+.|..+.+..   .....+++++
T Consensus        84 ~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g  163 (269)
T TIGR03015        84 AEDLLRMVAADFGLETEGRDKAALLRELEDFLIEQFAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVG  163 (269)
T ss_pred             HHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcC
Confidence            111111111111100000000     0      0001234569999999999988777766544321   1223345555


Q ss_pred             cCCc------ccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhC----CCCCHHHHHHHHhhccCcHHHHHHHHHHHH
Q 022641          193 NYIS------RIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEG----LNLDAEALSTLSSISQGDLRRAITYLQGAA  261 (294)
Q Consensus       193 ~~~~------~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~----~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~  261 (294)
                      ....      .....+.+|+. .+.++|++.+++.+++...+...+    ..+++++++.|++.|+|++|.+..++..+.
T Consensus       164 ~~~~~~~l~~~~~~~l~~r~~~~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~  243 (269)
T TIGR03015       164 QPEFRETLQSPQLQQLRQRIIASCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLL  243 (269)
T ss_pred             CHHHHHHHcCchhHHHHhheeeeeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHH
Confidence            3221      11234666754 789999999999999999887655    368999999999999999999888888775


Q ss_pred             HHh----CCCCChhhhhhhccccc
Q 022641          262 RLF----GSSITSKDLISVSGYPT  281 (294)
Q Consensus       262 ~~~----~~~it~~~v~~~~~~~~  281 (294)
                      ..+    ...|+.++|..++....
T Consensus       244 ~~a~~~~~~~i~~~~v~~~~~~~~  267 (269)
T TIGR03015       244 LSAFLEEKREIGGEEVREVIAEID  267 (269)
T ss_pred             HHHHHcCCCCCCHHHHHHHHHHhh
Confidence            554    56799999999887654

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.

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.73  E-value=2e-16  Score=139.47  Aligned_cols=171  Identities=20%  Similarity=0.203  Sum_probs=114.2

Q ss_pred             hhcCCCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCc----cCCc
Q 022641           53 EKYRPKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPEL----YKSR  115 (294)
Q Consensus        53 ~~~~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~----~~~~  115 (294)
                      +..-+..|+++.|.+..++.+...+..             ..+++++|+||||||||++++++++++..+..    ....
T Consensus       174 ~~~p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~  253 (512)
T TIGR03689       174 EEVPDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSY  253 (512)
T ss_pred             ecCCCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCcee
Confidence            445567899999999999888887632             23346999999999999999999999843211    1122


Q ss_pred             ceeecCCCCcc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH------------HHHHHHHH
Q 022641          116 VLELNASDDRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE------------DAQNALRR  177 (294)
Q Consensus       116 ~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~------------~~~~~L~~  177 (294)
                      ++.+..+...+      ...++..+.......          ....+.+|||||+|.+..            ...+.|+.
T Consensus       254 fl~v~~~eLl~kyvGete~~ir~iF~~Ar~~a----------~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~  323 (512)
T TIGR03689       254 FLNIKGPELLNKYVGETERQIRLIFQRAREKA----------SDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLS  323 (512)
T ss_pred             EEeccchhhcccccchHHHHHHHHHHHHHHHh----------hcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHH
Confidence            23333222111      112222222222111          012345999999998732            12356666


Q ss_pred             HHHhhc--CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCC
Q 022641          178 TMETYS--KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNL  234 (294)
Q Consensus       178 ~l~~~~--~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~  234 (294)
                      .++...  ..+.+|.+||.+..+++++++  ||. .|.|++|+.+++.++++.++.. .+.+
T Consensus       324 ~LDgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~-~l~l  384 (512)
T TIGR03689       324 ELDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTD-SLPL  384 (512)
T ss_pred             HhcccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhc-cCCc
Confidence            666443  456788899999999999998  887 7999999999999999998854 3444

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.73  E-value=1.3e-16  Score=150.54  Aligned_cols=208  Identities=18%  Similarity=0.177  Sum_probs=150.0

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCC----ccCCcceeecC
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE----LYKSRVLELNA  121 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~----~~~~~~~~~~~  121 (294)
                      ....|+.++.+|..++.++|+++.++.+.+.|.....+|++|+||||||||+++++++..+....    ..+..++.++.
T Consensus       163 ~~~~~l~~~~r~~~l~~vigr~~ei~~~i~iL~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l  242 (857)
T PRK10865        163 KYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDM  242 (857)
T ss_pred             HHhhhHHHHHhcCCCCcCCCCHHHHHHHHHHHhcCCcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEeh
Confidence            56678999999999999999999999999999998888999999999999999999999984321    12455555554


Q ss_pred             CCCc----chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------HHHHHHHHHHHhhcCcceEE
Q 022641          122 SDDR----GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------DAQNALRRTMETYSKVTRFF  189 (294)
Q Consensus       122 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------~~~~~L~~~l~~~~~~~~ii  189 (294)
                      ....    ....+...+..+......         ...+.||||||+|.+..        +..+.|...++.  ....+|
T Consensus       243 ~~l~ag~~~~g~~e~~lk~~~~~~~~---------~~~~~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l~~--g~l~~I  311 (857)
T PRK10865        243 GALVAGAKYRGEFEERLKGVLNDLAK---------QEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR--GELHCV  311 (857)
T ss_pred             hhhhhccchhhhhHHHHHHHHHHHHH---------cCCCeEEEEecHHHhccCCCCccchhHHHHhcchhhc--CCCeEE
Confidence            4321    111222222322221110         01235999999999852        256778877764  566778


Q ss_pred             EEecCCc-----ccchHhhccccEEEecCCCHHHHHHHHHHHHHH----hCCCCCHHHHHHHHhhccC------cHHHHH
Q 022641          190 FICNYIS-----RIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE----EGLNLDAEALSTLSSISQG------DLRRAI  254 (294)
Q Consensus       190 ~~~~~~~-----~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~----~~~~~~~~~l~~l~~~~~G------~~r~~~  254 (294)
                      .+|+...     ..++++.+||..|.+..|+.++...+++.+...    +++.++++++...+.++.+      -|..++
T Consensus       312 gaTt~~e~r~~~~~d~al~rRf~~i~v~eP~~~~~~~iL~~l~~~~e~~~~v~~~d~a~~~a~~ls~ry~~~~~~pdkAi  391 (857)
T PRK10865        312 GATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAILRGLKERYELHHHVQITDPAIVAAATLSHRYIADRQLPDKAI  391 (857)
T ss_pred             EcCCCHHHHHHhhhcHHHHhhCCEEEeCCCCHHHHHHHHHHHhhhhccCCCCCcCHHHHHHHHHHhhccccCCCCChHHH
Confidence            8876543     478999999999999999999999999877653    3567888888777665432      466788


Q ss_pred             HHHHHHHHHh
Q 022641          255 TYLQGAARLF  264 (294)
Q Consensus       255 ~~l~~~~~~~  264 (294)
                      .++..++...
T Consensus       392 ~LiD~aaa~~  401 (857)
T PRK10865        392 DLIDEAASSI  401 (857)
T ss_pred             HHHHHHhccc
Confidence            8887776543

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

Probab=99.72  E-value=3.3e-16  Score=122.64  Aligned_cols=197  Identities=21%  Similarity=0.242  Sum_probs=130.5

Q ss_pred             cchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           59 QVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      ++.++-|.+-.++.+++.+.-             ..++.++++||||||||.|++++++..      ...|+.+.++...
T Consensus       153 sy~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t------~a~firvvgsefv  226 (408)
T KOG0727|consen  153 SYADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT------TAAFIRVVGSEFV  226 (408)
T ss_pred             cccccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhcc------chheeeeccHHHH
Confidence            456777777777777666532             345569999999999999999999987      6777777766532


Q ss_pred             c------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHh---hc--
Q 022641          126 G------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMET---YS--  183 (294)
Q Consensus       126 ~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~---~~--  183 (294)
                      .      ..-+++.+.-...              +.+.+|||||+|.+.           .+.+..|+.++..   +.  
T Consensus       227 qkylgegprmvrdvfrlake--------------napsiifideidaiatkrfdaqtgadrevqril~ellnqmdgfdq~  292 (408)
T KOG0727|consen  227 QKYLGEGPRMVRDVFRLAKE--------------NAPSIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDGFDQT  292 (408)
T ss_pred             HHHhccCcHHHHHHHHHHhc--------------cCCcEEEeehhhhHhhhhccccccccHHHHHHHHHHHHhccCcCcc
Confidence            2      2223333332222              224599999999862           3355666666653   22  


Q ss_pred             CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhh----ccCcHHHHHHH
Q 022641          184 KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSI----SQGDLRRAITY  256 (294)
Q Consensus       184 ~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~----~~G~~r~~~~~  256 (294)
                      .++.+|++||....+++++++  |.. .|+|+-|+..+.+-++..+..+.++.- +-.++.++..    ++.++-.+   
T Consensus       293 ~nvkvimatnradtldpallrpgrldrkiefplpdrrqkrlvf~titskm~ls~-~vdle~~v~rpdkis~adi~ai---  368 (408)
T KOG0727|consen  293 TNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFSTITSKMNLSD-EVDLEDLVARPDKISGADINAI---  368 (408)
T ss_pred             cceEEEEecCcccccCHhhcCCccccccccCCCCchhhhhhhHHhhhhcccCCc-ccCHHHHhcCccccchhhHHHH---
Confidence            467899999999999999987  555 799999999999999988887755532 2224444433    44455444   


Q ss_pred             HHHHHHHh----CCCCChhhhhhhccc
Q 022641          257 LQGAARLF----GSSITSKDLISVSGY  279 (294)
Q Consensus       257 l~~~~~~~----~~~it~~~v~~~~~~  279 (294)
                      +|.+...+    .--+...+++++-..
T Consensus       369 cqeagm~avr~nryvvl~kd~e~ay~~  395 (408)
T KOG0727|consen  369 CQEAGMLAVRENRYVVLQKDFEKAYKT  395 (408)
T ss_pred             HHHHhHHHHHhcceeeeHHHHHHHHHh
Confidence            44444443    223666677665544

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=99.72  E-value=1.1e-15  Score=125.75  Aligned_cols=173  Identities=21%  Similarity=0.293  Sum_probs=130.0

Q ss_pred             ccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc------------------CCcceeecCCC-C
Q 022641           65 HQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY------------------KSRVLELNASD-D  124 (294)
Q Consensus        65 g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~------------------~~~~~~~~~~~-~  124 (294)
                      .++.++..+.+.+..++.++ ++|+||  +||+++|..+++.+.|....                  +..+..+.... .
T Consensus         6 ~q~~~~~~L~~~~~~~rl~hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~~~Cg~C~~C~~i~~~~HPD~~~i~p~~~~   83 (290)
T PRK07276          6 KQPKVFQRFQTILEQDRLNHAYLFSGD--FASFEMALFLAQSLFCEQKEGVLPCGHCRSCRLIEQGEFSDVTVIEPQGQV   83 (290)
T ss_pred             HHHHHHHHHHHHHHcCCcceeeeeeCC--ccHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCeeeecCCCCc
Confidence            56788899999999998877 799996  68999999999999886431                  12223332221 2


Q ss_pred             cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhc
Q 022641          125 RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLAS  204 (294)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~  204 (294)
                      ...+.+++....+...+.          .+++.|+|||++|.++....|.|++.+|+++.++.+|++|+.+..+++.++|
T Consensus        84 I~idqIR~l~~~~~~~p~----------~~~~kV~II~~ad~m~~~AaNaLLKtLEEPp~~t~~iL~t~~~~~lLpTI~S  153 (290)
T PRK07276         84 IKTDTIRELVKNFSQSGY----------EGKQQVFIIKDADKMHVNAANSLLKVIEEPQSEIYIFLLTNDENKVLPTIKS  153 (290)
T ss_pred             CCHHHHHHHHHHHhhCcc----------cCCcEEEEeehhhhcCHHHHHHHHHHhcCCCCCeEEEEEECChhhCchHHHH
Confidence            345666666555544332          2446799999999999999999999999999999999999999999999999


Q ss_pred             cccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHH
Q 022641          205 RCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYL  257 (294)
Q Consensus       205 r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l  257 (294)
                      ||+.+.|++ +.+++.+++    ..+|+  +.+....++..+ |++..++.++
T Consensus       154 Rcq~i~f~~-~~~~~~~~L----~~~g~--~~~~a~~la~~~-~s~~~A~~l~  198 (290)
T PRK07276        154 RTQIFHFPK-NEAYLIQLL----EQKGL--LKTQAELLAKLA-QSTSEAEKLA  198 (290)
T ss_pred             cceeeeCCC-cHHHHHHHH----HHcCC--ChHHHHHHHHHC-CCHHHHHHHh
Confidence            999999966 666666666    34554  444444555544 4788888776

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.72  E-value=1.6e-16  Score=153.75  Aligned_cols=179  Identities=12%  Similarity=0.131  Sum_probs=125.9

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchh----------------------------------
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGIN----------------------------------  128 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~----------------------------------  128 (294)
                      +.++|+||||||||.||+++|.+.      +.+++.+++++.....                                  
T Consensus      1631 KGILLiGPPGTGKTlLAKALA~es------~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~~~~e~~e~ 1704 (2281)
T CHL00206       1631 RGILVIGSIGTGRSYLVKYLATNS------YVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDLDTELLTM 1704 (2281)
T ss_pred             CceEEECCCCCCHHHHHHHHHHhc------CCceEEEEHHHHhhcccccccccccccccccccccccccccccchhhhhh
Confidence            359999999999999999999998      6666666554322100                                  


Q ss_pred             ---------------HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH-----HHHHHHHHHHhh-----c
Q 022641          129 ---------------VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED-----AQNALRRTMETY-----S  183 (294)
Q Consensus       129 ---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~-----~~~~L~~~l~~~-----~  183 (294)
                                     .++..+...              ....++||+|||||.+...     ..+.|+..|+..     .
T Consensus      1705 ~n~~~~~m~~~e~~~rIr~lFelA--------------Rk~SPCIIFIDEIDaL~~~ds~~ltL~qLLneLDg~~~~~s~ 1770 (2281)
T CHL00206       1705 MNALTMDMMPKIDRFYITLQFELA--------------KAMSPCIIWIPNIHDLNVNESNYLSLGLLVNSLSRDCERCST 1770 (2281)
T ss_pred             cchhhhhhhhhhhHHHHHHHHHHH--------------HHCCCeEEEEEchhhcCCCccceehHHHHHHHhccccccCCC
Confidence                           001111111              1133579999999999643     256677777643     2


Q ss_pred             CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHH--HHHHHHhhccC-cHHHHHHHH
Q 022641          184 KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAE--ALSTLSSISQG-DLRRAITYL  257 (294)
Q Consensus       184 ~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~--~l~~l~~~~~G-~~r~~~~~l  257 (294)
                      ..+.||.+||.+..+++++++  ||. .|.++.|+..+..+++.......++.+.++  .++.+++.|.| +.+.+.+++
T Consensus      1771 ~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA~~T~GfSGADLanLv 1850 (2281)
T CHL00206       1771 RNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLVALT 1850 (2281)
T ss_pred             CCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHHHHHHhCCCCCHHHHHHHH
Confidence            356788889999999999997  887 789999988888887765555556666543  47888988866 455566666


Q ss_pred             HHHHHHh----CCCCChhhhhhhccccc
Q 022641          258 QGAARLF----GSSITSKDLISVSGYPT  281 (294)
Q Consensus       258 ~~~~~~~----~~~it~~~v~~~~~~~~  281 (294)
                      ..|+..+    ...|+.+++..++....
T Consensus      1851 NEAaliAirq~ks~Id~~~I~~Al~Rq~ 1878 (2281)
T CHL00206       1851 NEALSISITQKKSIIDTNTIRSALHRQT 1878 (2281)
T ss_pred             HHHHHHHHHcCCCccCHHHHHHHHHHHH
Confidence            6666655    35699999998887654

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=99.72  E-value=2.1e-15  Score=125.23  Aligned_cols=174  Identities=17%  Similarity=0.259  Sum_probs=132.0

Q ss_pred             HHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCc-------cCCcceeecC-CCCcchhHHHHHHHHHH
Q 022641           68 EVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL-------YKSRVLELNA-SDDRGINVVRTKIKTFA  138 (294)
Q Consensus        68 ~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~-------~~~~~~~~~~-~~~~~~~~~~~~~~~~~  138 (294)
                      ..+..+.+.+..++.++ ++|+|+.|+||+.++..+++.++|...       ....+..++. ......+.++.....+.
T Consensus         3 ~~~~~l~~~i~~~~l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~i~vd~Ir~l~~~~~   82 (299)
T PRK07132          3 NWIKFLDNSATQNKISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKDLSKSEFLSAINKLY   82 (299)
T ss_pred             hHHHHHHHHHHhCCCCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCcCCHHHHHHHHHHhc
Confidence            45677888888877766 679999999999999999999977421       1113333431 22244556665555543


Q ss_pred             hhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEEecCCCHHH
Q 022641          139 AVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEV  218 (294)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~  218 (294)
                      ..+..         .+++.++|||+++.++....+.|++.+++++..+.+|++++.+..+.+.+.+||..+.|.|++.++
T Consensus        83 ~~~~~---------~~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~f~~l~~~~  153 (299)
T PRK07132         83 FSSFV---------QSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPDQQK  153 (299)
T ss_pred             cCCcc---------cCCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEEECCCCCHHH
Confidence            33211         135679999999999999999999999999999999999998899999999999999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHH
Q 022641          219 MSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYL  257 (294)
Q Consensus       219 ~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l  257 (294)
                      +..++..    .+  ++++....++..++| +..++.++
T Consensus       154 l~~~l~~----~~--~~~~~a~~~a~~~~~-~~~a~~~~  185 (299)
T PRK07132        154 ILAKLLS----KN--KEKEYNWFYAYIFSN-FEQAEKYI  185 (299)
T ss_pred             HHHHHHH----cC--CChhHHHHHHHHcCC-HHHHHHHH
Confidence            9988853    23  676777777777774 88777665

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.71  E-value=3.9e-16  Score=143.39  Aligned_cols=204  Identities=19%  Similarity=0.135  Sum_probs=139.3

Q ss_pred             CCCcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           56 RPKQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        56 ~~~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ....+.++.|.+..+..+.+.+..            ..+++++|+||||||||+++++++.++      +.+++.+++++
T Consensus       147 ~~~~~~di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~------~~~f~~is~~~  220 (644)
T PRK10733        147 IKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA------KVPFFTISGSD  220 (644)
T ss_pred             hhCcHHHHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHc------CCCEEEEehHH
Confidence            345678888988877766655421            113459999999999999999999998      66777776654


Q ss_pred             Cc------chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhhc
Q 022641          124 DR------GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTMETYS  183 (294)
Q Consensus       124 ~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~~~~  183 (294)
                      ..      ....++..+.....              ..+.+|||||+|.+..              ...+.|+..++.+.
T Consensus       221 ~~~~~~g~~~~~~~~~f~~a~~--------------~~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~  286 (644)
T PRK10733        221 FVEMFVGVGASRVRDMFEQAKK--------------AAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFE  286 (644)
T ss_pred             hHHhhhcccHHHHHHHHHHHHh--------------cCCcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhccc
Confidence            21      22233333332211              1235999999998732              13455665566544


Q ss_pred             --CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC----cHHHHH
Q 022641          184 --KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG----DLRRAI  254 (294)
Q Consensus       184 --~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G----~~r~~~  254 (294)
                        ..+.+|.+||.+..+++++.+  ||. .+.++.|+.+++.++++.+++...+. .+..+..+++.+.|    |+..++
T Consensus       287 ~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~-~~~d~~~la~~t~G~sgadl~~l~  365 (644)
T PRK10733        287 GNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLA-PDIDAAIIARGTPGFSGADLANLV  365 (644)
T ss_pred             CCCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCC-CcCCHHHHHhhCCCCCHHHHHHHH
Confidence              346678889999999999986  886 89999999999999999988654332 22336678888776    666665


Q ss_pred             HHHHHHHHHh-CCCCChhhhhhhcccc
Q 022641          255 TYLQGAARLF-GSSITSKDLISVSGYP  280 (294)
Q Consensus       255 ~~l~~~~~~~-~~~it~~~v~~~~~~~  280 (294)
                      +.....+... ...|+.+++..+....
T Consensus       366 ~eAa~~a~r~~~~~i~~~d~~~a~~~v  392 (644)
T PRK10733        366 NEAALFAARGNKRVVSMVEFEKAKDKI  392 (644)
T ss_pred             HHHHHHHHHcCCCcccHHHHHHHHHHH
Confidence            5554433322 4569999998887644

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

Probab=99.71  E-value=6.4e-16  Score=123.46  Aligned_cols=127  Identities=24%  Similarity=0.272  Sum_probs=107.8

Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecC-------------CcccchHhhccccEEEecCCCHHHHHHH
Q 022641          156 YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNY-------------ISRIIEPLASRCAKFRFKPLSEEVMSSR  222 (294)
Q Consensus       156 ~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~-------------~~~~~~~l~~r~~~i~~~~~~~~~~~~~  222 (294)
                      +++|||||+|+|+-++...|.+.++..-.+ .+|+++|.             ++.+++.+++|..+|...+++.++++.+
T Consensus       297 PGVLFIDEVhMLDiEcFTyL~kalES~iaP-ivifAsNrG~~~irGt~d~~sPhGip~dllDRl~Iirt~~y~~~e~r~I  375 (456)
T KOG1942|consen  297 PGVLFIDEVHMLDIECFTYLHKALESPIAP-IVIFASNRGMCTIRGTEDILSPHGIPPDLLDRLLIIRTLPYDEEEIRQI  375 (456)
T ss_pred             CcceEeeehhhhhhHHHHHHHHHhcCCCCc-eEEEecCCcceeecCCcCCCCCCCCCHHHhhheeEEeeccCCHHHHHHH
Confidence            569999999999999999999999874444 46777753             4668899999999999999999999999


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHhh-ccCcHHHHHHHHHHHHHHh----CCCCChhhhhhhcccccCC
Q 022641          223 VLHICNEEGLNLDAEALSTLSSI-SQGDLRRAITYLQGAARLF----GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       223 l~~~~~~~~~~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~~~  283 (294)
                      ++..++.+++.++++++..+++. +..++|.++++|.-+...+    ++.|..++++++...+-+.
T Consensus       376 i~~Ra~~E~l~~~e~a~~~l~~~gt~tsLRy~vqLl~p~~~~ak~~g~~~i~v~dvee~~~Lf~Da  441 (456)
T KOG1942|consen  376 IKIRAQVEGLQVEEEALDLLAEIGTSTSLRYAVQLLTPASILAKTNGRKEISVEDVEEVTELFLDA  441 (456)
T ss_pred             HHHHHhhhcceecHHHHHHHHhhccchhHHHHHHhcCHHHHHHHHcCCceeecccHHHHHHHHHhc
Confidence            99999999999999999999997 5678999999998555444    4579999998887665443

>TIGR01817 nifA Nif-specific regulatory protein

Probab=99.71  E-value=6.9e-16  Score=139.96  Aligned_cols=217  Identities=20%  Similarity=0.224  Sum_probs=150.3

Q ss_pred             hcCCCcchhhcccHHHHHHHHHHHHcC--CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHH
Q 022641           54 KYRPKQVKDVAHQEEVVRVLTNTLETA--NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVR  131 (294)
Q Consensus        54 ~~~~~~~~~~~g~~~~~~~l~~~l~~~--~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (294)
                      +.....++.++|....+..+.+.+..-  ...+++|+|++||||+++|+++.....   ....+++.++|..... ..+.
T Consensus       189 ~~~~~~~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s~---r~~~pfv~i~c~~~~~-~~~~  264 (534)
T TIGR01817       189 RRRSGKEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSP---RAKRPFVKVNCAALSE-TLLE  264 (534)
T ss_pred             ccccCccCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhCC---CCCCCeEEeecCCCCH-HHHH
Confidence            344457889999988888777766543  334699999999999999999988642   2356889999887533 2222


Q ss_pred             HHHHHHHhh-hcc-cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc--
Q 022641          132 TKIKTFAAV-AVG-SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS--  196 (294)
Q Consensus       132 ~~~~~~~~~-~~~-~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~--  196 (294)
                      ..+...... ..+ .....+....+..+.|+|||++.++...+..|+..++...           ..+++|++++...  
T Consensus       265 ~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~s~~~l~~  344 (534)
T TIGR01817       265 SELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEE  344 (534)
T ss_pred             HHHcCCCCCccCCCCcCCCCcccccCCCeEEEechhhCCHHHHHHHHHHHhcCcEEECCCCceEeecEEEEEeCCCCHHH
Confidence            111100000 000 0111222334567899999999999999999999997643           1357888776432  


Q ss_pred             -----ccchHhhcccc--EEEecCCC--HHHHHHHHHHHHHH----hC--CCCCHHHHHHHHhh-ccCcHHHHHHHHHHH
Q 022641          197 -----RIIEPLASRCA--KFRFKPLS--EEVMSSRVLHICNE----EG--LNLDAEALSTLSSI-SQGDLRRAITYLQGA  260 (294)
Q Consensus       197 -----~~~~~l~~r~~--~i~~~~~~--~~~~~~~l~~~~~~----~~--~~~~~~~l~~l~~~-~~G~~r~~~~~l~~~  260 (294)
                           .+...|..|+.  .|.++|+.  .+++..++.+++..    .+  +.+++++++.|..+ ++||+|++.++++.+
T Consensus       345 ~~~~~~f~~~L~~rl~~~~i~lPpLreR~eDi~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~~~WPGNvrEL~~v~~~a  424 (534)
T TIGR01817       345 AVAKGEFRADLYYRINVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRPLTITPSAIRVLMSCKWPGNVRELENCLERT  424 (534)
T ss_pred             HHHcCCCCHHHHHHhcCCeeeCCCcccccccHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhCCCCChHHHHHHHHHHH
Confidence                 24456777775  67888886  46676666666543    22  56899999999998 699999999999998


Q ss_pred             HHHh-CCCCChhhhh
Q 022641          261 ARLF-GSSITSKDLI  274 (294)
Q Consensus       261 ~~~~-~~~it~~~v~  274 (294)
                      +... +..|+.+++.
T Consensus       425 ~~~~~~~~I~~~~l~  439 (534)
T TIGR01817       425 ATLSRSGTITRSDFS  439 (534)
T ss_pred             HHhCCCCcccHHHCc
Confidence            8765 4568888875

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.

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

Probab=99.71  E-value=3.6e-16  Score=130.15  Aligned_cols=149  Identities=15%  Similarity=0.207  Sum_probs=110.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc------chhHHHHHHHHHHhhhcccCccCCCCCCCCc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR------GINVVRTKIKTFAAVAVGSGQRRGGYPCPPY  156 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (294)
                      ..++|+||||||||.+|+++++++      +..++.++++...      +...++..+........         ...++
T Consensus       149 lgllL~GPPGcGKTllAraiA~el------g~~~i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~---------~~~aP  213 (413)
T PLN00020        149 LILGIWGGKGQGKSFQCELVFKKM------GIEPIVMSAGELESENAGEPGKLIRQRYREAADIIK---------KKGKM  213 (413)
T ss_pred             eEEEeeCCCCCCHHHHHHHHHHHc------CCCeEEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhh---------ccCCC
Confidence            349999999999999999999999      7888888876533      34455555554433210         11245


Q ss_pred             EEEEEeCCCCCCHH-----------H-HHHHHHHHHh--------------hcCcceEEEEecCCcccchHhhc--cccE
Q 022641          157 KIIILDEADSMTED-----------A-QNALRRTMET--------------YSKVTRFFFICNYISRIIEPLAS--RCAK  208 (294)
Q Consensus       157 ~lliiDei~~l~~~-----------~-~~~L~~~l~~--------------~~~~~~ii~~~~~~~~~~~~l~~--r~~~  208 (294)
                      .+|+|||+|.+...           . ...|+.+++.              ....+.||+|||.+..++++|++  ||..
T Consensus       214 cVLFIDEIDA~~g~r~~~~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd~LDpALlRpGRfDk  293 (413)
T PLN00020        214 SCLFINDLDAGAGRFGTTQYTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFSTLYAPLIRDGRMEK  293 (413)
T ss_pred             eEEEEehhhhcCCCCCCCCcchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCCCcccCCHhHcCCCCCCc
Confidence            69999999976321           1 2456666543              23457789999999999999999  8875


Q ss_pred             EEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCc
Q 022641          209 FRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGD  249 (294)
Q Consensus       209 i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~  249 (294)
                      + +..|+.+++.+|++.+++..+  ++...+..|++...|.
T Consensus       294 ~-i~lPd~e~R~eIL~~~~r~~~--l~~~dv~~Lv~~f~gq  331 (413)
T PLN00020        294 F-YWAPTREDRIGVVHGIFRDDG--VSREDVVKLVDTFPGQ  331 (413)
T ss_pred             e-eCCCCHHHHHHHHHHHhccCC--CCHHHHHHHHHcCCCC
Confidence            4 457999999999999987754  5688899999988775

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.71  E-value=2e-16  Score=149.49  Aligned_cols=206  Identities=17%  Similarity=0.150  Sum_probs=149.8

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCC----CccCCcceeecCC
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP----ELYKSRVLELNAS  122 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~----~~~~~~~~~~~~~  122 (294)
                      ....+.+.-+...++.++|++..++.+.+++.....+|++|+||||||||++|+.++..+...    ...+..++.++..
T Consensus       165 ~~~~l~~~a~~~~~~~~igr~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l~~~  244 (821)
T CHL00095        165 FGTNLTKEAIDGNLDPVIGREKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIG  244 (821)
T ss_pred             HHHHHHHHHHcCCCCCCCCcHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeHH
Confidence            344566666677788999999999999999999888899999999999999999999987421    2234567777654


Q ss_pred             CCc----chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------HHHHHHHHHHHhhcCcceEEE
Q 022641          123 DDR----GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------DAQNALRRTMETYSKVTRFFF  190 (294)
Q Consensus       123 ~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------~~~~~L~~~l~~~~~~~~ii~  190 (294)
                      ...    ....+...+..+......          .+..||||||+|.+..        ...+.|...+..  ....+|.
T Consensus       245 ~l~ag~~~~ge~e~rl~~i~~~~~~----------~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~r--g~l~~Ig  312 (821)
T CHL00095        245 LLLAGTKYRGEFEERLKRIFDEIQE----------NNNIILVIDEVHTLIGAGAAEGAIDAANILKPALAR--GELQCIG  312 (821)
T ss_pred             HHhccCCCccHHHHHHHHHHHHHHh----------cCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHhC--CCcEEEE
Confidence            321    122233333433332211          1235999999997742        245667777764  5566777


Q ss_pred             EecCC-----cccchHhhccccEEEecCCCHHHHHHHHHHHHH----HhCCCCCHHHHHHHHhhccC------cHHHHHH
Q 022641          191 ICNYI-----SRIIEPLASRCAKFRFKPLSEEVMSSRVLHICN----EEGLNLDAEALSTLSSISQG------DLRRAIT  255 (294)
Q Consensus       191 ~~~~~-----~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~----~~~~~~~~~~l~~l~~~~~G------~~r~~~~  255 (294)
                      +|+..     ....+++.+||..+.+.+|+.++...+++.+..    ..++.++++++..+++++.|      -|+.++.
T Consensus       313 aTt~~ey~~~ie~D~aL~rRf~~I~v~ep~~~e~~aILr~l~~~~e~~~~v~i~deal~~i~~ls~~yi~~r~lPdkaid  392 (821)
T CHL00095        313 ATTLDEYRKHIEKDPALERRFQPVYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQYIADRFLPDKAID  392 (821)
T ss_pred             eCCHHHHHHHHhcCHHHHhcceEEecCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhccCccccCchHHHH
Confidence            77654     246789999999999999999998888876553    35677999999999988765      3888999


Q ss_pred             HHHHHHHHh
Q 022641          256 YLQGAARLF  264 (294)
Q Consensus       256 ~l~~~~~~~  264 (294)
                      ++..++...
T Consensus       393 lld~a~a~~  401 (821)
T CHL00095        393 LLDEAGSRV  401 (821)
T ss_pred             HHHHHHHHH
Confidence            999887643

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=99.70  E-value=1.3e-15  Score=128.37  Aligned_cols=135  Identities=24%  Similarity=0.331  Sum_probs=106.3

Q ss_pred             CCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCcc-------------------CCcceeecCCC----------CcchhH
Q 022641           80 ANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELY-------------------KSRVLELNASD----------DRGINV  129 (294)
Q Consensus        80 ~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~-------------------~~~~~~~~~~~----------~~~~~~  129 (294)
                      ++.++ ++|+||+|+|||++|..+++.+.|....                   +..++.+.+..          ...++.
T Consensus        18 ~r~~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~~~~~g~~~~~I~id~   97 (325)
T PRK08699         18 ERRPNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSDEPENGRKLLQIKIDA   97 (325)
T ss_pred             CCcceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecccccccccccCCCcCHHH
Confidence            34455 8999999999999999999999875421                   23455554421          134566


Q ss_pred             HHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEE
Q 022641          130 VRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKF  209 (294)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i  209 (294)
                      ++.........+.          .+++.|++||+++.++...++.|++.+++++....+|++|+.+..+.+.+.+||..+
T Consensus        98 iR~l~~~~~~~p~----------~~~~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~  167 (325)
T PRK08699         98 VREIIDNVYLTSV----------RGGLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKM  167 (325)
T ss_pred             HHHHHHHHhhCcc----------cCCceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhh
Confidence            6665544433221          234679999999999999999999999998878889999999999999999999999


Q ss_pred             EecCCCHHHHHHHHH
Q 022641          210 RFKPLSEEVMSSRVL  224 (294)
Q Consensus       210 ~~~~~~~~~~~~~l~  224 (294)
                      .|.|++.+++..+|.
T Consensus       168 ~~~~~~~~~~~~~L~  182 (325)
T PRK08699        168 VLPAPSHEEALAYLR  182 (325)
T ss_pred             cCCCCCHHHHHHHHH
Confidence            999999999999885

>PRK09183 transposase/IS protein; Provisional

Probab=99.70  E-value=4.6e-18  Score=139.32  Aligned_cols=201  Identities=11%  Similarity=0.140  Sum_probs=130.2

Q ss_pred             CCcccccccccccCCCCCcccCCCC--cccCCCCchHHHHhhccccccCCchhhhhcCCCcchhhccc-HHHHHHHHHHH
Q 022641            1 MRANFGKIHKSGKNKSPNFTQKFST--TQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQ-EEVVRVLTNTL   77 (294)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~-~~~~~~l~~~l   77 (294)
                      |+++|++++.++...++++.+++..  +.|...|.++...++++   .+.+|+.+.+..++|....+. ...+..|..+-
T Consensus        21 ~~~~~~~~~~~~~~~~~~~~e~l~~ll~~E~~~R~~~~~~~~~k---~a~~p~~~~l~~fd~~~~~~~~~~~i~~L~~~~   97 (259)
T PRK09183         21 LISAAPALAQQAVDQEWSYMDFLEHLLHEEKLARHQRKQAMYTR---MAAFPAVKTFEEYDFTFATGAPQKQLQSLRSLS   97 (259)
T ss_pred             HHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHH---hCCCCCCCcHhhcccccCCCCCHHHHHHHhcCC
Confidence            3567778888888999999999987  56777777777777777   788899888888888877664 55666665543


Q ss_pred             HcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcE
Q 022641           78 ETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYK  157 (294)
Q Consensus        78 ~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (294)
                      ......+++|+||+||||||++.+++..+...   +..+..++..+      +...+....... .... .........+
T Consensus        98 ~i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~---G~~v~~~~~~~------l~~~l~~a~~~~-~~~~-~~~~~~~~~d  166 (259)
T PRK09183         98 FIERNENIVLLGPSGVGKTHLAIALGYEAVRA---GIKVRFTTAAD------LLLQLSTAQRQG-RYKT-TLQRGVMAPR  166 (259)
T ss_pred             chhcCCeEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEEeHHH------HHHHHHHHHHCC-cHHH-HHHHHhcCCC
Confidence            34445689999999999999999999886321   22333332211      110110000000 0000 0000012346


Q ss_pred             EEEEeCCCCC--CHHHHHHHHHHHHhhcCcceEEEEecCCcc---------------cchHhhccccEEEecCCC
Q 022641          158 IIILDEADSM--TEDAQNALRRTMETYSKVTRFFFICNYISR---------------IIEPLASRCAKFRFKPLS  215 (294)
Q Consensus       158 lliiDei~~l--~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~---------------~~~~l~~r~~~i~~~~~~  215 (294)
                      +++|||++..  +....+.|+++++..+....+|+|||.+..               +.+++.+.+..|.|...+
T Consensus       167 lLiiDdlg~~~~~~~~~~~lf~li~~r~~~~s~iiTsn~~~~~w~~~~~~d~~~~~ai~dRl~~~~~~i~~~g~s  241 (259)
T PRK09183        167 LLIIDEIGYLPFSQEEANLFFQVIAKRYEKGSMILTSNLPFGQWDQTFAGDAALTSAMLDRLLHHSHVVQIKGES  241 (259)
T ss_pred             EEEEcccccCCCChHHHHHHHHHHHHHHhcCcEEEecCCCHHHHHHHhcCchhHHHHHHHHHhcceEEEeecCCC
Confidence            9999999985  455667899999887777778999986532               223444455678877655

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.70  E-value=2.2e-15  Score=127.07  Aligned_cols=228  Identities=19%  Similarity=0.132  Sum_probs=147.2

Q ss_pred             CCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccC-CcceeecCCC------------
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYK-SRVLELNASD------------  123 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~-~~~~~~~~~~------------  123 (294)
                      .+.|.+++|+++.+..|...+...+..+++|.|++|||||++++.+.+.+.+..... .+|. .++.+            
T Consensus        13 ~~pf~~ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~ar~~~~~l~~~~~~~~~pf~-~~p~~p~~~~~~~~~~~   91 (350)
T CHL00081         13 VFPFTAIVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTTIRALVDLLPEIEVVKDDPFN-SHPSDPELMSDEVREAI   91 (350)
T ss_pred             CCCHHHHhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHHHHHHHHHHhhcCccCCCCCC-CCCCChhhhchhhhhhh
Confidence            347899999999999999998888877899999999999999999988875332111 1111 11100            


Q ss_pred             --------------------CcchhHHHHHHHHHHhhhccc-CccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh
Q 022641          124 --------------------DRGINVVRTKIKTFAAVAVGS-GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY  182 (294)
Q Consensus       124 --------------------~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~  182 (294)
                                          ....+.+..-+........+. ....+....+.+++|++||++.+++..+..|++.+++.
T Consensus        92 ~~~~~~~~~~~~~~~~~lp~~~ted~l~G~iD~~~al~~g~~~~~~GlL~~A~~GiL~lDEInrL~~~~Q~~LLeam~e~  171 (350)
T CHL00081         92 QNGETIETEKIKIPMVDLPLGATEDRVCGTIDIEKALTEGVKAFEPGLLAKANRGILYVDEVNLLDDHLVDILLDSAASG  171 (350)
T ss_pred             cccccccceeccccceecCCCCchhhccCcccHHHHhhcCcccccCCeeeecCCCEEEecChHhCCHHHHHHHHHHHHhC
Confidence                                000000000000000000000 01233344566789999999999999999999999762


Q ss_pred             c-------------CcceEEEEecCCc-ccchHhhcccc-EEEecCCC-HHHHHHHHHHHHH------------------
Q 022641          183 S-------------KVTRFFFICNYIS-RIIEPLASRCA-KFRFKPLS-EEVMSSRVLHICN------------------  228 (294)
Q Consensus       183 ~-------------~~~~ii~~~~~~~-~~~~~l~~r~~-~i~~~~~~-~~~~~~~l~~~~~------------------  228 (294)
                      .             ..+.++.+.|... .+.+++..||. .+.+..++ .+...+++++...                  
T Consensus       172 ~~~ier~G~s~~~p~rfiviaT~np~eg~l~~~LldRf~l~i~l~~~~~~~~e~~il~~~~~~~~~~~~~~~~~~~~~~~  251 (350)
T CHL00081        172 WNTVEREGISIRHPARFVLVGSGNPEEGELRPQLLDRFGMHAEIRTVKDPELRVKIVEQRTSFDKNPQEFREKYEESQEE  251 (350)
T ss_pred             CeEEeeCCeeeecCCCEEEEeccCcccCCCCHHHHHHhCceeecCCCCChHHHHHHHHhhhccccChhhhhhhhcccccc
Confidence            2             2222333334333 47889999998 78888887 4666666665321                  


Q ss_pred             -----------HhCCCCCHHHHHHHHhhc---c-CcHHHHHHHHHHHHHHh----CCCCChhhhhhhcccccCCCC
Q 022641          229 -----------EEGLNLDAEALSTLSSIS---Q-GDLRRAITYLQGAARLF----GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       229 -----------~~~~~~~~~~l~~l~~~~---~-G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~~~~~  285 (294)
                                 -..+.++++.++++++.+   + -.+|..+.+++.+-..+    ...++.+||..+...+-.+..
T Consensus       252 ~~~~I~~ar~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~~vL~HR~  327 (350)
T CHL00081        252 LRSKIVAAQNLLPKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVITLCLRHRL  327 (350)
T ss_pred             CHHHHHHHHHhcCCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence                       023568899988888764   2 25888888777655555    567999999988776555533

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.70  E-value=5.9e-16  Score=145.77  Aligned_cols=194  Identities=23%  Similarity=0.340  Sum_probs=135.3

Q ss_pred             hhhcccHHHHHHHHHHHHcC-------CCC--cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHH
Q 022641           61 KDVAHQEEVVRVLTNTLETA-------NCP--HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVR  131 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~-------~~~--~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (294)
                      +.++||+.++..+.+.+...       ..|  .++|+||+|||||.+|+++++.++...   ..++.++++.........
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~~---~~~~~~dmse~~~~~~~~  642 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGGE---QNLITINMSEFQEAHTVS  642 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhCCC---cceEEEeHHHhhhhhhhc
Confidence            47789999999888887531       122  389999999999999999999986432   244555544322111111


Q ss_pred             HHHHHHHhhhccc-CccC-----CCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecC
Q 022641          132 TKIKTFAAVAVGS-GQRR-----GGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNY  194 (294)
Q Consensus       132 ~~~~~~~~~~~~~-~~~~-----~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~  194 (294)
                      ..+    ..+.+. +...     .......+.||+|||++.+++..++.|++++++..           .+..+|+|||.
T Consensus       643 ~l~----g~~~gyvg~~~~g~L~~~v~~~p~svvllDEieka~~~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSNl  718 (852)
T TIGR03345       643 RLK----GSPPGYVGYGEGGVLTEAVRRKPYSVVLLDEVEKAHPDVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNA  718 (852)
T ss_pred             ccc----CCCCCcccccccchHHHHHHhCCCcEEEEechhhcCHHHHHHHHHHhhcceeecCCCcEEeccccEEEEeCCC
Confidence            110    000000 0000     00112345799999999999999999999999765           56778899874


Q ss_pred             Cc-----------------------------ccchHhhccccEEEecCCCHHHHHHHHHHHHHH-------h-C--CCCC
Q 022641          195 IS-----------------------------RIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE-------E-G--LNLD  235 (294)
Q Consensus       195 ~~-----------------------------~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~-------~-~--~~~~  235 (294)
                      ..                             .+.++|++|+.+|.|.|++.+++..++...+..       . +  +.++
T Consensus       719 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEflnRi~iI~F~pLs~e~l~~Iv~~~L~~l~~rl~~~~gi~l~i~  798 (852)
T TIGR03345       719 GSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLGRMTVIPYLPLDDDVLAAIVRLKLDRIARRLKENHGAELVYS  798 (852)
T ss_pred             chHHHHHhccCcccCcchHHHHHHHHHHHHHhccHHHhcceeEEEeCCCCHHHHHHHHHHHHHHHHHHHHHhcCceEEEC
Confidence            21                             145788899999999999999999999887643       1 4  3589


Q ss_pred             HHHHHHHHhhccC---cHHHHHHHHHHHH
Q 022641          236 AEALSTLSSISQG---DLRRAITYLQGAA  261 (294)
Q Consensus       236 ~~~l~~l~~~~~G---~~r~~~~~l~~~~  261 (294)
                      +++++.|++.+.+   ..|.+.+.++...
T Consensus       799 d~a~~~La~~g~~~~~GAR~L~r~Ie~~i  827 (852)
T TIGR03345       799 EALVEHIVARCTEVESGARNIDAILNQTL  827 (852)
T ss_pred             HHHHHHHHHHcCCCCCChHHHHHHHHHHH
Confidence            9999999999876   6888888887644

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.

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

Probab=99.70  E-value=6e-16  Score=137.74  Aligned_cols=213  Identities=23%  Similarity=0.247  Sum_probs=143.2

Q ss_pred             hhhhcCCCcchhhcccHHHHHHHHHHHHcC------------CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCccee
Q 022641           51 WVEKYRPKQVKDVAHQEEVVRVLTNTLETA------------NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLE  118 (294)
Q Consensus        51 ~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~------------~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~  118 (294)
                      ...+.-.-.|+++-|.++++..+++.+...            +...|+||||||||||.+|+++|.++      ...|+.
T Consensus       662 GAPKIPnV~WdDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEc------sL~FlS  735 (953)
T KOG0736|consen  662 GAPKIPNVSWDDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATEC------SLNFLS  735 (953)
T ss_pred             CCCCCCccchhcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhc------eeeEEe
Confidence            333444457899999999999998887541            12359999999999999999999998      667776


Q ss_pred             ecCCC------CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH-------------HHHHHHHHHH
Q 022641          119 LNASD------DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE-------------DAQNALRRTM  179 (294)
Q Consensus       119 ~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~-------------~~~~~L~~~l  179 (294)
                      +.++.      +.+..++++.+.....              +.+.|||+||+|.+.+             +....|+.-|
T Consensus       736 VKGPELLNMYVGqSE~NVR~VFerAR~--------------A~PCVIFFDELDSlAP~RG~sGDSGGVMDRVVSQLLAEL  801 (953)
T KOG0736|consen  736 VKGPELLNMYVGQSEENVREVFERARS--------------AAPCVIFFDELDSLAPNRGRSGDSGGVMDRVVSQLLAEL  801 (953)
T ss_pred             ecCHHHHHHHhcchHHHHHHHHHHhhc--------------cCCeEEEeccccccCccCCCCCCccccHHHHHHHHHHHh
Confidence            65554      3345556666655433              3456999999999843             2456677666


Q ss_pred             Hhhc----CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHH-HHHHHhhc-----
Q 022641          180 ETYS----KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEA-LSTLSSIS-----  246 (294)
Q Consensus       180 ~~~~----~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-l~~l~~~~-----  246 (294)
                      +...    ..+-+|.+||.+..+++++++  ||. .+++.+....+-+..+-+.+.+ ...+++++ +..|++.|     
T Consensus       802 Dgls~~~s~~VFViGATNRPDLLDpALLRPGRFDKLvyvG~~~d~esk~~vL~AlTr-kFkLdedVdL~eiAk~cp~~~T  880 (953)
T KOG0736|consen  802 DGLSDSSSQDVFVIGATNRPDLLDPALLRPGRFDKLVYVGPNEDAESKLRVLEALTR-KFKLDEDVDLVEIAKKCPPNMT  880 (953)
T ss_pred             hcccCCCCCceEEEecCCCccccChhhcCCCccceeEEecCCccHHHHHHHHHHHHH-HccCCCCcCHHHHHhhCCcCCc
Confidence            6544    355678889999999999987  898 6788888776666555444432 34455544 77778765     


Q ss_pred             cCcHHHHHHHHHHHH--HHh-----C-----------CCCChhhhhhhcccccCCC
Q 022641          247 QGDLRRAITYLQGAA--RLF-----G-----------SSITSKDLISVSGYPTGGS  284 (294)
Q Consensus       247 ~G~~r~~~~~l~~~~--~~~-----~-----------~~it~~~v~~~~~~~~~~~  284 (294)
                      +.|+-.++.-.-.+|  +..     +           -.++++|+-+.+.+..+..
T Consensus       881 GADlYsLCSdA~l~AikR~i~~ie~g~~~~~e~~~~~v~V~~eDflks~~~l~PSv  936 (953)
T KOG0736|consen  881 GADLYSLCSDAMLAAIKRTIHDIESGTISEEEQESSSVRVTMEDFLKSAKRLQPSV  936 (953)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhhccccccccCCceEEEEHHHHHHHHHhcCCcc
Confidence            445544442221111  111     1           1278888888877766653

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.69  E-value=3.1e-15  Score=126.29  Aligned_cols=225  Identities=15%  Similarity=0.102  Sum_probs=140.3

Q ss_pred             cchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc-------CCCc---cCCcceeec--------
Q 022641           59 QVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF-------GPEL---YKSRVLELN--------  120 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~-------~~~~---~~~~~~~~~--------  120 (294)
                      .|..++|+++++..|.-.+-.+...+++|.|++|+|||+++++++..+.       ++..   ....+++.+        
T Consensus         2 pf~~ivgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~   81 (337)
T TIGR02030         2 PFTAIVGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAVRALAALLPEIKAVAGCPFNSSPSDPEMMCEEVRIRVDSQ   81 (337)
T ss_pred             CccccccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHHHHHHHhhcccccccCCCCCCCCCCccccChHHhhhhhcc
Confidence            4678999999999887777776666899999999999999999998772       1110   000000000        


Q ss_pred             --------------CCCCcchhHHHHHHHHHHhh-hcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc--
Q 022641          121 --------------ASDDRGINVVRTKIKTFAAV-AVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS--  183 (294)
Q Consensus       121 --------------~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~--  183 (294)
                                    .......+.+...+.-.... ........+....+.+++|+|||++.+++..++.|++.+++..  
T Consensus        82 ~~~~~~~~~~~~~~lP~~~t~d~l~G~~d~~~~l~~g~~~~~~GlL~~A~~GvL~lDEi~~L~~~~Q~~Ll~~l~~g~~~  161 (337)
T TIGR02030        82 EPLSIIKKPVPVVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLARANRGILYIDEVNLLEDHLVDVLLDVAASGWNV  161 (337)
T ss_pred             cccccccCCCCcCCCCCCCcccceecchhHhhHhhcCCEEeecCcceeccCCEEEecChHhCCHHHHHHHHHHHHhCCeE
Confidence                          00000000110000000000 0001112333334567899999999999999999999997642  


Q ss_pred             -----------CcceEEEEecCCc-ccchHhhcccc-EEEecCCCH-HHHHHHHHHHHH---------------------
Q 022641          184 -----------KVTRFFFICNYIS-RIIEPLASRCA-KFRFKPLSE-EVMSSRVLHICN---------------------  228 (294)
Q Consensus       184 -----------~~~~ii~~~~~~~-~~~~~l~~r~~-~i~~~~~~~-~~~~~~l~~~~~---------------------  228 (294)
                                 ..+.++.+.|... .+.+++.+||. .+.+.++.. ++..+++++...                     
T Consensus       162 v~r~G~~~~~~~r~iviat~np~eg~l~~~LldRf~l~i~l~~p~~~eer~eIL~~~~~~~~~~~~~~~~~~~e~~~~~~  241 (337)
T TIGR02030       162 VEREGISIRHPARFVLVGSGNPEEGELRPQLLDRFGLHAEIRTVRDVELRVEIVERRTEYDADPHAFCEKWQTEQEALQA  241 (337)
T ss_pred             EEECCEEEEcCCCEEEEeccccccCCCCHHHHhhcceEEECCCCCCHHHHHHHHHhhhhcccCchhhhhhhhhhhhcCHH
Confidence                       2233344444333 57889999998 678888865 666666665211                     


Q ss_pred             --------HhCCCCCHHHHHHHHhhc---cC-cHHHHHHHHHHHHHHh----CCCCChhhhhhhcccccCC
Q 022641          229 --------EEGLNLDAEALSTLSSIS---QG-DLRRAITYLQGAARLF----GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       229 --------~~~~~~~~~~l~~l~~~~---~G-~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~~~  283 (294)
                              -..+.++++.++++++.+   +. .+|..+.++..+..++    ...++.+||..++..+-.+
T Consensus       242 ~I~~a~~~~~~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~~vL~H  312 (337)
T TIGR02030       242 KIVNAQNLLPQVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAVLALRH  312 (337)
T ss_pred             HHHHHHHHhccCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Confidence                    023558888888877753   33 4788888777665555    4579999999877654444

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.

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

Probab=99.69  E-value=6.4e-16  Score=127.35  Aligned_cols=189  Identities=23%  Similarity=0.220  Sum_probs=127.6

Q ss_pred             CcchhhcccHHHHHHHHHHHHc--------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           58 KQVKDVAHQEEVVRVLTNTLET--------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~--------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      .+|.++-|.+.+++.+.+.+--              ....+++|+||||||||.+|++++++.      +..++-+..+.
T Consensus        89 v~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAKA~Akea------ga~fInv~~s~  162 (386)
T KOG0737|consen   89 VSFDDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAKAIAKEA------GANFINVSVSN  162 (386)
T ss_pred             eehhhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHHHHHHHc------CCCcceeeccc
Confidence            4678999999999888777532              122359999999999999999999999      88888888877


Q ss_pred             CcchhHHH--HHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH-------HHHHH----HHHHHH----hhcCcc
Q 022641          124 DRGINVVR--TKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE-------DAQNA----LRRTME----TYSKVT  186 (294)
Q Consensus       124 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~-------~~~~~----L~~~l~----~~~~~~  186 (294)
                      ..+.....  .....+...+.          .-.+.+|+|||++.+-.       +....    +...=+    .....+
T Consensus       163 lt~KWfgE~eKlv~AvFslAs----------Kl~P~iIFIDEvds~L~~R~s~dHEa~a~mK~eFM~~WDGl~s~~~~rV  232 (386)
T KOG0737|consen  163 LTSKWFGEAQKLVKAVFSLAS----------KLQPSIIFIDEVDSFLGQRRSTDHEATAMMKNEFMALWDGLSSKDSERV  232 (386)
T ss_pred             cchhhHHHHHHHHHHHHhhhh----------hcCcceeehhhHHHHHhhcccchHHHHHHHHHHHHHHhccccCCCCceE
Confidence            65533211  11111111111          11345999999997631       11111    111111    112235


Q ss_pred             eEEEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcH-HHHHHHHHHHHHH
Q 022641          187 RFFFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDL-RRAITYLQGAARL  263 (294)
Q Consensus       187 ~ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~-r~~~~~l~~~~~~  263 (294)
                      .|+.+||.++.++.++.+|+. .++++-|+..++.+|++-+++.+.+. ++=.+..++..+.|-- +.+.+++..++.+
T Consensus       233 lVlgATNRP~DlDeAiiRR~p~rf~V~lP~~~qR~kILkviLk~e~~e-~~vD~~~iA~~t~GySGSDLkelC~~Aa~~  310 (386)
T KOG0737|consen  233 LVLGATNRPFDLDEAIIRRLPRRFHVGLPDAEQRRKILKVILKKEKLE-DDVDLDEIAQMTEGYSGSDLKELCRLAALR  310 (386)
T ss_pred             EEEeCCCCCccHHHHHHHhCcceeeeCCCchhhHHHHHHHHhcccccC-cccCHHHHHHhcCCCcHHHHHHHHHHHhHh
Confidence            566778999999999999987 89999999999999999999988876 4445777888877743 3344444444433

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=99.69  E-value=2e-15  Score=128.05  Aligned_cols=205  Identities=18%  Similarity=0.178  Sum_probs=135.7

Q ss_pred             cccHHHHHHHHHHHHcC--CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhh
Q 022641           64 AHQEEVVRVLTNTLETA--NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVA  141 (294)
Q Consensus        64 ~g~~~~~~~l~~~l~~~--~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  141 (294)
                      +|....+..+.+.+..-  ...+|+|+|++||||+++|+++....   .....+++.++|..... ..+...+.......
T Consensus         2 iG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~s---~r~~~pfv~vnc~~~~~-~~l~~~lfG~~~g~   77 (329)
T TIGR02974         2 IGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLS---KRWQGPLVKLNCAALSE-NLLDSELFGHEAGA   77 (329)
T ss_pred             CcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHhc---CccCCCeEEEeCCCCCh-HHHHHHHhcccccc
Confidence            45554555444444332  22359999999999999999998654   22356889999886532 22221111100000


Q ss_pred             -cc-cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCC-------cccchH
Q 022641          142 -VG-SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYI-------SRIIEP  201 (294)
Q Consensus       142 -~~-~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~-------~~~~~~  201 (294)
                       .+ .....+....+..+.|+|||++.|+...+..|+.+++...           .++++|++++..       ..+.+.
T Consensus        78 ~~ga~~~~~G~~~~a~gGtL~Ldei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~at~~~l~~~~~~g~fr~d  157 (329)
T TIGR02974        78 FTGAQKRHQGRFERADGGTLFLDELATASLLVQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNADLPALAAEGRFRAD  157 (329)
T ss_pred             ccCcccccCCchhhCCCCEEEeCChHhCCHHHHHHHHHHHHcCcEEecCCCceeccceEEEEechhhHHHHhhcCchHHH
Confidence             00 0112233445667899999999999999999999997643           345788888643       234567


Q ss_pred             hhcccc--EEEecCCC--HHHHHHHHHHHHH----HhC----CCCCHHHHHHHHhh-ccCcHHHHHHHHHHHHHHh-CCC
Q 022641          202 LASRCA--KFRFKPLS--EEVMSSRVLHICN----EEG----LNLDAEALSTLSSI-SQGDLRRAITYLQGAARLF-GSS  267 (294)
Q Consensus       202 l~~r~~--~i~~~~~~--~~~~~~~l~~~~~----~~~----~~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~~-~~~  267 (294)
                      |..|+.  .|.++|+.  .+++..++.+++.    +.+    ..+++++++.|..+ +.||+|++.++++.++... +..
T Consensus       158 L~~rl~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvrEL~n~i~~~~~~~~~~~  237 (329)
T TIGR02974       158 LLDRLAFDVITLPPLRERQEDIMLLAEHFAIRMARELGLPLFPGFTPQAREQLLEYHWPGNVRELKNVVERSVYRHGLEE  237 (329)
T ss_pred             HHHHhcchhcCCCchhhhhhhHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHhCCCCchHHHHHHHHHHHHHhCCCCc
Confidence            788885  68888887  4666666665543    323    35899999999998 5999999999999988765 334


Q ss_pred             CChhh
Q 022641          268 ITSKD  272 (294)
Q Consensus       268 it~~~  272 (294)
                      ++.++
T Consensus       238 ~~~~~  242 (329)
T TIGR02974       238 APIDE  242 (329)
T ss_pred             cchhh
Confidence            55554

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

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

Probab=99.69  E-value=3.7e-16  Score=138.49  Aligned_cols=205  Identities=22%  Similarity=0.201  Sum_probs=148.8

Q ss_pred             CcchhhcccHHHHHHHHHHH---HcC---------CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC--
Q 022641           58 KQVKDVAHQEEVVRVLTNTL---ETA---------NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD--  123 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l---~~~---------~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~--  123 (294)
                      ..|.++.|.+++++.+.+.+   ..+         -+..++++||||||||.||++++-++      +.+++.+++++  
T Consensus       147 v~F~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA------~VPFf~iSGS~FV  220 (596)
T COG0465         147 VTFADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEA------GVPFFSISGSDFV  220 (596)
T ss_pred             cChhhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhccc------CCCceeccchhhh
Confidence            57889999999988776665   322         12349999999999999999999999      78888887765  


Q ss_pred             ----CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhhcC-
Q 022641          124 ----DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTMETYSK-  184 (294)
Q Consensus       124 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~~~~~-  184 (294)
                          ..+...+++.+.......              +++|+|||+|.+..              ...+.|+.-++.+.. 
T Consensus       221 emfVGvGAsRVRdLF~qAkk~a--------------P~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~~  286 (596)
T COG0465         221 EMFVGVGASRVRDLFEQAKKNA--------------PCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGN  286 (596)
T ss_pred             hhhcCCCcHHHHHHHHHhhccC--------------CCeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhccCCCC
Confidence                345566777766655443              24999999998742              256777777777663 


Q ss_pred             -cceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCc-HHHHHHHHHH
Q 022641          185 -VTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGD-LRRAITYLQG  259 (294)
Q Consensus       185 -~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~-~r~~~~~l~~  259 (294)
                       .+.++.+||.+.-+++++++  ||. .|.++.|+...+.++++-+++...+. .+-.+..+++.+.|- --...|++..
T Consensus       287 ~gviviaaTNRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~-~~Vdl~~iAr~tpGfsGAdL~nl~NE  365 (596)
T COG0465         287 EGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLA-EDVDLKKIARGTPGFSGADLANLLNE  365 (596)
T ss_pred             CceEEEecCCCcccchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCC-CcCCHHHHhhhCCCcccchHhhhHHH
Confidence             45566677888888899987  776 78999999999999998666544333 222255588887663 3345566666


Q ss_pred             HHHHh----CCCCChhhhhhhcccccCC
Q 022641          260 AARLF----GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       260 ~~~~~----~~~it~~~v~~~~~~~~~~  283 (294)
                      ++..+    ...|++.++.++.......
T Consensus       366 Aal~aar~n~~~i~~~~i~ea~drv~~G  393 (596)
T COG0465         366 AALLAARRNKKEITMRDIEEAIDRVIAG  393 (596)
T ss_pred             HHHHHHHhcCeeEeccchHHHHHHHhcC
Confidence            66665    5569999998887775444

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

Probab=99.68  E-value=7.3e-16  Score=121.26  Aligned_cols=205  Identities=20%  Similarity=0.260  Sum_probs=134.8

Q ss_pred             cchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC-
Q 022641           59 QVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD-  124 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~-  124 (294)
                      .+.++-|.++.++.|.+++--             ..+..+++|||||||||.+|++.+.+.      ...|..+.++.. 
T Consensus       169 ~YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT------~aTFLKLAgPQLV  242 (424)
T KOG0652|consen  169 QYSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQT------NATFLKLAGPQLV  242 (424)
T ss_pred             cccccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhc------cchHHHhcchHHH
Confidence            567888999999888877632             223359999999999999999999987      455554443321 


Q ss_pred             -----cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHH---Hhhc--
Q 022641          125 -----RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTM---ETYS--  183 (294)
Q Consensus       125 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l---~~~~--  183 (294)
                           .+...+++.+.-...              ..+.+|||||+|.+.           .+++...+.++   +.++  
T Consensus       243 QMfIGdGAkLVRDAFaLAKE--------------kaP~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQLDGFss~  308 (424)
T KOG0652|consen  243 QMFIGDGAKLVRDAFALAKE--------------KAPTIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSD  308 (424)
T ss_pred             hhhhcchHHHHHHHHHHhhc--------------cCCeEEEEechhhhccccccccccccHHHHHHHHHHHHhhcCCCCc
Confidence                 122333333322211              234599999999873           23444444444   4444  


Q ss_pred             CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHHHHH
Q 022641          184 KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITYLQG  259 (294)
Q Consensus       184 ~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~l~~  259 (294)
                      ..+.+|.+||...-++|++++  |.. .|+|+.|+.+.+..+++-...+..+. ++-.++.+++.+++ |-.++--.+-.
T Consensus       309 ~~vKviAATNRvDiLDPALlRSGRLDRKIEfP~Pne~aRarIlQIHsRKMnv~-~DvNfeELaRsTddFNGAQcKAVcVE  387 (424)
T KOG0652|consen  309 DRVKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARILQIHSRKMNVS-DDVNFEELARSTDDFNGAQCKAVCVE  387 (424)
T ss_pred             cceEEEeecccccccCHHHhhcccccccccCCCCChHHHHHHHHHhhhhcCCC-CCCCHHHHhhcccccCchhheeeehh
Confidence            356789999999999999987  554 79999999988888887766554432 33347788877643 33444444444


Q ss_pred             HHHHh----CCCCChhhhhhhcccccCCC
Q 022641          260 AARLF----GSSITSKDLISVSGYPTGGS  284 (294)
Q Consensus       260 ~~~~~----~~~it~~~v~~~~~~~~~~~  284 (294)
                      +...+    ..+++.+++.+.+.++....
T Consensus       388 AGMiALRr~atev~heDfmegI~eVqakK  416 (424)
T KOG0652|consen  388 AGMIALRRGATEVTHEDFMEGILEVQAKK  416 (424)
T ss_pred             hhHHHHhcccccccHHHHHHHHHHHHHhh
Confidence            44444    45689898877766655443

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

Probab=99.68  E-value=5.1e-16  Score=143.64  Aligned_cols=176  Identities=22%  Similarity=0.294  Sum_probs=123.4

Q ss_pred             hhhcccHHHHHHHHHHHHcC-------CC--CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHH
Q 022641           61 KDVAHQEEVVRVLTNTLETA-------NC--PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVR  131 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~-------~~--~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (294)
                      ..++||+.++..+...+...       ..  .+++|+||||||||.+|+.+|+.+      +.+++.++++.........
T Consensus       458 ~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l------~~~~i~id~se~~~~~~~~  531 (758)
T PRK11034        458 MLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL------GIELLRFDMSEYMERHTVS  531 (758)
T ss_pred             ceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHh------CCCcEEeechhhcccccHH
Confidence            35789999999998888631       11  249999999999999999999998      5667777765543322222


Q ss_pred             HHHHHHHhhhcccC-ccCCC-----CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecC
Q 022641          132 TKIKTFAAVAVGSG-QRRGG-----YPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNY  194 (294)
Q Consensus       132 ~~~~~~~~~~~~~~-~~~~~-----~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~  194 (294)
                      ..+.    .+.+.. ...++     .....+++|+|||++.+++..++.|++++++..           .++.+|+|||.
T Consensus       532 ~LiG----~~~gyvg~~~~g~L~~~v~~~p~sVlllDEieka~~~v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~  607 (758)
T PRK11034        532 RLIG----APPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNA  607 (758)
T ss_pred             HHcC----CCCCcccccccchHHHHHHhCCCcEEEeccHhhhhHHHHHHHHHHHhcCeeecCCCceecCCCcEEEEeCCc
Confidence            1111    110000 00000     012345799999999999999999999998542           34558888873


Q ss_pred             C-------------------------cccchHhhcccc-EEEecCCCHHHHHHHHHHHHH-------HhCC--CCCHHHH
Q 022641          195 I-------------------------SRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICN-------EEGL--NLDAEAL  239 (294)
Q Consensus       195 ~-------------------------~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~-------~~~~--~~~~~~l  239 (294)
                      .                         ..+.|+|++|+. ++.|+|++.+++..++...+.       ..++  .++++++
T Consensus       608 g~~~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~Rid~ii~f~~L~~~~l~~I~~~~l~~~~~~l~~~~i~l~~~~~~~  687 (758)
T PRK11034        608 GVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQAQLDQKGVSLEVSQEAR  687 (758)
T ss_pred             CHHHHhhcccCcccchhhHHHHHHHHHhcCHHHHccCCEEEEcCCCCHHHHHHHHHHHHHHHHHHHHHCCCCceECHHHH
Confidence            2                         124588999997 899999999999999887654       2344  4799999


Q ss_pred             HHHHhhc
Q 022641          240 STLSSIS  246 (294)
Q Consensus       240 ~~l~~~~  246 (294)
                      +.|++..
T Consensus       688 ~~l~~~~  694 (758)
T PRK11034        688 DWLAEKG  694 (758)
T ss_pred             HHHHHhC
Confidence            9999763

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

Probab=99.67  E-value=7.7e-15  Score=116.03  Aligned_cols=190  Identities=20%  Similarity=0.254  Sum_probs=134.3

Q ss_pred             hhcCCCcchhhcccHHHHHHHHHH----HHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchh
Q 022641           53 EKYRPKQVKDVAHQEEVVRVLTNT----LETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGIN  128 (294)
Q Consensus        53 ~~~~~~~~~~~~g~~~~~~~l~~~----l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~  128 (294)
                      +...+..+++++|.+..++.|.+-    +......|++|+|++|||||++++++..++...   +..++++...+.....
T Consensus        19 ~~~~~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~---GLRlIev~k~~L~~l~   95 (249)
T PF05673_consen   19 KHPDPIRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQ---GLRLIEVSKEDLGDLP   95 (249)
T ss_pred             CCCCCCCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhc---CceEEEECHHHhccHH
Confidence            556678899999988888766543    444445679999999999999999999987433   3667777666655555


Q ss_pred             HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-HHHHHHHHHHHH----hhcCcceEEEEecCCcccc----
Q 022641          129 VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-EDAQNALRRTME----TYSKVTRFFFICNYISRII----  199 (294)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-~~~~~~L~~~l~----~~~~~~~ii~~~~~~~~~~----  199 (294)
                      .+...+..   .             ..+-||++||+..=. ...-..|..+|+    ..+.++.+..|+|..+.+.    
T Consensus        96 ~l~~~l~~---~-------------~~kFIlf~DDLsFe~~d~~yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E~~~  159 (249)
T PF05673_consen   96 ELLDLLRD---R-------------PYKFILFCDDLSFEEGDTEYKALKSVLEGGLEARPDNVLIYATSNRRHLVPESFS  159 (249)
T ss_pred             HHHHHHhc---C-------------CCCEEEEecCCCCCCCcHHHHHHHHHhcCccccCCCcEEEEEecchhhccchhhh
Confidence            44444332   1             113499999976432 233455666665    5667888888887544322    


Q ss_pred             -------------------hHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHH-----HHHHHhhccCcHHHHH
Q 022641          200 -------------------EPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEA-----LSTLSSISQGDLRRAI  254 (294)
Q Consensus       200 -------------------~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-----l~~l~~~~~G~~r~~~  254 (294)
                                         -+|..||. .+.|.|++.++..++++.++...|+.++++.     ++......+.+.|.|.
T Consensus       160 d~~~~~~~eih~~d~~eEklSLsDRFGL~l~F~~~~q~~YL~IV~~~~~~~g~~~~~e~l~~~Al~wa~~rg~RSGRtA~  239 (249)
T PF05673_consen  160 DREDIQDDEIHPSDTIEEKLSLSDRFGLWLSFYPPDQEEYLAIVRHYAERYGLELDEEELRQEALQWALRRGGRSGRTAR  239 (249)
T ss_pred             hccCCCccccCcchHHHHHHhHHHhCCcEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHcCCCCHHHHH
Confidence                               13456787 8999999999999999999999999999644     4444445556788888


Q ss_pred             HHHHHHH
Q 022641          255 TYLQGAA  261 (294)
Q Consensus       255 ~~l~~~~  261 (294)
                      +.+...+
T Consensus       240 QF~~~l~  246 (249)
T PF05673_consen  240 QFIDDLA  246 (249)
T ss_pred             HHHHHHh
Confidence            7776554

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

Probab=99.67  E-value=8.3e-15  Score=126.71  Aligned_cols=213  Identities=23%  Similarity=0.240  Sum_probs=151.1

Q ss_pred             CcchhhcccHHHHHHHHHHHHcCCC--CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHH-HH
Q 022641           58 KQVKDVAHQEEVVRVLTNTLETANC--PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRT-KI  134 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~~~~--~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~  134 (294)
                      ....+++|+...+..+.+.+..-..  -+++|+|++||||-.+|++|.+.-   ...+.+|+.+||..... ..+.. ++
T Consensus       138 ~~~~~liG~S~am~~l~~~i~kvA~s~a~VLI~GESGtGKElvAr~IH~~S---~R~~~PFVavNcaAip~-~l~ESELF  213 (464)
T COG2204         138 SLGGELVGESPAMQQLRRLIAKVAPSDASVLITGESGTGKELVARAIHQAS---PRAKGPFIAVNCAAIPE-NLLESELF  213 (464)
T ss_pred             cccCCceecCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHhhC---cccCCCceeeecccCCH-HHHHHHhh
Confidence            3567899999999988888865433  359999999999999999998753   44467999999988643 22222 22


Q ss_pred             HHHHhhhcccCc-cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc------
Q 022641          135 KTFAAVAVGSGQ-RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS------  196 (294)
Q Consensus       135 ~~~~~~~~~~~~-~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~------  196 (294)
                      ..-.....+... +.+....+..+.||||||..++...|..|+.++++..           .+++||.+||..-      
T Consensus       214 GhekGAFTGA~~~r~G~fE~A~GGTLfLDEI~~mpl~~Q~kLLRvLqe~~~~rvG~~~~i~vdvRiIaaT~~dL~~~v~~  293 (464)
T COG2204         214 GHEKGAFTGAITRRIGRFEQANGGTLFLDEIGEMPLELQVKLLRVLQEREFERVGGNKPIKVDVRIIAATNRDLEEEVAA  293 (464)
T ss_pred             cccccCcCCcccccCcceeEcCCceEEeeccccCCHHHHHHHHHHHHcCeeEecCCCcccceeeEEEeecCcCHHHHHHc
Confidence            222211122222 3445556788999999999999999999999998533           3566888887542      


Q ss_pred             -ccchHhhccccE--EEecCCCH--HHHH----HHHHHHHHHhCC---CCCHHHHHHHHhh-ccCcHHHHHHHHHHHHHH
Q 022641          197 -RIIEPLASRCAK--FRFKPLSE--EVMS----SRVLHICNEEGL---NLDAEALSTLSSI-SQGDLRRAITYLQGAARL  263 (294)
Q Consensus       197 -~~~~~l~~r~~~--i~~~~~~~--~~~~----~~l~~~~~~~~~---~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~  263 (294)
                       .....|..|+.+  |.++|+.+  +++-    .++++.++..+.   .+++++++.|..+ +.||+|++.|.++.++..
T Consensus       294 G~FReDLyyRLnV~~i~iPpLRER~EDIp~L~~hfl~~~~~~~~~~~~~~s~~a~~~L~~y~WPGNVREL~N~ver~~il  373 (464)
T COG2204         294 GRFREDLYYRLNVVPLRLPPLRERKEDIPLLAEHFLKRFAAELGRPPKGFSPEALAALLAYDWPGNVRELENVVERAVIL  373 (464)
T ss_pred             CCcHHHHHhhhccceecCCcccccchhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCChHHHHHHHHHHHHHhc
Confidence             245667778875  55555542  3444    444445555543   5899999999988 799999999999988877


Q ss_pred             h-CCCCChhhhh
Q 022641          264 F-GSSITSKDLI  274 (294)
Q Consensus       264 ~-~~~it~~~v~  274 (294)
                      . +..|+.+++.
T Consensus       374 ~~~~~i~~~~l~  385 (464)
T COG2204         374 SEGPEIEVEDLP  385 (464)
T ss_pred             CCccccchhhcc
Confidence            6 4557777765

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

Probab=99.67  E-value=3.1e-15  Score=127.12  Aligned_cols=213  Identities=18%  Similarity=0.203  Sum_probs=145.2

Q ss_pred             cCCCcchhhcccHHHHHHHHHHHHcCC--CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHH
Q 022641           55 YRPKQVKDVAHQEEVVRVLTNTLETAN--CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRT  132 (294)
Q Consensus        55 ~~~~~~~~~~g~~~~~~~l~~~l~~~~--~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (294)
                      .....+.+++|.......+++-+....  ..+++++|++||||+.+|+.|...-  +.....+++.+||..........+
T Consensus        72 ~~~~~~~~LIG~~~~~~~~~eqik~~ap~~~~vLi~GetGtGKel~A~~iH~~s--~r~~~~PFI~~NCa~~~en~~~~e  149 (403)
T COG1221          72 LKSEALDDLIGESPSLQELREQIKAYAPSGLPVLIIGETGTGKELFARLIHALS--ARRAEAPFIAFNCAAYSENLQEAE  149 (403)
T ss_pred             ccchhhhhhhccCHHHHHHHHHHHhhCCCCCcEEEecCCCccHHHHHHHHHHhh--hcccCCCEEEEEHHHhCcCHHHHH
Confidence            334567899998777777777665532  2359999999999999999998332  222578999999987655433333


Q ss_pred             HHHHHHhhhcc-cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh-----------hcCcceEEEEecCC--ccc
Q 022641          133 KIKTFAAVAVG-SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMET-----------YSKVTRFFFICNYI--SRI  198 (294)
Q Consensus       133 ~~~~~~~~~~~-~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~-----------~~~~~~ii~~~~~~--~~~  198 (294)
                      .+........+ ...+.+....+..+.|++||++.+++..+..|+.++++           .+..+++|++|+..  ..+
T Consensus       150 LFG~~kGaftGa~~~k~Glfe~A~GGtLfLDEI~~LP~~~Q~kLl~~le~g~~~rvG~~~~~~~dVRli~AT~~~l~~~~  229 (403)
T COG1221         150 LFGHEKGAFTGAQGGKAGLFEQANGGTLFLDEIHRLPPEGQEKLLRVLEEGEYRRVGGSQPRPVDVRLICATTEDLEEAV  229 (403)
T ss_pred             HhccccceeecccCCcCchheecCCCEEehhhhhhCCHhHHHHHHHHHHcCceEecCCCCCcCCCceeeeccccCHHHHH
Confidence            22222222222 22244445567788999999999999999999999986           34567788887643  334


Q ss_pred             ch--Hhhcccc--EEEecCCCH--HHHHHHHHH----HHHHhCCC---CCHHHHHHHHhh-ccCcHHHHHHHHHHHHHHh
Q 022641          199 IE--PLASRCA--KFRFKPLSE--EVMSSRVLH----ICNEEGLN---LDAEALSTLSSI-SQGDLRRAITYLQGAARLF  264 (294)
Q Consensus       199 ~~--~l~~r~~--~i~~~~~~~--~~~~~~l~~----~~~~~~~~---~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~~  264 (294)
                      ..  .+.+|+.  .|+++|+..  .++..++.+    .+.+.+.+   .+++++..+..+ +.||+|++.|++++++...
T Consensus       230 ~~g~dl~~rl~~~~I~LPpLrER~~Di~~L~e~Fl~~~~~~l~~~~~~~~~~a~~~L~~y~~pGNirELkN~Ve~~~~~~  309 (403)
T COG1221         230 LAGADLTRRLNILTITLPPLRERKEDILLLAEHFLKSEARRLGLPLSVDSPEALRALLAYDWPGNIRELKNLVERAVAQA  309 (403)
T ss_pred             HhhcchhhhhcCceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCCCcHHHHHHHHHHHHHHh
Confidence            44  5666544  788888764  444444444    44444544   345778887777 6999999999999999877


Q ss_pred             -CCCCC
Q 022641          265 -GSSIT  269 (294)
Q Consensus       265 -~~~it  269 (294)
                       ...++
T Consensus       310 ~~~~~~  315 (403)
T COG1221         310 SGEGQD  315 (403)
T ss_pred             ccccCC
Confidence             33344

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

Probab=99.66  E-value=9.7e-16  Score=113.40  Aligned_cols=109  Identities=28%  Similarity=0.341  Sum_probs=81.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc------chhHHHHHHHHHHhhhcccCccCCCCCCCCcEE
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR------GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKI  158 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  158 (294)
                      ++|+||||||||++++.+++.+      +.+++.+++....      ....+...+.......             ++.+
T Consensus         1 ill~G~~G~GKT~l~~~la~~l------~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~-------------~~~v   61 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL------GFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKSA-------------KPCV   61 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT------TSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHTS-------------TSEE
T ss_pred             CEEECcCCCCeeHHHHHHHhhc------ccccccccccccccccccccccccccccccccccc-------------ccee
Confidence            6899999999999999999998      7778888876543      1223333333322211             2469


Q ss_pred             EEEeCCCCCCHHH-----------HHHHHHHHHhhcC---cceEEEEecCCcccchHhh-cccc-EEEec
Q 022641          159 IILDEADSMTEDA-----------QNALRRTMETYSK---VTRFFFICNYISRIIEPLA-SRCA-KFRFK  212 (294)
Q Consensus       159 liiDei~~l~~~~-----------~~~L~~~l~~~~~---~~~ii~~~~~~~~~~~~l~-~r~~-~i~~~  212 (294)
                      |+|||+|.+....           .+.|+..++....   ...+|++||....+++++. +||. .+.++
T Consensus        62 l~iDe~d~l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~~i~~~l~~~rf~~~i~~~  131 (132)
T PF00004_consen   62 LFIDEIDKLFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPDKIDPALLRSRFDRRIEFP  131 (132)
T ss_dssp             EEEETGGGTSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGGGSCHHHHSTTSEEEEEE-
T ss_pred             eeeccchhcccccccccccccccccceeeecccccccccccceeEEeeCChhhCCHhHHhCCCcEEEEcC
Confidence            9999999997664           6788888887665   4789999999999999999 9998 56653

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 ....

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

Probab=99.66  E-value=1.3e-15  Score=129.85  Aligned_cols=180  Identities=22%  Similarity=0.220  Sum_probs=130.1

Q ss_pred             hhcCCCcchhhcccHHHHHHHHHHHHcC------------CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           53 EKYRPKQVKDVAHQEEVVRVLTNTLETA------------NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        53 ~~~~~~~~~~~~g~~~~~~~l~~~l~~~------------~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      ....+..|+++.|.+.++..+...+--+            ....+++.||||+|||.|++++|.+.      ...++.+.
T Consensus       145 ~~~~~v~~~di~gl~~~k~~l~e~vi~p~lr~d~F~glr~p~rglLLfGPpgtGKtmL~~aiAsE~------~atff~iS  218 (428)
T KOG0740|consen  145 DTLRNVGWDDIAGLEDAKQSLKEAVILPLLRPDLFLGLREPVRGLLLFGPPGTGKTMLAKAIATES------GATFFNIS  218 (428)
T ss_pred             ccCCcccccCCcchhhHHHHhhhhhhhcccchHhhhccccccchhheecCCCCchHHHHHHHHhhh------cceEeecc
Confidence            3455667889999888887776654321            11249999999999999999999998      78888888


Q ss_pred             CCCCcchhHH--HHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH-----------H-HHHHHHHHHH---hhc
Q 022641          121 ASDDRGINVV--RTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE-----------D-AQNALRRTME---TYS  183 (294)
Q Consensus       121 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~-----------~-~~~~L~~~l~---~~~  183 (294)
                      +++..+...-  ...+..+....          ...++.++||||+|.+-.           . ..+.|++..-   ...
T Consensus       219 assLtsK~~Ge~eK~vralf~vA----------r~~qPsvifidEidslls~Rs~~e~e~srr~ktefLiq~~~~~s~~~  288 (428)
T KOG0740|consen  219 ASSLTSKYVGESEKLVRALFKVA----------RSLQPSVIFIDEIDSLLSKRSDNEHESSRRLKTEFLLQFDGKNSAPD  288 (428)
T ss_pred             HHHhhhhccChHHHHHHHHHHHH----------HhcCCeEEEechhHHHHhhcCCcccccchhhhhHHHhhhccccCCCC
Confidence            7765543321  12222221111          122346999999998721           1 2334444442   223


Q ss_pred             CcceEEEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC
Q 022641          184 KVTRFFFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG  248 (294)
Q Consensus       184 ~~~~ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G  248 (294)
                      ..+.+|.+||.++.+++++++||+ ++.++.|+.+.+..++.+.+...+-.+.+..+..|++.+.|
T Consensus       289 drvlvigaTN~P~e~Dea~~Rrf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~~~Teg  354 (428)
T KOG0740|consen  289 DRVLVIGATNRPWELDEAARRRFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLAKVTEG  354 (428)
T ss_pred             CeEEEEecCCCchHHHHHHHHHhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcC
Confidence            467788889999999999999998 78899999999999999999988777889999999988654

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=99.66  E-value=1.2e-14  Score=123.43  Aligned_cols=211  Identities=18%  Similarity=0.174  Sum_probs=140.2

Q ss_pred             cchhhcccHHHHHHHHHHHHcC--CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHH
Q 022641           59 QVKDVAHQEEVVRVLTNTLETA--NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKT  136 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~--~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  136 (294)
                      .+++++|....+..+.+.+..-  ...+|+|+|++||||+++|+++...-   .....+++.++|..... ..+...+..
T Consensus         4 ~~~~liG~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~s---~r~~~pfv~v~c~~~~~-~~~~~~lfg   79 (326)
T PRK11608          4 YKDNLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLS---SRWQGPFISLNCAALNE-NLLDSELFG   79 (326)
T ss_pred             ccCccEECCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhC---CccCCCeEEEeCCCCCH-HHHHHHHcc
Confidence            3456888877777666665442  23459999999999999999997543   22356888899887532 222221111


Q ss_pred             HHhh-hcc-cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCC-------c
Q 022641          137 FAAV-AVG-SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYI-------S  196 (294)
Q Consensus       137 ~~~~-~~~-~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~-------~  196 (294)
                      .... ..+ .....+....+..+.|+|||++.|+...+..|+.+++...           ..+++|++++..       .
T Consensus        80 ~~~~~~~g~~~~~~g~l~~a~gGtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~s~~~l~~l~~~g  159 (326)
T PRK11608         80 HEAGAFTGAQKRHPGRFERADGGTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEG  159 (326)
T ss_pred             ccccccCCcccccCCchhccCCCeEEeCChhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCchhHHHHHHcC
Confidence            0000 000 0011223344567899999999999999999999997533           236777777643       2


Q ss_pred             ccchHhhcccc--EEEecCCCH--HHHHHHHHHHH----HHhC----CCCCHHHHHHHHhh-ccCcHHHHHHHHHHHHHH
Q 022641          197 RIIEPLASRCA--KFRFKPLSE--EVMSSRVLHIC----NEEG----LNLDAEALSTLSSI-SQGDLRRAITYLQGAARL  263 (294)
Q Consensus       197 ~~~~~l~~r~~--~i~~~~~~~--~~~~~~l~~~~----~~~~----~~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~  263 (294)
                      .+.+.+..|+.  .|.++|+..  +++..++.+++    ...+    ..+++++++.|..+ +.||+|++.++++.++..
T Consensus       160 ~f~~dL~~~l~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~~s~~al~~L~~y~WPGNvrEL~~vl~~a~~~  239 (326)
T PRK11608        160 KFRADLLDRLAFDVVQLPPLRERQSDIMLMAEHFAIQMCRELGLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYR  239 (326)
T ss_pred             CchHHHHHhcCCCEEECCChhhhhhhHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHHh
Confidence            34567788875  688888864  45666665544    3333    35899999999988 799999999999998875


Q ss_pred             h-CCCCChhhh
Q 022641          264 F-GSSITSKDL  273 (294)
Q Consensus       264 ~-~~~it~~~v  273 (294)
                      . +..++.+++
T Consensus       240 ~~~~~~~~~~l  250 (326)
T PRK11608        240 HGTSEYPLDNI  250 (326)
T ss_pred             cCCCCCchhhc
Confidence            5 334544443

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

Probab=99.66  E-value=2.4e-15  Score=136.71  Aligned_cols=193  Identities=28%  Similarity=0.363  Sum_probs=137.3

Q ss_pred             hhhcccHHHHHHHHHHHHcC-------CCC--cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHH
Q 022641           61 KDVAHQEEVVRVLTNTLETA-------NCP--HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVR  131 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~-------~~~--~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (294)
                      ..++||++++..+.+.+...       +.|  .++|.||+|||||-||++||..+++.+   ..++.++++.-.....+.
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e---~aliR~DMSEy~EkHsVS  567 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDE---QALIRIDMSEYMEKHSVS  567 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCC---ccceeechHHHHHHHHHH
Confidence            46789999999998888642       222  399999999999999999999996542   566677776654444333


Q ss_pred             HHHHHHHhhhcccCc------cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecC
Q 022641          132 TKIKTFAAVAVGSGQ------RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNY  194 (294)
Q Consensus       132 ~~~~~~~~~~~~~~~------~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~  194 (294)
                          .+...+.+.-.      -........+.||++||+++.+++..+.|++++++..           .++.+|+|||.
T Consensus       568 ----rLIGaPPGYVGyeeGG~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVlDdGrLTD~~Gr~VdFrNtiIImTSN~  643 (786)
T COG0542         568 ----RLIGAPPGYVGYEEGGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNA  643 (786)
T ss_pred             ----HHhCCCCCCceeccccchhHhhhcCCCeEEEechhhhcCHHHHHHHHHHhcCCeeecCCCCEEecceeEEEEeccc
Confidence                33333332211      1112234567899999999999999999999998543           35668888863


Q ss_pred             Ccc----------------------------cchHhhcccc-EEEecCCCHHHHHHHHHHHHHH-------hCC--CCCH
Q 022641          195 ISR----------------------------IIEPLASRCA-KFRFKPLSEEVMSSRVLHICNE-------EGL--NLDA  236 (294)
Q Consensus       195 ~~~----------------------------~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~-------~~~--~~~~  236 (294)
                      ...                            ..|+|++|+. +|.|.|++.+.+..++...+..       .++  .+++
T Consensus       644 Gs~~i~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFLNRid~II~F~~L~~~~l~~Iv~~~L~~l~~~L~~~~i~l~~s~  723 (786)
T COG0542         644 GSEEILRDADGDDFADKEALKEAVMEELKKHFRPEFLNRIDEIIPFNPLSKEVLERIVDLQLNRLAKRLAERGITLELSD  723 (786)
T ss_pred             chHHHHhhccccccchhhhHHHHHHHHHHhhCCHHHHhhcccEEeccCCCHHHHHHHHHHHHHHHHHHHHhCCceEEECH
Confidence            211                            3578889998 9999999999999988876642       343  4799


Q ss_pred             HHHHHHHhhcc---CcHHHHHHHHHHH
Q 022641          237 EALSTLSSISQ---GDLRRAITYLQGA  260 (294)
Q Consensus       237 ~~l~~l~~~~~---G~~r~~~~~l~~~  260 (294)
                      ++...|++.+.   ..-|-+.+.++..
T Consensus       724 ~a~~~l~~~gyd~~~GARpL~R~Iq~~  750 (786)
T COG0542         724 EAKDFLAEKGYDPEYGARPLRRAIQQE  750 (786)
T ss_pred             HHHHHHHHhccCCCcCchHHHHHHHHH
Confidence            99999998753   2245555555543

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=99.65  E-value=1.4e-14  Score=129.37  Aligned_cols=217  Identities=18%  Similarity=0.169  Sum_probs=147.3

Q ss_pred             CCcchhhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHH
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKI  134 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  134 (294)
                      ...|++++|....+..+.+.+..  ....+++|+|++||||+++|+.+.+.-   .....+++.++|..... ..+...+
T Consensus       208 ~~~f~~iiG~S~~m~~~~~~i~~~A~~~~pVLI~GE~GTGKe~lA~~IH~~S---~r~~~pfv~inC~~l~e-~lleseL  283 (526)
T TIGR02329       208 RYRLDDLLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLS---GRRDFPFVAINCGAIAE-SLLEAEL  283 (526)
T ss_pred             ccchhheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCcCHHHHHHHHHHhc---CcCCCCEEEeccccCCh-hHHHHHh
Confidence            35678899998888877777643  333469999999999999999998653   23367899999887542 2222211


Q ss_pred             HHHHhhhccc---CccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc----
Q 022641          135 KTFAAVAVGS---GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS----  196 (294)
Q Consensus       135 ~~~~~~~~~~---~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~----  196 (294)
                      ..........   ....+....+..+.|||||++.|+...+..|+..+++..           .++++|++++...    
T Consensus       284 FG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~~~Q~~Ll~~L~~~~~~r~g~~~~~~~dvRiIaat~~~l~~~v  363 (526)
T TIGR02329       284 FGYEEGAFTGARRGGRTGLIEAAHRGTLFLDEIGEMPLPLQTRLLRVLEEREVVRVGGTEPVPVDVRVVAATHCALTTAV  363 (526)
T ss_pred             cCCcccccccccccccccchhhcCCceEEecChHhCCHHHHHHHHHHHhcCcEEecCCCceeeecceEEeccCCCHHHHh
Confidence            1111000000   012222334567899999999999999999999997633           2346888876542    


Q ss_pred             ---ccchHhhcccc--EEEecCCCH--HHHHHHHHHHHH----HhCCCCCHHHHHH-------HHhh-ccCcHHHHHHHH
Q 022641          197 ---RIIEPLASRCA--KFRFKPLSE--EVMSSRVLHICN----EEGLNLDAEALST-------LSSI-SQGDLRRAITYL  257 (294)
Q Consensus       197 ---~~~~~l~~r~~--~i~~~~~~~--~~~~~~l~~~~~----~~~~~~~~~~l~~-------l~~~-~~G~~r~~~~~l  257 (294)
                         .+...+..|+.  .|.++|+..  +++..++.+++.    ..++.+++++++.       |..+ ++||+|++.+++
T Consensus       364 ~~g~fr~dL~~rL~~~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~~~~~~a~~~~~~~~~~L~~y~WPGNvrEL~nvi  443 (526)
T TIGR02329       364 QQGRFRRDLFYRLSILRIALPPLRERPGDILPLAAEYLVQAAAALRLPDSEAAAQVLAGVADPLQRYPWPGNVRELRNLV  443 (526)
T ss_pred             hhcchhHHHHHhcCCcEEeCCCchhchhHHHHHHHHHHHHHHHHcCCCCCHHHHHHhHHHHHHHHhCCCCchHHHHHHHH
Confidence               23345666665  678888864  566665555554    3456789999887       7766 799999999999


Q ss_pred             HHHHHHh----CCCCChhhhhhhc
Q 022641          258 QGAARLF----GSSITSKDLISVS  277 (294)
Q Consensus       258 ~~~~~~~----~~~it~~~v~~~~  277 (294)
                      +.++...    +..|+.+++....
T Consensus       444 er~~i~~~~~~~~~I~~~~l~~~~  467 (526)
T TIGR02329       444 ERLALELSAMPAGALTPDVLRALA  467 (526)
T ss_pred             HHHHHhcccCCCCccCHHHhhhhc
Confidence            9988753    3568888875443

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

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

Probab=99.65  E-value=3.8e-15  Score=129.12  Aligned_cols=173  Identities=21%  Similarity=0.236  Sum_probs=112.5

Q ss_pred             hhhcccHHHHHHHHHHHHcC----------------CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC
Q 022641           61 KDVAHQEEVVRVLTNTLETA----------------NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD  124 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~----------------~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~  124 (294)
                      +.++|++.+++.+...+.+.                ...+++|+||||||||++|+++++.+      +.+++.++++..
T Consensus        71 ~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l------~~pf~~id~~~l  144 (412)
T PRK05342         71 QYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARIL------DVPFAIADATTL  144 (412)
T ss_pred             hHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHh------CCCceecchhhc
Confidence            35789999999886665321                13569999999999999999999988      667776666542


Q ss_pred             cch----hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhhc---
Q 022641          125 RGI----NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTMETYS---  183 (294)
Q Consensus       125 ~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~~~~---  183 (294)
                      ...    ......+.........      ......+++|+|||+|.++.              ..++.|+++|+...   
T Consensus       145 ~~~gyvG~d~e~~l~~l~~~~~~------~~~~a~~gIi~iDEIdkl~~~~~~~~~~~d~s~~~vQ~~LL~~Leg~~~~v  218 (412)
T PRK05342        145 TEAGYVGEDVENILLKLLQAADY------DVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASV  218 (412)
T ss_pred             ccCCcccchHHHHHHHHHHhccc------cHHHcCCcEEEEechhhhccccCCCCcCCCcccHHHHHHHHHHHhcCeEEe
Confidence            211    1122222222111100      01113456999999999964              37899999997421   


Q ss_pred             ----------CcceEEEEecCCc----------------------------------------------------ccchH
Q 022641          184 ----------KVTRFFFICNYIS----------------------------------------------------RIIEP  201 (294)
Q Consensus       184 ----------~~~~ii~~~~~~~----------------------------------------------------~~~~~  201 (294)
                                ....+|.|+|-.+                                                    .+.|+
T Consensus       219 ~~~gg~~~~~~~~~~i~t~nilfi~~Gaf~g~~~~~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~dL~~~gf~PE  298 (412)
T PRK05342        219 PPQGGRKHPQQEFIQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLIKFGLIPE  298 (412)
T ss_pred             CCCCCcCcCCCCeEEeccCCceeeecccccCcHHHHHHHHhhcccCCccccccccccchhHHHHHhcCHHHHHHHhhhHH
Confidence                      1122333332200                                                    13578


Q ss_pred             hhcccc-EEEecCCCHHHHHHHHHH----H-------HHHhCC--CCCHHHHHHHHhh
Q 022641          202 LASRCA-KFRFKPLSEEVMSSRVLH----I-------CNEEGL--NLDAEALSTLSSI  245 (294)
Q Consensus       202 l~~r~~-~i~~~~~~~~~~~~~l~~----~-------~~~~~~--~~~~~~l~~l~~~  245 (294)
                      |+.|+. ++.|.|++.+++..++..    .       +...++  .++++++..|++.
T Consensus       299 flgRld~iv~f~~L~~~~L~~Il~~~~~~l~~q~~~~l~~~~i~L~~t~~al~~Ia~~  356 (412)
T PRK05342        299 FIGRLPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKK  356 (412)
T ss_pred             HhCCCCeeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHh
Confidence            888987 789999999999999872    2       233444  4899999999986

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.65  E-value=6.2e-15  Score=127.93  Aligned_cols=214  Identities=15%  Similarity=0.108  Sum_probs=128.9

Q ss_pred             chhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHH--HHHH
Q 022641           60 VKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTK--IKTF  137 (294)
Q Consensus        60 ~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~  137 (294)
                      -..++|++++++.+..++..+.  +++|.||||||||++|++++.......    ++....+...... .+...  +...
T Consensus        19 ~~~i~gre~vI~lll~aalag~--hVLL~GpPGTGKT~LAraLa~~~~~~~----~F~~~~~~fttp~-DLfG~l~i~~~   91 (498)
T PRK13531         19 EKGLYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAFQNAR----AFEYLMTRFSTPE-EVFGPLSIQAL   91 (498)
T ss_pred             hhhccCcHHHHHHHHHHHccCC--CEEEECCCChhHHHHHHHHHHHhcccC----cceeeeeeecCcH-HhcCcHHHhhh
Confidence            3578899999999998888776  799999999999999999999873221    1222211110011 11000  0100


Q ss_pred             HhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc---------CcceE-EEEecCCc---ccchHhhc
Q 022641          138 AAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS---------KVTRF-FFICNYIS---RIIEPLAS  204 (294)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~---------~~~~i-i~~~~~~~---~~~~~l~~  204 (294)
                      .....-.....+  ......+|++||++.+++..++.|+..|++..         -+.++ ++++|...   ....++..
T Consensus        92 ~~~g~f~r~~~G--~L~~A~lLfLDEI~rasp~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN~LPE~g~~leAL~D  169 (498)
T PRK13531         92 KDEGRYQRLTSG--YLPEAEIVFLDEIWKAGPAILNTLLTAINERRFRNGAHEEKIPMRLLVTASNELPEADSSLEALYD  169 (498)
T ss_pred             hhcCchhhhcCC--ccccccEEeecccccCCHHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECCCCcccCCchHHhHh
Confidence            000000000011  11123499999999999999999999997544         12234 44455322   13358999


Q ss_pred             ccc-EEEecCCC-HHHHHHHHHHHHH-----------------------HhCCCCCHHHHHHHHhhc------c----Cc
Q 022641          205 RCA-KFRFKPLS-EEVMSSRVLHICN-----------------------EEGLNLDAEALSTLSSIS------Q----GD  249 (294)
Q Consensus       205 r~~-~i~~~~~~-~~~~~~~l~~~~~-----------------------~~~~~~~~~~l~~l~~~~------~----G~  249 (294)
                      ||. .+.+++++ .++...++.....                       -..+.+++.+++++.+..      .    -+
T Consensus       170 RFliri~vp~l~~~~~e~~lL~~~~~~~~~~~~~~~vis~eel~~lq~~v~~V~v~d~v~eyI~~L~~~lr~~r~~~~~S  249 (498)
T PRK13531        170 RMLIRLWLDKVQDKANFRSMLTSQQDENDNPVPASLQITDEEYQQWQKEIGKITLPDHVFELIFQLRQQLDALPNAPYVS  249 (498)
T ss_pred             hEEEEEECCCCCchHHHHHHHHcccccccCCCcccCCCCHHHHHHHHHHhcceeCCHHHHHHHHHHHHHHhcCCCCCCcC
Confidence            997 68888997 4555667654211                       023456777777776552      1    36


Q ss_pred             HHHHHHHHHHHHHHh----CCCCChhhhhhhcccccCC
Q 022641          250 LRRAITYLQGAARLF----GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       250 ~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~~~  283 (294)
                      +|..+.++..+...+    +..++.+|+. ++..+--+
T Consensus       250 pR~~~~l~~~akA~A~l~GR~~V~p~Dv~-ll~~vL~H  286 (498)
T PRK13531        250 DRRWKKAIRLLQASAFFSGRDAIAPIDLI-LLKDCLWH  286 (498)
T ss_pred             cHHHHHHHHHHHHHHHHCCCCCCCHHHHH-HhHHHhcc
Confidence            787777666544444    5569999998 65554433

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

Probab=99.65  E-value=8.9e-15  Score=129.37  Aligned_cols=184  Identities=22%  Similarity=0.197  Sum_probs=133.2

Q ss_pred             cchhhcccHHHHHHHHHHHHcCC-------------CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC-
Q 022641           59 QVKDVAHQEEVVRVLTNTLETAN-------------CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD-  124 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~~-------------~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~-  124 (294)
                      .|+++-|..+++..|.+.+..+.             ..+++|+||||||||.||.+++...      ...++.+.++.. 
T Consensus       665 ~w~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~------~~~fisvKGPElL  738 (952)
T KOG0735|consen  665 RWEDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNS------NLRFISVKGPELL  738 (952)
T ss_pred             CceecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhC------CeeEEEecCHHHH
Confidence            57788888888888887775421             1249999999999999999999987      777887776543 


Q ss_pred             -----cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHhhc--Ccc
Q 022641          125 -----RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMETYS--KVT  186 (294)
Q Consensus       125 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~~~--~~~  186 (294)
                           .+...++..+.....              +++.+||+||+|.+.           .++.+.|+..|+...  ..+
T Consensus       739 ~KyIGaSEq~vR~lF~rA~~--------------a~PCiLFFDEfdSiAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV  804 (952)
T KOG0735|consen  739 SKYIGASEQNVRDLFERAQS--------------AKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGV  804 (952)
T ss_pred             HHHhcccHHHHHHHHHHhhc--------------cCCeEEEeccccccCcccCCCCCCchHHHHHHHHHhhccccccceE
Confidence                 233445555554333              345799999999884           347888988887533  345


Q ss_pred             eEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC----cHHHHHHHHHH
Q 022641          187 RFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG----DLRRAITYLQG  259 (294)
Q Consensus       187 ~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G----~~r~~~~~l~~  259 (294)
                      .++.+|..+..+++++++  |+. .+..++|+..++.++++......-. -++-.++.++..+.|    |+..++...+.
T Consensus       805 ~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s~~~-~~~vdl~~~a~~T~g~tgADlq~ll~~A~l  883 (952)
T KOG0735|consen  805 YILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSNSLLK-DTDVDLECLAQKTDGFTGADLQSLLYNAQL  883 (952)
T ss_pred             EEEEecCCccccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhhccCC-ccccchHHHhhhcCCCchhhHHHHHHHHHH
Confidence            566667888899999987  776 6788888999999999876643222 244557888887654    77777777776


Q ss_pred             HHHH
Q 022641          260 AARL  263 (294)
Q Consensus       260 ~~~~  263 (294)
                      ++..
T Consensus       884 ~avh  887 (952)
T KOG0735|consen  884 AAVH  887 (952)
T ss_pred             HHHH
Confidence            6644

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=99.64  E-value=1.2e-14  Score=116.72  Aligned_cols=159  Identities=13%  Similarity=0.159  Sum_probs=116.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccC----------------CcceeecCC-CCcchhHHHHHHHHHHhhhcccCc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYK----------------SRVLELNAS-DDRGINVVRTKIKTFAAVAVGSGQ  146 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~----------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  146 (294)
                      .++|+||.|+||..+|.++++.+.|....+                ..+..+... .....+.+++....+.....    
T Consensus         9 A~Lf~G~~G~G~~~lA~~~A~~llC~~~~~~Cg~C~sC~~i~~~~HPDl~~i~p~~~~I~id~ir~l~~~l~~~s~----   84 (261)
T PRK05818          9 PLLLIERKGSFLKPFLYEYLTSIVCTKANGFCKTCESCLKILNGKYNDFYLIFDQKNPIKKEDALSIINKLNRPSV----   84 (261)
T ss_pred             ceeeeCCCCCcHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHhcCCCCCEEEecCCcccCCHHHHHHHHHHHccCch----
Confidence            389999999999999999999998864221                122222211 12345555555444332211    


Q ss_pred             cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEEecCC----------CH
Q 022641          147 RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPL----------SE  216 (294)
Q Consensus       147 ~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~----------~~  216 (294)
                           ..+.+.|+||+++++++..+.+.|++.+|+++.++.+|++|+.+..+++.++|||+.+.++++          +.
T Consensus        85 -----e~~~~KV~II~~ae~m~~~AaNaLLK~LEEPp~~t~fiLit~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~~~~~  159 (261)
T PRK05818         85 -----ESNGKKIYIIYGIEKLNKQSANSLLKLIEEPPKNTYGIFTTRNENNILNTILSRCVQYVVLSKEKKVPFKVESND  159 (261)
T ss_pred             -----hcCCCEEEEeccHhhhCHHHHHHHHHhhcCCCCCeEEEEEECChHhCchHhhhheeeeecCChhhhcccccccCh
Confidence                 113467999999999999999999999999999999999999999999999999999999887          44


Q ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHH
Q 022641          217 EVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGA  260 (294)
Q Consensus       217 ~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~  260 (294)
                      .++.+.+..     ...+++    .++...+|+...++.+++..
T Consensus       160 ~~i~~~L~~-----~~~~d~----~i~~~a~g~~~~a~~l~~~l  194 (261)
T PRK05818        160 RYFQYILLS-----FYSVDE----QLQAYNNGSFSKLKNIIETL  194 (261)
T ss_pred             HHHHHHHHH-----ccCccH----HHHHHcCCCHHHHHHHHHHH
Confidence            444444321     122444    66777899999999988854

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

Probab=99.64  E-value=7.8e-15  Score=137.26  Aligned_cols=189  Identities=24%  Similarity=0.328  Sum_probs=128.4

Q ss_pred             hhhcccHHHHHHHHHHHHcC-------CCC--cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHH
Q 022641           61 KDVAHQEEVVRVLTNTLETA-------NCP--HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVR  131 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~-------~~~--~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (294)
                      +.++||+.+++.+...+...       ..+  +++|+||+|||||.+|+++++.+      ...++.++++.........
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l------~~~~~~~d~se~~~~~~~~  527 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEAL------GVHLERFDMSEYMEKHTVS  527 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHh------cCCeEEEeCchhhhcccHH
Confidence            46789999999988887642       112  48999999999999999999998      4556666655432222111


Q ss_pred             HHHHHHHhhhccc-CccC-----CCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecC
Q 022641          132 TKIKTFAAVAVGS-GQRR-----GGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNY  194 (294)
Q Consensus       132 ~~~~~~~~~~~~~-~~~~-----~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~  194 (294)
                      ..+..    +.+. +...     .......+.+|+|||++.+++..++.|++++++..           .++.+|+|||.
T Consensus       528 ~lig~----~~gyvg~~~~~~l~~~~~~~p~~VvllDEieka~~~~~~~Ll~~ld~g~~~d~~g~~vd~~~~iii~Tsn~  603 (731)
T TIGR02639       528 RLIGA----PPGYVGFEQGGLLTEAVRKHPHCVLLLDEIEKAHPDIYNILLQVMDYATLTDNNGRKADFRNVILIMTSNA  603 (731)
T ss_pred             HHhcC----CCCCcccchhhHHHHHHHhCCCeEEEEechhhcCHHHHHHHHHhhccCeeecCCCcccCCCCCEEEECCCc
Confidence            11111    0000 0000     00012345799999999999999999999998642           34568888865


Q ss_pred             Cc-------------------------ccchHhhcccc-EEEecCCCHHHHHHHHHHHHHH-------hC--CCCCHHHH
Q 022641          195 IS-------------------------RIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNE-------EG--LNLDAEAL  239 (294)
Q Consensus       195 ~~-------------------------~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~-------~~--~~~~~~~l  239 (294)
                      ..                         .+.++|++|+. ++.|.|++.+++..+++..+..       .+  +.++++++
T Consensus       604 g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef~~Rid~Vi~F~pLs~e~l~~Iv~~~L~~l~~~l~~~~~~l~i~~~a~  683 (731)
T TIGR02639       604 GASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRNRLDAIIHFNPLSEEVLEKIVQKFVDELSKQLNEKNIKLELTDDAK  683 (731)
T ss_pred             chhhhhhccCCcchhhhHHHHHHHHHhhcChHHHhcCCeEEEcCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEeCHHHH
Confidence            31                         14578889997 8999999999999999988753       22  56899999


Q ss_pred             HHHHhhc---cCcHHHHHHHHHH
Q 022641          240 STLSSIS---QGDLRRAITYLQG  259 (294)
Q Consensus       240 ~~l~~~~---~G~~r~~~~~l~~  259 (294)
                      +.|++.+   .-..|.+...++.
T Consensus       684 ~~La~~~~~~~~GaR~l~r~i~~  706 (731)
T TIGR02639       684 KYLAEKGYDEEFGARPLARVIQE  706 (731)
T ss_pred             HHHHHhCCCcccCchHHHHHHHH
Confidence            9999863   1234555555544

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

Probab=99.64  E-value=3.1e-15  Score=126.68  Aligned_cols=153  Identities=17%  Similarity=0.223  Sum_probs=115.1

Q ss_pred             cCCCcchhhcccHHHHHHHHHHH----Hc---------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecC
Q 022641           55 YRPKQVKDVAHQEEVVRVLTNTL----ET---------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA  121 (294)
Q Consensus        55 ~~~~~~~~~~g~~~~~~~l~~~l----~~---------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~  121 (294)
                      -.|.+|+.++-.++.++.+.+-+    ..         ...+..||+||||||||+++.|+|+.+      +..++.++.
T Consensus       195 ~HpstF~TlaMd~~~K~~I~~Dl~~F~k~k~~YkrvGkawKRGYLLYGPPGTGKSS~IaAmAn~L------~ydIydLeL  268 (457)
T KOG0743|consen  195 PHPSTFETLAMDPDLKERIIDDLDDFIKGKDFYKRVGKAWKRGYLLYGPPGTGKSSFIAAMANYL------NYDIYDLEL  268 (457)
T ss_pred             CCCCCccccccChhHHHHHHHHHHHHHhcchHHHhcCcchhccceeeCCCCCCHHHHHHHHHhhc------CCceEEeee
Confidence            34567888887766665554433    22         123569999999999999999999999      889999988


Q ss_pred             CCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH------------------HHHHHHHHHHHhhc
Q 022641          122 SDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE------------------DAQNALRRTMETYS  183 (294)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~------------------~~~~~L~~~l~~~~  183 (294)
                      +.......++.++....                .+.||+|+|||.--.                  -....|+..++..-
T Consensus       269 t~v~~n~dLr~LL~~t~----------------~kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlw  332 (457)
T KOG0743|consen  269 TEVKLDSDLRHLLLATP----------------NKSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLW  332 (457)
T ss_pred             ccccCcHHHHHHHHhCC----------------CCcEEEEeecccccccccccccccccccCCcceeehHHhhhhhcccc
Confidence            87777666766655432                235999999997510                  13456888887544


Q ss_pred             C----cceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHH
Q 022641          184 K----VTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNE  229 (294)
Q Consensus       184 ~----~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~  229 (294)
                      .    ...+|+|||....++|+|++  |.. .|++...+.+..+.+..+++..
T Consensus       333 Sscg~ERIivFTTNh~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL~~  385 (457)
T KOG0743|consen  333 SSCGDERIIVFTTNHKEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYLGI  385 (457)
T ss_pred             ccCCCceEEEEecCChhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhcCC
Confidence            3    45789999999999999998  665 7999999999999888887753

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=99.64  E-value=1.8e-14  Score=128.68  Aligned_cols=216  Identities=19%  Similarity=0.203  Sum_probs=144.3

Q ss_pred             CcchhhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhc---C--CCccCCcceeecCCCCcchhHH
Q 022641           58 KQVKDVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLF---G--PELYKSRVLELNASDDRGINVV  130 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~---~--~~~~~~~~~~~~~~~~~~~~~~  130 (294)
                      ..|++++|....+..+.+.+..  ....+++|+|++||||+.+|+++.+.+.   .  +.....+|+.++|..... ..+
T Consensus       216 ~~f~~iiG~S~~m~~~~~~i~~~A~s~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~inCaal~e-~ll  294 (538)
T PRK15424        216 YVLGDLLGQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIAE-SLL  294 (538)
T ss_pred             cchhheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEeecccCCh-hhH
Confidence            4578899998888888777653  3334699999999999999999988731   0  233467899999987542 222


Q ss_pred             HHHHHHHHhhhccc---CccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc
Q 022641          131 RTKIKTFAAVAVGS---GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS  196 (294)
Q Consensus       131 ~~~~~~~~~~~~~~---~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~  196 (294)
                      ...+..........   ..+.+....+..+.|||||++.|+...+..|+..+++..           .++++|++|+..-
T Consensus       295 eseLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~~~Q~kLl~~L~e~~~~r~G~~~~~~~dvRiIaat~~~L  374 (538)
T PRK15424        295 EAELFGYEEGAFTGSRRGGRAGLFEIAHGGTLFLDEIGEMPLPLQTRLLRVLEEKEVTRVGGHQPVPVDVRVISATHCDL  374 (538)
T ss_pred             HHHhcCCccccccCccccccCCchhccCCCEEEEcChHhCCHHHHHHHHhhhhcCeEEecCCCceeccceEEEEecCCCH
Confidence            22211111100001   112233345667899999999999999999999998632           2347888876542


Q ss_pred             -------ccchHhhcccc--EEEecCCCH--HHHHHHHHHHHHH----hCCCCCHHHH-------HHHHhh-ccCcHHHH
Q 022641          197 -------RIIEPLASRCA--KFRFKPLSE--EVMSSRVLHICNE----EGLNLDAEAL-------STLSSI-SQGDLRRA  253 (294)
Q Consensus       197 -------~~~~~l~~r~~--~i~~~~~~~--~~~~~~l~~~~~~----~~~~~~~~~l-------~~l~~~-~~G~~r~~  253 (294)
                             .+...+..|+.  .|.++|+..  +++..++.+++.+    .+..++++++       +.|..+ ++||+|++
T Consensus       375 ~~~v~~g~Fr~dL~yrL~~~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~~~~~~a~~~~~~a~~~L~~y~WPGNvREL  454 (538)
T PRK15424        375 EEDVRQGRFRRDLFYRLSILRLQLPPLRERVADILPLAESFLKQSLAALSAPFSAALRQGLQQCETLLLHYDWPGNVREL  454 (538)
T ss_pred             HHHHhcccchHHHHHHhcCCeecCCChhhchhHHHHHHHHHHHHHHHHcCCCCCHHHHHhhHHHHHHHHhCCCCchHHHH
Confidence                   13345666665  677777764  5666666666654    4566787776       455555 79999999


Q ss_pred             HHHHHHHHHHhC----CCCChhhhh
Q 022641          254 ITYLQGAARLFG----SSITSKDLI  274 (294)
Q Consensus       254 ~~~l~~~~~~~~----~~it~~~v~  274 (294)
                      .|+++.++.+..    ..|+.+++.
T Consensus       455 ~nvier~~i~~~~~~~~~i~~~~l~  479 (538)
T PRK15424        455 RNLMERLALFLSVEPTPDLTPQFLQ  479 (538)
T ss_pred             HHHHHHHHHhcCCCCcCccCHHHhh
Confidence            999999887653    346665553

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.64  E-value=1.3e-14  Score=136.12  Aligned_cols=174  Identities=19%  Similarity=0.230  Sum_probs=122.2

Q ss_pred             CCCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           56 RPKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        56 ~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      ....|+++.|.+..+..+.+++..             ....+++|+||||||||++++++++++      +..++.+++.
T Consensus       173 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~------~~~~i~i~~~  246 (733)
T TIGR01243       173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEA------GAYFISINGP  246 (733)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHh------CCeEEEEecH
Confidence            345788999999999888887642             123469999999999999999999998      5666777654


Q ss_pred             CCcc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHhhcC-
Q 022641          123 DDRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMETYSK-  184 (294)
Q Consensus       123 ~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~~~~-  184 (294)
                      ...+      ...++..+.....              ..+.+|+|||+|.+.           ...++.|+..++.... 
T Consensus       247 ~i~~~~~g~~~~~l~~lf~~a~~--------------~~p~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~  312 (733)
T TIGR01243       247 EIMSKYYGESEERLREIFKEAEE--------------NAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGR  312 (733)
T ss_pred             HHhcccccHHHHHHHHHHHHHHh--------------cCCcEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhccccC
Confidence            3221      1223333322211              123599999998873           2356678888876543 


Q ss_pred             -cceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCC-HHHHHHHHhhccCcHH
Q 022641          185 -VTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLD-AEALSTLSSISQGDLR  251 (294)
Q Consensus       185 -~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~-~~~l~~l~~~~~G~~r  251 (294)
                       ...+|.++|.+..+++++.+  ||. .+.+++|+.+++.++++....  +..+. +..++.+++.+.|-..
T Consensus       313 ~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~--~~~l~~d~~l~~la~~t~G~~g  382 (733)
T TIGR01243       313 GRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTR--NMPLAEDVDLDKLAEVTHGFVG  382 (733)
T ss_pred             CCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhc--CCCCccccCHHHHHHhCCCCCH
Confidence             34566688988889888876  776 799999999999999986554  34443 4457888888877443

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.

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=99.64  E-value=2.1e-14  Score=124.36  Aligned_cols=217  Identities=18%  Similarity=0.180  Sum_probs=152.1

Q ss_pred             hcCCCcchhhcccHHHHHHHHHHHHcCCC--CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHH
Q 022641           54 KYRPKQVKDVAHQEEVVRVLTNTLETANC--PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVR  131 (294)
Q Consensus        54 ~~~~~~~~~~~g~~~~~~~l~~~l~~~~~--~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (294)
                      ......|++++|....+..+.........  ..++|.|.+||||..+|+++.+.   +...+.+|+.+||.... ...+.
T Consensus       238 ~~a~y~f~~Iig~S~~m~~~~~~akr~A~tdstVLi~GESGTGKElfA~~IH~~---S~R~~~PFIaiNCaAiP-e~LlE  313 (560)
T COG3829         238 LKAKYTFDDIIGESPAMLRVLELAKRIAKTDSTVLILGESGTGKELFARAIHNL---SPRANGPFIAINCAAIP-ETLLE  313 (560)
T ss_pred             cccccchhhhccCCHHHHHHHHHHHhhcCCCCcEEEecCCCccHHHHHHHHHhc---CcccCCCeEEEecccCC-HHHHH
Confidence            55567899999997777776666655433  35999999999999999999654   56668899999998863 33333


Q ss_pred             HHHHHHHhhhcccC---ccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh-----------cCcceEEEEecCCc-
Q 022641          132 TKIKTFAAVAVGSG---QRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY-----------SKVTRFFFICNYIS-  196 (294)
Q Consensus       132 ~~~~~~~~~~~~~~---~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~-----------~~~~~ii~~~~~~~-  196 (294)
                      ..+-.+......+.   .+++....+..+-||+|||+.|+...|..|++++++.           +.++++|.+||..- 
T Consensus       314 SELFGye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgempl~LQaKLLRVLQEkei~rvG~t~~~~vDVRIIAATN~nL~  393 (560)
T COG3829         314 SELFGYEKGAFTGASKGGKPGLFELANGGTLFLDEIGEMPLPLQAKLLRVLQEKEIERVGGTKPIPVDVRIIAATNRNLE  393 (560)
T ss_pred             HHHhCcCCccccccccCCCCcceeeccCCeEEehhhccCCHHHHHHHHHHHhhceEEecCCCCceeeEEEEEeccCcCHH
Confidence            32222222211111   1455556688899999999999999999999999753           34677899998642 


Q ss_pred             ------ccchHhhccccE--EEecCCC--HHHHHHHHHHHHH----HhCC---CCCHHHHHHHHhh-ccCcHHHHHHHHH
Q 022641          197 ------RIIEPLASRCAK--FRFKPLS--EEVMSSRVLHICN----EEGL---NLDAEALSTLSSI-SQGDLRRAITYLQ  258 (294)
Q Consensus       197 ------~~~~~l~~r~~~--i~~~~~~--~~~~~~~l~~~~~----~~~~---~~~~~~l~~l~~~-~~G~~r~~~~~l~  258 (294)
                            .+...|..|..+  |.++|+-  ++++..+..+.+.    +.+.   .+++++++.|.++ ++||+|++-|+++
T Consensus       394 ~~i~~G~FReDLYYRLNV~~i~iPPLReR~eDI~~L~~~Fl~k~s~~~~~~v~~ls~~a~~~L~~y~WPGNVRELeNviE  473 (560)
T COG3829         394 KMIAEGTFREDLYYRLNVIPITIPPLRERKEDIPLLAEYFLDKFSRRYGRNVKGLSPDALALLLRYDWPGNVRELENVIE  473 (560)
T ss_pred             HHHhcCcchhhheeeeceeeecCCCcccCcchHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHhCCCCchHHHHHHHHH
Confidence                  234455667764  5556653  3455555554444    3332   3899999999988 8999999999999


Q ss_pred             HHHHHh--CCCCChhhhh
Q 022641          259 GAARLF--GSSITSKDLI  274 (294)
Q Consensus       259 ~~~~~~--~~~it~~~v~  274 (294)
                      .+...+  +.-|+.+++-
T Consensus       474 R~v~~~~~~~~I~~~~lp  491 (560)
T COG3829         474 RAVNLVESDGLIDADDLP  491 (560)
T ss_pred             HHHhccCCcceeehhhcc
Confidence            999765  3336666654

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=99.64  E-value=1.9e-14  Score=133.45  Aligned_cols=215  Identities=16%  Similarity=0.119  Sum_probs=145.3

Q ss_pred             CcchhhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHH
Q 022641           58 KQVKDVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK  135 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (294)
                      ..|++++|....+..+.+.+..  .....++|+|++||||+++|+++.+...   ....+++.++|............+.
T Consensus       322 ~~~~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~s~---r~~~pfv~vnc~~~~~~~~~~elfg  398 (638)
T PRK11388        322 HTFDHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNESE---RAAGPYIAVNCQLYPDEALAEEFLG  398 (638)
T ss_pred             ccccceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHhCC---ccCCCeEEEECCCCChHHHHHHhcC
Confidence            4678899987777666555543  2223599999999999999999987642   2356888999887643111111111


Q ss_pred             HHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-------c
Q 022641          136 TFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-------R  197 (294)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-------~  197 (294)
                      .. . ........+....+..+.|+|||++.++...+..|++++++..           ..+++|++|+...       .
T Consensus       399 ~~-~-~~~~~~~~g~~~~a~~GtL~ldei~~l~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~t~~~l~~~~~~~~  476 (638)
T PRK11388        399 SD-R-TDSENGRLSKFELAHGGTLFLEKVEYLSPELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNR  476 (638)
T ss_pred             CC-C-cCccCCCCCceeECCCCEEEEcChhhCCHHHHHHHHHHHhcCcEEeCCCCceEEeeEEEEEeccCCHHHHHhcCC
Confidence            11 0 0011112222334567899999999999999999999997532           1456777776531       2


Q ss_pred             cchHhhcccc--EEEecCCCH--HHHHHHHHHHHHHh------CCCCCHHHHHHHHhhc-cCcHHHHHHHHHHHHHHh-C
Q 022641          198 IIEPLASRCA--KFRFKPLSE--EVMSSRVLHICNEE------GLNLDAEALSTLSSIS-QGDLRRAITYLQGAARLF-G  265 (294)
Q Consensus       198 ~~~~l~~r~~--~i~~~~~~~--~~~~~~l~~~~~~~------~~~~~~~~l~~l~~~~-~G~~r~~~~~l~~~~~~~-~  265 (294)
                      +...+..|+.  .|.++|+..  +++..++.+++...      .+.+++++++.|.++. +||+|++.++++.+.... +
T Consensus       477 f~~dL~~~l~~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvreL~~~l~~~~~~~~~  556 (638)
T PRK11388        477 FSRQLYYALHAFEITIPPLRMRREDIPALVNNKLRSLEKRFSTRLKIDDDALARLVSYRWPGNDFELRSVIENLALSSDN  556 (638)
T ss_pred             ChHHHhhhhceeEEeCCChhhhhhHHHHHHHHHHHHHHHHhCCCCCcCHHHHHHHHcCCCCChHHHHHHHHHHHHHhCCC
Confidence            3455666665  577777764  46666666655432      2468999999999984 999999999999987655 4


Q ss_pred             CCCChhhhhhhc
Q 022641          266 SSITSKDLISVS  277 (294)
Q Consensus       266 ~~it~~~v~~~~  277 (294)
                      ..|+.+++...+
T Consensus       557 ~~i~~~~lp~~~  568 (638)
T PRK11388        557 GRIRLSDLPEHL  568 (638)
T ss_pred             CeecHHHCchhh
Confidence            468888876544

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.63  E-value=2.4e-14  Score=135.89  Aligned_cols=196  Identities=23%  Similarity=0.318  Sum_probs=136.4

Q ss_pred             hhhcccHHHHHHHHHHHHcCC-------C--CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHH
Q 022641           61 KDVAHQEEVVRVLTNTLETAN-------C--PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVR  131 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~~-------~--~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (294)
                      ..++|++.++..+...+....       .  ..++|+||+|||||++|++++..+++.   ...++.++++.........
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~---~~~~i~~d~s~~~~~~~~~  641 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDD---EDAMVRIDMSEYMEKHSVA  641 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCC---CCcEEEEechhhcccchHH
Confidence            468899999999988886521       1  248999999999999999999998654   2456666665433222221


Q ss_pred             HHHHHHHhhhccc-CccCC-----CCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecC
Q 022641          132 TKIKTFAAVAVGS-GQRRG-----GYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNY  194 (294)
Q Consensus       132 ~~~~~~~~~~~~~-~~~~~-----~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~  194 (294)
                      ..+    ..+.+. +...+     ......+.+|+|||++.+++..++.|++++++..           .++.+|+|||.
T Consensus       642 ~l~----g~~~g~~g~~~~g~l~~~v~~~p~~vlllDeieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~  717 (852)
T TIGR03346       642 RLI----GAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNL  717 (852)
T ss_pred             Hhc----CCCCCccCcccccHHHHHHHcCCCcEEEEeccccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCc
Confidence            111    000000 00000     0011234699999999999999999999998653           34568888876


Q ss_pred             Ccc-------------------------cchHhhcccc-EEEecCCCHHHHHHHHHHHHHH-------hC--CCCCHHHH
Q 022641          195 ISR-------------------------IIEPLASRCA-KFRFKPLSEEVMSSRVLHICNE-------EG--LNLDAEAL  239 (294)
Q Consensus       195 ~~~-------------------------~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~-------~~--~~~~~~~l  239 (294)
                      ...                         ..++|..|+. ++.|.|++.+++.+++...+..       .+  +.++++++
T Consensus       718 g~~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel~~Rid~IivF~PL~~e~l~~I~~l~L~~l~~~l~~~~~~l~i~~~a~  797 (852)
T TIGR03346       718 GSQFIQELAGGDDYEEMREAVMEVLRAHFRPEFLNRIDEIVVFHPLGREQIARIVEIQLGRLRKRLAERKITLELSDAAL  797 (852)
T ss_pred             chHhHhhhcccccHHHHHHHHHHHHHhhcCHHHhcCcCeEEecCCcCHHHHHHHHHHHHHHHHHHHHHCCCeecCCHHHH
Confidence            321                         3467788886 8999999999999988876642       22  56899999


Q ss_pred             HHHHhh-c--cCcHHHHHHHHHHHHHH
Q 022641          240 STLSSI-S--QGDLRRAITYLQGAARL  263 (294)
Q Consensus       240 ~~l~~~-~--~G~~r~~~~~l~~~~~~  263 (294)
                      +.|++. +  .++.|.+.+.++.....
T Consensus       798 ~~L~~~~~~~~~gaR~L~~~i~~~i~~  824 (852)
T TIGR03346       798 DFLAEAGYDPVYGARPLKRAIQREIEN  824 (852)
T ss_pred             HHHHHhCCCCCCCchhHHHHHHHHHHH
Confidence            999997 3  58899988888876643

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.

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=99.62  E-value=4.5e-14  Score=127.13  Aligned_cols=215  Identities=19%  Similarity=0.217  Sum_probs=142.7

Q ss_pred             CCCcchhhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHH
Q 022641           56 RPKQVKDVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTK  133 (294)
Q Consensus        56 ~~~~~~~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  133 (294)
                      ....|++++|....+..+...+..  .....++|+|++||||+++|+++....   .....+++.++|..... ..+...
T Consensus       199 ~~~~f~~~ig~s~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~lA~aiH~~s---~r~~~pfv~inca~~~~-~~~e~e  274 (520)
T PRK10820        199 DDSAFSQIVAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLRS---PRGKKPFLALNCASIPD-DVVESE  274 (520)
T ss_pred             ccccccceeECCHHHHHHHHHHHHHhCCCCCEEEECCCCccHHHHHHHHHHhC---CCCCCCeEEeccccCCH-HHHHHH
Confidence            456788999987776666555532  233459999999999999999986543   23356888898877542 222211


Q ss_pred             HHHHHhhhccc--CccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc----
Q 022641          134 IKTFAAVAVGS--GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS----  196 (294)
Q Consensus       134 ~~~~~~~~~~~--~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~----  196 (294)
                      +-.........  ....+....+..+.|+|||++.++...+..|+..+++..           ..+++|++|+...    
T Consensus       275 lFG~~~~~~~~~~~~~~g~~e~a~~GtL~LdeI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~vRiI~st~~~l~~l~  354 (520)
T PRK10820        275 LFGHAPGAYPNALEGKKGFFEQANGGSVLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVELV  354 (520)
T ss_pred             hcCCCCCCcCCcccCCCChhhhcCCCEEEEeChhhCCHHHHHHHHHHHhcCCcccCCCCcceeeeeEEEEecCCCHHHHH
Confidence            11100000000  011122223567899999999999999999999997632           2346777775432    


Q ss_pred             ---ccchHhhcccc--EEEecCCCH--HHHHHHHHH----HHHHhCC---CCCHHHHHHHHhh-ccCcHHHHHHHHHHHH
Q 022641          197 ---RIIEPLASRCA--KFRFKPLSE--EVMSSRVLH----ICNEEGL---NLDAEALSTLSSI-SQGDLRRAITYLQGAA  261 (294)
Q Consensus       197 ---~~~~~l~~r~~--~i~~~~~~~--~~~~~~l~~----~~~~~~~---~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~  261 (294)
                         ...+.+..|+.  .|.++|+..  +++..++..    .+.+.+.   .+++++++.|..+ ++||+|++.+++..+.
T Consensus       355 ~~g~f~~dL~~rL~~~~i~lPpLreR~~Di~~L~~~fl~~~~~~~g~~~~~ls~~a~~~L~~y~WPGNvreL~nvl~~a~  434 (520)
T PRK10820        355 QKGEFREDLYYRLNVLTLNLPPLRDRPQDIMPLTELFVARFADEQGVPRPKLAADLNTVLTRYGWPGNVRQLKNAIYRAL  434 (520)
T ss_pred             HcCCccHHHHhhcCeeEEeCCCcccChhHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHhcCCCCCHHHHHHHHHHHHH
Confidence               23456777765  677888764  345544444    4444443   5899999999998 8999999999999888


Q ss_pred             HHh-CCCCChhhhh
Q 022641          262 RLF-GSSITSKDLI  274 (294)
Q Consensus       262 ~~~-~~~it~~~v~  274 (294)
                      ... +..|+.+++.
T Consensus       435 ~~~~~~~i~~~~~~  448 (520)
T PRK10820        435 TQLEGYELRPQDIL  448 (520)
T ss_pred             HhCCCCcccHHHcC
Confidence            765 4568888753

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.62  E-value=2.3e-14  Score=135.60  Aligned_cols=179  Identities=25%  Similarity=0.366  Sum_probs=123.1

Q ss_pred             hhhcccHHHHHHHHHHHHcC-------CCC--cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHH
Q 022641           61 KDVAHQEEVVRVLTNTLETA-------NCP--HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVR  131 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~-------~~~--~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (294)
                      +.++||+.++..+...+...       ..|  .++|+||+|||||++|+++++.+++..   ..++.++.+.......+.
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~---~~~~~~d~s~~~~~~~~~  585 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGSE---DAMIRLDMSEYMEKHTVS  585 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCc---cceEEEEchhccccccHH
Confidence            57889999999998887532       112  389999999999999999999997652   345566554432222121


Q ss_pred             HHHHHHHhhhccc-CccCC-----CCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecC
Q 022641          132 TKIKTFAAVAVGS-GQRRG-----GYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNY  194 (294)
Q Consensus       132 ~~~~~~~~~~~~~-~~~~~-----~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~  194 (294)
                      ..+    ..+.+. +...+     ......+.||+|||++.+++..++.|++++++..           .++.+|+|||.
T Consensus       586 ~l~----g~~~gyvg~~~~~~l~~~~~~~p~~VvllDeieka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~  661 (821)
T CHL00095        586 KLI----GSPPGYVGYNEGGQLTEAVRKKPYTVVLFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNL  661 (821)
T ss_pred             Hhc----CCCCcccCcCccchHHHHHHhCCCeEEEECChhhCCHHHHHHHHHHhccCceecCCCcEEecCceEEEEeCCc
Confidence            111    000000 00000     0112345799999999999999999999998642           46678888764


Q ss_pred             Ccc-------------------------------------cchHhhcccc-EEEecCCCHHHHHHHHHHHHHH-------
Q 022641          195 ISR-------------------------------------IIEPLASRCA-KFRFKPLSEEVMSSRVLHICNE-------  229 (294)
Q Consensus       195 ~~~-------------------------------------~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~-------  229 (294)
                      ...                                     +.|+|++|+. ++.|.|++.+++..++...+..       
T Consensus       662 g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~peflnRid~ii~F~pL~~~~l~~Iv~~~l~~l~~rl~~  741 (821)
T CHL00095        662 GSKVIETNSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLNRLDEIIVFRQLTKNDVWEIAEIMLKNLFKRLNE  741 (821)
T ss_pred             chHHHHhhccccCCcccccccccccHHHHHHHHHHHHHHhcCHHHhccCCeEEEeCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            210                                     2357889994 8999999999999998887753       


Q ss_pred             hC--CCCCHHHHHHHHhhc
Q 022641          230 EG--LNLDAEALSTLSSIS  246 (294)
Q Consensus       230 ~~--~~~~~~~l~~l~~~~  246 (294)
                      .+  +.+++++.+.|++.+
T Consensus       742 ~~i~l~~~~~~~~~La~~~  760 (821)
T CHL00095        742 QGIQLEVTERIKTLLIEEG  760 (821)
T ss_pred             CCcEEEECHHHHHHHHHhc
Confidence            23  458999999999863

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=99.62  E-value=5.9e-14  Score=126.33  Aligned_cols=212  Identities=20%  Similarity=0.198  Sum_probs=143.7

Q ss_pred             cchhhcccHHHHHHHHHHHHcC--CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHH
Q 022641           59 QVKDVAHQEEVVRVLTNTLETA--NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKT  136 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~--~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  136 (294)
                      .+..++|+...++.+.+.+..-  ...+++|+|++||||+++|+++.....   ....+++.++|..... ..+...+..
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~---r~~~p~v~v~c~~~~~-~~~e~~lfG  260 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASP---RADKPLVYLNCAALPE-SLAESELFG  260 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCC---cCCCCeEEEEcccCCh-HHHHHHhcC
Confidence            5678899988887777766543  234599999999999999999988642   2356888899887542 222211110


Q ss_pred             HHhhhc-cc-CccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-------
Q 022641          137 FAAVAV-GS-GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-------  196 (294)
Q Consensus       137 ~~~~~~-~~-~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-------  196 (294)
                      ...... +. ....+....+..+.|||||++.|+...+..|+..+++..           ..+++|++|+...       
T Consensus       261 ~~~g~~~ga~~~~~g~~~~a~gGtL~ldeI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~l~~~~~~~  340 (509)
T PRK05022        261 HVKGAFTGAISNRSGKFELADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRDLREEVRAG  340 (509)
T ss_pred             ccccccCCCcccCCcchhhcCCCEEEecChhhCCHHHHHHHHHHHhcCCEeeCCCCcceecceEEEEecCCCHHHHHHcC
Confidence            000000 00 011222334567899999999999999999999997533           2557888886542       


Q ss_pred             ccchHhhcccc--EEEecCCCH--HHHHHHHHHHHH----HhC---CCCCHHHHHHHHhh-ccCcHHHHHHHHHHHHHHh
Q 022641          197 RIIEPLASRCA--KFRFKPLSE--EVMSSRVLHICN----EEG---LNLDAEALSTLSSI-SQGDLRRAITYLQGAARLF  264 (294)
Q Consensus       197 ~~~~~l~~r~~--~i~~~~~~~--~~~~~~l~~~~~----~~~---~~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~~  264 (294)
                      .+...|..|+.  .|.++|+..  +++..++.+++.    +.+   +.+++++++.|..+ +.||+|++.++++.++...
T Consensus       341 ~f~~dL~~rl~~~~i~lPpLreR~eDI~~L~~~fl~~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvrEL~~~i~ra~~~~  420 (509)
T PRK05022        341 RFRADLYHRLSVFPLSVPPLRERGDDVLLLAGYFLEQNRARLGLRSLRLSPAAQAALLAYDWPGNVRELEHVISRAALLA  420 (509)
T ss_pred             CccHHHHhcccccEeeCCCchhchhhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCCCcHHHHHHHHHHHHHhc
Confidence            24566777765  577777764  455555554443    322   46899999999998 7999999999999988776


Q ss_pred             CC-------CCChhhhh
Q 022641          265 GS-------SITSKDLI  274 (294)
Q Consensus       265 ~~-------~it~~~v~  274 (294)
                      ..       .|+.+++.
T Consensus       421 ~~~~~~~~~~i~~~~l~  437 (509)
T PRK05022        421 RARGAGRIVTLEAQHLD  437 (509)
T ss_pred             CCCccCccceecHHHcC
Confidence            32       36666654

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

Probab=99.61  E-value=3.8e-15  Score=118.99  Aligned_cols=205  Identities=20%  Similarity=0.259  Sum_probs=140.3

Q ss_pred             CCcchhhcccHHHHHHHHHHHHcC-------------CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLETA-------------NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~~-------------~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ..++.++-|.+..++.+.+.+.-.             .+..+++||+||||||.||+++|++.      ...|+.+-++.
T Consensus       181 ~Ety~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqT------SATFlRvvGse  254 (440)
T KOG0726|consen  181 QETYADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQT------SATFLRVVGSE  254 (440)
T ss_pred             hhhhcccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhccc------chhhhhhhhHH
Confidence            346778889999999998887532             23359999999999999999999987      55565554443


Q ss_pred             ------CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHh---h-
Q 022641          124 ------DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMET---Y-  182 (294)
Q Consensus       124 ------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~---~-  182 (294)
                            ..+...++..+........              .++||||||.+.           ...+..++.+++.   + 
T Consensus       255 LiQkylGdGpklvRqlF~vA~e~ap--------------SIvFiDEIdAiGtKRyds~SggerEiQrtmLELLNQldGFd  320 (440)
T KOG0726|consen  255 LIQKYLGDGPKLVRELFRVAEEHAP--------------SIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFD  320 (440)
T ss_pred             HHHHHhccchHHHHHHHHHHHhcCC--------------ceEEeehhhhhccccccCCCccHHHHHHHHHHHHHhccCcc
Confidence                  2233445555554433332              499999999873           1244455555543   2 


Q ss_pred             -cCcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHH-HHHHH----hhccCcHHHH
Q 022641          183 -SKVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEA-LSTLS----SISQGDLRRA  253 (294)
Q Consensus       183 -~~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-l~~l~----~~~~G~~r~~  253 (294)
                       ...+.+|++||....+++++.+  |.. .|.|+.|+....+.++.-.-.  ++.+++++ ++.++    +.++.|+..+
T Consensus       321 srgDvKvimATnrie~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~IHTs--~Mtl~~dVnle~li~~kddlSGAdIkAi  398 (440)
T KOG0726|consen  321 SRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKKIFQIHTS--RMTLAEDVNLEELIMTKDDLSGADIKAI  398 (440)
T ss_pred             ccCCeEEEEecccccccCHhhcCCCccccccccCCCchhhhceeEEEeec--ccchhccccHHHHhhcccccccccHHHH
Confidence             3567899999999999999987  555 799999998888877743332  23344333 44433    3477888887


Q ss_pred             HHHHHHHHHHh-CCCCChhhhhhhcccccCC
Q 022641          254 ITYLQGAARLF-GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       254 ~~~l~~~~~~~-~~~it~~~v~~~~~~~~~~  283 (294)
                      +.-.-..+... +..++.+++.++...+-.+
T Consensus       399 ctEaGllAlRerRm~vt~~DF~ka~e~V~~~  429 (440)
T KOG0726|consen  399 CTEAGLLALRERRMKVTMEDFKKAKEKVLYK  429 (440)
T ss_pred             HHHHhHHHHHHHHhhccHHHHHHHHHHHHHh
Confidence            76666555544 4579999998877665444

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

Probab=99.61  E-value=5.3e-15  Score=137.23  Aligned_cols=208  Identities=27%  Similarity=0.419  Sum_probs=163.0

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCC--------------CC--cEEEECCCCCCHHHHHHHHHHHhcCCCc
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETAN--------------CP--HMLFYGPPGTGKTTTALAIAHQLFGPEL  111 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~--------------~~--~ill~Gp~G~GKT~la~~la~~~~~~~~  111 (294)
                      ..-|.++|+|....++.|.......+..|+....              ..  .++++||||+|||+.+...+.++     
T Consensus       307 ~~~~~~k~~p~~~k~~~~~~~~~~~~~~~l~~~k~~~~~sy~~~~~~ss~~~~~l~~G~pGigKT~~~h~~~k~~-----  381 (871)
T KOG1968|consen  307 GAGWTEKYQPTSSKALEGNASSSKKASKWLAKSKDKEKSSYKENEPDSSKKKALLLSGPPGIGKTTAAHKAAKEL-----  381 (871)
T ss_pred             ccccccccccccHHhhhcccchhhhhhhHHHhhhccccccccccCcchhhHHHHHhcCCCCCCchhhHhhhhhhc-----
Confidence            3579999999999999999888878888886530              00  15999999999999999999999     


Q ss_pred             cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCcc----CCCCCCCCcEEEEEeCCCCCCH---HHHHHHHHHHHhhcC
Q 022641          112 YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQR----RGGYPCPPYKIIILDEADSMTE---DAQNALRRTMETYSK  184 (294)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~lliiDei~~l~~---~~~~~L~~~l~~~~~  184 (294)
                       +..+++.|+++.++...+...+..+.....-....    ..........||++||+|.+..   ..+..|-.++..  .
T Consensus       382 -g~~v~E~Nas~~RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vil~devD~~~~~dRg~v~~l~~l~~k--s  458 (871)
T KOG1968|consen  382 -GFKVVEKNASDVRSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLILMDEVDGMFGEDRGGVSKLSSLCKK--S  458 (871)
T ss_pred             -ccceeecCccccccccHHHhhhhccccccchhhhhcccccccccccceeEEEEeccccccchhhhhHHHHHHHHHh--c
Confidence             88999999999998887777666644332211111    0011123345999999999876   345555556553  4


Q ss_pred             cceEEEEecCCcc-cchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHH
Q 022641          185 VTRFFFICNYISR-IIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARL  263 (294)
Q Consensus       185 ~~~ii~~~~~~~~-~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~  263 (294)
                      ...+|++||+... ..+.+.+-|..++|..|+.+.+...+..+|..+++.++++.++.+.+.++||+|.+++++++....
T Consensus       459 ~~Piv~~cndr~~p~sr~~~~~~~~l~f~kP~~~~i~~ri~si~~se~~ki~~~~l~~~s~~~~~DiR~~i~~lq~~~~~  538 (871)
T KOG1968|consen  459 SRPLVCTCNDRNLPKSRALSRACSDLRFSKPSSELIRSRIMSICKSEGIKISDDVLEEISKLSGGDIRQIIMQLQFWSLS  538 (871)
T ss_pred             cCCeEEEecCCCCccccchhhhcceeeecCCcHHHHHhhhhhhhcccceecCcHHHHHHHHhcccCHHHHHHHHhhhhcc
Confidence            5568899987654 345667778899999999999999999999999999999999999999999999999999998554

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.60  E-value=3.6e-14  Score=117.92  Aligned_cols=198  Identities=17%  Similarity=0.174  Sum_probs=126.1

Q ss_pred             cCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHH
Q 022641           55 YRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKI  134 (294)
Q Consensus        55 ~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  134 (294)
                      +.|..-..+.-.......+..++..++  +++|.||||||||++++.+++.+      +.+++.+++........+....
T Consensus        39 ~~p~~d~~y~f~~~~~~~vl~~l~~~~--~ilL~G~pGtGKTtla~~lA~~l------~~~~~rV~~~~~l~~~DliG~~  110 (327)
T TIGR01650        39 HVPDIDPAYLFDKATTKAICAGFAYDR--RVMVQGYHGTGKSTHIEQIAARL------NWPCVRVNLDSHVSRIDLVGKD  110 (327)
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhcCC--cEEEEeCCCChHHHHHHHHHHHH------CCCeEEEEecCCCChhhcCCCc
Confidence            344444456666666777777776544  79999999999999999999999      7778877766554432221110


Q ss_pred             HH-HHhhhcccCccCCCC--CCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh--------------cCcceEEEEecCCc-
Q 022641          135 KT-FAAVAVGSGQRRGGY--PCPPYKIIILDEADSMTEDAQNALRRTMETY--------------SKVTRFFFICNYIS-  196 (294)
Q Consensus       135 ~~-~~~~~~~~~~~~~~~--~~~~~~lliiDei~~l~~~~~~~L~~~l~~~--------------~~~~~ii~~~~~~~-  196 (294)
                      .. ............+..  ....+.+|++||++..+++.+..|..+++..              ...+++|.|+|... 
T Consensus       111 ~~~l~~g~~~~~f~~GpL~~A~~~g~illlDEin~a~p~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~  190 (327)
T TIGR01650       111 AIVLKDGKQITEFRDGILPWALQHNVALCFDEYDAGRPDVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGL  190 (327)
T ss_pred             eeeccCCcceeEEecCcchhHHhCCeEEEechhhccCHHHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCc
Confidence            00 000000000000100  1134568999999999999999999888731              13466788888632 


Q ss_pred             -----------ccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCC--CCHHHHHHHHhh---cc-----------C
Q 022641          197 -----------RIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLN--LDAEALSTLSSI---SQ-----------G  248 (294)
Q Consensus       197 -----------~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~--~~~~~l~~l~~~---~~-----------G  248 (294)
                                 .++.++++||. .+.+..|+.++..+++.....  ++.  .+++.++++++.   +.           -
T Consensus       191 Gd~~G~y~Gt~~l~~A~lDRF~i~~~~~Yp~~e~E~~Il~~~~~--~~~~~~~~~i~~~mV~la~~tR~~~~~~~i~~~~  268 (327)
T TIGR01650       191 GDTTGLYHGTQQINQAQMDRWSIVTTLNYLEHDNEAAIVLAKAK--GFDDTEGKDIINAMVRVADMTRNAFINGDISTVM  268 (327)
T ss_pred             CCCCcceeeeecCCHHHHhheeeEeeCCCCCHHHHHHHHHhhcc--CCCccchHHHHHHHHHHHHHHHhhhccCCccccc
Confidence                       36899999998 568999999999999876542  221  134555555543   21           1


Q ss_pred             cHHHHHHHHHHHHH
Q 022641          249 DLRRAITYLQGAAR  262 (294)
Q Consensus       249 ~~r~~~~~l~~~~~  262 (294)
                      ++|..+...+.+..
T Consensus       269 SpR~li~w~~~~~~  282 (327)
T TIGR01650       269 SPRTVITWAENAEI  282 (327)
T ss_pred             cHHHHHHHHHHHHh
Confidence            67777777665443

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.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=99.60  E-value=7.4e-14  Score=130.24  Aligned_cols=217  Identities=21%  Similarity=0.252  Sum_probs=140.2

Q ss_pred             hhhhhcCC--CcchhhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           50 PWVEKYRP--KQVKDVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        50 ~~~~~~~~--~~~~~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      .+.+.+..  ..|.+++|+...+..+.+.+..  ....+++|+|++|||||++|+++.....   ..+.+++.++|....
T Consensus       363 ~lt~~L~~~n~~~~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s~---r~~~~~v~i~c~~~~  439 (686)
T PRK15429        363 ALTEQLNNVDSEFGEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSG---RNNRRMVKMNCAAMP  439 (686)
T ss_pred             HHHHhhhhccccccceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcC---CCCCCeEEEecccCC
Confidence            34444444  4577899998777776655543  2334699999999999999999987652   235688888887653


Q ss_pred             chhHHHH-HHHHHHhhhccc-CccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEe
Q 022641          126 GINVVRT-KIKTFAAVAVGS-GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFIC  192 (294)
Q Consensus       126 ~~~~~~~-~~~~~~~~~~~~-~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~  192 (294)
                      . ..+.. .+........+. ....+......++.|+|||++.++...+..|+..+++..           ..+++|+++
T Consensus       440 ~-~~~~~~lfg~~~~~~~g~~~~~~g~le~a~~GtL~Ldei~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~t  518 (686)
T PRK15429        440 A-GLLESDLFGHERGAFTGASAQRIGRFELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAAT  518 (686)
T ss_pred             h-hHhhhhhcCcccccccccccchhhHHHhcCCCeEEEechhhCCHHHHHHHHHHHHhCCEEeCCCCCcccceEEEEEeC
Confidence            2 11111 111100000000 001111223456799999999999999999999997643           345788887


Q ss_pred             cCCc-------ccchHhhcccc--EEEecCCCH--HHHHHHHHHHHH----HhCC---CCCHHHHHHHHhh-ccCcHHHH
Q 022641          193 NYIS-------RIIEPLASRCA--KFRFKPLSE--EVMSSRVLHICN----EEGL---NLDAEALSTLSSI-SQGDLRRA  253 (294)
Q Consensus       193 ~~~~-------~~~~~l~~r~~--~i~~~~~~~--~~~~~~l~~~~~----~~~~---~~~~~~l~~l~~~-~~G~~r~~  253 (294)
                      +..-       .+...+..|+.  .|.++|+..  +++..++++++.    +.+.   .+++++++.|..+ +.||+|++
T Consensus       519 ~~~l~~~~~~~~f~~~L~~~l~~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~~s~~al~~L~~y~WPGNvrEL  598 (686)
T PRK15429        519 NRDLKKMVADREFRSDLYYRLNVFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPAETLRTLSNMEWPGNVREL  598 (686)
T ss_pred             CCCHHHHHHcCcccHHHHhccCeeEEeCCChhhhHhHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhCCCCCcHHHH
Confidence            6542       23345666765  577777754  455555555443    3332   4799999999887 79999999


Q ss_pred             HHHHHHHHHHh-CCCCCh
Q 022641          254 ITYLQGAARLF-GSSITS  270 (294)
Q Consensus       254 ~~~l~~~~~~~-~~~it~  270 (294)
                      .++++.++... +..|+.
T Consensus       599 ~~~i~~a~~~~~~~~i~~  616 (686)
T PRK15429        599 ENVIERAVLLTRGNVLQL  616 (686)
T ss_pred             HHHHHHHHHhCCCCcccc
Confidence            99999988765 334554

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.59  E-value=1.2e-13  Score=130.64  Aligned_cols=195  Identities=25%  Similarity=0.340  Sum_probs=128.8

Q ss_pred             cchhhcccHHHHHHHHHHHHcC-------CC--CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhH
Q 022641           59 QVKDVAHQEEVVRVLTNTLETA-------NC--PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINV  129 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~-------~~--~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (294)
                      -.+.++|++.++..+...+...       ..  ..++|+||+|||||++|+++++.+++..   ..++.++++.......
T Consensus       566 l~~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~~---~~~i~id~se~~~~~~  642 (857)
T PRK10865        566 LHHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMFDSD---DAMVRIDMSEFMEKHS  642 (857)
T ss_pred             hCCeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHhhcCC---CcEEEEEhHHhhhhhh
Confidence            3457889999999888887642       11  2489999999999999999999886432   3455565544322111


Q ss_pred             HHHHHHHHHhhhccc-CccCC-----CCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEe
Q 022641          130 VRTKIKTFAAVAVGS-GQRRG-----GYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFIC  192 (294)
Q Consensus       130 ~~~~~~~~~~~~~~~-~~~~~-----~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~  192 (294)
                      ....+    ..+.+. +...+     ......+++|+|||++.+++..++.|++++++..           .+..+|+||
T Consensus       643 ~~~Li----G~~pgy~g~~~~g~l~~~v~~~p~~vLllDEieka~~~v~~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TS  718 (857)
T PRK10865        643 VSRLV----GAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTS  718 (857)
T ss_pred             HHHHh----CCCCcccccchhHHHHHHHHhCCCCeEEEeehhhCCHHHHHHHHHHHhhCceecCCceEEeecccEEEEeC
Confidence            11111    000000 00000     0011234699999999999999999999998642           234578888


Q ss_pred             cCCc-------------------------ccchHhhcccc-EEEecCCCHHHHHHHHHHHHHH-------hC--CCCCHH
Q 022641          193 NYIS-------------------------RIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNE-------EG--LNLDAE  237 (294)
Q Consensus       193 ~~~~-------------------------~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~-------~~--~~~~~~  237 (294)
                      |...                         .+.++|.+|+. ++.|.|++.+++..++...+..       .+  +.++++
T Consensus       719 N~g~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PELlnRld~iivF~PL~~edl~~Iv~~~L~~l~~rl~~~gi~l~is~~  798 (857)
T PRK10865        719 NLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFINRIDEVVVFHPLGEQHIASIAQIQLQRLYKRLEERGYEIHISDE  798 (857)
T ss_pred             CcchHHHHHhccccchHHHHHHHHHHHcccccHHHHHhCCeeEecCCCCHHHHHHHHHHHHHHHHHHHHhCCCcCcCCHH
Confidence            7631                         13468889994 8999999999999998887754       13  357999


Q ss_pred             HHHHHHhhcc---CcHHHHHHHHHHH
Q 022641          238 ALSTLSSISQ---GDLRRAITYLQGA  260 (294)
Q Consensus       238 ~l~~l~~~~~---G~~r~~~~~l~~~  260 (294)
                      +++.|++.+-   -..|.+.+.++..
T Consensus       799 al~~L~~~gy~~~~GARpL~r~I~~~  824 (857)
T PRK10865        799 ALKLLSENGYDPVYGARPLKRAIQQQ  824 (857)
T ss_pred             HHHHHHHcCCCccCChHHHHHHHHHH
Confidence            9999998642   1245555555543

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=99.59  E-value=1.3e-13  Score=118.12  Aligned_cols=212  Identities=23%  Similarity=0.218  Sum_probs=148.2

Q ss_pred             cchhhcccHHHHHHHHHHHHcCCC--CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHH
Q 022641           59 QVKDVAHQEEVVRVLTNTLETANC--PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKT  136 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~~~--~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  136 (294)
                      .+.+++|+...+..+.+.+..-..  .+++|.|.+||||..+|++|.+.   +.....+++.+||......-.-.+.+..
T Consensus       221 ~~~~iIG~S~am~~ll~~i~~VA~Sd~tVLi~GETGtGKElvAraIH~~---S~R~~kPfV~~NCAAlPesLlESELFGH  297 (550)
T COG3604         221 EVGGIIGRSPAMRQLLKEIEVVAKSDSTVLIRGETGTGKELVARAIHQL---SPRRDKPFVKLNCAALPESLLESELFGH  297 (550)
T ss_pred             ccccceecCHHHHHHHHHHHHHhcCCCeEEEecCCCccHHHHHHHHHhh---CcccCCCceeeeccccchHHHHHHHhcc
Confidence            456899999999888888765433  35999999999999999999765   4455779999999886332211122222


Q ss_pred             HHhhhcc-cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-------c
Q 022641          137 FAAVAVG-SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-------R  197 (294)
Q Consensus       137 ~~~~~~~-~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-------~  197 (294)
                      ......+ ...+.+....++.+-||+|||+.++...|..|+.++.+..           -.+++|.+||..-       .
T Consensus       298 eKGAFTGA~~~r~GrFElAdGGTLFLDEIGelPL~lQaKLLRvLQegEieRvG~~r~ikVDVRiIAATNRDL~~~V~~G~  377 (550)
T COG3604         298 EKGAFTGAINTRRGRFELADGGTLFLDEIGELPLALQAKLLRVLQEGEIERVGGDRTIKVDVRVIAATNRDLEEMVRDGE  377 (550)
T ss_pred             cccccccchhccCcceeecCCCeEechhhccCCHHHHHHHHHHHhhcceeecCCCceeEEEEEEEeccchhHHHHHHcCc
Confidence            2211111 1234555667888999999999999999999999997532           3567899998642       2


Q ss_pred             cchHhhccccE--EEecCCCH--HH----HHHHHHHHHHHhCC---CCCHHHHHHHHhh-ccCcHHHHHHHHHHHHHHhC
Q 022641          198 IIEPLASRCAK--FRFKPLSE--EV----MSSRVLHICNEEGL---NLDAEALSTLSSI-SQGDLRRAITYLQGAARLFG  265 (294)
Q Consensus       198 ~~~~l~~r~~~--i~~~~~~~--~~----~~~~l~~~~~~~~~---~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~~~  265 (294)
                      .-..+..|..+  +.++|+-+  ++    ...++++...+.|.   .+++++++.+.++ +.||+|.+.|+++.++..++
T Consensus       378 FRaDLYyRLsV~Pl~lPPLRER~~DIplLA~~Fle~~~~~~gr~~l~ls~~Al~~L~~y~wPGNVRELen~veRavlla~  457 (550)
T COG3604         378 FRADLYYRLSVFPLELPPLRERPEDIPLLAGYFLEKFRRRLGRAILSLSAEALELLSSYEWPGNVRELENVVERAVLLAG  457 (550)
T ss_pred             chhhhhhcccccccCCCCcccCCccHHHHHHHHHHHHHHhcCCcccccCHHHHHHHHcCCCCCcHHHHHHHHHHHHHHhc
Confidence            33456667764  45555532  22    23344444444454   5899999999998 69999999999999998876


Q ss_pred             CCCChhhh
Q 022641          266 SSITSKDL  273 (294)
Q Consensus       266 ~~it~~~v  273 (294)
                      ..++..++
T Consensus       458 ~~~~~~d~  465 (550)
T COG3604         458 RLTRRGDL  465 (550)
T ss_pred             ccCCCcce
Confidence            66666663

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

Probab=99.59  E-value=1.2e-14  Score=114.92  Aligned_cols=205  Identities=20%  Similarity=0.218  Sum_probs=137.3

Q ss_pred             cchhhcccHHHHHHHHHHHHcC-------------CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           59 QVKDVAHQEEVVRVLTNTLETA-------------NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~-------------~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      ++.++-|.++.++.+++.+...             .+..++++||||||||.+|+++|+..      +..|+.+-++...
T Consensus       175 ty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrt------dacfirvigselv  248 (435)
T KOG0729|consen  175 TYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRT------DACFIRVIGSELV  248 (435)
T ss_pred             ccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhccc------CceEEeehhHHHH
Confidence            4568888999999998887542             33459999999999999999999987      7777777666543


Q ss_pred             chhH--HHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHh-----hcCcce
Q 022641          126 GINV--VRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMET-----YSKVTR  187 (294)
Q Consensus       126 ~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~-----~~~~~~  187 (294)
                      -.+.  -...+..+....          ...+..+||+||+|.+.           .+++...+.++..     ...+..
T Consensus       249 qkyvgegarmvrelf~ma----------rtkkaciiffdeidaiggarfddg~ggdnevqrtmleli~qldgfdprgnik  318 (435)
T KOG0729|consen  249 QKYVGEGARMVRELFEMA----------RTKKACIIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIK  318 (435)
T ss_pred             HHHhhhhHHHHHHHHHHh----------cccceEEEEeeccccccCccccCCCCCcHHHHHHHHHHHHhccCCCCCCCeE
Confidence            3222  112222222221          22345699999999873           3355556666543     335778


Q ss_pred             EEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHH-HHHHHhhc----cCcHHHHHHHHH-
Q 022641          188 FFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEA-LSTLSSIS----QGDLRRAITYLQ-  258 (294)
Q Consensus       188 ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-l~~l~~~~----~G~~r~~~~~l~-  258 (294)
                      ++++||.+..+++++++  |.. .++|.-|+.+-...+++-.++..  .++.+. ++.|+.+|    +.++|+++...- 
T Consensus       319 vlmatnrpdtldpallrpgrldrkvef~lpdlegrt~i~kihaksm--sverdir~ellarlcpnstgaeirsvcteagm  396 (435)
T KOG0729|consen  319 VLMATNRPDTLDPALLRPGRLDRKVEFGLPDLEGRTHIFKIHAKSM--SVERDIRFELLARLCPNSTGAEIRSVCTEAGM  396 (435)
T ss_pred             EEeecCCCCCcCHhhcCCcccccceeccCCcccccceeEEEecccc--ccccchhHHHHHhhCCCCcchHHHHHHHHhhH
Confidence            99999999999999987  555 79999999888888886655443  333333 44455554    456777665443 


Q ss_pred             HHHHHhCCCCChhhhhhhccccc
Q 022641          259 GAARLFGSSITSKDLISVSGYPT  281 (294)
Q Consensus       259 ~~~~~~~~~it~~~v~~~~~~~~  281 (294)
                      ++...-.+..|..++.+++..+.
T Consensus       397 fairarrk~atekdfl~av~kvv  419 (435)
T KOG0729|consen  397 FAIRARRKVATEKDFLDAVNKVV  419 (435)
T ss_pred             HHHHHHhhhhhHHHHHHHHHHHH
Confidence            23322255678888877776543

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

Probab=99.58  E-value=1.9e-13  Score=111.59  Aligned_cols=218  Identities=15%  Similarity=0.081  Sum_probs=138.6

Q ss_pred             hhhcccHHHH---HHHHHHHHc---CCCCcEEEECCCCCCHHHHHHHHHHHhcC---CCccCCcceeecCCCCcchhHHH
Q 022641           61 KDVAHQEEVV---RVLTNTLET---ANCPHMLFYGPPGTGKTTTALAIAHQLFG---PELYKSRVLELNASDDRGINVVR  131 (294)
Q Consensus        61 ~~~~g~~~~~---~~l~~~l~~---~~~~~ill~Gp~G~GKT~la~~la~~~~~---~~~~~~~~~~~~~~~~~~~~~~~  131 (294)
                      +..+|.+.+.   +.|.+.+..   .+.++++|+|++|.|||++++.+.+....   .+....+++.+......+...+.
T Consensus        34 ~rWIgY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y  113 (302)
T PF05621_consen   34 DRWIGYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFY  113 (302)
T ss_pred             CCeecCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHH
Confidence            3445655444   455555544   34478999999999999999999987632   12234577788777776766666


Q ss_pred             HHHHHHHhhhcccCccCCC--------CCCCCcEEEEEeCCCCC---CHHHHHHHHHHHHhhc--CcceEEEEecC----
Q 022641          132 TKIKTFAAVAVGSGQRRGG--------YPCPPYKIIILDEADSM---TEDAQNALRRTMETYS--KVTRFFFICNY----  194 (294)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~--------~~~~~~~lliiDei~~l---~~~~~~~L~~~l~~~~--~~~~ii~~~~~----  194 (294)
                      ..+......+.........        ...-+..+|||||+|.+   +...+..++..+....  -...+|+++..    
T Consensus       114 ~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~A~~  193 (302)
T PF05621_consen  114 SAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTREAYR  193 (302)
T ss_pred             HHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccHHHHH
Confidence            5555544444332221111        11234569999999986   2333444444443322  23445555432    


Q ss_pred             CcccchHhhccccEEEecCCCHH-HHHHHHHHHHHHh----CCC-CCHHHHHHHHhhccCcHHHHHHHHHHHHHHh----
Q 022641          195 ISRIIEPLASRCAKFRFKPLSEE-VMSSRVLHICNEE----GLN-LDAEALSTLSSISQGDLRRAITYLQGAARLF----  264 (294)
Q Consensus       195 ~~~~~~~l~~r~~~i~~~~~~~~-~~~~~l~~~~~~~----~~~-~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~----  264 (294)
                      ....++++.+||..+.+++...+ +...++...-..-    .-. -+++...+|.+.|+|.+..+..++..++..+    
T Consensus       194 al~~D~QLa~RF~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~l~~ll~~aA~~AI~sG  273 (302)
T PF05621_consen  194 ALRTDPQLASRFEPFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIGELSRLLNAAAIAAIRSG  273 (302)
T ss_pred             HhccCHHHHhccCCccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchHHHHHHHHHHHHHHHhcC
Confidence            23457899999999999888654 4444443322211    111 3567778999999999999999999988887    


Q ss_pred             CCCCChhhhhhhcc
Q 022641          265 GSSITSKDLISVSG  278 (294)
Q Consensus       265 ~~~it~~~v~~~~~  278 (294)
                      .+.||.+.+..+--
T Consensus       274 ~E~It~~~l~~~~~  287 (302)
T PF05621_consen  274 EERITREILDKIDW  287 (302)
T ss_pred             CceecHHHHhhCCC
Confidence            56799998877543

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

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

Probab=99.58  E-value=2.7e-14  Score=123.22  Aligned_cols=176  Identities=20%  Similarity=0.214  Sum_probs=113.0

Q ss_pred             cchhhcccHHHHHHHHHHHHc----------CC--------CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           59 QVKDVAHQEEVVRVLTNTLET----------AN--------CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~----------~~--------~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      --+.++||+.+++.+...+.+          ..        ..+++|+||||||||++|+++++.+      +.++..++
T Consensus        75 L~~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l------~~pf~~~d  148 (413)
T TIGR00382        75 LDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARIL------NVPFAIAD  148 (413)
T ss_pred             hcceecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhc------CCCeEEec
Confidence            334678999999988766621          11        2469999999999999999999887      55555555


Q ss_pred             CCCCcc----hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhh
Q 022641          121 ASDDRG----INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTMETY  182 (294)
Q Consensus       121 ~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~~~  182 (294)
                      +.....    .......+........      .......+++|+|||+|.+++              ..++.|+++++..
T Consensus       149 a~~L~~~gyvG~d~e~~L~~~~~~~~------~~l~~a~~gIV~lDEIdkl~~~~~~~s~~~dvsg~~vq~~LL~iLeG~  222 (413)
T TIGR00382       149 ATTLTEAGYVGEDVENILLKLLQAAD------YDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGT  222 (413)
T ss_pred             hhhccccccccccHHHHHHHHHHhCc------ccHHhcccceEEecccchhchhhccccccccccchhHHHHHHHHhhcc
Confidence            443211    1111222222111100      001122346999999999876              5789999999632


Q ss_pred             c-------------CcceEEEEecCCc--------------------------------------------------ccc
Q 022641          183 S-------------KVTRFFFICNYIS--------------------------------------------------RII  199 (294)
Q Consensus       183 ~-------------~~~~ii~~~~~~~--------------------------------------------------~~~  199 (294)
                      .             ....+|.|+|-.+                                                  .+.
T Consensus       223 ~~~v~~~~gr~~~~~~~i~i~TsNilfi~~Gaf~g~~~i~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~dl~~~g~~  302 (413)
T TIGR00382       223 VANVPPQGGRKHPYQEFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLI  302 (413)
T ss_pred             ceecccCCCccccCCCeEEEEcCCceeeecccccChHHHHHHHhhhccccccccccccchhhHHHHHHHHHHHHHHHhhH
Confidence            1             1234555554300                                                  134


Q ss_pred             hHhhcccc-EEEecCCCHHHHHHHHHHH----HH-------HhCC--CCCHHHHHHHHhhc
Q 022641          200 EPLASRCA-KFRFKPLSEEVMSSRVLHI----CN-------EEGL--NLDAEALSTLSSIS  246 (294)
Q Consensus       200 ~~l~~r~~-~i~~~~~~~~~~~~~l~~~----~~-------~~~~--~~~~~~l~~l~~~~  246 (294)
                      |+|+.|+. ++.|.|++.+++..++..-    .+       ..++  .+++++++.|++.+
T Consensus       303 PEflgRld~Iv~f~pL~~~~L~~Il~~~~n~l~kq~~~~l~~~gi~L~~t~~a~~~Ia~~~  363 (413)
T TIGR00382       303 PEFIGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKA  363 (413)
T ss_pred             HHHhCCCCeEeecCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCeEEEECHHHHHHHHHhC
Confidence            77888987 7889999999999988752    22       1243  47899999999873

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>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=99.57  E-value=2.8e-14  Score=116.05  Aligned_cols=188  Identities=21%  Similarity=0.291  Sum_probs=107.1

Q ss_pred             hcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHH--------
Q 022641           63 VAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKI--------  134 (294)
Q Consensus        63 ~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------  134 (294)
                      ++|++..++.|.+++..+..+.++|+||+|+|||++++.+.+.+.....   ..+.+..............+        
T Consensus         1 F~gR~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~---~~~y~~~~~~~~~~~~~~~~~~~~~~~~   77 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFINELKEKGY---KVVYIDFLEESNESSLRSFIEETSLADE   77 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHHHCT--EE---CCCHHCCTTBSHHHHHHHHHHHHHHHCH
T ss_pred             CCCHHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHHHhhhcCC---cEEEEecccchhhhHHHHHHHHHHHHHH
Confidence            4689999999999999887778999999999999999999998732221   22222222222222221110        


Q ss_pred             -HHHHhhhccc-Cc--------cCCC----------CCCCCcEEEEEeCCCCCC------HHHHHHHHHHHHh--hcCcc
Q 022641          135 -KTFAAVAVGS-GQ--------RRGG----------YPCPPYKIIILDEADSMT------EDAQNALRRTMET--YSKVT  186 (294)
Q Consensus       135 -~~~~~~~~~~-~~--------~~~~----------~~~~~~~lliiDei~~l~------~~~~~~L~~~l~~--~~~~~  186 (294)
                       .......... ..        ....          ....+..+|+|||++.+.      ......|...++.  ...+.
T Consensus        78 l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  157 (234)
T PF01637_consen   78 LSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNV  157 (234)
T ss_dssp             CHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTE
T ss_pred             HHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCc
Confidence             0001110000 00        0000          001223799999999987      4555667777765  23445


Q ss_pred             eEEEEecCCcc------cchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCC--CHHHHHHHHhhccCcHHHHH
Q 022641          187 RFFFICNYISR------IIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNL--DAEALSTLSSISQGDLRRAI  254 (294)
Q Consensus       187 ~ii~~~~~~~~------~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~--~~~~l~~l~~~~~G~~r~~~  254 (294)
                      .+|+++.....      -...+..|+..+.++|++.++..+++...+... ..+  +++.++.+...++|+|+.+.
T Consensus       158 ~~v~~~S~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~e~~~~~~~~~~~~-~~~~~~~~~~~~i~~~~gG~P~~l~  232 (234)
T PF01637_consen  158 SIVITGSSDSLMEEFLDDKSPLFGRFSHIELKPLSKEEAREFLKELFKEL-IKLPFSDEDIEEIYSLTGGNPRYLQ  232 (234)
T ss_dssp             EEEEEESSHHHHHHTT-TTSTTTT---EEEE----HHHHHHHHHHHHHCC-------HHHHHHHHHHHTT-HHHHH
T ss_pred             eEEEECCchHHHHHhhcccCccccccceEEEeeCCHHHHHHHHHHHHHHh-hcccCCHHHHHHHHHHhCCCHHHHh
Confidence            55555544221      123466777789999999999999999987665 544  99999999999999999764

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

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

Probab=99.57  E-value=5.7e-14  Score=105.74  Aligned_cols=140  Identities=34%  Similarity=0.364  Sum_probs=93.3

Q ss_pred             ccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHH-Hhhhcc
Q 022641           65 HQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTF-AAVAVG  143 (294)
Q Consensus        65 g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~  143 (294)
                      |++..+..+...+......+++|+||||+|||++++.+++.+..   ....++.+++................ ....  
T Consensus         2 ~~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~---~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~--   76 (151)
T cd00009           2 GQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFR---PGAPFLYLNASDLLEGLVVAELFGHFLVRLL--   76 (151)
T ss_pred             chHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhc---CCCCeEEEehhhhhhhhHHHHHhhhhhHhHH--
Confidence            56777888888887766668999999999999999999998842   13455556554433322222111100 0000  


Q ss_pred             cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc------CcceEEEEecCCc--ccchHhhcccc-EEEecC
Q 022641          144 SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS------KVTRFFFICNYIS--RIIEPLASRCA-KFRFKP  213 (294)
Q Consensus       144 ~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~------~~~~ii~~~~~~~--~~~~~l~~r~~-~i~~~~  213 (294)
                          .......+..+|+|||++.+.......+...++...      ....+|++++...  .+.+.+.+|+. .+.++|
T Consensus        77 ----~~~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~r~~~~i~~~~  151 (151)
T cd00009          77 ----FELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL  151 (151)
T ss_pred             ----HHhhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHhhhccEeecCC
Confidence                000112345699999999997777788888887753      5677888888766  67788999984 666653

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.

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

Probab=99.57  E-value=3.5e-13  Score=108.25  Aligned_cols=126  Identities=21%  Similarity=0.279  Sum_probs=104.1

Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEec------------CCcccchHhhccccEEEecCCCHHHHHHHH
Q 022641          156 YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICN------------YISRIIEPLASRCAKFRFKPLSEEVMSSRV  223 (294)
Q Consensus       156 ~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~------------~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l  223 (294)
                      +++|||||+|+|+-++...|-+.+++--. ..++++||            .++.++-.|++|..+|...|++.++++++|
T Consensus       289 pGVLFIDEvHMLDIEcFsFlNrAlE~d~~-PiiimaTNrgit~iRGTn~~SphGiP~D~lDR~lII~t~py~~~d~~~IL  367 (454)
T KOG2680|consen  289 PGVLFIDEVHMLDIECFSFLNRALENDMA-PIIIMATNRGITRIRGTNYRSPHGIPIDLLDRMLIISTQPYTEEDIKKIL  367 (454)
T ss_pred             cceEEEeeehhhhhHHHHHHHHHhhhccC-cEEEEEcCCceEEeecCCCCCCCCCcHHHhhhhheeecccCcHHHHHHHH
Confidence            57999999999999999999999986333 33555554            346688999999999999999999999999


Q ss_pred             HHHHHHhCCCCCHHHHHHHHhhc-cCcHHHHHHHHHHHHHHh----CCCCChhhhhhhcccccC
Q 022641          224 LHICNEEGLNLDAEALSTLSSIS-QGDLRRAITYLQGAARLF----GSSITSKDLISVSGYPTG  282 (294)
Q Consensus       224 ~~~~~~~~~~~~~~~l~~l~~~~-~G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~~  282 (294)
                      +..|..+.+.+++++++.|.... .-++|.+++++..+....    +..+..+++..+...+-+
T Consensus       368 ~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~LFlD  431 (454)
T KOG2680|consen  368 RIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYRLFLD  431 (454)
T ss_pred             HhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHHHHhh
Confidence            99999999999999999999874 567999999998777655    455778888777655433

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

Probab=99.57  E-value=5.6e-14  Score=123.75  Aligned_cols=204  Identities=16%  Similarity=0.155  Sum_probs=147.7

Q ss_pred             hhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC----
Q 022641           61 KDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD----  123 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~----  123 (294)
                      ..+.|....+..++..+..             ..++.++++||||||||.++++++++.      +..++.++++.    
T Consensus       184 ~~~gg~~~~~~~i~e~v~~pl~~~~~~~s~g~~~prg~Ll~gppg~Gkt~l~~aVa~e~------~a~~~~i~~peli~k  257 (693)
T KOG0730|consen  184 DDIGGLKRQLSVIRELVELPLRHPALFKSIGIKPPRGLLLYGPPGTGKTFLVRAVANEY------GAFLFLINGPELISK  257 (693)
T ss_pred             cccchhHHHHHHHHHHHHhhhcchhhhhhcCCCCCCCccccCCCCCChHHHHHHHHHHh------CceeEecccHHHHHh
Confidence            3455556666555555422             233459999999999999999999998      67777777653    


Q ss_pred             --CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH----------HHHHHHHHHHHhhc--CcceEE
Q 022641          124 --DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE----------DAQNALRRTMETYS--KVTRFF  189 (294)
Q Consensus       124 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~----------~~~~~L~~~l~~~~--~~~~ii  189 (294)
                        ..+...++..+........             +.+|+|||++.+.+          .....|+.+++...  .+.+++
T Consensus       258 ~~gEte~~LR~~f~~a~k~~~-------------psii~IdEld~l~p~r~~~~~~e~Rv~sqlltL~dg~~~~~~vivl  324 (693)
T KOG0730|consen  258 FPGETESNLRKAFAEALKFQV-------------PSIIFIDELDALCPKREGADDVESRVVSQLLTLLDGLKPDAKVIVL  324 (693)
T ss_pred             cccchHHHHHHHHHHHhccCC-------------CeeEeHHhHhhhCCcccccchHHHHHHHHHHHHHhhCcCcCcEEEE
Confidence              2344455555555443321             45999999999853          34567888888766  667778


Q ss_pred             EEecCCcccchHhhc-ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHH-HHHHHHHHHhCC
Q 022641          190 FICNYISRIIEPLAS-RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAI-TYLQGAARLFGS  266 (294)
Q Consensus       190 ~~~~~~~~~~~~l~~-r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~-~~l~~~~~~~~~  266 (294)
                      .++|.+..+++++++ ||. .+.+.-|+.....++++.+++..+.. ++..+..++..+.|-...-+ .++..++..+-.
T Consensus       325 ~atnrp~sld~alRRgRfd~ev~IgiP~~~~RldIl~~l~k~~~~~-~~~~l~~iA~~thGyvGaDL~~l~~ea~~~~~r  403 (693)
T KOG0730|consen  325 AATNRPDSLDPALRRGRFDREVEIGIPGSDGRLDILRVLTKKMNLL-SDVDLEDIAVSTHGYVGADLAALCREASLQATR  403 (693)
T ss_pred             EecCCccccChhhhcCCCcceeeecCCCchhHHHHHHHHHHhcCCc-chhhHHHHHHHccchhHHHHHHHHHHHHHHHhh
Confidence            888999999999996 887 79999999999999999999887766 67889999999988765544 344444443322


Q ss_pred             CCChhhhhhhcccccCCCC
Q 022641          267 SITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       267 ~it~~~v~~~~~~~~~~~~  285 (294)
                      . +++++..+.....+...
T Consensus       404 ~-~~~~~~~A~~~i~psa~  421 (693)
T KOG0730|consen  404 R-TLEIFQEALMGIRPSAL  421 (693)
T ss_pred             h-hHHHHHHHHhcCCchhh
Confidence            2 77788888777766644

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=99.57  E-value=2.1e-13  Score=125.47  Aligned_cols=221  Identities=14%  Similarity=0.073  Sum_probs=138.7

Q ss_pred             cchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc-----------CCC-----------------
Q 022641           59 QVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF-----------GPE-----------------  110 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~-----------~~~-----------------  110 (294)
                      .|..++|++.++..+.-.+..+...+++|.|++|||||++|+++++.+.           |..                 
T Consensus         2 pf~~ivGq~~~~~al~~~av~~~~g~vli~G~~GtgKs~lar~l~~~lp~~~~~~~~~~~c~p~~~~~~~~~~~~~~~~~   81 (633)
T TIGR02442         2 PFTAIVGQEDLKLALLLNAVDPRIGGVLIRGEKGTAKSTAARGLAALLPPIDVVAGCPFSCDPDDPEEWCEECRRKYRPS   81 (633)
T ss_pred             CcchhcChHHHHHHHHHHhhCCCCCeEEEEcCCCCcHHHHHHHHHHhCCCceeccCCcCCCCCCCccccChhhhhccccc
Confidence            4678999999999888888776666799999999999999999998872           100                 


Q ss_pred             -ccCCcceeecCCCCcchhHHHHHHHHHHhh-hcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----
Q 022641          111 -LYKSRVLELNASDDRGINVVRTKIKTFAAV-AVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----  183 (294)
Q Consensus       111 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----  183 (294)
                       ....+++.+....  ....+...+...... ........+....+..++|+|||++.++...++.|++.++...     
T Consensus        82 ~~~~~pfv~~p~~~--t~~~l~G~~d~~~~l~~g~~~~~~G~L~~A~~GiL~lDEi~~l~~~~q~~Ll~~le~g~~~v~r  159 (633)
T TIGR02442        82 EQRPVPFVNLPLGA--TEDRVVGSLDIERALREGEKAFQPGLLAEAHRGILYIDEVNLLDDHLVDVLLDAAAMGVNRVER  159 (633)
T ss_pred             ccCCCCeeeCCCCC--cHHHcCCcccHHHHhhcCCeeecCcceeecCCCeEEeChhhhCCHHHHHHHHHHHhcCCEEEEE
Confidence             0012222222211  110000000000000 0001112333344567899999999999999999999998642     


Q ss_pred             --------CcceEEEEecCC-cccchHhhcccc-EEEecCCC-HHHHHHHHHHHHH------------------------
Q 022641          184 --------KVTRFFFICNYI-SRIIEPLASRCA-KFRFKPLS-EEVMSSRVLHICN------------------------  228 (294)
Q Consensus       184 --------~~~~ii~~~~~~-~~~~~~l~~r~~-~i~~~~~~-~~~~~~~l~~~~~------------------------  228 (294)
                              ..+.+|.++|.. ..+.+++.+||. .+.+.++. .++..+++.+...                        
T Consensus       160 ~g~~~~~~~~~~lIat~np~eg~l~~~L~dR~~l~i~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~l~~~i~  239 (633)
T TIGR02442       160 EGLSVSHPARFVLIGTMNPEEGDLRPQLLDRFGLCVDVAAPRDPEERVEIIRRRLAFDADPEAFAARWAAEQEELRNRIA  239 (633)
T ss_pred             CCceeeecCCeEEEEecCCCCCCCCHHHHhhcceEEEccCCCchHHHHHHHHHHHhhccCcHHHHHHhhhhHHHHHHHHH
Confidence                    235566666654 346789999997 56676664 3444444443211                        


Q ss_pred             -----HhCCCCCHHHHHHHHhhc---c-CcHHHHHHHHHHHHHHh----CCCCChhhhhhhccccc
Q 022641          229 -----EEGLNLDAEALSTLSSIS---Q-GDLRRAITYLQGAARLF----GSSITSKDLISVSGYPT  281 (294)
Q Consensus       229 -----~~~~~~~~~~l~~l~~~~---~-G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~  281 (294)
                           ...+.++++.++++++.+   + ..+|..+.+++-+...+    ...++.+||..++..+-
T Consensus       240 ~ar~~~~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~lvL  305 (633)
T TIGR02442       240 RARSLLPSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAELVL  305 (633)
T ss_pred             HHHHhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHh
Confidence                 013568888888888764   2 14777777777654444    56799999987665544

A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.

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

Probab=99.56  E-value=1.1e-13  Score=112.23  Aligned_cols=184  Identities=21%  Similarity=0.276  Sum_probs=120.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc---CCCccCCcceeecCCCCcc------hhHHHHHHHHHHhhhcccCccCCCCCCCC
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF---GPELYKSRVLELNASDDRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPP  155 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~---~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (294)
                      ++++||||||||+|.+++|+.+.   ...+.....+++++....+      ...+...++.+.+....         .+.
T Consensus       180 iLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d---------~~~  250 (423)
T KOG0744|consen  180 ILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVED---------RGN  250 (423)
T ss_pred             EEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhC---------CCc
Confidence            89999999999999999999983   3345566778888765433      22333444444433222         112


Q ss_pred             cEEEEEeCCCCCCH---------------HHHHHHHHHHHhhc--CcceEEEEecCCcccchHhhcccc-EEEecCCCHH
Q 022641          156 YKIIILDEADSMTE---------------DAQNALRRTMETYS--KVTRFFFICNYISRIIEPLASRCA-KFRFKPLSEE  217 (294)
Q Consensus       156 ~~lliiDei~~l~~---------------~~~~~L~~~l~~~~--~~~~ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~  217 (294)
                      .-.++|||++.+..               ++.+.|+..++...  .++.++.|+|....++.+|.+|.. +..+.||+..
T Consensus       251 lVfvLIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDrlK~~~NvliL~TSNl~~siD~AfVDRADi~~yVG~Pt~~  330 (423)
T KOG0744|consen  251 LVFVLIDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDRLKRYPNVLILATSNLTDSIDVAFVDRADIVFYVGPPTAE  330 (423)
T ss_pred             EEEEEeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHhccCCCEEEEeccchHHHHHHHhhhHhhheeecCCccHH
Confidence            34789999998731               26788888888644  455566667888899999999999 7888999999


Q ss_pred             HHHHHHHHHHHH---hCCCC--------------CHHHHHHHHhhc-cCcHHHHHHHHHHHHHHh---CCCCChhhhhhh
Q 022641          218 VMSSRVLHICNE---EGLNL--------------DAEALSTLSSIS-QGDLRRAITYLQGAARLF---GSSITSKDLISV  276 (294)
Q Consensus       218 ~~~~~l~~~~~~---~~~~~--------------~~~~l~~l~~~~-~G~~r~~~~~l~~~~~~~---~~~it~~~v~~~  276 (294)
                      -+.++++..+.+   .|+-+              .+.....+.+.+ .|--...+..|-+.+...   ...++.+.+..+
T Consensus       331 ai~~IlkscieEL~~~gIi~~~~~s~~~~~~i~~~~~~~~~~~~~~~~gLSGRtlrkLP~Laha~y~~~~~v~~~~fl~a  410 (423)
T KOG0744|consen  331 AIYEILKSCIEELISSGIILFHQRSTGVKEFIKYQKALRNILIELSTVGLSGRTLRKLPLLAHAEYFRTFTVDLSNFLLA  410 (423)
T ss_pred             HHHHHHHHHHHHHHhcCeeeeeccchhhhHHhHhhHhHHHHHHHHhhcCCccchHhhhhHHHHHhccCCCccChHHHHHH
Confidence            999988876643   23221              122233333332 444445555666655443   235777766554


Q ss_pred             c
Q 022641          277 S  277 (294)
Q Consensus       277 ~  277 (294)
                      +
T Consensus       411 l  411 (423)
T KOG0744|consen  411 L  411 (423)
T ss_pred             H
Confidence            4

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

Probab=99.55  E-value=9.6e-14  Score=115.88  Aligned_cols=204  Identities=20%  Similarity=0.181  Sum_probs=132.3

Q ss_pred             cchhhcccHHHHHHHHHHHHc--------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchh-H
Q 022641           59 QVKDVAHQEEVVRVLTNTLET--------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGIN-V  129 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~--------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~-~  129 (294)
                      .+++++-++.+...+.+....        ...+|++||||||||||..|+-|++.-      +..+-.+.+.+..... .
T Consensus       353 pl~~ViL~psLe~Rie~lA~aTaNTK~h~apfRNilfyGPPGTGKTm~ArelAr~S------GlDYA~mTGGDVAPlG~q  426 (630)
T KOG0742|consen  353 PLEGVILHPSLEKRIEDLAIATANTKKHQAPFRNILFYGPPGTGKTMFARELARHS------GLDYAIMTGGDVAPLGAQ  426 (630)
T ss_pred             CcCCeecCHHHHHHHHHHHHHhcccccccchhhheeeeCCCCCCchHHHHHHHhhc------CCceehhcCCCccccchH
Confidence            477888888877777666532        234579999999999999999999986      6666666666654321 2


Q ss_pred             HHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCC---------CHHH---HHHHHHHHHhhcCcceEEEEecCCcc
Q 022641          130 VRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSM---------TEDA---QNALRRTMETYSKVTRFFFICNYISR  197 (294)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l---------~~~~---~~~L~~~l~~~~~~~~ii~~~~~~~~  197 (294)
                      ....+..+.+...         ...+.-+|||||+|.+         +...   +|.|+----+.+..+.++++||.+..
T Consensus       427 aVTkiH~lFDWak---------kS~rGLllFIDEADAFLceRnktymSEaqRsaLNAlLfRTGdqSrdivLvlAtNrpgd  497 (630)
T KOG0742|consen  427 AVTKIHKLFDWAK---------KSRRGLLLFIDEADAFLCERNKTYMSEAQRSALNALLFRTGDQSRDIVLVLATNRPGD  497 (630)
T ss_pred             HHHHHHHHHHHHh---------hcccceEEEehhhHHHHHHhchhhhcHHHHHHHHHHHHHhcccccceEEEeccCCccc
Confidence            2223333333221         1223459999999864         3333   33333222344567788999999999


Q ss_pred             cchHhhcccc-EEEecCCCHHHHHHHHHHHHHHh-------C---------------CC----CCHHHHHHHHhhccC-c
Q 022641          198 IIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEE-------G---------------LN----LDAEALSTLSSISQG-D  249 (294)
Q Consensus       198 ~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~-------~---------------~~----~~~~~l~~l~~~~~G-~  249 (294)
                      ++-++.+|+. +++|+-|..++...+|..++.+.       +               +.    ..+..+...++.+.| +
T Consensus       498 lDsAV~DRide~veFpLPGeEERfkll~lYlnkyi~~~~~~~~~~~~~~lfkk~sQ~i~l~~~~t~~~~~EaAkkTeGfS  577 (630)
T KOG0742|consen  498 LDSAVNDRIDEVVEFPLPGEEERFKLLNLYLNKYILKPATSGKPGKWSHLFKKESQRIKLAGFDTGRKCSEAAKKTEGFS  577 (630)
T ss_pred             hhHHHHhhhhheeecCCCChHHHHHHHHHHHHHHhcCcCCCCCCchhhHHHhhhhheeeeccchHHHHHHHHHHhccCCc
Confidence            9999999998 89999999999999998888542       1               11    245667777777765 4


Q ss_pred             HHHHHHHHH--HHHHHhCC--CCChhhhhhhc
Q 022641          250 LRRAITYLQ--GAARLFGS--SITSKDLISVS  277 (294)
Q Consensus       250 ~r~~~~~l~--~~~~~~~~--~it~~~v~~~~  277 (294)
                      -|.+-.+..  .++.|.+.  -++...+++.+
T Consensus       578 GREiakLva~vQAavYgsedcvLd~~lf~e~v  609 (630)
T KOG0742|consen  578 GREIAKLVASVQAAVYGSEDCVLDEALFDERV  609 (630)
T ss_pred             HHHHHHHHHHHHHHHhcccchhhHHHHHHHHH
Confidence            455544443  34444422  24444444443

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

Probab=99.55  E-value=6.8e-14  Score=127.44  Aligned_cols=206  Identities=19%  Similarity=0.211  Sum_probs=151.1

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCC----ccCCcceeecCC
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE----LYKSRVLELNAS  122 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~----~~~~~~~~~~~~  122 (294)
                      .....++.-+...++-++|++..++.+.+.|......|-+|+|+||+|||+++..+|......+    ..+..++.++.+
T Consensus       156 y~~dlt~~Ar~gklDPvIGRd~EI~r~iqIL~RR~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sLD~g  235 (786)
T COG0542         156 YTRDLTELAREGKLDPVIGRDEEIRRTIQILSRRTKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLG  235 (786)
T ss_pred             HhhhhHHHHhcCCCCCCcChHHHHHHHHHHHhccCCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEecHH
Confidence            3445556666677889999999999999999999999999999999999999999999984322    234556666544


Q ss_pred             CCcc----hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC---------HHHHHHHHHHHHhhcCcceEE
Q 022641          123 DDRG----INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT---------EDAQNALRRTMETYSKVTRFF  189 (294)
Q Consensus       123 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~---------~~~~~~L~~~l~~~~~~~~ii  189 (294)
                      ....    .....+.++.+......          .++-+|||||+|.+-         .+..|.|...+..  ....+|
T Consensus       236 ~LvAGakyRGeFEeRlk~vl~ev~~----------~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaLAR--GeL~~I  303 (786)
T COG0542         236 SLVAGAKYRGEFEERLKAVLKEVEK----------SKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALAR--GELRCI  303 (786)
T ss_pred             HHhccccccCcHHHHHHHHHHHHhc----------CCCeEEEEechhhhcCCCcccccccchhhhhHHHHhc--CCeEEE
Confidence            3221    12222333333322211          113599999999872         3367788888876  445567


Q ss_pred             EEecC-----CcccchHhhccccEEEecCCCHHHHHHHHHHHHH----HhCCCCCHHHHHHHHhhccC------cHHHHH
Q 022641          190 FICNY-----ISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICN----EEGLNLDAEALSTLSSISQG------DLRRAI  254 (294)
Q Consensus       190 ~~~~~-----~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~----~~~~~~~~~~l~~l~~~~~G------~~r~~~  254 (294)
                      .+|+.     ...-+++|.+||+.|.+..|+.++...+|+.+..    .+++.++++++...+.++..      -|-.++
T Consensus       304 GATT~~EYRk~iEKD~AL~RRFQ~V~V~EPs~e~ti~ILrGlk~~yE~hH~V~i~D~Al~aAv~LS~RYI~dR~LPDKAI  383 (786)
T COG0542         304 GATTLDEYRKYIEKDAALERRFQKVLVDEPSVEDTIAILRGLKERYEAHHGVRITDEALVAAVTLSDRYIPDRFLPDKAI  383 (786)
T ss_pred             EeccHHHHHHHhhhchHHHhcCceeeCCCCCHHHHHHHHHHHHHHHHHccCceecHHHHHHHHHHHHhhcccCCCCchHH
Confidence            76643     3346889999999999999999999999987665    46888999999998887643      467899


Q ss_pred             HHHHHHHHHh
Q 022641          255 TYLQGAARLF  264 (294)
Q Consensus       255 ~~l~~~~~~~  264 (294)
                      .++..++...
T Consensus       384 DLiDeA~a~~  393 (786)
T COG0542         384 DLLDEAGARV  393 (786)
T ss_pred             HHHHHHHHHH
Confidence            9999888665

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

Probab=99.55  E-value=2.5e-13  Score=115.97  Aligned_cols=155  Identities=25%  Similarity=0.198  Sum_probs=104.2

Q ss_pred             hhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhh
Q 022641           61 KDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAV  140 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  140 (294)
                      ..++|.+..+..+..++..++  +++|.||||||||++|+.+++.+      +.+++.+.+........+..........
T Consensus        24 ~~~~g~~~~~~~~l~a~~~~~--~vll~G~PG~gKT~la~~lA~~l------~~~~~~i~~t~~l~p~d~~G~~~~~~~~   95 (329)
T COG0714          24 KVVVGDEEVIELALLALLAGG--HVLLEGPPGVGKTLLARALARAL------GLPFVRIQCTPDLLPSDLLGTYAYAALL   95 (329)
T ss_pred             CeeeccHHHHHHHHHHHHcCC--CEEEECCCCccHHHHHHHHHHHh------CCCeEEEecCCCCCHHHhcCchhHhhhh
Confidence            347788888888877777776  79999999999999999999999      7888888877654443332211111110


Q ss_pred             --hcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc------------CcceEEEEec-----CCcccchH
Q 022641          141 --AVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS------------KVTRFFFICN-----YISRIIEP  201 (294)
Q Consensus       141 --~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~------------~~~~ii~~~~-----~~~~~~~~  201 (294)
                        ........+....+-..++++|||++.++..++.|+..|++..            ..+.++.|+|     ....++++
T Consensus        96 ~~~~~~~~~~gpl~~~~~~ill~DEInra~p~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~g~~~l~eA  175 (329)
T COG0714          96 LEPGEFRFVPGPLFAAVRVILLLDEINRAPPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEGTYPLPEA  175 (329)
T ss_pred             ccCCeEEEecCCcccccceEEEEeccccCCHHHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccCCCcCCCHH
Confidence              0000001111111111599999999999999999999998621            3344555557     34568999


Q ss_pred             hhccc-cEEEecCC-CHHHHHHHH
Q 022641          202 LASRC-AKFRFKPL-SEEVMSSRV  223 (294)
Q Consensus       202 l~~r~-~~i~~~~~-~~~~~~~~l  223 (294)
                      +++|| ..+.++.| +.++...++
T Consensus       176 ~ldRf~~~~~v~yp~~~~e~~~i~  199 (329)
T COG0714         176 LLDRFLLRIYVDYPDSEEEERIIL  199 (329)
T ss_pred             HHhhEEEEEecCCCCchHHHHHHH
Confidence            99999 58888888 444444443

>smart00350 MCM minichromosome maintenance proteins

Probab=99.54  E-value=9e-13  Score=118.47  Aligned_cols=219  Identities=16%  Similarity=0.149  Sum_probs=138.1

Q ss_pred             hhhhcCCCcchhhcccHHHHHHHHHHHHcCCC------------CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCccee
Q 022641           51 WVEKYRPKQVKDVAHQEEVVRVLTNTLETANC------------PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLE  118 (294)
Q Consensus        51 ~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~------------~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~  118 (294)
                      +.+.+...-...+.|++..+..+.-.+..+..            .|++|+|+||+|||++|+.+++.....     .++.
T Consensus       193 ~~~~l~~si~p~i~G~~~~k~~l~l~l~gg~~~~~~~~~~~r~~~~vLL~G~pGtGKs~lar~l~~~~~r~-----~~~~  267 (509)
T smart00350      193 IYERLSRSLAPSIYGHEDIKKAILLLLFGGVHKNLPDGMKIRGDINILLLGDPGTAKSQLLKYVEKTAPRA-----VYTT  267 (509)
T ss_pred             HHHHHHHhhCccccCcHHHHHHHHHHHhCCCccccCCCccccccceEEEeCCCChhHHHHHHHHHHHcCcc-----eEcC
Confidence            33444444455788999888888777766532            169999999999999999999876211     1111


Q ss_pred             ecCCCCcch--hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-------------
Q 022641          119 LNASDDRGI--NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-------------  183 (294)
Q Consensus       119 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-------------  183 (294)
                      ....+..+.  ...++.      .........+....+..++|+|||++.+++..+..|+..|+...             
T Consensus       268 ~~~~~~~~l~~~~~~~~------~~g~~~~~~G~l~~A~~Gil~iDEi~~l~~~~q~~L~e~me~~~i~i~k~G~~~~l~  341 (509)
T smart00350      268 GKGSSAVGLTAAVTRDP------ETREFTLEGGALVLADNGVCCIDEFDKMDDSDRTAIHEAMEQQTISIAKAGITTTLN  341 (509)
T ss_pred             CCCCCcCCccccceEcc------CcceEEecCccEEecCCCEEEEechhhCCHHHHHHHHHHHhcCEEEEEeCCEEEEec
Confidence            000111010  000000      00001112333445667899999999999999999999997532             


Q ss_pred             CcceEEEEecCCc-------------ccchHhhcccc--EEEecCCCHHHHHHHHHHHHHH-------------------
Q 022641          184 KVTRFFFICNYIS-------------RIIEPLASRCA--KFRFKPLSEEVMSSRVLHICNE-------------------  229 (294)
Q Consensus       184 ~~~~ii~~~~~~~-------------~~~~~l~~r~~--~i~~~~~~~~~~~~~l~~~~~~-------------------  229 (294)
                      ..+.+|.++|...             .+++++++||.  .+...+++.+.-..++++++..                   
T Consensus       342 ~~~~viAa~NP~~g~y~~~~~~~~n~~l~~~lLsRFdLi~~~~d~~~~~~d~~i~~~i~~~~~~~~~~~~~~~~~~~~~~  421 (509)
T smart00350      342 ARCSVLAAANPIGGRYDPKLTPEENIDLPAPILSRFDLLFVVLDEVDEERDRELAKHVVDLHRYSHPEPDEADEVPISQE  421 (509)
T ss_pred             CCcEEEEEeCCCCcccCCCcChhhccCCChHHhCceeeEEEecCCCChHHHHHHHHHHHHhhcccCccccccccccCCHH
Confidence            4566888887542             48899999996  3455667766666666554321                   


Q ss_pred             ------------hCCCCCHHHHHHHHhhc-----c-----------CcHHHHHHHHHHHHHHh----CCCCChhhhhhhc
Q 022641          230 ------------EGLNLDAEALSTLSSIS-----Q-----------GDLRRAITYLQGAARLF----GSSITSKDLISVS  277 (294)
Q Consensus       230 ------------~~~~~~~~~l~~l~~~~-----~-----------G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~  277 (294)
                                  -...+++++.++|.+.+     .           -.+|.+..++..+...+    +..++.+|+..++
T Consensus       422 ~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~Dv~~ai  501 (509)
T smart00350      422 FLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEADVEEAI  501 (509)
T ss_pred             HHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHH
Confidence                        11246788877776541     1           14677777776655555    6679999999887


Q ss_pred             ccc
Q 022641          278 GYP  280 (294)
Q Consensus       278 ~~~  280 (294)
                      .-+
T Consensus       502 ~l~  504 (509)
T smart00350      502 RLL  504 (509)
T ss_pred             HHH
Confidence            654

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=99.53  E-value=4e-15  Score=115.04  Aligned_cols=139  Identities=19%  Similarity=0.188  Sum_probs=64.5

Q ss_pred             cCCchhhhhcCCCcchhhcc-cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC
Q 022641           46 QSSQPWVEKYRPKQVKDVAH-QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD  124 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g-~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~  124 (294)
                      .+.+|....+...++..-.+ .+..+..+...-+.....+++|+||+|||||++|.++++++...   +..+..++..  
T Consensus        10 ~a~lp~~~~~~~~d~~~~~~~~~~~~~~l~~~~~~~~~~~l~l~G~~G~GKThLa~ai~~~~~~~---g~~v~f~~~~--   84 (178)
T PF01695_consen   10 QAGLPPDATLENFDFSNERGIDKAQIAQLAALEFIENGENLILYGPPGTGKTHLAVAIANEAIRK---GYSVLFITAS--   84 (178)
T ss_dssp             ------------------------HHHHHHHH-S-SC--EEEEEESTTSSHHHHHHHHHHHHHHT---T--EEEEEHH--
T ss_pred             ccccccccccccccccchhhHHHHHHHHHhcCCCcccCeEEEEEhhHhHHHHHHHHHHHHHhccC---CcceeEeecC--
Confidence            56666444454444443322 33444555444444455689999999999999999999998532   2223333211  


Q ss_pred             cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC--HHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          125 RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT--EDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                             +.+..+.................+.++|||||++...  ....+.|+++++.++.+..+|+|||...
T Consensus        85 -------~L~~~l~~~~~~~~~~~~~~~l~~~dlLilDDlG~~~~~~~~~~~l~~ii~~R~~~~~tIiTSN~~~  151 (178)
T PF01695_consen   85 -------DLLDELKQSRSDGSYEELLKRLKRVDLLILDDLGYEPLSEWEAELLFEIIDERYERKPTIITSNLSP  151 (178)
T ss_dssp             -------HHHHHHHCCHCCTTHCHHHHHHHTSSCEEEETCTSS---HHHHHCTHHHHHHHHHT-EEEEEESS-H
T ss_pred             -------ceeccccccccccchhhhcCccccccEecccccceeeecccccccchhhhhHhhcccCeEeeCCCch
Confidence                   1111111110000000000001234599999998764  4466779999998887778999998653

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.

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.53  E-value=7.8e-13  Score=117.96  Aligned_cols=212  Identities=20%  Similarity=0.195  Sum_probs=139.3

Q ss_pred             cchhhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHH
Q 022641           59 QVKDVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKT  136 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  136 (294)
                      .+..++|....+..+...+..  ....+++|+|++||||+++|+.+.....   ....+++.++|..... ..+...+..
T Consensus       137 ~~~~lig~s~~~~~l~~~i~~~a~~~~~vli~Ge~GtGK~~lA~~ih~~s~---~~~~~~v~v~c~~~~~-~~~~~~lfg  212 (445)
T TIGR02915       137 ALRGLITSSPGMQKICRTIEKIAPSDITVLLLGESGTGKEVLARALHQLSD---RKDKRFVAINCAAIPE-NLLESELFG  212 (445)
T ss_pred             cccceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhCC---cCCCCeEEEECCCCCh-HHHHHHhcC
Confidence            344677776666666665543  2334699999999999999999987642   2345788888877532 222221111


Q ss_pred             HHhhhccc--CccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-------
Q 022641          137 FAAVAVGS--GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-------  196 (294)
Q Consensus       137 ~~~~~~~~--~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-------  196 (294)
                      ........  ....+....+.++.|+|||++.|+...+..|+++++...           ..+++|++++...       
T Consensus       213 ~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~  292 (445)
T TIGR02915       213 YEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIAEG  292 (445)
T ss_pred             CCCCCcCCCccCCCCceeECCCCEEEEechhhCCHHHHHHHHHHHhhCeEEeCCCCceeeeceEEEEecCCCHHHHHHcC
Confidence            00000000  111222334567899999999999999999999998643           2457888886542       


Q ss_pred             ccchHhhcccc--EEEecCCCH--HHHHHHHHHHHH----HhC---CCCCHHHHHHHHhh-ccCcHHHHHHHHHHHHHHh
Q 022641          197 RIIEPLASRCA--KFRFKPLSE--EVMSSRVLHICN----EEG---LNLDAEALSTLSSI-SQGDLRRAITYLQGAARLF  264 (294)
Q Consensus       197 ~~~~~l~~r~~--~i~~~~~~~--~~~~~~l~~~~~----~~~---~~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~~  264 (294)
                      .+.+.|..|+.  .|.++|+..  +++..++.+++.    ..+   ..+++++++.|..+ ++||+|++.++++.++...
T Consensus       293 ~~~~~L~~~l~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNvreL~~~i~~a~~~~  372 (445)
T TIGR02915       293 TFREDLFYRIAEISITIPPLRSRDGDAVLLANAFLERFARELKRKTKGFTDDALRALEAHAWPGNVRELENKVKRAVIMA  372 (445)
T ss_pred             CccHHHHHHhccceecCCCchhchhhHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHhCCCCChHHHHHHHHHHHHHhC
Confidence            24455667765  677777753  344444444443    323   35899999999988 5999999999999988766


Q ss_pred             -CCCCChhhhh
Q 022641          265 -GSSITSKDLI  274 (294)
Q Consensus       265 -~~~it~~~v~  274 (294)
                       +..|+.+++.
T Consensus       373 ~~~~i~~~~l~  383 (445)
T TIGR02915       373 EGNQITAEDLG  383 (445)
T ss_pred             CCCcccHHHcC
Confidence             4568877764

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

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.53  E-value=8.9e-15  Score=109.27  Aligned_cols=116  Identities=23%  Similarity=0.219  Sum_probs=77.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDE  163 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDe  163 (294)
                      +++|+||||||||++++.+++.+      +..+..+++........+....... ................+..+++|||
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~------~~~~~~i~~~~~~~~~dl~g~~~~~-~~~~~~~~~~l~~a~~~~~il~lDE   73 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALL------GRPVIRINCSSDTTEEDLIGSYDPS-NGQFEFKDGPLVRAMRKGGILVLDE   73 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH------TCEEEEEE-TTTSTHHHHHCEEET--TTTTCEEE-CCCTTHHEEEEEEESS
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh------hcceEEEEeccccccccceeeeeec-ccccccccccccccccceeEEEECC
Confidence            48999999999999999999999      7788888877766655443211111 0000000011111123678999999


Q ss_pred             CCCCCHHHHHHHHHHHHhhc-------------C------cceEEEEecCCc----ccchHhhccc
Q 022641          164 ADSMTEDAQNALRRTMETYS-------------K------VTRFFFICNYIS----RIIEPLASRC  206 (294)
Q Consensus       164 i~~l~~~~~~~L~~~l~~~~-------------~------~~~ii~~~~~~~----~~~~~l~~r~  206 (294)
                      ++..++..++.|..+++...             .      ...+|+++|...    .+.+++++||
T Consensus        74 in~a~~~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~l~~al~~Rf  139 (139)
T PF07728_consen   74 INRAPPEVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKELSPALLDRF  139 (139)
T ss_dssp             CGG--HHHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTTTCHHHHTT-
T ss_pred             cccCCHHHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCcCCHHHHhhC
Confidence            99999999999999997422             1      277888888877    7889999987

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.

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

Probab=99.52  E-value=9.2e-13  Score=118.25  Aligned_cols=213  Identities=20%  Similarity=0.253  Sum_probs=141.7

Q ss_pred             cchhhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHH
Q 022641           59 QVKDVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKT  136 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  136 (294)
                      .+.+++|.......+.+.+..  .....++|+|++|||||++|+++....   .....+++.+++..... ..+...+..
T Consensus       136 ~~~~lig~s~~~~~l~~~~~~~~~~~~~vli~Ge~GtGK~~lA~~ih~~s---~~~~~~~i~i~c~~~~~-~~~~~~lfg  211 (469)
T PRK10923        136 PTTDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRHS---PRAKAPFIALNMAAIPK-DLIESELFG  211 (469)
T ss_pred             ccccceecCHHHHHHHHHHHHHhccCCeEEEEeCCCCcHHHHHHHHHhcC---CCCCCCeEeeeCCCCCH-HHHHHHhcC
Confidence            345678876666666555533  223359999999999999999998764   23356888888877522 222211111


Q ss_pred             HH-hhhcc-cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCC-------c
Q 022641          137 FA-AVAVG-SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYI-------S  196 (294)
Q Consensus       137 ~~-~~~~~-~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~-------~  196 (294)
                      .. ....+ .....+....+.++.|+|||++.++...+..|++.+++..           ..+++|++++..       .
T Consensus       212 ~~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l~~~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~  291 (469)
T PRK10923        212 HEKGAFTGANTIRQGRFEQADGGTLFLDEIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEG  291 (469)
T ss_pred             CCCCCCCCCCcCCCCCeeECCCCEEEEeccccCCHHHHHHHHHHHhcCcEEeCCCCCeEEeeEEEEEeCCCCHHHHHHcC
Confidence            00 00000 0011222334556799999999999999999999998643           234788887643       2


Q ss_pred             ccchHhhcccc--EEEecCCCH--HHHHHHHHHHHH----HhCC---CCCHHHHHHHHhh-ccCcHHHHHHHHHHHHHHh
Q 022641          197 RIIEPLASRCA--KFRFKPLSE--EVMSSRVLHICN----EEGL---NLDAEALSTLSSI-SQGDLRRAITYLQGAARLF  264 (294)
Q Consensus       197 ~~~~~l~~r~~--~i~~~~~~~--~~~~~~l~~~~~----~~~~---~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~~  264 (294)
                      .+.+.+..|+.  .|.++|+..  +++..++.+++.    ..+.   .+++++++.|..+ +.||+|++.++++.++...
T Consensus       292 ~~~~~L~~~l~~~~i~~PpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNv~eL~~~i~~~~~~~  371 (469)
T PRK10923        292 KFREDLFHRLNVIRVHLPPLRERREDIPRLARHFLQVAARELGVEAKLLHPETEAALTRLAWPGNVRQLENTCRWLTVMA  371 (469)
T ss_pred             CchHHHHHHhcceeecCCCcccchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhCCCCChHHHHHHHHHHHHHhC
Confidence            34567788875  677777754  555555555543    3232   4899999999988 7999999999999988766


Q ss_pred             -CCCCChhhhhh
Q 022641          265 -GSSITSKDLIS  275 (294)
Q Consensus       265 -~~~it~~~v~~  275 (294)
                       +..|+.+++..
T Consensus       372 ~~~~i~~~~l~~  383 (469)
T PRK10923        372 AGQEVLIQDLPG  383 (469)
T ss_pred             CCCcccHHHCcH
Confidence             55688888753

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

Probab=99.52  E-value=5.4e-13  Score=118.31  Aligned_cols=192  Identities=13%  Similarity=0.118  Sum_probs=130.1

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEE
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIIL  161 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llii  161 (294)
                      .++++|.||+|+|||.|++++++++.........++.+...+......+...+..........+          +.+|++
T Consensus       431 ~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~vfse~~~~~----------PSiIvL  500 (952)
T KOG0735|consen  431 HGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTLDGSSLEKIQKFLNNVFSEALWYA----------PSIIVL  500 (952)
T ss_pred             cccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEechhccchhHHHHHHHHHHHHHHHHhhC----------CcEEEE
Confidence            3569999999999999999999998633333333333344444455555555555554444333          349999


Q ss_pred             eCCCCCCH--------------HHHHHHHHHHHh---hcCcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHH
Q 022641          162 DEADSMTE--------------DAQNALRRTMET---YSKVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSS  221 (294)
Q Consensus       162 Dei~~l~~--------------~~~~~L~~~l~~---~~~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~  221 (294)
                      |++|.+..              .....|.+++..   ......+|.+++....+.+.+.+  +|+ ++.+++|..+++.+
T Consensus       501 Ddld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~R~~  580 (952)
T KOG0735|consen  501 DDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAVTRRKE  580 (952)
T ss_pred             cchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCCcchhHHHH
Confidence            99998732              012233344433   23344567777777777777665  555 78999999999999


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHhhccCc-HHHHHHHHHHHHHHh--------CCCCChhhhhhhcccccCC
Q 022641          222 RVLHICNEEGLNLDAEALSTLSSISQGD-LRRAITYLQGAARLF--------GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       222 ~l~~~~~~~~~~~~~~~l~~l~~~~~G~-~r~~~~~l~~~~~~~--------~~~it~~~v~~~~~~~~~~  283 (294)
                      +|.+.+++.......+.++.++..|+|- .+.+....+.+...+        .+-+|.+++.+.+..+.+-
T Consensus       581 IL~~~~s~~~~~~~~~dLd~ls~~TEGy~~~DL~ifVeRai~~a~leris~~~klltke~f~ksL~~F~P~  651 (952)
T KOG0735|consen  581 ILTTIFSKNLSDITMDDLDFLSVKTEGYLATDLVIFVERAIHEAFLERISNGPKLLTKELFEKSLKDFVPL  651 (952)
T ss_pred             HHHHHHHhhhhhhhhHHHHHHHHhcCCccchhHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHhcChH
Confidence            9999999887777888899999999884 444444444444333        2358999999888876654

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=99.52  E-value=2.4e-14  Score=110.96  Aligned_cols=117  Identities=27%  Similarity=0.358  Sum_probs=71.9

Q ss_pred             cchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC---------------
Q 022641           59 QVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD---------------  123 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~---------------  123 (294)
                      +|.+++||+.+++.+.-+...+  .|++|+||||||||++|+.+..-+-  ........++..-.               
T Consensus         1 Df~dI~GQe~aKrAL~iAAaG~--h~lLl~GppGtGKTmlA~~l~~lLP--~l~~~e~le~~~i~s~~~~~~~~~~~~~~   76 (206)
T PF01078_consen    1 DFSDIVGQEEAKRALEIAAAGG--HHLLLIGPPGTGKTMLARRLPSLLP--PLTEEEALEVSKIYSVAGLGPDEGLIRQR   76 (206)
T ss_dssp             -TCCSSSTHHHHHHHHHHHHCC----EEEES-CCCTHHHHHHHHHHCS----CCEECCESS--S-TT---S---EEEE--
T ss_pred             ChhhhcCcHHHHHHHHHHHcCC--CCeEEECCCCCCHHHHHHHHHHhCC--CCchHHHhhhccccccccCCCCCceecCC
Confidence            4789999999999998777754  4899999999999999999997662  11111111111000               


Q ss_pred             -CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh
Q 022641          124 -DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY  182 (294)
Q Consensus       124 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~  182 (294)
                       .+....- .....+.  ..+...+++....+.++|||+||+..++....+.|++.+++.
T Consensus        77 Pfr~phhs-~s~~~li--Ggg~~~~PGeislAh~GVLflDE~~ef~~~vld~Lr~ple~g  133 (206)
T PF01078_consen   77 PFRAPHHS-ASEAALI--GGGRPPRPGEISLAHRGVLFLDELNEFDRSVLDALRQPLEDG  133 (206)
T ss_dssp             -EEEE-TT---HHHHH--EEGGGEEE-CGGGGTTSEEEECETTTS-HHHHHHHHHHHHHS
T ss_pred             CcccCCCC-cCHHHHh--CCCcCCCcCHHHHhcCCEEEechhhhcCHHHHHHHHHHHHCC
Confidence             0000000 0001111  112233566777788999999999999999999999999863

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.51  E-value=1.8e-12  Score=101.11  Aligned_cols=192  Identities=20%  Similarity=0.261  Sum_probs=135.3

Q ss_pred             hhcCCCcchhhcccHHHHHHHHHH----HHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchh
Q 022641           53 EKYRPKQVKDVAHQEEVVRVLTNT----LETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGIN  128 (294)
Q Consensus        53 ~~~~~~~~~~~~g~~~~~~~l~~~----l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~  128 (294)
                      ..+.+..+.+++|-+..++.|.+-    +......|++|+|..|||||++++++..++...   +...++++..+.....
T Consensus        52 ~~~~~i~L~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~~---glrLVEV~k~dl~~Lp  128 (287)
T COG2607          52 PDPDPIDLADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYADE---GLRLVEVDKEDLATLP  128 (287)
T ss_pred             CCCCCcCHHHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHHhc---CCeEEEEcHHHHhhHH
Confidence            566777889999988888776543    333344569999999999999999999988433   3346777666655544


Q ss_pred             HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-HHHHHHHHHHHH----hhcCcceEEEEecCCcccch---
Q 022641          129 VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-EDAQNALRRTME----TYSKVTRFFFICNYISRIIE---  200 (294)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-~~~~~~L~~~l~----~~~~~~~ii~~~~~~~~~~~---  200 (294)
                      .+.+.+...                ..+-||++||+-.=. ...-..|...++    ..+.++.+..|+|..+.++.   
T Consensus       129 ~l~~~Lr~~----------------~~kFIlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNRRHLl~e~~~  192 (287)
T COG2607         129 DLVELLRAR----------------PEKFILFCDDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSNRRHLLPEDMK  192 (287)
T ss_pred             HHHHHHhcC----------------CceEEEEecCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecCCcccccHhhh
Confidence            444433332                223499999986543 334455666665    56677878888877654431   


Q ss_pred             -------------------Hhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH-----hhccCcHHHHHH
Q 022641          201 -------------------PLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLS-----SISQGDLRRAIT  255 (294)
Q Consensus       201 -------------------~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~-----~~~~G~~r~~~~  255 (294)
                                         .+..||. .+.|.|++.++...++..+++..++.++++.++.=+     ...+.+-|.+.+
T Consensus       193 dn~~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~~~~l~~~~e~l~~eAl~WAt~rg~RSGR~A~Q  272 (287)
T COG2607         193 DNEGSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDEYLKIVDHYAKHFGLDISDEELHAEALQWATTRGGRSGRVAWQ  272 (287)
T ss_pred             hCCCcccccChhHHHHHhhchhhhcceeecccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhcCCCccHhHHH
Confidence                               2345776 789999999999999999999999999876655433     334567788888


Q ss_pred             HHHHHHHH
Q 022641          256 YLQGAARL  263 (294)
Q Consensus       256 ~l~~~~~~  263 (294)
                      .++.++.-
T Consensus       273 F~~~~~g~  280 (287)
T COG2607         273 FIRDLAGR  280 (287)
T ss_pred             HHHHHHhh
Confidence            88877643

>PHA02244 ATPase-like protein

Probab=99.51  E-value=7.1e-13  Score=111.44  Aligned_cols=132  Identities=16%  Similarity=0.109  Sum_probs=87.6

Q ss_pred             HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCC
Q 022641           71 RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGG  150 (294)
Q Consensus        71 ~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (294)
                      ..+..|+..+.  +++|+||||||||++|+++++.+      +.+++.++...  ....+..    ...........+..
T Consensus       110 ~ri~r~l~~~~--PVLL~GppGtGKTtLA~aLA~~l------g~pfv~In~l~--d~~~L~G----~i~~~g~~~dgpLl  175 (383)
T PHA02244        110 ADIAKIVNANI--PVFLKGGAGSGKNHIAEQIAEAL------DLDFYFMNAIM--DEFELKG----FIDANGKFHETPFY  175 (383)
T ss_pred             HHHHHHHhcCC--CEEEECCCCCCHHHHHHHHHHHh------CCCEEEEecCh--HHHhhcc----cccccccccchHHH
Confidence            45566666554  69999999999999999999998      66676665321  0000000    00000000000000


Q ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh-----------cCcceEEEEecCC-----------cccchHhhccccE
Q 022641          151 YPCPPYKIIILDEADSMTEDAQNALRRTMETY-----------SKVTRFFFICNYI-----------SRIIEPLASRCAK  208 (294)
Q Consensus       151 ~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~-----------~~~~~ii~~~~~~-----------~~~~~~l~~r~~~  208 (294)
                      ......++|+|||++.+++..+..|..+++..           +..+++|+++|..           ..+.+++++||..
T Consensus       176 ~A~~~GgvLiLDEId~a~p~vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~~~~G~~~~y~G~k~L~~AllDRFv~  255 (383)
T PHA02244        176 EAFKKGGLFFIDEIDASIPEALIIINSAIANKFFDFADERVTAHEDFRVISAGNTLGKGADHIYVARNKIDGATLDRFAP  255 (383)
T ss_pred             HHhhcCCEEEEeCcCcCCHHHHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCCCccCcccccCCCcccCHHHHhhcEE
Confidence            00234569999999999999999999998632           3577899999873           4578999999999


Q ss_pred             EEecCCCH
Q 022641          209 FRFKPLSE  216 (294)
Q Consensus       209 i~~~~~~~  216 (294)
                      +.+..|+.
T Consensus       256 I~~dyp~~  263 (383)
T PHA02244        256 IEFDYDEK  263 (383)
T ss_pred             eeCCCCcH
Confidence            99988874

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

Probab=99.50  E-value=1.2e-13  Score=111.41  Aligned_cols=202  Identities=20%  Similarity=0.210  Sum_probs=130.6

Q ss_pred             CCcchhhcccHHHHHHHHHHHHcC-------------CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLETA-------------NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~~-------------~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ..+|+++-|.-..+..+++.+.-+             .+..++||||||+|||.++++++..+      +..++.+.++.
T Consensus       128 ~~s~~~~ggl~~qirelre~ielpl~np~lf~rvgIk~Pkg~ll~GppGtGKTlla~~Vaa~m------g~nfl~v~ss~  201 (388)
T KOG0651|consen  128 NISFENVGGLFYQIRELREVIELPLTNPELFLRVGIKPPKGLLLYGPPGTGKTLLARAVAATM------GVNFLKVVSSA  201 (388)
T ss_pred             ccCHHHhCChHHHHHHHHhheEeeccCchhccccCCCCCceeEEeCCCCCchhHHHHHHHHhc------CCceEEeeHhh
Confidence            347778888888888887776432             22249999999999999999999999      88888887665


Q ss_pred             Ccc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHhhc---
Q 022641          124 DRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMETYS---  183 (294)
Q Consensus       124 ~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~~~---  183 (294)
                      ..+      ...+++.+.......              +.+|++||+|...           ...+..|..+++...   
T Consensus       202 lv~kyiGEsaRlIRemf~yA~~~~--------------pciifmdeiDAigGRr~se~Ts~dreiqrTLMeLlnqmdgfd  267 (388)
T KOG0651|consen  202 LVDKYIGESARLIRDMFRYAREVI--------------PCIIFMDEIDAIGGRRFSEGTSSDREIQRTLMELLNQMDGFD  267 (388)
T ss_pred             hhhhhcccHHHHHHHHHHHHhhhC--------------ceEEeehhhhhhccEEeccccchhHHHHHHHHHHHHhhccch
Confidence            433      233444444333332              2599999999762           224455555555332   


Q ss_pred             --CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhC--CCCCHHHHHHHHhhccCcHHHHHHH
Q 022641          184 --KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEG--LNLDAEALSTLSSISQGDLRRAITY  256 (294)
Q Consensus       184 --~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~--~~~~~~~l~~l~~~~~G~~r~~~~~  256 (294)
                        ..+.+|+++|++..+.++|++  |.. .+.++-|+..-...+++-....-.  -.++.+++-.+.+..+|  -...+.
T Consensus       268 ~l~rVk~ImatNrpdtLdpaLlRpGRldrk~~iPlpne~~r~~I~Kih~~~i~~~Geid~eaivK~~d~f~g--ad~rn~  345 (388)
T KOG0651|consen  268 TLHRVKTIMATNRPDTLDPALLRPGRLDRKVEIPLPNEQARLGILKIHVQPIDFHGEIDDEAILKLVDGFNG--ADLRNV  345 (388)
T ss_pred             hcccccEEEecCCccccchhhcCCccccceeccCCcchhhceeeEeeccccccccccccHHHHHHHHhccCh--HHHhhh
Confidence              467799999999999999987  665 677776666666665533222111  13677777777777665  234455


Q ss_pred             HHHHHHHh----CCCCChhhhhhhcccc
Q 022641          257 LQGAARLF----GSSITSKDLISVSGYP  280 (294)
Q Consensus       257 l~~~~~~~----~~~it~~~v~~~~~~~  280 (294)
                      ++.+..++    ...+-.|++..++.+.
T Consensus       346 ~tEag~Fa~~~~~~~vl~Ed~~k~vrk~  373 (388)
T KOG0651|consen  346 CTEAGMFAIPEERDEVLHEDFMKLVRKQ  373 (388)
T ss_pred             cccccccccchhhHHHhHHHHHHHHHHH
Confidence            55554443    2335555555555443

>TIGR00368 Mg chelatase-related protein

Probab=99.49  E-value=1.7e-12  Score=115.39  Aligned_cols=156  Identities=23%  Similarity=0.274  Sum_probs=98.9

Q ss_pred             CcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc-c---------h
Q 022641           58 KQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR-G---------I  127 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~-~---------~  127 (294)
                      .+|.++.|+...++.+...+..+  .+++|+||||+|||++++.+...+..  .....+++...-... +         .
T Consensus       189 ~d~~dv~Gq~~~~~al~~aa~~g--~~vlliG~pGsGKTtlar~l~~llp~--~~~~~~le~~~i~s~~g~~~~~~~~~~  264 (499)
T TIGR00368       189 LDLKDIKGQQHAKRALEIAAAGG--HNLLLFGPPGSGKTMLASRLQGILPP--LTNEEAIETARIWSLVGKLIDRKQIKQ  264 (499)
T ss_pred             CCHHHhcCcHHHHhhhhhhccCC--CEEEEEecCCCCHHHHHHHHhcccCC--CCCcEEEeccccccchhhhcccccccc
Confidence            47899999999988877666544  47999999999999999999876521  111111111110000 0         0


Q ss_pred             hHHHH---HHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-------------CcceEEEE
Q 022641          128 NVVRT---KIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-------------KVTRFFFI  191 (294)
Q Consensus       128 ~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-------------~~~~ii~~  191 (294)
                      ...+.   ..........+...+++....+.+++|||||++.+++..++.|++.|+...             ..+.+|.+
T Consensus       265 ~Pf~~p~~s~s~~~~~ggg~~~~pG~i~lA~~GvLfLDEi~e~~~~~~~~L~~~LE~~~v~i~r~g~~~~~pa~frlIaa  344 (499)
T TIGR00368       265 RPFRSPHHSASKPALVGGGPIPLPGEISLAHNGVLFLDELPEFKRSVLDALREPIEDGSISISRASAKIFYPARFQLVAA  344 (499)
T ss_pred             CCccccccccchhhhhCCccccchhhhhccCCCeEecCChhhCCHHHHHHHHHHHHcCcEEEEecCcceeccCCeEEEEe
Confidence            00000   000000001111134455566778899999999999999999999998642             45678888


Q ss_pred             ecCC------c-----------------ccchHhhcccc-EEEecCCCHH
Q 022641          192 CNYI------S-----------------RIIEPLASRCA-KFRFKPLSEE  217 (294)
Q Consensus       192 ~~~~------~-----------------~~~~~l~~r~~-~i~~~~~~~~  217 (294)
                      +|.-      .                 .+..+|++||. .+.+++++..
T Consensus       345 ~Npcpcg~~~~~~~~c~c~~~~~~~y~~~is~pllDR~dl~~~~~~~~~~  394 (499)
T TIGR00368       345 MNPCPCGHYGGKNTHCRCSPQQISRYWNKLSGPFLDRIDLSVEVPLLPPE  394 (499)
T ss_pred             cCCcccCcCCCCcccccCCHHHHHHHhhhccHhHHhhCCEEEEEcCCCHH
Confidence            8742      1                 36788999998 6788877544

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=99.49  E-value=2.6e-14  Score=116.65  Aligned_cols=167  Identities=15%  Similarity=0.219  Sum_probs=93.6

Q ss_pred             CCCCcccCCCC--cccCCCCchHHHHhhccccccCCchhhhhcCCCcchhhcc-cHHHHHHHHHHH-HcCCCCcEEEECC
Q 022641           15 KSPNFTQKFST--TQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAH-QEEVVRVLTNTL-ETANCPHMLFYGP   90 (294)
Q Consensus        15 ~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g-~~~~~~~l~~~l-~~~~~~~ill~Gp   90 (294)
                      +.+.+.+++..  ..+..++..+...++++   .+++|..+.+...+++...+ +..+...+.... .-.+..+++|+||
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~---~a~~p~~k~~~~~d~~~~~~~~~~~l~~~~~~~~~~~~~~nl~l~G~  113 (254)
T COG1484          37 KEWGYAEFLEYLLEEEKLAREARKIERRLR---SASFPAKKTFEEFDFEFQPGIDKKALEDLASLVEFFERGENLVLLGP  113 (254)
T ss_pred             hcccHHHHHHHHHHHHHHHHHHHHHHHHHH---HhcCCccCCcccccccCCcchhHHHHHHHHHHHHHhccCCcEEEECC
Confidence            44554444433  22222333344444444   77888875555555554442 344444444333 2225558999999


Q ss_pred             CCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCc-cCCCCCCCCcEEEEEeCCCCCC-
Q 022641           91 PGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQ-RRGGYPCPPYKIIILDEADSMT-  168 (294)
Q Consensus        91 ~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~lliiDei~~l~-  168 (294)
                      ||||||+||.++++++. ..  +..+..+..++         .+..+......... ........+.+||||||++..+ 
T Consensus       114 ~G~GKThLa~Ai~~~l~-~~--g~sv~f~~~~e---------l~~~Lk~~~~~~~~~~~l~~~l~~~dlLIiDDlG~~~~  181 (254)
T COG1484         114 PGVGKTHLAIAIGNELL-KA--GISVLFITAPD---------LLSKLKAAFDEGRLEEKLLRELKKVDLLIIDDIGYEPF  181 (254)
T ss_pred             CCCcHHHHHHHHHHHHH-Hc--CCeEEEEEHHH---------HHHHHHHHHhcCchHHHHHHHhhcCCEEEEecccCccC
Confidence            99999999999999995 22  23333332222         11111111100000 0000112345699999999865 


Q ss_pred             -HHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          169 -EDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       169 -~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                       ....+.++++|..++.....++|+|.+.
T Consensus       182 ~~~~~~~~~q~I~~r~~~~~~~~tsN~~~  210 (254)
T COG1484         182 SQEEADLLFQLISRRYESRSLIITSNLSF  210 (254)
T ss_pred             CHHHHHHHHHHHHHHHhhccceeecCCCh
Confidence             4457788888888777666689998764

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.48  E-value=1.3e-12  Score=111.40  Aligned_cols=93  Identities=19%  Similarity=0.317  Sum_probs=67.4

Q ss_pred             CCcEEEEEeCCCCCCH------------HHHHHHHHHHHhhc----------CcceEEEEe----cCCcccchHhhcccc
Q 022641          154 PPYKIIILDEADSMTE------------DAQNALRRTMETYS----------KVTRFFFIC----NYISRIIEPLASRCA  207 (294)
Q Consensus       154 ~~~~lliiDei~~l~~------------~~~~~L~~~l~~~~----------~~~~ii~~~----~~~~~~~~~l~~r~~  207 (294)
                      ...++|||||+|++..            .+|..|+++++...          .+..+|+.+    ..+..+.|+|..|+.
T Consensus       246 e~~GIVfiDEiDKIa~~~~~~~~DvS~eGVQ~~LLkilEGt~v~~k~~~v~T~~ILFI~~GAF~~~kp~DlIPEl~GR~P  325 (441)
T TIGR00390       246 EQSGIIFIDEIDKIAKKGESSGADVSREGVQRDLLPIVEGSTVNTKYGMVKTDHILFIAAGAFQLAKPSDLIPELQGRFP  325 (441)
T ss_pred             HcCCEEEEEchhhhcccCCCCCCCCCccchhccccccccCceeeecceeEECCceeEEecCCcCCCChhhccHHHhCccc
Confidence            4678999999999842            37888999998522          233333333    235567899999999


Q ss_pred             -EEEecCCCHHHHHHHHHH-----------HHHHhCC--CCCHHHHHHHHhhc
Q 022641          208 -KFRFKPLSEEVMSSRVLH-----------ICNEEGL--NLDAEALSTLSSIS  246 (294)
Q Consensus       208 -~i~~~~~~~~~~~~~l~~-----------~~~~~~~--~~~~~~l~~l~~~~  246 (294)
                       ++.+.+++.+++..+|..           .++.+|+  .++++++..|++..
T Consensus       326 i~v~L~~L~~edL~rILteP~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A  378 (441)
T TIGR00390       326 IRVELQALTTDDFERILTEPKNSLIKQYKALMKTEGVNIEFSDEAIKRIAELA  378 (441)
T ss_pred             eEEECCCCCHHHHHHHhcCChhHHHHHHHHHHhhcCcEEEEeHHHHHHHHHHH
Confidence             799999999999988822           2344554  47999999998763

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.

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=99.47  E-value=3.9e-12  Score=113.88  Aligned_cols=211  Identities=21%  Similarity=0.232  Sum_probs=135.0

Q ss_pred             hhhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHH
Q 022641           61 KDVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFA  138 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  138 (294)
                      ..+++.......+...+..  ....++++.|++||||+++|+++....   .....+++.+++..... ..+...+....
T Consensus       143 ~~ii~~S~~~~~~~~~~~~~a~~~~~vli~Ge~GtGK~~lA~~ih~~s---~~~~~~~~~i~c~~~~~-~~~~~~lfg~~  218 (457)
T PRK11361        143 GHILTNSPAMMDICKDTAKIALSQASVLISGESGTGKELIARAIHYNS---RRAKGPFIKVNCAALPE-SLLESELFGHE  218 (457)
T ss_pred             cceecccHHHhHHHHHHHHHcCCCcEEEEEcCCCccHHHHHHHHHHhC---CCCCCCeEEEECCCCCH-HHHHHHhcCCC
Confidence            3466665555544444332  222369999999999999999997754   22356788888877532 22211111100


Q ss_pred             hhhc-c-cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-------cc
Q 022641          139 AVAV-G-SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-------RI  198 (294)
Q Consensus       139 ~~~~-~-~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-------~~  198 (294)
                      .... + .....+....+..+.|+|||++.++...+..|+..++...           ..+++|++++...       .+
T Consensus       219 ~~~~~~~~~~~~g~~~~a~~gtl~ld~i~~l~~~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~l~~~~~~g~~  298 (457)
T PRK11361        219 KGAFTGAQTLRQGLFERANEGTLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTF  298 (457)
T ss_pred             CCCCCCCCCCCCCceEECCCCEEEEechhhCCHHHHHHHHHHHhcCcEEeCCCCceeeeceEEEEeCCCCHHHHHHcCCc
Confidence            0000 0 0111223334567899999999999999999999997632           2357888886542       24


Q ss_pred             chHhhcccc--EEEecCCCH--HHHHHHHHHHHH----HhC---CCCCHHHHHHHHhh-ccCcHHHHHHHHHHHHHHh-C
Q 022641          199 IEPLASRCA--KFRFKPLSE--EVMSSRVLHICN----EEG---LNLDAEALSTLSSI-SQGDLRRAITYLQGAARLF-G  265 (294)
Q Consensus       199 ~~~l~~r~~--~i~~~~~~~--~~~~~~l~~~~~----~~~---~~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~~-~  265 (294)
                      .+.+..|+.  .|.++|+..  +++..++..++.    ..+   ..+++++++.|..+ ++||+|++.+.++.+.... +
T Consensus       299 ~~~l~~~l~~~~i~~ppLreR~~di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNv~eL~~~~~~~~~~~~~  378 (457)
T PRK11361        299 REDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIERAVVMNSG  378 (457)
T ss_pred             hHHHHHHhccceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHcCCCCCcHHHHHHHHHHHHHhCCC
Confidence            455666665  567777753  445544444433    222   35899999999988 6999999999999988766 4


Q ss_pred             CCCChhhhhh
Q 022641          266 SSITSKDLIS  275 (294)
Q Consensus       266 ~~it~~~v~~  275 (294)
                      ..|+.+++..
T Consensus       379 ~~i~~~~l~~  388 (457)
T PRK11361        379 PIIFSEDLPP  388 (457)
T ss_pred             CcccHHHChH
Confidence            5688888754

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=99.47  E-value=4.3e-12  Score=113.81  Aligned_cols=212  Identities=20%  Similarity=0.223  Sum_probs=140.5

Q ss_pred             hhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHh
Q 022641           62 DVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAA  139 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  139 (294)
                      .++|.......+...+..  .....+++.|.+||||+++|+++.....   ....+++.+++..... ..+...+.....
T Consensus       135 ~lig~s~~~~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~ih~~~~---~~~~~~~~~~c~~~~~-~~~~~~lfg~~~  210 (463)
T TIGR01818       135 ELIGEAPAMQEVFRAIGRLSRSDITVLINGESGTGKELVARALHRHSP---RANGPFIALNMAAIPK-DLIESELFGHEK  210 (463)
T ss_pred             ceeecCHHHHHHHHHHHHHhCcCCeEEEECCCCCCHHHHHHHHHHhCC---CCCCCeEEEeCCCCCH-HHHHHHhcCCCC
Confidence            466665555555544432  2233599999999999999999987642   2356888888877522 222222211000


Q ss_pred             hhc-c-cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-------ccc
Q 022641          140 VAV-G-SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-------RII  199 (294)
Q Consensus       140 ~~~-~-~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-------~~~  199 (294)
                      ... + .....+....+..+.|+|||++.++...+..|++.++...           ..+++|++++...       .+.
T Consensus       211 ~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l~~~~q~~ll~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~f~  290 (463)
T TIGR01818       211 GAFTGANTRRQGRFEQADGGTLFLDEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFR  290 (463)
T ss_pred             CCCCCcccCCCCcEEECCCCeEEEEchhhCCHHHHHHHHHHHhcCcEEECCCCceeeeeeEEEEeCCCCHHHHHHcCCcH
Confidence            000 0 0011122233456789999999999999999999998533           2456788776542       234


Q ss_pred             hHhhcccc--EEEecCCC--HHHHHHHHHHHHHH----hC---CCCCHHHHHHHHhh-ccCcHHHHHHHHHHHHHHh-CC
Q 022641          200 EPLASRCA--KFRFKPLS--EEVMSSRVLHICNE----EG---LNLDAEALSTLSSI-SQGDLRRAITYLQGAARLF-GS  266 (294)
Q Consensus       200 ~~l~~r~~--~i~~~~~~--~~~~~~~l~~~~~~----~~---~~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~~-~~  266 (294)
                      +.+..|+.  .|.++|+.  .+++..++.+++..    .+   ..+++++++.|..+ +.||+|++.++++.++... +.
T Consensus       291 ~~L~~rl~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNvreL~~~~~~~~~~~~~~  370 (463)
T TIGR01818       291 EDLFHRLNVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKLLDPEALERLKQLRWPGNVRQLENLCRWLTVMASGD  370 (463)
T ss_pred             HHHHHHhCcceecCCCcccchhhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCCCChHHHHHHHHHHHHHhCCCC
Confidence            56777765  78888887  56777776665542    23   35899999999988 6999999999999988776 45


Q ss_pred             CCChhhhhhhc
Q 022641          267 SITSKDLISVS  277 (294)
Q Consensus       267 ~it~~~v~~~~  277 (294)
                      .|+.+++...+
T Consensus       371 ~i~~~~l~~~~  381 (463)
T TIGR01818       371 EVLVSDLPAEL  381 (463)
T ss_pred             cccHHhchHHH
Confidence            68888875433

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

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

Probab=99.46  E-value=1.4e-12  Score=110.74  Aligned_cols=205  Identities=17%  Similarity=0.209  Sum_probs=135.3

Q ss_pred             cchhhcccHHHHHHHHHHHHcC----CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhH-HHHH
Q 022641           59 QVKDVAHQEEVVRVLTNTLETA----NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINV-VRTK  133 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~----~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~  133 (294)
                      .-..+.|++.....++.|+...    ....+.+.|.||+|||.+...+...+.+.. .....+.+|+........ ....
T Consensus       148 ~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~-~~~~~v~inc~sl~~~~aiF~kI  226 (529)
T KOG2227|consen  148 PPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSS-KSPVTVYINCTSLTEASAIFKKI  226 (529)
T ss_pred             CCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhc-ccceeEEEeeccccchHHHHHHH
Confidence            3457789999998888887653    334599999999999999998887773322 223457778776433332 2233


Q ss_pred             HHHHHhhhcccCcc--------CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh---hcCcceEEEEecCCc---ccc
Q 022641          134 IKTFAAVAVGSGQR--------RGGYPCPPYKIIILDEADSMTEDAQNALRRTMET---YSKVTRFFFICNYIS---RII  199 (294)
Q Consensus       134 ~~~~~~~~~~~~~~--------~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~---~~~~~~ii~~~~~~~---~~~  199 (294)
                      ...+.....+.+..        .........-++++||+|+|....+..|+.+++-   +.....+|.++|...   ..+
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            33332221111110        0001112456999999999987767777666653   334555666667543   345


Q ss_pred             hHhhcccc----EEEecCCCHHHHHHHHHHHHHHhCCCC-CHHHHHHHHhh---ccCcHHHHHHHHHHHHHHh
Q 022641          200 EPLASRCA----KFRFKPLSEEVMSSRVLHICNEEGLNL-DAEALSTLSSI---SQGDLRRAITYLQGAARLF  264 (294)
Q Consensus       200 ~~l~~r~~----~i~~~~~~~~~~~~~l~~~~~~~~~~~-~~~~l~~l~~~---~~G~~r~~~~~l~~~~~~~  264 (294)
                      +.|..++.    .+.|+|++.+++.+|+...+..+.... -+.+++.++..   ..||+|.++.+++.+...+
T Consensus       307 prL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~SGDlRkaLdv~R~aiEI~  379 (529)
T KOG2227|consen  307 PRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAPSGDLRKALDVCRRAIEIA  379 (529)
T ss_pred             hhhhhccCCCCceeeecCCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccCchhHHHHHHHHHHHHHHH
Confidence            56666543    799999999999999999887765543 34577777765   4799999999999777655

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=99.46  E-value=4.6e-12  Score=115.39  Aligned_cols=200  Identities=17%  Similarity=0.109  Sum_probs=126.4

Q ss_pred             HcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcc-cCccCCCCCCCCc
Q 022641           78 ETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVG-SGQRRGGYPCPPY  156 (294)
Q Consensus        78 ~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~  156 (294)
                      -.+...+++|.|+||||||++|+++++.+..    ..+|+.+....  ..+.+..-+........+ .....+....+.+
T Consensus        12 v~p~~g~vLl~G~~GtgKs~lar~l~~~~~~----~~pfv~i~~~~--t~d~L~G~idl~~~~~~g~~~~~~G~L~~A~~   85 (589)
T TIGR02031        12 VDPSLGGVAIRARAGTGKTALARALAEILPP----IMPFVELPLGV--TEDRLIGGIDVEESLAGGQRVTQPGLLDEAPR   85 (589)
T ss_pred             cCCCcceEEEEcCCCcHHHHHHHHHHHhCCc----CCCeEecCccc--chhhcccchhhhhhhhcCcccCCCCCeeeCCC
Confidence            3444557999999999999999999997622    12344444211  111110001000000001 1122333444667


Q ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHhhc-------------CcceEEEEecCCc---ccchHhhcccc-EEEecC-CCHHH
Q 022641          157 KIIILDEADSMTEDAQNALRRTMETYS-------------KVTRFFFICNYIS---RIIEPLASRCA-KFRFKP-LSEEV  218 (294)
Q Consensus       157 ~lliiDei~~l~~~~~~~L~~~l~~~~-------------~~~~ii~~~~~~~---~~~~~l~~r~~-~i~~~~-~~~~~  218 (294)
                      ++|+|||++.+++..++.|++.|++..             ..+.+|.++|...   .+.+++.+||. .+.+.. ++.++
T Consensus        86 GvL~lDEi~rl~~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~LldRf~l~v~~~~~~~~~e  165 (589)
T TIGR02031        86 GVLYVDMANLLDDGLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLDRLALHVSLEDVASQDL  165 (589)
T ss_pred             CcEeccchhhCCHHHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHHhccCeeecCCCCCHHH
Confidence            899999999999999999999998643             3456777777654   58889999998 455544 45555


Q ss_pred             HHHHHHHHHH-----------------------HhCCCCCHHHHHHHHhhc---c-CcHHHHHHHHHHHHHHh----CCC
Q 022641          219 MSSRVLHICN-----------------------EEGLNLDAEALSTLSSIS---Q-GDLRRAITYLQGAARLF----GSS  267 (294)
Q Consensus       219 ~~~~l~~~~~-----------------------~~~~~~~~~~l~~l~~~~---~-G~~r~~~~~l~~~~~~~----~~~  267 (294)
                      ..+++++...                       ...+.++++.+++|++.+   + ..+|..+.++.-+-..+    ...
T Consensus       166 r~eil~~~~~~~~~~~~~~~~~~~~~i~~ar~~~~~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~  245 (589)
T TIGR02031       166 RVEIVRRERCNEVFRMNDELELLRGQIEAARELLPQVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTE  245 (589)
T ss_pred             HHHHHHHHHHhhhhhcchhhHHHHHHHHHHHHhcCCccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCC
Confidence            6666655431                       123568899888888763   2 23777777776554444    567


Q ss_pred             CChhhhhhhcccccCC
Q 022641          268 ITSKDLISVSGYPTGG  283 (294)
Q Consensus       268 it~~~v~~~~~~~~~~  283 (294)
                      ++.+|+..++..+-.+
T Consensus       246 V~~~Dv~~a~~lvl~h  261 (589)
T TIGR02031       246 VTEEDLKLAVELVLLP  261 (589)
T ss_pred             CCHHHHHHHHHHHhhh
Confidence            9999999887665443

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

>PRK15115 response regulator GlrR; Provisional

Probab=99.46  E-value=8.4e-12  Score=111.31  Aligned_cols=191  Identities=19%  Similarity=0.211  Sum_probs=125.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhccc--CccCCCCCCCCcEEEE
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGS--GQRRGGYPCPPYKIII  160 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~lli  160 (294)
                      ..++|+|++|+|||++|+++.+...   ....+++.+++..... ..+...+..........  ....+.......+.|+
T Consensus       158 ~~vli~Ge~GtGk~~lA~~ih~~s~---r~~~~f~~i~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~  233 (444)
T PRK15115        158 VSVLINGQSGTGKEILAQAIHNASP---RASKPFIAINCGALPE-QLLESELFGHARGAFTGAVSNREGLFQAAEGGTLF  233 (444)
T ss_pred             CeEEEEcCCcchHHHHHHHHHHhcC---CCCCCeEEEeCCCCCH-HHHHHHhcCCCcCCCCCCccCCCCcEEECCCCEEE
Confidence            4699999999999999999988642   2356788888877532 22222111100000000  0112223345567999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-------ccchHhhcccc--EEEecCCCH--HH
Q 022641          161 LDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-------RIIEPLASRCA--KFRFKPLSE--EV  218 (294)
Q Consensus       161 iDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-------~~~~~l~~r~~--~i~~~~~~~--~~  218 (294)
                      |||++.|+...+..|+..++...           ..+++|++++..-       .+...+..++.  .|.++|+..  ++
T Consensus       234 l~~i~~l~~~~q~~L~~~l~~~~~~~~g~~~~~~~~~rii~~~~~~l~~~~~~~~f~~~l~~~l~~~~i~lPpLr~R~eD  313 (444)
T PRK15115        234 LDEIGDMPAPLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHRDLPKAMARGEFREDLYYRLNVVSLKIPALAERTED  313 (444)
T ss_pred             EEccccCCHHHHHHHHHHHhhCCEEeCCCCceeeeeEEEEEeCCCCHHHHHHcCCccHHHHHhhceeeecCCChHhcccc
Confidence            99999999999999999998643           1456777776431       23345555655  566677653  45


Q ss_pred             HHHHHHHHHHH----hC---CCCCHHHHHHHHhhc-cCcHHHHHHHHHHHHHHh-CCCCChhhhhhhc
Q 022641          219 MSSRVLHICNE----EG---LNLDAEALSTLSSIS-QGDLRRAITYLQGAARLF-GSSITSKDLISVS  277 (294)
Q Consensus       219 ~~~~l~~~~~~----~~---~~~~~~~l~~l~~~~-~G~~r~~~~~l~~~~~~~-~~~it~~~v~~~~  277 (294)
                      +..++.+++..    .+   ..+++++++.|..+. +||+|++.++++.++... +..|+.+++...+
T Consensus       314 i~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~WpgNvreL~~~i~~~~~~~~~~~i~~~~l~~~~  381 (444)
T PRK15115        314 IPLLANHLLRQAAERHKPFVRAFSTDAMKRLMTASWPGNVRQLVNVIEQCVALTSSPVISDALVEQAL  381 (444)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCCCChHHHHHHHHHHHHHhCCCCccChhhhhhhh
Confidence            55454554432    23   248999999999985 999999999999988755 5568888775444

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=99.45  E-value=2.2e-12  Score=110.13  Aligned_cols=92  Identities=22%  Similarity=0.328  Sum_probs=66.9

Q ss_pred             CcEEEEEeCCCCCC------------HHHHHHHHHHHHhhc----------CcceEEEEe----cCCcccchHhhcccc-
Q 022641          155 PYKIIILDEADSMT------------EDAQNALRRTMETYS----------KVTRFFFIC----NYISRIIEPLASRCA-  207 (294)
Q Consensus       155 ~~~lliiDei~~l~------------~~~~~~L~~~l~~~~----------~~~~ii~~~----~~~~~~~~~l~~r~~-  207 (294)
                      ..++|||||+|++.            ..+|..|+++++...          .+..||+.+    ..+..+.|+|..|+. 
T Consensus       249 ~~GIVfiDEiDKIa~~~~~~~~DvS~eGVQ~~LLki~EG~~v~~k~~~i~T~~ILFI~~GAF~~~kp~DlIPEl~GR~Pi  328 (443)
T PRK05201        249 QNGIVFIDEIDKIAARGGSSGPDVSREGVQRDLLPLVEGSTVSTKYGMVKTDHILFIASGAFHVSKPSDLIPELQGRFPI  328 (443)
T ss_pred             cCCEEEEEcchhhcccCCCCCCCCCccchhcccccccccceeeecceeEECCceeEEecCCcCCCChhhccHHHhCccce
Confidence            67899999999984            237888999998522          222233332    234567899999999 


Q ss_pred             EEEecCCCHHHHHHHHHH-----------HHHHhCC--CCCHHHHHHHHhhc
Q 022641          208 KFRFKPLSEEVMSSRVLH-----------ICNEEGL--NLDAEALSTLSSIS  246 (294)
Q Consensus       208 ~i~~~~~~~~~~~~~l~~-----------~~~~~~~--~~~~~~l~~l~~~~  246 (294)
                      ++.+.+++.+++..+|..           .++.+|+  .+++++++.|++.+
T Consensus       329 ~v~L~~L~~~dL~~ILteP~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A  380 (443)
T PRK05201        329 RVELDALTEEDFVRILTEPKASLIKQYQALLATEGVTLEFTDDAIRRIAEIA  380 (443)
T ss_pred             EEECCCCCHHHHHHHhcCChhHHHHHHHHHHhhcCcEEEEcHHHHHHHHHHH
Confidence            799999999999988832           2334555  47899999998763

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=99.44  E-value=5.3e-12  Score=115.16  Aligned_cols=126  Identities=15%  Similarity=0.134  Sum_probs=87.4

Q ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc---------------------CcceEEEEecCC--cccchHhhcccc--
Q 022641          153 CPPYKIIILDEADSMTEDAQNALRRTMETYS---------------------KVTRFFFICNYI--SRIIEPLASRCA--  207 (294)
Q Consensus       153 ~~~~~lliiDei~~l~~~~~~~L~~~l~~~~---------------------~~~~ii~~~~~~--~~~~~~l~~r~~--  207 (294)
                      .+..++|+|||++.|++..+..|++.+++..                     ..+++|+++|..  ..+.+.|.+||.  
T Consensus       215 ~AngGtL~Ldei~~L~~~~q~~Ll~~L~~~~i~~~g~~e~~~~~~~~~~~ip~dvrvIa~~~~~~l~~l~~~l~~rf~~y  294 (608)
T TIGR00764       215 RAHKGVLYIDEIKTMPLEVQQYLLTALQDKKFPITGQSENSSGAMVRTEPVPCDFILVASGNLDDLEGMHPALRSRIRGY  294 (608)
T ss_pred             ECCCCEEEEEChHhCCHHHHHHHHHHHHhCcEEecCccccccccccCCCCCccceEEEEECCHHHHhhcCHHHHHHhcCC
Confidence            4567899999999999999999999996422                     244577777754  467889999987  


Q ss_pred             -E-EEec---CCCHHHHH---HHHHHHHHHhC--CCCCHHHHHHHHhhc----------cCcHHHHHHHHHHHHHHh---
Q 022641          208 -K-FRFK---PLSEEVMS---SRVLHICNEEG--LNLDAEALSTLSSIS----------QGDLRRAITYLQGAARLF---  264 (294)
Q Consensus       208 -~-i~~~---~~~~~~~~---~~l~~~~~~~~--~~~~~~~l~~l~~~~----------~G~~r~~~~~l~~~~~~~---  264 (294)
                       . +.|.   |.+.+...   .++.+.+++.|  ..++++++..+.+.+          ..+.|.+-++++.+...+   
T Consensus       295 ~v~v~~~~~~~~~~e~~~~~~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~  374 (608)
T TIGR00764       295 GYEVYMKDTMPDTPENRDKLVQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSS  374 (608)
T ss_pred             eEEEEeeccCCCCHHHHHHHHHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhc
Confidence             2 3443   33444443   44444444553  358999999888542          245888888888875544   


Q ss_pred             -CCCCChhhhhhhcc
Q 022641          265 -GSSITSKDLISVSG  278 (294)
Q Consensus       265 -~~~it~~~v~~~~~  278 (294)
                       ...|+.+||.+++.
T Consensus       375 ~~~~I~~ehV~~Ai~  389 (608)
T TIGR00764       375 GKVYVTAEHVLKAKK  389 (608)
T ss_pred             CCceecHHHHHHHHH
Confidence             35699999987644

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=99.43  E-value=2.8e-11  Score=95.35  Aligned_cols=171  Identities=16%  Similarity=0.160  Sum_probs=127.0

Q ss_pred             HHHHHHHHcCCCCc-EEEECCCC-CCHHHHHHHHHHHhcCCC---ccCCcceeecCC-------CCcchhHHHHHHHHHH
Q 022641           71 RVLTNTLETANCPH-MLFYGPPG-TGKTTTALAIAHQLFGPE---LYKSRVLELNAS-------DDRGINVVRTKIKTFA  138 (294)
Q Consensus        71 ~~l~~~l~~~~~~~-ill~Gp~G-~GKT~la~~la~~~~~~~---~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~  138 (294)
                      ..+...+..++..| .+|.|..+ +||..++..+++.++|..   .....+..+...       ...+.+.+++....+.
T Consensus         3 ~~L~~~iq~~kLshAYLfeG~n~~~~~~~~~~f~~~~l~~~~i~~~~HPD~~~I~pe~~~~~~~~~I~IdqIReL~~~l~   82 (263)
T PRK06581          3 ERLEFNLKHNKLYNSWLIEAENIEQALKDLEKFIYIKLFKNSIPLENNPDYHFIARETSATSNAKNISIEQIRKLQDFLS   82 (263)
T ss_pred             HHHHHHHHcCcchheeeEeCCChhhHHHHHHHHHHHHHhccCcccCCCCCEEEEeccccccccCCcccHHHHHHHHHHHh
Confidence            45666777776655 89999998 999999999999987642   233445555432       2345667776655544


Q ss_pred             hhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEEecCCCHHH
Q 022641          139 AVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEV  218 (294)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~  218 (294)
                      ..+.          .+++.|++|++++.++..+.+.|++.+|+++....+|++|..+..+++.+++||..+.|..+....
T Consensus        83 ~~p~----------~g~~KViII~~ae~mt~~AANALLKtLEEPP~~t~fILit~~~~~LLpTIrSRCq~i~~~~p~~~~  152 (263)
T PRK06581         83 KTSA----------ISGYKVAIIYSAELMNLNAANSCLKILEDAPKNSYIFLITSRAASIISTIRSRCFKINVRSSILHA  152 (263)
T ss_pred             hCcc----------cCCcEEEEEechHHhCHHHHHHHHHhhcCCCCCeEEEEEeCChhhCchhHhhceEEEeCCCCCHHH
Confidence            4332          245679999999999999999999999999999999999999999999999999999999999888


Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHH
Q 022641          219 MSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAI  254 (294)
Q Consensus       219 ~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~  254 (294)
                      ..++....+.   ...+.+.++.|.+.+.-|-....
T Consensus       153 ~~e~~~~~~~---p~~~~~~l~~i~~~~~~d~~~w~  185 (263)
T PRK06581        153 YNELYSQFIQ---PIADNKTLDFINRFTTKDRELWL  185 (263)
T ss_pred             HHHHHHHhcc---cccccHHHHHHHHHhhhhHHHHH
Confidence            7777654442   22455557777666544444333

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=99.42  E-value=2.5e-11  Score=110.44  Aligned_cols=125  Identities=15%  Similarity=0.147  Sum_probs=85.7

Q ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc---------------------CcceEEEEecCC--cccchHhhcccc--
Q 022641          153 CPPYKIIILDEADSMTEDAQNALRRTMETYS---------------------KVTRFFFICNYI--SRIIEPLASRCA--  207 (294)
Q Consensus       153 ~~~~~lliiDei~~l~~~~~~~L~~~l~~~~---------------------~~~~ii~~~~~~--~~~~~~l~~r~~--  207 (294)
                      .+..++|+|||++.|++..+..|++.|++..                     -.+++|++++..  ..+++.|.+||.  
T Consensus       224 kAnGGtL~LDei~~L~~~~q~~Llr~L~~~~i~i~g~~e~~~~~~~~~~~ip~dvrvI~a~~~~ll~~~dpdL~~rfk~~  303 (637)
T PRK13765        224 KAHKGVLFIDEINTLDLESQQSLLTAMQEKKFPITGQSERSSGAMVRTEPVPCDFIMVAAGNLDALENMHPALRSRIKGY  303 (637)
T ss_pred             ECCCcEEEEeChHhCCHHHHHHHHHHHHhCCEEecccccccccccCCCcceeeeeEEEEecCcCHHHhhhHHHHHHhccC
Confidence            4567899999999999999999999996432                     134677777764  346788888874  


Q ss_pred             --EEEecC---CCHHHHHHHHHHHHHHh-----CCCCCHHHHHHHHhhc---cCc-------HHHHHHHHHHHHHHh---
Q 022641          208 --KFRFKP---LSEEVMSSRVLHICNEE-----GLNLDAEALSTLSSIS---QGD-------LRRAITYLQGAARLF---  264 (294)
Q Consensus       208 --~i~~~~---~~~~~~~~~l~~~~~~~-----~~~~~~~~l~~l~~~~---~G~-------~r~~~~~l~~~~~~~---  264 (294)
                        .+.|..   -+.+....+++.+.+..     -..++++++..|++.+   .|+       .|.+.+++..+...+   
T Consensus       304 ~v~v~f~~~~~d~~e~~~~~~~~iaqe~~~~G~l~~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~  383 (637)
T PRK13765        304 GYEVYMRDTMEDTPENRRKLVRFVAQEVKRDGKIPHFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSE  383 (637)
T ss_pred             eEEEEcccccCCCHHHHHHHHHHHHHHhhhccCCCCCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhh
Confidence              355543   34566667776555432     2368999999988763   232       677777777766555   


Q ss_pred             -CCCCChhhhhhhc
Q 022641          265 -GSSITSKDLISVS  277 (294)
Q Consensus       265 -~~~it~~~v~~~~  277 (294)
                       .+.++.+++.++.
T Consensus       384 ~~~~i~~~~v~~a~  397 (637)
T PRK13765        384 GAELTTAEHVLEAK  397 (637)
T ss_pred             ccceecHHHHHHHH
Confidence             3347777776554

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

Probab=99.42  E-value=1.6e-12  Score=112.20  Aligned_cols=153  Identities=17%  Similarity=0.201  Sum_probs=93.9

Q ss_pred             chhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCc-cCCcceeecCCCCcchhHHH-------
Q 022641           60 VKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPEL-YKSRVLELNASDDRGINVVR-------  131 (294)
Q Consensus        60 ~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~-~~~~~~~~~~~~~~~~~~~~-------  131 (294)
                      ++++++.+...+.+...+..+.  +++|+||||||||++|+.++..+..... ....++.+.... ...+.+.       
T Consensus       174 l~d~~i~e~~le~l~~~L~~~~--~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsy-SYeDFI~G~rP~~v  250 (459)
T PRK11331        174 LNDLFIPETTIETILKRLTIKK--NIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSY-SYEDFIQGYRPNGV  250 (459)
T ss_pred             hhcccCCHHHHHHHHHHHhcCC--CEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccc-cHHHHhcccCCCCC
Confidence            5577788888888888887654  8999999999999999999998854311 111222222110 0000000       


Q ss_pred             ------HHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH-HHHHHHHHHHhh----------------------
Q 022641          132 ------TKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED-AQNALRRTMETY----------------------  182 (294)
Q Consensus       132 ------~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~-~~~~L~~~l~~~----------------------  182 (294)
                            ..+..+.....        ....++.+|||||+++.+.. ....++.+++..                      
T Consensus       251 gy~~~~G~f~~~~~~A~--------~~p~~~~vliIDEINRani~kiFGel~~lLE~~~rg~~~~v~l~y~e~d~e~f~i  322 (459)
T PRK11331        251 GFRRKDGIFYNFCQQAK--------EQPEKKYVFIIDEINRANLSKVFGEVMMLMEHDKRGENWSVPLTYSENDEERFYV  322 (459)
T ss_pred             CeEecCchHHHHHHHHH--------hcccCCcEEEEehhhccCHHHhhhhhhhhccccccccccceeeeccccccccccC
Confidence                  00111100000        01123569999999999854 466677777631                      


Q ss_pred             cCcceEEEEecCCc----ccchHhhccccEEEecCC-CHHHHHHHH
Q 022641          183 SKVTRFFFICNYIS----RIIEPLASRCAKFRFKPL-SEEVMSSRV  223 (294)
Q Consensus       183 ~~~~~ii~~~~~~~----~~~~~l~~r~~~i~~~~~-~~~~~~~~l  223 (294)
                      +.++.+|.|+|...    .++.++++||..+.+.|. +......++
T Consensus       323 P~Nl~IIgTMNt~Drs~~~lD~AlrRRF~fi~i~p~~~~~~~~~~l  368 (459)
T PRK11331        323 PENVYIIGLMNTADRSLAVVDYALRRRFSFIDIEPGFDTPQFRNFL  368 (459)
T ss_pred             CCCeEEEEecCccccchhhccHHHHhhhheEEecCCCChHHHHHHH
Confidence            23556788887664    578999999999999874 444444443

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=99.40  E-value=1.2e-11  Score=109.97  Aligned_cols=221  Identities=19%  Similarity=0.212  Sum_probs=147.4

Q ss_pred             hhcccHHHHHHHHHHHHc-----CCCCcEEEECCCCCCHHHHHHHHHHHhc----CCCccCCcceeecCCCCcchhHHHH
Q 022641           62 DVAHQEEVVRVLTNTLET-----ANCPHMLFYGPPGTGKTTTALAIAHQLF----GPELYKSRVLELNASDDRGINVVRT  132 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~-----~~~~~ill~Gp~G~GKT~la~~la~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~  132 (294)
                      .+.+++.....+...+..     +....+.+.|-||||||+++..+.+.+.    ....-...++++|+-...+...+..
T Consensus       397 sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~Y~  476 (767)
T KOG1514|consen  397 SLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREIYE  476 (767)
T ss_pred             cccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHHHH
Confidence            344566666666655543     2223599999999999999999999885    2233456778888877666655554


Q ss_pred             HHHHHHhh-hcccCc--------cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh---cCcceEEEEecCCcc---
Q 022641          133 KIKTFAAV-AVGSGQ--------RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY---SKVTRFFFICNYISR---  197 (294)
Q Consensus       133 ~~~~~~~~-~~~~~~--------~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~---~~~~~ii~~~~~~~~---  197 (294)
                      .+...... ...+..        ...........||+|||+|.|-...++.|..+++-.   .....+|.++|....   
T Consensus       477 ~I~~~lsg~~~~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~IaNTmdlPEr  556 (767)
T KOG1514|consen  477 KIWEALSGERVTWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIAIANTMDLPER  556 (767)
T ss_pred             HHHHhcccCcccHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEEecccccCHHH
Confidence            44432211 111100        001123345679999999999776777777777643   345666667776442   


Q ss_pred             -cchHhhcccc--EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhh---ccCcHHHHHHHHHHHHHHhCC-----
Q 022641          198 -IIEPLASRCA--KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSI---SQGDLRRAITYLQGAARLFGS-----  266 (294)
Q Consensus       198 -~~~~l~~r~~--~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~---~~G~~r~~~~~l~~~~~~~~~-----  266 (294)
                       +...+.+|..  .+.|.|++.+++.+++...++.. -.++.++++.+++.   ..||.|.+++++..|+..+.+     
T Consensus       557 ~l~nrvsSRlg~tRi~F~pYth~qLq~Ii~~RL~~~-~~f~~~aielvarkVAavSGDaRraldic~RA~Eia~~~~~~~  635 (767)
T KOG1514|consen  557 LLMNRVSSRLGLTRICFQPYTHEQLQEIISARLKGL-DAFENKAIELVARKVAAVSGDARRALDICRRAAEIAEERNVKG  635 (767)
T ss_pred             HhccchhhhccceeeecCCCCHHHHHHHHHHhhcch-hhcchhHHHHHHHHHHhccccHHHHHHHHHHHHHHhhhhcccc
Confidence             2223445554  89999999999999998777543 34678888887765   579999999999999988722     


Q ss_pred             ------CCChhhhhhhcccccCC
Q 022641          267 ------SITSKDLISVSGYPTGG  283 (294)
Q Consensus       267 ------~it~~~v~~~~~~~~~~  283 (294)
                            .++..++..++.++.+.
T Consensus       636 k~~~~q~v~~~~v~~Ai~em~~~  658 (767)
T KOG1514|consen  636 KLAVSQLVGILHVMEAINEMLAS  658 (767)
T ss_pred             cccccceeehHHHHHHHHHHhhh
Confidence                  25777777777665544

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=99.39  E-value=3.6e-11  Score=111.55  Aligned_cols=157  Identities=17%  Similarity=0.109  Sum_probs=98.1

Q ss_pred             hhhhcCCCcchhhcccHHHHHHHHHHHHcCCC---------------------CcEEEECCCCCCHHHHHHHHHHHhcCC
Q 022641           51 WVEKYRPKQVKDVAHQEEVVRVLTNTLETANC---------------------PHMLFYGPPGTGKTTTALAIAHQLFGP  109 (294)
Q Consensus        51 ~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~---------------------~~ill~Gp~G~GKT~la~~la~~~~~~  109 (294)
                      ..+.+...-...+.|++.++..+.-.+..|..                     .+++|+|+||||||.+|+.+++.....
T Consensus       440 i~~~L~~SiaP~I~G~e~vK~ailL~L~gG~~k~~~~~~~~dg~~~~~~iRgdihVLLvGDPGTGKSqLAr~Ih~lspR~  519 (915)
T PTZ00111        440 IYRILLDSFAPSIKARNNVKIGLLCQLFSGNKNSSDFNKSPDACYKVDNFRGIINVLLCGDPGTAKSQLLHYTHLLSPRS  519 (915)
T ss_pred             HHHHHHHHhCCeEECCHHHHHHHHHHHhcCCccccccccccccccccccccCCceEEEeCCCCccHHHHHHHHHHhCCcc
Confidence            33444444445778999999888777765531                     159999999999999999998854211


Q ss_pred             C-ccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----
Q 022641          110 E-LYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----  183 (294)
Q Consensus       110 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----  183 (294)
                      . ..+..+..+++...         ...............+....+..++++|||++.++...+..|+++|+...     
T Consensus       520 ~ytsG~~~s~vgLTa~---------~~~~d~~tG~~~le~GaLvlAdgGtL~IDEidkms~~~Q~aLlEaMEqqtIsI~K  590 (915)
T PTZ00111        520 IYTSGKSSSSVGLTAS---------IKFNESDNGRAMIQPGAVVLANGGVCCIDELDKCHNESRLSLYEVMEQQTVTIAK  590 (915)
T ss_pred             ccCCCCCCccccccch---------hhhcccccCcccccCCcEEEcCCCeEEecchhhCCHHHHHHHHHHHhCCEEEEec
Confidence            0 01112222211110         00000001111223344455677899999999999999999999997532     


Q ss_pred             --------CcceEEEEecCCc-------------ccchHhhcccc--EEEecCCCH
Q 022641          184 --------KVTRFFFICNYIS-------------RIIEPLASRCA--KFRFKPLSE  216 (294)
Q Consensus       184 --------~~~~ii~~~~~~~-------------~~~~~l~~r~~--~i~~~~~~~  216 (294)
                              ..+.+|.++|+..             .+++++++||.  .+-+..++.
T Consensus       591 aGi~~tL~ar~rVIAAaNP~~gryd~~~s~~eni~Lp~~LLSRFDLIf~l~D~~d~  646 (915)
T PTZ00111        591 AGIVATLKAETAILASCNPINSRYNKNKAVIENINISPSLFTRFDLIYLVLDHIDQ  646 (915)
T ss_pred             CCcceecCCCeEEEEEcCCcccccCcccCcccccCCChHHhhhhcEEEEecCCCCh
Confidence                    4567888887632             36789999997  334455544

>PRK12377 putative replication protein; Provisional

Probab=99.39  E-value=2.8e-12  Score=103.85  Aligned_cols=152  Identities=18%  Similarity=0.229  Sum_probs=84.9

Q ss_pred             hhcCCCcchhhc----ccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc
Q 022641           53 EKYRPKQVKDVA----HQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG  126 (294)
Q Consensus        53 ~~~~~~~~~~~~----g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~  126 (294)
                      +.+...+|+.+.    ++..++.........  ....+++|+|||||||||||.++++.+...   +..+..+...+   
T Consensus        66 ~~~~~~tFdnf~~~~~~~~~a~~~a~~~a~~~~~~~~~l~l~G~~GtGKThLa~AIa~~l~~~---g~~v~~i~~~~---  139 (248)
T PRK12377         66 PLHRKCSFANYQVQNDGQRYALSQAKSIADELMTGCTNFVFSGKPGTGKNHLAAAIGNRLLAK---GRSVIVVTVPD---  139 (248)
T ss_pred             cccccCCcCCcccCChhHHHHHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHHc---CCCeEEEEHHH---
Confidence            445555676664    333344433333321  223579999999999999999999998532   22233332221   


Q ss_pred             hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCC--CCHHHHHHHHHHHHhhcC-cceEEEEecCCcc-----c
Q 022641          127 INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADS--MTEDAQNALRRTMETYSK-VTRFFFICNYISR-----I  198 (294)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~--l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~~-----~  198 (294)
                         +...+.......  ...........+.++|||||++.  .+...++.|+++++.++. ...+|++||....     +
T Consensus       140 ---l~~~l~~~~~~~--~~~~~~l~~l~~~dLLiIDDlg~~~~s~~~~~~l~~ii~~R~~~~~ptiitSNl~~~~l~~~~  214 (248)
T PRK12377        140 ---VMSRLHESYDNG--QSGEKFLQELCKVDLLVLDEIGIQRETKNEQVVLNQIIDRRTASMRSVGMLTNLNHEAMSTLL  214 (248)
T ss_pred             ---HHHHHHHHHhcc--chHHHHHHHhcCCCEEEEcCCCCCCCCHHHHHHHHHHHHHHHhcCCCEEEEcCCCHHHHHHHh
Confidence               111111110000  00000001123456999999954  466778899999998886 4678999986532     2


Q ss_pred             chHhhccc-----cEEEecCCC
Q 022641          199 IEPLASRC-----AKFRFKPLS  215 (294)
Q Consensus       199 ~~~l~~r~-----~~i~~~~~~  215 (294)
                      .+++.+|+     ..|.|...|
T Consensus       215 ~~ri~dRl~~~~~~~v~~~g~s  236 (248)
T PRK12377        215 GERVMDRMTMNGGRWVNFNWES  236 (248)
T ss_pred             hHHHHHHHhhCCCeEEEeCCcC
Confidence            33444443     246665544

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=99.39  E-value=6e-13  Score=94.73  Aligned_cols=113  Identities=25%  Similarity=0.217  Sum_probs=61.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcc-cCccCCCCCCCCcEEEEEe
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVG-SGQRRGGYPCPPYKIIILD  162 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~lliiD  162 (294)
                      |++|.|+||+|||++|+++|+.+      +..+..+......-...+...  .+...... .....+-..   ..++++|
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~------~~~f~RIq~tpdllPsDi~G~--~v~~~~~~~f~~~~GPif---~~ill~D   69 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSL------GLSFKRIQFTPDLLPSDILGF--PVYDQETGEFEFRPGPIF---TNILLAD   69 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHT------T--EEEEE--TT--HHHHHEE--EEEETTTTEEEEEE-TT----SSEEEEE
T ss_pred             CEeeECCCccHHHHHHHHHHHHc------CCceeEEEecCCCCcccceee--eeeccCCCeeEeecChhh---hceeeec
Confidence            58999999999999999999998      666666655432222222111  00000000 000111111   2499999


Q ss_pred             CCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-----ccchHhhcccc
Q 022641          163 EADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-----RIIEPLASRCA  207 (294)
Q Consensus       163 ei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-----~~~~~l~~r~~  207 (294)
                      |+++.++..+..|+++|+++.           ....+|.+.|...     .++.++++||.
T Consensus        70 EiNrappktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~DRF~  130 (131)
T PF07726_consen   70 EINRAPPKTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLDRFM  130 (131)
T ss_dssp             TGGGS-HHHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT--S------HHHHTTSS
T ss_pred             ccccCCHHHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhcccc
Confidence            999999999999999998644           3344555666543     57888888874

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.

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.39  E-value=7.5e-13  Score=101.57  Aligned_cols=106  Identities=24%  Similarity=0.318  Sum_probs=68.0

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEe
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILD  162 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiD  162 (294)
                      .+++|+||+|||||.+|+++++.+..  ....+++.++++...........+..+.........      .....||+||
T Consensus         4 ~~~ll~GpsGvGKT~la~~la~~l~~--~~~~~~~~~d~s~~~~~~~~~~~~~~l~~~~~~~v~------~~~~gVVllD   75 (171)
T PF07724_consen    4 SNFLLAGPSGVGKTELAKALAELLFV--GSERPLIRIDMSEYSEGDDVESSVSKLLGSPPGYVG------AEEGGVVLLD   75 (171)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHT---SSCCEEEEEEGGGHCSHHHCSCHCHHHHHHTTCHHH------HHHHTEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhcc--CCccchHHHhhhcccccchHHhhhhhhhhcccceee------ccchhhhhhH
Confidence            36999999999999999999999941  112467777776655422211111211111110000      0112399999


Q ss_pred             CCCCCCH-----------HHHHHHHHHHHhhc-----------CcceEEEEecCCc
Q 022641          163 EADSMTE-----------DAQNALRRTMETYS-----------KVTRFFFICNYIS  196 (294)
Q Consensus       163 ei~~l~~-----------~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~  196 (294)
                      |+|+.++           ..++.|++++++..           .++.+|+|+|...
T Consensus        76 EidKa~~~~~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~~  131 (171)
T PF07724_consen   76 EIDKAHPSNSGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFGA  131 (171)
T ss_dssp             TGGGCSHTTTTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSST
T ss_pred             HHhhccccccccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEeccccc
Confidence            9999999           99999999998532           3556788887543

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 ....

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=99.38  E-value=8.9e-11  Score=99.37  Aligned_cols=222  Identities=15%  Similarity=0.077  Sum_probs=134.0

Q ss_pred             CcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCcc-CCcc--------------------
Q 022641           58 KQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELY-KSRV--------------------  116 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~-~~~~--------------------  116 (294)
                      ..|..++|++..+..|....-......++|.|+.|+||||++++|+..|-..... +++|                    
T Consensus        14 ~pf~aivGqd~lk~aL~l~av~P~iggvLI~G~kGtaKSt~~Rala~LLp~~~~V~gc~f~cdP~~P~~~c~~c~~k~~e   93 (423)
T COG1239          14 LPFTAIVGQDPLKLALGLNAVDPQIGGALIAGEKGTAKSTLARALADLLPEIEVVIGCPFNCDPDDPEEMCDECRAKGDE   93 (423)
T ss_pred             cchhhhcCchHHHHHHhhhhcccccceeEEecCCCccHHHHHHHHHHhCCccceecCCCCCCCCCChhhhhHHHHhhccc
Confidence            4567889999999888766656666679999999999999999999988311110 0000                    


Q ss_pred             -----------eeecCCCCcchhHHHHHHHHHHhh-hcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh--
Q 022641          117 -----------LELNASDDRGINVVRTKIKTFAAV-AVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY--  182 (294)
Q Consensus       117 -----------~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~--  182 (294)
                                 -.++.......+.+-..+.-.... .......++....++++|+++||++.|+...++.|++.++..  
T Consensus        94 ~~~~~~~~r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~AnRGIlYvDEvnlL~d~lvd~LLd~aaeG~n  173 (423)
T COG1239          94 LEWLPREKRKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARANRGILYVDEVNLLDDHLVDALLDVAAEGVN  173 (423)
T ss_pred             cccccccceecceecCCCccchhhhccccCHHHHHhcCccccCCcchhhccCCEEEEeccccccHHHHHHHHHHHHhCCc
Confidence                       001111111111111000000000 011223455566788999999999999999999999999863  


Q ss_pred             -----------cCcceEEEEecCC-cccchHhhcccc-EEEecCC-CHHHHHHHHHHHHHHh------------------
Q 022641          183 -----------SKVTRFFFICNYI-SRIIEPLASRCA-KFRFKPL-SEEVMSSRVLHICNEE------------------  230 (294)
Q Consensus       183 -----------~~~~~ii~~~~~~-~~~~~~l~~r~~-~i~~~~~-~~~~~~~~l~~~~~~~------------------  230 (294)
                                 +..+.+|.|+|.. ..+.+.|+.||. .+...++ +.++..+++.+...-.                  
T Consensus       174 ~vereGisi~hpa~fvligTmNPEeGeLrpqLlDRfg~~v~~~~~~~~~~rv~Ii~r~~~f~~~Pe~f~~~~~~~~~~lR  253 (423)
T COG1239         174 DVEREGISIRHPARFLLIGTMNPEEGELRPQLLDRFGLEVDTHYPLDLEERVEIIRRRLAFEAVPEAFLEKYADAQRALR  253 (423)
T ss_pred             eeeeCceeeccCccEEEEeecCccccccchhhHhhhcceeeccCCCCHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHH
Confidence                       2455567777765 457889999987 6666555 4566666666544311                  


Q ss_pred             -----------CCCCCHHHHHHHHhhc-----cCcHHHHHHHHHH----HHHHhCCCCChhhhhhhcccc
Q 022641          231 -----------GLNLDAEALSTLSSIS-----QGDLRRAITYLQG----AARLFGSSITSKDLISVSGYP  280 (294)
Q Consensus       231 -----------~~~~~~~~l~~l~~~~-----~G~~r~~~~~l~~----~~~~~~~~it~~~v~~~~~~~  280 (294)
                                 .+.++++....+++.|     .| -|..+.....    ++.....+++.++++.+....
T Consensus       254 ~~ii~ar~~l~~V~l~~~~~~~ia~~~~~~~v~g-~radi~~~r~a~a~aa~~Gr~~v~~~Di~~a~~l~  322 (423)
T COG1239         254 ARIIAARSLLSEVELDDDAETKIAELCARLAVDG-HRADIVVVRAAKALAALRGRTEVEEEDIREAAELA  322 (423)
T ss_pred             HHHHHHHhccccccCcHHHHHHHHHHHHHhccCC-CchhhHHHHHHHHHHHhcCceeeehhhHHHHHhhh
Confidence                       2346666666666653     22 3333333332    222224567778887766543

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

Probab=99.37  E-value=1.4e-11  Score=114.99  Aligned_cols=186  Identities=20%  Similarity=0.134  Sum_probs=128.9

Q ss_pred             CcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC
Q 022641           58 KQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD  124 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~  124 (294)
                      ..|+++-|.+..+..|++.+..             ..++.++++||||||||..|++++..+. .......++.-.+.+-
T Consensus       262 v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~~itpPrgvL~~GppGTGkTl~araLa~~~s-~~~~kisffmrkgaD~  340 (1080)
T KOG0732|consen  262 VGFDSVGGLENYINQLKEMVLLPLLYPEFFDNFNITPPRGVLFHGPPGTGKTLMARALAAACS-RGNRKISFFMRKGADC  340 (1080)
T ss_pred             cCccccccHHHHHHHHHHHHHhHhhhhhHhhhcccCCCcceeecCCCCCchhHHHHhhhhhhc-ccccccchhhhcCchh
Confidence            3677888888899888887632             2234499999999999999999998872 1222333333333332


Q ss_pred             cch------hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH-----------HHHHHHHHHHHhhcC--c
Q 022641          125 RGI------NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE-----------DAQNALRRTMETYSK--V  185 (294)
Q Consensus       125 ~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~-----------~~~~~L~~~l~~~~~--~  185 (294)
                      .++      ..++-.+....              ...+.+|++||||.|.+           .....|+.+|+....  .
T Consensus       341 lskwvgEaERqlrllFeeA~--------------k~qPSIIffdeIdGlapvrSskqEqih~SIvSTLLaLmdGldsRgq  406 (1080)
T KOG0732|consen  341 LSKWVGEAERQLRLLFEEAQ--------------KTQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDSRGQ  406 (1080)
T ss_pred             hccccCcHHHHHHHHHHHHh--------------ccCceEEeccccccccccccchHHHhhhhHHHHHHHhccCCCCCCc
Confidence            221      12222222222              22346999999997742           245567888876554  4


Q ss_pred             ceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHH
Q 022641          186 TRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQ  258 (294)
Q Consensus       186 ~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~  258 (294)
                      +++|.+||.+..+.+++++  ||. .+.|+-|+.+...+++...-.+..-.++...+..+++.+.|..+.-+..|-
T Consensus       407 VvvigATnRpda~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrkw~~~i~~~l~~~la~~t~gy~gaDlkaLC  482 (1080)
T KOG0732|consen  407 VVVIGATNRPDAIDPALRRPGRFDREFYFPLPDVDARAKILDIHTRKWEPPISRELLLWLAEETSGYGGADLKALC  482 (1080)
T ss_pred             eEEEcccCCccccchhhcCCcccceeEeeeCCchHHHHHHHHHhccCCCCCCCHHHHHHHHHhccccchHHHHHHH
Confidence            5567778999999999966  676 788988889999999877666667778999999999998887776665444

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.36  E-value=3e-12  Score=103.80  Aligned_cols=184  Identities=22%  Similarity=0.292  Sum_probs=113.3

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHc---------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCC
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLET---------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKS  114 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~---------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~  114 (294)
                      |-.+..+..--+.++||+.+++.|.-++.+               -..+|+++.||+|+|||.||+.+|+.+      +.
T Consensus        50 PtP~eik~~Ld~YVIGQe~AKKvLsVAVYNHYKRl~~~~~~~dvEL~KSNILLiGPTGsGKTlLAqTLAk~L------nV  123 (408)
T COG1219          50 PTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQTLAKIL------NV  123 (408)
T ss_pred             CChHHHHHHhhhheecchhhhceeeeeehhHHHHHhccCCCCceeeeeccEEEECCCCCcHHHHHHHHHHHh------CC
Confidence            333333333334567998888655333221               123579999999999999999999999      77


Q ss_pred             cceeecCCCCcc----hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC--------------HHHHHHHH
Q 022641          115 RVLELNASDDRG----INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT--------------EDAQNALR  176 (294)
Q Consensus       115 ~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--------------~~~~~~L~  176 (294)
                      +|...++.....    ...+...+..+......      ....+.+++|+|||+|.+.              ..+++.|+
T Consensus       124 PFaiADATtLTEAGYVGEDVENillkLlqaady------dV~rAerGIIyIDEIDKIarkSeN~SITRDVSGEGVQQALL  197 (408)
T COG1219         124 PFAIADATTLTEAGYVGEDVENILLKLLQAADY------DVERAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALL  197 (408)
T ss_pred             CeeeccccchhhccccchhHHHHHHHHHHHccc------CHHHHhCCeEEEechhhhhccCCCCCcccccCchHHHHHHH
Confidence            777666554322    12333333333322110      0122456799999999873              34789999


Q ss_pred             HHHHhh-------------cC------cceEEEEe------------------------cC-------------------
Q 022641          177 RTMETY-------------SK------VTRFFFIC------------------------NY-------------------  194 (294)
Q Consensus       177 ~~l~~~-------------~~------~~~ii~~~------------------------~~-------------------  194 (294)
                      ++++.-             ..      ..-+++++                        +.                   
T Consensus       198 KiiEGTvasVPPqGGRKHP~Qe~iqvDT~NILFIcgGAF~GlekiI~~R~~~~~iGF~a~~~~~~~~~~~~~~l~~vepe  277 (408)
T COG1219         198 KIIEGTVASVPPQGGRKHPQQEFIQVDTSNILFICGGAFAGLEKIIKKRLGKKGIGFGAEVKSKSKKKEEGELLKQVEPE  277 (408)
T ss_pred             HHHcCceeccCCCCCCCCCccceEEEcccceeEEeccccccHHHHHHHhccCCcccccccccchhhhhhHHHHHHhcChH
Confidence            999731             11      11133332                        00                   


Q ss_pred             ---CcccchHhhcccc-EEEecCCCHHHHHHHHHH-----------HHHHhCC--CCCHHHHHHHHhh
Q 022641          195 ---ISRIIEPLASRCA-KFRFKPLSEEVMSSRVLH-----------ICNEEGL--NLDAEALSTLSSI  245 (294)
Q Consensus       195 ---~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~-----------~~~~~~~--~~~~~~l~~l~~~  245 (294)
                         .+.+.|+|..|+. +-.+.+++.+.+..+|..           ++...++  .++++++..+++.
T Consensus       278 DLvkFGLIPEfIGRlPvia~L~~Lde~aLv~ILtePkNAlvKQYq~Lf~~d~V~L~F~~~AL~~IA~~  345 (408)
T COG1219         278 DLVKFGLIPEFIGRLPVIATLEELDEDALVQILTEPKNALVKQYQKLFEMDGVELEFTEEALKAIAKK  345 (408)
T ss_pred             HHHHcCCcHHHhcccceeeehhhcCHHHHHHHHhcccHHHHHHHHHHhcccCceEEEcHHHHHHHHHH
Confidence               0125678888988 568899999888877743           2223343  3789999998876

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=99.35  E-value=2.6e-12  Score=98.26  Aligned_cols=143  Identities=19%  Similarity=0.205  Sum_probs=83.3

Q ss_pred             hcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhh
Q 022641           63 VAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAV  140 (294)
Q Consensus        63 ~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  140 (294)
                      ++|....+..+.+.+..  ....+++|+|++||||+.+|+++.+.   +.....+|+.++|..... ..+...+-.....
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~---s~r~~~pfi~vnc~~~~~-~~~e~~LFG~~~~   76 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNN---SPRKNGPFISVNCAALPE-ELLESELFGHEKG   76 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHC---STTTTS-EEEEETTTS-H-HHHHHHHHEBCSS
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHh---hhcccCCeEEEehhhhhc-chhhhhhhccccc
Confidence            35555555555555433  22346999999999999999999873   334467999999987633 2222211111000


Q ss_pred             h-cc-cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-------ccch
Q 022641          141 A-VG-SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-------RIIE  200 (294)
Q Consensus       141 ~-~~-~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-------~~~~  200 (294)
                      . .+ .....+....+..+.|+|||++.|++..|..|++++++..           .++++|++|+..-       .+.+
T Consensus        77 ~~~~~~~~~~G~l~~A~~GtL~Ld~I~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~st~~~l~~~v~~g~fr~  156 (168)
T PF00158_consen   77 AFTGARSDKKGLLEQANGGTLFLDEIEDLPPELQAKLLRVLEEGKFTRLGSDKPVPVDVRIIASTSKDLEELVEQGRFRE  156 (168)
T ss_dssp             SSTTTSSEBEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEECCTSSSEEE--EEEEEEESS-HHHHHHTTSS-H
T ss_pred             cccccccccCCceeeccceEEeecchhhhHHHHHHHHHHHHhhchhccccccccccccceEEeecCcCHHHHHHcCCChH
Confidence            0 00 0011122233567799999999999999999999998532           3667888887542       2345


Q ss_pred             HhhccccEE
Q 022641          201 PLASRCAKF  209 (294)
Q Consensus       201 ~l~~r~~~i  209 (294)
                      .|..|+..+
T Consensus       157 dLy~rL~~~  165 (168)
T PF00158_consen  157 DLYYRLNVF  165 (168)
T ss_dssp             HHHHHHTTE
T ss_pred             HHHHHhceE
Confidence            555555443

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 ....

>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=99.35  E-value=7e-12  Score=105.34  Aligned_cols=191  Identities=14%  Similarity=0.108  Sum_probs=106.9

Q ss_pred             cHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc-hhHHHHHHHHHHhhhc
Q 022641           66 QEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG-INVVRTKIKTFAAVAV  142 (294)
Q Consensus        66 ~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  142 (294)
                      ++..++.|.++|..  .....+.|+|++|+|||++|..+++.......++. ++-++...... ..........+.....
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~-v~wv~~~~~~~~~~~~~~i~~~l~~~~~   79 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDG-VIWVSLSKNPSLEQLLEQILRQLGEPDS   79 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTE-EEEEEEES-SCCHHHHHHHHHHHTCC-S
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeeccccccccccccc-cccccccccccccccccccccccccccc
Confidence            35677888888887  44455999999999999999999988421222222 22223222222 2223332222221111


Q ss_pred             cc--Ccc-------CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEEecC
Q 022641          143 GS--GQR-------RGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKP  213 (294)
Q Consensus       143 ~~--~~~-------~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~  213 (294)
                      ..  ...       .......++.+||+|+++...  ..+.+...+........+|+||+... +..........+.+.+
T Consensus        80 ~~~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~kilvTTR~~~-v~~~~~~~~~~~~l~~  156 (287)
T PF00931_consen   80 SISDPKDIEELQDQLRELLKDKRCLLVLDDVWDEE--DLEELREPLPSFSSGSKILVTTRDRS-VAGSLGGTDKVIELEP  156 (287)
T ss_dssp             TSSCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SHH--HH-------HCHHSS-EEEEEESCGG-GGTTHHSCEEEEECSS
T ss_pred             ccccccccccccccchhhhccccceeeeeeecccc--cccccccccccccccccccccccccc-cccccccccccccccc
Confidence            00  000       000112447899999987653  44445555555556778888887643 3333333366899999


Q ss_pred             CCHHHHHHHHHHHHHHhC---CCCCHHHHHHHHhhccCcHHHHHHHHHHH
Q 022641          214 LSEEVMSSRVLHICNEEG---LNLDAEALSTLSSISQGDLRRAITYLQGA  260 (294)
Q Consensus       214 ~~~~~~~~~l~~~~~~~~---~~~~~~~l~~l~~~~~G~~r~~~~~l~~~  260 (294)
                      ++.++..+++.+.+....   ..-.++..+.|++.|+|.|-.+..+....
T Consensus       157 L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l  206 (287)
T PF00931_consen  157 LSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYL  206 (287)
T ss_dssp             --HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            999999999998875443   12235667889999999887766655544

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.

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

Probab=99.33  E-value=1.6e-10  Score=91.34  Aligned_cols=231  Identities=17%  Similarity=0.156  Sum_probs=139.3

Q ss_pred             hccccccCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee
Q 022641           40 KMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL  119 (294)
Q Consensus        40 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~  119 (294)
                      .++.......|+....+|..+-....+...+..+...+..++ ..+.++|+.|+|||.+.+++...+....   ..++.+
T Consensus        10 ~l~~~g~~~~pf~~~~~~~~~~~~a~h~e~l~~l~~~i~d~q-g~~~vtGevGsGKTv~~Ral~~s~~~d~---~~~v~i   85 (269)
T COG3267          10 LLNHFGFSRLPFSWDIQPGLDYWAADHNEALLMLHAAIADGQ-GILAVTGEVGSGKTVLRRALLASLNEDQ---VAVVVI   85 (269)
T ss_pred             HHHHhhhccCCCccchhhhhhhhhhhhhHHHHHHHHHHhcCC-ceEEEEecCCCchhHHHHHHHHhcCCCc---eEEEEe
Confidence            344444555566666666555555556666666666665544 3689999999999999997776663211   111333


Q ss_pred             cCCCCcchhHHHHHHHHHHhhhcccCc----------cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHH---hhcCcc
Q 022641          120 NASDDRGINVVRTKIKTFAAVAVGSGQ----------RRGGYPCPPYKIIILDEADSMTEDAQNALRRTME---TYSKVT  186 (294)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~---~~~~~~  186 (294)
                      +.............+..+...+.....          ........++.++++||++.+..+..+.|+-..+   +.....
T Consensus        86 ~~~~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~~~g~r~v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l  165 (269)
T COG3267          86 DKPTLSDATLLEAIVADLESQPKVNVNAVLEQIDRELAALVKKGKRPVVLMVDEAHDLNDSALEALRLLTNLEEDSSKLL  165 (269)
T ss_pred             cCcchhHHHHHHHHHHHhccCccchhHHHHHHHHHHHHHHHHhCCCCeEEeehhHhhhChhHHHHHHHHHhhcccccCce
Confidence            333322222222222222110000000          0000111233799999999999888887765554   333445


Q ss_pred             eEEEEecCC------cccchHhhccccE-EEecCCCHHHHHHHHHHHHHHhCCC---CCHHHHHHHHhhccCcHHHHHHH
Q 022641          187 RFFFICNYI------SRIIEPLASRCAK-FRFKPLSEEVMSSRVLHICNEEGLN---LDAEALSTLSSISQGDLRRAITY  256 (294)
Q Consensus       187 ~ii~~~~~~------~~~~~~l~~r~~~-i~~~~~~~~~~~~~l~~~~~~~~~~---~~~~~l~~l~~~~~G~~r~~~~~  256 (294)
                      .+++++...      .....++..|+.+ +.++|++.++...+++..++..+..   ++++++..+...+.|-||.+-++
T Consensus       166 ~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~  245 (269)
T COG3267         166 SIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNL  245 (269)
T ss_pred             eeeecCCcccchhhchHHHHhhhheEEEEEecCCcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHH
Confidence            566666322      1234566779986 9999999999999999999876554   78999999999999988876665


Q ss_pred             HHHHHHH---h-CCCCChhhhh
Q 022641          257 LQGAARL---F-GSSITSKDLI  274 (294)
Q Consensus       257 l~~~~~~---~-~~~it~~~v~  274 (294)
                      +..|-.-   + +..|+...++
T Consensus       246 ~~~Al~~a~~a~~~~v~~a~~~  267 (269)
T COG3267         246 ATLALDAAYSAGEDGVSEAEIK  267 (269)
T ss_pred             HHHHHHHHHHcCCCccchhhcc
Confidence            5543322   2 3446655543

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

Probab=99.32  E-value=9.6e-12  Score=107.15  Aligned_cols=194  Identities=22%  Similarity=0.180  Sum_probs=118.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCC-cceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEe
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKS-RVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILD  162 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiD  162 (294)
                      .++|+||||||||.+|+.+.+-+...+..-. ..-.++..-..+...++.++..........+.      .+.-++||+|
T Consensus       258 GiLLyGPPGTGKTLiARqIGkMLNArePKIVNGPeIL~KYVGeSE~NvR~LFaDAEeE~r~~g~------~SgLHIIIFD  331 (744)
T KOG0741|consen  258 GILLYGPPGTGKTLIARQIGKMLNAREPKIVNGPEILNKYVGESEENVRKLFADAEEEQRRLGA------NSGLHIIIFD  331 (744)
T ss_pred             eEEEECCCCCChhHHHHHHHHHhcCCCCcccCcHHHHHHhhcccHHHHHHHHHhHHHHHHhhCc------cCCceEEEeh
Confidence            3999999999999999999999854332110 00012222334556677777665544322221      1234699999


Q ss_pred             CCCCCC-------------HHHHHHHHHHHHhhc--CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHH
Q 022641          163 EADSMT-------------EDAQNALRRTMETYS--KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVL  224 (294)
Q Consensus       163 ei~~l~-------------~~~~~~L~~~l~~~~--~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~  224 (294)
                      |+|.+.             ....+.|+.-|+.-.  .+..+|..||....++.+|++  |+. .+++.-|+++-+.++++
T Consensus       332 EiDAICKqRGS~~g~TGVhD~VVNQLLsKmDGVeqLNNILVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gRlQIl~  411 (744)
T KOG0741|consen  332 EIDAICKQRGSMAGSTGVHDTVVNQLLSKMDGVEQLNNILVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGRLQILK  411 (744)
T ss_pred             hhHHHHHhcCCCCCCCCccHHHHHHHHHhcccHHhhhcEEEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCceEEEE
Confidence            999762             346788887776433  467788889999999999987  776 57888888877776665


Q ss_pred             HHHH---HhCCCCCHHHHHHHHhhc----cCcHHHHHHHHHHHHHHh----C------------CCCChhhhhhhccccc
Q 022641          225 HICN---EEGLNLDAEALSTLSSIS----QGDLRRAITYLQGAARLF----G------------SSITSKDLISVSGYPT  281 (294)
Q Consensus       225 ~~~~---~~~~~~~~~~l~~l~~~~----~G~~r~~~~~l~~~~~~~----~------------~~it~~~v~~~~~~~~  281 (294)
                      -.-+   .++.-=++-.++.|+..+    +..+..++...+.-|..-    +            -.++++|+..++.++.
T Consensus       412 IHT~rMre~~~l~~dVdl~elA~lTKNfSGAEleglVksA~S~A~nR~vk~~~~~~~~~~~~e~lkV~r~DFl~aL~dVk  491 (744)
T KOG0741|consen  412 IHTKRMRENNKLSADVDLKELAALTKNFSGAELEGLVKSAQSFAMNRHVKAGGKVEVDPVAIENLKVTRGDFLNALEDVK  491 (744)
T ss_pred             hhhhhhhhcCCCCCCcCHHHHHHHhcCCchhHHHHHHHHHHHHHHHhhhccCcceecCchhhhheeecHHHHHHHHHhcC
Confidence            4332   233322233366666653    333333333333222110    1            1378888888877655


Q ss_pred             CC
Q 022641          282 GG  283 (294)
Q Consensus       282 ~~  283 (294)
                      +.
T Consensus       492 PA  493 (744)
T KOG0741|consen  492 PA  493 (744)
T ss_pred             cc
Confidence            54

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=99.31  E-value=2.2e-10  Score=102.22  Aligned_cols=191  Identities=19%  Similarity=0.212  Sum_probs=126.0

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhccc--CccCCCCCCCCcEEEE
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGS--GQRRGGYPCPPYKIII  160 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~lli  160 (294)
                      ..++++|.+|+||+++++++....   .....+++.+++..... ..+...+..........  ....+....+..+.|+
T Consensus       163 ~~vli~ge~g~gk~~~a~~ih~~s---~~~~~~~i~~~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~  238 (441)
T PRK10365        163 ATVLIHGDSGTGKELVARAIHASS---ARSEKPLVTLNCAALNE-SLLESELFGHEKGAFTGADKRREGRFVEADGGTLF  238 (441)
T ss_pred             CeEEEEecCCCCHHHHHHHHHHcC---CCCCCCeeeeeCCCCCH-HHHHHHhcCCCCCCcCCCCcCCCCceeECCCCEEE
Confidence            459999999999999999998754   22356888888886532 22222221111000000  0112223445678999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-------ccchHhhcccc--EEEecCCCH--HH
Q 022641          161 LDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-------RIIEPLASRCA--KFRFKPLSE--EV  218 (294)
Q Consensus       161 iDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-------~~~~~l~~r~~--~i~~~~~~~--~~  218 (294)
                      |||++.|+...+..|+..++...           ..+++|++|+...       .+.+.+..++.  .+.++|+..  ++
T Consensus       239 ldei~~l~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~~~~~~~~~~~~~~l~~~l~~~~i~~ppLreR~~D  318 (441)
T PRK10365        239 LDEIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVAIEVPSLRQRRED  318 (441)
T ss_pred             EeccccCCHHHHHHHHHHHccCcEEeCCCCceeeeceEEEEeCCCCHHHHHHcCCchHHHHHHhccceecCCChhhcchh
Confidence            99999999999999999997633           1345777775432       23455556665  566666653  35


Q ss_pred             HHHHHHHHHHH----hC---CCCCHHHHHHHHhhc-cCcHHHHHHHHHHHHHHh-CCCCChhhhhhhc
Q 022641          219 MSSRVLHICNE----EG---LNLDAEALSTLSSIS-QGDLRRAITYLQGAARLF-GSSITSKDLISVS  277 (294)
Q Consensus       219 ~~~~l~~~~~~----~~---~~~~~~~l~~l~~~~-~G~~r~~~~~l~~~~~~~-~~~it~~~v~~~~  277 (294)
                      +..++.+++.+    .+   ..+++++++.|..+. +||+|++.++++.++... +..|+.+++...+
T Consensus       319 i~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgN~reL~~~~~~~~~~~~~~~i~~~~l~~~~  386 (441)
T PRK10365        319 IPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAVERAVVLLTGEYISERELPLAI  386 (441)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCCCCHHHHHHHHHHHHHHhCCCCccchHhCchhh
Confidence            55555555443    23   348999999999985 999999999999988665 5568888876443

>PRK08116 hypothetical protein; Validated

Probab=99.30  E-value=3.4e-11  Score=99.34  Aligned_cols=156  Identities=19%  Similarity=0.199  Sum_probs=86.9

Q ss_pred             hhhcCCCcchhhccc---HHHHHHHHHHHHc----C-CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           52 VEKYRPKQVKDVAHQ---EEVVRVLTNTLET----A-NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        52 ~~~~~~~~~~~~~g~---~~~~~~l~~~l~~----~-~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      .+++...+|+.+...   ..+.......+..    . ....++|+|++|+||||||.++++.+...   +..++.++..+
T Consensus        76 ~~~~~~~tFdnf~~~~~~~~a~~~a~~y~~~~~~~~~~~~gl~l~G~~GtGKThLa~aia~~l~~~---~~~v~~~~~~~  152 (268)
T PRK08116         76 DEKFRNSTFENFLFDKGSEKAYKIARKYVKKFEEMKKENVGLLLWGSVGTGKTYLAACIANELIEK---GVPVIFVNFPQ  152 (268)
T ss_pred             CHHHHhcchhcccCChHHHHHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEEHHH
Confidence            456666777766532   2233333333321    1 22349999999999999999999998432   23344443222


Q ss_pred             CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCC--CCCHHHHHHHHHHHHhhcC-cceEEEEecCCcc---
Q 022641          124 DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEAD--SMTEDAQNALRRTMETYSK-VTRFFFICNYISR---  197 (294)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~--~l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~~---  197 (294)
                            +...+......................++|+|||++  ..+...++.|+.+++.++. ...+|+|||....   
T Consensus       153 ------ll~~i~~~~~~~~~~~~~~~~~~l~~~dlLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~~~eL~  226 (268)
T PRK08116        153 ------LLNRIKSTYKSSGKEDENEIIRSLVNADLLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLSLEELK  226 (268)
T ss_pred             ------HHHHHHHHHhccccccHHHHHHHhcCCCEEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHH
Confidence                  111111000000000000000011234699999995  4566678889999987653 4568899987532   


Q ss_pred             --cchHhhcc----ccEEEecCCCH
Q 022641          198 --IIEPLASR----CAKFRFKPLSE  216 (294)
Q Consensus       198 --~~~~l~~r----~~~i~~~~~~~  216 (294)
                        +..++.+|    |..+.+..++.
T Consensus       227 ~~~~~ri~sRl~e~~~~v~~~g~d~  251 (268)
T PRK08116        227 NQYGKRIYDRILEMCTPVENEGKSY  251 (268)
T ss_pred             HHHhHHHHHHHHHcCEEEEeeCcCh
Confidence              34566666    44677777663

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=99.29  E-value=4.3e-10  Score=92.90  Aligned_cols=214  Identities=19%  Similarity=0.206  Sum_probs=142.3

Q ss_pred             CCcchhhcccHHHHHHHHHHHHcCC--CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHH
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLETAN--CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKI  134 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~~~--~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  134 (294)
                      ...|+.+++....++.+..-...-.  -..++|.|.+||||-.+|++....   +.....+|+.+||........-.+. 
T Consensus       200 ~~~F~~~v~~S~~mk~~v~qA~k~AmlDAPLLI~GeTGTGKdLlAkaCH~~---S~R~~~pFlalNCA~lPe~~aEsEl-  275 (511)
T COG3283         200 VSGFEQIVAVSPKMKHVVEQAQKLAMLDAPLLITGETGTGKDLLAKACHLA---SPRHSKPFLALNCASLPEDAAESEL-  275 (511)
T ss_pred             ccchHHHhhccHHHHHHHHHHHHhhccCCCeEEecCCCchHHHHHHHHhhc---CcccCCCeeEeecCCCchhHhHHHH-
Confidence            3467788887666655544332211  124999999999999999987543   4455778999998876443222222 


Q ss_pred             HHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCC-------c
Q 022641          135 KTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYI-------S  196 (294)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~-------~  196 (294)
                         .....+...+.+....+..+-+++|||..+++..+..|+..+.+..           .++++|++|..+       .
T Consensus       276 ---FG~apg~~gk~GffE~AngGTVlLDeIgEmSp~lQaKLLRFL~DGtFRRVGee~Ev~vdVRVIcatq~nL~~lv~~g  352 (511)
T COG3283         276 ---FGHAPGDEGKKGFFEQANGGTVLLDEIGEMSPRLQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQVNLVELVQKG  352 (511)
T ss_pred             ---hcCCCCCCCccchhhhccCCeEEeehhhhcCHHHHHHHHHHhcCCceeecCCcceEEEEEEEEecccccHHHHHhcC
Confidence               1222223334455556778899999999999999999999997533           456788887543       1


Q ss_pred             ccchHhhccccEE--EecCCCH------HHHHHHHHHHHHHhCCC---CCHHHHHHHHhh-ccCcHHHHHHHHHHHHHHh
Q 022641          197 RIIEPLASRCAKF--RFKPLSE------EVMSSRVLHICNEEGLN---LDAEALSTLSSI-SQGDLRRAITYLQGAARLF  264 (294)
Q Consensus       197 ~~~~~l~~r~~~i--~~~~~~~------~~~~~~l~~~~~~~~~~---~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~~  264 (294)
                      .....+..|..++  +++|+-+      .-...++.+++.+.++.   ++++.+.++.++ +.||+|++-|.+=.++..-
T Consensus       353 ~fReDLfyRLNVLtl~~PpLRer~~di~pL~e~Fv~q~s~elg~p~pkl~~~~~~~L~~y~WpGNVRqL~N~iyRA~s~~  432 (511)
T COG3283         353 KFREDLFYRLNVLTLNLPPLRERPQDIMPLAELFVQQFSDELGVPRPKLAADLLTVLTRYAWPGNVRQLKNAIYRALTLL  432 (511)
T ss_pred             chHHHHHHHhheeeecCCccccCcccchHHHHHHHHHHHHHhCCCCCccCHHHHHHHHHcCCCccHHHHHHHHHHHHHHh
Confidence            2345566677654  4455432      23345566667666654   789999999987 7999999999777665444


Q ss_pred             -CCCCChhhhhhhc
Q 022641          265 -GSSITSKDLISVS  277 (294)
Q Consensus       265 -~~~it~~~v~~~~  277 (294)
                       +..++.+++.-..
T Consensus       433 Eg~~l~i~~i~Lp~  446 (511)
T COG3283         433 EGYELRIEDILLPD  446 (511)
T ss_pred             ccCccchhhcccCC
Confidence             5667777665443

>PRK09862 putative ATP-dependent protease; Provisional

Probab=99.29  E-value=1.6e-10  Score=102.43  Aligned_cols=219  Identities=22%  Similarity=0.226  Sum_probs=126.8

Q ss_pred             CcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec------CCCC-------
Q 022641           58 KQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN------ASDD-------  124 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~------~~~~-------  124 (294)
                      .++.++.|+...++.+.-.+.  ...+++|+||+|+|||++++.+...+...  .+...+++.      ....       
T Consensus       188 ~d~~~v~Gq~~~~~al~laa~--~G~~llliG~~GsGKTtLak~L~gllpp~--~g~e~le~~~i~s~~g~~~~~~~~~~  263 (506)
T PRK09862        188 HDLSDVIGQEQGKRGLEITAA--GGHNLLLIGPPGTGKTMLASRINGLLPDL--SNEEALESAAILSLVNAESVQKQWRQ  263 (506)
T ss_pred             cCeEEEECcHHHHhhhheecc--CCcEEEEECCCCCcHHHHHHHHhccCCCC--CCcEEEecchhhhhhccccccCCcCC
Confidence            367788899888777653333  33589999999999999999998766211  111111110      0000       


Q ss_pred             cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh-------------cCcceEEEE
Q 022641          125 RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY-------------SKVTRFFFI  191 (294)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~-------------~~~~~ii~~  191 (294)
                      +.....-.......-...+....++....+.+++|+|||++.++...++.|++.|++.             +..+.+|.+
T Consensus       264 rPfr~ph~~~s~~~l~GGg~~~~pG~l~~A~gGvLfLDEi~e~~~~~~~~L~~~LE~g~v~I~r~g~~~~~pa~f~lIAa  343 (506)
T PRK09862        264 RPFRSPHHSASLTAMVGGGAIPGPGEISLAHNGVLFLDELPEFERRTLDALREPIESGQIHLSRTRAKITYPARFQLVAA  343 (506)
T ss_pred             CCccCCCccchHHHHhCCCceehhhHhhhccCCEEecCCchhCCHHHHHHHHHHHHcCcEEEecCCcceeccCCEEEEEe
Confidence            0000000000000001111123445566678899999999999999999999999753             345667888


Q ss_pred             ecCCc---------------------ccchHhhcccc-EEEecCCCHHHHH----------HHHHHHHH------Hh---
Q 022641          192 CNYIS---------------------RIIEPLASRCA-KFRFKPLSEEVMS----------SRVLHICN------EE---  230 (294)
Q Consensus       192 ~~~~~---------------------~~~~~l~~r~~-~i~~~~~~~~~~~----------~~l~~~~~------~~---  230 (294)
                      +|...                     .+..++++||. .+.+++++.+++.          .+-+++.+      ..   
T Consensus       344 ~NP~pcG~~~~~~c~c~~~~~~~Y~~~ls~plLDRfdL~v~v~~~~~~~l~~~~~~~ess~~i~~rV~~ar~~q~~r~~~  423 (506)
T PRK09862        344 MNPSPTGHYQGNHNRCTPEQTLRYLNRLSGPFLDRFDLSLEIPLPPPGILSKTVVPGESSATVKQRVMAARERQFKRQNK  423 (506)
T ss_pred             ecCccceecCCCCCCcCHHHHHHHHhhCCHhHHhhccEEEEeCCCCHHHHhcccCCCCChHHHHHHHhhHHHHHHHHHHH
Confidence            77531                     36668999998 5788877432211          11111110      00   


Q ss_pred             -C-----------CCCCHHHHHHHH---hhccCcHHHHHHHHHHHHHHh----CCCCChhhhhhhcccc
Q 022641          231 -G-----------LNLDAEALSTLS---SISQGDLRRAITYLQGAARLF----GSSITSKDLISVSGYP  280 (294)
Q Consensus       231 -~-----------~~~~~~~l~~l~---~~~~G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~  280 (294)
                       +           +.++++..+.+.   ...+=+.|....+++-+...+    ...|+.+|+.+++.-.
T Consensus       424 ~n~~l~~~~l~~~~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR  492 (506)
T PRK09862        424 LNAWLDSPEIRQFCKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYR  492 (506)
T ss_pred             HhcccCHHHHHHHhCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhh
Confidence             1           223444433222   223345777777777555444    5679999999988754

>PRK07952 DNA replication protein DnaC; Validated

Probab=99.27  E-value=2.3e-11  Score=98.31  Aligned_cols=154  Identities=18%  Similarity=0.170  Sum_probs=86.9

Q ss_pred             hhhcCCCcchhhc----ccHHHHHHHHHHHHcC--CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           52 VEKYRPKQVKDVA----HQEEVVRVLTNTLETA--NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        52 ~~~~~~~~~~~~~----g~~~~~~~l~~~l~~~--~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      .+.+.+.+|+.+.    ++..++..+..+....  ...+++|+|++|||||+|+.++++++...   +..+..+...+  
T Consensus        63 ~~~~~~~tFdnf~~~~~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~~---g~~v~~it~~~--  137 (244)
T PRK07952         63 RPLHQNCSFENYRVECEGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLR---GKSVLIITVAD--  137 (244)
T ss_pred             CccccCCccccccCCCchHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEHHH--
Confidence            3456677787765    2334555555555432  22469999999999999999999998432   23333332211  


Q ss_pred             chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH--HHHHHHHHHHhhcC-cceEEEEecCCcc-----
Q 022641          126 GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED--AQNALRRTMETYSK-VTRFFFICNYISR-----  197 (294)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~--~~~~L~~~l~~~~~-~~~ii~~~~~~~~-----  197 (294)
                          +...+...... .............+.++|+|||++.....  ....|+++++.++. ...+|++||....     
T Consensus       138 ----l~~~l~~~~~~-~~~~~~~~l~~l~~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl~~~~l~~~  212 (244)
T PRK07952        138 ----IMSAMKDTFSN-SETSEEQLLNDLSNVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNSNMEEMTKL  212 (244)
T ss_pred             ----HHHHHHHHHhh-ccccHHHHHHHhccCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCCCHHHHHHH
Confidence                11111110000 00000000001224569999999887533  45678889987765 6778999987532     


Q ss_pred             cchHhhccc-----cEEEecCCC
Q 022641          198 IIEPLASRC-----AKFRFKPLS  215 (294)
Q Consensus       198 ~~~~l~~r~-----~~i~~~~~~  215 (294)
                      +.+++.+|+     ..+.|...+
T Consensus       213 ~g~ri~sRl~~~~~~~i~f~~~s  235 (244)
T PRK07952        213 LGERVMDRMRLGNSLWVIFNWDS  235 (244)
T ss_pred             hChHHHHHHHHCCceEEEeeCCc
Confidence            334444544     356666544

>PRK08485 DNA polymerase III subunit delta'; Validated

Probab=99.27  E-value=1.4e-10  Score=88.80  Aligned_cols=136  Identities=17%  Similarity=0.127  Sum_probs=109.7

Q ss_pred             CcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEec
Q 022641          114 SRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      ...+.+-..+...++.++..+........            .. -++|++++.++..+.+.|++.+++++.++.+|++|.
T Consensus        26 ~~~~~~f~~~~i~Vd~iReii~~~~~~~~------------~~-k~iI~~a~~l~~~A~NaLLK~LEEPp~~~~fiL~t~   92 (206)
T PRK08485         26 KKNLRFFIKEEFKIEDAKEVIAEAYIAES------------EE-KIIVIAAPSYGIEAQNALLKILEEPPKNICFIIVAK   92 (206)
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHhhCCC------------Cc-EEEEEchHhhCHHHHHHHHHHhcCCCCCeEEEEEeC
Confidence            33333334446677778777666544321            11 346889999999999999999999999999999999


Q ss_pred             CCcccchHhhccccE-------------EEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHH
Q 022641          194 YISRIIEPLASRCAK-------------FRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGA  260 (294)
Q Consensus       194 ~~~~~~~~l~~r~~~-------------i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~  260 (294)
                      .+..+++.+++||..             +.+.+++.+++.+.+.+ +.+++....+++++.|+....|.+|.++.+.+..
T Consensus        93 ~~~~llpTI~SRc~~~~~~~~~~~~~l~l~l~~l~~~~i~~~L~~-~~ke~~~~~~ea~~lIa~la~~s~r~~l~l~~q~  171 (206)
T PRK08485         93 SKNLLLPTIRSRLIIEKRKQKKPVKPLDLDLKKLDLKDIYEFLKE-LEKENKLSKEELKELIESLLKECVKYKIPLNEEE  171 (206)
T ss_pred             ChHhCchHHHhhheeccccccccccccccccCCCCHHHHHHHHHH-HHHcccccHHHHHHHHHHHHHHHHHHHcCccHHH
Confidence            999999999999985             77899999999999998 6777887888999999999999999997776665


Q ss_pred             HHH
Q 022641          261 ARL  263 (294)
Q Consensus       261 ~~~  263 (294)
                      ..+
T Consensus       172 l~~  174 (206)
T PRK08485        172 LEY  174 (206)
T ss_pred             HHH
Confidence            544

>PF13173 AAA_14: AAA domain

Probab=99.26  E-value=7.6e-11  Score=86.52  Aligned_cols=120  Identities=26%  Similarity=0.354  Sum_probs=77.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHH-HHHHHHhhhcccCccCCCCCCCCcEEEEE
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRT-KIKTFAAVAVGSGQRRGGYPCPPYKIIIL  161 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~llii  161 (294)
                      +.++|+||+||||||+++.+++.+.    ....++.++..+......... ....+.....           .+..+|+|
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~----~~~~~~yi~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~i~i   67 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLL----PPENILYINFDDPRDRRLADPDLLEYFLELIK-----------PGKKYIFI   67 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhc----ccccceeeccCCHHHHHHhhhhhHHHHHHhhc-----------cCCcEEEE
Confidence            4589999999999999999999883    124556666655433221110 1111111100           12359999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcc----cchHhhccccEEEecCCCHHHH
Q 022641          162 DEADSMTEDAQNALRRTMETYSKVTRFFFICNYISR----IIEPLASRCAKFRFKPLSEEVM  219 (294)
Q Consensus       162 Dei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~----~~~~l~~r~~~i~~~~~~~~~~  219 (294)
                      ||++.++ .....+..+.+.. ....+++++.....    ....+..|...+.+.|++-.|.
T Consensus        68 DEiq~~~-~~~~~lk~l~d~~-~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   68 DEIQYLP-DWEDALKFLVDNG-PNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             ehhhhhc-cHHHHHHHHHHhc-cCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            9999996 4555566565543 45678887765433    3456777888999999998764

>KOG0482 consensus DNA replication licensing factor, MCM7 component [Replication, recombination and repair]

Probab=99.26  E-value=7.9e-11  Score=101.02  Aligned_cols=228  Identities=18%  Similarity=0.191  Sum_probs=148.9

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCC------------CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCc
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANC------------PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSR  115 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~------------~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~  115 (294)
                      .-++.+++...-..++.|++++++.|+-.|-.+..            =|++|.|.||+.||.|++.+.+-..      ..
T Consensus       329 ~~d~yekLa~SiAPEIyGheDVKKaLLLlLVGgvd~~~~dGMKIRGdINicLmGDPGVAKSQLLkyi~rlap------Rg  402 (721)
T KOG0482|consen  329 EGDFYEKLAASIAPEIYGHEDVKKALLLLLVGGVDKSPGDGMKIRGDINICLMGDPGVAKSQLLKYISRLAP------RG  402 (721)
T ss_pred             cccHHHHHHHhhchhhccchHHHHHHHHHhhCCCCCCCCCCceeecceeEEecCCCchhHHHHHHHHHhcCc------cc
Confidence            34667777777777999999999999888754311            1499999999999999999988761      12


Q ss_pred             cee-ecCCCCcchhHHHHHHHHHHhhhcccC--ccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh-----------
Q 022641          116 VLE-LNASDDRGINVVRTKIKTFAAVAVGSG--QRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMET-----------  181 (294)
Q Consensus       116 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~-----------  181 (294)
                      ++. -.++++.+...  ..+.    -+....  ..-+....+..++++|||+|++.......+..+|+.           
T Consensus       403 vYTTGrGSSGVGLTA--AVmk----DpvTgEM~LEGGALVLAD~GICCIDEfDKM~e~DRtAIHEVMEQQTISIaKAGI~  476 (721)
T KOG0482|consen  403 VYTTGRGSSGVGLTA--AVMK----DPVTGEMVLEGGALVLADGGICCIDEFDKMDESDRTAIHEVMEQQTISIAKAGIN  476 (721)
T ss_pred             ceecCCCCCccccch--hhhc----CCCCCeeEeccceEEEccCceEeehhhhhhhhhhhHHHHHHHHhhhhhhhhhccc
Confidence            221 12333333211  1111    111111  111234456788999999999998888888888874           


Q ss_pred             --hcCcceEEEEecCCc-------------ccchHhhccccEE-------------------------------EecCCC
Q 022641          182 --YSKVTRFFFICNYIS-------------RIIEPLASRCAKF-------------------------------RFKPLS  215 (294)
Q Consensus       182 --~~~~~~ii~~~~~~~-------------~~~~~l~~r~~~i-------------------------------~~~~~~  215 (294)
                        ....++++.++|+..             .++.+|++||..+                               .|.|++
T Consensus       477 TtLNAR~sILaAANPayGRYnprrs~e~NI~LPaALLSRFDll~Li~D~pdrd~D~~LA~HiTyVH~H~~qp~~~fepl~  556 (721)
T KOG0482|consen  477 TTLNARTSILAAANPAYGRYNPRRSPEQNINLPAALLSRFDLLWLIQDRPDRDNDLRLAQHITYVHQHEEQPPLDFEPLD  556 (721)
T ss_pred             cchhhhHHhhhhcCccccccCcccChhHhcCCcHHHHHhhhhhhhhccCCcccchHHHHHHhHhhhccCCCCCccCCCCC
Confidence              223344555555432             2678899988532                               566777


Q ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHhh--------------ccCcHHHHHHHHHHHHHHh----CCCCChhhhhhhc
Q 022641          216 EEVMSSRVLHICNEEGLNLDAEALSTLSSI--------------SQGDLRRAITYLQGAARLF----GSSITSKDLISVS  277 (294)
Q Consensus       216 ~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~--------------~~G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~  277 (294)
                      .+.++.++. .|+.....++++..++|...              +.-.+|.++.++......+    ...+..++|.+++
T Consensus       557 ~~~mR~yI~-~ak~~~P~vp~~l~dyi~~AYv~~Rrea~~~~~~t~ttpRtLL~IlRls~AlarLRls~~V~~~DV~EAL  635 (721)
T KOG0482|consen  557 PNLMRRYIS-LAKRKNPVVPEALADYITGAYVELRREARSSKDFTYTTPRTLLGILRLSTALARLRLSDSVEEDDVNEAL  635 (721)
T ss_pred             HHHHHHHHH-HHhhcCCCCCHHHHHHHHHHHHHHHHHhhccCCCcccCHHHHHHHHHHHHHHHHhhhccccchhhHHHHH
Confidence            788888774 45555667888887777643              1346899888888766665    5668899999988


Q ss_pred             ccccCCCCCcc
Q 022641          278 GYPTGGSGGAF  288 (294)
Q Consensus       278 ~~~~~~~~~~~  288 (294)
                      ....-...+.+
T Consensus       636 RLme~sK~sL~  646 (721)
T KOG0482|consen  636 RLMEMSKDSLY  646 (721)
T ss_pred             HHHHhhhcccc
Confidence            77554444333

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=99.25  E-value=6.1e-10  Score=100.82  Aligned_cols=210  Identities=13%  Similarity=0.092  Sum_probs=132.0

Q ss_pred             cHHHHHHHHHHHHcC-CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhccc
Q 022641           66 QEEVVRVLTNTLETA-NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGS  144 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~-~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  144 (294)
                      ++..+..|.-..-.. ....++|.|++|+|||+++++++..+-.    ..+|+.+..+.  +.+.+..-+.--.....+.
T Consensus         8 ~~~~~~Al~l~av~p~~~gGv~i~g~~G~~ks~~~r~l~~llp~----~~p~r~~p~~~--t~~~L~Gg~Dl~~~l~~g~   81 (584)
T PRK13406          8 WADAALAAALLAVDPAGLGGVVLRARAGPVRDRWLAALRALLPA----GTPLRRLPPGI--ADDRLLGGLDLAATLRAGR   81 (584)
T ss_pred             HHHHHHHHHHhCcCccccceEEEEcCCCcHHHHHHHHHHHhcCC----CCCcccCCCCC--cHHHccCCchHHhHhhcCC
Confidence            445555544444444 4456999999999999999999988722    12443332221  2222211111111111122


Q ss_pred             C-ccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-------------CcceEEEEecC---CcccchHhhcccc
Q 022641          145 G-QRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-------------KVTRFFFICNY---ISRIIEPLASRCA  207 (294)
Q Consensus       145 ~-~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-------------~~~~ii~~~~~---~~~~~~~l~~r~~  207 (294)
                      . ..++....+.++||||||++.+++..++.|++.+++..             ..+.+|.+-|.   ...+..++++||.
T Consensus        82 ~~~~pGlla~Ah~GvL~lDe~n~~~~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~~~L~~~lLDRf~  161 (584)
T PRK13406         82 PVAQRGLLAEADGGVLVLAMAERLEPGTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEEDERAPAALADRLA  161 (584)
T ss_pred             cCCCCCceeeccCCEEEecCcccCCHHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcccCCCHHhHhheE
Confidence            1 45566667788999999999999999999999998632             23334443221   1347888999998


Q ss_pred             -EEEecCCCHHHHH-------HHHHHHHHHhCCCCCHHHHHHHHhhc--cC--cHHHHHHHHHHHHHHh----CCCCChh
Q 022641          208 -KFRFKPLSEEVMS-------SRVLHICNEEGLNLDAEALSTLSSIS--QG--DLRRAITYLQGAARLF----GSSITSK  271 (294)
Q Consensus       208 -~i~~~~~~~~~~~-------~~l~~~~~~~~~~~~~~~l~~l~~~~--~G--~~r~~~~~l~~~~~~~----~~~it~~  271 (294)
                       .+.+.+++..+..       .+......-.++.++++.++++++.+  .|  .+|..+.++.-+...+    ...|+.+
T Consensus       162 l~v~v~~~~~~~~~~~~~~~~~I~~AR~rl~~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~  241 (584)
T PRK13406        162 FHLDLDGLALRDAREIPIDADDIAAARARLPAVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEE  241 (584)
T ss_pred             EEEEcCCCChHHhcccCCCHHHHHHHHHHHccCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHH
Confidence             7888887765432       12211111146789999999887753  12  5688777777655555    5679999


Q ss_pred             hhhhhccccc
Q 022641          272 DLISVSGYPT  281 (294)
Q Consensus       272 ~v~~~~~~~~  281 (294)
                      ||..++..+-
T Consensus       242 dv~~Aa~lvL  251 (584)
T PRK13406        242 DLALAARLVL  251 (584)
T ss_pred             HHHHHHHHHH
Confidence            9998876543

>PRK08939 primosomal protein DnaI; Reviewed

Probab=99.25  E-value=3.1e-11  Score=101.19  Aligned_cols=137  Identities=16%  Similarity=0.183  Sum_probs=74.2

Q ss_pred             cCCchhhhhcCCCcchhhcc----cHHHHHHHHHHHHcC----CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcce
Q 022641           46 QSSQPWVEKYRPKQVKDVAH----QEEVVRVLTNTLETA----NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVL  117 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g----~~~~~~~l~~~l~~~----~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~  117 (294)
                      .+.+|.  .+...+|+++..    +..+......++...    ...+++|+||+|||||+|+.++++++...   +..+.
T Consensus       114 ~a~~p~--~~~~atf~~~~~~~~~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~~~---g~~v~  188 (306)
T PRK08939        114 SIYMPK--DLLQASLADIDLDDRDRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELAKK---GVSST  188 (306)
T ss_pred             HcCCCH--hHhcCcHHHhcCCChHHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHHHc---CCCEE
Confidence            455553  445556665542    333444445555532    23579999999999999999999998422   22222


Q ss_pred             eecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--HHHH-HHHHHHHhh-cCcceEEEEec
Q 022641          118 ELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--DAQN-ALRRTMETY-SKVTRFFFICN  193 (294)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--~~~~-~L~~~l~~~-~~~~~ii~~~~  193 (294)
                      .+..+.     .+. .+....   .............+.++|||||++.-+.  -... .|..+++.+ .....+|+|||
T Consensus       189 ~~~~~~-----l~~-~lk~~~---~~~~~~~~l~~l~~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSN  259 (306)
T PRK08939        189 LLHFPE-----FIR-ELKNSI---SDGSVKEKIDAVKEAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSN  259 (306)
T ss_pred             EEEHHH-----HHH-HHHHHH---hcCcHHHHHHHhcCCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECC
Confidence            222211     011 111100   0000000001123456999999987643  3343 344555655 46778999998


Q ss_pred             CCc
Q 022641          194 YIS  196 (294)
Q Consensus       194 ~~~  196 (294)
                      ...
T Consensus       260 l~~  262 (306)
T PRK08939        260 FDF  262 (306)
T ss_pred             CCH
Confidence            764

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=99.24  E-value=1.2e-11  Score=105.94  Aligned_cols=120  Identities=29%  Similarity=0.382  Sum_probs=76.4

Q ss_pred             CcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec------CCCCcchhHHH
Q 022641           58 KQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN------ASDDRGINVVR  131 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~------~~~~~~~~~~~  131 (294)
                      .+|.|+.||+..++.+.-+...+.  |++++||||||||.+|+.+..-+  +.......++++      .........+.
T Consensus       176 ~D~~DV~GQ~~AKrAleiAAAGgH--nLl~~GpPGtGKTmla~Rl~~lL--Ppls~~E~lE~s~I~s~~g~~~~~~~~~~  251 (490)
T COG0606         176 PDFKDVKGQEQAKRALEIAAAGGH--NLLLVGPPGTGKTMLASRLPGLL--PPLSIPEALEVSAIHSLAGDLHEGCPLKI  251 (490)
T ss_pred             cchhhhcCcHHHHHHHHHHHhcCC--cEEEecCCCCchHHhhhhhcccC--CCCChHHHHHHHHHhhhcccccccCccce
Confidence            388999999999999886666554  89999999999999999987765  111111111111      00000000000


Q ss_pred             --------HHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh
Q 022641          132 --------TKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMET  181 (294)
Q Consensus       132 --------~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~  181 (294)
                              .......-...+....++....+.++||||||+..+.....+.|.+-|++
T Consensus       252 ~rPFr~PHHsaS~~aLvGGG~~p~PGeIsLAH~GVLFLDElpef~~~iLe~LR~PLE~  309 (490)
T COG0606         252 HRPFRAPHHSASLAALVGGGGVPRPGEISLAHNGVLFLDELPEFKRSILEALREPLEN  309 (490)
T ss_pred             eCCccCCCccchHHHHhCCCCCCCCCceeeecCCEEEeeccchhhHHHHHHHhCcccc
Confidence                    00000001111233456677788999999999999999999999988875

>smart00763 AAA_PrkA PrkA AAA domain

Probab=99.24  E-value=2.4e-10  Score=96.32  Aligned_cols=93  Identities=10%  Similarity=-0.044  Sum_probs=65.3

Q ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcC-----------cceEEEEecCC-------cccchHhhccccEEEec
Q 022641          151 YPCPPYKIIILDEADSMTEDAQNALRRTMETYSK-----------VTRFFFICNYI-------SRIIEPLASRCAKFRFK  212 (294)
Q Consensus       151 ~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~-----------~~~ii~~~~~~-------~~~~~~l~~r~~~i~~~  212 (294)
                      ...+.++++-++|+...+.+.++.|+.++++...           ...+|+++|..       .....+|.+||..+.++
T Consensus       232 l~~aNrGi~~f~Ei~K~~~~~l~~LL~~~qE~~v~~~~~~~~~~~d~liia~sNe~e~~~~~~~k~~eaf~dR~~~i~vp  311 (361)
T smart00763      232 LNRANRGILEFVEMFKADIKFLHPLLTATQEGNIKGTGGFAMIPIDGLIIAHSNESEWQRFKSNKKNEALLDRIIKVKVP  311 (361)
T ss_pred             cccccCceEEEeehhcCCHHHHHHHhhhhhcceEecCCcccccccceEEEEeCCHHHHhhhhccccchhhhhceEEEeCC
Confidence            3446789999999999999999999999985331           23356666654       24578999999988887


Q ss_pred             CC-CHHHHHHHHHHHHHHh---CCCCCHHHHHHHH
Q 022641          213 PL-SEEVMSSRVLHICNEE---GLNLDAEALSTLS  243 (294)
Q Consensus       213 ~~-~~~~~~~~l~~~~~~~---~~~~~~~~l~~l~  243 (294)
                      .+ +..+-.++.++.+...   +..+.+.+++.++
T Consensus       312 Y~l~~~~E~~Iy~k~~~~s~~~~~~~aP~~le~aa  346 (361)
T smart00763      312 YCLRVSEEAQIYEKLLRNSDLTEAHIAPHTLEMAA  346 (361)
T ss_pred             CcCCHHHHHHHHHHHhccCcCcccccCchHHHHHH
Confidence            55 5567777777776543   3345555544443

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK06835 DNA replication protein DnaC; Validated

Probab=99.21  E-value=1.7e-10  Score=97.55  Aligned_cols=123  Identities=20%  Similarity=0.190  Sum_probs=72.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEe
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILD  162 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiD  162 (294)
                      .+++|+||+|+|||||+.++++++...   +..++.+...+.      ...+........... ..........++||||
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~---g~~V~y~t~~~l------~~~l~~~~~~~~~~~-~~~~~~l~~~DLLIID  253 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDR---GKSVIYRTADEL------IEILREIRFNNDKEL-EEVYDLLINCDLLIID  253 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHC---CCeEEEEEHHHH------HHHHHHHHhccchhH-HHHHHHhccCCEEEEe
Confidence            679999999999999999999998533   234444433221      111111000000000 0000011234699999


Q ss_pred             CCCCC--CHHHHHHHHHHHHhhcC-cceEEEEecCCcc-----cchHhhccc----cEEEecCCC
Q 022641          163 EADSM--TEDAQNALRRTMETYSK-VTRFFFICNYISR-----IIEPLASRC----AKFRFKPLS  215 (294)
Q Consensus       163 ei~~l--~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~~-----~~~~l~~r~----~~i~~~~~~  215 (294)
                      |++..  ++...+.|+.+++.+.. ...+|++||....     +.+++.+|+    ..+.|...+
T Consensus       254 DlG~e~~t~~~~~~Lf~iin~R~~~~k~tIiTSNl~~~el~~~~~eri~SRL~~~~~~i~~~G~d  318 (329)
T PRK06835        254 DLGTEKITEFSKSELFNLINKRLLRQKKMIISTNLSLEELLKTYSERISSRLLGNFTLLKFYGED  318 (329)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHhHHHHHHHHcCCEEEEecCcC
Confidence            99765  45667889999988764 4678999986532     234555554    356665544

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=99.19  E-value=1.2e-10  Score=105.54  Aligned_cols=219  Identities=19%  Similarity=0.142  Sum_probs=132.1

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHcCCC------------CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcce
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANC------------PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVL  117 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~------------~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~  117 (294)
                      ...+.+...-...+.|++.+++.+.-.|..+..            -|+||+|.||||||.+.+.+.+.+       ..-+
T Consensus       275 ~i~~~l~~SiaPsIyG~e~VKkAilLqLfgGv~k~~~~g~~iRGDInILLvGDPgtaKSqlLk~v~~~a-------Pr~v  347 (682)
T COG1241         275 DIYDILIKSIAPSIYGHEDVKKAILLQLFGGVKKNLPDGTRIRGDIHILLVGDPGTAKSQLLKYVAKLA-------PRGV  347 (682)
T ss_pred             cHHHHHHHHhcccccCcHHHHHHHHHHhcCCCcccCCCCcccccceeEEEcCCCchhHHHHHHHHHhhC-------CceE
Confidence            444555555556788999999988888876432            259999999999999999999876       1222


Q ss_pred             eecC--CCCcchh--HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh-----------
Q 022641          118 ELNA--SDDRGIN--VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY-----------  182 (294)
Q Consensus       118 ~~~~--~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~-----------  182 (294)
                      ..++  +...+..  ..++..     . ..+....+....+.+++++|||+|.++......|...|+..           
T Consensus       348 ytsgkgss~~GLTAav~rd~~-----t-ge~~LeaGALVlAD~Gv~cIDEfdKm~~~dr~aihEaMEQQtIsIaKAGI~a  421 (682)
T COG1241         348 YTSGKGSSAAGLTAAVVRDKV-----T-GEWVLEAGALVLADGGVCCIDEFDKMNEEDRVAIHEAMEQQTISIAKAGITA  421 (682)
T ss_pred             EEccccccccCceeEEEEccC-----C-CeEEEeCCEEEEecCCEEEEEeccCCChHHHHHHHHHHHhcEeeecccceee
Confidence            2222  2211111  010000     0 01112334455677889999999999999999999999852           


Q ss_pred             --cCcceEEEEecCCcc-------------cchHhhccccEEEe--cCCCHHHHHH------------------------
Q 022641          183 --SKVTRFFFICNYISR-------------IIEPLASRCAKFRF--KPLSEEVMSS------------------------  221 (294)
Q Consensus       183 --~~~~~ii~~~~~~~~-------------~~~~l~~r~~~i~~--~~~~~~~~~~------------------------  221 (294)
                        +..+.++.++|+...             ++++|++||..|.+  .-++.+.-..                        
T Consensus       422 tLnARcsvLAAaNP~~Gryd~~~~~~enI~l~~~lLSRFDLifvl~D~~d~~~D~~ia~hil~~h~~~~~~~~~~~~~~~  501 (682)
T COG1241         422 TLNARCSVLAAANPKFGRYDPKKTVAENINLPAPLLSRFDLIFVLKDDPDEEKDEEIAEHILDKHRGEEPEETISLDGVD  501 (682)
T ss_pred             ecchhhhhhhhhCCCCCcCCCCCCHHHhcCCChhHHhhCCeeEEecCCCCccchHHHHHHHHHHHhcccccccccccccc
Confidence              234456666665542             67889999984433  3333221111                        


Q ss_pred             --------HHHHHH---HH-hCCCCCHHHHHHHHhhcc-----C-----------cHHHHHHHHHHHHHHh----CCCCC
Q 022641          222 --------RVLHIC---NE-EGLNLDAEALSTLSSISQ-----G-----------DLRRAITYLQGAARLF----GSSIT  269 (294)
Q Consensus       222 --------~l~~~~---~~-~~~~~~~~~l~~l~~~~~-----G-----------~~r~~~~~l~~~~~~~----~~~it  269 (294)
                              +|+++.   ++ -...+++++.+.|.+..-     +           ..|++-.+++.+-..+    +..++
T Consensus       502 ~~~~~~~~~lrkYI~YAR~~v~P~lt~ea~e~l~~~Yv~~Rk~~~~~~~~~~~piT~RqLEsiiRLaeA~Ak~rLS~~V~  581 (682)
T COG1241         502 EVEERDFELLRKYISYARKNVTPVLTEEAREELEDYYVEMRKKSALVEEKRTIPITARQLESIIRLAEAHAKMRLSDVVE  581 (682)
T ss_pred             ccccCcHHHHHHHHHHHhccCCcccCHHHHHHHHHHHHHhhhccccccccCcccccHHHHHHHHHHHHHHHhhhccCCCC
Confidence                    122221   11 113578888888776531     1           1444444444444333    67799


Q ss_pred             hhhhhhhccccc
Q 022641          270 SKDLISVSGYPT  281 (294)
Q Consensus       270 ~~~v~~~~~~~~  281 (294)
                      .+|+..+.....
T Consensus       582 ~eD~~eAi~lv~  593 (682)
T COG1241         582 EEDVDEAIRLVD  593 (682)
T ss_pred             HHHHHHHHHHHH
Confidence            999988876544

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.19  E-value=7.6e-10  Score=93.51  Aligned_cols=151  Identities=22%  Similarity=0.293  Sum_probs=98.6

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc----hhHHHHHHHHHHhhhcccCccCCCCCCCCcEE
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG----INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKI  158 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  158 (294)
                      .|++|.||+|+|||.||+.||+-+      +.++.-+++....-    .+.+...+..+.......      ...++.+|
T Consensus       227 SNvLllGPtGsGKTllaqTLAr~l------dVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~n------VekAQqGI  294 (564)
T KOG0745|consen  227 SNVLLLGPTGSGKTLLAQTLARVL------DVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYN------VEKAQQGI  294 (564)
T ss_pred             ccEEEECCCCCchhHHHHHHHHHh------CCCeEEecccchhhcccccccHHHHHHHHHHHccCC------HHHHhcCe
Confidence            579999999999999999999999      78888777765321    123333333333222111      11235679


Q ss_pred             EEEeCCCCCC--------------HHHHHHHHHHHHhhc-------------Cc------ceEEEEec------------
Q 022641          159 IILDEADSMT--------------EDAQNALRRTMETYS-------------KV------TRFFFICN------------  193 (294)
Q Consensus       159 liiDei~~l~--------------~~~~~~L~~~l~~~~-------------~~------~~ii~~~~------------  193 (294)
                      ++|||+|.+.              ..+++.|+++++..-             ..      .-|++++.            
T Consensus       295 VflDEvDKi~~~~~~i~~~RDVsGEGVQQaLLKllEGtvVnVpeK~~~~~~rgd~vqiDTtnILFiasGAF~~Ldk~I~r  374 (564)
T KOG0745|consen  295 VFLDEVDKITKKAESIHTSRDVSGEGVQQALLKLLEGTVVNVPEKGSRRKPRGDTVQIDTTNILFIASGAFVGLDKIISR  374 (564)
T ss_pred             EEEehhhhhcccCccccccccccchhHHHHHHHHhcccEEcccCCCCCCCCCCCeEEEeccceEEEecccccchHHHHHH
Confidence            9999999884              347889999997210             00      01222220            


Q ss_pred             -----------C-----------------------------------CcccchHhhcccc-EEEecCCCHHHHHHHHHH-
Q 022641          194 -----------Y-----------------------------------ISRIIEPLASRCA-KFRFKPLSEEVMSSRVLH-  225 (294)
Q Consensus       194 -----------~-----------------------------------~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~-  225 (294)
                                 .                                   .+.+.|+|..||. ++.|.+++.+++..+|.. 
T Consensus       375 R~~d~slGFg~~s~~~vr~~~~~~s~~~~~~~~~~~lL~~~~~~DLisfGmIPEfVGRfPVlVplh~L~~~~Lv~VLtEP  454 (564)
T KOG0745|consen  375 RLDDKSLGFGAPSSKGVRANMATKSGVENDAEKRDELLEKVESGDLISFGMIPEFVGRFPVLVPLHSLDEDQLVRVLTEP  454 (564)
T ss_pred             hhcchhcccCCCCCccchhhcccccCcchhHHHHHHHHhhccccchhhhcCcHHHhcccceEeeccccCHHHHHHHHhcc
Confidence                       0                                   0115688999998 689999999988877743 


Q ss_pred             ----------HHHHhCC--CCCHHHHHHHHhh
Q 022641          226 ----------ICNEEGL--NLDAEALSTLSSI  245 (294)
Q Consensus       226 ----------~~~~~~~--~~~~~~l~~l~~~  245 (294)
                                ++...++  .+++++++.|++.
T Consensus       455 knaL~~Qyk~lf~~~nV~L~fTe~Al~~IAq~  486 (564)
T KOG0745|consen  455 KNALGKQYKKLFGMDNVELHFTEKALEAIAQL  486 (564)
T ss_pred             hhhHHHHHHHHhccCCeeEEecHHHHHHHHHH
Confidence                      2222233  4799999999876

>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]

Probab=99.19  E-value=1.2e-10  Score=102.36  Aligned_cols=224  Identities=17%  Similarity=0.144  Sum_probs=130.0

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHcCCC------------CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcce
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANC------------PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVL  117 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~------------~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~  117 (294)
                      ...+++...-+..+.|++.++..+.-.+..|-.            .|++|+|.||+|||.++++.+.-+       ..-+
T Consensus       334 nly~~lv~Sl~PsIyGhe~VK~GilL~LfGGv~K~a~eg~~lRGDinv~iVGDPgt~KSQfLk~v~~fs-------PR~v  406 (764)
T KOG0480|consen  334 NLYKNLVNSLFPSIYGHELVKAGILLSLFGGVHKSAGEGTSLRGDINVCIVGDPGTGKSQFLKAVCAFS-------PRSV  406 (764)
T ss_pred             hHHHHHHHhhCccccchHHHHhhHHHHHhCCccccCCCCccccCCceEEEeCCCCccHHHHHHHHhccC-------Ccce
Confidence            334444455566788999999888877765421            259999999999999999998755       2222


Q ss_pred             eecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh-------------hcC
Q 022641          118 ELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMET-------------YSK  184 (294)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~-------------~~~  184 (294)
                      +.++...............  ..........+..-.+.++++.|||+|+++...+..|++.|+.             .+.
T Consensus       407 YtsGkaSSaAGLTaaVvkD--~esgdf~iEAGALmLADnGICCIDEFDKMd~~dqvAihEAMEQQtISIaKAGv~aTLnA  484 (764)
T KOG0480|consen  407 YTSGKASSAAGLTAAVVKD--EESGDFTIEAGALMLADNGICCIDEFDKMDVKDQVAIHEAMEQQTISIAKAGVVATLNA  484 (764)
T ss_pred             EecCcccccccceEEEEec--CCCCceeeecCcEEEccCceEEechhcccChHhHHHHHHHHHhheehheecceEEeecc
Confidence            2222111000000000000  0000001122333456778999999999999889999999984             223


Q ss_pred             cceEEEEecCCc-------------ccchHhhcccc--EEEecCC-----------------------------CHHHHH
Q 022641          185 VTRFFFICNYIS-------------RIIEPLASRCA--KFRFKPL-----------------------------SEEVMS  220 (294)
Q Consensus       185 ~~~ii~~~~~~~-------------~~~~~l~~r~~--~i~~~~~-----------------------------~~~~~~  220 (294)
                      ..+|+.++|+..             .+..++++||.  .|-+..+                             +.++++
T Consensus       485 RtSIlAAANPv~GhYdR~ktl~eNi~msApimSRFDL~FiLlD~~nE~~D~~ia~hIld~h~~i~~~~~~~~~~~~e~vr  564 (764)
T KOG0480|consen  485 RTSILAAANPVGGHYDRKKTLRENINMSAPIMSRFDLFFILLDDCNEVVDYAIARHILDLHRGIDDATERVCVYTLEQVR  564 (764)
T ss_pred             hhhhhhhcCCcCCccccccchhhhcCCCchhhhhhcEEEEEecCCchHHHHHHHHHHHHHhccccccccccccccHHHHH
Confidence            444666666432             25678899987  3444444                             445555


Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHhhcc--------C--------cHHHHHHHHH---HHHHHh-CCCCChhhhhhhcccc
Q 022641          221 SRVLHICNEEGLNLDAEALSTLSSISQ--------G--------DLRRAITYLQ---GAARLF-GSSITSKDLISVSGYP  280 (294)
Q Consensus       221 ~~l~~~~~~~~~~~~~~~l~~l~~~~~--------G--------~~r~~~~~l~---~~~~~~-~~~it~~~v~~~~~~~  280 (294)
                      .++.... .....++.++-+.|.+...        |        ..|++-.++.   ..|+.. ...+|.+++.++....
T Consensus       565 kYi~yAR-~~~P~ls~ea~~~lve~Y~~lR~~~~~~~~~~s~~ITvRqLESlIRLsEA~Ar~~~~devt~~~v~ea~eLl  643 (764)
T KOG0480|consen  565 KYIRYAR-NFKPKLSKEASEMLVEKYKGLRQRDAQGNNRSSYRITVRQLESLIRLSEARARVECRDEVTKEDVEEAVELL  643 (764)
T ss_pred             HHHHHHH-hcCccccHHHHHHHHHHHHHHHHhhccccCcccccccHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHHHHH
Confidence            5543322 3334467777666665421        1        2344444443   333333 6779999999888765


Q ss_pred             cCC
Q 022641          281 TGG  283 (294)
Q Consensus       281 ~~~  283 (294)
                      ..+
T Consensus       644 k~S  646 (764)
T KOG0480|consen  644 KKS  646 (764)
T ss_pred             Hhh
Confidence            554

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=99.18  E-value=6.5e-10  Score=89.77  Aligned_cols=176  Identities=22%  Similarity=0.267  Sum_probs=114.6

Q ss_pred             hhcccHHHHHHHHHHH----HcCCCCc---EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee----cCCCCcchhHH
Q 022641           62 DVAHQEEVVRVLTNTL----ETANCPH---MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL----NASDDRGINVV  130 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l----~~~~~~~---ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~----~~~~~~~~~~~  130 (294)
                      .+.||.-+++.+...+    .++.++.   +-|+|++||||+.+++.+++.++........+..+    +.+.....+..
T Consensus        83 ~lfGQHla~~~Vv~alk~~~~n~~p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~~~ie~Y  162 (344)
T KOG2170|consen   83 ALFGQHLAKQLVVNALKSHWANPNPRKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHASKIEDY  162 (344)
T ss_pred             HhhchHHHHHHHHHHHHHHhcCCCCCCCeEEEecCCCCCchhHHHHHHHHHHHhccccchhHHHhhhhccCCChHHHHHH
Confidence            5667766666555554    3443322   77899999999999999999986544333333333    23333333333


Q ss_pred             HHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-------CcceEEEEecCCcc------
Q 022641          131 RTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-------KVTRFFFICNYISR------  197 (294)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-------~~~~ii~~~~~~~~------  197 (294)
                      +..+.........         ..++.+.|+||+|.|++...+.|...++.++       .+..+|+.+|....      
T Consensus       163 k~eL~~~v~~~v~---------~C~rslFIFDE~DKmp~gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg~eI~~~a  233 (344)
T KOG2170|consen  163 KEELKNRVRGTVQ---------ACQRSLFIFDEVDKLPPGLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGGSEIARIA  233 (344)
T ss_pred             HHHHHHHHHHHHH---------hcCCceEEechhhhcCHhHHHHHhhhhccccccccccccceEEEEEcCCcchHHHHHH
Confidence            3333332222211         2345699999999999999999999988433       45668888865331      


Q ss_pred             -----------------cchHhh-------------cc------c-cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHH
Q 022641          198 -----------------IIEPLA-------------SR------C-AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALS  240 (294)
Q Consensus       198 -----------------~~~~l~-------------~r------~-~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~  240 (294)
                                       +-+.+.             ++      . ..|.|.|++...++..++-.+.++|...+++.++
T Consensus       234 L~~~~~g~~re~~~l~~~E~~L~~~~~n~~~~Gl~~S~li~~~lid~fIPFLPLek~hV~~C~r~el~~rg~~~d~~~~e  313 (344)
T KOG2170|consen  234 LENARNGKPREQLRLKSFEPALMQSAFNEKAGGLVHSRLISNNLIDHFIPFLPLEKRHVRSCIRAELRKRGLAPDQDFVE  313 (344)
T ss_pred             HHHHHcCCCcccchhhhhhHHHHHhhhccccccccccccchhhHHhhccCcCcccHHHHHHHHHHHHHhcccccchHHHH
Confidence                             001110             11      1 2678889999999999999888999888888888


Q ss_pred             HHHhhc
Q 022641          241 TLSSIS  246 (294)
Q Consensus       241 ~l~~~~  246 (294)
                      .+++..
T Consensus       314 rva~~l  319 (344)
T KOG2170|consen  314 RVANSL  319 (344)
T ss_pred             HHHHhh
Confidence            888763

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A

Probab=99.17  E-value=9.5e-09  Score=82.59  Aligned_cols=167  Identities=20%  Similarity=0.209  Sum_probs=106.3

Q ss_pred             HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCC
Q 022641           71 RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGG  150 (294)
Q Consensus        71 ~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (294)
                      ..+..++....  .-.+.||+|||||.+++.+++.+      +..++.++++...+...+...+........        
T Consensus        23 ~~l~~al~~~~--~~~~~GpagtGKtetik~La~~l------G~~~~vfnc~~~~~~~~l~ril~G~~~~Ga--------   86 (231)
T PF12774_consen   23 LTLTQALSLNL--GGALSGPAGTGKTETIKDLARAL------GRFVVVFNCSEQMDYQSLSRILKGLAQSGA--------   86 (231)
T ss_dssp             HHHHHHHCTTT--EEEEESSTTSSHHHHHHHHHHCT------T--EEEEETTSSS-HHHHHHHHHHHHHHT---------
T ss_pred             HHHHHHhccCC--CCCCcCCCCCCchhHHHHHHHHh------CCeEEEecccccccHHHHHHHHHHHhhcCc--------
Confidence            34444454332  46789999999999999999999      999999999999998888888877776542        


Q ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh--------------------hcCcceEEEEecCC----cccchHhhccc
Q 022641          151 YPCPPYKIIILDEADSMTEDAQNALRRTMET--------------------YSKVTRFFFICNYI----SRIIEPLASRC  206 (294)
Q Consensus       151 ~~~~~~~lliiDei~~l~~~~~~~L~~~l~~--------------------~~~~~~ii~~~~~~----~~~~~~l~~r~  206 (294)
                             .+++||+++++.+....+.+.+..                    ......+++|.|..    ..+++.+..-|
T Consensus        87 -------W~cfdefnrl~~~vLS~i~~~i~~i~~al~~~~~~~~~~g~~i~l~~~~~iFiT~np~y~gr~~LP~nLk~lF  159 (231)
T PF12774_consen   87 -------WLCFDEFNRLSEEVLSVISQQIQSIQDALRAKQKSFTLEGQEIKLNPNCGIFITMNPGYAGRSELPENLKALF  159 (231)
T ss_dssp             -------EEEEETCCCSSHHHHHHHHHHHHHHHHHHHCTSSEEEETTCEEE--TT-EEEEEE-B-CCCC--S-HHHCTTE
T ss_pred             -------hhhhhhhhhhhHHHHHHHHHHHHHHHHhhcccccccccCCCEEEEccceeEEEeeccccCCcccCCHhHHHHh
Confidence                   899999999998877666555532                    11234566676633    46888899999


Q ss_pred             cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH-------hh------ccCcHHHHHHHHHHHHHH
Q 022641          207 AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLS-------SI------SQGDLRRAITYLQGAARL  263 (294)
Q Consensus       207 ~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~-------~~------~~G~~r~~~~~l~~~~~~  263 (294)
                      ..+.+..|+...+.+++   +...|..-.......+.       ++      .+-.+|.+..++..+...
T Consensus       160 Rpvam~~PD~~~I~ei~---L~s~GF~~a~~La~kl~~l~~l~~~~lS~q~hydfgLRalk~vl~~a~~~  226 (231)
T PF12774_consen  160 RPVAMMVPDLSLIAEIL---LLSQGFKDAKSLAKKLVSLFQLCKEQLSKQDHYDFGLRALKSVLRMAGSL  226 (231)
T ss_dssp             EEEE--S--HHHHHHHH---HHCCCTSSHHHHHHHHHHHHHHHHHCS-SSTT---SHHHHHHHHHHHHHH
T ss_pred             heeEEeCCCHHHHHHHH---HHHcCchhHHHHHHHHHHHHHHHHHhhccCccccccHHHHHHHHHHHHHH
Confidence            99999999977777665   34445432222222222       11      234688888888877654

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=99.16  E-value=2.1e-10  Score=85.38  Aligned_cols=125  Identities=19%  Similarity=0.223  Sum_probs=76.2

Q ss_pred             ccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhc
Q 022641           65 HQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAV  142 (294)
Q Consensus        65 g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  142 (294)
                      |....++.+.+.+..  .....++|+|++||||+++|+.+...-..   ....++.+++....     .+.+...     
T Consensus         2 G~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~~~---~~~~~~~~~~~~~~-----~~~l~~a-----   68 (138)
T PF14532_consen    2 GKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYSGR---ANGPFIVIDCASLP-----AELLEQA-----   68 (138)
T ss_dssp             -SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTTTT---CCS-CCCCCHHCTC-----HHHHHHC-----
T ss_pred             CCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhcCc---cCCCeEEechhhCc-----HHHHHHc-----
Confidence            444444444444433  22346999999999999999999876421   22344444433322     1122221     


Q ss_pred             ccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh-cCcceEEEEecCCc-------ccchHhhcccc--EEEec
Q 022641          143 GSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY-SKVTRFFFICNYIS-------RIIEPLASRCA--KFRFK  212 (294)
Q Consensus       143 ~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~-~~~~~ii~~~~~~~-------~~~~~l~~r~~--~i~~~  212 (294)
                                  +.+.|+|+|++.++...+..|+..++.. ..+.++|+++....       .+.+.|..++.  .|.++
T Consensus        69 ------------~~gtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~RlI~ss~~~l~~l~~~~~~~~~L~~~l~~~~i~lP  136 (138)
T PF14532_consen   69 ------------KGGTLYLKNIDRLSPEAQRRLLDLLKRQERSNVRLIASSSQDLEELVEEGRFSPDLYYRLSQLEIHLP  136 (138)
T ss_dssp             ------------TTSEEEEECGCCS-HHHHHHHHHHHHHCTTTTSEEEEEECC-CCCHHHHSTHHHHHHHHCSTCEEEE-
T ss_pred             ------------CCCEEEECChHHCCHHHHHHHHHHHHhcCCCCeEEEEEeCCCHHHHhhccchhHHHHHHhCCCEEeCC
Confidence                        2349999999999999999999999864 46778888886432       35567777765  67776


Q ss_pred             CC
Q 022641          213 PL  214 (294)
Q Consensus       213 ~~  214 (294)
                      |+
T Consensus       137 pL  138 (138)
T PF14532_consen  137 PL  138 (138)
T ss_dssp             --
T ss_pred             CC
Confidence            64

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.15  E-value=6.3e-10  Score=91.23  Aligned_cols=128  Identities=20%  Similarity=0.271  Sum_probs=82.3

Q ss_pred             CcEEEEEeCCCCCCH------------HHHHHHHHHHHhhc----------CcceEEEEe----cCCcccchHhhcccc-
Q 022641          155 PYKIIILDEADSMTE------------DAQNALRRTMETYS----------KVTRFFFIC----NYISRIIEPLASRCA-  207 (294)
Q Consensus       155 ~~~lliiDei~~l~~------------~~~~~L~~~l~~~~----------~~~~ii~~~----~~~~~~~~~l~~r~~-  207 (294)
                      +.+++||||||.+..            .++.-|+.+++...          .+..+|.++    ..|+.+.|+|..||. 
T Consensus       250 ~~GIvFIDEIDKIa~~~~~g~~dvSREGVQRDlLPlvEGstV~TKyG~VkTdHILFIasGAFh~sKPSDLiPELQGRfPI  329 (444)
T COG1220         250 QNGIVFIDEIDKIAKRGGSGGPDVSREGVQRDLLPLVEGSTVSTKYGPVKTDHILFIASGAFHVAKPSDLIPELQGRFPI  329 (444)
T ss_pred             hcCeEEEehhhHHHhcCCCCCCCcchhhhcccccccccCceeeccccccccceEEEEecCceecCChhhcChhhcCCCce
Confidence            367999999998732            35666888887422          233233332    456778999999999 


Q ss_pred             EEEecCCCHHHHHHHHHH-----------HHHHhCCC--CCHHHHHHHHhhc---c---Cc--HHHHHH----HHHHHHH
Q 022641          208 KFRFKPLSEEVMSSRVLH-----------ICNEEGLN--LDAEALSTLSSIS---Q---GD--LRRAIT----YLQGAAR  262 (294)
Q Consensus       208 ~i~~~~~~~~~~~~~l~~-----------~~~~~~~~--~~~~~l~~l~~~~---~---G~--~r~~~~----~l~~~~~  262 (294)
                      .+++.+++.++...+|..           .++.+++.  ++++++..|++.+   +   -|  .|.+-.    +|+..+.
T Consensus       330 RVEL~~Lt~~Df~rILtep~~sLikQY~aLlkTE~v~l~FtddaI~~iAeiA~~vN~~~ENIGARRLhTvlErlLediSF  409 (444)
T COG1220         330 RVELDALTKEDFERILTEPKASLIKQYKALLKTEGVELEFTDDAIKRIAEIAYQVNEKTENIGARRLHTVLERLLEDISF  409 (444)
T ss_pred             EEEcccCCHHHHHHHHcCcchHHHHHHHHHHhhcCeeEEecHHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHHHhCc
Confidence            799999999998887743           23345554  7899999998863   1   12  233333    3333333


Q ss_pred             Hh----CC--CCChhhhhhhcccccC
Q 022641          263 LF----GS--SITSKDLISVSGYPTG  282 (294)
Q Consensus       263 ~~----~~--~it~~~v~~~~~~~~~  282 (294)
                      .+    +.  .|+.+.|.+-++....
T Consensus       410 eA~d~~g~~v~Id~~yV~~~l~~l~~  435 (444)
T COG1220         410 EAPDMSGQKVTIDAEYVEEKLGDLVA  435 (444)
T ss_pred             cCCcCCCCeEEEcHHHHHHHHHHHhc
Confidence            33    11  3777777777765433

>PRK06921 hypothetical protein; Provisional

Probab=99.15  E-value=5.3e-10  Score=92.10  Aligned_cols=122  Identities=18%  Similarity=0.184  Sum_probs=69.7

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEE
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII  160 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lli  160 (294)
                      ...+++|+||+|+|||||+.++++++....  +..++.+...+.  ...+...+.......         ....+.++||
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l~~~~--g~~v~y~~~~~l--~~~l~~~~~~~~~~~---------~~~~~~dlLi  182 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANELMRKK--GVPVLYFPFVEG--FGDLKDDFDLLEAKL---------NRMKKVEVLF  182 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHhhhc--CceEEEEEHHHH--HHHHHHHHHHHHHHH---------HHhcCCCEEE
Confidence            345799999999999999999999984321  233333332211  111111111110000         0112346999


Q ss_pred             EeCCCC-------CCHHHHHHHHHHHHhhcC-cceEEEEecCCcc----cchHhhc----ccc--EEEecCCC
Q 022641          161 LDEADS-------MTEDAQNALRRTMETYSK-VTRFFFICNYISR----IIEPLAS----RCA--KFRFKPLS  215 (294)
Q Consensus       161 iDei~~-------l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~~----~~~~l~~----r~~--~i~~~~~~  215 (294)
                      |||++.       .+.-..+.|+.+++.+.. ...+|++||....    +.+.+.+    |+.  .+.+...|
T Consensus       183 IDDl~~~~~g~e~~t~~~~~~lf~iin~R~~~~k~tIitsn~~~~el~~~~~~l~sRi~~r~~~~~i~~~g~s  255 (266)
T PRK06921        183 IDDLFKPVNGKPRATEWQIEQMYSVLNYRYLNHKPILISSELTIDELLDIDEALGSRIVEMCKDYLVIIKGDS  255 (266)
T ss_pred             EeccccccCCCccCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHhhhhhHHHHHHHHhccCeEEEecCcc
Confidence            999944       344456778999987764 4668888886532    1234444    343  56665554

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=99.14  E-value=6e-10  Score=98.68  Aligned_cols=187  Identities=24%  Similarity=0.248  Sum_probs=126.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccC---ccCCCCCCCCcEEEE
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSG---QRRGGYPCPPYKIII  160 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~lli  160 (294)
                      .+++.|.+||||-.+++++...-   . ...+++.+|+..... ..+...+-.+......+.   ...+.......+-+|
T Consensus       338 pvll~GEtGtGKe~laraiH~~s---~-~~gpfvAvNCaAip~-~liesELFGy~~GafTga~~kG~~g~~~~A~gGtlF  412 (606)
T COG3284         338 PVLLQGETGTGKEVLARAIHQNS---E-AAGPFVAVNCAAIPE-ALIESELFGYVAGAFTGARRKGYKGKLEQADGGTLF  412 (606)
T ss_pred             CeEecCCcchhHHHHHHHHHhcc---c-ccCCeEEEEeccchH-HhhhHHHhccCccccccchhccccccceecCCCccH
Confidence            49999999999999999997653   3 567888898887533 222222222221111111   123444556778999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhhc----------CcceEEEEecCCc-------ccchHhhcccc--EEEecCCCH-HHHH
Q 022641          161 LDEADSMTEDAQNALRRTMETYS----------KVTRFFFICNYIS-------RIIEPLASRCA--KFRFKPLSE-EVMS  220 (294)
Q Consensus       161 iDei~~l~~~~~~~L~~~l~~~~----------~~~~ii~~~~~~~-------~~~~~l~~r~~--~i~~~~~~~-~~~~  220 (294)
                      +|||+.++...+..|+.++.+..          -.+.+|.+|+..-       .....+..|..  .|.++|+.. .+..
T Consensus       413 ldeIgd~p~~~Qs~LLrVl~e~~v~p~g~~~~~vdirvi~ath~dl~~lv~~g~fredLyyrL~~~~i~lP~lr~R~d~~  492 (606)
T COG3284         413 LDEIGDMPLALQSRLLRVLQEGVVTPLGGTRIKVDIRVIAATHRDLAQLVEQGRFREDLYYRLNAFVITLPPLRERSDRI  492 (606)
T ss_pred             HHHhhhchHHHHHHHHHHHhhCceeccCCcceeEEEEEEeccCcCHHHHHHcCCchHHHHHHhcCeeeccCchhcccccH
Confidence            99999999999999999998532          2345666665432       23345566666  677777753 3444


Q ss_pred             HHHHHHHHHh---CCCCCHHHHHHHHhh-ccCcHHHHHHHHHHHHHHh-CCCCChhhhhh
Q 022641          221 SRVLHICNEE---GLNLDAEALSTLSSI-SQGDLRRAITYLQGAARLF-GSSITSKDLIS  275 (294)
Q Consensus       221 ~~l~~~~~~~---~~~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~~-~~~it~~~v~~  275 (294)
                      ..|.++..++   .+.+++++++.|..+ ++||+|++.++++.++... +..|...++-.
T Consensus       493 ~~l~~~~~~~~~~~~~l~~~~~~~l~~~~WPGNirel~~v~~~~~~l~~~g~~~~~dlp~  552 (606)
T COG3284         493 PLLDRILKRENDWRLQLDDDALARLLAYRWPGNIRELDNVIERLAALSDGGRIRVSDLPP  552 (606)
T ss_pred             HHHHHHHHHccCCCccCCHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCCCCeeEcccCCH
Confidence            5555555544   367899999998776 8999999999999998877 34455555433

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=99.13  E-value=3.8e-09  Score=90.44  Aligned_cols=106  Identities=15%  Similarity=0.229  Sum_probs=62.0

Q ss_pred             cHHHHHHHHHH-HHcCCCCcEEEECCCCCCHHHHHHHHHHH-hcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcc
Q 022641           66 QEEVVRVLTNT-LETANCPHMLFYGPPGTGKTTTALAIAHQ-LFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVG  143 (294)
Q Consensus        66 ~~~~~~~l~~~-l~~~~~~~ill~Gp~G~GKT~la~~la~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  143 (294)
                      ....+..|.+. -......|+++.||+||||||++.+++.. .+            ......+..   .++..+..... 
T Consensus       192 ~r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla~~l~~~~a~------------~sG~f~T~a---~Lf~~L~~~~l-  255 (449)
T TIGR02688       192 ARQKLLLLARLLPLVEPNYNLIELGPKGTGKSYIYNNLSPYVIL------------ISGGTITVA---KLFYNISTRQI-  255 (449)
T ss_pred             hHHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHHHHHhHHHHH------------HcCCcCcHH---HHHHHHHHHHH-
Confidence            34444444443 12234458999999999999999999887 31            111111222   22222222111 


Q ss_pred             cCccCCCCCCCCcEEEEEeCCCCCC----HHHHHHHHHHHHhhc---------CcceEEEEecC
Q 022641          144 SGQRRGGYPCPPYKIIILDEADSMT----EDAQNALRRTMETYS---------KVTRFFFICNY  194 (294)
Q Consensus       144 ~~~~~~~~~~~~~~lliiDei~~l~----~~~~~~L~~~l~~~~---------~~~~ii~~~~~  194 (294)
                             ....+.++|+|||+.+++    .+..+.+...|+...         ...++++++|-
T Consensus       256 -------g~v~~~DlLI~DEvgylp~~~~~~~v~imK~yMesg~fsRG~~~~~a~as~vfvGNi  312 (449)
T TIGR02688       256 -------GLVGRWDVVAFDEVATLKFAKPKELIGILKNYMESGSFTRGDETKSSDASFVFLGNV  312 (449)
T ss_pred             -------hhhccCCEEEEEcCCCCcCCchHHHHHHHHHHHHhCceeccceeeeeeeEEEEEccc
Confidence                   123456799999999975    235567777776432         35567777764

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=99.11  E-value=1.4e-09  Score=96.69  Aligned_cols=160  Identities=19%  Similarity=0.168  Sum_probs=99.9

Q ss_pred             hcCCCcchhhcccHHHHHHHHHHHHcCCC------------CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecC
Q 022641           54 KYRPKQVKDVAHQEEVVRVLTNTLETANC------------PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA  121 (294)
Q Consensus        54 ~~~~~~~~~~~g~~~~~~~l~~~l~~~~~------------~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~  121 (294)
                      .+...-...+.|+++.++.++-.|+.|..            -||||+|.||||||.+++.+.+-+.      .. +..++
T Consensus       422 lLa~SiAPsIye~edvKkglLLqLfGGt~k~~~~~~~~R~~INILL~GDPGtsKSqlLqyv~~l~p------Rg-~yTSG  494 (804)
T KOG0478|consen  422 LLARSIAPSIYELEDVKKGLLLQLFGGTRKEDEKSGRFRGDINILLVGDPGTSKSQLLQYCHRLLP------RG-VYTSG  494 (804)
T ss_pred             HHHHhhchhhhcccchhhhHHHHHhcCCcccccccccccccceEEEecCCCcCHHHHHHHHHHhCC------cc-eeecC
Confidence            33333344777999999888777765422            2599999999999999999998762      11 11111


Q ss_pred             --CCCcchhHHHHHHHHHHhhhcc---cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh-------------hc
Q 022641          122 --SDDRGINVVRTKIKTFAAVAVG---SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMET-------------YS  183 (294)
Q Consensus       122 --~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~-------------~~  183 (294)
                        +...+.       .........   .-...+....+.+++++|||+|+|+......|.++|+.             .+
T Consensus       495 kGsSavGL-------TayVtrd~dtkqlVLesGALVLSD~GiCCIDEFDKM~dStrSvLhEvMEQQTvSIAKAGII~sLN  567 (804)
T KOG0478|consen  495 KGSSAVGL-------TAYVTKDPDTRQLVLESGALVLSDNGICCIDEFDKMSDSTRSVLHEVMEQQTLSIAKAGIIASLN  567 (804)
T ss_pred             Cccchhcc-------eeeEEecCccceeeeecCcEEEcCCceEEchhhhhhhHHHHHHHHHHHHHhhhhHhhcceeeecc
Confidence              111110       000000000   00112333456778999999999999999999999984             34


Q ss_pred             CcceEEEEecCCc-------------ccchHhhcccc--EEEecCCCHHHHHHHHHHHH
Q 022641          184 KVTRFFFICNYIS-------------RIIEPLASRCA--KFRFKPLSEEVMSSRVLHIC  227 (294)
Q Consensus       184 ~~~~ii~~~~~~~-------------~~~~~l~~r~~--~i~~~~~~~~~~~~~l~~~~  227 (294)
                      ...+|+.++|+..             .+++.|++||.  .+-+.++++..=+.+..++.
T Consensus       568 AR~SVLAaANP~~skynp~k~i~eNI~LpptLLSRFDLIylllD~~DE~~Dr~La~Hiv  626 (804)
T KOG0478|consen  568 ARCSVLAAANPIRSKYNPNKSIIENINLPPTLLSRFDLIFLLLDKPDERSDRRLADHIV  626 (804)
T ss_pred             ccceeeeeeccccccCCCCCchhhccCCChhhhhhhcEEEEEecCcchhHHHHHHHHHH
Confidence            5666777776321             27899999999  45567777654444444444

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=99.10  E-value=2.2e-09  Score=79.93  Aligned_cols=99  Identities=28%  Similarity=0.322  Sum_probs=56.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHH----------------HHHHHHHHhhhcccCc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVV----------------RTKIKTFAAVAVGSGQ  146 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~  146 (294)
                      .+++|+||||||||++++.++..+....   ..++.++++........                .............   
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---   76 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPG---GGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARK---   76 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCC---CCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHh---
Confidence            4699999999999999999999984332   13455544432211100                0111111111110   


Q ss_pred             cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHH--------HHHhhcCcceEEEEecC
Q 022641          147 RRGGYPCPPYKIIILDEADSMTEDAQNALRR--------TMETYSKVTRFFFICNY  194 (294)
Q Consensus       147 ~~~~~~~~~~~lliiDei~~l~~~~~~~L~~--------~l~~~~~~~~ii~~~~~  194 (294)
                             ....+|+|||++.+..........        ..........+|+++|.
T Consensus        77 -------~~~~viiiDei~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  125 (148)
T smart00382       77 -------LKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTND  125 (148)
T ss_pred             -------cCCCEEEEECCcccCCHHHHHHHHhhhhhHHHHHHHhcCCCEEEEEeCC
Confidence                   013599999999997654443322        22334456778888885

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.

>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=99.10  E-value=6.1e-10  Score=92.00  Aligned_cols=147  Identities=18%  Similarity=0.193  Sum_probs=85.6

Q ss_pred             HHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCc-cCCCCC
Q 022641           74 TNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQ-RRGGYP  152 (294)
Q Consensus        74 ~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~  152 (294)
                      ..++..+  .+++|+||+|||||++++.+.+.+...   ......++.+.......+    +........... ..-+..
T Consensus        27 ~~l~~~~--~pvLl~G~~GtGKT~li~~~l~~l~~~---~~~~~~~~~s~~Tts~~~----q~~ie~~l~k~~~~~~gP~   97 (272)
T PF12775_consen   27 DLLLSNG--RPVLLVGPSGTGKTSLIQNFLSSLDSD---KYLVITINFSAQTTSNQL----QKIIESKLEKRRGRVYGPP   97 (272)
T ss_dssp             HHHHHCT--EEEEEESSTTSSHHHHHHHHHHCSTTC---CEEEEEEES-TTHHHHHH----HHCCCTTECECTTEEEEEE
T ss_pred             HHHHHcC--CcEEEECCCCCchhHHHHhhhccCCcc---ccceeEeeccCCCCHHHH----HHHHhhcEEcCCCCCCCCC
Confidence            3344443  379999999999999999987765211   112333444443333222    222222111110 011123


Q ss_pred             CCCcEEEEEeCCCCCCH------HHHHHHHHHHHhhc------------CcceEEEEecCC---cccchHhhccccEEEe
Q 022641          153 CPPYKIIILDEADSMTE------DAQNALRRTMETYS------------KVTRFFFICNYI---SRIIEPLASRCAKFRF  211 (294)
Q Consensus       153 ~~~~~lliiDei~~l~~------~~~~~L~~~l~~~~------------~~~~ii~~~~~~---~~~~~~l~~r~~~i~~  211 (294)
                      .+++.+++|||++.-.+      ...+.|.++++...            .++.++.+++..   ..+.+++.+.|.++.+
T Consensus        98 ~~k~lv~fiDDlN~p~~d~ygtq~~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~~Gr~~is~R~~r~f~i~~~  177 (272)
T PF12775_consen   98 GGKKLVLFIDDLNMPQPDKYGTQPPIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPTGGRNPISPRFLRHFNILNI  177 (272)
T ss_dssp             SSSEEEEEEETTT-S---TTS--HHHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESSTTT--SHHHHHHTTEEEEE-
T ss_pred             CCcEEEEEecccCCCCCCCCCCcCHHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCCCCCCCCChHHhhheEEEEe
Confidence            45777999999986532      24678888887422            234466666653   2478899999999999


Q ss_pred             cCCCHHHHHHHHHHHHHH
Q 022641          212 KPLSEEVMSSRVLHICNE  229 (294)
Q Consensus       212 ~~~~~~~~~~~l~~~~~~  229 (294)
                      ++|+.+.+..+...++..
T Consensus       178 ~~p~~~sl~~If~~il~~  195 (272)
T PF12775_consen  178 PYPSDESLNTIFSSILQS  195 (272)
T ss_dssp             ---TCCHHHHHHHHHHHH
T ss_pred             cCCChHHHHHHHHHHHhh
Confidence            999999999998888764

>PF05729 NACHT: NACHT domain

Probab=99.10  E-value=1.1e-09  Score=84.18  Aligned_cols=145  Identities=15%  Similarity=0.148  Sum_probs=82.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCC---cceeecCCCCcch---hHHHHHHHHHHhhhcccCcc--CCCCCCCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKS---RVLELNASDDRGI---NVVRTKIKTFAAVAVGSGQR--RGGYPCPP  155 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~---~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~--~~~~~~~~  155 (294)
                      -++|+|++|+|||++++.++..+........   .++.+........   ..+...+.............  ........
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~   81 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEELLQELLEKNK   81 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHHHHHHHHHcCC
Confidence            3799999999999999999998854433221   1222222221111   12222222211111000000  00011244


Q ss_pred             cEEEEEeCCCCCCHHH--------HHHHHHHHHh-hcCcceEEEEecCCcc-cchHhhccccEEEecCCCHHHHHHHHHH
Q 022641          156 YKIIILDEADSMTEDA--------QNALRRTMET-YSKVTRFFFICNYISR-IIEPLASRCAKFRFKPLSEEVMSSRVLH  225 (294)
Q Consensus       156 ~~lliiDei~~l~~~~--------~~~L~~~l~~-~~~~~~ii~~~~~~~~-~~~~l~~r~~~i~~~~~~~~~~~~~l~~  225 (294)
                      +-+++||.+|.+....        ...|..++.. ......++++++.... ...........+.+.|++.+++..++++
T Consensus        82 ~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  161 (166)
T PF05729_consen   82 RVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEEDIKQYLRK  161 (166)
T ss_pred             ceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHHHHHHHHH
Confidence            5699999999986532        2345555554 4566778888865432 1222233335899999999999999988


Q ss_pred             HHH
Q 022641          226 ICN  228 (294)
Q Consensus       226 ~~~  228 (294)
                      +++
T Consensus       162 ~f~  164 (166)
T PF05729_consen  162 YFS  164 (166)
T ss_pred             Hhh
Confidence            774

>TIGR01128 holA DNA polymerase III, delta subunit

Probab=99.10  E-value=7e-09  Score=87.82  Aligned_cols=132  Identities=14%  Similarity=0.157  Sum_probs=109.8

Q ss_pred             CCcEEEEEeCCCCCC-HHHHHHHHHHHHhhcCcceEEEEecCCcc---cchHhh--ccccEEEecCCCHHHHHHHHHHHH
Q 022641          154 PPYKIIILDEADSMT-EDAQNALRRTMETYSKVTRFFFICNYISR---IIEPLA--SRCAKFRFKPLSEEVMSSRVLHIC  227 (294)
Q Consensus       154 ~~~~lliiDei~~l~-~~~~~~L~~~l~~~~~~~~ii~~~~~~~~---~~~~l~--~r~~~i~~~~~~~~~~~~~l~~~~  227 (294)
                      +.+.+++|++++.+. ....+.|..+++..+....+|+.++....   +...+.  +++..+.+.+++..++..++...+
T Consensus        45 ~~~kliii~~~~~~~~~~~~~~L~~~l~~~~~~~~~i~~~~~~~~~~~~~k~~~~~~~~~~i~~~~~~~~~~~~~i~~~~  124 (302)
T TIGR01128        45 SERRLVELRNPEGKPGAKGLKALEEYLANPPPDTLLLIEAPKLDKRKKLTKWLKALKNAQIVECKTPKEQELPRWIQARL  124 (302)
T ss_pred             cCCeEEEEECCCCCCCHHHHHHHHHHHhcCCCCEEEEEecCCCCHhHHHHHHHHHhcCeeEEEecCCCHHHHHHHHHHHH
Confidence            345799999999986 45678899999998888777777764322   112233  488999999999999999999999


Q ss_pred             HHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh-CCCCChhhhhhhcccccCCCC
Q 022641          228 NEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF-GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       228 ~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~-~~~it~~~v~~~~~~~~~~~~  285 (294)
                      ++.|+.+++++++.+++.++||++.+.+.++..+.+. ++.||.++|..++....+...
T Consensus       125 ~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~~~~~~i  183 (302)
T TIGR01128       125 KKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSDSARFNV  183 (302)
T ss_pred             HHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhhhhcCCH
Confidence            9999999999999999999999999999999999886 457999999999987666544

subunit around DNA forming a DNA sliding clamp.

>PRK05629 hypothetical protein; Validated

Probab=99.09  E-value=7.6e-09  Score=88.06  Aligned_cols=188  Identities=13%  Similarity=0.071  Sum_probs=134.9

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEe
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILD  162 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiD  162 (294)
                      +.++|+|+----.-.....+.+.+.........+..+++.+.. ...+   +. ....          ...+.+.+|+++
T Consensus         7 ~vyL~~G~e~~l~~~~~~~i~~~~~~~~~~~~n~~~~d~~e~~-~~~l---~~-~~t~----------slF~~~rlV~v~   71 (318)
T PRK05629          7 PVHLVLGDDEFLAERARLNIVHDIRSSMADSLQVTTLKASEVS-QGEL---LD-ALSP----------SLFGEDRVIVLT   71 (318)
T ss_pred             ceEEEEeCHHHHHHHHHHHHHHHHhccCCCCCceEEeecccCC-HHHH---HH-hhCc----------CccCCceEEEEe
Confidence            4588998655333334444555554444445566777655432 2222   21 1111          123456799999


Q ss_pred             CCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCc---ccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHH
Q 022641          163 EADSMTEDAQNALRRTMETYSKVTRFFFICNYIS---RIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEAL  239 (294)
Q Consensus       163 ei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~---~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l  239 (294)
                      +.+.......+.+...+..++....+|+++....   .+.+.+...+..+.+.++...++..++...++..|..++++++
T Consensus        72 ~~~~~~~~~~~~l~~~l~~~~~~~~Lil~~~~~~~~kk~~K~l~k~~~~ve~~~~~~~~l~~wi~~~~~~~g~~i~~~A~  151 (318)
T PRK05629         72 NMEQAGKEPTDLALSAAVDPSPGIYLIIMHSGGGRTKSMVPKLEKIAVVHEAAKLKPRERPGWVTQEFKNHGVRPTPDVV  151 (318)
T ss_pred             ChHhcChhHHHHHHHHHhCCCCCeEEEEEcCCcchhhHHHHHHHhcceEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            9877666567778888888777777777664321   1233566667789999999999999999999999999999999


Q ss_pred             HHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhcccccCCCC
Q 022641          240 STLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       240 ~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~~~~~~~  285 (294)
                      +.+++.+++|+..+.+.++.++.+.++.||.++|..++....+.++
T Consensus       152 ~~L~~~~g~dl~~l~~EleKL~~~~~~~It~e~V~~~v~~~~~~~i  197 (318)
T PRK05629        152 HALLEGVGSDLRELASAISQLVEDTQGNVTVEKVRAYYVGVAEVSG  197 (318)
T ss_pred             HHHHHHHCccHHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCccchH
Confidence            9999999999999999999988777778999999999887655443

>PRK07452 DNA polymerase III subunit delta; Validated

Probab=99.08  E-value=7.4e-09  Score=88.59  Aligned_cols=185  Identities=16%  Similarity=0.183  Sum_probs=131.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEe
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILD  162 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiD  162 (294)
                      +.++|+|+-.--+...+..+.+.+..+......+..+++.+..   .+...+......+          ..+.+.+|+++
T Consensus         2 ~~yll~G~e~~l~~~~~~~l~~~~~~~~~~~fn~~~~d~~~~~---~~~~~~~~~~t~p----------ff~~~rlVvv~   68 (326)
T PRK07452          2 PIYLYWGEDDFALNQAIEKLIDQVVDPEWKSFNYSRLDGDDAD---QAIQALNEAMTPP----------FGSGGRLVWLK   68 (326)
T ss_pred             CEEEEEcChHHHHHHHHHHHHHHhCCchhhhcchhhcCCccch---HHHHHHHHhcCCC----------CCCCceEEEEe
Confidence            4589999988777777788877664433334445555544321   1223333322221          22346799999


Q ss_pred             CCCCC---CHHHHHHHHHHHHhhcCcceEEEEec-CC---cccchHhhccccEEEecCC---CHHHHHHHHHHHHHHhCC
Q 022641          163 EADSM---TEDAQNALRRTMETYSKVTRFFFICN-YI---SRIIEPLASRCAKFRFKPL---SEEVMSSRVLHICNEEGL  232 (294)
Q Consensus       163 ei~~l---~~~~~~~L~~~l~~~~~~~~ii~~~~-~~---~~~~~~l~~r~~~i~~~~~---~~~~~~~~l~~~~~~~~~  232 (294)
                      +.+.+   +....+.|..+++.++....+|+++. ..   ......+...+....|.++   +.+++..++...+++.|+
T Consensus        69 ~~~~~~~~~~~~~~~L~~~l~~~~~~~~li~~~~~~~d~r~k~~k~l~k~~~~~~~~~~~~~~~~~l~~~i~~~~~~~g~  148 (326)
T PRK07452         69 NSPLCQGCSEELLAELERTLPLIPENTHLLLTNTKKPDGRLKSTKLLQKLAEEKEFSLIPPWDTEGLKQLVERTAQELGV  148 (326)
T ss_pred             CchhhccCCHHHHHHHHHHHcCCCCCcEEEEEeCCCcchHHHHHHHHHHceeEEEecCCCcccHHHHHHHHHHHHHHcCC
Confidence            98654   56677889999998888777777643 22   1233445555666666554   457799999999999999


Q ss_pred             CCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---CCCCChhhhhhhcccc
Q 022641          233 NLDAEALSTLSSISQGDLRRAITYLQGAARLF---GSSITSKDLISVSGYP  280 (294)
Q Consensus       233 ~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---~~~it~~~v~~~~~~~  280 (294)
                      .+++++++.|++.+++|++.+.+.++..+.+.   +..||.++|..++...
T Consensus       149 ~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~  199 (326)
T PRK07452        149 KLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNT  199 (326)
T ss_pred             CCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccC
Confidence            99999999999999999999999999999884   4579999999998864

>PRK14700 recombination factor protein RarA; Provisional

Probab=99.02  E-value=2.2e-09  Score=87.70  Aligned_cols=96  Identities=16%  Similarity=0.178  Sum_probs=80.2

Q ss_pred             cceEEEEe--cCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHh------CCCCCHHHHHHHHhhccCcHHHHHHH
Q 022641          185 VTRFFFIC--NYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEE------GLNLDAEALSTLSSISQGDLRRAITY  256 (294)
Q Consensus       185 ~~~ii~~~--~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~------~~~~~~~~l~~l~~~~~G~~r~~~~~  256 (294)
                      ...+|.+|  |+.+.+.+++++||+++.|.|++.+++..++++.+...      .+.+++++++.|++.++||.|.++|.
T Consensus         8 ~i~LIGATTENP~f~vn~ALlSR~~v~~l~~L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~~a~GDaR~aLN~   87 (300)
T PRK14700          8 KIILIGATTENPTYYLNDALVSRLFILRLKRLSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHNYNEGDCRKILNL   87 (300)
T ss_pred             cEEEEeecCCCccceecHhhhhhhheeeecCCCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHHhcCCHHHHHHHH
Confidence            34455555  67788999999999999999999999999999999752      35799999999999999999999999


Q ss_pred             HHHHHHHh--CC--CCChhhhhhhcccc
Q 022641          257 LQGAARLF--GS--SITSKDLISVSGYP  280 (294)
Q Consensus       257 l~~~~~~~--~~--~it~~~v~~~~~~~  280 (294)
                      |+.+....  ..  .||.+.+++++...
T Consensus        88 LE~a~~~~~~~~~~~it~~~~~~~~~~~  115 (300)
T PRK14700         88 LERMFLISTRGDEIYLNKELFDQAVGET  115 (300)
T ss_pred             HHHHHhhccccCCCccCHHHHHHHHhHH
Confidence            99977533  22  29999999888653

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.01  E-value=3.8e-08  Score=95.68  Aligned_cols=189  Identities=15%  Similarity=0.135  Sum_probs=117.6

Q ss_pred             CCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHH
Q 022641           56 RPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK  135 (294)
Q Consensus        56 ~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (294)
                      .|..-..++-++.....+...   ...+-++|+||+|.||||++..+....    . ....+.+...+......+...+.
T Consensus         9 ~p~~~~~~~~R~rl~~~l~~~---~~~~~~~v~apaG~GKTtl~~~~~~~~----~-~~~w~~l~~~d~~~~~f~~~l~~   80 (903)
T PRK04841          9 RPVRLHNTVVRERLLAKLSGA---NNYRLVLVTSPAGYGKTTLISQWAAGK----N-NLGWYSLDESDNQPERFASYLIA   80 (903)
T ss_pred             CCCCccccCcchHHHHHHhcc---cCCCeEEEECCCCCCHHHHHHHHHHhC----C-CeEEEecCcccCCHHHHHHHHHH
Confidence            355566778888777766532   233569999999999999999988654    1 23334444444333333333333


Q ss_pred             HHHhhhcccCc-------cCC--------------CCCCCCcEEEEEeCCCCCCHHH-HHHHHHHHHhhcCcceEEEEec
Q 022641          136 TFAAVAVGSGQ-------RRG--------------GYPCPPYKIIILDEADSMTEDA-QNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       136 ~~~~~~~~~~~-------~~~--------------~~~~~~~~lliiDei~~l~~~~-~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      .+.........       ...              ......+-+|||||+|.++... .+.|..++...+....+|++++
T Consensus        81 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR  160 (903)
T PRK04841         81 ALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSR  160 (903)
T ss_pred             HHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeC
Confidence            33211111000       000              0012456799999999997444 4567777777778888888886


Q ss_pred             CCcccc-hHhhc--cccEEEec--CCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHH
Q 022641          194 YISRII-EPLAS--RCAKFRFK--PLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAIT  255 (294)
Q Consensus       194 ~~~~~~-~~l~~--r~~~i~~~--~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~  255 (294)
                      ....+. ..+.-  .+..+...  +++.+|...++...+   +..++++.+..+.+.|+|+|-.+.-
T Consensus       161 ~~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~~---~~~~~~~~~~~l~~~t~Gwp~~l~l  224 (903)
T PRK04841        161 NLPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQRL---SSPIEAAESSRLCDDVEGWATALQL  224 (903)
T ss_pred             CCCCCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhcc---CCCCCHHHHHHHHHHhCChHHHHHH
Confidence            533331 22222  22334443  889999999886433   6778999999999999999976543

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

Probab=99.00  E-value=8e-09  Score=93.16  Aligned_cols=167  Identities=22%  Similarity=0.257  Sum_probs=101.7

Q ss_pred             cccHHHHHHHHHHHHcC---------CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcch--hHHHH
Q 022641           64 AHQEEVVRVLTNTLETA---------NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGI--NVVRT  132 (294)
Q Consensus        64 ~g~~~~~~~l~~~l~~~---------~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~  132 (294)
                      .+.+..+..+...+.-.         ..+.++|+|+||||||++++++|+++      +..++++++......  .....
T Consensus       404 ~~~~~~~~~l~~vl~p~~~~s~~~~~~~~~vLLhG~~g~GK~t~V~~vas~l------g~h~~evdc~el~~~s~~~~et  477 (953)
T KOG0736|consen  404 PGLEAKVLELVAVLSPQKQPSGALLTLNPSVLLHGPPGSGKTTVVRAVASEL------GLHLLEVDCYELVAESASHTET  477 (953)
T ss_pred             ccchHHHHHHHHHhCcccCcchhccccceEEEEeCCCCCChHHHHHHHHHHh------CCceEeccHHHHhhcccchhHH
Confidence            34555555555555322         22349999999999999999999999      788888776443211  11111


Q ss_pred             HHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCC--------CHHHHHHHHHHHH--hh---cCcceEEEEecCCcccc
Q 022641          133 KIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSM--------TEDAQNALRRTME--TY---SKVTRFFFICNYISRII  199 (294)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l--------~~~~~~~L~~~l~--~~---~~~~~ii~~~~~~~~~~  199 (294)
                      .+........          ...+.+|++-++|-+        +...+..+...+.  .+   ..+..++.+++....++
T Consensus       478 kl~~~f~~a~----------~~~pavifl~~~dvl~id~dgged~rl~~~i~~~ls~e~~~~~~~~~ivv~t~~s~~~lp  547 (953)
T KOG0736|consen  478 KLQAIFSRAR----------RCSPAVLFLRNLDVLGIDQDGGEDARLLKVIRHLLSNEDFKFSCPPVIVVATTSSIEDLP  547 (953)
T ss_pred             HHHHHHHHHh----------hcCceEEEEeccceeeecCCCchhHHHHHHHHHHHhcccccCCCCceEEEEeccccccCC
Confidence            2222111110          112336666666554        2233333333333  11   23445667777888899


Q ss_pred             hHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHH-HHHHHhhccC
Q 022641          200 EPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEA-LSTLSSISQG  248 (294)
Q Consensus       200 ~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-l~~l~~~~~G  248 (294)
                      +.+++.+. .|.++.++++++.++++.++....  ++.+. ++.++.++.|
T Consensus       548 ~~i~~~f~~ei~~~~lse~qRl~iLq~y~~~~~--~n~~v~~k~~a~~t~g  596 (953)
T KOG0736|consen  548 ADIQSLFLHEIEVPALSEEQRLEILQWYLNHLP--LNQDVNLKQLARKTSG  596 (953)
T ss_pred             HHHHHhhhhhccCCCCCHHHHHHHHHHHHhccc--cchHHHHHHHHHhcCC
Confidence            99998876 899999999999999999986543  44333 4556666543

>PRK06585 holA DNA polymerase III subunit delta; Reviewed

Probab=99.00  E-value=8.2e-08  Score=82.77  Aligned_cols=191  Identities=16%  Similarity=0.107  Sum_probs=132.5

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEE
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII  160 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lli  160 (294)
                      ..+.++|+|+-.......+..+.+.+.........+..+++.+..  ..+...+..+...+          ..+.+.+|+
T Consensus        19 ~~~~yll~G~e~~li~~~~~~l~~~~~~~~~~~fn~~~~~~~e~~--~~~~~~~~~~~t~s----------lF~~~rlVi   86 (343)
T PRK06585         19 KIRAVLLYGPDRGLVRERARRLAKSVVPDLDDPFAVVRLDGDDLD--ADPARLEDEANAIS----------LFGGRRLIW   86 (343)
T ss_pred             CCeEEEEeCCchHHHHHHHHHHHHHhcCCCCCCcceeeccHHHhh--cCHHHHHHHHhCCC----------CCCCceEEE
Confidence            446699999999888888888887764332222334444332211  01223333332222          234457999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCc---ccchHhh--ccccEEEecCCCHHHHHHHHHHHHHHhCCCCC
Q 022641          161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYIS---RIIEPLA--SRCAKFRFKPLSEEVMSSRVLHICNEEGLNLD  235 (294)
Q Consensus       161 iDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~---~~~~~l~--~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~  235 (294)
                      +.+.+   ....+.|..+++..+....+|+.+....   .+...+.  .....+.+.+++..++..++...++..|+.++
T Consensus        87 v~~~~---~~~~~~L~~~l~~~~~~~~lil~~~~~~~~~kl~k~~~~~~~~~~v~~~~~~~~~l~~~i~~~~~~~g~~i~  163 (343)
T PRK06585         87 VRAGS---KNLAAALKALLESPPGDAFIVIEAGDLKKGSSLRKLFETAAYAAAIPCYADDERDLARLIDDELAEAGLRIT  163 (343)
T ss_pred             EECCc---hhHHHHHHHHHcCCCCCcEEEEEcCCCCcccHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHHHHCCCCCC
Confidence            99654   3345567778877666676766553321   1222221  23346888899999999999999999999999


Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHHHh--CCCCChhhhhhhcccccCCCCC
Q 022641          236 AEALSTLSSISQGDLRRAITYLQGAARLF--GSSITSKDLISVSGYPTGGSGG  286 (294)
Q Consensus       236 ~~~l~~l~~~~~G~~r~~~~~l~~~~~~~--~~~it~~~v~~~~~~~~~~~~~  286 (294)
                      +++++.+++.++||++.+.+.++..+.+.  +..||.++|..+++...+.+..
T Consensus       164 ~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~~~e~~if  216 (343)
T PRK06585        164 PDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGDASALSLD  216 (343)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCcccccHH
Confidence            99999999999999999999999999986  3579999999999987776553

>PRK07914 hypothetical protein; Reviewed

Probab=98.98  E-value=5.6e-08  Score=82.81  Aligned_cols=187  Identities=11%  Similarity=0.057  Sum_probs=135.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcC-CCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEE
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFG-PELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIIL  161 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llii  161 (294)
                      +..+|+|+----.......+.+.+.. ++.....+..+++.+... .   . +......          ...+.+.+|++
T Consensus         6 ~iYll~G~E~~l~~~~~~~i~~~~~~~~~~~~~n~~~~d~~~~~~-~---~-i~~~~t~----------plF~~rRlV~v   70 (320)
T PRK07914          6 PLHLVLGDEELLVERAVAAVLRSARQRAGTADVPVSRMRAGDVST-Y---E-LAELLSP----------SLFAEERVVVL   70 (320)
T ss_pred             ceEEEEecHHHHHHHHHHHHHHHHhcCcCCCCCceEEeccccCCH-H---H-HHHhcCC----------CCCCCceEEEE
Confidence            45888988766666666666665543 244455666666654422 1   1 2222211          12355679999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCc---ccchHhhcc-ccEEEecCC-CHHHHHHHHHHHHHHhCCCCCH
Q 022641          162 DEADSMTEDAQNALRRTMETYSKVTRFFFICNYIS---RIIEPLASR-CAKFRFKPL-SEEVMSSRVLHICNEEGLNLDA  236 (294)
Q Consensus       162 Dei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~---~~~~~l~~r-~~~i~~~~~-~~~~~~~~l~~~~~~~~~~~~~  236 (294)
                      ++...+.....+.|..+++..+....+|++.+...   .+...+... +..+.+.++ +..++..++...++..|+.+++
T Consensus        71 ~~~~~~~~~~~~~l~~~l~~~~~~t~lil~~~~~~~~kk~~K~L~k~g~~~v~~~~~~~~~~l~~wi~~~a~~~g~~i~~  150 (320)
T PRK07914         71 EAAAEAGKDAAALILSAAADLPPGTVLVVVHSGGGRAKALANQLRKLGAEVHPCARITKAAERADFVRKEFRSLRVKVDD  150 (320)
T ss_pred             eChHhccHHHHHHHHHHHhCCCCCeEEEEEecCCcchhHHHHHHHHCCCEEEecCCCCCHHHHHHHHHHHHHHcCCCCCH
Confidence            99877766667788889988777777777654322   122345544 347899988 9999999999999999999999


Q ss_pred             HHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhcccccCCC
Q 022641          237 EALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTGGS  284 (294)
Q Consensus       237 ~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~~~~~~  284 (294)
                      ++++.|++.++||+..+.+.++.++.+.++.||.++|..++......+
T Consensus       151 ~A~~~L~~~~g~dl~~l~~EleKL~~~~~~~It~e~V~~~v~~~~~~~  198 (320)
T PRK07914        151 DTVTALLDAVGSDLRELASACSQLVADTGGAVDAAAVRRYHSGKAEVK  198 (320)
T ss_pred             HHHHHHHHHHCccHHHHHHHHHHHhcCCCCCcCHHHHHHHcCCCeech
Confidence            999999999999999999999988766677899999999998765543

>PRK05574 holA DNA polymerase III subunit delta; Reviewed

Probab=98.96  E-value=1.5e-07  Score=81.16  Aligned_cols=199  Identities=16%  Similarity=0.171  Sum_probs=130.2

Q ss_pred             HHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCC
Q 022641           72 VLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGY  151 (294)
Q Consensus        72 ~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (294)
                      .+...+..+-.+.++|+|+-=.=+...+..+...+..+......+..+++.+. ...   ..+..+...+          
T Consensus         7 ~~~~~~~~~~~~~~li~G~d~~l~~~~~~~i~~~~~~~~~~~~~~~~~d~~~~-~~~---~l~~~~~t~~----------   72 (340)
T PRK05574          7 QLEKQLKKGLAPLYLLYGDEPLLLQEAKDAIRAAARAQGFDERNVFTFDGSET-DWD---DVLEACQSLP----------   72 (340)
T ss_pred             HHHHHHhCCCCceEEEEcCcHHHHHHHHHHHHHHHHcCCCceeeEEEeecCCC-CHH---HHHHHhhccC----------
Confidence            34455555544568999976433334444554443222333344555555432 222   2222222221          


Q ss_pred             CCCCcEEEEEeCCCCCCHHH----HHHHHHHHHhhcC--cceEEEEecCCc---cc---chHhhccccEEEecCCCHHHH
Q 022641          152 PCPPYKIIILDEADSMTEDA----QNALRRTMETYSK--VTRFFFICNYIS---RI---IEPLASRCAKFRFKPLSEEVM  219 (294)
Q Consensus       152 ~~~~~~lliiDei~~l~~~~----~~~L~~~l~~~~~--~~~ii~~~~~~~---~~---~~~l~~r~~~i~~~~~~~~~~  219 (294)
                      ..+.+.+++|++++.+....    ...|...+ ....  ...+++..+...   .+   .+.+..++..+.+.+++..++
T Consensus        73 lF~~~klvii~~~~~l~~~~~~~~l~~l~~~l-~~~~~~~~~li~~~~~~~~~~k~~k~~k~~~~~~~~~~~~~~~~~~~  151 (340)
T PRK05574         73 LFSDRKLVELRLPEFLTGAKGEKALKRLEAYL-NPLPHPDLLLIVRLPKLDKAKKKSAWFKALKKKAVVVEAQPPKEAEL  151 (340)
T ss_pred             ccccCeEEEEECCCCCCchhHHHHHHHHHHhc-cCCCCCcEEEEEECCcCCHHHHhhHHHHHHHhCceEEEcCCCCHHHH
Confidence            22345799999999986542    23333333 2232  233444433221   22   456667888999999999999


Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh-CCCCChhhhhhhcccccCCCC
Q 022641          220 SSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF-GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       220 ~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~-~~~it~~~v~~~~~~~~~~~~  285 (294)
                      ..++...++..|+.+++++++.+++.++||+..+.+.++..+.+. +..||.++|..++....+.+.
T Consensus       152 ~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~~~~~~~  218 (340)
T PRK05574        152 PQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPDSARFDV  218 (340)
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhhhhcCCH
Confidence            999999999999999999999999999999999999999999887 344999999999888666544

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=98.96  E-value=6.5e-09  Score=96.71  Aligned_cols=154  Identities=23%  Similarity=0.319  Sum_probs=100.7

Q ss_pred             hhhcccHHHHHHHHHHHHcCCC------Cc--EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc------
Q 022641           61 KDVAHQEEVVRVLTNTLETANC------PH--MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG------  126 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~~~------~~--ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~------  126 (294)
                      +.++||++++..+..++...+.      +.  ++|.||.|+|||-+|+++|..+++.   ...++.++.+....      
T Consensus       562 ~~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgs---e~~~IriDmse~~evsklig  638 (898)
T KOG1051|consen  562 ERVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYVFGS---EENFIRLDMSEFQEVSKLIG  638 (898)
T ss_pred             hhccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHHHcCC---ccceEEechhhhhhhhhccC
Confidence            4678999999999888865321      22  8999999999999999999999654   34555555543100      


Q ss_pred             ---hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEe
Q 022641          127 ---INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFIC  192 (294)
Q Consensus       127 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~  192 (294)
                         .+........+...          .....+.||++|||+..++..++.|+++++.+.           .++.||+|+
T Consensus       639 sp~gyvG~e~gg~Ltea----------vrrrP~sVVLfdeIEkAh~~v~n~llq~lD~GrltDs~Gr~Vd~kN~I~IMTs  708 (898)
T KOG1051|consen  639 SPPGYVGKEEGGQLTEA----------VKRRPYSVVLFEEIEKAHPDVLNILLQLLDRGRLTDSHGREVDFKNAIFIMTS  708 (898)
T ss_pred             CCcccccchhHHHHHHH----------HhcCCceEEEEechhhcCHHHHHHHHHHHhcCccccCCCcEeeccceEEEEec
Confidence               00001111111111          122445799999999999999999999998644           356678886


Q ss_pred             cCC--------c--------------------------------ccchHhhcccc-EEEecCCCHHHHHHHHHHHH
Q 022641          193 NYI--------S--------------------------------RIIEPLASRCA-KFRFKPLSEEVMSSRVLHIC  227 (294)
Q Consensus       193 ~~~--------~--------------------------------~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~  227 (294)
                      |..        .                                ...+++.+|+. .+.|.|++.+++.+++....
T Consensus       709 n~~~~~i~~~~~~~~~l~~~~~~~~~~~~~k~~v~~~~~~~~~~~~r~Ef~nrid~i~lf~~l~~~~~~~i~~~~~  784 (898)
T KOG1051|consen  709 NVGSSAIANDASLEEKLLDMDEKRGSYRLKKVQVSDAVRIYNKQFFRKEFLNRIDELDLNLPLDRDELIEIVNKQL  784 (898)
T ss_pred             ccchHhhhcccccccccccchhhhhhhhhhhhhhhhhhhcccccccChHHhcccceeeeecccchhhHhhhhhhHH
Confidence            431        1                                01234455555 66778888777776665544

>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]

Probab=98.93  E-value=1e-08  Score=90.31  Aligned_cols=151  Identities=19%  Similarity=0.247  Sum_probs=91.8

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCC------------cEEEECCCCCCHHHHHHHHHHHhcCCCccCC
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCP------------HMLFYGPPGTGKTTTALAIAHQLFGPELYKS  114 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~------------~ill~Gp~G~GKT~la~~la~~~~~~~~~~~  114 (294)
                      .+.|..++.-..---.+.|+..++..+.-.+..|...            |+||+|.||||||..++.+++..      ..
T Consensus       435 kd~~i~~rIiaSiaPsIyGh~~VK~AvAlaLfGGv~kn~~~khkvRGDinvLL~GDPGTaKSQFLKY~eK~s------~R  508 (854)
T KOG0477|consen  435 KDPPIKERIIASIAPSIYGHEDVKRAVALALFGGVPKNPGGKHKVRGDINVLLLGDPGTAKSQFLKYAEKTS------PR  508 (854)
T ss_pred             cCccHHHHHHHhhCchhhchHHHHHHHHHHHhcCCccCCCCCceeccceeEEEecCCCccHHHHHHHHHhcC------cc
Confidence            3445555533333346779999999998888765332            49999999999999999998875      22


Q ss_pred             cceeecCCC-Ccch--hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh----------
Q 022641          115 RVLELNASD-DRGI--NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMET----------  181 (294)
Q Consensus       115 ~~~~~~~~~-~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~----------  181 (294)
                      .++....+. ..+.  +..+.      .....+....+....+.+++++|||+|.++......+...|+.          
T Consensus       509 AV~tTGqGASavGLTa~v~Kd------PvtrEWTLEaGALVLADkGvClIDEFDKMndqDRtSIHEAMEQQSISISKAGI  582 (854)
T KOG0477|consen  509 AVFTTGQGASAVGLTAYVRKD------PVTREWTLEAGALVLADKGVCLIDEFDKMNDQDRTSIHEAMEQQSISISKAGI  582 (854)
T ss_pred             eeEeccCCccccceeEEEeeC------CccceeeeccCeEEEccCceEEeehhhhhcccccchHHHHHHhcchhhhhhhH
Confidence            222221111 0110  00000      0001112223345567788999999999987766666666653          


Q ss_pred             ---hcCcceEEEEecCCc-------------ccchHhhccccEE
Q 022641          182 ---YSKVTRFFFICNYIS-------------RIIEPLASRCAKF  209 (294)
Q Consensus       182 ---~~~~~~ii~~~~~~~-------------~~~~~l~~r~~~i  209 (294)
                         ....+.+|.++|+..             .+...+++||.++
T Consensus       583 VtsLqArctvIAAanPigGRY~~s~tFaqNV~ltePIlSRFDiL  626 (854)
T KOG0477|consen  583 VTSLQARCTVIAAANPIGGRYNPSLTFAQNVDLTEPILSRFDIL  626 (854)
T ss_pred             HHHHHhhhhhheecCCCCCccCCccchhhccccccchhhhccee
Confidence               334566777776521             2557788998754

>PLN03210 Resistant to P

Probab=98.93  E-value=2.2e-08  Score=98.94  Aligned_cols=195  Identities=15%  Similarity=0.084  Sum_probs=108.2

Q ss_pred             CCcchhhcccHHHHHHHHHHHHcC--CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCccee---ecCCC--------
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLETA--NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLE---LNASD--------  123 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~~--~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~---~~~~~--------  123 (294)
                      +..+++++|.+..++.+..++...  ..+.+.|+|++|+||||+|+++++.+.... .+..++.   +....        
T Consensus       180 ~~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~~F-~g~vfv~~~~v~~~~~~~~~~~~  258 (1153)
T PLN03210        180 SNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLSRQF-QSSVFIDRAFISKSMEIYSSANP  258 (1153)
T ss_pred             CcccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHHhhcC-CeEEEeeccccccchhhcccccc
Confidence            346778999999999998887533  334599999999999999999988873322 1111110   00000        


Q ss_pred             -Ccc--hhHHHHHHHHHHhhhcccC---ccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcc
Q 022641          124 -DRG--INVVRTKIKTFAAVAVGSG---QRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISR  197 (294)
Q Consensus       124 -~~~--~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~  197 (294)
                       ...  .......+..+........   .........++-+|+|||++..  ...+.|............||+||.+..-
T Consensus       259 ~~~~~~~~l~~~~l~~il~~~~~~~~~~~~~~~~L~~krvLLVLDdv~~~--~~l~~L~~~~~~~~~GsrIIiTTrd~~v  336 (1153)
T PLN03210        259 DDYNMKLHLQRAFLSEILDKKDIKIYHLGAMEERLKHRKVLIFIDDLDDQ--DVLDALAGQTQWFGSGSRIIVITKDKHF  336 (1153)
T ss_pred             cccchhHHHHHHHHHHHhCCCCcccCCHHHHHHHHhCCeEEEEEeCCCCH--HHHHHHHhhCccCCCCcEEEEEeCcHHH
Confidence             000  0000111111111000000   0000112345679999998753  4455555444433455678888876432


Q ss_pred             cchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCC--HHHHHHHHhhccCcHHHHHHH
Q 022641          198 IIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLD--AEALSTLSSISQGDLRRAITY  256 (294)
Q Consensus       198 ~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~--~~~l~~l~~~~~G~~r~~~~~  256 (294)
                      +..  ..-..++.+..++.++..+++.+.+-......+  .+....++++|+|.|=.+..+
T Consensus       337 l~~--~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~~c~GLPLAl~vl  395 (1153)
T PLN03210        337 LRA--HGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVL  395 (1153)
T ss_pred             HHh--cCCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhCCCcHHHHHH
Confidence            211  011247888999999999999887754332211  234566888899977554433

syringae 6; Provisional

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

Probab=98.91  E-value=5.7e-10  Score=82.26  Aligned_cols=110  Identities=21%  Similarity=0.297  Sum_probs=60.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCc--cCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCC--------CCC
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPEL--YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRG--------GYP  152 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~  152 (294)
                      ..++++||+|+|||+++..+++.+.....  ....++.+++........+...+...............        ...
T Consensus         5 ~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l~   84 (131)
T PF13401_consen    5 RILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDALD   84 (131)
T ss_dssp             --EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHHH
T ss_pred             cccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHHH
Confidence            35999999999999999999998731100  02344444443333322222222222221111100000        000


Q ss_pred             CCCcEEEEEeCCCCC-CHHHHHHHHHHHHhhcCcceEEEEecC
Q 022641          153 CPPYKIIILDEADSM-TEDAQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       153 ~~~~~lliiDei~~l-~~~~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      .....+|+|||+|.+ +....+.|..+.+  ...+.+|+++.+
T Consensus        85 ~~~~~~lviDe~~~l~~~~~l~~l~~l~~--~~~~~vvl~G~~  125 (131)
T PF13401_consen   85 RRRVVLLVIDEADHLFSDEFLEFLRSLLN--ESNIKVVLVGTP  125 (131)
T ss_dssp             HCTEEEEEEETTHHHHTHHHHHHHHHHTC--SCBEEEEEEESS
T ss_pred             hcCCeEEEEeChHhcCCHHHHHHHHHHHh--CCCCeEEEEECh
Confidence            012259999999999 8888888877766  466677777765

>PRK05907 hypothetical protein; Provisional

Probab=98.88  E-value=5.7e-07  Score=75.72  Aligned_cols=191  Identities=13%  Similarity=0.105  Sum_probs=133.5

Q ss_pred             HHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCC
Q 022641           70 VRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRG  149 (294)
Q Consensus        70 ~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (294)
                      ...+.+.+..+. +.++++|..-   ......+.+.+..++.     ..+++.+. .   +...+......+        
T Consensus         7 ~~~~~~~~~~~~-~~y~~~g~~~---~~~~~~l~~~~~~~~~-----~~fdg~~~-~---~~~ii~~aetlP--------   65 (311)
T PRK05907          7 FKDFSQYYEEKR-PAVIVIGSSS---EEDKDIFIELLVSGRK-----SEFDGQGL-L---QQELLSWTEHFG--------   65 (311)
T ss_pred             HHHHHHHHhcCC-ceEEEecCCc---HHHHHHHHHHhCCCcc-----ceecCCCC-C---HHHHHHHHhcCC--------
Confidence            345555677777 8899999877   5555666555532221     22322221 2   233333333332        


Q ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEE-EEecCCcccchHhhc---cccEE----EecCCCHHHHHH
Q 022641          150 GYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFF-FICNYISRIIEPLAS---RCAKF----RFKPLSEEVMSS  221 (294)
Q Consensus       150 ~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii-~~~~~~~~~~~~l~~---r~~~i----~~~~~~~~~~~~  221 (294)
                        ..+.+.+|++.+.+.+.....+.|..+++++++...+| ++.+  ..-.+.+..   ....+    .+.++...++..
T Consensus        66 --fFaerRlV~v~~~~~~~~~~~~~L~~Yl~np~~~~~liv~~~~--~d~~kkl~K~i~k~~~v~~~~e~~~l~e~~L~~  141 (311)
T PRK05907         66 --LFASQETIGIYQAEKMSSSTQEFLIRYARNPNPHLTLFLFTTK--QECFSSLSKKLSSALCLSLFGEWFADRDKRIAQ  141 (311)
T ss_pred             --cccCeEEEEEecccccccccHHHHHHHHhCCCCCeEEEEEEec--ccHHHHHHHHHhhcceeccccccCCCCHHHHHH
Confidence              23456688888877776666788999999988865555 4442  111122222   24445    899999999999


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHhhc-cCcHHHHHHHHHHHHHHh--CCCCChhhhhhhcccccCCCC
Q 022641          222 RVLHICNEEGLNLDAEALSTLSSIS-QGDLRRAITYLQGAARLF--GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       222 ~l~~~~~~~~~~~~~~~l~~l~~~~-~G~~r~~~~~l~~~~~~~--~~~it~~~v~~~~~~~~~~~~  285 (294)
                      ++...+++.|..+++++++.+++.+ +||+..+.+.++.++.+.  ++.||.++|..++......+.
T Consensus       142 Wi~~~~~~~g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~~s~e~nI  208 (311)
T PRK05907        142 LLIQRAKELGISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVVKKEAASL  208 (311)
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhcCcccccH
Confidence            9999999999999999999999999 699999999999999985  567999999999988776654

>PRK08487 DNA polymerase III subunit delta; Validated

Probab=98.85  E-value=8.8e-07  Score=75.73  Aligned_cols=195  Identities=18%  Similarity=0.107  Sum_probs=132.8

Q ss_pred             HHHHHHHcCCC-CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCC
Q 022641           72 VLTNTLETANC-PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGG  150 (294)
Q Consensus        72 ~l~~~l~~~~~-~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (294)
                      ++...+..+.. +.++|+|.-=--....+..+.+.+...+. ... +..+   ..+   +...+..+...+         
T Consensus         5 ~l~~~lk~~~l~~vyll~GeE~yli~~~~~~i~~~~~~~~~-~~~-~~~~---~~~---~~~i~~~~~t~p---------   67 (328)
T PRK08487          5 ELDTLLKQNKLPNAFLLYGEDEFQIELYAKKISEKFKPENE-LKT-LYFD---EYD---FEQAKDFLSQSS---------   67 (328)
T ss_pred             HHHHHHhcCCCCceEEEecCchhHHHHHHHHHHHHhcCchH-hhh-hchh---hcc---HHHHHHHHhccc---------
Confidence            45555666543 55899998777777777777766532221 111 1111   112   223333333222         


Q ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcc---cchHhhcc--ccEEEecCCCHHHHHHHHHH
Q 022641          151 YPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISR---IIEPLASR--CAKFRFKPLSEEVMSSRVLH  225 (294)
Q Consensus       151 ~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~---~~~~l~~r--~~~i~~~~~~~~~~~~~l~~  225 (294)
                       ..+.+.+|++.+...........|...++..+....+|+..+....   +...+...  ...+.+.+++..++..++..
T Consensus        68 -lF~~~rlViv~~~~~~~~~~~~~L~~~l~~~~~~~~lv~~~~~~~k~kkl~k~~~~~k~~~~v~~~~~~~~~l~~~i~~  146 (328)
T PRK08487         68 -LFGGKNLLIIKLDKKIPKKELKLLIELCEKNSDNYFIIELYGADSKTKDIEKLFQKKDEAVFVRFFKPNAREALELLQE  146 (328)
T ss_pred             -ccCCceEEEEecccccCHHHHHHHHHHHhcCCCCEEEEEecCCcchhHHHHHHhccCCCceEEEeeCCCHHHHHHHHHH
Confidence             2345679999987766666667888888876655544443333221   11222222  34789999999999999999


Q ss_pred             HHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhcccccCCCC
Q 022641          226 ICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       226 ~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~~~~~~~  285 (294)
                      .++..|+.+++++++.++..+++|...+.+-++.++.+.+ .||.++|..++....+.+.
T Consensus       147 ~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~-~It~edV~~~v~~~~e~~v  205 (328)
T PRK08487        147 RAKELGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE-PITLKDIQELVFGLGSVSF  205 (328)
T ss_pred             HHHHhCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC-CCCHHHHHHHhcccccccH
Confidence            9999999999999999999999999999999999999854 7999999999988766544

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=98.84  E-value=1.3e-07  Score=69.80  Aligned_cols=24  Identities=46%  Similarity=0.700  Sum_probs=22.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+.++|+||+||||++.-++..+.
T Consensus         7 ki~ITG~PGvGKtTl~~ki~e~L~   30 (179)
T COG1618           7 KIFITGRPGVGKTTLVLKIAEKLR   30 (179)
T ss_pred             EEEEeCCCCccHHHHHHHHHHHHH
Confidence            489999999999999999998884

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

Probab=98.80  E-value=7.3e-09  Score=81.05  Aligned_cols=46  Identities=26%  Similarity=0.419  Sum_probs=32.2

Q ss_pred             hhcccHHHHHHHHHHHH---cCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           62 DVAHQEEVVRVLTNTLE---TANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~---~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|++..++.+...+.   .+..++++|+|++|+|||++++.+...+.
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~   49 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLA   49 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            36899999999999983   23345699999999999999999988874

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=98.79  E-value=3.7e-10  Score=96.17  Aligned_cols=146  Identities=21%  Similarity=0.203  Sum_probs=75.3

Q ss_pred             hhhcccHHHHHHHHHHHHcCCC------------CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchh
Q 022641           61 KDVAHQEEVVRVLTNTLETANC------------PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGIN  128 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~~~------------~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~  128 (294)
                      ..+.|++..+..+.-.+..+..            -|++|+|.||+|||.+.+.+++-.       ...+..++.......
T Consensus        24 P~i~g~~~iK~aill~L~~~~~~~~~~~~~~r~~ihiLlvGdpg~gKS~ll~~~~~~~-------pr~v~~~g~~~s~~g   96 (331)
T PF00493_consen   24 PSIYGHEDIKKAILLQLFGGVEKNDPDGTRIRGNIHILLVGDPGTGKSQLLKYVAKLA-------PRSVYTSGKGSSAAG   96 (331)
T ss_dssp             STTTT-HHHHHHHCCCCTT--SCCCCT-TEE--S--EEEECSCHHCHHHHHHCCCCT--------SSEEEEECCGSTCCC
T ss_pred             CcCcCcHHHHHHHHHHHHhccccccccccccccccceeeccchhhhHHHHHHHHHhhC-------CceEEECCCCcccCC
Confidence            3666888888777655544321            259999999999999999875443       222222211110000


Q ss_pred             HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh-------------hcCcceEEEEecCC
Q 022641          129 VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMET-------------YSKVTRFFFICNYI  195 (294)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~-------------~~~~~~ii~~~~~~  195 (294)
                      ........  .....+....+....+.+++++|||++.+.......|.+.|+.             .+..+.++.++|+.
T Consensus        97 Lta~~~~d--~~~~~~~leaGalvlad~GiccIDe~dk~~~~~~~~l~eaMEqq~isi~kagi~~~l~ar~svlaa~NP~  174 (331)
T PF00493_consen   97 LTASVSRD--PVTGEWVLEAGALVLADGGICCIDEFDKMKEDDRDALHEAMEQQTISIAKAGIVTTLNARCSVLAAANPK  174 (331)
T ss_dssp             CCEEECCC--GGTSSECEEE-HHHHCTTSEEEECTTTT--CHHHHHHHHHHHCSCEEECTSSSEEEEE---EEEEEE--T
T ss_pred             ccceeccc--cccceeEEeCCchhcccCceeeecccccccchHHHHHHHHHHcCeeccchhhhcccccchhhhHHHHhhh
Confidence            00000000  0000011112222334567999999999999999999999985             23456678888755


Q ss_pred             c-------------ccchHhhccccEEE--ecCCC
Q 022641          196 S-------------RIIEPLASRCAKFR--FKPLS  215 (294)
Q Consensus       196 ~-------------~~~~~l~~r~~~i~--~~~~~  215 (294)
                      .             .+++.+++||..+.  ..+++
T Consensus       175 ~g~~~~~~~~~~ni~l~~~LLSRFDLif~l~D~~d  209 (331)
T PF00493_consen  175 FGRYDPNKSLSENINLPPPLLSRFDLIFLLRDKPD  209 (331)
T ss_dssp             T--S-TTS-CGCCT-S-CCCHCC-SEEECC--TTT
T ss_pred             hhhcchhhhhHHhcccchhhHhhcCEEEEeccccc
Confidence            3             26778999998442  34554

; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.

>PHA00729 NTP-binding motif containing protein

Probab=98.77  E-value=1.3e-07  Score=75.06  Aligned_cols=125  Identities=17%  Similarity=0.156  Sum_probs=67.7

Q ss_pred             HHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCC-ccCCcceeecCCC---CcchhHHHHHHHHHHhhhcccCccCC
Q 022641           74 TNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE-LYKSRVLELNASD---DRGINVVRTKIKTFAAVAVGSGQRRG  149 (294)
Q Consensus        74 ~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~-~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (294)
                      ...+..+...+++|+|+|||||||+|.++++.+.... .............   ..+...+...+.......        
T Consensus         9 ~~~l~~~~f~nIlItG~pGvGKT~LA~aLa~~l~~~l~~l~~~~~~~d~~~~~~fid~~~Ll~~L~~a~~~~--------   80 (226)
T PHA00729          9 VSAYNNNGFVSAVIFGKQGSGKTTYALKVARDVFWKLNNLSTKDDAWQYVQNSYFFELPDALEKIQDAIDND--------   80 (226)
T ss_pred             HHHHhcCCeEEEEEECCCCCCHHHHHHHHHHHHHhhcccccchhhHHhcCCcEEEEEHHHHHHHHHHHHhcC--------
Confidence            3344455556899999999999999999999872000 0000000011111   112222222232211110        


Q ss_pred             CCCCCCcEEEEEeCCCCCCHH-HHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHH
Q 022641          150 GYPCPPYKIIILDEADSMTED-AQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLH  225 (294)
Q Consensus       150 ~~~~~~~~lliiDei~~l~~~-~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~  225 (294)
                          .+.++|||||++--... .+..     +    .      ....+.+.+.+++|+..+.+.+++.+++...++.
T Consensus        81 ----~~~dlLIIDd~G~~~~~~~wh~-----~----~------~~~yf~L~~aLrSR~~l~il~~ls~edL~~~Lr~  138 (226)
T PHA00729         81 ----YRIPLIIFDDAGIWLSKYVWYE-----D----Y------MKTFYKIYALIRTRVSAVIFTTPSPEDLAFYLRE  138 (226)
T ss_pred             ----CCCCEEEEeCCchhhcccchhh-----h----c------cchHHHHHHHHHhhCcEEEEecCCHHHHHHHHHh
Confidence                12358999997542111 0000     0    0      0122445678888999999999999988888865

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

Probab=98.74  E-value=4.1e-07  Score=79.24  Aligned_cols=155  Identities=15%  Similarity=0.248  Sum_probs=90.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC-Ccch------hHHHHHHHHHHhhhcccCccCCCCCCCCc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD-DRGI------NVVRTKIKTFAAVAVGSGQRRGGYPCPPY  156 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~-~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (294)
                      .++|.||||+|||+||..+|..-      ..+|+.+-... ..+.      ..+...+......+.              
T Consensus       540 SvLl~Gp~~sGKTaLAA~iA~~S------~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYkS~l--------------  599 (744)
T KOG0741|consen  540 SVLLEGPPGSGKTALAAKIALSS------DFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKSPL--------------  599 (744)
T ss_pred             EEEEecCCCCChHHHHHHHHhhc------CCCeEEEeChHHccCccHHHHHHHHHHHHHHhhcCcc--------------
Confidence            49999999999999999999876      67777664332 2222      233334444333332              


Q ss_pred             EEEEEeCCCCC------CHHHHH----HHHHHHHhhcCc--ceEEEEecCCcccch--Hhhcccc-EEEecCCCH-HHHH
Q 022641          157 KIIILDEADSM------TEDAQN----ALRRTMETYSKV--TRFFFICNYISRIIE--PLASRCA-KFRFKPLSE-EVMS  220 (294)
Q Consensus       157 ~lliiDei~~l------~~~~~~----~L~~~l~~~~~~--~~ii~~~~~~~~~~~--~l~~r~~-~i~~~~~~~-~~~~  220 (294)
                      .+|++|++++|      .+...+    .|+-++...+..  ..+|+.|.....+..  .+.+.|. .+.++.++. +++.
T Consensus       600 siivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpnl~~~~~~~  679 (744)
T KOG0741|consen  600 SIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPNLTTGEQLL  679 (744)
T ss_pred             eEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCccCchHHHH
Confidence            49999999876      244444    444444443433  445555554433332  2344555 788888876 6777


Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHhhccC-----cHHHHHHHHHHHHHH
Q 022641          221 SRVLHICNEEGLNLDAEALSTLSSISQG-----DLRRAITYLQGAARL  263 (294)
Q Consensus       221 ~~l~~~~~~~~~~~~~~~l~~l~~~~~G-----~~r~~~~~l~~~~~~  263 (294)
                      +++.    ..+. ++++..+.+++.--+     .+..++.+++.+...
T Consensus       680 ~vl~----~~n~-fsd~~~~~~~~~~~~~~~~vgIKklL~lie~a~q~  722 (744)
T KOG0741|consen  680 EVLE----ELNI-FSDDEVRAIAEQLLSKKVNVGIKKLLMLIEMARQD  722 (744)
T ss_pred             HHHH----HccC-CCcchhHHHHHHHhccccchhHHHHHHHHHHHhcc
Confidence            7763    2222 455555555544222     267777777765543

>PF14516 AAA_35: AAA-like domain

Probab=98.73  E-value=2e-06  Score=73.51  Aligned_cols=201  Identities=14%  Similarity=0.087  Sum_probs=114.1

Q ss_pred             hhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC-----cchhH-HHHHHH
Q 022641           62 DVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD-----RGINV-VRTKIK  135 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~-----~~~~~-~~~~~~  135 (294)
                      -.+.++.+-+.+.+.+... +..+.|.||..+|||++...+.+.+...   +..++.++....     .+... ++....
T Consensus        12 ~Yi~R~~~e~~~~~~i~~~-G~~~~I~apRq~GKTSll~~l~~~l~~~---~~~~v~id~~~~~~~~~~~~~~f~~~~~~   87 (331)
T PF14516_consen   12 FYIERPPAEQECYQEIVQP-GSYIRIKAPRQMGKTSLLLRLLERLQQQ---GYRCVYIDLQQLGSAIFSDLEQFLRWFCE   87 (331)
T ss_pred             cccCchHHHHHHHHHHhcC-CCEEEEECcccCCHHHHHHHHHHHHHHC---CCEEEEEEeecCCCcccCCHHHHHHHHHH
Confidence            3456665666666666553 2369999999999999999999888433   334444443321     11111 111111


Q ss_pred             HHHhhhc-------------ccCcc-------CCCCCCCCcEEEEEeCCCCCCH--HHHHHHHHHH----Hhhc-----C
Q 022641          136 TFAAVAV-------------GSGQR-------RGGYPCPPYKIIILDEADSMTE--DAQNALRRTM----ETYS-----K  184 (294)
Q Consensus       136 ~~~~~~~-------------~~~~~-------~~~~~~~~~~lliiDei~~l~~--~~~~~L~~~l----~~~~-----~  184 (294)
                      .+.....             +....       .......++-||+|||+|.+..  .....++..+    +...     .
T Consensus        88 ~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~~~  167 (331)
T PF14516_consen   88 EISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPIWQ  167 (331)
T ss_pred             HHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCcccc
Confidence            1111100             00000       0001225677999999998854  2233344444    3222     2


Q ss_pred             cceEEEEecCCcccchHh----hccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHH
Q 022641          185 VTRFFFICNYISRIIEPL----ASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGA  260 (294)
Q Consensus       185 ~~~ii~~~~~~~~~~~~l----~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~  260 (294)
                      ..+++++......+....    .+....+.+++.+.+|+..+++    ..+..+++..++.|...++|.|--...++..+
T Consensus       168 ~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~----~~~~~~~~~~~~~l~~~tgGhP~Lv~~~~~~l  243 (331)
T PF14516_consen  168 KLRLILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQ----RYGLEFSQEQLEQLMDWTGGHPYLVQKACYLL  243 (331)
T ss_pred             eEEEEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHH----hhhccCCHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            344555543222111111    1334478999999999988774    45677888889999999999997766666666


Q ss_pred             HHHhCCCCChhhh
Q 022641          261 ARLFGSSITSKDL  273 (294)
Q Consensus       261 ~~~~~~~it~~~v  273 (294)
                      +.   ..++.+++
T Consensus       244 ~~---~~~~~~~l  253 (331)
T PF14516_consen  244 VE---EQITLEQL  253 (331)
T ss_pred             HH---ccCcHHHH
Confidence            54   24454444

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=98.73  E-value=1.6e-07  Score=91.10  Aligned_cols=146  Identities=16%  Similarity=0.236  Sum_probs=97.7

Q ss_pred             HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCC
Q 022641           71 RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGG  150 (294)
Q Consensus        71 ~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (294)
                      ..+.+++..++  .++|-|.||+|||+++.++|+..      +..++.+|.++....-   +.+........++......
T Consensus      1534 ~rVlRAmqv~k--pilLEGsPGVGKTSlItaLAr~t------G~kliRINLSeQTdL~---DLfGsd~Pve~~Gef~w~d 1602 (4600)
T COG5271        1534 RRVLRAMQVGK--PILLEGSPGVGKTSLITALARKT------GKKLIRINLSEQTDLC---DLFGSDLPVEEGGEFRWMD 1602 (4600)
T ss_pred             HHHHHHHhcCC--ceeecCCCCccHHHHHHHHHHHh------cCceEEeeccccchHH---HHhCCCCCcccCceeEecc
Confidence            34555555555  59999999999999999999998      7888888877653321   1111111000000000000


Q ss_pred             ----CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc--------------CcceEEEEecC------CcccchHhhccc
Q 022641          151 ----YPCPPYKIIILDEADSMTEDAQNALRRTMETYS--------------KVTRFFFICNY------ISRIIEPLASRC  206 (294)
Q Consensus       151 ----~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~--------------~~~~ii~~~~~------~~~~~~~l~~r~  206 (294)
                          ..-.+++-+++||+...+..+.+.|-..++.+.              ++.+++.+-|+      ...++..+.+||
T Consensus      1603 apfL~amr~G~WVlLDEiNLaSQSVlEGLNacLDhR~eayIPEld~~f~~HpnfrVFAaqNPq~qggGRKgLPkSF~nRF 1682 (4600)
T COG5271        1603 APFLHAMRDGGWVLLDEINLASQSVLEGLNACLDHRREAYIPELDKTFDVHPNFRVFAAQNPQDQGGGRKGLPKSFLNRF 1682 (4600)
T ss_pred             cHHHHHhhcCCEEEeehhhhhHHHHHHHHHHHHhhccccccccccceeeccCCeeeeeecCchhcCCCcccCCHHHhhhh
Confidence                011345699999999999999999988887543              33444444443      245899999999


Q ss_pred             cEEEecCCCHHHHHHHHHHHH
Q 022641          207 AKFRFKPLSEEVMSSRVLHIC  227 (294)
Q Consensus       207 ~~i~~~~~~~~~~~~~l~~~~  227 (294)
                      .++.+..++.+++..+.....
T Consensus      1683 svV~~d~lt~dDi~~Ia~~~y 1703 (4600)
T COG5271        1683 SVVKMDGLTTDDITHIANKMY 1703 (4600)
T ss_pred             heEEecccccchHHHHHHhhC
Confidence            999999999999988875544

>KOG0481 consensus DNA replication licensing factor, MCM5 component [Replication, recombination and repair]

Probab=98.73  E-value=1e-07  Score=82.43  Aligned_cols=219  Identities=18%  Similarity=0.168  Sum_probs=124.3

Q ss_pred             hhhhcCCCcchhhcccHHHHHHHHHHHHcCCCC------------cEEEECCCCCCHHHHHHHHHHHhcCCCccCCccee
Q 022641           51 WVEKYRPKQVKDVAHQEEVVRVLTNTLETANCP------------HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLE  118 (294)
Q Consensus        51 ~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~------------~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~  118 (294)
                      ..+.....-...+.|+++.++.+.-.|+.|...            |++|.|.|||.||.+++.+-+-.      ...++.
T Consensus       321 ~Ye~is~sIAPSIfG~~DiKkAiaClLFgGsrK~LpDg~~lRGDINVLLLGDPgtAKSQlLKFvEkvs------PIaVYT  394 (729)
T KOG0481|consen  321 VYERISKSIAPSIFGHEDIKKAIACLLFGGSRKRLPDGVTLRGDINVLLLGDPGTAKSQLLKFVEKVS------PIAVYT  394 (729)
T ss_pred             HHHHHhhccCchhcCchhHHHHHHHHhhcCccccCCCcceeccceeEEEecCCchhHHHHHHHHHhcC------ceEEEe
Confidence            344444444446779999999998888775332            49999999999999999987653      112221


Q ss_pred             ecCCCCcchh-----HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh------------
Q 022641          119 LNASDDRGIN-----VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMET------------  181 (294)
Q Consensus       119 ~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~------------  181 (294)
                        ...+.+..     .+++-..  ..+-.    .-+....+..++++|||+|++.++..-.+.+.|+.            
T Consensus       395 --SGKGSSAAGLTASV~RD~~t--ReFyl----EGGAMVLADgGVvCIDEFDKMre~DRVAIHEAMEQQTISIAKAGITT  466 (729)
T KOG0481|consen  395 --SGKGSSAAGLTASVIRDPST--REFYL----EGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITT  466 (729)
T ss_pred             --cCCCcccccceeeEEecCCc--ceEEE----ecceEEEecCCEEEeehhhccCchhhhHHHHHHHhhhHHHhhhccee
Confidence              11111110     1110000  00000    01223456678999999999998887778877763            


Q ss_pred             -hcCcceEEEEecCCcc-------------cchHhhccccEEEec-----------------------------------
Q 022641          182 -YSKVTRFFFICNYISR-------------IIEPLASRCAKFRFK-----------------------------------  212 (294)
Q Consensus       182 -~~~~~~ii~~~~~~~~-------------~~~~l~~r~~~i~~~-----------------------------------  212 (294)
                       ....++++.++|..+.             ..+.+++||..|.+-                                   
T Consensus       467 ~LNSRtSVLAAANpvfGRyDd~Kt~~dNIDf~~TILSRFDmIFIVKD~h~~~~D~~lAkHVI~vH~~~~n~~~~~~~~~~  546 (729)
T KOG0481|consen  467 TLNSRTSVLAAANPVFGRYDDTKTGEDNIDFMPTILSRFDMIFIVKDEHDEERDITLAKHVINVHVSKANAQTDSQEENE  546 (729)
T ss_pred             eecchhhhhhhcCCccccccccCCcccccchhhhHhhhccEEEEEeccCcchhhhHHHHHhhhhhccccccccCccccCC
Confidence             2234455555565432             346788888743221                                   


Q ss_pred             -CCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhcc--------------------CcHHH---HHHHHHHHHHHh-CCC
Q 022641          213 -PLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQ--------------------GDLRR---AITYLQGAARLF-GSS  267 (294)
Q Consensus       213 -~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~--------------------G~~r~---~~~~l~~~~~~~-~~~  267 (294)
                       ..+.+.++.++.+...+-+..+++++.+.|....=                    =.+|+   ++.+-+.+++.. +..
T Consensus       547 ~ei~~~~~KryI~YcR~kc~PrLs~~AaekL~~~yV~~R~~~~q~e~~s~~rssIPITVRQLEAIiRI~ESLAKm~Ls~~  626 (729)
T KOG0481|consen  547 GEIPIEKLKRYIQYCRLKCGPRLSAEAAEKLSSRYVTMRKGVRQHEQDSDKRSSIPITVRQLEAIIRIAESLAKMELSPF  626 (729)
T ss_pred             CcccHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHhHHHHHHHHhhhcccccCCCceeHHHHHHHHHHHHHHHhhcCCcc
Confidence             11223444444443344566788888777664310                    02333   333333344333 455


Q ss_pred             CChhhhhhhcccccCC
Q 022641          268 ITSKDLISVSGYPTGG  283 (294)
Q Consensus       268 it~~~v~~~~~~~~~~  283 (294)
                      .|.+|+.+++..+.-+
T Consensus       627 ate~hV~EA~RLF~vS  642 (729)
T KOG0481|consen  627 ATEAHVEEALRLFQVS  642 (729)
T ss_pred             ccHHHHHHHHHHHhHh
Confidence            7888888887765544

>PRK10536 hypothetical protein; Provisional

Probab=98.72  E-value=1.7e-07  Score=75.59  Aligned_cols=60  Identities=15%  Similarity=0.176  Sum_probs=44.5

Q ss_pred             cCCchhhh-hcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           46 QSSQPWVE-KYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        46 ~~~~~~~~-~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+.+|+.. .....++..+.+.......+..++...  ..++++||+|||||+++.+++.+..
T Consensus        39 ~~~~p~~~~~~~~~~~~~i~p~n~~Q~~~l~al~~~--~lV~i~G~aGTGKT~La~a~a~~~l   99 (262)
T PRK10536         39 MGGVEAIGMARDSRDTSPILARNEAQAHYLKAIESK--QLIFATGEAGCGKTWISAAKAAEAL   99 (262)
T ss_pred             hccCCccccchhhcCCccccCCCHHHHHHHHHHhcC--CeEEEECCCCCCHHHHHHHHHHHHH
Confidence            45566655 445556666777776777777777664  4799999999999999999999653

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=98.71  E-value=2.8e-08  Score=70.36  Aligned_cols=23  Identities=48%  Similarity=0.925  Sum_probs=21.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      |.|+||||+|||+++..|++.+.
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~   23 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLL   23 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHH
Confidence            57999999999999999999884

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

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=98.68  E-value=6.6e-09  Score=79.50  Aligned_cols=63  Identities=13%  Similarity=0.270  Sum_probs=35.8

Q ss_pred             CcEEEEEeCCCCC---CHHHHHHHHHHHHhhcCcceEEEEecC--CcccchHhhcc--ccEEEecCCCHHHHH
Q 022641          155 PYKIIILDEADSM---TEDAQNALRRTMETYSKVTRFFFICNY--ISRIIEPLASR--CAKFRFKPLSEEVMS  220 (294)
Q Consensus       155 ~~~lliiDei~~l---~~~~~~~L~~~l~~~~~~~~ii~~~~~--~~~~~~~l~~r--~~~i~~~~~~~~~~~  220 (294)
                      ..++++|||++.+   .+...+.+..+++   ....+|.+-..  ...+.+++.+|  +.++.+.+-+.+.+.
T Consensus        95 ~~~liviDEIG~mEl~~~~F~~~v~~~l~---s~~~vi~vv~~~~~~~~l~~i~~~~~~~i~~vt~~NRd~l~  164 (168)
T PF03266_consen   95 SSDLIVIDEIGKMELKSPGFREAVEKLLD---SNKPVIGVVHKRSDNPFLEEIKRRPDVKIFEVTEENRDALP  164 (168)
T ss_dssp             CCHEEEE---STTCCC-CHHHHHHHHHHC---TTSEEEEE--SS--SCCHHHHHTTTTSEEEE--TTTCCCHH
T ss_pred             CCCEEEEeccchhhhcCHHHHHHHHHHHc---CCCcEEEEEecCCCcHHHHHHHhCCCcEEEEeChhHHhhHh
Confidence            4469999999987   3556777888877   23334444433  34567888887  557877776655443

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.

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.68  E-value=8e-08  Score=77.81  Aligned_cols=195  Identities=18%  Similarity=0.210  Sum_probs=116.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCc-cCCCCCCCCcEEEEEe
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQ-RRGGYPCPPYKIIILD  162 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~lliiD  162 (294)
                      .++|.||.|.|||.+|+.+-..-.........|+++||...++.......+........+... ..+....+..+++++|
T Consensus       210 p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghvkgaftga~~~r~gllrsadggmlfld  289 (531)
T COG4650         210 PILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHVKGAFTGARESREGLLRSADGGMLFLD  289 (531)
T ss_pred             CeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecCchHHHHHHhhhccccccchhhhhhhhccCCCceEehH
Confidence            499999999999999998865443344457899999999888877666666655443332222 2344456778899999


Q ss_pred             CCCCCCHHHHHHHHHHHHhhcC-----------cceEEEEe-cCC------cccchHhhccccEEEecCCCHHHHH----
Q 022641          163 EADSMTEDAQNALRRTMETYSK-----------VTRFFFIC-NYI------SRIIEPLASRCAKFRFKPLSEEVMS----  220 (294)
Q Consensus       163 ei~~l~~~~~~~L~~~l~~~~~-----------~~~ii~~~-~~~------~~~~~~l~~r~~~i~~~~~~~~~~~----  220 (294)
                      |++.+..+.+..|++.+++-..           ...+|.-| .+.      ......+..|+....|.-|...+..    
T Consensus       290 eigelgadeqamllkaieekrf~pfgsdr~v~sdfqliagtvrdlrq~vaeg~fredl~arinlwtf~lpgl~qr~edie  369 (531)
T COG4650         290 EIGELGADEQAMLLKAIEEKRFYPFGSDRQVSSDFQLIAGTVRDLRQLVAEGKFREDLYARINLWTFTLPGLRQRQEDIE  369 (531)
T ss_pred             hhhhcCccHHHHHHHHHHhhccCCCCCccccccchHHhhhhHHHHHHHHhccchHHHHHHhhheeeeeccccccCccccC
Confidence            9999999999999999986321           11111111 110      0112233344444444333321111    


Q ss_pred             ----HHHHHHHHHhC--CCCCHHHHHH-HH------hhccCcHHHHHHHHHHHHHHh-CCCCChhhhhhhcc
Q 022641          221 ----SRVLHICNEEG--LNLDAEALST-LS------SISQGDLRRAITYLQGAARLF-GSSITSKDLISVSG  278 (294)
Q Consensus       221 ----~~l~~~~~~~~--~~~~~~~l~~-l~------~~~~G~~r~~~~~l~~~~~~~-~~~it~~~v~~~~~  278 (294)
                          --+.+.+...|  +.+..++-.. ++      ....||.|.+--.+...+..+ +..||.+.|+.-+.
T Consensus       370 pnldyelerha~~~g~~vrfntearra~l~fa~spqa~w~gnfrelsasvtrmatlad~grit~~~ve~ei~  441 (531)
T COG4650         370 PNLDYELERHASLTGDSVRFNTEARRAWLAFATSPQATWRGNFRELSASVTRMATLADSGRITLDVVEDEIN  441 (531)
T ss_pred             CCccHHHHHHHHhhCceeeeehHHHHHHHHhccCcchhhcccHHHHhHHHHHHHHHhcCCceeHHHHHHHHH
Confidence                12333444444  3344444322 22      125789999887777666555 66788877765443

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

Probab=98.67  E-value=3.8e-06  Score=73.46  Aligned_cols=190  Identities=19%  Similarity=0.195  Sum_probs=111.8

Q ss_pred             HHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC-cchhHHHHHHHHHHhhhcccCc
Q 022641           68 EVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD-RGINVVRTKIKTFAAVAVGSGQ  146 (294)
Q Consensus        68 ~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  146 (294)
                      .....+.+.+..... .++|+||.+|||||+++.+.+.+..      ..+.++..+. .......+....+......   
T Consensus        24 ~~~~~l~~~~~~~~~-i~~i~GpR~~GKTtll~~l~~~~~~------~~iy~~~~d~~~~~~~l~d~~~~~~~~~~~---   93 (398)
T COG1373          24 KLLPRLIKKLDLRPF-IILILGPRQVGKTTLLKLLIKGLLE------EIIYINFDDLRLDRIELLDLLRAYIELKER---   93 (398)
T ss_pred             hhhHHHHhhcccCCc-EEEEECCccccHHHHHHHHHhhCCc------ceEEEEecchhcchhhHHHHHHHHHHhhcc---
Confidence            444455555544443 7999999999999999888887722      1344443333 2223333333333332211   


Q ss_pred             cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCc----ccchHhhccccEEEecCCCHHHHHH-
Q 022641          147 RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYIS----RIIEPLASRCAKFRFKPLSEEVMSS-  221 (294)
Q Consensus       147 ~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~----~~~~~l~~r~~~i~~~~~~~~~~~~-  221 (294)
                              +...++|||++.+.. -...+..+.+..+.  .+++++....    .....+..|...+.+.|++..|... 
T Consensus        94 --------~~~yifLDEIq~v~~-W~~~lk~l~d~~~~--~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Efl~~  162 (398)
T COG1373          94 --------EKSYIFLDEIQNVPD-WERALKYLYDRGNL--DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREFLKL  162 (398)
T ss_pred             --------CCceEEEecccCchh-HHHHHHHHHccccc--eEEEECCchhhhccchhhhcCCCceeEEECCCCHHHHHhh
Confidence                    345999999999853 33344444444333  4555554332    3456677888899999999988865 


Q ss_pred             ------------HHHHHHHHhCCC----CCH------HHH-----HHHHhhcc-CcHHHHHHHHHHHHHHhCCCCChhhh
Q 022641          222 ------------RVLHICNEEGLN----LDA------EAL-----STLSSISQ-GDLRRAITYLQGAARLFGSSITSKDL  273 (294)
Q Consensus       222 ------------~l~~~~~~~~~~----~~~------~~l-----~~l~~~~~-G~~r~~~~~l~~~~~~~~~~it~~~v  273 (294)
                                  .+..++..-|.+    .+.      +.+     ..+.+..+ -+...+..++.+++...+..++...+
T Consensus       163 ~~~~~~~~~~~~~f~~Yl~~GGfP~~v~~~~~~~~~~~~~~~~~~~Di~~~~~~~~~~~~k~i~~~l~~~~g~~~s~~~l  242 (398)
T COG1373         163 KGEEIEPSKLELLFEKYLETGGFPESVKADLSEKKLKEYLDTILKRDIIERGKIENADLMKRILRFLASNIGSPISYSSL  242 (398)
T ss_pred             cccccchhHHHHHHHHHHHhCCCcHHHhCcchhhHHHHHHHHHHHHHHHHHcCcccHHHHHHHHHHHHhhcCCccCHHHH
Confidence                        466677665654    111      111     12333332 24445556666777666777888887


Q ss_pred             hhhcc
Q 022641          274 ISVSG  278 (294)
Q Consensus       274 ~~~~~  278 (294)
                      ...+.
T Consensus       243 a~~l~  247 (398)
T COG1373         243 ARELK  247 (398)
T ss_pred             HHHHh
Confidence            77764

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=98.64  E-value=8.4e-08  Score=75.65  Aligned_cols=120  Identities=22%  Similarity=0.277  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHH----HHHhhhccc
Q 022641           69 VVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK----TFAAVAVGS  144 (294)
Q Consensus        69 ~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~  144 (294)
                      ....+...+.++ .+..++.||||||||+++..+...+...   +..++.+.+.. .....+.....    .+.......
T Consensus         6 Q~~a~~~~l~~~-~~~~~l~G~aGtGKT~~l~~~~~~~~~~---g~~v~~~apT~-~Aa~~L~~~~~~~a~Ti~~~l~~~   80 (196)
T PF13604_consen    6 QREAVRAILTSG-DRVSVLQGPAGTGKTTLLKALAEALEAA---GKRVIGLAPTN-KAAKELREKTGIEAQTIHSFLYRI   80 (196)
T ss_dssp             HHHHHHHHHHCT-CSEEEEEESTTSTHHHHHHHHHHHHHHT---T--EEEEESSH-HHHHHHHHHHTS-EEEHHHHTTEE
T ss_pred             HHHHHHHHHhcC-CeEEEEEECCCCCHHHHHHHHHHHHHhC---CCeEEEECCcH-HHHHHHHHhhCcchhhHHHHHhcC
Confidence            344444455443 3458889999999999999988877321   23344333322 22222332211    000000000


Q ss_pred             Cc--cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCC
Q 022641          145 GQ--RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYI  195 (294)
Q Consensus       145 ~~--~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~  195 (294)
                      ..  ........+..+|||||+..++......|+..+..  ....+|+++...
T Consensus        81 ~~~~~~~~~~~~~~~vliVDEasmv~~~~~~~ll~~~~~--~~~klilvGD~~  131 (196)
T PF13604_consen   81 PNGDDEGRPELPKKDVLIVDEASMVDSRQLARLLRLAKK--SGAKLILVGDPN  131 (196)
T ss_dssp             CCEECCSSCC-TSTSEEEESSGGG-BHHHHHHHHHHS-T---T-EEEEEE-TT
T ss_pred             CcccccccccCCcccEEEEecccccCHHHHHHHHHHHHh--cCCEEEEECCcc
Confidence            00  00111134567999999999999888888877765  456688887544

>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=98.61  E-value=1.6e-05  Score=68.09  Aligned_cols=109  Identities=14%  Similarity=0.126  Sum_probs=68.5

Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhhc--CcceEEEEecCCc---------------ccchHhhccc-c-EEEecCC
Q 022641          154 PPYKIIILDEADSMTEDAQNALRRTMETYS--KVTRFFFICNYIS---------------RIIEPLASRC-A-KFRFKPL  214 (294)
Q Consensus       154 ~~~~lliiDei~~l~~~~~~~L~~~l~~~~--~~~~ii~~~~~~~---------------~~~~~l~~r~-~-~i~~~~~  214 (294)
                      .++-|++|||+|+++++....++..+...-  .++.+|++.+...               ......+.++ + .+.++++
T Consensus       171 ~~~iViiIDdLDR~~~~~i~~~l~~ik~~~~~~~i~~Il~~D~~~l~~ai~~~~~~~~~~~~~~~yLeKiiq~~~~lP~~  250 (325)
T PF07693_consen  171 KKRIVIIIDDLDRCSPEEIVELLEAIKLLLDFPNIIFILAFDPEILEKAIEKNYGEGFDEIDGREYLEKIIQVPFSLPPP  250 (325)
T ss_pred             CceEEEEEcchhcCCcHHHHHHHHHHHHhcCCCCeEEEEEecHHHHHHHHHhhcCcccccccHHHHHHhhcCeEEEeCCC
Confidence            457799999999999887777776666433  3555666664221               1223344444 3 6899999


Q ss_pred             CHHHHHHHHHHHHHHhCCC----CC---------------HHHHHHHHhh---ccCcHHHHHHHHHHHHH
Q 022641          215 SEEVMSSRVLHICNEEGLN----LD---------------AEALSTLSSI---SQGDLRRAITYLQGAAR  262 (294)
Q Consensus       215 ~~~~~~~~l~~~~~~~~~~----~~---------------~~~l~~l~~~---~~G~~r~~~~~l~~~~~  262 (294)
                      +..++..++...+......    .+               ...+..+...   ..++||.+.+.+.....
T Consensus       251 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~npR~ikr~iN~~~~  320 (325)
T PF07693_consen  251 SPSDLERYLNELLESLESETNESDDIETLSNSASNENLRIDEILNDIIDSIDFSIGNPRDIKRFINSLSL  320 (325)
T ss_pred             CHHHHHHHHHHHHHHhhhccccccchhhhhhcchhhhhhHHHHHHHHHHhhhhcCCCHHHHHHHHHHHHH
Confidence            9999998888876543221    11               1233344432   35789988887776554

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 [].

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=98.60  E-value=8.9e-07  Score=73.09  Aligned_cols=165  Identities=14%  Similarity=0.107  Sum_probs=93.1

Q ss_pred             hhcccHHHHHHHHHHHH----cCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHH
Q 022641           62 DVAHQEEVVRVLTNTLE----TANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTF  137 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~----~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  137 (294)
                      .+.|..+....+.+|+.    .|....++++||.|+|||.+....... ..+...+.-.+.+|+.-....-.+.+...++
T Consensus        25 ~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~-~q~~~E~~l~v~Lng~~~~dk~al~~I~rql  103 (408)
T KOG2228|consen   25 NLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSD-IQENGENFLLVRLNGELQTDKIALKGITRQL  103 (408)
T ss_pred             ceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhh-HHhcCCeEEEEEECccchhhHHHHHHHHHHH
Confidence            45566555555555554    466666999999999999998776655 2233334444555655444333333333333


Q ss_pred             HhhhcccCcc----------------CCCCCCCCcEEEEEeCCCCCCHHH-HHH---HHHHHHhhcCcceEEEEecCC--
Q 022641          138 AAVAVGSGQR----------------RGGYPCPPYKIIILDEADSMTEDA-QNA---LRRTMETYSKVTRFFFICNYI--  195 (294)
Q Consensus       138 ~~~~~~~~~~----------------~~~~~~~~~~lliiDei~~l~~~~-~~~---L~~~l~~~~~~~~ii~~~~~~--  195 (294)
                      ..........                .+....+..-+.|+||+|..-+.. +-.   |+++.+....++++|..|...  
T Consensus       104 ~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrld~  183 (408)
T KOG2228|consen  104 ALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRLDI  183 (408)
T ss_pred             HHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeeccccH
Confidence            2221111110                122222333566778999774432 333   344444555667777766544  


Q ss_pred             -cccchHhhcccc--EEEe-cCCCHHHHHHHHHHHH
Q 022641          196 -SRIIEPLASRCA--KFRF-KPLSEEVMSSRVLHIC  227 (294)
Q Consensus       196 -~~~~~~l~~r~~--~i~~-~~~~~~~~~~~l~~~~  227 (294)
                       ..+-+++.+||.  .|.+ ++.+-.+...+++..+
T Consensus       184 lE~LEKRVKSRFshr~I~m~~~~~l~~yv~l~r~ll  219 (408)
T KOG2228|consen  184 LELLEKRVKSRFSHRVIFMLPSLPLGDYVDLYRKLL  219 (408)
T ss_pred             HHHHHHHHHhhcccceeeccCCCChHHHHHHHHHHh
Confidence             345678889996  3555 4456788888887666

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

Probab=98.57  E-value=2.4e-07  Score=71.62  Aligned_cols=109  Identities=16%  Similarity=0.216  Sum_probs=79.8

Q ss_pred             CCCcEEEEEeCC----CCCCHHHHHHHHHHHHhhcCcceEEEEec-CCc---ccchHhhccccEEEecCCCHHHHHHHHH
Q 022641          153 CPPYKIIILDEA----DSMTEDAQNALRRTMETYSKVTRFFFICN-YIS---RIIEPLASRCAKFRFKPLSEEVMSSRVL  224 (294)
Q Consensus       153 ~~~~~lliiDei----~~l~~~~~~~L~~~l~~~~~~~~ii~~~~-~~~---~~~~~l~~r~~~i~~~~~~~~~~~~~l~  224 (294)
                      .+.+.+|+|.++    +.........|...+...+....+|+.++ ...   .+...+...+.++.+.++...++..+++
T Consensus        55 F~~~klvii~~~~~l~~~~~~~~~~~l~~~l~~~~~~~~lii~~~~~~~~~~k~~k~l~~~~~~~~~~~~~~~~~~~~i~  134 (172)
T PF06144_consen   55 FGDKKLVIIKNAPFLKDKLKKKEIKALIEYLSNPPPDCILIIFSEEKLDKRKKLYKALKKQAIVIECKKPKEQELPRWIK  134 (172)
T ss_dssp             SSSEEEEEEE-----TT-S-TTHHHHHHHHTTT--SSEEEEEEES-S--HHHHHHHHHTTTEEEEEE----TTTHHHHHH
T ss_pred             cCCCeEEEEecCccccccccHHHHHHHHHHHhCCCCCEEEEEEeCCchhhhhhHHHHHhcccceEEecCCCHHHHHHHHH
Confidence            345679999998    44566778889999998888888888877 222   2445566677789999999999999999


Q ss_pred             HHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHH
Q 022641          225 HICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA  261 (294)
Q Consensus       225 ~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~  261 (294)
                      ..+++.|+.+++++++.+++.+++|++.+.+.++..+
T Consensus       135 ~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~EleKL~  171 (172)
T PF06144_consen  135 ERAKKNGLKIDPDAAQYLIERVGNDLSLLQNELEKLS  171 (172)
T ss_dssp             HHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHcCCCCCHHHHHHHHHHhChHHHHHHHHHHHhc
Confidence            9999999999999999999999999999999998765

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

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

Probab=98.55  E-value=5.3e-06  Score=69.72  Aligned_cols=197  Identities=18%  Similarity=0.163  Sum_probs=109.7

Q ss_pred             hhhcccHHHHHHHHHHHHcCCC---CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcch----------
Q 022641           61 KDVAHQEEVVRVLTNTLETANC---PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGI----------  127 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~~~---~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~----------  127 (294)
                      ..+.+++..+..|...+.....   .+++|+|.+|||||.+++.+.+....      +.+-+++..-...          
T Consensus         6 ~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~------~~vw~n~~ecft~~~lle~IL~~   79 (438)
T KOG2543|consen    6 PNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNL------ENVWLNCVECFTYAILLEKILNK   79 (438)
T ss_pred             cCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCC------cceeeehHHhccHHHHHHHHHHH
Confidence            4567888899999888866432   34799999999999999999998722      2222222111111          


Q ss_pred             ---------------hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC---HHHHHHHHHHHHhhcCcceEE
Q 022641          128 ---------------NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT---EDAQNALRRTMETYSKVTRFF  189 (294)
Q Consensus       128 ---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~---~~~~~~L~~~l~~~~~~~~ii  189 (294)
                                     ..+.+.+..+......       ...++.-+|++|++|.+.   ....+.|+++-+-.+.+...|
T Consensus        80 ~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~-------t~~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i~i  152 (438)
T KOG2543|consen   80 SQLADKDGDKVEGDAENFSDFIYLLVQWPAA-------TNRDQKVFLILDNADALRDMDAILLQCLFRLYELLNEPTIVI  152 (438)
T ss_pred             hccCCCchhhhhhHHHHHHHHHHHHHhhHHh-------hccCceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCceEE
Confidence                           1111112221111000       111345699999999874   445666666665555555444


Q ss_pred             EEecCCcccchHhh---cc-c-cEEEecCCCHHHHHHHHHHHHH-HhCCCCCHHHH----HHHHhhccCcHHHHHHHHHH
Q 022641          190 FICNYISRIIEPLA---SR-C-AKFRFKPLSEEVMSSRVLHICN-EEGLNLDAEAL----STLSSISQGDLRRAITYLQG  259 (294)
Q Consensus       190 ~~~~~~~~~~~~l~---~r-~-~~i~~~~~~~~~~~~~l~~~~~-~~~~~~~~~~l----~~l~~~~~G~~r~~~~~l~~  259 (294)
                      +.+.....  ....   +. + ..+.|+.++.++...++.+--. +...++-.+-+    +.....|. |+..+..++..
T Consensus       153 ils~~~~e--~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~~~p~~r~~~~ya~fl~v~l~vF~~~cr-d~~eL~~~~~~  229 (438)
T KOG2543|consen  153 ILSAPSCE--KQYLINTGTLEIVVLHFPQYSVEETQVILSRDNPGKRKLDVYAQFLHVLLQVFYMACR-DVNELRSLISL  229 (438)
T ss_pred             EEeccccH--HHhhcccCCCCceEEecCCCCHHHHHHHHhcCCccccchHHHHHHHHHHHHHHHHHhC-CHHHHHHHHHH
Confidence            44433321  1111   11 1 2789999999999999854322 11111111222    22333355 99999888887


Q ss_pred             HHHHhCCCCChhhh
Q 022641          260 AARLFGSSITSKDL  273 (294)
Q Consensus       260 ~~~~~~~~it~~~v  273 (294)
                      +....-+.|+...+
T Consensus       230 ~wpky~epi~~~~i  243 (438)
T KOG2543|consen  230 AWPKYCEPITKGKI  243 (438)
T ss_pred             HHHhhccccccCCC
Confidence            76554344444433

>PHA02774 E1; Provisional

Probab=98.54  E-value=9.9e-07  Score=78.66  Aligned_cols=136  Identities=23%  Similarity=0.337  Sum_probs=84.3

Q ss_pred             HHHHHHHHHHcCCC-CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCccee-ecCCCCcchhHHHHHHHHHHhhhcccCc
Q 022641           69 VVRVLTNTLETANC-PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLE-LNASDDRGINVVRTKIKTFAAVAVGSGQ  146 (294)
Q Consensus        69 ~~~~l~~~l~~~~~-~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (294)
                      ....|+.++..... ..++|+||||||||+++.+|++.+      ...++. +|..+..-       +..          
T Consensus       420 fl~~lk~~l~~~PKknciv~~GPP~TGKS~fa~sL~~~L------~G~vi~fvN~~s~Fw-------Lqp----------  476 (613)
T PHA02774        420 FLTALKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFL------KGKVISFVNSKSHFW-------LQP----------  476 (613)
T ss_pred             HHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHh------CCCEEEEEECccccc-------cch----------
Confidence            44667777765443 459999999999999999999987      333322 34321111       111          


Q ss_pred             cCCCCCCCCcEEEEEeCCCCCCHH-HHHHHHHHHHhhc-------------CcceEEEEecCCccc---chHhhccccEE
Q 022641          147 RRGGYPCPPYKIIILDEADSMTED-AQNALRRTMETYS-------------KVTRFFFICNYISRI---IEPLASRCAKF  209 (294)
Q Consensus       147 ~~~~~~~~~~~lliiDei~~l~~~-~~~~L~~~l~~~~-------------~~~~ii~~~~~~~~~---~~~l~~r~~~i  209 (294)
                            ....++++|||+-.-... ....|+.+++..+             ....+|+|||.....   ...|.+|+..+
T Consensus       477 ------l~d~ki~vlDD~t~~~w~y~d~~Lrn~LdG~~v~lD~Khk~~~q~k~pPlIITSN~d~~~~~~~~yL~sRi~~f  550 (613)
T PHA02774        477 ------LADAKIALLDDATHPCWDYIDTYLRNALDGNPVSIDCKHKAPVQIKCPPLLITSNIDVKAEDRYKYLHSRITVF  550 (613)
T ss_pred             ------hccCCEEEEecCcchHHHHHHHHHHHHcCCCcceeeecccCcccccCCCEEEecCCCcccchhhHHhhhhEEEE
Confidence                  112359999999332112 2335677776532             124588999865433   34566788777


Q ss_pred             EecC-------------CCHHHHHHHHHHHHHHhCCC
Q 022641          210 RFKP-------------LSEEVMSSRVLHICNEEGLN  233 (294)
Q Consensus       210 ~~~~-------------~~~~~~~~~l~~~~~~~~~~  233 (294)
                      .|+.             ++....+.++++...+-.+.
T Consensus       551 ~F~n~~P~d~~G~P~f~ltd~~WKsFF~rlw~~LdL~  587 (613)
T PHA02774        551 EFPNPFPLDENGNPVFELTDANWKSFFERLWSQLDLS  587 (613)
T ss_pred             ECCCCCCcCCCCCEeeeeCchhHHHHHHHHHHHcCCC
Confidence            6642             34578889998888775543

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=98.53  E-value=5.4e-07  Score=87.70  Aligned_cols=150  Identities=19%  Similarity=0.284  Sum_probs=101.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhccc-CccCCCC--CCCCcEEEE
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGS-GQRRGGY--PCPPYKIII  160 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~--~~~~~~lli  160 (294)
                      .++|.||..+|||+++..+++..      +..|+.+|.......   .+.+..+.....+. ..+.+..  ...++.-|+
T Consensus       890 P~LiQGpTSSGKTSMI~yla~~t------ghkfVRINNHEHTdl---qeYiGTyvTdd~G~lsFkEGvLVeAlR~GyWIV  960 (4600)
T COG5271         890 PLLIQGPTSSGKTSMILYLARET------GHKFVRINNHEHTDL---QEYIGTYVTDDDGSLSFKEGVLVEALRRGYWIV  960 (4600)
T ss_pred             cEEEecCCCCCcchHHHHHHHHh------CccEEEecCcccchH---HHHhhceeecCCCceeeehhHHHHHHhcCcEEE
Confidence            49999999999999999999998      778888876554332   22222222111110 0011100  113445999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhhc--------------CcceEEEEecCCc------ccchHhhccccEEEecCCCHHHHH
Q 022641          161 LDEADSMTEDAQNALRRTMETYS--------------KVTRFFFICNYIS------RIIEPLASRCAKFRFKPLSEEVMS  220 (294)
Q Consensus       161 iDei~~l~~~~~~~L~~~l~~~~--------------~~~~ii~~~~~~~------~~~~~l~~r~~~i~~~~~~~~~~~  220 (294)
                      +||+...+.++.+.|-+++++..              +.+.++.|-|+|.      .+..++++||..++|...+.+++.
T Consensus       961 LDELNLApTDVLEaLNRLLDDNRelfIPETqevV~PHp~F~lFATQNppg~YgGRK~LSrAFRNRFlE~hFddipedEle 1040 (4600)
T COG5271         961 LDELNLAPTDVLEALNRLLDDNRELFIPETQEVVVPHPNFRLFATQNPPGGYGGRKGLSRAFRNRFLEMHFDDIPEDELE 1040 (4600)
T ss_pred             eeccccCcHHHHHHHHHhhccccceecCCcceeeccCCCeeEEeecCCCccccchHHHHHHHHhhhHhhhcccCcHHHHH
Confidence            99999999999999999997422              3444444445442      367899999999999999999999


Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHhhcc
Q 022641          221 SRVLHICNEEGLNLDAEALSTLSSISQ  247 (294)
Q Consensus       221 ~~l~~~~~~~~~~~~~~~l~~l~~~~~  247 (294)
                      .+|..     ++.+.+.-...+++...
T Consensus      1041 ~ILh~-----rc~iapSyakKiVeVyr 1062 (4600)
T COG5271        1041 EILHG-----RCEIAPSYAKKIVEVYR 1062 (4600)
T ss_pred             HHHhc-----cCccCHHHHHHHHHHHH
Confidence            99954     44566766666666543

>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=98.53  E-value=7.5e-06  Score=65.82  Aligned_cols=137  Identities=14%  Similarity=0.092  Sum_probs=72.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc---------------chhHHHHHHHHHHhhhcccCccC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR---------------GINVVRTKIKTFAAVAVGSGQRR  148 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~~~  148 (294)
                      ++++.|++|+|||+++..+...+....   ..++.+......               ..+.+...+............+.
T Consensus        15 r~viIG~sGSGKT~li~~lL~~~~~~f---~~I~l~t~~~n~~~~~~i~p~~i~~~~~~e~le~~l~~~k~~I~k~~~k~   91 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTLIKSLLYYLRHKF---DHIFLITPEYNNEYYKYIWPDHIFKVFDKEELEYILIRQKEKIEKYIKKS   91 (241)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhhcccC---CEEEEEecCCchhhhhhcchhhccccccHHHHHHHHHHHHHHHHHHhhhh
Confidence            599999999999999999987762211   111111111100               01111111111111000000000


Q ss_pred             CCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHH-hhcCcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHH
Q 022641          149 GGYPCPPYKIIILDEADSMTEDAQNALRRTME-TYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVL  224 (294)
Q Consensus       149 ~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~-~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~  224 (294)
                      .......+.+||+||+..-.. ....+..++. .+.....+|+++.....+++.++.-+..+-+-..+..++..+++
T Consensus        92 ~~~k~~~~~LiIlDD~~~~~~-k~~~l~~~~~~gRH~~is~i~l~Q~~~~lp~~iR~n~~y~i~~~~s~~dl~~i~~  167 (241)
T PF04665_consen   92 PQKKNNPRFLIILDDLGDKKL-KSKILRQFFNNGRHYNISIIFLSQSYFHLPPNIRSNIDYFIIFNNSKRDLENIYR  167 (241)
T ss_pred             cccCCCCCeEEEEeCCCCchh-hhHHHHHHHhcccccceEEEEEeeecccCCHHHhhcceEEEEecCcHHHHHHHHH
Confidence            111134467999999865211 1223444443 34456778899988899999988877754444567666655543

This is thought to be an ATPase involved in viral DNA packaging [].

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=98.50  E-value=3.4e-07  Score=68.81  Aligned_cols=51  Identities=12%  Similarity=0.137  Sum_probs=37.8

Q ss_pred             CCcEEEEEeCCCCC-C--HHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhcccc
Q 022641          154 PPYKIIILDEADSM-T--EDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       154 ~~~~lliiDei~~l-~--~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      ...++|||||+... +  .-..+.++++++..+....+|+|++...   +.+..+..
T Consensus        94 ~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p---~~l~e~AD  147 (159)
T cd00561          94 GEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAP---KELIEAAD  147 (159)
T ss_pred             CCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCC---HHHHHhCc
Confidence            45789999999765 2  1235678889999999999999997754   45555544

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.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=98.48  E-value=2.6e-06  Score=78.41  Aligned_cols=187  Identities=17%  Similarity=0.171  Sum_probs=115.4

Q ss_pred             cCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHH
Q 022641           55 YRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKI  134 (294)
Q Consensus        55 ~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  134 (294)
                      ..|......+-++.....|....   ..+-++|.-|.|.||||++..++..+  ........+.++.++........-.+
T Consensus        13 ~~P~~~~~~v~R~rL~~~L~~~~---~~RL~li~APAGfGKttl~aq~~~~~--~~~~~v~Wlslde~dndp~rF~~yLi   87 (894)
T COG2909          13 VRPVRPDNYVVRPRLLDRLRRAN---DYRLILISAPAGFGKTTLLAQWRELA--ADGAAVAWLSLDESDNDPARFLSYLI   87 (894)
T ss_pred             CCCCCcccccccHHHHHHHhcCC---CceEEEEeCCCCCcHHHHHHHHHHhc--CcccceeEeecCCccCCHHHHHHHHH
Confidence            33445556666666655554222   22349999999999999999998733  33334445556666555555544444


Q ss_pred             HHHHhhhcccCccCC---------------------CCCCCCcEEEEEeCCCCCCHH-HHHHHHHHHHhhcCcceEEEEe
Q 022641          135 KTFAAVAVGSGQRRG---------------------GYPCPPYKIIILDEADSMTED-AQNALRRTMETYSKVTRFFFIC  192 (294)
Q Consensus       135 ~~~~~~~~~~~~~~~---------------------~~~~~~~~lliiDei~~l~~~-~~~~L~~~l~~~~~~~~ii~~~  192 (294)
                      ..+.......+....                     .....++-+++|||.|.++.. ....+...++..+.+..+|++|
T Consensus        88 ~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~S  167 (894)
T COG2909          88 AALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTS  167 (894)
T ss_pred             HHHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEe
Confidence            443322221111000                     012244569999999999754 4556777788889999999999


Q ss_pred             cCCcccc-hHhhccccEEEec----CCCHHHHHHHHHHHHHHhC-CCCCHHHHHHHHhhccCcH
Q 022641          193 NYISRII-EPLASRCAKFRFK----PLSEEVMSSRVLHICNEEG-LNLDAEALSTLSSISQGDL  250 (294)
Q Consensus       193 ~~~~~~~-~~l~~r~~~i~~~----~~~~~~~~~~l~~~~~~~~-~~~~~~~l~~l~~~~~G~~  250 (294)
                      .....+. ..++=|-..+++.    .++.+|..+++.    ..+ ..++...++.|.+.++|=+
T Consensus       168 R~rP~l~la~lRlr~~llEi~~~~Lrf~~eE~~~fl~----~~~~l~Ld~~~~~~L~~~teGW~  227 (894)
T COG2909         168 RSRPQLGLARLRLRDELLEIGSEELRFDTEEAAAFLN----DRGSLPLDAADLKALYDRTEGWA  227 (894)
T ss_pred             ccCCCCcccceeehhhHHhcChHhhcCChHHHHHHHH----HcCCCCCChHHHHHHHhhcccHH
Confidence            7554332 2232232333332    457788888874    344 8899999999999999843

>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=98.46  E-value=2.5e-05  Score=67.38  Aligned_cols=75  Identities=15%  Similarity=0.309  Sum_probs=51.4

Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhh------cCcceEEEEecCCc---ccchHhhccc-cEEEecCCCHHHHHHHHH
Q 022641          155 PYKIIILDEADSMTEDAQNALRRTMETY------SKVTRFFFICNYIS---RIIEPLASRC-AKFRFKPLSEEVMSSRVL  224 (294)
Q Consensus       155 ~~~lliiDei~~l~~~~~~~L~~~l~~~------~~~~~ii~~~~~~~---~~~~~l~~r~-~~i~~~~~~~~~~~~~l~  224 (294)
                      .+.||+||++.+-... .+.+.+.+.+.      ..-..||++|++..   .+.+++-++. ..|.+.-.+.+..+.++.
T Consensus       148 ~~PVVVIdnF~~k~~~-~~~iy~~laeWAa~Lv~~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak~yV~  226 (431)
T PF10443_consen  148 RRPVVVIDNFLHKAEE-NDFIYDKLAEWAASLVQNNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAKQYVL  226 (431)
T ss_pred             cCCEEEEcchhccCcc-cchHHHHHHHHHHHHHhcCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHHHHHH
Confidence            3579999999765433 44444444321      24456788886543   4566776664 489999999999999998


Q ss_pred             HHHHHh
Q 022641          225 HICNEE  230 (294)
Q Consensus       225 ~~~~~~  230 (294)
                      ..+...
T Consensus       227 ~~L~~~  232 (431)
T PF10443_consen  227 SQLDED  232 (431)
T ss_pred             HHhccc
Confidence            888653

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 [].

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=98.44  E-value=1.8e-06  Score=79.04  Aligned_cols=108  Identities=18%  Similarity=0.188  Sum_probs=61.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHh--------------------hhcc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAA--------------------VAVG  143 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------~~~~  143 (294)
                      ..+|+|+|||||||++..+...+..........+.+.++.......+.+.+.....                    ...+
T Consensus       169 ~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~~~~~~~~~~~~a~TiHrlLg  248 (615)
T PRK10875        169 ISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEEASTLHRLLG  248 (615)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhccccchhhhhcCCCchHHHHHHhC
Confidence            49999999999999999988776321111112344444444444444333321100                    0001


Q ss_pred             cCccC-----CCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecC
Q 022641          144 SGQRR-----GGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       144 ~~~~~-----~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      .....     .....-..++|||||+.+++......|++.+   +...++|+++..
T Consensus       249 ~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd~~lm~~ll~al---~~~~rlIlvGD~  301 (615)
T PRK10875        249 AQPGSQRLRYHAGNPLHLDVLVVDEASMVDLPMMARLIDAL---PPHARVIFLGDR  301 (615)
T ss_pred             cCCCccchhhccccCCCCCeEEEChHhcccHHHHHHHHHhc---ccCCEEEEecch
Confidence            00000     0011123479999999999888777777665   566788888853

>PHA02624 large T antigen; Provisional

Probab=98.40  E-value=2.2e-06  Score=76.77  Aligned_cols=115  Identities=21%  Similarity=0.245  Sum_probs=69.0

Q ss_pred             HHHHHHcCCC-CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCC
Q 022641           73 LTNTLETANC-PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGY  151 (294)
Q Consensus        73 l~~~l~~~~~-~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (294)
                      ++.++..-.. ..++|+||||||||+++.+|++.+      +..++.++.+...+.-    .+..+.+            
T Consensus       421 lk~~l~giPKk~~il~~GPpnTGKTtf~~sLl~~L------~G~vlsVNsPt~ks~F----wL~pl~D------------  478 (647)
T PHA02624        421 LKLIVENVPKRRYWLFKGPVNSGKTTLAAALLDLC------GGKSLNVNCPPDKLNF----ELGCAID------------  478 (647)
T ss_pred             HHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHc------CCeEEEeeCCcchhHH----Hhhhhhh------------
Confidence            3344433232 349999999999999999999998      5556666644432211    1111111            


Q ss_pred             CCCCcEEEEEeCCCCCCH-------H----HHHHHHHHHHhh-c-------------CcceEEEEecCCcccchHhhccc
Q 022641          152 PCPPYKIIILDEADSMTE-------D----AQNALRRTMETY-S-------------KVTRFFFICNYISRIIEPLASRC  206 (294)
Q Consensus       152 ~~~~~~lliiDei~~l~~-------~----~~~~L~~~l~~~-~-------------~~~~ii~~~~~~~~~~~~l~~r~  206 (294)
                          ..+++|||+-.-..       .    -...|+..++.. +             .-...|+|+|... ++..+.-||
T Consensus       479 ----~~~~l~dD~t~~~~~~~~Lp~G~~~dNl~~lRn~LDG~V~v~ld~KH~n~~q~~~PPlliT~Ney~-iP~T~~~Rf  553 (647)
T PHA02624        479 ----QFMVVFEDVKGQPADNKDLPSGQGMNNLDNLRDYLDGSVPVNLEKKHLNKRSQIFPPGIVTMNEYL-IPQTVKARF  553 (647)
T ss_pred             ----ceEEEeeeccccccccccCCcccccchhhHHHhhcCCCCccccchhccCchhccCCCeEEeecCcc-cchhHHHHH
Confidence                23889999843211       1    124566666643 1             1123777887754 677888888


Q ss_pred             c-EEEecCC
Q 022641          207 A-KFRFKPL  214 (294)
Q Consensus       207 ~-~i~~~~~  214 (294)
                      . .+.|.+-
T Consensus       554 ~~~~~F~~k  562 (647)
T PHA02624        554 AKVLDFKPK  562 (647)
T ss_pred             HHhcccccc
Confidence            7 6777553

>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=98.39  E-value=1.5e-06  Score=74.71  Aligned_cols=118  Identities=15%  Similarity=0.153  Sum_probs=62.9

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC------C-cchhHHHHHHHHHHhhhcccCccCCCCCCC
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD------D-RGINVVRTKIKTFAAVAVGSGQRRGGYPCP  154 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~------~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (294)
                      +++++|+||+|+|||+|.-.+...+.........|..+-..-      . ...+.+......+               ..
T Consensus        62 ~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~Fm~~vh~~l~~~~~~~~~l~~va~~l---------------~~  126 (362)
T PF03969_consen   62 PKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHEFMLDVHSRLHQLRGQDDPLPQVADEL---------------AK  126 (362)
T ss_pred             CceEEEECCCCCchhHHHHHHHHhCCccccccccccHHHHHHHHHHHHHhCCCccHHHHHHHH---------------Hh
Confidence            456999999999999999999888732211111111110000      0 0000111111111               12


Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHh-hcCcceEEEEecCCcc--------------cchHhhccccEEEecCC
Q 022641          155 PYKIIILDEADSMTEDAQNALRRTMET-YSKVTRFFFICNYISR--------------IIEPLASRCAKFRFKPL  214 (294)
Q Consensus       155 ~~~lliiDei~~l~~~~~~~L~~~l~~-~~~~~~ii~~~~~~~~--------------~~~~l~~r~~~i~~~~~  214 (294)
                      +..+|++||++--+....-.|..+++. +...+++|+|+|.+..              ..+.+.++|.++.+...
T Consensus       127 ~~~lLcfDEF~V~DiaDAmil~rLf~~l~~~gvvlVaTSN~~P~~Ly~~gl~r~~Flp~I~~l~~~~~vv~ld~~  201 (362)
T PF03969_consen  127 ESRLLCFDEFQVTDIADAMILKRLFEALFKRGVVLVATSNRPPEDLYKNGLQRERFLPFIDLLKRRCDVVELDGG  201 (362)
T ss_pred             cCCEEEEeeeeccchhHHHHHHHHHHHHHHCCCEEEecCCCChHHHcCCcccHHHHHHHHHHHHhceEEEEecCC
Confidence            334999999987665443333334433 2356667777775422              12445667887777654

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

>PRK04296 thymidine kinase; Provisional

Probab=98.38  E-value=4.2e-06  Score=65.67  Aligned_cols=94  Identities=17%  Similarity=0.185  Sum_probs=52.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC-CCcc-----------------hhHHHHHHHHHHhhhcccC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS-DDRG-----------------INVVRTKIKTFAAVAVGSG  145 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~-~~~~-----------------~~~~~~~~~~~~~~~~~~~  145 (294)
                      ..+++||+|+||||++..++.++...   +..++.+.+. +.+.                 .....+.+..+..      
T Consensus         4 i~litG~~GsGKTT~~l~~~~~~~~~---g~~v~i~k~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~------   74 (190)
T PRK04296          4 LEFIYGAMNSGKSTELLQRAYNYEER---GMKVLVFKPAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE------   74 (190)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHc---CCeEEEEeccccccccCCcEecCCCCcccceEeCChHHHHHHHHh------
Confidence            47899999999999999998887432   1222222211 0000                 0001111111111      


Q ss_pred             ccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecC
Q 022641          146 QRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       146 ~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                            ...+.++|+|||++.++.+....|.+.+..  ....+|+++..
T Consensus        75 ------~~~~~dvviIDEaq~l~~~~v~~l~~~l~~--~g~~vi~tgl~  115 (190)
T PRK04296         75 ------EGEKIDCVLIDEAQFLDKEQVVQLAEVLDD--LGIPVICYGLD  115 (190)
T ss_pred             ------hCCCCCEEEEEccccCCHHHHHHHHHHHHH--cCCeEEEEecC
Confidence                  113457999999999987655555555543  45556776643

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=98.38  E-value=2.2e-06  Score=74.34  Aligned_cols=111  Identities=22%  Similarity=0.328  Sum_probs=60.0

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHH-H-HHHHHHHhhhcc
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVV-R-TKIKTFAAVAVG  143 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~  143 (294)
                      |..+...+.+.+....+.++++.||.|||||++.+++...+...   +..+. +.++.......+ . ..+..+...+..
T Consensus         6 Q~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~~~---~~~~~-~~a~tg~AA~~i~~G~T~hs~f~i~~~   81 (364)
T PF05970_consen    6 QRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYLRSR---GKKVL-VTAPTGIAAFNIPGGRTIHSFFGIPIN   81 (364)
T ss_pred             HHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHhccc---cceEE-EecchHHHHHhccCCcchHHhcCcccc
Confidence            44555566666666666679999999999999999999887321   11122 222221111111 0 011111111111


Q ss_pred             cCc---------cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHH
Q 022641          144 SGQ---------RRGGYPCPPYKIIILDEADSMTEDAQNALRRTME  180 (294)
Q Consensus       144 ~~~---------~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~  180 (294)
                      ...         .........-++|||||+-+++......+-..+.
T Consensus        82 ~~~~~~~~~~~~~~~~~~l~~~~~lIiDEism~~~~~l~~i~~~lr  127 (364)
T PF05970_consen   82 NNEKSQCKISKNSRLRERLRKADVLIIDEISMVSADMLDAIDRRLR  127 (364)
T ss_pred             ccccccccccccchhhhhhhhheeeecccccchhHHHHHHHHHhhh
Confidence            000         0111123445799999999998887766544443

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>KOG0479 consensus DNA replication licensing factor, MCM3 component [Replication, recombination and repair]

Probab=98.37  E-value=4.8e-06  Score=73.46  Aligned_cols=156  Identities=14%  Similarity=0.141  Sum_probs=95.5

Q ss_pred             hhcccHHHHHHHHHHHHcCCC------------CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee--cCCCCcch
Q 022641           62 DVAHQEEVVRVLTNTLETANC------------PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL--NASDDRGI  127 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~~~~------------~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~--~~~~~~~~  127 (294)
                      .+.|++-+++.+.-.|-.|-.            =|++++|.|.+.||.|++.+.+.+..       -+..  .++++.+.
T Consensus       302 SI~GH~~vKkAillLLlGGvEk~L~NGshlRGDINiLlvGDPSvAKSQLLRyVLntApl-------AI~TTGRGSSGVGL  374 (818)
T KOG0479|consen  302 SIYGHDYVKKAILLLLLGGVEKNLENGSHLRGDINILLVGDPSVAKSQLLRYVLNTAPL-------AIATTGRGSSGVGL  374 (818)
T ss_pred             ccccHHHHHHHHHHHHhccceeccCCCceeccceeEEEecCchHHHHHHHHHHHhcccc-------cccccCCCCCCccc
Confidence            567999888888777644311            14999999999999999999887621       1111  11221111


Q ss_pred             hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh-------------hcCcceEEEEecC
Q 022641          128 NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMET-------------YSKVTRFFFICNY  194 (294)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~-------------~~~~~~ii~~~~~  194 (294)
                      ......-..    ........+....+.+++++|||+|+++....-.+..+|+.             ....++++.++|+
T Consensus       375 TAAVTtD~e----TGERRLEAGAMVLADRGVVCIDEFDKMsDiDRvAIHEVMEQqtVTIaKAGIHasLNARCSVlAAANP  450 (818)
T KOG0479|consen  375 TAAVTTDQE----TGERRLEAGAMVLADRGVVCIDEFDKMSDIDRVAIHEVMEQQTVTIAKAGIHASLNARCSVLAAANP  450 (818)
T ss_pred             eeEEeeccc----cchhhhhcCceEEccCceEEehhcccccchhHHHHHHHHhcceEEeEeccchhhhccceeeeeecCc
Confidence            100000000    00000112334556788999999999998888888888874             3456778888875


Q ss_pred             Cc-------------ccchHhhcccc--EEEecCCCHHHHHHHHHHHHH
Q 022641          195 IS-------------RIIEPLASRCA--KFRFKPLSEEVMSSRVLHICN  228 (294)
Q Consensus       195 ~~-------------~~~~~l~~r~~--~i~~~~~~~~~~~~~l~~~~~  228 (294)
                      ..             .+++.+++||.  .+-+...+...=..+-.++++
T Consensus       451 vyG~Yd~~k~P~eNIgLpDSLLSRFDLlFv~lD~~d~~~D~~iSeHVLR  499 (818)
T KOG0479|consen  451 VYGQYDQSKTPMENIGLPDSLLSRFDLLFVVLDDIDADIDRMISEHVLR  499 (818)
T ss_pred             cccccCCCCChhhccCCcHHHHhhhcEEEEEeccccchHHHHHHHHHHH
Confidence            42             27899999998  455555555444444444444

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

Probab=98.37  E-value=9e-05  Score=63.58  Aligned_cols=198  Identities=17%  Similarity=0.157  Sum_probs=126.3

Q ss_pred             HHHHHHcC-CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCC
Q 022641           73 LTNTLETA-NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGY  151 (294)
Q Consensus        73 l~~~l~~~-~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (294)
                      +...+..+ ..+-++++|+-=-=....+..+..... .+........... .   ...+...........          
T Consensus         6 ~~~~l~~~~~~~v~ll~G~d~~l~~e~~~~i~~~~~-~~~~~~~~~~~~~-~---~~~~~~~~~~~~s~~----------   70 (334)
T COG1466           6 LAKHLKKKNLMPVYLLYGEDEGLLEEAADAILKRAL-ADGFDENYSFFDD-S---ELDWADLLSELESPS----------   70 (334)
T ss_pred             HHHHHhcCCCccEEEEecCChhHHHHHHHHHHHHHh-ccchhhHHhhccc-c---cCCHHHHHHHhhccc----------
Confidence            34444444 334589999876555556666666552 1111111111111 1   111222222222221          


Q ss_pred             CCCCcEEEEEeCCCCCC-HHHHHHHHHHHHhhc-CcceEEEEecCCcc---cchHhhcc--ccEEEecCCCHHHHHHHHH
Q 022641          152 PCPPYKIIILDEADSMT-EDAQNALRRTMETYS-KVTRFFFICNYISR---IIEPLASR--CAKFRFKPLSEEVMSSRVL  224 (294)
Q Consensus       152 ~~~~~~lliiDei~~l~-~~~~~~L~~~l~~~~-~~~~ii~~~~~~~~---~~~~l~~r--~~~i~~~~~~~~~~~~~l~  224 (294)
                      ..+...+++|....... ......+.......+ ....+++.++....   ....+..-  ...+.+.|++..++..++.
T Consensus        71 lF~~~~~v~l~~~~~~~~~~~~~~l~~~~~~~p~~~~~l~~~~~kl~~~~~~~k~~~~~~~~~~~~~~~~~~~~l~~~i~  150 (334)
T COG1466          71 LFGEKRLVVLKNAEKKPNKDKNLALLELAALLPSTDLLLLVESNKLDKAKKLTKWLKKLAKAVVVECKPLDEAELPQWIK  150 (334)
T ss_pred             cccCCeeEEEECCCCCcCchhHHHHHHHHcCCCCCCEEEEEecCCcchHHHHHHHHHHhccCceEecCCCCHHHHHHHHH
Confidence            22334689999888765 444555555665555 44444444433322   21222221  4589999999999999999


Q ss_pred             HHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh-CCCCChhhhhhhcccccCCCC
Q 022641          225 HICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF-GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       225 ~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~-~~~it~~~v~~~~~~~~~~~~  285 (294)
                      ..++..|+.+++++++.++...+||...+.+.++..+.+. ++.||.++|..++......+.
T Consensus       151 ~~~~~~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~~~~~~~  212 (334)
T COG1466         151 KRAKELGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSDVAEFNI  212 (334)
T ss_pred             HHHHHcCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhccccCCH
Confidence            9999999999999999999999999999999999999988 348999999999988776654

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=98.32  E-value=6.6e-06  Score=75.24  Aligned_cols=118  Identities=19%  Similarity=0.247  Sum_probs=64.6

Q ss_pred             HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCcc-CCcceeecCCCCcchhHHHHHHHHHHh----------
Q 022641           71 RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELY-KSRVLELNASDDRGINVVRTKIKTFAA----------  139 (294)
Q Consensus        71 ~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~----------  139 (294)
                      ..+...+..   +..+|+|+|||||||++..+...+...... ...-+.+.+........+.+.+.....          
T Consensus       152 ~A~~~al~~---~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~~~~~l~~~~~~~~  228 (586)
T TIGR01447       152 VAVALALKS---NFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKAVKNLAAAEALIA  228 (586)
T ss_pred             HHHHHHhhC---CeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHhhhcccccchhhhh
Confidence            344444443   359999999999999999988776321110 111233444443333333333222100          


Q ss_pred             ----------hhcccCc-----cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecC
Q 022641          140 ----------VAVGSGQ-----RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       140 ----------~~~~~~~-----~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                                ...+...     ..........++|||||+.+++......|++.+   +....+|+++..
T Consensus       229 ~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMvd~~l~~~ll~al---~~~~rlIlvGD~  295 (586)
T TIGR01447       229 ALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMVDLPLMAKLLKAL---PPNTKLILLGDK  295 (586)
T ss_pred             ccccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccCCHHHHHHHHHhc---CCCCEEEEECCh
Confidence                      0000000     000011124579999999999988777776655   456778888743

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=98.32  E-value=5.8e-06  Score=77.68  Aligned_cols=120  Identities=19%  Similarity=0.180  Sum_probs=64.6

Q ss_pred             HHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHH-------HHHHHh
Q 022641           67 EEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTK-------IKTFAA  139 (294)
Q Consensus        67 ~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~  139 (294)
                      +.....+..+..   .+.++|+|+||||||++++++...+..... ... +.+.++.......+.+.       +..+..
T Consensus       326 ~~Q~~Ai~~~~~---~~~~iitGgpGTGKTt~l~~i~~~~~~~~~-~~~-v~l~ApTg~AA~~L~e~~g~~a~Tih~lL~  400 (720)
T TIGR01448       326 EEQKQALDTAIQ---HKVVILTGGPGTGKTTITRAIIELAEELGG-LLP-VGLAAPTGRAAKRLGEVTGLTASTIHRLLG  400 (720)
T ss_pred             HHHHHHHHHHHh---CCeEEEECCCCCCHHHHHHHHHHHHHHcCC-Cce-EEEEeCchHHHHHHHHhcCCccccHHHHhh
Confidence            344444444432   236999999999999999999887732210 022 22333332222222221       111111


Q ss_pred             hhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecC
Q 022641          140 VAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      .................++|||||+.+++......|+..+   +....+|+++..
T Consensus       401 ~~~~~~~~~~~~~~~~~~llIvDEaSMvd~~~~~~Ll~~~---~~~~rlilvGD~  452 (720)
T TIGR01448       401 YGPDTFRHNHLEDPIDCDLLIVDESSMMDTWLALSLLAAL---PDHARLLLVGDT  452 (720)
T ss_pred             ccCCccchhhhhccccCCEEEEeccccCCHHHHHHHHHhC---CCCCEEEEECcc
Confidence            1000000000011234679999999999988777777654   456778888743

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>PRK13695 putative NTPase; Provisional

Probab=98.32  E-value=1.1e-05  Score=62.55  Aligned_cols=70  Identities=16%  Similarity=0.261  Sum_probs=45.2

Q ss_pred             CcEEEEEeCCCCCC---HHHHHHHHHHHHhhcCcceEEEEecCCc--ccchHhhcccc--EEEecCCCHHHHHHHHHHHH
Q 022641          155 PYKIIILDEADSMT---EDAQNALRRTMETYSKVTRFFFICNYIS--RIIEPLASRCA--KFRFKPLSEEVMSSRVLHIC  227 (294)
Q Consensus       155 ~~~lliiDei~~l~---~~~~~~L~~~l~~~~~~~~ii~~~~~~~--~~~~~l~~r~~--~i~~~~~~~~~~~~~l~~~~  227 (294)
                      +.++|++||++.+.   ....+.+..+++   ....+|++++...  ...+++..+..  ++.+.+-+.+++...+.+..
T Consensus        96 ~~~~lllDE~~~~e~~~~~~~~~l~~~~~---~~~~~i~v~h~~~~~~~~~~i~~~~~~~i~~~~~~~r~~~~~~~~~~~  172 (174)
T PRK13695         96 EADVIIIDEIGKMELKSPKFVKAVEEVLD---SEKPVIATLHRRSVHPFVQEIKSRPGGRVYELTPENRDSLPFEILNRL  172 (174)
T ss_pred             CCCEEEEECCCcchhhhHHHHHHHHHHHh---CCCeEEEEECchhhHHHHHHHhccCCcEEEEEcchhhhhHHHHHHHHH
Confidence            56799999976553   334555666653   3456777887643  34556666554  78888888887777665543

>PRK04132 replication factor C small subunit; Provisional

Probab=98.31  E-value=6.7e-07  Score=84.01  Aligned_cols=51  Identities=49%  Similarity=0.999  Sum_probs=47.7

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHH
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTT   98 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~l   98 (294)
                      ..||.++|+|..|++++|++..+..|..++..+..++++|+||||+||+..
T Consensus         6 ~~~~~~k~RP~~f~dIiGqe~i~~~Lk~~i~~~~i~h~l~~g~~g~~~cl~   56 (846)
T PRK04132          6 EKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKCLT   56 (846)
T ss_pred             cccHHHhhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEECCCCCCcccc
Confidence            459999999999999999999999999999999999999999999999643

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.28  E-value=4.6e-05  Score=64.44  Aligned_cols=48  Identities=21%  Similarity=0.085  Sum_probs=39.2

Q ss_pred             EEEecCCCHHHHHHHHHHHHHHhCC---CCCHHHHHHHHhhccCcHHHHHH
Q 022641          208 KFRFKPLSEEVMSSRVLHICNEEGL---NLDAEALSTLSSISQGDLRRAIT  255 (294)
Q Consensus       208 ~i~~~~~~~~~~~~~l~~~~~~~~~---~~~~~~l~~l~~~~~G~~r~~~~  255 (294)
                      .+.+++++.+|.+.+++.+....-+   ..++...+.+.-.++||+|++.+
T Consensus       258 ~i~v~~~s~~E~~~ll~yy~~~~~l~~~~~~~~~~e~~~~~s~GNp~el~k  308 (309)
T PF10236_consen  258 PIEVPRLSKEEARSLLEYYADSGWLRSRVDEELVLEKLFLSSNGNPRELEK  308 (309)
T ss_pred             eEEeCCCCHHHHHHHHHHHHHCCccccCCCCHHHHHHHHHhcCCCHHHhcc
Confidence            7899999999999999988865443   24566778888888999998764

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).

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=98.28  E-value=7e-06  Score=78.38  Aligned_cols=193  Identities=11%  Similarity=0.006  Sum_probs=112.3

Q ss_pred             cccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc-CCCccCCcceeecCCCCcchhHHHHHHHHHHhhhc
Q 022641           64 AHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF-GPELYKSRVLELNASDDRGINVVRTKIKTFAAVAV  142 (294)
Q Consensus        64 ~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  142 (294)
                      +|++..++.+...+.......+-++|-.|+||||||+.+-+... -...++...+.+-..+........+.+..+.....
T Consensus       161 VG~e~~~~kl~~~L~~d~~~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~~~  240 (889)
T KOG4658|consen  161 VGLETMLEKLWNRLMEDDVGIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLLDE  240 (889)
T ss_pred             ccHHHHHHHHHHHhccCCCCEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccCCc
Confidence            99999999999999888777899999999999999999988774 22222222222211121122222222222211111


Q ss_pred             ccCcc--------CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEEecCC
Q 022641          143 GSGQR--------RGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPL  214 (294)
Q Consensus       143 ~~~~~--------~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~  214 (294)
                      .....        .......++-+|++||+..=.  .++.+...+-.......+++||+... +-.........+++.-+
T Consensus       241 ~~~~~~~~~~~~~i~~~L~~krfllvLDDIW~~~--dw~~I~~~~p~~~~g~KvvlTTRs~~-V~~~~m~~~~~~~v~~L  317 (889)
T KOG4658|consen  241 EWEDKEEDELASKLLNLLEGKRFLLVLDDIWEEV--DWDKIGVPFPSRENGSKVVLTTRSEE-VCGRAMGVDYPIEVECL  317 (889)
T ss_pred             ccchhhHHHHHHHHHHHhccCceEEEEecccccc--cHHhcCCCCCCccCCeEEEEEeccHh-hhhccccCCcccccccc
Confidence            11110        001223566799999996521  23333322222233467888886643 11222233456788888


Q ss_pred             CHHHHHHHHHHHHHHhCCC--C-CHHHHHHHHhhccCcHHHHHHHHHH
Q 022641          215 SEEVMSSRVLHICNEEGLN--L-DAEALSTLSSISQGDLRRAITYLQG  259 (294)
Q Consensus       215 ~~~~~~~~l~~~~~~~~~~--~-~~~~l~~l~~~~~G~~r~~~~~l~~  259 (294)
                      +.++.-+.+.+.+-.....  . -++....+++.|+|-|-.+..+-..
T Consensus       318 ~~~eaW~LF~~~v~~~~~~~~~~i~~lak~v~~kC~GLPLAl~viG~~  365 (889)
T KOG4658|consen  318 TPEEAWDLFQKKVGPNTLGSHPDIEELAKEVAEKCGGLPLALNVLGGL  365 (889)
T ss_pred             CccccHHHHHHhhccccccccccHHHHHHHHHHHhCChHHHHHHHHHH
Confidence            9999999998777433222  1 3667778888899977655544443

>COG3899 Predicted ATPase [General function prediction only]

Probab=98.27  E-value=2.2e-05  Score=75.00  Aligned_cols=107  Identities=15%  Similarity=0.120  Sum_probs=70.6

Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhhc--Cc--ceEEEEecCCcccchHhhc--cccEEEecCCCHHHHHHHHHHHH
Q 022641          154 PPYKIIILDEADSMTEDAQNALRRTMETYS--KV--TRFFFICNYISRIIEPLAS--RCAKFRFKPLSEEVMSSRVLHIC  227 (294)
Q Consensus       154 ~~~~lliiDei~~l~~~~~~~L~~~l~~~~--~~--~~ii~~~~~~~~~~~~l~~--r~~~i~~~~~~~~~~~~~l~~~~  227 (294)
                      .++-++|+||+|..++...+.|-.++....  ..  ..+..+.+..........+  ....|.+.|++..+...++...+
T Consensus       153 ~~plVi~leDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l  232 (849)
T COG3899         153 EHPLVIVLEDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATL  232 (849)
T ss_pred             cCCeEEEEecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHh
Confidence            347799999999999988888887777643  00  0111111111122222222  33489999999999999998877


Q ss_pred             HHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHH
Q 022641          228 NEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA  261 (294)
Q Consensus       228 ~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~  261 (294)
                      .. ....+.+..+.+.+.+.|||==+...++...
T Consensus       233 ~~-~~~~~~p~~~~i~~kt~GnPfFi~e~lk~l~  265 (849)
T COG3899         233 GC-TKLLPAPLLELIFEKTKGNPFFIEEFLKALY  265 (849)
T ss_pred             CC-cccccchHHHHHHHHhcCCCccHHHHHHHHH
Confidence            43 2456778889999999998765555555443

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=98.25  E-value=4.7e-06  Score=64.38  Aligned_cols=51  Identities=10%  Similarity=0.150  Sum_probs=36.1

Q ss_pred             CCcEEEEEeCCCCCCH---HHHHHHHHHHHhhcCcceEEEEecCCcccchHhhcccc
Q 022641          154 PPYKIIILDEADSMTE---DAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       154 ~~~~lliiDei~~l~~---~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      .+.++|||||+...-.   -..+.+.++++..+....+|+|++...   +++.....
T Consensus       114 ~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p---~~Lie~AD  167 (191)
T PRK05986        114 ESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAP---RELIEAAD  167 (191)
T ss_pred             CCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCC---HHHHHhCc
Confidence            5678999999865421   124567788888899999999997654   45555444

>PTZ00202 tuzin; Provisional

Probab=98.25  E-value=4.4e-05  Score=66.18  Aligned_cols=52  Identities=15%  Similarity=0.231  Sum_probs=43.4

Q ss_pred             cCCCcchhhcccHHHHHHHHHHHHcCC---CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           55 YRPKQVKDVAHQEEVVRVLTNTLETAN---CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        55 ~~~~~~~~~~g~~~~~~~l~~~l~~~~---~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..|....+++|++.....|...+....   .+.++|+|++|||||++++.+...+
T Consensus       256 ~lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l  310 (550)
T PTZ00202        256 SAPAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKE  310 (550)
T ss_pred             CCCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcC
Confidence            346678899999999999999886432   2358999999999999999999877

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=98.24  E-value=1.5e-05  Score=62.65  Aligned_cols=99  Identities=17%  Similarity=0.243  Sum_probs=65.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCC
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEA  164 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei  164 (294)
                      ++|.|+.|+|||+..+.|+...+..     .   +  ......+...    .+...                -++.+||+
T Consensus        55 lvl~G~QG~GKStf~~~L~~~~~~d-----~---~--~~~~~kd~~~----~l~~~----------------~iveldEl  104 (198)
T PF05272_consen   55 LVLVGKQGIGKSTFFRKLGPEYFSD-----S---I--NDFDDKDFLE----QLQGK----------------WIVELDEL  104 (198)
T ss_pred             eeEecCCcccHHHHHHHHhHHhccC-----c---c--ccCCCcHHHH----HHHHh----------------HheeHHHH
Confidence            8999999999999999997664211     1   1  1111122221    11111                28999999


Q ss_pred             CCCCHHHHHHHHHHHH---------------hhcCcceEEEEecCCcccch-HhhccccEEEecC
Q 022641          165 DSMTEDAQNALRRTME---------------TYSKVTRFFFICNYISRIIE-PLASRCAKFRFKP  213 (294)
Q Consensus       165 ~~l~~~~~~~L~~~l~---------------~~~~~~~ii~~~~~~~~~~~-~l~~r~~~i~~~~  213 (294)
                      +.+.....+.|...+.               ..+...++|.+||...-+.+ .--+|+..+.+..
T Consensus       105 ~~~~k~~~~~lK~~iT~~~~~~R~pY~~~~~~~~R~~~figTtN~~~~L~D~TGnRRf~~v~v~~  169 (198)
T PF05272_consen  105 DGLSKKDVEALKSFITRRTDTYRPPYGRDPEEFPRRAVFIGTTNDDDFLKDPTGNRRFWPVEVSK  169 (198)
T ss_pred             hhcchhhHHHHHHHhcccceeeecCCcCcceeeceeEEEEeccCCcceeeCCCCCeEEEEEEEcC
Confidence            9999888888888884               23355667888888765544 4556888777765

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=98.22  E-value=1.5e-05  Score=60.73  Aligned_cols=23  Identities=48%  Similarity=0.845  Sum_probs=21.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++|+||||+|||+++..++..+.
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~   24 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIA   24 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHH
Confidence            68999999999999999999873

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.

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=98.21  E-value=8.9e-05  Score=61.16  Aligned_cols=156  Identities=17%  Similarity=0.217  Sum_probs=91.3

Q ss_pred             HHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCC
Q 022641           72 VLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGY  151 (294)
Q Consensus        72 ~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (294)
                      .+.+.+...+ .|.+|+|.+|+||+++++..+.-.      +..++.+......+...+++.++........        
T Consensus        22 ri~RvL~~~~-Gh~LLvG~~GsGr~sl~rLaa~i~------~~~~~~i~~~~~y~~~~f~~dLk~~~~~ag~--------   86 (268)
T PF12780_consen   22 RISRVLSQPR-GHALLVGVGGSGRQSLARLAAFIC------GYEVFQIEITKGYSIKDFKEDLKKALQKAGI--------   86 (268)
T ss_dssp             HHHHHHCSTT-EEEEEECTTTSCHHHHHHHHHHHT------TEEEE-TTTSTTTHHHHHHHHHHHHHHHHHC--------
T ss_pred             HHHHHHcCCC-CCeEEecCCCccHHHHHHHHHHHh------ccceEEEEeeCCcCHHHHHHHHHHHHHHHhc--------
Confidence            4444454433 479999999999999999877665      6677777766665666666555554433221        


Q ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHHH------------------------------------------HhhcCcceEE
Q 022641          152 PCPPYKIIILDEADSMTEDAQNALRRTM------------------------------------------ETYSKVTRFF  189 (294)
Q Consensus       152 ~~~~~~lliiDei~~l~~~~~~~L~~~l------------------------------------------~~~~~~~~ii  189 (294)
                       .+++.+++++|-+-......+.+-.++                                          +....+..++
T Consensus        87 -~~~~~vfll~d~qi~~~~fLe~in~LL~sGeip~LF~~eE~~~i~~~l~~~~~~~~~~~~~~~~~~~F~~rvr~nLHiv  165 (268)
T PF12780_consen   87 -KGKPTVFLLTDSQIVDESFLEDINSLLSSGEIPNLFTKEELDNIISSLREEAKAEGISDSRESLYEFFIERVRKNLHIV  165 (268)
T ss_dssp             -S-S-EEEEEECCCSSSCHHHHHHHHHHHCSS-TTTS-TCHHHHHHHHHHHHHHHCT--SSHHHHHHHHHHHHCCCEEEE
T ss_pred             -cCCCeEEEecCcccchHhHHHHHHHHHhCCCCCCCccHHHHHHHHHHhHHHHHHcCCCCchHHHHHHHHHHHHhheeEE
Confidence             133458888887655332211111111                                          1223455677


Q ss_pred             EEecCCcc-------cchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHh
Q 022641          190 FICNYISR-------IIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSS  244 (294)
Q Consensus       190 ~~~~~~~~-------~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~  244 (294)
                      ++.++...       ..|++.++|.+.-+.+.+.+-+..+-.+.++.... ++++.-+.+++
T Consensus       166 l~~sp~~~~~r~~~~~fPaL~~~ctIdW~~~W~~eaL~~Va~~~l~~~~~-~~~~~~~~l~~  226 (268)
T PF12780_consen  166 LCMSPVGPNFRDRCRSFPALVNCCTIDWFDPWPEEALLSVANKFLSDIEL-LSEELKKSLAE  226 (268)
T ss_dssp             EEESTTTTCCCHHHHHHCCHHHHSEEEEEES--HHHHHHHHHHHCCHHHT-SS--HHHHHHH
T ss_pred             EEECCCCchHHHHHHhCcchhcccEEEeCCcCCHHHHHHHHHHHHHhhcc-cchhHHHHHHH
Confidence            66654322       35778888999999999999998888776654321 34444444443

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=98.19  E-value=4.4e-06  Score=59.71  Aligned_cols=53  Identities=26%  Similarity=0.364  Sum_probs=37.2

Q ss_pred             hhhcccHHHHHHHHHHH----HcCCCC-c--EEEECCCCCCHHHHHHHHHHHhcCCCccC
Q 022641           61 KDVAHQEEVVRVLTNTL----ETANCP-H--MLFYGPPGTGKTTTALAIAHQLFGPELYK  113 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l----~~~~~~-~--ill~Gp~G~GKT~la~~la~~~~~~~~~~  113 (294)
                      ..+.||.-+.+.+.+++    .+..++ .  +.|.|++|||||.+++.||+.++......
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~ly~~G~~S   84 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHLYKSGMKS   84 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHHHhcccCC
Confidence            46778876666555554    333221 1  66899999999999999999987544333

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

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=98.18  E-value=9.2e-06  Score=76.65  Aligned_cols=113  Identities=14%  Similarity=0.185  Sum_probs=63.7

Q ss_pred             HHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHH-------HHHHHh
Q 022641           67 EEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTK-------IKTFAA  139 (294)
Q Consensus        67 ~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~  139 (294)
                      +.....+...+...  +.++|+|+||||||++++++...+...   +..+..+. +.......+...       +..+..
T Consensus       355 ~~Q~~Av~~i~~s~--~~~il~G~aGTGKTtll~~i~~~~~~~---g~~V~~~A-pTg~Aa~~L~~~~g~~a~Ti~~~~~  428 (744)
T TIGR02768       355 EEQYEAVRHVTGSG--DIAVVVGRAGTGKSTMLKAAREAWEAA---GYRVIGAA-LSGKAAEGLQAESGIESRTLASLEY  428 (744)
T ss_pred             HHHHHHHHHHhcCC--CEEEEEecCCCCHHHHHHHHHHHHHhC---CCeEEEEe-CcHHHHHHHHhccCCceeeHHHHHh
Confidence            44445554444332  368999999999999999998776322   23333332 221111111110       011100


Q ss_pred             hhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEe
Q 022641          140 VAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFIC  192 (294)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~  192 (294)
                      .     .........+.++|||||+.+++......|+.....  ....+|+++
T Consensus       429 ~-----~~~~~~~~~~~~llIvDEasMv~~~~~~~Ll~~~~~--~~~kliLVG  474 (744)
T TIGR02768       429 A-----WANGRDLLSDKDVLVIDEAGMVGSRQMARVLKEAEE--AGAKVVLVG  474 (744)
T ss_pred             h-----hccCcccCCCCcEEEEECcccCCHHHHHHHHHHHHh--cCCEEEEEC
Confidence            0     011112234668999999999998887777765543  355677776

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=98.17  E-value=4e-05  Score=66.40  Aligned_cols=149  Identities=12%  Similarity=0.146  Sum_probs=72.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCC-ccCCcceeecCCCCc--chhHHHHHHHHHHhhhcccCcc-----CCCCCCC
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPE-LYKSRVLELNASDDR--GINVVRTKIKTFAAVAVGSGQR-----RGGYPCP  154 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~-~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~  154 (294)
                      ..++|+||+|+||||++..+|..+.... ..+..+..+.....+  ....+..... ....+......     .......
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~-~lgvpv~~~~~~~~l~~~L~~~~  253 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGD-IMGIPVKAIESFKDLKEEITQSK  253 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhh-cCCcceEeeCcHHHHHHHHHHhC
Confidence            4599999999999999999998773211 112233333332221  1111211111 11111111000     0001124


Q ss_pred             CcEEEEEeCCCCCCHH--HHHHHHHHHHhhcC--cceEEEEecCCcccchHhhccc-----cEEEecCCCHHHHHHHHHH
Q 022641          155 PYKIIILDEADSMTED--AQNALRRTMETYSK--VTRFFFICNYISRIIEPLASRC-----AKFRFKPLSEEVMSSRVLH  225 (294)
Q Consensus       155 ~~~lliiDei~~l~~~--~~~~L~~~l~~~~~--~~~ii~~~~~~~~~~~~l~~r~-----~~i~~~~~~~~~~~~~l~~  225 (294)
                      +.++|+||.+++.+.+  ....+..+++....  ...+++.++....-...+.+++     .-+-|..++.......+-.
T Consensus       254 ~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~~~~~~~~~~~~~~~~I~TKlDet~~~G~~l~  333 (388)
T PRK12723        254 DFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDVKEIFHQFSPFSYKTVIFTKLDETTCVGNLIS  333 (388)
T ss_pred             CCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHHHHHHHHhcCCCCCEEEEEeccCCCcchHHHH
Confidence            5789999999998643  34566666665432  2334444433322222333333     2455666665544444444


Q ss_pred             HHHHhCC
Q 022641          226 ICNEEGL  232 (294)
Q Consensus       226 ~~~~~~~  232 (294)
                      ++...++
T Consensus       334 ~~~~~~~  340 (388)
T PRK12723        334 LIYEMRK  340 (388)
T ss_pred             HHHHHCC
Confidence            4444433

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=98.17  E-value=3e-06  Score=75.70  Aligned_cols=94  Identities=13%  Similarity=0.217  Sum_probs=60.0

Q ss_pred             cCCCCCcccCCCCcccCCCCchHHHHhhccccccCCc-----------hhh--hhcCCCcchhhcccHHHHHHHHHHHH-
Q 022641           13 KNKSPNFTQKFSTTQSSPEKSEDEVKRKMAPVLQSSQ-----------PWV--EKYRPKQVKDVAHQEEVVRVLTNTLE-   78 (294)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~--~~~~~~~~~~~~g~~~~~~~l~~~l~-   78 (294)
                      ....+++.+++....+.|......-+|-+.-+.....           .+.  ..-+...|+++.|.++.+..+...+. 
T Consensus        15 ~~~~~sl~eyL~~vk~~p~~~~~A~~R~~~~Ig~~~vv~~~~~~~~~rif~~~~i~ry~fF~d~yGlee~ieriv~~l~~   94 (644)
T PRK15455         15 KEEEFSLQEYLELCKQDPSAYANAAERLLMAIGEPEMVDTAKDPRLSRIFSNRVIKRYPAFEEFYGMEEAIEQIVSYFRH   94 (644)
T ss_pred             hcccccHHHHHHHHhcChHHHhhHHHHHHHHhCCceeeecCccchhhhhhcccccccccchhcccCcHHHHHHHHHHHHH
Confidence            4555677777666555555444444444332211110           011  01223356789999999998888772 


Q ss_pred             -----cCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           79 -----TANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        79 -----~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                           ....+.++|+||||+|||+|++.|++.+
T Consensus        95 Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~l  127 (644)
T PRK15455         95 AAQGLEEKKQILYLLGPVGGGKSSLAERLKSLM  127 (644)
T ss_pred             HHHhcCCCCceEEEecCCCCCchHHHHHHHHHH
Confidence                 2344569999999999999999999987

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=98.16  E-value=1.9e-05  Score=74.21  Aligned_cols=194  Identities=18%  Similarity=0.161  Sum_probs=120.9

Q ss_pred             chhhccc-HHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCC----ccCCcceeecCCC----CcchhHH
Q 022641           60 VKDVAHQ-EEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE----LYKSRVLELNASD----DRGINVV  130 (294)
Q Consensus        60 ~~~~~g~-~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~----~~~~~~~~~~~~~----~~~~~~~  130 (294)
                      ..-++|+ +..++.+.+.+......|-+|+|.||+|||.++..+++....-+    .....++.++...    ......+
T Consensus       185 ldPvigr~deeirRvi~iL~Rrtk~NPvLVG~~gvgktaiv~gla~ri~~G~vp~~l~~~~l~~l~~g~l~aGa~~rge~  264 (898)
T KOG1051|consen  185 LDPVIGRHDEEIRRVIEILSRKTKNNPVLVGEPGVGKTAIVEGLAQRIATGDVPETLKDKKLIALDFGSLVAGAKRRGEF  264 (898)
T ss_pred             CCCccCCchHHHHHHHHHHhccCCCCceEEecCCCCchhHHHHHHHHhhcCCCCccccccceEEEEhhhcccCcccchHH
Confidence            3456677 78888888888888878999999999999999999999874221    1223334343321    1223344


Q ss_pred             HHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------HHHHHHHHHHHhhcCcceEEEEecCC-----cc
Q 022641          131 RTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------DAQNALRRTMETYSKVTRFFFICNYI-----SR  197 (294)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------~~~~~L~~~l~~~~~~~~ii~~~~~~-----~~  197 (294)
                      ...+..+......         .+..-||+|||++.+..        ...+.|...+...  ...+|.+|...     ..
T Consensus       265 E~rlk~l~k~v~~---------~~~gvILfigelh~lvg~g~~~~~~d~~nlLkp~L~rg--~l~~IGatT~e~Y~k~ie  333 (898)
T KOG1051|consen  265 EERLKELLKEVES---------GGGGVILFLGELHWLVGSGSNYGAIDAANLLKPLLARG--GLWCIGATTLETYRKCIE  333 (898)
T ss_pred             HHHHHHHHHHHhc---------CCCcEEEEecceeeeecCCCcchHHHHHHhhHHHHhcC--CeEEEecccHHHHHHHHh
Confidence            4455554433221         12345999999998732        2345555555432  26677666422     12


Q ss_pred             cchHhhccccEEEecCCCHHHHHHHHHHHHHH----hCCCCCHHHHHHHHhhc------cCcHHHHHHHHHHHHHHh
Q 022641          198 IIEPLASRCAKFRFKPLSEEVMSSRVLHICNE----EGLNLDAEALSTLSSIS------QGDLRRAITYLQGAARLF  264 (294)
Q Consensus       198 ~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~----~~~~~~~~~l~~l~~~~------~G~~r~~~~~l~~~~~~~  264 (294)
                      -++++-+||..+.++-|+.++...++......    +|..+++..+...+..+      ..-+..++.+.+.++...
T Consensus       334 kdPalErrw~l~~v~~pS~~~~~~iL~~l~~~~e~~hg~~~s~~a~~~a~~~s~~~~t~r~lpd~aidl~dEa~a~~  410 (898)
T KOG1051|consen  334 KDPALERRWQLVLVPIPSVENLSLILPGLSERYEVHHGVRISDESLFSAAQLSARYITLSFLPDCAIDLEDEAAALV  410 (898)
T ss_pred             hCcchhhCcceeEeccCcccchhhhhhhhhhhhccccCCcccccccccccchhhhhcccCcCchhcccHHHHHHHHH
Confidence            46889999999989889888777677665554    45556555544433322      334566666666665443

>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=98.15  E-value=2e-06  Score=62.27  Aligned_cols=22  Identities=45%  Similarity=0.881  Sum_probs=21.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+||||+||||+++.|++.+
T Consensus         2 I~I~G~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERL   23 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7899999999999999999998

...

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=98.15  E-value=2.2e-05  Score=59.81  Aligned_cols=51  Identities=10%  Similarity=0.121  Sum_probs=35.7

Q ss_pred             CCcEEEEEeCCCCCCH---HHHHHHHHHHHhhcCcceEEEEecCCcccchHhhcccc
Q 022641          154 PPYKIIILDEADSMTE---DAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       154 ~~~~lliiDei~~l~~---~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      ...++|||||+...-.   -..+.+.++++..+....+|+|++...   +.+.....
T Consensus        96 ~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p---~~l~e~AD  149 (173)
T TIGR00708        96 PELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCP---QDLLELAD  149 (173)
T ss_pred             CCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCC---HHHHHhCc
Confidence            4678999999863211   123457788888999999999997654   55555554

Alternate name: corrinoid adenosyltransferase.

>PRK14532 adenylate kinase; Provisional

Probab=98.15  E-value=0.00012  Score=57.50  Aligned_cols=23  Identities=30%  Similarity=0.732  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++|.||||+||||+++.+++.+
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~   24 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEER   24 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999987

>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=98.14  E-value=8e-06  Score=64.19  Aligned_cols=36  Identities=17%  Similarity=0.317  Sum_probs=21.7

Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecC
Q 022641          156 YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       156 ~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      ..+||+||++.+++.....+   +-.....+.+|++++.
T Consensus       120 ~~~iIvDEaQN~t~~~~k~i---lTR~g~~skii~~GD~  155 (205)
T PF02562_consen  120 NAFIIVDEAQNLTPEELKMI---LTRIGEGSKIIITGDP  155 (205)
T ss_dssp             SEEEEE-SGGG--HHHHHHH---HTTB-TT-EEEEEE--
T ss_pred             ceEEEEecccCCCHHHHHHH---HcccCCCcEEEEecCc
Confidence            47999999999987765544   4445567788888754

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=98.13  E-value=1.2e-05  Score=69.53  Aligned_cols=23  Identities=48%  Similarity=0.676  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++.|.||||||.+|..++..+
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHh
Confidence            48999999999999999999998

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK08118 topology modulation protein; Reviewed

Probab=98.13  E-value=3.8e-05  Score=58.94  Aligned_cols=23  Identities=30%  Similarity=0.615  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|+||||+||||+|+.|++.+
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l   25 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKL   25 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999998

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=98.11  E-value=3e-06  Score=61.68  Aligned_cols=33  Identities=36%  Similarity=0.588  Sum_probs=27.4

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL  119 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~  119 (294)
                      ..|||+++|.|||||||++..+|...      +..++.+
T Consensus         6 ~~PNILvtGTPG~GKstl~~~lae~~------~~~~i~i   38 (176)
T KOG3347|consen    6 ERPNILVTGTPGTGKSTLAERLAEKT------GLEYIEI   38 (176)
T ss_pred             cCCCEEEeCCCCCCchhHHHHHHHHh------CCceEeh
Confidence            45799999999999999999999876      5555544

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=98.10  E-value=4.2e-05  Score=67.41  Aligned_cols=147  Identities=20%  Similarity=0.180  Sum_probs=72.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc-CCCccCCcceeecCCCCcchhHHHHHHHHHHh---hhcccCccCC-----CCCC
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF-GPELYKSRVLELNASDDRGINVVRTKIKTFAA---VAVGSGQRRG-----GYPC  153 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~-----~~~~  153 (294)
                      ..++|+||+|+||||++..|+..+. ...  +..+..++....+... . ..+..+..   .+........     ....
T Consensus       222 ~~i~~vGptGvGKTTt~~kLA~~~~~~~~--g~~V~li~~D~~r~~a-~-eqL~~~a~~~~vp~~~~~~~~~l~~~l~~~  297 (424)
T PRK05703        222 GVVALVGPTGVGKTTTLAKLAARYALLYG--KKKVALITLDTYRIGA-V-EQLKTYAKIMGIPVEVVYDPKELAKALEQL  297 (424)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHhcC--CCeEEEEECCccHHHH-H-HHHHHHHHHhCCceEccCCHHhHHHHHHHh
Confidence            3589999999999999999988773 121  2233334433322111 0 11111111   1100000000     0012


Q ss_pred             CCcEEEEEeCCCCCC--HHHHHHHHHHHHh-h-cCcceEEEEecCCcccchHhhcccc-----EEEecCCCHHHHHHHHH
Q 022641          154 PPYKIIILDEADSMT--EDAQNALRRTMET-Y-SKVTRFFFICNYISRIIEPLASRCA-----KFRFKPLSEEVMSSRVL  224 (294)
Q Consensus       154 ~~~~lliiDei~~l~--~~~~~~L~~~l~~-~-~~~~~ii~~~~~~~~~~~~l~~r~~-----~i~~~~~~~~~~~~~l~  224 (294)
                      ...++|+||..++.+  ....+.|..+++. . +....+++.++.......++..+|.     .+-+..++......-+.
T Consensus       298 ~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~~~~~~f~~~~~~~vI~TKlDet~~~G~i~  377 (424)
T PRK05703        298 RDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLKDIYKHFSRLPLDGLIFTKLDETSSLGSIL  377 (424)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHHHHHHHhCCCCCCEEEEecccccccccHHH
Confidence            346899999998764  4456667777762 1 2234455555544333344444432     34455555444333344


Q ss_pred             HHHHHhCCC
Q 022641          225 HICNEEGLN  233 (294)
Q Consensus       225 ~~~~~~~~~  233 (294)
                      .++...+++
T Consensus       378 ~~~~~~~lP  386 (424)
T PRK05703        378 SLLIESGLP  386 (424)
T ss_pred             HHHHHHCCC
Confidence            444444443

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=98.10  E-value=3.8e-05  Score=63.41  Aligned_cols=29  Identities=31%  Similarity=0.407  Sum_probs=25.0

Q ss_pred             HcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           78 ETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        78 ~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+...+++|.||+|+||||+++.++..+
T Consensus       107 ~~~~~~~~~i~g~~g~GKttl~~~l~~~~  135 (270)
T TIGR02858       107 RNNRVLNTLIISPPQCGKTTLLRDLARIL  135 (270)
T ss_pred             hCCCeeEEEEEcCCCCCHHHHHHHHhCcc
Confidence            34444689999999999999999999887

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.

>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=98.09  E-value=8.6e-06  Score=60.79  Aligned_cols=22  Identities=45%  Similarity=0.912  Sum_probs=20.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++||||+||||+++.+++.+
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~   23 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRL   23 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHC
Confidence            6899999999999999999887

...

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=98.09  E-value=6.8e-05  Score=64.24  Aligned_cols=135  Identities=14%  Similarity=0.163  Sum_probs=71.8

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhc-CCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCC-----CCCCCC
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQLF-GPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRG-----GYPCPP  155 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~  155 (294)
                      ...+.|+||.|+||||++.-||..+. ........++.++.-..-....+. .....+..+......+.     ......
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk-~Ya~im~vp~~vv~~~~el~~ai~~l~~  281 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLK-TYADIMGVPLEVVYSPKELAEAIEALRD  281 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHH-HHHHHhCCceEEecCHHHHHHHHHHhhc
Confidence            45699999999999999999988874 222223333333322221111111 11111222111111100     011234


Q ss_pred             cEEEEEeCCCCCC--HHHHHHHHHHHHhh-cCcceEEEEecCCcccchHhhcccc-----EEEecCCCHH
Q 022641          156 YKIIILDEADSMT--EDAQNALRRTMETY-SKVTRFFFICNYISRIIEPLASRCA-----KFRFKPLSEE  217 (294)
Q Consensus       156 ~~lliiDei~~l~--~~~~~~L~~~l~~~-~~~~~ii~~~~~~~~~~~~l~~r~~-----~i~~~~~~~~  217 (294)
                      .++|++|=+++-.  ......|..+++.. +....+++.++....-..++..+|.     -+-|..+++.
T Consensus       282 ~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei~~~f~~~~i~~~I~TKlDET  351 (407)
T COG1419         282 CDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIKQFSLFPIDGLIFTKLDET  351 (407)
T ss_pred             CCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecCcchHHHHHHHHHhccCCcceeEEEccccc
Confidence            5799999998753  45566677776654 3345566666666555666666554     3444455543

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.08  E-value=2e-05  Score=58.07  Aligned_cols=24  Identities=38%  Similarity=0.574  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++++.||+|+|||+++..++..+.
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~   25 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELL   25 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHH
Confidence            689999999999999999888874

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=98.08  E-value=1.8e-05  Score=61.50  Aligned_cols=43  Identities=35%  Similarity=0.505  Sum_probs=35.6

Q ss_pred             ccHHHHHHHHHHHHcC-CCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           65 HQEEVVRVLTNTLETA-NCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        65 g~~~~~~~l~~~l~~~-~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .|..++..+.+.+... ..++++|.+|+|+|||.++..++.++.
T Consensus         7 ~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~   50 (184)
T PF04851_consen    7 YQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELA   50 (184)
T ss_dssp             HHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhccc
Confidence            4677778888888776 556899999999999999998777773

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>PRK14974 cell division protein FtsY; Provisional

Probab=98.07  E-value=3.6e-05  Score=65.49  Aligned_cols=24  Identities=46%  Similarity=0.530  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+||+|+||||++..++..+.
T Consensus       142 vi~~~G~~GvGKTTtiakLA~~l~  165 (336)
T PRK14974        142 VIVFVGVNGTGKTTTIAKLAYYLK  165 (336)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999998773

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

Probab=98.07  E-value=1.4e-05  Score=65.25  Aligned_cols=29  Identities=31%  Similarity=0.392  Sum_probs=24.8

Q ss_pred             CCCCcEEEECCCCCCHHHHHHHHHHHhcC
Q 022641           80 ANCPHMLFYGPPGTGKTTTALAIAHQLFG  108 (294)
Q Consensus        80 ~~~~~ill~Gp~G~GKT~la~~la~~~~~  108 (294)
                      +.+..++|+||+|+|||++++.+++.+..
T Consensus        14 ~~Gqr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          14 GKGQRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhcccc
Confidence            44557999999999999999999988743

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.

>PRK07261 topology modulation protein; Provisional

Probab=98.06  E-value=2.6e-05  Score=60.16  Aligned_cols=23  Identities=26%  Similarity=0.476  Sum_probs=21.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|+||+||||+++.++..+
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~   24 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHY   24 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999876

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=98.05  E-value=2.2e-05  Score=67.43  Aligned_cols=24  Identities=38%  Similarity=0.559  Sum_probs=22.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+||+|+||||++..|+..+
T Consensus       138 ~ii~lvGptGvGKTTtiakLA~~~  161 (374)
T PRK14722        138 GVFALMGPTGVGKTTTTAKLAARC  161 (374)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHH
Confidence            469999999999999999999886

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=98.05  E-value=7.6e-05  Score=58.24  Aligned_cols=22  Identities=32%  Similarity=0.632  Sum_probs=21.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+||||+||||+++.+++.+
T Consensus         2 i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7899999999999999999987

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.

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=98.04  E-value=3.3e-05  Score=60.73  Aligned_cols=34  Identities=38%  Similarity=0.464  Sum_probs=27.4

Q ss_pred             HHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           73 LTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        73 l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +...+......|.++.|||||||||+++-+++-+
T Consensus       128 li~~ly~~g~lntLiigpP~~GKTTlLRdiaR~~  161 (308)
T COG3854         128 LIKDLYQNGWLNTLIIGPPQVGKTTLLRDIARLL  161 (308)
T ss_pred             HHHHHHhcCceeeEEecCCCCChHHHHHHHHHHh
Confidence            3444445555679999999999999999999987

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=98.02  E-value=4.1e-05  Score=73.66  Aligned_cols=114  Identities=13%  Similarity=0.136  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHH-------HHHHHHHh
Q 022641           67 EEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVR-------TKIKTFAA  139 (294)
Q Consensus        67 ~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~  139 (294)
                      +.....+..++....  .++|+|++||||||+++.+...+...   +..++.+.++. .....+.       ..+..+..
T Consensus       349 ~eQr~Av~~il~s~~--v~vv~G~AGTGKTT~l~~~~~~~e~~---G~~V~~~ApTG-kAA~~L~e~tGi~a~TI~sll~  422 (988)
T PRK13889        349 GEQADALAHVTDGRD--LGVVVGYAGTGKSAMLGVAREAWEAA---GYEVRGAALSG-IAAENLEGGSGIASRTIASLEH  422 (988)
T ss_pred             HHHHHHHHHHhcCCC--eEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEecCcH-HHHHHHhhccCcchhhHHHHHh
Confidence            344444444443322  57899999999999998876655211   23333332211 1111111       01111110


Q ss_pred             hhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEec
Q 022641          140 VAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                         .  ...+.......++|||||+.+++......|++....  ....+|+++.
T Consensus       423 ---~--~~~~~~~l~~~~vlIVDEASMv~~~~m~~LL~~a~~--~garvVLVGD  469 (988)
T PRK13889        423 ---G--WGQGRDLLTSRDVLVIDEAGMVGTRQLERVLSHAAD--AGAKVVLVGD  469 (988)
T ss_pred             ---h--hcccccccccCcEEEEECcccCCHHHHHHHHHhhhh--CCCEEEEECC
Confidence               0  001112234567999999999998888888776654  4566777774

>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=98.02  E-value=8.6e-06  Score=64.08  Aligned_cols=146  Identities=16%  Similarity=0.230  Sum_probs=68.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCC-----------CCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRG-----------GYP  152 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~  152 (294)
                      .++|+||+|+||||++--+|..+... .....++..+....-..+.++..... ...+........           ...
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~-~~~v~lis~D~~R~ga~eQL~~~a~~-l~vp~~~~~~~~~~~~~~~~~l~~~~   80 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLK-GKKVALISADTYRIGAVEQLKTYAEI-LGVPFYVARTESDPAEIAREALEKFR   80 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEESTSSTHHHHHHHHHHHH-HTEEEEESSTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhc-cccceeecCCCCCccHHHHHHHHHHH-hccccchhhcchhhHHHHHHHHHHHh
Confidence            48999999999999999999988533 22333333332222222223222221 111110000000           001


Q ss_pred             CCCcEEEEEeCCCCCCH--HHHHHHHHHHHhhcC-cceEEEEecCCcccchHhhc---cc--cEEEecCCCHHHHHHHHH
Q 022641          153 CPPYKIIILDEADSMTE--DAQNALRRTMETYSK-VTRFFFICNYISRIIEPLAS---RC--AKFRFKPLSEEVMSSRVL  224 (294)
Q Consensus       153 ~~~~~lliiDei~~l~~--~~~~~L~~~l~~~~~-~~~ii~~~~~~~~~~~~l~~---r~--~~i~~~~~~~~~~~~~l~  224 (294)
                      ..+.++|+||-.++.+.  .....|.++++.... ...+++.++........+..   .+  .-+-+..+++.....-+-
T Consensus        81 ~~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~~~~~~~~~~~lIlTKlDet~~~G~~l  160 (196)
T PF00448_consen   81 KKGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQALAFYEAFGIDGLILTKLDETARLGALL  160 (196)
T ss_dssp             HTTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHHHHHHHHSSTCEEEEESTTSSSTTHHHH
T ss_pred             hcCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHHHHHHHHHhhcccCceEEEEeecCCCCcccce
Confidence            12357999999988763  445666666665433 34444444433322222222   22  244555665543333333


Q ss_pred             HHHHHhC
Q 022641          225 HICNEEG  231 (294)
Q Consensus       225 ~~~~~~~  231 (294)
                      ..+...+
T Consensus       161 ~~~~~~~  167 (196)
T PF00448_consen  161 SLAYESG  167 (196)
T ss_dssp             HHHHHHT
T ss_pred             eHHHHhC
Confidence            3333333

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 ....

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=98.00  E-value=5.3e-05  Score=73.36  Aligned_cols=104  Identities=14%  Similarity=0.161  Sum_probs=60.6

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHH----HHHhhhcccCccCCCCCCCCcE
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK----TFAAVAVGSGQRRGGYPCPPYK  157 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~  157 (294)
                      .+..+|.|++||||||+++.+...+...   +..++.+.++ ......+.+...    .+.......  ..+........
T Consensus       397 ~r~~~v~G~AGTGKTt~l~~~~~~~e~~---G~~V~g~ApT-gkAA~~L~e~~Gi~a~TIas~ll~~--~~~~~~l~~~~  470 (1102)
T PRK13826        397 ARIAAVVGRAGAGKTTMMKAAREAWEAA---GYRVVGGALA-GKAAEGLEKEAGIQSRTLSSWELRW--NQGRDQLDNKT  470 (1102)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEEcCc-HHHHHHHHHhhCCCeeeHHHHHhhh--ccCccCCCCCc
Confidence            3468999999999999999998765221   3344433222 111122211100    000000000  01112344567


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEec
Q 022641          158 IIILDEADSMTEDAQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       158 lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      +|||||+.+++......|++....  ....+|+++.
T Consensus       471 vlVIDEAsMv~~~~m~~Ll~~~~~--~garvVLVGD  504 (1102)
T PRK13826        471 VFVLDEAGMVASRQMALFVEAVTR--AGAKLVLVGD  504 (1102)
T ss_pred             EEEEECcccCCHHHHHHHHHHHHh--cCCEEEEECC
Confidence            999999999999988888887764  4566777774

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.98  E-value=6.5e-05  Score=66.98  Aligned_cols=24  Identities=38%  Similarity=0.624  Sum_probs=21.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|+||+|+||||++..|+..+
T Consensus       351 ~vIaLVGPtGvGKTTtaakLAa~l  374 (559)
T PRK12727        351 GVIALVGPTGAGKTTTIAKLAQRF  374 (559)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            459999999999999999999876

>PRK14528 adenylate kinase; Provisional

Probab=97.98  E-value=0.00028  Score=55.19  Aligned_cols=24  Identities=42%  Similarity=0.855  Sum_probs=22.0

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++++.||||+||||+++.+++.+
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~~   25 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCERL   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            358999999999999999999887

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=97.97  E-value=8.4e-05  Score=60.82  Aligned_cols=160  Identities=21%  Similarity=0.186  Sum_probs=94.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchh----------------HHHHHHHHHHhhhcccCcc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGIN----------------VVRTKIKTFAAVAVGSGQR  147 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~~~  147 (294)
                      ...++|-+|.|||+.++.++...       ...+....+...+..                .+...+.......      
T Consensus        96 l~~vyg~~g~gKt~a~~~y~~s~-------p~~~l~~~~p~~~a~~~i~~i~~~~~~~~~~~~~d~~~~~~~~l------  162 (297)
T COG2842          96 LVVVYGYAGLGKTQAAKNYAPSN-------PNALLIEADPSYTALVLILIICAAAFGATDGTINDLTERLMIRL------  162 (297)
T ss_pred             eEEEeccccchhHHHHHhhcccC-------ccceeecCChhhHHHHHHHHHHHHHhcccchhHHHHHHHHHHHH------
Confidence            58999999999999999998764       222223222221111                1111111111111      


Q ss_pred             CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCC--------cccchHhhcccc---EEEecCCCH
Q 022641          148 RGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYI--------SRIIEPLASRCA---KFRFKPLSE  216 (294)
Q Consensus       148 ~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~--------~~~~~~l~~r~~---~i~~~~~~~  216 (294)
                           ....++|++||++.|+...++.|....++..-.  +++++++.        ....-.+.+|..   .+...-++.
T Consensus       163 -----~~~~~~iivDEA~~L~~~ale~lr~i~d~~Gi~--~vLvG~prL~~~l~~~~~~~~rl~srv~v~~~~~~~~~d~  235 (297)
T COG2842         163 -----RDTVRLIIVDEADRLPYRALEELRRIHDKTGIG--VVLVGMPRLFKVLRRPEDELSRLYSRVRVGKLLGEKFPDA  235 (297)
T ss_pred             -----ccCcceeeeehhhccChHHHHHHHHHHHhhCce--EEEecChHHHhccccchHHHHHHHHHhhhHhhhhhhhhhh
Confidence                 234569999999999999999999998874433  44444332        111222333322   122122332


Q ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCC
Q 022641          217 EVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS  267 (294)
Q Consensus       217 ~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~  267 (294)
                      .+...+....+    ...++..+..+...++|++|.+-..+..+..++...
T Consensus       236 d~~~~~~~~~l----~~~~~~~v~~~~~~~~g~~~~L~~~l~~~~~~a~~~  282 (297)
T COG2842         236 DELAEIAALVL----PTEDELVLMQVIKETEGNIRRLDKILAGAVGTARSN  282 (297)
T ss_pred             HHHHHHHHhhC----ccchHHHHHHHHHhcchhHhHHHHHHhhhhhhhhhc
Confidence            44444433222    225777888888889999999999888887776433

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=97.96  E-value=0.00024  Score=54.37  Aligned_cols=57  Identities=11%  Similarity=0.218  Sum_probs=40.2

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEE
Q 022641          154 PPYKIIILDEA-DSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFR  210 (294)
Q Consensus       154 ~~~~lliiDei-~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~  210 (294)
                      .++.+|+=||- +.+++.....+++++++.......++.+.+...+...+..|+..++
T Consensus       154 ~~P~vLlADEPTGNLDp~~s~~im~lfeeinr~GtTVl~ATHd~~lv~~~~~rvl~l~  211 (223)
T COG2884         154 NQPAVLLADEPTGNLDPDLSWEIMRLFEEINRLGTTVLMATHDLELVNRMRHRVLALE  211 (223)
T ss_pred             cCCCeEeecCCCCCCChHHHHHHHHHHHHHhhcCcEEEEEeccHHHHHhccCcEEEEe
Confidence            56789999996 5788988888999998877655544444454555566666665544

>PF13245 AAA_19: Part of AAA domain

Probab=97.94  E-value=1.6e-05  Score=52.21  Aligned_cols=25  Identities=52%  Similarity=0.792  Sum_probs=18.9

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      +.+++.||||+|||+++..+...+.
T Consensus        11 ~~~vv~g~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen   11 PLFVVQGPPGTGKTTTLAARIAELL   35 (76)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHH
Confidence            3477799999999977666666653

>TIGR00767 rho transcription termination factor Rho

Probab=97.92  E-value=2.6e-05  Score=67.15  Aligned_cols=28  Identities=29%  Similarity=0.372  Sum_probs=24.3

Q ss_pred             CCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           80 ANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        80 ~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      +.++.++|+||+|+|||++++.+++...
T Consensus       166 g~Gq~~~IvG~~g~GKTtL~~~i~~~I~  193 (415)
T TIGR00767       166 GKGQRGLIVAPPKAGKTVLLQKIAQAIT  193 (415)
T ss_pred             CCCCEEEEECCCCCChhHHHHHHHHhhc
Confidence            4555699999999999999999999874

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

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=97.92  E-value=0.00017  Score=55.20  Aligned_cols=110  Identities=15%  Similarity=0.196  Sum_probs=56.6

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhh--hcccCccC----CCCCCCC
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAV--AVGSGQRR----GGYPCPP  155 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~----~~~~~~~  155 (294)
                      ...+.|.||+|+|||||++.++......   . .-+.++..+...... ..........  ..+.+.+.    ......+
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~i~G~~~~~---~-G~v~~~g~~~~~~~~-~~~~~~~i~~~~qLS~G~~qrl~laral~~~  100 (163)
T cd03216          26 GEVHALLGENGAGKSTLMKILSGLYKPD---S-GEILVDGKEVSFASP-RDARRAGIAMVYQLSVGERQMVEIARALARN  100 (163)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCCC---C-eEEEECCEECCcCCH-HHHHhcCeEEEEecCHHHHHHHHHHHHHhcC
Confidence            3469999999999999999998765211   1 112222211110000 0000000000  00000000    0011234


Q ss_pred             cEEEEEeCCC-CCCHHHHHHHHHHHHhhc-CcceEEEEecCCc
Q 022641          156 YKIIILDEAD-SMTEDAQNALRRTMETYS-KVTRFFFICNYIS  196 (294)
Q Consensus       156 ~~lliiDei~-~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~~  196 (294)
                      +.++++||.- .++......+.+.+.... ....+|+++.+..
T Consensus       101 p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~  143 (163)
T cd03216         101 ARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLD  143 (163)
T ss_pred             CCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence            5699999965 678888888888887653 3455677776543

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.91  E-value=0.00011  Score=56.85  Aligned_cols=24  Identities=42%  Similarity=0.610  Sum_probs=22.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      -++|+|+||+||||+++.+++.+.
T Consensus         3 LiIlTGyPgsGKTtfakeLak~L~   26 (261)
T COG4088           3 LIILTGYPGSGKTTFAKELAKELR   26 (261)
T ss_pred             eEEEecCCCCCchHHHHHHHHHHH
Confidence            489999999999999999999984

>PF08303 tRNA_lig_kinase: tRNA ligase kinase domain; InterPro: IPR015966 This entry represents a kinase domain found in fungal tRNA ligases []

Probab=97.91  E-value=0.001  Score=49.84  Aligned_cols=124  Identities=14%  Similarity=0.165  Sum_probs=68.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc---hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEE
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG---INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIIL  161 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llii  161 (294)
                      ++=++.+||||||++.+|.+.+      +. +-.+...+..+   ...+...+..+..              ....++|.
T Consensus         2 lvPIAtiGCGKTTva~aL~~LF------g~-wgHvQnDnI~~k~~~~f~~~~l~~L~~--------------~~~~vVia   60 (168)
T PF08303_consen    2 LVPIATIGCGKTTVALALSNLF------GE-WGHVQNDNITGKRKPKFIKAVLELLAK--------------DTHPVVIA   60 (168)
T ss_pred             EeeecCCCcCHHHHHHHHHHHc------CC-CCccccCCCCCCCHHHHHHHHHHHHhh--------------CCCCEEEE
Confidence            4457899999999999999876      21 11122222222   2223233333211              12349999


Q ss_pred             eCCCCCCHHHHHHHHHHHHhhcC-------cceEEEEecCCccc--------chHhhcccc---EEEecCCCHHHHHHHH
Q 022641          162 DEADSMTEDAQNALRRTMETYSK-------VTRFFFICNYISRI--------IEPLASRCA---KFRFKPLSEEVMSSRV  223 (294)
Q Consensus       162 Dei~~l~~~~~~~L~~~l~~~~~-------~~~ii~~~~~~~~~--------~~~l~~r~~---~i~~~~~~~~~~~~~l  223 (294)
                      |-=++. ......|+..++....       ...+|...=.....        .+++..|-.   .|............++
T Consensus        61 DRNNh~-~reR~ql~~~~~~~~~~yl~~~~~~r~VaL~fv~~~~~~~i~~it~~RV~~RGDNHQTika~~~~~~~~~~Im  139 (168)
T PF08303_consen   61 DRNNHQ-KRERKQLFEDVSQLKPDYLPYDTNVRFVALNFVHDDDLDEIRRITQDRVLARGDNHQTIKADSKDEKKVEGIM  139 (168)
T ss_pred             eCCCch-HHHHHHHHHHHHHhcccccccCCCeEEEEEEccCCCCHHHHHHHHHHHHHhcCcCcceeecCCCCHHHHHHHH
Confidence            987666 4456677777766444       55555544111111        123334432   5666666667777777


Q ss_pred             HHHHHHh
Q 022641          224 LHICNEE  230 (294)
Q Consensus       224 ~~~~~~~  230 (294)
                      ...+++.
T Consensus       140 ~gFi~rf  146 (168)
T PF08303_consen  140 EGFIKRF  146 (168)
T ss_pred             HHHHHhc
Confidence            7766553

Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.91  E-value=1.6e-05  Score=63.35  Aligned_cols=22  Identities=45%  Similarity=0.697  Sum_probs=19.6

Q ss_pred             CcEEEECCCCCCHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~  104 (294)
                      ..++|+|+||+|||++|+.++.
T Consensus        13 ~~~liyG~~G~GKtt~a~~~~~   34 (220)
T TIGR01618        13 NMYLIYGKPGTGKTSTIKYLPG   34 (220)
T ss_pred             cEEEEECCCCCCHHHHHHhcCC
Confidence            3499999999999999999864

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=97.89  E-value=0.00017  Score=53.87  Aligned_cols=95  Identities=16%  Similarity=0.182  Sum_probs=54.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC------CCcchhHHHHHHHHHHhhhcccCccCCCCCCCCc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS------DDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPY  156 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (294)
                      ..+.|.||+|+||||+++.++.......   .. +.++..      ...+....+. +.-...            ...++
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~~~~~~---G~-i~~~~~~~i~~~~~lS~G~~~r-v~lara------------l~~~p   89 (144)
T cd03221          27 DRIGLVGRNGAGKSTLLKLIAGELEPDE---GI-VTWGSTVKIGYFEQLSGGEKMR-LALAKL------------LLENP   89 (144)
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCCCCCc---eE-EEECCeEEEEEEccCCHHHHHH-HHHHHH------------HhcCC
Confidence            4689999999999999999987652111   11 111110      0011111111 111111            11234


Q ss_pred             EEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          157 KIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       157 ~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                      .++++||.. .++......+.+.+...  ...+++++....
T Consensus        90 ~illlDEP~~~LD~~~~~~l~~~l~~~--~~til~~th~~~  128 (144)
T cd03221          90 NLLLLDEPTNHLDLESIEALEEALKEY--PGTVILVSHDRY  128 (144)
T ss_pred             CEEEEeCCccCCCHHHHHHHHHHHHHc--CCEEEEEECCHH
Confidence            599999965 67888888888888765  245677776543

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>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=97.88  E-value=0.00019  Score=56.45  Aligned_cols=22  Identities=45%  Similarity=0.847  Sum_probs=21.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |+|+||||+||||+++.|+..+
T Consensus         2 I~i~G~pGsGKst~a~~La~~~   23 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKY   23 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            8999999999999999999987

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.88  E-value=1.4e-05  Score=68.44  Aligned_cols=29  Identities=28%  Similarity=0.352  Sum_probs=24.8

Q ss_pred             CCCCcEEEECCCCCCHHHHHHHHHHHhcC
Q 022641           80 ANCPHMLFYGPPGTGKTTTALAIAHQLFG  108 (294)
Q Consensus        80 ~~~~~ill~Gp~G~GKT~la~~la~~~~~  108 (294)
                      ++.+..+|+||+|+|||+|++.+++....
T Consensus       167 GkGQR~lIvgppGvGKTTLaK~Ian~I~~  195 (416)
T PRK09376        167 GKGQRGLIVAPPKAGKTVLLQNIANSITT  195 (416)
T ss_pred             ccCceEEEeCCCCCChhHHHHHHHHHHHh
Confidence            45556999999999999999999998743

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=97.87  E-value=7.1e-05  Score=59.00  Aligned_cols=43  Identities=9%  Similarity=0.112  Sum_probs=30.9

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC-cceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK-VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~  196 (294)
                      .++.++++||.. .++......+.+.+..... ...+|+++.+..
T Consensus       128 ~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~  172 (194)
T cd03213         128 SNPSLLFLDEPTSGLDSSSALQVMSLLRRLADTGRTIICSIHQPS  172 (194)
T ss_pred             cCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEEecCch
Confidence            456799999965 5778888888888876543 455777776654

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>PRK00625 shikimate kinase; Provisional

Probab=97.86  E-value=1.7e-05  Score=61.02  Aligned_cols=31  Identities=26%  Similarity=0.435  Sum_probs=26.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      +|+|+|.||+||||+++.+++.+      +.+++.++
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l------~~~~id~D   32 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFL------SLPFFDTD   32 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh------CCCEEEhh
Confidence            58999999999999999999998      56665554

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.86  E-value=9e-05  Score=65.31  Aligned_cols=25  Identities=36%  Similarity=0.518  Sum_probs=22.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ..++|+|++|+||||++..+|..+.
T Consensus        96 ~vI~lvG~~GsGKTTtaakLA~~L~  120 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAAKLARYFK  120 (437)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHH
Confidence            3489999999999999999998874

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=97.85  E-value=0.00023  Score=55.05  Aligned_cols=102  Identities=18%  Similarity=0.144  Sum_probs=54.9

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHhcCCCc---c-CCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCc
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQLFGPEL---Y-KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPY  156 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~~~~~~---~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (294)
                      ....+.|.||.|+|||||++.++..+.....   . +..+..+......+...- ..+.-...            ...++
T Consensus        24 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~i~~~~q~~~LSgGq~-qrv~lara------------l~~~p   90 (177)
T cd03222          24 EGEVIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQYIDLSGGEL-QRVAIAAA------------LLRNA   90 (177)
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcCCCCCCcEEEECCEEEEEEcccCCCCHHHH-HHHHHHHH------------HhcCC
Confidence            3446999999999999999999876521110   0 000000100000111111 11111111            11234


Q ss_pred             EEEEEeCCC-CCCHHHHHHHHHHHHhhcC--cceEEEEecCC
Q 022641          157 KIIILDEAD-SMTEDAQNALRRTMETYSK--VTRFFFICNYI  195 (294)
Q Consensus       157 ~lliiDei~-~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~  195 (294)
                      .++++||.- .++......+.+.+.....  ...+++++.+.
T Consensus        91 ~lllLDEPts~LD~~~~~~l~~~l~~~~~~~~~tiiivsH~~  132 (177)
T cd03222          91 TFYLFDEPSAYLDIEQRLNAARAIRRLSEEGKKTALVVEHDL  132 (177)
T ss_pred             CEEEEECCcccCCHHHHHHHHHHHHHHHHcCCCEEEEEECCH
Confidence            699999975 6777777777777765432  25577777654

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>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=97.85  E-value=0.00094  Score=49.86  Aligned_cols=30  Identities=33%  Similarity=0.522  Sum_probs=25.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      ++|+|++|+|||++++.++..+      +.+++..+
T Consensus         2 I~i~G~~GsGKst~a~~la~~~------~~~~~~~~   31 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKKL------GLPYLDTG   31 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh------CCceeccc
Confidence            7899999999999999999998      55555443

>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid []

Probab=97.85  E-value=0.00019  Score=56.00  Aligned_cols=143  Identities=24%  Similarity=0.275  Sum_probs=65.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCC
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEA  164 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei  164 (294)
                      ++|+||+|||||.++-.+|+..      +.+++..+.-.-            +.....+.+........+-+. +++||-
T Consensus         4 ~~i~GpT~tGKt~~ai~lA~~~------g~pvI~~Driq~------------y~~l~v~Sgrp~~~el~~~~R-iyL~~r   64 (233)
T PF01745_consen    4 YLIVGPTGTGKTALAIALAQKT------GAPVISLDRIQC------------YPELSVGSGRPTPSELKGTRR-IYLDDR   64 (233)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH--------EEEEE-SGGG-------------GGGTTTTT---SGGGTT-EE-EES---
T ss_pred             EEEECCCCCChhHHHHHHHHHh------CCCEEEecceec------------ccccccccCCCCHHHHcccce-eeeccc
Confidence            6899999999999999999999      667665542211            111111111100001111223 788875


Q ss_pred             CC----CC-HHHHHHHHHHHHhhcCcceEEEEecCCcccchHh----h-cccc--EEEecCCCHHHHHHHHHHHHHHh-C
Q 022641          165 DS----MT-EDAQNALRRTMETYSKVTRFFFICNYISRIIEPL----A-SRCA--KFRFKPLSEEVMSSRVLHICNEE-G  231 (294)
Q Consensus       165 ~~----l~-~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l----~-~r~~--~i~~~~~~~~~~~~~l~~~~~~~-~  231 (294)
                      .-    ++ ....+.|...+.......-+|+-+...+.+..-.    . ..+.  +..+.-++.+.......+..++. .
T Consensus        65 ~l~~G~i~a~ea~~~Li~~v~~~~~~~~~IlEGGSISLl~~m~~~~~w~~~f~w~i~rl~l~d~~~f~~ra~~Rv~~ML~  144 (233)
T PF01745_consen   65 PLSDGIINAEEAHERLISEVNSYSAHGGLILEGGSISLLNCMAQDPYWSLDFRWHIRRLRLPDEEVFMARAKRRVRQMLR  144 (233)
T ss_dssp             -GGG-S--HHHHHHHHHHHHHTTTTSSEEEEEE--HHHHHHHHH-TTTSSSSEEEEEE-----HHHHHHHHHHHHHHHHS
T ss_pred             cccCCCcCHHHHHHHHHHHHHhccccCceEEeCchHHHHHHHHhcccccCCCeEEEEEEECCChHHHHHHHHHHHHHhcC
Confidence            32    23 3355667788887777777777775544332111    1 1222  45555556555555444444332 1


Q ss_pred             C-CCCHHHHHHHHhhc
Q 022641          232 L-NLDAEALSTLSSIS  246 (294)
Q Consensus       232 ~-~~~~~~l~~l~~~~  246 (294)
                      . .-.+..+++++...
T Consensus       145 p~~~~~Sll~EL~~lW  160 (233)
T PF01745_consen  145 PDSSGPSLLEELVALW  160 (233)
T ss_dssp             --SSS--HHHHHHHHH
T ss_pred             CCCCCCcHHHHHHHHH
Confidence            1 22356777777764

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>PF13337 Lon_2: Putative ATP-dependent Lon protease

Probab=97.85  E-value=0.00013  Score=63.57  Aligned_cols=171  Identities=12%  Similarity=0.174  Sum_probs=89.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEe
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILD  162 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiD  162 (294)
                      -|++=.||.|||||++=+.+..          ..+.++++.....    .++........        -..+..++|++|
T Consensus       209 ~NliELgPrGTGKS~vy~eiSp----------~~~liSGG~~T~A----~LFyn~~~~~~--------GlV~~~D~VafD  266 (457)
T PF13337_consen  209 YNLIELGPRGTGKSYVYKEISP----------YGILISGGQVTVA----KLFYNMSTGQI--------GLVGRWDVVAFD  266 (457)
T ss_pred             cceEEEcCCCCCceeehhhcCc----------ccEEEECCCcchH----HheeeccCCcc--------eeeeeccEEEEE
Confidence            4699999999999999666632          2333443332111    11111111100        012345799999


Q ss_pred             CCCCCC---HHHHHHHHHHHHhhc---------CcceEEEEecCCcc-------------c-----chHhhccccE----
Q 022641          163 EADSMT---EDAQNALRRTMETYS---------KVTRFFFICNYISR-------------I-----IEPLASRCAK----  208 (294)
Q Consensus       163 ei~~l~---~~~~~~L~~~l~~~~---------~~~~ii~~~~~~~~-------------~-----~~~l~~r~~~----  208 (294)
                      |+..+.   ++..+.|...|+...         ....+++++|-...             +     +.++++|++.    
T Consensus       267 Ev~~i~f~d~d~i~imK~YMesG~fsRG~~~i~a~as~vf~GNi~~~v~~~~~~~~lf~~lP~~~~DsAflDRiH~~iPG  346 (457)
T PF13337_consen  267 EVAGIKFKDKDEIQIMKDYMESGSFSRGKEEINADASMVFVGNINQSVENMLKTSHLFEPLPEEMRDSAFLDRIHGYIPG  346 (457)
T ss_pred             eccCcccCChHHHHHHHHHHhccceeecccccccceeEEEEcCcCCcchhccccchhhhhcCHHHHHHHHHhHhheeccC
Confidence            999885   556677888887433         45668888875422             1     3567778772    


Q ss_pred             EEecCCCH-----------HHHHHHHHHHHHHhCCCCCHHHHHHHHhhc-cCcHHHHHHHHHHHHHHh-----CCCCChh
Q 022641          209 FRFKPLSE-----------EVMSSRVLHICNEEGLNLDAEALSTLSSIS-QGDLRRAITYLQGAARLF-----GSSITSK  271 (294)
Q Consensus       209 i~~~~~~~-----------~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~-~G~~r~~~~~l~~~~~~~-----~~~it~~  271 (294)
                      .+++....           +-..++++.+.+..   + .+.++...+.. +-+.|....+-..++.+.     ...+|.+
T Consensus       347 WeiPk~~~e~~t~~~gl~~Dy~aE~l~~LR~~~---~-~~~~~~~~~lg~~~~~RD~~AV~kt~SgllKLL~P~~~~~~e  422 (457)
T PF13337_consen  347 WEIPKIRPEMFTNGYGLIVDYFAEILHELRKQS---Y-SDAVDKYFKLGSNLSQRDTKAVKKTVSGLLKLLFPHGEFTKE  422 (457)
T ss_pred             ccccccCHHHccCCceeeHHHHHHHHHHHHHHH---H-HHHHHhhEeeCCCcchhhHHHHHHHHHHHHHhhCCCCCCCHH
Confidence            24444433           33444444433211   1 12233333332 123333333333332222     5678888


Q ss_pred             hhhhhccc
Q 022641          272 DLISVSGY  279 (294)
Q Consensus       272 ~v~~~~~~  279 (294)
                      +++.++..
T Consensus       423 e~~~~l~~  430 (457)
T PF13337_consen  423 ELEECLRP  430 (457)
T ss_pred             HHHHHHHH
Confidence            88777654

>PRK00131 aroK shikimate kinase; Reviewed

Probab=97.84  E-value=2.3e-05  Score=60.61  Aligned_cols=25  Identities=32%  Similarity=0.555  Sum_probs=23.1

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +..++|+|+||+|||++++.+++.+
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~l   28 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKRL   28 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHh
Confidence            3469999999999999999999998

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=97.84  E-value=0.00025  Score=55.05  Aligned_cols=44  Identities=16%  Similarity=0.216  Sum_probs=32.7

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCcc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYISR  197 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~  197 (294)
                      .++.++++||.- .++......+.+.+........+|+++.+...
T Consensus       115 ~~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~  159 (178)
T cd03247         115 QDAPIVLLDEPTVGLDPITERQLLSLIFEVLKDKTLIWITHHLTG  159 (178)
T ss_pred             cCCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEecCHHH
Confidence            456799999965 67888888888888766555667777766543

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.

>PRK06547 hypothetical protein; Provisional

Probab=97.83  E-value=3.8e-05  Score=59.09  Aligned_cols=32  Identities=34%  Similarity=0.345  Sum_probs=25.5

Q ss_pred             HHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           75 NTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        75 ~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.......++|.|++|+||||+++.+++.+
T Consensus         8 ~~~~~~~~~~i~i~G~~GsGKTt~a~~l~~~~   39 (172)
T PRK06547          8 ARLCGGGMITVLIDGRSGSGKTTLAGALAART   39 (172)
T ss_pred             HHhhcCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            33444444458888999999999999999986

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=97.83  E-value=0.00032  Score=54.07  Aligned_cols=44  Identities=20%  Similarity=0.329  Sum_probs=32.5

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCcc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYISR  197 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~  197 (294)
                      .+++++++||-- .++......+.+++........+++++.+...
T Consensus       113 ~~p~llllDEP~~gLD~~~~~~l~~~l~~~~~~~tii~~sh~~~~  157 (171)
T cd03228         113 RDPPILILDEATSALDPETEALILEALRALAKGKTVIVIAHRLST  157 (171)
T ss_pred             cCCCEEEEECCCcCCCHHHHHHHHHHHHHhcCCCEEEEEecCHHH
Confidence            456799999964 67888888888888776555667777766543

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF00519 PPV_E1_C: Papillomavirus helicase; InterPro: IPR001177 Papillomaviruses are a large family of DNA tumour viruses which give rise to warts in their host species

Probab=97.83  E-value=6.3e-05  Score=63.89  Aligned_cols=131  Identities=22%  Similarity=0.309  Sum_probs=73.7

Q ss_pred             HHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee-cCCCCcchhHHHHHHHHHHhhhcccCcc
Q 022641           70 VRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL-NASDDRGINVVRTKIKTFAAVAVGSGQR  147 (294)
Q Consensus        70 ~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (294)
                      +..++.++..-...| ++|+|||.||||..+..|.+-+      +..++.. |..+..=       ++.+          
T Consensus       249 l~~lk~~Lkg~PKKnClvi~GPPdTGKS~F~~SLi~Fl------~GkViSf~Ns~ShFW-------LqPL----------  305 (432)
T PF00519_consen  249 LIALKQFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFL------KGKVISFVNSKSHFW-------LQPL----------  305 (432)
T ss_dssp             HHHHHHHHHTBTTSSEEEEESSCCCSHHHHHHHHHHHH------TSEEE-GGGTTSCGG-------GGGG----------
T ss_pred             HHHHHHHHhCCCcccEEEEECCCCCchhHHHHHHHHHh------CCEEEEecCCCCccc-------ccch----------
Confidence            356677776544444 9999999999999999999988      5555543 2221110       1111          


Q ss_pred             CCCCCCCCcEEEEEeCCCCCCHHHHH-HHHHHHHhhc-------------CcceEEEEecCCc---ccchHhhccccEEE
Q 022641          148 RGGYPCPPYKIIILDEADSMTEDAQN-ALRRTMETYS-------------KVTRFFFICNYIS---RIIEPLASRCAKFR  210 (294)
Q Consensus       148 ~~~~~~~~~~lliiDei~~l~~~~~~-~L~~~l~~~~-------------~~~~ii~~~~~~~---~~~~~l~~r~~~i~  210 (294)
                            ....+-+|||+-.-.-.-.+ .|+..++..+             .-..+++|||..-   .-...|.+|...+.
T Consensus       306 ------~d~Ki~llDDAT~~cW~Y~D~ylRNaLDGN~vsiD~KHkap~Qik~PPLlITsN~dv~~~~~~~YLhSRi~~f~  379 (432)
T PF00519_consen  306 ------ADAKIALLDDATYPCWDYIDTYLRNALDGNPVSIDCKHKAPVQIKCPPLLITSNIDVKKDDRWKYLHSRITCFE  379 (432)
T ss_dssp             ------CT-SSEEEEEE-HHHHHHHHHHTHHHHCTSEEEEEESSSEEEEEE---EEEEESS-TTTSCCCHHHCTTEEEEE
T ss_pred             ------hcCcEEEEcCCcccHHHHHHHHHHhccCCCeeeeeccCCCceEeecCceEEecCCCCCcchhhhhhhheEEEEE
Confidence                  11238899998543222222 2556665422             1123778887543   23456788988877


Q ss_pred             ecCC-------------CHHHHHHHHHHHHHH
Q 022641          211 FKPL-------------SEEVMSSRVLHICNE  229 (294)
Q Consensus       211 ~~~~-------------~~~~~~~~l~~~~~~  229 (294)
                      |+.+             +....+.++++...+
T Consensus       380 F~n~~P~d~~G~P~y~ltd~~WksFF~rlw~~  411 (432)
T PF00519_consen  380 FPNPFPLDENGNPVYELTDANWKSFFRRLWSQ  411 (432)
T ss_dssp             --S-S-BSTTSSBSS---HHHHHHHHHHHTCC
T ss_pred             cCCccccCCCCCeeEEeccChHHHHHHHHHHh
Confidence            7532             346677777666643

The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication []. It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins []. The E1 protein is a 70 kDa polypeptide with a central DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase []. In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other []. Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity []. The entry represents the C-terminal region of E1, containing both the DNA-binding and ATPase/helical domains.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1TUE_K 1R9W_A 2V9P_B 2GXA_I 1KSX_J 1KSY_A 1F08_B.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=97.83  E-value=0.00031  Score=54.94  Aligned_cols=51  Identities=12%  Similarity=0.237  Sum_probs=33.2

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCc-ceEEEEecCCcccchHhhcc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKV-TRFFFICNYISRIIEPLASR  205 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~-~~ii~~~~~~~~~~~~l~~r  205 (294)
                      .++.++++||.- .|+++.....+..+...... ..++++|.. ......+.+|
T Consensus       153 M~P~vmLFDEPTSALDPElv~EVL~vm~~LA~eGmTMivVTHE-M~FAr~Vadr  205 (240)
T COG1126         153 MDPKVMLFDEPTSALDPELVGEVLDVMKDLAEEGMTMIIVTHE-MGFAREVADR  205 (240)
T ss_pred             CCCCEEeecCCcccCCHHHHHHHHHHHHHHHHcCCeEEEEech-hHHHHHhhhe
Confidence            467899999986 46888888888888765543 445566543 3333444444

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=97.83  E-value=0.00027  Score=60.33  Aligned_cols=24  Identities=29%  Similarity=0.400  Sum_probs=22.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++++|++|+||||+++++....
T Consensus       161 ~nili~G~tgSGKTTll~aL~~~i  184 (332)
T PRK13900        161 KNIIISGGTSTGKTTFTNAALREI  184 (332)
T ss_pred             CcEEEECCCCCCHHHHHHHHHhhC
Confidence            489999999999999999999877

>PRK03839 putative kinase; Provisional

Probab=97.83  E-value=1.9e-05  Score=61.50  Aligned_cols=23  Identities=39%  Similarity=0.621  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|+||+||||+++.+++.+
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~   24 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKL   24 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999998

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=97.83  E-value=7.2e-05  Score=67.57  Aligned_cols=43  Identities=16%  Similarity=0.177  Sum_probs=33.5

Q ss_pred             CCCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCC
Q 022641          153 CPPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYI  195 (294)
Q Consensus       153 ~~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~  195 (294)
                      ..+++++||||+- .++++....+++.+.+.-..+.+|-++..+
T Consensus       531 L~kP~~v~LDEATsALDe~~e~~l~q~l~~~lp~~tvISV~Hr~  574 (604)
T COG4178         531 LHKPKWVFLDEATSALDEETEDRLYQLLKEELPDATVISVGHRP  574 (604)
T ss_pred             HcCCCEEEEecchhccChHHHHHHHHHHHhhCCCCEEEEeccch
Confidence            3578899999985 578888999999998765666677777554

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=97.83  E-value=0.00024  Score=54.58  Aligned_cols=23  Identities=30%  Similarity=0.313  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|+||+|||++|..++..+
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~   25 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQS   25 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHc
Confidence            48999999999999999999886

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.82  E-value=0.00013  Score=62.70  Aligned_cols=145  Identities=19%  Similarity=0.214  Sum_probs=68.9

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc--chhHHHHHHHHHHhhhcccCccCC-------C-CC
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR--GINVVRTKIKTFAAVAVGSGQRRG-------G-YP  152 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~-------~-~~  152 (294)
                      ..++|+||+|+||||++..|+..+...   +..+..+++...+  ....+...... ...+........       . ..
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~~~---GkkVglI~aDt~RiaAvEQLk~yae~-lgipv~v~~d~~~L~~aL~~lk~  317 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFHGK---KKTVGFITTDHSRIGTVQQLQDYVKT-IGFEVIAVRDEAAMTRALTYFKE  317 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHc---CCcEEEEecCCcchHHHHHHHHHhhh-cCCcEEecCCHHHHHHHHHHHHh
Confidence            458999999999999999999887422   2223333333222  22222211111 011100000000       0 00


Q ss_pred             CCCcEEEEEeCCCCCC--HHHHHHHHHHHHhhcCcce-EEEEecCCcccchHhhcccc-----EEEecCCCHHHHHHHHH
Q 022641          153 CPPYKIIILDEADSMT--EDAQNALRRTMETYSKVTR-FFFICNYISRIIEPLASRCA-----KFRFKPLSEEVMSSRVL  224 (294)
Q Consensus       153 ~~~~~lliiDei~~l~--~~~~~~L~~~l~~~~~~~~-ii~~~~~~~~~~~~l~~r~~-----~i~~~~~~~~~~~~~l~  224 (294)
                      ..+.++|+||-.++..  ......|...+........ +++.++....-...+..+|.     -+-|..++.......+-
T Consensus       318 ~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~~~F~~~~idglI~TKLDET~k~G~iL  397 (436)
T PRK11889        318 EARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIITNFKDIHIDGIVFTKFDETASSGELL  397 (436)
T ss_pred             ccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHHHHhcCCCCCEEEEEcccCCCCccHHH
Confidence            1135799999998875  4456667777764333322 22222222211123333332     45555565544444444


Q ss_pred             HHHHHhC
Q 022641          225 HICNEEG  231 (294)
Q Consensus       225 ~~~~~~~  231 (294)
                      .++...+
T Consensus       398 ni~~~~~  404 (436)
T PRK11889        398 KIPAVSS  404 (436)
T ss_pred             HHHHHHC
Confidence            4444433

>PRK13947 shikimate kinase; Provisional

Probab=97.82  E-value=2.1e-05  Score=60.64  Aligned_cols=30  Identities=30%  Similarity=0.431  Sum_probs=25.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL  119 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~  119 (294)
                      +|+|+|+||+|||++++.+++.+      +.+++..
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~l------g~~~id~   32 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTL------SFGFIDT   32 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHh------CCCEEEC
Confidence            69999999999999999999998      5555543

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=97.81  E-value=0.00028  Score=53.55  Aligned_cols=108  Identities=19%  Similarity=0.264  Sum_probs=55.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc--hhHHHHHHHHHHhhhcccCccC----CCCCCCCc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG--INVVRTKIKTFAAVAVGSGQRR----GGYPCPPY  156 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~  156 (294)
                      ..+.|+||.|+||||+++.++..+...    ..-+.++......  .......+...  ...+.+.+.    ......++
T Consensus        26 ~~~~i~G~nGsGKStll~~l~g~~~~~----~G~i~~~~~~~~~~~~~~~~~~i~~~--~qlS~G~~~r~~l~~~l~~~~   99 (157)
T cd00267          26 EIVALVGPNGSGKSTLLRAIAGLLKPT----SGEILIDGKDIAKLPLEELRRRIGYV--PQLSGGQRQRVALARALLLNP   99 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCCC----ccEEEECCEEcccCCHHHHHhceEEE--eeCCHHHHHHHHHHHHHhcCC
Confidence            469999999999999999998765211    1111222211100  00000000000  000000000    00001234


Q ss_pred             EEEEEeCCC-CCCHHHHHHHHHHHHhhcCc-ceEEEEecCCc
Q 022641          157 KIIILDEAD-SMTEDAQNALRRTMETYSKV-TRFFFICNYIS  196 (294)
Q Consensus       157 ~lliiDei~-~l~~~~~~~L~~~l~~~~~~-~~ii~~~~~~~  196 (294)
                      .++++||.. .++......+.+.+...... ..+++++....
T Consensus       100 ~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~  141 (157)
T cd00267         100 DLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPE  141 (157)
T ss_pred             CEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence            699999976 67777777888887765433 55677776544

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=97.81  E-value=0.00025  Score=55.19  Aligned_cols=43  Identities=14%  Similarity=0.206  Sum_probs=31.4

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC--cceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      .++.++++||.- .++......+.+.+.....  ...+|+++....
T Consensus       114 ~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~  159 (180)
T cd03214         114 QEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLN  159 (180)
T ss_pred             cCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            467899999965 6788888888888876543  456777776544

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.

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=97.81  E-value=2.3e-05  Score=59.38  Aligned_cols=32  Identities=25%  Similarity=0.416  Sum_probs=27.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      ++++|+|++|+||||+.+.+|+.+      +.+|+..+
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L------~~~F~D~D   34 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKAL------NLPFIDTD   34 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHc------CCCcccch
Confidence            479999999999999999999999      66666554

>PRK13808 adenylate kinase; Provisional

Probab=97.80  E-value=0.00068  Score=57.40  Aligned_cols=23  Identities=39%  Similarity=0.803  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|+||||+||||++..|+..+
T Consensus         2 rIiv~GpPGSGK~T~a~~LA~~y   24 (333)
T PRK13808          2 RLILLGPPGAGKGTQAQRLVQQY   24 (333)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999987

>PRK06762 hypothetical protein; Provisional

Probab=97.80  E-value=0.00041  Score=53.18  Aligned_cols=23  Identities=35%  Similarity=0.574  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|+||+||||+|+.+++.+
T Consensus         4 li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          4 LIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999987

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=97.80  E-value=0.00047  Score=53.29  Aligned_cols=41  Identities=17%  Similarity=0.237  Sum_probs=29.9

Q ss_pred             cEEEEEeCCC-CCCHHHHHHHHHHHHhhc-CcceEEEEecCCc
Q 022641          156 YKIIILDEAD-SMTEDAQNALRRTMETYS-KVTRFFFICNYIS  196 (294)
Q Consensus       156 ~~lliiDei~-~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~~  196 (294)
                      +.++++||.- .++......+.+.+.... ....+|+++.+..
T Consensus       108 p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~~  150 (176)
T cd03238         108 GTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNLD  150 (176)
T ss_pred             CCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHH
Confidence            6899999964 577887787887777643 3456777776654

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>PRK02496 adk adenylate kinase; Provisional

Probab=97.79  E-value=0.00035  Score=54.57  Aligned_cols=23  Identities=48%  Similarity=0.992  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||||+||||+++.+++.+
T Consensus         3 ~i~i~G~pGsGKst~a~~la~~~   25 (184)
T PRK02496          3 RLIFLGPPGAGKGTQAVVLAEHL   25 (184)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999987

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=97.79  E-value=2.3e-05  Score=58.91  Aligned_cols=22  Identities=36%  Similarity=0.596  Sum_probs=20.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|.|||||||+++.|+ .+
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~-~l   23 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR-EL   23 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH-Hh
Confidence            58999999999999999999 66

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=97.78  E-value=0.00026  Score=55.38  Aligned_cols=24  Identities=33%  Similarity=0.490  Sum_probs=18.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++.||+|+|||+.+..++-..
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~~   48 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALEA   48 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHH
Confidence            479999999999999554444443

>cd01131 PilT Pilus retraction ATPase PilT

Probab=97.78  E-value=0.00039  Score=54.99  Aligned_cols=24  Identities=38%  Similarity=0.566  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+||+|+||||++.+++..+.
T Consensus         3 lilI~GptGSGKTTll~~ll~~~~   26 (198)
T cd01131           3 LVLVTGPTGSGKSTTLAAMIDYIN   26 (198)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            489999999999999999988873

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.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=97.77  E-value=7.8e-05  Score=54.39  Aligned_cols=24  Identities=33%  Similarity=0.382  Sum_probs=22.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|.|+.|+||||+++.+++.+.
T Consensus        24 ~i~l~G~lGaGKTtl~~~l~~~lg   47 (133)
T TIGR00150        24 VVLLKGDLGAGKTTLVQGLLQGLG   47 (133)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcC
Confidence            599999999999999999999983

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.

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=97.76  E-value=0.00052  Score=53.10  Aligned_cols=23  Identities=48%  Similarity=0.881  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.||||+||||+|+.|++.+
T Consensus         2 riiilG~pGaGK~T~A~~La~~~   24 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKL   24 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999996

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=97.76  E-value=0.00063  Score=52.56  Aligned_cols=43  Identities=16%  Similarity=0.279  Sum_probs=30.9

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC-cceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK-VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~  196 (294)
                      .++.++++||.- .++......+.+.+..... ...+|+++.+..
T Consensus       113 ~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~~  157 (173)
T cd03246         113 GNPRILVLDEPNSHLDVEGERALNQAIAALKAAGATRIVIAHRPE  157 (173)
T ss_pred             cCCCEEEEECCccccCHHHHHHHHHHHHHHHhCCCEEEEEeCCHH
Confidence            456799999965 6788888888888876543 456777776654

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=97.76  E-value=3.4e-05  Score=62.47  Aligned_cols=37  Identities=41%  Similarity=0.575  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           68 EVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        68 ~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .....+..++....  ..++.||||||||+++..+...+
T Consensus         5 ~Q~~Ai~~~~~~~~--~~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen    5 SQREAIQSALSSNG--ITLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             HHHHHHHHHCTSSE---EEEE-STTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCC--CEEEECCCCCChHHHHHHHHHHh
Confidence            34445544444332  38999999999999888888776

>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=97.75  E-value=0.00012  Score=56.07  Aligned_cols=112  Identities=19%  Similarity=0.202  Sum_probs=58.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCc---c-C-CcceeecCCCCcchhHHHHHHHHHHhhhcccCccC----CCCCC
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPEL---Y-K-SRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRR----GGYPC  153 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~---~-~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~  153 (294)
                      ..+.|.||.|+||||+++.++..+.....   . + ..+..+..........+.+.+........+.+.+.    .....
T Consensus        28 e~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~~~~~~i~~~~q~~~~~~~tv~~nl~~~~~~~LS~G~~~rv~laral~  107 (166)
T cd03223          28 DRLLITGPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLFLPQRPYLPLGTLREQLIYPWDDVLSGGEQQRLAFARLLL  107 (166)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCCCCceEEECCCceEEEECCCCccccccHHHHhhccCCCCCCHHHHHHHHHHHHHH
Confidence            35999999999999999999987521110   0 0 01111111111111112222211000001111100    00112


Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                      .++.++++||.- .++......+.+.+.+.  ...+|+++.+..
T Consensus       108 ~~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~  149 (166)
T cd03223         108 HKPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPS  149 (166)
T ss_pred             cCCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChh
Confidence            456799999975 57888888888888775  355777776643

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

>PLN02674 adenylate kinase

Probab=97.75  E-value=0.00099  Score=54.08  Aligned_cols=25  Identities=32%  Similarity=0.647  Sum_probs=23.0

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+++|.||||+||||.++.|++.+
T Consensus        31 ~~~i~l~G~PGsGKgT~a~~La~~~   55 (244)
T PLN02674         31 DKRLILIGPPGSGKGTQSPIIKDEY   55 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHc
Confidence            3569999999999999999999987

>PRK13949 shikimate kinase; Provisional

Probab=97.75  E-value=3.2e-05  Score=59.48  Aligned_cols=23  Identities=39%  Similarity=0.582  Sum_probs=22.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++|+|+||+||||+++.+++.+
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l   25 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALAREL   25 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999998

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=97.75  E-value=0.00083  Score=56.81  Aligned_cols=23  Identities=39%  Similarity=0.481  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|+||+||||+++.+++.+
T Consensus         4 liil~G~pGSGKSTla~~L~~~~   26 (300)
T PHA02530          4 IILTVGVPGSGKSTWAREFAAKN   26 (300)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHC
Confidence            47889999999999999999987

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=97.75  E-value=0.00037  Score=69.97  Aligned_cols=124  Identities=21%  Similarity=0.223  Sum_probs=66.7

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcC-CCccCCcceeecCCCCcchhHHHH------HHHHHH
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFG-PELYKSRVLELNASDDRGINVVRT------KIKTFA  138 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~  138 (294)
                      .+.....+..++.... +.++|.|.+||||||+++.+...+.. ....+..++.+. +.......+.+      .+..+.
T Consensus       837 t~~Qr~Av~~iLts~d-r~~~IqG~AGTGKTT~l~~i~~~~~~l~e~~g~~V~glA-PTgkAa~~L~e~Gi~A~TIasfL  914 (1623)
T PRK14712        837 TSGQRAATRMILETSD-RFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLG-PTHRAVGEMRSAGVDAQTLASFL  914 (1623)
T ss_pred             CHHHHHHHHHHHhCCC-ceEEEEeCCCCCHHHHHHHHHHHHHHHhhccCceEEEEe-chHHHHHHHHHhCchHhhHHHHh
Confidence            3444555555565432 46999999999999998887665421 000122233332 21111111111      111111


Q ss_pred             hhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecC
Q 022641          139 AVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      .... ...........+..++||||+.+++...+..|+..++.  ....+|+++..
T Consensus       915 ~~~~-~~~~~~~~~~~~~~llIVDEASMV~~~~m~~ll~~~~~--~garvVLVGD~  967 (1623)
T PRK14712        915 HDTQ-LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAA--GGGRAVASGDT  967 (1623)
T ss_pred             cccc-chhhcccCCCCCCcEEEEEccccccHHHHHHHHHhhhh--CCCEEEEEcch
Confidence            1100 00001111223467999999999999888888888764  34668888743

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=97.75  E-value=6.6e-05  Score=58.05  Aligned_cols=43  Identities=12%  Similarity=0.292  Sum_probs=30.6

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCc-ceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKV-TRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~-~~ii~~~~~~~  196 (294)
                      .++.++++||.. .++......+.+.+...... ..+|+++.+..
T Consensus       112 ~~p~illlDEPt~~LD~~~~~~l~~~l~~~~~~g~tiii~th~~~  156 (173)
T cd03230         112 HDPELLILDEPTSGLDPESRREFWELLRELKKEGKTILLSSHILE  156 (173)
T ss_pred             cCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHH
Confidence            456799999965 57788888888888776433 55677776543

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>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=97.75  E-value=3.5e-05  Score=58.26  Aligned_cols=23  Identities=35%  Similarity=0.541  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++|+|+||+|||++++.++..+
T Consensus         1 ~i~l~G~~GsGKstla~~la~~l   23 (154)
T cd00464           1 NIVLIGMMGAGKTTVGRLLAKAL   23 (154)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999988

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.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=97.74  E-value=0.0007  Score=57.40  Aligned_cols=24  Identities=25%  Similarity=0.506  Sum_probs=22.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++++||+|+||||+++++...+
T Consensus       145 ~~ili~G~tGsGKTTll~al~~~~  168 (308)
T TIGR02788       145 KNIIISGGTGSGKTTFLKSLVDEI  168 (308)
T ss_pred             CEEEEECCCCCCHHHHHHHHHccC
Confidence            489999999999999999998776

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=97.73  E-value=0.00058  Score=57.49  Aligned_cols=37  Identities=30%  Similarity=0.396  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           68 EVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        68 ~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .....|..++...  .+++++||+|+||||+++++...+
T Consensus       120 ~~~~~L~~~v~~~--~~ilI~G~tGSGKTTll~al~~~i  156 (299)
T TIGR02782       120 AQRDVLREAVLAR--KNILVVGGTGSGKTTLANALLAEI  156 (299)
T ss_pred             HHHHHHHHHHHcC--CeEEEECCCCCCHHHHHHHHHHHh
Confidence            3445566666543  489999999999999999999886

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=97.73  E-value=0.00032  Score=58.38  Aligned_cols=49  Identities=24%  Similarity=0.413  Sum_probs=34.0

Q ss_pred             cchhhcccHHHHHHHHHHHHcC--CCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           59 QVKDVAHQEEVVRVLTNTLETA--NCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~--~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      +++++.........+.+.+...  ...+++++||+|+||||++.++...+.
T Consensus       102 sle~l~~~~~~~~~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~all~~i~  152 (270)
T PF00437_consen  102 SLEDLGESGSIPEEIAEFLRSAVRGRGNILISGPTGSGKTTLLNALLEEIP  152 (270)
T ss_dssp             CHCCCCHTHHCHHHHHHHHHHCHHTTEEEEEEESTTSSHHHHHHHHHHHCH
T ss_pred             cHhhccCchhhHHHHHHHHhhccccceEEEEECCCccccchHHHHHhhhcc
Confidence            4555554444444555554433  234799999999999999999998873

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=97.73  E-value=0.00024  Score=72.01  Aligned_cols=124  Identities=20%  Similarity=0.210  Sum_probs=67.6

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcC-CCccCCcceeecCCCCcchhHHHH------HHHHHH
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFG-PELYKSRVLELNASDDRGINVVRT------KIKTFA  138 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~  138 (294)
                      .+.....+..++... .+.++|.|.+||||||+++.+...+.. ....+..++.+.+ .......+.+      .+..+.
T Consensus       969 t~~Q~~Av~~il~s~-dr~~~I~G~AGTGKTT~l~~v~~~~~~l~~~~~~~V~glAP-TgrAAk~L~e~Gi~A~TI~s~L 1046 (1747)
T PRK13709        969 TSGQRAATRMILEST-DRFTVVQGYAGVGKTTQFRAVMSAVNTLPESERPRVVGLGP-THRAVGEMRSAGVDAQTLASFL 1046 (1747)
T ss_pred             CHHHHHHHHHHHhCC-CcEEEEEeCCCCCHHHHHHHHHHHHHHhhcccCceEEEECC-cHHHHHHHHhcCcchhhHHHHh
Confidence            344455555555443 246999999999999999998877521 0111223333322 2111111111      111111


Q ss_pred             hhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecC
Q 022641          139 AVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      .... ..............++||||+.+++......|++.+..  ....+|+++..
T Consensus      1047 ~~~~-~~~~~~~~~~~~~~llIVDEaSMv~~~~m~~Ll~~~~~--~garvVLVGD~ 1099 (1747)
T PRK13709       1047 HDTQ-LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAA--GGGRAVSSGDT 1099 (1747)
T ss_pred             cccc-cccccccCCCCCCcEEEEEccccccHHHHHHHHHhhhc--CCCEEEEecch
Confidence            1000 00000111223457999999999999888888888764  34668888743

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=97.73  E-value=4.5e-05  Score=61.98  Aligned_cols=21  Identities=29%  Similarity=0.556  Sum_probs=19.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~  105 (294)
                      +++.|+||+|||++++.+...
T Consensus         1 ~vv~G~pGsGKSt~i~~~~~~   21 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKKLLKD   21 (234)
T ss_pred             CEEEcCCCCCHHHHHHHHHHh
Confidence            579999999999999999887

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>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=97.72  E-value=4.1e-05  Score=49.33  Aligned_cols=22  Identities=41%  Similarity=0.605  Sum_probs=20.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.+.|++|+|||++++.+++.+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6889999999999999999886

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.

>PRK14530 adenylate kinase; Provisional

Probab=97.70  E-value=4.3e-05  Score=61.29  Aligned_cols=24  Identities=38%  Similarity=0.800  Sum_probs=22.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|+||||+||||+++.|++.+
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~   27 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEF   27 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            469999999999999999999998

>COG1485 Predicted ATPase [General function prediction only]

Probab=97.70  E-value=4.9e-05  Score=63.60  Aligned_cols=25  Identities=24%  Similarity=0.272  Sum_probs=22.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      +.+.++|+.|+|||+|.-.+-..+.
T Consensus        66 ~GlYl~GgVGrGKT~LMD~Fy~~lp   90 (367)
T COG1485          66 RGLYLWGGVGRGKTMLMDLFYESLP   90 (367)
T ss_pred             ceEEEECCCCccHHHHHHHHHhhCC
Confidence            4599999999999999999888873

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=97.70  E-value=0.00013  Score=56.93  Aligned_cols=42  Identities=17%  Similarity=0.307  Sum_probs=29.7

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC-cceEEEEecCC
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK-VTRFFFICNYI  195 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~  195 (294)
                      .++.++++||.- .++......+.+.+..... ...+|+++.+.
T Consensus       121 ~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~  164 (182)
T cd03215         121 RDPRVLILDEPTRGVDVGAKAEIYRLIRELADAGKAVLLISSEL  164 (182)
T ss_pred             cCCCEEEECCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCH
Confidence            456799999964 5788878888888776532 45567777654

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>PRK06217 hypothetical protein; Validated

Probab=97.69  E-value=4.4e-05  Score=59.63  Aligned_cols=23  Identities=35%  Similarity=0.564  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|.|++|+||||+++.|++.+
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l   25 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERL   25 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999998

>PRK00279 adk adenylate kinase; Reviewed

Probab=97.69  E-value=0.0007  Score=54.30  Aligned_cols=23  Identities=43%  Similarity=0.793  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+++||||+||||+++.+++.+
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~   24 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKY   24 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            38999999999999999999988

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=97.69  E-value=0.00032  Score=54.80  Aligned_cols=23  Identities=48%  Similarity=0.566  Sum_probs=20.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++++||||+|||+++..++....
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~   24 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGL   24 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH
Confidence            78999999999999999887763

A related protein is found in archaea.

>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=97.69  E-value=3.3e-05  Score=56.34  Aligned_cols=22  Identities=45%  Similarity=0.644  Sum_probs=20.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |+|.|+||+||||+++.|++.+
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            6899999999999999999985

...

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=97.68  E-value=0.00053  Score=56.74  Aligned_cols=93  Identities=20%  Similarity=0.296  Sum_probs=48.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec-------CC---CCcchhHHHHHHHHHHhhhcccCccCCCCCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN-------AS---DDRGINVVRTKIKTFAAVAVGSGQRRGGYPC  153 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~-------~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (294)
                      -++|+|.||+|||++++.|...+...   +..+..++       ..   +.......+..+........+          
T Consensus         3 Liil~G~P~SGKTt~a~~L~~~~~~~---~~~v~~i~~~~~~~~~~~y~~~~~Ek~~R~~l~s~v~r~ls----------   69 (270)
T PF08433_consen    3 LIILCGLPCSGKTTRAKELKKYLEEK---GKEVVIISDDSLGIDRNDYADSKKEKEARGSLKSAVERALS----------   69 (270)
T ss_dssp             EEEEE--TTSSHHHHHHHHHHHHHHT---T--EEEE-THHHH-TTSSS--GGGHHHHHHHHHHHHHHHHT----------
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHHHhc---CCEEEEEcccccccchhhhhchhhhHHHHHHHHHHHHHhhc----------
Confidence            38999999999999999999987331   12222222       11   112233444444444433322          


Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEE
Q 022641          154 PPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFI  191 (294)
Q Consensus       154 ~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~  191 (294)
                       +..++|+|+..++ .+..-.|+.+-....-..++|.+
T Consensus        70 -~~~iVI~Dd~nYi-Kg~RYelyclAr~~~~~~c~i~~  105 (270)
T PF08433_consen   70 -KDTIVILDDNNYI-KGMRYELYCLARAYGTTFCVIYC  105 (270)
T ss_dssp             -T-SEEEE-S---S-HHHHHHHHHHHHHTT-EEEEEEE
T ss_pred             -cCeEEEEeCCchH-HHHHHHHHHHHHHcCCCEEEEEE
Confidence             2259999999887 56667777766655544444443

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=97.67  E-value=0.00022  Score=56.12  Aligned_cols=43  Identities=16%  Similarity=0.208  Sum_probs=30.4

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC-cceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK-VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~  196 (294)
                      .++.++++||.. .++......+.+.+..... ...+|+++.+..
T Consensus       125 ~~p~vlllDEP~~~LD~~~~~~l~~~l~~~~~~~~tiiivtH~~~  169 (192)
T cd03232         125 AKPSILFLDEPTSGLDSQAAYNIVRFLKKLADSGQAILCTIHQPS  169 (192)
T ss_pred             cCCcEEEEeCCCcCCCHHHHHHHHHHHHHHHHcCCEEEEEEcCCh
Confidence            456799999965 5777777778877776532 456777776643

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.66  E-value=0.00013  Score=63.38  Aligned_cols=145  Identities=14%  Similarity=0.159  Sum_probs=67.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCcc-------CCCCCCCCc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQR-------RGGYPCPPY  156 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~  156 (294)
                      .++|+||+|+||||++..++..+....  +..+..+++...+....  ..+........-....       .........
T Consensus       225 vi~lvGptGvGKTTtaaKLA~~~~~~~--G~~V~Lit~Dt~R~aA~--eQLk~yAe~lgvp~~~~~~~~~l~~~l~~~~~  300 (432)
T PRK12724        225 VVFFVGPTGSGKTTSIAKLAAKYFLHM--GKSVSLYTTDNYRIAAI--EQLKRYADTMGMPFYPVKDIKKFKETLARDGS  300 (432)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhc--CCeEEEecccchhhhHH--HHHHHHHHhcCCCeeehHHHHHHHHHHHhCCC
Confidence            488999999999999999997652111  12222222222111111  1111111110000000       000001345


Q ss_pred             EEEEEeCCCCCC--HHHHHHHHHHHHhh----cCcceEEEEecCCcccchHhhcccc-----EEEecCCCHHHHHHHHHH
Q 022641          157 KIIILDEADSMT--EDAQNALRRTMETY----SKVTRFFFICNYISRIIEPLASRCA-----KFRFKPLSEEVMSSRVLH  225 (294)
Q Consensus       157 ~lliiDei~~l~--~~~~~~L~~~l~~~----~~~~~ii~~~~~~~~~~~~l~~r~~-----~i~~~~~~~~~~~~~l~~  225 (294)
                      ++|+||=.++.+  ....+.|..++...    +....+++.++....-...+..+|.     -+-|..++.......+-.
T Consensus       301 D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~~~~f~~~~~~glIlTKLDEt~~~G~il~  380 (432)
T PRK12724        301 ELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTVLKAYESLNYRRILLTKLDEADFLGSFLE  380 (432)
T ss_pred             CEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHHHHHhcCCCCCEEEEEcccCCCCccHHHH
Confidence            799999877654  45566676666542    2233344444433322233333332     455555665444444444


Q ss_pred             HHHHhCC
Q 022641          226 ICNEEGL  232 (294)
Q Consensus       226 ~~~~~~~  232 (294)
                      ++...+.
T Consensus       381 i~~~~~l  387 (432)
T PRK12724        381 LADTYSK  387 (432)
T ss_pred             HHHHHCC
Confidence            4444443

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=97.65  E-value=0.0014  Score=54.16  Aligned_cols=49  Identities=27%  Similarity=0.422  Sum_probs=36.5

Q ss_pred             CcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           58 KQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+++++--.+...+.+..++.... ..++|+||+|+||||+++++...+.
T Consensus        57 ~~l~~lg~~~~~~~~l~~~~~~~~-GlilisG~tGSGKTT~l~all~~i~  105 (264)
T cd01129          57 LDLEKLGLKPENLEIFRKLLEKPH-GIILVTGPTGSGKTTTLYSALSELN  105 (264)
T ss_pred             CCHHHcCCCHHHHHHHHHHHhcCC-CEEEEECCCCCcHHHHHHHHHhhhC
Confidence            455566555666677777765433 3699999999999999999988763

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.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=97.65  E-value=0.0015  Score=57.65  Aligned_cols=53  Identities=26%  Similarity=0.307  Sum_probs=41.6

Q ss_pred             CCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCC
Q 022641           56 RPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP  109 (294)
Q Consensus        56 ~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~  109 (294)
                      ...+++.+...+.....+.+++..+. ..++++||.|+||||+..++...++.+
T Consensus       233 ~~l~l~~Lg~~~~~~~~~~~~~~~p~-GliLvTGPTGSGKTTTLY~~L~~ln~~  285 (500)
T COG2804         233 VILDLEKLGMSPFQLARLLRLLNRPQ-GLILVTGPTGSGKTTTLYAALSELNTP  285 (500)
T ss_pred             ccCCHHHhCCCHHHHHHHHHHHhCCC-eEEEEeCCCCCCHHHHHHHHHHHhcCC
Confidence            34566777777777778887776654 258999999999999999999998543

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=97.65  E-value=0.00039  Score=57.15  Aligned_cols=22  Identities=36%  Similarity=0.694  Sum_probs=21.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+|+||+||||+|+.+++.+
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l   23 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKL   23 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHH
Confidence            7899999999999999999987

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.

>KOG1808 consensus AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.65  E-value=0.00016  Score=72.72  Aligned_cols=146  Identities=22%  Similarity=0.311  Sum_probs=88.3

Q ss_pred             HHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCC-
Q 022641           72 VLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGG-  150 (294)
Q Consensus        72 ~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  150 (294)
                      .+..+...+ .-.++|.||.|+|||.++..++++.      +..++.++.......   .+.+..+.....+...-+.+ 
T Consensus       431 ~~~~a~~~~-~~pillqG~tssGKtsii~~la~~~------g~~~vrinnhehtd~---qeyig~y~~~~~g~l~freg~  500 (1856)
T KOG1808|consen  431 DLARAISSG-KFPILLQGPTSSGKTSIIKELARAT------GKNIVRINNHEHTDL---QEYIGTYVADDNGDLVFREGV  500 (1856)
T ss_pred             HHHHHHhcC-CCCeEEecCcCcCchhHHHHHHHHh------ccCceehhccccchH---HHHHHhhhcCCCCCeeeehhH
Confidence            333334333 2359999999999999999999998      667777665443332   22333222211111110000 


Q ss_pred             --CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----Cc---------ceEEEEecCC------cccchHhhccccE
Q 022641          151 --YPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----KV---------TRFFFICNYI------SRIIEPLASRCAK  208 (294)
Q Consensus       151 --~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----~~---------~~ii~~~~~~------~~~~~~l~~r~~~  208 (294)
                        ....+...+++||++..+.+..+.|.++++...     ..         ..++.+-|.+      ..+..++.+|+..
T Consensus       501 LV~Alr~G~~~vlD~lnla~~dvL~aLnrllddnRel~ipe~~rlv~~h~~f~lfatqn~~~~y~grk~lsRa~~~rf~e  580 (1856)
T KOG1808|consen  501 LVQALRNGDWIVLDELNLAPHDVLEALNRLLDDNRELFIPETQRLVKAHPEFMLFATQNPPGTYGGRKILSRALRNRFIE  580 (1856)
T ss_pred             HHHHHHhCCEEEeccccccchHHHHHHHhhhhhhccccccccceeeccCcchhhhhhccCccccchhhhhhhcccccchh
Confidence              011234699999999999999999999998622     11         1122222332      2245677888888


Q ss_pred             EEecCCCHHHHHHHHHHHH
Q 022641          209 FRFKPLSEEVMSSRVLHIC  227 (294)
Q Consensus       209 i~~~~~~~~~~~~~l~~~~  227 (294)
                      ++|...+.++...++...+
T Consensus       581 ~~f~~~~e~e~~~i~~~~~  599 (1856)
T KOG1808|consen  581 LHFDDIGEEELEEILEHRC  599 (1856)
T ss_pred             hhhhhcCchhhhhhhcccc
Confidence            8887777777777765544

>COG1119 ModF ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]

Probab=97.63  E-value=0.00081  Score=53.69  Aligned_cols=54  Identities=20%  Similarity=0.283  Sum_probs=37.7

Q ss_pred             CCcEEEEEeC-CCCCCHHHHHHHHHHHHhhc---CcceEEEEecCCcccchHhhcccc
Q 022641          154 PPYKIIILDE-ADSMTEDAQNALRRTMETYS---KVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       154 ~~~~lliiDe-i~~l~~~~~~~L~~~l~~~~---~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      .++.+||+|| ++.++....+.|++.+.+..   ....++++|.....+++-+-++..
T Consensus       188 ~~P~LLiLDEP~~GLDl~~re~ll~~l~~~~~~~~~~~ll~VtHh~eEi~~~~th~ll  245 (257)
T COG1119         188 KDPELLILDEPAQGLDLIAREQLLNRLEELAASPGAPALLFVTHHAEEIPPCFTHRLL  245 (257)
T ss_pred             cCCCEEEecCccccCChHHHHHHHHHHHHHhcCCCCceEEEEEcchhhcccccceEEE
Confidence            4577999999 56777777777777776533   345588888887777766655543

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=97.63  E-value=5.5e-05  Score=56.14  Aligned_cols=22  Identities=45%  Similarity=0.699  Sum_probs=21.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.+.|||||||||+++.++..+
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~   24 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHL   24 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHh
Confidence            6789999999999999999998

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=97.63  E-value=6.5e-05  Score=58.19  Aligned_cols=24  Identities=25%  Similarity=0.403  Sum_probs=22.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.++|+|+||+||||+++.+++.+
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~   26 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVL   26 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhh
Confidence            369999999999999999999987

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.62  E-value=5.8e-05  Score=56.85  Aligned_cols=22  Identities=36%  Similarity=0.655  Sum_probs=20.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+|+||+||||+++.++..+
T Consensus         2 i~l~G~~GsGKST~a~~l~~~~   23 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAERL   23 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhhc
Confidence            6899999999999999999986

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.62  E-value=0.00062  Score=54.33  Aligned_cols=45  Identities=22%  Similarity=0.413  Sum_probs=30.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRT  132 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (294)
                      .+.|+||||+|||+++..++......   +..++.++... .....+..
T Consensus        14 i~~i~G~~GsGKT~l~~~~~~~~~~~---g~~v~yi~~e~-~~~~rl~~   58 (209)
T TIGR02237        14 ITQIYGPPGSGKTNICMILAVNAARQ---GKKVVYIDTEG-LSPERFKQ   58 (209)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECCC-CCHHHHHH
Confidence            38999999999999999998876432   34555565554 33343433

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.62  E-value=0.00023  Score=61.00  Aligned_cols=95  Identities=16%  Similarity=0.171  Sum_probs=50.0

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc--hhHHHHHHHHHHhhhcccCccCCC--------CC
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG--INVVRTKIKTFAAVAVGSGQRRGG--------YP  152 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~--------~~  152 (294)
                      ..++|+||+|+||||++..++..+...   +..+..+++...+.  ...+....... ..+......+..        ..
T Consensus       207 ~ii~lvGptGvGKTTt~akLA~~l~~~---g~~V~lItaDtyR~gAveQLk~yae~l-gvpv~~~~dp~dL~~al~~l~~  282 (407)
T PRK12726        207 RIISLIGQTGVGKTTTLVKLGWQLLKQ---NRTVGFITTDTFRSGAVEQFQGYADKL-DVELIVATSPAELEEAVQYMTY  282 (407)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCCccCccHHHHHHHHhhcC-CCCEEecCCHHHHHHHHHHHHh
Confidence            358999999999999999999876322   22333344333322  22332222211 111100000000        00


Q ss_pred             CCCcEEEEEeCCCCCC--HHHHHHHHHHHHh
Q 022641          153 CPPYKIIILDEADSMT--EDAQNALRRTMET  181 (294)
Q Consensus       153 ~~~~~lliiDei~~l~--~~~~~~L~~~l~~  181 (294)
                      ....++|+||=+++.+  ....+.|..+.+.
T Consensus       283 ~~~~D~VLIDTAGr~~~d~~~l~EL~~l~~~  313 (407)
T PRK12726        283 VNCVDHILIDTVGRNYLAEESVSEISAYTDV  313 (407)
T ss_pred             cCCCCEEEEECCCCCccCHHHHHHHHHHhhc
Confidence            1245799999998864  4455556555544

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=97.62  E-value=0.00098  Score=60.20  Aligned_cols=37  Identities=16%  Similarity=0.258  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           68 EVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        68 ~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +...+|...+....  .+++.|+.||||||=+-.+..+.
T Consensus        54 ~~r~~il~~ve~nq--vlIviGeTGsGKSTQipQyL~ea   90 (674)
T KOG0922|consen   54 KYRDQILYAVEDNQ--VLIVIGETGSGKSTQIPQYLAEA   90 (674)
T ss_pred             HHHHHHHHHHHHCC--EEEEEcCCCCCccccHhHHHHhc
Confidence            34456666666554  69999999999999776666554

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=97.61  E-value=5.4e-05  Score=57.89  Aligned_cols=22  Identities=45%  Similarity=0.773  Sum_probs=20.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++||+|+||||+++.+++.+
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRL   22 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhc
Confidence            5789999999999999999987

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.

>PRK13948 shikimate kinase; Provisional

Probab=97.61  E-value=8.6e-05  Score=57.61  Aligned_cols=33  Identities=18%  Similarity=0.317  Sum_probs=28.0

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      ..+++|+|.+|+||||+++.+++.+      +..++..+
T Consensus        10 ~~~I~LiG~~GsGKSTvg~~La~~l------g~~~iD~D   42 (182)
T PRK13948         10 VTWVALAGFMGTGKSRIGWELSRAL------MLHFIDTD   42 (182)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHc------CCCEEECC
Confidence            4579999999999999999999998      66666554

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=97.61  E-value=9.6e-05  Score=57.43  Aligned_cols=43  Identities=9%  Similarity=0.233  Sum_probs=30.5

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC--cceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      .++.++++||.- .++......+.+.+.....  ...+++++.+..
T Consensus       117 ~~p~llilDEP~~~LD~~~~~~l~~~l~~~~~~~~~tiii~sH~~~  162 (178)
T cd03229         117 MDPDVLLLDEPTSALDPITRREVRALLKSLQAQLGITVVLVTHDLD  162 (178)
T ss_pred             CCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            456799999964 6788888888888876544  356777776543

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK06696 uridine kinase; Validated

Probab=97.61  E-value=0.00013  Score=58.93  Aligned_cols=42  Identities=21%  Similarity=0.290  Sum_probs=32.2

Q ss_pred             cHHHHHHHHHHHHc---CCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           66 QEEVVRVLTNTLET---ANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        66 ~~~~~~~l~~~l~~---~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      +...+..|.+.+..   +....|.|.|++|+||||+|+.|+..+.
T Consensus         3 ~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~~l~   47 (223)
T PRK06696          3 RKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEEIK   47 (223)
T ss_pred             HHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45566777776643   3333489999999999999999999883

>TIGR01613 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain

Probab=97.61  E-value=0.00024  Score=60.13  Aligned_cols=131  Identities=19%  Similarity=0.223  Sum_probs=69.9

Q ss_pred             hhhcc-cHHHHHHHHHHHHc---CCC---CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHH
Q 022641           61 KDVAH-QEEVVRVLTNTLET---ANC---PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTK  133 (294)
Q Consensus        61 ~~~~g-~~~~~~~l~~~l~~---~~~---~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  133 (294)
                      .++.+ .+..+.-+.+++..   +..   ..++++|+.|+|||+++..+..-+ +..     ......+.  .       
T Consensus        48 ~~~~~~d~~~~~~l~~~lg~~L~~~~~~~~~~~l~G~g~nGKStl~~~l~~l~-G~~-----~~~~~~~~--~-------  112 (304)
T TIGR01613        48 LETFGGDNELIEYLQRVIGYSLTGNYTEQKLFFLYGNGGNGKSTFQNLLSNLL-GDY-----ATTAVASL--K-------  112 (304)
T ss_pred             HHHhCCCHHHHHHHHHHHhHHhcCCCCceEEEEEECCCCCcHHHHHHHHHHHh-Chh-----hccCCcch--h-------
Confidence            44443 44556666666532   211   128999999999999999887655 221     11000000  0       


Q ss_pred             HHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHH--------------hhcCcceEEEEecCCccc-
Q 022641          134 IKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTME--------------TYSKVTRFFFICNYISRI-  198 (294)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~--------------~~~~~~~ii~~~~~~~~~-  198 (294)
                      +......      ...........+++.||++.-.....+.|..+..              .......+|++||....+ 
T Consensus       113 ~~~~~~~------~f~~a~l~gk~l~~~~E~~~~~~~~~~~lK~lt~gd~i~~~~k~k~~~~~~~~~~~i~~tN~~P~~~  186 (304)
T TIGR01613       113 MNEFQEH------RFGLARLEGKRAVIGDEVQKGYRDDESTFKSLTGGDTITARFKNKDPFEFTPKFTLVQSTNHLPRIR  186 (304)
T ss_pred             hhhccCC------CchhhhhcCCEEEEecCCCCCccccHHhhhhhhcCCeEEeecccCCcEEEEEeeEEEEEcCCCCccC
Confidence            0000000      0000011234589999987532223345555553              122345688889876554 


Q ss_pred             --chHhhccccEEEec
Q 022641          199 --IEPLASRCAKFRFK  212 (294)
Q Consensus       199 --~~~l~~r~~~i~~~  212 (294)
                        ..++.+|+.+|.|+
T Consensus       187 ~~~~a~~RR~~vi~f~  202 (304)
T TIGR01613       187 GFDGGIKRRLRIIPFT  202 (304)
T ss_pred             CCChhheeeEEEEecc
Confidence              46788999888775

This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.60  E-value=0.00015  Score=60.53  Aligned_cols=24  Identities=38%  Similarity=0.606  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+||+|+||||++..++..+.
T Consensus       196 vi~~vGptGvGKTTt~~kLa~~~~  219 (282)
T TIGR03499       196 VIALVGPTGVGKTTTLAKLAARFV  219 (282)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            589999999999999999998873

>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=97.60  E-value=0.0003  Score=54.32  Aligned_cols=23  Identities=48%  Similarity=0.559  Sum_probs=20.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++++|+||+|||+++..++..+.
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~~~   25 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLK   25 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH
Confidence            78999999999999999998873

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.

>PRK14531 adenylate kinase; Provisional

Probab=97.60  E-value=8.1e-05  Score=58.10  Aligned_cols=23  Identities=43%  Similarity=0.806  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++||||+||||+++.+++.+
T Consensus         4 ~i~i~G~pGsGKsT~~~~la~~~   26 (183)
T PRK14531          4 RLLFLGPPGAGKGTQAARLCAAH   26 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            59999999999999999999987

>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=97.59  E-value=0.001  Score=50.12  Aligned_cols=20  Identities=45%  Similarity=0.818  Sum_probs=19.1

Q ss_pred             EECCCCCCHHHHHHHHHHHh
Q 022641           87 FYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        87 l~Gp~G~GKT~la~~la~~~  106 (294)
                      |.||||+||||+++.|++.+
T Consensus         1 i~G~PgsGK~t~~~~la~~~   20 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRY   20 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHH
T ss_pred             CcCCCCCChHHHHHHHHHhc
Confidence            68999999999999999998

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 ....

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=97.59  E-value=0.0009  Score=57.65  Aligned_cols=25  Identities=32%  Similarity=0.517  Sum_probs=22.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ..++|+||+|+||||+++++...+.
T Consensus       123 g~ili~G~tGSGKTT~l~al~~~i~  147 (343)
T TIGR01420       123 GLILVTGPTGSGKSTTLASMIDYIN  147 (343)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhhC
Confidence            4699999999999999999998763

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.

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=97.59  E-value=0.001  Score=62.95  Aligned_cols=121  Identities=15%  Similarity=0.153  Sum_probs=65.6

Q ss_pred             HHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcc----
Q 022641           68 EVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVG----  143 (294)
Q Consensus        68 ~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----  143 (294)
                      ..+..|...+....  .++|.||+|+||||-+-.++-+...   .....+.+..+.......+...+........+    
T Consensus        53 ~~~~~i~~ai~~~~--vvii~getGsGKTTqlP~~lle~g~---~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VG  127 (845)
T COG1643          53 AVRDEILKAIEQNQ--VVIIVGETGSGKTTQLPQFLLEEGL---GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVG  127 (845)
T ss_pred             HHHHHHHHHHHhCC--EEEEeCCCCCChHHHHHHHHHhhhc---ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceee
Confidence            44566777776654  5999999999999998877766511   11112222222211222222222222222111    


Q ss_pred             cCccC-----------------------CCCCCCCcEEEEEeCCCCCCH--H-HHHHHHHHHHhhcCcceEEEEec
Q 022641          144 SGQRR-----------------------GGYPCPPYKIIILDEADSMTE--D-AQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       144 ~~~~~-----------------------~~~~~~~~~lliiDei~~l~~--~-~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      ...+.                       ......++++|||||+|.=+-  + .+..|.+++...+....+|+++.
T Consensus       128 Y~iRfe~~~s~~Trik~mTdGiLlrei~~D~~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIimSA  203 (845)
T COG1643         128 YSIRFESKVSPRTRIKVMTDGILLREIQNDPLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMSA  203 (845)
T ss_pred             EEEEeeccCCCCceeEEeccHHHHHHHhhCcccccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEEec
Confidence            00000                       012346788999999997442  2 34556666777666677777763

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=97.59  E-value=0.0011  Score=56.68  Aligned_cols=24  Identities=38%  Similarity=0.664  Sum_probs=22.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++++||+|+||||+++++....
T Consensus       163 ~nilI~G~tGSGKTTll~aLl~~i  186 (344)
T PRK13851        163 LTMLLCGPTGSGKTTMSKTLISAI  186 (344)
T ss_pred             CeEEEECCCCccHHHHHHHHHccc
Confidence            489999999999999999999876

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.58  E-value=0.00013  Score=62.41  Aligned_cols=28  Identities=29%  Similarity=0.338  Sum_probs=24.9

Q ss_pred             CCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           80 ANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        80 ~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++.+..+|+||+|||||++++.+++.+.
T Consensus       131 GkGQR~LIvG~pGtGKTTLl~~la~~i~  158 (380)
T PRK12608        131 GKGQRGLIVAPPRAGKTVLLQQIAAAVA  158 (380)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHHH
Confidence            5566799999999999999999999874

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=97.58  E-value=9.3e-05  Score=57.09  Aligned_cols=24  Identities=38%  Similarity=0.682  Sum_probs=22.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++|+|++|+||||+++.++..+
T Consensus         5 ~~I~liG~~GaGKStl~~~La~~l   28 (172)
T PRK05057          5 RNIFLVGPMGAGKSTIGRQLAQQL   28 (172)
T ss_pred             CEEEEECCCCcCHHHHHHHHHHHc
Confidence            469999999999999999999987

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=97.56  E-value=0.0013  Score=51.91  Aligned_cols=24  Identities=25%  Similarity=0.296  Sum_probs=21.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+||.|+||||+++.++...
T Consensus        26 ~~~~ltGpNg~GKSTllr~i~~~~   49 (199)
T cd03283          26 NGILITGSNMSGKSTFLRTIGVNV   49 (199)
T ss_pred             cEEEEECCCCCChHHHHHHHHHHH
Confidence            468999999999999999998654

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 slid

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.55  E-value=0.00066  Score=59.49  Aligned_cols=23  Identities=39%  Similarity=0.577  Sum_probs=20.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+||+|+||||++..|+..+
T Consensus       193 vi~lvGpnG~GKTTtlakLA~~~  215 (420)
T PRK14721        193 VYALIGPTGVGKTTTTAKLAARA  215 (420)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            49999999999999999998764

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=97.55  E-value=0.0012  Score=52.47  Aligned_cols=25  Identities=32%  Similarity=0.449  Sum_probs=22.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ..+.|.||+|+|||||++.++....
T Consensus        34 e~~~i~G~nGsGKSTLl~~l~G~~~   58 (202)
T cd03233          34 EMVLVLGRPGSGCSTLLKALANRTE   58 (202)
T ss_pred             cEEEEECCCCCCHHHHHHHhcccCC
Confidence            4699999999999999999998763

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.55  E-value=0.00061  Score=55.07  Aligned_cols=36  Identities=31%  Similarity=0.567  Sum_probs=26.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      .++|+||||+|||+++..++.+....   +..++.++..
T Consensus        25 i~~i~G~~GsGKT~l~~~la~~~~~~---~~~v~yi~~e   60 (225)
T PRK09361         25 ITQIYGPPGSGKTNICLQLAVEAAKN---GKKVIYIDTE   60 (225)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEECC
Confidence            38999999999999999999876422   3344445444

>PTZ00088 adenylate kinase 1; Provisional

Probab=97.55  E-value=9.4e-05  Score=59.65  Aligned_cols=23  Identities=30%  Similarity=0.639  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.||||+||||+++.+++.+
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~   30 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKE   30 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            49999999999999999999998

>TIGR00174 miaA tRNA isopentenyltransferase (miaA)

Probab=97.54  E-value=0.0017  Score=54.05  Aligned_cols=22  Identities=32%  Similarity=0.703  Sum_probs=20.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+||+|+|||+++..+++.+
T Consensus         2 i~i~G~t~~GKs~la~~l~~~~   23 (287)
T TIGR00174         2 IFIMGPTAVGKSQLAIQLAKKL   23 (287)
T ss_pred             EEEECCCCCCHHHHHHHHHHhC
Confidence            7899999999999999999987

Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.

>KOG3928 consensus Mitochondrial ribosome small subunit component, mediator of apoptosis DAP3 [Translation, ribosomal structure and biogenesis]

Probab=97.54  E-value=0.0053  Score=52.67  Aligned_cols=54  Identities=9%  Similarity=0.009  Sum_probs=40.7

Q ss_pred             cccEEEecCCCHHHHHHHHHHHHHHhCCC---CCHHHHHHHHhhccCcHHHHHHHHH
Q 022641          205 RCAKFRFKPLSEEVMSSRVLHICNEEGLN---LDAEALSTLSSISQGDLRRAITYLQ  258 (294)
Q Consensus       205 r~~~i~~~~~~~~~~~~~l~~~~~~~~~~---~~~~~l~~l~~~~~G~~r~~~~~l~  258 (294)
                      -|..|++++++.+|...++.++...+=+.   .+++....+.-+++|||+....++.
T Consensus       402 pf~pi~v~nYt~~E~~~~i~YYl~~nwl~kkv~~Ee~~kql~fLSngNP~l~~~lca  458 (461)
T KOG3928|consen  402 PFVPIEVENYTLDEFEALIDYYLQSNWLLKKVPGEENIKQLYFLSNGNPSLMERLCA  458 (461)
T ss_pred             CcCccccCCCCHHHHHHHHHHHHHhhHHHhhcCcccchhhhhhhcCCCHHHHHHHHH
Confidence            45578999999999999999988754221   3477788888889999965554443

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=97.54  E-value=0.00059  Score=56.63  Aligned_cols=24  Identities=46%  Similarity=0.617  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+||+|+||||++..+|..+.
T Consensus        74 vi~l~G~~G~GKTTt~akLA~~l~   97 (272)
T TIGR00064        74 VILFVGVNGVGKTTTIAKLANKLK   97 (272)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHH
Confidence            488999999999999999998773

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.

>PRK05973 replicative DNA helicase; Provisional

Probab=97.54  E-value=0.00058  Score=55.17  Aligned_cols=23  Identities=35%  Similarity=0.481  Sum_probs=20.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.|+||+|||+++..++...
T Consensus        66 l~LIaG~PG~GKT~lalqfa~~~   88 (237)
T PRK05973         66 LVLLGARPGHGKTLLGLELAVEA   88 (237)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            38999999999999999988776

>PRK13946 shikimate kinase; Provisional

Probab=97.53  E-value=0.00011  Score=57.43  Aligned_cols=32  Identities=25%  Similarity=0.369  Sum_probs=26.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      .+|+|+|++|+|||++++.+++.+      +.+++..+
T Consensus        11 ~~I~l~G~~GsGKsti~~~LA~~L------g~~~id~D   42 (184)
T PRK13946         11 RTVVLVGLMGAGKSTVGRRLATML------GLPFLDAD   42 (184)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc------CCCeECcC
Confidence            469999999999999999999998      55555443

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=97.53  E-value=0.00011  Score=57.42  Aligned_cols=24  Identities=29%  Similarity=0.512  Sum_probs=22.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.++|.||||+||||+++.+++.+
T Consensus         4 ~ii~i~G~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360         4 KIIFIVGGPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999999887

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.

>PF13479 AAA_24: AAA domain

Probab=97.52  E-value=8.7e-05  Score=59.40  Aligned_cols=20  Identities=55%  Similarity=1.077  Sum_probs=18.3

Q ss_pred             cEEEECCCCCCHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIA  103 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la  103 (294)
                      .++|+|+||+|||+++..+-
T Consensus         5 ~~lIyG~~G~GKTt~a~~~~   24 (213)
T PF13479_consen    5 KILIYGPPGSGKTTLAASLP   24 (213)
T ss_pred             EEEEECCCCCCHHHHHHhCC
Confidence            59999999999999999883

>cd03243 ABC_MutS_homologs 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

Probab=97.52  E-value=0.0012  Score=52.35  Aligned_cols=22  Identities=32%  Similarity=0.365  Sum_probs=20.0

Q ss_pred             CcEEEECCCCCCHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~  104 (294)
                      ..++|+||.|+||||+++.++.
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            3599999999999999999984

Members of the MutS family also possess 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 clamps, and recognition of specific DNA stru

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.51  E-value=0.0021  Score=52.32  Aligned_cols=23  Identities=26%  Similarity=0.332  Sum_probs=20.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|+||+|||+++..++...
T Consensus        27 ~~~i~G~~GsGKt~l~~~~~~~~   49 (234)
T PRK06067         27 LILIEGDHGTGKSVLSQQFVYGA   49 (234)
T ss_pred             EEEEECCCCCChHHHHHHHHHHH
Confidence            48999999999999999998765

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=97.51  E-value=0.00087  Score=51.40  Aligned_cols=32  Identities=25%  Similarity=0.319  Sum_probs=24.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      ++++|++|+|||++|..++...      +.+++.+...
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~------~~~~~y~at~   33 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAEL------GGPVTYIATA   33 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhc------CCCeEEEEcc
Confidence            6899999999999999998763      3455555433

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.

>PRK11823 DNA repair protein RadA; Provisional

Probab=97.49  E-value=0.0011  Score=59.15  Aligned_cols=36  Identities=33%  Similarity=0.501  Sum_probs=26.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      .++|+|+||+|||+++..++......   +..++.++..
T Consensus        82 ~~lI~G~pG~GKTtL~lq~a~~~a~~---g~~vlYvs~E  117 (446)
T PRK11823         82 VVLIGGDPGIGKSTLLLQVAARLAAA---GGKVLYVSGE  117 (446)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEcc
Confidence            48999999999999999999876311   3344555443

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.49  E-value=0.00095  Score=69.37  Aligned_cols=121  Identities=14%  Similarity=0.201  Sum_probs=68.9

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHH-------HH
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKT-------FA  138 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~  138 (294)
                      .+.....+..++.+ ..+..+|.|++|||||++++.+...+...   +..++.+. +.......+.+....       ..
T Consensus       431 s~~Q~~Av~~il~s-~~~v~ii~G~aGTGKTt~l~~l~~~~~~~---G~~V~~lA-PTgrAA~~L~e~~g~~A~Ti~~~l  505 (1960)
T TIGR02760       431 SPSNKDAVSTLFTS-TKRFIIINGFGGTGSTEIAQLLLHLASEQ---GYEIQIIT-AGSLSAQELRQKIPRLASTFITWV  505 (1960)
T ss_pred             CHHHHHHHHHHHhC-CCCeEEEEECCCCCHHHHHHHHHHHHHhc---CCeEEEEe-CCHHHHHHHHHHhcchhhhHHHHH
Confidence            44555566655554 33468999999999999999998876322   33444443 222222222221110       00


Q ss_pred             hhhcccC-------ccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEec
Q 022641          139 AVAVGSG-------QRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       139 ~~~~~~~-------~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      .......       ...........++||+||+.+++......|++....  ....+|+++.
T Consensus       506 ~~l~~~~~~~tv~~fl~~~~~l~~~~vlIVDEAsMl~~~~~~~Ll~~a~~--~garvVlvGD  565 (1960)
T TIGR02760       506 KNLFNDDQDHTVQGLLDKSSPFSNKDIFVVDEANKLSNNELLKLIDKAEQ--HNSKLILLND  565 (1960)
T ss_pred             HhhcccccchhHHHhhcccCCCCCCCEEEEECCCCCCHHHHHHHHHHHhh--cCCEEEEEcC
Confidence            0000000       000111224567999999999999888888877654  4466777764

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=97.48  E-value=0.00015  Score=55.98  Aligned_cols=30  Identities=33%  Similarity=0.583  Sum_probs=25.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL  119 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~  119 (294)
                      +++|+|++|+|||++++.+++.+      +.+++..
T Consensus         4 ~i~~~G~~GsGKst~~~~la~~l------g~~~~d~   33 (171)
T PRK03731          4 PLFLVGARGCGKTTVGMALAQAL------GYRFVDT   33 (171)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh------CCCEEEc
Confidence            58999999999999999999998      5555543

>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]

Probab=97.48  E-value=0.0011  Score=49.00  Aligned_cols=23  Identities=30%  Similarity=0.573  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      -+++.|++|+||||++++++.++
T Consensus        14 ~i~vmGvsGsGKSTigk~L~~~l   36 (191)
T KOG3354|consen   14 VIVVMGVSGSGKSTIGKALSEEL   36 (191)
T ss_pred             eEEEEecCCCChhhHHHHHHHHh
Confidence            38999999999999999999999

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=97.47  E-value=0.00039  Score=58.56  Aligned_cols=23  Identities=35%  Similarity=0.676  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+|||+++..+++.+
T Consensus         6 ~i~i~GptgsGKt~la~~la~~~   28 (307)
T PRK00091          6 VIVIVGPTASGKTALAIELAKRL   28 (307)
T ss_pred             EEEEECCCCcCHHHHHHHHHHhC
Confidence            48999999999999999999987

>PRK10867 signal recognition particle protein; Provisional

Probab=97.46  E-value=0.00078  Score=59.37  Aligned_cols=24  Identities=42%  Similarity=0.484  Sum_probs=21.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++++|++|+||||++..+|..+.
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~l~  125 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKYLK  125 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHH
Confidence            389999999999999999998773

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=97.45  E-value=0.0017  Score=51.89  Aligned_cols=22  Identities=27%  Similarity=0.427  Sum_probs=19.9

Q ss_pred             CcEEEECCCCCCHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~  104 (294)
                      +.++|+||.|+|||++++.++.
T Consensus        30 ~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          30 SIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            4599999999999999999984

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

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=97.44  E-value=0.00079  Score=63.04  Aligned_cols=44  Identities=18%  Similarity=0.294  Sum_probs=33.1

Q ss_pred             CCCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          153 CPPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       153 ~~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                      ..++.+|++||+- .+++.....+.+.+........+|+++....
T Consensus       625 l~~P~ILlLDEaTSaLD~~sE~~I~~~L~~~~~~~T~I~IaHRl~  669 (709)
T COG2274         625 LSKPKILLLDEATSALDPETEAIILQNLLQILQGRTVIIIAHRLS  669 (709)
T ss_pred             ccCCCEEEEeCcccccCHhHHHHHHHHHHHHhcCCeEEEEEccch
Confidence            3678899999985 5677777778888877776677788876543

>cd03239 ABC_SMC_head The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms

Probab=97.44  E-value=0.0033  Score=48.75  Aligned_cols=55  Identities=18%  Similarity=0.280  Sum_probs=34.3

Q ss_pred             CcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCc-ceEEEEecCCcccchHhhccccEEEe
Q 022641          155 PYKIIILDEAD-SMTEDAQNALRRTMETYSKV-TRFFFICNYISRIIEPLASRCAKFRF  211 (294)
Q Consensus       155 ~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~-~~ii~~~~~~~~~~~~l~~r~~~i~~  211 (294)
                      ++.++++||.. .++......+.+.+...... ..+|+++.....+  ...+|+..++.
T Consensus       116 ~p~llilDEp~~~LD~~~~~~i~~~L~~~~~~g~tiIiiSH~~~~~--~~adrvi~i~~  172 (178)
T cd03239         116 PSPFYVLDEIDAALDPTNRRRVSDMIKEMAKHTSQFIVITLKKEMF--ENADKLIGVLF  172 (178)
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHHHHHhCCCEEEEEECCHHHH--hhCCeEEEEEE
Confidence            34699999987 56777777777777654333 5677777664422  23444444443

SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.44  E-value=0.0012  Score=57.35  Aligned_cols=24  Identities=42%  Similarity=0.612  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+|+||+|||+++..++..+.
T Consensus        84 lvLI~G~pG~GKStLllq~a~~~a  107 (372)
T cd01121          84 VILIGGDPGIGKSTLLLQVAARLA  107 (372)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHH
Confidence            389999999999999999998763

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.

>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]

Probab=97.43  E-value=0.0011  Score=59.09  Aligned_cols=39  Identities=31%  Similarity=0.342  Sum_probs=28.6

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |+.+++.+......  ....+++-|+|+|||.++..++..+
T Consensus        41 Q~~al~a~~~~~~~--~~~gvivlpTGaGKT~va~~~~~~~   79 (442)
T COG1061          41 QEEALDALVKNRRT--ERRGVIVLPTGAGKTVVAAEAIAEL   79 (442)
T ss_pred             HHHHHHHHHhhccc--CCceEEEeCCCCCHHHHHHHHHHHh
Confidence            44444444444443  3458899999999999999999988

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=97.42  E-value=0.0025  Score=50.57  Aligned_cols=23  Identities=30%  Similarity=0.323  Sum_probs=20.0

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~  105 (294)
                      ..++|+||.|+|||++++.++..
T Consensus        30 ~~~~l~G~n~~GKstll~~i~~~   52 (204)
T cd03282          30 RFHIITGPNMSGKSTYLKQIALL   52 (204)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            35999999999999999998744

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

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=97.42  E-value=0.00038  Score=54.83  Aligned_cols=53  Identities=13%  Similarity=0.083  Sum_probs=31.3

Q ss_pred             CcEEEEEeCCCCCC-HHHH-----HHHHHHHH-hhcCcceEEEEecCCcccchHhhcccc
Q 022641          155 PYKIIILDEADSMT-EDAQ-----NALRRTME-TYSKVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       155 ~~~lliiDei~~l~-~~~~-----~~L~~~l~-~~~~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      ...+|||||++..- ....     ....+.+. .+....-++++|..+..++..++..+.
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~~~~~~~~l~~hRh~g~diiliTQ~~~~id~~ir~lve  138 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKKVPEIIEFLAQHRHYGWDIILITQSPSQIDKFIRDLVE  138 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T----HHHHGGGGCCCTT-EEEEEES-GGGB-HHHHCCEE
T ss_pred             CCcEEEEECChhhcCCCccccccchHHHHHHHHhCcCCcEEEEEeCCHHHHhHHHHHHHh
Confidence            45699999999752 2211     12224443 344566789999999988888887655

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=97.42  E-value=0.0026  Score=55.92  Aligned_cols=24  Identities=38%  Similarity=0.504  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+|++|+||||++..+|..+.
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~~l~  125 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAYYYQ  125 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999998774

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.

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=97.42  E-value=0.0029  Score=48.28  Aligned_cols=23  Identities=39%  Similarity=0.546  Sum_probs=20.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+++||.|+|||+++++++-.+
T Consensus        23 ~~~i~G~NgsGKS~~l~~i~~~~   45 (162)
T cd03227          23 LTIITGPNGSGKSTILDAIGLAL   45 (162)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            58999999999999999976655

These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.

>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=97.41  E-value=0.00031  Score=59.36  Aligned_cols=46  Identities=28%  Similarity=0.417  Sum_probs=38.8

Q ss_pred             hhhcccHHHHHHHHHHHHcC------CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           61 KDVAHQEEVVRVLTNTLETA------NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~------~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++.|.++.+..+...+...      ..+.++|.||+|+|||++++.|.+-+
T Consensus        61 ~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~l  112 (358)
T PF08298_consen   61 DEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRGL  112 (358)
T ss_pred             ccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999998877542      33459999999999999999999887

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=97.41  E-value=0.0037  Score=50.99  Aligned_cols=39  Identities=31%  Similarity=0.369  Sum_probs=27.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcC-CC--------ccCCcceeecCCC
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFG-PE--------LYKSRVLELNASD  123 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~-~~--------~~~~~~~~~~~~~  123 (294)
                      .+|+||+|+|||+++..++..+.. ..        .....++.++..+
T Consensus         4 ~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~Ed   51 (239)
T cd01125           4 SALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAED   51 (239)
T ss_pred             eEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEECCC
Confidence            589999999999999999887531 11        1234566666655

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.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=97.40  E-value=0.00014  Score=56.47  Aligned_cols=23  Identities=30%  Similarity=0.411  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+||||+++.|+..+
T Consensus         3 ~~~i~G~sGsGKttl~~~l~~~~   25 (179)
T TIGR02322         3 LIYVVGPSGAGKDTLLDYARARL   25 (179)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999886

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.

>PRK14529 adenylate kinase; Provisional

Probab=97.40  E-value=0.0019  Score=51.70  Aligned_cols=23  Identities=30%  Similarity=0.715  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++|.||||+||||.++.|++.+
T Consensus         2 ~I~l~G~PGsGK~T~a~~La~~~   24 (223)
T PRK14529          2 NILIFGPNGSGKGTQGALVKKKY   24 (223)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            48999999999999999999998

>TIGR01351 adk adenylate kinases

Probab=97.40  E-value=0.00017  Score=57.66  Aligned_cols=22  Identities=45%  Similarity=0.844  Sum_probs=20.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+||||+||||+++.|++.+
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~   23 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKY   23 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7899999999999999999887

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.

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.40  E-value=0.00012  Score=58.48  Aligned_cols=25  Identities=32%  Similarity=0.375  Sum_probs=22.1

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ...+.|.||+|||||||.+.++--.
T Consensus        29 GEfvsilGpSGcGKSTLLriiAGL~   53 (248)
T COG1116          29 GEFVAILGPSGCGKSTLLRLIAGLE   53 (248)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3459999999999999999999866

>PRK08233 hypothetical protein; Provisional

Probab=97.40  E-value=0.00014  Score=56.62  Aligned_cols=23  Identities=30%  Similarity=0.407  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|.|+||+||||++..|+..+
T Consensus         5 iI~I~G~~GsGKtTla~~L~~~l   27 (182)
T PRK08233          5 IITIAAVSGGGKTTLTERLTHKL   27 (182)
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            47889999999999999999987

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=97.39  E-value=0.00034  Score=54.75  Aligned_cols=37  Identities=27%  Similarity=0.269  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           68 EVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        68 ~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .....|...+..+  .+++|+||+|+||||++++++..+
T Consensus        13 ~~~~~l~~~v~~g--~~i~I~G~tGSGKTTll~aL~~~i   49 (186)
T cd01130          13 LQAAYLWLAVEAR--KNILISGGTGSGKTTLLNALLAFI   49 (186)
T ss_pred             HHHHHHHHHHhCC--CEEEEECCCCCCHHHHHHHHHhhc
Confidence            3444555555554  379999999999999999999876

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=97.39  E-value=0.00031  Score=59.59  Aligned_cols=31  Identities=29%  Similarity=0.425  Sum_probs=26.6

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL  119 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~  119 (294)
                      .+|+|+|++|+|||++++.++..+      +.+++.+
T Consensus       134 ~~I~l~G~~GsGKStvg~~La~~L------g~~~id~  164 (309)
T PRK08154        134 RRIALIGLRGAGKSTLGRMLAARL------GVPFVEL  164 (309)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHc------CCCEEeH
Confidence            359999999999999999999998      6666643

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=97.39  E-value=0.0021  Score=63.69  Aligned_cols=37  Identities=22%  Similarity=0.330  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           68 EVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        68 ~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+..+...+....  .++|+|++|+||||.+=.+..+.
T Consensus        70 ~~~~~Il~~l~~~~--vvii~g~TGSGKTTqlPq~lle~  106 (1283)
T TIGR01967        70 AKREDIAEAIAENQ--VVIIAGETGSGKTTQLPKICLEL  106 (1283)
T ss_pred             HHHHHHHHHHHhCc--eEEEeCCCCCCcHHHHHHHHHHc
Confidence            33466667776544  69999999999999887666554

This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=97.38  E-value=0.0017  Score=52.75  Aligned_cols=110  Identities=18%  Similarity=0.184  Sum_probs=57.5

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc--hhHHHHHHHHHHhhh-------------cccC
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG--INVVRTKIKTFAAVA-------------VGSG  145 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~-------------~~~~  145 (294)
                      ....+-|+|.+||||||+++.+.......    .--+.+.+.+...  .....+.+..+....             .+++
T Consensus        38 ~ge~~glVGESG~GKSTlgr~i~~L~~pt----~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGG  113 (268)
T COG4608          38 EGETLGLVGESGCGKSTLGRLILGLEEPT----SGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGG  113 (268)
T ss_pred             CCCEEEEEecCCCCHHHHHHHHHcCcCCC----CceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCch
Confidence            34469999999999999999998865211    1112222222111  211222222221110             0111


Q ss_pred             ccC----CCCCCCCcEEEEEeCCCC-CCHHHHHHHHHHHHhhc--CcceEEEEecC
Q 022641          146 QRR----GGYPCPPYKIIILDEADS-MTEDAQNALRRTMETYS--KVTRFFFICNY  194 (294)
Q Consensus       146 ~~~----~~~~~~~~~lliiDei~~-l~~~~~~~L~~~l~~~~--~~~~ii~~~~~  194 (294)
                      +..    .....-++.+++.||.-. ++...+..++.++.+..  ....+++++.+
T Consensus       114 QrQRi~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~~~~lt~lFIsHD  169 (268)
T COG4608         114 QRQRIGIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQEELGLTYLFISHD  169 (268)
T ss_pred             hhhhHHHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHHHHhCCeEEEEEEE
Confidence            100    001124577999999764 45666666666665443  34556777754

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.38  E-value=0.0025  Score=51.60  Aligned_cols=23  Identities=26%  Similarity=0.342  Sum_probs=19.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++||+|||||+++..++..+
T Consensus        26 ~~~i~G~~G~GKTtl~~~~~~~~   48 (230)
T PRK08533         26 LILIEGDESTGKSILSQRLAYGF   48 (230)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            59999999999999986666555

>PRK14527 adenylate kinase; Provisional

Probab=97.37  E-value=0.00019  Score=56.43  Aligned_cols=25  Identities=44%  Similarity=0.777  Sum_probs=22.6

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +..++++||||+||||+++.+++.+
T Consensus         6 ~~~i~i~G~pGsGKsT~a~~La~~~   30 (191)
T PRK14527          6 NKVVIFLGPPGAGKGTQAERLAQEL   30 (191)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            3469999999999999999999887

>PLN02200 adenylate kinase family protein

Probab=97.37  E-value=0.00022  Score=57.83  Aligned_cols=23  Identities=30%  Similarity=0.508  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||||+||||+++.+++.+
T Consensus        45 ii~I~G~PGSGKsT~a~~La~~~   67 (234)
T PLN02200         45 ITFVLGGPGSGKGTQCEKIVETF   67 (234)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999987

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=97.37  E-value=0.002  Score=59.05  Aligned_cols=40  Identities=15%  Similarity=0.211  Sum_probs=29.4

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEec
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      .++.++++||.- .++......+.+.+........+|+++.
T Consensus       487 ~~~~iliLDE~TSaLD~~te~~I~~~l~~~~~~~TvIiItH  527 (529)
T TIGR02868       487 ADAPILLLDEPTEHLDAGTESELLEDLLAALSGKTVVVITH  527 (529)
T ss_pred             cCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEec
Confidence            577899999986 4677777778888876655555666654

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>cd01394 radB RadB

Probab=97.37  E-value=0.0041  Score=49.95  Aligned_cols=36  Identities=36%  Similarity=0.616  Sum_probs=26.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      .++|+|+||+|||+++..++......   +..++.++..
T Consensus        21 i~~i~G~~GsGKT~l~~~~a~~~~~~---g~~v~yi~~e   56 (218)
T cd01394          21 VTQVYGPPGTGKTNIAIQLAVETAGQ---GKKVAYIDTE   56 (218)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEECC
Confidence            38999999999999999999887322   3345555543

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=97.37  E-value=0.0013  Score=61.47  Aligned_cols=37  Identities=30%  Similarity=0.353  Sum_probs=27.9

Q ss_pred             ccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHH
Q 022641           65 HQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALA  101 (294)
Q Consensus        65 g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~  101 (294)
                      .|..++..+..-+......+.++.||+|+|||.++-.
T Consensus       239 ~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l  275 (630)
T TIGR00643       239 AQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAAL  275 (630)
T ss_pred             HHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHH
Confidence            4666666666666555556799999999999997643

>PTZ00293 thymidine kinase; Provisional

Probab=97.37  E-value=0.00022  Score=56.19  Aligned_cols=23  Identities=26%  Similarity=0.225  Sum_probs=19.3

Q ss_pred             cEEEECCCCCCHHH-HHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTT-TALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~-la~~la~~~  106 (294)
                      .-+++||-|+|||+ |++.+.+..
T Consensus         6 i~vi~GpMfSGKTteLLr~i~~y~   29 (211)
T PTZ00293          6 ISVIIGPMFSGKTTELMRLVKRFT   29 (211)
T ss_pred             EEEEECCCCChHHHHHHHHHHHHH
Confidence            46889999999999 888877654

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.36  E-value=0.00022  Score=55.26  Aligned_cols=25  Identities=36%  Similarity=0.383  Sum_probs=22.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ..++|+|++|+||||+++.++..+.
T Consensus         8 ~~I~i~G~~GsGKst~a~~l~~~l~   32 (176)
T PRK05541          8 YVIWITGLAGSGKTTIAKALYERLK   32 (176)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            3699999999999999999999883

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=97.36  E-value=0.00014  Score=61.50  Aligned_cols=23  Identities=35%  Similarity=0.508  Sum_probs=21.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.||+||||||+++.+|--.
T Consensus        31 f~vllGPSGcGKSTlLr~IAGLe   53 (338)
T COG3839          31 FVVLLGPSGCGKSTLLRMIAGLE   53 (338)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            59999999999999999999754

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=97.36  E-value=0.0063  Score=54.85  Aligned_cols=49  Identities=24%  Similarity=0.375  Sum_probs=35.5

Q ss_pred             CcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           58 KQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ..+.++--.+.....+..++.... ..++++||+|+||||++.++.+.+.
T Consensus       219 ~~l~~Lg~~~~~~~~l~~~~~~~~-GlilitGptGSGKTTtL~a~L~~l~  267 (486)
T TIGR02533       219 LDLETLGMSPELLSRFERLIRRPH-GIILVTGPTGSGKTTTLYAALSRLN  267 (486)
T ss_pred             CCHHHcCCCHHHHHHHHHHHhcCC-CEEEEEcCCCCCHHHHHHHHHhccC
Confidence            345555445666667776665443 3589999999999999998887763

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.36  E-value=0.00019  Score=53.79  Aligned_cols=24  Identities=29%  Similarity=0.493  Sum_probs=21.6

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|+||+|||||++.+.+|...
T Consensus        30 e~iaitGPSG~GKStllk~va~Li   53 (223)
T COG4619          30 EFIAITGPSGCGKSTLLKIVASLI   53 (223)
T ss_pred             ceEEEeCCCCccHHHHHHHHHhcc
Confidence            359999999999999999999865

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=97.36  E-value=0.0018  Score=60.13  Aligned_cols=42  Identities=21%  Similarity=0.397  Sum_probs=31.5

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCC
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYI  195 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~  195 (294)
                      .+++++++||.- .+++.....+.+.+........+|++|.+.
T Consensus       497 ~~~~ililDEptsaLD~~t~~~i~~~l~~~~~~~tvI~VtHr~  539 (582)
T PRK11176        497 RDSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRL  539 (582)
T ss_pred             hCCCEEEEECccccCCHHHHHHHHHHHHHHhCCCEEEEEecch
Confidence            567899999975 567777777888887765566677777664

>KOG2383 consensus Predicted ATPase [General function prediction only]

Probab=97.36  E-value=0.0016  Score=55.54  Aligned_cols=25  Identities=28%  Similarity=0.352  Sum_probs=20.6

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++.+.|+|..|||||+|--.+-.++
T Consensus       114 PkGlYlYG~VGcGKTmLMDlFy~~~  138 (467)
T KOG2383|consen  114 PKGLYLYGSVGCGKTMLMDLFYDAL  138 (467)
T ss_pred             CceEEEecccCcchhHHHHHHhhcC
Confidence            3459999999999999987776554

>PRK04040 adenylate kinase; Provisional

Probab=97.35  E-value=0.00018  Score=56.33  Aligned_cols=23  Identities=35%  Similarity=0.475  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|+||+||||+++.+++.+
T Consensus         4 ~i~v~G~pG~GKtt~~~~l~~~l   26 (188)
T PRK04040          4 VVVVTGVPGVGKTTVLNKALEKL   26 (188)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999987

>cd03240 ABC_Rad50 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains

Probab=97.35  E-value=0.0013  Score=52.23  Aligned_cols=43  Identities=19%  Similarity=0.261  Sum_probs=31.1

Q ss_pred             CCcEEEEEeCCC-CCCHHHHH-HHHHHHHhhcC--cceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQN-ALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~-~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      .++.++++||.. .+++.... .+.+.+.....  ...+|+++....
T Consensus       138 ~~p~illlDEP~~~LD~~~~~~~l~~~l~~~~~~~~~~iiiitH~~~  184 (204)
T cd03240         138 SNCGILALDEPTTNLDEENIEESLAEIIEERKSQKNFQLIVITHDEE  184 (204)
T ss_pred             cCCCEEEEcCCccccCHHHHHHHHHHHHHHHHhccCCEEEEEEecHH
Confidence            467899999975 67777777 88888876544  446777776643

The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=97.35  E-value=0.00014  Score=55.61  Aligned_cols=21  Identities=43%  Similarity=0.589  Sum_probs=18.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~  105 (294)
                      |+|+|++|||||||++.|++.
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            789999999999999999987

>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]

Probab=97.34  E-value=0.003  Score=58.30  Aligned_cols=227  Identities=14%  Similarity=0.077  Sum_probs=124.1

Q ss_pred             hhcCCCcchhhcccHHHHHHHHHH------HHcCCCCcEEEEC----CCCCCHHHHHHHHHHHhcC----CCccCCccee
Q 022641           53 EKYRPKQVKDVAHQEEVVRVLTNT------LETANCPHMLFYG----PPGTGKTTTALAIAHQLFG----PELYKSRVLE  118 (294)
Q Consensus        53 ~~~~~~~~~~~~g~~~~~~~l~~~------l~~~~~~~ill~G----p~G~GKT~la~~la~~~~~----~~~~~~~~~~  118 (294)
                      +..+|..+.++.+++.........      ........+...|    ++|++++..+..+.....-    .......+..
T Consensus        96 ~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~iv~~~~~~~~~~~~~~~~~~~~  175 (647)
T COG1067          96 PAGRPESFSELLGQKAEEKAEYLSYLILLALLGPIEQQIILYGYNALLPGVLYAVAARIVLYEAKILKRSAVSVPKNFVE  175 (647)
T ss_pred             cccCCcchHHHHHhhhhHHHHHHhhhhHHHhhchhhhhhhhcccccccchhhHHHHHHHHHhhhhcccchhhhhhhhhhh
Confidence            445566777777776555433222      1222223477777    9999999998766555310    0001111111


Q ss_pred             ec---CCCCc--chhHHHHHHHHHHhhhccc--------CccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh---
Q 022641          119 LN---ASDDR--GINVVRTKIKTFAAVAVGS--------GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY---  182 (294)
Q Consensus       119 ~~---~~~~~--~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~---  182 (294)
                      ..   .....  .......++.........+        ...++....+..++|||||+..|....++.+++.+...   
T Consensus       176 ~~~~~~~p~v~a~~~~~~~LlG~Vr~~~~qG~l~~~~~~~i~pGaVHkAngGVLiIdei~lL~~~~~w~~LKa~~~k~~~  255 (647)
T COG1067         176 LSPLDGAPVVFATGAIADQLLGSVRHDPYQGGLGTTGHIRVKPGAVHKANGGVLIIDEIGLLAQPLQWKLLKALLDKEQP  255 (647)
T ss_pred             hccccCCcEEecCCCChhhcceeEEEcCCCCccCCCCcccccCcccccccCcEEEEEhhhhhCcHHHHHHHHHHHhcccc
Confidence            10   00000  0111112222222222221        12456667788999999999999966666666555422   


Q ss_pred             ------------------cCcceEEEEecCC--cc---cchHhhccccE-EEecCC---CHHHHHHHHHHHHH----H-h
Q 022641          183 ------------------SKVTRFFFICNYI--SR---IIEPLASRCAK-FRFKPL---SEEVMSSRVLHICN----E-E  230 (294)
Q Consensus       183 ------------------~~~~~ii~~~~~~--~~---~~~~l~~r~~~-i~~~~~---~~~~~~~~l~~~~~----~-~  230 (294)
                                        +-...+|+++|..  ..   .++.+..-+.. ..|...   ++++...+++.+++    . +
T Consensus       256 ~~~~~~~s~~~~v~~e~vP~d~klI~~Gn~~~l~~l~~~~~~r~~g~~y~ae~~~~m~~~~~nr~k~~~~~~q~v~~d~~  335 (647)
T COG1067         256 IWGSSEPSSGAPVRPESVPLDLKLILAGNREDLEDLHEPDRSRIEGFGYEAEFEDTMPITDANRSKLVQFYVQELARDGN  335 (647)
T ss_pred             ccCcCccccCcccCCCCcccceEEEeeCCHHHHHhhcccCHHHHhhcceEEEEcCCCCCChHHHHHHHHHHHHHHHhcCC
Confidence                              2344566666532  12   23333333322 444432   45666666555554    3 2


Q ss_pred             CCCCCHHHHHHHHhhcc----------CcHHHHHHHHHHHHHHh----CCCCChhhhhhhccc
Q 022641          231 GLNLDAEALSTLSSISQ----------GDLRRAITYLQGAARLF----GSSITSKDLISVSGY  279 (294)
Q Consensus       231 ~~~~~~~~l~~l~~~~~----------G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~  279 (294)
                      -..++.+++..|.....          =.+|.+.++++.++..+    .+.|+.+||.+++..
T Consensus       336 ip~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~  398 (647)
T COG1067         336 IPHLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQK  398 (647)
T ss_pred             CCCCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHh
Confidence            34589999888776521          26888889888777666    234999999998876

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=97.34  E-value=0.00045  Score=58.50  Aligned_cols=36  Identities=25%  Similarity=0.449  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           69 VVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        69 ~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ....|..++..+.  |++++|++|+||||+++++....
T Consensus       133 ~~~~L~~~v~~~~--nilI~G~tGSGKTTll~aL~~~i  168 (323)
T PRK13833        133 QASVIRSAIDSRL--NIVISGGTGSGKTTLANAVIAEI  168 (323)
T ss_pred             HHHHHHHHHHcCC--eEEEECCCCCCHHHHHHHHHHHH
Confidence            3455566666543  89999999999999999999876

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=97.34  E-value=0.00043  Score=59.69  Aligned_cols=26  Identities=31%  Similarity=0.395  Sum_probs=23.1

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ...++++||+|+||||+++++.+.+.
T Consensus       134 ~glilI~GpTGSGKTTtL~aLl~~i~  159 (358)
T TIGR02524       134 EGIVFITGATGSGKSTLLAAIIRELA  159 (358)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHh
Confidence            34699999999999999999998873

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=97.33  E-value=0.00081  Score=54.48  Aligned_cols=46  Identities=9%  Similarity=0.231  Sum_probs=32.7

Q ss_pred             CCCcEEEEEeCC-CCCCHHHHHHHHHHHHhhcC-cceEEEEecCCccc
Q 022641          153 CPPYKIIILDEA-DSMTEDAQNALRRTMETYSK-VTRFFFICNYISRI  198 (294)
Q Consensus       153 ~~~~~lliiDei-~~l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~~~  198 (294)
                      ..+++++++||- ..++...+..+.++|.+... ...+++++.+...+
T Consensus       155 ~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~~eg~tIl~vtHDL~~v  202 (254)
T COG1121         155 AQNPDLLLLDEPFTGVDVAGQKEIYDLLKELRQEGKTVLMVTHDLGLV  202 (254)
T ss_pred             ccCCCEEEecCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEeCCcHHh
Confidence            357789999994 56778888888888876655 45566667665543

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=97.33  E-value=0.0021  Score=59.59  Aligned_cols=42  Identities=19%  Similarity=0.345  Sum_probs=31.4

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCC
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYI  195 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~  195 (294)
                      .++.++++||.- .++......+.+.+........+|++|.+.
T Consensus       486 ~~~~illLDEpts~LD~~~~~~i~~~L~~~~~~~tiIiitH~~  528 (571)
T TIGR02203       486 KDAPILILDEATSALDNESERLVQAALERLMQGRTTLVIAHRL  528 (571)
T ss_pred             cCCCEEEEeCccccCCHHHHHHHHHHHHHHhCCCEEEEEehhh
Confidence            567899999975 577777778888887765556677777654

This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.

>cd01878 HflX HflX subfamily

Probab=97.32  E-value=0.016  Score=45.86  Aligned_cols=24  Identities=25%  Similarity=0.288  Sum_probs=21.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+|++|+|||+++..+...-
T Consensus        42 ~~I~iiG~~g~GKStLl~~l~~~~   65 (204)
T cd01878          42 PTVALVGYTNAGKSTLFNALTGAD   65 (204)
T ss_pred             CeEEEECCCCCCHHHHHHHHhcch
Confidence            569999999999999999988753

A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.

>TIGR00376 DNA helicase, putative

Probab=97.32  E-value=0.00058  Score=63.53  Aligned_cols=40  Identities=35%  Similarity=0.544  Sum_probs=30.7

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++.....+..++...  +.++|.||||||||+++..+..++.
T Consensus       159 n~~Q~~Av~~~l~~~--~~~lI~GpPGTGKT~t~~~ii~~~~  198 (637)
T TIGR00376       159 NESQKEAVSFALSSK--DLFLIHGPPGTGKTRTLVELIRQLV  198 (637)
T ss_pred             CHHHHHHHHHHhcCC--CeEEEEcCCCCCHHHHHHHHHHHHH
Confidence            566666676666432  3689999999999999998888763

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	294
1sxj_D	353	Crystal Structure Of The Eukaryotic Clamp Loader (R		9e-75
2chq_A	319	Replication Factor C Adpnp Complex Length = 319		3e-63
2chg_A	226	Replication Factor C Domains 1 And 2 Length = 226		3e-63
1iqp_A	327	Crystal Structure Of The Clamp Loader Small Subunit		2e-61
1sxj_B	323	Crystal Structure Of The Eukaryotic Clamp Loader (R		1e-50
1sxj_C	340	Crystal Structure Of The Eukaryotic Clamp Loader (R		4e-50
1sxj_E	354	Crystal Structure Of The Eukaryotic Clamp Loader (R		9e-30
3u5z_B	324	Structure Of T4 Bacteriophage Clamp Loader Bound To		2e-16
1njg_A	250	Nucleotide-Free Form Of An Isolated E. Coli Clamp L		6e-13
3glf_B	395	Crystal Structure Of The Ecoli Clamp Loader Bound T		9e-13
3glh_B	376	Crystal Structure Of The E. Coli Clamp Loader Bound		1e-12
1jr3_A	373	Crystal Structure Of The Processivity Clamp Loader		1e-12
1xxi_B	368	Adp Bound E. Coli Clamp Loader Complex Length = 368		1e-12
3glg_B	395	Crystal Structure Of A Mutant (Gammat157a) E. Coli		1e-12
1sxj_A	516	Crystal Structure Of The Eukaryotic Clamp Loader (R		2e-11
1ixr_C	312	Ruva-Ruvb Complex Length = 312		6e-05
1ixs_B	318	Structure Of Ruvb Complexed With Ruva Domain Iii Le		7e-05
1hqc_A	324	Structure Of Ruvb From Thermus Thermophilus Hb8 Len		8e-05
3pvs_A	447	Structure And Biochemical Activities Of Escherichia		1e-04
1in8_A	334	Thermotoga Maritima Ruvb T158v Length = 334		2e-04
1j7k_A	334	Thermotoga Maritima Ruvb P216g Mutant Length = 334		2e-04
1in5_A	334	Thermogota Maritima Ruvb A156s Mutant Length = 334		2e-04
1in7_A	334	Thermotoga Maritima Ruvb R170a Length = 334		2e-04
1in4_A	334	Thermotoga Maritima Ruvb Holliday Junction Branch M		2e-04
1in6_A	334	Thermotoga Maritima Ruvb K64r Mutant Length = 334		4e-04

>pdb|1SXJ|D Chain D, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 353

Iteration: 1
 Score =  276 bits (706), Expect = 9e-75,   Method: Compositional matrix adjust.
 Identities = 130/218 (59%), Positives = 160/218 (73%), Gaps = 2/218 (0%)
Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL 106
           + QPWVEKYRPK + +V  Q+  V VL  TL++AN PHMLFYGPPGTGKT+T LA+  +L
Sbjct: 23  AQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKEL 82
Query: 107 FGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRG--GYPCPPYKIIILDEA 164
           +GP+L KSR+LELNASD+RGI++VR K+K FA + V    +     YPCPPYKIIILDEA
Sbjct: 83  YGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEA 142
Query: 165 DSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVL 224
           DSMT DAQ+ALRRTMETYS VTRF  ICNY++RII+PLAS+C+KFRFK L       R+ 
Sbjct: 143 DSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLR 202
Query: 225 HICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAAR 262
            I  +E +  D   L  +  IS GDLRR IT LQ A++
Sbjct: 203 FISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK 240

>pdb|2CHQ|A Chain A, Replication Factor C Adpnp Complex Length = 319

Iteration: 1
 Score =  238 bits (607), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 117/217 (53%), Positives = 150/217 (69%), Gaps = 9/217 (4%)
Query: 45  LQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAH 104
           +++ + WVEKYRP+ + +V  Q+EV++ L   +E  N PH+LF GPPGTGKT TA+A+A 
Sbjct: 1   MENFEIWVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALAR 60
Query: 105 QLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEA 164
            LFG E ++   +E+NASD+RGI+VVR KIK FA  A   G         P+KII LDEA
Sbjct: 61  DLFG-ENWRDNFIEMNASDERGIDVVRHKIKEFARTAPIGG--------APFKIIFLDEA 111
Query: 165 DSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVL 224
           D++T DAQ ALRRTME YSK  RF   CNY+SRIIEP+ SRCA FRFKP+ +E M  R+L
Sbjct: 112 DALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLL 171
Query: 225 HICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA 261
            IC +EG+ +  + L  L  IS GD R+AI  LQGAA
Sbjct: 172 EICEKEGVKITEDGLEALIYISGGDFRKAINALQGAA 208

>pdb|2CHG|A Chain A, Replication Factor C Domains 1 And 2 Length = 226

Iteration: 1
 Score =  238 bits (607), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 117/219 (53%), Positives = 151/219 (68%), Gaps = 9/219 (4%)
Query: 45  LQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAH 104
           +++ + WVEKYRP+ + +V  Q+EV++ L   +E  N PH+LF GPPGTGKT TA+A+A 
Sbjct: 1   MENFEIWVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALAR 60
Query: 105 QLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEA 164
            LFG E ++   +E+NASD+RGI+VVR KIK FA  A   G         P+KII LDEA
Sbjct: 61  DLFG-ENWRDNFIEMNASDERGIDVVRHKIKEFARTAPIGG--------APFKIIFLDEA 111
Query: 165 DSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVL 224
           D++T DAQ ALRRTME YSK  RF   CNY+SRIIEP+ SRCA FRFKP+ +E M  R+L
Sbjct: 112 DALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLL 171
Query: 225 HICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARL 263
            IC +EG+ +  + L  L  IS GD R+AI  LQGAA +
Sbjct: 172 EICEKEGVKITEDGLEALIYISGGDFRKAINALQGAAAI 210

>pdb|1IQP|A Chain A, Crystal Structure Of The Clamp Loader Small Subunit From Pyrococcus Furiosus Length = 327

Iteration: 1
 Score =  232 bits (592), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 115/230 (50%), Positives = 155/230 (67%), Gaps = 10/230 (4%)
Query: 48  SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF 107
            +PWVEKYRP+++ D+  QE +V+ L + ++T + PH+LF GPPG GKTT ALA+A +LF
Sbjct: 12  EKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELF 71
Query: 108 GPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSM 167
           G E ++   LELNASD+RGINV+R K+K FA      G          +KII LDEAD++
Sbjct: 72  G-ENWRHNFLELNASDERGINVIREKVKEFARTKPIGG--------ASFKIIFLDEADAL 122
Query: 168 TEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHIC 227
           T+DAQ ALRRTME +S   RF   CNY S+IIEP+ SRCA FRF+PL +E ++ R+ +I 
Sbjct: 123 TQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIA 182
Query: 228 NEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVS 277
             EGL L  E L  +  I++GD+RRAI  LQ AA L    IT +++  V+
Sbjct: 183 ENEGLELTEEGLQAILYIAEGDMRRAINILQAAAAL-DKKITDENVFMVA 231

>pdb|1SXJ|B Chain B, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 323

Iteration: 1
 Score =  196 bits (499), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 102/218 (46%), Positives = 133/218 (61%), Gaps = 8/218 (3%)
Query: 41  MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 100
           M+  L    PWVEKYRP+ + D+   +E +  L    +  N PHM+  G PG GKTT+  
Sbjct: 1   MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH 60
Query: 101 AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII 160
            +AH+L G   Y   VLELNASDDRGI+VVR +IK FA       Q++   P   +KI+I
Sbjct: 61  CLAHELLGRS-YADGVLELNASDDRGIDVVRNQIKHFA-------QKKLHLPPGKHKIVI 112
Query: 161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 220
           LDEADSMT  AQ ALRRTME YS  TRF F CN  ++IIEPL S+CA  R+  LS+E + 
Sbjct: 113 LDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVL 172
Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQ 258
            R+L I   E +    + L  +   ++GD+R+AI  LQ
Sbjct: 173 KRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQ 210

>pdb|1SXJ|C Chain C, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 340

Iteration: 1
 Score =  194 bits (494), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 97/209 (46%), Positives = 135/209 (64%), Gaps = 9/209 (4%)
Query: 50  PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP 109
           PWVEKYRP+ + +V  Q EV+  +   ++    PH+LFYGPPGTGKT+T +A+A +++G 
Sbjct: 14  PWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGK 73
Query: 110 ELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE 169
             Y + VLELNASDDRGI+VVR +IK FA+        R  +    +K+IILDEAD+MT 
Sbjct: 74  N-YSNMVLELNASDDRGIDVVRNQIKDFAST-------RQIF-SKGFKLIILDEADAMTN 124
Query: 170 DAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE 229
            AQNALRR +E Y+K TRF  + NY  ++   L S+C +FRF+PL +E +  R+ ++   
Sbjct: 125 AAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVH 184
Query: 230 EGLNLDAEALSTLSSISQGDLRRAITYLQ 258
           E L L   A   L  +S GD+RR +  LQ
Sbjct: 185 EKLKLSPNAEKALIELSNGDMRRVLNVLQ 213

>pdb|1SXJ|E Chain E, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 354

Iteration: 1
 Score =  127 bits (318), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 82/242 (33%), Positives = 125/242 (51%), Gaps = 35/242 (14%)
Query: 51  WVEKYRPKQVKDVAHQEEVVRVLTNTLETA-----NCPHMLFYGPPGTGKTTTALAIAHQ 105
           WV+KYRPK +  ++H EE    LTN L++      + PH+L YGP GTGK T  +A+   
Sbjct: 4   WVDKYRPKSLNALSHNEE----LTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLES 59
Query: 106 LFGPELYK------------SRVLELNASD----------DRGIN---VVRTKIKTFAAV 140
           +FGP +Y+            +R LELN             D G N   V++  +K  A +
Sbjct: 60  IFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQM 119
Query: 141 AVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIE 200
                Q         YK +I++EA+S+T+DAQ ALRRTME YSK  R   +C+ +S II 
Sbjct: 120 EQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIA 179
Query: 201 PLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDA-EALSTLSSISQGDLRRAITYLQG 259
           P+ S+C   R    S+  +S+ +  +   E + L+  + L  ++  S G+LR ++  L+ 
Sbjct: 180 PIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLES 239
Query: 260 AA 261
            A
Sbjct: 240 MA 241

>pdb|3U5Z|B Chain B, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4 Clamp, Primer-Template Dna, And Atp Analog Length = 324

Iteration: 1
 Score = 82.8 bits (203), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 107/231 (46%), Gaps = 32/231 (13%)
Query: 41  MAPVLQSSQPWVEKYRPKQVKDV---AHQEEVVRVLTNTLETANCPHMLFYGP-PGTGKT 96
           M  V +      +KYRP  + +    A  +E  + +T+       PH++ + P PGTGKT
Sbjct: 6   MITVNEKEHILEQKYRPSTIDECILPAFDKETFKSITSK---GKIPHIILHSPSPGTGKT 62
Query: 97  TTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPY 156
           T A A+ H +    ++      +N SD + I+ VR  +  FA+ A   G++         
Sbjct: 63  TVAKALCHDVNADMMF------VNGSDCK-IDFVRGPLTNFASAASFDGRQ--------- 106
Query: 157 KIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRF-KPL 214
           K+I++DE D S   ++Q  LR  ME YS         N I  II+PL SRC    F +P 
Sbjct: 107 KVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPT 166
Query: 215 SEE------VMSSRVLHICNEEGLNL-DAEALSTLSSISQGDLRRAITYLQ 258
            E+       M  R+  IC  EG+ + D + ++ L   +  D R+ I  L 
Sbjct: 167 DEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGELD 217

>pdb|1NJG|A Chain A, Nucleotide-Free Form Of An Isolated E. Coli Clamp Loader Gamma Subunit Length = 250

Iteration: 1
 Score = 71.2 bits (173), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 99/227 (43%), Gaps = 27/227 (11%)
Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQ 105
           S Q    K+RP+   DV  QE V+  L N L      H  LF G  G GKT+ A  +A  
Sbjct: 9   SYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKG 68
Query: 106 LFGP---------------ELYKSRVLELNASDDRGINVVRTKIKTFAAVA--VGSGQRR 148
           L                  E+ + R ++L   D       RTK++    +   V     R
Sbjct: 69  LNCETGITATPCGVCDNCREIEQGRFVDLIEID----AASRTKVEDTRDLLDNVQYAPAR 124
Query: 149 GGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAK 208
           G      +K+ ++DE   ++  + NAL +T+E   +  +F        ++   + SRC +
Sbjct: 125 G-----RFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQ 179
Query: 209 FRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAIT 255
           F  K L  E +  ++ HI NEE +  +  AL  L+  ++G LR A++
Sbjct: 180 FHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALS 226

>pdb|3GLF|B Chain B, Crystal Structure Of The Ecoli Clamp Loader Bound To Primer-template Dna Length = 395

Iteration: 1
 Score = 70.9 bits (172), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 99/227 (43%), Gaps = 27/227 (11%)
Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQ 105
           S Q    K+RP+   DV  QE V+  L N L      H  LF G  G GKT+ A  +A  
Sbjct: 24  SYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKG 83
Query: 106 LFGP---------------ELYKSRVLELNASDDRGINVVRTKIKTFAAVA--VGSGQRR 148
           L                  E+ + R ++L   D       RTK++    +   V     R
Sbjct: 84  LNCETGITATPCGVCDNCREIEQGRFVDLIEID----AASRTKVEDTRDLLDNVQYAPAR 139
Query: 149 GGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAK 208
           G +     K+ ++DE   ++  + NAL +T+E   +  +F        ++   + SRC +
Sbjct: 140 GRF-----KVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQ 194
Query: 209 FRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAIT 255
           F  K L  E +  ++ HI NEE +  +  AL  L+  ++G LR A++
Sbjct: 195 FHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALS 241

>pdb|3GLH|B Chain B, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi Peptide Length = 376

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 99/227 (43%), Gaps = 27/227 (11%)
Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQ 105
           S Q    K+RP+   DV  QE V+  L N L      H  LF G  G GKT+ A  +A  
Sbjct: 5   SYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKG 64
Query: 106 LFGP---------------ELYKSRVLELNASDDRGINVVRTKIKTFAAVA--VGSGQRR 148
           L                  E+ + R ++L   D       RTK++    +   V     R
Sbjct: 65  LNCETGITATPCGVCDNCREIEQGRFVDLIEID----AASRTKVEDTRDLLDNVQYAPAR 120
Query: 149 GGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAK 208
           G +     K+ ++DE   ++  + NAL +T+E   +  +F        ++   + SRC +
Sbjct: 121 GRF-----KVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQ 175
Query: 209 FRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAIT 255
           F  K L  E +  ++ HI NEE +  +  AL  L+  ++G LR A++
Sbjct: 176 FHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALS 222

>pdb|1JR3|A Chain A, Crystal Structure Of The Processivity Clamp Loader Gamma Complex Of E. Coli Dna Polymerase Iii Length = 373

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 99/227 (43%), Gaps = 27/227 (11%)
Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQ 105
           S Q    K+RP+   DV  QE V+  L N L      H  LF G  G GKT+ A  +A  
Sbjct: 2   SYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKG 61
Query: 106 LFGP---------------ELYKSRVLELNASDDRGINVVRTKIKTFAAVA--VGSGQRR 148
           L                  E+ + R ++L   D       RTK++    +   V     R
Sbjct: 62  LNCETGITATPCGVCDNCREIEQGRFVDLIEID----AASRTKVEDTRDLLDNVQYAPAR 117
Query: 149 GGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAK 208
           G +     K+ ++DE   ++  + NAL +T+E   +  +F        ++   + SRC +
Sbjct: 118 GRF-----KVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQ 172
Query: 209 FRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAIT 255
           F  K L  E +  ++ HI NEE +  +  AL  L+  ++G LR A++
Sbjct: 173 FHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALS 219

>pdb|1XXI|B Chain B, Adp Bound E. Coli Clamp Loader Complex Length = 368

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 99/227 (43%), Gaps = 27/227 (11%)
Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQ 105
           S Q    K+RP+   DV  QE V+  L N L      H  LF G  G GKT+ A  +A  
Sbjct: 2   SYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKG 61
Query: 106 LFGP---------------ELYKSRVLELNASDDRGINVVRTKIKTFAAVA--VGSGQRR 148
           L                  E+ + R ++L   D       RTK++    +   V     R
Sbjct: 62  LNCETGITATPCGVCDNCREIEQGRFVDLIEID----AASRTKVEDTRDLLDNVQYAPAR 117
Query: 149 GGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAK 208
           G +     K+ ++DE   ++  + NAL +T+E   +  +F        ++   + SRC +
Sbjct: 118 GRF-----KVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQ 172
Query: 209 FRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAIT 255
           F  K L  E +  ++ HI NEE +  +  AL  L+  ++G LR A++
Sbjct: 173 FHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALS 219

>pdb|3GLG|B Chain B, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp Loader Bound To Primer-Template Dna Length = 395

Iteration: 1
 Score = 70.1 bits (170), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 99/227 (43%), Gaps = 27/227 (11%)
Query: 47  SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHM-LFYGPPGTGKTTTALAIAHQ 105
           S Q    K+RP+   DV  QE V+  L N L      H  LF G  G GKT+ A  +A  
Sbjct: 24  SYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKG 83
Query: 106 LFGP---------------ELYKSRVLELNASDDRGINVVRTKIKTFAAVA--VGSGQRR 148
           L                  E+ + R ++L   D       RTK++    +   V     R
Sbjct: 84  LNCETGITATPCGVCDNCREIEQGRFVDLIEID----AASRTKVEDTRDLLDNVQYAPAR 139
Query: 149 GGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAK 208
           G +     K+ ++DE   ++  + NAL +T+E   +  +F        ++   + SRC +
Sbjct: 140 GRF-----KVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATADPQKLPVTILSRCLQ 194
Query: 209 FRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAIT 255
           F  K L  E +  ++ HI NEE +  +  AL  L+  ++G LR A++
Sbjct: 195 FHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALS 241

>pdb|1SXJ|A Chain A, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 516

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/241 (24%), Positives = 94/241 (39%), Gaps = 33/241 (13%)
Query: 42  APVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH----------------- 84
            P + S + W  KY P  ++ V   +  V  L N L  AN  +                 
Sbjct: 20  GPHMASDKLWTVKYAPTNLQQVCGNKGSVMKLKNWL--ANWENSKKNSFKHAGKDGSGVF 77
Query: 85  --MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINV----VRTKIKTFA 138
              + YGPPG GKTT A  +A +L         +LE NASD R   +    V+  +   +
Sbjct: 78  RAAMLYGPPGIGKTTAAHLVAQEL------GYDILEQNASDVRSKTLLNAGVKNALDNMS 131
Query: 139 AVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKV-TRFFFICNYISR 197
            V               + +II+DE D M+   +  + +  +   K  T    ICN  + 
Sbjct: 132 VVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNL 191
Query: 198 -IIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITY 256
             + P    C   +F+      + SR++ I   E   LD   +  L   ++GD+R+ I  
Sbjct: 192 PKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINL 251
Query: 257 L 257
           L
Sbjct: 252 L 252

>pdb|1IXR|C Chain C, Ruva-Ruvb Complex Length = 312

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 5/56 (8%)
Query: 56  RPKQVKDVAHQEEVVRVLTNTLETANC-----PHMLFYGPPGTGKTTTALAIAHQL 106
           RPK + +   QE + + L   LE A        H+L +GPPG GKTT A  IAH+L
Sbjct: 7   RPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL 62

>pdb|1IXS|B Chain B, Structure Of Ruvb Complexed With Ruva Domain Iii Length = 318

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 5/56 (8%)
Query: 56  RPKQVKDVAHQEEVVRVLTNTLETANC-----PHMLFYGPPGTGKTTTALAIAHQL 106
           RPK + +   QE + + L   LE A        H+L +GPPG GKTT A  IAH+L
Sbjct: 7   RPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL 62

>pdb|1HQC|A Chain A, Structure Of Ruvb From Thermus Thermophilus Hb8 Length = 324

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 5/56 (8%)
Query: 56  RPKQVKDVAHQEEVVRVLTNTLETANC-----PHMLFYGPPGTGKTTTALAIAHQL 106
           RPK + +   QE + + L   LE A        H+L +GPPG GKTT A  IAH+L
Sbjct: 7   RPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL 62

>pdb|3PVS|A Chain A, Structure And Biochemical Activities Of Escherichia Coli Mgsa Length = 447

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 51/225 (22%), Positives = 90/225 (40%), Gaps = 27/225 (12%)
Query: 49  QPWVEKYRPKQVKDVAHQEEVV---RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQ 105
           QP   + RP+ +     Q+ ++   + L   +E  +   M+ +GPPGTGKTT A  IA  
Sbjct: 14  QPLAARMRPENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIAR- 72
Query: 106 LFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEAD 165
                 Y +  +E  ++   G+  +R  I+  A     +G+R          I+ +DE  
Sbjct: 73  ------YANADVERISAVTSGVKEIREAIER-ARQNRNAGRR---------TILFVDEVH 116
Query: 166 SMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLH 225
              +  Q+A    +E  +         N    +   L SR   +  K LS E +   +  
Sbjct: 117 RFNKSQQDAFLPHIEDGTITFIGATTENPSFELNSALLSRARVYLLKSLSTEDIEQVLTQ 176
Query: 226 ICNE-------EGLNLDAEALSTLSSISQGDLRRAITYLQGAARL 263
              +       + + L  E    ++ +  GD RRA+  L+  A +
Sbjct: 177 AMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTLEMMADM 221

>pdb|1IN8|A Chain A, Thermotoga Maritima Ruvb T158v Length = 334

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 52  VEKYRPKQVKDVAHQEEVVRVLTNTLETAN-----CPHMLFYGPPGTGKTTTALAIAHQL 106
           V+  RPK + +   QE V + L+  LE A        H+L  GPPG GKTT A  IA +L
Sbjct: 16  VQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL 75

>pdb|1J7K|A Chain A, Thermotoga Maritima Ruvb P216g Mutant Length = 334

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 52  VEKYRPKQVKDVAHQEEVVRVLTNTLETAN-----CPHMLFYGPPGTGKTTTALAIAHQL 106
           V+  RPK + +   QE V + L+  LE A        H+L  GPPG GKTT A  IA +L
Sbjct: 16  VQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL 75

>pdb|1IN5|A Chain A, Thermogota Maritima Ruvb A156s Mutant Length = 334

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 52  VEKYRPKQVKDVAHQEEVVRVLTNTLETAN-----CPHMLFYGPPGTGKTTTALAIAHQL 106
           V+  RPK + +   QE V + L+  LE A        H+L  GPPG GKTT A  IA +L
Sbjct: 16  VQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL 75

>pdb|1IN7|A Chain A, Thermotoga Maritima Ruvb R170a Length = 334

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 52  VEKYRPKQVKDVAHQEEVVRVLTNTLETAN-----CPHMLFYGPPGTGKTTTALAIAHQL 106
           V+  RPK + +   QE V + L+  LE A        H+L  GPPG GKTT A  IA +L
Sbjct: 16  VQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL 75

>pdb|1IN4|A Chain A, Thermotoga Maritima Ruvb Holliday Junction Branch Migration Motor Length = 334

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 52  VEKYRPKQVKDVAHQEEVVRVLTNTLETAN-----CPHMLFYGPPGTGKTTTALAIAHQL 106
           V+  RPK + +   QE V + L+  LE A        H+L  GPPG GKTT A  IA +L
Sbjct: 16  VQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL 75

>pdb|1IN6|A Chain A, Thermotoga Maritima Ruvb K64r Mutant Length = 334

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 52  VEKYRPKQVKDVAHQEEVVRVLTNTLETAN-----CPHMLFYGPPGTGKTTTALAIAHQL 106
           V+  RPK + +   QE V + L+  LE A        H+L  GPPG G+TT A  IA +L
Sbjct: 16  VQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGRTTLAHIIASEL 75

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	294
2chg_A	226	Replication factor C small subunit; DNA-binding pr	1e-132
2chq_A	319	Replication factor C small subunit; DNA-binding pr	1e-129
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	1e-128
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	1e-127
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	1e-125
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	1e-124
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	1e-105
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	1e-104
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	1e-101
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	1e-26
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	2e-26
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	2e-23
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	7e-15
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	2e-14
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	3e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-12
3pvs_A	447	Replication-associated recombination protein A; ma	1e-10
3pvs_A	447	Replication-associated recombination protein A; ma	1e-05
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	6e-10
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	4e-09
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	4e-09
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	1e-08
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	7e-08
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	3e-07
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	8e-07
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	1e-06
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	2e-06
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-05
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-05
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-05
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	3e-05
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	7e-05
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	7e-05
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	8e-05
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	2e-04
2qgz_A	308	Helicase loader, putative primosome component; str	2e-04
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	2e-04
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	4e-04
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	5e-04
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	6e-04
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	7e-04
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	7e-04
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	7e-04
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	7e-04
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	8e-04
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	9e-04

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus} Length = 226

 Score =  371 bits (956), Expect = e-132
 Identities = 116/234 (49%), Positives = 155/234 (66%), Gaps = 10/234 (4%)

Query: 45  LQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAH 104
           +++ + WVEKYRP+ + +V  Q+EV++ L   +E  N PH+LF GPPGTGKT TA+A+A 
Sbjct: 1   MENFEIWVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALAR 60

Query: 105 QLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEA 164
            LFG E ++   +E+NASD+RGI+VVR KIK FA        R       P+KII LDEA
Sbjct: 61  DLFG-ENWRDNFIEMNASDERGIDVVRHKIKEFA--------RTAPIGGAPFKIIFLDEA 111

Query: 165 DSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVL 224
           D++T DAQ ALRRTME YSK  RF   CNY+SRIIEP+ SRCA FRFKP+ +E M  R+L
Sbjct: 112 DALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLL 171

Query: 225 HICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
            IC +EG+ +  + L  L  IS GD R+AI  LQGAA +    + +  +  ++ 
Sbjct: 172 EICEKEGVKITEDGLEALIYISGGDFRKAINALQGAAAIGE-VVDADTIYQITA 224

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A Length = 319

 Score =  369 bits (950), Expect = e-129
 Identities = 115/237 (48%), Positives = 154/237 (64%), Gaps = 10/237 (4%)

Query: 45  LQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAH 104
           +++ + WVEKYRP+ + +V  Q+EV++ L   +E  N PH+LF GPPGTGKT TA+A+A 
Sbjct: 1   MENFEIWVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALAR 60

Query: 105 QLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEA 164
            LFG   ++   +E+NASD+RGI+VVR KIK FA        R       P+KII LDEA
Sbjct: 61  DLFGEN-WRDNFIEMNASDERGIDVVRHKIKEFA--------RTAPIGGAPFKIIFLDEA 111

Query: 165 DSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVL 224
           D++T DAQ ALRRTME YSK  RF   CNY+SRIIEP+ SRCA FRFKP+ +E M  R+L
Sbjct: 112 DALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLL 171

Query: 225 HICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPT 281
            IC +EG+ +  + L  L  IS GD R+AI  LQGAA +    + +  +  ++    
Sbjct: 172 EICEKEGVKITEDGLEALIYISGGDFRKAINALQGAAAIGE-VVDADTIYQITATAR 227

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20 Length = 327

 Score =  366 bits (941), Expect = e-128
 Identities = 115/241 (47%), Positives = 157/241 (65%), Gaps = 10/241 (4%)

Query: 40  KMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTA 99
           ++  V    +PWVEKYRP+++ D+  QE +V+ L + ++T + PH+LF GPPG GKTT A
Sbjct: 4   EIREVKVLEKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAA 63

Query: 100 LAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKII 159
           LA+A +LFG   ++   LELNASD+RGINV+R K+K FA        R        +KII
Sbjct: 64  LALARELFGEN-WRHNFLELNASDERGINVIREKVKEFA--------RTKPIGGASFKII 114

Query: 160 ILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVM 219
            LDEAD++T+DAQ ALRRTME +S   RF   CNY S+IIEP+ SRCA FRF+PL +E +
Sbjct: 115 FLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDI 174

Query: 220 SSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGY 279
           + R+ +I   EGL L  E L  +  I++GD+RRAI  LQ AA L    IT +++  V+  
Sbjct: 175 AKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALDK-KITDENVFMVASR 233

Query: 280 P 280
            
Sbjct: 234 A 234

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 323

 Score =  365 bits (938), Expect = e-127
 Identities = 104/240 (43%), Positives = 140/240 (58%), Gaps = 9/240 (3%)

Query: 41  MAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTAL 100
           M+  L    PWVEKYRP+ + D+   +E +  L    +  N PHM+  G PG GKTT+  
Sbjct: 1   MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH 60

Query: 101 AIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII 160
            +AH+L G   Y   VLELNASDDRGI+VVR +IK FA       Q++   P   +KI+I
Sbjct: 61  CLAHELLGRS-YADGVLELNASDDRGIDVVRNQIKHFA-------QKKLHLPPGKHKIVI 112

Query: 161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMS 220
           LDEADSMT  AQ ALRRTME YS  TRF F CN  ++IIEPL S+CA  R+  LS+E + 
Sbjct: 113 LDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVL 172

Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYP 280
            R+L I   E +    + L  +   ++GD+R+AI  LQ      G  + + ++  +   P
Sbjct: 173 KRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHG-LVNADNVFKIVDSP 231

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 353

 Score =  361 bits (927), Expect = e-125
 Identities = 136/265 (51%), Positives = 176/265 (66%), Gaps = 10/265 (3%)

Query: 23  FSTTQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANC 82
           F     + ++   ++  + +    + QPWVEKYRPK + +V  Q+  V VL  TL++AN 
Sbjct: 2   FEGFGPNKKRKISKLAAEQS---LAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANL 58

Query: 83  PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAV 142
           PHMLFYGPPGTGKT+T LA+  +L+GP+L KSR+LELNASD+RGI++VR K+K FA + V
Sbjct: 59  PHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTV 118

Query: 143 --GSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIE 200
              S      YPCPPYKIIILDEADSMT DAQ+ALRRTMETYS VTRF  ICNY++RII+
Sbjct: 119 SKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIID 178

Query: 201 PLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGA 260
           PLAS+C+KFRFK L       R+  I  +E +  D   L  +  IS GDLRR IT LQ A
Sbjct: 179 PLASQCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSA 238

Query: 261 ARLFG-----SSITSKDLISVSGYP 280
           ++         +ITS  +  ++G  
Sbjct: 239 SKGAQYLGDGKNITSTQVEELAGVV 263

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 340

 Score =  356 bits (916), Expect = e-124
 Identities = 99/239 (41%), Positives = 141/239 (58%), Gaps = 13/239 (5%)

Query: 46  QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQ 105
           + + PWVEKYRP+ + +V  Q EV+  +   ++    PH+LFYGPPGTGKT+T +A+A +
Sbjct: 10  KENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALARE 69

Query: 106 LFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEAD 165
           ++G   Y + VLELNASDDRGI+VVR +IK FA+                +K+IILDEAD
Sbjct: 70  IYGKN-YSNMVLELNASDDRGIDVVRNQIKDFASTRQ--------IFSKGFKLIILDEAD 120

Query: 166 SMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLH 225
           +MT  AQNALRR +E Y+K TRF  + NY  ++   L S+C +FRF+PL +E +  R+ +
Sbjct: 121 AMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIAN 180

Query: 226 ICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGS----SITSKDLISVSGYP 280
           +   E L L   A   L  +S GD+RR +  LQ       +     I+   +    G P
Sbjct: 181 VLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAP 239

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 354

 Score =  309 bits (794), Expect = e-105
 Identities = 77/260 (29%), Positives = 128/260 (49%), Gaps = 27/260 (10%)

Query: 49  QPWVEKYRPKQVKDVAHQEEVVRVLTN-TLETANCPHMLFYGPPGTGKTTTALAIAHQLF 107
             WV+KYRPK +  ++H EE+   L + + +  + PH+L YGP GTGK T  +A+   +F
Sbjct: 2   SLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIF 61

Query: 108 GPELYKSRV-----------------------LELNASDDRGIN--VVRTKIKTFAAVAV 142
           GP +Y+ ++                       LE+  SD    +  V++  +K  A +  
Sbjct: 62  GPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQ 121

Query: 143 GSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPL 202
              Q         YK +I++EA+S+T+DAQ ALRRTME YSK  R   +C+ +S II P+
Sbjct: 122 VDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPI 181

Query: 203 ASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDA-EALSTLSSISQGDLRRAITYLQGAA 261
            S+C   R    S+  +S+ +  +   E + L+  + L  ++  S G+LR ++  L+  A
Sbjct: 182 KSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMA 241

Query: 262 RLFGSSITSKDLISVSGYPT 281
                ++ S   I    +  
Sbjct: 242 LNNELALKSSSPIIKPDWII 261

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B* Length = 324

 Score =  305 bits (782), Expect = e-104
 Identities = 66/252 (26%), Positives = 103/252 (40%), Gaps = 28/252 (11%)

Query: 40  KMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGP-PGTGKTTT 98
            M  V +      +KYRP  + +            +       PH++ + P PGTGKTT 
Sbjct: 5   SMITVNEKEHILEQKYRPSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTV 64

Query: 99  ALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKI 158
           A A+ H +         ++ +N SD + I+ VR  +  FA+ A               K+
Sbjct: 65  AKALCHDVNAD------MMFVNGSDCK-IDFVRGPLTNFASAAS---------FDGRQKV 108

Query: 159 IILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEE 217
           I++DE D S   ++Q  LR  ME YS         N I  II+PL SRC    F   ++E
Sbjct: 109 IVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDE 168

Query: 218 -------VMSSRVLHICNEEGLNL-DAEALSTLSSISQGDLRRAITYLQGAARLFGSSIT 269
                   M  R+  IC  EG+ + D + ++ L   +  D R+ I  L   +      + 
Sbjct: 169 DKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGELDSYSS--KGVLD 226

Query: 270 SKDLISVSGYPT 281
           +  L  V+    
Sbjct: 227 AGILSLVTNDRG 238

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 516

 Score =  306 bits (784), Expect = e-101
 Identities = 60/280 (21%), Positives = 102/280 (36%), Gaps = 30/280 (10%)

Query: 24  STTQSSPEKSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLE----- 78
            ++      S         P + S + W  KY P  ++ V   +  V  L N L      
Sbjct: 2   GSSHHHHHHSSGLEVLFQGPHMASDKLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENS 61

Query: 79  ------------TANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG 126
                       +      + YGPPG GKTT A  +A +L         +LE NASD R 
Sbjct: 62  KKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL------GYDILEQNASDVRS 115

Query: 127 INVVRTKIKTFA----AVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY 182
             ++   +K        V               + +II+DE D M+   +  + +  +  
Sbjct: 116 KTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFC 175

Query: 183 SKVTRFF-FICNYIS-RIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALS 240
            K +     ICN  +   + P    C   +F+      + SR++ I   E   LD   + 
Sbjct: 176 RKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVID 235

Query: 241 TLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYP 280
            L   ++GD+R+ I  L   +     +I  +++  +S   
Sbjct: 236 RLIQTTRGDIRQVINLLSTISTTTK-TINHENINEISKAW 274

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A* Length = 250

 Score =  103 bits (259), Expect = 1e-26
 Identities = 59/246 (23%), Positives = 106/246 (43%), Gaps = 33/246 (13%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQL---FGP 109
           K+RP+   DV  QE V+  L N L      H  LF G  G GKT+ A  +A  L    G 
Sbjct: 16  KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 75

Query: 110 ------------ELYKSR---VLELNASDDRGINVVRTKIKT--FAAVAVGSGQRRGGYP 152
                       E+ + R   ++E++A+    +   R  +    +A              
Sbjct: 76  TATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARG---------- 125

Query: 153 CPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFK 212
              +K+ ++DE   ++  + NAL +T+E   +  +F        ++   + SRC +F  K
Sbjct: 126 --RFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLK 183

Query: 213 PLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKD 272
            L  E +  ++ HI NEE +  +  AL  L+  ++G LR A++    A       ++++ 
Sbjct: 184 ALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQA 243

Query: 273 LISVSG 278
           + ++ G
Sbjct: 244 VSAMLG 249

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E* Length = 334

 Score =  105 bits (264), Expect = 2e-26
 Identities = 46/241 (19%), Positives = 79/241 (32%), Gaps = 45/241 (18%)

Query: 66  QEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLF-----GPE--------- 110
                  L  + +     H +L    PG G      A++  L      G +         
Sbjct: 7   LRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQ 66

Query: 111 LYKSR----VLELNASDDR---GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDE 163
           L ++        L     +   G++ VR   +     A   G           K++ + +
Sbjct: 67  LMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGG----------AKVVWVTD 116

Query: 164 ADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRV 223
           A  +T+ A NAL +T+E     T FF       R++  L SRC      P  E+   + +
Sbjct: 117 AALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWL 176

Query: 224 LHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA--------RLFGSSITSKDLIS 275
                   + +  +AL     +S G    A+   QG          +    S+ S D  S
Sbjct: 177 -----SREVTMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYS 231

Query: 276 V 276
           +
Sbjct: 232 L 232

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B* Length = 373

 Score = 97.3 bits (243), Expect = 2e-23
 Identities = 62/261 (23%), Positives = 106/261 (40%), Gaps = 63/261 (24%)

Query: 54  KYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQL---FGP 109
           K+RP+   DV  QE V+  L N L      H  LF G  G GKT+ A  +A  L    G 
Sbjct: 9   KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 68

Query: 110 ------------ELYKSR---VLELNASDDRGINVVRTKIKT--FAAVAVGSGQRRGGYP 152
                       E+ + R   ++E++A+    +   R  +    +A              
Sbjct: 69  TATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARG---------- 118

Query: 153 CPPYKIIILDEADSMTEDAQNALRRTME---TYSKVTRFFFICNYISRIIEPLA------ 203
              +K+ ++DE   ++  + NAL +T+E    + K     F+          LA      
Sbjct: 119 --RFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVK-----FL----------LATTDPQK 161

Query: 204 ------SRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYL 257
                 SRC +F  K L  E +  ++ HI NEE +  +  AL  L+  ++G LR A++  
Sbjct: 162 LPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLT 221

Query: 258 QGAARLFGSSITSKDLISVSG 278
             A       ++++ + ++ G
Sbjct: 222 DQAIASGDGQVSTQAVSAMLG 242

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D* Length = 368

 Score = 73.1 bits (179), Expect = 7e-15
 Identities = 49/298 (16%), Positives = 93/298 (31%), Gaps = 74/298 (24%)

Query: 53  EKYRPKQV-KDVAHQEEVVRVLTN----TLETANCPH-MLFYGPPGTGKTTTALAIA--- 103
           +   P+Q  + +  Q    R          E       +L  G PGTGKT  A+ +A   
Sbjct: 35  DALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQAL 94

Query: 104 -----------HQLFGPELYKSR-----------------------VLELNASDDRGINV 129
                       ++F  E+ K+                        + E++  + R    
Sbjct: 95  GPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGF 154

Query: 130 ----------VRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTM 179
                     ++++++      V   +  G     P  ++ +DE   +  ++ + L R +
Sbjct: 155 LALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIP-GVLFIDEVHMLDIESFSFLNRAL 213

Query: 180 E-TYSKVTRFFFICNYISRIIEP------------LASRCAKFRFKPLSEEVMSSRVLHI 226
           E   + V       N     I              L  R       P SE+     +   
Sbjct: 214 ESDMAPV--LIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIR 271

Query: 227 CNEEGLNLDAEALSTLSSI-SQGDLRRAITYL----QGAARLFGSSITSKDLISVSGY 279
           C EE + +  +A + L+ I  +  LR AI  +        +  G+ +   D+  V   
Sbjct: 272 CEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSL 329

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20 Length = 389

 Score = 71.7 bits (175), Expect = 2e-14
 Identities = 44/261 (16%), Positives = 88/261 (33%), Gaps = 49/261 (18%)

Query: 43  PVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETA------NCPHMLFYGPPGTGKT 96
            ++     +   Y PK++    H+E+ ++ L   L         + P     G PGTGKT
Sbjct: 2   AIVVDDSVFSPSYVPKRLP---HREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKT 58

Query: 97  TTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPC--- 153
            T   +       +   +R + +N    R    +  +I      ++     R G      
Sbjct: 59  VTLRKLWELY--KDKTTARFVYINGFIYRNFTAIIGEIAR----SLNIPFPRRGLSRDEF 112

Query: 154 -----------PPYKIIILDEADSMTEDAQNALRRTMETYSKVTR----FFFICN---YI 195
                        Y  ++LD+A ++  D  +   R  +   K+         + +    +
Sbjct: 113 LALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVL 172

Query: 196 SRIIEPLASRCA--KFRFKPLSE----EVMSSRVLH-----ICNEEGLNLDAE--ALSTL 242
           + +             RF P ++    +++  R          +E+ L + A+     T 
Sbjct: 173 NNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTP 232

Query: 243 SSISQGDLRRAITYLQGAARL 263
              ++GD R AI  L  +A  
Sbjct: 233 LDTNRGDARLAIDILYRSAYA 253

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus} Length = 384

 Score = 71.3 bits (174), Expect = 3e-14
 Identities = 35/223 (15%), Positives = 76/223 (34%), Gaps = 27/223 (12%)

Query: 67  EEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG 126
            +    +   ++       LF G  GTGKT  +  I +++   +       ++  +    
Sbjct: 30  RDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNC 89

Query: 127 INVVRTKIKTFAAVA---------------VGSGQRRGGYPCPPYKIIILDEADSMTE-- 169
             V  T     +++A                    +          II LDE D++ +  
Sbjct: 90  REVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRR 149

Query: 170 DAQNALRRTMETYSKVTRFFFICN---YISRIIEPLASRCAK-FRFKPLS----EEVMSS 221
                L + + + + ++    I N       +   + S       FKP      + ++S 
Sbjct: 150 GGDIVLYQLLRSDANIS-VIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSK 208

Query: 222 RVLHICNEEGLNLDA-EALSTLSSISQGDLRRAITYLQGAARL 263
              +   +   + +    ++ +S+   GD R+A+  L  AA+L
Sbjct: 209 YAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQL 251

>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 = 64.5 bits (156), Expect = 9e-12
 Identities = 49/313 (15%), Positives = 86/313 (27%), Gaps = 72/313 (23%)

Query: 5   FGKIHKSGKNK---------SPNF---TQKFSTTQSSPEKSEDEVKRKMAPVLQSSQPWV 52
           F  +    +             N+        T Q  P         +   +   +Q   
Sbjct: 68  FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV-- 125

Query: 53  EKYRPKQVKDVAHQEEVVRVLTNTLETANCPH--MLFYGPPGTGKTTTALAIA-----HQ 105
             +    V     + +    L   L     P   +L  G  G+GKT  AL +        
Sbjct: 126 --FAKYNVS----RLQPYLKLRQALLELR-PAKNVLIDGVLGSGKTWVALDVCLSYKVQC 178

Query: 106 LFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPC-PPYKIIILDEA 164
                    ++  LN  +      V   ++        +   R  +      +I      
Sbjct: 179 KMD-----FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI------ 227

Query: 165 DSMTEDAQNALRRTM--ETYSK---VTRFFFICNYISRIIEPLASRCAKF----RFKPLS 215
                  Q  LRR +  + Y     V     + N  ++        C K     RFK ++
Sbjct: 228 ----HSIQAELRRLLKSKPYENCLLVLL--NVQN--AKAWNAFNLSC-KILLTTRFKQVT 278

Query: 216 EEVMSSRVLHICNEE---GLNLDAEALSTLSS---ISQGDLRRAITYLQG---AARLFGS 266
           + + ++   HI  +     L  D E  S L         DL R +  L        +   
Sbjct: 279 DFLSAATTTHISLDHHSMTLTPD-EVKSLLLKYLDCRPQDLPREV--LTTNPRRLSIIAE 335

Query: 267 SITSKDLISVSGY 279
           SI  +D ++    
Sbjct: 336 SI--RDGLATWDN 346

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli} Length = 447

 Score = 60.6 bits (148), Expect = 1e-10
 Identities = 28/105 (26%), Positives = 48/105 (45%), Gaps = 11/105 (10%)

Query: 46  QSSQPWVEKYRPKQVKDVAHQEEVV---RVLTNTLETANCPHMLFYGPPGTGKTTTALAI 102
            + QP   + RP+ +     Q+ ++   + L   +E  +   M+ +GPPGTGKTT A  I
Sbjct: 11  NTFQPLAARMRPENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVI 70

Query: 103 AHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQR 147
           A          + V  ++A    G+  +R  I+  A     +G+R
Sbjct: 71  ARYA------NADVERISAVTS-GVKEIREAIER-ARQNRNAGRR 107

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli} Length = 447

 Score = 45.2 bits (108), Expect = 1e-05
 Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 7/86 (8%)

Query: 198 IIEPLASRCAKFRFKPLSEEVMSS---RVLHICN----EEGLNLDAEALSTLSSISQGDL 250
           +   L SR   +  K LS E +     + +         + + L  E    ++ +  GD 
Sbjct: 149 LNSALLSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDA 208

Query: 251 RRAITYLQGAARLFGSSITSKDLISV 276
           RRA+  L+  A +     + K ++  
Sbjct: 209 RRALNTLEMMADMAEVDDSGKRVLKP 234

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus} Length = 386

 Score = 58.1 bits (140), Expect = 6e-10
 Identities = 39/225 (17%), Positives = 79/225 (35%), Gaps = 25/225 (11%)

Query: 64  AHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD 123
               ++  +L          ++  YG  GTGKT     +  +L    L K + + +N   
Sbjct: 27  DQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQ 86

Query: 124 DRGINVVRTKIKTFAAVAVGSG----------QRRGGYPCPPYKIIILDEADSM-TEDAQ 172
                 V   +     V V               +         +I+LDE D+   +   
Sbjct: 87  IDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYND 146

Query: 173 NALRRTMETYSKVTR----FFFICN---YISRIIEPLASRCAKFR--FKPLS----EEVM 219
           + L +     S+V +    F  I N   ++  +   + S  ++    F P +    E+++
Sbjct: 147 DILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDIL 206

Query: 220 SSRVLHICNEEGLNLDA-EALSTLSSISQGDLRRAITYLQGAARL 263
           + R         L  +  +  + L++   GD RRA+  L+ +  +
Sbjct: 207 TKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEI 251

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20 Length = 305

 Score = 55.5 bits (134), Expect = 4e-09
 Identities = 38/237 (16%), Positives = 83/237 (35%), Gaps = 44/237 (18%)

Query: 66  QEEVVRVLTNTLETA-NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSR---VLELN- 120
            ++ +  L   +E +      L  G   +     +L +   +   E +  +   VLE++ 
Sbjct: 2   AKDQLETLKRIIEKSEGISI-LINGEDLSYPREVSLELPEYV---EKFPPKASDVLEIDP 57

Query: 121 ASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTME 180
             ++ GI+ +RT IK F   +               K +I+ + + MT+ A NA  + +E
Sbjct: 58  EGENIGIDDIRT-IKDFLNYSPELYT---------RKYVIVHDCERMTQQAANAFLKALE 107

Query: 181 ---TYSKVTRFFFICN--YISRIIEPLASRCAKFR------FKPLSEEVMSSRVLHIC-N 228
               Y+       + N      ++  + SR  +        F+ L +E +      +   
Sbjct: 108 EPPEYAV-----IVLNTRRWHYLLPTIKSRVFRVVVNVPKEFRDLVKEKIGDLWEELPLL 162

Query: 229 EEGLNLDAEALSTLSSISQGDLRRAITYL-------QGAARLFGSSITSKDLISVSG 278
           E       EA    +    G L  ++  L       +  ++     +  ++L+    
Sbjct: 163 ERDFKTALEAYKLGAEKLSG-LMESLKVLETEKLLKKVLSKGLEGYLACRELLERFS 218

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A* Length = 309

 Score = 55.5 bits (133), Expect = 4e-09
 Identities = 37/171 (21%), Positives = 60/171 (35%), Gaps = 29/171 (16%)

Query: 84  HMLFYGPPGTGKTTTALAIAHQLFGP-ELYKSRVLELNASDDRGINVVRTKIKTFAAVAV 142
           HM F G PGTGKTT AL +A  L     + K  ++ +   D  G  +  T  KT   +  
Sbjct: 69  HMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEVLKR 128

Query: 143 GSGQRRGGYPCPPYKIIILDEADSMT---------EDAQNALRRTMETYSKVTRFFFICN 193
             G            ++ +DEA  +          ++A   L + ME          +  
Sbjct: 129 AMG-----------GVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDL-VVILAG 176

Query: 194 YISRIIEPLASR-------CAKFRFKPLSEEVMSSRVLHICNEEGLNLDAE 237
           Y  R+     S             F   S+E +     H+ +++   +  E
Sbjct: 177 YADRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPE 227

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix} Length = 387

 Score = 54.4 bits (130), Expect = 1e-08
 Identities = 41/227 (18%), Positives = 73/227 (32%), Gaps = 30/227 (13%)

Query: 67  EEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF---GPELYKSRVLELNASD 123
             +  VL   L      + L YG  GTGKT  A  +  +L           + + +NA  
Sbjct: 29  RRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARH 88

Query: 124 DRGINVVRTKI----------KTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT----- 168
                 V + I             +   V     +         II+LDE D +      
Sbjct: 89  RETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGG 148

Query: 169 EDAQNALRRTMETYSKVTRFFFIC-----NYISRIIEPLASRCAKFR--FKPLSEE---- 217
           +D    + R  +          +       ++  +   + S   +    F P +      
Sbjct: 149 QDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRD 208

Query: 218 VMSSRVLHICNEEGLNLDA-EALSTLSSISQGDLRRAITYLQGAARL 263
           ++ +R     N   L+ D     + L++   GD RRA+  L+ A  +
Sbjct: 209 ILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLLRVAGEI 255

>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* Length = 334

 Score = 51.8 bits (125), Expect = 7e-08
 Identities = 26/73 (35%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 39  RKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANC-----PHMLFYGPPGT 93
             + P        V+  RPK + +   QE V + L+  LE A        H+L  GPPG 
Sbjct: 3   EFLTPERTVYDSGVQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGL 62

Query: 94  GKTTTALAIAHQL 106
           GKTT A  IA +L
Sbjct: 63  GKTTLAHIIASEL 75

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp} Length = 338

 Score = 50.3 bits (121), Expect = 3e-07
 Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 35  DEVKRKMAPVLQSSQPWVEK-YRPKQVKDVAHQEEVVRVLTNTLETANC-----PHMLFY 88
           + + R +     S     E   RP        QE + + L   +  A        H+LF 
Sbjct: 2   NAMDRIVEIEKYSFDETYETSLRPSNFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFS 61

Query: 89  GPPGTGKTTTALAIAHQL 106
           GP G GKTT A  I++++
Sbjct: 62  GPAGLGKTTLANIISYEM 79

>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* Length = 324

 Score = 48.7 bits (117), Expect = 8e-07
 Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 5/56 (8%)

Query: 56  RPKQVKDVAHQEEVVRVLTNTLETANC-----PHMLFYGPPGTGKTTTALAIAHQL 106
           RPK + +   QE + + L   LE A        H+L +GPPG GKTT A  IAH+L
Sbjct: 7   RPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL 62

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A* Length = 456

 Score = 48.4 bits (115), Expect = 1e-06
 Identities = 22/81 (27%), Positives = 30/81 (37%), Gaps = 6/81 (7%)

Query: 32  KSEDEVKRKMAPVLQSSQPWVEK-YRPKQVKDVAHQEEVVRVLTNTLETANCP-----HM 85
           KS  + +R  +          E     +    +  QE         +E           +
Sbjct: 7   KSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAV 66

Query: 86  LFYGPPGTGKTTTALAIAHQL 106
           L  GPPGTGKT  ALAIA +L
Sbjct: 67  LLAGPPGTGKTALALAIAQEL 87

>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 Length = 377

 Score = 47.3 bits (112), Expect = 2e-06
 Identities = 34/164 (20%), Positives = 56/164 (34%), Gaps = 32/164 (19%)

Query: 81  NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAV 140
                LF GP  +GKTT A A+     G      + L +N   DR    +   I  F  V
Sbjct: 170 RY--WLFKGPIDSGKTTLAAALLELCGG------KALNVNLPLDRLNFELGVAIDQFLVV 221

Query: 141 ---AVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTR------FFFI 191
                G+G      P        ++  D++ +    +++  +E      R          
Sbjct: 222 FEDVKGTGGESRDLPSGQG----INNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVT 277

Query: 192 CNYISRIIEPLASRCAK---FRFKP-------LSEEVMSSRVLH 225
            N    + + L +R  K   FR K         SE ++  R++ 
Sbjct: 278 MN-EYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQ 320

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

 Score = 44.5 bits (106), Expect = 1e-05
 Identities = 19/33 (57%), Positives = 21/33 (63%), Gaps = 7/33 (21%)

Query: 86  LFYGPPGTGKTTTALAIAHQL---F----GPEL 111
           LFYGPPG GKT  A AIA++    F    GPEL
Sbjct: 53  LFYGPPGCGKTLLAKAIANECQANFISIKGPEL 85

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

 Score = 43.7 bits (104), Expect = 3e-05
 Identities = 16/33 (48%), Positives = 19/33 (57%), Gaps = 7/33 (21%)

Query: 86  LFYGPPGTGKTTTALAIAHQL---F----GPEL 111
           L  GPPG GKT  A A+A++    F    GPEL
Sbjct: 48  LLAGPPGCGKTLLAKAVANESGLNFISVKGPEL 80

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus} Length = 604

 Score = 43.2 bits (102), Expect = 7e-05
 Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 2/81 (2%)

Query: 32  KSEDEVKRKMAPVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPP 91
            +  E    +   ++ +     +   K +  V  QE  V V+          H+L  G P
Sbjct: 12  LAPREYGESLELGIEFTTTEEIEVPEKLIDQVIGQEHAVEVIK--TAANQKRHVLLIGEP 69

Query: 92  GTGKTTTALAIAHQLFGPELY 112
           GTGK+    A+A  L    L 
Sbjct: 70  GTGKSMLGQAMAELLPTETLE 90

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426} Length = 202

 Score = 42.0 bits (99), Expect = 7e-05
 Identities = 10/55 (18%), Positives = 17/55 (30%)

Query: 52  VEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL 106
           +          +       R +           +  +G  G GKT    AIA++L
Sbjct: 24  LSDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANEL 78

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

 Score = 42.3 bits (100), Expect = 8e-05
 Identities = 16/33 (48%), Positives = 19/33 (57%), Gaps = 7/33 (21%)

Query: 86  LFYGPPGTGKTTTALAIAHQ-------LFGPEL 111
           L YGPPGTGKT  A A+A +       + G EL
Sbjct: 55  LLYGPPGTGKTLLAKAVATETNATFIRVVGSEL 87

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A* Length = 180

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 26/157 (16%), Positives = 52/157 (33%), Gaps = 37/157 (23%)

Query: 85  MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD-------DRGINVVRTKIKTF 137
           + F G PG GKT  A+A    ++  E    R    +  D                 +KT 
Sbjct: 41  LTFVGSPGVGKTHLAVATLKAIY--EKKGIRGYFFDTKDLIFRLKHLMDEGKDTKFLKTV 98

Query: 138 AAVAVGSGQRRGGYPCPPYKIIILDE--ADSMTEDAQNAL-----RRTMETYSKVTRFFF 190
                               +++LD+  ++ +++  +  +      R    Y+ +     
Sbjct: 99  LN----------------SPVLVLDDLGSERLSDWQRELISYIITYR----YNNLKSTII 138

Query: 191 ICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHIC 227
             NY  +  E  + R +      L E V+ S++  + 
Sbjct: 139 TTNYSLQREEESSVRISADLASRLGENVV-SKIYEMN 174

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3} Length = 308

 Score = 41.4 bits (97), Expect = 2e-04
 Identities = 10/39 (25%), Positives = 16/39 (41%)

Query: 68  EVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL 106
             +        +A    +  YG  G GK+    A+AH+L
Sbjct: 138 SAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHEL 176

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae} Length = 318

 Score = 41.4 bits (96), Expect = 2e-04
 Identities = 22/214 (10%), Positives = 68/214 (31%), Gaps = 27/214 (12%)

Query: 67  EEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP----ELYKSRVLELNAS 122
             +   + ++L ++            + K      +  +L       EL     + ++A 
Sbjct: 30  TRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDAL 89

Query: 123 DDRGINVVRTKI----------KTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDA- 171
           +  G++ +  KI             +  A+               +I++   +++  +  
Sbjct: 90  ELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKI 149

Query: 172 -QNALRRTMETYSKVTRFFFICN---YISRIIEPLASRCAKFR---FKPLS----EEVMS 220
            Q   +      SK++    +      I   I  + S  A F       +     ++++ 
Sbjct: 150 LQYFEKWISSKNSKLS-IICVGGHNVTIREQINIMPSLKAHFTEIKLNKVDKNELQQMII 208

Query: 221 SRVLHICNEEGLNLDAEALSTLSSISQGDLRRAI 254
           +R+  +     + ++ +   T+ +  +    + I
Sbjct: 209 TRLKSLLKPFHVKVNDKKEMTIYNNIREGQNQKI 242

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A Length = 800

 Score = 41.1 bits (96), Expect = 4e-04
 Identities = 20/62 (32%), Positives = 23/62 (37%), Gaps = 13/62 (20%)

Query: 81  NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS-----------DDRGINV 129
             P  L  GPPGTGKT T+  I + L         VL    S              G+ V
Sbjct: 370 QRPLSLIQGPPGTGKTVTSATIVYHLARQ--GNGPVLVCAPSNIAVDQLTEKIHQTGLKV 427

Query: 130 VR 131
           VR
Sbjct: 428 VR 429

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C Length = 322

 Score = 40.0 bits (94), Expect = 5e-04
 Identities = 12/21 (57%), Positives = 16/21 (76%)

Query: 85  MLFYGPPGTGKTTTALAIAHQ 105
           +L YGPPGTGK+  A A+A +
Sbjct: 54  ILLYGPPGTGKSYLAKAVATE 74

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

 Score = 39.8 bits (93), Expect = 6e-04
 Identities = 17/109 (15%), Positives = 33/109 (30%), Gaps = 30/109 (27%)

Query: 85  MLFYGPPGTGKTTTALAIAHQL---F----GPELYKSRVLELNASDDRGINVVRTKIKTF 137
           +  +G  G GK+     +  ++          EL      E          ++R + +  
Sbjct: 39  LGIWGGKGQGKSFQCELVFRKMGINPIMMSAGELESGNAGE-------PAKLIRQRYREA 91

Query: 138 AAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVT 186
           A +       R G  C     + +++ D+       A R    T   V 
Sbjct: 92  AEII------RKGNMC----CLFINDLDAG------AGRMGGTTQYTVN 124

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

 Score = 39.8 bits (93), Expect = 7e-04
 Identities = 29/107 (27%), Positives = 41/107 (38%), Gaps = 32/107 (29%)

Query: 86  LFYGPPGTGKTTTALAIAHQL-------FGPELYKSRVLELNASDDRGINVVRTKIKTFA 138
           L YGPPGTGKT  A A+A++         GPE+      E         + +R   K F 
Sbjct: 242 LLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGE-------SESNLR---KAFE 291

Query: 139 AVAVGSGQRRGGYPCPPYKIIILDEADSMT---EDAQNAL-RRTMET 181
                  +     P     II +DE D++    E     + RR +  
Sbjct: 292 -------EAEKNAPA----IIFIDELDAIAPKREKTHGEVERRIVSQ 327

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

 Score = 39.6 bits (93), Expect = 7e-04
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 85  MLFYGPPGTGKTTTALAIAHQ 105
           +L +GPPG GKT  A A+A +
Sbjct: 57  LLLFGPPGNGKTLLARAVATE 77

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens} Length = 357

 Score = 39.7 bits (93), Expect = 7e-04
 Identities = 12/21 (57%), Positives = 14/21 (66%)

Query: 85  MLFYGPPGTGKTTTALAIAHQ 105
           +L +GPPGTGKT     IA Q
Sbjct: 120 ILLFGPPGTGKTLIGKCIASQ 140

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score = 39.7 bits (93), Expect = 7e-04
 Identities = 11/21 (52%), Positives = 16/21 (76%)

Query: 85  MLFYGPPGTGKTTTALAIAHQ 105
           +L +GPPGTGK+  A A+A +
Sbjct: 48  ILLFGPPGTGKSYLAKAVATE 68

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae} Length = 802

 Score = 39.9 bits (93), Expect = 8e-04
 Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 13/62 (20%)

Query: 81  NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVL---ELNASDD--------RGINV 129
             P  L  GPPGTGKT T+  I + L   +++K R+L     N + D         G+ V
Sbjct: 374 QRPLSLIQGPPGTGKTVTSATIVYHLS--KIHKDRILVCAPSNVAVDHLAAKLRDLGLKV 431

Query: 130 VR 131
           VR
Sbjct: 432 VR 433

>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 Length = 350

 Score = 39.4 bits (92), Expect = 9e-04
 Identities = 23/99 (23%), Positives = 39/99 (39%), Gaps = 5/99 (5%)

Query: 41  MAPVLQSSQPWVEKYRPKQV---KDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTT 97
           M   +   QP     + + V     +  QE++   L  T        +L +G  GTGK+T
Sbjct: 1   MTTAVARLQPSASGAKTRPVFPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKST 60

Query: 98  TALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKT 136
              A+A  L  PE+       +++ +   I    T + T
Sbjct: 61  AVRALAALL--PEIEAVEGCPVSSPNVEMIPDWATVLST 97

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	294
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.98
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.98
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.97
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.97
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.97
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.97
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.97
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.97
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.97
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.97
3pvs_A	447	Replication-associated recombination protein A; ma	99.96
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.96
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.95
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.94
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.94
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.93
3bos_A	242	Putative DNA replication factor; P-loop containing	99.92
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.92
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.92
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.91
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.91
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.91
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.91
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.91
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	99.91
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.9
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.9
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.9
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.89
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.89
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.89
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	99.89
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.89
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.89
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.89
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.88
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	99.88
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.88
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.87
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.87
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.87
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.87
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.86
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.86
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.85
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.85
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.85
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.85
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.85
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.84
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.84
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.83
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	99.83
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.83
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.83
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	99.82
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.82
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.8
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.8
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.8
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.79
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.79
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.79
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.79
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.77
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.77
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.77
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.76
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.76
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.76
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.75
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.75
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.74
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.74
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	99.72
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.72
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.72
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.68
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.67
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.65
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.64
3co5_A	143	Putative two-component system transcriptional RES	99.62
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.61
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.61
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.59
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.58
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.55
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	99.48
2fna_A	357	Conserved hypothetical protein; structural genomic	99.47
3f8t_A	506	Predicted ATPase involved in replication control,	99.41
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	99.35
2qgz_A	308	Helicase loader, putative primosome component; str	99.32
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.28
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	99.26
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	99.21
1tue_A	212	Replication protein E1; helicase, replication, E1E	99.17
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.17
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	99.15
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	99.05
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.04
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	98.95
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.87
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	98.83
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	98.81
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	98.76
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	98.67
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	98.66
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	98.6
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	98.45
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.44
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	98.38
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	98.33
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.23
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	98.17
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	98.1
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	98.07
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	98.02
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	97.96
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.94
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	97.92
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	97.91
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	97.88
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	97.86
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	97.85
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	97.85
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	97.84
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	97.84
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	97.81
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	97.8
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	97.79
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.79
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	97.78
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.78
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	97.77
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	97.76
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	97.76
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	97.75
1via_A	175	Shikimate kinase; structural genomics, transferase	97.73
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	97.73
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	97.71
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	97.71
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	97.7
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	97.67
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	97.64
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	97.63
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	97.61
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	97.61
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.6
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.59
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	97.58
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	97.57
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	97.57
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.57
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	97.57
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	97.56
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	97.56
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	97.55
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	97.55
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	97.54
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	97.53
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	97.52
1u94_A	356	RECA protein, recombinase A; homologous recombinat	97.52
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	97.52
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	97.52
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	97.51
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	97.5
3b6e_A	216	Interferon-induced helicase C domain-containing P;	97.5
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.49
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	97.48
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	97.46
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	97.46
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	97.46
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	97.46
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.45
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	97.45
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	97.44
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	97.44
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	97.44
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.44
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	97.43
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	97.42
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	97.42
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	97.42
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	97.41
3h1t_A	590	Type I site-specific restriction-modification syst	97.41
2vli_A	183	Antibiotic resistance protein; transferase, tunica	97.4
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	97.4
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.4
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	97.39
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	97.38
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	97.38
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	97.37
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	97.37
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	97.35
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	97.35
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	97.35
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	97.35
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	97.34
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	97.33
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	97.32
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	97.32
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	97.32
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	97.31
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	97.31
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	97.31
1nrj_B	218	SR-beta, signal recognition particle receptor beta	97.31
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	97.31
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	97.3
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	97.29
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	97.28
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	97.27
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	97.27
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	97.27
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	97.26
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.26
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	97.26
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	97.26
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	97.25
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	97.25
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	97.24
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	97.23
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	97.23
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	97.23
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	97.22
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	97.22
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	97.22
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	97.22
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	97.22
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	97.21
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	97.2
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	97.2
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	97.2
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	97.16
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	97.16
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	97.15
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	97.15
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	97.15
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	97.13
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	97.13
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	97.13
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	97.11
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	97.11
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	97.11
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	97.1
3bor_A	237	Human initiation factor 4A-II; translation initiat	97.1
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	97.07
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	97.06
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	97.06
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	97.05
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	97.05
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	97.03
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	97.03
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	97.02
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	97.02
2hf9_A	226	Probable hydrogenase nickel incorporation protein	97.02
3llu_A	196	RAS-related GTP-binding protein C; structural geno	97.01
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	97.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	96.99
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	96.98
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	96.98
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	96.98
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	96.98
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	96.98
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	96.97
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.95
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	96.95
1p9r_A	418	General secretion pathway protein E; bacterial typ	96.95
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	96.95
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	96.93
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	96.93
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	96.92
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	96.91
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	96.9
2eyu_A	261	Twitching motility protein PILT; pilus retraction	96.89
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	96.89
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	96.88
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	96.88
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	96.88
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	96.87
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	96.85
4a74_A	231	DNA repair and recombination protein RADA; hydrola	96.85
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	96.85
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	96.85
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	96.84
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.84
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	96.84
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	96.83
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	96.83
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	96.83
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	96.82
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	96.82
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	96.8
3io5_A	333	Recombination and repair protein; storage dimer, i	96.8
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	96.79
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	96.78
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	96.78
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	96.78
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	96.77
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	96.76
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	96.76
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	96.76
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	96.75
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	96.74
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	96.73
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	96.73
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.72
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	96.72
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	96.71
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	96.7
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	96.7
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	96.7
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	96.68
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	96.68
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	96.68
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	96.68
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	96.68
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	96.67
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	96.67
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	96.66
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.65
2z43_A	324	DNA repair and recombination protein RADA; archaea	96.65
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	96.65
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	96.64
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	96.63
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	96.63
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	96.63
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	96.63
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	96.63
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	96.63
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	96.62
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	96.62
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	96.61
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	96.6
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	96.59
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	96.58
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	96.58
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	96.57
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	96.57
3th5_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	95.59
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	96.56
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	96.56
1b0u_A	262	Histidine permease; ABC transporter, transport pro	96.56
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	96.56
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	96.54
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	96.54
1sgw_A	214	Putative ABC transporter; structural genomics, P p	96.54
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	96.53
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	96.53
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	96.53
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	96.53
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.53
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	96.53
2ged_A	193	SR-beta, signal recognition particle receptor beta	96.53
2ewv_A	372	Twitching motility protein PILT; pilus retraction	96.52
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	96.51
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	96.5
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	96.49
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	96.49
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	96.49
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.49
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	96.48
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	96.48
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.48
2xxa_A	433	Signal recognition particle protein; protein trans	96.48
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	96.47
3szr_A	608	Interferon-induced GTP-binding protein MX1; interf	96.47
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	96.46
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	96.45
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	96.45
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	96.45
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	96.45
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	96.45
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	96.45
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	96.44
1g6h_A	257	High-affinity branched-chain amino acid transport	96.44
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	96.44
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	96.44
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	96.44
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	96.43
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	96.43
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	96.43
1ji0_A	240	ABC transporter; ATP binding protein, structural g	96.43
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	96.42
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	96.42
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	96.42
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	96.42
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.42
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	96.41
2ghi_A	260	Transport protein; multidrug resistance protein, M	96.4
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.4
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	96.4
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	96.4
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	96.38
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	96.38
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	96.37
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	96.37
3kta_A	182	Chromosome segregation protein SMC; structural mai	96.37
2wji_A	165	Ferrous iron transport protein B homolog; membrane	96.37
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	96.36
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	96.35
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	96.35
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	96.34
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	96.34
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	96.32
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	96.32
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	96.32
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	96.32
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	96.3
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	96.29
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	96.28
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	96.27
2og2_A	359	Putative signal recognition particle receptor; nuc	96.26
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	96.26
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	96.26
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	96.25
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	96.24
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	96.23
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	96.23
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	96.22
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	96.22
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	96.21
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	96.21
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	96.21
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	96.2
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	96.2
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	96.19
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	96.19
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	96.19
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	96.17
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	96.17
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	96.17
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	96.16
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	96.16
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	96.15
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	96.14
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	96.14
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	96.13
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	96.12
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	96.1
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	96.1
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	96.1
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	96.09
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	96.08
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	96.08
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	96.08
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	96.07
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	96.07
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	96.06
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	96.05
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	96.05
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	96.04
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	96.04
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	96.04
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	96.03
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	96.01
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	96.01
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	96.0
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	96.0
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	96.0
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	95.98
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	95.98
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	95.97
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	95.97
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	95.96
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.95
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	95.94
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	95.94
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	95.94
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	95.93
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	95.93
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	95.92
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	95.92
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	95.92
3ice_A	422	Transcription termination factor RHO; transcriptio	95.92
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	95.91
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	95.91
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	95.91
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	95.9
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	95.9
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.9
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	95.89
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	95.87
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	95.85
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	95.84
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	95.84
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	95.83
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	95.81
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	95.8
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	95.8
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	95.8
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	95.79
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	95.79
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	95.79
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	95.78
1yks_A	440	Genome polyprotein [contains: flavivirin protease	95.78
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	95.77
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	95.76
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	95.76
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	95.75
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	95.74

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

Probab=99.98  E-value=5.4e-31  Score=223.90  Aligned_cols=216  Identities=29%  Similarity=0.433  Sum_probs=176.5

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD  124 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~  124 (294)
                      ....||.++|+|..+++++|++..+..+..++..+..++ ++++||||||||++++++++.+      +..++.+++++.
T Consensus        11 ~~~~~~~~k~rP~~~~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l------~~~~~~i~~~~~   84 (324)
T 3u61_B           11 EKEHILEQKYRPSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDV------NADMMFVNGSDC   84 (324)
T ss_dssp             TTCSSHHHHSCCCSTTTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHT------TEEEEEEETTTC
T ss_pred             cccchHHHhhCCCCHHHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHh------CCCEEEEccccc
Confidence            567799999999999999999999999999999888777 5666779999999999999998      778888988764


Q ss_pred             cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-HHHHHHHHHHHHhhcCcceEEEEecCCcccchHhh
Q 022641          125 RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-EDAQNALRRTMETYSKVTRFFFICNYISRIIEPLA  203 (294)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~  203 (294)
                      . ...++..+..+.....         ..+++.+|+|||+|.++ ...++.|+..++.++....+|+++|....+.+++.
T Consensus        85 ~-~~~i~~~~~~~~~~~~---------~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~  154 (324)
T 3u61_B           85 K-IDFVRGPLTNFASAAS---------FDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQ  154 (324)
T ss_dssp             C-HHHHHTHHHHHHHBCC---------CSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHH
T ss_pred             C-HHHHHHHHHHHHhhcc---------cCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHH
Confidence            3 5555555554433211         12356799999999999 99999999999998889999999999999999999


Q ss_pred             ccccEEEecCCCHHH-------HHHHHHHHHHHhCCCCCH-HHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhh
Q 022641          204 SRCAKFRFKPLSEEV-------MSSRVLHICNEEGLNLDA-EALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLIS  275 (294)
Q Consensus       204 ~r~~~i~~~~~~~~~-------~~~~l~~~~~~~~~~~~~-~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~  275 (294)
                      +||..+.|++|+.++       +...+...+..+++.+++ ++++.+++.++||+|.+++.++.++  ....||.+++..
T Consensus       155 sR~~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~gd~R~a~~~L~~~~--~~~~i~~~~v~~  232 (324)
T 3u61_B          155 SRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGELDSYS--SKGVLDAGILSL  232 (324)
T ss_dssp             HHSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCBSCHHHHHHHHHHTCSCTTHHHHHHHHHG--GGTCBCC-----
T ss_pred             hhCcEEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHhCCCCHHHHHHHHHHHh--ccCCCCHHHHHH
Confidence            999999999999877       445566667788999988 9999999999999999999999888  456699999988


Q ss_pred             hccc
Q 022641          276 VSGY  279 (294)
Q Consensus       276 ~~~~  279 (294)
                      ++..
T Consensus       233 ~~~~  236 (324)
T 3u61_B          233 VTND  236 (324)
T ss_dssp             ----
T ss_pred             HhCC
Confidence            7765

>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=99.98  E-value=4.8e-30  Score=206.28  Aligned_cols=222  Identities=52%  Similarity=0.880  Sum_probs=188.4

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcch
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGI  127 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~  127 (294)
                      ..||.++|.|..+.+++|++..+..+..++..+..++++|+||+|||||++++.+++.+.+. .....++.+++......
T Consensus         4 ~~~~~~~~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~-~~~~~~~~~~~~~~~~~   82 (226)
T 2chg_A            4 FEIWVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGE-NWRDNFIEMNASDERGI   82 (226)
T ss_dssp             CCCHHHHTSCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHGG-GGGGGEEEEETTCTTCH
T ss_pred             hhhHHHhcCCCCHHHHcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHhcc-ccccceEEeccccccCh
Confidence            45899999999999999999999999999998877789999999999999999999987432 22345666777666665


Q ss_pred             hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhcccc
Q 022641          128 NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      ..+...+.......        .....++.+|+|||++.++...++.|+..++.......+|+++|....+.+++.+|+.
T Consensus        83 ~~~~~~~~~~~~~~--------~~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~  154 (226)
T 2chg_A           83 DVVRHKIKEFARTA--------PIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCA  154 (226)
T ss_dssp             HHHHHHHHHHHTSC--------CSTTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSE
T ss_pred             HHHHHHHHHHhccc--------CCCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCc
Confidence            55554444433221        0112356799999999999999999999999888888899999998889999999999


Q ss_pred             EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhccc
Q 022641          208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGY  279 (294)
Q Consensus       208 ~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~  279 (294)
                      .+.++|++.+++..++.+.+...+..+++++++.+++.++||+|.+++.++.++... +.||.++++.+++.
T Consensus       155 ~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~l~~~l~~~~~~~-~~I~~~~v~~~~~~  225 (226)
T 2chg_A          155 VFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQGAAAIG-EVVDADTIYQITAT  225 (226)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SCBCHHHHHHHHHT
T ss_pred             eeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhcC-ceecHHHHHHHhcC
Confidence            999999999999999999999999999999999999999999999999999988775 78999999998764

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.97  E-value=4.4e-31  Score=227.03  Aligned_cols=236  Identities=57%  Similarity=0.929  Sum_probs=191.8

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      ....||.++|+|..+++++|++..+..+..++..+..++++|+||||||||++++++++.+.++......+..+++++..
T Consensus        22 ~~~~~~~~k~~p~~~~~i~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~  101 (353)
T 1sxj_D           22 LAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDER  101 (353)
T ss_dssp             ----CHHHHTCCSSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCC
T ss_pred             ccCccHHHhcCCCCHHHhhCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEcccccc
Confidence            45679999999999999999999999999999988777899999999999999999999975432234567778877766


Q ss_pred             chhHHHHHHHHHHhhhcccCc--cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhh
Q 022641          126 GINVVRTKIKTFAAVAVGSGQ--RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLA  203 (294)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~  203 (294)
                      +...+...+..+.........  .........+.+|+|||++.++...++.|++.+++.+....+|+++|.+..+.+++.
T Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~  181 (353)
T 1sxj_D          102 GISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLA  181 (353)
T ss_dssp             CHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHH
T ss_pred             chHHHHHHHHHHhhhcccccchhhcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhh
Confidence            666555555444332111000  000011235579999999999999999999999998888889999999999999999


Q ss_pred             ccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCC-----CCChhhhhhhcc
Q 022641          204 SRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGS-----SITSKDLISVSG  278 (294)
Q Consensus       204 ~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~-----~it~~~v~~~~~  278 (294)
                      +||..+.|.|++.+++..++..++..+++.+++++++.+++.++||+|.+++.++.++.+.+.     .||.+++..+++
T Consensus       182 sR~~~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~~~~~~It~~~v~~~~~  261 (353)
T 1sxj_D          182 SQCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAG  261 (353)
T ss_dssp             HHSEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSSCHHHHHHHHHHTHHHHHHHCSCCCCCHHHHHHHHT
T ss_pred             ccCceEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCccCccccHHHHHHHhC
Confidence            999999999999999999999999989999999999999999999999999999988876532     799999998887


Q ss_pred             ccc
Q 022641          279 YPT  281 (294)
Q Consensus       279 ~~~  281 (294)
                      ...
T Consensus       262 ~~~  264 (353)
T 1sxj_D          262 VVP  264 (353)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.97  E-value=1.2e-30  Score=223.16  Aligned_cols=227  Identities=43%  Similarity=0.753  Sum_probs=192.5

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG  126 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~  126 (294)
                      ...||.++|+|..+.+++|++.++..|..++..+..++++|+||||||||++++++++.+.+... ...+..+++++..+
T Consensus        11 ~~~~~~~k~rp~~~~~~~g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~~~~~-~~~~~~~~~~~~~~   89 (340)
T 1sxj_C           11 ENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNY-SNMVLELNASDDRG   89 (340)
T ss_dssp             -CCCHHHHTCCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSH-HHHEEEECTTSCCS
T ss_pred             cCCchHHHhCCCcHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCc-cceEEEEcCccccc
Confidence            35699999999999999999999999999999998888999999999999999999999865432 23466677776666


Q ss_pred             hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccc
Q 022641          127 INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRC  206 (294)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~  206 (294)
                      ...++..+..+......        ..+.+.+++|||+|.++...++.|++.++.++....+|+++|.+..+.+++.+||
T Consensus        90 ~~~ir~~i~~~~~~~~~--------~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~  161 (340)
T 1sxj_C           90 IDVVRNQIKDFASTRQI--------FSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQC  161 (340)
T ss_dssp             HHHHHTHHHHHHHBCCS--------SSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTS
T ss_pred             HHHHHHHHHHHHhhccc--------CCCCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhc
Confidence            66666655544422110        1123679999999999999999999999999999999999999999999999999


Q ss_pred             cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCC----CCChhhhhhhcccccC
Q 022641          207 AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGS----SITSKDLISVSGYPTG  282 (294)
Q Consensus       207 ~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~----~it~~~v~~~~~~~~~  282 (294)
                      ..+.|.|++.+++..++.++++.+++.+++++++.+++.++|++|.+++.++.++.....    .||.+++..+++...+
T Consensus       162 ~~~~~~~l~~~~~~~~l~~~~~~~~~~i~~~~~~~i~~~s~G~~r~~~~~l~~~~~~~~~~~~~~it~~~v~~~~~~~~~  241 (340)
T 1sxj_C          162 TRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRP  241 (340)
T ss_dssp             EEEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTTCHHHHHHHTTTTTTTTCSSSCCCBCHHHHHHHTTCCCH
T ss_pred             eeEeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCcccccccHHHHHHHhCCCCH
Confidence            999999999999999999999888999999999999999999999999999987765542    6999999988876543

>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=99.97  E-value=1.1e-30  Score=222.13  Aligned_cols=227  Identities=50%  Similarity=0.840  Sum_probs=188.1

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      ....||.++|+|..|++++|++..+..+..++..+..++++|+||||+|||++|+++++.+.+.. ....++.+++++..
T Consensus        10 ~~~~~~~~k~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l~~~~-~~~~~~~~~~~~~~   88 (327)
T 1iqp_A           10 VLEKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGEN-WRHNFLELNASDER   88 (327)
T ss_dssp             HTTSCHHHHTCCCSTTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGG-HHHHEEEEETTCHH
T ss_pred             ccCCchhhccCCCCHHHhhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCc-ccCceEEeeccccC
Confidence            45679999999999999999999999999999998888899999999999999999999974332 12345667766654


Q ss_pred             chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhcc
Q 022641          126 GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASR  205 (294)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r  205 (294)
                      +...++..+..+.....        ...+++.+|+|||+|.++...++.|+..++..+....+|+++|.+..+.+++.+|
T Consensus        89 ~~~~~~~~~~~~~~~~~--------~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr  160 (327)
T 1iqp_A           89 GINVIREKVKEFARTKP--------IGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSR  160 (327)
T ss_dssp             HHHTTHHHHHHHHHSCC--------GGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHT
T ss_pred             chHHHHHHHHHHHhhCC--------cCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhh
Confidence            44444443333321110        0013457999999999999999999999999888889999999999999999999


Q ss_pred             ccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhcccccC
Q 022641          206 CAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTG  282 (294)
Q Consensus       206 ~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~~~~  282 (294)
                      |..+.|+|++.+++..++..++..+++.+++++++.+++.++||+|.+++.++.++.. ...||.+++..+++...+
T Consensus       161 ~~~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~~~~~l~~~~~~-~~~i~~~~v~~~~~~~~~  236 (327)
T 1iqp_A          161 CAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAAL-DKKITDENVFMVASRARP  236 (327)
T ss_dssp             EEEEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTTCHHHHHHHHHHHHTT-CSEECHHHHHHHTTCCCH
T ss_pred             CcEEEecCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHhc-CCCCCHHHHHHHHCCCCH
Confidence            9999999999999999999999989999999999999999999999999999987754 446899999888776543

>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=99.97  E-value=1.6e-30  Score=220.49  Aligned_cols=225  Identities=52%  Similarity=0.882  Sum_probs=188.4

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcch
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGI  127 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~  127 (294)
                      ..||.++|+|..+++++|++..+..+..++..+..++++|+||+|||||++|+.+++.+.+... ...++.+++++..+.
T Consensus         4 ~~~~~~k~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~-~~~~~~~~~~~~~~~   82 (319)
T 2chq_A            4 FEIWVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENW-RDNFIEMNASDERGI   82 (319)
T ss_dssp             --CTTTTTSCSSGGGSCSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHHHTTCH-HHHCEEEETTSTTCT
T ss_pred             cccHHHhcCCCCHHHHhCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHhcCCcc-cCCeEEEeCccccCh
Confidence            4699999999999999999999999999999888788999999999999999999999854432 235667777765554


Q ss_pred             hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhcccc
Q 022641          128 NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      ..++..+..+.....        ...+++.+|+|||+|.++...++.|++.++..+..+.+|+++|....+.+++.+||.
T Consensus        83 ~~~~~~~~~~~~~~~--------~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~  154 (319)
T 2chq_A           83 DVVRHKIKEFARTAP--------IGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCA  154 (319)
T ss_dssp             TTSSHHHHHHHHSCC--------SSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCE
T ss_pred             HHHHHHHHHHHhcCC--------CCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCe
Confidence            444444443331110        112346799999999999999999999999888889999999999999999999999


Q ss_pred             EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhcccccC
Q 022641          208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPTG  282 (294)
Q Consensus       208 ~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~~~~  282 (294)
                      .+.|.|++.+++..++..++..+++.+++++++.+++.++||+|.+++.++.++.. ...||.+++..+++...+
T Consensus       155 ~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G~~r~~~~~l~~~~~~-~~~i~~~~v~~~~~~~~~  228 (319)
T 2chq_A          155 VFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQGAAAI-GEVVDADTIYQITATARP  228 (319)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHTTCCCBCHHHHHHHHHTTTTCHHHHHHHHHHHHHS-SSCBCHHHHHHHTTCCCH
T ss_pred             EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc-CCCCCHHHHHHHHCCCCH
Confidence            99999999999999999999999999999999999999999999999999988765 567999999988876543

>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=99.97  E-value=1.6e-29  Score=214.65  Aligned_cols=226  Identities=44%  Similarity=0.707  Sum_probs=191.2

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG  126 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~  126 (294)
                      ...||.++|+|..+++++|++..+..+..++..+..++++|+||+|+|||++++.+++.+.+.. ....++.+++++..+
T Consensus         7 ~~~~~~~~~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~-~~~~~~~~~~~~~~~   85 (323)
T 1sxj_B            7 LQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRS-YADGVLELNASDDRG   85 (323)
T ss_dssp             CCCCHHHHTCCSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGG-HHHHEEEECTTSCCS
T ss_pred             ccCcHHHhcCCCCHHHHHCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCc-ccCCEEEecCccccC
Confidence            3569999999999999999999999999999998888899999999999999999999975432 123466677777656


Q ss_pred             hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccc
Q 022641          127 INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRC  206 (294)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~  206 (294)
                      ...++..+..+......       ...+++.+|+|||+|.++...++.|++.++..+....+|++++....+.+++.+||
T Consensus        86 ~~~i~~~~~~~~~~~~~-------~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~  158 (323)
T 1sxj_B           86 IDVVRNQIKHFAQKKLH-------LPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQC  158 (323)
T ss_dssp             HHHHHTHHHHHHHBCCC-------CCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTS
T ss_pred             hHHHHHHHHHHHhcccc-------CCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhc
Confidence            66666655554321111       01234679999999999999999999999998888999999999999999999999


Q ss_pred             cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhccccc
Q 022641          207 AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSGYPT  281 (294)
Q Consensus       207 ~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~~~~  281 (294)
                      ..+.|.|++.+++..++..++...++.+++++++.+++.++||+|.+++.++.++.. .+.|+.+++..+++...
T Consensus       159 ~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~a~~~l~~~~~~-~~~i~~~~v~~~~~~~~  232 (323)
T 1sxj_B          159 AILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAG-HGLVNADNVFKIVDSPH  232 (323)
T ss_dssp             EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHHHHHHHH-HSSBCHHHHHHHHTSCC
T ss_pred             eEEeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhc-CCCcCHHHHHHHHCCCC
Confidence            999999999999999999999999999999999999999999999999999988754 35699999988887643

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=99.97  E-value=1.5e-28  Score=212.74  Aligned_cols=224  Identities=25%  Similarity=0.372  Sum_probs=185.8

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCccC-------------
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYK-------------  113 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~~-------------  113 (294)
                      ..||.++|+|..+++++|++..+..+..++..+..++ ++|+||+|+|||++++.+++.+.+.....             
T Consensus         3 ~~~l~~k~rp~~~~~~vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~   82 (373)
T 1jr3_A            3 YQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREI   82 (373)
T ss_dssp             CCCHHHHTCCCSTTTSCSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSSHHHHHH
T ss_pred             cHHHHHhhCCCchhhccCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHH
Confidence            4689999999999999999999999999998887655 79999999999999999999986543211             


Q ss_pred             -----CcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceE
Q 022641          114 -----SRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       114 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~i  188 (294)
                           ..++.++.........++..+..+...          ...+++.+|+|||+|.++...++.|++.+++.+....+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----------~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~  152 (373)
T 1jr3_A           83 EQGRFVDLIEIDAASRTKVEDTRDLLDNVQYA----------PARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKF  152 (373)
T ss_dssp             HTSCCSSCEEEETTCSCCSSCHHHHHHHTTSC----------CSSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEE
T ss_pred             hccCCCceEEecccccCCHHHHHHHHHHHhhc----------cccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEE
Confidence                 123444443333334444444332211          11234679999999999999999999999998888999


Q ss_pred             EEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCC
Q 022641          189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSI  268 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  268 (294)
                      |++++....+.+.+.+||..+.|.|++.+++..++..++...++.+++++++.+++.++||+|.+.++++.+..+.+..|
T Consensus       153 Il~~~~~~~l~~~l~sr~~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~a~~~l~~~~~G~~r~~~~~l~~~~~~~~~~i  232 (373)
T 1jr3_A          153 LLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQV  232 (373)
T ss_dssp             EEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHSSSCHHHHHHHHHHHHHHTTTCB
T ss_pred             EEEeCChHhCcHHHHhheeEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhcCCcc
Confidence            99999888899999999999999999999999999999999999999999999999999999999999999887777789


Q ss_pred             Chhhhhhhccccc
Q 022641          269 TSKDLISVSGYPT  281 (294)
Q Consensus       269 t~~~v~~~~~~~~  281 (294)
                      |.++|..+++...
T Consensus       233 ~~~~v~~~~~~~~  245 (373)
T 1jr3_A          233 STQAVSAMLGTLD  245 (373)
T ss_dssp             CHHHHHHHTTCCC
T ss_pred             cHHHHHHHhCCCC
Confidence            9999998887643

>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=99.97  E-value=1.7e-28  Score=199.88  Aligned_cols=222  Identities=25%  Similarity=0.376  Sum_probs=177.7

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCC-cEEEECCCCCCHHHHHHHHHHHhcCCCccC------------
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCP-HMLFYGPPGTGKTTTALAIAHQLFGPELYK------------  113 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~-~ill~Gp~G~GKT~la~~la~~~~~~~~~~------------  113 (294)
                      ...||.++|.|..+.+++|++..+..+..++..+..+ .++|+||+|+|||++++.+++.+.+.....            
T Consensus         9 ~~~~~~~~~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (250)
T 1njg_A            9 SYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCRE   88 (250)
T ss_dssp             --CCHHHHTCCCSGGGCCSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHH
T ss_pred             HHHHHhhccCCccHHHHhCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHH
Confidence            3568999999999999999999999999999887654 489999999999999999999885432110            


Q ss_pred             ------CcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcce
Q 022641          114 ------SRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTR  187 (294)
Q Consensus       114 ------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~  187 (294)
                            ..++.++.........+...+..+..          .....++.+|+|||++.++...++.|+..++..+....
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~  158 (250)
T 1njg_A           89 IEQGRFVDLIEIDAASRTKVEDTRDLLDNVQY----------APARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVK  158 (250)
T ss_dssp             HHTTCCSSEEEEETTCGGGHHHHHHHHHSCCC----------SCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEE
T ss_pred             HhccCCcceEEecCcccccHHHHHHHHHHhhh----------chhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceE
Confidence                  01222332222222222222221110          01123467999999999999999999999998778888


Q ss_pred             EEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCC
Q 022641          188 FFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS  267 (294)
Q Consensus       188 ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~  267 (294)
                      +|++++....+.+.+.+|+..+.++|++.+++.+++..++...+..+++++++.+++.++|++|.+.++++.+.......
T Consensus       159 ~i~~t~~~~~~~~~l~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~~~~~~~~~~~~~~~~~~  238 (250)
T 1njg_A          159 FLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQ  238 (250)
T ss_dssp             EEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHTTCHHHHHHHHHHHHTTTTSS
T ss_pred             EEEEeCChHhCCHHHHHHhhhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhccCce
Confidence            99999998888899999999999999999999999999999999999999999999999999999999999998777778


Q ss_pred             CChhhhhhhcc
Q 022641          268 ITSKDLISVSG  278 (294)
Q Consensus       268 it~~~v~~~~~  278 (294)
                      ||.++++++++
T Consensus       239 i~~~~v~~~~~  249 (250)
T 1njg_A          239 VSTQAVSAMLG  249 (250)
T ss_dssp             BCHHHHHHHSC
T ss_pred             ecHHHHHHHhC
Confidence            99999998875

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.97  E-value=2.8e-29  Score=215.87  Aligned_cols=221  Identities=34%  Similarity=0.584  Sum_probs=170.1

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHH-HcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCcc----------------
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTL-ETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELY----------------  112 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l-~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~----------------  112 (294)
                      ||+++|+|..|++++|++..+..+..++ ..+..++++|+||+|+||||+++++++.+.++...                
T Consensus         3 ~w~~kyrP~~~~~~vg~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~~~~~~~~   82 (354)
T 1sxj_E            3 LWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRK   82 (354)
T ss_dssp             -CTTTTCCCSGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC---------------
T ss_pred             cchhccCCCCHHHhcCCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceeeccccccc
Confidence            8999999999999999999999999999 77777789999999999999999999987554321                


Q ss_pred             -------CCcceeecCCCCcchh--HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc
Q 022641          113 -------KSRVLELNASDDRGIN--VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS  183 (294)
Q Consensus       113 -------~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~  183 (294)
                             ...++.++..+.....  .++..+..+.....-...........++.+++|||++.++...++.|++.+++.+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~vlilDE~~~L~~~~~~~L~~~le~~~  162 (354)
T 1sxj_E           83 LELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYS  162 (354)
T ss_dssp             ---CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCHHHHHHHHHHHHHST
T ss_pred             ceeeeecccceEEecHhhcCCcchHHHHHHHHHHHHhccccccccccccCCCCeEEEEeCccccCHHHHHHHHHHHHhhc
Confidence                   0123334433221111  2333333332211000000000013456799999999999999999999999988


Q ss_pred             CcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCC-HHHHHHHHhhccCcHHHHHHHHHHHHH
Q 022641          184 KVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLD-AEALSTLSSISQGDLRRAITYLQGAAR  262 (294)
Q Consensus       184 ~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~-~~~l~~l~~~~~G~~r~~~~~l~~~~~  262 (294)
                      ....+|++|+.+..+.+++.+||..+.|+|++.+++..++.+++..+++.++ +++++.+++.++||+|.+++.++.++.
T Consensus       163 ~~~~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~i~~~~~G~~r~a~~~l~~~~~  242 (354)
T 1sxj_E          163 KNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMAL  242 (354)
T ss_dssp             TTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHHHHHTHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            8889999999999999999999999999999999999999999999999999 999999999999999999999998887


Q ss_pred             HhCCCCCh
Q 022641          263 LFGSSITS  270 (294)
Q Consensus       263 ~~~~~it~  270 (294)
                      +....||.
T Consensus       243 ~~~~~i~~  250 (354)
T 1sxj_E          243 NNELALKS  250 (354)
T ss_dssp             TTTTEECS
T ss_pred             hCCCCcCc
Confidence            65434554

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.96  E-value=1.2e-28  Score=216.43  Aligned_cols=214  Identities=24%  Similarity=0.367  Sum_probs=175.5

Q ss_pred             chhhhhcCCCcchhhcccHHHH---HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           49 QPWVEKYRPKQVKDVAHQEEVV---RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        49 ~~~~~~~~~~~~~~~~g~~~~~---~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      .||.++++|..+++++|+++.+   ..|...+..+..++++|+||||||||++|+.+++.+      +..++.+++... 
T Consensus        14 ~pla~r~rP~~l~~ivGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~------~~~f~~l~a~~~-   86 (447)
T 3pvs_A           14 QPLAARMRPENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYA------NADVERISAVTS-   86 (447)
T ss_dssp             CCHHHHTCCCSTTTCCSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHHHT------TCEEEEEETTTC-
T ss_pred             CChHHHhCCCCHHHhCCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHHHh------CCCeEEEEeccC-
Confidence            5999999999999999999999   889999999988899999999999999999999998      667777776553 


Q ss_pred             chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEe--cCCcccchHhh
Q 022641          126 GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFIC--NYISRIIEPLA  203 (294)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~--~~~~~~~~~l~  203 (294)
                      +...++..+........          ..++.+|||||+|.++...++.|+..+++  ..+.+|++|  |....+.+++.
T Consensus        87 ~~~~ir~~~~~a~~~~~----------~~~~~iLfIDEI~~l~~~~q~~LL~~le~--~~v~lI~att~n~~~~l~~aL~  154 (447)
T 3pvs_A           87 GVKEIREAIERARQNRN----------AGRRTILFVDEVHRFNKSQQDAFLPHIED--GTITFIGATTENPSFELNSALL  154 (447)
T ss_dssp             CHHHHHHHHHHHHHHHH----------TTCCEEEEEETTTCC------CCHHHHHT--TSCEEEEEESSCGGGSSCHHHH
T ss_pred             CHHHHHHHHHHHHHhhh----------cCCCcEEEEeChhhhCHHHHHHHHHHHhc--CceEEEecCCCCcccccCHHHh
Confidence            45555555554433321          12356999999999999999999999997  446666666  44467889999


Q ss_pred             ccccEEEecCCCHHHHHHHHHHHHHH-------hCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhC------CCCCh
Q 022641          204 SRCAKFRFKPLSEEVMSSRVLHICNE-------EGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFG------SSITS  270 (294)
Q Consensus       204 ~r~~~i~~~~~~~~~~~~~l~~~~~~-------~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~------~~it~  270 (294)
                      +||.++.|.+++.+++..++.+.+..       .++.+++++++.|++.++||+|.++++++.++..+.      ..||.
T Consensus       155 sR~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~Gd~R~lln~Le~a~~~a~~~~~~~~~It~  234 (447)
T 3pvs_A          155 SRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTLEMMADMAEVDDSGKRVLKP  234 (447)
T ss_dssp             TTEEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCBCTTSCEECCH
T ss_pred             CceeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccccCCCCccCH
Confidence            99999999999999999999999986       456799999999999999999999999999998874      25999


Q ss_pred             hhhhhhccccc
Q 022641          271 KDLISVSGYPT  281 (294)
Q Consensus       271 ~~v~~~~~~~~  281 (294)
                      +++.+++....
T Consensus       235 e~v~~~l~~~~  245 (447)
T 3pvs_A          235 ELLTEIAGERS  245 (447)
T ss_dssp             HHHHHHHTCCC
T ss_pred             HHHHHHHhhhh
Confidence            99999998753

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.96  E-value=1.3e-27  Score=214.51  Aligned_cols=225  Identities=26%  Similarity=0.407  Sum_probs=173.4

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHc-----------------CCCCcEEEECCCCCCHHHHHHHHHHHhcC
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLET-----------------ANCPHMLFYGPPGTGKTTTALAIAHQLFG  108 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~-----------------~~~~~ill~Gp~G~GKT~la~~la~~~~~  108 (294)
                      ....+|+++|+|..+++++|++..++.+..|+..                 +..+.++|+||||||||++|+++++++  
T Consensus        24 ~~~~lW~ekyrP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l--  101 (516)
T 1sxj_A           24 ASDKLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL--  101 (516)
T ss_dssp             --CCCHHHHTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT--
T ss_pred             ccCCCcccccCCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc--
Confidence            4567999999999999999999999999999875                 123579999999999999999999998  


Q ss_pred             CCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccC----CCCCCCCcEEEEEeCCCCCCHHH---HHHHHHHHHh
Q 022641          109 PELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRR----GGYPCPPYKIIILDEADSMTEDA---QNALRRTMET  181 (294)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~lliiDei~~l~~~~---~~~L~~~l~~  181 (294)
                          +..++.+++++......+...+........-.....    ......++.+|+|||+|.++...   .+.|+..++.
T Consensus       102 ----~~~~i~in~s~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~~  177 (516)
T 1sxj_A          102 ----GYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRK  177 (516)
T ss_dssp             ----TCEEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHH
T ss_pred             ----CCCEEEEeCCCcchHHHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccchhhHHHHHHHHHHHHh
Confidence                788899999887766544333222111100000000    00123567899999999997543   4778888876


Q ss_pred             hcCcceEEEEecCCc-ccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHH
Q 022641          182 YSKVTRFFFICNYIS-RIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGA  260 (294)
Q Consensus       182 ~~~~~~ii~~~~~~~-~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~  260 (294)
                      .  ...+|++++... ...+.+.+||..+.|++|+.+++..++..++..+++.+++++++.|++.++||+|.++++++.+
T Consensus       178 ~--~~~iIli~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~~~l~~la~~s~GdiR~~i~~L~~~  255 (516)
T 1sxj_A          178 T--STPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTI  255 (516)
T ss_dssp             C--SSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTTCHHHHHHHHTHH
T ss_pred             c--CCCEEEEEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence            3  344677776543 3446788999999999999999999999999999999999999999999999999999999987


Q ss_pred             HHHhCCCCChhhhhhhccc
Q 022641          261 ARLFGSSITSKDLISVSGY  279 (294)
Q Consensus       261 ~~~~~~~it~~~v~~~~~~  279 (294)
                      +. ....|+.+++..++..
T Consensus       256 ~~-~~~~It~~~v~~~~~~  273 (516)
T 1sxj_A          256 ST-TTKTINHENINEISKA  273 (516)
T ss_dssp             HH-HSSCCCTTHHHHHHHH
T ss_pred             Hh-cCCCCchHHHHHHHHh
Confidence            75 3667999998877663

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

Probab=99.95  E-value=1.7e-26  Score=197.25  Aligned_cols=211  Identities=18%  Similarity=0.214  Sum_probs=169.9

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHc-----CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecC
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLET-----ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA  121 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~-----~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~  121 (294)
                      ....|.++|+|..|++++|++..+..+..++..     ...++++|+||||||||++|+++++.+      +..++.+++
T Consensus        15 ~~~~~~~~~~p~~~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~------~~~~~~~~~   88 (338)
T 3pfi_A           15 FDETYETSLRPSNFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEM------SANIKTTAA   88 (338)
T ss_dssp             --------CCCCSGGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHT------TCCEEEEEG
T ss_pred             hhhhhhhccCCCCHHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHh------CCCeEEecc
Confidence            445799999999999999999999999888865     334579999999999999999999998      667777877


Q ss_pred             CCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcC-----------------
Q 022641          122 SDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSK-----------------  184 (294)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~-----------------  184 (294)
                      ............+..                ...+.+|||||++.++...++.|+..+++...                 
T Consensus        89 ~~~~~~~~~~~~~~~----------------~~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~  152 (338)
T 3pfi_A           89 PMIEKSGDLAAILTN----------------LSEGDILFIDEIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDL  152 (338)
T ss_dssp             GGCCSHHHHHHHHHT----------------CCTTCEEEEETGGGCCHHHHHHHHHHHHTSCC---------CCCCCCCC
T ss_pred             hhccchhHHHHHHHh----------------ccCCCEEEEechhhcCHHHHHHHHHHHHhccchhhcccCccccceecCC
Confidence            665444444333322                12346999999999999999999999987431                 


Q ss_pred             -cceEEEEecCCcccchHhhccc-cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHH
Q 022641          185 -VTRFFFICNYISRIIEPLASRC-AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAAR  262 (294)
Q Consensus       185 -~~~ii~~~~~~~~~~~~l~~r~-~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~  262 (294)
                       .+.+|++||....+.+++.+|| ..+.+++|+.+++..++.+.+...+..+++++++.+++.++|++|.+.++++.+..
T Consensus       153 ~~~~~i~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l~~~~~  232 (338)
T 3pfi_A          153 PKFTLIGATTRAGMLSNPLRDRFGMQFRLEFYKDSELALILQKAALKLNKTCEEKAALEIAKRSRSTPRIALRLLKRVRD  232 (338)
T ss_dssp             CCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHTTTTCHHHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCccccCHHHHhhcCEEeeCCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence             2678889999888999999999 58999999999999999999999999999999999999999999999999998765


Q ss_pred             Hh----CCCCChhhhhhhccc
Q 022641          263 LF----GSSITSKDLISVSGY  279 (294)
Q Consensus       263 ~~----~~~it~~~v~~~~~~  279 (294)
                      .+    ...|+.+++..++..
T Consensus       233 ~a~~~~~~~i~~~~~~~~~~~  253 (338)
T 3pfi_A          233 FADVNDEEIITEKRANEALNS  253 (338)
T ss_dssp             HHHHTTCSEECHHHHHHHHHH
T ss_pred             HHHhhcCCccCHHHHHHHHHH
Confidence            44    445899998877765

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

Probab=99.94  E-value=2e-25  Score=192.86  Aligned_cols=225  Identities=21%  Similarity=0.247  Sum_probs=166.2

Q ss_pred             cCCchhhhhcCCCc-chhhcccHHHHHH---HHHHHHcCCCC--cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee
Q 022641           46 QSSQPWVEKYRPKQ-VKDVAHQEEVVRV---LTNTLETANCP--HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL  119 (294)
Q Consensus        46 ~~~~~~~~~~~~~~-~~~~~g~~~~~~~---l~~~l~~~~~~--~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~  119 (294)
                      ....++.++++|.. |++++|++..+..   +...+..+..+  +++|+||||||||++|+++++.+.+.    .+++.+
T Consensus        28 ~~~l~l~~~~~p~~~~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~~~----~~~~~~  103 (368)
T 3uk6_A           28 IRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPD----TPFTAI  103 (368)
T ss_dssp             CCSCCBCTTSCBCSEETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHCSS----CCEEEE
T ss_pred             hhccCcccccCcCcchhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhccc----CCcccc
Confidence            34556778899998 9999999988765   45556666554  79999999999999999999998431    123323


Q ss_pred             cCCCC----cc---------------------------------------------------hhHHHHHHHHHHhhhccc
Q 022641          120 NASDD----RG---------------------------------------------------INVVRTKIKTFAAVAVGS  144 (294)
Q Consensus       120 ~~~~~----~~---------------------------------------------------~~~~~~~~~~~~~~~~~~  144 (294)
                      ++...    ..                                                   ...++..+..........
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~  183 (368)
T 3uk6_A          104 AGSEIFSLEMSKTEALTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREE  183 (368)
T ss_dssp             EGGGGSCSSSCHHHHHHHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHH
T ss_pred             cchhhhhcccchhHHHHHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhh
Confidence            22110    00                                                   112222222211111000


Q ss_pred             CccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEec------------CCcccchHhhccccEEEec
Q 022641          145 GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICN------------YISRIIEPLASRCAKFRFK  212 (294)
Q Consensus       145 ~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~------------~~~~~~~~l~~r~~~i~~~  212 (294)
                      +     .....+++|||||+|.++...++.|++.++...... ++++++            .+..+++++.+||..+.|+
T Consensus       184 g-----~~~~~~~vl~IDEi~~l~~~~~~~L~~~le~~~~~~-~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~~i~~~  257 (368)
T 3uk6_A          184 G-----KAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPV-LIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTT  257 (368)
T ss_dssp             T-----C---CBCEEEEESGGGSBHHHHHHHHHHTTCTTCCE-EEEEESCSEEECBTSSCEEETTCCHHHHTTEEEEEEC
T ss_pred             c-----cccccCceEEEhhccccChHHHHHHHHHhhCcCCCe-eeeecccceeeeeccCCCCcccCCHHHHhhccEEEec
Confidence            0     001123599999999999999999999998866554 444444            3556889999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhcc-CcHHHHHHHHHHHHHHh----CCCCChhhhhhhcccc
Q 022641          213 PLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQ-GDLRRAITYLQGAARLF----GSSITSKDLISVSGYP  280 (294)
Q Consensus       213 ~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~-G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~  280 (294)
                      ||+.+++..++++.+...+..+++++++.+++.+. |++|.++++++.+...+    ...||.+++..++...
T Consensus       258 ~~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll~~a~~~A~~~~~~~It~~~v~~a~~~~  330 (368)
T 3uk6_A          258 PYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLF  330 (368)
T ss_dssp             CCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHh
Confidence            99999999999999999999999999999999998 99999999999988765    4579999999988763

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

Probab=99.94  E-value=3.8e-25  Score=187.85  Aligned_cols=208  Identities=22%  Similarity=0.268  Sum_probs=168.8

Q ss_pred             hhhcCCCcchhhcccHHHHHHHHHHHHc-----CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc
Q 022641           52 VEKYRPKQVKDVAHQEEVVRVLTNTLET-----ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG  126 (294)
Q Consensus        52 ~~~~~~~~~~~~~g~~~~~~~l~~~l~~-----~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~  126 (294)
                      .++|+|..|++++|++..+..+..++..     ....+++|+||||||||++|+++++.+      +..++.+++.....
T Consensus         3 ~~~~~p~~~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~------~~~~~~~~~~~~~~   76 (324)
T 1hqc_A            3 DLALRPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL------GVNLRVTSGPAIEK   76 (324)
T ss_dssp             --CCCCCSTTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHH------TCCEEEECTTTCCS
T ss_pred             ccccCcccHHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHh------CCCEEEEeccccCC
Confidence            4689999999999999999888887753     234579999999999999999999998      56677777766544


Q ss_pred             hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc------------------CcceE
Q 022641          127 INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS------------------KVTRF  188 (294)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~------------------~~~~i  188 (294)
                      ...+...+..               ....+.+|+|||++.++...++.|+..++...                  ..+.+
T Consensus        77 ~~~l~~~l~~---------------~~~~~~~l~lDEi~~l~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~  141 (324)
T 1hqc_A           77 PGDLAAILAN---------------SLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTL  141 (324)
T ss_dssp             HHHHHHHHTT---------------TCCTTCEEEETTTTSCCHHHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEE
T ss_pred             hHHHHHHHHH---------------hccCCCEEEEECCcccccchHHHHHHHHHhhhhHHhccccccccccccCCCCEEE
Confidence            4333322211               01234699999999999999999999998753                  24678


Q ss_pred             EEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---
Q 022641          189 FFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---  264 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---  264 (294)
                      |+++|....+.+++.+||. .+.+++|+.+++..++.+.+...+..+++++++.++++++|++|.+.++++.+...+   
T Consensus       142 i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l~~~~~~a~~~  221 (324)
T 1hqc_A          142 IGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQVA  221 (324)
T ss_dssp             EEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHSCSCHHHHHHHHHHHTTTSTTT
T ss_pred             EEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHh
Confidence            8899988888899999994 999999999999999999998888999999999999999999999999999887655   


Q ss_pred             -CCCCChhhhhhhcccc
Q 022641          265 -GSSITSKDLISVSGYP  280 (294)
Q Consensus       265 -~~~it~~~v~~~~~~~  280 (294)
                       ...|+.+++..++...
T Consensus       222 ~~~~i~~~~~~~~~~~~  238 (324)
T 1hqc_A          222 GEEVITRERALEALAAL  238 (324)
T ss_dssp             SCSCCCHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHh
Confidence             3468988887776543

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=99.93  E-value=1.3e-23  Score=178.70  Aligned_cols=217  Identities=19%  Similarity=0.249  Sum_probs=163.4

Q ss_pred             ccccCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcC-----CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcce
Q 022641           43 PVLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETA-----NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVL  117 (294)
Q Consensus        43 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~-----~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~  117 (294)
                      +.......|.+.++|..+++++|++..+..+...+..+     ...+++|+||||+||||++++++..+      +..+.
T Consensus         7 ~~~~~~~~~~~~lr~~~l~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l------~~~~~   80 (334)
T 1in4_A            7 PERTVYDSGVQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL------QTNIH   80 (334)
T ss_dssp             ----------CTTSCSSGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHH------TCCEE
T ss_pred             cchHHHHHHHHHcCCccHHHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHh------CCCEE
Confidence            33344457899999999999999999998888777643     33579999999999999999999998      34444


Q ss_pred             eecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc--------------
Q 022641          118 ELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS--------------  183 (294)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~--------------  183 (294)
                      ..++........+......    .            ....+++|||++.+.+...+.|+..++...              
T Consensus        81 ~~sg~~~~~~~~l~~~~~~----~------------~~~~v~~iDE~~~l~~~~~e~L~~~~~~~~~~i~~~~~~~~~~i  144 (334)
T 1in4_A           81 VTSGPVLVKQGDMAAILTS----L------------ERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSI  144 (334)
T ss_dssp             EEETTTCCSHHHHHHHHHH----C------------CTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC-----------
T ss_pred             EEechHhcCHHHHHHHHHH----c------------cCCCEEEEcchhhcCHHHHHHHHHHHHhcccceeeccCcccccc
Confidence            3444333232223222111    0            123599999999999888888887776532              


Q ss_pred             ----CcceEEEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHH
Q 022641          184 ----KVTRFFFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQ  258 (294)
Q Consensus       184 ----~~~~ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~  258 (294)
                          ..+.++.+++.+..+...+++||. .+.++|++.+++.+++++.+...++.++++++..|++.+.|++|.+.++++
T Consensus       145 ~~~l~~~~li~at~~~~~Ls~~l~sR~~l~~~Ld~~~~~~l~~iL~~~~~~~~~~~~~~~~~~ia~~~~G~~R~a~~ll~  224 (334)
T 1in4_A          145 RIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTK  224 (334)
T ss_dssp             ----CCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHHH
T ss_pred             cccCCCeEEEEecCCcccCCHHHHHhcCceeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhcCCChHHHHHHHH
Confidence                124566677888889999999997 689999999999999999998889999999999999999999999999998


Q ss_pred             HHHHHh----CCCCChhhhhhhccccc
Q 022641          259 GAARLF----GSSITSKDLISVSGYPT  281 (294)
Q Consensus       259 ~~~~~~----~~~it~~~v~~~~~~~~  281 (294)
                      .+..++    ...||.++++.++....
T Consensus       225 ~~~~~a~~~~~~~It~~~v~~al~~~~  251 (334)
T 1in4_A          225 RVRDMLTVVKADRINTDIVLKTMEVLN  251 (334)
T ss_dssp             HHHHHHHHHTCSSBCHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCCCcCHHHHHHHHHHhC
Confidence            776554    45799999999887754

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=99.92  E-value=1.5e-24  Score=176.34  Aligned_cols=210  Identities=12%  Similarity=0.172  Sum_probs=160.8

Q ss_pred             CchhhhhcCC-Ccchhhcc---cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           48 SQPWVEKYRP-KQVKDVAH---QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        48 ~~~~~~~~~~-~~~~~~~g---~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ..|+..++.| ..|+++++   ++..+..+..++..+..++++|+||||||||++++.+++.+...   +..+..+++..
T Consensus        14 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~---~~~~~~~~~~~   90 (242)
T 3bos_A           14 QLSLPVHLPDDETFTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANEL---ERRSFYIPLGI   90 (242)
T ss_dssp             CCEEECCCCTTCSTTTSCC--CCHHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEEGGG
T ss_pred             hcCCCCCCCCCCChhhccCCCCCHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEEHHH
Confidence            4577778887 78888886   36788888888887667789999999999999999999988432   23444444433


Q ss_pred             CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHH--HHHHHHHHHhhcCcc--eEEEEecCCc---
Q 022641          124 DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDA--QNALRRTMETYSKVT--RFFFICNYIS---  196 (294)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~--~~~L~~~l~~~~~~~--~ii~~~~~~~---  196 (294)
                      ....  .    .....            ...+..+|+|||++.+....  ++.|+..++......  .+|++++...   
T Consensus        91 ~~~~--~----~~~~~------------~~~~~~vliiDe~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~  152 (242)
T 3bos_A           91 HASI--S----TALLE------------GLEQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEA  152 (242)
T ss_dssp             GGGS--C----GGGGT------------TGGGSSEEEEETGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTT
T ss_pred             HHHH--H----HHHHH------------hccCCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHH
Confidence            2110  0    00000            01234599999999997544  777888877654332  4777776443   


Q ss_pred             -ccchHhhccc---cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---CCCCC
Q 022641          197 -RIIEPLASRC---AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---GSSIT  269 (294)
Q Consensus       197 -~~~~~l~~r~---~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---~~~it  269 (294)
                       ...+.+.+||   ..+.+++|+.+++..++...+...+..+++++++.+++.++||+|.+.+.++.+..++   +..||
T Consensus       153 ~~~~~~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~l~~~l~~~~~~a~~~~~~It  232 (242)
T 3bos_A          153 GFVLPDLVSRMHWGLTYQLQPMMDDEKLAALQRRAAMRGLQLPEDVGRFLLNRMARDLRTLFDVLDRLDKASMVHQRKLT  232 (242)
T ss_dssp             TCCCHHHHHHHHHSEEEECCCCCGGGHHHHHHHHHHHTTCCCCHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHTCCCC
T ss_pred             HHhhhhhhhHhhcCceEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCCCc
Confidence             3458899999   7999999999999999999999999999999999999999999999999999888765   66799


Q ss_pred             hhhhhhhcc
Q 022641          270 SKDLISVSG  278 (294)
Q Consensus       270 ~~~v~~~~~  278 (294)
                      .++++.++.
T Consensus       233 ~~~v~~~l~  241 (242)
T 3bos_A          233 IPFVKEMLR  241 (242)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHhh
Confidence            999998875

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=99.92  E-value=7.1e-24  Score=180.38  Aligned_cols=183  Identities=21%  Similarity=0.302  Sum_probs=149.7

Q ss_pred             cccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCccC------------------CcceeecCC--
Q 022641           64 AHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYK------------------SRVLELNAS--  122 (294)
Q Consensus        64 ~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~~------------------~~~~~~~~~--  122 (294)
                      .-++...+.+...+..++.++ ++|+||+|+|||++|+.+++.+.|.....                  ..+..+++.  
T Consensus         5 pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~   84 (334)
T 1a5t_A            5 PWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKG   84 (334)
T ss_dssp             GGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTT
T ss_pred             CchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEecccc
Confidence            345777888889998888777 99999999999999999999998764321                  345555553  


Q ss_pred             -CCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchH
Q 022641          123 -DDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEP  201 (294)
Q Consensus       123 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~  201 (294)
                       ...+.+.++..+..+...+          ..+++.++||||+|.++...++.|++.+++++..+.+|++|+.+..++++
T Consensus        85 ~~~~~i~~ir~l~~~~~~~~----------~~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~~~l~~t  154 (334)
T 1a5t_A           85 KNTLGVDAVREVTEKLNEHA----------RLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLAT  154 (334)
T ss_dssp             CSSBCHHHHHHHHHHTTSCC----------TTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHH
T ss_pred             CCCCCHHHHHHHHHHHhhcc----------ccCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHH
Confidence             3455666666554433221          12456799999999999999999999999988899999999999999999


Q ss_pred             hhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHH
Q 022641          202 LASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA  261 (294)
Q Consensus       202 l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~  261 (294)
                      +++||..+.|+|++.+++..++...+     .++++++..+++.++|++|.++++++...
T Consensus       155 i~SRc~~~~~~~~~~~~~~~~L~~~~-----~~~~~~~~~l~~~s~G~~r~a~~~l~~~~  209 (334)
T 1a5t_A          155 LRSRCRLHYLAPPPEQYAVTWLSREV-----TMSQDALLAALRLSAGSPGAALALFQGDN  209 (334)
T ss_dssp             HHTTSEEEECCCCCHHHHHHHHHHHC-----CCCHHHHHHHHHHTTTCHHHHHHTTSSHH
T ss_pred             HhhcceeeeCCCCCHHHHHHHHHHhc-----CCCHHHHHHHHHHcCCCHHHHHHHhccch
Confidence            99999999999999999999997654     67999999999999999999999887544

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

Probab=99.92  E-value=8.7e-24  Score=180.25  Aligned_cols=205  Identities=20%  Similarity=0.238  Sum_probs=150.0

Q ss_pred             CCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ..+|+++.|.+.+++.|.+.+..             ..+..+||+||||||||++|+++|.++      +.+++.++++.
T Consensus       144 ~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~------~~~f~~v~~s~  217 (405)
T 4b4t_J          144 DSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHT------DCKFIRVSGAE  217 (405)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHH------TCEEEEEEGGG
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhh------CCCceEEEhHH
Confidence            45799999999999998877632             233469999999999999999999999      88888888776


Q ss_pred             Ccc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhhc
Q 022641          124 DRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTMETYS  183 (294)
Q Consensus       124 ~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~~~~  183 (294)
                      ..+      ...++..+......              .+.+|||||+|.+..              .....|+..|+...
T Consensus       218 l~sk~vGese~~vr~lF~~Ar~~--------------aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~  283 (405)
T 4b4t_J          218 LVQKYIGEGSRMVRELFVMAREH--------------APSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFE  283 (405)
T ss_dssp             GSCSSTTHHHHHHHHHHHHHHHT--------------CSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTT
T ss_pred             hhccccchHHHHHHHHHHHHHHh--------------CCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccC
Confidence            543      23344444433322              235999999998732              23556777777543


Q ss_pred             --CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHHH
Q 022641          184 --KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITYL  257 (294)
Q Consensus       184 --~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~l  257 (294)
                        ..+.+|++||.+..+++++++  ||. .|.+++|+.+++.++++.+++...+. ++-.+..|++.+.| +...+.+++
T Consensus       284 ~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~-~dvdl~~lA~~t~G~SGADi~~l~  362 (405)
T 4b4t_J          284 TSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLT-RGINLRKVAEKMNGCSGADVKGVC  362 (405)
T ss_dssp             CCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCC-SSCCHHHHHHHCCSCCHHHHHHHH
T ss_pred             CCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCC-ccCCHHHHHHHCCCCCHHHHHHHH
Confidence              456788999999999999998  887 89999999999999998887654332 22247888888765 334444555


Q ss_pred             HHHHHHh----CCCCChhhhhhhcccccC
Q 022641          258 QGAARLF----GSSITSKDLISVSGYPTG  282 (294)
Q Consensus       258 ~~~~~~~----~~~it~~~v~~~~~~~~~  282 (294)
                      ..|+..+    ...||.+|+..++..+..
T Consensus       363 ~eA~~~Air~~~~~vt~~Df~~Al~~v~~  391 (405)
T 4b4t_J          363 TEAGMYALRERRIHVTQEDFELAVGKVMN  391 (405)
T ss_dssp             HHHHHHHHHTTCSBCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCcCHHHHHHHHHHHhC
Confidence            5555444    456999999998876543

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

Probab=99.91  E-value=4.4e-23  Score=182.51  Aligned_cols=125  Identities=22%  Similarity=0.248  Sum_probs=111.2

Q ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEec---------C----CcccchHhhccccEEEecCCCHHHHHHHH
Q 022641          157 KIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICN---------Y----ISRIIEPLASRCAKFRFKPLSEEVMSSRV  223 (294)
Q Consensus       157 ~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~---------~----~~~~~~~l~~r~~~i~~~~~~~~~~~~~l  223 (294)
                      .|+||||+|.|+...++.|++.+++++.. .+|+++|         .    +..+++.+++||..+.|+|++.+++.+++
T Consensus       297 ~VliIDEa~~l~~~a~~aLlk~lEe~~~~-~~il~tn~~~~~i~~~~~~~~~~~l~~~i~sR~~~~~~~~~~~~e~~~iL  375 (456)
T 2c9o_A          297 GVLFVDEVHMLDIECFTYLHRALESSIAP-IVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQII  375 (456)
T ss_dssp             CEEEEESGGGCBHHHHHHHHHHTTSTTCC-EEEEEECCSEEECBTTSSCEEETTCCHHHHTTEEEEECCCCCHHHHHHHH
T ss_pred             eEEEEechhhcCHHHHHHHHHHhhccCCC-EEEEecCCccccccccccccccccCChhHHhhcceeeCCCCCHHHHHHHH
Confidence            59999999999999999999999998877 5666773         3    56788999999999999999999999999


Q ss_pred             HHHHHHhCCCCCHHHHHHHHhhc-cCcHHHHHHHHHHHHHHh----CCCCChhhhhhhcccccC
Q 022641          224 LHICNEEGLNLDAEALSTLSSIS-QGDLRRAITYLQGAARLF----GSSITSKDLISVSGYPTG  282 (294)
Q Consensus       224 ~~~~~~~~~~~~~~~l~~l~~~~-~G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~~  282 (294)
                      ++++..++..++++++..++..+ .|++|.++++++.+...+    ...|+.++|..+++.+.+
T Consensus       376 ~~~~~~~~~~~~~~~~~~i~~~a~~g~~r~a~~ll~~a~~~A~~~~~~~v~~~~v~~~~~~~~d  439 (456)
T 2c9o_A          376 KIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYD  439 (456)
T ss_dssp             HHHHHHHTCCBCHHHHHHHHHHHHHSCHHHHHHTHHHHHHHHHHTTCSSBCHHHHHHHHHHSCC
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhcCCCccCHHHHHHHHHHhcC
Confidence            99999999999999999999999 999999999999885554    457999999999877543

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

Probab=99.91  E-value=3.5e-23  Score=173.59  Aligned_cols=214  Identities=22%  Similarity=0.230  Sum_probs=161.7

Q ss_pred             hhhhcCCCcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCccee
Q 022641           51 WVEKYRPKQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLE  118 (294)
Q Consensus        51 ~~~~~~~~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~  118 (294)
                      |.+++.+..|++++|++..++.+..++..            ....+++|+||||||||++|+++++.+      +..++.
T Consensus        11 ~~~~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~------~~~~~~   84 (297)
T 3b9p_A           11 IVEGGAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATEC------SATFLN   84 (297)
T ss_dssp             TBCCSSCCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHT------TCEEEE
T ss_pred             hccCCCCCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHh------CCCeEE
Confidence            55667788999999999999999888743            124569999999999999999999998      667777


Q ss_pred             ecCCCCcch------hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHh
Q 022641          119 LNASDDRGI------NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMET  181 (294)
Q Consensus       119 ~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~  181 (294)
                      ++++.....      ...+..+.....              ..+.+|+|||++.+.           ...++.|+..++.
T Consensus        85 i~~~~l~~~~~~~~~~~~~~~~~~~~~--------------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~  150 (297)
T 3b9p_A           85 ISAASLTSKYVGDGEKLVRALFAVARH--------------MQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDG  150 (297)
T ss_dssp             EESTTTSSSSCSCHHHHHHHHHHHHHH--------------TCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHH
T ss_pred             eeHHHHhhcccchHHHHHHHHHHHHHH--------------cCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhc
Confidence            776654321      122222222111              124699999998873           3456667777776


Q ss_pred             hc-----CcceEEEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHH-
Q 022641          182 YS-----KVTRFFFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAI-  254 (294)
Q Consensus       182 ~~-----~~~~ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~-  254 (294)
                      ..     ..+.+|++||.+..+++++.+||. .+.+++|+.++...+++.++...+..++++.++.+++.+.|..+..+ 
T Consensus       151 ~~~~~~~~~v~vi~~tn~~~~l~~~l~~R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~l~  230 (297)
T 3b9p_A          151 LPGNPDGDRIVVLAATNRPQELDEAALRRFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLT  230 (297)
T ss_dssp             CC------CEEEEEEESCGGGBCHHHHHHCCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHHHH
T ss_pred             ccccCCCCcEEEEeecCChhhCCHHHHhhCCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHH
Confidence            54     346788889999999999999996 88999999999999999999888888999999999999999776544 


Q ss_pred             HHHHHHHHHh----------------CCCCChhhhhhhcccccCCC
Q 022641          255 TYLQGAARLF----------------GSSITSKDLISVSGYPTGGS  284 (294)
Q Consensus       255 ~~l~~~~~~~----------------~~~it~~~v~~~~~~~~~~~  284 (294)
                      .+++.++..+                ...|+.+++..++....+..
T Consensus       231 ~l~~~a~~~a~r~~~~~~~~~~~~~~~~~i~~~d~~~a~~~~~~s~  276 (297)
T 3b9p_A          231 ALAKDAALEPIRELNVEQVKCLDISAMRAITEQDFHSSLKRIRRSV  276 (297)
T ss_dssp             HHHHHHTTHHHHTCC--------CCCCCCCCHHHHHHHTTSCCCSS
T ss_pred             HHHHHHHHHHHHHHhhhhcccccccccCCcCHHHHHHHHHHcCCCC
Confidence            5555544332                13699999999998877654

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

Probab=99.91  E-value=2.2e-23  Score=176.58  Aligned_cols=196  Identities=20%  Similarity=0.212  Sum_probs=145.0

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHH----------cC--CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcce
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLE----------TA--NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVL  117 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~----------~~--~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~  117 (294)
                      .|..++.+..|++++|++.+++.|..++.          .+  ...+++|+||||||||++|+++++++      +..++
T Consensus         7 ~~~~~~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~------~~~~~   80 (322)
T 3eie_A            7 AILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEA------NSTFF   80 (322)
T ss_dssp             CSEEECCCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHH------TCEEE
T ss_pred             ceeecCCCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHH------CCCEE
Confidence            45567778889999999999999988872          11  22469999999999999999999998      67777


Q ss_pred             eecCCCCcc--hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH-----------HHHHHHHHHHHhh--
Q 022641          118 ELNASDDRG--INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE-----------DAQNALRRTMETY--  182 (294)
Q Consensus       118 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~-----------~~~~~L~~~l~~~--  182 (294)
                      .++++...+  .......+.........          ..+.+|+|||+|.+..           ..++.|+..++..  
T Consensus        81 ~v~~~~l~~~~~g~~~~~~~~~f~~a~~----------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~  150 (322)
T 3eie_A           81 SVSSSDLVSKWMGESEKLVKQLFAMARE----------NKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGN  150 (322)
T ss_dssp             EEEHHHHHTTTGGGHHHHHHHHHHHHHH----------TSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGT
T ss_pred             EEchHHHhhcccchHHHHHHHHHHHHHh----------cCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhccccc
Confidence            777644211  11112222222111111          1236999999998843           3467777777643  


Q ss_pred             -cCcceEEEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHHHHH
Q 022641          183 -SKVTRFFFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITYLQG  259 (294)
Q Consensus       183 -~~~~~ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~l~~  259 (294)
                       ...+.+|++||.+..+++++.+||. .+.+++|+.+++..+++.++...+..+++..+..|++.+.| +.+.+.++++.
T Consensus       151 ~~~~v~vi~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~~t~g~sg~di~~l~~~  230 (322)
T 3eie_A          151 DSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKD  230 (322)
T ss_dssp             SCCCEEEEEEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHHTTTTCCHHHHHHHHHH
T ss_pred             cCCceEEEEecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence             3456778889999999999999997 79999999999999999999887778899999999999877 45555555554


Q ss_pred             HH
Q 022641          260 AA  261 (294)
Q Consensus       260 ~~  261 (294)
                      ++
T Consensus       231 a~  232 (322)
T 3eie_A          231 AL  232 (322)
T ss_dssp             HT
T ss_pred             HH
Confidence            43

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

Probab=99.91  E-value=5.7e-23  Score=178.47  Aligned_cols=218  Identities=19%  Similarity=0.203  Sum_probs=161.8

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcce
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVL  117 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~  117 (294)
                      .|.+++.+..|++++|++.+++.|..++..            ....+++|+||||||||++|+++++++      +..++
T Consensus       104 ~~~~~~~~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~------~~~~~  177 (389)
T 3vfd_A          104 EIVDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAES------NATFF  177 (389)
T ss_dssp             TTBCCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHT------TCEEE
T ss_pred             hhhccCCCCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhh------cCcEE
Confidence            577888999999999999999999888732            223579999999999999999999998      77888


Q ss_pred             eecCCCCcchhH--HHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCC-----------CHHHHHHHHHHHHhhc-
Q 022641          118 ELNASDDRGINV--VRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSM-----------TEDAQNALRRTMETYS-  183 (294)
Q Consensus       118 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l-----------~~~~~~~L~~~l~~~~-  183 (294)
                      .+++........  ....+.........          ..+.+|||||+|.+           ....++.|+..++... 
T Consensus       178 ~v~~~~l~~~~~g~~~~~~~~~~~~a~~----------~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~  247 (389)
T 3vfd_A          178 NISAASLTSKYVGEGEKLVRALFAVARE----------LQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQS  247 (389)
T ss_dssp             EECSCCC-------CHHHHHHHHHHHHH----------SSSEEEEEETGGGGC--------CTHHHHHHHHHHHHHHHC-
T ss_pred             EeeHHHhhccccchHHHHHHHHHHHHHh----------cCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhcccc
Confidence            888876543211  11111111111110          12359999999988           2345566777776543 


Q ss_pred             ---CcceEEEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHH-HHH
Q 022641          184 ---KVTRFFFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAIT-YLQ  258 (294)
Q Consensus       184 ---~~~~ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~-~l~  258 (294)
                         ..+.+|++||.+..+.+++.+||. .+.+++|+.+++..++..++...+..++++.+..|++.+.|..+..+. ++.
T Consensus       248 ~~~~~v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~~~~g~~~~~l~~L~~  327 (389)
T 3vfd_A          248 AGDDRVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAK  327 (389)
T ss_dssp             ----CEEEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             cCCCCEEEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence               456788899999999999999997 799999999999999999998888999999999999999997765554 444


Q ss_pred             HHHHHh----------------CCCCChhhhhhhcccccCC
Q 022641          259 GAARLF----------------GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       259 ~~~~~~----------------~~~it~~~v~~~~~~~~~~  283 (294)
                      .++...                ...|+.+++..++....+.
T Consensus       328 ~a~~~~~rel~~~~~~~~~~~~~~~i~~~d~~~al~~~~~s  368 (389)
T 3vfd_A          328 DAALGPIRELKPEQVKNMSASEMRNIRLSDFTESLKKIKRS  368 (389)
T ss_dssp             HHTTHHHHTSCCC---CCSSSCCCCCCHHHHHHHHHHCCCS
T ss_pred             HHHHHHHHhhhhhhhhccchhhcCCcCHHHHHHHHHHcCCC
Confidence            443322                1358888998888766554

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

Probab=99.91  E-value=3.7e-23  Score=177.15  Aligned_cols=192  Identities=19%  Similarity=0.203  Sum_probs=139.3

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcce
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVL  117 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~  117 (294)
                      .+..++.+..|++++|++.+++.|..++..            ....+++|+||||||||++|+++++++      +.+++
T Consensus        40 ~~~~~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~------~~~~~  113 (355)
T 2qp9_X           40 AILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEA------NSTFF  113 (355)
T ss_dssp             -------CCCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHH------TCEEE
T ss_pred             hhcccCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHh------CCCEE
Confidence            345567788999999999999999887731            122469999999999999999999998      66777


Q ss_pred             eecCCCCc------chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH-----------HHHHHHHHHHH
Q 022641          118 ELNASDDR------GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE-----------DAQNALRRTME  180 (294)
Q Consensus       118 ~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~-----------~~~~~L~~~l~  180 (294)
                      .+++.+..      ....++..+.....              ..+.+|||||+|.+..           ...+.|+..++
T Consensus       114 ~v~~~~l~~~~~g~~~~~~~~~f~~a~~--------------~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~  179 (355)
T 2qp9_X          114 SVSSSDLVSKWMGESEKLVKQLFAMARE--------------NKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMN  179 (355)
T ss_dssp             EEEHHHHHSCC---CHHHHHHHHHHHHH--------------TSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHH
T ss_pred             EeeHHHHhhhhcchHHHHHHHHHHHHHH--------------cCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhh
Confidence            77654321      12222222222111              1246999999999863           24667777777


Q ss_pred             hh---cCcceEEEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHH
Q 022641          181 TY---SKVTRFFFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAIT  255 (294)
Q Consensus       181 ~~---~~~~~ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~  255 (294)
                      ..   ...+.+|++||.+..+++++++||. .+.+++|+.+++..+++.++...+..+++..+..|++.+.| +.+.+.+
T Consensus       180 ~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~~t~G~sg~dl~~  259 (355)
T 2qp9_X          180 GVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAV  259 (355)
T ss_dssp             HCC---CCEEEEEEESCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHHHTTTCCHHHHHH
T ss_pred             cccccCCCeEEEeecCCcccCCHHHHcccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHcCCCCHHHHHH
Confidence            53   3467788899999999999999996 89999999999999999999877777899999999999988 4555555


Q ss_pred             HHHHHH
Q 022641          256 YLQGAA  261 (294)
Q Consensus       256 ~l~~~~  261 (294)
                      +++.++
T Consensus       260 l~~~A~  265 (355)
T 2qp9_X          260 VVKDAL  265 (355)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            555544

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

Probab=99.91  E-value=8.7e-23  Score=176.69  Aligned_cols=209  Identities=21%  Similarity=0.216  Sum_probs=150.8

Q ss_pred             CCCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           56 RPKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        56 ~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      -+.+|+++.|.+.+++.|.+.+..             ..+.+++|+||||||||++|+++|.++      +.+++.++++
T Consensus       176 p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~------~~~f~~v~~s  249 (434)
T 4b4t_M          176 PTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQT------NATFLKLAAP  249 (434)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHH------TCEEEEEEGG
T ss_pred             CCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHh------CCCEEEEehh
Confidence            345799999999999988876421             233469999999999999999999999      8888888876


Q ss_pred             CCcc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------H---HHHHHHHHHHHhh
Q 022641          123 DDRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------E---DAQNALRRTMETY  182 (294)
Q Consensus       123 ~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~---~~~~~L~~~l~~~  182 (294)
                      +..+      ...++..+.......              +.+|+|||+|.+.           .   .....|+..++..
T Consensus       250 ~l~~~~vGese~~ir~lF~~A~~~a--------------P~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~  315 (434)
T 4b4t_M          250 QLVQMYIGEGAKLVRDAFALAKEKA--------------PTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGF  315 (434)
T ss_dssp             GGCSSCSSHHHHHHHHHHHHHHHHC--------------SEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTS
T ss_pred             hhhhcccchHHHHHHHHHHHHHhcC--------------CeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhcc
Confidence            6433      223444443333322              3599999999761           1   1344567777654


Q ss_pred             c--CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHH
Q 022641          183 S--KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITY  256 (294)
Q Consensus       183 ~--~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~  256 (294)
                      .  ..+.+|++||.+..+++++++  ||. .|.|++|+.+++.++++.+++...+. ++-.++.|++.+.| +...+.++
T Consensus       316 ~~~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~-~dvdl~~lA~~t~G~sGADi~~l  394 (434)
T 4b4t_M          316 SSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTD-DDINWQELARSTDEFNGAQLKAV  394 (434)
T ss_dssp             CSSCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBC-SCCCHHHHHHHCSSCCHHHHHHH
T ss_pred             CCCCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCC-CcCCHHHHHHhCCCCCHHHHHHH
Confidence            4  356788899999999999987  887 89999999999999999888764432 11237778887765 33444444


Q ss_pred             HHHHHHHh----CCCCChhhhhhhcccccCCCC
Q 022641          257 LQGAARLF----GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       257 l~~~~~~~----~~~it~~~v~~~~~~~~~~~~  285 (294)
                      +..|+..+    ...|+.+|+..++..+.+...
T Consensus       395 ~~eA~~~a~r~~~~~i~~~Df~~Al~~v~~~~~  427 (434)
T 4b4t_M          395 TVEAGMIALRNGQSSVKHEDFVEGISEVQARKS  427 (434)
T ss_dssp             HHHHHHHHHHHTCSSBCHHHHHHHHHSCSSSCC
T ss_pred             HHHHHHHHHHcCCCCcCHHHHHHHHHHHhCCCC
Confidence            44444433    557999999999988877644

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

Probab=99.90  E-value=1.6e-22  Score=173.02  Aligned_cols=207  Identities=19%  Similarity=0.220  Sum_probs=148.8

Q ss_pred             hcCCCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           54 KYRPKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        54 ~~~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      +--..+|+++.|.+.+++.|.+.+..             ..+..+||+||||||||++|+++|.++      +.+++.++
T Consensus       175 ~~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~------~~~fi~v~  248 (437)
T 4b4t_I          175 KSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQT------SATFLRIV  248 (437)
T ss_dssp             SSCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHH------TCEEEEEE
T ss_pred             cCCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHh------CCCEEEEE
Confidence            33456899999999999988877632             223469999999999999999999999      88888888


Q ss_pred             CCCCcch------hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHH
Q 022641          121 ASDDRGI------NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTME  180 (294)
Q Consensus       121 ~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~  180 (294)
                      +++..+.      ..++..+......              .+.||+|||+|.+..              .....|+..++
T Consensus       249 ~s~l~sk~vGesek~ir~lF~~Ar~~--------------aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lD  314 (437)
T 4b4t_I          249 GSELIQKYLGDGPRLCRQIFKVAGEN--------------APSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLD  314 (437)
T ss_dssp             SGGGCCSSSSHHHHHHHHHHHHHHHT--------------CSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHH
T ss_pred             HHHhhhccCchHHHHHHHHHHHHHhc--------------CCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhh
Confidence            7654332      2333333333222              235999999998721              23455666666


Q ss_pred             hhc--CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHH-HHHHHHhhccC-cHHHH
Q 022641          181 TYS--KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAE-ALSTLSSISQG-DLRRA  253 (294)
Q Consensus       181 ~~~--~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~-~l~~l~~~~~G-~~r~~  253 (294)
                      ...  ..+.+|++||.+..+++++++  ||. .|.|+.|+.+++.++++.+++..  .++++ .++.|++.+.| +...+
T Consensus       315 g~~~~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~--~l~~dvdl~~LA~~T~GfSGADI  392 (437)
T 4b4t_I          315 GFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKM--NLSEDVNLETLVTTKDDLSGADI  392 (437)
T ss_dssp             HCCCSSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTS--CBCSCCCHHHHHHHCCSCCHHHH
T ss_pred             CcCCCCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCC--CCCCcCCHHHHHHhCCCCCHHHH
Confidence            533  456789999999999999998  887 79999999999999998888653  33333 37788887655 33344


Q ss_pred             HHHHHHHHHHh----CCCCChhhhhhhcccccC
Q 022641          254 ITYLQGAARLF----GSSITSKDLISVSGYPTG  282 (294)
Q Consensus       254 ~~~l~~~~~~~----~~~it~~~v~~~~~~~~~  282 (294)
                      .+++..|+..+    ...|+.+|+..++..+.+
T Consensus       393 ~~l~~eA~~~Air~~~~~It~eDf~~Al~rv~~  425 (437)
T 4b4t_I          393 QAMCTEAGLLALRERRMQVTAEDFKQAKERVMK  425 (437)
T ss_dssp             HHHHHHHHHHHHHTTCSCBCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCccCHHHHHHHHHHHhC
Confidence            44455554444    456999999998876543

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

Probab=99.90  E-value=4e-22  Score=171.05  Aligned_cols=218  Identities=18%  Similarity=0.166  Sum_probs=159.7

Q ss_pred             hhhcCCCcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee
Q 022641           52 VEKYRPKQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL  119 (294)
Q Consensus        52 ~~~~~~~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~  119 (294)
                      .+++.+..|++++|++..++.|.+++..            ....+++|+||||||||++|+++++.+      +..++.+
T Consensus        75 ~~~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~------~~~~~~i  148 (357)
T 3d8b_A           75 MDHGPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQS------GATFFSI  148 (357)
T ss_dssp             BCCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHT------TCEEEEE
T ss_pred             ccCCCCCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHc------CCeEEEE
Confidence            3456788999999999999999888742            234569999999999999999999998      6777777


Q ss_pred             cCCCCcch--hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHhh----
Q 022641          120 NASDDRGI--NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMETY----  182 (294)
Q Consensus       120 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~~----  182 (294)
                      ++++....  ......+........          ...+.+|||||+|.+.           ...++.|+..++..    
T Consensus       149 ~~~~l~~~~~g~~~~~~~~~~~~a~----------~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~  218 (357)
T 3d8b_A          149 SASSLTSKWVGEGEKMVRALFAVAR----------CQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSS  218 (357)
T ss_dssp             EGGGGCCSSTTHHHHHHHHHHHHHH----------HTCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC----C
T ss_pred             ehHHhhccccchHHHHHHHHHHHHH----------hcCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccccC
Confidence            77654321  111112222111111          0124699999998773           23456677777642    


Q ss_pred             cCcceEEEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHHHHHH
Q 022641          183 SKVTRFFFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITYLQGA  260 (294)
Q Consensus       183 ~~~~~ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~l~~~  260 (294)
                      ...+.+|++||.+..+.+++.+||. .+.+++|+.+++..++..++...+..++++.++.+++.+.| ..+.+..+++.+
T Consensus       219 ~~~v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~~a  298 (357)
T 3d8b_A          219 EDRILVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCREA  298 (357)
T ss_dssp             CCCEEEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             CCCEEEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence            3466788899999999999999998 78999999999999999999888888999999999999888 444455555554


Q ss_pred             HHHh----------------CCCCChhhhhhhcccccCCCC
Q 022641          261 ARLF----------------GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       261 ~~~~----------------~~~it~~~v~~~~~~~~~~~~  285 (294)
                      +...                ...|+.+++..++....+...
T Consensus       299 ~~~~ir~l~~~~~~~~~~~~~~~i~~~d~~~al~~~~ps~~  339 (357)
T 3d8b_A          299 SLGPIRSLQTADIATITPDQVRPIAYIDFENAFRTVRPSVS  339 (357)
T ss_dssp             HTHHHHHCCC----------CCCBCHHHHHHHHHHHGGGCC
T ss_pred             HHHHHHHhhhhhhccccccccCCcCHHHHHHHHHhcCCCCC
Confidence            3222                246999999999888776543

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

Probab=99.90  E-value=3.2e-22  Score=173.28  Aligned_cols=206  Identities=18%  Similarity=0.159  Sum_probs=148.4

Q ss_pred             CCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ..+|+++.|.+..++.|.+.+..             ..+..+||+||||||||++|+++|.++      +.+++.+++++
T Consensus       177 ~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~------~~~~~~v~~s~  250 (437)
T 4b4t_L          177 EITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATI------GANFIFSPASG  250 (437)
T ss_dssp             SSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHH------TCEEEEEEGGG
T ss_pred             CCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHh------CCCEEEEehhh
Confidence            34789999999999988887632             233469999999999999999999999      88888888776


Q ss_pred             Ccch------hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhhc
Q 022641          124 DRGI------NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTMETYS  183 (294)
Q Consensus       124 ~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~~~~  183 (294)
                      ..+.      ..++..+......              .+.||||||+|.+..              .....|+..++...
T Consensus       251 l~sk~~Gese~~ir~~F~~A~~~--------------~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~  316 (437)
T 4b4t_L          251 IVDKYIGESARIIREMFAYAKEH--------------EPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFD  316 (437)
T ss_dssp             TCCSSSSHHHHHHHHHHHHHHHS--------------CSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSS
T ss_pred             hccccchHHHHHHHHHHHHHHhc--------------CCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhccc
Confidence            5432      2233333322221              245999999998731              23556777777544


Q ss_pred             --CcceEEEEecCCcccchHhhcc--cc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHHH
Q 022641          184 --KVTRFFFICNYISRIIEPLASR--CA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITYL  257 (294)
Q Consensus       184 --~~~~ii~~~~~~~~~~~~l~~r--~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~l  257 (294)
                        ..+.+|++||.+..++++++++  |. .|.|+.|+.+++..+++.+++..... ++-.+..+++.|.| +...+.+++
T Consensus       317 ~~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~-~d~dl~~lA~~t~G~sGADi~~l~  395 (437)
T 4b4t_L          317 NLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKT-GEFDFEAAVKMSDGFNGADIRNCA  395 (437)
T ss_dssp             CTTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBC-SCCCHHHHHHTCCSCCHHHHHHHH
T ss_pred             CCCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCC-cccCHHHHHHhCCCCCHHHHHHHH
Confidence              3567899999999999999874  76 79999999999999999888654332 22347888888765 334444445


Q ss_pred             HHHHHHh----CCCCChhhhhhhcccccCC
Q 022641          258 QGAARLF----GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       258 ~~~~~~~----~~~it~~~v~~~~~~~~~~  283 (294)
                      ..|+..+    ...|+.+|+..++..+.+.
T Consensus       396 ~eA~~~air~~~~~i~~~d~~~Al~~v~~~  425 (437)
T 4b4t_L          396 TEAGFFAIRDDRDHINPDDLMKAVRKVAEV  425 (437)
T ss_dssp             HHHHHHHHHTTCSSBCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHHhc
Confidence            5544443    4569999999988776543

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=99.89  E-value=2e-22  Score=168.41  Aligned_cols=173  Identities=18%  Similarity=0.203  Sum_probs=140.6

Q ss_pred             ccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc-CCCccCCcceeecCCC-CcchhHHHHHHHHHHhhhc
Q 022641           65 HQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF-GPELYKSRVLELNASD-DRGINVVRTKIKTFAAVAV  142 (294)
Q Consensus        65 g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~-~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  142 (294)
                      |+++++..|...+..++.++++|+||||+|||+++.++++... |.. ....+..+++++ ..+.+.++..+..+...+.
T Consensus         1 g~~~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~-~~~d~~~l~~~~~~~~id~ir~li~~~~~~p~   79 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPP-KASDVLEIDPEGENIGIDDIRTIKDFLNYSPE   79 (305)
T ss_dssp             ---CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCC-CTTTEEEECCSSSCBCHHHHHHHHHHHTSCCS
T ss_pred             ChHHHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHHhCchhhc-cCCCEEEEcCCcCCCCHHHHHHHHHHHhhccc
Confidence            6788899999999988877799999999999999999998641 211 245677787764 5677777776665543221


Q ss_pred             ccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEEecCCCHHHHHHH
Q 022641          143 GSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSR  222 (294)
Q Consensus       143 ~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~  222 (294)
                                .+++.++||||+|.++...++.|++.+++++..+.+|++|+.+..+.+++++|  .+.|.|++.+++..+
T Consensus        80 ----------~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR--~~~f~~l~~~~i~~~  147 (305)
T 2gno_A           80 ----------LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR--VFRVVVNVPKEFRDL  147 (305)
T ss_dssp             ----------SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT--SEEEECCCCHHHHHH
T ss_pred             ----------cCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce--eEeCCCCCHHHHHHH
Confidence                      23467999999999999999999999999999999999999999999999999  999999999999999


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHH
Q 022641          223 VLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQG  259 (294)
Q Consensus       223 l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~  259 (294)
                      +.+.+   +  ++++++    ..+.||+|.++++++.
T Consensus       148 L~~~~---~--i~~~~~----~~~~g~~~~al~~l~~  175 (305)
T 2gno_A          148 VKEKI---G--DLWEEL----PLLERDFKTALEAYKL  175 (305)
T ss_dssp             HHHHH---T--THHHHC----GGGGTCHHHHHHHHHH
T ss_pred             HHHHh---C--CCHHHH----HHHCCCHHHHHHHHHH
Confidence            98877   2  566665    5579999999988863

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

Probab=99.89  E-value=2.7e-21  Score=163.39  Aligned_cols=188  Identities=18%  Similarity=0.158  Sum_probs=139.1

Q ss_pred             cCCCcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           55 YRPKQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        55 ~~~~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      ..+..|+++.|.+.+++.|.+.+..            ....+++|+||||||||++|+++++++.     ...++.++++
T Consensus         6 ~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~-----~~~~~~i~~~   80 (322)
T 1xwi_A            6 RPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEAN-----NSTFFSISSS   80 (322)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHTT-----SCEEEEEECC
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHcC-----CCcEEEEEhH
Confidence            3456899999999999999887631            1224699999999999999999999872     3455666655


Q ss_pred             CCc------chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHhh---
Q 022641          123 DDR------GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMETY---  182 (294)
Q Consensus       123 ~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~~---  182 (294)
                      +..      ....++..+.....              ..+.+|+|||+|.+.           ....+.|+..++..   
T Consensus        81 ~l~~~~~g~~~~~~~~lf~~a~~--------------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~  146 (322)
T 1xwi_A           81 DLVSKWLGESEKLVKNLFQLARE--------------NKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVD  146 (322)
T ss_dssp             SSCCSSCCSCHHHHHHHHHHHHH--------------TSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSC
T ss_pred             HHHhhhhhHHHHHHHHHHHHHHh--------------cCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhccccc
Confidence            432      22333333332221              124599999999882           23456677777653   


Q ss_pred             cCcceEEEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCc-HHHHHHHHHHH
Q 022641          183 SKVTRFFFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGD-LRRAITYLQGA  260 (294)
Q Consensus       183 ~~~~~ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~-~r~~~~~l~~~  260 (294)
                      ...+.+|++||.+..+++++++||. .+.+++|+.+++..+++.++...+..+++..+..|++.+.|. .+.+..+++.+
T Consensus       147 ~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~A  226 (322)
T 1xwi_A          147 NDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVRDA  226 (322)
T ss_dssp             CTTEEEEEEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             CCCEEEEEecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence            3557788889999999999999996 899999999999999999988777778999999999998874 45555555554


Q ss_pred             H
Q 022641          261 A  261 (294)
Q Consensus       261 ~  261 (294)
                      +
T Consensus       227 ~  227 (322)
T 1xwi_A          227 L  227 (322)
T ss_dssp             H
T ss_pred             H
Confidence            4

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

Probab=99.89  E-value=4.2e-22  Score=163.49  Aligned_cols=209  Identities=18%  Similarity=0.132  Sum_probs=153.0

Q ss_pred             hhhhcCCCcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCccee
Q 022641           51 WVEKYRPKQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLE  118 (294)
Q Consensus        51 ~~~~~~~~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~  118 (294)
                      |.+++.+..|++++|.+..++.+...+..            ....+++|+||||||||++|++++..+      +.+++.
T Consensus         2 ~~~~~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~------~~~~~~   75 (257)
T 1lv7_A            2 LTEDQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA------KVPFFT   75 (257)
T ss_dssp             EEECSSCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH------TCCEEE
T ss_pred             CCccCCCCCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHc------CCCEEE
Confidence            66778889999999999999877665432            123469999999999999999999998      556677


Q ss_pred             ecCCCCcc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHH
Q 022641          119 LNASDDRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRT  178 (294)
Q Consensus       119 ~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~  178 (294)
                      +++.+...      ...+...+.....              ..+.+++|||+|.+..              ...+.++..
T Consensus        76 i~~~~~~~~~~~~~~~~~~~~~~~a~~--------------~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~  141 (257)
T 1lv7_A           76 ISGSDFVEMFVGVGASRVRDMFEQAKK--------------AAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVE  141 (257)
T ss_dssp             ECSCSSTTSCCCCCHHHHHHHHHHHHT--------------TCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHH
T ss_pred             EeHHHHHHHhhhhhHHHHHHHHHHHHH--------------cCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHH
Confidence            77654322      2223333332211              1235999999976532              345556666


Q ss_pred             HHhh--cCcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCH-HHHHHHHhhccC-cHH
Q 022641          179 METY--SKVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDA-EALSTLSSISQG-DLR  251 (294)
Q Consensus       179 l~~~--~~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~-~~l~~l~~~~~G-~~r  251 (294)
                      ++..  .....+|++||.+..+++++.+  ||. .+.+++|+.+++.++++.+++..  .+++ ..+..++..+.| ++|
T Consensus       142 l~~~~~~~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~--~l~~~~~~~~la~~~~G~~~~  219 (257)
T 1lv7_A          142 MDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRV--PLAPDIDAAIIARGTPGFSGA  219 (257)
T ss_dssp             HHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTS--CBCTTCCHHHHHHTCTTCCHH
T ss_pred             hhCcccCCCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcC--CCCccccHHHHHHHcCCCCHH
Confidence            6643  3456788889999888899887  776 78999999999999998887543  3433 336778889999 999


Q ss_pred             HHHHHHHHHHHHh----CCCCChhhhhhhccccc
Q 022641          252 RAITYLQGAARLF----GSSITSKDLISVSGYPT  281 (294)
Q Consensus       252 ~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~  281 (294)
                      .+.+++..++..+    ...|+.+++..++....
T Consensus       220 dl~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~  253 (257)
T 1lv7_A          220 DLANLVNEAALFAARGNKRVVSMVEFEKAKDKIM  253 (257)
T ss_dssp             HHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHh
Confidence            9999999887766    35799999999887653

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

Probab=99.89  E-value=5.6e-22  Score=171.20  Aligned_cols=203  Identities=19%  Similarity=0.203  Sum_probs=145.4

Q ss_pred             CcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC
Q 022641           58 KQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD  124 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~  124 (294)
                      .+|+++.|.+.+++.|.+.+..             ..++.+||+||||||||++|+++|.++      +.+++.++++..
T Consensus       206 vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~------~~~fi~vs~s~L  279 (467)
T 4b4t_H          206 VTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRT------DATFIRVIGSEL  279 (467)
T ss_dssp             CCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHH------TCEEEEEEGGGG
T ss_pred             CCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhcc------CCCeEEEEhHHh
Confidence            5789999999999998876532             234569999999999999999999999      788888887654


Q ss_pred             cc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhhc-
Q 022641          125 RG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTMETYS-  183 (294)
Q Consensus       125 ~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~~~~-  183 (294)
                      .+      ...++..+......              .+.+|||||+|.+..              .....++..++... 
T Consensus       280 ~sk~vGesek~ir~lF~~Ar~~--------------aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~  345 (467)
T 4b4t_H          280 VQKYVGEGARMVRELFEMARTK--------------KACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDP  345 (467)
T ss_dssp             CCCSSSHHHHHHHHHHHHHHHT--------------CSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCC
T ss_pred             hcccCCHHHHHHHHHHHHHHhc--------------CCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCC
Confidence            33      22344444333322              235999999998731              13445566665433 


Q ss_pred             -CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHH-HHHHHHhhccC-cHHHHHHHH
Q 022641          184 -KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAE-ALSTLSSISQG-DLRRAITYL  257 (294)
Q Consensus       184 -~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~-~l~~l~~~~~G-~~r~~~~~l  257 (294)
                       ..+.+|++||.+..+++++++  ||. .|.|+.|+.+++.++|+.+++...  ++.+ .++.|++.|.| +...+.+++
T Consensus       346 ~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~--l~~dvdl~~LA~~T~GfSGADI~~l~  423 (467)
T 4b4t_H          346 RGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMS--VERGIRWELISRLCPNSTGAELRSVC  423 (467)
T ss_dssp             TTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSC--BCSSCCHHHHHHHCCSCCHHHHHHHH
T ss_pred             CCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCC--CCCCCCHHHHHHHCCCCCHHHHHHHH
Confidence             356788899999999999988  998 899999999999999988876533  3322 36778887765 233333444


Q ss_pred             HHHHHHh----CCCCChhhhhhhcccccC
Q 022641          258 QGAARLF----GSSITSKDLISVSGYPTG  282 (294)
Q Consensus       258 ~~~~~~~----~~~it~~~v~~~~~~~~~  282 (294)
                      ..|+..+    ...|+.+++..++..+..
T Consensus       424 ~eAa~~Air~~~~~it~~Df~~Al~kV~~  452 (467)
T 4b4t_H          424 TEAGMFAIRARRKVATEKDFLKAVDKVIS  452 (467)
T ss_dssp             HHHHHHHHHHTCSSBCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCccCHHHHHHHHHHHhc
Confidence            4444333    567999999988877543

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

Probab=99.89  E-value=2.5e-21  Score=159.31  Aligned_cols=204  Identities=18%  Similarity=0.122  Sum_probs=140.8

Q ss_pred             CcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           58 KQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      ..|++++|++..+..+.+++..            ....+++|+||||||||++|+++++++      +.+++.+++.+..
T Consensus         3 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~------~~~~~~~~~~~~~   76 (262)
T 2qz4_A            3 VSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEA------QVPFLAMAGAEFV   76 (262)
T ss_dssp             CCTTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHH------TCCEEEEETTTTS
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHh------CCCEEEechHHHH
Confidence            4688999999999888776531            233469999999999999999999998      6677777766532


Q ss_pred             c------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH------------HHH---HHHHHHHHh--h
Q 022641          126 G------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE------------DAQ---NALRRTMET--Y  182 (294)
Q Consensus       126 ~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~------------~~~---~~L~~~l~~--~  182 (294)
                      .      ...+...+.....              ..+.+|+|||+|.+..            ...   ..|+..++.  .
T Consensus        77 ~~~~~~~~~~~~~~~~~a~~--------------~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~  142 (262)
T 2qz4_A           77 EVIGGLGAARVRSLFKEARA--------------RAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGT  142 (262)
T ss_dssp             SSSTTHHHHHHHHHHHHHHH--------------TCSEEEEEECC-------------------CHHHHHHHHHHHTCCT
T ss_pred             hhccChhHHHHHHHHHHHHh--------------cCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCC
Confidence            2      1112222222111              1235999999999832            222   334444443  2


Q ss_pred             cCcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHH-HHHHHhhccCc-HHHHHHHH
Q 022641          183 SKVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEA-LSTLSSISQGD-LRRAITYL  257 (294)
Q Consensus       183 ~~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-l~~l~~~~~G~-~r~~~~~l  257 (294)
                      .....+|+++|.+..+++++.+  ||. .+.+++|+.+++.++++.++...+...+.+. +..++..+.|. .+.+.+++
T Consensus       143 ~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~  222 (262)
T 2qz4_A          143 TDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANIC  222 (262)
T ss_dssp             TCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHH
T ss_pred             CCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHH
Confidence            3456788889999888899988  996 8999999999999999999998888777664 57888888764 45666777


Q ss_pred             HHHHHHh----CCCCChhhhhhhccccc
Q 022641          258 QGAARLF----GSSITSKDLISVSGYPT  281 (294)
Q Consensus       258 ~~~~~~~----~~~it~~~v~~~~~~~~  281 (294)
                      +.++..+    ...|+.+++..++....
T Consensus       223 ~~a~~~a~~~~~~~i~~~d~~~a~~~~~  250 (262)
T 2qz4_A          223 NEAALHAAREGHTSVHTLNFEYAVERVL  250 (262)
T ss_dssp             HHHHTC--------CCBCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhc
Confidence            7666554    34699999998887643

>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=99.89  E-value=2.9e-21  Score=167.81  Aligned_cols=230  Identities=18%  Similarity=0.213  Sum_probs=166.6

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHc----CCCC--cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLET----ANCP--HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~----~~~~--~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      ...+|..+|.|   ++++|++..+..+..++..    ....  +++|+||+|+|||++++.+++.+.+..  +..++.++
T Consensus         6 ~~~~l~~~~~p---~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~--~~~~~~i~   80 (389)
T 1fnn_A            6 DDSVFSPSYVP---KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKT--TARFVYIN   80 (389)
T ss_dssp             CGGGGSTTCCC---SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSC--CCEEEEEE
T ss_pred             CHhhcCCccCC---CCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhc--CeeEEEEe
Confidence            44567777877   6789999999888888765    3333  799999999999999999999984332  34567777


Q ss_pred             CCCCcchhH-HHHHHHHHHhhhcccCccCC---------CCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc----Ccc
Q 022641          121 ASDDRGINV-VRTKIKTFAAVAVGSGQRRG---------GYPCPPYKIIILDEADSMTEDAQNALRRTMETYS----KVT  186 (294)
Q Consensus       121 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~----~~~  186 (294)
                      +........ +......+.......+....         .....++.+|+|||++.++...+..|+.+++...    ...
T Consensus        81 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~  160 (389)
T 1fnn_A           81 GFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRI  160 (389)
T ss_dssp             TTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCE
T ss_pred             CccCCCHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCE
Confidence            665443322 22222211000000000000         0001345699999999999988999998887644    377


Q ss_pred             eEEEEecCC---cccchHhhcccc--EEEecCCCHHHHHHHHHHHHHHh--CCCCCHHHHHHHHhhc---------cCcH
Q 022641          187 RFFFICNYI---SRIIEPLASRCA--KFRFKPLSEEVMSSRVLHICNEE--GLNLDAEALSTLSSIS---------QGDL  250 (294)
Q Consensus       187 ~ii~~~~~~---~~~~~~l~~r~~--~i~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~l~~l~~~~---------~G~~  250 (294)
                      .+|++++..   ..+.+.+.+||.  .+.|+|++.+++..++...+...  ...+++++++.+++.+         +||+
T Consensus       161 ~iI~~~~~~~~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~  240 (389)
T 1fnn_A          161 ALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDA  240 (389)
T ss_dssp             EEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCH
T ss_pred             EEEEEECCchHHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCCcH
Confidence            788888876   457788888887  79999999999999999988752  2468999999999998         8999


Q ss_pred             HHHHHHHHHHHHHh----CCCCChhhhhhhccccc
Q 022641          251 RRAITYLQGAARLF----GSSITSKDLISVSGYPT  281 (294)
Q Consensus       251 r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~  281 (294)
                      |.++++++.+...+    ...|+.+++..++....
T Consensus       241 r~~~~~l~~a~~~a~~~~~~~i~~~~v~~~~~~~~  275 (389)
T 1fnn_A          241 RLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEVL  275 (389)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHh
Confidence            99999999887765    35699999988776654

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

Probab=99.89  E-value=6.8e-22  Score=164.76  Aligned_cols=211  Identities=17%  Similarity=0.168  Sum_probs=147.1

Q ss_pred             cCCCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecC
Q 022641           55 YRPKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA  121 (294)
Q Consensus        55 ~~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~  121 (294)
                      ..+..|++++|++..++.+..++..             ....+++|+||||||||++|+++++.+      +..++.+++
T Consensus        11 ~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~------~~~~~~v~~   84 (285)
T 3h4m_A           11 RPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATET------NATFIRVVG   84 (285)
T ss_dssp             SCCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHT------TCEEEEEEG
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHh------CCCEEEEeh
Confidence            3356789999999999999887743             344569999999999999999999998      667777665


Q ss_pred             CCCcc--hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCC-----------CHHHHHHHHHHHHhh-----c
Q 022641          122 SDDRG--INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSM-----------TEDAQNALRRTMETY-----S  183 (294)
Q Consensus       122 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l-----------~~~~~~~L~~~l~~~-----~  183 (294)
                      .....  .......+.........          ..+.+|+|||+|.+           ....+..|..+++..     .
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~  154 (285)
T 3h4m_A           85 SELVKKFIGEGASLVKDIFKLAKE----------KAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDAR  154 (285)
T ss_dssp             GGGCCCSTTHHHHHHHHHHHHHHH----------TCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSS
T ss_pred             HHHHHhccchHHHHHHHHHHHHHH----------cCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCCC
Confidence            44322  11111222221111111          12359999999987           334555666555532     3


Q ss_pred             CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHHHHH
Q 022641          184 KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITYLQG  259 (294)
Q Consensus       184 ~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~l~~  259 (294)
                      ....+|++||.+..+++++.+  ||. .+.+++|+.+++.++++..+...+.. ++..+..++..+.| +++.+..++..
T Consensus       155 ~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~-~~~~~~~l~~~~~g~~~~~i~~l~~~  233 (285)
T 3h4m_A          155 GDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLA-EDVNLEEIAKMTEGCVGAELKAICTE  233 (285)
T ss_dssp             SSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBC-TTCCHHHHHHHCTTCCHHHHHHHHHH
T ss_pred             CCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCC-CcCCHHHHHHHcCCCCHHHHHHHHHH
Confidence            467788899999999999998  886 89999999999999999887654433 23346777777766 45555555555


Q ss_pred             HHHHh----CCCCChhhhhhhcccccC
Q 022641          260 AARLF----GSSITSKDLISVSGYPTG  282 (294)
Q Consensus       260 ~~~~~----~~~it~~~v~~~~~~~~~  282 (294)
                      +...+    ...|+.+++..++.....
T Consensus       234 a~~~a~~~~~~~I~~~d~~~al~~~~~  260 (285)
T 3h4m_A          234 AGMNAIRELRDYVTMDDFRKAVEKIME  260 (285)
T ss_dssp             HHHHHHHTTCSSBCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccCcCCHHHHHHHHHHHHh
Confidence            55444    456999999999887543

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

Probab=99.88  E-value=6.3e-22  Score=166.86  Aligned_cols=202  Identities=21%  Similarity=0.224  Sum_probs=148.1

Q ss_pred             hhcccHHHHHHHHHHHH---------------cCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCc-cCCcceeecCCCCc
Q 022641           62 DVAHQEEVVRVLTNTLE---------------TANCPHMLFYGPPGTGKTTTALAIAHQLFGPEL-YKSRVLELNASDDR  125 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~---------------~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~-~~~~~~~~~~~~~~  125 (294)
                      +++|++..++.+..++.               .....+++|+||||||||++|+++++.+.+... ...+++.+++....
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~l~  111 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDLV  111 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGGGTC
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHHHhh
Confidence            68999999988877654               233346999999999999999999999843221 23356666654432


Q ss_pred             ch--hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCC---------CHHHHHHHHHHHHhhcCcceEEEEecC
Q 022641          126 GI--NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSM---------TEDAQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       126 ~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l---------~~~~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      ..  ......+.......             .+++|+|||+|.+         +...++.|++.++.......+|+++|.
T Consensus       112 ~~~~g~~~~~~~~~~~~~-------------~~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~~~i~~~~~  178 (309)
T 3syl_A          112 GQYIGHTAPKTKEVLKRA-------------MGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLVVILAGYA  178 (309)
T ss_dssp             CSSTTCHHHHHHHHHHHH-------------TTSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTTCEEEEEECH
T ss_pred             hhcccccHHHHHHHHHhc-------------CCCEEEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCCEEEEEeCCh
Confidence            21  11111111111111             1249999999977         778899999999998888888888875


Q ss_pred             Cc-----ccchHhhccc-cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhh--------ccCcHHHHHHHHHHH
Q 022641          195 IS-----RIIEPLASRC-AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSI--------SQGDLRRAITYLQGA  260 (294)
Q Consensus       195 ~~-----~~~~~l~~r~-~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~--------~~G~~r~~~~~l~~~  260 (294)
                      ..     .+.+++.+|| ..+.|++|+.+++..+++.++...+..+++++++.+++.        +.||+|.+.++++.+
T Consensus       179 ~~~~~~~~~~~~l~~R~~~~i~~~~~~~~~~~~il~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~gn~r~l~~~l~~a  258 (309)
T 3syl_A          179 DRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRAYIGLRRNQPHFANARSIRNALDRA  258 (309)
T ss_dssp             HHHHHHHHHSTTHHHHEEEEEEECCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHTTSSSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhhCHHHHHhCCeEEEcCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHH
Confidence            42     2468999999 599999999999999999999999999999999999886        459999999999988


Q ss_pred             HHHh--------CCCCChhhhhhh
Q 022641          261 ARLF--------GSSITSKDLISV  276 (294)
Q Consensus       261 ~~~~--------~~~it~~~v~~~  276 (294)
                      ....        ...++.+++..+
T Consensus       259 ~~~~~~r~~~~~~~~~~~~~l~~i  282 (309)
T 3syl_A          259 RLRQANRLFTASSGPLDARALSTI  282 (309)
T ss_dssp             HHHHHHHHHHC---CEEHHHHHEE
T ss_pred             HHHHHHHHHhccCCCCCHHHHhhc
Confidence            7422        244555555443

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

Probab=99.88  E-value=1.6e-21  Score=168.76  Aligned_cols=201  Identities=21%  Similarity=0.209  Sum_probs=145.5

Q ss_pred             CcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC
Q 022641           58 KQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD  124 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~  124 (294)
                      ..|+++.|.+.+++.|.+.+..             ..++.++|+||||||||++|+++|.++      +.+++.+++++.
T Consensus       169 v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~------~~~~~~v~~~~l  242 (428)
T 4b4t_K          169 VTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANST------KAAFIRVNGSEF  242 (428)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHH------TCEEEEEEGGGT
T ss_pred             CCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHh------CCCeEEEecchh
Confidence            4789999999999988877632             233459999999999999999999999      888888887654


Q ss_pred             cc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC--------------HHHHHHHHHHHHhhc-
Q 022641          125 RG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT--------------EDAQNALRRTMETYS-  183 (294)
Q Consensus       125 ~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--------------~~~~~~L~~~l~~~~-  183 (294)
                      .+      ...++..+......              .+.+|+|||+|.+.              ....+.|+..++... 
T Consensus       243 ~~~~~Ge~e~~ir~lF~~A~~~--------------aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~  308 (428)
T 4b4t_K          243 VHKYLGEGPRMVRDVFRLAREN--------------APSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQ  308 (428)
T ss_dssp             CCSSCSHHHHHHHHHHHHHHHT--------------CSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCS
T ss_pred             hccccchhHHHHHHHHHHHHHc--------------CCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCC
Confidence            33      23344444433322              23599999998651              124667778887643 


Q ss_pred             -CcceEEEEecCCcccchHhhc--ccc-EEEec-CCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHHH
Q 022641          184 -KVTRFFFICNYISRIIEPLAS--RCA-KFRFK-PLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITYL  257 (294)
Q Consensus       184 -~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~-~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~l  257 (294)
                       ..+.+|++||.+..+++++++  ||. .|.|+ +|+.+++..+++.+++...+. ++..++.|++.|.| +...+.+++
T Consensus       309 ~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~-~~~dl~~lA~~t~G~sgadi~~l~  387 (428)
T 4b4t_K          309 STNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLA-PEADLDSLIIRNDSLSGAVIAAIM  387 (428)
T ss_dssp             SCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBC-TTCCHHHHHHHTTTCCHHHHHHHH
T ss_pred             CCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCC-cccCHHHHHHHCCCCCHHHHHHHH
Confidence             356788999999999999997  887 78895 788999999998888654332 22347888887765 334444555


Q ss_pred             HHHHHHh----CCCCChhhhhhhccc
Q 022641          258 QGAARLF----GSSITSKDLISVSGY  279 (294)
Q Consensus       258 ~~~~~~~----~~~it~~~v~~~~~~  279 (294)
                      ..|+..+    ...|+.+++..++..
T Consensus       388 ~eA~~~a~r~~~~~i~~~d~~~A~~~  413 (428)
T 4b4t_K          388 QEAGLRAVRKNRYVILQSDLEEAYAT  413 (428)
T ss_dssp             HHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHHH
Confidence            5555444    456999999998865

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

Probab=99.88  E-value=8e-22  Score=171.18  Aligned_cols=230  Identities=20%  Similarity=0.217  Sum_probs=162.5

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHc----CCCCcEEEECCCCCCHHHHHHHHHHHhcCCC---ccCCcceeec
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLET----ANCPHMLFYGPPGTGKTTTALAIAHQLFGPE---LYKSRVLELN  120 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~----~~~~~ill~Gp~G~GKT~la~~la~~~~~~~---~~~~~~~~~~  120 (294)
                      ..+|...+.|   ++++|++..+..+..++..    +..++++|+||||||||++++.+++.+....   ..+..++.++
T Consensus         9 ~~~l~~~~~p---~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~   85 (387)
T 2v1u_A            9 RWVLLPDYVP---DVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVN   85 (387)
T ss_dssp             HHHHSTTCCC---SCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEE
T ss_pred             HHhcCCccCC---CCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEE
Confidence            3455556666   7789999999999998843    3456799999999999999999999873210   1145667777


Q ss_pred             CCCCcchhHHH-HHHHHHHhhhcccCccC---------CCCCCCCcEEEEEeCCCCCCHH--HHHHHHHHHHhh-----c
Q 022641          121 ASDDRGINVVR-TKIKTFAAVAVGSGQRR---------GGYPCPPYKIIILDEADSMTED--AQNALRRTMETY-----S  183 (294)
Q Consensus       121 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~---------~~~~~~~~~lliiDei~~l~~~--~~~~L~~~l~~~-----~  183 (294)
                      +....+...+. .....+.......+...         ......++.+|+|||+|.+...  .++.|..+++..     .
T Consensus        86 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~  165 (387)
T 2v1u_A           86 ARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDR  165 (387)
T ss_dssp             TTTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC---
T ss_pred             CCcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCC
Confidence            76544433221 11111100000000000         0001234669999999999765  677777777644     4


Q ss_pred             CcceEEEEecCC---cccchHhhccc--cEEEecCCCHHHHHHHHHHHHHH--hCCCCCHHHHHHHHhhcc---CcHHHH
Q 022641          184 KVTRFFFICNYI---SRIIEPLASRC--AKFRFKPLSEEVMSSRVLHICNE--EGLNLDAEALSTLSSISQ---GDLRRA  253 (294)
Q Consensus       184 ~~~~ii~~~~~~---~~~~~~l~~r~--~~i~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~l~~l~~~~~---G~~r~~  253 (294)
                      ....+|+++|..   ..+.+.+.+|+  ..+.|+|++.+++..++...+..  .+..+++++++.+++.++   ||+|.+
T Consensus       166 ~~~~~I~~t~~~~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~  245 (387)
T 2v1u_A          166 VWVSLVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRA  245 (387)
T ss_dssp             --CEEEEECSCSTTSSSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSSHHHHHHHHHHSSSCCHHHH
T ss_pred             ceEEEEEEECCCchHhhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhccCHHHH
Confidence            566788888876   56788999999  58999999999999999999876  456789999999999988   999999


Q ss_pred             HHHHHHHHHHh----CCCCChhhhhhhcccc
Q 022641          254 ITYLQGAARLF----GSSITSKDLISVSGYP  280 (294)
Q Consensus       254 ~~~l~~~~~~~----~~~it~~~v~~~~~~~  280 (294)
                      +++++.+...+    ...|+.+++..++...
T Consensus       246 ~~~l~~a~~~a~~~~~~~i~~~~v~~a~~~~  276 (387)
T 2v1u_A          246 LDLLRVAGEIAERRREERVRREHVYSARAEI  276 (387)
T ss_dssp             HHHHHHHHHHHHHTTCSCBCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence            99999888765    3569999998887654

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

Probab=99.87  E-value=3.5e-21  Score=162.28  Aligned_cols=207  Identities=17%  Similarity=0.235  Sum_probs=148.0

Q ss_pred             hhhcccHHHHHHHHHHHHc--------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc
Q 022641           61 KDVAHQEEVVRVLTNTLET--------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG  126 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~--------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~  126 (294)
                      +.++|++.++..+...+..              ....+++|+||||||||++|+++++.+      +.+++.++++....
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l------~~~~~~i~~~~~~~   88 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA------NAPFIKVEATKFTE   88 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH------TCCEEEEEGGGGSS
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHh------CCCEEEEcchhccc
Confidence            4688999999988887754              234579999999999999999999998      55666666554321


Q ss_pred             --------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHH------------HHHHHHHHHhh----
Q 022641          127 --------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDA------------QNALRRTMETY----  182 (294)
Q Consensus       127 --------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~------------~~~L~~~l~~~----  182 (294)
                              ...+...+........         ....+.+|+|||+|.++...            ++.|++.++..    
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~~  159 (310)
T 1ofh_A           89 VGYVGKEVDSIIRDLTDSAGGAID---------AVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVST  159 (310)
T ss_dssp             CCSGGGSTTHHHHHHHHTTTTCHH---------HHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEEE
T ss_pred             CCccCccHHHHHHHHHHHhhHHHh---------hccCCCEEEEEChhhcCccccccccchhHHHHHHHHHHHhcCCeEec
Confidence                    1112222221100000         00113599999999997543            78899999863    


Q ss_pred             ------cCcceEEEEe----cCCcccchHhhcccc-EEEecCCCHHHHHHHHHH-----------HHHHhCC--CCCHHH
Q 022641          183 ------SKVTRFFFIC----NYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLH-----------ICNEEGL--NLDAEA  238 (294)
Q Consensus       183 ------~~~~~ii~~~----~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~-----------~~~~~~~--~~~~~~  238 (294)
                            .....+|+++    +.+..+.+++.+||. .+.|+||+.+++..++++           .+...+.  .+++++
T Consensus       160 ~~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~R~~~~i~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~a  239 (310)
T 1ofh_A          160 KHGMVKTDHILFIASGAFQVARPSDLIPELQGRLPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDA  239 (310)
T ss_dssp             TTEEEECTTCEEEEEECCSSSCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHHTTCEEEECHHH
T ss_pred             ccccccCCcEEEEEcCCcccCCcccCCHHHHhhCCceEEcCCcCHHHHHHHHHhhHHHHHHHHHHHHHhcCCeeccCHHH
Confidence                  1355666664    355678899999997 699999999999999982           2333453  589999


Q ss_pred             HHHHHhhc--------cCcHHHHHHHHHHHHHH-----h--CC---CCChhhhhhhcccccC
Q 022641          239 LSTLSSIS--------QGDLRRAITYLQGAARL-----F--GS---SITSKDLISVSGYPTG  282 (294)
Q Consensus       239 l~~l~~~~--------~G~~r~~~~~l~~~~~~-----~--~~---~it~~~v~~~~~~~~~  282 (294)
                      ++.|++.+        .||+|.+.++++.+...     .  ..   .||.+++.+++.....
T Consensus       240 ~~~l~~~~~~~~~~~~~g~~R~l~~~l~~~~~~~~~~~~~~~~~~~~i~~~~v~~~l~~~~~  301 (310)
T 1ofh_A          240 VKKIAEAAFRVNEKTENIGARRLHTVMERLMDKISFSASDMNGQTVNIDAAYVADALGEVVE  301 (310)
T ss_dssp             HHHHHHHHHHHHHHSCCCTTHHHHHHHHHHSHHHHHHGGGCTTCEEEECHHHHHHHTCSSSS
T ss_pred             HHHHHHHhhhhcccccccCcHHHHHHHHHHHHhhhcCCccccCCEEEEeeHHHHHHHHhhhh
Confidence            99999987        79999999999986522     1  11   3999999999987543

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=99.87  E-value=1.5e-21  Score=171.56  Aligned_cols=213  Identities=15%  Similarity=0.147  Sum_probs=152.4

Q ss_pred             cchhhc-c--cHHHHHHHHHHHHcCC-CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHH
Q 022641           59 QVKDVA-H--QEEVVRVLTNTLETAN-CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKI  134 (294)
Q Consensus        59 ~~~~~~-g--~~~~~~~l~~~l~~~~-~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  134 (294)
                      +|++++ |  +......+..+..... .++++|+||||+||||+++++++.+... ..+..++.+++...     .....
T Consensus       103 tfd~fv~g~~n~~a~~~~~~~a~~~~~~~~lll~Gp~G~GKTtLa~aia~~l~~~-~~~~~v~~v~~~~~-----~~~~~  176 (440)
T 2z4s_A          103 TFENFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQN-EPDLRVMYITSEKF-----LNDLV  176 (440)
T ss_dssp             SGGGCCCCTTTHHHHHHHHHHHHSTTSSCCEEEECSSSSSHHHHHHHHHHHHHHH-CCSSCEEEEEHHHH-----HHHHH
T ss_pred             ChhhcCCCCchHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHh-CCCCeEEEeeHHHH-----HHHHH
Confidence            677776 4  4555566666666544 5679999999999999999999987321 11334455544331     11111


Q ss_pred             HHHHhhhcccCccCCCCCCC-CcEEEEEeCCCCCCH--HHHHHHHHHHHhhcC-cceEEEEecCC-cc---cchHhhccc
Q 022641          135 KTFAAVAVGSGQRRGGYPCP-PYKIIILDEADSMTE--DAQNALRRTMETYSK-VTRFFFICNYI-SR---IIEPLASRC  206 (294)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~-~~~lliiDei~~l~~--~~~~~L~~~l~~~~~-~~~ii~~~~~~-~~---~~~~l~~r~  206 (294)
                      ..+.........    .... +.++|+|||++.+..  ..++.|+..++.... ...+|++++.+ ..   +.+++.+||
T Consensus       177 ~~~~~~~~~~~~----~~~~~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~sR~  252 (440)
T 2z4s_A          177 DSMKEGKLNEFR----EKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRF  252 (440)
T ss_dssp             HHHHTTCHHHHH----HHHTTTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHHHH
T ss_pred             HHHHcccHHHHH----HHhcCCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHhhc
Confidence            111100000000    0001 346999999999875  677888888876443 45567777653 32   678999999


Q ss_pred             ---cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh---CCCCChhhhhhhcccc
Q 022641          207 ---AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF---GSSITSKDLISVSGYP  280 (294)
Q Consensus       207 ---~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~---~~~it~~~v~~~~~~~  280 (294)
                         ..+.+.+|+.+++..++.+.+...++.+++++++.|+..++||+|.+.++++.+..++   +..||.+++..++...
T Consensus       253 ~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~~e~l~~la~~~~gn~R~l~~~L~~~~~~a~~~~~~It~~~~~~~l~~~  332 (440)
T 2z4s_A          253 QMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGKEVDLKEAILLLKDF  332 (440)
T ss_dssp             HSSBCCBCCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHCCSCHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHTSTT
T ss_pred             cCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence               4899999999999999999999999999999999999999999999999999887766   5679999999999876


Q ss_pred             c
Q 022641          281 T  281 (294)
Q Consensus       281 ~  281 (294)
                      .
T Consensus       333 ~  333 (440)
T 2z4s_A          333 I  333 (440)
T ss_dssp             T
T ss_pred             h
Confidence            5

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

Probab=99.87  E-value=1.8e-21  Score=165.67  Aligned_cols=221  Identities=17%  Similarity=0.139  Sum_probs=160.7

Q ss_pred             chhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchh
Q 022641           49 QPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGIN  128 (294)
Q Consensus        49 ~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~  128 (294)
                      .+|.+++.|..+.+++|++..+..+...+..+.  +++|+||||||||++|+++++.+      +..+..+++.......
T Consensus        15 ~~~~~~~~~~~~~~i~g~~~~~~~l~~~l~~~~--~vll~G~pGtGKT~la~~la~~~------~~~~~~i~~~~~~~~~   86 (331)
T 2r44_A           15 RNKIKEVIDEVGKVVVGQKYMINRLLIGICTGG--HILLEGVPGLAKTLSVNTLAKTM------DLDFHRIQFTPDLLPS   86 (331)
T ss_dssp             HHHHHHHHHHHTTTCCSCHHHHHHHHHHHHHTC--CEEEESCCCHHHHHHHHHHHHHT------TCCEEEEECCTTCCHH
T ss_pred             HHHHHHHHHHhccceeCcHHHHHHHHHHHHcCC--eEEEECCCCCcHHHHHHHHHHHh------CCCeEEEecCCCCChh
Confidence            479999999999999999999999988887754  79999999999999999999988      5556666654332222


Q ss_pred             HHHHHHHHHHhhhccc--CccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh-----------cCcceEEEEecCC
Q 022641          129 VVRTKIKTFAAVAVGS--GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY-----------SKVTRFFFICNYI  195 (294)
Q Consensus       129 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~-----------~~~~~ii~~~~~~  195 (294)
                      .+   +..........  ....+..   ..++|+|||++.++...++.|++.+++.           +..+.++.++|..
T Consensus        87 ~l---~g~~~~~~~~~~~~~~~g~l---~~~vl~iDEi~~~~~~~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~  160 (331)
T 2r44_A           87 DL---IGTMIYNQHKGNFEVKKGPV---FSNFILADEVNRSPAKVQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPV  160 (331)
T ss_dssp             HH---HEEEEEETTTTEEEEEECTT---CSSEEEEETGGGSCHHHHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTT
T ss_pred             hc---CCceeecCCCCceEeccCcc---cccEEEEEccccCCHHHHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCC
Confidence            11   11000000000  0000100   1369999999999999999999999864           3345566666643


Q ss_pred             c-----ccchHhhcccc-EEEecCCCHHHHHHHHHHHHHH----------------------hCCCCCHHHHHHHHhhc-
Q 022641          196 S-----RIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNE----------------------EGLNLDAEALSTLSSIS-  246 (294)
Q Consensus       196 ~-----~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~----------------------~~~~~~~~~l~~l~~~~-  246 (294)
                      .     .+++++.+||. .+.+.+|+.++..+++++.+..                      .++.+++++++++++.+ 
T Consensus       161 ~~~~~~~l~~~l~~Rf~~~i~i~~p~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~v~~~~~~~~~i~~~~~  240 (331)
T 2r44_A          161 EQEGTYPLPEAQVDRFMMKIHLTYLDKESELEVMRRVSNMNFNYQVQKIVSKNDVLEIRNEINKVTISESLEKYIIELVF  240 (331)
T ss_dssp             CCSCCCCCCHHHHTTSSEEEECCCCCHHHHHHHHHHHHCTTCCCCCCCCSCHHHHHHHHHHHHTCBCCHHHHHHHHHHHH
T ss_pred             cccCcccCCHHHHhheeEEEEcCCCCHHHHHHHHHhccccCcchhccccCCHHHHHHHHHHhccCCCCHHHHHHHHHHHH
Confidence            2     37899999998 5999999999999999887653                      26678999999888753 


Q ss_pred             ----cC---------------cHHHHHHHHHHHHHHh----CCCCChhhhhhhcccccCC
Q 022641          247 ----QG---------------DLRRAITYLQGAARLF----GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       247 ----~G---------------~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~~~  283 (294)
                          .|               ++|.++++++.+...+    ...|+.+++..++.....+
T Consensus       241 ~~r~~~~~~~~~~~~~~~~~~s~R~~~~ll~~a~a~A~l~g~~~v~~~dv~~~~~~vl~~  300 (331)
T 2r44_A          241 ATRFPAEYGLEAEASYILYGASTRAAINLNRVAKAMAFFNNRDYVLPEDIKEVAYDILNH  300 (331)
T ss_dssp             HHHSGGGGTCHHHHHHEEECCCHHHHHHHHHHHHHHHHHTTCSBCCHHHHHHHHHHHHTT
T ss_pred             HHhccccccccccccccccCcChhHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhHh
Confidence                23               6999999888766554    3459999999887765433

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

Probab=99.87  E-value=8.4e-21  Score=167.13  Aligned_cols=192  Identities=18%  Similarity=0.164  Sum_probs=140.5

Q ss_pred             hhhcCCCcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee
Q 022641           52 VEKYRPKQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL  119 (294)
Q Consensus        52 ~~~~~~~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~  119 (294)
                      ...+.+..|++++|++.++..|..++..            ....+++|+||||||||++|+++++++.     +..++.+
T Consensus       125 ~~~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~~-----~~~~~~v  199 (444)
T 2zan_A          125 VIERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEAN-----NSTFFSI  199 (444)
T ss_dssp             BCCCCCCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHCC-----SSEEEEE
T ss_pred             eccCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHcC-----CCCEEEE
Confidence            3456677899999999999999887731            2235699999999999999999999872     3456666


Q ss_pred             cCCCCcch------hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHhh
Q 022641          120 NASDDRGI------NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMETY  182 (294)
Q Consensus       120 ~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~~  182 (294)
                      ++++..+.      ..++..+.....              ..+.+|||||+|.+.           ....+.|+..++..
T Consensus       200 ~~~~l~~~~~g~~~~~~~~~f~~a~~--------------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~  265 (444)
T 2zan_A          200 SSSDLVSKWLGESEKLVKNLFQLARE--------------NKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGV  265 (444)
T ss_dssp             CCC---------CCCTHHHHHHHHHH--------------SCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCS
T ss_pred             eHHHHHhhhcchHHHHHHHHHHHHHH--------------cCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCc
Confidence            66543221      122222222211              124699999999883           23556666666552


Q ss_pred             ---cCcceEEEEecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHHH
Q 022641          183 ---SKVTRFFFICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITYL  257 (294)
Q Consensus       183 ---~~~~~ii~~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~l  257 (294)
                         ...+.+|++||.+..+++++++||. .+.+++|+.+++..+++.++...+..+++..+..|++.+.| +.+.+.+++
T Consensus       266 ~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~  345 (444)
T 2zan_A          266 GVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIV  345 (444)
T ss_dssp             SCCCSSCEEEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             ccCCCCEEEEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence               4567788899999999999999997 89999999999999999988777667899999999999988 455555666


Q ss_pred             HHHHH
Q 022641          258 QGAAR  262 (294)
Q Consensus       258 ~~~~~  262 (294)
                      +.++.
T Consensus       346 ~~a~~  350 (444)
T 2zan_A          346 RDALM  350 (444)
T ss_dssp             HHHHT
T ss_pred             HHHHH
Confidence            65553

>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=99.86  E-value=6.7e-21  Score=165.32  Aligned_cols=231  Identities=21%  Similarity=0.191  Sum_probs=159.3

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHc----CCCCcEEEECCCCCCHHHHHHHHHHHhcCC----Ccc-CCcc
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLET----ANCPHMLFYGPPGTGKTTTALAIAHQLFGP----ELY-KSRV  116 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~----~~~~~ill~Gp~G~GKT~la~~la~~~~~~----~~~-~~~~  116 (294)
                      ....+|..++.|   ++++|++..+..+..++..    ...++++|+||||||||++++.+++.+...    ... +..+
T Consensus         8 ~~~~~l~~~~~p---~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~   84 (384)
T 2qby_B            8 NPKVFIDPLSVF---KEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQ   84 (384)
T ss_dssp             CTTTTTCHHHHC---SSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEE
T ss_pred             ccHhhcCCccCC---CCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceE
Confidence            445678788888   7789999999888876653    344579999999999999999999987321    011 4556


Q ss_pred             eeecCCCCc-chh-HHHHHHHHHHhhhccc-CccCC-------CCCCCCcEEEEEeCCCCCCHHH-HHH-HHHHHHhhcC
Q 022641          117 LELNASDDR-GIN-VVRTKIKTFAAVAVGS-GQRRG-------GYPCPPYKIIILDEADSMTEDA-QNA-LRRTMETYSK  184 (294)
Q Consensus       117 ~~~~~~~~~-~~~-~~~~~~~~~~~~~~~~-~~~~~-------~~~~~~~~lliiDei~~l~~~~-~~~-L~~~l~~~~~  184 (294)
                      +.+++.... +.. .+...+..+....... +....       ........+|+|||+|.+.... .+. +..++... .
T Consensus        85 ~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~-~  163 (384)
T 2qby_B           85 AYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSD-A  163 (384)
T ss_dssp             EEEEHHHHCSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSS-S
T ss_pred             EEEECccCCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCC-c
Confidence            666654332 221 1222222211000000 00000       0000112399999999986542 444 44444443 6


Q ss_pred             cceEEEEecCC---cccchHhhccc-cEEEecCCCHHHHHHHHHHHHHH--hCCCCCHHHHHHHHhhcc---CcHHHHHH
Q 022641          185 VTRFFFICNYI---SRIIEPLASRC-AKFRFKPLSEEVMSSRVLHICNE--EGLNLDAEALSTLSSISQ---GDLRRAIT  255 (294)
Q Consensus       185 ~~~ii~~~~~~---~~~~~~l~~r~-~~i~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~l~~l~~~~~---G~~r~~~~  255 (294)
                      ...+|+++|..   ..+.+++.+|+ ..+.|+|++.+++..++...+..  .+..+++++++.+++.++   ||+|.+++
T Consensus       164 ~~~iI~~t~~~~~~~~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~G~~r~a~~  243 (384)
T 2qby_B          164 NISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVN  243 (384)
T ss_dssp             CEEEEEECSSTTTTTTSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCCSHHHHHHHHHHHTTCCCHHHHHH
T ss_pred             ceEEEEEECCCchHhhhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcCHHHHHHHHHHHHhccCCHHHHHH
Confidence            77888888876   56788888886 59999999999999999998875  345789999999999988   99999999


Q ss_pred             HHHHHHHHhC--CCCChhhhhhhcccc
Q 022641          256 YLQGAARLFG--SSITSKDLISVSGYP  280 (294)
Q Consensus       256 ~l~~~~~~~~--~~it~~~v~~~~~~~  280 (294)
                      +++.+...+.  ..|+.+++..++...
T Consensus       244 ~l~~a~~~a~~~~~i~~~~v~~~~~~~  270 (384)
T 2qby_B          244 LLFRAAQLASGGGIIRKEHVDKAIVDY  270 (384)
T ss_dssp             HHHHHHHHTTSSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCccCHHHHHHHHHHH
Confidence            9999987763  569999999887664

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

Probab=99.86  E-value=2e-20  Score=156.88  Aligned_cols=210  Identities=19%  Similarity=0.196  Sum_probs=142.6

Q ss_pred             cCCCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecC
Q 022641           55 YRPKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA  121 (294)
Q Consensus        55 ~~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~  121 (294)
                      ..+..|+++.|.+..++.|..++..             ....+++|+||||||||++|++++..+      +..++.+++
T Consensus         9 ~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~------~~~~i~v~~   82 (301)
T 3cf0_A            9 VPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC------QANFISIKG   82 (301)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHT------TCEEEEECH
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHh------CCCEEEEEh
Confidence            3456789999999999988887753             233469999999999999999999998      566776665


Q ss_pred             CCCc------chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH--------------HHHHHHHHHHh
Q 022641          122 SDDR------GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED--------------AQNALRRTMET  181 (294)
Q Consensus       122 ~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~--------------~~~~L~~~l~~  181 (294)
                      ++..      ....+...+.....              ..+.+|+|||+|.+...              .++.|+..++.
T Consensus        83 ~~l~~~~~g~~~~~~~~~f~~a~~--------------~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~  148 (301)
T 3cf0_A           83 PELLTMWFGESEANVREIFDKARQ--------------AAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDG  148 (301)
T ss_dssp             HHHHHHHHTTCTTHHHHHHHHHHH--------------TCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHS
T ss_pred             HHHHhhhcCchHHHHHHHHHHHHh--------------cCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhc
Confidence            4321      11122222222211              12469999999987543              35778888874


Q ss_pred             h--cCcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHH
Q 022641          182 Y--SKVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAIT  255 (294)
Q Consensus       182 ~--~~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~  255 (294)
                      .  ...+.+|++||.+..+++++++  ||. .+.+++|+.+++.++++.+++..+.. ++..+..++..+.| ..+.+.+
T Consensus       149 ~~~~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~-~~~~~~~la~~~~g~sg~dl~~  227 (301)
T 3cf0_A          149 MSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVA-KDVDLEFLAKMTNGFSGADLTE  227 (301)
T ss_dssp             SCTTSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC-SSCCHHHHHHTCSSCCHHHHHH
T ss_pred             ccCCCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCC-ccchHHHHHHHcCCCCHHHHHH
Confidence            3  3467788999999999999988  886 89999999999999999888765442 22224555555433 1223333


Q ss_pred             HHHHHHHHh-----------------------------CCCCChhhhhhhcccccCCCC
Q 022641          256 YLQGAARLF-----------------------------GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       256 ~l~~~~~~~-----------------------------~~~it~~~v~~~~~~~~~~~~  285 (294)
                      +++.++..+                             ...|+.+++..++....++..
T Consensus       228 l~~~a~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~al~~~~~s~~  286 (301)
T 3cf0_A          228 ICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVS  286 (301)
T ss_dssp             HHHHHHHHHHHHHHHHHC--------------------CCCBCHHHHHHHHTTCCCSSC
T ss_pred             HHHHHHHHHHHHHHHhhhhhhhhcccccccccccccccCCccCHHHHHHHHHHcCCCCC
Confidence            333332211                             035888999999988776543

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.85  E-value=1.8e-20  Score=156.31  Aligned_cols=215  Identities=7%  Similarity=0.035  Sum_probs=144.7

Q ss_pred             hcccHHHHHHHHHH----HHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCC----ccCCcceeecCCCCcchhHHH-HH
Q 022641           63 VAHQEEVVRVLTNT----LETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE----LYKSRVLELNASDDRGINVVR-TK  133 (294)
Q Consensus        63 ~~g~~~~~~~l~~~----l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~----~~~~~~~~~~~~~~~~~~~~~-~~  133 (294)
                      +.+++..+..+...    +..+.+++++|+||||||||++++.+++++....    .....++.+|+....+...+. ..
T Consensus        22 L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I  101 (318)
T 3te6_A           22 LKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKI  101 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHH
Confidence            77888777766544    4557777899999999999999999999984221    113467788887655443322 22


Q ss_pred             HHHHHhhhcccCc---------cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh---hcCcceEEEEecCCc----c
Q 022641          134 IKTFAAVAVGSGQ---------RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMET---YSKVTRFFFICNYIS----R  197 (294)
Q Consensus       134 ~~~~~~~~~~~~~---------~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~---~~~~~~ii~~~~~~~----~  197 (294)
                      ...+.......+.         ...........+++|||+|.+.  .++.|+.+++-   ......+|+++|...    .
T Consensus       102 ~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~--~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~~~~  179 (318)
T 3te6_A          102 WFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLL--SEKILQYFEKWISSKNSKLSIICVGGHNVTIREQ  179 (318)
T ss_dssp             HHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSC--CTHHHHHHHHHHHCSSCCEEEEEECCSSCCCHHH
T ss_pred             HHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhh--cchHHHHHHhcccccCCcEEEEEEecCcccchhh
Confidence            2222111000000         0000012345799999999997  56666666652   234567788887753    2


Q ss_pred             cchHhhcccc--EEEecCCCHHHHHHHHHHHHHHhCC-----------------------------------CCCHHHHH
Q 022641          198 IIEPLASRCA--KFRFKPLSEEVMSSRVLHICNEEGL-----------------------------------NLDAEALS  240 (294)
Q Consensus       198 ~~~~l~~r~~--~i~~~~~~~~~~~~~l~~~~~~~~~-----------------------------------~~~~~~l~  240 (294)
                      +.+++.+|+.  .|.|+|++.+++..++++.+....-                                   .+++++++
T Consensus       180 L~~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ai~  259 (318)
T 3te6_A          180 INIMPSLKAHFTEIKLNKVDKNELQQMIITRLKSLLKPFHVKVNDKKEMTIYNNIREGQNQKIPDNVIVINHKINNKITQ  259 (318)
T ss_dssp             HHTCHHHHTTEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEECTTCCEEECCCC--------CTTEEEECEECCHHHHH
T ss_pred             cchhhhccCCceEEEeCCCCHHHHHHHHHHHHHhhhccccccccccccccccccccccccccccccccccccccCHHHHH
Confidence            4556778884  7999999999999999999976421                                   36999999


Q ss_pred             HHHh---hccCcHHHHHHHHHHHHHHhC-------------CCCChhhhhhhccc
Q 022641          241 TLSS---ISQGDLRRAITYLQGAARLFG-------------SSITSKDLISVSGY  279 (294)
Q Consensus       241 ~l~~---~~~G~~r~~~~~l~~~~~~~~-------------~~it~~~v~~~~~~  279 (294)
                      .+++   ...||.|.++++|..+...++             ..||.+.+.+++.+
T Consensus       260 ~~A~~vA~~~GD~R~Al~ilr~A~~~ae~e~~~k~~~~~~~~~i~~~~~~~~~~~  314 (318)
T 3te6_A          260 LIAKNVANVSGSTEKAFKICEAAVEISKKDFVRKGGLQKGKLVVSQEMVPRYFSE  314 (318)
T ss_dssp             HHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTTEETTEECCSEECCTHHHHH
T ss_pred             HHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHhccCCCCCcEEeeHHHHHHHHHH
Confidence            9998   478999999999999987762             13666666655543

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=99.85  E-value=1.2e-20  Score=160.13  Aligned_cols=206  Identities=14%  Similarity=0.126  Sum_probs=144.3

Q ss_pred             cchhhc---ccHHHHHHHHHHHHcCC--CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHH
Q 022641           59 QVKDVA---HQEEVVRVLTNTLETAN--CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTK  133 (294)
Q Consensus        59 ~~~~~~---g~~~~~~~l~~~l~~~~--~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  133 (294)
                      +|++++   ++......+..++....  ..+++|+||||||||++++++++.+...   +..++.+++....  ..+...
T Consensus         9 ~f~~fv~g~~~~~a~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~~~~---~~~~~~i~~~~~~--~~~~~~   83 (324)
T 1l8q_A            9 TLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKR---GYRVIYSSADDFA--QAMVEH   83 (324)
T ss_dssp             CSSSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHT---TCCEEEEEHHHHH--HHHHHH
T ss_pred             CcccCCCCCcHHHHHHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHHHHC---CCEEEEEEHHHHH--HHHHHH
Confidence            556665   35556666777776653  3569999999999999999999987432   3455666543321  111111


Q ss_pred             HHHH-HhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--HHHHHHHHHHHhhc-CcceEEEEecCC-c---ccchHhhcc
Q 022641          134 IKTF-AAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--DAQNALRRTMETYS-KVTRFFFICNYI-S---RIIEPLASR  205 (294)
Q Consensus       134 ~~~~-~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--~~~~~L~~~l~~~~-~~~~ii~~~~~~-~---~~~~~l~~r  205 (294)
                      +... ......        ...+.++|+|||++.++.  ..++.++..++... ....+|++++.+ .   .+.+++.+|
T Consensus        84 ~~~~~~~~~~~--------~~~~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~sR  155 (324)
T 1l8q_A           84 LKKGTINEFRN--------MYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSR  155 (324)
T ss_dssp             HHHTCHHHHHH--------HHHTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHH
T ss_pred             HHcCcHHHHHH--------HhcCCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhhc
Confidence            1100 000000        001135999999999975  56777777776533 334566666543 3   478899999


Q ss_pred             c---cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHH-------h-CCCC-Chhhh
Q 022641          206 C---AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARL-------F-GSSI-TSKDL  273 (294)
Q Consensus       206 ~---~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~-------~-~~~i-t~~~v  273 (294)
                      |   ..+.++| +.+++..++...+...++.+++++++.|++.+ ||+|.+.+.++.+..+       . ...| |.+++
T Consensus       156 ~~~~~~i~l~~-~~~e~~~il~~~~~~~~~~l~~~~l~~l~~~~-g~~r~l~~~l~~~~~~~~~~l~~~~~~~i~t~~~i  233 (324)
T 1l8q_A          156 FEGGILVEIEL-DNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-KNVREIEGKIKLIKLKGFEGLERKERKERDKLMQI  233 (324)
T ss_dssp             HHTSEEEECCC-CHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-SSHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHH
T ss_pred             ccCceEEEeCC-CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhC-CCHHHHHHHHHHHHHcCHHHhccccccCCCCHHHH
Confidence            9   5899999 99999999999999999999999999999999 9999999999987766       2 2347 88888


Q ss_pred             hhhccc
Q 022641          274 ISVSGY  279 (294)
Q Consensus       274 ~~~~~~  279 (294)
                      .+++..
T Consensus       234 ~~~~~~  239 (324)
T 1l8q_A          234 VEFVAN  239 (324)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877764

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

Probab=99.85  E-value=2.3e-20  Score=164.10  Aligned_cols=204  Identities=23%  Similarity=0.208  Sum_probs=148.1

Q ss_pred             CCcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD  124 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~  124 (294)
                      ...|+++.|.+..+..+.+.+..            ..+.+++|+||||||||++|++++.++      +.+++.+++++.
T Consensus        12 ~~~f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~------~~~f~~is~~~~   85 (476)
T 2ce7_A           12 RVTFKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEA------NVPFFHISGSDF   85 (476)
T ss_dssp             CCCGGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHH------TCCEEEEEGGGT
T ss_pred             CCCHHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHc------CCCeeeCCHHHH
Confidence            45789999999998877776532            123459999999999999999999998      667777776543


Q ss_pred             cc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhh--
Q 022641          125 RG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTMETY--  182 (294)
Q Consensus       125 ~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~~~--  182 (294)
                      ..      ....+..+.....              ..+.+|||||+|.+..              ..++.|+..++..  
T Consensus        86 ~~~~~g~~~~~~r~lf~~A~~--------------~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~  151 (476)
T 2ce7_A           86 VELFVGVGAARVRDLFAQAKA--------------HAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDS  151 (476)
T ss_dssp             TTCCTTHHHHHHHHHHHHHHH--------------TCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCG
T ss_pred             HHHHhcccHHHHHHHHHHHHh--------------cCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCC
Confidence            22      1222233222221              1246999999998742              2456677777643  


Q ss_pred             cCcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHH-HHHHHHhhccCcH-HHHHHHH
Q 022641          183 SKVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAE-ALSTLSSISQGDL-RRAITYL  257 (294)
Q Consensus       183 ~~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~-~l~~l~~~~~G~~-r~~~~~l  257 (294)
                      ...+.+|++||.+..+++++++  ||. .+.+++|+.+++.++++.+++..  .++++ .+..++..+.|+. +.+.+++
T Consensus       152 ~~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~--~l~~~v~l~~la~~t~G~sgadL~~lv  229 (476)
T 2ce7_A          152 KEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNK--PLAEDVNLEIIAKRTPGFVGADLENLV  229 (476)
T ss_dssp             GGTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTS--CBCTTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             CCCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhC--CCcchhhHHHHHHhcCCCcHHHHHHHH
Confidence            3456788889999888888886  887 89999999999999998877643  33333 3788999999977 7788888


Q ss_pred             HHHHHHh----CCCCChhhhhhhcccccC
Q 022641          258 QGAARLF----GSSITSKDLISVSGYPTG  282 (294)
Q Consensus       258 ~~~~~~~----~~~it~~~v~~~~~~~~~  282 (294)
                      ..++..+    ...|+.+++..++.....
T Consensus       230 ~~Aal~A~~~~~~~I~~~dl~~al~~v~~  258 (476)
T 2ce7_A          230 NEAALLAAREGRDKITMKDFEEAIDRVIA  258 (476)
T ss_dssp             HHHHHHHHHTTCSSBCHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHcCCCeecHHHHHHHHHHHhc
Confidence            8777655    356999999998876543

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=99.85  E-value=2.2e-20  Score=153.95  Aligned_cols=214  Identities=18%  Similarity=0.174  Sum_probs=138.8

Q ss_pred             CcchhhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHH
Q 022641           58 KQVKDVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIK  135 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (294)
                      .+|++++|+...+..+...+..  ....+++|+||||||||++|+++++....   ...+++.++++.... ..+...+.
T Consensus         3 ~~f~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~~~---~~~~~~~v~~~~~~~-~~~~~~l~   78 (265)
T 2bjv_A            3 EYKDNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSR---WQGPFISLNCAALNE-NLLDSELF   78 (265)
T ss_dssp             -------CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTSTT---TTSCEEEEEGGGSCH-HHHHHHHH
T ss_pred             cccccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhcCc---cCCCeEEEecCCCCh-hHHHHHhc
Confidence            3577889998888777665543  33457999999999999999999987632   135677777766422 21211110


Q ss_pred             HHHh-hhcccCc-cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh-----------cCcceEEEEecCCc------
Q 022641          136 TFAA-VAVGSGQ-RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY-----------SKVTRFFFICNYIS------  196 (294)
Q Consensus       136 ~~~~-~~~~~~~-~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~-----------~~~~~ii~~~~~~~------  196 (294)
                      .... ...+... ..+.......++|+|||++.++...++.|++.++..           ...+.+|+++|...      
T Consensus        79 g~~~~~~~g~~~~~~~~l~~a~~~~l~lDEi~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~~~~~~~~~  158 (265)
T 2bjv_A           79 GHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPMMVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNE  158 (265)
T ss_dssp             CCC---------CCCCHHHHTTTSEEEEESGGGSCHHHHHHHHHHHHHCEECCCCC--CEECCCEEEEEESSCHHHHHHH
T ss_pred             CCcccccccccccccchhhhcCCcEEEEechHhcCHHHHHHHHHHHHhCCeecCCCcccccCCeEEEEecCcCHHHHHHc
Confidence            0000 0000000 000000123569999999999999999999999864           24577899998742      


Q ss_pred             -ccchHhhcccc--EEEecCCCH--HHHHHHHHHH----HHHhCC----CCCHHHHHHHHhh-ccCcHHHHHHHHHHHHH
Q 022641          197 -RIIEPLASRCA--KFRFKPLSE--EVMSSRVLHI----CNEEGL----NLDAEALSTLSSI-SQGDLRRAITYLQGAAR  262 (294)
Q Consensus       197 -~~~~~l~~r~~--~i~~~~~~~--~~~~~~l~~~----~~~~~~----~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~  262 (294)
                       .+.+++.+|+.  .+.++|+..  +++..++.++    +...+.    .+++++++.|..+ +.||+|.+.++++.+..
T Consensus       159 ~~~~~~L~~Rl~~~~i~lp~L~~R~~di~~l~~~~l~~~~~~~~~~~~~~~~~~a~~~L~~~~~~gn~reL~~~l~~~~~  238 (265)
T 2bjv_A          159 GTFRADLLDALAFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVY  238 (265)
T ss_dssp             TSSCHHHHHHHCSEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCSSCCCBCHHHHHHHHHSCCTTHHHHHHHHHHHHHH
T ss_pred             CCccHHHHHhhcCcEEeCCChhhhhHHHHHHHHHHHHHHHHHhCCCcccCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Confidence             35688899985  578888865  5666555444    334454    6899999999877 49999999999999876


Q ss_pred             Hh-CCCCChhhhhh
Q 022641          263 LF-GSSITSKDLIS  275 (294)
Q Consensus       263 ~~-~~~it~~~v~~  275 (294)
                      .. +..|+.+++..
T Consensus       239 ~~~~~~i~~~~l~~  252 (265)
T 2bjv_A          239 RHGTSDYPLDDIII  252 (265)
T ss_dssp             HHCCSSSCBCCCCS
T ss_pred             hCCCCcCcHHHcch
Confidence            65 55688887743

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=99.85  E-value=1.2e-20  Score=161.74  Aligned_cols=227  Identities=16%  Similarity=0.097  Sum_probs=147.1

Q ss_pred             hhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCC-----CccCC-------------
Q 022641           53 EKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP-----ELYKS-------------  114 (294)
Q Consensus        53 ~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~-----~~~~~-------------  114 (294)
                      ..-.+..|++++|++..+..+..........+++|+||||||||++|+++++.+...     ..+.+             
T Consensus        16 ~~~~~~~f~~i~G~~~~~~~l~~~~~~~~~~~vLl~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (350)
T 1g8p_A           16 KTRPVFPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEMIPDWATVL   95 (350)
T ss_dssp             --CCCCCGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSGGGSCTTCCCS
T ss_pred             CCCCCCCchhccChHHHHHHHHHHhhCCCCceEEEECCCCccHHHHHHHHHHhCccccccccccccccccccccchhhhh
Confidence            344567899999999888776665554445579999999999999999999987320     00000             


Q ss_pred             ---------cceeecCCCCcchhHHHHH---HHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh
Q 022641          115 ---------RVLELNASDDRGINVVRTK---IKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY  182 (294)
Q Consensus       115 ---------~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~  182 (294)
                               .++.+.  .......+...   ...+....  .....+....+..++|+|||++.++...++.|+..++..
T Consensus        96 ~~~~~~~~~~~~~~~--~~~~~~~l~g~~~~~~~~~~~~--~~~~~g~~~~a~~~vl~iDEi~~l~~~~~~~Ll~~le~~  171 (350)
T 1g8p_A           96 STNVIRKPTPVVDLP--LGVSEDRVVGALDIERAISKGE--KAFEPGLLARANRGYLYIDECNLLEDHIVDLLLDVAQSG  171 (350)
T ss_dssp             CCCEEEECCCEEEEC--TTCCHHHHHCEECHHHHHHHCG--GGEECCHHHHHTTEEEEETTGGGSCHHHHHHHHHHHHHS
T ss_pred             ccccccCCCcccccC--CCcchhhheeechhhhhhcCCc--eeecCceeeecCCCEEEEeChhhCCHHHHHHHHHHHhcC
Confidence                     011100  00011111100   00000000  000001011123569999999999999999999999873


Q ss_pred             c-------------CcceEEEEecCCc-ccchHhhccccE-EEecCCC-HHHHHHHHHHH--------------------
Q 022641          183 S-------------KVTRFFFICNYIS-RIIEPLASRCAK-FRFKPLS-EEVMSSRVLHI--------------------  226 (294)
Q Consensus       183 ~-------------~~~~ii~~~~~~~-~~~~~l~~r~~~-i~~~~~~-~~~~~~~l~~~--------------------  226 (294)
                      .             ..+.+|+++|... .+.+++.+||.. +.+++|+ .++..+++.+.                    
T Consensus       172 ~~~~~~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~R~~~~~~l~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~  251 (350)
T 1g8p_A          172 ENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLDRFGLSVEVLSPRDVETRVEVIRRRDTYDADPKAFLEEWRPKDMD  251 (350)
T ss_dssp             EEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHTTCSEEEECCCCCSHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             ceEEEecceEEeeCCceEEEEEeCCCCCCCCHHHHhhcceEEEcCCCCcHHHHHHHHHHHHhcccCchhhccccccchHH
Confidence            2             3566777888643 788999999985 9999995 55555666552                    


Q ss_pred             ---------HHHhCCCCCHHHHHHHHhhccC----cHHHHHHHHHHHHHHh---C-CCCChhhhhhhcccccCC
Q 022641          227 ---------CNEEGLNLDAEALSTLSSISQG----DLRRAITYLQGAARLF---G-SSITSKDLISVSGYPTGG  283 (294)
Q Consensus       227 ---------~~~~~~~~~~~~l~~l~~~~~G----~~r~~~~~l~~~~~~~---~-~~it~~~v~~~~~~~~~~  283 (294)
                               ....++.+++++++.|++.+.|    ++|.+.++++.+...+   + ..|+.+++..++.....+
T Consensus       252 ~~~~i~~~~~~~~~~~ls~~~~~~l~~~~~~~~~~~~R~~~~ll~~a~~~A~~~~~~~v~~~~v~~a~~~~l~~  325 (350)
T 1g8p_A          252 IRNQILEARERLPKVEAPNTALYDCAALCIALGSDGLRGELTLLRSARALAALEGATAVGRDHLKRVATMALSH  325 (350)
T ss_dssp             HHHHHHHHHHHGGGCBCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHHHHHHHTTCSBCCHHHHHHHHHHHHGG
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHHhh
Confidence                     1123467999999999998766    8999999998776655   3 459999999887764433

>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=99.84  E-value=5.2e-20  Score=159.60  Aligned_cols=221  Identities=18%  Similarity=0.236  Sum_probs=151.5

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHc----CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLET----ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~----~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ..++...+.|   ++++|++..+..+..++..    ....+++|+||+|||||++++.+++.+......+..++.+++..
T Consensus        10 ~~~l~~~~~p---~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~   86 (386)
T 2qby_A           10 REYLLPDYIP---DELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQ   86 (386)
T ss_dssp             GGGGSSSCCC---SCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHH
T ss_pred             hhhCCCccCC---CCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCC
Confidence            3455555655   6789999999999988874    34457999999999999999999998732110023445554332


Q ss_pred             CcchhH-------------------HHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC----HHHHHHHHHHHH
Q 022641          124 DRGINV-------------------VRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT----EDAQNALRRTME  180 (294)
Q Consensus       124 ~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~----~~~~~~L~~~l~  180 (294)
                      ......                   .......+.....         ....+.+|+|||++.+.    ......|+..++
T Consensus        87 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~---------~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~  157 (386)
T 2qby_A           87 IDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVR---------DYGSQVVIVLDEIDAFVKKYNDDILYKLSRINS  157 (386)
T ss_dssp             HCSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHH---------TCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHh---------ccCCeEEEEEcChhhhhccCcCHHHHHHhhchh
Confidence            111110                   0011111111100         01235699999999875    344555666665


Q ss_pred             hh-cCcceEEEEecCC---cccchHhhccc--cEEEecCCCHHHHHHHHHHHHHHhC--CCCCHHHHHHHHhhcc---Cc
Q 022641          181 TY-SKVTRFFFICNYI---SRIIEPLASRC--AKFRFKPLSEEVMSSRVLHICNEEG--LNLDAEALSTLSSISQ---GD  249 (294)
Q Consensus       181 ~~-~~~~~ii~~~~~~---~~~~~~l~~r~--~~i~~~~~~~~~~~~~l~~~~~~~~--~~~~~~~l~~l~~~~~---G~  249 (294)
                      .. .....+|++++..   ..+.+.+.+|+  ..+.++|++.+++.+++...+....  ..+++++++.+++.++   |+
T Consensus       158 ~~~~~~~~~I~~~~~~~~~~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~  237 (386)
T 2qby_A          158 EVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGD  237 (386)
T ss_dssp             SCCC--EEEEEEESCGGGGGGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCC
T ss_pred             hcCCCeEEEEEEECCCChHhhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCC
Confidence            42 3466788888866   35677888888  5899999999999999999886533  5689999999999988   99


Q ss_pred             HHHHHHHHHHHHHHh----CCCCChhhhhhhcccc
Q 022641          250 LRRAITYLQGAARLF----GSSITSKDLISVSGYP  280 (294)
Q Consensus       250 ~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~  280 (294)
                      +|.++++++.+...+    ...|+.+++..++...
T Consensus       238 ~r~~~~ll~~a~~~a~~~~~~~i~~~~v~~a~~~~  272 (386)
T 2qby_A          238 ARRALDLLRVSGEIAERMKDTKVKEEYVYMAKEEI  272 (386)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHH
Confidence            999999999887665    2479999998776554

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

Probab=99.84  E-value=9.6e-21  Score=170.51  Aligned_cols=218  Identities=21%  Similarity=0.233  Sum_probs=141.8

Q ss_pred             chhhcccHHHHHHHHHHHHc------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHH
Q 022641           60 VKDVAHQEEVVRVLTNTLET------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTK  133 (294)
Q Consensus        60 ~~~~~g~~~~~~~l~~~l~~------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  133 (294)
                      .+++.|.++++..+...+..      ...++++|+||||||||+++++++..+      ...+..+++........+...
T Consensus        80 ~~di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l------~~~~~~i~~~~~~~~~~~~g~  153 (543)
T 3m6a_A           80 DEEHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSL------GRKFVRISLGGVRDESEIRGH  153 (543)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHHH------TCEEEEECCCC----------
T ss_pred             HHHhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHhc------CCCeEEEEecccchhhhhhhH
Confidence            34688999888777655421      234579999999999999999999998      566666665543221111111


Q ss_pred             HHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH----HHHHHHHHHHhhc---------------CcceEEEEecC
Q 022641          134 IKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED----AQNALRRTMETYS---------------KVTRFFFICNY  194 (294)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~----~~~~L~~~l~~~~---------------~~~~ii~~~~~  194 (294)
                      ...+....................+++|||++.++..    .++.|++.++...               ..+.+|+++|.
T Consensus       154 ~~~~ig~~~~~~~~~~~~a~~~~~vl~lDEid~l~~~~~~~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~ttN~  233 (543)
T 3m6a_A          154 RRTYVGAMPGRIIQGMKKAGKLNPVFLLDEIDKMSSDFRGDPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATANN  233 (543)
T ss_dssp             ----------CHHHHHHTTCSSSEEEEEEESSSCC---------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEECSS
T ss_pred             HHHHhccCchHHHHHHHHhhccCCEEEEhhhhhhhhhhccCHHHHHHHHHhhhhcceeecccCCeeecccceEEEeccCc
Confidence            0000000000000000001123459999999999876    3477888876432               45678889999


Q ss_pred             CcccchHhhccccEEEecCCCHHHHHHHHHHHHH-----Hh-----CCCCCHHHHHHHHhhc--cCcHHHHHHHHHHHHH
Q 022641          195 ISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICN-----EE-----GLNLDAEALSTLSSIS--QGDLRRAITYLQGAAR  262 (294)
Q Consensus       195 ~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~-----~~-----~~~~~~~~l~~l~~~~--~G~~r~~~~~l~~~~~  262 (294)
                      ...++++|++||.++.|++|+.++...++.+++.     ..     ++.++++++..+++.+  .|++|.+.+.++.++.
T Consensus       234 ~~~l~~aL~~R~~vi~~~~~~~~e~~~Il~~~l~~~~~~~~~~~~~~i~i~~~~l~~l~~~~~~~~~vR~L~~~i~~~~~  313 (543)
T 3m6a_A          234 LATIPGPLRDRMEIINIAGYTEIEKLEIVKDHLLPKQIKEHGLKKSNLQLRDQAILDIIRYYTREAGVRSLERQLAAICR  313 (543)
T ss_dssp             TTTSCHHHHHHEEEEECCCCCHHHHHHHHHHTHHHHHHHHTTCCGGGCEECHHHHHHHHHHHCCCSSSHHHHHHHHHHHH
T ss_pred             cccCCHHHHhhcceeeeCCCCHHHHHHHHHHHHHHHHHHHcCCCcccccCCHHHHHHHHHhCChhhchhHHHHHHHHHHH
Confidence            9999999999999999999999999999988763     23     3457899999988753  4788888777766544


Q ss_pred             Hh----------CCCCChhhhhhhcccccCC
Q 022641          263 LF----------GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       263 ~~----------~~~it~~~v~~~~~~~~~~  283 (294)
                      .+          ...||.+++.++++.....
T Consensus       314 ~aa~~~~~~~~~~~~It~~~l~~~Lg~~~~~  344 (543)
T 3m6a_A          314 KAAKAIVAEERKRITVTEKNLQDFIGKRIFR  344 (543)
T ss_dssp             HHHHHHHTTCCSCCEECTTTTHHHHCSCCSC
T ss_pred             HHHHHHHhcCCcceecCHHHHHHHhCCcccC
Confidence            33          1249999999999876543

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.83  E-value=1.2e-19  Score=152.01  Aligned_cols=209  Identities=18%  Similarity=0.222  Sum_probs=144.2

Q ss_pred             hhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHh
Q 022641           62 DVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAA  139 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  139 (294)
                      +++|+...+..+...+..  ....+++|+||||||||++|+++++....   .+.+++.+++..... ..+...+   ..
T Consensus         3 ~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~---~~~~~v~v~~~~~~~-~l~~~~l---fg   75 (304)
T 1ojl_A            3 HMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSAR---SDRPLVTLNCAALNE-SLLESEL---FG   75 (304)
T ss_dssp             CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHSSC---SSSCCCEEECSSCCH-HHHHHHH---TC
T ss_pred             CcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhCcc---cCCCeEEEeCCCCCh-HHHHHHh---cC
Confidence            577887777777766654  33456999999999999999999987522   245778888876532 1111111   10


Q ss_pred             hhccc--C---ccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-------
Q 022641          140 VAVGS--G---QRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-------  196 (294)
Q Consensus       140 ~~~~~--~---~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-------  196 (294)
                      ...+.  +   ...+.......++|||||++.++...+..|+..++...           ..+.+|++||...       
T Consensus        76 ~~~g~~tg~~~~~~g~~~~a~~g~L~LDEi~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~l~~~v~~g  155 (304)
T 1ojl_A           76 HEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAG  155 (304)
T ss_dssp             CCSSCCC---CCCCCHHHHHTTSEEEEESCTTCCHHHHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSCHHHHHHHT
T ss_pred             ccccccCchhhhhcCHHHhcCCCEEEEeccccCCHHHHHHHHHHHhcCEeeecCCcccccCCeEEEEecCccHHHHHHhC
Confidence            00000  0   00000011234699999999999999999999998753           3577899998752       


Q ss_pred             ccchHhhcccc--EEEecCCC--HHHHHHHHHHHHH----HhC---CCCCHHHHHHHHhhc-cCcHHHHHHHHHHHHHHh
Q 022641          197 RIIEPLASRCA--KFRFKPLS--EEVMSSRVLHICN----EEG---LNLDAEALSTLSSIS-QGDLRRAITYLQGAARLF  264 (294)
Q Consensus       197 ~~~~~l~~r~~--~i~~~~~~--~~~~~~~l~~~~~----~~~---~~~~~~~l~~l~~~~-~G~~r~~~~~l~~~~~~~  264 (294)
                      .+.+.+.+|+.  .+.++|+.  .+++..++.+++.    ..+   ..+++++++.+..++ .||+|.+.++++.+....
T Consensus       156 ~fr~~L~~Rl~~~~i~lPpL~eR~edi~~l~~~~l~~~~~~~~~~~~~~s~~a~~~L~~~~wpGnvReL~~~l~~~~~~~  235 (304)
T 1ojl_A          156 RFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLL  235 (304)
T ss_dssp             SSCHHHHHHHSSEEEECCCSGGGGGGHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHHCCCSSHHHHHHHHHHHHHHHC
T ss_pred             CcHHHHHhhcCeeEEeccCHHHhHhhHHHHHHHHHHHHHHHhccCccCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhC
Confidence            24567888875  56788877  4666666665544    333   468999999999986 999999999999988776


Q ss_pred             -CCCCChhhhhhhc
Q 022641          265 -GSSITSKDLISVS  277 (294)
Q Consensus       265 -~~~it~~~v~~~~  277 (294)
                       +..|+.+++...+
T Consensus       236 ~~~~i~~~~l~~~~  249 (304)
T 1ojl_A          236 TGEYISERELPLAI  249 (304)
T ss_dssp             CSSSBCGGGSCGGG
T ss_pred             CCCcccHHhhhhhh
Confidence             4568888886544

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

Probab=99.83  E-value=2.6e-20  Score=165.12  Aligned_cols=198  Identities=15%  Similarity=0.190  Sum_probs=144.3

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCC----ccCCcceeecC
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE----LYKSRVLELNA  121 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~----~~~~~~~~~~~  121 (294)
                      ....+|.++++|..++.++|++..+..+...+.....++++|+||||||||++|+++++.+.+..    ..+..++.+++
T Consensus       165 ~~~~~l~~~~r~~~ld~iiGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~  244 (468)
T 3pxg_A          165 SLARDLTAIAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDM  244 (468)
T ss_dssp             SSCCBHHHHTTSSCSCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC--
T ss_pred             HHHHHHHHHHhcCCCCCccCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeC
Confidence            66779999999999999999999999999999988888999999999999999999999984322    23556666665


Q ss_pred             CCCc---chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCc--
Q 022641          122 SDDR---GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYIS--  196 (294)
Q Consensus       122 ~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~--  196 (294)
                      +...   ....+...+.....              ..+.+||||    .....++.|+..++.  ....+|.+||...  
T Consensus       245 ~~~~~g~~e~~~~~~~~~~~~--------------~~~~iLfiD----~~~~a~~~L~~~L~~--g~v~vI~at~~~e~~  304 (468)
T 3pxg_A          245 GTKYRGEFEDRLKKVMDEIRQ--------------AGNIILFID----AAIDASNILKPSLAR--GELQCIGATTLDEYR  304 (468)
T ss_dssp             --------CTTHHHHHHHHHT--------------CCCCEEEEC----C--------CCCTTS--SSCEEEEECCTTTTH
T ss_pred             CccccchHHHHHHHHHHHHHh--------------cCCeEEEEe----CchhHHHHHHHhhcC--CCEEEEecCCHHHHH
Confidence            5110   01122233332221              123499999    344566777777764  4677888888764  


Q ss_pred             ---ccchHhhccccEEEecCCCHHHHHHHHHHHHHH----hCCCCCHHHHHHHHhhccC------cHHHHHHHHHHHHHH
Q 022641          197 ---RIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE----EGLNLDAEALSTLSSISQG------DLRRAITYLQGAARL  263 (294)
Q Consensus       197 ---~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~----~~~~~~~~~l~~l~~~~~G------~~r~~~~~l~~~~~~  263 (294)
                         .+++++.+||..+.+++|+.++...+++.++..    +++.++++++..++..+.+      -++.++++++.++..
T Consensus       305 ~~~~~~~al~~Rf~~i~v~~p~~e~~~~iL~~~~~~~~~~~~~~i~~~al~~l~~~s~~~~~~~~lp~~ai~ll~~a~~~  384 (468)
T 3pxg_A          305 KYIEKDAALERRFQPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAGSK  384 (468)
T ss_dssp             HHHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHHHHHH
T ss_pred             HHhhcCHHHHHhCccceeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhccCcCCcHHHHHHHHHHHH
Confidence               578999999999999999999999999987765    7788999999999987653      366799988877653

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

Probab=99.83  E-value=7.5e-20  Score=154.24  Aligned_cols=196  Identities=22%  Similarity=0.313  Sum_probs=138.9

Q ss_pred             hhhcccHHHHHHHHHHHHcCC---------CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHH
Q 022641           61 KDVAHQEEVVRVLTNTLETAN---------CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVR  131 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~~---------~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (294)
                      ..++|+..++..+...+....         ..+++|+||||||||++|+++++.+.+.   ..+++.++++.........
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~---~~~~~~~~~~~~~~~~~~~   93 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT---EEAMIRIDMTEYMEKHAVS   93 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSC---GGGEEEEEGGGCCSTTHHH
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCC---CcceEEeecccccccccHH
Confidence            467899999988888876531         1259999999999999999999998443   2345556554433322221


Q ss_pred             HHHHHHHhhhccc-CccCC-----CCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecC
Q 022641          132 TKIKTFAAVAVGS-GQRRG-----GYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNY  194 (294)
Q Consensus       132 ~~~~~~~~~~~~~-~~~~~-----~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~  194 (294)
                      ..+..    ..+. +....     .......++|+|||++.+++..++.|++.++...           .+..+|++||.
T Consensus        94 ~l~g~----~~~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn~  169 (311)
T 4fcw_A           94 RLIGA----PPGYVGYEEGGQLTEAVRRRPYSVILFDAIEKAHPDVFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSNL  169 (311)
T ss_dssp             HHHCC----CTTSTTTTTCCHHHHHHHHCSSEEEEEETGGGSCHHHHHHHHHHHHHSEEECTTSCEEECTTEEEEEEEST
T ss_pred             HhcCC----CCccccccccchHHHHHHhCCCeEEEEeChhhcCHHHHHHHHHHHhcCEEEcCCCCEEECCCcEEEEeccc
Confidence            11100    0000 00000     0001224699999999999999999999998754           24558888988


Q ss_pred             --------------------------CcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHh---------CCCCCHHH
Q 022641          195 --------------------------ISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEE---------GLNLDAEA  238 (294)
Q Consensus       195 --------------------------~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~---------~~~~~~~~  238 (294)
                                                ...+.++|.+||. .+.|.||+.+++..++...+...         .+.+++++
T Consensus       170 ~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~R~~~~~~~~p~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~  249 (311)
T 4fcw_A          170 GSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQMSYLRARLAEKRISLELTEAA  249 (311)
T ss_dssp             THHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHHTHHHHHHHHTTTCEEEECHHH
T ss_pred             CHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHhcCCeEEEeCCCCHHHHHHHHHHHHHHHHHHHHhCCcEEEeCHHH
Confidence                                      3456788999995 88999999999999999877642         34589999


Q ss_pred             HHHHHhhc---cCcHHHHHHHHHHHHHH
Q 022641          239 LSTLSSIS---QGDLRRAITYLQGAARL  263 (294)
Q Consensus       239 l~~l~~~~---~G~~r~~~~~l~~~~~~  263 (294)
                      ++.|++++   .||+|.+.+.++.+...
T Consensus       250 ~~~l~~~~~~~~gn~R~L~~~i~~~~~~  277 (311)
T 4fcw_A          250 KDFLAERGYDPVFGARPLRRVIQRELET  277 (311)
T ss_dssp             HHHHHHHSCBTTTBTTTHHHHHHHHTHH
T ss_pred             HHHHHHhCCCccCCchhHHHHHHHHHHH
Confidence            99999974   59999999999876653

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

Probab=99.83  E-value=1.1e-21  Score=162.03  Aligned_cols=210  Identities=19%  Similarity=0.177  Sum_probs=142.4

Q ss_pred             cCCCcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           55 YRPKQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        55 ~~~~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      +.+..|++++|++..+..+...+..            ....+++|+||||||||++|+++++++      ..+++.+++.
T Consensus         5 ~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~------~~~~~~v~~~   78 (268)
T 2r62_A            5 KPNVRFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA------HVPFFSMGGS   78 (268)
T ss_dssp             CCCCCSTTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHH------TCCCCCCCSC
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHh------CCCEEEechH
Confidence            3456788999998888877776541            223459999999999999999999998      4455555544


Q ss_pred             CCcch------hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH---------------HHHHHHHHHHh
Q 022641          123 DDRGI------NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED---------------AQNALRRTMET  181 (294)
Q Consensus       123 ~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~---------------~~~~L~~~l~~  181 (294)
                      .....      ..+...+.....              ..+.+|+|||+|.+...               .++.|+..++.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~a~~--------------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~  144 (268)
T 2r62_A           79 SFIEMFVGLGASRVRDLFETAKK--------------QAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDG  144 (268)
T ss_dssp             TTTTSCSSSCSSSSSTTHHHHHH--------------SCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTC
T ss_pred             HHHHhhcchHHHHHHHHHHHHHh--------------cCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhC
Confidence            32110      111111111111              12359999999998643               23345555554


Q ss_pred             hc---CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHH
Q 022641          182 YS---KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAI  254 (294)
Q Consensus       182 ~~---~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~  254 (294)
                      ..   ..+.+|+++|.+..+++++.+  ||. .+.+++|+.+++.++++.+++...+. ++..+..+++.+.| ..|.+.
T Consensus       145 ~~~~~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~-~~~~~~~la~~~~g~~g~dl~  223 (268)
T 2r62_A          145 FGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLA-NDVNLQEVAKLTAGLAGADLA  223 (268)
T ss_dssp             SSCSCSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCC-SSCCTTTTTSSSCSSCHHHHH
T ss_pred             cccCCCCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCC-CccCHHHHHHHcCCCCHHHHH
Confidence            32   236688888988888888888  775 79999999999999998877543221 23336677877776 456777


Q ss_pred             HHHHHHHHHh----CCCCChhhhhhhcccccCCCC
Q 022641          255 TYLQGAARLF----GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       255 ~~l~~~~~~~----~~~it~~~v~~~~~~~~~~~~  285 (294)
                      ++++.++..+    ...|+.+++..++....+...
T Consensus       224 ~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~  258 (268)
T 2r62_A          224 NIINEAALLAGRNNQKEVRQQHLKEAVERGIAGLE  258 (268)
T ss_dssp             HHHHHHHHTTSSSCCCSCCHHHHHTSCTTCCCCCC
T ss_pred             HHHHHHHHHHHHhccCCcCHHHHHHHHHHHhhcch
Confidence            7777777666    356999999999988766543

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=99.82  E-value=7.6e-20  Score=156.29  Aligned_cols=195  Identities=11%  Similarity=0.059  Sum_probs=154.3

Q ss_pred             HHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCC
Q 022641           74 TNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPC  153 (294)
Q Consensus        74 ~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (294)
                      .+.+.....+.++|+||+|+||++.+..+++.+.+.......++.++.  .   ..++.........+..          
T Consensus        10 ~~~l~~~~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~--~---~~~~~l~~~~~~~plf----------   74 (343)
T 1jr3_D           10 RAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDP--N---TDWNAIFSLCQAMSLF----------   74 (343)
T ss_dssp             HHHHHHCCCSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECCT--T---CCHHHHHHHHHHHHHC----------
T ss_pred             HHHHhcCCCcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEecC--C---CCHHHHHHHhcCcCCc----------
Confidence            334443344569999999999999999999988644322222333432  1   3344444444333322          


Q ss_pred             CCcEEEEEeCCCC-CCHHHHHHHHHHHHhhcCcceEEEEecC------CcccchHhhccccEEEecCCCHHHHHHHHHHH
Q 022641          154 PPYKIIILDEADS-MTEDAQNALRRTMETYSKVTRFFFICNY------ISRIIEPLASRCAKFRFKPLSEEVMSSRVLHI  226 (294)
Q Consensus       154 ~~~~lliiDei~~-l~~~~~~~L~~~l~~~~~~~~ii~~~~~------~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~  226 (294)
                      +++.+++|||++. ++...++.|++.+++++....+|++++.      ...+.+.+.+||..+.|.+++..++..++.++
T Consensus        75 ~~~kvvii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~~~~l~~~l~~~  154 (343)
T 1jr3_D           75 ASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAAR  154 (343)
T ss_dssp             CSCEEEEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTTHHHHHHHHH
T ss_pred             cCCeEEEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCCHHHHHHHHHHH
Confidence            3457999999999 9988999999999999989988888865      34578899999999999999999999999999


Q ss_pred             HHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh-CCCCChhhhhhhcccccCC
Q 022641          227 CNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF-GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       227 ~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~-~~~it~~~v~~~~~~~~~~  283 (294)
                      ++.+|+.+++++++.+++.++||+|.+.+.++.++.+. ++.||.++|..+++.....
T Consensus       155 ~~~~g~~i~~~a~~~l~~~~~gdl~~~~~elekl~l~~~~~~It~e~V~~~~~~~~~~  212 (343)
T 1jr3_D          155 AKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGKLTLPRVEQAVNDAAHF  212 (343)
T ss_dssp             HHHTTCEECHHHHHHHHHSSTTCHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHCCC
T ss_pred             HHHcCCCCCHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHhhhhcC
Confidence            99999999999999999999999999999999999875 5579999999988776544

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

Probab=99.82  E-value=1.4e-19  Score=160.27  Aligned_cols=209  Identities=17%  Similarity=0.149  Sum_probs=149.9

Q ss_pred             hcCCCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           54 KYRPKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        54 ~~~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      ...+..|++++|.+..++.|.+++..             ....+++|+||||||||++|+++++++      +.+++.++
T Consensus       197 ~~~~~~~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~------~~~fv~vn  270 (489)
T 3hu3_A          197 SLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET------GAFFFLIN  270 (489)
T ss_dssp             HHTCCCGGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHC------SSEEEEEE
T ss_pred             ccCCCCHHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHh------CCCEEEEE
Confidence            45667889999999999999887753             334569999999999999999999998      67788887


Q ss_pred             CCCCcc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HHHHHHHHHHHHhhc
Q 022641          121 ASDDRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------EDAQNALRRTMETYS  183 (294)
Q Consensus       121 ~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~~~~~L~~~l~~~~  183 (294)
                      +....+      ...+...+.....              ..+.+|||||+|.+.           ...++.|+..++...
T Consensus       271 ~~~l~~~~~g~~~~~~~~~f~~A~~--------------~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~  336 (489)
T 3hu3_A          271 GPEIMSKLAGESESNLRKAFEEAEK--------------NAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLK  336 (489)
T ss_dssp             HHHHHTSCTTHHHHHHHHHHHHHHH--------------TCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSC
T ss_pred             chHhhhhhcchhHHHHHHHHHHHHh--------------cCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhccc
Confidence            643221      1122222222211              123699999997663           256788999998543


Q ss_pred             --CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCc-HHHHHHHH
Q 022641          184 --KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGD-LRRAITYL  257 (294)
Q Consensus       184 --~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~-~r~~~~~l  257 (294)
                        ..+.+|.+||.+..+++++.+  ||. .+.+++|+.+++.++++.++....+. .+..+..++..+.|. .+.+..++
T Consensus       337 ~~~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~-~~~~l~~la~~t~g~s~~dL~~L~  415 (489)
T 3hu3_A          337 QRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLA-DDVDLEQVANETHGHVGADLAALC  415 (489)
T ss_dssp             TTSCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBC-TTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             cCCceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCc-chhhHHHHHHHccCCcHHHHHHHH
Confidence              456788889999889999988  776 79999999999999999887654333 233467788887763 45555566


Q ss_pred             HHHHHHh--C-------------------CCCChhhhhhhcccccCC
Q 022641          258 QGAARLF--G-------------------SSITSKDLISVSGYPTGG  283 (294)
Q Consensus       258 ~~~~~~~--~-------------------~~it~~~v~~~~~~~~~~  283 (294)
                      ..++..+  +                   ..|+.+++..++....+.
T Consensus       416 ~~A~~~a~r~~~~~i~~~~~~~~~~~~~~~~vt~edf~~Al~~~~ps  462 (489)
T 3hu3_A          416 SEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPS  462 (489)
T ss_dssp             HHHHHHHHHTTTTTCCTTCSSCCHHHHHHCCBCHHHHHHHHTSHHHH
T ss_pred             HHHHHHHHHhccccccccccccchhhcccCcCCHHHHHHHHHhCCch
Confidence            6665444  1                   137888998888876654

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=99.80  E-value=6e-19  Score=167.23  Aligned_cols=208  Identities=17%  Similarity=0.189  Sum_probs=144.9

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCC----ccCCcceeecC
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE----LYKSRVLELNA  121 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~----~~~~~~~~~~~  121 (294)
                      ....+|.++++|..++.++|++..+..+..++.....++++|+||||||||++++++++.+.+..    ..+..++.+++
T Consensus       155 ~~~~~l~~~~r~~~ld~viGr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~  234 (854)
T 1qvr_A          155 QYGIDLTRLAAEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQM  234 (854)
T ss_dssp             HHEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC
T ss_pred             HHHHhHHHHHhcCCCcccCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeeh
Confidence            45668999999999999999999999999999988888899999999999999999999873211    12456666766


Q ss_pred             CCCcch----hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC--------HHHHHHHHHHHHhhcCcceEE
Q 022641          122 SDDRGI----NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT--------EDAQNALRRTMETYSKVTRFF  189 (294)
Q Consensus       122 ~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--------~~~~~~L~~~l~~~~~~~~ii  189 (294)
                      +.....    ......+.........         ...+.+|||||+|.+.        ....+.|..+++.  ....+|
T Consensus       235 ~~l~~g~~~~g~~~~~l~~~~~~~~~---------~~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l~~--~~i~~I  303 (854)
T 1qvr_A          235 GSLLAGAKYRGEFEERLKAVIQEVVQ---------SQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALAR--GELRLI  303 (854)
T ss_dssp             -----------CHHHHHHHHHHHHHT---------TCSSEEEEECCC-------------------HHHHHT--TCCCEE
T ss_pred             HHhhccCccchHHHHHHHHHHHHHHh---------cCCCeEEEEecHHHHhccCCccchHHHHHHHHHHHhC--CCeEEE
Confidence            543211    1111222222221111         0124599999999986        3445667777765  455677


Q ss_pred             EEecCCc----ccchHhhccccEEEecCCCHHHHHHHHHHHHH----HhCCCCCHHHHHHHHhhccCc------HHHHHH
Q 022641          190 FICNYIS----RIIEPLASRCAKFRFKPLSEEVMSSRVLHICN----EEGLNLDAEALSTLSSISQGD------LRRAIT  255 (294)
Q Consensus       190 ~~~~~~~----~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~----~~~~~~~~~~l~~l~~~~~G~------~r~~~~  255 (294)
                      ++++...    .+++++.+||..+.+++|+.++...+++.++.    .+++.++++++..+++.+.|.      +..++.
T Consensus       304 ~at~~~~~~~~~~d~aL~rRf~~i~l~~p~~~e~~~iL~~~~~~~~~~~~~~i~~~al~~~~~ls~r~i~~~~lp~kai~  383 (854)
T 1qvr_A          304 GATTLDEYREIEKDPALERRFQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAID  383 (854)
T ss_dssp             EEECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCTHHHHHH
T ss_pred             EecCchHHhhhccCHHHHhCCceEEeCCCCHHHHHHHHHhhhhhhhhhcCCCCCHHHHHHHHHHHhhhcccccChHHHHH
Confidence            7777553    36789999999999999999999999987765    457889999999999987543      788898


Q ss_pred             HHHHHHHHh
Q 022641          256 YLQGAARLF  264 (294)
Q Consensus       256 ~l~~~~~~~  264 (294)
                      ++..++...
T Consensus       384 lldea~a~~  392 (854)
T 1qvr_A          384 LIDEAAARL  392 (854)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888777554

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=99.80  E-value=1.1e-18  Score=163.83  Aligned_cols=225  Identities=16%  Similarity=0.136  Sum_probs=160.2

Q ss_pred             cccCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCC----ccCCcceee
Q 022641           44 VLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE----LYKSRVLEL  119 (294)
Q Consensus        44 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~----~~~~~~~~~  119 (294)
                      ......+|.++++|..++.++|++..+..+.+.+......+++|+||||||||++|+++++.+.+..    .....++.+
T Consensus       169 l~~~~~~l~~~~~~~~~d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~  248 (758)
T 1r6b_X          169 LENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSL  248 (758)
T ss_dssp             CCSSSCBHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEEC
T ss_pred             HHHHhHhHHHHHhcCCCCCccCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEE
Confidence            3467889999999999999999999999999999888888899999999999999999999874321    123334444


Q ss_pred             cCCCCc----chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC---------HHHHHHHHHHHHhhcCcc
Q 022641          120 NASDDR----GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT---------EDAQNALRRTMETYSKVT  186 (294)
Q Consensus       120 ~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~---------~~~~~~L~~~l~~~~~~~  186 (294)
                      +.....    ........+.........          ..+.+|||||+|.+.         ....+.|..+++.  ...
T Consensus       249 ~~~~l~~~~~~~g~~e~~l~~~~~~~~~----------~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~~--~~~  316 (758)
T 1r6b_X          249 DIGSLLAGTKYRGDFEKRFKALLKQLEQ----------DTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSS--GKI  316 (758)
T ss_dssp             CCC---CCCCCSSCHHHHHHHHHHHHSS----------SSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSS--CCC
T ss_pred             cHHHHhccccccchHHHHHHHHHHHHHh----------cCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHHhC--CCe
Confidence            332211    111122222222222111          124699999999982         2334555555543  456


Q ss_pred             eEEEEecCC-----cccchHhhccccEEEecCCCHHHHHHHHHHHHHH----hCCCCCHHHHHHHHhhccC------cHH
Q 022641          187 RFFFICNYI-----SRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE----EGLNLDAEALSTLSSISQG------DLR  251 (294)
Q Consensus       187 ~ii~~~~~~-----~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~----~~~~~~~~~l~~l~~~~~G------~~r  251 (294)
                      .+|++++..     ...++++.+||..+.+++|+.++...+++.++..    +++.++++++..++..+.|      .+.
T Consensus       317 ~~I~at~~~~~~~~~~~d~aL~~Rf~~i~v~~p~~~e~~~il~~l~~~~~~~~~v~~~~~al~~~~~~s~~~i~~~~lp~  396 (758)
T 1r6b_X          317 RVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPD  396 (758)
T ss_dssp             EEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSCTTH
T ss_pred             EEEEEeCchHHhhhhhcCHHHHhCceEEEcCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhcccccCch
Confidence            677777643     3456889999999999999999999999987765    6888999999999988655      355


Q ss_pred             HHHHHHHHHHHHh--------CCCCChhhhhhhcccc
Q 022641          252 RAITYLQGAARLF--------GSSITSKDLISVSGYP  280 (294)
Q Consensus       252 ~~~~~l~~~~~~~--------~~~it~~~v~~~~~~~  280 (294)
                      .++.++..++...        ...++.+++..++...
T Consensus       397 ~~i~lld~a~~~~~~~~~~~~~~~v~~~di~~~~~~~  433 (758)
T 1r6b_X          397 KAIDVIDEAGARARLMPVSKRKKTVNVADIESVVARI  433 (758)
T ss_dssp             HHHHHHHHHHHHHHHSSSCCCCCSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcccccccCCccCHHHHHHHHHHh
Confidence            7888887766442        2458999998877653

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

Probab=99.80  E-value=1.9e-18  Score=141.42  Aligned_cols=206  Identities=23%  Similarity=0.234  Sum_probs=136.0

Q ss_pred             hcCCCcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecC
Q 022641           54 KYRPKQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA  121 (294)
Q Consensus        54 ~~~~~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~  121 (294)
                      ...+..|++++|.+..+..+.+....            ...++++|+|||||||||++++++..+      ...++.+++
T Consensus         9 ~~~~~~~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~------~~~~i~~~~   82 (254)
T 1ixz_A            9 EAPKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA------RVPFITASG   82 (254)
T ss_dssp             CCCSCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHT------TCCEEEEEH
T ss_pred             CCCCCCHHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHh------CCCEEEeeH
Confidence            34456789999998888776655432            112359999999999999999999987      455555554


Q ss_pred             CCCcc--hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhhcC-
Q 022641          122 SDDRG--INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTMETYSK-  184 (294)
Q Consensus       122 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~~~~~-  184 (294)
                      .+...  .......+.........          ..+.++++||++.+..              ...+.++..++.... 
T Consensus        83 ~~~~~~~~~~~~~~i~~~~~~~~~----------~~~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~~  152 (254)
T 1ixz_A           83 SDFVEMFVGVGAARVRDLFETAKR----------HAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKD  152 (254)
T ss_dssp             HHHHHSCTTHHHHHHHHHHHHHTT----------SSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTT
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHh----------cCCeEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCCC
Confidence            32110  11111111111111100          1235999999976521              123455555554332 


Q ss_pred             -cceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHH-HHHHHhhccCcH-HHHHHHHH
Q 022641          185 -VTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEA-LSTLSSISQGDL-RRAITYLQ  258 (294)
Q Consensus       185 -~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-l~~l~~~~~G~~-r~~~~~l~  258 (294)
                       ...++.++|.+..+++++.+  ||. .+.+++|+.+++.++++..++  +..++++. +..+++.+.|+. |.+.+++.
T Consensus       153 ~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~--~~~~~~~~~~~~la~~~~G~~~~dl~~~~~  230 (254)
T 1ixz_A          153 TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHAR--GKPLAEDVDLALLAKRTPGFVGADLENLLN  230 (254)
T ss_dssp             CCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHT--TSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHc--CCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence             34566677888889999988  665 799999999999999987763  45555443 888999998865 77778887


Q ss_pred             HHHHHh----CCCCChhhhhhhc
Q 022641          259 GAARLF----GSSITSKDLISVS  277 (294)
Q Consensus       259 ~~~~~~----~~~it~~~v~~~~  277 (294)
                      .++..+    ...||.+++.+++
T Consensus       231 ~a~~~a~~~~~~~I~~~dl~~a~  253 (254)
T 1ixz_A          231 EAALLAAREGRRKITMKDLEEAA  253 (254)
T ss_dssp             HHHHHHHHTTCSSBCHHHHHHHT
T ss_pred             HHHHHHHHhcCCCcCHHHHHHHh
Confidence            777655    3469999998875

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=99.79  E-value=3.3e-19  Score=147.46  Aligned_cols=162  Identities=13%  Similarity=0.170  Sum_probs=110.0

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc---hhHHHHHHHHHHhhhcccCccCCCCCCCCcE
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG---INVVRTKIKTFAAVAVGSGQRRGGYPCPPYK  157 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (294)
                      ...+++|+||||||||++|+++++.+      +.+++.+++++...   .......+........          .....
T Consensus        63 ~~~~vLl~G~~GtGKT~la~~ia~~~------~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~----------~~~~~  126 (272)
T 1d2n_A           63 PLVSVLLEGPPHSGKTALAAKIAEES------NFPFIKICSPDKMIGFSETAKCQAMKKIFDDAY----------KSQLS  126 (272)
T ss_dssp             SEEEEEEECSTTSSHHHHHHHHHHHH------TCSEEEEECGGGCTTCCHHHHHHHHHHHHHHHH----------TSSEE
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHh------CCCEEEEeCHHHhcCCchHHHHHHHHHHHHHHH----------hcCCc
Confidence            33469999999999999999999997      66777776554221   1111111121111110          12356


Q ss_pred             EEEEeCCCCC----------CHHHHHHHHHHHHh---hcCcceEEEEecCCcccch-Hhhcccc-EEEecCCCH-HHHHH
Q 022641          158 IIILDEADSM----------TEDAQNALRRTMET---YSKVTRFFFICNYISRIIE-PLASRCA-KFRFKPLSE-EVMSS  221 (294)
Q Consensus       158 lliiDei~~l----------~~~~~~~L~~~l~~---~~~~~~ii~~~~~~~~~~~-~l~~r~~-~i~~~~~~~-~~~~~  221 (294)
                      +|+|||+|.+          ....++.|...++.   ....+.+|+++|.+..+.+ .+.+||. .+.++|++. +++..
T Consensus       127 vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~~l~~~~l~~rf~~~i~~p~l~~r~~i~~  206 (272)
T 1d2n_A          127 CVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLE  206 (272)
T ss_dssp             EEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTTTSSEEEECCCEEEHHHHHH
T ss_pred             EEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCEEEEEecCChhhcchhhhhcccceEEcCCCccHHHHHHH
Confidence            9999999887          44556666666654   2334557778888766655 5778864 789988887 66666


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHhhccC-----cHHHHHHHHHHHHHH
Q 022641          222 RVLHICNEEGLNLDAEALSTLSSISQG-----DLRRAITYLQGAARL  263 (294)
Q Consensus       222 ~l~~~~~~~~~~~~~~~l~~l~~~~~G-----~~r~~~~~l~~~~~~  263 (294)
                      ++.+    . ..++++.+..+++.+.|     ++|.++++++.+...
T Consensus       207 i~~~----~-~~~~~~~~~~l~~~~~g~~~~g~ir~l~~~l~~a~~~  248 (272)
T 1d2n_A          207 ALEL----L-GNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQM  248 (272)
T ss_dssp             HHHH----H-TCSCHHHHHHHHHHHTTSEEEECHHHHHHHHHHHTTS
T ss_pred             HHHh----c-CCCCHHHHHHHHHHhcCCCccccHHHHHHHHHHHhhh
Confidence            5543    2 34789999999999877     999999999988764

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

Probab=99.79  E-value=1.7e-18  Score=153.09  Aligned_cols=210  Identities=22%  Similarity=0.206  Sum_probs=147.0

Q ss_pred             CCCcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           56 RPKQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        56 ~~~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      .+..|++++|.+..+..+.+....            ....+++|+||||||||+++++++..+      ...++.+++++
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~------~~~~i~i~g~~   99 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA------RVPFITASGSD   99 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHT------TCCEEEEEGGG
T ss_pred             CCCCHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHh------CCCEEEEehhH
Confidence            567899999999998877766532            112359999999999999999999998      56777777655


Q ss_pred             Ccch--hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhhc--Cc
Q 022641          124 DRGI--NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTMETYS--KV  185 (294)
Q Consensus       124 ~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~~~~--~~  185 (294)
                      ....  ......+.......          ....+.+++|||+|.+..              ...+.|+..++...  ..
T Consensus       100 ~~~~~~g~~~~~v~~lfq~a----------~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~~~  169 (499)
T 2dhr_A          100 FVEMFVGVGAARVRDLFETA----------KRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTA  169 (499)
T ss_dssp             GTSSCTTHHHHHHHHHTTTS----------SSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCSSCC
T ss_pred             HHHhhhhhHHHHHHHHHHHH----------HhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcccccCcc
Confidence            3221  11111122111111          011235999999987631              23345555555433  34


Q ss_pred             ceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHH-HHHHHhhccCcH-HHHHHHHHHH
Q 022641          186 TRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEA-LSTLSSISQGDL-RRAITYLQGA  260 (294)
Q Consensus       186 ~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-l~~l~~~~~G~~-r~~~~~l~~~  260 (294)
                      ..++.++|.+..+++++.+  ||. .+.+++|+.+++.++++.+++  +..+++++ +..++..+.|+. |.+.+++..+
T Consensus       170 viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~--~~~l~~dv~l~~lA~~t~G~~gadL~~lv~~A  247 (499)
T 2dhr_A          170 IVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHAR--GKPLAEDVDLALLAKRTPGFVGADLENLLNEA  247 (499)
T ss_dssp             CEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTS--SSCCCCSSTTHHHHTTSCSCCHHHHHHHHHHH
T ss_pred             EEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHh--cCCCChHHHHHHHHHhcCCCCHHHHHHHHHHH
Confidence            5567777888888889988  565 899999999999999976653  45555444 888999999987 8888999988


Q ss_pred             HHHh----CCCCChhhhhhhcccccCC
Q 022641          261 ARLF----GSSITSKDLISVSGYPTGG  283 (294)
Q Consensus       261 ~~~~----~~~it~~~v~~~~~~~~~~  283 (294)
                      +..+    ...|+.+++..++......
T Consensus       248 a~~A~~~~~~~It~~dl~~al~~v~~~  274 (499)
T 2dhr_A          248 ALLAAREGRRKITMKDLEEAADRVMML  274 (499)
T ss_dssp             HHHHTTTCCSSCCSHHHHHHHHHHTTC
T ss_pred             HHHHHHhCCCccCHHHHHHHHHHHhcc
Confidence            8766    2469999999988876543

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=99.79  E-value=2.8e-18  Score=148.36  Aligned_cols=207  Identities=18%  Similarity=0.202  Sum_probs=137.7

Q ss_pred             hhhcccHHHHHHHHHHHH----c--------------------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCC
Q 022641           61 KDVAHQEEVVRVLTNTLE----T--------------------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPE  110 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~----~--------------------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~  110 (294)
                      +.++|++.+++.|..++.    .                          ....+++|+||||||||++|+++++.+    
T Consensus        21 ~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l----   96 (376)
T 1um8_A           21 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHL----   96 (376)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHT----
T ss_pred             hHccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHh----
Confidence            357899999988887762    0                          123569999999999999999999998    


Q ss_pred             ccCCcceeecCCCCcch----hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH--------------HH
Q 022641          111 LYKSRVLELNASDDRGI----NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED--------------AQ  172 (294)
Q Consensus       111 ~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~--------------~~  172 (294)
                        +.+++.+++......    ......+.........      ......+++|+|||++.+...              .+
T Consensus        97 --~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~------~~~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~  168 (376)
T 1um8_A           97 --DIPIAISDATSLTEAGYVGEDVENILTRLLQASDW------NVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQ  168 (376)
T ss_dssp             --TCCEEEEEGGGCC--------CTHHHHHHHHHTTT------CHHHHTTSEEEEETGGGC--------------CHHHH
T ss_pred             --CCCEEEecchhhhhcCcCCccHHHHHHHHHhhccc------hhhhcCCeEEEEcCHHHHhhhcCCCceecccchHHHH
Confidence              566666665443211    1111111111111000      000112359999999999877              88


Q ss_pred             HHHHHHHHhhc---------------------CcceEEEEecC-------------------------------------
Q 022641          173 NALRRTMETYS---------------------KVTRFFFICNY-------------------------------------  194 (294)
Q Consensus       173 ~~L~~~l~~~~---------------------~~~~ii~~~~~-------------------------------------  194 (294)
                      +.|+++++...                     .+..+|+++|.                                     
T Consensus       169 ~~Ll~~le~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~R~~~~~~g~~~~~~~~~~~~~~~~~~~~  248 (376)
T 1um8_A          169 QALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQT  248 (376)
T ss_dssp             HHHHHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCH
T ss_pred             HHHHHHhhccceecccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHHHhcccccCCCchhhhccchhHHHhhcCH
Confidence            99999998531                     33456666551                                     


Q ss_pred             ----CcccchHhhcccc-EEEecCCCHHHHHHHHHH----HHH----H---h--CCCCCHHHHHHHHhhcc---CcHHHH
Q 022641          195 ----ISRIIEPLASRCA-KFRFKPLSEEVMSSRVLH----ICN----E---E--GLNLDAEALSTLSSISQ---GDLRRA  253 (294)
Q Consensus       195 ----~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~----~~~----~---~--~~~~~~~~l~~l~~~~~---G~~r~~  253 (294)
                          ...+.++|.+|+. ++.|+|++.+++..++..    ++.    .   .  ++.+++++++.|++.+.   |++|.+
T Consensus       249 ~~l~~~~~~p~l~~R~~~~i~~~~l~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~L  328 (376)
T 1um8_A          249 HDLVTYGLIPELIGRLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKTGARGL  328 (376)
T ss_dssp             HHHHHTTCCHHHHTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTGGGH
T ss_pred             HHHhhcCCChHHhcCCCceeeccCCCHHHHHHHHhhhHHHHHHHHHHHHhhcCceEEECHHHHHHHHHHhcccccCcHHH
Confidence                1125688899994 899999999999998862    221    1   1  34589999999999854   999999


Q ss_pred             HHHHHHHHHHh-----C-----CCCChhhhhhhccc
Q 022641          254 ITYLQGAARLF-----G-----SSITSKDLISVSGY  279 (294)
Q Consensus       254 ~~~l~~~~~~~-----~-----~~it~~~v~~~~~~  279 (294)
                      .+.++.+....     .     ..||.+++......
T Consensus       329 ~~~le~~~~~~~~~~~~~~~~~~~i~~~~v~~~~~~  364 (376)
T 1um8_A          329 RAIIEDFCLDIMFDLPKLKGSEVRITKDCVLKQAEP  364 (376)
T ss_dssp             HHHHHHHHHHHHHTGGGGTTSEEEECHHHHTTSSCC
T ss_pred             HHHHHHHHHHHHhhccCCCCCEEEEeHHHhcCCCCc
Confidence            99998876542     1     13888888876655

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.79  E-value=5.1e-19  Score=138.32  Aligned_cols=166  Identities=18%  Similarity=0.170  Sum_probs=116.6

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCc----cCCcceeecCC
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPEL----YKSRVLELNAS  122 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~----~~~~~~~~~~~  122 (294)
                      ...||.+++.|..+++++|++..+..+..++......+++|+||+|||||++++.+++.+.+...    .+..++.+++.
T Consensus         8 ~~~~l~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (195)
T 1jbk_A            8 YTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMG   87 (195)
T ss_dssp             HEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHH
T ss_pred             HhHHHHHHHhhccccccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeHH
Confidence            35689999999999999999999999999998877778999999999999999999998743211    13344444432


Q ss_pred             CC----cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH--------HHHHHHHHHHhhcCcceEEE
Q 022641          123 DD----RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED--------AQNALRRTMETYSKVTRFFF  190 (294)
Q Consensus       123 ~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~--------~~~~L~~~l~~~~~~~~ii~  190 (294)
                      ..    .........+.........         ..++.+|+|||++.+...        ..+.|...++.  ....+|+
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~l~~~~~~--~~~~~i~  156 (195)
T 1jbk_A           88 ALVAGAKYRGEFEERLKGVLNDLAK---------QEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR--GELHCVG  156 (195)
T ss_dssp             HHHTTTCSHHHHHHHHHHHHHHHHH---------STTTEEEEEETGGGGTT------CCCCHHHHHHHHHT--TSCCEEE
T ss_pred             HHhccCCccccHHHHHHHHHHHHhh---------cCCCeEEEEeCHHHHhccCcccchHHHHHHHHHhhcc--CCeEEEE
Confidence            21    1112222222222221110         122459999999998532        35666666654  4566788


Q ss_pred             EecCCc-----ccchHhhccccEEEecCCCHHHHHHHH
Q 022641          191 ICNYIS-----RIIEPLASRCAKFRFKPLSEEVMSSRV  223 (294)
Q Consensus       191 ~~~~~~-----~~~~~l~~r~~~i~~~~~~~~~~~~~l  223 (294)
                      +++...     .+++++.+||..+.+.+|+.+++.+++
T Consensus       157 ~~~~~~~~~~~~~~~~l~~r~~~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          157 ATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             EECHHHHHHHTTTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             eCCHHHHHHHHhcCHHHHHHhceeecCCCCHHHHHHHh
Confidence            887654     578999999999999999999988764

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

Probab=99.77  E-value=2.2e-17  Score=136.91  Aligned_cols=204  Identities=23%  Similarity=0.240  Sum_probs=134.2

Q ss_pred             CCCcchhhcccHHHHHHHHHHHHc------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           56 RPKQVKDVAHQEEVVRVLTNTLET------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        56 ~~~~~~~~~g~~~~~~~l~~~l~~------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      .+..|++++|.+..+..+.+....            ...++++|+||+||||||++++++..+      ...++.+++.+
T Consensus        35 ~~~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~------~~~~i~~~~~~  108 (278)
T 1iy2_A           35 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA------RVPFITASGSD  108 (278)
T ss_dssp             CCCCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHT------TCCEEEEEHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHc------CCCEEEecHHH
Confidence            456789999999888777665432            112359999999999999999999987      45555555432


Q ss_pred             Ccc--hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC-----------HH---HHHHHHHHHHhhc--Cc
Q 022641          124 DRG--INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT-----------ED---AQNALRRTMETYS--KV  185 (294)
Q Consensus       124 ~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~-----------~~---~~~~L~~~l~~~~--~~  185 (294)
                      ...  .......+.........          ..+.++++||++.+.           ..   ..+.++..++...  ..
T Consensus       109 ~~~~~~~~~~~~i~~~~~~~~~----------~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~~~~  178 (278)
T 1iy2_A          109 FVEMFVGVGAARVRDLFETAKR----------HAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTA  178 (278)
T ss_dssp             HHHSTTTHHHHHHHHHHHHHHT----------SCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTCCTTCC
T ss_pred             HHHHHhhHHHHHHHHHHHHHHh----------cCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCCCCC
Confidence            110  01111111111111110          113599999997652           11   2233444444322  23


Q ss_pred             ceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHH-HHHHHhhccCcH-HHHHHHHHHH
Q 022641          186 TRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEA-LSTLSSISQGDL-RRAITYLQGA  260 (294)
Q Consensus       186 ~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-l~~l~~~~~G~~-r~~~~~l~~~  260 (294)
                      ..++.++|.+..+++++.+  ||. .+.+++|+.+++.++++.+++  +..+++++ +..++..+.|+. +.+.++++.+
T Consensus       179 ~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~--~~~~~~~~~~~~la~~~~G~~~~dl~~l~~~a  256 (278)
T 1iy2_A          179 IVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHAR--GKPLAEDVDLALLAKRTPGFVGADLENLLNEA  256 (278)
T ss_dssp             EEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHT--TSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             EEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHc--cCCCCcccCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            4566677888889999987  665 799999999999999987764  45555443 788999999876 6777788777


Q ss_pred             HHHh----CCCCChhhhhhhc
Q 022641          261 ARLF----GSSITSKDLISVS  277 (294)
Q Consensus       261 ~~~~----~~~it~~~v~~~~  277 (294)
                      +..+    ...|+.+++.+++
T Consensus       257 ~~~a~~~~~~~I~~~dl~~a~  277 (278)
T 1iy2_A          257 ALLAAREGRRKITMKDLEEAA  277 (278)
T ss_dssp             HHHHHHTTCCSBCHHHHHHHT
T ss_pred             HHHHHHhCCCCcCHHHHHHHh
Confidence            6654    3469999998875

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

Probab=99.77  E-value=1.1e-18  Score=161.36  Aligned_cols=209  Identities=17%  Similarity=0.144  Sum_probs=145.2

Q ss_pred             CCCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           56 RPKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        56 ~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      ....|+++.|.+..+..|.+++..             ..+.+++|+||||||||++|+++|+++      +.+++.++++
T Consensus       199 ~~v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~el------g~~~~~v~~~  272 (806)
T 3cf2_A          199 NEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET------GAFFFLINGP  272 (806)
T ss_dssp             SSCCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTT------TCEEEEEEHH
T ss_pred             CCCChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHh------CCeEEEEEhH
Confidence            345789999998888888877632             123459999999999999999999998      7788888765


Q ss_pred             CCcc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH-----------HHHHHHHHHHHhhc--
Q 022641          123 DDRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE-----------DAQNALRRTMETYS--  183 (294)
Q Consensus       123 ~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~-----------~~~~~L~~~l~~~~--  183 (294)
                      +..+      ...++..+.....              ..+.||+|||+|.+.+           ...+.|+..|+...  
T Consensus       273 ~l~sk~~gese~~lr~lF~~A~~--------------~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~  338 (806)
T 3cf2_A          273 EIMSKLAGESESNLRKAFEEAEK--------------NAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQR  338 (806)
T ss_dssp             HHHSSCTTHHHHHHHHHHHHHTT--------------SCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGG
T ss_pred             HhhcccchHHHHHHHHHHHHHHH--------------cCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhccccc
Confidence            4322      2233333333221              2346999999998842           35667777787644  


Q ss_pred             CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCc-HHHHHHHHHH
Q 022641          184 KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGD-LRRAITYLQG  259 (294)
Q Consensus       184 ~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~-~r~~~~~l~~  259 (294)
                      ..+.+|.+||.+..+++++++  ||. .|.++.|+.+++.++++.+++..... ++..+..|+..+.|- ...+..+++.
T Consensus       339 ~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~-~dvdl~~lA~~T~GfsgaDL~~Lv~e  417 (806)
T 3cf2_A          339 AHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLA-DDVDLEQVANETHGHVGADLAALCSE  417 (806)
T ss_dssp             GCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEEC-TTCCHHHHHHHCCSCCHHHHHHHHHH
T ss_pred             CCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCC-cccCHHHHHHhcCCCCHHHHHHHHHH
Confidence            356678889999999999998  887 79999999999999998766432221 233477888887652 3333334443


Q ss_pred             HHHHh---------------------CCCCChhhhhhhcccccCCCC
Q 022641          260 AARLF---------------------GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       260 ~~~~~---------------------~~~it~~~v~~~~~~~~~~~~  285 (294)
                      ++..+                     ...++.+++..++....+...
T Consensus       418 A~~~A~~r~~~~i~~~~~~~~~e~~~~~~v~~~Df~~Al~~~~ps~~  464 (806)
T 3cf2_A          418 AALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSAL  464 (806)
T ss_dssp             HHHHHHHHHHHHGGGTCCCCSHHHHHHCEECTTHHHHHHSSSSCCCC
T ss_pred             HHHHHHHhccccccccccccchhhhccceeeHHHHHHHHHhCCCccc
Confidence            33222                     124788888888888776543

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

Probab=99.77  E-value=4.3e-18  Score=159.68  Aligned_cols=198  Identities=15%  Similarity=0.193  Sum_probs=143.1

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCC----ccCCcceeecC
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPE----LYKSRVLELNA  121 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~----~~~~~~~~~~~  121 (294)
                      ....+|.+++++..++.++|++..++.+..++......|++|+||||||||++|+++++.+.+..    ..+..++.++.
T Consensus       165 ~~~~~l~~~~~~~~ld~iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~~~~  244 (758)
T 3pxi_A          165 SLARDLTAIAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDM  244 (758)
T ss_dssp             SSCCBHHHHTTSSCSCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC--
T ss_pred             HHHHHHHHHHhhCCCCCccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEEecc
Confidence            56779999999999999999999999999999988888999999999999999999999974321    22445555555


Q ss_pred             CCC---cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCc--
Q 022641          122 SDD---RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYIS--  196 (294)
Q Consensus       122 ~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~--  196 (294)
                      ...   .....+...+.....              ..+.+||||    .....++.|+..++.  ....+|.+||...  
T Consensus       245 g~~~~G~~e~~l~~~~~~~~~--------------~~~~iLfiD----~~~~~~~~L~~~l~~--~~v~~I~at~~~~~~  304 (758)
T 3pxi_A          245 GTKYRGEFEDRLKKVMDEIRQ--------------AGNIILFID----AAIDASNILKPSLAR--GELQCIGATTLDEYR  304 (758)
T ss_dssp             --------CTTHHHHHHHHHT--------------CCCCEEEEC----C--------CCCTTS--SSCEEEEECCTTTTH
T ss_pred             cccccchHHHHHHHHHHHHHh--------------cCCEEEEEc----CchhHHHHHHHHHhc--CCEEEEeCCChHHHH
Confidence            111   011123333333221              123599999    334566777777763  5677888888766  


Q ss_pred             ---ccchHhhccccEEEecCCCHHHHHHHHHHHHHH----hCCCCCHHHHHHHHhhccC------cHHHHHHHHHHHHHH
Q 022641          197 ---RIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE----EGLNLDAEALSTLSSISQG------DLRRAITYLQGAARL  263 (294)
Q Consensus       197 ---~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~----~~~~~~~~~l~~l~~~~~G------~~r~~~~~l~~~~~~  263 (294)
                         .+++++.+||..+.+++|+.+++..+++.++..    +++.++++++..+++.+.+      .+..++.++..++..
T Consensus       305 ~~~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~~~~~~~~~~~i~~~al~~~~~~s~~~i~~~~~p~~ai~ll~~a~~~  384 (758)
T 3pxi_A          305 KYIEKDAALERRFQPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAGSK  384 (758)
T ss_dssp             HHHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHHHHHH
T ss_pred             HHhhccHHHHhhCcEEEeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhcccccCcCCcHHHHHHHHHHHH
Confidence               578999999999999999999999999977755    6788999999999887543      467888888877643

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

Probab=99.76  E-value=6.2e-18  Score=158.61  Aligned_cols=186  Identities=20%  Similarity=0.304  Sum_probs=134.9

Q ss_pred             hhhcccHHHHHHHHHHHHcCC-------CC--cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHH-
Q 022641           61 KDVAHQEEVVRVLTNTLETAN-------CP--HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVV-  130 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~~-------~~--~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~-  130 (294)
                      ..++|++..+..+...+....       .+  +++|+||||||||++|+++++.++..   ..+++.++++........ 
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~---~~~~i~i~~s~~~~~~~~~  567 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIFGD---EESMIRIDMSEYMEKHSTS  567 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSC---TTCEEEEEGGGGCSSCCCC
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCC---CcceEEEechhcccccccc
Confidence            467899999988888776422       12  59999999999999999999998433   346667766543221110 


Q ss_pred             HHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCcc--
Q 022641          131 RTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYISR--  197 (294)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~~--  197 (294)
                      ...+......             ..+++|+|||++.+++..++.|++++++..           .++.+|++||.+..  
T Consensus       568 ~~~l~~~~~~-------------~~~~vl~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~  634 (758)
T 3pxi_A          568 GGQLTEKVRR-------------KPYSVVLLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEK  634 (758)
T ss_dssp             ---CHHHHHH-------------CSSSEEEEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCC
T ss_pred             cchhhHHHHh-------------CCCeEEEEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhH
Confidence            0011111100             123499999999999999999999999733           35688999986432  


Q ss_pred             ----------cchHhhccc-cEEEecCCCHHHHHHHHHHHHHHh---------CCCCCHHHHHHHHhh---ccCcHHHHH
Q 022641          198 ----------IIEPLASRC-AKFRFKPLSEEVMSSRVLHICNEE---------GLNLDAEALSTLSSI---SQGDLRRAI  254 (294)
Q Consensus       198 ----------~~~~l~~r~-~~i~~~~~~~~~~~~~l~~~~~~~---------~~~~~~~~l~~l~~~---~~G~~r~~~  254 (294)
                                +.++|.+|| ..+.|+|++.+++..++...+...         .+.+++++++.|++.   ..|++|.+.
T Consensus       635 ~~~~~~~~~~f~p~l~~Rl~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~L~  714 (758)
T 3pxi_A          635 DKVMGELKRAFRPEFINRIDEIIVFHSLEKKHLTEIVSLMSDQLTKRLKEQDLSIELTDAAKAKVAEEGVDLEYGARPLR  714 (758)
T ss_dssp             HHHHHHHHHHSCHHHHTTSSEEEECC--CHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHGGGCCTTTTTTTHH
T ss_pred             HHHHHHHHhhCCHHHHhhCCeEEecCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEECHHHHHHHHHhCCCCCCCChHHH
Confidence                      678899999 499999999999999998877642         345899999999875   468899888


Q ss_pred             HHHHHHHH
Q 022641          255 TYLQGAAR  262 (294)
Q Consensus       255 ~~l~~~~~  262 (294)
                      +.++.+..
T Consensus       715 ~~i~~~v~  722 (758)
T 3pxi_A          715 RAIQKHVE  722 (758)
T ss_dssp             HHHHHHTH
T ss_pred             HHHHHHHH
Confidence            88886543

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

Probab=99.76  E-value=2.8e-19  Score=165.32  Aligned_cols=207  Identities=18%  Similarity=0.187  Sum_probs=124.2

Q ss_pred             CcchhhcccHHHHHHHHHHHHcC-------------CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC-
Q 022641           58 KQVKDVAHQEEVVRVLTNTLETA-------------NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD-  123 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~~-------------~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~-  123 (294)
                      ..|+++.|.++.++.|.+.+...             ....+||+||||||||.+|+++|.++      +.+++.++.++ 
T Consensus       474 v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~------~~~f~~v~~~~l  547 (806)
T 3cf2_A          474 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC------QANFISIKGPEL  547 (806)
T ss_dssp             CCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTT------TCEEEECCHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHh------CCceEEeccchh
Confidence            46788999999999888776321             22349999999999999999999998      77777776543 


Q ss_pred             -----CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhhcC
Q 022641          124 -----DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTMETYSK  184 (294)
Q Consensus       124 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~~~~~  184 (294)
                           ..+...++..+......              .+.||||||+|.+..              ...+.|+..|+....
T Consensus       548 ~s~~vGese~~vr~lF~~Ar~~--------------~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~  613 (806)
T 3cf2_A          548 LTMWFGESEANVREIFDKARQA--------------APCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMST  613 (806)
T ss_dssp             HTTTCSSCHHHHHHHHHHHHTT--------------CSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCS
T ss_pred             hccccchHHHHHHHHHHHHHHc--------------CCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCC
Confidence                 23444555555554332              235999999998732              145678888886543


Q ss_pred             --cceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhc----cCcHHHHHH
Q 022641          185 --VTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSIS----QGDLRRAIT  255 (294)
Q Consensus       185 --~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~----~G~~r~~~~  255 (294)
                        .+.+|.+||.+..+++++++  ||. .|+++.|+.+++.++++.++++..+. ++-.+..|++.+    +.|+..+++
T Consensus       614 ~~~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~-~~~dl~~la~~t~g~SGadi~~l~~  692 (806)
T 3cf2_A          614 KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVA-KDVDLEFLAKMTNGFSGADLTEICQ  692 (806)
T ss_dssp             SSSEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--C-CC----------------CHHHHHH
T ss_pred             CCCEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCC-CCCCHHHHHHhCCCCCHHHHHHHHH
Confidence              45667788999999999998  998 89999999999999998777543322 233466677664    457776665


Q ss_pred             HHHHHHHHh--------------------------CCCCChhhhhhhcccccCCCC
Q 022641          256 YLQGAARLF--------------------------GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       256 ~l~~~~~~~--------------------------~~~it~~~v~~~~~~~~~~~~  285 (294)
                      .....+...                          ...|+++|+..++....++..
T Consensus       693 ~A~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~df~~al~~~~pSvs  748 (806)
T 3cf2_A          693 RACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVS  748 (806)
T ss_dssp             HHHHHHHHHHHC-----------------------CCC----CCTTTC--------
T ss_pred             HHHHHHHHHHHHhhhhhhhhhccCccccccccccccCccCHHHHHHHHHhCCCCCC
Confidence            443322111                          124899999999998887643

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=99.76  E-value=1.1e-17  Score=157.22  Aligned_cols=183  Identities=21%  Similarity=0.243  Sum_probs=133.9

Q ss_pred             hhhcccHHHHHHHHHHHHcCC-------C--CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcch----
Q 022641           61 KDVAHQEEVVRVLTNTLETAN-------C--PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGI----  127 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~~-------~--~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~----  127 (294)
                      ..++|++..+..+...+....       .  .+++|+||||||||++|+++++.+      +..++.++++.....    
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l------~~~~~~i~~s~~~~~~~~~  531 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL------GIELLRFDMSEYMERHTVS  531 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH------TCEEEEEEGGGCSSSSCCS
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHh------cCCEEEEechhhcchhhHh
Confidence            457899999988877765321       1  259999999999999999999998      456666665432111    


Q ss_pred             --------hHH---HHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------Cc
Q 022641          128 --------NVV---RTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KV  185 (294)
Q Consensus       128 --------~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~  185 (294)
                              ..-   ...+.....             ...+.+|+|||++.+++..++.|++++++..           .+
T Consensus       532 ~l~g~~~g~~g~~~~~~l~~~~~-------------~~~~~vl~lDEi~~~~~~~~~~Ll~~le~~~~~~~~g~~~~~~~  598 (758)
T 1r6b_X          532 RLIGAPPGYVGFDQGGLLTDAVI-------------KHPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRN  598 (758)
T ss_dssp             SSCCCCSCSHHHHHTTHHHHHHH-------------HCSSEEEEEETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTT
T ss_pred             hhcCCCCCCcCccccchHHHHHH-------------hCCCcEEEEeCccccCHHHHHHHHHHhcCcEEEcCCCCEEecCC
Confidence                    000   001111110             1224699999999999999999999999643           34


Q ss_pred             ceEEEEecCCc-------------------------ccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHh---------
Q 022641          186 TRFFFICNYIS-------------------------RIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEE---------  230 (294)
Q Consensus       186 ~~ii~~~~~~~-------------------------~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~---------  230 (294)
                      +.+|++||...                         .+.++|.+||. ++.|+|++.+++..++...+...         
T Consensus       599 ~~iI~tsN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~  678 (758)
T 1r6b_X          599 VVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGV  678 (758)
T ss_dssp             EEEEEEECSSCC-----------------CHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHTTE
T ss_pred             eEEEEecCcchhhhhhcccCccccchHHHHHHHHHHhcCHHHHhhCCcceeeCCCCHHHHHHHHHHHHHHHHHHHHHCCc
Confidence            66888888643                         46788999995 89999999999999999887632         


Q ss_pred             CCCCCHHHHHHHHhhc---cCcHHHHHHHHHHHHH
Q 022641          231 GLNLDAEALSTLSSIS---QGDLRRAITYLQGAAR  262 (294)
Q Consensus       231 ~~~~~~~~l~~l~~~~---~G~~r~~~~~l~~~~~  262 (294)
                      .+.+++++++.|++.+   +++.|.+.+.++.+..
T Consensus       679 ~~~~~~~a~~~l~~~~~~~~~g~R~l~~~i~~~~~  713 (758)
T 1r6b_X          679 SLEVSQEARNWLAEKGYDRAMGARPMARVIQDNLK  713 (758)
T ss_dssp             EEEECHHHHHHHHHHHCBTTTBTTTHHHHHHHHHT
T ss_pred             EEEeCHHHHHHHHHhCCCcCCCchHHHHHHHHHHH
Confidence            2468999999999875   4458888888877664

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

Probab=99.75  E-value=1.4e-16  Score=131.35  Aligned_cols=213  Identities=16%  Similarity=0.130  Sum_probs=133.9

Q ss_pred             CCcchhhcccHHHHHHHHHHHHc-------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLET-------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      ...|+++.|.+.+++.|.+.+..             ...++++|+||||||||+++++++..+      +..++.+++.+
T Consensus         6 ~~~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~------~~~~i~i~g~~   79 (274)
T 2x8a_A            6 NVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANES------GLNFISVKGPE   79 (274)
T ss_dssp             ------CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHT------TCEEEEEETTT
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHc------CCCEEEEEcHH
Confidence            45788999999998888765421             122359999999999999999999987      55677777765


Q ss_pred             Ccch--hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH-----------HHHHHHHHHHHhhc--CcceE
Q 022641          124 DRGI--NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE-----------DAQNALRRTMETYS--KVTRF  188 (294)
Q Consensus       124 ~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~-----------~~~~~L~~~l~~~~--~~~~i  188 (294)
                      ....  ......+..+......          ..+.++++||++.+..           ...+.++..++...  ....+
T Consensus        80 l~~~~~~~~~~~i~~vf~~a~~----------~~p~i~~~Deid~~~~~r~~~~~~~~~~~~~~~l~~Lsgg~~~~~~i~  149 (274)
T 2x8a_A           80 LLNMYVGESERAVRQVFQRAKN----------SAPCVIFFDEVDALCPRRSDRETGASVRVVNQLLTEMDGLEARQQVFI  149 (274)
T ss_dssp             TCSSTTHHHHHHHHHHHHHHHH----------TCSEEEEEETCTTTCC---------CTTHHHHHHHHHHTCCSTTCEEE
T ss_pred             HHhhhhhHHHHHHHHHHHHHHh----------cCCCeEeeehhhhhhcccCCCcchHHHHHHHHHHHhhhcccccCCEEE
Confidence            4332  1122222222211100          1135999999998631           13445566665433  24456


Q ss_pred             EEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHh-CCCCC-HHHHHHHHhh------ccCcHHHHHHHH
Q 022641          189 FFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEE-GLNLD-AEALSTLSSI------SQGDLRRAITYL  257 (294)
Q Consensus       189 i~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~-~~~~~-~~~l~~l~~~------~~G~~r~~~~~l  257 (294)
                      +.++|.+..+++++++  ||. .|.+++|+.+++.++++.+++.. ...++ +-.+..++..      +++|+..+++..
T Consensus       150 ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~la~~~~~~g~sgadl~~l~~~a  229 (274)
T 2x8a_A          150 MAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVREA  229 (274)
T ss_dssp             EEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHHHTCSGGGSCCHHHHHHHHHHH
T ss_pred             EeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHHHHhhccCCcCHHHHHHHHHHH
Confidence            6778999999999987  887 79999999999999998877542 22222 2336666653      344665555433


Q ss_pred             HHHHHHh------------CCCCChhhhhhhcccccCCCC
Q 022641          258 QGAARLF------------GSSITSKDLISVSGYPTGGSG  285 (294)
Q Consensus       258 ~~~~~~~------------~~~it~~~v~~~~~~~~~~~~  285 (294)
                      ...+...            ...|+.+|+..++....++..
T Consensus       230 ~~~a~~~~~~~~~~~~~~~~~~i~~~df~~al~~~~ps~~  269 (274)
T 2x8a_A          230 SICALRQEMARQKSGNEKGELKVSHKHFEEAFKKVRSSIS  269 (274)
T ss_dssp             HHHHHHHHC-----------CCBCHHHHHHHHTTCCCCC-
T ss_pred             HHHHHHHHHhhccccccccCCeecHHHHHHHHHHhcCCCC
Confidence            3222110            125999999999999887643

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.75  E-value=2.9e-18  Score=133.34  Aligned_cols=159  Identities=16%  Similarity=0.178  Sum_probs=110.4

Q ss_pred             cCCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCc----cCCcceeecC
Q 022641           46 QSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPEL----YKSRVLELNA  121 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~----~~~~~~~~~~  121 (294)
                      ....+|.++++|..+++++|++..+..+..++......+++|+||+|||||++++.+++.+.+...    .+..++.+++
T Consensus         7 ~~~~~l~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (187)
T 2p65_A            7 KYSRDLTALARAGKLDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLDL   86 (187)
T ss_dssp             TTEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEEECH
T ss_pred             HHHHHHHHHHhccccchhhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEEEeH
Confidence            456789999999999999999999999999998877778999999999999999999999843211    1334444432


Q ss_pred             CCCc----chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC---------HHHHHHHHHHHHhhcCcceE
Q 022641          122 SDDR----GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT---------EDAQNALRRTMETYSKVTRF  188 (294)
Q Consensus       122 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~---------~~~~~~L~~~l~~~~~~~~i  188 (294)
                      ....    ........+.........         ...+.+|+|||++.+.         ....+.|...++.  ....+
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~~l~~~~~~--~~~~i  155 (187)
T 2p65_A           87 SSLIAGAKYRGDFEERLKSILKEVQD---------AEGQVVMFIDEIHTVVGAGAVAEGALDAGNILKPMLAR--GELRC  155 (187)
T ss_dssp             HHHHHHCCSHHHHHHHHHHHHHHHHH---------TTTSEEEEETTGGGGSSSSSSCTTSCCTHHHHHHHHHT--TCSCE
T ss_pred             HHhhcCCCchhHHHHHHHHHHHHHHh---------cCCceEEEEeCHHHhcccccccccchHHHHHHHHHHhc--CCeeE
Confidence            2110    111111122222111111         0124599999999986         3456667777654  45668


Q ss_pred             EEEecCCc-----ccchHhhccccEEEecCCC
Q 022641          189 FFICNYIS-----RIIEPLASRCAKFRFKPLS  215 (294)
Q Consensus       189 i~~~~~~~-----~~~~~l~~r~~~i~~~~~~  215 (294)
                      |++++...     .+++++.+||..+.+++|+
T Consensus       156 i~~~~~~~~~~~~~~~~~l~~R~~~i~i~~p~  187 (187)
T 2p65_A          156 IGATTVSEYRQFIEKDKALERRFQQILVEQPS  187 (187)
T ss_dssp             EEEECHHHHHHHTTTCHHHHHHEEEEECCSCC
T ss_pred             EEecCHHHHHHHHhccHHHHHhcCcccCCCCC
Confidence            88887654     5789999999999998875

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.74  E-value=4.1e-17  Score=144.44  Aligned_cols=209  Identities=15%  Similarity=0.129  Sum_probs=134.3

Q ss_pred             hhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhh
Q 022641           61 KDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAV  140 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  140 (294)
                      ..++|++..++.+...+..+.  +++|+||||||||++|+++++.+..    ...+...++... ....+   +......
T Consensus        22 ~~ivGq~~~i~~l~~al~~~~--~VLL~GpPGtGKT~LAraLa~~l~~----~~~f~~~~~~~~-t~~dL---~G~~~~~   91 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAFQN----ARAFEYLMTRFS-TPEEV---FGPLSIQ   91 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHTC--EEEEECCSSSSHHHHHHHGGGGBSS----CCEEEEECCTTC-CHHHH---HCCBC--
T ss_pred             hhhHHHHHHHHHHHHHHhcCC--eeEeecCchHHHHHHHHHHHHHHhh----hhHHHHHHHhcC-CHHHh---cCcccHH
Confidence            468899999999988888775  8999999999999999999987621    112222222211 11111   1100000


Q ss_pred             h---cccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc----------CcceEEEEecCCcc---cchHhhc
Q 022641          141 A---VGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS----------KVTRFFFICNYISR---IIEPLAS  204 (294)
Q Consensus       141 ~---~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~----------~~~~ii~~~~~~~~---~~~~l~~  204 (294)
                      .   .+.............++|+|||++.+++..++.|+..+++..          ....+|++||....   ..+++.+
T Consensus        92 ~~~~~g~~~~~~~g~l~~~~IL~IDEI~r~~~~~q~~LL~~lee~~v~i~G~~~~~~~~~iI~ATN~lpe~~~~~~aLld  171 (500)
T 3nbx_X           92 ALKDEGRYERLTSGYLPEAEIVFLDEIWKAGPAILNTLLTAINERQFRNGAHVEKIPMRLLVAASNELPEADSSLEALYD  171 (500)
T ss_dssp             --------CBCCTTSGGGCSEEEEESGGGCCHHHHHHHHHHHHSSEEECSSSEEECCCCEEEEEESSCCCTTCTTHHHHT
T ss_pred             HHhhchhHHhhhccCCCcceeeeHHhHhhhcHHHHHHHHHHHHHHhccCCCCcCCcchhhhhhccccCCCccccHHHHHH
Confidence            0   000000000011134699999999999999999999997532          11235777875322   3468999


Q ss_pred             ccc-EEEecCCCH-HHHHHHHHHHH-----------------------HHhCCCCCHHHHHHHHhhc----------cCc
Q 022641          205 RCA-KFRFKPLSE-EVMSSRVLHIC-----------------------NEEGLNLDAEALSTLSSIS----------QGD  249 (294)
Q Consensus       205 r~~-~i~~~~~~~-~~~~~~l~~~~-----------------------~~~~~~~~~~~l~~l~~~~----------~G~  249 (294)
                      ||. .+.+++|+. ++...++....                       ...++.+++++++++++..          +.+
T Consensus       172 RF~~~i~v~~p~~~ee~~~IL~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~v~v~d~v~e~i~~l~~~lr~~r~~~~iS  251 (500)
T 3nbx_X          172 RMLIRLWLDKVQDKANFRSMLTSQQDENDNPVPDALQVTDEEYERWQKEIGEITLPDHVFELIFMLRQQLDKLPDAPYVS  251 (500)
T ss_dssp             TCCEEEECCSCCCHHHHHHHHTCCCCTTSCCSCTTTSBCHHHHHHHHHHHTTCBCCHHHHHHHHHHHHHHHHCSSSCCCC
T ss_pred             HHHHHHHHHHhhhhhhHHHHHhcccccCCCCCCccceecHHHHHHHHhcCCcccCchHHHHHHHHHHHHhhcCCCCCccc
Confidence            987 588889887 66677775432                       1235678999999888765          457


Q ss_pred             HHHHHHHHHHHHHHh----CCCCChhhhhhhcccc
Q 022641          250 LRRAITYLQGAARLF----GSSITSKDLISVSGYP  280 (294)
Q Consensus       250 ~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~  280 (294)
                      +|.++.++..+...+    ...++.+|+. ++..+
T Consensus       252 ~R~~~~llr~A~A~A~l~gr~~Vt~eDv~-~a~~v  285 (500)
T 3nbx_X          252 DRRWKKAIRLLQASAFFSGRSAVAPVDLI-LLKDC  285 (500)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCSBCCGGGGG-GGGGT
T ss_pred             hhHHHHHHHHHHHHHhhcCCccccchHHH-HHHhh
Confidence            898777777655444    4568999998 55443

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=99.74  E-value=6.5e-18  Score=145.35  Aligned_cols=206  Identities=20%  Similarity=0.204  Sum_probs=135.1

Q ss_pred             hhcccHHHHHHHHHHHHc---------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc
Q 022641           62 DVAHQEEVVRVLTNTLET---------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG  126 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~---------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~  126 (294)
                      .++|++.+++.+...+..               ....+++|+||||||||++|+++++.+      +.+++.++++....
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~------~~~~~~~~~~~l~~   89 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLL------DVPFTMADATTLTE   89 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHT------TCCEEEEEHHHHTT
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHc------CCCEEEechHHhcc
Confidence            468999999988887731               133569999999999999999999998      67788777654322


Q ss_pred             hhH----HHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH--------------HHHHHHHHHHhhc-----
Q 022641          127 INV----VRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED--------------AQNALRRTMETYS-----  183 (294)
Q Consensus       127 ~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~--------------~~~~L~~~l~~~~-----  183 (294)
                      ...    ....+.........      ......+++|+|||++.++..              .++.|++.|+...     
T Consensus        90 ~~~~g~~~~~~~~~~~~~~~~------~~~~~~~~vl~lDEid~l~~~~~~~~~~~~~~~~~~~~~Ll~~leg~~~~~~~  163 (363)
T 3hws_A           90 AGYVGEDVENIIQKLLQKCDY------DVQKAQRGIVYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEGTVAAVPP  163 (363)
T ss_dssp             CHHHHHHHTHHHHHHHHHTTT------CHHHHHHCEEEEECHHHHCCCSSCC---CHHHHHHHHHHHHHHHHCC------
T ss_pred             cccccccHHHHHHHHHHHhhh------hHHhcCCcEEEEeChhhhcccccccccccccchHHHHHHHHHHhcCceeeccC
Confidence            111    11111221111100      000012359999999988754              8999999998210     


Q ss_pred             ----------------CcceEEEEecCC----------cc-----------------------------------cchHh
Q 022641          184 ----------------KVTRFFFICNYI----------SR-----------------------------------IIEPL  202 (294)
Q Consensus       184 ----------------~~~~ii~~~~~~----------~~-----------------------------------~~~~l  202 (294)
                                      .+..+|++++..          ..                                   +.++|
T Consensus       164 ~~~~~~~~~~~~~i~tsn~~~i~~g~~~~l~~~i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~~~~~~~l  243 (363)
T 3hws_A          164 QGGRKHPQQEFLQVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEF  243 (363)
T ss_dssp             ----------CCCCCTTSSEEEEEECCTTHHHHHHHHHCCCC------------CCSCHHHHHHTCCHHHHHHHTCCHHH
T ss_pred             ccccccCCCceEEEECCCceEEecCCcHHHHHHHHHhhhccccCCccccccccccchhhHHHHHhCCHHHHHHcCCCHHH
Confidence                            223345554431          01                                   57889


Q ss_pred             hcccc-EEEecCCCHHHHHHHHHH----HHH-------HhC--CCCCHHHHHHHHhh---ccCcHHHHHHHHHHHHHHh-
Q 022641          203 ASRCA-KFRFKPLSEEVMSSRVLH----ICN-------EEG--LNLDAEALSTLSSI---SQGDLRRAITYLQGAARLF-  264 (294)
Q Consensus       203 ~~r~~-~i~~~~~~~~~~~~~l~~----~~~-------~~~--~~~~~~~l~~l~~~---~~G~~r~~~~~l~~~~~~~-  264 (294)
                      .+|+. ++.|.|++.+++.+++..    ++.       ..+  +.+++++++.|++.   .+|+.|.+.+.++.+.... 
T Consensus       244 ~~R~~~~~~~~pl~~~~~~~I~~~~~~~l~~~~~~~~~~~~~~l~~~~~a~~~L~~~~~~~~~gaR~L~~~ie~~~~~~l  323 (363)
T 3hws_A          244 IGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTM  323 (363)
T ss_dssp             HTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTTTTHHHHHHHHHHHHH
T ss_pred             hcccCeeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHHHHHhhcCCccCchHHHHHHHHHHHHHH
Confidence            99998 566899999999888875    322       123  34799999999975   4677888888888766443 


Q ss_pred             -----C-C----CCChhhhhhhccc
Q 022641          265 -----G-S----SITSKDLISVSGY  279 (294)
Q Consensus       265 -----~-~----~it~~~v~~~~~~  279 (294)
                           . .    .||.++|+.....
T Consensus       324 ~~~~~~~~~~~~~I~~~~v~~~~~~  348 (363)
T 3hws_A          324 YDLPSMEDVEKVVIDESVIDGQSEP  348 (363)
T ss_dssp             HSTTTCCCSEEEECHHHHTTCCSCC
T ss_pred             HhcccccCCceeEEcHHHHhCcCCc
Confidence                 1 1    2666676665543

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=99.72  E-value=2.7e-17  Score=150.29  Aligned_cols=224  Identities=18%  Similarity=0.187  Sum_probs=149.6

Q ss_pred             hhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc-----
Q 022641           51 WVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR-----  125 (294)
Q Consensus        51 ~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~-----  125 (294)
                      ...+++|..+++++|++.+++.+...+..+.  +++|+||||||||++|++++..+.+...   ..+.+.+....     
T Consensus        31 ~~~~~rp~~l~~i~G~~~~l~~l~~~i~~g~--~vll~Gp~GtGKTtlar~ia~~l~~~~~---~~~~~~~~~~~~~~p~  105 (604)
T 3k1j_A           31 EEIEVPEKLIDQVIGQEHAVEVIKTAANQKR--HVLLIGEPGTGKSMLGQAMAELLPTETL---EDILVFPNPEDENMPR  105 (604)
T ss_dssp             GGSCCCSSHHHHCCSCHHHHHHHHHHHHTTC--CEEEECCTTSSHHHHHHHHHHTSCCSSC---EEEEEECCTTCTTSCE
T ss_pred             CcccccccccceEECchhhHhhccccccCCC--EEEEEeCCCCCHHHHHHHHhccCCcccC---CeEEEeCCcccccCCc
Confidence            3457889999999999999999999998775  8999999999999999999997743210   11111100000     


Q ss_pred             -------chhHHHHHHHH----------------------------------------------HHhhhcc-----cCc-
Q 022641          126 -------GINVVRTKIKT----------------------------------------------FAAVAVG-----SGQ-  146 (294)
Q Consensus       126 -------~~~~~~~~~~~----------------------------------------------~~~~~~~-----~~~-  146 (294)
                             ....+......                                              +......     .+. 
T Consensus       106 i~~~p~g~~~~~~e~~~~~~~~~~~~r~~~~~~~~~~~~~nl~v~~~~~~~~~~v~~~~~~~~~L~G~~~~~~~~~g~~~  185 (604)
T 3k1j_A          106 IKTVPACQGRRIVEKYREKAKSQESVKSSNMRLKSTVLVPKLLVDNCGRTKAPFIDATGAHAGALLGDVRHDPFQSGGLG  185 (604)
T ss_dssp             EEEEETTHHHHHHHHHHHHHHHHTCC-----------CCCEEEECCTTCSSCCEEECTTCCHHHHHCEECCCCC----CC
T ss_pred             EEEEecchHHHHHHHHHHhhccchhhhhhcccccccccccceeeccccCCCCCEEEcCCCCHHhcCceEEechhhcCCcc
Confidence                   00000000000                                              0000000     000 


Q ss_pred             -------cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc---------------------CcceEEEEecCC--c
Q 022641          147 -------RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS---------------------KVTRFFFICNYI--S  196 (294)
Q Consensus       147 -------~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~---------------------~~~~ii~~~~~~--~  196 (294)
                             ..+....+.+++|||||++.+++..++.|++.|++..                     ..+.+|+++|..  .
T Consensus       186 ~g~~~~i~~g~~~~a~~gvL~LDEi~~l~~~~q~~Ll~~Le~~~~~~~g~~~~~~~~~l~~~~~p~~~~vI~atn~~~~~  265 (604)
T 3k1j_A          186 TPAHERVEPGMIHRAHKGVLFIDEIATLSLKMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNLDTVD  265 (604)
T ss_dssp             CCGGGGEECCHHHHTTTSEEEETTGGGSCHHHHHHHHHHHHHSEECCBCSCTTSGGGGCBCSCEECCCEEEEEECHHHHH
T ss_pred             ccccccccCceeeecCCCEEEEechhhCCHHHHHHHHHHHHcCcEEecccccccccccCCCCccceeEEEEEecCHHHHh
Confidence                   0011112355699999999999999999999998432                     355688889875  5


Q ss_pred             ccchHhhcccc----EEEecC---CCHHHHHHHHHHHHHHhC-----CCCCHHHHHHHHhhc---cC-------cHHHHH
Q 022641          197 RIIEPLASRCA----KFRFKP---LSEEVMSSRVLHICNEEG-----LNLDAEALSTLSSIS---QG-------DLRRAI  254 (294)
Q Consensus       197 ~~~~~l~~r~~----~i~~~~---~~~~~~~~~l~~~~~~~~-----~~~~~~~l~~l~~~~---~G-------~~r~~~  254 (294)
                      .+.++|.+||.    .+.|++   ...+.+..+++.++...+     ..++++++..|++++   .|       ++|.+.
T Consensus       266 ~l~~~l~~R~~v~~i~i~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ls~eAl~~Li~~~~r~~g~r~~l~~~~R~l~  345 (604)
T 3k1j_A          266 KMHPALRSRIRGYGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEIVREAQKRAGRKGHLTLRLRDLG  345 (604)
T ss_dssp             HSCHHHHHHHHHHSEEEECCSEEECCHHHHHHHHHHHHHHHHHHCSSCCBBHHHHHHHHHHHHHTTCSTTEEECCHHHHH
T ss_pred             hcCHHHHHHhhccceEeeccccccCCHHHHHHHHHHHHHHHhhccCcccCCHHHHHHHHHHHhhhhccccccccCHHHHH
Confidence            68999999995    455543   245667777766655322     568999999999865   56       699999


Q ss_pred             HHHHHHHHHh----CCCCChhhhhhhccc
Q 022641          255 TYLQGAARLF----GSSITSKDLISVSGY  279 (294)
Q Consensus       255 ~~l~~~~~~~----~~~it~~~v~~~~~~  279 (294)
                      ++++.+...+    ...|+.+++.+++..
T Consensus       346 ~llr~A~~~A~~~~~~~I~~edv~~A~~~  374 (604)
T 3k1j_A          346 GIVRAAGDIAVKKGKKYVEREDVIEAVKM  374 (604)
T ss_dssp             HHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCcccccHHHHHHHHHh
Confidence            9999877665    456999999888743

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=99.72  E-value=1.4e-17  Score=157.83  Aligned_cols=201  Identities=22%  Similarity=0.277  Sum_probs=137.6

Q ss_pred             chhhcccHHHHHHHHHHHHcCC-------C--CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHH
Q 022641           60 VKDVAHQEEVVRVLTNTLETAN-------C--PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVV  130 (294)
Q Consensus        60 ~~~~~g~~~~~~~l~~~l~~~~-------~--~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~  130 (294)
                      +..++|++..+..+...+....       .  .+++|+||||||||++|+++++.+.+.   +.+++.++++........
T Consensus       557 ~~~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~~~---~~~~i~i~~~~~~~~~~~  633 (854)
T 1qvr_A          557 HKRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT---EEAMIRIDMTEYMEKHAV  633 (854)
T ss_dssp             HHHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSS---GGGEEEECTTTCCSSGGG
T ss_pred             hcccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCC---CCcEEEEechhccchhHH
Confidence            3568899999988888775431       1  259999999999999999999998543   346667776654332111


Q ss_pred             HHHHHHHHhh-hccc-CccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCC--
Q 022641          131 RTKIKTFAAV-AVGS-GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYI--  195 (294)
Q Consensus       131 ~~~~~~~~~~-~~~~-~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~--  195 (294)
                      ...+...... .... +..........+++|+|||++.+++..++.|++++++..           .++.+|++||..  
T Consensus       634 s~l~g~~~~~~G~~~~g~l~~~~~~~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~~~~  713 (854)
T 1qvr_A          634 SRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSP  713 (854)
T ss_dssp             GGC--------------CHHHHHHHCSSEEEEESSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHH
T ss_pred             HHHcCCCCCCcCccccchHHHHHHhCCCeEEEEecccccCHHHHHHHHHHhccCceECCCCCEeccCCeEEEEecCcChH
Confidence            1111000000 0000 000000001224699999999999999999999998653           245588888862  


Q ss_pred             ------------------------cccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHh---------CCCCCHHHHHH
Q 022641          196 ------------------------SRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEE---------GLNLDAEALST  241 (294)
Q Consensus       196 ------------------------~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~---------~~~~~~~~l~~  241 (294)
                                              ..+.++|.+|+. ++.|.|++.+++..++...+...         .+.+++++++.
T Consensus       714 ~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~Rl~~~i~~~pl~~edi~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~  793 (854)
T 1qvr_A          714 LILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDF  793 (854)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHTCSBCCBCCCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHH
T ss_pred             HHhhhcccccchHHHHHHHHHHHHhhCCHHHHHhcCeEEeCCCCCHHHHHHHHHHHHHHHHHHHHhCCceEEECHHHHHH
Confidence                                    234577889995 78899999999999998877531         24589999999


Q ss_pred             HHhhc---cCcHHHHHHHHHHHHHH
Q 022641          242 LSSIS---QGDLRRAITYLQGAARL  263 (294)
Q Consensus       242 l~~~~---~G~~r~~~~~l~~~~~~  263 (294)
                      |++++   .|++|.+.++++.+...
T Consensus       794 L~~~~~~~~gn~R~L~~~i~~~~~~  818 (854)
T 1qvr_A          794 LAERGYDPVFGARPLRRVIQRELET  818 (854)
T ss_dssp             HHHHHCBTTTBTSTHHHHHHHHTHH
T ss_pred             HHHcCCCCCCChHHHHHHHHHHHHH
Confidence            99975   59999999998876544

>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=99.72  E-value=1.6e-16  Score=138.90  Aligned_cols=230  Identities=17%  Similarity=0.196  Sum_probs=145.4

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHH-Hc---C---CCCcEEE--ECCCCCCHHHHHHHHHHHhcCCC---ccCCc
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTL-ET---A---NCPHMLF--YGPPGTGKTTTALAIAHQLFGPE---LYKSR  115 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l-~~---~---~~~~ill--~Gp~G~GKT~la~~la~~~~~~~---~~~~~  115 (294)
                      ..++...+.|   ..++|++..+..|..++ ..   +   ....++|  +||+|+|||++++.+++.+....   ..+..
T Consensus        12 ~~~~~~~~~p---~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~   88 (412)
T 1w5s_A           12 RRVFDENYIP---PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVK   88 (412)
T ss_dssp             GGGGSTTCCC---SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEE
T ss_pred             HhhcCCccCC---CCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCcee
Confidence            3344445555   67899999888888877 42   2   3446888  99999999999999998873210   01234


Q ss_pred             ceeecCCCCcchh-HHHHHHHHHHhhhcccCccCCC---------CCCCCcEEEEEeCCCCCC------HHHHHHHHHHH
Q 022641          116 VLELNASDDRGIN-VVRTKIKTFAAVAVGSGQRRGG---------YPCPPYKIIILDEADSMT------EDAQNALRRTM  179 (294)
Q Consensus       116 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~lliiDei~~l~------~~~~~~L~~~l  179 (294)
                      ++.+++....... .+...+..+.......+.....         ....++.+|+|||+|.+.      ...+..|+..+
T Consensus        89 ~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~  168 (412)
T 1w5s_A           89 QAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVH  168 (412)
T ss_dssp             EEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHH
Confidence            4555543222222 2222211110000000000000         001345699999999974      35566667777


Q ss_pred             Hhhc-----CcceEEEEecCCc---ccc---hHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCC--CCCHHHHHHHHhh
Q 022641          180 ETYS-----KVTRFFFICNYIS---RII---EPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGL--NLDAEALSTLSSI  245 (294)
Q Consensus       180 ~~~~-----~~~~ii~~~~~~~---~~~---~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~--~~~~~~l~~l~~~  245 (294)
                      ....     .++.+|++++.+.   .+.   +.+.+++. .+.++|++.++..+++...+...+.  .++++++..+++.
T Consensus       169 ~~~~~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~  248 (412)
T 1w5s_A          169 EEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDV  248 (412)
T ss_dssp             HHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHH
T ss_pred             HhcccCCCCceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHH
Confidence            6544     4566777776543   222   44555554 5999999999999999888765433  4789999999999


Q ss_pred             cc------CcHHHHHHHHHHHHHHh----CCCCChhhhhhhcccc
Q 022641          246 SQ------GDLRRAITYLQGAARLF----GSSITSKDLISVSGYP  280 (294)
Q Consensus       246 ~~------G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~  280 (294)
                      ++      |++|.+..++..+...+    ...++.+++..++...
T Consensus       249 ~~~~~~~~G~p~~~~~l~~~a~~~a~~~~~~~i~~~~v~~~~~~~  293 (412)
T 1w5s_A          249 YGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSEN  293 (412)
T ss_dssp             HCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC
T ss_pred             HHHhccCCCcHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            99      99999999998766543    3458888887766543

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.68  E-value=6.2e-18  Score=153.53  Aligned_cols=215  Identities=17%  Similarity=0.096  Sum_probs=134.8

Q ss_pred             CCcchhhcccHHHHHHHHHHHHcCCCC-----------cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLETANCP-----------HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~~~~~~-----------~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      ..-...++|++.++..+...+..+...           +++|+||||||||++|+++++.+....+..  ....++....
T Consensus       291 ~~l~~~I~G~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~~~~r~~~~~--~~~~~~~~l~  368 (595)
T 3f9v_A          291 SSIAPSIYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISRVAPRAVYTT--GKGSTAAGLT  368 (595)
T ss_dssp             HHTSSTTSCCHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSSTTCSCEECCC--TTCSTTTTSE
T ss_pred             HhhcchhcChHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHHHHHHHHhCCCceecC--CCcccccccc
Confidence            333457889999988887777665311           799999999999999999998762111000  0001111110


Q ss_pred             chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-------------CcceEEEEe
Q 022641          126 GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-------------KVTRFFFIC  192 (294)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-------------~~~~ii~~~  192 (294)
                      . ......      .........+....+.+++|+|||++.+++..++.|++.|++..             ..+.+|.++
T Consensus       369 ~-~~~~~~------~~g~~~~~~G~l~~A~~gil~IDEid~l~~~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaat  441 (595)
T 3f9v_A          369 A-AVVREK------GTGEYYLEAGALVLADGGIAVIDEIDKMRDEDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAG  441 (595)
T ss_dssp             E-ECSSGG------GTSSCSEEECHHHHHSSSEECCTTTTCCCSHHHHHHHHHHHSSSEEEESSSSEEEECCCCEEEEEE
T ss_pred             c-eeeecc------ccccccccCCeeEecCCCcEEeehhhhCCHhHhhhhHHHHhCCEEEEecCCcEEEecCceEEEEEc
Confidence            0 000000      00000000111111234699999999999999999999998533             355688888


Q ss_pred             cCCc-------------ccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHh-------------------------CCC
Q 022641          193 NYIS-------------RIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEE-------------------------GLN  233 (294)
Q Consensus       193 ~~~~-------------~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~-------------------------~~~  233 (294)
                      |...             .+++++++||. .+.+.+++..+...+.++++..+                         ...
T Consensus       442 Np~~G~~~~~~~~~~ni~l~~aLl~RFDl~~~~~~~~~~e~~~i~~~il~~~~~~~~~~~l~~~~l~~~i~~ar~~~~p~  521 (595)
T 3f9v_A          442 NPKFGRYISERPVSDNINLPPTILSRFDLIFILKDQPGEQDRELANYILDVHSGKSTKNIIDIDTLRKYIAYARKYVTPK  521 (595)
T ss_dssp             CCTTCCSCTTSCSCTTTCSCSSSGGGCSCCEEECCTTHHHHHHHHHHHHTTTCCCSSSSTTCCTTTHHHHHHHHHHHCCC
T ss_pred             CCcCCccCcccCchhccCCCHHHHhhCeEEEEeCCCCCHHHHHHHHHHHHHhhccccccCCCHHHHHHHHHHHHHhCCCC
Confidence            8765             78899999995 44454544443555555544322                         225


Q ss_pred             CCHHHHHHHHhh---------------ccCcHHHHHHHHHHHHHHh----CCCCChhhhhhhcccc
Q 022641          234 LDAEALSTLSSI---------------SQGDLRRAITYLQGAARLF----GSSITSKDLISVSGYP  280 (294)
Q Consensus       234 ~~~~~l~~l~~~---------------~~G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~  280 (294)
                      +++++.+.|.+.               .++++|.+..++..+...+    +..++.+|+..++...
T Consensus       522 ls~ea~~~l~~~y~~lR~~~~~~~~~~~~~s~R~l~~lirla~a~A~l~~~~~V~~~dv~~Ai~l~  587 (595)
T 3f9v_A          522 ITSEAKNLITDFFVEMRKKSSETPDSPILITPRQLEALIRISEAYAKMALKAEVTREDAERAINIM  587 (595)
T ss_dssp             CCCCTHHHHHHHHTTSSCSCCBCSSSCBCSSTTTTTHHHHHHHHHHHTTSSCCSSHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHhhccCCCccccccHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHHH
Confidence            666666666665               4678999888888766555    5679999999887643

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.67  E-value=4.3e-16  Score=116.15  Aligned_cols=132  Identities=17%  Similarity=0.178  Sum_probs=92.5

Q ss_pred             hhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHh
Q 022641           62 DVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAA  139 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  139 (294)
                      +++|+...+..+...+..  ....+++|+||||||||++|+++++....   .+.+++ +++............+...  
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~~~---~~~~~v-~~~~~~~~~~~~~~~~~~a--   75 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGRN---AQGEFV-YRELTPDNAPQLNDFIALA--   75 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSSTT---TTSCCE-EEECCTTTSSCHHHHHHHH--
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhCCc---cCCCEE-EECCCCCcchhhhcHHHHc--
Confidence            567888888777776643  34457999999999999999999886522   134566 7666543332222222211  


Q ss_pred             hhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCc-------ccchHhhcccc--EEE
Q 022641          140 VAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYIS-------RIIEPLASRCA--KFR  210 (294)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~-------~~~~~l~~r~~--~i~  210 (294)
                                     ..++|+|||++.++...+..|+..+...+....+|++||.+.       .+.+.+..|+.  .|.
T Consensus        76 ---------------~~g~l~ldei~~l~~~~q~~Ll~~l~~~~~~~~~I~~t~~~~~~~~~~~~~~~~L~~rl~~~~i~  140 (145)
T 3n70_A           76 ---------------QGGTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDTSLVELAASNHIIAELYYCFAMTQIA  140 (145)
T ss_dssp             ---------------TTSCEEEECGGGSCHHHHHHHHHHHHSSSCSSCEEEEESSCHHHHHHHSCCCHHHHHHHHHHEEE
T ss_pred             ---------------CCcEEEEcChHHCCHHHHHHHHHHHhhcCCCEEEEEECCcCHHHHHHcCCCCHHHHHHhcCCEEe
Confidence                           124899999999999999999999988777888999998653       34566777765  677


Q ss_pred             ecCC
Q 022641          211 FKPL  214 (294)
Q Consensus       211 ~~~~  214 (294)
                      ++|+
T Consensus       141 lPpL  144 (145)
T 3n70_A          141 CLPL  144 (145)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7775

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

Probab=99.65  E-value=2.8e-15  Score=124.95  Aligned_cols=150  Identities=13%  Similarity=0.177  Sum_probs=97.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc------hhHHHHHHHHHHhhhcccCccCCCCCCCCc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPY  156 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (294)
                      ..++|+||||||||++|+++++++      +.+++.++++....      ...+...+........          ...+
T Consensus        37 ~~lLl~GppGtGKT~la~aiA~~l------~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~----------~~~~  100 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQCELVFRKM------GINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIR----------KGNM  100 (293)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHH------TCCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHHT----------TSSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh------CCCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHHh----------cCCC
Confidence            358999999999999999999999      77888887644322      1122222222211100          1224


Q ss_pred             EEEEEeCCCCCCH-------------HHHHHHHHHHHh-------------hcCcceEEEEecCCcccchHhhc--cccE
Q 022641          157 KIIILDEADSMTE-------------DAQNALRRTMET-------------YSKVTRFFFICNYISRIIEPLAS--RCAK  208 (294)
Q Consensus       157 ~lliiDei~~l~~-------------~~~~~L~~~l~~-------------~~~~~~ii~~~~~~~~~~~~l~~--r~~~  208 (294)
                      .+|+|||+|.+..             ..++.|+++++.             ....+.+|+|||.+..+++++++  ||..
T Consensus       101 ~vl~iDEiD~~~~~~~~~~~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~R~d~  180 (293)
T 3t15_A          101 CCLFINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEK  180 (293)
T ss_dssp             CCEEEECCC--------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCCC--CHHHHHHHEEE
T ss_pred             eEEEEechhhhcCCCCCCccccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcccCCHHHhCCCCCce
Confidence            5999999998754             234778888762             12457799999999999999986  7764


Q ss_pred             EEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhh-ccCcHH
Q 022641          209 FRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSI-SQGDLR  251 (294)
Q Consensus       209 i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~-~~G~~r  251 (294)
                      +.+ .|+.+++.++++.++...+  ++.+.+..+... ++.++.
T Consensus       181 ~i~-~P~~~~r~~Il~~~~~~~~--~~~~~l~~~~~~~~~~~l~  221 (293)
T 3t15_A          181 FYW-APTREDRIGVCTGIFRTDN--VPAEDVVKIVDNFPGQSID  221 (293)
T ss_dssp             EEE-CCCHHHHHHHHHHHHGGGC--CCHHHHHHHHHHSCSCCHH
T ss_pred             eEe-CcCHHHHHHHHHHhccCCC--CCHHHHHHHhCCCCcccHH
Confidence            333 4599999999998887554  556666665554 455554

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

Probab=99.64  E-value=1.4e-14  Score=125.72  Aligned_cols=128  Identities=17%  Similarity=0.198  Sum_probs=88.9

Q ss_pred             CcEEEEEeCCCCCCH------------HHHHHHHHHHHhh----------cCcceEEEEe----cCCcccchHhhccccE
Q 022641          155 PYKIIILDEADSMTE------------DAQNALRRTMETY----------SKVTRFFFIC----NYISRIIEPLASRCAK  208 (294)
Q Consensus       155 ~~~lliiDei~~l~~------------~~~~~L~~~l~~~----------~~~~~ii~~~----~~~~~~~~~l~~r~~~  208 (294)
                      .+.++++||+|.+..            ..++.|+++++..          ..++.+|+++    +.+..+.++|++|+.+
T Consensus       250 ~~~il~~DEidki~~~~~~~~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dlipel~~R~~i  329 (444)
T 1g41_A          250 QNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLPI  329 (444)
T ss_dssp             HHCEEEEETGGGGSCCSSCSSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHTTCCE
T ss_pred             cCCeeeHHHHHHHhhccCCCCCCchHHHHHHHHHHHhcccccccccceecCCcEEEEeccccccCChhhcchHHhcccce
Confidence            356999999998842            2677999999852          2345566666    2444566899999995


Q ss_pred             -EEecCCCHHHHHHHHHH-----------HHHHhCC--CCCHHHHHHHHhh--------ccCcHHHHHHHHHHHHHHh--
Q 022641          209 -FRFKPLSEEVMSSRVLH-----------ICNEEGL--NLDAEALSTLSSI--------SQGDLRRAITYLQGAARLF--  264 (294)
Q Consensus       209 -i~~~~~~~~~~~~~l~~-----------~~~~~~~--~~~~~~l~~l~~~--------~~G~~r~~~~~l~~~~~~~--  264 (294)
                       +.|++++.++...++..           .+..++.  .++++++..|++.        -++..|.+.+.++.+....  
T Consensus       330 ~i~l~~lt~~e~~~Il~~~~~~l~~q~~~~~~~~~~~l~~~~~al~~i~~~a~~~~~~t~~~GaR~L~~~ie~~~~~~~~  409 (444)
T 1g41_A          330 RVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLMDKISF  409 (444)
T ss_dssp             EEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHH
T ss_pred             eeeCCCCCHHHHHHHHHHHHHhHHHHHHHHhcccCceEEECHHHHHHHHHHHHHhccCCccCCchHHHHHHHHHHHHHHh
Confidence             89999999999999831           2222343  4899999999985        2456677666666544322  


Q ss_pred             ---C---C--CCChhhhhhhcccccC
Q 022641          265 ---G---S--SITSKDLISVSGYPTG  282 (294)
Q Consensus       265 ---~---~--~it~~~v~~~~~~~~~  282 (294)
                         +   .  .||.+.+...++....
T Consensus       410 ~~~~~~~~~~~i~~~~v~~~l~~~~~  435 (444)
T 1g41_A          410 SASDMNGQTVNIDAAYVADALGEVVE  435 (444)
T ss_dssp             HGGGCTTCEEEECHHHHHHHHTTTTT
T ss_pred             hccccCCCeEEEeHHHHHHhcCcccc
Confidence               1   1  3888888888776543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.62  E-value=8.8e-16  Score=114.18  Aligned_cols=128  Identities=13%  Similarity=0.129  Sum_probs=87.7

Q ss_pred             hhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHh
Q 022641           62 DVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAA  139 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  139 (294)
                      +++|+...+..+.+.+..  ....+++|+||||||||++|+++++..      . +++.+++....... ....+..   
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~------~-~~~~~~~~~~~~~~-~~~~~~~---   73 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNG------T-PWVSPARVEYLIDM-PMELLQK---   73 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTT------S-CEECCSSTTHHHHC-HHHHHHH---
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhC------C-CeEEechhhCChHh-hhhHHHh---
Confidence            567887777777776643  344579999999999999999998765      2 67777776532211 1111111   


Q ss_pred             hhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-CcceEEEEecCCc-c----cchHhhcccc--EEEe
Q 022641          140 VAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-KVTRFFFICNYIS-R----IIEPLASRCA--KFRF  211 (294)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~~-~----~~~~l~~r~~--~i~~  211 (294)
                                    .+.++|+|||++.++...+..|++.++... ..+++|++||... .    +.+.+..|+.  .|.+
T Consensus        74 --------------a~~~~l~lDei~~l~~~~q~~Ll~~l~~~~~~~~~iI~~tn~~~~~~~~~~~~~L~~rl~~~~i~l  139 (143)
T 3co5_A           74 --------------AEGGVLYVGDIAQYSRNIQTGITFIIGKAERCRVRVIASCSYAAGSDGISCEEKLAGLFSESVVRI  139 (143)
T ss_dssp             --------------TTTSEEEEEECTTCCHHHHHHHHHHHHHHTTTTCEEEEEEEECTTTC--CHHHHHHHHSSSEEEEE
T ss_pred             --------------CCCCeEEEeChHHCCHHHHHHHHHHHHhCCCCCEEEEEecCCCHHHHHhCccHHHHHHhcCcEEeC
Confidence                          112499999999999999999999998764 4577888887542 2    4456677765  5777


Q ss_pred             cCC
Q 022641          212 KPL  214 (294)
Q Consensus       212 ~~~  214 (294)
                      +|+
T Consensus       140 PpL  142 (143)
T 3co5_A          140 PPL  142 (143)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=99.61  E-value=1.5e-14  Score=125.01  Aligned_cols=211  Identities=19%  Similarity=0.215  Sum_probs=139.9

Q ss_pred             hhhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHH
Q 022641           61 KDVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFA  138 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  138 (294)
                      ..++|....+..+.+.+..  ....+++|+|++||||+++|+.+.....   ....+++.+++..... ..+...+-...
T Consensus       137 ~~~ig~s~~m~~l~~~i~~~a~~~~~vli~Ge~GtGK~~lAr~ih~~s~---r~~~~fv~v~~~~~~~-~~~~~elfg~~  212 (387)
T 1ny5_A          137 EEYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSD---RSKEPFVALNVASIPR-DIFEAELFGYE  212 (387)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHST---TTTSCEEEEETTTSCH-HHHHHHHHCBC
T ss_pred             hhhhhccHHhhHHHHHHHHhcCCCCCeEEecCCCcCHHHHHHHHHHhcC---CCCCCeEEEecCCCCH-HHHHHHhcCCC
Confidence            4567776666666555543  2223599999999999999999987642   2346788888886532 22221111110


Q ss_pred             hhhc-cc-CccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-------cc
Q 022641          139 AVAV-GS-GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-------RI  198 (294)
Q Consensus       139 ~~~~-~~-~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-------~~  198 (294)
                      .... +. ....+....+..+.|+|||++.++...+..|++.+++..           ..+++|++||...       ..
T Consensus       213 ~g~~tga~~~~~g~~~~a~~gtlfldei~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~l~~~~~~g~f  292 (387)
T 1ny5_A          213 KGAFTGAVSSKEGFFELADGGTLFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKF  292 (387)
T ss_dssp             TTSSTTCCSCBCCHHHHTTTSEEEEESGGGCCHHHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSCHHHHHHTTSS
T ss_pred             CCCCCCcccccCCceeeCCCcEEEEcChhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCCCCHHHHHHcCCc
Confidence            0000 00 011111223456799999999999999999999998632           3567888888642       24


Q ss_pred             chHhhcccc--EEEecCCCH--HHHHHHHHHHHH----HhCC---CCCHHHHHHHHhh-ccCcHHHHHHHHHHHHHHh-C
Q 022641          199 IEPLASRCA--KFRFKPLSE--EVMSSRVLHICN----EEGL---NLDAEALSTLSSI-SQGDLRRAITYLQGAARLF-G  265 (294)
Q Consensus       199 ~~~l~~r~~--~i~~~~~~~--~~~~~~l~~~~~----~~~~---~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~~-~  265 (294)
                      .+.+..|+.  .+.++|+..  +++..++.+.+.    +.+.   .+++++++.+..+ +.||+|++.+.++.++... +
T Consensus       293 r~dl~~rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~l~~~~wpGNvreL~~~i~~~~~~~~~  372 (387)
T 1ny5_A          293 REDLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELKNVIERAVLFSEG  372 (387)
T ss_dssp             CHHHHHHHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHHHHSCCTTHHHHHHHHHHHHHHHCCS
T ss_pred             cHHHHHhhcCCeecCCcchhccccHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHHhCCC
Confidence            556667765  577777754  666666655543    3343   3799999999987 5999999999999998876 4


Q ss_pred             CCCChhhhhh
Q 022641          266 SSITSKDLIS  275 (294)
Q Consensus       266 ~~it~~~v~~  275 (294)
                      ..|+.+++..
T Consensus       373 ~~i~~~~l~~  382 (387)
T 1ny5_A          373 KFIDRGELSC  382 (387)
T ss_dssp             SEECHHHHHH
T ss_pred             CcCcHHHCcH
Confidence            4588777754

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=99.59  E-value=1.5e-14  Score=124.05  Aligned_cols=199  Identities=18%  Similarity=0.166  Sum_probs=131.8

Q ss_pred             hhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHh
Q 022641           62 DVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAA  139 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  139 (294)
                      .++|.......+...+..  .....++++|++||||+.+|+++.......    ..++.+++............+.....
T Consensus       130 ~~ig~s~~~~~~~~~~~~~a~~~~~vli~GesGtGKe~lAr~ih~~s~r~----~~fv~vnc~~~~~~~~~~~lfg~~~g  205 (368)
T 3dzd_A          130 EFVGEHPKILEIKRLIPKIAKSKAPVLITGESGTGKEIVARLIHRYSGRK----GAFVDLNCASIPQELAESELFGHEKG  205 (368)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHTSCSCEEEECCTTSSHHHHHHHHHHHHCCC----SCEEEEESSSSCTTTHHHHHHEECSC
T ss_pred             cccccchHHHHHHhhhhhhhccchhheEEeCCCchHHHHHHHHHHhcccc----CCcEEEEcccCChHHHHHHhcCcccc
Confidence            466776665555544432  223459999999999999999998776221    22888888875432221111111000


Q ss_pred             hhccc-CccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-------ccch
Q 022641          140 VAVGS-GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-------RIIE  200 (294)
Q Consensus       140 ~~~~~-~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-------~~~~  200 (294)
                      ...+. ..+.+....+..+.|+|||++.++...+..|++.+++..           ..+++|.+||...       ...+
T Consensus       206 ~~tga~~~~~g~~~~a~~gtlfldei~~l~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~l~~~v~~g~fr~  285 (368)
T 3dzd_A          206 AFTGALTRKKGKLELADQGTLFLDEVGELDQRVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNKNLEEEIKKGNFRE  285 (368)
T ss_dssp             SSSSCCCCEECHHHHTTTSEEEEETGGGSCHHHHHHHHHHHHHSEECCBTCCCBEECCCEEEEEESSCHHHHHHTTSSCH
T ss_pred             ccCCcccccCChHhhcCCCeEEecChhhCCHHHHHHHHHHHHhCCcccCCCCcceeeeeEEEEecCCCHHHHHHcCCccH
Confidence            00000 001111122455799999999999999999999998643           2466888887542       2445


Q ss_pred             Hhhcccc--EEEecCCCH--HHHHHHHHHHHHH----hC---CCCCHHHHHHHHhhc-cCcHHHHHHHHHHHHHHh
Q 022641          201 PLASRCA--KFRFKPLSE--EVMSSRVLHICNE----EG---LNLDAEALSTLSSIS-QGDLRRAITYLQGAARLF  264 (294)
Q Consensus       201 ~l~~r~~--~i~~~~~~~--~~~~~~l~~~~~~----~~---~~~~~~~l~~l~~~~-~G~~r~~~~~l~~~~~~~  264 (294)
                      .+..|+.  .|.++|+..  +++..++.+.+.+    .+   ..+++++++.|..+. +||+|++.|.++.++...
T Consensus       286 dL~~rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpGNvreL~n~i~~~~~~~  361 (368)
T 3dzd_A          286 DLYYRLSVFQIYLPPLRERGKDVILLAEYFLKKFAKEYKKNCFELSEETKEYLMKQEWKGNVRELKNLIERAVILC  361 (368)
T ss_dssp             HHHHHHTSEEEECCCGGGSTTHHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHTCCCTTHHHHHHHHHHHHHHTC
T ss_pred             HHHHHhCCeEEeCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhCCCCcHHHHHHHHHHHHHHhC
Confidence            6778877  577888876  6777666665543    33   348999999999985 999999999999988765

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.58  E-value=1.5e-13  Score=117.31  Aligned_cols=189  Identities=14%  Similarity=0.157  Sum_probs=120.5

Q ss_pred             cchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc------chhHHHH
Q 022641           59 QVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR------GINVVRT  132 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~  132 (294)
                      ....++|++..+..|..++..+  +.++|+||+|+|||++++.+++..      +  ++.+++....      +...+..
T Consensus        10 ~~~~~~gR~~el~~L~~~l~~~--~~v~i~G~~G~GKT~Ll~~~~~~~------~--~~~~~~~~~~~~~~~~~~~~~~~   79 (350)
T 2qen_A           10 RREDIFDREEESRKLEESLENY--PLTLLLGIRRVGKSSLLRAFLNER------P--GILIDCRELYAERGHITREELIK   79 (350)
T ss_dssp             SGGGSCSCHHHHHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHHHHS------S--EEEEEHHHHHHTTTCBCHHHHHH
T ss_pred             ChHhcCChHHHHHHHHHHHhcC--CeEEEECCCcCCHHHHHHHHHHHc------C--cEEEEeecccccccCCCHHHHHH
Confidence            4467899999999999998875  589999999999999999999875      2  3333322110      1111111


Q ss_pred             HHHH-HHh------h--------hcccCccCCCC----------C-CCCcEEEEEeCCCCCCH-------HHHHHHHHHH
Q 022641          133 KIKT-FAA------V--------AVGSGQRRGGY----------P-CPPYKIIILDEADSMTE-------DAQNALRRTM  179 (294)
Q Consensus       133 ~~~~-~~~------~--------~~~~~~~~~~~----------~-~~~~~lliiDei~~l~~-------~~~~~L~~~l  179 (294)
                      .+.. +..      .        ...........          . ..++.+|+|||+|.+..       .....|...+
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            1111 000      0        00000000000          0 00256999999999753       4455555555


Q ss_pred             HhhcCcceEEEEecCCccc---------chHhhccc-cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCc
Q 022641          180 ETYSKVTRFFFICNYISRI---------IEPLASRC-AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGD  249 (294)
Q Consensus       180 ~~~~~~~~ii~~~~~~~~~---------~~~l~~r~-~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~  249 (294)
                      +.. .+..+|+++.....+         ...+..|. ..+.+.|++.++..+++...+...+..++++.+..+++.++|+
T Consensus       160 ~~~-~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~~~~~~~~i~~~tgG~  238 (350)
T 2qen_A          160 DSL-PNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNLDVPENEIEEAVELLDGI  238 (350)
T ss_dssp             HHC-TTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHTTC
T ss_pred             Hhc-CCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCC
Confidence            543 466777777543211         11233354 4899999999999999998887778889999999999999999


Q ss_pred             HHHHHHHHH
Q 022641          250 LRRAITYLQ  258 (294)
Q Consensus       250 ~r~~~~~l~  258 (294)
                      |..+..+..
T Consensus       239 P~~l~~~~~  247 (350)
T 2qen_A          239 PGWLVVFGV  247 (350)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            986655443

>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=99.48  E-value=6.8e-14  Score=108.16  Aligned_cols=134  Identities=13%  Similarity=0.190  Sum_probs=79.7

Q ss_pred             hhcCCCcchhhcc----cHHHHHHHHHHHHcC---CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           53 EKYRPKQVKDVAH----QEEVVRVLTNTLETA---NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        53 ~~~~~~~~~~~~g----~~~~~~~l~~~l~~~---~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      ++|++.+|+++++    ++.++..+..++...   ...+++|+||+|+||||++++++..+....  +..++.++.    
T Consensus         2 ~r~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~--g~~~~~~~~----   75 (180)
T 3ec2_A            2 KRYWNANLDTYHPKNVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKK--GIRGYFFDT----   75 (180)
T ss_dssp             CSCTTCCSSSCCCCSHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHS--CCCCCEEEH----
T ss_pred             chhhhCccccccCCCHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHc--CCeEEEEEH----
Confidence            4678888888875    455556666666542   245699999999999999999999873111  112222221    


Q ss_pred             chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCC--CCCHHHHHHHHHHHHhhc-CcceEEEEecCCcc
Q 022641          126 GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEAD--SMTEDAQNALRRTMETYS-KVTRFFFICNYISR  197 (294)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~--~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~~~  197 (294)
                        ..+...+.........   ........+.++|+|||++  .+++.....|..+++... ....+|++||....
T Consensus        76 --~~~~~~~~~~~~~~~~---~~~~~~~~~~~llilDE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~~~~  145 (180)
T 3ec2_A           76 --KDLIFRLKHLMDEGKD---TKFLKTVLNSPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNYSLQ  145 (180)
T ss_dssp             --HHHHHHHHHHHHHTCC---SHHHHHHHTCSEEEEETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCCCSC
T ss_pred             --HHHHHHHHHHhcCchH---HHHHHHhcCCCEEEEeCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCCChh
Confidence              1111111111100000   0000001134699999998  567777788888887654 55678888887653

>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=99.47  E-value=1.2e-12  Score=112.00  Aligned_cols=188  Identities=17%  Similarity=0.141  Sum_probs=116.4

Q ss_pred             cchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC-----cchhHHHHH
Q 022641           59 QVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD-----RGINVVRTK  133 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~  133 (294)
                      ....++|++..+..|.. +..   +.++|+||+|+|||++++.+++.+      ...++.+++...     .+.......
T Consensus        11 ~~~~~~gR~~el~~L~~-l~~---~~v~i~G~~G~GKT~L~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (357)
T 2fna_A           11 NRKDFFDREKEIEKLKG-LRA---PITLVLGLRRTGKSSIIKIGINEL------NLPYIYLDLRKFEERNYISYKDFLLE   80 (357)
T ss_dssp             SGGGSCCCHHHHHHHHH-TCS---SEEEEEESTTSSHHHHHHHHHHHH------TCCEEEEEGGGGTTCSCCCHHHHHHH
T ss_pred             CHHHhcChHHHHHHHHH-hcC---CcEEEECCCCCCHHHHHHHHHHhc------CCCEEEEEchhhccccCCCHHHHHHH
Confidence            34678999999999988 765   589999999999999999999987      223344443321     121111111


Q ss_pred             HHHHHhh-----------hc-------cc-Ccc------CCCC---------CCC-CcEEEEEeCCCCCCH----HHHHH
Q 022641          134 IKTFAAV-----------AV-------GS-GQR------RGGY---------PCP-PYKIIILDEADSMTE----DAQNA  174 (294)
Q Consensus       134 ~~~~~~~-----------~~-------~~-~~~------~~~~---------~~~-~~~lliiDei~~l~~----~~~~~  174 (294)
                      +......           ..       .. ...      ....         ... ++.+|+|||+|.+..    .....
T Consensus        81 l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~vlvlDe~~~~~~~~~~~~~~~  160 (357)
T 2fna_A           81 LQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPA  160 (357)
T ss_dssp             HHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHH
T ss_pred             HHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCCCCeEEEEECHHHhhccCchhHHHH
Confidence            1111100           00       00 000      0000         001 367999999999753    33444


Q ss_pred             HHHHHHhhcCcceEEEEecCCccc---------chHhhccc-cEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHh
Q 022641          175 LRRTMETYSKVTRFFFICNYISRI---------IEPLASRC-AKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSS  244 (294)
Q Consensus       175 L~~~l~~~~~~~~ii~~~~~~~~~---------~~~l~~r~-~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~  244 (294)
                      |....+.. ....+|++++....+         ...+..|+ ..+.+.|++.++..+++...+...+...++.  ..+++
T Consensus       161 l~~~~~~~-~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~--~~i~~  237 (357)
T 2fna_A          161 LAYAYDNL-KRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDY--EVVYE  237 (357)
T ss_dssp             HHHHHHHC-TTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCCH--HHHHH
T ss_pred             HHHHHHcC-CCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCCCCcH--HHHHH
Confidence            54454442 466788887653211         11244454 5899999999999999998887667766554  88899


Q ss_pred             hccCcHHHHHHHHHH
Q 022641          245 ISQGDLRRAITYLQG  259 (294)
Q Consensus       245 ~~~G~~r~~~~~l~~  259 (294)
                      .++|+|..+..++..
T Consensus       238 ~t~G~P~~l~~~~~~  252 (357)
T 2fna_A          238 KIGGIPGWLTYFGFI  252 (357)
T ss_dssp             HHCSCHHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHHH
Confidence            999999876655443

>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family; helicase, MCM homolog, DNA replication, ATP-binding, DNA-binding; 1.90A {Methanopyrus kandleri AV19}

Probab=99.41  E-value=1.1e-12  Score=113.22  Aligned_cols=215  Identities=14%  Similarity=0.070  Sum_probs=133.6

Q ss_pred             hhcCCCcchhhcccHHHHHHHHHHHHcCC-----CCcEEEECCCCCCHHHHHHHH-HHHhcCCCccCCcceeecCCCCcc
Q 022641           53 EKYRPKQVKDVAHQEEVVRVLTNTLETAN-----CPHMLFYGPPGTGKTTTALAI-AHQLFGPELYKSRVLELNASDDRG  126 (294)
Q Consensus        53 ~~~~~~~~~~~~g~~~~~~~l~~~l~~~~-----~~~ill~Gp~G~GKT~la~~l-a~~~~~~~~~~~~~~~~~~~~~~~  126 (294)
                      +.+...-.. +.|++.++..+.-.+..+.     .-|++|.|+||| ||.+|+.+ ++.+       ........ ...+
T Consensus       206 ~~l~~sIap-I~G~e~vK~aLll~L~GG~~k~rgdihVLL~G~PGt-KS~Lar~i~~~i~-------pR~~ft~g-~~ss  275 (506)
T 3f8t_A          206 TTFARAIAP-LPGAEEVGKMLALQLFSCVGKNSERLHVLLAGYPVV-CSEILHHVLDHLA-------PRGVYVDL-RRTE  275 (506)
T ss_dssp             HHHHHHHCC-STTCHHHHHHHHHHHTTCCSSGGGCCCEEEESCHHH-HHHHHHHHHHHTC-------SSEEEEEG-GGCC
T ss_pred             HHHHHHhcc-cCCCHHHHHHHHHHHcCCccccCCceeEEEECCCCh-HHHHHHHHHHHhC-------CCeEEecC-CCCC
Confidence            344333334 8899998888887776653     126999999999 99999999 5543       11111111 0001


Q ss_pred             hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh---------cCcceEEEEecCCc-
Q 022641          127 INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY---------SKVTRFFFICNYIS-  196 (294)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~---------~~~~~ii~~~~~~~-  196 (294)
                      ...+   ...... ..+.....+....+..++|+|||++.+++..+..|++.|++.         +..+.+|.++|... 
T Consensus       276 ~~gL---t~s~r~-~tG~~~~~G~l~LAdgGvl~lDEIn~~~~~~qsaLlEaMEe~~VtI~G~~lparf~VIAA~NP~~~  351 (506)
T 3f8t_A          276 LTDL---TAVLKE-DRGWALRAGAAVLADGGILAVDHLEGAPEPHRWALMEAMDKGTVTVDGIALNARCAVLAAINPGEQ  351 (506)
T ss_dssp             HHHH---SEEEEE-SSSEEEEECHHHHTTTSEEEEECCTTCCHHHHHHHHHHHHHSEEEETTEEEECCCEEEEEECCCC-
T ss_pred             ccCc---eEEEEc-CCCcccCCCeeEEcCCCeeehHhhhhCCHHHHHHHHHHHhCCcEEECCEEcCCCeEEEEEeCcccc
Confidence            0000   000000 001111223333455679999999999999999999999963         46677888888753 


Q ss_pred             ----------ccchHhhccccEEE--ec-------------CCCHHHHHHHHHHHH-HHhCCCCCHHHHHHHHhhc----
Q 022641          197 ----------RIIEPLASRCAKFR--FK-------------PLSEEVMSSRVLHIC-NEEGLNLDAEALSTLSSIS----  246 (294)
Q Consensus       197 ----------~~~~~l~~r~~~i~--~~-------------~~~~~~~~~~l~~~~-~~~~~~~~~~~l~~l~~~~----  246 (294)
                                .++.++++||..+.  +.             .++.+++++++...- ..-.+.+++++.++|.+..    
T Consensus       352 yd~~~s~~~~~Lp~alLDRFDLi~i~~d~pd~e~d~e~~~~~ls~e~L~~yi~~ar~~~~~p~ls~ea~~yI~~~y~~tR  431 (506)
T 3f8t_A          352 WPSDPPIARIDLDQDFLSHFDLIAFLGVDPRPGEPEEQDTEVPSYTLLRRYLLYAIREHPAPELTEEARKRLEHWYETRR  431 (506)
T ss_dssp             -CCSCGGGGCCSCHHHHTTCSEEEETTC--------------CCHHHHHHHHHHHHHHCSCCEECHHHHHHHHHHHHHHH
T ss_pred             cCCCCCccccCCChHHhhheeeEEEecCCCChhHhhcccCCCCCHHHHHHHHHHHHhcCCCceeCHHHHHHHHHHHHHHh
Confidence                      68889999996332  22             234455555554333 1225678898877776531    


Q ss_pred             --------------cCcHHHHHHHHHHHHHHh----CCCCChhhhhhhccccc
Q 022641          247 --------------QGDLRRAITYLQGAARLF----GSSITSKDLISVSGYPT  281 (294)
Q Consensus       247 --------------~G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~~~  281 (294)
                                    +-.+|.+..++..+-..+    +..++.+|+..++.-..
T Consensus       432 ~~~~~~~~~~~~~~giSpR~leaLiRlA~A~A~L~gR~~V~~eDV~~Ai~L~~  484 (506)
T 3f8t_A          432 EEVEERLGMGLPTLPVTRRQLESVERLAKAHARMRLSDDVEPEDVDIAAELVD  484 (506)
T ss_dssp             HHHHHHHHTTCCCCCCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHH
T ss_pred             cCcccccccccccccccHHHHHHHHHHHHHHHHHcCcCCCCHHHHHHHHHHHH
Confidence                          235677777766555444    56799999998876543

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=99.35  E-value=9.7e-13  Score=98.13  Aligned_cols=112  Identities=17%  Similarity=0.251  Sum_probs=74.2

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccC
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSG  145 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (294)
                      +..++..+..+    ....++|+||+|+|||+++++++..+...   +..++.++..+....        .+        
T Consensus        24 n~~~~~~l~~~----~g~~~~l~G~~G~GKTtL~~~i~~~~~~~---g~~~~~~~~~~~~~~--------~~--------   80 (149)
T 2kjq_A           24 NAELVYVLRHK----HGQFIYVWGEEGAGKSHLLQAWVAQALEA---GKNAAYIDAASMPLT--------DA--------   80 (149)
T ss_dssp             THHHHHHCCCC----CCSEEEEESSSTTTTCHHHHHHHHHHHTT---TCCEEEEETTTSCCC--------GG--------
T ss_pred             cHHHHHHHHhc----CCCEEEEECCCCCCHHHHHHHHHHHHHhc---CCcEEEEcHHHhhHH--------HH--------
Confidence            34444444333    44579999999999999999999988432   334555555443322        00        


Q ss_pred             ccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCc-ce-EEEEecCCcc-c--chHhhcccc
Q 022641          146 QRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKV-TR-FFFICNYISR-I--IEPLASRCA  207 (294)
Q Consensus       146 ~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~-~~-ii~~~~~~~~-~--~~~l~~r~~  207 (294)
                             ..+.++|+|||++.+....++.|+.+++..... .. +|++++.+.. +  .+.+.+|+.
T Consensus        81 -------~~~~~lLilDE~~~~~~~~~~~l~~li~~~~~~g~~~iiits~~~p~~l~~~~~L~SRl~  140 (149)
T 2kjq_A           81 -------AFEAEYLAVDQVEKLGNEEQALLFSIFNRFRNSGKGFLLLGSEYTPQQLVIREDLRTRMA  140 (149)
T ss_dssp             -------GGGCSEEEEESTTCCCSHHHHHHHHHHHHHHHHTCCEEEEEESSCTTTSSCCHHHHHHGG
T ss_pred             -------HhCCCEEEEeCccccChHHHHHHHHHHHHHHHcCCcEEEEECCCCHHHccccHHHHHHHh
Confidence                   012359999999999876688888888765543 33 7788875322 1  288899886

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=99.32  E-value=2.4e-12  Score=107.76  Aligned_cols=132  Identities=17%  Similarity=0.222  Sum_probs=71.4

Q ss_pred             hhhcCCCcchhhccc----HHHHHHHHHHHHcC---CCCcEEEECCCCCCHHHHHHHHHHHhc-CCCccCCcceeecCCC
Q 022641           52 VEKYRPKQVKDVAHQ----EEVVRVLTNTLETA---NCPHMLFYGPPGTGKTTTALAIAHQLF-GPELYKSRVLELNASD  123 (294)
Q Consensus        52 ~~~~~~~~~~~~~g~----~~~~~~l~~~l~~~---~~~~ill~Gp~G~GKT~la~~la~~~~-~~~~~~~~~~~~~~~~  123 (294)
                      .+.+.+.+|+++.+.    ..+...+..++...   ...+++|+||||||||++|.++++.+. ..   +..+..++.+.
T Consensus       115 ~~~~~~~tfd~f~~~~~~~~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~---g~~v~~~~~~~  191 (308)
T 2qgz_A          115 PKSYRHIHLSDIDVNNASRMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKK---GVSTTLLHFPS  191 (308)
T ss_dssp             CGGGGSCCGGGSCCCSHHHHHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHS---CCCEEEEEHHH
T ss_pred             CHHHHhCCHhhCcCCChHHHHHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHHHHhc---CCcEEEEEHHH
Confidence            345667788888752    33455666777653   245799999999999999999999884 22   12333332211


Q ss_pred             CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH--HHH-HHHHHHHhh-cCcceEEEEecCC
Q 022641          124 DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED--AQN-ALRRTMETY-SKVTRFFFICNYI  195 (294)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~--~~~-~L~~~l~~~-~~~~~ii~~~~~~  195 (294)
                               .+..+.................+.++|||||++..+..  .++ .|..+++.. .....+|++||.+
T Consensus       192 ---------l~~~l~~~~~~~~~~~~~~~~~~~~lLiiDdig~~~~~~~~~~~ll~~ll~~r~~~~~~~IitSN~~  258 (308)
T 2qgz_A          192 ---------FAIDVKNAISNGSVKEEIDAVKNVPVLILDDIGAEQATSWVRDEVLQVILQYRMLEELPTFFTSNYS  258 (308)
T ss_dssp             ---------HHHHHHCCCC----CCTTHHHHTSSEEEEETCCC------CTTTTHHHHHHHHHHHTCCEEEEESSC
T ss_pred             ---------HHHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCCCCCHHHHHHHHHHHHHHHHHCCCcEEEECCCC
Confidence                     11111110000000000000123459999999765432  233 333466654 3456789999854

>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=99.28  E-value=1.7e-11  Score=125.93  Aligned_cols=151  Identities=17%  Similarity=0.133  Sum_probs=101.5

Q ss_pred             HHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcc-cCccCCCC
Q 022641           73 LTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVG-SGQRRGGY  151 (294)
Q Consensus        73 l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~  151 (294)
                      +..++..+  .+++|+||||||||++|+.+....     .+..+..++.+...+...+...+......... .+..-+..
T Consensus      1260 l~~~l~~~--~~vLL~GPpGtGKT~la~~~l~~~-----~~~~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~~~~P~ 1332 (2695)
T 4akg_A         1260 FYDLLNSK--RGIILCGPPGSGKTMIMNNALRNS-----SLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPK 1332 (2695)
T ss_dssp             HHHHHHHT--CEEEEECSTTSSHHHHHHHHHHSC-----SSCEEEEEECCTTCCHHHHHHHHHHHBCCEEETTTEEEEEB
T ss_pred             HHHHHHCC--CeEEEECCCCCCHHHHHHHHHhcC-----CCCceEEEEeecCCCHHHHHHHHHHHhhhccccCCccccCC
Confidence            34444444  379999999999999996665543     14566677777776665555544443221100 00000001


Q ss_pred             CCCCcEEEEEeCCCCCCH------HHHHHHHHHHHhhc------------CcceEEEEecCC-----cccchHhhccccE
Q 022641          152 PCPPYKIIILDEADSMTE------DAQNALRRTMETYS------------KVTRFFFICNYI-----SRIIEPLASRCAK  208 (294)
Q Consensus       152 ~~~~~~lliiDei~~l~~------~~~~~L~~~l~~~~------------~~~~ii~~~~~~-----~~~~~~l~~r~~~  208 (294)
                      ..+++.||+|||++....      ...+.|.+.++...            .++.+|.++|++     ..+++++.+||.+
T Consensus      1333 ~~gk~~VlFiDEinmp~~d~yg~q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllRrf~v 1412 (2695)
T 4akg_A         1333 SDIKNLVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAI 1412 (2695)
T ss_dssp             SSSSCEEEEEETTTCSCCCSSSCCHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHTTEEE
T ss_pred             CCCceEEEEecccccccccccCchhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhheeeE
Confidence            134567999999876432      36788888887422            235678888887     4689999999999


Q ss_pred             EEecCCCHHHHHHHHHHHHHHh
Q 022641          209 FRFKPLSEEVMSSRVLHICNEE  230 (294)
Q Consensus       209 i~~~~~~~~~~~~~l~~~~~~~  230 (294)
                      +.+++|+.+.+..|+..++...
T Consensus      1413 i~i~~P~~~~l~~I~~~il~~~ 1434 (2695)
T 4akg_A         1413 LYLGYPSGKSLSQIYEIYYKAI 1434 (2695)
T ss_dssp             EECCCCTTTHHHHHHHHHHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHHHHH
Confidence            9999999999999999888643

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=99.26  E-value=3.5e-12  Score=100.30  Aligned_cols=133  Identities=14%  Similarity=0.131  Sum_probs=72.0

Q ss_pred             hhhhcCCCcchhhccc----HHHHHHHHHHHHcCC----CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           51 WVEKYRPKQVKDVAHQ----EEVVRVLTNTLETAN----CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        51 ~~~~~~~~~~~~~~g~----~~~~~~l~~~l~~~~----~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      +.+++.+.+|+++++.    ..++..+..++....    ..+++|+||+|||||++++++++.+...   +..++.+++.
T Consensus        15 ~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~---~~~~~~~~~~   91 (202)
T 2w58_A           15 MPREILRASLSDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKR---NVSSLIVYVP   91 (202)
T ss_dssp             SCGGGGCCCTTSSCCSSHHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTT---TCCEEEEEHH
T ss_pred             CCHHHHcCCHhhccCCChhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEEhH
Confidence            3456777888888863    235566677776542    1579999999999999999999988432   2233333322


Q ss_pred             CCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH--HHHHHH-HHHHhh-cCcceEEEEecCC
Q 022641          123 DDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED--AQNALR-RTMETY-SKVTRFFFICNYI  195 (294)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~--~~~~L~-~~l~~~-~~~~~ii~~~~~~  195 (294)
                      .      +...+.....   ............+.++|+|||++.....  .+..++ .+++.. .....+|++||..
T Consensus        92 ~------~~~~~~~~~~---~~~~~~~~~~~~~~~~lilDei~~~~~~~~~~~~ll~~~l~~~~~~~~~~i~tsn~~  159 (202)
T 2w58_A           92 E------LFRELKHSLQ---DQTMNEKLDYIKKVPVLMLDDLGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNFD  159 (202)
T ss_dssp             H------HHHHHHHC------CCCHHHHHHHHHSSEEEEEEECCC---CCGGGTTHHHHHHHHHHTTCCEEEEESSC
T ss_pred             H------HHHHHHHHhc---cchHHHHHHHhcCCCEEEEcCCCCCcCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCC
Confidence            1      0000000000   0000000000001249999999876433  233233 455544 3556788888854

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=99.21  E-value=1.1e-10  Score=94.17  Aligned_cols=134  Identities=18%  Similarity=0.232  Sum_probs=85.4

Q ss_pred             HHHHHHHHcC-CC-CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccC
Q 022641           71 RVLTNTLETA-NC-PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRR  148 (294)
Q Consensus        71 ~~l~~~l~~~-~~-~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (294)
                      ..+..|+... .. ..++|+||||||||+++.++++.+.      . .-.++..+.           .+....       
T Consensus        91 ~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~~~------l-~G~vn~~~~-----------~f~l~~-------  145 (267)
T 1u0j_A           91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVP------F-YGCVNWTNE-----------NFPFND-------  145 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHSS------C-EEECCTTCS-----------SCTTGG-------
T ss_pred             HHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhhhc------c-cceeecccc-----------cccccc-------
Confidence            4566677654 32 3499999999999999999999751      1 111121110           000000       


Q ss_pred             CCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHH--------hhc-----CcceEEEEecCC-----------cccchHhhc
Q 022641          149 GGYPCPPYKIIILDEADSMTEDAQNALRRTME--------TYS-----KVTRFFFICNYI-----------SRIIEPLAS  204 (294)
Q Consensus       149 ~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~--------~~~-----~~~~ii~~~~~~-----------~~~~~~l~~  204 (294)
                          .....+++.||..... +..+.+..+++        ...     ....+|++||..           ....+.|.+
T Consensus       146 ----~~~k~i~l~Ee~~~~~-d~~~~lr~i~~G~~~~id~K~k~~~~v~~tPvIitsN~~i~~~~~g~~~s~~~~~~L~s  220 (267)
T 1u0j_A          146 ----CVDKMVIWWEEGKMTA-KVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQD  220 (267)
T ss_dssp             ----GSSCSEEEECSCCEET-TTHHHHHHHHTTCCEEC------CCEECCCCEEEEESSCTTCEEETTEEECTTHHHHHT
T ss_pred             ----ccccEEEEeccccchh-HHHHHHHHHhCCCcEEEecCcCCcccccCCCEEEEecCCcccccccCccchhhhHHHhh
Confidence                0112377777776654 44556777776        222     456789999862           134578999


Q ss_pred             cccEEEec--------CCCHHHHHHHHHHHHHHhCCCCC
Q 022641          205 RCAKFRFK--------PLSEEVMSSRVLHICNEEGLNLD  235 (294)
Q Consensus       205 r~~~i~~~--------~~~~~~~~~~l~~~~~~~~~~~~  235 (294)
                      |+..+.|.        +++.++++.++... +.+..+++
T Consensus       221 R~~~f~F~~~~p~~~~~lt~~~~~~f~~w~-~~~~~~~~  258 (267)
T 1u0j_A          221 RMFKFELTRRLDHDFGKVTKQEVKDFFRWA-KDHVVEVE  258 (267)
T ss_dssp             TEEEEECCSCCCTTSCCCCHHHHHHHHHHH-HHTCCCCC
T ss_pred             hEEEEECCCcCCcccCCCCHHHHHHHHHHH-HHcCCCCc
Confidence            99999998        89999999999844 66666554

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=99.17  E-value=9.2e-11  Score=90.47  Aligned_cols=133  Identities=17%  Similarity=0.237  Sum_probs=79.2

Q ss_pred             HHHHHHHHHHHcCCC-CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCc
Q 022641           68 EVVRVLTNTLETANC-PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQ  146 (294)
Q Consensus        68 ~~~~~l~~~l~~~~~-~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (294)
                      ..+..+..++..... .+++|+||||||||++|.++++.+.      ..++.+..+.. ..  .       .. .     
T Consensus        43 ~f~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a~ala~~l~------g~i~~fans~s-~f--~-------l~-~-----  100 (212)
T 1tue_A           43 TFLGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQ------GAVISFVNSTS-HF--W-------LE-P-----  100 (212)
T ss_dssp             HHHHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHT------CEECCCCCSSS-CG--G-------GG-G-----
T ss_pred             HHHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhC------CCeeeEEeccc-hh--h-------hc-c-----
Confidence            345666666664322 3599999999999999999999882      22222111100 00  0       00 0     


Q ss_pred             cCCCCCCCCcEEEEEeCCCCCCHHH-HHHHHHHHHhhc-------------CcceEEEEecCC---cccchHhhccccEE
Q 022641          147 RRGGYPCPPYKIIILDEADSMTEDA-QNALRRTMETYS-------------KVTRFFFICNYI---SRIIEPLASRCAKF  209 (294)
Q Consensus       147 ~~~~~~~~~~~lliiDei~~l~~~~-~~~L~~~l~~~~-------------~~~~ii~~~~~~---~~~~~~l~~r~~~i  209 (294)
                            ..+..+++|||++.-.... ...+..+++..+             ....+|+|||..   ....+.+.+|+..+
T Consensus       101 ------l~~~kIiiLDEad~~~~~~~d~~lrn~ldG~~~~iD~Khr~~~~~~~~PlIITtN~~~~~~~~~~~L~SRi~~f  174 (212)
T 1tue_A          101 ------LTDTKVAMLDDATTTCWTYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLESRITVF  174 (212)
T ss_dssp             ------GTTCSSEEEEEECHHHHHHHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHTSCEEE
T ss_pred             ------cCCCCEEEEECCCchhHHHHHHHHHHHhCCCcccHHHhhcCccccCCCCEEEecCCCcccccchhhhhhhEEEE
Confidence                  0112499999998532222 235666666532             134699999974   33456899999988


Q ss_pred             EecC-------------CCHHHHHHHHHHHHH
Q 022641          210 RFKP-------------LSEEVMSSRVLHICN  228 (294)
Q Consensus       210 ~~~~-------------~~~~~~~~~l~~~~~  228 (294)
                      .|+.             ++....+.++++...
T Consensus       175 ~F~~~~p~~~~g~p~~~~~~~~wk~ff~~~~~  206 (212)
T 1tue_A          175 EFPNAFPFDKNGNPVYEINDKNWKCFFERTWS  206 (212)
T ss_dssp             ECCSCCCBCTTSCBSCCCCHHHHHHHHHHHTG
T ss_pred             EcCCCCCCCCCCCeeEEeCcchHHHHHHHHHH
Confidence            7762             234566666665553

>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=99.17  E-value=3e-09  Score=109.65  Aligned_cols=169  Identities=22%  Similarity=0.250  Sum_probs=120.2

Q ss_pred             HHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCcc
Q 022641           68 EVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQR  147 (294)
Q Consensus        68 ~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (294)
                      +....+..++..+.  ..++.||+|||||++++.+|+.+      +..++.+++++......+...+..+....      
T Consensus       633 r~~~tl~~Al~~~~--~~~l~GpaGtGKTe~vk~LA~~l------g~~~v~~nc~e~ld~~~lg~~~~g~~~~G------  698 (2695)
T 4akg_A          633 IGFATLTDSLHQKY--GGCFFGPAGTGKTETVKAFGQNL------GRVVVVFNCDDSFDYQVLSRLLVGITQIG------  698 (2695)
T ss_dssp             HHHHHHHHHHHTTC--EEEEECCTTSCHHHHHHHHHHTT------TCCCEEEETTSSCCHHHHHHHHHHHHHHT------
T ss_pred             HHHHHHHHHHHhCC--CCcccCCCCCCcHHHHHHHHHHh------CCcEEEEECCCCCChhHhhHHHHHHHhcC------
Confidence            33345555565554  58999999999999999999999      89999999999888877766665555432      


Q ss_pred             CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHH-------hh-------------cCcceEEEEecC----CcccchHhh
Q 022641          148 RGGYPCPPYKIIILDEADSMTEDAQNALRRTME-------TY-------------SKVTRFFFICNY----ISRIIEPLA  203 (294)
Q Consensus       148 ~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~-------~~-------------~~~~~ii~~~~~----~~~~~~~l~  203 (294)
                               ..+++||+++++++.+..+.+.+.       ..             ...+.+++|.|+    ...+++++.
T Consensus       699 ---------aw~~~DE~nr~~~evLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy~g~~eLP~~Lk  769 (2695)
T 4akg_A          699 ---------AWGCFDEFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLK  769 (2695)
T ss_dssp             ---------CEEEEETTTSSCHHHHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCSSSSCCCCHHHH
T ss_pred             ---------CEeeehhhhhcChHHHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCccCcccccHHHH
Confidence                     389999999999987777643332       21             234557777774    346899999


Q ss_pred             ccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHh-------h------ccCcHHHHHHHHHHHHH
Q 022641          204 SRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSS-------I------SQGDLRRAITYLQGAAR  262 (294)
Q Consensus       204 ~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~-------~------~~G~~r~~~~~l~~~~~  262 (294)
                      +||..+.+..|+.+.+.+++..   ..|....+.....++.       .      .+..+|.+..+|..+..
T Consensus       770 ~~Fr~v~m~~Pd~~~i~ei~l~---s~Gf~~a~~la~kiv~~~~l~~e~ls~q~hydfglRalksvL~~ag~  838 (2695)
T 4akg_A          770 KSFREFSMKSPQSGTIAEMILQ---IMGFEDSKSLASKIVHFLELLSSKCSSMNHYHFGLRTLKGVLRNCSP  838 (2695)
T ss_dssp             TTEEEEECCCCCHHHHHHHHHH---HHHCSSHHHHHHHHHHHHHHHHHHSCCCTTCCCSHHHHHHHHHHHHH
T ss_pred             hheEEEEeeCCCHHHHHHHHHH---hcCCCchHHHHHHHHHHHHHHHHHhCcCCcccccHHHHHHHHHHHHH
Confidence            9999999999999888887643   3455444444433332       1      12367777777765543

>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=99.15  E-value=6.6e-11  Score=104.67  Aligned_cols=142  Identities=15%  Similarity=0.180  Sum_probs=80.1

Q ss_pred             cCCchhhhhcCCCcchhhc-ccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC
Q 022641           46 QSSQPWVEKYRPKQVKDVA-HQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD  124 (294)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~-g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~  124 (294)
                      ..+.||.++|+|..++++. +|..++..+..++..+.. +++|.|+||||||+++..++..+.....  ..++.+ +...
T Consensus         9 ~~~~~~~~~~~p~~~~~Ln~~Q~~av~~~~~~i~~~~~-~~li~G~aGTGKT~ll~~~~~~l~~~~~--~~il~~-a~T~   84 (459)
T 3upu_A            9 HHSSGLVPRGSHMTFDDLTEGQKNAFNIVMKAIKEKKH-HVTINGPAGTGATTLTKFIIEALISTGE--TGIILA-APTH   84 (459)
T ss_dssp             ------------CCSSCCCHHHHHHHHHHHHHHHSSSC-EEEEECCTTSCHHHHHHHHHHHHHHTTC--CCEEEE-ESSH
T ss_pred             CccCCCccccCCCccccCCHHHHHHHHHHHHHHhcCCC-EEEEEeCCCCCHHHHHHHHHHHHHhcCC--ceEEEe-cCcH
Confidence            4567999999999999987 788888888888877653 8999999999999999999998854322  122222 2222


Q ss_pred             cchhHHHHHH-------HHHHhhhcccCc------cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEE
Q 022641          125 RGINVVRTKI-------KTFAAVAVGSGQ------RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFI  191 (294)
Q Consensus       125 ~~~~~~~~~~-------~~~~~~~~~~~~------~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~  191 (294)
                      .....+...+       ..+.........      ........+.++|+|||++.++...+..|+..+.   ....++++
T Consensus        85 ~Aa~~l~~~~~~~~~T~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiDE~~~~~~~~~~~l~~~~~---~~~~~~~v  161 (459)
T 3upu_A           85 AAKKILSKLSGKEASTIHSILKINPVTYEENVLFEQKEVPDLAKCRVLICDEVSMYDRKLFKILLSTIP---PWCTIIGI  161 (459)
T ss_dssp             HHHHHHHHHHSSCEEEHHHHHTEEEEECSSCEEEEECSCCCCSSCSEEEESCGGGCCHHHHHHHHHHSC---TTCEEEEE
T ss_pred             HHHHHHHhhhccchhhHHHHhccCcccccccchhcccccccccCCCEEEEECchhCCHHHHHHHHHhcc---CCCEEEEE
Confidence            2222222111       011110000000      0111223456799999999999888887777653   45567777


Q ss_pred             ecC
Q 022641          192 CNY  194 (294)
Q Consensus       192 ~~~  194 (294)
                      +..
T Consensus       162 GD~  164 (459)
T 3upu_A          162 GDN  164 (459)
T ss_dssp             ECT
T ss_pred             CCH
Confidence            744

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=99.05  E-value=1.6e-09  Score=112.45  Aligned_cols=150  Identities=15%  Similarity=0.152  Sum_probs=101.3

Q ss_pred             HHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhccc--CccCCC
Q 022641           73 LTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGS--GQRRGG  150 (294)
Q Consensus        73 l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~  150 (294)
                      +..++..+.  +++|+||+|||||.++..+...+.     +..++.++.+.......+...+..........  +...+.
T Consensus      1297 l~~ll~~~~--pvLL~GptGtGKT~li~~~L~~l~-----~~~~~~infS~~Tta~~l~~~~e~~~e~~~~~~~G~~~~p 1369 (3245)
T 3vkg_A         1297 LHAWLSEHR--PLILCGPPGSGKTMTLTSTLRAFP-----DFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRP 1369 (3245)
T ss_dssp             HHHHHHTTC--CCEEESSTTSSHHHHHHHHGGGCT-----TEEEEEECCCTTCCHHHHHHHHHHHEEEEECTTSCEEEEE
T ss_pred             HHHHHHCCC--cEEEECCCCCCHHHHHHHHHHhCC-----CCceEEEEeeCCCCHHHHHHHHhhcceEEeccCCCcccCC
Confidence            344455444  699999999999998876654441     34567788888777666655554322211110  100000


Q ss_pred             CCCCCcEEEEEeCCCCCCH------HHHHHHHHHHHhhc------------CcceEEEEecCC-----cccchHhhcccc
Q 022641          151 YPCPPYKIIILDEADSMTE------DAQNALRRTMETYS------------KVTRFFFICNYI-----SRIIEPLASRCA  207 (294)
Q Consensus       151 ~~~~~~~lliiDei~~l~~------~~~~~L~~~l~~~~------------~~~~ii~~~~~~-----~~~~~~l~~r~~  207 (294)
                      ...++..|++|||++.-..      ...+.|.++++...            .++.+|.++|++     ..+.+++.+||.
T Consensus      1370 ~~~Gk~~VlFiDDiNmp~~D~yGtQ~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp~~gGr~~l~~Rf~r~F~ 1449 (3245)
T 3vkg_A         1370 TQLGKWLVVFCDEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLRHAP 1449 (3245)
T ss_dssp             SSTTCEEEEEETTTTCCCCCTTSCCHHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECCTTSTTCCCCCHHHHTTCC
T ss_pred             CcCCceEEEEecccCCCCccccccccHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCCCCCCCccCCHHHHhhce
Confidence            1125567999999987543      37888999988532            234577788876     358899999999


Q ss_pred             EEEecCCCHHHHHHHHHHHHHH
Q 022641          208 KFRFKPLSEEVMSSRVLHICNE  229 (294)
Q Consensus       208 ~i~~~~~~~~~~~~~l~~~~~~  229 (294)
                      ++.++.|+.+.+..|+..++..
T Consensus      1450 vi~i~~ps~esL~~If~til~~ 1471 (3245)
T 3vkg_A         1450 ILLVDFPSTSSLTQIYGTFNRA 1471 (3245)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHH
T ss_pred             EEEeCCCCHHHHHHHHHHHHHH
Confidence            9999999999999998776653

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.04  E-value=8.8e-09  Score=94.07  Aligned_cols=194  Identities=11%  Similarity=0.028  Sum_probs=107.5

Q ss_pred             CCCcchhhcccHHHHHHHHHHHHc--CCCCcEEEECCCCCCHHHHHHHHHHHhcC-CCccCCcceeecCCCCcchhHHHH
Q 022641           56 RPKQVKDVAHQEEVVRVLTNTLET--ANCPHMLFYGPPGTGKTTTALAIAHQLFG-PELYKSRVLELNASDDRGINVVRT  132 (294)
Q Consensus        56 ~~~~~~~~~g~~~~~~~l~~~l~~--~~~~~ill~Gp~G~GKT~la~~la~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  132 (294)
                      -|.....++|++..+..|..++..  +..+.++|+||+|+|||++|..+++.... ...+...++.++.+.. ....+..
T Consensus       119 ~P~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~  197 (591)
T 1z6t_A          119 VPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLM  197 (591)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHH
T ss_pred             CCCCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHH
Confidence            355667899999999999999974  23345999999999999999998743200 0001111222222221 1111111


Q ss_pred             HHHHHHhhhcc-cC--ccCCCC-------------CCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          133 KIKTFAAVAVG-SG--QRRGGY-------------PCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       133 ~~~~~~~~~~~-~~--~~~~~~-------------~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                      .+..+...... ..  ......             ...++-+|||||++..  .       .++.......+|+||+...
T Consensus       198 ~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~--~-------~l~~l~~~~~ilvTsR~~~  268 (591)
T 1z6t_A          198 KLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS--W-------VLKAFDSQCQILLTTRDKS  268 (591)
T ss_dssp             HHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCH--H-------HHHTTCSSCEEEEEESCGG
T ss_pred             HHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCH--H-------HHHHhcCCCeEEEECCCcH
Confidence            12111111100 00  000000             0013569999999762  1       2334466778888887654


Q ss_pred             ccchHhhccccEEE-ecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHH
Q 022641          197 RIIEPLASRCAKFR-FKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA  261 (294)
Q Consensus       197 ~~~~~l~~r~~~i~-~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~  261 (294)
                      ... ........+. +.+++.++..+++...+... ..-.++....|++.|+|.|-.+..+...+.
T Consensus       269 ~~~-~~~~~~~~v~~l~~L~~~ea~~L~~~~~~~~-~~~~~~~~~~i~~~~~G~PLal~~~a~~l~  332 (591)
T 1z6t_A          269 VTD-SVMGPKYVVPVESSLGKEKGLEILSLFVNMK-KADLPEQAHSIIKECKGSPLVVSLIGALLR  332 (591)
T ss_dssp             GGT-TCCSCEEEEECCSSCCHHHHHHHHHHHHTSC-GGGSCTHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHH-hcCCCceEeecCCCCCHHHHHHHHHHHhCCC-cccccHHHHHHHHHhCCCcHHHHHHHHHHh
Confidence            211 1111111222 25899999999998776321 111246788899999999877665555443

>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=98.95  E-value=1.1e-08  Score=92.39  Aligned_cols=182  Identities=11%  Similarity=0.083  Sum_probs=102.6

Q ss_pred             cccHHHHHHHHHHHHcC---CCCcEEEECCCCCCHHHHHHHHHH---HhcCCCccCCcceeecCCCCc--ch-hHHHHHH
Q 022641           64 AHQEEVVRVLTNTLETA---NCPHMLFYGPPGTGKTTTALAIAH---QLFGPELYKSRVLELNASDDR--GI-NVVRTKI  134 (294)
Q Consensus        64 ~g~~~~~~~l~~~l~~~---~~~~ill~Gp~G~GKT~la~~la~---~~~~~~~~~~~~~~~~~~~~~--~~-~~~~~~~  134 (294)
                      +|++..+..|.+++...   ..+.+.|+|+.|+|||+||..+++   ......+....++  +.+...  +. ......+
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv--~vs~~~~~~~~~~~~~il  208 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWL--KDSGTAPKSTFDLFTDIL  208 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEE--ECCCCSTTHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEE--EECCCCCCCHHHHHHHHH
Confidence            49999999999998655   334589999999999999999997   2222222222222  333321  11 2222222


Q ss_pred             HHHHhhhc-ccCccCCC------------CCCCC-cEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccch
Q 022641          135 KTFAAVAV-GSGQRRGG------------YPCPP-YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIE  200 (294)
Q Consensus       135 ~~~~~~~~-~~~~~~~~------------~~~~~-~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~  200 (294)
                      ..+..... ........            ....+ +-+||||+++....  . .+.    . .....||+||+...- ..
T Consensus       209 ~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~--~-~~~----~-~~gs~ilvTTR~~~v-~~  279 (549)
T 2a5y_B          209 LMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEET--I-RWA----Q-ELRLRCLVTTRDVEI-SN  279 (549)
T ss_dssp             HHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHH--H-HHH----H-HTTCEEEEEESBGGG-GG
T ss_pred             HHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchh--h-ccc----c-cCCCEEEEEcCCHHH-HH
Confidence            22211100 00000000            11233 78999999988421  1 111    1 155678888875431 11


Q ss_pred             HhhccccEEEecCCCHHHHHHHHHHHHHHhCC-CCCHHHHHHHHhhccCcHHHHHHH
Q 022641          201 PLASRCAKFRFKPLSEEVMSSRVLHICNEEGL-NLDAEALSTLSSISQGDLRRAITY  256 (294)
Q Consensus       201 ~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~-~~~~~~l~~l~~~~~G~~r~~~~~  256 (294)
                      ........+.+.+++.++..+++.+.+..... .-.++....|++.|+|.|=.+..+
T Consensus       280 ~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~GlPLAl~~~  336 (549)
T 2a5y_B          280 AASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMF  336 (549)
T ss_dssp             GCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HcCCCCeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHhCCChHHHHHH
Confidence            11112246999999999999999766421111 111345778999999988665544

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.87  E-value=2.6e-07  Score=96.32  Aligned_cols=168  Identities=20%  Similarity=0.217  Sum_probs=119.7

Q ss_pred             HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCC
Q 022641           71 RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGG  150 (294)
Q Consensus        71 ~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (294)
                      ..|..++....  ...+.||+|||||.+++.+|+.+      +..++.++|++......+...+..+....         
T Consensus       595 ~tl~~Al~~~~--gg~~~GPaGtGKTet~k~La~~l------gr~~~vfnC~~~~d~~~~g~i~~G~~~~G---------  657 (3245)
T 3vkg_A          595 LTLTQALESRM--GGNPFGPAGTGKTETVKALGSQL------GRFVLVFCCDEGFDLQAMSRIFVGLCQCG---------  657 (3245)
T ss_dssp             HHHHHHHHTTC--EEEEECSTTSSHHHHHHHHHHHT------TCCEEEEECSSCCCHHHHHHHHHHHHHHT---------
T ss_pred             HHHHHHHHhcC--CCCCCCCCCCCHHHHHHHHHHHh------CCeEEEEeCCCCCCHHHHHHHHhhHhhcC---------
Confidence            44555555444  46799999999999999999999      89999999999888777766665555432         


Q ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh---------------------hcCcceEEEEecC----CcccchHhhcc
Q 022641          151 YPCPPYKIIILDEADSMTEDAQNALRRTMET---------------------YSKVTRFFFICNY----ISRIIEPLASR  205 (294)
Q Consensus       151 ~~~~~~~lliiDei~~l~~~~~~~L~~~l~~---------------------~~~~~~ii~~~~~----~~~~~~~l~~r  205 (294)
                            ..+++||+++++.+....+.+.+..                     ....+.+++|.|+    ...+++.+..+
T Consensus       658 ------aW~cfDEfNrl~~~vLSvv~~qi~~I~~a~~~~~~~~~~~~G~~i~l~~~~~vfiTmNpgY~gr~eLP~nLk~l  731 (3245)
T 3vkg_A          658 ------AWGCFDEFNRLEERILSAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGYAGRSNLPDNLKKL  731 (3245)
T ss_dssp             ------CEEEEETTTSSCHHHHHHHHHHHHHHHHHHHHTCSEECCC---CEECCTTCEEEECBCCCGGGCCCSCHHHHTT
T ss_pred             ------cEEEehhhhcCCHHHHHHHHHHHHHHHHHHHcCCCeEEecCCCEEeecCCeEEEEEeCCCccCcccChHHHHhh
Confidence                  2889999999999887776665541                     1124557777774    34689999999


Q ss_pred             ccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHh---h----------ccCcHHHHHHHHHHHHHHh
Q 022641          206 CAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSS---I----------SQGDLRRAITYLQGAARLF  264 (294)
Q Consensus       206 ~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~---~----------~~G~~r~~~~~l~~~~~~~  264 (294)
                      |..+.+..|+.+.+.+++.   -..|..-.......+..   .          .+-.+|.+..+|..|....
T Consensus       732 Fr~v~m~~Pd~~~i~ei~L---~s~Gf~~a~~La~k~~~~~~l~~e~LS~Q~HYDfGLRalKsVL~~AG~lk  800 (3245)
T 3vkg_A          732 FRSMAMIKPDREMIAQVML---YSQGFKTAEVLAGKIVPLFKLCQEQLSAQSHYDFGLRALKSVLVSAGGIK  800 (3245)
T ss_dssp             EEEEECCSCCHHHHHHHHH---HTTTCSCHHHHHHHHHHHHHHHHHSSCCCTTCCCSHHHHHHHHHHHHHHH
T ss_pred             cEEEEEeCCCHHHHHHHHH---HHcccchHHHHHHHHHHHHHHHHHHhCCCCCCCCChHHHHHHHHHHHHHH
Confidence            9999999999998888863   34555433333333332   1          2235888888887666543

>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=98.83  E-value=1.4e-07  Score=93.09  Aligned_cols=193  Identities=11%  Similarity=0.051  Sum_probs=111.8

Q ss_pred             CCCcchhhcccHHHHHHHHHHHHcC--CCCcEEEECCCCCCHHHHHHHHHHHh--cCCCccCCcceeecCCCCcchhHHH
Q 022641           56 RPKQVKDVAHQEEVVRVLTNTLETA--NCPHMLFYGPPGTGKTTTALAIAHQL--FGPELYKSRVLELNASDDRGINVVR  131 (294)
Q Consensus        56 ~~~~~~~~~g~~~~~~~l~~~l~~~--~~~~ill~Gp~G~GKT~la~~la~~~--~~~~~~~~~~~~~~~~~~~~~~~~~  131 (294)
                      -|.....++|++..+..|.+.+...  ..+.+.|+|+.|+|||+||..+++..  ....+ ...++-++.+...... ..
T Consensus       119 ~p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~-~~~~~~v~~~~~~~~~-~~  196 (1249)
T 3sfz_A          119 VPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCF-SGGVHWVSIGKQDKSG-LL  196 (1249)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTS-TTCEEEEECCSCCHHH-HH
T ss_pred             CCCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhC-CCeEEEEEECCcCchH-HH
Confidence            4555667999999999999999643  33458999999999999999887653  11111 2222233333221111 11


Q ss_pred             HHHHHHHhhhcccCc---c-CC------------CCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCC
Q 022641          132 TKIKTFAAVAVGSGQ---R-RG------------GYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYI  195 (294)
Q Consensus       132 ~~~~~~~~~~~~~~~---~-~~------------~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~  195 (294)
                      ..+..+.........   . ..            .....++-+||||+++..  .       .++.......+|+||+..
T Consensus       197 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~--~-------~~~~~~~~~~ilvTtR~~  267 (1249)
T 3sfz_A          197 MKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDP--W-------VLKAFDNQCQILLTTRDK  267 (1249)
T ss_dssp             HHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCH--H-------HHTTTCSSCEEEEEESST
T ss_pred             HHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCH--H-------HHHhhcCCCEEEEEcCCH
Confidence            112211111110000   0 00            000123679999999863  1       233345677888888765


Q ss_pred             cccchHhhccccEEEecC-CCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHH
Q 022641          196 SRIIEPLASRCAKFRFKP-LSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA  261 (294)
Q Consensus       196 ~~~~~~l~~r~~~i~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~  261 (294)
                      .-. .........+.+.+ ++.++..+++...+... ..-.++....|++.|+|.|=.+..+...+.
T Consensus       268 ~~~-~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~-~~~~~~~~~~i~~~~~glPLal~~~~~~l~  332 (1249)
T 3sfz_A          268 SVT-DSVMGPKHVVPVESGLGREKGLEILSLFVNMK-KEDLPAEAHSIIKECKGSPLVVSLIGALLR  332 (1249)
T ss_dssp             TTT-TTCCSCBCCEECCSSCCHHHHHHHHHHHHTSC-STTCCTHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHH-HhhcCCceEEEecCCCCHHHHHHHHHHhhCCC-hhhCcHHHHHHHHHhCCCHHHHHHHHHHhh
Confidence            321 12223334788886 99999999998766322 122245688899999998876655554443

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=98.81  E-value=1.3e-07  Score=89.47  Aligned_cols=177  Identities=14%  Similarity=0.104  Sum_probs=94.7

Q ss_pred             cccHHHHHHHHHHHHc-CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhc
Q 022641           64 AHQEEVVRVLTNTLET-ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAV  142 (294)
Q Consensus        64 ~g~~~~~~~l~~~l~~-~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  142 (294)
                      +|++..+..|.+++.. ...+.+.|+|+.|+|||+||..+++...-...+...++-++.+.......+...+........
T Consensus       131 VGRe~eLeeL~elL~~~d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~~i~  210 (1221)
T 1vt4_I          131 VSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQID  210 (1221)
T ss_dssp             CCCHHHHHHHHHHHHHCCSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHHHHC
T ss_pred             CCcHHHHHHHHHHHhccCCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHhhcC
Confidence            8999999999999876 334569999999999999999998642001111222222333332222222122221111100


Q ss_pred             cc-CccC-----------------C---CCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchH
Q 022641          143 GS-GQRR-----------------G---GYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEP  201 (294)
Q Consensus       143 ~~-~~~~-----------------~---~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~  201 (294)
                      .. ....                 .   .....++-+|||||++.  ...+..       ++....+|+||+...... .
T Consensus       211 ~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd--~eqLe~-------f~pGSRILVTTRd~~Va~-~  280 (1221)
T 1vt4_I          211 PNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQN--AKAWNA-------FNLSCKILLTTRFKQVTD-F  280 (1221)
T ss_dssp             SSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCC--HHHHHH-------HHSSCCEEEECSCSHHHH-H
T ss_pred             cccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcCh--HHHHHh-------hCCCeEEEEeccChHHHH-h
Confidence            00 0000                 0   00123567999999988  222222       236677888887654321 1


Q ss_pred             hhc-cccEEEec----CCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHH
Q 022641          202 LAS-RCAKFRFK----PLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYL  257 (294)
Q Consensus       202 l~~-r~~~i~~~----~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l  257 (294)
                      +.. +...+.++    +++.++..+++.+.+.   .. ..+..   .+.|+|.|-.+..+.
T Consensus       281 l~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g---~~-~eeL~---~eICgGLPLALkLaG  334 (1221)
T 1vt4_I          281 LSAATTTHISLDHHSMTLTPDEVKSLLLKYLD---CR-PQDLP---REVLTTNPRRLSIIA  334 (1221)
T ss_dssp             HHHHSSCEEEECSSSSCCCHHHHHHHHHHHHC---CC-TTTHH---HHHCCCCHHHHHHHH
T ss_pred             cCCCeEEEecCccccCCcCHHHHHHHHHHHcC---CC-HHHHH---HHHhCCCHHHHHHHH
Confidence            211 12345544    7899999999987642   21 22222   233777665544433

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=98.76  E-value=7.9e-08  Score=73.58  Aligned_cols=67  Identities=13%  Similarity=0.265  Sum_probs=46.6

Q ss_pred             CcEEEEEeCCC---CCCHHHHHHHHHHHHhhcCcceEEEEec--CCcccchHhhcc--ccEEEecCCCHHHHHHHH
Q 022641          155 PYKIIILDEAD---SMTEDAQNALRRTMETYSKVTRFFFICN--YISRIIEPLASR--CAKFRFKPLSEEVMSSRV  223 (294)
Q Consensus       155 ~~~lliiDei~---~l~~~~~~~L~~~l~~~~~~~~ii~~~~--~~~~~~~~l~~r--~~~i~~~~~~~~~~~~~l  223 (294)
                      ++.++++||++   .+++...+.+.+.++.  ....+|+++.  +.......+.+|  +.++.+.+.+.+++...+
T Consensus        99 ~p~llilDEigp~~~ld~~~~~~l~~~l~~--~~~~~i~~~H~~h~~~~~~~i~~r~~~~i~~~~~~~r~~~~~~l  172 (178)
T 1ye8_A           99 RRKVIIIDEIGKMELFSKKFRDLVRQIMHD--PNVNVVATIPIRDVHPLVKEIRRLPGAVLIELTPENRDVILEDI  172 (178)
T ss_dssp             TTCEEEECCCSTTGGGCHHHHHHHHHHHTC--TTSEEEEECCSSCCSHHHHHHHTCTTCEEEECCTTTTTTHHHHH
T ss_pred             CCCEEEEeCCCCcccCCHHHHHHHHHHHhc--CCCeEEEEEccCCCchHHHHHHhcCCcEEEEecCcCHHHHHHHH
Confidence            34699999964   4567788888888876  3444666663  445566778787  668888888766665544

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=98.67  E-value=9.5e-09  Score=79.21  Aligned_cols=55  Identities=11%  Similarity=0.050  Sum_probs=37.6

Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEec------CCcccchHhhcccc-EEEec
Q 022641          155 PYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICN------YISRIIEPLASRCA-KFRFK  212 (294)
Q Consensus       155 ~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~------~~~~~~~~l~~r~~-~i~~~  212 (294)
                      +.++|+|||++.++++..+.|..+.+.   ...+++++.      .++...+.+++++. +..+.
T Consensus        76 ~~dvviIDE~Q~~~~~~~~~l~~l~~~---~~~Vi~~Gl~~~f~~~~f~~~~~ll~~ad~v~~l~  137 (184)
T 2orw_A           76 DTRGVFIDEVQFFNPSLFEVVKDLLDR---GIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKK  137 (184)
T ss_dssp             TEEEEEECCGGGSCTTHHHHHHHHHHT---TCEEEEEEESBCTTSCBCHHHHHHHHHCSEEEECC
T ss_pred             CCCEEEEECcccCCHHHHHHHHHHHHC---CCCEEEEeeccccccCCccchHHHHHHhhheEEee
Confidence            468999999999987777777766654   445666654      44455677777775 33443

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=98.66  E-value=2.6e-08  Score=77.54  Aligned_cols=59  Identities=12%  Similarity=0.135  Sum_probs=39.7

Q ss_pred             cEEEEEeCCCCC--CH-HHH--HHHHHHHH-hhcCcceEEEEecCCcccchHhhcccc-EEEecCC
Q 022641          156 YKIIILDEADSM--TE-DAQ--NALRRTME-TYSKVTRFFFICNYISRIIEPLASRCA-KFRFKPL  214 (294)
Q Consensus       156 ~~lliiDei~~l--~~-~~~--~~L~~~l~-~~~~~~~ii~~~~~~~~~~~~l~~r~~-~i~~~~~  214 (294)
                      ..+|||||++.+  +. ...  ..++..++ .......+|++++.+..+..++++|+. .+++.++
T Consensus        88 ~~vliIDEAq~l~~~~~~~~e~~rll~~l~~~r~~~~~iil~tq~~~~l~~~lr~ri~~~~~l~~~  153 (199)
T 2r2a_A           88 GSIVIVDEAQDVWPARSAGSKIPENVQWLNTHRHQGIDIFVLTQGPKLLDQNLRTLVRKHYHIASN  153 (199)
T ss_dssp             TCEEEETTGGGTSBCCCTTCCCCHHHHGGGGTTTTTCEEEEEESCGGGBCHHHHTTEEEEEEEEEC
T ss_pred             ceEEEEEChhhhccCccccchhHHHHHHHHhcCcCCeEEEEECCCHHHHhHHHHHHhheEEEEcCc
Confidence            459999999998  21 111  12333333 333455789999998889999999987 5666653

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=98.60  E-value=6.5e-08  Score=74.35  Aligned_cols=116  Identities=14%  Similarity=0.110  Sum_probs=65.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee---cCCCCcchhHHHHHHH-------------------HHHhh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL---NASDDRGINVVRTKIK-------------------TFAAV  140 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~-------------------~~~~~  140 (294)
                      .++++++++|.||||+|-+++-++.+...   .+..+   ......+...+...+.                   .....
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G~---rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a  105 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHGK---NVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAAC  105 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTTC---CEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHH
Confidence            46999999999999999999998854422   22222   1111111111111100                   00000


Q ss_pred             hcccCccCCCCCCCCcEEEEEeCCC------CCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhcccc
Q 022641          141 AVGSGQRRGGYPCPPYKIIILDEAD------SMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       141 ~~~~~~~~~~~~~~~~~lliiDei~------~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      ..............++++|||||+.      .++   .+.+++++...+....+|+|+|...   +++.....
T Consensus       106 ~~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~---~~ev~~~l~~Rp~~~~vIlTGr~ap---~~l~e~AD  172 (196)
T 1g5t_A          106 MAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLP---LEEVISALNARPGHQTVIITGRGCH---RDILDLAD  172 (196)
T ss_dssp             HHHHHHHHHHTTCTTCSEEEEETHHHHHHTTSSC---HHHHHHHHHTSCTTCEEEEECSSCC---HHHHHHCS
T ss_pred             HHHHHHHHHHHhcCCCCEEEEeCCCccccCCCCC---HHHHHHHHHhCcCCCEEEEECCCCc---HHHHHhCc
Confidence            0000000001123567899999994      444   3458888899999999999998865   45555544

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=98.45  E-value=1.2e-06  Score=72.57  Aligned_cols=22  Identities=23%  Similarity=0.347  Sum_probs=20.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|+||||+|||+++..++..
T Consensus       125 viLI~GpPGsGKTtLAlqlA~~  146 (331)
T 2vhj_A          125 MVIVTGKGNSGKTPLVHALGEA  146 (331)
T ss_dssp             EEEEECSCSSSHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHh
Confidence            4799999999999999999987

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=98.44  E-value=4.1e-07  Score=82.32  Aligned_cols=119  Identities=22%  Similarity=0.248  Sum_probs=65.8

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHH-------HHHH
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKI-------KTFA  138 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~  138 (294)
                      .+.....+...+.   .+.++|+||||||||+++..++..+...   +..+..+ +........+.+..       ..+.
T Consensus       191 ~~~Q~~Av~~~~~---~~~~~I~G~pGTGKTt~i~~l~~~l~~~---g~~Vl~~-ApT~~Aa~~L~e~~~~~a~Tih~ll  263 (574)
T 3e1s_A          191 SEEQASVLDQLAG---HRLVVLTGGPGTGKSTTTKAVADLAESL---GLEVGLC-APTGKAARRLGEVTGRTASTVHRLL  263 (574)
T ss_dssp             CHHHHHHHHHHTT---CSEEEEECCTTSCHHHHHHHHHHHHHHT---TCCEEEE-ESSHHHHHHHHHHHTSCEEEHHHHT
T ss_pred             CHHHHHHHHHHHh---CCEEEEEcCCCCCHHHHHHHHHHHHHhc---CCeEEEe-cCcHHHHHHhHhhhcccHHHHHHHH
Confidence            3444455544442   3469999999999999999999877322   2233322 22222222222211       1111


Q ss_pred             hhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCC
Q 022641          139 AVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYI  195 (294)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~  195 (294)
                      .... ...........+.++|||||++.++......|+..+   +....+|+++...
T Consensus       264 ~~~~-~~~~~~~~~~~~~dvlIIDEasml~~~~~~~Ll~~~---~~~~~lilvGD~~  316 (574)
T 3e1s_A          264 GYGP-QGFRHNHLEPAPYDLLIVDEVSMMGDALMLSLLAAV---PPGARVLLVGDTD  316 (574)
T ss_dssp             TEET-TEESCSSSSCCSCSEEEECCGGGCCHHHHHHHHTTS---CTTCEEEEEECTT
T ss_pred             cCCc-chhhhhhcccccCCEEEEcCccCCCHHHHHHHHHhC---cCCCEEEEEeccc
Confidence            1110 001111112235679999999999988776666544   4566788887543

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=98.38  E-value=4.1e-06  Score=65.81  Aligned_cols=167  Identities=13%  Similarity=0.142  Sum_probs=86.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhh-----cccCc-cCCC---CCCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVA-----VGSGQ-RRGG---YPCP  154 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~-~~~~---~~~~  154 (294)
                      ++++.|++||||||++..++..+...   +..+..+..........+ ..+..+...+     ..... ....   ....
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~---G~~V~v~d~D~q~~~~~~-al~~gl~~~~~~~~~~~~~~~~e~~l~~~L~~   83 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQ---GVRVMAGVVETHGRAETE-ALLNGLPQQPLLRTEYRGMTLEEMDLDALLKA   83 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHT---TCCEEEEECCCTTCHHHH-HHHTTSCBCCCEEEEETTEEEEECCHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHC---CCCEEEEEeCCCCChhHH-HHhcCccccCcceeecCCcccccccHHHHHhc
Confidence            59999999999999999999987432   223333333222121111 1111111000     00000 0000   0012


Q ss_pred             CcEEEEEeCCCCCCHH------HHHHHHHHHHhhcCcceEEEEecCC------------------cccchHhhccccEEE
Q 022641          155 PYKIIILDEADSMTED------AQNALRRTMETYSKVTRFFFICNYI------------------SRIIEPLASRCAKFR  210 (294)
Q Consensus       155 ~~~lliiDei~~l~~~------~~~~L~~~l~~~~~~~~ii~~~~~~------------------~~~~~~l~~r~~~i~  210 (294)
                      ++++++|||+.+.+..      ..+.+...   ......++.|+|..                  ..+++.+...+..|.
T Consensus        84 ~pdlvIVDElG~~~~~~~r~~~~~qDV~~~---l~sgidVitT~Nlqh~esl~d~v~~itg~~v~e~vpd~~~~~a~~v~  160 (228)
T 2r8r_A           84 APSLVLVDELAHTNAPGSRHTKRWQDIQEL---LAAGIDVYTTVNVQHLESLNDQVRGITGVQVRETLPDWVLQEAFDLV  160 (228)
T ss_dssp             CCSEEEESCTTCBCCTTCSSSBHHHHHHHH---HHTTCEEEEEEEGGGBGGGHHHHHHHHSCCCCSCBCHHHHHTCSEEE
T ss_pred             CCCEEEEeCCCCCCcccchhHHHHHHHHHH---HcCCCCEEEEccccccccHHHHHHHHcCCCcCCcCccHHHhhCCeEE
Confidence            4579999999886321      22222222   23455677777622                  236778888887777


Q ss_pred             ecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhh-ccCcHHHHHH-HHHHHH
Q 022641          211 FKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSI-SQGDLRRAIT-YLQGAA  261 (294)
Q Consensus       211 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~-~~G~~r~~~~-~l~~~~  261 (294)
                      +--++++++.+.+    +.-++...+.+-..+... +.||+-.+.. .|..++
T Consensus       161 lvD~~p~~l~~rl----~~g~vy~~~~~~~a~~~~f~~~nl~~lrelal~~~a  209 (228)
T 2r8r_A          161 LIDLPPRELLERL----RDGKVYVPEQARAAIDAFFTQTNLTALREMAMQTAA  209 (228)
T ss_dssp             EBCCCHHHHHHHH----HTTCCCCTTCCHHHHHHHCCHHHHHHHHHHHHHHHH
T ss_pred             EecCCHHHHHHHH----HCCCccChhHHHHHHHhhhchhhHHHHHHHHHHHHH
Confidence            7677777766664    333343344443444444 3566665555 444444

>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=98.33  E-value=2.6e-06  Score=67.34  Aligned_cols=94  Identities=16%  Similarity=0.086  Sum_probs=52.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC-c----------------chhHHHHHHHHHHhhhcccCc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD-R----------------GINVVRTKIKTFAAVAVGSGQ  146 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~-~----------------~~~~~~~~~~~~~~~~~~~~~  146 (294)
                      .++++||+|+||||++..++..+....   ..+..+..... +                ......+....+...      
T Consensus        14 i~litG~mGsGKTT~ll~~~~r~~~~g---~kVli~~~~~d~r~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~------   84 (223)
T 2b8t_A           14 IEFITGPMFAGKTAELIRRLHRLEYAD---VKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSN------   84 (223)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTT---CCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHST------
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhcC---CEEEEEEeccCchHHHHHHHhcCCCccccccCCHHHHHHHHHHH------
Confidence            488999999999999999888873221   11111111100 0                000011111111110      


Q ss_pred             cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEec
Q 022641          147 RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       147 ~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                          ....+.++|+|||++.++.+..+.+..+.+ .  ...+|+++.
T Consensus        85 ----~~~~~~dvViIDEaQ~l~~~~ve~l~~L~~-~--gi~Vil~Gl  124 (223)
T 2b8t_A           85 ----SFNDETKVIGIDEVQFFDDRICEVANILAE-N--GFVVIISGL  124 (223)
T ss_dssp             ----TSCTTCCEEEECSGGGSCTHHHHHHHHHHH-T--TCEEEEECC
T ss_pred             ----hhCCCCCEEEEecCccCcHHHHHHHHHHHh-C--CCeEEEEec
Confidence                011235799999999998776666654443 2  566788775

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=98.23  E-value=3.7e-06  Score=76.77  Aligned_cols=108  Identities=19%  Similarity=0.199  Sum_probs=58.0

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCC-ccCCcceeecCCCCcchhHHHHHHHHHHhhh-------------cccCccC
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPE-LYKSRVLELNASDDRGINVVRTKIKTFAAVA-------------VGSGQRR  148 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~  148 (294)
                      +.++++|+||||||+++..+...+.... ..+..+. +-++.......+.+.+.......             .......
T Consensus       165 ~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vl-l~APTg~AA~~L~e~~~~~~~~l~l~~~~~~~~~~~~~Tih~l  243 (608)
T 1w36_D          165 RISVISGGPGTGKTTTVAKLLAALIQMADGERCRIR-LAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEDASTLHRL  243 (608)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEE-EEBSSHHHHHHHHHHHTHHHHHSSCCSCCCCSCSCCCBTTTSC
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHHHHhhhcCCCeEE-EEeCChhHHHHHHHHHHHHHhcCCCCHHHHhccchhhhhhHhh
Confidence            4699999999999999998887763210 1122232 22333223333332222111100             0000000


Q ss_pred             ------------CCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecC
Q 022641          149 ------------GGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       149 ------------~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                                  ........++|||||++.++......|+..   .+....+|+++..
T Consensus       244 l~~~~~~~~~~~~~~~~l~~d~lIIDEAsml~~~~~~~Ll~~---l~~~~~liLvGD~  298 (608)
T 1w36_D          244 LGAQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLIDA---LPDHARVIFLGDR  298 (608)
T ss_dssp             C-----------CTTSCCSCSEEEECSGGGCBHHHHHHHHHT---CCTTCEEEEEECT
T ss_pred             hccCCCchHHHhccCCCCCCCEEEEechhhCCHHHHHHHHHh---CCCCCEEEEEcch
Confidence                        000112467999999999987665555544   4566778888754

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=98.17  E-value=3.4e-06  Score=65.73  Aligned_cols=118  Identities=12%  Similarity=0.041  Sum_probs=58.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC-Cc-chhHHHHHHHHHHh-hhcccCccCCCCCCCCcEEEE
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD-DR-GINVVRTKIKTFAA-VAVGSGQRRGGYPCPPYKIII  160 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~lli  160 (294)
                      ..+++||.|+||||.+..++..+...   +..++.+.... .+ +...+...+..... ...............+.++|+
T Consensus        30 l~vitG~MgsGKTT~lL~~a~r~~~~---g~kVli~k~~~d~R~ge~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~dvVi  106 (214)
T 2j9r_A           30 IEVICGSMFSGKSEELIRRVRRTQFA---KQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSASKDIFKHITEEMDVIA  106 (214)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHT---TCCEEEEECC-----------------CCEEECSSGGGGGGGCCSSCCEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHC---CCEEEEEEeccCCcchHHHHHhhcCCeeEEeecCCHHHHHHHHhcCCCEEE
Confidence            36799999999999999888887422   23333333221 11 11111111110000 000000000000112468999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhhcCcceEEEEec------CCcccchHhhcccc
Q 022641          161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICN------YISRIIEPLASRCA  207 (294)
Q Consensus       161 iDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~------~~~~~~~~l~~r~~  207 (294)
                      |||++.++++..+.|..+.+   ....+|+++.      .++.-.+.|+..+.
T Consensus       107 IDEaQF~~~~~V~~l~~l~~---~~~~Vi~~Gl~~DF~~~~F~~~~~Ll~~AD  156 (214)
T 2j9r_A          107 IDEVQFFDGDIVEVVQVLAN---RGYRVIVAGLDQDFRGLPFGQVPQLMAIAE  156 (214)
T ss_dssp             ECCGGGSCTTHHHHHHHHHH---TTCEEEEEECSBCTTSCBCTTHHHHHHHCS
T ss_pred             EECcccCCHHHHHHHHHHhh---CCCEEEEEecccccccCccccHHHHHHhcc
Confidence            99999998777765554433   3556777774      33444445554443

>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=98.10  E-value=0.00019  Score=56.35  Aligned_cols=23  Identities=30%  Similarity=0.595  Sum_probs=21.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++|+||||+||||+++.|++.+
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            48899999999999999999887

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=98.07  E-value=9.5e-06  Score=81.92  Aligned_cols=27  Identities=30%  Similarity=0.388  Sum_probs=24.0

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      +..+++|+||||||||+||.+++.++.
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~ 1452 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQ 1452 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            445799999999999999999998874

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=98.02  E-value=6.2e-06  Score=63.21  Aligned_cols=100  Identities=13%  Similarity=0.078  Sum_probs=48.9

Q ss_pred             cEEEECCCCCCHH-HHHHHHHHHhcCCCccCCcceeecCC-CCcchhHHHHHHHHHHhh-hcccCccCCCCCCCCcEEEE
Q 022641           84 HMLFYGPPGTGKT-TTALAIAHQLFGPELYKSRVLELNAS-DDRGINVVRTKIKTFAAV-AVGSGQRRGGYPCPPYKIII  160 (294)
Q Consensus        84 ~ill~Gp~G~GKT-~la~~la~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~lli  160 (294)
                      ..+++||.|+||| +|++++.+....    +..++.+.+. +.+....+...+...... ......... ......++|+
T Consensus        22 l~fiyG~MgsGKTt~Ll~~i~n~~~~----~~kvl~~kp~~D~R~~~~i~S~~g~~~~A~~~~~~~d~~-~~~~~~DvIl   96 (195)
T 1w4r_A           22 IQVILGPMFSGKSTELMRRVRRFQIA----QYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVA-QEALGVAVIG   96 (195)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHT----TCCEEEEEETTCCCGGGSCCHHHHHHSEEEEESSGGGGH-HHHHTCSEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHc----CCeEEEEccccCccchhhhhhccCCcccceecCCHHHHH-HhccCCCEEE
Confidence            4899999999999 888888776532    2344444322 111111111111100000 000000000 0011246999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhhcCcceEEEEe
Q 022641          161 LDEADSMTEDAQNALRRTMETYSKVTRFFFIC  192 (294)
Q Consensus       161 iDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~  192 (294)
                      |||++.+ ++..+.+ ..+.+  ....||+++
T Consensus        97 IDEaQFf-k~~ve~~-~~L~~--~gk~VI~~G  124 (195)
T 1w4r_A           97 IDEGQFF-PDIVEFC-EAMAN--AGKTVIVAA  124 (195)
T ss_dssp             ESSGGGC-TTHHHHH-HHHHH--TTCEEEEEE
T ss_pred             EEchhhh-HHHHHHH-HHHHH--CCCeEEEEe
Confidence            9999999 5544444 45543  344566665

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=97.96  E-value=0.00022  Score=55.90  Aligned_cols=23  Identities=35%  Similarity=0.611  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++|+||||+||||+++.|++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999999999999987

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=97.94  E-value=2e-06  Score=66.35  Aligned_cols=24  Identities=17%  Similarity=0.189  Sum_probs=21.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ..+++||.|+||||.+..+++.+.
T Consensus        10 i~v~~G~mgsGKTT~ll~~a~r~~   33 (191)
T 1xx6_A           10 VEVIVGPMYSGKSEELIRRIRRAK   33 (191)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHH
Confidence            489999999999999999988873

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=97.92  E-value=0.00013  Score=55.44  Aligned_cols=22  Identities=36%  Similarity=0.486  Sum_probs=20.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|.|+||+||||+++.+++.
T Consensus         4 ~I~i~G~~GsGKST~a~~L~~~   25 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWAREFIAK   25 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEecCCCCCHHHHHHHHHhh
Confidence            4899999999999999999983

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=97.91  E-value=4.5e-05  Score=61.02  Aligned_cols=38  Identities=26%  Similarity=0.308  Sum_probs=27.7

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.....+..++..   .+++++||+|+|||.++..++..+
T Consensus        95 ~~~Q~~ai~~~~~~---~~~ll~~~tG~GKT~~a~~~~~~~  132 (237)
T 2fz4_A           95 RDYQEKALERWLVD---KRGCIVLPTGSGKTHVAMAAINEL  132 (237)
T ss_dssp             CHHHHHHHHHHTTT---SEEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHhC---CCEEEEeCCCCCHHHHHHHHHHHc
Confidence            34444455554443   259999999999999999888776

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=97.88  E-value=9.8e-06  Score=62.15  Aligned_cols=24  Identities=25%  Similarity=0.405  Sum_probs=22.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|+||+|+||||+++.+++.+
T Consensus         6 ~~i~l~G~~GsGKst~a~~La~~l   29 (185)
T 3trf_A            6 TNIYLIGLMGAGKTSVGSQLAKLT   29 (185)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            479999999999999999999998

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=97.86  E-value=1.3e-05  Score=60.98  Aligned_cols=24  Identities=17%  Similarity=0.321  Sum_probs=22.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+|+||+||||+++.|++.+
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l   27 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            358999999999999999999998

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=97.85  E-value=2.5e-05  Score=60.12  Aligned_cols=69  Identities=17%  Similarity=0.203  Sum_probs=40.5

Q ss_pred             CCCcEEEEEeCCCCC---CHHHHHHHHHHHHhhcCcceEEEE-e--cCC-cccchHhhcc--ccEEEecCCCHHHHHHHH
Q 022641          153 CPPYKIIILDEADSM---TEDAQNALRRTMETYSKVTRFFFI-C--NYI-SRIIEPLASR--CAKFRFKPLSEEVMSSRV  223 (294)
Q Consensus       153 ~~~~~lliiDei~~l---~~~~~~~L~~~l~~~~~~~~ii~~-~--~~~-~~~~~~l~~r--~~~i~~~~~~~~~~~~~l  223 (294)
                      ..++++++|||++.+   +...++.|.++++..  ...++.+ +  ... ..+.+++..+  +.++.+.+-+.+.+..-+
T Consensus       103 ~~~~dvlilDE~g~~~~~~~~~~~~l~~~l~~~--~~~ilgti~vsh~~~~~~vd~i~~~~~~~i~~~~~~nr~~~~~~i  180 (189)
T 2i3b_A          103 GPGQRVCVIDEIGKMELFSQLFIQAVRQTLSTP--GTIILGTIPVPKGKPLALVEEIRNRKDVKVFNVTKENRNHLLPDI  180 (189)
T ss_dssp             SSCCCCEEECCCSTTTTTCSHHHHHHHHHHHCS--SCCEEEECCCCCSSCCTTHHHHHTTCCSEEEECCSSSGGGHHHHH
T ss_pred             ccCCCEEEEeCCCccccccHHHHHHHHHHHhCC--CcEEEEEeecCCCCchHHHHHHeecCCcEEEEeChHhHHHHHHHH
Confidence            456789999998766   345677777787753  2233312 2  221 2445666554  347777776665555444

>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=97.85  E-value=3.5e-05  Score=61.55  Aligned_cols=22  Identities=27%  Similarity=0.392  Sum_probs=17.9

Q ss_pred             CcEEEECCCCCCHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~  104 (294)
                      .++++.||+|+|||+++..+.-
T Consensus        77 ~~~~i~g~TGsGKTt~~~~~~~   98 (235)
T 3llm_A           77 SVVIIRGATGCGKTTQVPQFIL   98 (235)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEeCCCCCcHHhHHHHHh
Confidence            3799999999999987665543

>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=97.84  E-value=0.00042  Score=56.13  Aligned_cols=24  Identities=33%  Similarity=0.526  Sum_probs=21.9

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..|+|+|+||+||||+++.++..+
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~L   28 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKIL   28 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHH
Confidence            358999999999999999999984

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=97.84  E-value=3.7e-05  Score=60.49  Aligned_cols=102  Identities=12%  Similarity=0.053  Sum_probs=51.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecC--CCCcchhHHHHHHHHHHhh-hcccCccCCCCCCCCcEEEE
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA--SDDRGINVVRTKIKTFAAV-AVGSGQRRGGYPCPPYKIII  160 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~lli  160 (294)
                      ..+++||.|+||||.+-..+..+...   +..++.+..  +...+ ..+...+...... ..... ........+.++|+
T Consensus        21 l~v~~G~MgsGKTT~lL~~~~r~~~~---g~kvli~kp~~D~Ryg-~~i~sr~G~~~~a~~i~~~-~di~~~~~~~dvVi   95 (234)
T 2orv_A           21 IQVILGPMFSGKSTELMRRVRRFQIA---QYKCLVIKYAKDTRYS-SSFCTHDRNTMEALPACLL-RDVAQEALGVAVIG   95 (234)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTT---TCCEEEEEETTCCCC------------CEEEEESSG-GGGHHHHTTCSEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHC---CCeEEEEeecCCccch-HHHHhhcCCeeEEEecCCH-HHHHHHhccCCEEE
Confidence            37899999999998887777776432   222222221  11111 1111111000000 00000 00000002357999


Q ss_pred             EeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecC
Q 022641          161 LDEADSMTEDAQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       161 iDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      |||++.+..  ...+.+.+.+  ....+|+++.+
T Consensus        96 IDEaQF~~~--v~el~~~l~~--~gi~VI~~GL~  125 (234)
T 2orv_A           96 IDEGQFFPD--IVEFCEAMAN--AGKTVIVAALD  125 (234)
T ss_dssp             ESSGGGCTT--HHHHHHHHHH--TTCEEEEECCS
T ss_pred             EEchhhhhh--HHHHHHHHHh--CCCEEEEEecc
Confidence            999999974  6666677766  45567777743

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=97.81  E-value=1.6e-05  Score=61.85  Aligned_cols=24  Identities=38%  Similarity=0.494  Sum_probs=22.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+||+|+||||+++.+++.+
T Consensus        26 ~~i~l~G~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           26 VRIFLTGYMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHc
Confidence            469999999999999999999998

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=97.80  E-value=0.0006  Score=54.62  Aligned_cols=26  Identities=31%  Similarity=0.570  Sum_probs=23.0

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+..++|+||||+||||+++.|++.+
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            33459999999999999999999987

>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=97.79  E-value=9.3e-05  Score=64.34  Aligned_cols=23  Identities=26%  Similarity=0.268  Sum_probs=21.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|+||+||||+++.++..+
T Consensus       260 lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          260 VVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             EEEEESCTTSSHHHHHHHHTGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            48999999999999999998876

>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=97.79  E-value=0.00032  Score=55.02  Aligned_cols=34  Identities=29%  Similarity=0.364  Sum_probs=26.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      .++|+||+|+|||+++..++...      +..++.++...
T Consensus        22 ~~~i~G~~GsGKTtl~~~l~~~~------~~~v~~i~~~~   55 (220)
T 2cvh_A           22 LTQVYGPYASGKTTLALQTGLLS------GKKVAYVDTEG   55 (220)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH------CSEEEEEESSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc------CCcEEEEECCC
Confidence            48999999999999999998822      44555555544

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=97.78  E-value=1.7e-05  Score=59.77  Aligned_cols=30  Identities=33%  Similarity=0.548  Sum_probs=26.0

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCccee
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLE  118 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~  118 (294)
                      .+++|+|++|+||||+++.|++.+      +.+++.
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~l------g~~~id   37 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLAL------KLEVLD   37 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHH------TCCEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh------CCCEEE
Confidence            579999999999999999999998      555554

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.78  E-value=0.0001  Score=74.63  Aligned_cols=98  Identities=17%  Similarity=0.232  Sum_probs=59.2

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchh---------------------HHHHHHHHHHhh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGIN---------------------VVRTKIKTFAAV  140 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~~~~~  140 (294)
                      ..+++|+||||||||+++.+++.+....   +..+..+........-                     ........+.. 
T Consensus      1081 g~~vll~G~~GtGKT~la~~~~~ea~k~---Ge~~~Fit~ee~~~~L~a~~~G~dl~~l~~~~pd~~e~~~~i~~~l~~- 1156 (2050)
T 3cmu_A         1081 GRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR- 1156 (2050)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHHHTT---TCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHH-
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEEccccHHHHHHHHcCCChhHheeecCcchHHHHHHHHHHHH-
Confidence            3469999999999999999999987433   2233333333211110                     01111111111 


Q ss_pred             hcccCccCCCCCCCCcEEEEEeCCCCCCHH------------------HHHHHHHHHHhhcCcceEEEEecCC
Q 022641          141 AVGSGQRRGGYPCPPYKIIILDEADSMTED------------------AQNALRRTMETYSKVTRFFFICNYI  195 (294)
Q Consensus       141 ~~~~~~~~~~~~~~~~~lliiDei~~l~~~------------------~~~~L~~~l~~~~~~~~ii~~~~~~  195 (294)
                                  ..+.++||||++..+.+.                  ....|++++...+...++++++|..
T Consensus      1157 ------------~~~~dlvVIDsl~~L~~~~e~~~~~g~~~~gl~aR~~~~~L~~L~~~l~e~~stiI~tN~~ 1217 (2050)
T 3cmu_A         1157 ------------SGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQI 1217 (2050)
T ss_dssp             ------------HTCCSEEEESCGGGCCCHHHHHSCTTCCCTTHHHHHHHHHHHHHHHHHHTTTCEEEEEECC
T ss_pred             ------------hCCCCEEEECCcccccccccccccccccchhHHHHHHHHHHHHHHHHHHhCCeEEEEecCC
Confidence                        123469999999998431                  1245777777777777777777765

>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=97.77  E-value=2e-05  Score=59.52  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+||||+++.|++.+
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l   25 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKEL   25 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999998

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=97.76  E-value=0.001  Score=59.48  Aligned_cols=70  Identities=13%  Similarity=0.161  Sum_probs=49.2

Q ss_pred             CcEEEEEeCCCCCC----HHHHHHHHHHHHhhc-CcceEEEEecCCc--ccchHhhcccc-EEEecCCCHHHHHHHHH
Q 022641          155 PYKIIILDEADSMT----EDAQNALRRTMETYS-KVTRFFFICNYIS--RIIEPLASRCA-KFRFKPLSEEVMSSRVL  224 (294)
Q Consensus       155 ~~~lliiDei~~l~----~~~~~~L~~~l~~~~-~~~~ii~~~~~~~--~~~~~l~~r~~-~i~~~~~~~~~~~~~l~  224 (294)
                      .+-+|||||++.+.    ......|.++..... ..+.+|++|..+.  .+...+++.|. .|.|...+..+...++.
T Consensus       343 P~ivvVIDE~~~L~~~~~~~~~~~L~~Iar~GRa~GIhLIlaTQRPs~d~I~~~Iran~~~RI~lrv~s~~Dsr~ILd  420 (574)
T 2iut_A          343 PTIVVVVDEFADMMMIVGKKVEELIARIAQKARAAGIHLILATQRPSVDVITGLIKANIPTRIAFQVSSKIDSRTILD  420 (574)
T ss_dssp             CEEEEEESCCTTHHHHTCHHHHHHHHHHHHHCTTTTEEEEEEESCCCTTTSCHHHHHTCCEEEEECCSCHHHHHHHHS
T ss_pred             CcEEEEEeCHHHHhhhhhHHHHHHHHHHHHHHhhCCeEEEEEecCcccccccHHHHhhhccEEEEEcCCHHHHHHhcC
Confidence            35699999999773    344555666665543 4566777787766  56777777776 78888888888877763

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=97.76  E-value=4.4e-05  Score=65.19  Aligned_cols=26  Identities=38%  Similarity=0.411  Sum_probs=23.0

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ....++|+||+|+||||+++.++...
T Consensus       168 ~~~~i~l~G~~GsGKSTl~~~l~~~~  193 (377)
T 1svm_A          168 KKRYWLFKGPIDSGKTTLAAALLELC  193 (377)
T ss_dssp             TCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            33469999999999999999999876

>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=97.75  E-value=2.2e-05  Score=59.86  Aligned_cols=25  Identities=40%  Similarity=0.681  Sum_probs=23.0

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|+|+||+||||+++.+++.+
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHh
Confidence            3469999999999999999999988

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=97.73  E-value=2.2e-05  Score=59.67  Aligned_cols=23  Identities=43%  Similarity=0.668  Sum_probs=22.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++|+|+||+||||+++.|++.+
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l   28 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDL   28 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc
Confidence            59999999999999999999998

>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=97.73  E-value=2.5e-05  Score=59.81  Aligned_cols=24  Identities=38%  Similarity=0.704  Sum_probs=22.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.++|+|+||+||||+++.|++.+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l   26 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKAL   26 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc
Confidence            359999999999999999999988

>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=97.71  E-value=0.0012  Score=57.35  Aligned_cols=25  Identities=36%  Similarity=0.470  Sum_probs=22.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFG  108 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~  108 (294)
                      .++++|++|+||||++..++..+..
T Consensus       102 vIlivG~~G~GKTTt~~kLA~~l~~  126 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTVAKLARYFQK  126 (443)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             EEEEECcCCCCHHHHHHHHHHHHHH
Confidence            4899999999999999999988743

>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=97.71  E-value=2.3e-05  Score=60.08  Aligned_cols=24  Identities=46%  Similarity=0.625  Sum_probs=22.2

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHH
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~  105 (294)
                      ..+++|+|++|+||||+++.+++.
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            346999999999999999999998

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=97.70  E-value=3.1e-05  Score=58.56  Aligned_cols=24  Identities=38%  Similarity=0.682  Sum_probs=22.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+||+|+||||+++.++..+
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l   28 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQL   28 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh
Confidence            369999999999999999999987

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=97.67  E-value=2.9e-05  Score=60.33  Aligned_cols=36  Identities=11%  Similarity=0.164  Sum_probs=26.9

Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEe
Q 022641          154 PPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFIC  192 (294)
Q Consensus       154 ~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~  192 (294)
                      .+.++|+|||++.++++..+.+..+.+   ....||+.+
T Consensus       100 ~~~dvV~IDEaQFf~~~~v~~l~~la~---~gi~Vi~~G  135 (219)
T 3e2i_A          100 TNVDVIGIDEVQFFDDEIVSIVEKLSA---DGHRVIVAG  135 (219)
T ss_dssp             TTCSEEEECCGGGSCTHHHHHHHHHHH---TTCEEEEEE
T ss_pred             cCCCEEEEechhcCCHHHHHHHHHHHH---CCCEEEEee
Confidence            456799999999999888888877763   344566555

>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=97.64  E-value=0.00029  Score=54.90  Aligned_cols=23  Identities=43%  Similarity=0.793  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++|.||||+||+|.++.|++.+
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~   24 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEK   24 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999999988

>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=97.63  E-value=0.00044  Score=60.03  Aligned_cols=24  Identities=38%  Similarity=0.400  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++++||+|+||||++..++..+.
T Consensus        99 vI~lvG~~GsGKTTt~~kLA~~l~  122 (433)
T 3kl4_A           99 IIMLVGVQGSGKTTTAGKLAYFYK  122 (433)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999998873

>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=97.61  E-value=0.00065  Score=57.59  Aligned_cols=23  Identities=43%  Similarity=0.647  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+||||++++++..+
T Consensus       125 ~i~I~GptGSGKTTlL~~l~g~~  147 (356)
T 3jvv_A          125 LVLVTGPTGSGKSTTLAAMLDYL  147 (356)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhcc
Confidence            79999999999999999998876

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=97.61  E-value=4.7e-05  Score=61.54  Aligned_cols=23  Identities=43%  Similarity=0.697  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+||||+++.|+..+
T Consensus         3 li~I~G~~GSGKSTla~~La~~~   25 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQET   25 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHhcC
Confidence            47899999999999999999988

>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=97.60  E-value=0.00055  Score=57.86  Aligned_cols=41  Identities=15%  Similarity=0.160  Sum_probs=28.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCc---cCCcceeecCCCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPEL---YKSRVLELNASDD  124 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~---~~~~~~~~~~~~~  124 (294)
                      .++|+||||+|||+++..++.....+..   .+..++.++....
T Consensus       124 i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~  167 (343)
T 1v5w_A          124 ITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENT  167 (343)
T ss_dssp             EEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCC
Confidence            4899999999999999999987532211   2345555555543

>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=97.59  E-value=3.9e-05  Score=58.01  Aligned_cols=22  Identities=32%  Similarity=0.523  Sum_probs=20.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||||+||||+++.+ ..+
T Consensus         3 ~I~l~G~~GsGKsT~a~~L-~~~   24 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL-KER   24 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH-HHT
T ss_pred             EEEEECCCCCCHHHHHHHH-HHC
Confidence            5899999999999999999 665

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=97.58  E-value=0.00013  Score=60.01  Aligned_cols=23  Identities=39%  Similarity=0.574  Sum_probs=21.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||||+||||+++.++..+
T Consensus        35 livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           35 AFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             EEEEECCTTSCTHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            38999999999999999999886

>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=97.57  E-value=5.5e-05  Score=59.70  Aligned_cols=25  Identities=36%  Similarity=0.693  Sum_probs=22.9

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ...++|+|+||+||||+++.|++.+
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            3469999999999999999999988

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=97.57  E-value=5.6e-05  Score=58.77  Aligned_cols=24  Identities=29%  Similarity=0.469  Sum_probs=22.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+|++|+||||+++.|+..+
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            359999999999999999999987

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=97.57  E-value=0.00021  Score=71.54  Aligned_cols=23  Identities=35%  Similarity=0.566  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++||||||||++|++++.+.
T Consensus      1084 ~~l~~G~~g~GKT~la~~~~~~~ 1106 (1706)
T 3cmw_A         1084 IVEIYGPESSGKTTLTLQVIAAA 1106 (1706)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCChHHHHHHHHHHh
Confidence            39999999999999999999876

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=97.57  E-value=6.3e-05  Score=63.21  Aligned_cols=30  Identities=27%  Similarity=0.507  Sum_probs=25.8

Q ss_pred             HHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           77 LETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        77 l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +..+..++++|+|++|+||||+++.++..+
T Consensus        19 i~~g~~~~i~l~G~~G~GKTTl~~~la~~l   48 (359)
T 2ga8_A           19 IEDNYRVCVILVGSPGSGKSTIAEELCQII   48 (359)
T ss_dssp             TTTCSCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             hccCCeeEEEEECCCCCcHHHHHHHHHHHh
Confidence            345555679999999999999999999988

>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=97.56  E-value=4.9e-05  Score=57.42  Aligned_cols=23  Identities=30%  Similarity=0.495  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+||||+++.|++.+
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~l   26 (173)
T 1e6c_A            4 PIFMVGARGCGMTTVGRELARAL   26 (173)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999988

>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=97.56  E-value=6.8e-05  Score=58.25  Aligned_cols=23  Identities=48%  Similarity=0.917  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|+|+||+||||+++.|++.+
T Consensus        22 ~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           22 RVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            59999999999999999999988

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=97.55  E-value=5.2e-05  Score=58.52  Aligned_cols=25  Identities=28%  Similarity=0.480  Sum_probs=22.9

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ...++|+|++|+||||+++.|++.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            3469999999999999999999988

>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=97.55  E-value=4.6e-05  Score=58.69  Aligned_cols=24  Identities=42%  Similarity=0.574  Sum_probs=22.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+|+||+||||+++.+++.+
T Consensus         6 ~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            6 ALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            358999999999999999999987

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=97.54  E-value=6.1e-05  Score=58.53  Aligned_cols=26  Identities=35%  Similarity=0.537  Sum_probs=23.3

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ....++|+||+|+||||+++.++..+
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            44569999999999999999999887

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=97.53  E-value=5.3e-05  Score=57.98  Aligned_cols=23  Identities=48%  Similarity=0.907  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+||||+++.+++.+
T Consensus         6 ~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            6 AVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999987

>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=97.52  E-value=4.9e-05  Score=58.37  Aligned_cols=24  Identities=29%  Similarity=0.461  Sum_probs=22.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+|+||+||||+++.|++.+
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l   27 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNL   27 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            358999999999999999999987

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=97.52  E-value=0.00044  Score=58.60  Aligned_cols=24  Identities=33%  Similarity=0.506  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+|+||+|||+++..++..+.
T Consensus        65 ii~I~G~pGsGKTtLal~la~~~~   88 (356)
T 1u94_A           65 IVEIYGPESSGKTTLTLQVIAAAQ   88 (356)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            599999999999999999998763

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=97.52  E-value=0.0016  Score=51.06  Aligned_cols=43  Identities=19%  Similarity=0.263  Sum_probs=26.9

Q ss_pred             CCCcEEEEEeCCCCCC--HHHHHHHHHHHHhhcCcceEEEEecCC
Q 022641          153 CPPYKIIILDEADSMT--EDAQNALRRTMETYSKVTRFFFICNYI  195 (294)
Q Consensus       153 ~~~~~lliiDei~~l~--~~~~~~L~~~l~~~~~~~~ii~~~~~~  195 (294)
                      ....++||+||+|.+.  ......+..++...+....+++.|...
T Consensus       156 ~~~~~~lViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  200 (220)
T 1t6n_A          156 LKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATL  200 (220)
T ss_dssp             CTTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCC
T ss_pred             cccCCEEEEcCHHHHhcccCcHHHHHHHHHhCCCcCeEEEEEeec
Confidence            3456799999999873  344455556666555555565555433

>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=97.52  E-value=8.2e-05  Score=57.78  Aligned_cols=27  Identities=30%  Similarity=0.357  Sum_probs=23.6

Q ss_pred             CCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           80 ANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        80 ~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .....+.|+||+|+||||+++.++..+
T Consensus        23 ~~g~~i~l~G~sGsGKSTl~~~La~~l   49 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTLACALNQML   49 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            344469999999999999999999987

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=97.51  E-value=0.0044  Score=50.39  Aligned_cols=23  Identities=22%  Similarity=0.400  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++.|+||+|+||||+++.|+...
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            48899999999999999999876

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=97.50  E-value=7.1e-05  Score=56.26  Aligned_cols=23  Identities=22%  Similarity=0.349  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+||||+++.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l   24 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSL   24 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999988

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=97.50  E-value=0.00013  Score=57.05  Aligned_cols=24  Identities=33%  Similarity=0.527  Sum_probs=20.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++.+|+|+|||.++..++...
T Consensus        49 ~~~li~~~tGsGKT~~~~~~~~~~   72 (216)
T 3b6e_A           49 KNIIICLPTGSGKTRVAVYIAKDH   72 (216)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHHH
Confidence            479999999999999988877654

>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=97.49  E-value=0.00035  Score=59.12  Aligned_cols=24  Identities=38%  Similarity=0.527  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+||||+|||+++..++..+.
T Consensus        63 iv~I~G~pGsGKTtLal~la~~~~   86 (349)
T 2zr9_A           63 VIEIYGPESSGKTTVALHAVANAQ   86 (349)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            499999999999999999987763

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=97.48  E-value=7.5e-05  Score=57.51  Aligned_cols=23  Identities=30%  Similarity=0.543  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|+||+||||+++.+++.+
T Consensus         5 ~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            5 VVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999987

>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=97.46  E-value=9.8e-05  Score=58.85  Aligned_cols=24  Identities=38%  Similarity=0.699  Sum_probs=22.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++|.|++|+||||+++.|++.+
T Consensus        17 ~~I~l~G~~GsGKsT~a~~La~~l   40 (233)
T 1ak2_A           17 VRAVLLGPPGAGKGTQAPKLAKNF   40 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            469999999999999999999998

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=97.46  E-value=0.00015  Score=58.47  Aligned_cols=23  Identities=30%  Similarity=0.437  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|+||+||||+++.++..+
T Consensus        34 ~i~l~G~~GsGKSTla~~L~~~l   56 (253)
T 2p5t_B           34 AILLGGQSGAGKTTIHRIKQKEF   56 (253)
T ss_dssp             EEEEESCGGGTTHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            48999999999999999999987

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=97.46  E-value=7.4e-05  Score=57.80  Aligned_cols=24  Identities=25%  Similarity=0.501  Sum_probs=22.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+|+||+||||+++.|++.+
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~l   36 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEKY   36 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            369999999999999999999988

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=97.46  E-value=7.1e-05  Score=59.15  Aligned_cols=24  Identities=25%  Similarity=0.429  Sum_probs=22.6

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|.||||+||||+++.|++.+
T Consensus         6 ~~I~l~G~~GsGKsT~~~~La~~l   29 (222)
T 1zak_A            6 LKVMISGAPASGKGTQCELIKTKY   29 (222)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            469999999999999999999998

>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=97.45  E-value=0.00078  Score=56.96  Aligned_cols=24  Identities=29%  Similarity=0.350  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+||||+|||+++..++..+.
T Consensus        63 i~~I~GppGsGKSTLal~la~~~~   86 (356)
T 3hr8_A           63 IVEIFGQESSGKTTLALHAIAEAQ   86 (356)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999998863

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=97.45  E-value=6.5e-05  Score=57.76  Aligned_cols=23  Identities=30%  Similarity=0.432  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|.|+||+||||+++.|++.+
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l   25 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEIL   25 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            48999999999999999999988

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=97.44  E-value=0.00044  Score=54.49  Aligned_cols=41  Identities=22%  Similarity=0.332  Sum_probs=24.0

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhhcCcceEEEEecC
Q 022641          154 PPYKIIILDEADSMTED-AQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       154 ~~~~lliiDei~~l~~~-~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      .+..+||+||+|.+... ....+..++...+....+++.|..
T Consensus       154 ~~~~~iViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~lSAT  195 (224)
T 1qde_A          154 DKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSAT  195 (224)
T ss_dssp             TTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESS
T ss_pred             hhCcEEEEcChhHHhhhhhHHHHHHHHHhCCccCeEEEEEee
Confidence            44579999999986432 233455555554555555555433

>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=97.44  E-value=0.0001  Score=55.82  Aligned_cols=23  Identities=39%  Similarity=0.651  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+||||+++.++..+
T Consensus        10 ~i~l~G~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A           10 IYVLMGVSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHhh
Confidence            58999999999999999999886

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=97.44  E-value=9.3e-05  Score=57.67  Aligned_cols=24  Identities=29%  Similarity=0.610  Sum_probs=22.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+||+|+||||+++.|+..+
T Consensus        13 ~~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           13 PPLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            459999999999999999999886

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.44  E-value=0.00015  Score=62.89  Aligned_cols=96  Identities=19%  Similarity=0.229  Sum_probs=50.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCc----------cCCCCCCC
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQ----------RRGGYPCP  154 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~  154 (294)
                      .++.|+||||||+++..++..        .....+.+.. .....+++.+... ........          ........
T Consensus       164 ~~I~G~aGsGKTt~I~~~~~~--------~~~lVlTpT~-~aa~~l~~kl~~~-~~~~~~~~~V~T~dsfL~~~~~~~~~  233 (446)
T 3vkw_A          164 VLVDGVPGCGKTKEILSRVNF--------EEDLILVPGR-QAAEMIRRRANAS-GIIVATKDNVRTVDSFLMNYGKGARC  233 (446)
T ss_dssp             EEEEECTTSCHHHHHHHHCCT--------TTCEEEESCH-HHHHHHHHHHTTT-SCCCCCTTTEEEHHHHHHTTTSSCCC
T ss_pred             EEEEcCCCCCHHHHHHHHhcc--------CCeEEEeCCH-HHHHHHHHHhhhc-CccccccceEEEeHHhhcCCCCCCCC
Confidence            789999999999999777531        1222222221 2233333333210 00000000          00000111


Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecC
Q 022641          155 PYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       155 ~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      ..++|||||+..++......++..+    ....+|+++..
T Consensus       234 ~~d~liiDE~sm~~~~~l~~l~~~~----~~~~vilvGD~  269 (446)
T 3vkw_A          234 QFKRLFIDEGLMLHTGCVNFLVEMS----LCDIAYVYGDT  269 (446)
T ss_dssp             CCSEEEEETGGGSCHHHHHHHHHHT----TCSEEEEEECT
T ss_pred             cCCEEEEeCcccCCHHHHHHHHHhC----CCCEEEEecCc
Confidence            2579999999999988877776553    22567777743

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=97.43  E-value=7.5e-05  Score=58.82  Aligned_cols=24  Identities=29%  Similarity=0.585  Sum_probs=22.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|.|+||+||||+++.|++.+
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            359999999999999999999998

>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=97.42  E-value=6.4e-05  Score=57.80  Aligned_cols=24  Identities=42%  Similarity=0.594  Sum_probs=21.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+||+|+||||+++.++...
T Consensus        10 ~~i~l~G~~GsGKSTl~~~La~~~   33 (191)
T 1zp6_A           10 NILLLSGHPGSGKSTIAEALANLP   33 (191)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTCS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhcc
Confidence            359999999999999999998753

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=97.42  E-value=0.00011  Score=57.81  Aligned_cols=23  Identities=26%  Similarity=0.572  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|.||||+||+|.++.|++.+
T Consensus        31 iI~llGpPGsGKgTqa~~L~~~~   53 (217)
T 3umf_A           31 VIFVLGGPGSGKGTQCEKLVQKF   53 (217)
T ss_dssp             EEEEECCTTCCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            48889999999999999999988

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=97.42  E-value=8.3e-05  Score=58.99  Aligned_cols=24  Identities=29%  Similarity=0.555  Sum_probs=22.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+|+||+||||+++.|++.+
T Consensus         8 ~~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            8 LRAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            469999999999999999999987

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=97.41  E-value=0.00011  Score=56.13  Aligned_cols=23  Identities=13%  Similarity=0.369  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+||||+++.++..+
T Consensus         7 ~i~i~GpsGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A            7 TLVLLGAHGVGRRHIKNTLITKH   29 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            58999999999999999999875

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=97.41  E-value=0.00037  Score=63.46  Aligned_cols=41  Identities=24%  Similarity=0.344  Sum_probs=29.4

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      |...+..+...+..+. .++++++|+|+|||.++-.++..+.
T Consensus       183 Q~~ai~~~~~~~~~~~-~~~ll~~~TGsGKT~~~~~~~~~l~  223 (590)
T 3h1t_A          183 QQIAINRAVQSVLQGK-KRSLITMATGTGKTVVAFQISWKLW  223 (590)
T ss_dssp             HHHHHHHHHHHHHTTC-SEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCC-CceEEEecCCCChHHHHHHHHHHHH
Confidence            4445555555554443 4689999999999999888887764

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=97.40  E-value=7.6e-05  Score=56.91  Aligned_cols=24  Identities=42%  Similarity=0.657  Sum_probs=18.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+|+||+||||+++.+++.+
T Consensus         6 ~~I~l~G~~GsGKST~a~~La~~l   29 (183)
T 2vli_A            6 PIIWINGPFGVGKTHTAHTLHERL   29 (183)
T ss_dssp             CEEEEECCC----CHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            358999999999999999999987

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=97.40  E-value=9.8e-05  Score=57.39  Aligned_cols=23  Identities=26%  Similarity=0.512  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|+|++|+||||+++.|++.+
T Consensus        17 ~I~l~G~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           17 VIFVLGGPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999887

>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=97.40  E-value=0.0016  Score=55.31  Aligned_cols=24  Identities=50%  Similarity=0.566  Sum_probs=21.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+||||+|||+++..++..+.
T Consensus        76 li~I~G~pGsGKTtlal~la~~~~   99 (366)
T 1xp8_A           76 ITEIYGPESGGKTTLALAIVAQAQ   99 (366)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCChHHHHHHHHHHHH
Confidence            489999999999999999988763

>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=97.39  E-value=8.8e-05  Score=56.98  Aligned_cols=23  Identities=30%  Similarity=0.583  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+||||+++.+++.+
T Consensus         8 ~I~l~G~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A            8 VVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999987

>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=97.38  E-value=0.0005  Score=58.22  Aligned_cols=23  Identities=30%  Similarity=0.379  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+||+|+|||+++..++...
T Consensus       133 i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          133 ITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            38999999999999999999876

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=97.38  E-value=0.00015  Score=56.59  Aligned_cols=38  Identities=24%  Similarity=0.402  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHcC--CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           69 VVRVLTNTLETA--NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        69 ~~~~l~~~l~~~--~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++.|...+...  ....+.|.||+|+||||+++.|+..+
T Consensus         7 ~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~~~   46 (208)
T 3c8u_A            7 LCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAAAL   46 (208)
T ss_dssp             HHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            444554544432  23358999999999999999999987

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=97.37  E-value=0.00014  Score=58.58  Aligned_cols=24  Identities=38%  Similarity=0.502  Sum_probs=22.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+|++|+||||+++.++..+
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~~l   72 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMARSL   72 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhc
Confidence            479999999999999999999988

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=97.37  E-value=0.00065  Score=52.72  Aligned_cols=40  Identities=23%  Similarity=0.347  Sum_probs=23.6

Q ss_pred             CCcEEEEEeCCCCCCH-HHHHHHHHHHHhhcCcceEEEEec
Q 022641          154 PPYKIIILDEADSMTE-DAQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       154 ~~~~lliiDei~~l~~-~~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      ....+||+||+|.+.. .....+..++...+....+++.|.
T Consensus       145 ~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SA  185 (206)
T 1vec_A          145 DHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSA  185 (206)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHHHSCTTCEEEEEES
T ss_pred             ccCCEEEEEChHHhHhhCcHHHHHHHHHhCCccceEEEEEe
Confidence            4567999999997643 333444555555454455555443

>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=97.35  E-value=0.00012  Score=55.94  Aligned_cols=23  Identities=30%  Similarity=0.525  Sum_probs=21.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|+||+|+|||||++.|....
T Consensus         3 pIVi~GPSG~GK~Tl~~~L~~~~   25 (186)
T 1ex7_A            3 PIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            48999999999999999998876

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=97.35  E-value=0.0009  Score=57.28  Aligned_cols=28  Identities=21%  Similarity=0.133  Sum_probs=20.8

Q ss_pred             cCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           79 TANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        79 ~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+...++++.+|+|+|||..+...+-..
T Consensus        41 ~~~~~~~lv~a~TGsGKT~~~~~~~~~~   68 (395)
T 3pey_A           41 HNPPRNMIAQSQSGTGKTAAFSLTMLTR   68 (395)
T ss_dssp             CSSCCCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHH
Confidence            4444679999999999998766554443

>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=97.35  E-value=0.00015  Score=57.40  Aligned_cols=24  Identities=42%  Similarity=0.648  Sum_probs=22.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|+||+|+||||+++.++..+
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            358999999999999999999987

>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=97.35  E-value=0.0021  Score=53.02  Aligned_cols=23  Identities=35%  Similarity=0.421  Sum_probs=20.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.|+||+||||+++.+++.+
T Consensus         4 ~I~l~G~~GsGKST~a~~L~~~~   26 (301)
T 1ltq_A            4 IILTIGCPGSGKSTWAREFIAKN   26 (301)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            48999999999999999999863

>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=97.34  E-value=0.00012  Score=57.55  Aligned_cols=23  Identities=30%  Similarity=0.502  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++|+|+||+||||+++.|++.+
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            48999999999999999999987

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=97.33  E-value=0.00014  Score=56.87  Aligned_cols=24  Identities=25%  Similarity=0.374  Sum_probs=22.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .|+|.|+||+||||+++.|++.+.
T Consensus         6 ~I~i~G~~GsGKsT~~~~L~~~l~   29 (213)
T 2plr_A            6 LIAFEGIDGSGKSSQATLLKDWIE   29 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHh
Confidence            589999999999999999999883

>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=97.32  E-value=0.00013  Score=57.08  Aligned_cols=25  Identities=28%  Similarity=0.396  Sum_probs=22.2

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +..++|+||+|+||||+++.|+..+
T Consensus         8 g~~i~l~GpsGsGKsTl~~~L~~~~   32 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVREAVFKDP   32 (208)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHST
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhhC
Confidence            3459999999999999999999876

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=97.32  E-value=0.00014  Score=60.48  Aligned_cols=23  Identities=39%  Similarity=0.709  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+|||+++..+++.+
T Consensus         7 ~i~i~GptGsGKTtla~~La~~l   29 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLAMALADAL   29 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999997

>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=97.32  E-value=0.0019  Score=54.63  Aligned_cols=43  Identities=9%  Similarity=0.216  Sum_probs=31.6

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc--CcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS--KVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~--~~~~ii~~~~~~~  196 (294)
                      .++.+|++||.- .|++.....+++++....  ....+|++|.+..
T Consensus       180 ~~P~lLLlDEPTs~LD~~~~~~i~~lL~~l~~~~g~Tii~vTHdl~  225 (366)
T 3tui_C          180 SNPKVLLCDQATSALDPATTRSILELLKDINRRLGLTILLITHEMD  225 (366)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHSCCEEEEEESCHH
T ss_pred             cCCCEEEEECCCccCCHHHHHHHHHHHHHHHHhCCCEEEEEecCHH
Confidence            567899999964 578888888888887653  2556777776643

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=97.31  E-value=0.0052  Score=46.19  Aligned_cols=18  Identities=33%  Similarity=0.552  Sum_probs=16.7

Q ss_pred             cEEEECCCCCCHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALA  101 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~  101 (294)
                      .+.|+||+|+||||+++.
T Consensus        11 i~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A           11 LVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             EEEEECCTTSCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            589999999999999995

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=97.31  E-value=0.00033  Score=54.41  Aligned_cols=40  Identities=23%  Similarity=0.236  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHcC---CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           67 EEVVRVLTNTLETA---NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        67 ~~~~~~l~~~l~~~---~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ...++.+.+.+...   ....+.|+|++|+||||+++.++..+
T Consensus         4 ~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~   46 (201)
T 1rz3_A            4 RDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTL   46 (201)
T ss_dssp             HHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34555566665542   22348999999999999999999876

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=97.31  E-value=0.00015  Score=56.32  Aligned_cols=23  Identities=30%  Similarity=0.644  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.|++|+||||+++.|++.+
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l   24 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKL   24 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHhc
Confidence            48999999999999999999988

>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=97.31  E-value=0.0033  Score=49.09  Aligned_cols=27  Identities=22%  Similarity=0.426  Sum_probs=23.1

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ....++|+|++|+|||+++..+....+
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~~~   37 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTDSV   37 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            345699999999999999999987653

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=97.31  E-value=0.00027  Score=65.02  Aligned_cols=41  Identities=32%  Similarity=0.405  Sum_probs=31.6

Q ss_pred             ccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           65 HQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        65 g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      -++...+.+..++...  +..+|.||||||||+++..+..++.
T Consensus       190 LN~~Q~~AV~~al~~~--~~~lI~GPPGTGKT~ti~~~I~~l~  230 (646)
T 4b3f_X          190 LDTSQKEAVLFALSQK--ELAIIHGPPGTGKTTTVVEIILQAV  230 (646)
T ss_dssp             CCHHHHHHHHHHHHCS--SEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhcCC--CceEEECCCCCCHHHHHHHHHHHHH
Confidence            3677777888777643  2589999999999998877776663

>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=97.30  E-value=0.0012  Score=55.33  Aligned_cols=36  Identities=19%  Similarity=0.409  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           69 VVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        69 ~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +...+.-.+..+.  .++|+||+|+||||++++++...
T Consensus       160 ~l~~l~~~i~~g~--~v~i~G~~GsGKTTll~~l~g~~  195 (330)
T 2pt7_A          160 AISAIKDGIAIGK--NVIVCGGTGSGKTTYIKSIMEFI  195 (330)
T ss_dssp             HHHHHHHHHHHTC--CEEEEESTTSCHHHHHHHGGGGS
T ss_pred             HHhhhhhhccCCC--EEEEECCCCCCHHHHHHHHhCCC
Confidence            4445544555554  79999999999999999999876

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=97.29  E-value=0.00073  Score=52.42  Aligned_cols=21  Identities=24%  Similarity=0.173  Sum_probs=16.8

Q ss_pred             CcEEEECCCCCCHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIA  103 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la  103 (294)
                      .++++.+|+|+|||..+...+
T Consensus        39 ~~~li~~~TGsGKT~~~~~~~   59 (207)
T 2gxq_A           39 KDLIGQARTGTGKTLAFALPI   59 (207)
T ss_dssp             CCEEEECCTTSCHHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHHHHH
Confidence            479999999999998744433

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=97.28  E-value=0.0039  Score=55.25  Aligned_cols=68  Identities=10%  Similarity=0.099  Sum_probs=44.0

Q ss_pred             EEEEEeCCCCCCH----HHHHHHHHHHHhhc-CcceEEEEecCCc--ccchHhhcccc-EEEecCCCHHHHHHHHH
Q 022641          157 KIIILDEADSMTE----DAQNALRRTMETYS-KVTRFFFICNYIS--RIIEPLASRCA-KFRFKPLSEEVMSSRVL  224 (294)
Q Consensus       157 ~lliiDei~~l~~----~~~~~L~~~l~~~~-~~~~ii~~~~~~~--~~~~~l~~r~~-~i~~~~~~~~~~~~~l~  224 (294)
                      -+|+|||+..+-.    ...+.|..+..... ....+|++|..+.  .+...+.+.+. .|.|.-.+..+.+.++.
T Consensus       299 ivlvIDE~~~ll~~~~~~~~~~l~~Lar~gRa~GI~LIlaTQrp~~dvl~~~i~~n~~~RI~lrv~s~~dsr~ilg  374 (512)
T 2ius_A          299 IVVLVDEFADLMMTVGKKVEELIARLAQKARAAGIHLVLATQRPSVDVITGLIKANIPTRIAFTVSSKIDSRTILD  374 (512)
T ss_dssp             EEEEEETHHHHHHHHHHHHHHHHHHHHHHCGGGTEEEEEEESCCCTTTSCHHHHHHCCEEEEECCSSHHHHHHHHS
T ss_pred             EEEEEeCHHHHHhhhhHHHHHHHHHHHHHhhhCCcEEEEEecCCccccccHHHHhhcCCeEEEEcCCHHHHHHhcC
Confidence            4899999976532    22333444434333 3566788887765  46666777665 78888888888887764

>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=97.27  E-value=0.0016  Score=53.72  Aligned_cols=25  Identities=32%  Similarity=0.526  Sum_probs=22.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ..++|+||+|+||||++..++..+.
T Consensus       106 ~vi~lvG~~GsGKTTl~~~LA~~l~  130 (296)
T 2px0_A          106 KYIVLFGSTGAGKTTTLAKLAAISM  130 (296)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4599999999999999999998874

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=97.27  E-value=0.0002  Score=56.58  Aligned_cols=23  Identities=30%  Similarity=0.686  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.|+||+||||+++.|++.+
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            48999999999999999999987

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=97.27  E-value=0.0002  Score=55.56  Aligned_cols=24  Identities=29%  Similarity=0.508  Sum_probs=21.8

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|+||+|+||||+++.++..+
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             cEEEEECcCCCCHHHHHHHHHhhC
Confidence            468999999999999999999875

>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=97.26  E-value=0.00022  Score=55.07  Aligned_cols=24  Identities=21%  Similarity=0.402  Sum_probs=21.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+||+|+|||||++.|+...
T Consensus        20 ~~ivl~GPSGaGKsTL~~~L~~~~   43 (197)
T 3ney_A           20 KTLVLIGASGVGRSHIKNALLSQN   43 (197)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CEEEEECcCCCCHHHHHHHHHhhC
Confidence            358999999999999999999875

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=97.26  E-value=0.0011  Score=66.59  Aligned_cols=25  Identities=32%  Similarity=0.474  Sum_probs=22.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+++|+||||||||+++..++....
T Consensus        35 ~i~lI~G~pGsGKT~LAlqla~~~~   59 (1706)
T 3cmw_A           35 RIVEIYGPESSGKTTLTLQVIAAAQ   59 (1706)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4699999999999999999988753

>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=97.26  E-value=0.00021  Score=57.43  Aligned_cols=25  Identities=36%  Similarity=0.648  Sum_probs=22.7

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ...++|+||+|+||||+++.+++.+
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            3469999999999999999999887

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=97.25  E-value=0.00015  Score=55.48  Aligned_cols=24  Identities=42%  Similarity=0.544  Sum_probs=22.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+|++|+||||+++.++..+
T Consensus        14 ~~i~l~G~~GsGKsT~~~~L~~~l   37 (186)
T 2yvu_A           14 IVVWLTGLPGSGKTTIATRLADLL   37 (186)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHH
Confidence            358999999999999999999987

>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=97.25  E-value=0.0002  Score=55.18  Aligned_cols=22  Identities=27%  Similarity=0.374  Sum_probs=21.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.|+|++|+||||+++.+++.+
T Consensus        15 IgltG~~GSGKSTva~~L~~~l   36 (192)
T 2grj_A           15 IGVTGKIGTGKSTVCEILKNKY   36 (192)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHhc
Confidence            8999999999999999999986

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=97.24  E-value=0.00018  Score=56.17  Aligned_cols=24  Identities=25%  Similarity=0.407  Sum_probs=22.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..|+|+|++|+||||+++.|++.+
T Consensus        11 ~~I~l~G~~GsGKST~~~~L~~~l   34 (212)
T 2wwf_A           11 KFIVFEGLDRSGKSTQSKLLVEYL   34 (212)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHH
Confidence            359999999999999999999987

>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=97.23  E-value=0.00033  Score=54.78  Aligned_cols=28  Identities=29%  Similarity=0.439  Sum_probs=23.9

Q ss_pred             cCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           79 TANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        79 ~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ...+..++|+|++|+||||+++.++..+
T Consensus        22 ~~~~~~i~~~G~~GsGKsT~~~~l~~~l   49 (211)
T 1m7g_A           22 NQRGLTIWLTGLSASGKSTLAVELEHQL   49 (211)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHh
Confidence            3444469999999999999999999987

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=97.23  E-value=0.00023  Score=55.36  Aligned_cols=25  Identities=28%  Similarity=0.375  Sum_probs=22.2

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +..+.|+||+|+||||+++.++..+
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhh
Confidence            3468999999999999999998876

>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=97.23  E-value=0.011  Score=43.45  Aligned_cols=23  Identities=17%  Similarity=0.398  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++.|++|+|||+++..+....
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            48999999999999999988654

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=97.22  E-value=0.00023  Score=55.20  Aligned_cols=24  Identities=25%  Similarity=0.468  Sum_probs=21.9

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|+||+|+||||+++.+...+
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            359999999999999999999876

>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=97.22  E-value=0.00016  Score=56.15  Aligned_cols=22  Identities=32%  Similarity=0.406  Sum_probs=20.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+|++|+||||+++.++. +
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-~   24 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-L   24 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-T
T ss_pred             EEEEECCCCcCHHHHHHHHHH-C
Confidence            489999999999999999998 6

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=97.22  E-value=0.00021  Score=54.95  Aligned_cols=23  Identities=39%  Similarity=0.481  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+||||+++.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l   24 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYL   24 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999999986

>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=97.22  E-value=0.00021  Score=55.88  Aligned_cols=25  Identities=20%  Similarity=0.310  Sum_probs=22.6

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +..|+|+|++|+||||+++.|++.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l   33 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEAL   33 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            3469999999999999999999987

>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=97.21  E-value=0.0002  Score=55.55  Aligned_cols=24  Identities=29%  Similarity=0.494  Sum_probs=22.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..|+|+|++|+||||+++.|++.+
T Consensus         5 ~~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            5 ALIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHTS
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHH
Confidence            469999999999999999999876

>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=97.20  E-value=0.00027  Score=56.06  Aligned_cols=24  Identities=33%  Similarity=0.540  Sum_probs=22.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|.||+|+||||+++.+++.+
T Consensus        10 ~~i~i~G~~GsGKsTla~~la~~l   33 (233)
T 3r20_A           10 LVVAVDGPAGTGKSSVSRGLARAL   33 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            359999999999999999999988

>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=97.20  E-value=0.0002  Score=54.90  Aligned_cols=23  Identities=43%  Similarity=0.668  Sum_probs=20.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+||||+++.++...
T Consensus         4 ii~l~G~~GaGKSTl~~~L~~~~   26 (189)
T 2bdt_A            4 LYIITGPAGVGKSTTCKRLAAQL   26 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCcHHHHHHHHhccc
Confidence            47899999999999999998754

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=97.20  E-value=0.0014  Score=53.74  Aligned_cols=38  Identities=11%  Similarity=0.080  Sum_probs=27.1

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+...+.+..++..   .+.++.+|+|+|||.++..++...
T Consensus       115 ~~~Q~~ai~~~l~~---~~~ll~~~tGsGKT~~~~~~~~~~  152 (282)
T 1rif_A          115 HWYQKDAVFEGLVN---RRRILNLPTSAGRSLIQALLARYY  152 (282)
T ss_dssp             CHHHHHHHHHHHHH---SEEEECCCTTSCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhc---CCeEEEcCCCCCcHHHHHHHHHHH
Confidence            44445555555554   247889999999999998877764

>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=97.16  E-value=0.00021  Score=55.60  Aligned_cols=21  Identities=33%  Similarity=0.319  Sum_probs=19.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~  104 (294)
                      .+.|+||+|+||||+++.++.
T Consensus         4 ~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999987

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=97.16  E-value=0.00036  Score=56.26  Aligned_cols=24  Identities=42%  Similarity=0.645  Sum_probs=22.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|.||+|+||||+++.+++.+
T Consensus        28 ~~I~I~G~~GsGKSTl~k~La~~L   51 (252)
T 4e22_A           28 PVITVDGPSGAGKGTLCKALAESL   51 (252)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhc
Confidence            469999999999999999999887

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=97.15  E-value=0.0016  Score=61.06  Aligned_cols=32  Identities=25%  Similarity=0.346  Sum_probs=22.8

Q ss_pred             HHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHH
Q 022641           72 VLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        72 ~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .+..++..+.  +++++||+|+|||+++..+...
T Consensus       101 ~i~~~l~~~~--~vii~gpTGSGKTtllp~ll~~  132 (773)
T 2xau_A          101 EFLKLYQNNQ--IMVFVGETGSGKTTQIPQFVLF  132 (773)
T ss_dssp             HHHHHHHHCS--EEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHHHHhCCC--eEEEECCCCCCHHHHHHHHHHH
Confidence            3444444443  6999999999999977766544

>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=97.15  E-value=0.0003  Score=54.68  Aligned_cols=23  Identities=30%  Similarity=0.491  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+|++|+||||+++.++..+
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~l   26 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAAL   26 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            58999999999999999999988

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=97.15  E-value=0.00029  Score=55.36  Aligned_cols=44  Identities=16%  Similarity=0.222  Sum_probs=34.5

Q ss_pred             hcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           63 VAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        63 ~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +..+......+...+.....+.++|+|++|+||||++..++..+
T Consensus        11 l~~~~~~~~~~~~~~~~~~~~~i~i~G~~g~GKTTl~~~l~~~~   54 (221)
T 2wsm_A           11 LAENKRLAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERI   54 (221)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             HhhcHHHHHHHHHhhcccCceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            33555666666666655566679999999999999999999886

>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=97.13  E-value=0.0016  Score=53.97  Aligned_cols=43  Identities=19%  Similarity=0.315  Sum_probs=30.7

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                      .++.+|++||.- .|++.....+.+.+........+|+++.+..
T Consensus       207 ~~p~iLlLDEPts~LD~~~~~~i~~~l~~l~~~~Tvi~itH~l~  250 (306)
T 3nh6_A          207 KAPGIILLDEATSALDTSNERAIQASLAKVCANRTTIVVAHRLS  250 (306)
T ss_dssp             HCCSEEEEECCSSCCCHHHHHHHHHHHHHHHTTSEEEEECCSHH
T ss_pred             hCCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEEcChH
Confidence            356799999975 5677777777777776555566777776544

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=97.13  E-value=0.002  Score=54.43  Aligned_cols=24  Identities=21%  Similarity=0.224  Sum_probs=19.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++.+|+|+|||..+...+...
T Consensus        45 ~~~l~~~~TGsGKT~~~~~~~~~~   68 (367)
T 1hv8_A           45 YNIVAQARTGSGKTASFAIPLIEL   68 (367)
T ss_dssp             SEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHHHHHHHH
Confidence            479999999999999876655554

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=97.13  E-value=0.00019  Score=59.93  Aligned_cols=23  Identities=26%  Similarity=0.603  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+|||+|+..|++.+
T Consensus        42 lIvI~GPTgsGKTtLa~~LA~~l   64 (339)
T 3a8t_A           42 LLVLMGATGTGKSRLSIDLAAHF   64 (339)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTTS
T ss_pred             eEEEECCCCCCHHHHHHHHHHHC
Confidence            59999999999999999999987

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=97.11  E-value=0.0018  Score=53.65  Aligned_cols=39  Identities=23%  Similarity=0.359  Sum_probs=23.8

Q ss_pred             CcEEEEEeCCCCCCH--HHHHHHHHHHHhhcCcceEEEEec
Q 022641          155 PYKIIILDEADSMTE--DAQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       155 ~~~lliiDei~~l~~--~~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      .-.+|||||+|.+..  .....+..++...+....+++.|.
T Consensus       235 ~l~~lVlDEad~l~~~~~~~~~~~~i~~~~~~~~q~i~~SA  275 (300)
T 3fmo_B          235 KIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSA  275 (300)
T ss_dssp             GCSEEEETTHHHHHHSTTHHHHHHHHHTTSCTTCEEEEEES
T ss_pred             hceEEEEeCHHHHhhccCcHHHHHHHHHhCCCCCEEEEEec
Confidence            456999999998743  334445555555455555555553

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=97.11  E-value=0.00035  Score=55.00  Aligned_cols=24  Identities=25%  Similarity=0.490  Sum_probs=21.8

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|+||+|+||||+++.++...
T Consensus        24 ~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           24 YPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            359999999999999999999865

>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=97.10  E-value=0.00079  Score=55.41  Aligned_cols=24  Identities=38%  Similarity=0.787  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+.|.||+|+||||+++.++..+.
T Consensus        33 ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           33 FIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            489999999999999999998873

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=97.10  E-value=0.00098  Score=53.08  Aligned_cols=41  Identities=17%  Similarity=0.288  Sum_probs=24.0

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhhcCcceEEEEecC
Q 022641          154 PPYKIIILDEADSMTED-AQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       154 ~~~~lliiDei~~l~~~-~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      ....+||+||+|.+... ....+..++...+....+++.|..
T Consensus       172 ~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT  213 (237)
T 3bor_A          172 KWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSAT  213 (237)
T ss_dssp             TTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSS
T ss_pred             ccCcEEEECCchHhhccCcHHHHHHHHHhCCCCCeEEEEEEe
Confidence            34579999999976322 233445555555555555555533

>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=97.07  E-value=0.00035  Score=57.54  Aligned_cols=23  Identities=30%  Similarity=0.631  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+|||+++..+++.+
T Consensus        12 ~i~i~GptgsGKt~la~~La~~~   34 (316)
T 3foz_A           12 AIFLMGPTASGKTALAIELRKIL   34 (316)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECCCccCHHHHHHHHHHhC
Confidence            48899999999999999999987

>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=97.06  E-value=0.00038  Score=52.84  Aligned_cols=23  Identities=35%  Similarity=0.569  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+||||+++.++..+
T Consensus         7 ~i~l~G~~GsGKST~~~~L~~~l   29 (179)
T 2pez_A            7 TVWLTGLSGAGKTTVSMALEEYL   29 (179)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            58999999999999999999976

>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=97.05  E-value=0.00042  Score=54.55  Aligned_cols=24  Identities=21%  Similarity=0.373  Sum_probs=21.8

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+||+|+|||||++.++...
T Consensus        17 ~ii~l~GpsGsGKSTLlk~L~g~~   40 (219)
T 1s96_A           17 TLYIVSAPSGAGKSSLIQALLKTQ   40 (219)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHhccC
Confidence            358999999999999999999876

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=97.05  E-value=0.0015  Score=52.52  Aligned_cols=19  Identities=21%  Similarity=0.263  Sum_probs=15.9

Q ss_pred             CcEEEECCCCCCHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALA  101 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~  101 (294)
                      .++++.+|+|+|||.....
T Consensus        81 ~~~lv~a~TGsGKT~~~~~   99 (249)
T 3ber_A           81 RDIIGLAETGSGKTGAFAL   99 (249)
T ss_dssp             CCEEEECCTTSCHHHHHHH
T ss_pred             CCEEEEcCCCCCchhHhHH
Confidence            4799999999999987543

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=97.03  E-value=0.00041  Score=58.11  Aligned_cols=23  Identities=26%  Similarity=0.624  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+|||+++..|+..+
T Consensus         9 lI~I~GptgSGKTtla~~La~~l   31 (340)
T 3d3q_A            9 LIVIVGPTASGKTELSIEVAKKF   31 (340)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT
T ss_pred             eEEEECCCcCcHHHHHHHHHHHc
Confidence            58999999999999999999987

>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=97.03  E-value=0.00045  Score=53.84  Aligned_cols=25  Identities=20%  Similarity=0.438  Sum_probs=22.3

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ...+.|.||+|+||||+++.++..+
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3469999999999999999999876

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=97.02  E-value=0.0023  Score=55.09  Aligned_cols=24  Identities=21%  Similarity=0.278  Sum_probs=18.5

Q ss_pred             cCCCCcEEEECCCCCCHHHHHHHH
Q 022641           79 TANCPHMLFYGPPGTGKTTTALAI  102 (294)
Q Consensus        79 ~~~~~~ill~Gp~G~GKT~la~~l  102 (294)
                      .+...++++.+|+|+|||..+-..
T Consensus        61 ~~~~~~~lv~apTGsGKT~~~~~~   84 (412)
T 3fht_A           61 AEPPQNLIAQSQSGTGKTAAFVLA   84 (412)
T ss_dssp             SSSCCCEEEECCTTSCHHHHHHHH
T ss_pred             cCCCCeEEEECCCCchHHHHHHHH
Confidence            343457999999999999886443

>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=97.02  E-value=0.00034  Score=57.75  Aligned_cols=23  Identities=35%  Similarity=0.603  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.||+|+|||+++..+++.+
T Consensus         5 ~i~i~GptgsGKt~la~~La~~~   27 (322)
T 3exa_A            5 LVAIVGPTAVGKTKTSVMLAKRL   27 (322)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHTT
T ss_pred             EEEEECCCcCCHHHHHHHHHHhC
Confidence            48899999999999999999887

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=97.02  E-value=0.00068  Score=53.42  Aligned_cols=42  Identities=19%  Similarity=0.215  Sum_probs=32.7

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++.....++..+.....+.++|+|++|+|||+++..++...+
T Consensus        22 ~~~~a~~~r~~~~~~~~~~i~ivG~~gvGKTtl~~~l~~~~~   63 (226)
T 2hf9_A           22 NKRLADKNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDNLK   63 (226)
T ss_dssp             HHHHHHHHHHHHHHTTCEEEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHhCCCeEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            344555666666555566799999999999999999998874

>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=97.01  E-value=0.0066  Score=46.53  Aligned_cols=22  Identities=23%  Similarity=0.472  Sum_probs=19.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++++|++|+|||+|++.+...
T Consensus        22 ki~~vG~~~vGKTsLi~~l~~~   43 (196)
T 3llu_A           22 RILLMGLRRSGKSSIQKVVFHK   43 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhc
Confidence            4999999999999999877654

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=97.00  E-value=0.0086  Score=47.69  Aligned_cols=18  Identities=33%  Similarity=0.475  Sum_probs=15.3

Q ss_pred             CcEEEECCCCCCHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTAL  100 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~  100 (294)
                      .++++.+|+|+|||....
T Consensus        67 ~~~l~~a~TGsGKT~~~~   84 (245)
T 3dkp_A           67 RELLASAPTGSGKTLAFS   84 (245)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CCEEEECCCCCcHHHHHH
Confidence            369999999999998743

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=96.99  E-value=0.0023  Score=50.61  Aligned_cols=24  Identities=25%  Similarity=0.289  Sum_probs=17.7

Q ss_pred             CcEEEECCCCCCHHHHHH-HHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTAL-AIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~-~la~~~  106 (294)
                      .++++.+|+|+|||.... .+...+
T Consensus        62 ~~~l~~a~TGsGKT~~~~l~~l~~l   86 (230)
T 2oxc_A           62 LDLIVQAKSGTGKTCVFSTIALDSL   86 (230)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CCEEEECCCCCcHHHHHHHHHHHHH
Confidence            479999999999998743 333443

>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=96.98  E-value=0.0031  Score=49.44  Aligned_cols=22  Identities=23%  Similarity=0.374  Sum_probs=19.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|.|.+|+|||+|+..+...-
T Consensus        16 ivlvGd~~VGKTsLi~r~~~~~   37 (216)
T 4dkx_A           16 LVFLGEQSVGKTSLITRFMYDS   37 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECcCCcCHHHHHHHHHhCC
Confidence            9999999999999999987654

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=96.98  E-value=0.0075  Score=51.74  Aligned_cols=24  Identities=25%  Similarity=0.250  Sum_probs=18.6

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++.+|+|+|||..+...+-..
T Consensus        59 ~~~li~a~TGsGKT~~~~~~~~~~   82 (400)
T 1s2m_A           59 RDILARAKNGTGKTAAFVIPTLEK   82 (400)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCEEEECCCCcHHHHHHHHHHHHH
Confidence            369999999999998765555443

>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=96.98  E-value=0.00016  Score=56.31  Aligned_cols=42  Identities=12%  Similarity=0.043  Sum_probs=21.7

Q ss_pred             ccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           65 HQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        65 g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++...+.+.........-.++++|++|+|||+++..+....
T Consensus        13 ~~~~~~~~m~~~~~~~~~~ki~vvG~~~~GKSsLi~~l~~~~   54 (204)
T 4gzl_A           13 GLVPRGSHMENLYFQGQAIKCVVVGDGAVGKTCLLISYTTNA   54 (204)
T ss_dssp             -----------------CEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             CcccchhHHHhHhhcCCeEEEEEECcCCCCHHHHHHHHHhCC
Confidence            344444444444444444469999999999999999998654

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=96.98  E-value=0.00032  Score=54.76  Aligned_cols=22  Identities=45%  Similarity=0.554  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .+.|.||.|+|||||++.++..
T Consensus        24 ~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           24 IVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             EEEEECCTTSSTTHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            6899999999999999999876

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=96.98  E-value=0.00039  Score=54.30  Aligned_cols=23  Identities=39%  Similarity=0.414  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+||+|+||||+++.++..+
T Consensus         8 ~i~i~G~~GsGKSTl~~~l~~~~   30 (211)
T 3asz_A            8 VIGIAGGTASGKTTLAQALARTL   30 (211)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999986

>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=96.97  E-value=0.00056  Score=55.08  Aligned_cols=23  Identities=22%  Similarity=0.304  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|.|+|++|+||||+++.|+..+
T Consensus        24 iI~I~G~~GSGKST~a~~L~~~l   46 (252)
T 1uj2_A           24 LIGVSGGTASGKSSVCAKIVQLL   46 (252)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999987

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=96.95  E-value=0.002  Score=51.19  Aligned_cols=23  Identities=26%  Similarity=0.255  Sum_probs=21.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+|||+++..++...
T Consensus        26 ~~~i~G~~GsGKTtl~~~l~~~~   48 (243)
T 1n0w_A           26 ITEMFGEFRTGKTQICHTLAVTC   48 (243)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHH
Confidence            59999999999999999999864

>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=96.95  E-value=0.00055  Score=50.90  Aligned_cols=24  Identities=25%  Similarity=0.360  Sum_probs=22.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|.||.|+||||+++.++..+
T Consensus        34 e~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           34 IMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            358999999999999999999987

>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=96.95  E-value=0.0013  Score=56.89  Aligned_cols=48  Identities=21%  Similarity=0.268  Sum_probs=32.8

Q ss_pred             cchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           59 QVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++++--.......+...+ ......++|+||+|+||||++++++..+.
T Consensus       145 ~l~~Lg~~~~~~~~L~~l~-~~~ggii~I~GpnGSGKTTlL~allg~l~  192 (418)
T 1p9r_A          145 DLHSLGMTAHNHDNFRRLI-KRPHGIILVTGPTGSGKSTTLYAGLQELN  192 (418)
T ss_dssp             CGGGSCCCHHHHHHHHHHH-TSSSEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             CHHHcCCCHHHHHHHHHHH-HhcCCeEEEECCCCCCHHHHHHHHHhhcC
Confidence            3444443444444555554 33334589999999999999999999873

>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=96.95  E-value=0.00052  Score=53.93  Aligned_cols=22  Identities=41%  Similarity=0.489  Sum_probs=20.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+|++|+||||+++.|+. +
T Consensus         6 ~I~i~G~~GSGKST~~~~L~~-l   27 (218)
T 1vht_A            6 IVALTGGIGSGKSTVANAFAD-L   27 (218)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH-T
T ss_pred             EEEEECCCCCCHHHHHHHHHH-c
Confidence            589999999999999999987 5

>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=96.93  E-value=0.00091  Score=50.83  Aligned_cols=23  Identities=22%  Similarity=0.302  Sum_probs=20.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+|+..+...-
T Consensus         9 ki~v~G~~~vGKSsli~~l~~~~   31 (184)
T 1m7b_A            9 KIVVVGDSQCGKTALLHVFAKDC   31 (184)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            48999999999999999998754

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=96.93  E-value=0.00075  Score=53.76  Aligned_cols=24  Identities=33%  Similarity=0.524  Sum_probs=22.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|+|++|+||||+++.++..+
T Consensus        17 ~~i~i~G~~gsGKst~~~~l~~~l   40 (236)
T 1q3t_A           17 IQIAIDGPASSGKSTVAKIIAKDF   40 (236)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            459999999999999999999987

>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=96.92  E-value=0.00084  Score=59.51  Aligned_cols=43  Identities=12%  Similarity=0.195  Sum_probs=31.9

Q ss_pred             ccHHHHHHHHHHH--HcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           65 HQEEVVRVLTNTL--ETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        65 g~~~~~~~l~~~l--~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ..+++.+.+++..  ......+|+|+|.+|+||||++++|++.+.
T Consensus       376 ~rpeV~~vLr~~~~~~~~~~~~I~l~GlsGsGKSTIa~~La~~L~  420 (511)
T 1g8f_A          376 SYPEVVKILRESNPPRPKQGFSIVLGNSLTVSREQLSIALLSTFL  420 (511)
T ss_dssp             SCHHHHHHHHHHSCCGGGCCEEEEECTTCCSCHHHHHHHHHHHHT
T ss_pred             cChhhHHHHHHhcccccccceEEEecccCCCCHHHHHHHHHHHHH
Confidence            4455555666554  222334699999999999999999999993

>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=96.91  E-value=0.005  Score=46.10  Aligned_cols=23  Identities=17%  Similarity=0.332  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+++..+...-
T Consensus         9 ~i~v~G~~~~GKSsli~~l~~~~   31 (177)
T 1wms_A            9 KVILLGDGGVGKSSLMNRYVTNK   31 (177)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            49999999999999999998654

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=96.90  E-value=0.002  Score=50.45  Aligned_cols=21  Identities=33%  Similarity=0.282  Sum_probs=16.8

Q ss_pred             CcEEEECCCCCCHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIA  103 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la  103 (294)
                      .++++.+|+|+|||......+
T Consensus        42 ~~~lv~a~TGsGKT~~~~~~~   62 (219)
T 1q0u_A           42 ESMVGQSQTGTGKTHAYLLPI   62 (219)
T ss_dssp             CCEEEECCSSHHHHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHHHHH
Confidence            479999999999998754443

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=96.89  E-value=0.00087  Score=54.27  Aligned_cols=26  Identities=31%  Similarity=0.540  Sum_probs=22.7

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ....++|+||+|+||||+++.++..+
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~l~g~~   49 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIASMIDYI   49 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCccHHHHHHHHHHhC
Confidence            33469999999999999999999876

>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=96.89  E-value=0.00066  Score=51.32  Aligned_cols=24  Identities=17%  Similarity=0.178  Sum_probs=20.9

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      -.++++|++|+|||+++..+...-
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            359999999999999999988653

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=96.88  E-value=0.0015  Score=54.39  Aligned_cols=23  Identities=26%  Similarity=0.287  Sum_probs=21.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|.||+|+||||+++.+...+
T Consensus        94 iigI~GpsGSGKSTl~~~L~~ll  116 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTSRVLKALL  116 (321)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            38999999999999999999887

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=96.88  E-value=0.00069  Score=53.20  Aligned_cols=23  Identities=35%  Similarity=0.598  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+|++|+||||+++.++..+
T Consensus         5 ~i~i~G~~gsGkst~~~~l~~~~   27 (219)
T 2h92_A            5 NIALDGPAAAGKSTIAKRVASEL   27 (219)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            58999999999999999999987

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=96.88  E-value=0.0049  Score=48.55  Aligned_cols=40  Identities=15%  Similarity=0.237  Sum_probs=23.9

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhhcCcceEEEEec
Q 022641          154 PPYKIIILDEADSMTED-AQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       154 ~~~~lliiDei~~l~~~-~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      .+.++||+||+|.+... ....+..++...+....+++.|.
T Consensus       166 ~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SA  206 (228)
T 3iuy_A          166 RSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSA  206 (228)
T ss_dssp             TTCCEEEECCHHHHHHTTCHHHHHHHHHHSCSSCEEEEEES
T ss_pred             ccceEEEEECHHHHhccchHHHHHHHHHhCCcCCeEEEEEe
Confidence            45679999999986432 23344455555555555555543

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=96.87  E-value=0.00077  Score=53.24  Aligned_cols=24  Identities=33%  Similarity=0.426  Sum_probs=21.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+||+|+|||++++.++..+
T Consensus        24 ~~~~i~G~~GsGKTtl~~~l~~~~   47 (235)
T 2w0m_A           24 FFIALTGEPGTGKTIFSLHFIAKG   47 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHH
Confidence            358999999999999999999765

>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=96.85  E-value=0.00085  Score=55.46  Aligned_cols=26  Identities=35%  Similarity=0.588  Sum_probs=22.9

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ....+.|+||+|+|||||++.|+..+
T Consensus       125 ~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          125 KKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             TCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            33469999999999999999999886

>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=96.85  E-value=0.0018  Score=51.10  Aligned_cols=23  Identities=30%  Similarity=0.379  Sum_probs=21.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+||+|+||||+++.++..+
T Consensus        27 ~~~l~G~nGsGKSTll~~l~g~~   49 (231)
T 4a74_A           27 ITEVFGEFGSGKTQLAHTLAVMV   49 (231)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            49999999999999999999865

>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=96.85  E-value=0.0051  Score=45.58  Aligned_cols=23  Identities=17%  Similarity=0.375  Sum_probs=20.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+++..+...-
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            48999999999999999998765

>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=96.84  E-value=0.00073  Score=53.60  Aligned_cols=24  Identities=42%  Similarity=0.704  Sum_probs=22.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|.||+|+||||+++.++..+.
T Consensus        28 ~i~i~G~~GsGKsT~~~~l~~~l~   51 (229)
T 4eaq_A           28 FITFEGPEGSGKTTVINEVYHRLV   51 (229)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHh
Confidence            489999999999999999999983

>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=96.84  E-value=0.00057  Score=52.85  Aligned_cols=23  Identities=26%  Similarity=0.244  Sum_probs=20.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~  105 (294)
                      ..+.|+|++|+||||+++.|++.
T Consensus         9 ~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHC
Confidence            35899999999999999999874

>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=96.84  E-value=0.00024  Score=55.54  Aligned_cols=23  Identities=22%  Similarity=0.306  Sum_probs=21.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.|++|+||||+++.|++.+
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l   24 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAF   24 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            37899999999999999999987

>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=96.83  E-value=0.0014  Score=50.99  Aligned_cols=23  Identities=22%  Similarity=0.302  Sum_probs=20.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+|+..+...-
T Consensus        30 ki~vvG~~~vGKSsLi~~l~~~~   52 (205)
T 1gwn_A           30 KIVVVGDSQCGKTALLHVFAKDC   52 (205)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            49999999999999999998764

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=96.83  E-value=0.014  Score=57.28  Aligned_cols=42  Identities=21%  Similarity=0.275  Sum_probs=30.7

Q ss_pred             hcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHH
Q 022641           63 VAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        63 ~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~  104 (294)
                      -..|..++..+...+.++.+.+++++||+|+|||.++...+-
T Consensus       605 t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~  646 (1151)
T 2eyq_A          605 TPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAF  646 (1151)
T ss_dssp             CHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHH
Confidence            345566666666666667666899999999999988764443

>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=96.83  E-value=0.00089  Score=55.48  Aligned_cols=25  Identities=32%  Similarity=0.357  Sum_probs=22.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ..+.|+||+|+||||+++.++..+.
T Consensus       103 ~vi~lvG~nGsGKTTll~~Lagll~  127 (304)
T 1rj9_A          103 RVVLVVGVNGVGKTTTIAKLGRYYQ  127 (304)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHH
Confidence            3589999999999999999998874

>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=96.82  E-value=0.00061  Score=55.88  Aligned_cols=22  Identities=27%  Similarity=0.442  Sum_probs=20.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|.|+|++|+||||+++.|+ .+
T Consensus        77 iI~I~G~~GSGKSTva~~La-~l   98 (281)
T 2f6r_A           77 VLGLTGISGSGKSSVAQRLK-NL   98 (281)
T ss_dssp             EEEEEECTTSCHHHHHHHHH-HH
T ss_pred             EEEEECCCCCCHHHHHHHHH-HC
Confidence            49999999999999999999 45

>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=96.82  E-value=0.00047  Score=52.89  Aligned_cols=23  Identities=35%  Similarity=0.544  Sum_probs=21.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+|||++|..+++..
T Consensus        36 ~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           36 GVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             EEEEECCCTTTTHHHHHHHHTTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            48999999999999999999875

>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=96.80  E-value=0.0059  Score=44.88  Aligned_cols=23  Identities=17%  Similarity=0.463  Sum_probs=20.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++.|++|+|||+++..+....
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            48999999999999999998764

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=96.80  E-value=0.00057  Score=56.43  Aligned_cols=24  Identities=17%  Similarity=0.357  Sum_probs=20.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+||||+|||+|+..++..+.
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~   53 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYM   53 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHH
Confidence            389999999999999988877763

>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=96.79  E-value=0.00042  Score=53.95  Aligned_cols=23  Identities=30%  Similarity=0.345  Sum_probs=20.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+|++|+||||+++.++..+
T Consensus        23 ~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           23 IIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTTS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            48899999999999999998764

>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=96.78  E-value=0.00096  Score=50.04  Aligned_cols=25  Identities=20%  Similarity=0.033  Sum_probs=22.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      +.+.|+|++|+||||++..++..+.
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~l~   29 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAAAV   29 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhhH
Confidence            4589999999999999999999873

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=96.78  E-value=0.0049  Score=48.84  Aligned_cols=40  Identities=18%  Similarity=0.373  Sum_probs=23.8

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhhcCcceEEEEec
Q 022641          154 PPYKIIILDEADSMTED-AQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       154 ~~~~lliiDei~~l~~~-~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      ....+||+||+|.+... ....+..++...+....+++.|.
T Consensus       170 ~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SA  210 (236)
T 2pl3_A          170 TDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSA  210 (236)
T ss_dssp             TTCCEEEETTHHHHHHTTTHHHHHHHHHTSCTTSEEEEEES
T ss_pred             ccccEEEEeChHHHhcCCcHHHHHHHHHhCCCCCeEEEEEe
Confidence            44569999999976432 23445555555555554554443

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=96.78  E-value=0.00052  Score=54.44  Aligned_cols=24  Identities=33%  Similarity=0.443  Sum_probs=15.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHH-HHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIA-HQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la-~~~  106 (294)
                      ..+.|+||+|+||||+++.++ ..+
T Consensus        28 ~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           28 VILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CEEEEECSCC----CHHHHHHC---
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcCC
Confidence            358999999999999999999 664

>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=96.77  E-value=0.0087  Score=44.11  Aligned_cols=23  Identities=22%  Similarity=0.417  Sum_probs=20.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++.|++|+|||+++..+...-
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            58999999999999999998754

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=96.76  E-value=0.0038  Score=55.15  Aligned_cols=23  Identities=22%  Similarity=0.301  Sum_probs=17.9

Q ss_pred             cCCCCcEEEECCCCCCHHHHHHH
Q 022641           79 TANCPHMLFYGPPGTGKTTTALA  101 (294)
Q Consensus        79 ~~~~~~ill~Gp~G~GKT~la~~  101 (294)
                      .+...++++.||+|+|||.....
T Consensus       128 ~~~~~~~l~~a~TGsGKT~~~~l  150 (479)
T 3fmp_B          128 AEPPQNLIAQSQSGTGKTAAFVL  150 (479)
T ss_dssp             SBSCCEEEEECCSSSSHHHHHHH
T ss_pred             cCCCCcEEEEcCCCCchhHHHHH
Confidence            34346899999999999987543

>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=96.76  E-value=0.015  Score=50.36  Aligned_cols=23  Identities=22%  Similarity=0.332  Sum_probs=20.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++|+||+|+|||||++.++....
T Consensus        34 I~lvG~sGaGKSTLln~L~g~~~   56 (418)
T 2qag_C           34 LMVVGESGLGKSTLINSLFLTDL   56 (418)
T ss_dssp             EEEECCTTSSHHHHHHHHTTCCC
T ss_pred             EEEECCCCCcHHHHHHHHhCCCC
Confidence            79999999999999999987653

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=96.76  E-value=0.0047  Score=53.20  Aligned_cols=41  Identities=20%  Similarity=0.313  Sum_probs=25.3

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhhcCcceEEEEecC
Q 022641          154 PPYKIIILDEADSMTED-AQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       154 ~~~~lliiDei~~l~~~-~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      ...++||+||+|.+... ....+..++........+++.|..
T Consensus       182 ~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT  223 (414)
T 3eiq_A          182 KYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSAT  223 (414)
T ss_dssp             TTCCEEEECSHHHHHHTTTHHHHHHHHTTSCTTCEEEEECSC
T ss_pred             ccCcEEEEECHHHhhccCcHHHHHHHHHhCCCCCeEEEEEEe
Confidence            34569999999986432 234455556555556666666543

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=96.75  E-value=0.00095  Score=53.48  Aligned_cols=23  Identities=26%  Similarity=0.273  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+||+|+||||+++.++..+
T Consensus        27 iigI~G~~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           27 LIGVSGGTASGKSTVCEKIMELL   49 (245)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999876

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=96.74  E-value=0.0076  Score=53.37  Aligned_cols=24  Identities=38%  Similarity=0.492  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+|++|+||||++..|+..+.
T Consensus       103 vI~ivG~~GvGKTTl~~kLA~~l~  126 (504)
T 2j37_W          103 VIMFVGLQGSGKTTTCSKLAYYYQ  126 (504)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999998773

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=96.73  E-value=0.0073  Score=52.02  Aligned_cols=24  Identities=29%  Similarity=0.243  Sum_probs=18.6

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++.+|+|+|||......+-+.
T Consensus        75 ~~~lv~a~TGsGKT~~~~~~~~~~   98 (410)
T 2j0s_A           75 RDVIAQSQSGTGKTATFSISVLQC   98 (410)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCEEEECCCCCCchHHHHHHHHHH
Confidence            369999999999997766554443

>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=96.73  E-value=0.0011  Score=50.16  Aligned_cols=24  Identities=38%  Similarity=0.440  Sum_probs=21.9

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.++|+|++|+||||++..+...+
T Consensus         7 ~~i~i~G~sGsGKTTl~~~l~~~l   30 (174)
T 1np6_A            7 PLLAFAAWSGTGKTTLLKKLIPAL   30 (174)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhc
Confidence            458999999999999999999886

>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=96.72  E-value=0.0011  Score=57.79  Aligned_cols=26  Identities=23%  Similarity=0.450  Sum_probs=22.2

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +...++|+||+|+|||+|+..++...
T Consensus       150 kGq~~~i~G~sGvGKTtL~~~l~~~~  175 (473)
T 1sky_E          150 KGGKIGLFGGAGVGKTVLIQELIHNI  175 (473)
T ss_dssp             TTCEEEEECCSSSCHHHHHHHHHHHH
T ss_pred             cCCEEEEECCCCCCccHHHHHHHhhh
Confidence            33469999999999999999988765

>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=96.72  E-value=0.00064  Score=53.25  Aligned_cols=23  Identities=22%  Similarity=0.342  Sum_probs=20.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+|||+|+..+...-
T Consensus        29 ki~vvG~~~vGKSsL~~~l~~~~   51 (214)
T 3q3j_B           29 KLVLVGDVQCGKTAMLQVLAKDC   51 (214)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            49999999999999999998754

>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=96.71  E-value=0.00091  Score=53.27  Aligned_cols=43  Identities=9%  Similarity=0.202  Sum_probs=31.2

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC--cceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      .++.+|++||.- .|++.....+.+.+.+...  ...+|++|.+..
T Consensus       162 ~~p~llllDEPts~LD~~~~~~i~~~l~~l~~~~g~tvi~vtHd~~  207 (235)
T 3tif_A          162 NNPPIILADQPTWALDSKTGEKIMQLLKKLNEEDGKTVVVVTHDIN  207 (235)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHCCEEEEECSCHH
T ss_pred             cCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHHcCCEEEEEcCCHH
Confidence            567799999964 5788888888888776532  456777776654

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=96.70  E-value=0.0042  Score=56.59  Aligned_cols=97  Identities=12%  Similarity=0.064  Sum_probs=55.6

Q ss_pred             HHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccC
Q 022641           69 VVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRR  148 (294)
Q Consensus        69 ~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (294)
                      ..+.+...+... ....+|+|++|.|||+++..++..+.      ..+ .+.++...+...+.............  .. 
T Consensus       180 Q~~al~~~~~~~-~~~~vlta~RGRGKSa~lG~~~a~~~------~~~-~vtAP~~~a~~~l~~~~~~~i~~~~P--d~-  248 (671)
T 2zpa_A          180 QQQLLKQLMTMP-PGVAAVTAARGRGKSALAGQLISRIA------GRA-IVTAPAKASTDVLAQFAGEKFRFIAP--DA-  248 (671)
T ss_dssp             HHHHHHHHTTCC-SEEEEEEECTTSSHHHHHHHHHHHSS------SCE-EEECSSCCSCHHHHHHHGGGCCBCCH--HH-
T ss_pred             HHHHHHHHHHhh-hCeEEEecCCCCCHHHHHHHHHHHHH------hCc-EEECCCHHHHHHHHHHhhCCeEEeCc--hh-
Confidence            334444444322 23589999999999999999999883      222 44555555555554433221100000  00 


Q ss_pred             CCCCCCCcEEEEEeCCCCCCHHHHHHHH
Q 022641          149 GGYPCPPYKIIILDEADSMTEDAQNALR  176 (294)
Q Consensus       149 ~~~~~~~~~lliiDei~~l~~~~~~~L~  176 (294)
                      ........++|||||+-.++......|+
T Consensus       249 ~~~~~~~~dlliVDEAAaIp~pll~~ll  276 (671)
T 2zpa_A          249 LLASDEQADWLVVDEAAAIPAPLLHQLV  276 (671)
T ss_dssp             HHHSCCCCSEEEEETGGGSCHHHHHHHH
T ss_pred             hhhCcccCCEEEEEchhcCCHHHHHHHH
Confidence            0011224579999999999877555444

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=96.70  E-value=0.01  Score=50.65  Aligned_cols=40  Identities=23%  Similarity=0.331  Sum_probs=25.2

Q ss_pred             CCCcEEEEEeCCCCCCH--HHHHHHHHHHHhhcCcceEEEEe
Q 022641          153 CPPYKIIILDEADSMTE--DAQNALRRTMETYSKVTRFFFIC  192 (294)
Q Consensus       153 ~~~~~lliiDei~~l~~--~~~~~L~~~l~~~~~~~~ii~~~  192 (294)
                      ....++||+||+|.+..  .....+..++...+....+++.|
T Consensus       150 ~~~~~~vViDEaH~~~~~~~~~~~~~~~~~~~~~~~~~i~~S  191 (391)
T 1xti_A          150 LKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFS  191 (391)
T ss_dssp             CTTCSEEEECSHHHHTSSHHHHHHHHHHHHTSCSSSEEEEEE
T ss_pred             ccccCEEEEeCHHHHhhccchHHHHHHHHhhCCCCceEEEEE
Confidence            34567999999998753  44455555665555455555554

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=96.70  E-value=0.0016  Score=59.56  Aligned_cols=39  Identities=38%  Similarity=0.565  Sum_probs=29.5

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++.....+...+.   .+..+|.||||||||+++..+...+.
T Consensus       182 n~~Q~~av~~~l~---~~~~li~GppGTGKT~~~~~~i~~l~  220 (624)
T 2gk6_A          182 NHSQVYAVKTVLQ---RPLSLIQGPPGTGKTVTSATIVYHLA  220 (624)
T ss_dssp             CHHHHHHHHHHHT---CSEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhc---CCCeEEECCCCCCHHHHHHHHHHHHH
Confidence            4556666666553   24689999999999999988887763

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=96.68  E-value=0.0064  Score=55.13  Aligned_cols=44  Identities=20%  Similarity=0.366  Sum_probs=32.1

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCcc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYISR  197 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~  197 (294)
                      .+++++++||.- .+++.....+.+.+........+|+++.+...
T Consensus       494 ~~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~t~i~itH~l~~  538 (578)
T 4a82_A          494 NNPPILILDEATSALDLESESIIQEALDVLSKDRTTLIVAHRLST  538 (578)
T ss_dssp             HCCSEEEEESTTTTCCHHHHHHHHHHHHHHTTTSEEEEECSSGGG
T ss_pred             cCCCEEEEECccccCCHHHHHHHHHHHHHHcCCCEEEEEecCHHH
Confidence            356799999975 57777777788887766555667777766553

>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=96.68  E-value=0.013  Score=45.03  Aligned_cols=23  Identities=22%  Similarity=0.417  Sum_probs=20.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+|||+|+..+...-
T Consensus        16 ki~v~G~~~~GKSsli~~l~~~~   38 (206)
T 2bov_A           16 KVIMVGSGGVGKSALTLQFMYDE   38 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            49999999999999999998654

>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=96.68  E-value=0.01  Score=44.71  Aligned_cols=23  Identities=22%  Similarity=0.417  Sum_probs=20.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+|+..+...-
T Consensus        20 ki~v~G~~~~GKSsli~~l~~~~   42 (187)
T 2a9k_A           20 KVIMVGSGGVGKSALTLQFMYDE   42 (187)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhhCC
Confidence            49999999999999999998754

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=96.68  E-value=0.00079  Score=50.71  Aligned_cols=22  Identities=32%  Similarity=0.588  Sum_probs=19.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .+++.|++|+|||+++..+...
T Consensus        11 ~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B           11 KLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHCSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4999999999999999998643

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=96.68  E-value=0.018  Score=52.38  Aligned_cols=55  Identities=7%  Similarity=0.132  Sum_probs=35.3

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC-cceEEEEecCCcccchHhhccccEE
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK-VTRFFFICNYISRIIEPLASRCAKF  209 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~~~~~~l~~r~~~i  209 (294)
                      .++.++++||-- .|++.....+..++..... ...+|+++.+.. ....+.+|..++
T Consensus       238 ~~p~llllDEPts~LD~~~~~~l~~~l~~l~~~g~tvi~vtHdl~-~~~~~~drv~vl  294 (608)
T 3j16_B          238 QEADVYMFDEPSSYLDVKQRLNAAQIIRSLLAPTKYVICVEHDLS-VLDYLSDFVCII  294 (608)
T ss_dssp             SCCSEEEEECTTTTCCHHHHHHHHHHHHGGGTTTCEEEEECSCHH-HHHHHCSEEEEE
T ss_pred             hCCCEEEEECcccCCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHH-HHHHhCCEEEEE
Confidence            456799999964 6788888888888876544 345666665433 223444444433

>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=96.67  E-value=0.0011  Score=55.11  Aligned_cols=24  Identities=29%  Similarity=0.252  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+.|.||+|+||||+++.|+..+.
T Consensus        92 ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           92 IIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCchHHHHHHHHHhhcc
Confidence            489999999999999999998873

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=96.67  E-value=0.0019  Score=49.81  Aligned_cols=23  Identities=22%  Similarity=0.235  Sum_probs=20.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+|||+|+..+...-
T Consensus        26 ki~vvG~~~~GKSsli~~l~~~~   48 (201)
T 3oes_A           26 KVVILGYRCVGKTSLAHQFVEGE   48 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            49999999999999999998754

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=96.66  E-value=0.012  Score=51.61  Aligned_cols=23  Identities=39%  Similarity=0.444  Sum_probs=20.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++.+|+|+|||..+-.++...
T Consensus        25 ~~ll~~~tG~GKT~~~~~~~~~~   47 (494)
T 1wp9_A           25 NCLIVLPTGLGKTLIAMMIAEYR   47 (494)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHH
Confidence            79999999999999988886665

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.65  E-value=0.013  Score=48.66  Aligned_cols=24  Identities=33%  Similarity=0.415  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      -++|.|+||+|||+++..++..+.
T Consensus        70 l~li~G~pG~GKTtl~l~ia~~~a   93 (315)
T 3bh0_A           70 FVLIAARPSMGKTAFALKQAKNMS   93 (315)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHH
Confidence            499999999999999999997763

>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=96.65  E-value=0.0034  Score=52.49  Aligned_cols=41  Identities=17%  Similarity=0.291  Sum_probs=28.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCC---ccCCcceeecCCCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPE---LYKSRVLELNASDD  124 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~---~~~~~~~~~~~~~~  124 (294)
                      .++|+||||+|||+++..++.....+.   ..+..++.++....
T Consensus       109 i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~  152 (324)
T 2z43_A          109 MTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGT  152 (324)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSC
T ss_pred             EEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCC
Confidence            499999999999999999998763321   01334555555543

>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=96.65  E-value=0.0093  Score=44.57  Aligned_cols=23  Identities=17%  Similarity=0.309  Sum_probs=20.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+++..+...-
T Consensus        17 ~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           17 KYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            49999999999999999998765

>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=96.64  E-value=0.001  Score=56.82  Aligned_cols=23  Identities=22%  Similarity=0.553  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.||+|+|||+++..++..+
T Consensus         4 ~i~i~GptgsGKttla~~La~~~   26 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSIQLAQKF   26 (409)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHH
T ss_pred             EEEEECcchhhHHHHHHHHHHHC
Confidence            48899999999999999999987

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=96.63  E-value=0.0073  Score=48.08  Aligned_cols=41  Identities=17%  Similarity=0.250  Sum_probs=24.4

Q ss_pred             CCCcEEEEEeCCCCCCHH-HHHHHHHHHHhhcCcceEEEEec
Q 022641          153 CPPYKIIILDEADSMTED-AQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       153 ~~~~~lliiDei~~l~~~-~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      .....+||+||+|.+... ....+..++...+....+++.|.
T Consensus       174 ~~~~~~lViDEah~l~~~~~~~~~~~i~~~~~~~~q~~~~SA  215 (242)
T 3fe2_A          174 LRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSA  215 (242)
T ss_dssp             CTTCCEEEETTHHHHHHTTCHHHHHHHHTTSCSSCEEEEEES
T ss_pred             cccccEEEEeCHHHHhhhCcHHHHHHHHHhCCccceEEEEEe
Confidence            345679999999986432 23344555555555555555443

>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=96.63  E-value=0.00052  Score=52.05  Aligned_cols=23  Identities=17%  Similarity=0.257  Sum_probs=20.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+|+..+....
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            48999999999999999998654

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=96.63  E-value=0.0042  Score=54.15  Aligned_cols=21  Identities=24%  Similarity=0.314  Sum_probs=17.3

Q ss_pred             CcEEEECCCCCCHHHHH-HHHH
Q 022641           83 PHMLFYGPPGTGKTTTA-LAIA  103 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la-~~la  103 (294)
                      .++++.||+|+|||..+ ..+.
T Consensus         3 ~~~lv~a~TGsGKT~~~l~~~l   24 (431)
T 2v6i_A            3 ELTVLDLHPGAGKTRRVLPQLV   24 (431)
T ss_dssp             CEEEEECCTTSCTTTTHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH
Confidence            57999999999999986 4444

>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=96.63  E-value=0.0062  Score=46.24  Aligned_cols=23  Identities=26%  Similarity=0.384  Sum_probs=20.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+|||+|+..+...-
T Consensus        13 ki~v~G~~~~GKSsli~~l~~~~   35 (195)
T 3bc1_A           13 KFLALGDSGVGKTSVLYQYTDGK   35 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            49999999999999999998754

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=96.63  E-value=0.0016  Score=57.87  Aligned_cols=38  Identities=29%  Similarity=0.268  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           67 EEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        67 ~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+...+...+..+.  +++|+||+|+||||++++++..+
T Consensus       247 ~~~l~~l~~~v~~g~--~i~I~GptGSGKTTlL~aL~~~i  284 (511)
T 2oap_1          247 SGVLAYLWLAIEHKF--SAIVVGETASGKTTTLNAIMMFI  284 (511)
T ss_dssp             HHHHHHHHHHHHTTC--CEEEEESTTSSHHHHHHHHGGGS
T ss_pred             HHHHHHHHHHHhCCC--EEEEECCCCCCHHHHHHHHHhhC
Confidence            444555555555544  69999999999999999998766

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=96.63  E-value=0.0047  Score=52.79  Aligned_cols=41  Identities=22%  Similarity=0.332  Sum_probs=24.3

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhhcCcceEEEEecC
Q 022641          154 PPYKIIILDEADSMTED-AQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       154 ~~~~lliiDei~~l~~~-~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      .+.++||+||+|.+... ....+..++...+....+++.|..
T Consensus       161 ~~~~~vIiDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT  202 (394)
T 1fuu_A          161 DKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSAT  202 (394)
T ss_dssp             TTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSS
T ss_pred             hhCcEEEEEChHHhhCCCcHHHHHHHHHhCCCCceEEEEEEe
Confidence            45679999999986432 233344455554555555555543

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=96.62  E-value=0.004  Score=51.92  Aligned_cols=24  Identities=21%  Similarity=0.281  Sum_probs=18.9

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++.+|+|+|||..+...+.+.
T Consensus        32 ~~~lv~~~TGsGKT~~~~~~~~~~   55 (337)
T 2z0m_A           32 KNVVVRAKTGSGKTAAYAIPILEL   55 (337)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCcHHHHHHHHHHhh
Confidence            379999999999998776555443

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=96.62  E-value=0.0082  Score=53.42  Aligned_cols=38  Identities=11%  Similarity=0.080  Sum_probs=26.8

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.....+..++..   .+++++||+|+|||..+..++...
T Consensus       115 ~~~Q~~ai~~~~~~---~~~ll~~~tGsGKT~~~~~~~~~~  152 (510)
T 2oca_A          115 HWYQKDAVFEGLVN---RRRILNLPTSAGRSLIQALLARYY  152 (510)
T ss_dssp             CHHHHHHHHHHHHH---SEEEEECCSTTTHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhc---CCcEEEeCCCCCHHHHHHHHHHHH
Confidence            34444444444443   469999999999999997777664

>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=96.61  E-value=0.00063  Score=52.18  Aligned_cols=23  Identities=26%  Similarity=0.339  Sum_probs=20.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+|+..+...-
T Consensus        25 ki~~vG~~~~GKSsl~~~l~~~~   47 (194)
T 3reg_A           25 KIVVVGDGAVGKTCLLLAFSKGE   47 (194)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            49999999999999999998764

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=96.60  E-value=0.0016  Score=50.54  Aligned_cols=24  Identities=17%  Similarity=0.098  Sum_probs=22.6

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..|.|.|++|+|||++++.+++.+
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~~l   30 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAEHY   30 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHh
Confidence            469999999999999999999999

>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=96.59  E-value=0.0012  Score=52.62  Aligned_cols=44  Identities=9%  Similarity=0.103  Sum_probs=30.5

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHH---hhcCcceEEEEecCCcc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTME---TYSKVTRFFFICNYISR  197 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~---~~~~~~~ii~~~~~~~~  197 (294)
                      .++.++++||.- .|++.....+.+.+.   .......+|++|.+...
T Consensus       144 ~~p~lllLDEPts~LD~~~~~~i~~~l~~~~~~~~~~tviivtH~~~~  191 (237)
T 2cbz_A          144 SNADIYLFDDPLSAVDAHVGKHIFENVIGPKGMLKNKTRILVTHSMSY  191 (237)
T ss_dssp             HCCSEEEEESTTTTSCHHHHHHHHHHTTSTTSTTTTSEEEEECSCSTT
T ss_pred             cCCCEEEEeCcccccCHHHHHHHHHHHHHHHhhcCCCEEEEEecChHH
Confidence            356799999965 578888888888773   22334567777766543

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=96.58  E-value=0.0035  Score=50.71  Aligned_cols=41  Identities=12%  Similarity=0.291  Sum_probs=24.2

Q ss_pred             CCCcEEEEEeCCCCCCHH-HHHHHHHHHHhhcCcceEEEEec
Q 022641          153 CPPYKIIILDEADSMTED-AQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       153 ~~~~~lliiDei~~l~~~-~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      ..+..+|||||+|.+... ....+..++...+....+++.|.
T Consensus       199 ~~~l~~lViDEah~l~~~~~~~~l~~i~~~~~~~~q~l~~SA  240 (262)
T 3ly5_A          199 YKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSA  240 (262)
T ss_dssp             CTTCCEEEECSHHHHHHTTCHHHHHHHHHHSCSSSEEEEECS
T ss_pred             cccCCEEEEcChHHHhhhhHHHHHHHHHHhCCCCCeEEEEEe
Confidence            345679999999986432 23344555555555555555443

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=96.58  E-value=0.0012  Score=52.62  Aligned_cols=43  Identities=9%  Similarity=0.182  Sum_probs=30.6

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC--cceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      .++.++++||.- .|++.....+.+.+.....  ...+|++|.+..
T Consensus       143 ~~p~lllLDEPts~LD~~~~~~~~~~l~~l~~~~g~tvi~vtHd~~  188 (240)
T 2onk_A          143 IQPRLLLLDEPLSAVDLKTKGVLMEELRFVQREFDVPILHVTHDLI  188 (240)
T ss_dssp             TCCSSBEEESTTSSCCHHHHHHHHHHHHHHHHHHTCCEEEEESCHH
T ss_pred             cCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            567799999964 6788888888887766532  455777776543

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=96.57  E-value=0.009  Score=54.25  Aligned_cols=43  Identities=23%  Similarity=0.362  Sum_probs=32.6

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                      .++.++++||.- .+++.....+.+.+........+|+++.+..
T Consensus       496 ~~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~tvi~itH~l~  539 (587)
T 3qf4_A          496 KKPKVLILDDCTSSVDPITEKRILDGLKRYTKGCTTFIITQKIP  539 (587)
T ss_dssp             TCCSEEEEESCCTTSCHHHHHHHHHHHHHHSTTCEEEEEESCHH
T ss_pred             cCCCEEEEECCcccCCHHHHHHHHHHHHHhCCCCEEEEEecChH
Confidence            467799999975 5788878888888877656667788887654

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=96.57  E-value=0.001  Score=52.62  Aligned_cols=42  Identities=7%  Similarity=0.070  Sum_probs=29.8

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc-CcceEEEEecCC
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS-KVTRFFFICNYI  195 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~  195 (294)
                      .++.++++||.- .|++.....+.+.+.... ....+|++|.+.
T Consensus       157 ~~p~lllLDEPt~~LD~~~~~~~~~~l~~l~~~g~tvi~vtHd~  200 (224)
T 2pcj_A          157 NEPILLFADEPTGNLDSANTKRVMDIFLKINEGGTSIVMVTHER  200 (224)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEECSCH
T ss_pred             cCCCEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEcCCH
Confidence            567899999964 578887777777776543 245677777653

>3th5_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTPase, GTP binding, protein binding, signali protein; HET: GNP; 2.30A {Homo sapiens}

Probab=95.59  E-value=0.00036  Score=54.13  Aligned_cols=26  Identities=15%  Similarity=0.209  Sum_probs=21.2

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..-.++++|++|+|||+|+..+....
T Consensus        29 ~~~ki~v~G~~~~GKSsli~~l~~~~   54 (204)
T 3th5_A           29 QAIKCVVVGDGAVGKTCLLISYTTNA   54 (204)
Confidence            33459999999999999998887543

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=96.56  E-value=0.0068  Score=46.38  Aligned_cols=23  Identities=17%  Similarity=0.436  Sum_probs=20.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+|+..+...-
T Consensus         9 ki~v~G~~~~GKSsli~~l~~~~   31 (208)
T 3clv_A            9 KTVLLGESSVGKSSIVLRLTKDT   31 (208)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            49999999999999999998764

>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=96.56  E-value=0.0022  Score=53.27  Aligned_cols=24  Identities=29%  Similarity=0.285  Sum_probs=21.8

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|+||+|+||||+++.|+..+
T Consensus        81 ~iigI~G~~GsGKSTl~~~L~~~l  104 (308)
T 1sq5_A           81 YIISIAGSVAVGKSTTARVLQALL  104 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Confidence            358999999999999999999876

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=96.56  E-value=0.0013  Score=53.27  Aligned_cols=42  Identities=10%  Similarity=0.252  Sum_probs=29.5

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc-CcceEEEEecCC
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS-KVTRFFFICNYI  195 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~  195 (294)
                      .++.+|++||.- .|++.....+.+.+.... ....+|++|.+.
T Consensus       170 ~~p~lllLDEPts~LD~~~~~~~~~~l~~l~~~g~tvi~vtHd~  213 (262)
T 1b0u_A          170 MEPDVLLFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEM  213 (262)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHTTCCEEEECSCH
T ss_pred             cCCCEEEEeCCCccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            467799999964 578887777777776543 245577777653

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=96.56  E-value=0.0017  Score=51.24  Aligned_cols=22  Identities=36%  Similarity=0.683  Sum_probs=21.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +-|.||||+||||+++.|++.+
T Consensus        11 ~~~~G~pGsGKsT~a~~L~~~~   32 (230)
T 3gmt_A           11 LILLGAPGAGKGTQANFIKEKF   32 (230)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             eeeECCCCCCHHHHHHHHHHHh
Confidence            8899999999999999999988

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=96.54  E-value=0.0012  Score=59.16  Aligned_cols=41  Identities=32%  Similarity=0.408  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHH--HcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           67 EEVVRVLTNTL--ETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        67 ~~~~~~l~~~l--~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ..+...++...  .......++|+|++|+||||+++.|+..+.
T Consensus       352 peV~~vLR~~~~~~~~~G~iI~LiG~sGSGKSTLar~La~~L~  394 (552)
T 3cr8_A          352 PEVLAELHRQTPPRERQGFTVFFTGLSGAGKSTLARALAARLM  394 (552)
T ss_dssp             HHHHHHHHHHSCCGGGSCEEEEEEESSCHHHHHHHHHHHHHHH
T ss_pred             cchhhhhhhhcccccccceEEEEECCCCChHHHHHHHHHHhhc
Confidence            34444444433  222334699999999999999999999983

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=96.54  E-value=0.004  Score=61.85  Aligned_cols=45  Identities=16%  Similarity=0.359  Sum_probs=32.0

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCccc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYISRI  198 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~  198 (294)
                      .++.+|++||+- .++......+.+.+++......+|+++.....+
T Consensus      1234 r~~~ILiLDEaTSaLD~~tE~~Iq~~l~~~~~~~TvI~IAHRLsTi 1279 (1321)
T 4f4c_A         1234 RNPKILLLDEATSALDTESEKVVQEALDRAREGRTCIVIAHRLNTV 1279 (1321)
T ss_dssp             SCCSEEEEESCCCSTTSHHHHHHHHHHTTTSSSSEEEEECSSSSTT
T ss_pred             hCCCEEEEeCccccCCHHHHHHHHHHHHHHcCCCEEEEeccCHHHH
Confidence            456799999986 456666677777887766666677777665543

>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=96.54  E-value=0.0014  Score=51.38  Aligned_cols=24  Identities=42%  Similarity=0.524  Sum_probs=21.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|.||.|+|||||++.++..+
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl~   59 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTYL   59 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            358999999999999999998765

>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=96.53  E-value=0.0024  Score=49.96  Aligned_cols=24  Identities=33%  Similarity=0.498  Sum_probs=22.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .|+|.|++|+||||+++.++..+.
T Consensus         8 ~i~~eG~~gsGKsT~~~~l~~~l~   31 (213)
T 4edh_A            8 FVTLEGPEGAGKSTNRDYLAERLR   31 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999999884

>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=96.53  E-value=0.0031  Score=53.50  Aligned_cols=28  Identities=32%  Similarity=0.489  Sum_probs=23.7

Q ss_pred             CCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           80 ANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        80 ~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      +....+.|+|+||+||||++..++..+.
T Consensus        77 ~~~~~I~i~G~~G~GKSTl~~~L~~~l~  104 (355)
T 3p32_A           77 GNAHRVGITGVPGVGKSTAIEALGMHLI  104 (355)
T ss_dssp             CCSEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3444699999999999999999998863

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=96.53  E-value=0.0033  Score=58.55  Aligned_cols=22  Identities=32%  Similarity=0.377  Sum_probs=18.2

Q ss_pred             CCcEEEECCCCCCHHHHHHHHH
Q 022641           82 CPHMLFYGPPGTGKTTTALAIA  103 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la  103 (294)
                      ..+++++||+|+|||+.+....
T Consensus        46 ~~~~lv~apTGsGKT~~~~l~i   67 (715)
T 2va8_A           46 GNRLLLTSPTGSGKTLIAEMGI   67 (715)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHH
T ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Confidence            3579999999999999985443

>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=96.53  E-value=0.0013  Score=55.52  Aligned_cols=24  Identities=29%  Similarity=0.346  Sum_probs=21.6

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|.||+|||||||++.++...
T Consensus        31 e~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           31 EILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCchHHHHHHHHhcCC
Confidence            358999999999999999999865

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.53  E-value=0.0016  Score=51.95  Aligned_cols=23  Identities=35%  Similarity=0.429  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||||+|||+++..++..+
T Consensus        25 ~~~i~G~~GsGKTtl~~~~~~~~   47 (247)
T 2dr3_A           25 VVLLSGGPGTGKTIFSQQFLWNG   47 (247)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            58999999999999998887765

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=96.53  E-value=0.0076  Score=54.87  Aligned_cols=44  Identities=20%  Similarity=0.301  Sum_probs=32.0

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCcc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYISR  197 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~  197 (294)
                      .++.++++||.- .+++.....+.+.+.+......+|+++.+...
T Consensus       508 ~~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~t~i~itH~l~~  552 (598)
T 3qf4_B          508 ANPKILILDEATSNVDTKTEKSIQAAMWKLMEGKTSIIIAHRLNT  552 (598)
T ss_dssp             TCCSEEEECCCCTTCCHHHHHHHHHHHHHHHTTSEEEEESCCTTH
T ss_pred             cCCCEEEEECCccCCCHHHHHHHHHHHHHHcCCCEEEEEecCHHH
Confidence            456799999975 56777777777777765556667778876553

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=96.53  E-value=0.0034  Score=47.85  Aligned_cols=24  Identities=25%  Similarity=0.530  Sum_probs=21.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++++|++|+|||+++..+....
T Consensus        49 ~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           49 PSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            459999999999999999998754

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=96.52  E-value=0.0019  Score=55.18  Aligned_cols=25  Identities=32%  Similarity=0.551  Sum_probs=22.4

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ...++|+||+|+||||+++.++..+
T Consensus       136 g~~i~ivG~~GsGKTTll~~l~~~~  160 (372)
T 2ewv_A          136 MGLILVTGPTGSGKSTTIASMIDYI  160 (372)
T ss_dssp             SEEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhc
Confidence            3469999999999999999999876

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=96.51  E-value=0.0017  Score=53.78  Aligned_cols=24  Identities=38%  Similarity=0.505  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+.|+||+|+||||+++.++..+.
T Consensus       102 vi~lvG~nGsGKTTll~~Lag~l~  125 (302)
T 3b9q_A          102 VIMIVGVNGGGKTTSLGKLAHRLK  125 (302)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            389999999999999999998873

>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=96.50  E-value=0.0071  Score=46.06  Aligned_cols=24  Identities=29%  Similarity=0.483  Sum_probs=21.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+|++|+|||+|+..+...-+
T Consensus        25 ki~v~G~~~~GKSsli~~l~~~~~   48 (191)
T 3dz8_A           25 KLLIIGNSSVGKTSFLFRYADDTF   48 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEECCCCcCHHHHHHHHhcCCC
Confidence            399999999999999999988753

>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=96.49  E-value=0.0018  Score=55.20  Aligned_cols=43  Identities=12%  Similarity=0.240  Sum_probs=29.8

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhhcC--cceEEEEecCCc
Q 022641          154 PPYKIIILDEA-DSMTEDAQNALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei-~~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      .++.+|++||- -.|++.....++..+.....  ...+|++|.+..
T Consensus       150 ~~P~lLLLDEPts~LD~~~~~~l~~~l~~l~~~~g~tii~vTHd~~  195 (381)
T 3rlf_A          150 AEPSVFLLDEPLSNLDAALRVQMRIEISRLHKRLGRTMIYVTHDQV  195 (381)
T ss_dssp             HCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHCCEEEEECSCHH
T ss_pred             cCCCEEEEECCCcCCCHHHHHHHHHHHHHHHHhCCCEEEEEECCHH
Confidence            35679999995 46788777777777765432  456777776543

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=96.49  E-value=0.0018  Score=54.89  Aligned_cols=43  Identities=12%  Similarity=0.218  Sum_probs=30.0

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhhcC--cceEEEEecCCc
Q 022641          154 PPYKIIILDEA-DSMTEDAQNALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei-~~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      .++.+|++||- ..|+......+...+.....  ...+|++|.+..
T Consensus       150 ~~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  195 (362)
T 2it1_A          150 KEPEVLLLDEPLSNLDALLRLEVRAELKRLQKELGITTVYVTHDQA  195 (362)
T ss_dssp             TCCSEEEEESGGGGSCHHHHHHHHHHHHHHHHHHTCEEEEEESCHH
T ss_pred             cCCCEEEEECccccCCHHHHHHHHHHHHHHHHhCCCEEEEECCCHH
Confidence            56789999995 46787777777777765432  456777776643

>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=96.49  E-value=0.0016  Score=52.80  Aligned_cols=42  Identities=12%  Similarity=0.239  Sum_probs=29.7

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc-CcceEEEEecCC
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS-KVTRFFFICNYI  195 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~  195 (294)
                      .++.+|++||.- .|++.....+.+.+.... ....+|++|.+.
T Consensus       176 ~~p~lllLDEPts~LD~~~~~~~~~~l~~l~~~g~tvi~vtHd~  219 (263)
T 2olj_A          176 MEPKIMLFDEPTSALDPEMVGEVLSVMKQLANEGMTMVVVTHEM  219 (263)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHTTCEEEEECSCH
T ss_pred             CCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEcCCH
Confidence            567899999964 578887777777776543 245577777553

>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=96.49  E-value=0.0017  Score=54.28  Aligned_cols=23  Identities=43%  Similarity=0.606  Sum_probs=21.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+||+|+||||+++.++..+
T Consensus       131 vi~lvG~nGaGKTTll~~Lag~l  153 (328)
T 3e70_C          131 VIMFVGFNGSGKTTTIAKLANWL  153 (328)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            48999999999999999999877

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=96.48  E-value=0.0025  Score=54.23  Aligned_cols=34  Identities=24%  Similarity=0.418  Sum_probs=25.9

Q ss_pred             HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           71 RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        71 ~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.-.+..+.  .++|+||+|+||||++++++...
T Consensus       166 ~~l~~~i~~G~--~i~ivG~sGsGKSTll~~l~~~~  199 (361)
T 2gza_A          166 SFLRRAVQLER--VIVVAGETGSGKTTLMKALMQEI  199 (361)
T ss_dssp             HHHHHHHHTTC--CEEEEESSSSCHHHHHHHHHTTS
T ss_pred             HHHHHHHhcCC--EEEEECCCCCCHHHHHHHHHhcC
Confidence            33433344443  79999999999999999998865

>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=96.48  E-value=0.0018  Score=54.81  Aligned_cols=43  Identities=9%  Similarity=0.255  Sum_probs=29.9

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhhcC--cceEEEEecCCc
Q 022641          154 PPYKIIILDEA-DSMTEDAQNALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei-~~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      .++.+|++||- ..|++.....+...+.....  ...+|++|.+..
T Consensus       150 ~~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  195 (359)
T 2yyz_A          150 KQPKVLLFDEPLSNLDANLRMIMRAEIKHLQQELGITSVYVTHDQA  195 (359)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHCCEEEEEESCHH
T ss_pred             cCCCEEEEECCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEcCCHH
Confidence            56779999995 46788777777777765432  456777776543

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=96.48  E-value=0.005  Score=52.98  Aligned_cols=41  Identities=17%  Similarity=0.144  Sum_probs=27.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCc---cCCcceeecCCCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPEL---YKSRVLELNASDD  124 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~---~~~~~~~~~~~~~  124 (294)
                      .+.|+||||+|||+|+..++-....+..   ....++.++....
T Consensus       180 i~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~  223 (400)
T 3lda_A          180 ITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGT  223 (400)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSC
T ss_pred             EEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCc
Confidence            4999999999999999988755432211   1234555665543

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=96.48  E-value=0.022  Score=49.49  Aligned_cols=24  Identities=33%  Similarity=0.390  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++++|++|+||||++..|+..+.
T Consensus       102 vI~ivG~~GvGKTT~a~~LA~~l~  125 (433)
T 2xxa_A          102 VVLMAGLQGAGKTTSVGKLGKFLR  125 (433)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            488899999999999999998874

>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=96.47  E-value=0.002  Score=52.37  Aligned_cols=43  Identities=21%  Similarity=0.362  Sum_probs=31.7

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC-cceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK-VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~  196 (294)
                      .++.+|++||.- .|++.....+.+.+..... ...+|++|.+..
T Consensus       181 ~~p~lLlLDEPts~LD~~~~~~l~~~l~~l~~~g~tviivtHd~~  225 (267)
T 2zu0_C          181 LEPELCILDESDSGLDIDALKVVADGVNSLRDGKRSFIIVTHYQR  225 (267)
T ss_dssp             HCCSEEEEESTTTTCCHHHHHHHHHHHHTTCCSSCEEEEECSSGG
T ss_pred             hCCCEEEEeCCCCCCCHHHHHHHHHHHHHHHhcCCEEEEEeeCHH
Confidence            357799999965 5788888889988887643 455777776543

>3szr_A Interferon-induced GTP-binding protein MX1; interferon-induced antiviral GTPase, membrane associated, PR binding; 3.50A {Homo sapiens} PDB: 3zys_B

Probab=96.47  E-value=0.0084  Score=54.63  Aligned_cols=24  Identities=21%  Similarity=0.364  Sum_probs=21.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.+.|+||+|+||||++++++...
T Consensus        46 p~iaIvG~nGsGKSTLL~~I~Gl~   69 (608)
T 3szr_A           46 PAIAVIGDQSSGKSSVLEALSGVA   69 (608)
T ss_dssp             CCEECCCCTTSCHHHHHHHHHSCC
T ss_pred             CeEEEECCCCChHHHHHHHHhCCC
Confidence            559999999999999999998754

>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=96.46  E-value=0.0019  Score=51.95  Aligned_cols=43  Identities=21%  Similarity=0.246  Sum_probs=31.2

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC-cceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK-VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~  196 (294)
                      .++.+|++||.- .|++.....+.+.+..... ...+|++|.+..
T Consensus       160 ~~p~lllLDEPts~LD~~~~~~l~~~l~~l~~~g~tvi~vtHd~~  204 (250)
T 2d2e_A          160 LEPTYAVLDETDSGLDIDALKVVARGVNAMRGPNFGALVITHYQR  204 (250)
T ss_dssp             HCCSEEEEECGGGTTCHHHHHHHHHHHHHHCSTTCEEEEECSSSG
T ss_pred             cCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhcCCEEEEEecCHH
Confidence            356799999964 5788888888888877643 456777776544

>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=96.45  E-value=0.0019  Score=54.90  Aligned_cols=43  Identities=9%  Similarity=0.256  Sum_probs=30.2

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhhcC--cceEEEEecCCc
Q 022641          154 PPYKIIILDEA-DSMTEDAQNALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei-~~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      .++.+|++||- ..|+......+...+.....  ...+|++|.+..
T Consensus       158 ~~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  203 (372)
T 1v43_A          158 VEPDVLLMDEPLSNLDAKLRVAMRAEIKKLQQKLKVTTIYVTHDQV  203 (372)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHTCEEEEEESCHH
T ss_pred             cCCCEEEEcCCCccCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCHH
Confidence            56779999995 46788877777777765432  456777776643

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=96.45  E-value=0.0016  Score=53.17  Aligned_cols=52  Identities=12%  Similarity=0.132  Sum_probs=34.5

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc--CcceEEEEecCCcccchHhhccc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS--KVTRFFFICNYISRIIEPLASRC  206 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~--~~~~ii~~~~~~~~~~~~l~~r~  206 (294)
                      .++.+|++||.- .|++.....+.+++.+..  ....+|++|.+...+ ..+.+|+
T Consensus       160 ~~P~lLlLDEPts~LD~~~~~~i~~~l~~l~~~~g~tvi~vtHdl~~~-~~~~drv  214 (275)
T 3gfo_A          160 MEPKVLILDEPTAGLDPMGVSEIMKLLVEMQKELGITIIIATHDIDIV-PLYCDNV  214 (275)
T ss_dssp             TCCSEEEEECTTTTCCHHHHHHHHHHHHHHHHHHCCEEEEEESCCSSG-GGGCSEE
T ss_pred             cCCCEEEEECccccCCHHHHHHHHHHHHHHHhhCCCEEEEEecCHHHH-HHhCCEE
Confidence            567899999964 578888877877776643  245677777665433 2334443

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=96.45  E-value=0.0018  Score=54.67  Aligned_cols=43  Identities=14%  Similarity=0.289  Sum_probs=29.8

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhhcC--cceEEEEecCCc
Q 022641          154 PPYKIIILDEA-DSMTEDAQNALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei-~~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      .++.+|++||- ..|+......+...+.....  ...+|++|.+..
T Consensus       162 ~~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  207 (355)
T 1z47_A          162 PRPQVLLFDEPFAAIDTQIRRELRTFVRQVHDEMGVTSVFVTHDQE  207 (355)
T ss_dssp             TCCSEEEEESTTCCSSHHHHHHHHHHHHHHHHHHTCEEEEECSCHH
T ss_pred             cCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEECCCHH
Confidence            56789999995 46788777777777765432  456777776543

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=96.45  E-value=0.0069  Score=56.71  Aligned_cols=41  Identities=22%  Similarity=0.244  Sum_probs=31.4

Q ss_pred             ccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHH
Q 022641           65 HQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        65 g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .|..++..+...+..+...++++.||+|+|||..+...+-.
T Consensus       372 ~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~  412 (780)
T 1gm5_A          372 AQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILD  412 (780)
T ss_dssp             HHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHH
Confidence            46666777777776776678999999999999987655443

>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=96.45  E-value=0.0018  Score=49.93  Aligned_cols=23  Identities=17%  Similarity=0.362  Sum_probs=20.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.|++|+|||||++.+....
T Consensus         7 kv~lvG~~g~GKSTLl~~l~~~~   29 (199)
T 2f9l_A            7 KVVLIGDSGVGKSNLLSRFTRNE   29 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            48999999999999999998764

>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=96.45  E-value=0.0019  Score=53.26  Aligned_cols=25  Identities=24%  Similarity=0.147  Sum_probs=22.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ..++|.||||+||||++..++..+.
T Consensus        36 ~~~~i~G~~G~GKTTl~~~ia~~~~   60 (296)
T 1cr0_A           36 EVIMVTSGSGMGKSTFVRQQALQWG   60 (296)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            3599999999999999999998873

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=96.44  E-value=0.001  Score=54.71  Aligned_cols=24  Identities=21%  Similarity=0.412  Sum_probs=18.8

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..|.|+||+|+||||+++.++..+
T Consensus         6 ~iIgItG~sGSGKSTva~~L~~~l   29 (290)
T 1a7j_A            6 PIISVTGSSGAGTSTVKHTFDQIF   29 (290)
T ss_dssp             CEEEEESCC---CCTHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            358999999999999999999876

>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=96.44  E-value=0.0016  Score=52.61  Aligned_cols=43  Identities=14%  Similarity=0.202  Sum_probs=30.6

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC-cceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK-VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~  196 (294)
                      .++.+|++||.- .|++.....+.+.+..... ...+|++|.+..
T Consensus       170 ~~p~lllLDEPts~LD~~~~~~l~~~l~~l~~~g~tvi~vtHd~~  214 (257)
T 1g6h_A          170 TNPKMIVMDEPIAGVAPGLAHDIFNHVLELKAKGITFLIIEHRLD  214 (257)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEECSCCS
T ss_pred             cCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHCCCEEEEEecCHH
Confidence            467799999964 6788888878777766432 456777776644

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=96.44  E-value=0.003  Score=59.39  Aligned_cols=39  Identities=38%  Similarity=0.565  Sum_probs=29.4

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++.....+...+.   .+..+|.||||||||+++..+...+.
T Consensus       358 n~~Q~~Av~~~l~---~~~~lI~GppGTGKT~ti~~~i~~l~  396 (800)
T 2wjy_A          358 NHSQVYAVKTVLQ---RPLSLIQGPPGTGKTVTSATIVYHLA  396 (800)
T ss_dssp             CHHHHHHHHHHHT---SSEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhcc---CCeEEEEcCCCCCHHHHHHHHHHHHH
Confidence            4555566665554   24689999999999999988887764

>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=96.44  E-value=0.0016  Score=52.24  Aligned_cols=43  Identities=26%  Similarity=0.395  Sum_probs=31.1

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                      .++.+|++||.- .|++.....+.+.+........+|++|.+..
T Consensus       162 ~~p~lllLDEPts~LD~~~~~~i~~~l~~~~~g~tviivtH~~~  205 (247)
T 2ff7_A          162 NNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLS  205 (247)
T ss_dssp             TCCSEEEECCCCSCCCHHHHHHHHHHHHHHHTTSEEEEECSSGG
T ss_pred             cCCCEEEEeCCcccCCHHHHHHHHHHHHHHcCCCEEEEEeCCHH
Confidence            467799999965 5778777777777776544556777776644

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=96.44  E-value=0.0075  Score=53.10  Aligned_cols=38  Identities=26%  Similarity=0.308  Sum_probs=27.6

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+...+.+..++..   .++++.||+|+|||.++..++...
T Consensus        95 ~~~Q~~ai~~i~~~---~~~ll~~~TGsGKT~~~l~~i~~~  132 (472)
T 2fwr_A           95 RDYQEKALERWLVD---KRGCIVLPTGSGKTHVAMAAINEL  132 (472)
T ss_dssp             CHHHHHHHHHHTTT---TEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhc---CCEEEEeCCCCCHHHHHHHHHHHc
Confidence            44445555545443   259999999999999998887776

>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=96.43  E-value=0.0017  Score=51.48  Aligned_cols=43  Identities=5%  Similarity=0.039  Sum_probs=29.4

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHH-HHhhcCcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRT-METYSKVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~-l~~~~~~~~ii~~~~~~~  196 (294)
                      .++.++++||.- .+++.....+.+. +........+|++|.+..
T Consensus       147 ~~p~lllLDEPts~LD~~~~~~i~~~l~~~~~~~~tvi~vtH~~~  191 (229)
T 2pze_A          147 KDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKME  191 (229)
T ss_dssp             SCCSEEEEESTTTTSCHHHHHHHHHHCCCCCTTTSEEEEECCCHH
T ss_pred             cCCCEEEEECcccCCCHHHHHHHHHHHHHHhhCCCEEEEEcCChH
Confidence            457799999964 5788888888875 344333456777776543

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=96.43  E-value=0.0017  Score=47.78  Aligned_cols=23  Identities=17%  Similarity=0.359  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++.|++|+|||+++..+...-
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~~   25 (161)
T 2dyk_A            3 KVVIVGRPNVGKSSLFNRLLKKR   25 (161)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            58999999999999999998653

>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=96.43  E-value=0.0018  Score=52.86  Aligned_cols=24  Identities=33%  Similarity=0.465  Sum_probs=21.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+||+|+||||++..++..+
T Consensus        31 ~i~~i~G~~GsGKTtl~~~l~~~~   54 (279)
T 1nlf_A           31 TVGALVSPGGAGKSMLALQLAAQI   54 (279)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHH
Confidence            359999999999999999999765

>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=96.43  E-value=0.0017  Score=51.91  Aligned_cols=42  Identities=10%  Similarity=0.197  Sum_probs=30.2

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc-CcceEEEEecCC
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS-KVTRFFFICNYI  195 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~  195 (294)
                      .++.+|++||.- .|++.....+.+.+.... ....+|++|.+.
T Consensus       156 ~~p~lllLDEPts~LD~~~~~~l~~~l~~~~~~g~tvi~vtHd~  199 (240)
T 1ji0_A          156 SRPKLLMMDEPSLGLAPILVSEVFEVIQKINQEGTTILLVEQNA  199 (240)
T ss_dssp             TCCSEEEEECTTTTCCHHHHHHHHHHHHHHHHTTCCEEEEESCH
T ss_pred             cCCCEEEEcCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEecCH
Confidence            567899999964 578888877777776653 345577777654

>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=96.42  E-value=0.0016  Score=49.88  Aligned_cols=24  Identities=21%  Similarity=0.444  Sum_probs=21.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|.|++|+|||||++.++....
T Consensus        31 kv~lvG~~g~GKSTLl~~l~~~~~   54 (191)
T 1oix_A           31 KVVLIGDSGVGKSNLLSRFTRNEF   54 (191)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSCC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCCC
Confidence            389999999999999999987653

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=96.42  E-value=0.00081  Score=50.70  Aligned_cols=23  Identities=26%  Similarity=0.302  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+|++|+||||+++.++..+
T Consensus         4 ~v~IvG~SGsGKSTL~~~L~~~~   26 (171)
T 2f1r_A            4 ILSIVGTSDSGKTTLITRMMPIL   26 (171)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999999987

>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=96.42  E-value=0.0017  Score=52.71  Aligned_cols=42  Identities=12%  Similarity=0.162  Sum_probs=29.7

Q ss_pred             CcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC--cceEEEEecCCc
Q 022641          155 PYKIIILDEAD-SMTEDAQNALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       155 ~~~lliiDei~-~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      ++.+|++||-- .|++.....+.+.+.....  ...+|++|.+..
T Consensus       165 ~p~lLllDEPts~LD~~~~~~i~~~l~~l~~~~~~tvi~vtHdl~  209 (266)
T 4g1u_C          165 TPRWLFLDEPTSALDLYHQQHTLRLLRQLTRQEPLAVCCVLHDLN  209 (266)
T ss_dssp             CCEEEEECCCCSSCCHHHHHHHHHHHHHHHHHSSEEEEEECSCHH
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHHHHcCCCEEEEEEcCHH
Confidence            78899999964 5788888888877766532  345677775543

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=96.42  E-value=0.0018  Score=52.76  Aligned_cols=43  Identities=19%  Similarity=0.305  Sum_probs=32.2

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC--cceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      .++.+|++||.- .|++.....+.+.+.....  ...+|++|.+..
T Consensus       173 ~~p~lllLDEPts~LD~~~~~~i~~~l~~~~~~~g~tviivtHd~~  218 (271)
T 2ixe_A          173 RKPRLLILDNATSALDAGNQLRVQRLLYESPEWASRTVLLITQQLS  218 (271)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHHCTTTTTSEEEEECSCHH
T ss_pred             cCCCEEEEECCccCCCHHHHHHHHHHHHHHHhhcCCEEEEEeCCHH
Confidence            567899999964 5788888888888887643  556777776643

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=96.42  E-value=0.0045  Score=51.68  Aligned_cols=23  Identities=30%  Similarity=0.274  Sum_probs=21.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||||+|||+++..++...
T Consensus       100 i~~i~G~~gsGKT~la~~la~~~  122 (322)
T 2i1q_A          100 VTEFAGVFGSGKTQIMHQSCVNL  122 (322)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            48999999999999999999874

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=96.41  E-value=0.0018  Score=52.15  Aligned_cols=42  Identities=14%  Similarity=0.203  Sum_probs=30.0

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc-CcceEEEEecCC
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS-KVTRFFFICNYI  195 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~  195 (294)
                      .++.+|++||.- .|++.....+.+.+.... ....+|++|.+.
T Consensus       163 ~~p~lllLDEPts~LD~~~~~~l~~~l~~l~~~g~tiiivtHd~  206 (256)
T 1vpl_A          163 VNPRLAILDEPTSGLDVLNAREVRKILKQASQEGLTILVSSHNM  206 (256)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEEECCH
T ss_pred             cCCCEEEEeCCccccCHHHHHHHHHHHHHHHhCCCEEEEEcCCH
Confidence            567899999964 678887777777776643 345677777654

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=96.40  E-value=0.0018  Score=52.32  Aligned_cols=43  Identities=26%  Similarity=0.414  Sum_probs=31.5

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                      .++.++++||.- .|++.....+.+.+........+|++|.+..
T Consensus       172 ~~p~lllLDEPts~LD~~~~~~i~~~l~~l~~~~tviivtH~~~  215 (260)
T 2ghi_A          172 KDPKIVIFDEATSSLDSKTEYLFQKAVEDLRKNRTLIIIAHRLS  215 (260)
T ss_dssp             HCCSEEEEECCCCTTCHHHHHHHHHHHHHHTTTSEEEEECSSGG
T ss_pred             cCCCEEEEECccccCCHHHHHHHHHHHHHhcCCCEEEEEcCCHH
Confidence            356799999964 5788888888888876655566777776654

>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=96.40  E-value=0.0021  Score=53.19  Aligned_cols=24  Identities=33%  Similarity=0.476  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+||+|+||||++..++..+.
T Consensus       106 vi~ivG~~GsGKTTl~~~LA~~l~  129 (306)
T 1vma_A          106 VIMVVGVNGTGKTTSCGKLAKMFV  129 (306)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCChHHHHHHHHHHHHH
Confidence            389999999999999999998873

>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=96.40  E-value=0.0018  Score=51.99  Aligned_cols=38  Identities=21%  Similarity=0.323  Sum_probs=27.1

Q ss_pred             EEEEeCCC-CCCHHHHHHHHHHHHhhc-CcceEEEEecCC
Q 022641          158 IIILDEAD-SMTEDAQNALRRTMETYS-KVTRFFFICNYI  195 (294)
Q Consensus       158 lliiDei~-~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~  195 (294)
                      +|++||.- .|++.....+.+.+.... ....+|++|.+.
T Consensus       154 lllLDEPts~LD~~~~~~l~~~l~~l~~~g~tviivtHd~  193 (249)
T 2qi9_C          154 LLLLDEPMNSLDVAQQSALDKILSALSQQGLAIVMSSHDL  193 (249)
T ss_dssp             EEEESSTTTTCCHHHHHHHHHHHHHHHHTTCEEEEECSCH
T ss_pred             EEEEECCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            99999964 578888888887777653 345567777553

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=96.40  E-value=0.016  Score=51.89  Aligned_cols=96  Identities=14%  Similarity=0.123  Sum_probs=0.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCccC---------------------------------------------------
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFGPELYK---------------------------------------------------  113 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~~~~~~---------------------------------------------------  113 (294)
                      +.|+||.|+|||||++.++..+......-                                                   
T Consensus        28 ~gLiGpNGaGKSTLlkiL~Gl~~p~~G~i~~~~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  107 (538)
T 3ozx_A           28 LGVLGKNGVGKTTVLKILAGEIIPNFGDPNSKVGKDEVLKRFRGKEIYNYFKELYSNELKIVHKIQYVEYASKFLKGTVN  107 (538)
T ss_dssp             EEEECCTTSSHHHHHHHHTTSSCCCTTCTTSCCCHHHHHHHHTTSTTHHHHHHHHTTCCCEEEECSCTTGGGTTCCSBHH
T ss_pred             EEEECCCCCcHHHHHHHHhcCCCCCCCccccccchhhHHhhcCCeeHHHHHHHHhhcccchhhccchhhhhhhhccCcHH


Q ss_pred             ---------------------CcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeC-CCCCCHHH
Q 022641          114 ---------------------SRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDE-ADSMTEDA  171 (294)
Q Consensus       114 ---------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDe-i~~l~~~~  171 (294)
                                           .....-......+...-+-.+.........              +|++|| ...|+...
T Consensus       108 ~~l~~~~~~~~~~~~l~~l~l~~~~~~~~~~LSgGe~Qrv~iA~aL~~~p~--------------illlDEPts~LD~~~  173 (538)
T 3ozx_A          108 EILTKIDERGKKDEVKELLNMTNLWNKDANILSGGGLQRLLVAASLLREAD--------------VYIFDQPSSYLDVRE  173 (538)
T ss_dssp             HHHHHHCCSSCHHHHHHHTTCGGGTTSBGGGCCHHHHHHHHHHHHHHSCCS--------------EEEEESTTTTCCHHH
T ss_pred             HHhhcchhHHHHHHHHHHcCCchhhcCChhhCCHHHHHHHHHHHHHHcCCC--------------EEEEECCcccCCHHH


Q ss_pred             HHHHHHHHHhhcCcceEEEEecC
Q 022641          172 QNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       172 ~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      ...+++++........+|+++.+
T Consensus       174 ~~~l~~~l~~l~~g~tii~vsHd  196 (538)
T 3ozx_A          174 RMNMAKAIRELLKNKYVIVVDHD  196 (538)
T ss_dssp             HHHHHHHHHHHCTTSEEEEECSC
T ss_pred             HHHHHHHHHHHhCCCEEEEEEeC

>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=96.38  E-value=0.0016  Score=52.13  Aligned_cols=23  Identities=30%  Similarity=0.471  Sum_probs=21.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+||+|+|||||++.++..+
T Consensus        30 ~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           30 IIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            58999999999999999998765

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=96.38  E-value=0.0018  Score=48.39  Aligned_cols=22  Identities=27%  Similarity=0.468  Sum_probs=20.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|.|++|+|||++|..+.+.
T Consensus        18 gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           18 GVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHc
Confidence            5999999999999999999875

>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=96.37  E-value=0.0021  Score=54.70  Aligned_cols=43  Identities=7%  Similarity=0.232  Sum_probs=29.9

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhhcC--cceEEEEecCCc
Q 022641          154 PPYKIIILDEA-DSMTEDAQNALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei-~~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      .++.+|++||- ..|++.....+...+.....  ...+|++|.+..
T Consensus       156 ~~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  201 (372)
T 1g29_1          156 RKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIYVTHDQV  201 (372)
T ss_dssp             TCCSEEEEECTTTTSCHHHHHHHHHHHHHHHHHHTCEEEEEESCHH
T ss_pred             cCCCEEEECCCCccCCHHHHHHHHHHHHHHHHhcCCEEEEECCCHH
Confidence            46779999995 46788777777777765432  456777776543

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=96.37  E-value=0.021  Score=54.39  Aligned_cols=21  Identities=24%  Similarity=0.252  Sum_probs=18.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~  104 (294)
                      .++|+||.|+||||+++.++-
T Consensus       664 i~~ItGpNGsGKSTlLr~ial  684 (934)
T 3thx_A          664 FHIITGPNMGGKSTYIRQTGV  684 (934)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            389999999999999999853

>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=96.37  E-value=0.002  Score=48.89  Aligned_cols=23  Identities=30%  Similarity=0.398  Sum_probs=21.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+|+||.|+|||+++.+|.-.+
T Consensus        28 ~~~i~G~NGsGKStll~ai~~~l   50 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILFVL   50 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHH
Confidence            47999999999999999998876

>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=96.37  E-value=0.0021  Score=47.85  Aligned_cols=22  Identities=27%  Similarity=0.466  Sum_probs=19.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|.|++|+|||+|+..+...
T Consensus         5 ~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            5 EIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999753

>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=96.36  E-value=0.0017  Score=49.38  Aligned_cols=21  Identities=29%  Similarity=0.528  Sum_probs=19.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~  104 (294)
                      .++|+|++|+|||+|+..++.
T Consensus         4 kv~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999999875

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=96.35  E-value=0.002  Score=52.72  Aligned_cols=43  Identities=19%  Similarity=0.396  Sum_probs=29.4

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC-cceE--EEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK-VTRF--FFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~-~~~i--i~~~~~~~  196 (294)
                      .++.+|++||.- .|++.....+.+++..... ...+  |++|.+..
T Consensus       178 ~~p~lLlLDEPts~LD~~~~~~l~~~l~~l~~~g~tv~~iivtHd~~  224 (279)
T 2ihy_A          178 GQPQVLILDEPAAGLDFIARESLLSILDSLSDSYPTLAMIYVTHFIE  224 (279)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHHCTTCEEEEEESCGG
T ss_pred             CCCCEEEEeCCccccCHHHHHHHHHHHHHHHHCCCEEEEEEEecCHH
Confidence            467799999964 5788877777777765432 3345  77776644

>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B* 3thy_B* 3thz_B*

Probab=96.35  E-value=0.022  Score=54.12  Aligned_cols=22  Identities=27%  Similarity=0.341  Sum_probs=19.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|+||.|+||||+.+.++..
T Consensus       675 i~~ItGPNGaGKSTlLr~i~~i  696 (918)
T 3thx_B          675 VMIITGPNMGGKSSYIKQVALI  696 (918)
T ss_dssp             EEEEESCCCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCchHHHHHHHHHH
Confidence            4899999999999999998743

>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=96.34  E-value=0.0036  Score=47.57  Aligned_cols=32  Identities=19%  Similarity=0.208  Sum_probs=24.5

Q ss_pred             HHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHH
Q 022641           73 LTNTLETANCPHMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        73 l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~  105 (294)
                      +.+ +.......++++|++|+|||+++..+...
T Consensus         8 ~~~-~~~~~~~~i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A            8 IWR-LFNHQEHKVIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             HHH-HHTTSCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             HHH-hcCCCccEEEEECCCCCCHHHHHHHHhcC
Confidence            444 34444456999999999999999999843

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=96.34  E-value=0.0019  Score=51.09  Aligned_cols=24  Identities=33%  Similarity=0.429  Sum_probs=19.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..|+|.|++|+||||+++.+++.+
T Consensus        26 ~~I~~eG~~GsGKsT~~~~l~~~l   49 (227)
T 3v9p_A           26 KFITFEGIDGAGKTTHLQWFCDRL   49 (227)
T ss_dssp             CEEEEECCC---CHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            359999999999999999999988

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=96.32  E-value=0.0022  Score=52.10  Aligned_cols=43  Identities=23%  Similarity=0.338  Sum_probs=31.1

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc-CcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS-KVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~~  196 (294)
                      .++.+|++||.- .|++.....+.+.+.... ....+|++|.+..
T Consensus       155 ~~p~lllLDEPts~LD~~~~~~l~~~l~~l~~~g~tii~vtHd~~  199 (266)
T 2yz2_A          155 HEPDILILDEPLVGLDREGKTDLLRIVEKWKTLGKTVILISHDIE  199 (266)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEECSCCT
T ss_pred             cCCCEEEEcCccccCCHHHHHHHHHHHHHHHHcCCEEEEEeCCHH
Confidence            567899999965 578888888888877653 3456777776544

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=96.32  E-value=0.012  Score=44.85  Aligned_cols=23  Identities=22%  Similarity=0.416  Sum_probs=19.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+|+..+...-
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            39999999999999999987543

>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=96.32  E-value=0.0055  Score=53.85  Aligned_cols=23  Identities=43%  Similarity=0.547  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+||+|+||||+++.|+..+
T Consensus       295 VI~LVGpNGSGKTTLl~~LAgll  317 (503)
T 2yhs_A          295 VILMVGVNGVGKTTTIGKLARQF  317 (503)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCcccHHHHHHHHHHHh
Confidence            38999999999999999999877

>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=96.32  E-value=0.0016  Score=54.85  Aligned_cols=42  Identities=19%  Similarity=0.277  Sum_probs=30.1

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhhc--CcceEEEEecCC
Q 022641          154 PPYKIIILDEA-DSMTEDAQNALRRTMETYS--KVTRFFFICNYI  195 (294)
Q Consensus       154 ~~~~lliiDei-~~l~~~~~~~L~~~l~~~~--~~~~ii~~~~~~  195 (294)
                      .++.+|++||- ..|++.....+...+....  ....+|++|.+.
T Consensus       144 ~~P~lLLLDEP~s~LD~~~~~~l~~~l~~l~~~~g~tii~vTHd~  188 (348)
T 3d31_A          144 TNPKILLLDEPLSALDPRTQENAREMLSVLHKKNKLTVLHITHDQ  188 (348)
T ss_dssp             SCCSEEEEESSSTTSCHHHHHHHHHHHHHHHHHTTCEEEEEESCH
T ss_pred             cCCCEEEEECccccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            56789999995 4678887777777776543  245677777654

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=96.30  E-value=0.0074  Score=56.07  Aligned_cols=33  Identities=27%  Similarity=0.265  Sum_probs=22.9

Q ss_pred             ccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHH
Q 022641           65 HQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIA  103 (294)
Q Consensus        65 g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la  103 (294)
                      .|...+..+.    .  ..++++.||+|+|||+.+....
T Consensus        29 ~Q~~~i~~i~----~--~~~~lv~apTGsGKT~~~~l~i   61 (702)
T 2p6r_A           29 PQAEAVEKVF----S--GKNLLLAMPTAAGKTLLAEMAM   61 (702)
T ss_dssp             CCHHHHHHHT----T--CSCEEEECSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHh----C--CCcEEEEcCCccHHHHHHHHHH
Confidence            4555554432    2  3479999999999999984433

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=96.29  E-value=0.013  Score=54.60  Aligned_cols=18  Identities=33%  Similarity=0.338  Sum_probs=16.2

Q ss_pred             CcEEEECCCCCCHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTAL  100 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~  100 (294)
                      .+++++||+|+|||..+.
T Consensus        40 ~~~lv~apTGsGKT~~~~   57 (720)
T 2zj8_A           40 KNALISIPTASGKTLIAE   57 (720)
T ss_dssp             CEEEEECCGGGCHHHHHH
T ss_pred             CcEEEEcCCccHHHHHHH
Confidence            489999999999999883

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=96.28  E-value=0.04  Score=46.13  Aligned_cols=24  Identities=17%  Similarity=0.314  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      -++|.|+||+|||+++..++..+.
T Consensus        48 LiiIaG~pG~GKTt~al~ia~~~a   71 (338)
T 4a1f_A           48 LVIIGARPSMGKTSLMMNMVLSAL   71 (338)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHH
Confidence            399999999999999999998763

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=96.27  E-value=0.0023  Score=51.54  Aligned_cols=42  Identities=17%  Similarity=0.241  Sum_probs=30.5

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC--cceEEEEecCC
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK--VTRFFFICNYI  195 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~  195 (294)
                      .++.+|++||.- .|++.....+.+.+.....  ...+|++|.+.
T Consensus       145 ~~p~lllLDEPts~LD~~~~~~l~~~l~~l~~~~g~tvi~vtHd~  189 (253)
T 2nq2_C          145 SECKLILLDEPTSALDLANQDIVLSLLIDLAQSQNMTVVFTTHQP  189 (253)
T ss_dssp             TTCSEEEESSSSTTSCHHHHHHHHHHHHHHHHTSCCEEEEEESCH
T ss_pred             cCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEecCH
Confidence            467799999965 5788888888888776532  45677777654

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=96.26  E-value=0.0028  Score=53.69  Aligned_cols=23  Identities=39%  Similarity=0.556  Sum_probs=21.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      +.|+||+|+||||+++.++..+.
T Consensus       160 i~lvG~nGsGKTTll~~Lag~l~  182 (359)
T 2og2_A          160 IMIVGVNGGGKTTSLGKLAHRLK  182 (359)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEcCCCChHHHHHHHHHhhcc
Confidence            89999999999999999999873

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=96.26  E-value=0.012  Score=57.29  Aligned_cols=24  Identities=25%  Similarity=0.162  Sum_probs=19.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++++||+|+|||..+...+...
T Consensus       200 ~dvLV~ApTGSGKTlva~l~i~~~  223 (1108)
T 3l9o_A          200 ESVLVSAHTSAGKTVVAEYAIAQS  223 (1108)
T ss_dssp             CCEEEECCSSSHHHHHHHHHHHHH
T ss_pred             CCEEEECCCCCChHHHHHHHHHHH
Confidence            479999999999999876554443

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=96.26  E-value=0.0045  Score=58.19  Aligned_cols=38  Identities=37%  Similarity=0.596  Sum_probs=27.6

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++.....+...+.   .+.++|.||||||||+++..+...+
T Consensus       362 n~~Q~~Av~~~l~---~~~~lI~GppGTGKT~~i~~~i~~l  399 (802)
T 2xzl_A          362 NSSQSNAVSHVLQ---RPLSLIQGPPGTGKTVTSATIVYHL  399 (802)
T ss_dssp             CHHHHHHHHHHTT---CSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhc---CCCEEEECCCCCCHHHHHHHHHHHH
Confidence            4555566655553   3468999999999999987776654

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=96.25  E-value=0.0022  Score=51.16  Aligned_cols=23  Identities=17%  Similarity=0.228  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.|++|+||||+++.+++.+
T Consensus         4 ~i~~~G~~g~GKtt~~~~l~~~l   26 (241)
T 2ocp_A            4 RLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHC
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999987

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=96.24  E-value=0.038  Score=48.26  Aligned_cols=37  Identities=27%  Similarity=0.171  Sum_probs=26.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      -++|.|+||+|||+++..++.......  +.++..++..
T Consensus       202 l~ii~G~pg~GKT~lal~ia~~~a~~~--g~~vl~~slE  238 (444)
T 2q6t_A          202 LNIIAARPAMGKTAFALTIAQNAALKE--GVGVGIYSLE  238 (444)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTT--CCCEEEEESS
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHhC--CCeEEEEECC
Confidence            389999999999999999998763211  2345555443

>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=96.23  E-value=0.0032  Score=56.83  Aligned_cols=23  Identities=26%  Similarity=0.353  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|+|++|+||||+++.|++.+
T Consensus       398 ~I~l~GlsGSGKSTiA~~La~~L  420 (573)
T 1m8p_A          398 TIFLTGYMNSGKDAIARALQVTL  420 (573)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEeecCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999997

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=96.23  E-value=0.0029  Score=49.81  Aligned_cols=23  Identities=17%  Similarity=0.216  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|.|.|++|||||++++.|++.+
T Consensus        16 iI~i~g~~gsGk~~i~~~la~~l   38 (223)
T 3hdt_A           16 IITIEREYGSGGRIVGKKLAEEL   38 (223)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999998

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=96.22  E-value=0.017  Score=52.90  Aligned_cols=30  Identities=23%  Similarity=0.333  Sum_probs=21.2

Q ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHHHHhhc
Q 022641          154 PPYKIIILDEADSMTEDAQNALRRTMETYS  183 (294)
Q Consensus       154 ~~~~lliiDei~~l~~~~~~~L~~~l~~~~  183 (294)
                      .+..+|||||++.++......+..+++..+
T Consensus       317 ~~l~~lVlDEAH~l~~~~~~~l~~Il~~l~  346 (666)
T 3o8b_A          317 GAYDIIICDECHSTDSTTILGIGTVLDQAE  346 (666)
T ss_dssp             TSCSEEEETTTTCCSHHHHHHHHHHHHHTT
T ss_pred             CcccEEEEccchhcCccHHHHHHHHHHhhh
Confidence            456799999999998776555555555443

>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=96.22  E-value=0.003  Score=46.76  Aligned_cols=23  Identities=17%  Similarity=0.316  Sum_probs=20.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+++..+....
T Consensus         7 ~i~v~G~~~~GKssl~~~l~~~~   29 (168)
T 1z2a_A            7 KMVVVGNGAVGKSSMIQRYCKGI   29 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            48999999999999999998754

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=96.21  E-value=0.014  Score=58.15  Aligned_cols=26  Identities=19%  Similarity=0.279  Sum_probs=22.5

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+..+.|+||+|+||||+++.+.+.+
T Consensus       443 ~G~~vaivG~sGsGKSTll~ll~~~~  468 (1321)
T 4f4c_A          443 AGQTVALVGSSGCGKSTIISLLLRYY  468 (1321)
T ss_dssp             TTCEEEEEECSSSCHHHHHHHHTTSS
T ss_pred             CCcEEEEEecCCCcHHHHHHHhcccc
Confidence            33459999999999999999998876

>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=96.21  E-value=0.0011  Score=50.83  Aligned_cols=23  Identities=22%  Similarity=0.307  Sum_probs=20.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+++..+....
T Consensus        20 ki~v~G~~~~GKssli~~l~~~~   42 (194)
T 2atx_A           20 KCVVVGDGAVGKTCLLMSYANDA   42 (194)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            49999999999999999998764

>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=96.21  E-value=0.0026  Score=54.50  Aligned_cols=43  Identities=21%  Similarity=0.246  Sum_probs=31.4

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          154 PPYKIIILDEA-DSMTEDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei-~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                      .++.+|++||- ..|++.....+...+........+|+++.+..
T Consensus       172 ~~P~lLLLDEPts~LD~~~~~~l~~~l~~~~~~~tvi~vtHd~e  215 (390)
T 3gd7_A          172 SKAKILLLDEPSAHLDPVTYQIIRRTLKQAFADCTVILCEARIE  215 (390)
T ss_dssp             TTCCEEEEESHHHHSCHHHHHHHHHHHHTTTTTSCEEEECSSSG
T ss_pred             cCCCEEEEeCCccCCCHHHHHHHHHHHHHHhCCCEEEEEEcCHH
Confidence            46779999995 45777777888888876555566777776643

>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=96.20  E-value=0.0024  Score=54.42  Aligned_cols=24  Identities=17%  Similarity=0.224  Sum_probs=22.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+.|+||+|+|||||++.|+..+.
T Consensus       172 k~~IvG~nGsGKSTLlk~L~gl~~  195 (365)
T 1lw7_A          172 TVAILGGESSGKSVLVNKLAAVFN  195 (365)
T ss_dssp             EEEEECCTTSHHHHHHHHHHHHTT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            489999999999999999999873

>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=96.20  E-value=0.0027  Score=55.23  Aligned_cols=24  Identities=42%  Similarity=0.576  Sum_probs=22.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|+|++|+||||++..++..+
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~l  123 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARYI  123 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            369999999999999999999887

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=96.19  E-value=0.0048  Score=55.38  Aligned_cols=41  Identities=29%  Similarity=0.368  Sum_probs=29.8

Q ss_pred             cHHHHHHHHHHH--HcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           66 QEEVVRVLTNTL--ETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        66 ~~~~~~~l~~~l--~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++...++...  .......++|+|++|+||||+++.|++.+
T Consensus       354 r~eV~~~lr~~~~~~~~~~~~I~l~G~~GsGKSTia~~La~~L  396 (546)
T 2gks_A          354 RPEVAEILAETYVPKHKQGFCVWLTGLPCAGKSTIAEILATML  396 (546)
T ss_dssp             CHHHHHHHHHHSCCGGGCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             chhHHHHHHHhhccccccceEEEccCCCCCCHHHHHHHHHHHh
Confidence            345555555555  22223358999999999999999999987

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=96.19  E-value=0.00085  Score=52.26  Aligned_cols=23  Identities=17%  Similarity=0.213  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.|++|+|||+|+..+...-
T Consensus        11 ki~i~G~~~~GKTsli~~l~~~~   33 (212)
T 2j0v_A           11 KCVTVGDGAVGKTCMLICYTSNK   33 (212)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            49999999999999999998654

>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=96.19  E-value=0.003  Score=47.18  Aligned_cols=23  Identities=35%  Similarity=0.574  Sum_probs=19.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++.|++|+|||+|+..+...-
T Consensus         6 ki~i~G~~~vGKSsl~~~l~~~~   28 (175)
T 2nzj_A            6 RVVLLGDPGVGKTSLASLFAGKQ   28 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCC-
T ss_pred             EEEEECCCCccHHHHHHHHhcCC
Confidence            49999999999999999987543

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=96.17  E-value=0.0039  Score=46.71  Aligned_cols=25  Identities=36%  Similarity=0.339  Sum_probs=21.4

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ...++++|++|+|||+++..+...-
T Consensus         8 ~~~i~v~G~~~~GKssl~~~l~~~~   32 (178)
T 2lkc_A            8 PPVVTIMGHVDHGKTTLLDAIRHSK   32 (178)
T ss_dssp             CCEEEEESCTTTTHHHHHHHHHTTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCc
Confidence            3469999999999999999997643

>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=96.17  E-value=0.014  Score=44.82  Aligned_cols=23  Identities=17%  Similarity=0.299  Sum_probs=20.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+|||+|+..+...-
T Consensus        31 ki~vvG~~~vGKSsli~~l~~~~   53 (201)
T 2hup_A           31 KLVLVGDASVGKTCVVQRFKTGA   53 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhhCC
Confidence            49999999999999999997654

>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=96.17  E-value=0.0028  Score=50.33  Aligned_cols=24  Identities=25%  Similarity=0.426  Sum_probs=22.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .|+|.|++|+||||+++.++..+.
T Consensus        29 ~i~~eG~~GsGKsT~~~~l~~~l~   52 (236)
T 3lv8_A           29 FIVIEGLEGAGKSTAIQVVVETLQ   52 (236)
T ss_dssp             EEEEEESTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            589999999999999999999883

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=96.16  E-value=0.0038  Score=49.10  Aligned_cols=24  Identities=38%  Similarity=0.488  Sum_probs=22.0

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..|+|.|++|+||||+++.+++.+
T Consensus        22 ~~i~~~G~~g~GKst~~~~l~~~l   45 (223)
T 3ld9_A           22 MFITFEGIDGSGKTTQSHLLAEYL   45 (223)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            348999999999999999999987

>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=96.16  E-value=0.0016  Score=55.02  Aligned_cols=24  Identities=25%  Similarity=0.324  Sum_probs=20.8

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|+||+|+|||||++.|+...
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            359999999999999999997543

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=96.15  E-value=0.0025  Score=51.61  Aligned_cols=41  Identities=17%  Similarity=0.297  Sum_probs=31.6

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                      .++.++++||.- .|++.....+.+.+.....  .+|++|.+..
T Consensus       145 ~~p~lllLDEPts~LD~~~~~~l~~~L~~~~~--tviivtHd~~  186 (263)
T 2pjz_A          145 SQPEIVGLDEPFENVDAARRHVISRYIKEYGK--EGILVTHELD  186 (263)
T ss_dssp             TCCSEEEEECTTTTCCHHHHHHHHHHHHHSCS--EEEEEESCGG
T ss_pred             hCCCEEEEECCccccCHHHHHHHHHHHHHhcC--cEEEEEcCHH
Confidence            467799999964 6788888889999887655  6777776643

>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=0.0043  Score=49.49  Aligned_cols=22  Identities=41%  Similarity=0.496  Sum_probs=19.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|+|+||+|||+++..++..
T Consensus        32 l~~i~G~pG~GKT~l~l~~~~~   53 (251)
T 2zts_A           32 TVLLTGGTGTGKTTFAAQFIYK   53 (251)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHH
Confidence            4999999999999999887754

>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=96.14  E-value=0.0033  Score=56.16  Aligned_cols=23  Identities=26%  Similarity=0.431  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+++|.||+||||+++.+++.+
T Consensus        37 lIvlvGlpGSGKSTia~~La~~L   59 (520)
T 2axn_A           37 VIVMVGLPARGKTYISKKLTRYL   59 (520)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            48999999999999999999887

>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=96.13  E-value=0.0018  Score=54.83  Aligned_cols=24  Identities=38%  Similarity=0.396  Sum_probs=21.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|.||+|+|||||++.++...
T Consensus        32 e~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           32 ERFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC
Confidence            458999999999999999999765

>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=96.12  E-value=0.0036  Score=46.37  Aligned_cols=23  Identities=17%  Similarity=0.398  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++.|++|+|||+++..+...-
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            48999999999999999998654

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=96.10  E-value=0.0034  Score=47.60  Aligned_cols=22  Identities=27%  Similarity=0.466  Sum_probs=20.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|.|++|+|||+|+..+...
T Consensus         9 ~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            9 EIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4999999999999999999864

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=96.10  E-value=0.0042  Score=48.61  Aligned_cols=24  Identities=33%  Similarity=0.357  Sum_probs=22.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..|+|.|++|+||||+++.+++.+
T Consensus         6 ~~i~~eG~~g~GKst~~~~l~~~l   29 (216)
T 3tmk_A            6 KLILIEGLDRTGKTTQCNILYKKL   29 (216)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            458999999999999999999998

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=96.10  E-value=0.004  Score=52.38  Aligned_cols=27  Identities=33%  Similarity=0.421  Sum_probs=23.0

Q ss_pred             CCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           80 ANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        80 ~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .....+.|+||||+||||+++.++..+
T Consensus        53 ~~g~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           53 GRAIRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             CCSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHhh
Confidence            344469999999999999999999765

>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=96.09  E-value=0.0055  Score=50.71  Aligned_cols=22  Identities=23%  Similarity=0.434  Sum_probs=20.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|.||+|+|||||++.++ ..
T Consensus       167 i~~l~G~sG~GKSTLln~l~-~~  188 (302)
T 2yv5_A          167 ICILAGPSGVGKSSILSRLT-GE  188 (302)
T ss_dssp             EEEEECSTTSSHHHHHHHHH-SC
T ss_pred             EEEEECCCCCCHHHHHHHHH-Hh
Confidence            58999999999999999998 44

>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=96.08  E-value=0.0039  Score=46.28  Aligned_cols=23  Identities=22%  Similarity=0.339  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+++..+...-
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~~   30 (170)
T 1z08_A            8 KVVLLGEGCVGKTSLVLRYCENK   30 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHCC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            48999999999999999998654

>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=96.08  E-value=0.0024  Score=48.20  Aligned_cols=24  Identities=29%  Similarity=0.379  Sum_probs=20.0

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHH
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~  104 (294)
                      ....++++|++|+|||+++..+..
T Consensus        17 ~~~~i~v~G~~~~GKssli~~l~~   40 (183)
T 1moz_A           17 KELRILILGLDGAGKTTILYRLQI   40 (183)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CccEEEEECCCCCCHHHHHHHHhc
Confidence            334599999999999999988753

>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=96.08  E-value=0.024  Score=49.08  Aligned_cols=24  Identities=38%  Similarity=0.398  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++++|++|+||||++..++..+.
T Consensus       100 vi~i~G~~GsGKTT~~~~LA~~l~  123 (425)
T 2ffh_A          100 LWFLVGLQGSGKTTTAAKLALYYK  123 (425)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            488889999999999999999884

>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=96.07  E-value=0.0037  Score=46.42  Aligned_cols=21  Identities=29%  Similarity=0.480  Sum_probs=18.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~  104 (294)
                      .+++.|++|+|||+|+..+..
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            489999999999999999863

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=96.07  E-value=0.0087  Score=50.56  Aligned_cols=24  Identities=33%  Similarity=0.473  Sum_probs=21.6

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|+|+||+|||||...+...+
T Consensus        75 ~~v~lvG~pgaGKSTLln~L~~~~   98 (349)
T 2www_A           75 FRVGLSGPPGAGKSTFIEYFGKML   98 (349)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHh
Confidence            459999999999999999999865

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=96.06  E-value=0.018  Score=55.60  Aligned_cols=21  Identities=24%  Similarity=0.183  Sum_probs=17.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~  104 (294)
                      ++++.+|+|+|||.++.....
T Consensus       103 ~vLV~apTGSGKTlva~lai~  123 (1010)
T 2xgj_A          103 SVLVSAHTSAGKTVVAEYAIA  123 (1010)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEECCCCCChHHHHHHHHH
Confidence            799999999999998754443

>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=96.05  E-value=0.0044  Score=45.72  Aligned_cols=24  Identities=25%  Similarity=0.315  Sum_probs=21.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+++.|++|+|||+++..+...-+
T Consensus         2 ki~~~G~~~~GKssl~~~l~~~~~   25 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKLGEI   25 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHCS
T ss_pred             EEEEECCCCCCHHHHHHHHHcCCc
Confidence            489999999999999999987653

>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=96.05  E-value=0.0041  Score=46.69  Aligned_cols=23  Identities=22%  Similarity=0.401  Sum_probs=20.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+++..+....
T Consensus        10 ~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A           10 KVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            49999999999999999988754

>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=96.04  E-value=0.0042  Score=45.94  Aligned_cols=23  Identities=17%  Similarity=0.496  Sum_probs=20.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++.|++|+|||+++..+...-
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            48999999999999999998754

>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=96.04  E-value=0.003  Score=51.90  Aligned_cols=43  Identities=5%  Similarity=0.039  Sum_probs=29.5

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHH-HHhhcCcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRT-METYSKVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~-l~~~~~~~~ii~~~~~~~  196 (294)
                      .++.++++||.- .|++.....+.+. +........+|++|.+..
T Consensus       176 ~~p~lllLDEPts~LD~~~~~~i~~~ll~~~~~~~tviivtHd~~  220 (290)
T 2bbs_A          176 KDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKME  220 (290)
T ss_dssp             SCCSEEEEESTTTTCCHHHHHHHHHHCCCCCTTTSEEEEECCCHH
T ss_pred             CCCCEEEEECCcccCCHHHHHHHHHHHHHHhhCCCEEEEEecCHH
Confidence            457799999965 5788888888875 333333456777776643

>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=96.04  E-value=0.0038  Score=51.61  Aligned_cols=23  Identities=30%  Similarity=0.307  Sum_probs=20.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|.||+|+|||||++.++...
T Consensus       171 iv~l~G~sG~GKSTll~~l~g~~  193 (301)
T 1u0l_A          171 ISTMAGLSGVGKSSLLNAINPGL  193 (301)
T ss_dssp             EEEEECSTTSSHHHHHHHHSTTC
T ss_pred             eEEEECCCCCcHHHHHHHhcccc
Confidence            48999999999999999997654

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=96.03  E-value=0.0069  Score=55.27  Aligned_cols=23  Identities=26%  Similarity=0.351  Sum_probs=17.4

Q ss_pred             CcEEEECCCCCCHHHHH-HHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTA-LAIAHQ  105 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la-~~la~~  105 (294)
                      .++++.+|+|+|||... -.+...
T Consensus       187 ~dvlv~a~TGSGKT~~~~lpil~~  210 (618)
T 2whx_A          187 RLTIMDLHPGAGKTKRILPSIVRE  210 (618)
T ss_dssp             CEEEECCCTTSSTTTTHHHHHHHH
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHH
Confidence            47999999999999963 434433

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=96.01  E-value=0.0041  Score=46.16  Aligned_cols=22  Identities=23%  Similarity=0.513  Sum_probs=19.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++++|++|+|||+++..+...
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            4899999999999999999764

>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=96.01  E-value=0.0014  Score=53.10  Aligned_cols=23  Identities=17%  Similarity=0.174  Sum_probs=21.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|.|++|+||||+++.|++.+
T Consensus        26 ~I~ieG~~GsGKST~~~~L~~~l   48 (263)
T 1p5z_B           26 KISIEGNIAAGKSTFVNILKQLC   48 (263)
T ss_dssp             EEEEECSTTSSHHHHHTTTGGGC
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            58999999999999999999886

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=96.00  E-value=0.0039  Score=48.71  Aligned_cols=24  Identities=29%  Similarity=0.376  Sum_probs=22.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .|+|.|++|+||||.++.+++.+.
T Consensus         5 ~i~~eG~~gsGKsT~~~~l~~~l~   28 (213)
T 4tmk_A            5 YIVIEGLEGAGKTTARNVVVETLE   28 (213)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            589999999999999999999884

>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=96.00  E-value=0.0044  Score=45.89  Aligned_cols=23  Identities=17%  Similarity=0.411  Sum_probs=20.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++.|++|+|||+++..+...-
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~~   30 (170)
T 1r2q_A            8 KLVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            48999999999999999998653

>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=96.00  E-value=0.01  Score=51.23  Aligned_cols=23  Identities=17%  Similarity=0.234  Sum_probs=20.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+||+|+||||+++.++...
T Consensus        71 ~valvG~nGaGKSTLln~L~Gl~   93 (413)
T 1tq4_A           71 NVAVTGETGSGKSSFINTLRGIG   93 (413)
T ss_dssp             EEEEEECTTSSHHHHHHHHHTCC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCC
Confidence            69999999999999999998743

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=95.98  E-value=0.0049  Score=47.90  Aligned_cols=29  Identities=28%  Similarity=0.324  Sum_probs=24.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      +-|+|..|+||||+++.++. +      +.+++..+
T Consensus        12 iglTGgigsGKStv~~~l~~-~------g~~vidaD   40 (210)
T 4i1u_A           12 IGLTGGIGSGKTTVADLFAA-R------GASLVDTD   40 (210)
T ss_dssp             EEEECCTTSCHHHHHHHHHH-T------TCEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHH-C------CCcEEECc
Confidence            89999999999999999987 6      66666554

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=95.98  E-value=0.021  Score=49.89  Aligned_cols=36  Identities=25%  Similarity=0.220  Sum_probs=26.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      -++|.|+||+|||+++..++..+...   +..+..++..
T Consensus       199 liiIaG~pG~GKTtlal~ia~~~a~~---g~~vl~fSlE  234 (444)
T 3bgw_A          199 FVLIAARPSMGKTAFALKQAKNMSDN---DDVVNLHSLE  234 (444)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHHHT---TCEEEEECSS
T ss_pred             EEEEEeCCCCChHHHHHHHHHHHHHc---CCEEEEEECC
Confidence            39999999999999999999887422   3344444443

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=95.97  E-value=0.044  Score=49.07  Aligned_cols=24  Identities=29%  Similarity=0.524  Sum_probs=19.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++.+|+|+|||..+...+...
T Consensus        23 ~~~l~~~~tGsGKT~~~~~~~~~~   46 (556)
T 4a2p_A           23 KNALICAPTGSGKTFVSILICEHH   46 (556)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCChHHHHHHHHHHHH
Confidence            469999999999998876665444

>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=95.97  E-value=0.0038  Score=46.32  Aligned_cols=23  Identities=22%  Similarity=0.452  Sum_probs=20.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+++..+...-
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            48999999999999999998643

>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=95.96  E-value=0.0036  Score=47.00  Aligned_cols=22  Identities=27%  Similarity=0.487  Sum_probs=20.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|+|++|+|||+|+..+...
T Consensus         6 ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            6 KVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999865

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.95  E-value=0.0048  Score=51.46  Aligned_cols=23  Identities=35%  Similarity=0.492  Sum_probs=21.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++|+|++|+||||++..++..+.
T Consensus       108 I~ivG~~G~GKTT~~~~LA~~l~  130 (320)
T 1zu4_A          108 FMLVGVNGTGKTTSLAKMANYYA  130 (320)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH
Confidence            88999999999999999998873

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C

Probab=95.94  E-value=0.0073  Score=46.48  Aligned_cols=22  Identities=14%  Similarity=0.232  Sum_probs=4.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|+|++|+|||+|+..+...
T Consensus        22 ~i~v~G~~~~GKssli~~l~~~   43 (208)
T 2yc2_C           22 KVAVVGEATVGKSALISMFTSK   43 (208)
T ss_dssp             EEEEC-----------------
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4999999999999999998766

>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=95.94  E-value=0.0035  Score=46.41  Aligned_cols=21  Identities=33%  Similarity=0.626  Sum_probs=18.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~  104 (294)
                      .++++|++|+|||+|+..+..
T Consensus         4 ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            489999999999999998853

>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=95.94  E-value=0.0049  Score=45.77  Aligned_cols=23  Identities=30%  Similarity=0.408  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++.|++|+|||+++..+...-
T Consensus         9 ~i~v~G~~~~GKssl~~~l~~~~   31 (171)
T 1upt_A            9 RILILGLDGAGKTTILYRLQVGE   31 (171)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            59999999999999999997644

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=95.93  E-value=0.0047  Score=52.12  Aligned_cols=30  Identities=20%  Similarity=0.216  Sum_probs=25.6

Q ss_pred             HHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           77 LETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        77 l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.-+....+.|.||+|+|||||++.++...
T Consensus        66 l~i~~Gq~~gIiG~nGaGKTTLl~~I~g~~   95 (347)
T 2obl_A           66 LTCGIGQRIGIFAGSGVGKSTLLGMICNGA   95 (347)
T ss_dssp             SCEETTCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             eeecCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            444455579999999999999999999987

>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=95.93  E-value=0.005  Score=46.75  Aligned_cols=22  Identities=14%  Similarity=0.095  Sum_probs=19.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+|++|+|||+|+..+....
T Consensus        23 i~ivG~~~vGKSsL~~~~~~~~   44 (184)
T 3ihw_A           23 VGIVGNLSSGKSALVHRYLTGT   44 (184)
T ss_dssp             EEEECCTTSCHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            9999999999999998887654

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=95.92  E-value=0.005  Score=54.03  Aligned_cols=26  Identities=23%  Similarity=0.379  Sum_probs=22.8

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.+.|+||.|+|||||++.|+..+
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            44579999999999999999998865

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=95.92  E-value=0.0048  Score=46.22  Aligned_cols=23  Identities=22%  Similarity=0.416  Sum_probs=20.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++.|++|+|||+|+..+...-
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            49999999999999999997543

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=95.92  E-value=0.0052  Score=53.59  Aligned_cols=30  Identities=20%  Similarity=0.248  Sum_probs=25.3

Q ss_pred             HHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           77 LETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        77 l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.-.....+.|.||+|+|||||++.++...
T Consensus       152 l~i~~Gq~~~IvG~sGsGKSTLl~~Iag~~  181 (438)
T 2dpy_A          152 LTVGRGQRMGLFAGSGVGKSVLLGMMARYT  181 (438)
T ss_dssp             SCCBTTCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             EEecCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            444455579999999999999999999987

>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=95.92  E-value=0.0075  Score=51.22  Aligned_cols=35  Identities=29%  Similarity=0.330  Sum_probs=27.2

Q ss_pred             HHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           72 VLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        72 ~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+--.+..++...+.|+||+|+|||+++..+++..
T Consensus       164 aID~~~pi~rGQr~~IvG~sG~GKTtLl~~Iar~i  198 (422)
T 3ice_A          164 VLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSI  198 (422)
T ss_dssp             HHHHHSCCBTTCEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             eeeeeeeecCCcEEEEecCCCCChhHHHHHHHHHH
Confidence            33333444556679999999999999999998875

>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=95.91  E-value=0.005  Score=46.79  Aligned_cols=23  Identities=17%  Similarity=0.463  Sum_probs=20.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+++..+....
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            49999999999999999998764

>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=95.91  E-value=0.0051  Score=46.53  Aligned_cols=23  Identities=17%  Similarity=0.476  Sum_probs=20.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++.|++|+|||+|+..+....
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            48999999999999999998654

>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=95.91  E-value=0.0049  Score=54.38  Aligned_cols=24  Identities=25%  Similarity=0.372  Sum_probs=22.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++++|.||+||||+++.+++.+.
T Consensus        41 ~IvlvGlpGsGKSTia~~La~~l~   64 (469)
T 1bif_A           41 LIVMVGLPARGKTYISKKLTRYLN   64 (469)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            599999999999999999999873

>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=95.90  E-value=0.005  Score=46.97  Aligned_cols=23  Identities=22%  Similarity=0.380  Sum_probs=20.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+|||+|+..+...-
T Consensus        27 ki~v~G~~~~GKSsLi~~l~~~~   49 (193)
T 2oil_A           27 KVVLIGESGVGKTNLLSRFTRNE   49 (193)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            49999999999999999998754

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=95.90  E-value=0.047  Score=48.32  Aligned_cols=109  Identities=15%  Similarity=0.133  Sum_probs=57.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhh-c--ccCcc-CCC--------
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVA-V--GSGQR-RGG--------  150 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~--~~~~~-~~~--------  150 (294)
                      .+.+|.-+.|+|||..+-+++..+..... ..+++.+.+..  -...+...+..+.... .  -.+.. ...        
T Consensus        57 ~~~ilad~~GlGKT~~ai~~i~~~~~~~~-~~~~LIv~P~~--l~~qw~~e~~~~~~~~~v~~~~g~~~~~~~~~~~ivi  133 (500)
T 1z63_A           57 FGICLADDMGLGKTLQTIAVFSDAKKENE-LTPSLVICPLS--VLKNWEEELSKFAPHLRFAVFHEDRSKIKLEDYDIIL  133 (500)
T ss_dssp             CCEEECCCTTSCHHHHHHHHHHHHHHTTC-CSSEEEEECST--THHHHHHHHHHHCTTSCEEECSSSTTSCCGGGSSEEE
T ss_pred             CCEEEEeCCCCcHHHHHHHHHHHHHhcCC-CCCEEEEccHH--HHHHHHHHHHHHCCCceEEEEecCchhccccCCcEEE
Confidence            36899999999999999888877642221 12333343332  3344555554432110 0  00000 000        


Q ss_pred             -----------CCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCC
Q 022641          151 -----------YPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYI  195 (294)
Q Consensus       151 -----------~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~  195 (294)
                                 ......++||+||+|++.... ....+.+.......++.+++.+.
T Consensus       134 ~t~~~l~~~~~l~~~~~~~vIvDEaH~~kn~~-~~~~~~l~~l~~~~~l~LTaTP~  188 (500)
T 1z63_A          134 TTYAVLLRDTRLKEVEWKYIVIDEAQNIKNPQ-TKIFKAVKELKSKYRIALTGTPI  188 (500)
T ss_dssp             EEHHHHTTCHHHHTCCEEEEEEETGGGGSCTT-SHHHHHHHTSCEEEEEEECSSCS
T ss_pred             eeHHHHhccchhcCCCcCEEEEeCccccCCHh-HHHHHHHHhhccCcEEEEecCCC
Confidence                       011346799999999984221 12334444444455566666543

>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=95.90  E-value=0.0048  Score=56.00  Aligned_cols=24  Identities=33%  Similarity=0.502  Sum_probs=22.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..|+|+|.+|+||||+++.|++.+
T Consensus        53 ~lIvLtGlsGSGKSTlAr~La~~L   76 (630)
T 1x6v_B           53 CTVWLTGLSGAGKTTVSMALEEYL   76 (630)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHH
Confidence            359999999999999999999987

>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=95.89  E-value=0.0045  Score=47.21  Aligned_cols=24  Identities=17%  Similarity=0.372  Sum_probs=20.9

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHH
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~  105 (294)
                      ...++++|++|+|||+++..+...
T Consensus        23 ~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           23 LPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            346999999999999999998754

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=95.87  E-value=0.038  Score=49.36  Aligned_cols=24  Identities=29%  Similarity=0.498  Sum_probs=19.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++.+|+|+|||..+...+...
T Consensus        20 ~~~l~~~~tGsGKT~~~~~~~~~~   43 (555)
T 3tbk_A           20 KNTIICAPTGCGKTFVSLLICEHH   43 (555)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEeCCCChHHHHHHHHHHHH
Confidence            479999999999998876666544

>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=95.85  E-value=0.0057  Score=46.51  Aligned_cols=23  Identities=17%  Similarity=0.395  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+|||+|+..+...-
T Consensus        23 ki~vvG~~~vGKTsLi~~l~~~~   45 (187)
T 3c5c_A           23 NLAILGRRGAGKSALTVKFLTKR   45 (187)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCcHHHHHHHHHhCC
Confidence            39999999999999999988654

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=95.84  E-value=0.0058  Score=45.91  Aligned_cols=23  Identities=22%  Similarity=0.501  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+++..+...-
T Consensus        14 ki~v~G~~~~GKSsli~~l~~~~   36 (181)
T 2efe_B           14 KLVLLGDVGAGKSSLVLRFVKDQ   36 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHCC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            39999999999999999998654

>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=95.84  E-value=0.0069  Score=44.40  Aligned_cols=24  Identities=33%  Similarity=0.433  Sum_probs=21.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ..+|+||.|+|||+++.++.-.+.
T Consensus        25 ~~~I~G~NGsGKStil~Ai~~~l~   48 (149)
T 1f2t_A           25 INLIIGQNGSGKSSLLDAILVGLY   48 (149)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Confidence            479999999999999999987663

>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=95.83  E-value=0.0048  Score=46.28  Aligned_cols=23  Identities=17%  Similarity=0.430  Sum_probs=20.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++.|++|+|||+|+..+....
T Consensus        11 ~i~v~G~~~~GKssli~~l~~~~   33 (181)
T 2fn4_A           11 KLVVVGGGGVGKSALTIQFIQSY   33 (181)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            49999999999999999998764

>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=95.81  E-value=0.0048  Score=46.18  Aligned_cols=23  Identities=22%  Similarity=0.366  Sum_probs=20.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+|+..+...-
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            49999999999999999998654

>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=95.80  E-value=0.0048  Score=46.68  Aligned_cols=21  Identities=29%  Similarity=0.395  Sum_probs=19.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~  105 (294)
                      ++++|++|+|||++|..++..
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~   22 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD   22 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCCcHHHHHHHHHhc
Confidence            689999999999999999854

>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=95.80  E-value=0.006  Score=45.76  Aligned_cols=24  Identities=25%  Similarity=0.488  Sum_probs=21.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+++.|++|+|||+|+..+...-.
T Consensus        12 ~i~v~G~~~~GKssli~~l~~~~~   35 (180)
T 2g6b_A           12 KVMLVGDSGVGKTCLLVRFKDGAF   35 (180)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSCC
T ss_pred             EEEEECcCCCCHHHHHHHHHhCCC
Confidence            499999999999999999987543

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=95.80  E-value=0.0052  Score=46.74  Aligned_cols=23  Identities=22%  Similarity=0.356  Sum_probs=20.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~  105 (294)
                      ..+++.|++|+|||+++..+...
T Consensus        24 ~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 3pqc_A           24 GEVAFVGRSNVGKSSLLNALFNR   46 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHTS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35999999999999999998765

>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=95.79  E-value=0.0061  Score=45.96  Aligned_cols=23  Identities=17%  Similarity=0.481  Sum_probs=20.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+|||+++..+....
T Consensus        20 ki~v~G~~~~GKSsl~~~l~~~~   42 (183)
T 3kkq_A           20 KLVVVGDGGVGKSALTIQFFQKI   42 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            38999999999999999998664

>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=95.79  E-value=0.0045  Score=46.81  Aligned_cols=22  Identities=32%  Similarity=0.462  Sum_probs=19.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++++|++|+|||+|+..+...
T Consensus        18 ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           18 RILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4999999999999999998654

>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=95.79  E-value=0.0065  Score=46.48  Aligned_cols=22  Identities=32%  Similarity=0.446  Sum_probs=19.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|+|++|+|||+|+..+...
T Consensus         8 kv~lvG~~~vGKSsL~~~~~~~   29 (192)
T 2cjw_A            8 RVVLIGEQGVGKSTLANIFAGV   29 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999999864

>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=95.78  E-value=0.005  Score=47.01  Aligned_cols=24  Identities=29%  Similarity=0.409  Sum_probs=21.0

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+++.|++|+|||+++..+...-
T Consensus        24 ~ki~~vG~~~vGKSsli~~l~~~~   47 (190)
T 1m2o_B           24 GKLLFLGLDNAGKTTLLHMLKNDR   47 (190)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCC
Confidence            359999999999999999998643

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=95.78  E-value=0.021  Score=49.83  Aligned_cols=22  Identities=27%  Similarity=0.233  Sum_probs=17.4

Q ss_pred             CcEEEECCCCCCHHHHH-HHHHH
Q 022641           83 PHMLFYGPPGTGKTTTA-LAIAH  104 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la-~~la~  104 (294)
                      .++++.||+|+|||..+ ..+..
T Consensus         9 ~~vlv~a~TGSGKT~~~l~~~l~   31 (440)
T 1yks_A            9 MTTVLDFHPGAGKTRRFLPQILA   31 (440)
T ss_dssp             CEEEECCCTTSSTTTTHHHHHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHH
Confidence            47999999999999985 43444

>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=95.77  E-value=0.0063  Score=46.25  Aligned_cols=23  Identities=26%  Similarity=0.405  Sum_probs=20.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|++|+|||+|+..+...-
T Consensus        24 ki~vvG~~~~GKSsli~~l~~~~   46 (189)
T 2gf9_A           24 KLLLIGNSSVGKTSFLFRYADDS   46 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            49999999999999999998754

>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=95.76  E-value=0.0063  Score=46.38  Aligned_cols=23  Identities=35%  Similarity=0.592  Sum_probs=19.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.|++|+|||+|++.+....
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            39999999999999998776654

>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=95.76  E-value=0.0045  Score=46.46  Aligned_cols=23  Identities=13%  Similarity=0.153  Sum_probs=20.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+++.|++|+|||+|+..+...-
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            38999999999999999998754

>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=95.75  E-value=0.0052  Score=46.42  Aligned_cols=23  Identities=26%  Similarity=0.391  Sum_probs=20.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+|+..+...-
T Consensus        12 ki~v~G~~~~GKSsli~~l~~~~   34 (186)
T 2bme_A           12 KFLVIGNAGTGKSCLLHQFIEKK   34 (186)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            49999999999999999998654

>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=95.74  E-value=0.0066  Score=46.46  Aligned_cols=23  Identities=17%  Similarity=0.459  Sum_probs=20.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++|++|+|||+|+..+...-
T Consensus        30 ki~v~G~~~vGKSsli~~l~~~~   52 (196)
T 2atv_A           30 KLAIFGRAGVGKSALVVRFLTKR   52 (196)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            59999999999999999998754

---

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	294
d1njfa_	239	c.37.1.20 (A:) delta prime subunit of DNA polymera	6e-54
d1iqpa2	231	c.37.1.20 (A:2-232) Replication factor C {Archaeon	3e-53
d1sxjd2	237	c.37.1.20 (D:26-262) Replication factor C2 {Baker'	1e-52
d1sxjb2	224	c.37.1.20 (B:7-230) Replication factor C4 {Baker's	2e-47
d1sxjc2	227	c.37.1.20 (C:12-238) Replication factor C3 {Baker'	1e-41
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	8e-36
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	5e-35
d2gnoa2	198	c.37.1.20 (A:11-208) gamma subunit of DNA polymera	2e-34
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	6e-27
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	1e-26
d1a5ta2	207	c.37.1.20 (A:1-207) delta prime subunit of DNA pol	2e-23
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	5e-23
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	5e-15
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	1e-13
d1g8pa_	333	c.37.1.20 (A:) ATPase subunit of magnesium chelata	3e-07
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	5e-06
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	5e-06
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	1e-05
d1qvra3	315	c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus	2e-05
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	2e-05
d1tuea_	205	c.37.1.20 (A:) Replication protein E1 helicase dom	2e-04
d2i3ba1	189	c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57	3e-04
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	9e-04
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	0.001
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	0.002
g1ii8.1	369	c.37.1.12 (A:,B:) Rad50 {Archaeon Pyrococcus furio	0.003
d1ly1a_	152	c.37.1.1 (A:) Polynucleotide kinase, kinase domain	0.003
d1zp6a1	176	c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {	0.004
d1pjra1	318	c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillu	0.004

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 239

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

 Score =  173 bits (440), Expect = 6e-54
 Identities = 55/245 (22%), Positives = 100/245 (40%), Gaps = 29/245 (11%)

Query: 53  EKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPEL 111
            K+RP+   DV  QE V+  L N L      H  LF G  G GKT+ A  +A  L     
Sbjct: 4   RKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETG 63

Query: 112 YKSR------------------VLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPC 153
             +                   ++E++A+    +   R  +                   
Sbjct: 64  ITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGR-------- 115

Query: 154 PPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKP 213
             +K+ ++DE   ++  + NAL +T+E   +  +F        ++   + SRC +F  K 
Sbjct: 116 --FKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKA 173

Query: 214 LSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDL 273
           L  E +  ++ HI NEE +  +  AL  L+  ++G LR A++    A       ++++ +
Sbjct: 174 LDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAV 233

Query: 274 ISVSG 278
            ++ G
Sbjct: 234 SAMLG 238

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 231

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score =  171 bits (434), Expect = 3e-53
 Identities = 114/230 (49%), Positives = 154/230 (66%), Gaps = 10/230 (4%)

Query: 48  SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF 107
            +PWVEKYRP+++ D+  QE +V+ L + ++T + PH+LF GPPG GKTT ALA+A +LF
Sbjct: 11  EKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELF 70

Query: 108 GPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSM 167
             E ++   LELNASD+RGINV+R K+K FA      G          +KII LDEAD++
Sbjct: 71  -GENWRHNFLELNASDERGINVIREKVKEFARTKPIGGAS--------FKIIFLDEADAL 121

Query: 168 TEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHIC 227
           T+DAQ ALRRTME +S   RF   CNY S+IIEP+ SRCA FRF+PL +E ++ R+ +I 
Sbjct: 122 TQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIA 181

Query: 228 NEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVS 277
             EGL L  E L  +  I++GD+RRAI  LQ AA L    IT +++  V+
Sbjct: 182 ENEGLELTEEGLQAILYIAEGDMRRAINILQAAAAL-DKKITDENVFMVA 230

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  170 bits (430), Expect = 1e-52
 Identities = 134/236 (56%), Positives = 167/236 (70%), Gaps = 7/236 (2%)

Query: 50  PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP 109
           PWVEKYRPK + +V  Q+  V VL  TL++AN PHMLFYGPPGTGKT+T LA+  +L+GP
Sbjct: 1   PWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGP 60

Query: 110 ELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRG--GYPCPPYKIIILDEADSM 167
           +L KSR+LELNASD+RGI++VR K+K FA + V    +     YPCPPYKIIILDEADSM
Sbjct: 61  DLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSM 120

Query: 168 TEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHIC 227
           T DAQ+ALRRTMETYS VTRF  ICNY++RII+PLAS+C+KFRFK L       R+  I 
Sbjct: 121 TADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFIS 180

Query: 228 NEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF-----GSSITSKDLISVSG 278
            +E +  D   L  +  IS GDLRR IT LQ A++       G +ITS  +  ++G
Sbjct: 181 EQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAG 236

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 224

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  156 bits (394), Expect = 2e-47
 Identities = 101/229 (44%), Positives = 136/229 (59%), Gaps = 9/229 (3%)

Query: 50  PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP 109
           PWVEKYRP+ + D+   +E +  L    +  N PHM+  G PG GKTT+   +AH+L G 
Sbjct: 4   PWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGR 63

Query: 110 ELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE 169
             Y   VLELNASDDRGI+VVR +IK FA       Q++   P   +KI+ILDEADSMT 
Sbjct: 64  S-YADGVLELNASDDRGIDVVRNQIKHFA-------QKKLHLPPGKHKIVILDEADSMTA 115

Query: 170 DAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE 229
            AQ ALRRTME YS  TRF F CN  ++IIEPL S+CA  R+  LS+E +  R+L I   
Sbjct: 116 GAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKL 175

Query: 230 EGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG 278
           E +    + L  +   ++GD+R+AI  LQ      G  + + ++  +  
Sbjct: 176 EDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHG-LVNADNVFKIVD 223

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 227

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  141 bits (356), Expect = 1e-41
 Identities = 97/233 (41%), Positives = 136/233 (58%), Gaps = 13/233 (5%)

Query: 50  PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP 109
           PWVEKYRP+ + +V  Q EV+  +   ++    PH+LFYGPPGTGKT+T +A+A +++G 
Sbjct: 3   PWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGK 62

Query: 110 ELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE 169
             Y + VLELNASDDRGI+VVR +IK F                  +K+IILDEAD+MT 
Sbjct: 63  N-YSNMVLELNASDDRGIDVVRNQIKDF--------ASTRQIFSKGFKLIILDEADAMTN 113

Query: 170 DAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNE 229
            AQNALRR +E Y+K TRF  + NY  ++   L S+C +FRF+PL +E +  R+ ++   
Sbjct: 114 AAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVH 173

Query: 230 EGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSS----ITSKDLISVSG 278
           E L L   A   L  +S GD+RR +  LQ       +     I+   +    G
Sbjct: 174 EKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCG 226

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 252

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  127 bits (318), Expect = 8e-36
 Identities = 76/249 (30%), Positives = 123/249 (49%), Gaps = 29/249 (11%)

Query: 51  WVEKYRPKQVKDVAHQEEVVRVLTNTLETA-NCPHMLFYGPPGTGKTTTALAIAHQLFGP 109
           WV+KYRPK +  ++H EE+   L +  +   + PH+L YGP GTGK T  +A+   +FGP
Sbjct: 1   WVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGP 60

Query: 110 ELYKS-----------------------RVLELNASDDRGIN--VVRTKIKTFAAVAVGS 144
            +Y+                          LE+  SD    +  V++  +K  A +    
Sbjct: 61  GVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVD 120

Query: 145 GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLAS 204
            Q         YK +I++EA+S+T+DAQ ALRRTME YSK  R   +C+ +S II P+ S
Sbjct: 121 FQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKS 180

Query: 205 RCAKFRFKPLSEEVMSSRVLHICNEEGLNLDA-EALSTLSSISQGDLRRAITYLQGAARL 263
           +C   R    S+  +S+ +  +   E + L+  + L  ++  S G+LR ++  L+  A  
Sbjct: 181 QCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMA-- 238

Query: 264 FGSSITSKD 272
             + +  K 
Sbjct: 239 LNNELALKS 247

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 253

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  125 bits (313), Expect = 5e-35
 Identities = 53/253 (20%), Positives = 92/253 (36%), Gaps = 30/253 (11%)

Query: 49  QPWVEKYRPKQVKDVAHQEEVVRVLTNTLE-----------------TANCPHMLFYGPP 91
           + W  KY P  ++ V   +  V  L N L                  +      + YGPP
Sbjct: 2   KLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPP 61

Query: 92  GTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGY 151
           G GKTT A  +A +L    L +      NASD R   ++   +K         G  +   
Sbjct: 62  GIGKTTAAHLVAQELGYDILEQ------NASDVRSKTLLNAGVKNALDNMSVVGYFKHNE 115

Query: 152 PCPP----YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRII--EPLASR 205
                   + +II+DE D M+   +  + +  +   K +    +      +    P    
Sbjct: 116 EAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRV 175

Query: 206 CAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFG 265
           C   +F+      + SR++ I   E   LD   +  L   ++GD+R+ I  L        
Sbjct: 176 CLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLS-TISTTT 234

Query: 266 SSITSKDLISVSG 278
            +I  +++  +S 
Sbjct: 235 KTINHENINEISK 247

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]} Length = 198

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

 Score =  121 bits (305), Expect = 2e-34
 Identities = 33/202 (16%), Positives = 65/202 (32%), Gaps = 19/202 (9%)

Query: 70  VRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA-SDDRGIN 128
           +  L   +E +    +L  G   +     +L +   +       S VLE++   ++ GI+
Sbjct: 3   LETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGID 62

Query: 129 VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRF 188
            +R  IK F   +               K +I+ + + MT+ A NA  + +E   +    
Sbjct: 63  DIR-TIKDFLNYSPELYT---------RKYVIVHDCERMTQQAANAFLKALEEPPEYAVI 112

Query: 189 FFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHI-------CNEEGLNLDAEALST 241
                    ++  + SR  +       E     +             E       EA   
Sbjct: 113 VLNTRRWHYLLPTIKSRVFRVVVNVPKEFRDLVKEKIGDLWEELPLLERDFKTALEAYKL 172

Query: 242 LSSISQGDLRRAITYLQGAARL 263
            +    G L  ++  L+    L
Sbjct: 173 GAEKLSG-LMESLKVLETEKLL 193

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

 Score =  103 bits (256), Expect = 6e-27
 Identities = 40/219 (18%), Positives = 73/219 (33%), Gaps = 14/219 (6%)

Query: 53  EKYRPKQVKDVAHQEEVVRVLTNTLETA-----NCPHMLFYGPPGTGKTTTALAIAHQLF 107
           +  RPK + +   QE V + L+  LE A        H+L  GPPG GKTT A  IA +L 
Sbjct: 1   QFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQ 60

Query: 108 GPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSM 167
                 S  + +   D   I     +        +    +        Y  I   + D M
Sbjct: 61  TNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDEIHRLNKAV--EELLYSAIEDFQIDIM 118

Query: 168 TEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFR---FKPLSEEVMSSRVL 224
                +A  +++    +   F  +       +     R            + + +   + 
Sbjct: 119 IGKGPSA--KSIRIDIQ--PFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIK 174

Query: 225 HICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARL 263
              +   + ++  A   ++  S+G  R AI   +    +
Sbjct: 175 RAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDM 213

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]} Length = 239

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

 Score =  102 bits (255), Expect = 1e-26
 Identities = 46/232 (19%), Positives = 75/232 (32%), Gaps = 45/232 (19%)

Query: 56  RPKQVKDVAHQEEVVRVLTNTLETA-----NCPHMLFYGPPGTGKTTTALAIAHQLFGPE 110
           RPK + +   QE + + L   LE A        H+L +GPPG GKTT A  IAH+L    
Sbjct: 4   RPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELG--- 60

Query: 111 LYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED 170
                 + L  +    I          A                   I+ +DE   ++  
Sbjct: 61  ------VNLRVTSGPAIEKPGDLAAILAN------------SLEEGDILFIDEIHRLSRQ 102

Query: 171 AQNALRRTMETY----------------SKVTRFFFICNYISRIIEPLASR---CAKFRF 211
           A+  L   ME +                 ++ RF  I       +               
Sbjct: 103 AEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHL 162

Query: 212 KPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARL 263
           +  + E ++  V+      G+ +  EA   +   S+G +R A    +     
Sbjct: 163 EYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRDF 214

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

 Score = 92.9 bits (229), Expect = 2e-23
 Identities = 36/206 (17%), Positives = 62/206 (30%), Gaps = 17/206 (8%)

Query: 66  QEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD 124
                  L  + +     H +L    PG G      A++  L   +    +         
Sbjct: 7   LRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQ 66

Query: 125 RGINVVRTKIKTFAAVAVGSGQR-----------RGGYPCPPYKIIILDEADSMTEDAQN 173
                      T A     +                       K++ + +A  +T+ A N
Sbjct: 67  LMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAAN 126

Query: 174 ALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLN 233
           AL +T+E     T FF       R++  L SRC      P  E+   + +        + 
Sbjct: 127 ALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWL-----SREVT 181

Query: 234 LDAEALSTLSSISQGDLRRAITYLQG 259
           +  +AL     +S G    A+   QG
Sbjct: 182 MSQDALLAALRLSAGSPGAALALFQG 207

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]} Length = 362

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

 Score = 94.7 bits (235), Expect = 5e-23
 Identities = 28/203 (13%), Positives = 49/203 (24%), Gaps = 22/203 (10%)

Query: 83  PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAV-- 140
            + LF GP  +GKTT A A+     G        L +N   DR    +   I  F  V  
Sbjct: 155 RYWLFKGPIDSGKTTLAAALLELCGGK------ALNVNLPLDRLNFELGVAIDQFLVVFE 208

Query: 141 -AVGSGQRRGGYPCPPYKIIILDEADSMTED------AQNALRRTMETYSKVTRFFFICN 193
              G+G      P        ++  D++ +            +   +            N
Sbjct: 209 DVKGTGGESRDLPS----GQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMN 264

Query: 194 -YISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSS-ISQGDLR 251
            Y                      +    R   +  +  +      L  L       +  
Sbjct: 265 EYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFA 324

Query: 252 RAITYLQG-AARLFGSSITSKDL 273
           ++I               +    
Sbjct: 325 QSIQSRIVEWKERLDKEFSLSVY 347

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]} Length = 287

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

 Score = 71.7 bits (174), Expect = 5e-15
 Identities = 32/279 (11%), Positives = 71/279 (25%), Gaps = 49/279 (17%)

Query: 44  VLQSSQPWVEKYRPKQVKDVAHQ-EEVVRVLTNTLETANCP-----HMLFYGPPGTGKTT 97
           + +  + + E Y P +++    + E + R+  N L +              G  G GKTT
Sbjct: 2   LFKDRRVFDENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTT 61

Query: 98  TALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYP----- 152
            A     ++      +   ++    +      + T +           Q RG        
Sbjct: 62  LAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILK 121

Query: 153 --------------CPPYKIIILDEADSMTEDAQNALRRTMETYSK------------VT 186
                             +   +  +  +  +    L R  E                 +
Sbjct: 122 ALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVAS 181

Query: 187 RFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLN--LDAEAL----- 239
               +     +I +  +    K          + + +         +   +   L     
Sbjct: 182 DVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISD 241

Query: 240 -STLSSISQGDLRRAITYLQGAARLF----GSSITSKDL 273
                    G  RRAI  L+ A  +       S++   +
Sbjct: 242 VYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLV 280

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 276

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 67.1 bits (162), Expect = 1e-13
 Identities = 38/254 (14%), Positives = 70/254 (27%), Gaps = 37/254 (14%)

Query: 44  VLQSSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETA------NCPHMLFYGPPGTGKTT 97
           ++     +   Y PK++    H+E+ ++ L   L         + P     G PGTGKT 
Sbjct: 2   IVVDDSVFSPSYVPKRLP---HREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTV 58

Query: 98  TALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGY------ 151
           T   +          +   +      +    +                 R          
Sbjct: 59  TLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEH 118

Query: 152 --PCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKF 209
                 Y  ++LD+A ++  D  +   R  +   K+  F      +      L +     
Sbjct: 119 LRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPST 178

Query: 210 --RFKPLSEEVMSSRVLHICN----------------EEGLNLDAE--ALSTLSSISQGD 249
                             I +                E+ L + A+     T    ++GD
Sbjct: 179 RGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGD 238

Query: 250 LRRAITYLQGAARL 263
            R AI  L  +A  
Sbjct: 239 ARLAIDILYRSAYA 252

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]} Length = 333

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]

 Score = 48.4 bits (114), Expect = 3e-07
 Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 62  DVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA 121
            +  QE++   L  T        +L +G  GTGK+T   A+A  L  PE+       +++
Sbjct: 8   AIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALL--PEIEAVEGCPVSS 65

Query: 122 SDDRGI 127
            +   I
Sbjct: 66  PNVEMI 71

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]} Length = 247

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

 Score = 44.5 bits (105), Expect = 5e-06
 Identities = 52/250 (20%), Positives = 84/250 (33%), Gaps = 53/250 (21%)

Query: 61  KDVAHQEEVVRVLTNTLETANCPH------------MLFYGPPGTGKTTTALAIAHQLFG 108
           KDVA  EE    L   +E    P             +L  GPPG GKT  A A+A +   
Sbjct: 9   KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA-- 66

Query: 109 PELYKSRVLELNASD--DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADS 166
               +   +  + SD  +  + V   +++     A      +   PC    I+ +DE D+
Sbjct: 67  ----RVPFITASGSDFVEMFVGVGAARVRDLFETA------KRHAPC----IVFIDEIDA 112

Query: 167 M-------TEDAQNALRRT-------METYSKVTRFFFIC--NYISRIIEPL--ASRCAK 208
           +            +   +T       M+ + K T    +   N    +   L    R  +
Sbjct: 113 VGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDR 172

Query: 209 FRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG----DLRRAITY-LQGAARL 263
                  +     ++L I        +   L+ L+  + G    DL   +      AAR 
Sbjct: 173 QIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAARE 232

Query: 264 FGSSITSKDL 273
               IT KDL
Sbjct: 233 GRRKITMKDL 242

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]} Length = 273

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

 Score = 44.6 bits (104), Expect = 5e-06
 Identities = 19/166 (11%), Positives = 43/166 (25%), Gaps = 15/166 (9%)

Query: 62  DVAHQEEVVRVLTNTLETANCPHM----LFYGPPGTGKTTTALAIAHQLFGPELYKSRVL 117
           D   +  +   L   ++           L  G PG+GKT+   AI  +  G  +      
Sbjct: 8   DKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIV----- 62

Query: 118 ELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRR 177
            ++    +  +    ++                       II            +   R 
Sbjct: 63  -IDNDTFKQQHPNFDELV-KLYEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRT 120

Query: 178 TMETYSKVTR----FFFICNYISRIIEPLASRCAKFRFKPLSEEVM 219
           T       T      +    Y+  + +  +      R++ +  +  
Sbjct: 121 TDVPIQTATMLQAKGYETKMYVMAVPKINSYLGTIERYETMYADDP 166

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 309

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

 Score = 43.7 bits (102), Expect = 1e-05
 Identities = 21/139 (15%), Positives = 41/139 (29%), Gaps = 26/139 (18%)

Query: 56  RPKQVKD-----VAHQEEVVRVLTNT---------LETANCP-----HMLFYGPPGTGKT 96
            P+++       +  Q +  R +            L+          ++L  GP G GKT
Sbjct: 4   TPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKT 63

Query: 97  TTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPY 156
             A  +A     P +                     +  T +A        + G      
Sbjct: 64  EIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNG------ 117

Query: 157 KIIILDEADSMTEDAQNAL 175
            I+ +DE D + +  + + 
Sbjct: 118 -IVFIDEIDKICKKGEYSG 135

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]} Length = 315

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]

 Score = 43.2 bits (101), Expect = 2e-05
 Identities = 33/136 (24%), Positives = 51/136 (37%), Gaps = 20/136 (14%)

Query: 61  KDVAHQEEVVRVLTNTLETA----NCPH-----MLFYGPPGTGKTTTALAIAHQLFGPEL 111
           K V  Q+E +R + + +  A      P+      LF GP G GKT  A  +A  LF  E 
Sbjct: 23  KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEE 82

Query: 112 YKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCP-----PYKIIILDEADS 166
              R+      +   ++      +   A     G   GG         PY +I+ DE + 
Sbjct: 83  AMIRIDMTEYMEKHAVS------RLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDEIEK 136

Query: 167 MTEDAQNALRRTMETY 182
              D  N L + ++  
Sbjct: 137 AHPDVFNILLQILDDG 152

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]} Length = 256

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 47/259 (18%), Positives = 77/259 (29%), Gaps = 71/259 (27%)

Query: 61  KDVAHQEEVVRVLTNTLETANCPH------------MLFYGPPGTGKTTTALAIAHQLFG 108
            DVA  +E    +   +E    P             +L  GPPGTGKT  A AIA +   
Sbjct: 12  ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA-- 69

Query: 109 PELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQR---------RGGYPCPPYKII 159
                             +         F  + VG G           +   PC    II
Sbjct: 70  -----------------KVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPC----II 108

Query: 160 ILDEADSM-------TEDAQNALRRT-------METYSKVTRFFFIC--NYISRIIEPLA 203
            +DE D++            +   +T       M+ +        I   N    +++P  
Sbjct: 109 FIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPD-VLDPAL 167

Query: 204 SRCAKFRFK---PLSEEVMSSRVLHICN-----EEGLNLDAEALSTLSSISQGDLRRAIT 255
            R  +F  +    L +     ++L +          ++    A  T    S  DL   + 
Sbjct: 168 LRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGT-PGFSGADLANLVN 226

Query: 256 Y-LQGAARLFGSSITSKDL 273
                AAR     ++  + 
Sbjct: 227 EAALFAARGNKRVVSMVEF 245

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]} Length = 205

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]

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 20/75 (26%)

Query: 51  WVEKYRPKQVKDVAHQEEVVRVLT----------NTLET-------ANCPHMLFYGPPGT 93
           W+ ++R  ++ +      +V+ L             L++        NC  ++F GP  T
Sbjct: 8   WI-RFRCSKIDEGGDWRPIVQFLRYQQIEFITFLGALKSFLKGTPKKNC--LVFCGPANT 64

Query: 94  GKTTTALAIAHQLFG 108
           GK+   ++  H + G
Sbjct: 65  GKSYFGMSFIHFIQG 79

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]} Length = 189

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]

 Score = 38.5 bits (88), Expect = 3e-04
 Identities = 10/23 (43%), Positives = 12/23 (52%)

Query: 84  HMLFYGPPGTGKTTTALAIAHQL 106
           H+   GPPG GKTT     +  L
Sbjct: 3   HVFLTGPPGVGKTTLIHKASEVL 25

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]} Length = 246

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

 Score = 37.6 bits (86), Expect = 9e-04
 Identities = 20/183 (10%), Positives = 50/183 (27%), Gaps = 5/183 (2%)

Query: 85  MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA-SDDRGINVVRTKIKTFAAVAVG 143
           +L  GPP +GKT  A  IA +   P +      ++   S+      ++          + 
Sbjct: 43  VLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLS 102

Query: 144 SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLA 203
                       Y  I    ++ +   A   L +      +        +    + E   
Sbjct: 103 CVVVDDIERLLDYVPIGPRFSNLVL-QALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEM 161

Query: 204 SRC--AKFRFKPLSEEVMSSRVL-HICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGA 260
                       ++        L  + N +       A           +++ +  ++ +
Sbjct: 162 LNAFSTTIHVPNIATGEQLLEALELLGNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMS 221

Query: 261 ARL 263
            ++
Sbjct: 222 LQM 224

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]} Length = 321

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 10/128 (7%), Positives = 23/128 (17%), Gaps = 40/128 (31%)

Query: 84  HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVG 143
            ++  G   +GKT    A+   L                          +     +    
Sbjct: 125 MVIVTGKGNSGKTPLVHALGEAL-----------------GGKDKYATVRFGEPLSGYNT 167

Query: 144 SGQRR-------GGYPCPPYKIIILDEADSM------------TEDAQNALRRTMETYSK 184
                                +I++D   ++                   L   +   + 
Sbjct: 168 DFNVFVDDIARAMLQHR----VIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAA 223

Query: 185 VTRFFFIC 192
                 I 
Sbjct: 224 SRGCVVIA 231

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]} Length = 283

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]

 Score = 37.0 bits (84), Expect = 0.002
 Identities = 10/38 (26%), Positives = 16/38 (42%)

Query: 75  NTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELY 112
             L+    P  L  G   TGK++      ++L  P +Y
Sbjct: 22  EKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIY 59

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]} Length = 152

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]

 Score = 35.1 bits (79), Expect = 0.003
 Identities = 19/138 (13%), Positives = 44/138 (31%), Gaps = 5/138 (3%)

Query: 86  LFYGPPGTGKTTTALAIAHQLFG-PELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGS 144
           L  G PG+GK+T A     +  G   + +    +   + +       TK K      +  
Sbjct: 6   LTIGCPGSGKSTWAREFIAKNPGFYNINRDDYRQSIMAHEERDEYKYTKKKEGIVTGMQF 65

Query: 145 GQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLAS 204
              +           ++    ++  + + A     + Y             + +++    
Sbjct: 66  DTAKSILYGGDSVKGVIISDTNLNPERRLAWETFAKEYGWKVEHKVFDVPWTELVK---- 121

Query: 205 RCAKFRFKPLSEEVMSSR 222
           R +K   K +  +V+ S 
Sbjct: 122 RNSKRGTKAVPIDVLRSM 139

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]} Length = 176

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]

 Score = 35.3 bits (80), Expect = 0.004
 Identities = 21/155 (13%), Positives = 40/155 (25%), Gaps = 6/155 (3%)

Query: 86  LFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSG 145
           L  G PG+GK+T A A+A+    P       +  ++ D  G                 + 
Sbjct: 8   LLSGHPGSGKSTIAEALANLPGVP------KVHFHSDDLWGYIKHGRIDPWLPQSHQQNR 61

Query: 146 QRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASR 205
                      +         +    +          ++   +  +    +  IE    R
Sbjct: 62  MIMQIAADVAGRYAKEGYFVILDGVVRPDWLPAFTALARPLHYIVLRTTAAEAIERCLDR 121

Query: 206 CAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALS 240
                  PL    + S+   +   E   L      
Sbjct: 122 GGDSLSDPLVVADLHSQFADLGAFEHHVLPVSGKD 156

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]} Length = 318

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]

 Score = 35.8 bits (81), Expect = 0.004
 Identities = 26/172 (15%), Positives = 48/172 (27%), Gaps = 30/172 (17%)

Query: 48  SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALA-IAHQL 106
           S+  +     +Q + V   E  + ++                  G+GKT      IA+ +
Sbjct: 5   SEQLLAHLNKEQQEAVRTTEGPLLIM---------------AGAGSGKTRVLTHRIAYLM 49

Query: 107 FGPELYKSRVLELNAS------------DDRGINVVRTKIKTFAAVAVGSGQRRGGYPCP 154
               +    +L +  +               G       I TF ++ V   +R       
Sbjct: 50  AEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDVWISTFHSMCVRILRRDIDRIGI 109

Query: 155 PYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRC 206
                ILD  D ++        + ++      R   I   IS     L    
Sbjct: 110 NRNFSILDPTDQLSVMKTILKEKNIDPKKFEPR--TILGTISAAKNELLPPE 159

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	294
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	100.0
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	100.0
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	100.0
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	100.0
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	100.0
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.98
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.98
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.97
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.96
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.94
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.91
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.91
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.87
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.85
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.83
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.83
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.81
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	99.81
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.8
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.75
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	99.74
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.71
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.68
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.67
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.67
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.67
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.64
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.63
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	99.46
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.4
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.35
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	99.25
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.23
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.71
d1tuea_	205	Replication protein E1 helicase domain {Human papi	98.64
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.59
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.57
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	98.36
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	98.35
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	98.32
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	98.31
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	98.31
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.26
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	98.21
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	98.19
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	98.14
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	98.12
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.08
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	98.07
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	98.06
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	98.05
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	98.03
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	98.02
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	98.01
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.01
d1okkd2	207	GTPase domain of the signal recognition particle r	98.0
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.99
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.96
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	97.92
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.92
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	97.92
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.91
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	97.89
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.89
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.89
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	97.88
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.87
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.85
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.84
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.82
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.79
d2awna2	232	Maltose transport protein MalK, N-terminal domain	97.78
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	97.78
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	97.77
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	97.76
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	97.76
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.76
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	97.74
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	97.72
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	97.72
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	97.71
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	97.7
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	97.66
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	97.64
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.63
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	97.61
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.58
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	97.58
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.57
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	97.52
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	97.49
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	97.47
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	97.46
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	97.45
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	97.44
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	97.42
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	97.42
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	97.41
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	97.31
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	97.27
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	97.22
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	97.22
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	97.17
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	97.17
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	97.16
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	97.15
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.14
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	97.14
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	97.13
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	97.07
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	97.07
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	97.03
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	97.02
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	97.01
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	96.99
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	96.96
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	96.94
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.93
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	96.93
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	96.91
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	96.89
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	96.89
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	96.88
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	96.85
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	96.84
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.84
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	96.84
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	96.83
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.83
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	96.82
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	96.81
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	96.8
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	96.76
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	96.75
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	96.75
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	96.75
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	96.74
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	96.72
d1g2912	240	Maltose transport protein MalK, N-terminal domain	96.69
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.68
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	96.68
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	96.67
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.66
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	96.66
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	96.65
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.63
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	96.63
d1nrjb_	209	Signal recognition particle receptor beta-subunit	96.62
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	96.62
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	96.59
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	96.58
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	96.57
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	96.56
d2fh5b1	207	Signal recognition particle receptor beta-subunit	96.56
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.56
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	96.56
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	96.54
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	96.54
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	96.53
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	96.49
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	96.47
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	96.46
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	96.46
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	96.46
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	96.45
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	96.42
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	96.41
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	96.41
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	96.38
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.38
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	96.37
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	96.36
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	96.35
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	96.34
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	96.34
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	96.32
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	96.31
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	96.31
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	96.29
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	96.29
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	96.28
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	96.28
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	96.27
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	96.27
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	96.26
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	96.26
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	96.25
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	96.22
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	96.21
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	96.19
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	96.18
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	96.16
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	96.15
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	96.15
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	96.14
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	96.13
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	96.13
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	96.13
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	96.12
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	96.11
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	96.1
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	96.1
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	96.08
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	96.08
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	96.06
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	96.05
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	96.02
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	96.0
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	96.0
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.95
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	95.95
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	95.94
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	95.93
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	95.92
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	95.89
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	95.84
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	95.82
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	95.78
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	95.76
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	95.72
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	95.63
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	95.63
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	95.62
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	95.61
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	95.59
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	95.54
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	95.54
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	95.51
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	95.41
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	95.36
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	95.35
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	95.32
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	95.31
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	95.28
d1d0xa2	712	Myosin S1, motor domain {Dictyostelium discoideum	95.23
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	95.23
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	95.21
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	95.17
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	95.15
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	95.09
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	95.03
d1lkxa_	684	Myosin S1, motor domain {Dictyostelium discoideum,	94.94
d1xpua3	289	Transcription termination factor Rho, ATPase domai	94.85
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	94.84
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	94.8
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	94.65
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	94.62
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	94.51
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	94.5
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	94.5
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	94.49
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.43
d1br2a2	710	Myosin S1, motor domain {Chicken (Gallus gallus),	94.4
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	94.39
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	94.36
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	94.31
d1w7ja2	730	Myosin S1, motor domain {Chicken (Gallus gallus),	94.05
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	93.97
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	93.85
d2mysa2	794	Myosin S1, motor domain {Chicken (Gallus gallus),	93.85
d1kk8a2	789	Myosin S1, motor domain {Bay scallop (Aequipecten	93.8
d1c9ka_	180	Adenosylcobinamide kinase/adenosylcobinamide phosp	93.51
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	93.22
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	93.16
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	93.14
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	93.14
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	93.13
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	92.98
d1d2ea3	196	Elongation factor Tu (EF-Tu), N-terminal (G) domai	92.92
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	92.9
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	92.23
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	92.2
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	92.15
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	92.08
d1jqlb_	140	delta subunit of DNA polymerase III, N-domain {Esc	91.78
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	91.49
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	91.44
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	91.26
d2olra1	313	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	91.2
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	91.17
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	91.16
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	90.67
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	90.66
d1ii2a1	323	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	90.28
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	90.18
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	90.17
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	90.16
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	89.96
d1zunb3	222	Sulfate adenylate transferase subunit cysN/C, EF-T	88.92
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	88.81
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	88.69
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	88.52
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	87.73
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	87.63
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	87.62
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	87.54
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	87.47
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	85.68
d2akab1	299	Dynamin G domain {Rat (Rattus norvegicus) [TaxId:	85.35
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	84.96
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	84.75
d1f60a3	239	Elongation factor eEF-1alpha, N-terminal (G) domai	84.53
d1wgla_	59	Toll-interacting protein {Human (Homo sapiens) [Ta	83.25
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	82.82
d1jnya3	224	Elongation factor eEF-1alpha, N-terminal (G) domai	82.47
d2qn6a3	205	Initiation factor eIF2 gamma subunit, N-terminal (	82.35
d1jwyb_	306	Dynamin G domain {Dictyostelium discoideum [TaxId:	82.31
d1kk1a3	195	Initiation factor eIF2 gamma subunit, N-terminal (	82.01
d1u0sy_	118	CheY protein {Thermotoga maritima [TaxId: 2336]}	81.93
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	81.35
d1qkka_	140	Transcriptional regulatory protein DctD, receiver	80.86
d1f6va_	91	C-terminal domain of B transposition protein {Bact	80.78
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	80.78

>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=100.00  E-value=1.5e-37  Score=248.70  Aligned_cols=222  Identities=45%  Similarity=0.715  Sum_probs=195.8

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcch
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGI  127 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~  127 (294)
                      ..||+++|+|+.+++++|+++.+..|..|+..+..++++|+||||||||++|+.+++++.+.. ....++++++++..+.
T Consensus         2 ~~pw~eKyrP~~~~d~ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~-~~~~~~~~n~~~~~~~   80 (224)
T d1sxjb2           2 QLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRS-YADGVLELNASDDRGI   80 (224)
T ss_dssp             CCCHHHHTCCSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGG-HHHHEEEECTTSCCSH
T ss_pred             CCchHhHhCCCCHHHhcCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHhccc-cccccccccccccCCc
Confidence            469999999999999999999999999999999999999999999999999999999985432 2345778888888888


Q ss_pred             hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhcccc
Q 022641          128 NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      ..+......+......       ....+..++||||+|.++...++.|+..++..+....++++++....+.+++++||.
T Consensus        81 ~~i~~~~~~~~~~~~~-------~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~  153 (224)
T d1sxjb2          81 DVVRNQIKHFAQKKLH-------LPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCA  153 (224)
T ss_dssp             HHHHTHHHHHHHBCCC-------CCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSE
T ss_pred             eehhhHHHHHHHhhcc-------CCCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHH
Confidence            7777766665543322       123456799999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhcc
Q 022641          208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVSG  278 (294)
Q Consensus       208 ~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~~  278 (294)
                      .+.|++|+.+++..++.+++.++++.+++++++.+++.++||+|.+++.|+.+... ...|+.+.|.+++.
T Consensus       154 ~i~~~~~~~~~i~~~l~~i~~~e~~~i~~~~l~~I~~~s~Gd~R~ai~~Lq~~~~~-~~~i~~~~i~~~~d  223 (224)
T d1sxjb2         154 ILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAG-HGLVNADNVFKIVD  223 (224)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHHHHHHHH-HSSBCHHHHHHHHT
T ss_pred             HhhhcccchhhhHHHHHHHHHhcccCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHc-CCCcCHHHHHHHhC
Confidence            99999999999999999999999999999999999999999999999999987654 55799999988764

>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=100.00  E-value=5.6e-37  Score=245.89  Aligned_cols=222  Identities=44%  Similarity=0.763  Sum_probs=191.6

Q ss_pred             chhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchh
Q 022641           49 QPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGIN  128 (294)
Q Consensus        49 ~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~  128 (294)
                      .||+++|+|+.+++++|+++.++.|..|+..+..++++|+||||+|||++|+++++++.+... ...+.+.+.++..+..
T Consensus         2 ~pw~ekyrP~~~~divg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~-~~~~~e~~~~~~~~~~   80 (227)
T d1sxjc2           2 LPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNY-SNMVLELNASDDRGID   80 (227)
T ss_dssp             CCHHHHTCCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSH-HHHEEEECTTSCCSHH
T ss_pred             CchhhhhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhhcCCC-cceeEEecccccCCee
Confidence            599999999999999999999999999999999999999999999999999999999854322 2345667777766666


Q ss_pred             HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccE
Q 022641          129 VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAK  208 (294)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~  208 (294)
                      ..............        ....+..+++|||++.++...++.|+..++.......+++++|....+.+++++||..
T Consensus        81 ~~~~~~~~~~~~~~--------~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~  152 (227)
T d1sxjc2          81 VVRNQIKDFASTRQ--------IFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTR  152 (227)
T ss_dssp             HHHTHHHHHHHBCC--------SSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEE
T ss_pred             eeecchhhcccccc--------ccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhh
Confidence            55544444333211        1223456999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh----CCCCChhhhhhhccc
Q 022641          209 FRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF----GSSITSKDLISVSGY  279 (294)
Q Consensus       209 i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~  279 (294)
                      +.|.+++.+++..++.+++..+++.+++++++.|++.++||+|.+++.|+.+..+.    ...||.++|.+++|.
T Consensus       153 i~~~~~~~~~i~~~l~~I~~~e~i~i~~~~l~~i~~~s~Gd~R~ain~Lq~~~~~~~~~~~~~It~~~v~e~~g~  227 (227)
T d1sxjc2         153 FRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGA  227 (227)
T ss_dssp             EECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTTCHHHHHHHTTTTTTTTCSSSCCCBCHHHHHHHTTC
T ss_pred             hccccccccccccccccccccccccCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCCCCCeeCHHHHHHHhCc
Confidence            99999999999999999999999999999999999999999999999999887665    356999999999873

>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=100.00  E-value=1.1e-35  Score=239.79  Aligned_cols=218  Identities=25%  Similarity=0.390  Sum_probs=188.2

Q ss_pred             hhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCccC----------------
Q 022641           51 WVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYK----------------  113 (294)
Q Consensus        51 ~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~~----------------  113 (294)
                      +.+||+|..|++++|++..++.|..++..++.++ ++|+||||+|||++|+.+++.+.+.....                
T Consensus         2 ~~~KyrP~~~~dlig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~   81 (239)
T d1njfa_           2 LARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQG   81 (239)
T ss_dssp             HHHHTCCSSGGGSCSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHT
T ss_pred             chhhhCCCCHHHccChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchHHHHHHcC
Confidence            4689999999999999999999999999988777 89999999999999999999986543211                


Q ss_pred             --CcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEE
Q 022641          114 --SRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFI  191 (294)
Q Consensus       114 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~  191 (294)
                        ..+++++.++....+.++..+..+...          ...++..++||||+|.++...++.|++.+++++....+|++
T Consensus        82 ~~~~~~~~~~~~~~~i~~ir~~~~~~~~~----------~~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~  151 (239)
T d1njfa_          82 RFVDLIEIDAASRTKVEDTRDLLDNVQYA----------PARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLA  151 (239)
T ss_dssp             CCTTEEEEETTCSSSHHHHHHHHHSCCCS----------CSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEE
T ss_pred             CCCeEEEecchhcCCHHHHHHHHHHHHhc----------cccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEE
Confidence              134566666665666565544433211          12234579999999999999999999999999999999999


Q ss_pred             ecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChh
Q 022641          192 CNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSK  271 (294)
Q Consensus       192 ~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~  271 (294)
                      ||....+.+++.+||..+.|++++.+++..++.+++..++..+++++++.|+..++||+|.++++++.+.....+.|+.+
T Consensus       152 tn~~~~i~~~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~~~~~~~l~~i~~~s~Gd~R~ain~l~~~~~~~~~~I~~~  231 (239)
T d1njfa_         152 TTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQ  231 (239)
T ss_dssp             ESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHTTTCHHHHHHHHHHHHHHTTTSBCHH
T ss_pred             cCCccccChhHhhhhcccccccCcHHHhhhHHHHHHhhhccCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCCCcCHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999888777889999


Q ss_pred             hhhhhcc
Q 022641          272 DLISVSG  278 (294)
Q Consensus       272 ~v~~~~~  278 (294)
                      +|.+++|
T Consensus       232 ~v~~~lg  238 (239)
T d1njfa_         232 AVSAMLG  238 (239)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHhC
Confidence            9999886

>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=100.00  E-value=9.4e-37  Score=246.19  Aligned_cols=229  Identities=59%  Similarity=0.976  Sum_probs=193.4

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhH
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINV  129 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (294)
                      ||+++|+|..+++++|+++.++.|..|+..+..++++|+||||+|||++++++++++.+..........++.+...+...
T Consensus         1 ~w~~ky~P~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~   80 (237)
T d1sxjd2           1 PWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISI   80 (237)
T ss_dssp             CHHHHTCCSSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHH
T ss_pred             CcchhhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchH
Confidence            89999999999999999999999999999999899999999999999999999999865555566677777777766655


Q ss_pred             HHHHHHHHHhhhcccCcc--CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhcccc
Q 022641          130 VRTKIKTFAAVAVGSGQR--RGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      ....+.............  .......+..++||||++.++....+.++..++.......+|++++....+.+++.+||.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~  160 (237)
T d1sxjd2          81 VREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCS  160 (237)
T ss_dssp             HTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSE
T ss_pred             HHHHHHHHhhhhhhhhhHHHHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccccccccccccccccchhh
Confidence            555544433222111110  011123456699999999999999999999999988888899999999999999999999


Q ss_pred             EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh-----CCCCChhhhhhhcc
Q 022641          208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF-----GSSITSKDLISVSG  278 (294)
Q Consensus       208 ~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~-----~~~it~~~v~~~~~  278 (294)
                      .+.|+|++.+++..+|.+++.++++.+++++++.|++.++||+|.+++.|++++...     ++.||.++|++++|
T Consensus       161 ~i~f~~~~~~~~~~~L~~i~~~e~i~i~~~~l~~ia~~s~gd~R~ai~~L~~~~~~~~~~~~~~~It~~~i~e~~g  236 (237)
T d1sxjd2         161 KFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAG  236 (237)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSSCHHHHHHHHHHTHHHHHHHCSCCCCCHHHHHHHHT
T ss_pred             hhccccccccccchhhhhhhhhhcCcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhcCCCCccCHHHHHHhhC
Confidence            999999999999999999999999999999999999999999999999999876544     46699999998876

>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=100.00  E-value=4.4e-36  Score=241.23  Aligned_cols=220  Identities=51%  Similarity=0.873  Sum_probs=189.7

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcch
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGI  127 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~  127 (294)
                      .+||+++|+|..+++++|+++.++.|..|+..+..++++|+||||+|||++|+++++++.+.. ....++++++++..+.
T Consensus        11 ~~~w~~ky~P~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l~~~~-~~~~~~e~n~s~~~~~   89 (231)
T d1iqpa2          11 EKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGEN-WRHNFLELNASDERGI   89 (231)
T ss_dssp             TSCHHHHTCCCSTTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGG-HHHHEEEEETTCHHHH
T ss_pred             hchHHHHhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHHhcc-cCCCeeEEecCcccch
Confidence            469999999999999999999999999999999999999999999999999999999985432 2346777888877666


Q ss_pred             hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhcccc
Q 022641          128 NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      ..++.............        ..+..++++||++.+....++.|+..++.......+|+++|....+++++.+||.
T Consensus        90 ~~~~~~~~~~~~~~~~~--------~~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~  161 (231)
T d1iqpa2          90 NVIREKVKEFARTKPIG--------GASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCA  161 (231)
T ss_dssp             HTTHHHHHHHHHSCCGG--------GCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEE
T ss_pred             hHHHHHHHHHHhhhhcc--------CCCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccc
Confidence            55555444433222111        1345699999999999999999999999989999999999999999999999999


Q ss_pred             EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCCCCChhhhhhhc
Q 022641          208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGSSITSKDLISVS  277 (294)
Q Consensus       208 ~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~it~~~v~~~~  277 (294)
                      .+.+.+++..++..++++++..+++.+++++++.|++.++||+|.+++.|+.++.. ...||.++|..+.
T Consensus       162 ~i~~~~~~~~~~~~~l~~~~~~e~i~i~~~~l~~I~~~~~gdiR~ai~~Lq~~~~~-~~~it~e~v~~v~  230 (231)
T d1iqpa2         162 IFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAAL-DKKITDENVFMVA  230 (231)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTTCHHHHHHHHHHHHTT-CSEECHHHHHHHT
T ss_pred             cccccccchhhHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc-CCCcCHHHHHhhh
Confidence            99999999999999999999999999999999999999999999999999988765 5668998887653

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.98  E-value=3.2e-31  Score=215.43  Aligned_cols=213  Identities=35%  Similarity=0.602  Sum_probs=160.0

Q ss_pred             hhhhcCCCcchhhcccHHHHHHHHHHHHcCC-CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCC---------------
Q 022641           51 WVEKYRPKQVKDVAHQEEVVRVLTNTLETAN-CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKS---------------  114 (294)
Q Consensus        51 ~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~-~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~---------------  114 (294)
                      |.++|+|..+++++|++..+..|..++..+. .++++|+||||||||++|+++++++.+......               
T Consensus         1 W~eky~P~~~~diig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~   80 (252)
T d1sxje2           1 WVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKL   80 (252)
T ss_dssp             CTTTTCCCSGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC----------------
T ss_pred             CCcccCCCCHHHccCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccccccccccchh
Confidence            8999999999999999999999999987664 457999999999999999999999854321111               


Q ss_pred             --------cceeecCCCCc--chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcC
Q 022641          115 --------RVLELNASDDR--GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSK  184 (294)
Q Consensus       115 --------~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~  184 (294)
                              ....+...+..  ........+....................+..+++|||+|.++...++.|++.++.+..
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d~l~~~~~~~l~~~~e~~~~  160 (252)
T d1sxje2          81 ELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSK  160 (252)
T ss_dssp             --CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCHHHHHHHHHHHHHSTT
T ss_pred             hhhhccCCccceeeecccccCCcceeeehhhhhhhhhhhhhhhcccccCCCceEEEeccccccccccchhhhcccccccc
Confidence                    01111111111  11111222222111111111111122234567999999999999999999999999888


Q ss_pred             cceEEEEecCCcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCC-HHHHHHHHhhccCcHHHHHHHHHHHHHH
Q 022641          185 VTRFFFICNYISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLD-AEALSTLSSISQGDLRRAITYLQGAARL  263 (294)
Q Consensus       185 ~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~-~~~l~~l~~~~~G~~r~~~~~l~~~~~~  263 (294)
                      .+.+|++||....+++++.+||..++|+||+.+++.+++.+++..+++.++ +++++.|+..++||+|.+++.||.++..
T Consensus       161 ~~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~~~~~~~~l~~i~~~s~Gd~R~ai~~Lq~~~~~  240 (252)
T d1sxje2         161 NIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMALN  240 (252)
T ss_dssp             TEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHHHHHTHHHHT
T ss_pred             cccceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCcHHHHHHHHHHHHHc
Confidence            999999999999999999999999999999999999999999999998764 7889999999999999999999988764

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.98  E-value=3.2e-31  Score=215.60  Aligned_cols=223  Identities=26%  Similarity=0.407  Sum_probs=171.8

Q ss_pred             hhhhhcCCCcchhhcccHHHHHHHHHHHHc-----------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCcc
Q 022641           50 PWVEKYRPKQVKDVAHQEEVVRVLTNTLET-----------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELY  112 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~-----------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~  112 (294)
                      .|+++|+|..|++++|+++.++.|..|+..                 +..++++|+||||||||++|+++|+++      
T Consensus         3 lW~eky~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~------   76 (253)
T d1sxja2           3 LWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL------   76 (253)
T ss_dssp             CHHHHTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT------
T ss_pred             ccccCcCCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHH------
Confidence            699999999999999999999999999853                 233569999999999999999999998      


Q ss_pred             CCcceeecCCCCcchhHHHHHHHHHHhhhcccCc----cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh-cCcce
Q 022641          113 KSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQ----RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY-SKVTR  187 (294)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~-~~~~~  187 (294)
                      +..++.++.++..+...+...+............    ........+..++++||++.+....+..+...++.. .....
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~~~~~~~~  156 (253)
T d1sxja2          77 GYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTP  156 (253)
T ss_dssp             TCEEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHHCSSC
T ss_pred             HhhhhccccccchhhHHHHHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeeccccccchhhhhHHHhhhhcccccc
Confidence            7788889988887776665544333222111110    112233456779999999998766555444444321 23334


Q ss_pred             EEEEecC-CcccchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHhCC
Q 022641          188 FFFICNY-ISRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLFGS  266 (294)
Q Consensus       188 ii~~~~~-~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~  266 (294)
                      ++++++. .....+.+.+||..+.|++|+.+++..++++++.++++.+++++++.|++.++||+|.+++.|++++.. .+
T Consensus       157 ii~i~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~~~l~~i~~~s~GDiR~ai~~L~~~~~~-~~  235 (253)
T d1sxja2         157 LILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTT-TK  235 (253)
T ss_dssp             EEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTTCHHHHHHHHTHHHHH-SS
T ss_pred             cccccccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCCHHHHHHHHHhCCCcHHHHHHHHHHHHHc-CC
Confidence            5555554 344566788999999999999999999999999999999999999999999999999999999987765 66


Q ss_pred             CCChhhhhhhccc
Q 022641          267 SITSKDLISVSGY  279 (294)
Q Consensus       267 ~it~~~v~~~~~~  279 (294)
                      .++.+.+.++...
T Consensus       236 ~i~~~~~~~~~~~  248 (253)
T d1sxja2         236 TINHENINEISKA  248 (253)
T ss_dssp             CCCTTHHHHHHHH
T ss_pred             CCCHHHHHHHhch
Confidence            7898888776644

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=99.97  E-value=2.9e-29  Score=202.02  Aligned_cols=205  Identities=19%  Similarity=0.259  Sum_probs=172.8

Q ss_pred             hcCCCcchhhcccHHHHHHHHHHHHc-----CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchh
Q 022641           54 KYRPKQVKDVAHQEEVVRVLTNTLET-----ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGIN  128 (294)
Q Consensus        54 ~~~~~~~~~~~g~~~~~~~l~~~l~~-----~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~  128 (294)
                      -++|..|++++|++++++.|..|+..     ...++++|+||||||||++|+++++++      +..+..++++......
T Consensus         2 ~~RP~~~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~------~~~~~~~~~~~~~~~~   75 (238)
T d1in4a2           2 FLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL------QTNIHVTSGPVLVKQG   75 (238)
T ss_dssp             TTSCSSGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHH------TCCEEEEETTTCCSHH
T ss_pred             CCCCCcHHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhcc------CCCcccccCcccccHH
Confidence            46899999999999999999998853     245789999999999999999999999      7778888888877666


Q ss_pred             HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc------------------CcceEEE
Q 022641          129 VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS------------------KVTRFFF  190 (294)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~------------------~~~~ii~  190 (294)
                      .+...+...                .++.++++||++.++...++.+...++...                  .++.+|+
T Consensus        76 ~~~~~~~~~----------------~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~  139 (238)
T d1in4a2          76 DMAAILTSL----------------ERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVG  139 (238)
T ss_dssp             HHHHHHHHC----------------CTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEEEE
T ss_pred             HHHHHHHhh----------------ccCCchHHHHHHHhhhHHHhhcccceeeeeeeeeecCcccccccccCCCCeEEEE
Confidence            554433321                123599999999999998888888887532                  3667899


Q ss_pred             EecCCcccchHhhcccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh----C
Q 022641          191 ICNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF----G  265 (294)
Q Consensus       191 ~~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~----~  265 (294)
                      +||......+++++||. .+.|++++.+++..+++.++..++..+++++++.+++.++||+|.++++++.++..+    .
T Consensus       140 at~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~~s~gd~R~ai~~l~~~~~~~~~~~~  219 (238)
T d1in4a2         140 ATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTVVKA  219 (238)
T ss_dssp             EESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHHTC
T ss_pred             ecCCCccccccceeeeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhcC
Confidence            99999999999999987 679999999999999999999999999999999999999999999999999765433    5


Q ss_pred             CCCChhhhhhhcccc
Q 022641          266 SSITSKDLISVSGYP  280 (294)
Q Consensus       266 ~~it~~~v~~~~~~~  280 (294)
                      ..||.+.+.+++...
T Consensus       220 ~~it~~~~~~al~~l  234 (238)
T d1in4a2         220 DRINTDIVLKTMEVL  234 (238)
T ss_dssp             SSBCHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHhh
Confidence            579999998887643

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=99.96  E-value=2.4e-28  Score=196.67  Aligned_cols=204  Identities=21%  Similarity=0.238  Sum_probs=166.6

Q ss_pred             cCCCcchhhcccHHHHHHHHHHHHc-----CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhH
Q 022641           55 YRPKQVKDVAHQEEVVRVLTNTLET-----ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINV  129 (294)
Q Consensus        55 ~~~~~~~~~~g~~~~~~~l~~~l~~-----~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (294)
                      ++|++|++++|++++++.|..|+..     ...++++|+||||||||++|+++++++      ...+..++++.......
T Consensus         3 ~RP~~~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~------~~~~~~~~~~~~~~~~~   76 (239)
T d1ixsb2           3 LRPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL------GVNLRVTSGPAIEKPGD   76 (239)
T ss_dssp             CCCCSGGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHH------TCCEEEEETTTCCSHHH
T ss_pred             cCCCCHHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHh------CCCeEeccCCccccchh
Confidence            5799999999999999999988864     235789999999999999999999999      67778888777665544


Q ss_pred             HHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhh------------------cCcceEEEE
Q 022641          130 VRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETY------------------SKVTRFFFI  191 (294)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~------------------~~~~~ii~~  191 (294)
                      ....+....               ....+++|||+|.++...++.++..++..                  .....++++
T Consensus        77 ~~~~~~~~~---------------~~~~i~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~i~~  141 (239)
T d1ixsb2          77 LAAILANSL---------------EEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGA  141 (239)
T ss_dssp             HHHHHHTTC---------------CTTCEEEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTTCCCEEEEECCCCEEEEE
T ss_pred             hHHHHHhhc---------------cCCCeeeeecccccchhHHHhhhhhhhhhhhhhhhccchhhhhcccCCCCEEEEee
Confidence            433332211               12349999999999999999999988752                  124557777


Q ss_pred             ecCCcc-cchHhhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHHHHh----CC
Q 022641          192 CNYISR-IIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAARLF----GS  266 (294)
Q Consensus       192 ~~~~~~-~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~----~~  266 (294)
                      ++.+.. ..+.+.++|..+.+.+++.+++..++.+++..+++.++++.+..+++.++||+|.++++++.+..++    .+
T Consensus       142 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~~~~~l~~ia~~s~gd~R~a~~~l~~~~~~a~~~~~~  221 (239)
T d1ixsb2         142 TTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQVAGEE  221 (239)
T ss_dssp             ESCCSSCSCGGGGGCSEEEECCCCCHHHHHHHHHHHHGGGCCCBCHHHHHHHHHHTTSSHHHHHHHHHHHHHHHTTSCCS
T ss_pred             ccCcccccchhhcccceeeEeeccChhhhhHHHHHHHHHhCCccchHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhCCC
Confidence            766554 4556666788999999999999999999999999999999999999999999999999999887665    35


Q ss_pred             CCChhhhhhhccc
Q 022641          267 SITSKDLISVSGY  279 (294)
Q Consensus       267 ~it~~~v~~~~~~  279 (294)
                      .||.+.+.+++..
T Consensus       222 ~It~~~~~~~l~~  234 (239)
T d1ixsb2         222 VITRERALEALAA  234 (239)
T ss_dssp             CBCHHHHHHHHHH
T ss_pred             CcCHHHHHHHHhh
Confidence            6999999988764

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=99.94  E-value=5.3e-26  Score=178.12  Aligned_cols=180  Identities=21%  Similarity=0.299  Sum_probs=145.4

Q ss_pred             cccHHHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCccC------------------CcceeecCCC-
Q 022641           64 AHQEEVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYK------------------SRVLELNASD-  123 (294)
Q Consensus        64 ~g~~~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~~------------------~~~~~~~~~~-  123 (294)
                      ..++...+.|...+..++.++ ++|+||+|+|||++|+.+++.+.|.....                  ..+..+.... 
T Consensus         5 Pw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~   84 (207)
T d1a5ta2           5 PWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKG   84 (207)
T ss_dssp             GGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTT
T ss_pred             cccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhc
Confidence            467788899999999999888 99999999999999999999997653221                  1223332222 


Q ss_pred             --CcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchH
Q 022641          124 --DRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEP  201 (294)
Q Consensus       124 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~  201 (294)
                        ....+.++.....+....          ..++..++||||+|.++...++.|++.|++++.+..+|++|+....+.++
T Consensus        85 ~~~i~~~~ir~l~~~~~~~~----------~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~t  154 (207)
T d1a5ta2          85 KNTLGVDAVREVTEKLNEHA----------RLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLAT  154 (207)
T ss_dssp             CSSBCHHHHHHHHHHTTSCC----------TTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHH
T ss_pred             ccccccchhhHHhhhhhhcc----------ccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChhhhhhh
Confidence              233455555444332221          22456799999999999999999999999999999999999999999999


Q ss_pred             hhccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHH
Q 022641          202 LASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQ  258 (294)
Q Consensus       202 l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~  258 (294)
                      +++||..+.|.+++.+++..++.     +...+++++++.+++.++|++|.++++||
T Consensus       155 I~SRc~~i~~~~~~~~~~~~~L~-----~~~~~~~~~~~~i~~~s~Gs~r~al~~le  206 (207)
T d1a5ta2         155 LRSRCRLHYLAPPPEQYAVTWLS-----REVTMSQDALLAALRLSAGSPGAALALFQ  206 (207)
T ss_dssp             HHTTSEEEECCCCCHHHHHHHHH-----HHCCCCHHHHHHHHHHTTTCHHHHHHTTS
T ss_pred             hcceeEEEecCCCCHHHHHHHHH-----HcCCCCHHHHHHHHHHcCCCHHHHHHHhC
Confidence            99999999999999999998884     35678999999999999999999999875

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=99.91  E-value=7e-24  Score=170.48  Aligned_cols=203  Identities=19%  Similarity=0.140  Sum_probs=145.3

Q ss_pred             CCcchhhcccHHHHHHHHHHHH------------cCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCC
Q 022641           57 PKQVKDVAHQEEVVRVLTNTLE------------TANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDD  124 (294)
Q Consensus        57 ~~~~~~~~g~~~~~~~l~~~l~------------~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~  124 (294)
                      ..+|+++.|.++.++.|.+.+.            ...+++++|+||||||||++|+++|+++      +.+++.+++++.
T Consensus         8 ~~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~------~~~~~~i~~~~l   81 (256)
T d1lv7a_           8 KTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA------KVPFFTISGSDF   81 (256)
T ss_dssp             CCCGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH------TCCEEEECSCSS
T ss_pred             CCCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHc------CCCEEEEEhHHh
Confidence            4578999999999988876542            1223459999999999999999999999      788888887765


Q ss_pred             cc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC--------------HHHHHHHHHHHHhhc-
Q 022641          125 RG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT--------------EDAQNALRRTMETYS-  183 (294)
Q Consensus       125 ~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--------------~~~~~~L~~~l~~~~-  183 (294)
                      .+      ...++..+......              .+.+|+|||+|.+.              ....+.|+..++... 
T Consensus        82 ~~~~~g~~~~~l~~~f~~A~~~--------------~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~  147 (256)
T d1lv7a_          82 VEMFVGVGASRVRDMFEQAKKA--------------APCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEG  147 (256)
T ss_dssp             TTSCCCCCHHHHHHHHHHHHTT--------------CSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCS
T ss_pred             hhcchhHHHHHHHHHHHHHHHc--------------CCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCC
Confidence            33      33344444433221              23599999998752              123456777777433 


Q ss_pred             -CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC-cHHHHHHHHH
Q 022641          184 -KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG-DLRRAITYLQ  258 (294)
Q Consensus       184 -~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G-~~r~~~~~l~  258 (294)
                       ..+.+|.+||.+..+++++++  ||. .+.|++|+.+++..+++.++.+..+. .+..+..+++.+.| +.+.+.++++
T Consensus       148 ~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~G~s~adi~~l~~  226 (256)
T d1lv7a_         148 NEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLA-PDIDAAIIARGTPGFSGADLANLVN  226 (256)
T ss_dssp             SSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC-TTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcC-cccCHHHHHHhCCCCCHHHHHHHHH
Confidence             456778899999999999986  886 89999999999999999888654443 34457788888765 3444444454


Q ss_pred             HHHHHh----CCCCChhhhhhhcccc
Q 022641          259 GAARLF----GSSITSKDLISVSGYP  280 (294)
Q Consensus       259 ~~~~~~----~~~it~~~v~~~~~~~  280 (294)
                      .++..+    ...|+.+++..++..+
T Consensus       227 ~A~~~a~~~~~~~i~~~d~~~Al~rv  252 (256)
T d1lv7a_         227 EAALFAARGNKRVVSMVEFEKAKDKI  252 (256)
T ss_dssp             HHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCccCHHHHHHHHHHH
Confidence            443322    4569999999887654

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=99.91  E-value=3.1e-24  Score=171.95  Aligned_cols=203  Identities=22%  Similarity=0.220  Sum_probs=139.5

Q ss_pred             CcchhhcccHHHHHHHHHHHH------------cCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           58 KQVKDVAHQEEVVRVLTNTLE------------TANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~------------~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      .+|++++|.+++++.|.+.+.            ...+.+++|+||||||||++|+++++++      +.+++.+++++..
T Consensus         6 ~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~------~~~~~~i~~~~l~   79 (247)
T d1ixza_           6 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA------RVPFITASGSDFV   79 (247)
T ss_dssp             CCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHT------TCCEEEEEHHHHH
T ss_pred             CcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHc------CCCEEEEEhHHhh
Confidence            478999999999888766541            1223459999999999999999999998      7888888765532


Q ss_pred             ch--hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------------HHHHHHHHHHHhhc--Ccce
Q 022641          126 GI--NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------------DAQNALRRTMETYS--KVTR  187 (294)
Q Consensus       126 ~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------------~~~~~L~~~l~~~~--~~~~  187 (294)
                      +.  ......+..+.....          ...+.||+|||+|.+..              ...+.|+..++...  ..+.
T Consensus        80 ~~~~g~~~~~l~~~f~~a~----------~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vi  149 (247)
T d1ixza_          80 EMFVGVGAARVRDLFETAK----------RHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIV  149 (247)
T ss_dssp             HSCTTHHHHHHHHHHHHHT----------TSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEE
T ss_pred             hccccHHHHHHHHHHHHHH----------HcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEE
Confidence            21  111122222221111          11246999999987621              13556777777543  3455


Q ss_pred             EEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC----cHHHHHHHHHHH
Q 022641          188 FFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG----DLRRAITYLQGA  260 (294)
Q Consensus       188 ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G----~~r~~~~~l~~~  260 (294)
                      +|.+||.+..+++++++  ||. .|+|++|+.+++..+++.++...... .+..+..+++.+.|    |++.+++.....
T Consensus       150 vi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~lv~~A~l~  228 (247)
T d1ixza_         150 VMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLA-EDVDLALLAKRTPGFVGADLENLLNEAALL  228 (247)
T ss_dssp             EEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBC-TTCCHHHHHHTCTTCCHHHHHHHHHHHHHH
T ss_pred             EEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCc-cccCHHHHHHHCCCCCHHHHHHHHHHHHHH
Confidence            67789999999999984  887 89999999999999999888654433 33457888888776    555555433322


Q ss_pred             HHHh-CCCCChhhhhhhc
Q 022641          261 ARLF-GSSITSKDLISVS  277 (294)
Q Consensus       261 ~~~~-~~~it~~~v~~~~  277 (294)
                      +... .+.|+.+++.+++
T Consensus       229 a~~~~~~~i~~~d~~~A~  246 (247)
T d1ixza_         229 AAREGRRKITMKDLEEAA  246 (247)
T ss_dssp             HHHTTCSSBCHHHHHHHT
T ss_pred             HHHcCCCCcCHHHHHHhh
Confidence            2222 5679999998875

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.87  E-value=1.7e-21  Score=157.44  Aligned_cols=176  Identities=20%  Similarity=0.207  Sum_probs=124.5

Q ss_pred             cchhhcccHHHHHHHHHHHHc-----------C--CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           59 QVKDVAHQEEVVRVLTNTLET-----------A--NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~-----------~--~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      .|+++.|.++.++.|.+.+..           +  .++.++|+||||||||++++++++++      +.+++.++++...
T Consensus         2 ~~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~------~~~~~~i~~~~l~   75 (258)
T d1e32a2           2 GYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET------GAFFFLINGPEIM   75 (258)
T ss_dssp             CGGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHT------TCEEEEECHHHHT
T ss_pred             ChhhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHh------CCeEEEEEchhhc
Confidence            588999999999888887521           1  23469999999999999999999998      7778877754322


Q ss_pred             c------hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH-----------HHHHHHHHHHh--hcCcc
Q 022641          126 G------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED-----------AQNALRRTMET--YSKVT  186 (294)
Q Consensus       126 ~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~-----------~~~~L~~~l~~--~~~~~  186 (294)
                      +      ...++..+......              .+.+|+|||+|.+...           ....++..+..  ....+
T Consensus        76 ~~~~g~~~~~l~~~f~~A~~~--------------~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~v  141 (258)
T d1e32a2          76 SKLAGESESNLRKAFEEAEKN--------------APAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV  141 (258)
T ss_dssp             TSCTTHHHHHHHHHHHHHHHT--------------CSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCE
T ss_pred             ccccccHHHHHHHHHHHHHhc--------------CCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccccCCc
Confidence            1      22333333332221              2459999999998422           23444444443  23446


Q ss_pred             eEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccC----cHHHHHH
Q 022641          187 RFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQG----DLRRAIT  255 (294)
Q Consensus       187 ~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G----~~r~~~~  255 (294)
                      .+|++||.+..+++++++  ||. .|.+++|+.+++..+++.+++...+. ++..+..|++.|.|    |++.+++
T Consensus       142 lvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~G~s~adl~~lv~  216 (258)
T d1e32a2         142 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLA-DDVDLEQVANETHGHVGADLAALCS  216 (258)
T ss_dssp             EEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBC-TTCCHHHHHHHCTTCCHHHHHHHHH
T ss_pred             cEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccc-cccchhhhhhcccCCCHHHHHHHHH
Confidence            678899999999999987  887 89999999999999999888643332 22347888888766    5555544

>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=99.85  E-value=6.6e-20  Score=149.56  Aligned_cols=228  Identities=18%  Similarity=0.206  Sum_probs=151.0

Q ss_pred             CchhhhhcCCCcchhhcccHHHHHHHHHHHHc------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecC
Q 022641           48 SQPWVEKYRPKQVKDVAHQEEVVRVLTNTLET------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA  121 (294)
Q Consensus        48 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~  121 (294)
                      .-++.+.|.|.   .++|++..++.+.+++..      ...++++|+||||||||++++.+++.+....  ...++.+++
T Consensus         6 ~~~l~~~y~p~---~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~--~~~~~~~~~   80 (276)
T d1fnna2           6 DSVFSPSYVPK---RLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKT--TARFVYING   80 (276)
T ss_dssp             GGGGSTTCCCS---CCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSC--CCEEEEEET
T ss_pred             cccCCCCCCCC---CCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhccc--CCcEEEecc
Confidence            34667778775   458998888888887753      2335799999999999999999999984322  334444554


Q ss_pred             CCCcchhHHHHHHHHHHhhhcccCccC----------CCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh----hcCcce
Q 022641          122 SDDRGINVVRTKIKTFAAVAVGSGQRR----------GGYPCPPYKIIILDEADSMTEDAQNALRRTMET----YSKVTR  187 (294)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~----~~~~~~  187 (294)
                      ...........................          .........++++|+++.+.......+...+..    ......
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (276)
T d1fnna2          81 FIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIA  160 (276)
T ss_dssp             TTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEE
T ss_pred             hhhhhhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhhhhhhHHHHHhccccccccceE
Confidence            443332222111111000000000000          000112345889999999987766655544432    223455


Q ss_pred             EEEEecCC---cccchHhhcccc--EEEecCCCHHHHHHHHHHHHHHhC--CCCCHHHHHHHHhh---------ccCcHH
Q 022641          188 FFFICNYI---SRIIEPLASRCA--KFRFKPLSEEVMSSRVLHICNEEG--LNLDAEALSTLSSI---------SQGDLR  251 (294)
Q Consensus       188 ii~~~~~~---~~~~~~l~~r~~--~i~~~~~~~~~~~~~l~~~~~~~~--~~~~~~~l~~l~~~---------~~G~~r  251 (294)
                      +|++++..   ..+.+.+.+|+.  .+.|+|++.+++.+++++++....  ..+++++++.+++.         +.||+|
T Consensus       161 ~i~~~~~~~~~~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~~~~~~~~~~~~~~l~~ia~~~~~~~~~~~~~G~~R  240 (276)
T d1fnna2         161 LVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDAR  240 (276)
T ss_dssp             EEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHH
T ss_pred             EeecCCchhhhhhcchhhhhhhcchhccccchhHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhhhhhhhhhcCCCHH
Confidence            66777654   346677878764  699999999999999999887633  34899999998875         479999


Q ss_pred             HHHHHHHHHHHHh----CCCCChhhhhhhcccc
Q 022641          252 RAITYLQGAARLF----GSSITSKDLISVSGYP  280 (294)
Q Consensus       252 ~~~~~l~~~~~~~----~~~it~~~v~~~~~~~  280 (294)
                      .++++++.+...+    ...|+.+||+++..+.
T Consensus       241 ~a~~ll~~a~~~A~~~~~~~I~~edv~~A~~~~  273 (276)
T d1fnna2         241 LAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEV  273 (276)
T ss_dssp             HHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence            9999999887766    4579999999987653

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.83  E-value=4.1e-20  Score=142.74  Aligned_cols=138  Identities=17%  Similarity=0.195  Sum_probs=114.2

Q ss_pred             HHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC-CcchhHHHHHHHHHHhhhcccCcc
Q 022641           69 VVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD-DRGINVVRTKIKTFAAVAVGSGQR  147 (294)
Q Consensus        69 ~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  147 (294)
                      .++-+.+++..+..++++|+||+|+|||++|..+++........+..++.+.+.. ..+.+.+++....+...+      
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~------   75 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSP------   75 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCC------
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCCCHHHHHHHHHHHhhCc------
Confidence            3567788888888889999999999999999999998755555556777777643 346788887555543322      


Q ss_pred             CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccchHhhccccEEEecCCCH
Q 022641          148 RGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCAKFRFKPLSE  216 (294)
Q Consensus       148 ~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~~i~~~~~~~  216 (294)
                          ..+++.++||||+|.|+..+++.|++.||+++..+.+|++|+.+..+.+++++||+.+.|++|..
T Consensus        76 ----~~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~TI~SRC~~i~~~~p~~  140 (198)
T d2gnoa2          76 ----ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVPKE  140 (198)
T ss_dssp             ----SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCHH
T ss_pred             ----ccCCCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChhhCHHHHhcceEEEeCCCchH
Confidence                12456799999999999999999999999999999999999999999999999999999987753

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.83  E-value=2.5e-19  Score=143.50  Aligned_cols=221  Identities=16%  Similarity=0.144  Sum_probs=161.6

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCC----CccCCcceeecCC
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGP----ELYKSRVLELNAS  122 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~----~~~~~~~~~~~~~  122 (294)
                      .+..+.++-+...++.++|++..++.+.+.|......|++|+||||+|||+++..+++.....    ...+..++.++.+
T Consensus         4 ~~~dlt~~a~~~~ld~~igRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~   83 (268)
T d1r6bx2           4 FTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIG   83 (268)
T ss_dssp             SSCBHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC
T ss_pred             HhHHHHHHHHcCCCCcccChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeec
Confidence            445566666666777899999999999999999888999999999999999999999987421    2334567777654


Q ss_pred             CCc----chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC---------HHHHHHHHHHHHhhcCcceEE
Q 022641          123 DDR----GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT---------EDAQNALRRTMETYSKVTRFF  189 (294)
Q Consensus       123 ~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~---------~~~~~~L~~~l~~~~~~~~ii  189 (294)
                      ...    ....+...+..+......          .+..++||||+|.+-         .+..+.|...+..  ....+|
T Consensus        84 ~liag~~~~g~~e~r~~~i~~~~~~----------~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~r--g~i~vI  151 (268)
T d1r6bx2          84 SLLAGTKYRGDFEKRFKALLKQLEQ----------DTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSS--GKIRVI  151 (268)
T ss_dssp             ---CCCCCSSCHHHHHHHHHHHHSS----------SSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSS--CCCEEE
T ss_pred             hHhccCccchhHHHHHHHHHHHhhc----------cCCceEEecchHHHhcCCCCCCccccHHHHhhHHHhC--CCCeEE
Confidence            432    234455555544443321          224599999999882         2345566666653  566777


Q ss_pred             EEecC-----CcccchHhhccccEEEecCCCHHHHHHHHHHHH----HHhCCCCCHHHHHHHHhhcc------CcHHHHH
Q 022641          190 FICNY-----ISRIIEPLASRCAKFRFKPLSEEVMSSRVLHIC----NEEGLNLDAEALSTLSSISQ------GDLRRAI  254 (294)
Q Consensus       190 ~~~~~-----~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~----~~~~~~~~~~~l~~l~~~~~------G~~r~~~  254 (294)
                      .+|+.     ....+++|.+||..|.+.+|+.++...+++.+.    ..+++.++++++..+++++.      .-|..++
T Consensus       152 gatT~eey~~~~e~d~al~rrF~~I~V~Eps~e~t~~IL~~~~~~~e~~h~v~~~~~al~~~v~ls~ryi~~~~~PdKAI  231 (268)
T d1r6bx2         152 GSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAI  231 (268)
T ss_dssp             EEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSCTTHHHH
T ss_pred             EeCCHHHHHHHHhhcHHHHhhhcccccCCCCHHHHHHHHHHhhHHHhccCCEEeChHHHHHHHHHHHhhccCCCCCcHHH
Confidence            77753     234578899999999999999999999998755    45789999999999887743      4699999


Q ss_pred             HHHHHHHHHh--------CCCCChhhhhhhccc
Q 022641          255 TYLQGAARLF--------GSSITSKDLISVSGY  279 (294)
Q Consensus       255 ~~l~~~~~~~--------~~~it~~~v~~~~~~  279 (294)
                      .++..++...        ...++.+++..++..
T Consensus       232 dllDea~a~~~~~~~~~~~~~i~~~di~~~i~~  264 (268)
T d1r6bx2         232 DVIDEAGARARLMPVSKRKKTVNVADIESVVAR  264 (268)
T ss_dssp             HHHHHHHHHHHHSSSCCCCCSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhccccCcccCCHHHHHHHHHH
Confidence            9999887654        234788888776654

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.81  E-value=6.3e-19  Score=137.78  Aligned_cols=186  Identities=17%  Similarity=0.208  Sum_probs=126.0

Q ss_pred             cchhhc-c--cHHHHHHHHHHHHcCCCC--cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcch--hHH-
Q 022641           59 QVKDVA-H--QEEVVRVLTNTLETANCP--HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGI--NVV-  130 (294)
Q Consensus        59 ~~~~~~-g--~~~~~~~l~~~l~~~~~~--~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~--~~~-  130 (294)
                      +|++++ |  ++.+...+..+....+..  .++|+||+|||||||+.++++++...   +..++.++..+....  ..+ 
T Consensus         8 tFdnF~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~   84 (213)
T d1l8qa2           8 TLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKR---GYRVIYSSADDFAQAMVEHLK   84 (213)
T ss_dssp             CSSSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHT---TCCEEEEEHHHHHHHHHHHHH
T ss_pred             ChhhccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHHhccC---ccceEEechHHHHHHHHHHHH
Confidence            566654 4  566667777777654432  39999999999999999999998432   123333332221100  000 


Q ss_pred             HHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC--HHHHHHHHHHHHhhc-CcceEEEEecCCc----ccchHhh
Q 022641          131 RTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT--EDAQNALRRTMETYS-KVTRFFFICNYIS----RIIEPLA  203 (294)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--~~~~~~L~~~l~~~~-~~~~ii~~~~~~~----~~~~~l~  203 (294)
                      ......+....            ...++|+|||+|.+.  +..+..|+.+++... ....+|++++.+.    ...+.+.
T Consensus        85 ~~~~~~~~~~~------------~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~  152 (213)
T d1l8qa2          85 KGTINEFRNMY------------KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLV  152 (213)
T ss_dssp             HTCHHHHHHHH------------HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHH
T ss_pred             ccchhhHHHHH------------hhccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHH
Confidence            00001111111            012599999999985  556777888887644 4566777776543    2467888


Q ss_pred             cccc---EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHHH
Q 022641          204 SRCA---KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGAA  261 (294)
Q Consensus       204 ~r~~---~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~~  261 (294)
                      +|+.   .+.++ |+.+++..++++.+...|+.++++++++|++.+ .++|.+...+...+
T Consensus       153 SRL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~yl~~~~-~~~R~L~~~l~~l~  211 (213)
T d1l8qa2         153 SRFEGGILVEIE-LDNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-KNVREIEGKIKLIK  211 (213)
T ss_dssp             HHHHTSEEEECC-CCHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-SSHHHHHHHHHHHH
T ss_pred             HHhhCceEEEEC-CCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc-CcHHHHHHHHHHhh
Confidence            8876   77885 577889999999999999999999999999998 57998877776654

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.81  E-value=4.1e-19  Score=145.60  Aligned_cols=230  Identities=18%  Similarity=0.182  Sum_probs=140.8

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHH----HcCCCC-----cEEEECCCCCCHHHHHHHHHHHhcCC---CccCC
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTL----ETANCP-----HMLFYGPPGTGKTTTALAIAHQLFGP---ELYKS  114 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l----~~~~~~-----~ill~Gp~G~GKT~la~~la~~~~~~---~~~~~  114 (294)
                      ...++..+|.|.   .+.|++..++.|..++    ..+..+     +++|+||||||||++++++++.+...   .....
T Consensus         5 ~~~~l~~~~~P~---~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~   81 (287)
T d1w5sa2           5 DRRVFDENYIPP---ELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTV   81 (287)
T ss_dssp             CGGGGSTTCCCS---SCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCE
T ss_pred             ChhhcCCccCCC---CCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCc
Confidence            344677888885   4567666666665544    333322     25678999999999999999987321   11122


Q ss_pred             cceeecCCCCcchhHHHHHHHHHHhhhcc-cCccC---------CCCCCCCcEEEEEeCCCCCC------HHHHHHHHHH
Q 022641          115 RVLELNASDDRGINVVRTKIKTFAAVAVG-SGQRR---------GGYPCPPYKIIILDEADSMT------EDAQNALRRT  178 (294)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~---------~~~~~~~~~lliiDei~~l~------~~~~~~L~~~  178 (294)
                      .+..+++...................... .+...         .........++++||++.+.      ......+..+
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l  161 (287)
T d1w5sa2          82 KQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRV  161 (287)
T ss_dssp             EEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTH
T ss_pred             eeeeeccccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccchhHHHHHHHH
Confidence            33334433332222111111110000000 00000         00001234588999998762      3444555555


Q ss_pred             HHhhc-----CcceEEEEecCCc------ccchHhhccc-cEEEecCCCHHHHHHHHHHHHHHhC--CCCCHHHHHHHHh
Q 022641          179 METYS-----KVTRFFFICNYIS------RIIEPLASRC-AKFRFKPLSEEVMSSRVLHICNEEG--LNLDAEALSTLSS  244 (294)
Q Consensus       179 l~~~~-----~~~~ii~~~~~~~------~~~~~l~~r~-~~i~~~~~~~~~~~~~l~~~~~~~~--~~~~~~~l~~l~~  244 (294)
                      ++...     ....+|++++...      ...+++.+|+ ..+.|+|++.+++.+++..+++...  ..+++++++.+++
T Consensus       162 ~~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~  241 (287)
T d1w5sa2         162 HEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISD  241 (287)
T ss_dssp             HHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHH
T ss_pred             HHhcchhhcccceeEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHH
Confidence            54322     3445666665443      2345666665 4899999999999999999987643  3489999999998


Q ss_pred             hc------cCcHHHHHHHHHHHHHHh----CCCCChhhhhhhccc
Q 022641          245 IS------QGDLRRAITYLQGAARLF----GSSITSKDLISVSGY  279 (294)
Q Consensus       245 ~~------~G~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~~  279 (294)
                      .+      .||+|.++++|+.++..+    ...||.++|++++.+
T Consensus       242 ~~~~~~~~~gd~R~ai~~l~~a~~~A~~~~~~~It~~~V~~A~~e  286 (287)
T d1w5sa2         242 VYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSE  286 (287)
T ss_dssp             HHCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHH
T ss_pred             HHhccccCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhc
Confidence            65      699999999999888766    467999999988754

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=6.6e-21  Score=154.35  Aligned_cols=176  Identities=20%  Similarity=0.236  Sum_probs=116.3

Q ss_pred             cchhhcccHHHHHHHHHHHHc-----------C--CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           59 QVKDVAHQEEVVRVLTNTLET-----------A--NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~-----------~--~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      +|+++.|.++.++.|.+.+..           +  ...+++|+||||||||++++++|.++      +.+++.+++++..
T Consensus         5 ~f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~------~~~~~~~~~~~l~   78 (265)
T d1r7ra3           5 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC------QANFISIKGPELL   78 (265)
T ss_dssp             SCSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHT------TCEEEEECHHHHH
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHh------CCcEEEEEHHHhh
Confidence            788888888777766665421           2  23469999999999999999999999      7788877754321


Q ss_pred             ------chhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH--------------HHHHHHHHHHhh--c
Q 022641          126 ------GINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED--------------AQNALRRTMETY--S  183 (294)
Q Consensus       126 ------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~--------------~~~~L~~~l~~~--~  183 (294)
                            ....++..+......              .+.+|+|||+|.+...              ..+.|+..++..  .
T Consensus        79 ~~~~~~~~~~l~~~f~~A~~~--------------~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~  144 (265)
T d1r7ra3          79 TMWFGESEANVREIFDKARQA--------------APCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTK  144 (265)
T ss_dssp             TSCTTTHHHHHHHHHHHHHHT--------------CSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC-----
T ss_pred             hccccchHHHHHHHHHHHHhc--------------CCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCC
Confidence                  123333333332222              2359999999987421              234455555432  2


Q ss_pred             CcceEEEEecCCcccchHhhc--ccc-EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhcc----CcHHHHHH
Q 022641          184 KVTRFFFICNYISRIIEPLAS--RCA-KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSISQ----GDLRRAIT  255 (294)
Q Consensus       184 ~~~~ii~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~----G~~r~~~~  255 (294)
                      .++.+|++||.+..+++++++  ||. .|.+++|+.+++.++++.+++..... .+..+..|++.+.    +|+..+++
T Consensus       145 ~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~g~s~~di~~lv~  222 (265)
T d1r7ra3         145 KNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVA-KDVDLEFLAKMTNGFSGADLTEICQ  222 (265)
T ss_dssp             -CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC-----CCCCHHHHHHHCSSCCHHHHHHHH
T ss_pred             CCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCch-hhhhHHHHHhcCCCCCHHHHHHHHH
Confidence            346788889999999999986  787 89999999999999998776532221 1223566666654    45554443

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=99.75  E-value=7.2e-18  Score=142.33  Aligned_cols=207  Identities=17%  Similarity=0.177  Sum_probs=143.8

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcC----CCccCCcceeecCC
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFG----PELYKSRVLELNAS  122 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~----~~~~~~~~~~~~~~  122 (294)
                      .+..+.+.-+...++.++|++..++.+.+.|......|++|+||||+|||+++..+|+....    ....+..++.++.+
T Consensus         8 ~~~~l~~~a~~g~ld~~~gr~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~   87 (387)
T d1qvra2           8 YGIDLTRLAAEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMG   87 (387)
T ss_dssp             HEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-
T ss_pred             HHHHHHHHHHcCCCCCCcCcHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHh
Confidence            34455566666777889999999999999999998899999999999999999999998742    23445677888766


Q ss_pred             CCcch----hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCC--------HHHHHHHHHHHHhhcCcceEEE
Q 022641          123 DDRGI----NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMT--------EDAQNALRRTMETYSKVTRFFF  190 (294)
Q Consensus       123 ~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~--------~~~~~~L~~~l~~~~~~~~ii~  190 (294)
                      .....    ..+...+..+......         ...+.||||||+|.+-        .+..+.|...|..  ....+|.
T Consensus        88 ~l~ag~~~~g~~e~r~~~i~~~~~~---------~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~r--g~~~~I~  156 (387)
T d1qvra2          88 SLLAGAKYRGEFEERLKAVIQEVVQ---------SQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALAR--GELRLIG  156 (387)
T ss_dssp             ----------CHHHHHHHHHHHHHT---------TCSSEEEEECCC-------------------HHHHHT--TCCCEEE
T ss_pred             hhhcccCcchhHHHHHHHHHHHhcc---------CCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhC--CCcceee
Confidence            54332    2333333333332211         0123589999999983        2346778888876  5566777


Q ss_pred             EecCC----cccchHhhccccEEEecCCCHHHHHHHHHHHHH----HhCCCCCHHHHHHHHhhc------cCcHHHHHHH
Q 022641          191 ICNYI----SRIIEPLASRCAKFRFKPLSEEVMSSRVLHICN----EEGLNLDAEALSTLSSIS------QGDLRRAITY  256 (294)
Q Consensus       191 ~~~~~----~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~----~~~~~~~~~~l~~l~~~~------~G~~r~~~~~  256 (294)
                      +|+..    ..-+++|.+||+.|.+.+|+.++...+|+....    .+++.++++++..++++|      ..-|..++.+
T Consensus       157 ~tT~~ey~~~e~d~al~rrF~~v~v~ep~~~~~~~il~~~~~~~e~~h~v~~~~~ai~~~v~ls~ryi~~r~~PdKAidl  236 (387)
T d1qvra2         157 ATTLDEYREIEKDPALERRFQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAIDL  236 (387)
T ss_dssp             EECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCTHHHHHHH
T ss_pred             ecCHHHHHHhcccHHHHHhcccccCCCCcHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHhcccccccccChhhHHHH
Confidence            77432    234688999999999999999999999987664    468999999999988874      3579999999


Q ss_pred             HHHHHHHh
Q 022641          257 LQGAARLF  264 (294)
Q Consensus       257 l~~~~~~~  264 (294)
                      ++.++...
T Consensus       237 ld~a~a~~  244 (387)
T d1qvra2         237 IDEAAARL  244 (387)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99988664

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.74  E-value=2.6e-17  Score=131.38  Aligned_cols=212  Identities=18%  Similarity=0.171  Sum_probs=139.9

Q ss_pred             hhcccHHHHHHHHHHHHcC--CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHh
Q 022641           62 DVAHQEEVVRVLTNTLETA--NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAA  139 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~~--~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  139 (294)
                      +++|+...++.+.+.+..-  ....++|+|++|||||++|+++....   ......++.+++............+.....
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~s---~~~~~~~~~~~~~~~~~~~~~~~lfg~~~~   77 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLS---DRSKEPFVALNVASIPRDIFEAELFGYEKG   77 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHS---TTTTSCEEEEETTTSCHHHHHHHHHCBCTT
T ss_pred             CeEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhc---CCcccccccchhhhhhhcccHHHhcCcccC
Confidence            3567766776666665442  22359999999999999999998653   223456666766655333222222111000


Q ss_pred             hhcc-cCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCCc-------ccch
Q 022641          140 VAVG-SGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYIS-------RIIE  200 (294)
Q Consensus       140 ~~~~-~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~~-------~~~~  200 (294)
                      ...+ .....+.....+.+.|+|||++.++...+..|++.++...           ..+++|++++.+.       .+.+
T Consensus        78 ~~~~~~~~~~g~l~~a~gGtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~~~~~~~~~~~RlI~~s~~~l~~l~~~~~f~~  157 (247)
T d1ny5a2          78 AFTGAVSSKEGFFELADGGTLFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFRE  157 (247)
T ss_dssp             SSTTCCSCBCCHHHHTTTSEEEEESGGGCCHHHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSCHHHHHHTTSSCH
T ss_pred             CcCCcccccCCHHHccCCCEEEEeChHhCCHHHHHHHHHHHHhCCEEECCCCCceecCeEEEEecCCCHHHHHHcCCCcH
Confidence            0000 0001111122445699999999999999999999997532           2456888886542       3556


Q ss_pred             Hhhcccc--EEEecCCC--HHHHHHHHHHHHH----HhCC---CCCHHHHHHHHhh-ccCcHHHHHHHHHHHHHHh-CCC
Q 022641          201 PLASRCA--KFRFKPLS--EEVMSSRVLHICN----EEGL---NLDAEALSTLSSI-SQGDLRRAITYLQGAARLF-GSS  267 (294)
Q Consensus       201 ~l~~r~~--~i~~~~~~--~~~~~~~l~~~~~----~~~~---~~~~~~l~~l~~~-~~G~~r~~~~~l~~~~~~~-~~~  267 (294)
                      .|..|+.  .|.++|+.  .+++..++..++.    +.+.   .+++++++.|..+ +.||++++.++++.++... +..
T Consensus       158 ~L~~~l~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~ls~~al~~L~~~~WPGNl~EL~~~l~~a~~~~~~~~  237 (247)
T d1ny5a2         158 DLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELKNVIERAVLFSEGKF  237 (247)
T ss_dssp             HHHHHHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHHHHSCCTTHHHHHHHHHHHHHHHCCSSE
T ss_pred             HHHhhcCeeeecCCChhhchhhHhhhhhhhhhhhhhhcCCCCCCCCHHHHHHHHhCCCCCHHHHHHHHHHHHHHhCCCCe
Confidence            6777765  67888885  3567665555544    3343   3789999999988 5999999999999988777 556


Q ss_pred             CChhhhhhh
Q 022641          268 ITSKDLISV  276 (294)
Q Consensus       268 it~~~v~~~  276 (294)
                      |+.+++..+
T Consensus       238 I~~~dl~~l  246 (247)
T d1ny5a2         238 IDRGELSCL  246 (247)
T ss_dssp             ECHHHHHHH
T ss_pred             ECHHHcccc
Confidence            999988664

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=99.71  E-value=7e-17  Score=128.83  Aligned_cols=157  Identities=13%  Similarity=0.160  Sum_probs=100.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc---hhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEE
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG---INVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIII  160 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lli  160 (294)
                      .++|+||||||||++|+++|+++      +.+++.+++++...   .......+..+.....          ...+.+|+
T Consensus        42 ~vLL~GppGtGKT~la~alA~~~------~~~~~~i~~~~~~~g~~~~~~~~~i~~if~~A~----------~~~p~il~  105 (246)
T d1d2na_          42 SVLLEGPPHSGKTALAAKIAEES------NFPFIKICSPDKMIGFSETAKCQAMKKIFDDAY----------KSQLSCVV  105 (246)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH------TCSEEEEECGGGCTTCCHHHHHHHHHHHHHHHH----------TSSEEEEE
T ss_pred             EEEEECcCCCCHHHHHHHHhhcc------cccccccccccccccccccchhhhhhhhhhhhh----------hcccceee
Confidence            49999999999999999999999      78888887654321   1111122222221111          12346999


Q ss_pred             EeCCCCC----------CHHHHHHHHHHHHhhcC---cceEEEEecCCcccchH-hhcccc-EEEecCCC-HHHHHHHHH
Q 022641          161 LDEADSM----------TEDAQNALRRTMETYSK---VTRFFFICNYISRIIEP-LASRCA-KFRFKPLS-EEVMSSRVL  224 (294)
Q Consensus       161 iDei~~l----------~~~~~~~L~~~l~~~~~---~~~ii~~~~~~~~~~~~-l~~r~~-~i~~~~~~-~~~~~~~l~  224 (294)
                      |||+|.+          .....+.|+..++....   ++.+|.|||.+..+++. +.+||. .+.++.++ .+++..++.
T Consensus       106 iDEid~l~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~tTn~~~~ld~~~~~~rF~~~i~~P~~~~r~~il~~l~  185 (246)
T d1d2na_         106 VDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEALE  185 (246)
T ss_dssp             ECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTTTSSEEEECCCEEEHHHHHHHHH
T ss_pred             hhhhhhHhhhcccccchhHHHHHHHHHHhcCCCccccceeeeeccCChhhccchhhcCccceEEecCCchhHHHHHHHHH
Confidence            9999865          23445667777665432   35677788988777654 667887 67775544 344444442


Q ss_pred             HHHHHhCCCCCHHHHHHHHhhccC-----cHHHHHHHHHHHH
Q 022641          225 HICNEEGLNLDAEALSTLSSISQG-----DLRRAITYLQGAA  261 (294)
Q Consensus       225 ~~~~~~~~~~~~~~l~~l~~~~~G-----~~r~~~~~l~~~~  261 (294)
                          .. ..+++..+..+++.+.|     .++.++..++.+.
T Consensus       186 ----~~-~~~~~~~~~~i~~~~~g~~~~~~ik~ll~~ie~a~  222 (246)
T d1d2na_         186 ----LL-GNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSL  222 (246)
T ss_dssp             ----HH-TCSCHHHHHHHHHHHTTSEEEECHHHHHHHHHHHT
T ss_pred             ----hc-cCCChHHHHHHHHHcCCCccchhHHHHHHHHHHHH
Confidence                22 34677777888877665     4777777766443

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.68  E-value=1.3e-16  Score=120.66  Aligned_cols=166  Identities=19%  Similarity=0.179  Sum_probs=119.9

Q ss_pred             CCchhhhhcCCCcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcC----CCccCCcceeecCC
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFG----PELYKSRVLELNAS  122 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~----~~~~~~~~~~~~~~  122 (294)
                      +...+.++-+...++.++|++..++.+...+......|++|+||||+|||+++..+|+....    ....+..++.++.+
T Consensus         8 ~~~dlt~~a~~g~ld~~igRd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~   87 (195)
T d1jbka_           8 YTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMG   87 (195)
T ss_dssp             HEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHH
T ss_pred             HHHHHHHHHHcCCCCCCcCcHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHH
Confidence            34455666666777889999999999999999988899999999999999999999998742    23445667777644


Q ss_pred             CC----cchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCH--------HHHHHHHHHHHhhcCcceEEE
Q 022641          123 DD----RGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTE--------DAQNALRRTMETYSKVTRFFF  190 (294)
Q Consensus       123 ~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~--------~~~~~L~~~l~~~~~~~~ii~  190 (294)
                      ..    .....+...+..........         ....||+|||+|.+-.        +..+.|...++.  ....+|.
T Consensus        88 ~LiAg~~~rG~~E~rl~~il~e~~~~---------~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~r--g~l~~Ig  156 (195)
T d1jbka_          88 ALVAGAKYRGEFEERLKGVLNDLAKQ---------EGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR--GELHCVG  156 (195)
T ss_dssp             HHHTTTCSHHHHHHHHHHHHHHHHHS---------TTTEEEEEETGGGGTT------CCCCHHHHHHHHHT--TSCCEEE
T ss_pred             HHhccCCccHHHHHHHHHHHHHHhcC---------CCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHhC--CCceEEe
Confidence            32    23344555454444332110         1134999999998832        134788888885  5566777


Q ss_pred             EecCC-----cccchHhhccccEEEecCCCHHHHHHHH
Q 022641          191 ICNYI-----SRIIEPLASRCAKFRFKPLSEEVMSSRV  223 (294)
Q Consensus       191 ~~~~~-----~~~~~~l~~r~~~i~~~~~~~~~~~~~l  223 (294)
                      +|...     ..-+++|.+||+.|.+.+|+.++...+|
T Consensus       157 atT~eey~~~~e~d~aL~rrF~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         157 ATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             EECHHHHHHHTTTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             cCCHHHHHHHHHcCHHHHhcCCEeecCCCCHHHHHHHh
Confidence            77532     3457899999999999999999887765

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=99.67  E-value=3.7e-17  Score=135.08  Aligned_cols=148  Identities=19%  Similarity=0.273  Sum_probs=97.8

Q ss_pred             hhcccHHHHHHHHHHHHc--------------CCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcch
Q 022641           62 DVAHQEEVVRVLTNTLET--------------ANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGI  127 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~--------------~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~  127 (294)
                      .++||+++++.+..++.+              ..+.+++|+||||||||.+|+++|+.+      ..+++.++++.....
T Consensus        15 ~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~------~~~~~~i~~s~~~~~   88 (309)
T d1ofha_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA------NAPFIKVEATKFTEV   88 (309)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH------TCCEEEEEGGGGSSC
T ss_pred             cccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhcc------ccchhcccccccccc
Confidence            468999999988776631              134579999999999999999999998      566777766543211


Q ss_pred             --------hHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHH------------HHHHHHHHHHhhc----
Q 022641          128 --------NVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTED------------AQNALRRTMETYS----  183 (294)
Q Consensus       128 --------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~------------~~~~L~~~l~~~~----  183 (294)
                              ..+...+........         ...++.+|+|||+|.+.+.            .++.|+..++...    
T Consensus        89 ~~~~~~~~~~~~~~f~~a~~~~~---------~~~~~~IIf~DEIdki~~~~~~~~~~~~~~gv~~~LL~~~dg~~~~~~  159 (309)
T d1ofha_          89 GYVGKEVDSIIRDLTDSAGGAID---------AVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTK  159 (309)
T ss_dssp             CSGGGSTTHHHHHHHHTTTTCHH---------HHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEEET
T ss_pred             eeEeeeccccccccchhhhcccc---------cccCCceEEehhhhhhhhhccCcccchhhhHHHHHhhHHhcCCEEecC
Confidence                    122222211111000         0011359999999998532            4566888887421    


Q ss_pred             ------CcceEEEE----ecCCcccchHhhcccc-EEEecCCCHHHHHHHHH
Q 022641          184 ------KVTRFFFI----CNYISRIIEPLASRCA-KFRFKPLSEEVMSSRVL  224 (294)
Q Consensus       184 ------~~~~ii~~----~~~~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~  224 (294)
                            .+..++++    .+.+..+.+++.+|+. .+.+.+|+..++.+++.
T Consensus       160 ~~~i~~s~ilfi~~ga~~~~~~~~~~p~l~~R~~~~i~~~~~~~~~~~~Il~  211 (309)
T d1ofha_         160 HGMVKTDHILFIASGAFQVARPSDLIPELQGRLPIRVELTALSAADFERILT  211 (309)
T ss_dssp             TEEEECTTCEEEEEECCSSSCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHH
T ss_pred             CeEEEccceeEEeccchhhcCcccchhhhhhhhheeeeccCCCHHHHHHHHH
Confidence                  12223333    2456678899999998 79999999999998864

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=99.67  E-value=3.8e-16  Score=130.73  Aligned_cols=219  Identities=17%  Similarity=0.120  Sum_probs=128.9

Q ss_pred             CcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcC-------C----------Ccc--------
Q 022641           58 KQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFG-------P----------ELY--------  112 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~-------~----------~~~--------  112 (294)
                      .+|.+++||+.+++.|.-.+...+..|++|.||||||||++|+.++.-+..       .          ...        
T Consensus         4 ~~f~~I~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~lar~~~~iLp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (333)
T d1g8pa_           4 FPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEMIPDWATVLSTNVI   83 (333)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSGGGSCTTCCCSCCCEE
T ss_pred             CChhhccCcHHHHHHHHHHHhccCCCeEEEECCCCccHHHHHHHHHHhCCCchhhccCccccCccccccchhhccccCcc
Confidence            378999999999987765554333357999999999999999999986610       0          000        


Q ss_pred             --CCcceeecCCCCcchhHHHHHHHHH-HhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc------
Q 022641          113 --KSRVLELNASDDRGINVVRTKIKTF-AAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS------  183 (294)
Q Consensus       113 --~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~------  183 (294)
                        ..++...  ........+...+... ...........+....+.+++++|||++.+++..++.|++.|++..      
T Consensus        84 ~~~~~~~~~--~~~~~~~~l~G~~d~~~~~~~g~~~~~~G~l~~A~~gvl~iDEi~~~~~~~~~aLl~~me~~~v~i~r~  161 (333)
T d1g8pa_          84 RKPTPVVDL--PLGVSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLEDHIVDLLLDVAQSGENVVERD  161 (333)
T ss_dssp             EECCCEEEE--CTTCCHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGSCHHHHHHHHHHHHHSEEEECCT
T ss_pred             cccCceeec--cCCCCcccccCcchhhhccccCcceeeccccccccccEeecccHHHHHHHHHHHHhhhhcCCeEEeccc
Confidence              0001111  1111111111000000 0000111112222333456799999999999999999999998643      


Q ss_pred             -------CcceEEEEecCC-cccchHhhcccc-EEEecCCC-HHHHHHHHHHHH--------------------------
Q 022641          184 -------KVTRFFFICNYI-SRIIEPLASRCA-KFRFKPLS-EEVMSSRVLHIC--------------------------  227 (294)
Q Consensus       184 -------~~~~ii~~~~~~-~~~~~~l~~r~~-~i~~~~~~-~~~~~~~l~~~~--------------------------  227 (294)
                             ..+.++.++|.. ..+.+++++||. .+.+..+. ......++....                          
T Consensus       162 g~~~~~p~~f~liaa~Np~~~~l~~~llDRf~~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  241 (333)
T d1g8pa_         162 GLSIRHPARFVLVGSGNPEEGDLRPQLLDRFGLSVEVLSPRDVETRVEVIRRRDTYDADPKAFLEEWRPKDMDIRNQILE  241 (333)
T ss_dssp             TCCEEEECCEEEEEEECSCSCCCCHHHHTTCSEEEECCCCCSHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CceecCCCCEEEEEecCccccccccchhhhhcceeeccCcchhhHHHHHHHhhhhcccChHHHHHHHHHHHHHHHHHHHH
Confidence                   345566666754 458899999998 57776664 232222221110                          


Q ss_pred             ---HHhCCCCCHHHHHHHHhh---ccC-cHHHHHHHHHHHHHHh----CCCCChhhhhhhcc
Q 022641          228 ---NEEGLNLDAEALSTLSSI---SQG-DLRRAITYLQGAARLF----GSSITSKDLISVSG  278 (294)
Q Consensus       228 ---~~~~~~~~~~~l~~l~~~---~~G-~~r~~~~~l~~~~~~~----~~~it~~~v~~~~~  278 (294)
                         .-..+.++++....+...   .+. ++|....+++-+...+    ...|+.+||.+++.
T Consensus       242 ~~~~l~~v~~~~~~~~~~~~~~~~~~~~S~R~~~~llrvArtiA~L~gr~~V~~~di~~a~~  303 (333)
T d1g8pa_         242 ARERLPKVEAPNTALYDCAALCIALGSDGLRGELTLLRSARALAALEGATAVGRDHLKRVAT  303 (333)
T ss_dssp             HHHHGGGCBCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHHHHHHHTTCSBCCHHHHHHHHH
T ss_pred             HhhcccceecCHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence               011345666666655544   222 6788777776554444    56799999988554

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.67  E-value=1.3e-15  Score=125.85  Aligned_cols=166  Identities=22%  Similarity=0.269  Sum_probs=117.5

Q ss_pred             hhhcccHHHHHHHHHHHHc-------CCC--CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcch----
Q 022641           61 KDVAHQEEVVRVLTNTLET-------ANC--PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGI----  127 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~-------~~~--~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~----  127 (294)
                      +.++||+.+++.+...+..       ...  .+++|+||+|||||.+|+.+|+.+      ..+++.++++.....    
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l------~~~~i~~d~s~~~~~~~~~   95 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL------GIELLRFDMSEYMERHTVS   95 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH------TCEEEEEEGGGCSSSSCCS
T ss_pred             CeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhc------cCCeeEeccccccchhhhh
Confidence            5788999999988877742       111  148999999999999999999998      455666654432111    


Q ss_pred             --------h---HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------Cc
Q 022641          128 --------N---VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KV  185 (294)
Q Consensus       128 --------~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~  185 (294)
                              +   .....+.....             ...+.++++||++.++++.++.|++++++..           .+
T Consensus        96 ~l~g~~~gy~g~~~~~~l~~~~~-------------~~~~~vvl~DeieKa~~~V~~~lLqild~G~ltd~~Gr~vdf~n  162 (315)
T d1r6bx3          96 RLIGAPPGYVGFDQGGLLTDAVI-------------KHPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRN  162 (315)
T ss_dssp             SSCCCCSCSHHHHHTTHHHHHHH-------------HCSSEEEEEETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTT
T ss_pred             hhcccCCCccccccCChhhHHHH-------------hCccchhhhcccccccchHhhhhHHhhccceecCCCCCccCccc
Confidence                    0   01011111111             1234699999999999999999999998532           34


Q ss_pred             ceEEEEecCCc-------------------------ccchHhhcccc-EEEecCCCHHHHHHHHHHHHHH-------hC-
Q 022641          186 TRFFFICNYIS-------------------------RIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNE-------EG-  231 (294)
Q Consensus       186 ~~ii~~~~~~~-------------------------~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~-------~~-  231 (294)
                      ..+|+|+|...                         .+.++|.+|+. ++.|.|++.+++..++...+..       .+ 
T Consensus       163 ~iiI~Tsnig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEflnRid~ii~f~~l~~~~~~~I~~~~l~~~~~~l~~~~i  242 (315)
T d1r6bx3         163 VVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGV  242 (315)
T ss_dssp             EEEEEEECSSCC-----------------CHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHTTE
T ss_pred             eEEEeccchhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHHHhhhhhhhcccchhhhHHHHHHHHHHHHHHHHHHhcCc
Confidence            55778876321                         25688999998 7999999999999887776642       23 


Q ss_pred             -CCCCHHHHHHHHhh
Q 022641          232 -LNLDAEALSTLSSI  245 (294)
Q Consensus       232 -~~~~~~~l~~l~~~  245 (294)
                       +.++++++..|++.
T Consensus       243 ~l~~~~~a~~~l~~~  257 (315)
T d1r6bx3         243 SLEVSQEARNWLAEK  257 (315)
T ss_dssp             EEEECHHHHHHHHHH
T ss_pred             chhhHHHHHHHHHHh
Confidence             34799999999876

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=99.64  E-value=1.7e-15  Score=127.08  Aligned_cols=173  Identities=19%  Similarity=0.222  Sum_probs=112.0

Q ss_pred             hhhcccHHHHHHHHHHHH------------------------------cCCCCcEEEECCCCCCHHHHHHHHHHHhcCCC
Q 022641           61 KDVAHQEEVVRVLTNTLE------------------------------TANCPHMLFYGPPGTGKTTTALAIAHQLFGPE  110 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~------------------------------~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~  110 (294)
                      +.++||+++++.+..+++                              .....|++|+||+|||||.+|+.||+.+    
T Consensus        17 ~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~~~----   92 (364)
T d1um8a_          17 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHL----   92 (364)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHT----
T ss_pred             CeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHhhc----
Confidence            468899999988876663                              1244579999999999999999999987    


Q ss_pred             ccCCcceeecCCCCcchh----HHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeCCCC--------------CCHHHH
Q 022641          111 LYKSRVLELNASDDRGIN----VVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDEADS--------------MTEDAQ  172 (294)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDei~~--------------l~~~~~  172 (294)
                        ..+++.++++......    .....+..+.......      ....+++++++||++.              .++..+
T Consensus        93 --~~~~ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~------v~~~~~~iv~lDEieK~~~~s~~~~~~~d~a~~~V~  164 (364)
T d1um8a_          93 --DIPIAISDATSLTEAGYVGEDVENILTRLLQASDWN------VQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQ  164 (364)
T ss_dssp             --TCCEEEEEGGGCC--------CTHHHHHHHHHTTTC------HHHHTTSEEEEETGGGC--------------CHHHH
T ss_pred             --ccceeehhhhhcccchhhHhhhccchhhhhhhchhH------HHHhhcccchhhhhhhhccccccccccccccchHHH
Confidence              5666666655432211    1112222222211110      0112345999999998              556789


Q ss_pred             HHHHHHHHhhc-------------CcceEEEEecC---------------------------------------------
Q 022641          173 NALRRTMETYS-------------KVTRFFFICNY---------------------------------------------  194 (294)
Q Consensus       173 ~~L~~~l~~~~-------------~~~~ii~~~~~---------------------------------------------  194 (294)
                      +.|+++++...             ....++.++|-                                             
T Consensus       165 ~~lLqild~~~~~~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (364)
T d1um8a_         165 QALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQT  244 (364)
T ss_dssp             HHHHHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCH
T ss_pred             HhhhhhhcCceeccCCCCCCcCCcceeEEEeehhhhhhhcccchhhhhhhhhhcccccccccccccchhhhhhhhccccH
Confidence            99999998311             11112222211                                             


Q ss_pred             ----CcccchHhhcccc-EEEecCCCHHHHHHHHHH-----------HHHHhCCC--CCHHHHHHHHhh
Q 022641          195 ----ISRIIEPLASRCA-KFRFKPLSEEVMSSRVLH-----------ICNEEGLN--LDAEALSTLSSI  245 (294)
Q Consensus       195 ----~~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~-----------~~~~~~~~--~~~~~l~~l~~~  245 (294)
                          ...+.|+|..|+. ++.|.|++.+++..++..           .++.+|+.  +++++++.|++.
T Consensus       245 ~~~~~~~f~PEf~gRi~~iv~f~~L~~~~l~~Il~~~~~~l~kq~~~~l~~~gi~L~~td~a~~~la~~  313 (364)
T d1um8a_         245 HDLVTYGLIPELIGRLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQL  313 (364)
T ss_dssp             HHHHHTTCCHHHHTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHH
T ss_pred             HHHhhhhhHHHHHHHhcchhhHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHh
Confidence                0125688999998 789999999999999853           23334554  789999999986

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=99.63  E-value=1.8e-15  Score=124.65  Aligned_cols=181  Identities=24%  Similarity=0.357  Sum_probs=119.1

Q ss_pred             hhhcccHHHHHHHHHHHHc-------CCCC--cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHH
Q 022641           61 KDVAHQEEVVRVLTNTLET-------ANCP--HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVR  131 (294)
Q Consensus        61 ~~~~g~~~~~~~l~~~l~~-------~~~~--~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (294)
                      +.++||+++++.+...+..       ...|  .++|+||+|||||.+|+.+++.+++.   ...++.++++.........
T Consensus        23 ~~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~---~~~~~~~~~~~~~~~~~~~   99 (315)
T d1qvra3          23 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT---EEAMIRIDMTEYMEKHAVS   99 (315)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSS---GGGEEEECTTTCCSSGGGG
T ss_pred             CeEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCC---CcceEEEeccccccchhhh
Confidence            4778999999888776642       1222  37899999999999999999998543   3456666655433221111


Q ss_pred             HHHHHHH---hhhcccCccCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhc-----------CcceEEEEecCC--
Q 022641          132 TKIKTFA---AVAVGSGQRRGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYS-----------KVTRFFFICNYI--  195 (294)
Q Consensus       132 ~~~~~~~---~~~~~~~~~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~-----------~~~~ii~~~~~~--  195 (294)
                      ..+..-.   ....+ +.-........+.|+++||++..++..++.|++++++..           .+..+|+|||..  
T Consensus       100 ~L~g~~~gyvG~~~~-~~l~~~~~~~p~~Vvl~DEieK~~~~v~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~tsnlG~~  178 (315)
T d1qvra3         100 RLIGAPPGYVGYEEG-GQLTEAVRRRPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSP  178 (315)
T ss_dssp             GC---------------CHHHHHHHCSSEEEEESSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHH
T ss_pred             hhcCCCCCCcCcccC-ChHHHHHHhCCCcEEEEehHhhcCHHHHHHHHHHhccCceeCCCCcEecCcceEEEEecccChH
Confidence            1110000   00000 000000001234699999999999999999999997532           345577888742  


Q ss_pred             ------------------------cccchHhhcccc-EEEecCCCHHHHHHHHHHHHHH-------hC--CCCCHHHHHH
Q 022641          196 ------------------------SRIIEPLASRCA-KFRFKPLSEEVMSSRVLHICNE-------EG--LNLDAEALST  241 (294)
Q Consensus       196 ------------------------~~~~~~l~~r~~-~i~~~~~~~~~~~~~l~~~~~~-------~~--~~~~~~~l~~  241 (294)
                                              ..+.++|.+|+. ++.|.|++.+++..++...+.+       .+  +.+++++++.
T Consensus       179 ~i~~~~~~~~~~~~~~~~~~~~l~~~f~pEflnRid~Ii~F~~L~~~~~~~I~~~~l~~l~~rl~~~~i~l~i~~~~~~~  258 (315)
T d1qvra3         179 LILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDF  258 (315)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHTCSBCCBCCCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHH
T ss_pred             HHhhhcccccchhhhhHHHHHHHHhhcCHHHHhcCCeeeeccchhhhhhHHHHHHHHHHHHHHHHhccccccccHHHHHH
Confidence                                    226788999998 6789999999999998765543       23  3479999999


Q ss_pred             HHhh
Q 022641          242 LSSI  245 (294)
Q Consensus       242 l~~~  245 (294)
                      |++.
T Consensus       259 L~~~  262 (315)
T d1qvra3         259 LAER  262 (315)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            9987

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=99.46  E-value=1.3e-15  Score=127.51  Aligned_cols=177  Identities=17%  Similarity=0.107  Sum_probs=100.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEe
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILD  162 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiD  162 (294)
                      +.++|+||||||||++|.++++.+      +..++.+++++..+...+........... .............+.++++|
T Consensus       155 ~~~~~~g~~~~gk~~~~~~~~~~~------~~~~i~in~s~~rs~~~l~~~~~~~~~l~-d~~~~~~~~~~~~~~~~~~D  227 (362)
T d1svma_         155 RYWLFKGPIDSGKTTLAAALLELC------GGKALNVNLPLDRLNFELGVAIDQFLVVF-EDVKGTGGESRDLPSGQGIN  227 (362)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH------CCEEECCSSCTTTHHHHHGGGTTCSCEEE-TTCCCSTTTTTTCCCCSHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc------CCCEEEEECcchhhHHHHHhHHHHHHHHH-HHHHHhhhhccCCCCeEEEe
Confidence            469999999999999999999999      88899999888765443322211110000 00000001111223455666


Q ss_pred             CCCCCCHHHHHHHHHHHHhhc--------------CcceEEEEecCCcccchHhhcccc-EEEecC-CCHHHHHHHHHHH
Q 022641          163 EADSMTEDAQNALRRTMETYS--------------KVTRFFFICNYISRIIEPLASRCA-KFRFKP-LSEEVMSSRVLHI  226 (294)
Q Consensus       163 ei~~l~~~~~~~L~~~l~~~~--------------~~~~ii~~~~~~~~~~~~l~~r~~-~i~~~~-~~~~~~~~~l~~~  226 (294)
                      |+|.+        ...++...              ....+|+|||..... .....|+. .+.+.+ +.......++..+
T Consensus       228 eiD~l--------~~~~dg~~~~~~~~~~~~~~~~~~~p~i~ttN~~~~~-~~r~~Rf~~~i~~~~~~~~~~~~~~l~~i  298 (362)
T d1svma_         228 NLDNL--------RDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVP-KTLQARFVKQIDFRPKDYLKHCLERSEFL  298 (362)
T ss_dssp             HHHTT--------HHHHHCSSCEEECCSSSCCEEECCCCEEEEECSCCCC-HHHHTTEEEEEECCCCHHHHHHHHTCTHH
T ss_pred             hHhhc--------ccccCCcchhhhhhhhhchhhhccCCceeeccccccc-ccccccCceEEeecCCCcHHHHHHHHHHH
Confidence            66554        22233211              012378889864321 12233665 344433 3445555777788


Q ss_pred             HHHhCCCCCHHHHHH-HHhhccCcHHHHHHHHHHHHH-HhCCCCChhhhhh
Q 022641          227 CNEEGLNLDAEALST-LSSISQGDLRRAITYLQGAAR-LFGSSITSKDLIS  275 (294)
Q Consensus       227 ~~~~~~~~~~~~l~~-l~~~~~G~~r~~~~~l~~~~~-~~~~~it~~~v~~  275 (294)
                      ++.+.+..+.+.+.. +...+++|++.+++.+...+. .....++...+..
T Consensus       299 ~~~~~l~~~~~~L~~li~~~s~~D~~~~i~~~~~~~~~~l~~ei~~~~~~~  349 (362)
T d1svma_         299 LEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQK  349 (362)
T ss_dssp             HHTTCTTCHHHHHHHHHHHSCGGGSCGGGHHHHHHHHHHHHHHCCHHHHHH
T ss_pred             hcccCCCCCHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHhhhccHHHHHH
Confidence            888888888777766 446678889988876654332 2233455544443

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=99.40  E-value=9.3e-13  Score=107.35  Aligned_cols=120  Identities=13%  Similarity=0.097  Sum_probs=77.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc------hhHHHHHHHHHHhhhcccCccCCCCCCCCcE
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG------INVVRTKIKTFAAVAVGSGQRRGGYPCPPYK  157 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (294)
                      +++|+||||||||.+|+++|.++..    ..+++.+++++..+      ...++..+.....                +.
T Consensus       125 ~~l~~G~pG~GKT~la~ala~~~~~----~~~~~~~~~~~~~~~~~G~~e~~~~~~f~~a~~----------------~~  184 (321)
T d1w44a_         125 MVIVTGKGNSGKTPLVHALGEALGG----KDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQ----------------HR  184 (321)
T ss_dssp             EEEEECSSSSCHHHHHHHHHHHHHT----TSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHH----------------CS
T ss_pred             eEEEECCCCccHHHHHHHHHHHhcC----CCCeEEEEhhHhhhcccchHHHHHHHHHHHHhh----------------cc
Confidence            3667999999999999999999721    24566777666443      3344444443321                13


Q ss_pred             EEEEeCCCCCCH------------HHHHHHHHHHHhhc--CcceEEEEecCCcccchHh----h--cccc-EEEecCCCH
Q 022641          158 IIILDEADSMTE------------DAQNALRRTMETYS--KVTRFFFICNYISRIIEPL----A--SRCA-KFRFKPLSE  216 (294)
Q Consensus       158 lliiDei~~l~~------------~~~~~L~~~l~~~~--~~~~ii~~~~~~~~~~~~l----~--~r~~-~i~~~~~~~  216 (294)
                      +|||||+|.+..            ...+.|+..++.+.  ..+.+|.+||. ..+++.+    .  .||. .+.+.+|+.
T Consensus       185 ilf~DEid~~~~~r~~~~~~~~~~r~v~~lL~e~dg~~~~~~v~viaatN~-~~~~~~i~~~~~r~~Rf~~~v~v~~pd~  263 (321)
T d1w44a_         185 VIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNP-TSNDDKIVELVKEASRSNSTSLVISTDV  263 (321)
T ss_dssp             EEEEECCTTTC-----------CCHHHHHHHHHHHHHHHHHTCEEEEECCC-CCCCHHHHHHHHHHHHHSCSEEEEECSS
T ss_pred             EEEeehhhhhccccccCCCCCcchhhhhhhhhhccccccCCCeEEEEeCCC-cccccchhhhhhccCcccceeecCCCCh
Confidence            999999999842            24456666666433  34667777774 3333333    2  3555 788888887


Q ss_pred             HHHHHHHH
Q 022641          217 EVMSSRVL  224 (294)
Q Consensus       217 ~~~~~~l~  224 (294)
                      +....++.
T Consensus       264 ~~r~~il~  271 (321)
T d1w44a_         264 DGEWQVLT  271 (321)
T ss_dssp             TTEEEEEE
T ss_pred             HHHHHHHH
Confidence            77766664

>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=99.35  E-value=2.1e-11  Score=98.45  Aligned_cols=187  Identities=17%  Similarity=0.146  Sum_probs=109.4

Q ss_pred             cchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecC-----CCCcchhHHHHH
Q 022641           59 QVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA-----SDDRGINVVRTK  133 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~  133 (294)
                      .-++++|++..++.+...    ..+.++|+||+|+|||++++.+++.+      +..+..++.     ............
T Consensus        10 ~~~~f~GR~~el~~l~~~----~~~~i~i~G~~G~GKTsLl~~~~~~~------~~~~~~i~~~~~~~~~~~~~~~~~~~   79 (283)
T d2fnaa2          10 NRKDFFDREKEIEKLKGL----RAPITLVLGLRRTGKSSIIKIGINEL------NLPYIYLDLRKFEERNYISYKDFLLE   79 (283)
T ss_dssp             SGGGSCCCHHHHHHHHHT----CSSEEEEEESTTSSHHHHHHHHHHHH------TCCEEEEEGGGGTTCSCCCHHHHHHH
T ss_pred             ChhhCCChHHHHHHHHhc----cCCEEEEEcCCCCcHHHHHHHHHHHC------CCCeEEEEeccccccccccHHHHHHH
Confidence            467899999998887653    44579999999999999999999987      333222221     111112222221


Q ss_pred             HHHHHhhhc----------ccC---------c----cC--C----------CCCCCCcEEEEEeCCCCCCHH----HHHH
Q 022641          134 IKTFAAVAV----------GSG---------Q----RR--G----------GYPCPPYKIIILDEADSMTED----AQNA  174 (294)
Q Consensus       134 ~~~~~~~~~----------~~~---------~----~~--~----------~~~~~~~~lliiDei~~l~~~----~~~~  174 (294)
                      +........          ...         .    ..  .          .....++.++++||++.+...    ....
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~~~~~~~~~  159 (283)
T d2fnaa2          80 LQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPA  159 (283)
T ss_dssp             HHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHH
T ss_pred             HHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhcccchHHHHHH
Confidence            111111000          000         0    00  0          002245678999999876432    2333


Q ss_pred             HHHHHHhhcCcceEEEEecCCccc---------chHh-hccccEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHh
Q 022641          175 LRRTMETYSKVTRFFFICNYISRI---------IEPL-ASRCAKFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSS  244 (294)
Q Consensus       175 L~~~l~~~~~~~~ii~~~~~~~~~---------~~~l-~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~  244 (294)
                      +...... ......++++.....+         ...+ .+++..+.+.|++.++..+++.+.+...++..+  .++.+.+
T Consensus       160 l~~~~~~-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~~~--~~~~i~~  236 (283)
T d2fnaa2         160 LAYAYDN-LKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFK--DYEVVYE  236 (283)
T ss_dssp             HHHHHHH-CTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCC--CHHHHHH
T ss_pred             HHHHHHh-hhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCCCHH--HHHHHHH
Confidence            4444433 3445555554332111         1112 223457999999999999999999887776544  4788999


Q ss_pred             hccCcHHHHHHHHH
Q 022641          245 ISQGDLRRAITYLQ  258 (294)
Q Consensus       245 ~~~G~~r~~~~~l~  258 (294)
                      .++|.|..+..+..
T Consensus       237 ~~~G~P~~L~~~~~  250 (283)
T d2fnaa2         237 KIGGIPGWLTYFGF  250 (283)
T ss_dssp             HHCSCHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHH
Confidence            99999975443333

>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=99.25  E-value=1.1e-10  Score=99.75  Aligned_cols=56  Identities=23%  Similarity=0.401  Sum_probs=46.1

Q ss_pred             hhcccHHHHHHHHHHHHcC--------------CCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC
Q 022641           62 DVAHQEEVVRVLTNTLETA--------------NCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD  123 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~~--------------~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~  123 (294)
                      .++||+.+++.|.-+++++              .+.|+||+||+|||||.||+.||+.+      +.+|+.++++.
T Consensus        15 yVvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~l------~VPFv~~daT~   84 (443)
T d1g41a_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA------NAPFIKVEATK   84 (443)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHT------TCCEEEEEGGG
T ss_pred             cccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHHHh------CCCEEEeecce
Confidence            5789999999887777542              24589999999999999999999998      77777776654

>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=99.23  E-value=2e-10  Score=92.73  Aligned_cols=185  Identities=11%  Similarity=0.097  Sum_probs=107.2

Q ss_pred             hhcccHHHHHHHHHHHHcC---CCCcEEEECCCCCCHHHHHHHHHHHhcC--CCccCCcceeecCCCCcchhHHHHHHHH
Q 022641           62 DVAHQEEVVRVLTNTLETA---NCPHMLFYGPPGTGKTTTALAIAHQLFG--PELYKSRVLELNASDDRGINVVRTKIKT  136 (294)
Q Consensus        62 ~~~g~~~~~~~l~~~l~~~---~~~~ill~Gp~G~GKT~la~~la~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~  136 (294)
                      .++|++..++.+..++...   ....+.|+|..|+|||+||+.+.+....  ...+... +-+..+...+...+...+..
T Consensus        21 ~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~-~Wv~vs~~~~~~~l~~~~~~   99 (277)
T d2a5yb3          21 TCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSI-VWLKDSGTAPKSTFDLFTDI   99 (277)
T ss_dssp             CSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEE-EEEECCCCSTTHHHHHHHHH
T ss_pred             ceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceE-EEEEecCCCCHHHHHHHHHH
Confidence            4669999999998888542   2234889999999999999999887521  1111111 12233333333333333333


Q ss_pred             HHhhhcccC-c---cCC-------------CCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCcccc
Q 022641          137 FAAVAVGSG-Q---RRG-------------GYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYISRII  199 (294)
Q Consensus       137 ~~~~~~~~~-~---~~~-------------~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~  199 (294)
                      ......... .   ...             .....++.++|+|+++..  .....    +.  ....++|+||+.. .+.
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~--~~~~~----~~--~~~srilvTTR~~-~v~  170 (277)
T d2a5yb3         100 LLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQE--ETIRW----AQ--ELRLRCLVTTRDV-EIS  170 (277)
T ss_dssp             HHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCH--HHHHH----HH--HTTCEEEEEESBG-GGG
T ss_pred             HHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHH--hhhhh----hc--ccCceEEEEeehH-HHH
Confidence            222111100 0   000             011346779999999753  22221    22  2345678888754 334


Q ss_pred             hHhhccccEEEecCCCHHHHHHHHHHHHHHhCC-CCCHHHHHHHHhhccCcHHHHHHH
Q 022641          200 EPLASRCAKFRFKPLSEEVMSSRVLHICNEEGL-NLDAEALSTLSSISQGDLRRAITY  256 (294)
Q Consensus       200 ~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~-~~~~~~l~~l~~~~~G~~r~~~~~  256 (294)
                      ..+...+..+.+.+++.++..+++...+..... .-.++....|++.|+|.|=.+..+
T Consensus       171 ~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~GlPLAl~~i  228 (277)
T d2a5yb3         171 NAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMF  228 (277)
T ss_dssp             GGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HhcCCCCceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHhCCCHHHHHHH
Confidence            455556678999999999999998653321111 112455788999999998654443

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.71  E-value=2.2e-08  Score=74.77  Aligned_cols=23  Identities=39%  Similarity=0.673  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+|||||++.++..+
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l   24 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCcHHHHHHHHHHhcC
Confidence            48999999999999999999987

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=98.64  E-value=8.5e-08  Score=71.53  Aligned_cols=117  Identities=20%  Similarity=0.327  Sum_probs=71.1

Q ss_pred             HHHHHHHHHHHcCCCCc-EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCc
Q 022641           68 EVVRVLTNTLETANCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQ  146 (294)
Q Consensus        68 ~~~~~l~~~l~~~~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (294)
                      .-+..+..++......+ ++|+|||+||||.++.++.+-+      ...++....+.  + ...   +..+         
T Consensus        38 ~Fl~~l~~~l~~~PKkn~i~~~GP~~TGKS~f~~sl~~~l------~G~vis~~N~~--s-~F~---Lq~l---------   96 (205)
T d1tuea_          38 TFLGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFI------QGAVISFVNST--S-HFW---LEPL---------   96 (205)
T ss_dssp             HHHHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHH------TCEECCCCCSS--S-CGG---GGGG---------
T ss_pred             HHHHHHHHHHcCCCCceEEEEECCCCccHHHHHHHHHHHh------CCEEEeccCCC--C-Ccc---cccc---------
Confidence            44466777776554445 9999999999999999999987      33332221111  0 000   0111         


Q ss_pred             cCCCCCCCCcEEEEEeCCCCCCHHHHHH-HHHHHHhhc-------------CcceEEEEecCCc---ccchHhhccccEE
Q 022641          147 RRGGYPCPPYKIIILDEADSMTEDAQNA-LRRTMETYS-------------KVTRFFFICNYIS---RIIEPLASRCAKF  209 (294)
Q Consensus       147 ~~~~~~~~~~~lliiDei~~l~~~~~~~-L~~~l~~~~-------------~~~~ii~~~~~~~---~~~~~l~~r~~~i  209 (294)
                             ....++++||+........+. +..+++..+             ....+|+|+|..-   .-...|.+|..++
T Consensus        97 -------~~~kv~l~dD~t~~~~~~~d~~lK~ll~G~~vsvd~KhK~~vqi~~pPliITsN~~~~~~d~~~~L~sRi~~f  169 (205)
T d1tuea_          97 -------TDTKVAMLDDATTTCWTYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLESRITVF  169 (205)
T ss_dssp             -------TTCSSEEEEEECHHHHHHHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHTSCEEE
T ss_pred             -------cCCeEEEEeccccchHHHHHHHHHhccCCCeeeeecccCCcccccCCCEEEEcCCCCCccccchhhhheEEEE
Confidence                   112489999986655444444 455665311             1234788887542   2346788999988


Q ss_pred             Eec
Q 022641          210 RFK  212 (294)
Q Consensus       210 ~~~  212 (294)
                      .|+
T Consensus       170 ~F~  172 (205)
T d1tuea_         170 EFP  172 (205)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            886

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.59  E-value=2.9e-08  Score=79.39  Aligned_cols=33  Identities=30%  Similarity=0.519  Sum_probs=28.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      .++|+||||||||++|++++.++      ...++.++++
T Consensus        34 ~ilL~GpPGtGKT~la~~la~~~------~~~~~~i~~d   66 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSLRSAIFEET------QGNVIVIDND   66 (273)
T ss_dssp             EEEEECCTTSCTHHHHHHHHHHT------TTCCEEECTH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh------hcceEEEecH
Confidence            49999999999999999999998      5667777653

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=98.57  E-value=1.8e-07  Score=77.59  Aligned_cols=123  Identities=16%  Similarity=0.124  Sum_probs=65.6

Q ss_pred             HHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCc
Q 022641           67 EEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQ  146 (294)
Q Consensus        67 ~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (294)
                      +..+..+...+..   +..+|+||||||||+++..+...+.........-+.+-++.......+.+.+............
T Consensus       151 ~~Q~~A~~~al~~---~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~~~~~~  227 (359)
T d1w36d1         151 NWQKVAAAVALTR---RISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDE  227 (359)
T ss_dssp             CHHHHHHHHHHTB---SEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCCSC
T ss_pred             cHHHHHHHHHHcC---CeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHHHHHhhcCchhh
Confidence            3444555555533   3599999999999999877665552111111122333444444444444333322111100000


Q ss_pred             -------------c------------CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCC
Q 022641          147 -------------R------------RGGYPCPPYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYI  195 (294)
Q Consensus       147 -------------~------------~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~  195 (294)
                                   .            .........++|||||+.+++......++.   ..+....+|+++...
T Consensus       228 ~~~~~~~~~~t~~~ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~~~l~~~ll~---~~~~~~~lILvGD~~  298 (359)
T d1w36d1         228 QKKRIPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLID---ALPDHARVIFLGDRD  298 (359)
T ss_dssp             CCCSCSCCCBTTTSCC-----------CTTSCCSCSEEEECSGGGCBHHHHHHHHH---TCCTTCEEEEEECTT
T ss_pred             hhhhhhhhhhHHHHHHhhhhcchHHHHhhhcccccceeeehhhhccCHHHHHHHHH---HhcCCCEEEEECChh
Confidence                         0            000111245799999999998766555554   445667788888553

>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=98.36  E-value=1.2e-07  Score=69.55  Aligned_cols=30  Identities=30%  Similarity=0.575  Sum_probs=25.9

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCccee
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLE  118 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~  118 (294)
                      .+|+|+|||||||||+++.|++.+      +.+++.
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L------~~~~id   32 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQL------NMEFYD   32 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHT------TCEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh------CCCeEe
Confidence            469999999999999999999998      555554

>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=98.35  E-value=1.2e-07  Score=70.05  Aligned_cols=31  Identities=32%  Similarity=0.573  Sum_probs=26.5

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCccee
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLE  118 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~  118 (294)
                      .++|+|+||||+||||+++.|++.+      +..++.
T Consensus         4 ~~~I~i~G~pGsGKTTia~~La~~l------~~~~i~   34 (173)
T d1rkba_           4 LPNILLTGTPGVGKTTLGKELASKS------GLKYIN   34 (173)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHH------CCEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH------CCcEEe
Confidence            4679999999999999999999998      555553

>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=98.32  E-value=5.4e-06  Score=59.54  Aligned_cols=23  Identities=35%  Similarity=0.421  Sum_probs=20.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|+||||+||||+|+.+....
T Consensus         4 lIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            37899999999999999987765

>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=98.31  E-value=9.9e-07  Score=65.21  Aligned_cols=80  Identities=13%  Similarity=0.098  Sum_probs=45.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCCCCCCcEEEEEeC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGYPCPPYKIIILDE  163 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiDe  163 (294)
                      -++++|+||+||||+|+.++...      +  +..++..+..........+......               +..+|+|.
T Consensus        16 liil~G~pGsGKST~a~~l~~~~------~--~~~i~~D~~~~~~~~~~~~~~~l~~---------------g~~vIiD~   72 (172)
T d1yj5a2          16 VVVAVGFPGAGKSTFIQEHLVSA------G--YVHVNRDTLGSWQRCVSSCQAALRQ---------------GKRVVIDN   72 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHTGGG------T--CEEEEHHHHCSHHHHHHHHHHHHHT---------------TCCEEEES
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc------C--CEEEchHHHHHHHHHHHHHHHHHHC---------------CCCceeeC
Confidence            49999999999999999887654      2  2334333333333332222222211               12577887


Q ss_pred             CCCCCHHHHHHHHHHHHhhcCcce
Q 022641          164 ADSMTEDAQNALRRTMETYSKVTR  187 (294)
Q Consensus       164 i~~l~~~~~~~L~~~l~~~~~~~~  187 (294)
                      ... .......+..+.........
T Consensus        73 t~~-~~~~R~~~~~~a~~~~~~~~   95 (172)
T d1yj5a2          73 TNP-DVPSRARYIQCAKDAGVPCR   95 (172)
T ss_dssp             CCC-SHHHHHHHHHHHHHHTCCEE
T ss_pred             cCC-CHHHHHHHHHHHHhcCCCEE
Confidence            654 45566666666655444433

>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=98.31  E-value=2.1e-07  Score=68.47  Aligned_cols=32  Identities=31%  Similarity=0.594  Sum_probs=27.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      |+++|+|+||+||||+++.+++.+      +.+|+..+
T Consensus         2 p~IvliG~~G~GKSTig~~La~~l------~~~fiD~D   33 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGRRLAKAL------GVGLLDTD   33 (165)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH------TCCEEEHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHh------CCCeEeec
Confidence            578999999999999999999999      66776543

>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=98.26  E-value=1.9e-06  Score=61.02  Aligned_cols=92  Identities=23%  Similarity=0.232  Sum_probs=47.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhccc---Cc-------------
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGS---GQ-------------  146 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-------------  146 (294)
                      +..+|.+|+|+|||.++-.+....      +..++.+.... .-...+...+..........   +.             
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~~~------~~~vli~~P~~-~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSV-AATLGFGAYMSKAHGVDPNIRTGVRTITTGSPITYSTY   81 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHHTT------TCCEEEEESCH-HHHHHHHHHHHHHHSCCCEEECSSCEECCCCSEEEEEH
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHc------CCcEEEEcChH-HHHHHHHHHHHHHhhccccccccccccccccceEEEee
Confidence            348999999999999886655443      33333332222 12222222222221110000   00             


Q ss_pred             ----cCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh
Q 022641          147 ----RRGGYPCPPYKIIILDEADSMTEDAQNALRRTMET  181 (294)
Q Consensus       147 ----~~~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~  181 (294)
                          ........+.++||+||+|.++......+..+++.
T Consensus        82 ~~~~~~~~~~~~~~~~vIiDE~H~~~~~~~~~~~~~l~~  120 (136)
T d1a1va1          82 GKFLADGGCSGGAYDIIICDECHSTDATSILGIGTVLDQ  120 (136)
T ss_dssp             HHHHHTTGGGGCCCSEEEEETTTCCSHHHHHHHHHHHHH
T ss_pred             eeeccccchhhhcCCEEEEecccccCHHHHHHHHHHHHH
Confidence                00011224567999999999987765555555543

>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=98.21  E-value=4.1e-07  Score=66.62  Aligned_cols=30  Identities=37%  Similarity=0.525  Sum_probs=26.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL  119 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~  119 (294)
                      ||+|+|+||+||||+++.||+.+      +.+++..
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l------~~~~~d~   31 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDL------DLVFLDS   31 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH------TCEEEEH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHh------CCCEEec
Confidence            68999999999999999999999      7777754

>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=98.19  E-value=3.5e-07  Score=68.41  Aligned_cols=24  Identities=17%  Similarity=0.259  Sum_probs=22.6

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+|+|+|||||||||+|+.|++.+
T Consensus         8 K~I~i~G~~GsGKTTla~~La~~~   31 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVNKLAAVF   31 (192)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            459999999999999999999998

>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=98.14  E-value=6.9e-07  Score=66.57  Aligned_cols=25  Identities=40%  Similarity=0.634  Sum_probs=23.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++++|+|||||||||+++.++..+.
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~   26 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHH
Confidence            4799999999999999999999983

>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=98.12  E-value=7.9e-07  Score=65.64  Aligned_cols=30  Identities=23%  Similarity=0.388  Sum_probs=26.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceee
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLEL  119 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~  119 (294)
                      .|+|+|+||+||||+++.+|+.+      +.+++..
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~L------g~~~id~   33 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARAL------GYEFVDT   33 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHH------TCEEEEH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh------CCCEEeh
Confidence            58899999999999999999999      6776653

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=98.08  E-value=6.3e-06  Score=58.11  Aligned_cols=18  Identities=33%  Similarity=0.368  Sum_probs=15.4

Q ss_pred             CcEEEECCCCCCHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTAL  100 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~  100 (294)
                      .+.+|.+|+|+|||..+-
T Consensus         8 ~~~il~~~tGsGKT~~~~   25 (140)
T d1yksa1           8 MTTVLDFHPGAGKTRRFL   25 (140)
T ss_dssp             CEEEECCCTTSSTTTTHH
T ss_pred             CcEEEEcCCCCChhHHHH
Confidence            479999999999997663

>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=98.07  E-value=1.1e-06  Score=64.73  Aligned_cols=26  Identities=46%  Similarity=0.639  Sum_probs=23.3

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..-+|+|+||||+||||+++.|++.+
T Consensus         4 k~~~I~i~G~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHh
Confidence            34469999999999999999999987

>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=98.06  E-value=1.3e-06  Score=64.27  Aligned_cols=23  Identities=39%  Similarity=0.651  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||||+||||+++.|++.+
T Consensus         8 iivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           8 IYVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999999999999998

>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=98.05  E-value=8.1e-07  Score=65.68  Aligned_cols=32  Identities=31%  Similarity=0.474  Sum_probs=26.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNA  121 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~  121 (294)
                      .++|.||||+||||+++.+++.+      +.+++.++.
T Consensus         6 iI~l~G~~GsGKSTia~~La~~l------g~~~~~~~~   37 (176)
T d1zp6a1           6 ILLLSGHPGSGKSTIAEALANLP------GVPKVHFHS   37 (176)
T ss_dssp             EEEEEECTTSCHHHHHHHHHTCS------SSCEEEECT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh------CCCEEEecH
Confidence            58899999999999999999887      566665543

>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=98.03  E-value=1.4e-06  Score=64.08  Aligned_cols=23  Identities=43%  Similarity=0.668  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||||+||||+|+.|++.+
T Consensus         4 lI~i~G~~GsGKTTva~~L~~~~   26 (176)
T d2bdta1           4 LYIITGPAGVGKSTTCKRLAAQL   26 (176)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999987

>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=98.02  E-value=2.4e-06  Score=63.03  Aligned_cols=24  Identities=17%  Similarity=0.321  Sum_probs=22.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.|+|+||||+||||+|+.|++.+
T Consensus         4 kiI~l~G~~GsGKsTva~~L~~~l   27 (178)
T d1qhxa_           4 RMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            358999999999999999999998

>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=98.01  E-value=2e-05  Score=58.42  Aligned_cols=23  Identities=48%  Similarity=0.917  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++|.||||+||||+++.|++.+
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            58999999999999999999998

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.01  E-value=2.1e-05  Score=59.64  Aligned_cols=40  Identities=25%  Similarity=0.286  Sum_probs=29.0

Q ss_pred             cccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           64 AHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        64 ~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .-++-..+.+..++..   .+.++.+|+|+|||.++..++.++
T Consensus        70 ~Lr~yQ~eav~~~~~~---~~~ll~~~tG~GKT~~a~~~~~~~  109 (206)
T d2fz4a1          70 SLRDYQEKALERWLVD---KRGCIVLPTGSGKTHVAMAAINEL  109 (206)
T ss_dssp             CCCHHHHHHHHHHTTT---SEEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CcCHHHHHHHHHHHhC---CCcEEEeCCCCCceehHHhHHHHh
Confidence            3445555566555543   247888999999999998888876

>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=98.00  E-value=9.4e-06  Score=61.32  Aligned_cols=26  Identities=31%  Similarity=0.318  Sum_probs=22.6

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      +..++|+||+|+||||++--||..+.
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~~~   31 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRYYQ   31 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            34589999999999999999998874

>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=97.99  E-value=1.8e-06  Score=63.91  Aligned_cols=24  Identities=25%  Similarity=0.296  Sum_probs=22.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .|+|+|+||+||||+|+.|++.+.
T Consensus         8 ~I~l~G~~GsGKTTia~~La~~L~   31 (183)
T d1m8pa3           8 TIFLTGYMNSGKDAIARALQVTLN   31 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            488999999999999999999983

>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=97.96  E-value=6.8e-06  Score=62.18  Aligned_cols=24  Identities=42%  Similarity=0.470  Sum_probs=21.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+||+|+||||++.-||..+.
T Consensus        11 vi~lvGptGvGKTTTiAKLA~~~~   34 (211)
T d2qy9a2          11 VILMVGVNGVGKTTTIGKLARQFE   34 (211)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            378899999999999999998874

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=97.92  E-value=4.1e-05  Score=60.24  Aligned_cols=124  Identities=17%  Similarity=0.212  Sum_probs=69.7

Q ss_pred             HHHHHHHHcC-CCCc-EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccC
Q 022641           71 RVLTNTLETA-NCPH-MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRR  148 (294)
Q Consensus        71 ~~l~~~l~~~-~~~~-ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (294)
                      ..+..++... ...+ ++|+||+++|||+++.++.+.+      +. +..++.+.... .     +.             
T Consensus        91 ~~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l------g~-~~~~~~~~~~f-~-----l~-------------  144 (267)
T d1u0ja_          91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV------PF-YGCVNWTNENF-P-----FN-------------  144 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS------SC-EEECCTTCSSC-T-----TG-------------
T ss_pred             HHHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh------cc-hhhccccCCCc-c-----cc-------------
Confidence            4555566433 3334 8999999999999999999876      21 11222111100 0     00             


Q ss_pred             CCCCCCCcEEEEEeCCCCCCHHHHHHHHHHHHh--------------hcCcceEEEEecCCcc----------cchHhhc
Q 022641          149 GGYPCPPYKIIILDEADSMTEDAQNALRRTMET--------------YSKVTRFFFICNYISR----------IIEPLAS  204 (294)
Q Consensus       149 ~~~~~~~~~lliiDei~~l~~~~~~~L~~~l~~--------------~~~~~~ii~~~~~~~~----------~~~~l~~  204 (294)
                         ......++++||...-. ...+.+..++..              ......+|+++|+...          -...+.+
T Consensus       145 ---~l~~k~~~~~~e~~~~~-~~~~~~K~l~gGd~i~v~~K~k~~~~~~~~p~li~s~n~i~~~~~~~~~~~~~~~~l~~  220 (267)
T d1u0ja_         145 ---DCVDKMVIWWEEGKMTA-KVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQD  220 (267)
T ss_dssp             ---GGSSCSEEEECSCCEET-TTHHHHHHHHTTCCEEC------CCEECCCCEEEEESSCTTCEEETTEEECTTHHHHHT
T ss_pred             ---ccCCCEEEEEeCCCccc-cHHHHHHHhcCCCceEeecccCCCcEeeCCeEEEEeCCCcccccCCCccccccchHhhh
Confidence               01123489999986543 344566666642              1133345555555432          2467999


Q ss_pred             cccEEEecC--------CCHHHHHHHHH
Q 022641          205 RCAKFRFKP--------LSEEVMSSRVL  224 (294)
Q Consensus       205 r~~~i~~~~--------~~~~~~~~~l~  224 (294)
                      |+..+.|..        +..+++..++.
T Consensus       221 R~~~~~F~~~~p~~~~~i~~~e~k~f~~  248 (267)
T d1u0ja_         221 RMFKFELTRRLDHDFGKVTKQEVKDFFR  248 (267)
T ss_dssp             TEEEEECCSCCCTTSCCCCHHHHHHHHH
T ss_pred             hEEEEECCCcCCCccCCCCHHHHHHHHH
Confidence            998877753        33455555553

>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=97.92  E-value=1.3e-05  Score=60.57  Aligned_cols=96  Identities=23%  Similarity=0.233  Sum_probs=50.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhh---hcccCccCCC-----------
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAV---AVGSGQRRGG-----------  150 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~-----------  150 (294)
                      ++|+||+|+||||++.-||..+...   +..+..+.+...+... . +.+..+...   ..........           
T Consensus        13 i~lvGp~GvGKTTTiaKLA~~~~~~---g~kV~lit~Dt~R~gA-~-eQL~~~a~~l~v~~~~~~~~~~~~~~~~~~~~~   87 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAAKLALYYKGK---GRRPLLVAADTQRPAA-R-EQLRLLGEKVGVPVLEVMDGESPESIRRRVEEK   87 (207)
T ss_dssp             EEEECCTTTTHHHHHHHHHHHHHHT---TCCEEEEECCSSCHHH-H-HHHHHHHHHHTCCEEECCTTCCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEEecccccchH-H-HHHHHHHHhcCCccccccccchhhHHHHHHHHH
Confidence            7889999999999999999887432   2333333333322211 1 122222211   1111100000           


Q ss_pred             CCCCCcEEEEEeCCCCCC--HHHHHHHHHHHHhhcCc
Q 022641          151 YPCPPYKIIILDEADSMT--EDAQNALRRTMETYSKV  185 (294)
Q Consensus       151 ~~~~~~~lliiDei~~l~--~~~~~~L~~~l~~~~~~  185 (294)
                      ......++|+||=+++.+  ......|..+.+.....
T Consensus        88 ~~~~~~d~vlIDTaGr~~~d~~~~~el~~~~~~~~~~  124 (207)
T d1ls1a2          88 ARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPD  124 (207)
T ss_dssp             HHHHTCCEEEEECCCCSSCCHHHHHHHHHHHHHHCCS
T ss_pred             HhhccCcceeecccccchhhhhhHHHHHHHHhhcCCc
Confidence            012345799999998764  45566666666554443

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.92  E-value=3.2e-06  Score=62.85  Aligned_cols=23  Identities=35%  Similarity=0.583  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +|+|.||||+||||+++.|++.+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            48999999999999999999998

>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=97.91  E-value=2e-06  Score=64.75  Aligned_cols=26  Identities=27%  Similarity=0.475  Sum_probs=23.0

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+..|+|.||||+||||+++.|++.+
T Consensus         5 kp~iI~i~G~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_           5 KPNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            33458999999999999999999988

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=97.89  E-value=2.9e-06  Score=63.60  Aligned_cols=25  Identities=24%  Similarity=0.371  Sum_probs=23.0

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.+|+|.||||+||||+++.|++.+
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3469999999999999999999998

>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=97.89  E-value=1.8e-05  Score=59.82  Aligned_cols=146  Identities=15%  Similarity=0.097  Sum_probs=65.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc--hhHHHHHHHHHHhhhcccCccCCCC----------
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG--INVVRTKIKTFAAVAVGSGQRRGGY----------  151 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~----------  151 (294)
                      .++|+||+|+||||++--||..+...   +..+..+.....+.  ...++.. .................          
T Consensus        14 vi~lvGptGvGKTTTiAKLA~~~~~~---g~kV~lit~Dt~R~ga~eQL~~~-a~~l~v~~~~~~~~~~~~~~~~~a~~~   89 (211)
T d1j8yf2          14 VIMLVGVQGTGKATTAGKLAYFYKKK---GFKVGLVGADVYRPAALEQLQQL-GQQIGVPVYGEPGEKDVVGIAKRGVEK   89 (211)
T ss_dssp             EEEEECSCCC----HHHHHHHHHHHT---TCCEEEEECCCSSHHHHHHHHHH-HHHHTCCEECCTTCCCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC---CCceEEEEeeccccchhHHHHHh-ccccCcceeecccchhhhHHHHHHHHH
Confidence            37889999999999999999877422   22333333333222  2222211 11111111111111000          


Q ss_pred             -CCCCcEEEEEeCCCCCCH----HHHHHHHHHHHhhcC-cceEEEEecCCcccchHhhccc-----cEEEecCCCHHHHH
Q 022641          152 -PCPPYKIIILDEADSMTE----DAQNALRRTMETYSK-VTRFFFICNYISRIIEPLASRC-----AKFRFKPLSEEVMS  220 (294)
Q Consensus       152 -~~~~~~lliiDei~~l~~----~~~~~L~~~l~~~~~-~~~ii~~~~~~~~~~~~l~~r~-----~~i~~~~~~~~~~~  220 (294)
                       .....++|+||=+++.+.    .....+..+.+.... ...+++.++........+..++     .-+-+..++.....
T Consensus        90 ~~~~~~d~IlIDTaGr~~~~~~~~~~~el~~~~~~~~~~~~~LVl~a~~~~~~~~~~~~~~~~~~~~~lI~TKlDet~~~  169 (211)
T d1j8yf2          90 FLSEKMEIIIVDTAGRHGYGEEAALLEEMKNIYEAIKPDEVTLVIDASIGQKAYDLASKFNQASKIGTIIITKMDGTAKG  169 (211)
T ss_dssp             HHHTTCSEEEEECCCSCCTTCHHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGHHHHHHHHHHHCTTEEEEEECTTSCSCH
T ss_pred             hhccCCceEEEecCCcCccchhhHHHHHHHHHHhhcCCceEEEEEecccCcchHHHHhhhhcccCcceEEEecccCCCcc
Confidence             123457999999987532    123445555554433 3334444443333233333322     23556666665544


Q ss_pred             HHHHHHHHHhCCC
Q 022641          221 SRVLHICNEEGLN  233 (294)
Q Consensus       221 ~~l~~~~~~~~~~  233 (294)
                      --+-..+...+++
T Consensus       170 G~~l~~~~~~~lP  182 (211)
T d1j8yf2         170 GGALSAVAATGAT  182 (211)
T ss_dssp             HHHHHHHHTTTCC
T ss_pred             cHHHHHHHHHCcC
Confidence            4444444444443

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=97.89  E-value=5.6e-06  Score=62.85  Aligned_cols=23  Identities=35%  Similarity=0.525  Sum_probs=21.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++|+||+|+||||++.-||..+.
T Consensus        14 i~lvGptGvGKTTTiAKLAa~~~   36 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLAKMFV   36 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH
Confidence            78999999999999999998874

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=97.88  E-value=5e-05  Score=58.71  Aligned_cols=44  Identities=25%  Similarity=0.385  Sum_probs=33.4

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCcc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYISR  197 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~  197 (294)
                      .++.++++||.- .|++.....+.+.+........+|++|.+...
T Consensus       156 ~~p~ililDEpts~LD~~~~~~i~~~l~~l~~~~Tvi~itH~l~~  200 (241)
T d2pmka1         156 NNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLST  200 (241)
T ss_dssp             TCCSEEEECCCCSCCCHHHHHHHHHHHHHHHTTSEEEEECSSGGG
T ss_pred             cccchhhhhCCccccCHHHHHHHHHHHHHHhCCCEEEEEECCHHH
Confidence            567899999975 57888888888888776666678888876543

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=97.87  E-value=5.3e-06  Score=62.18  Aligned_cols=24  Identities=38%  Similarity=0.699  Sum_probs=22.0

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..++|.||||+||||+++.|++.+
T Consensus         4 ~riil~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           4 VRAVLLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            358899999999999999999998

>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=97.85  E-value=4.6e-06  Score=61.03  Aligned_cols=25  Identities=36%  Similarity=0.412  Sum_probs=22.9

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      |.+.|+|++|+|||||++.+++.+.
T Consensus         3 Pvi~itG~~GSGKTTL~~~L~~~l~   27 (170)
T d1np6a_           3 PLLAFAAWSGTGKTTLLKKLIPALC   27 (170)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            5789999999999999999999873

>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=97.84  E-value=5.4e-06  Score=62.45  Aligned_cols=24  Identities=25%  Similarity=0.497  Sum_probs=22.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.++|.||||+||||+|+.|++.+
T Consensus         9 ~iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_           9 SVIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            458999999999999999999987

>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=97.82  E-value=4.9e-06  Score=62.40  Aligned_cols=24  Identities=33%  Similarity=0.547  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .|+|+|+||+||||+|+.|++.+.
T Consensus        21 vI~L~G~pGSGKTTiAk~La~~l~   44 (195)
T d1x6va3          21 TVWLTGLSGAGKTTVSMALEEYLV   44 (195)
T ss_dssp             EEEEESSCHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            377999999999999999999883

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=97.79  E-value=8.1e-06  Score=61.11  Aligned_cols=24  Identities=29%  Similarity=0.526  Sum_probs=22.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      -.++|.||||+||||+++.|+..+
T Consensus         7 mrIiliG~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSRITKHF   30 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHB
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHH
Confidence            458999999999999999999987

>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=97.78  E-value=5.1e-05  Score=58.12  Aligned_cols=43  Identities=9%  Similarity=0.164  Sum_probs=29.1

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhh--cCcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETY--SKVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~--~~~~~ii~~~~~~~  196 (294)
                      .++.+|++||-- .|++.....+...+.+.  .....+|++|.+..
T Consensus       147 ~~P~illlDEPts~LD~~~~~~i~~~l~~l~~~~g~tii~vTHd~~  192 (232)
T d2awna2         147 AEPSVFLLDEPLSNLDAALRVQMRIEISRLHKRLGRTMIYVTHDQV  192 (232)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHSCCEEEEEESCHH
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            467799999964 57777766666666543  24566778876543

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.78  E-value=7.1e-05  Score=58.32  Aligned_cols=43  Identities=21%  Similarity=0.376  Sum_probs=32.9

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                      .++.++++||.- .|++.....+.+.+........+|++|.+..
T Consensus       171 ~~p~ililDEpts~LD~~t~~~i~~~l~~l~~~~TvI~itH~~~  214 (255)
T d2hyda1         171 NNPPILILDEATSALDLESESIIQEALDVLSKDRTTLIVAHRLS  214 (255)
T ss_dssp             HCCSEEEEESTTTTCCHHHHHHHHHHHHHHTTTSEEEEECSSGG
T ss_pred             cCCCEEEEeCccccCCHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            356799999975 5778888888888877666666788886654

>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=97.77  E-value=9.4e-06  Score=60.30  Aligned_cols=23  Identities=35%  Similarity=0.600  Sum_probs=21.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +|+|.||||+||||+++.|++.+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            48899999999999999999998

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.76  E-value=0.00012  Score=57.00  Aligned_cols=43  Identities=23%  Similarity=0.405  Sum_probs=32.1

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~  196 (294)
                      .++.++++||.- .|++.....+++.+........+|++|.+..
T Consensus       169 ~~p~ililDEpts~LD~~~~~~i~~~l~~l~~~~Tvi~itH~l~  212 (253)
T d3b60a1         169 RDSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRLS  212 (253)
T ss_dssp             HCCSEEEEETTTSSCCHHHHHHHHHHHHHHHTTSEEEEECSCGG
T ss_pred             cCCCEEEeccccccCCHHHHHHHHHHHHHhccCCEEEEEECCHH
Confidence            356799999975 5678777788888877666666788886654

>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=97.76  E-value=7.3e-06  Score=61.62  Aligned_cols=24  Identities=29%  Similarity=0.510  Sum_probs=22.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.|+|.||||+||||+++.|++.+
T Consensus         9 ~iI~l~G~pGSGKsT~a~~La~~~   32 (194)
T d3adka_           9 KIIFVVGGPGSGKGTQCEKIVQKY   32 (194)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999999987

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.76  E-value=8.5e-06  Score=61.17  Aligned_cols=24  Identities=29%  Similarity=0.488  Sum_probs=22.3

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.|+|.||||+||||.|+.|++.+
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            358999999999999999999988

>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=97.74  E-value=9.3e-06  Score=60.25  Aligned_cols=23  Identities=39%  Similarity=0.790  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.||||+||||+++.|+..+
T Consensus         4 rIvl~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999998

>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=97.72  E-value=8.7e-06  Score=60.31  Aligned_cols=23  Identities=30%  Similarity=0.502  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++|.||||+||||.++.|++.+
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999998

>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=97.72  E-value=1.2e-05  Score=61.58  Aligned_cols=25  Identities=40%  Similarity=0.628  Sum_probs=22.9

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|.|.|.||||+||||+++.|++.+
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~   27 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEAL   27 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            3568888999999999999999998

>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=97.71  E-value=9.4e-05  Score=56.82  Aligned_cols=43  Identities=9%  Similarity=0.228  Sum_probs=30.7

Q ss_pred             CCcEEEEEeCC-CCCCHHHHHHHHHHHHhhc--CcceEEEEecCCc
Q 022641          154 PPYKIIILDEA-DSMTEDAQNALRRTMETYS--KVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei-~~l~~~~~~~L~~~l~~~~--~~~~ii~~~~~~~  196 (294)
                      .++.+|++||- -.+++.....+.+.+.+..  ....+|++|.+..
T Consensus       153 ~~P~iLllDEPts~LD~~~~~~i~~ll~~l~~~~g~tii~vTHd~~  198 (239)
T d1v43a3         153 VEPDVLLMDEPLSNLDAKLRVAMRAEIKKLQQKLKVTTIYVTHDQV  198 (239)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHTCEEEEEESCHH
T ss_pred             cCCCceeecCCcccCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCHH
Confidence            56789999995 4678877777777776643  2566788886644

>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=97.70  E-value=0.00011  Score=59.48  Aligned_cols=38  Identities=21%  Similarity=0.434  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           67 EEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        67 ~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.....+..++..+.  |++++||+|+||||+++++....
T Consensus       153 ~~~~~~l~~~v~~~~--nili~G~tgSGKTT~l~al~~~i  190 (323)
T d1g6oa_         153 EQAISAIKDGIAIGK--NVIVCGGTGSGKTTYIKSIMEFI  190 (323)
T ss_dssp             HHHHHHHHHHHHHTC--CEEEEESTTSSHHHHHHHHGGGS
T ss_pred             HHHHHHHHHHHHhCC--CEEEEeeccccchHHHHHHhhhc
Confidence            455566666676665  79999999999999999998766

>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=97.66  E-value=4.9e-05  Score=58.76  Aligned_cols=52  Identities=10%  Similarity=0.116  Sum_probs=34.1

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC-cceEEEEecCCcccchHhhccc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK-VTRFFFICNYISRIIEPLASRC  206 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~-~~~ii~~~~~~~~~~~~l~~r~  206 (294)
                      .++.+|++||-- .+++.....+.+++.+... ...+++++.+.... ..+.+|+
T Consensus       156 ~~P~lLllDEPt~gLD~~~~~~i~~~i~~l~~~g~til~~tH~l~~~-~~~~drv  209 (240)
T d1ji0a_         156 SRPKLLMMDEPSLGLAPILVSEVFEVIQKINQEGTTILLVEQNALGA-LKVAHYG  209 (240)
T ss_dssp             TCCSEEEEECTTTTCCHHHHHHHHHHHHHHHHTTCCEEEEESCHHHH-HHHCSEE
T ss_pred             hCCCEeeecCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHH-HHhCCEE
Confidence            567899999964 6788888888777776433 45577777654322 2444444

>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=97.64  E-value=1.7e-05  Score=58.85  Aligned_cols=24  Identities=29%  Similarity=0.425  Sum_probs=22.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .|+|.|+||+||||+++.|++.+.
T Consensus         3 iI~i~G~~GsGKsT~~~~L~~~l~   26 (190)
T d1khta_           3 VVVVTGVPGVGSTTSSQLAMDNLR   26 (190)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            589999999999999999999883

>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=97.63  E-value=0.00036  Score=53.35  Aligned_cols=48  Identities=19%  Similarity=0.229  Sum_probs=39.8

Q ss_pred             cchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           59 QVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        59 ~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|..-..|......+...+..+...+.+|+|.+|+|||-++-..+...
T Consensus        53 P~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~  100 (233)
T d2eyqa3          53 PFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLA  100 (233)
T ss_dssp             CSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHH
T ss_pred             ccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHH
Confidence            344455678888899999999988889999999999999998777665

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=97.61  E-value=3.1e-05  Score=58.25  Aligned_cols=23  Identities=39%  Similarity=0.444  Sum_probs=18.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |.++++|+|+|||.++..++...
T Consensus        25 n~lv~~pTGsGKT~i~~~~~~~~   47 (200)
T d1wp9a1          25 NCLIVLPTGLGKTLIAMMIAEYR   47 (200)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEeCCCCcHHHHHHHHHHHH
Confidence            68999999999998766665443

>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=97.58  E-value=4.5e-05  Score=56.93  Aligned_cols=22  Identities=32%  Similarity=0.359  Sum_probs=20.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |.|.||+|+||||+|+.|+..+
T Consensus        25 IgI~G~~GSGKSTla~~L~~~l   46 (198)
T d1rz3a_          25 LGIDGLSRSGKTTLANQLSQTL   46 (198)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6699999999999999999877

>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=97.58  E-value=2.3e-05  Score=60.00  Aligned_cols=22  Identities=36%  Similarity=0.593  Sum_probs=20.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |.|.||||+||||+|+.|+..+
T Consensus         6 IaIdGp~GsGKgT~ak~La~~l   27 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAKDF   27 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5677999999999999999998

>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=97.57  E-value=2e-05  Score=59.75  Aligned_cols=22  Identities=27%  Similarity=0.481  Sum_probs=20.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|.||+||||+|+.|++.+
T Consensus         5 i~l~GlpgsGKSTla~~L~~~l   26 (213)
T d1bifa1           5 IVMVGLPARGKTYISKKLTRYL   26 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            8899999999999999999877

>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=97.52  E-value=0.00038  Score=53.98  Aligned_cols=43  Identities=16%  Similarity=0.271  Sum_probs=31.3

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhcC--cceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYSK--VTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~~--~~~ii~~~~~~~  196 (294)
                      .++.++++||.- .+++.....+.+.+.+...  ...+|++|.+..
T Consensus       168 ~~p~ililDEpTs~LD~~~~~~i~~~l~~l~~~~~~Tvi~itH~l~  213 (251)
T d1jj7a_         168 RKPCVLILDDATSALDANSQLQVEQLLYESPERYSRSVLLITQHLS  213 (251)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHTCGGGGGCEEEEECSCHH
T ss_pred             cCCcEEEecCcCcccChhhHHHHHHHHHHHhhhcCCEEEEEeCCHH
Confidence            567899999974 6788888888888876443  456777776643

>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=97.49  E-value=5.3e-05  Score=57.38  Aligned_cols=31  Identities=29%  Similarity=0.443  Sum_probs=25.1

Q ss_pred             HHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           76 TLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        76 ~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .....++..|+|+|.||+||||+|+.|++.+
T Consensus        18 ~~~~~kg~vIwltGlsGsGKTTia~~L~~~l   48 (208)
T d1m7ga_          18 ELRNQRGLTIWLTGLSASGKSTLAVELEHQL   48 (208)
T ss_dssp             HHHTSSCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             HHhCCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3444444469999999999999999999876

>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=97.47  E-value=0.00025  Score=54.57  Aligned_cols=43  Identities=14%  Similarity=0.182  Sum_probs=29.6

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc-CcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS-KVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~~  196 (294)
                      .++.+|++||.- .+++.....+.+++.+.. ....++++|.+..
T Consensus       150 ~~p~illLDEPt~gLD~~~~~~i~~~i~~~~~~g~tii~~tH~l~  194 (238)
T d1vpla_         150 VNPRLAILDEPTSGLDVLNAREVRKILKQASQEGLTILVSSHNML  194 (238)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEEECCHH
T ss_pred             cCCCEEEecCCCCCCCHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            567799999964 577777777777776543 3456777775543

>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=97.46  E-value=0.0011  Score=55.20  Aligned_cols=49  Identities=20%  Similarity=0.283  Sum_probs=38.4

Q ss_pred             CcchhhcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           58 KQVKDVAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        58 ~~~~~~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++.++--.+.....+.+++.... .-++|+||+|+||||++.++.+.+.
T Consensus       135 ~~l~~LG~~~~~~~~l~~l~~~~~-GliLvtGpTGSGKSTTl~~~l~~~~  183 (401)
T d1p9ra_         135 LDLHSLGMTAHNHDNFRRLIKRPH-GIILVTGPTGSGKSTTLYAGLQELN  183 (401)
T ss_dssp             CCGGGSCCCHHHHHHHHHHHTSSS-EEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             hhhhhhcccHHHHHHHHHHHhhhh-ceEEEEcCCCCCccHHHHHHhhhhc
Confidence            456666666777777777765543 3599999999999999999999884

>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=97.45  E-value=3e-05  Score=57.67  Aligned_cols=23  Identities=30%  Similarity=0.432  Sum_probs=21.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.|++|+||||+++.|++.+
T Consensus         3 iivi~G~~GsGKTT~~~~La~~L   25 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAKVKEIL   25 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37889999999999999999998

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.44  E-value=7.6e-05  Score=56.19  Aligned_cols=38  Identities=16%  Similarity=0.231  Sum_probs=25.3

Q ss_pred             CcEEEEEeCCCCCCH----HHHHHHHHHHHhhcCcceEEEEe
Q 022641          155 PYKIIILDEADSMTE----DAQNALRRTMETYSKVTRFFFIC  192 (294)
Q Consensus       155 ~~~lliiDei~~l~~----~~~~~L~~~l~~~~~~~~ii~~~  192 (294)
                      ..++||+||+|.+..    ...+.++..+.....+..+++.|
T Consensus       138 ~~~~ii~DE~h~~~~~~r~~~~~~~l~~i~~~~~~~~~l~lS  179 (202)
T d2p6ra3         138 AVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLS  179 (202)
T ss_dssp             GCCEEEETTGGGGGCTTTHHHHHHHHHHHHHHCTTCEEEEEE
T ss_pred             hhhhccccHHHHhcccccchHHHHHHHHHHhcCCCCcEEEEc
Confidence            456999999998742    23455666666666666666655

>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=97.42  E-value=4.7e-05  Score=56.84  Aligned_cols=23  Identities=26%  Similarity=0.501  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|+||+|+|||++++.|+...
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHhC
Confidence            38899999999999999999886

>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=97.42  E-value=4e-05  Score=56.99  Aligned_cols=23  Identities=30%  Similarity=0.525  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|+||+|+|||++++.|+++.
T Consensus         3 pIvl~GpsG~GK~tl~~~L~~~~   25 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHC
T ss_pred             eEEEECCCCCCHHHHHHHHHHhC
Confidence            48999999999999999999886

>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=97.41  E-value=0.00012  Score=56.54  Aligned_cols=23  Identities=30%  Similarity=0.471  Sum_probs=21.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+||+|+|||||++.++..+
T Consensus        30 ~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          30 IIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhh
Confidence            59999999999999999998765

>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=97.31  E-value=7.2e-05  Score=55.32  Aligned_cols=23  Identities=22%  Similarity=0.518  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+||||+++.|....
T Consensus         4 iivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           4 VVVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            58999999999999999998886

>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=97.27  E-value=0.0043  Score=44.44  Aligned_cols=22  Identities=18%  Similarity=0.407  Sum_probs=20.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+|++|||||+|+..+...-
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~~   27 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999998754

>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=97.22  E-value=0.00031  Score=53.86  Aligned_cols=52  Identities=17%  Similarity=0.237  Sum_probs=31.8

Q ss_pred             CcEEEEEeCC-CCCCHHHHHHHHHHHHhhc-CcceEEEEecCCcccchHhhcccc
Q 022641          155 PYKIIILDEA-DSMTEDAQNALRRTMETYS-KVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       155 ~~~lliiDei-~~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      .+.+|++||- ..|+......+.+++.... ....+++++.+... ...+.+|+.
T Consensus       150 ~p~llllDEPt~gLD~~~~~~i~~~i~~l~~~g~tii~vtHdl~~-~~~~~dri~  203 (231)
T d1l7vc_         150 AGQLLLLDEPMNSLDVAQQSALDKILSALCQQGLAIVMSSHDLNH-TLRHAHRAW  203 (231)
T ss_dssp             TCCEEEESSCSTTCCHHHHHHHHHHHHHHHHTTCEEEECCCCHHH-HHHHCSBCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHH-HHHHCCEEE
Confidence            4479999995 4677777777777776543 34456666654332 234445543

>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=97.22  E-value=0.00024  Score=51.37  Aligned_cols=21  Identities=19%  Similarity=0.292  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~  105 (294)
                      ++|+|++|+|||+|+..+...
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999988764

>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=97.17  E-value=0.00056  Score=49.00  Aligned_cols=22  Identities=27%  Similarity=0.487  Sum_probs=19.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|+|+||+|||+|..++...
T Consensus         3 kI~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3899999999999999998754

>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=97.17  E-value=0.00013  Score=52.96  Aligned_cols=24  Identities=21%  Similarity=0.047  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+.|+|++|+|||||+..++..+.
T Consensus         3 ii~I~G~~gSGKTTli~~l~~~L~   26 (165)
T d1xjca_           3 VWQVVGYKHSGKTTLMEKWVAAAV   26 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHH
Confidence            367999999999999999999884

>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=97.16  E-value=0.0012  Score=51.23  Aligned_cols=52  Identities=13%  Similarity=0.163  Sum_probs=33.3

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc-CcceEEEEecCCcccchHhhccc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS-KVTRFFFICNYISRIIEPLASRC  206 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~-~~~~ii~~~~~~~~~~~~l~~r~  206 (294)
                      .++.+|++||-- .+++.....+++.+.+.. ....+++++.+...+ ..+.+|.
T Consensus       167 ~~P~llilDEPt~gLD~~~~~~i~~~i~~l~~~g~til~vsHdl~~~-~~~~Drv  220 (254)
T d1g6ha_         167 TNPKMIVMDEPIAGVAPGLAHDIFNHVLELKAKGITFLIIEHRLDIV-LNYIDHL  220 (254)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEECSCCSTT-GGGCSEE
T ss_pred             hCcCchhhcCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEeCcHHHH-HHhCCEE
Confidence            467799999964 577777777777776543 345677777554432 2444544

>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=97.15  E-value=0.00039  Score=49.55  Aligned_cols=24  Identities=25%  Similarity=0.324  Sum_probs=22.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|.|+=|+|||++++.+++.+-
T Consensus        35 ii~L~G~LGaGKTtfvr~~~~~lg   58 (158)
T d1htwa_          35 MVYLNGDLGAGKTTLTRGMLQGIG   58 (158)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             EEEEecCCCccHHHHHHHHHhhcc
Confidence            388999999999999999999983

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.14  E-value=0.00033  Score=54.64  Aligned_cols=43  Identities=21%  Similarity=0.207  Sum_probs=36.4

Q ss_pred             cccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           64 AHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        64 ~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      -.|..++..+..-+..+...+-+|.|..|+|||-++-..+...
T Consensus        86 ~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~  128 (264)
T d1gm5a3          86 NAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDN  128 (264)
T ss_dssp             HHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHH
Confidence            3677888888888888888889999999999999987776554

>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=97.14  E-value=0.002  Score=46.67  Aligned_cols=25  Identities=20%  Similarity=0.274  Sum_probs=20.9

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHH
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~  105 (294)
                      +.-.++|+|.+|+|||+|+..+...
T Consensus        14 k~~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          14 QEHKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CeEEEEEECCCCCCHHHHHHHHhcC
Confidence            3345999999999999999988654

>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=97.13  E-value=0.00091  Score=48.43  Aligned_cols=23  Identities=22%  Similarity=0.504  Sum_probs=20.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++++|++|||||+|+..+...-+
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~~f   31 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKGQF   31 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSCC
T ss_pred             EEEECCCCcCHHHHHHHHHhCCC
Confidence            89999999999999999986543

>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=97.07  E-value=0.00017  Score=53.01  Aligned_cols=23  Identities=13%  Similarity=0.369  Sum_probs=21.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+|||++.+.|.++.
T Consensus         5 ~ivl~Gpsg~GK~tl~~~L~~~~   27 (178)
T d1kgda_           5 TLVLLGAHGVGRRHIKNTLITKH   27 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             cEEEECCCCCCHHHHHHHHHHhC
Confidence            58999999999999999998875

>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=97.07  E-value=0.0002  Score=53.90  Aligned_cols=23  Identities=22%  Similarity=0.388  Sum_probs=21.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||+|+|||+|.+.|....
T Consensus         4 livi~GPSG~GK~tl~~~L~~~~   26 (205)
T d1s96a_           4 LYIVSAPSGAGKSSLIQALLKTQ   26 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            58999999999999999999885

>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=97.03  E-value=0.00018  Score=54.44  Aligned_cols=22  Identities=23%  Similarity=0.347  Sum_probs=20.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |.|+||+|+||||+++.|+..+
T Consensus         5 IgI~G~~gSGKSTla~~L~~~l   26 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQLL   26 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6699999999999999999987

>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=97.02  E-value=0.0019  Score=46.32  Aligned_cols=22  Identities=23%  Similarity=0.374  Sum_probs=19.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++.|.+|||||+|+..+...-
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~~   24 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYDS   24 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7899999999999999987643

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.01  E-value=0.0019  Score=48.62  Aligned_cols=41  Identities=22%  Similarity=0.344  Sum_probs=26.1

Q ss_pred             CCCcEEEEEeCCCCCCHH-HHHHHHHHHHhhcCcceEEEEec
Q 022641          153 CPPYKIIILDEADSMTED-AQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       153 ~~~~~lliiDei~~l~~~-~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      ..+-..+++||+|.+... ..+.+.++++..+....+++.|.
T Consensus       149 l~~l~~lVlDEad~lld~~f~~~v~~I~~~~~~~~Q~vl~SA  190 (212)
T d1qdea_         149 TDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSA  190 (212)
T ss_dssp             CTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEES
T ss_pred             cCcceEEeehhhhhhcccchHHHHHHHHHhCCCCCeEEEEEe
Confidence            345668999999987432 34556666666665555555543

>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=96.99  E-value=0.0002  Score=52.83  Aligned_cols=22  Identities=18%  Similarity=0.259  Sum_probs=20.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|.+|||||+|+..+...-
T Consensus         8 ivviG~~~vGKTsli~~~~~~~   29 (183)
T d1mh1a_           8 CVVVGDGAVGKTCLLISYTTNA   29 (183)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            8999999999999999987754

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.96  E-value=0.003  Score=47.72  Aligned_cols=41  Identities=20%  Similarity=0.313  Sum_probs=27.1

Q ss_pred             CCcEEEEEeCCCCCCHH-HHHHHHHHHHhhcCcceEEEEecC
Q 022641          154 PPYKIIILDEADSMTED-AQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       154 ~~~~lliiDei~~l~~~-~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      ..-..+++||+|.+... ..+.+..+++..+....+++.+..
T Consensus       154 ~~l~~lVlDEaD~ll~~~f~~~~~~Il~~~~~~~Q~il~SAT  195 (218)
T d2g9na1         154 KYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSAT  195 (218)
T ss_dssp             TTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESC
T ss_pred             ccceEEEeeecchhhcCchHHHHHHHHHhCCCCCeEEEEEec
Confidence            34569999999987432 345566666666666666666543

>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=96.94  E-value=0.00043  Score=50.05  Aligned_cols=23  Identities=13%  Similarity=0.284  Sum_probs=20.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.|++|||||+|+..+...-
T Consensus         6 Kv~liG~~~vGKTsLl~~~~~~~   28 (167)
T d1xtqa1           6 KIAILGYRSVGKSSLTIQFVEGQ   28 (167)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            38999999999999999987643

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=96.93  E-value=0.00027  Score=50.51  Aligned_cols=23  Identities=26%  Similarity=0.320  Sum_probs=20.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++|+|+||||||+|+..+...-+
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~~   25 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGEI   25 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhcCCC
Confidence            78999999999999999987653

>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=96.93  E-value=0.0016  Score=46.77  Aligned_cols=22  Identities=18%  Similarity=0.475  Sum_probs=19.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|++|||||+|+..+...-
T Consensus         6 i~viG~~~vGKTsli~~l~~~~   27 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            8999999999999999987654

>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=96.91  E-value=0.0026  Score=45.78  Aligned_cols=22  Identities=23%  Similarity=0.427  Sum_probs=19.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|++|+|||+++..+...-
T Consensus         7 ivlvG~~~vGKTsli~~~~~~~   28 (168)
T d1u8za_           7 VIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999987643

>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=96.89  E-value=0.0014  Score=47.56  Aligned_cols=22  Identities=18%  Similarity=0.440  Sum_probs=19.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+|.+|||||+|+..+...-
T Consensus         9 v~lvG~~~vGKTsLi~r~~~~~   30 (173)
T d2fn4a1           9 LVVVGGGGVGKSALTIQFIQSY   30 (173)
T ss_dssp             EEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            9999999999999999887654

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.89  E-value=0.0055  Score=45.73  Aligned_cols=39  Identities=18%  Similarity=0.348  Sum_probs=26.2

Q ss_pred             CCcEEEEEeCCCCCC-HHHHHHHHHHHHhhcCcceEEEEe
Q 022641          154 PPYKIIILDEADSMT-EDAQNALRRTMETYSKVTRFFFIC  192 (294)
Q Consensus       154 ~~~~lliiDei~~l~-~~~~~~L~~~l~~~~~~~~ii~~~  192 (294)
                      ..-..+++||+|.+- .+..+.+..+++..+....+++.|
T Consensus       142 ~~l~~lV~DEaD~l~~~~f~~~v~~I~~~l~~~~Q~il~S  181 (206)
T d1s2ma1         142 SDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFS  181 (206)
T ss_dssp             TTCCEEEEESHHHHSSHHHHHHHHHHHTTSCSSCEEEEEE
T ss_pred             ccceEEEeechhhhhhhhhHHHHHHHHHhCCCCCEEEEEE
Confidence            445589999999875 345566677776666655555554

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=96.88  E-value=0.033  Score=40.04  Aligned_cols=22  Identities=23%  Similarity=0.318  Sum_probs=19.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .|+|+|.+|+|||+|+..+...
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5999999999999999998754

>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=96.85  E-value=0.00055  Score=52.62  Aligned_cols=23  Identities=22%  Similarity=0.236  Sum_probs=20.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||||+|||+++..++...
T Consensus        36 ~~li~G~pGsGKT~l~lq~~~~~   58 (251)
T d1szpa2          36 ITELFGEFRTGKSQLCHTLAVTC   58 (251)
T ss_dssp             EEEEEESTTSSHHHHHHHHTTTT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHh
Confidence            49999999999999999887654

>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=96.84  E-value=0.0055  Score=46.71  Aligned_cols=24  Identities=25%  Similarity=0.235  Sum_probs=21.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.++|+||.+.|||++++.++-..
T Consensus        42 ~~~iiTGpN~~GKSt~lk~i~l~~   65 (234)
T d1wb9a2          42 RMLIITGPNMGGKSTYMRQTALIA   65 (234)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEeccCchhhHHHHHHHHHHH
Confidence            458999999999999999988765

>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=96.84  E-value=0.00053  Score=55.33  Aligned_cols=27  Identities=33%  Similarity=0.412  Sum_probs=23.2

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      +...|-|+||||+|||||+..++..+.
T Consensus        53 ~~~~IgitG~pGaGKSTLi~~l~~~~~   79 (327)
T d2p67a1          53 NTLRLGVTGTPGAGKSTFLEAFGMLLI   79 (327)
T ss_dssp             CSEEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CceEEEeeCCCCCCHHHHHHHHHHHHH
Confidence            334499999999999999999998874

>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=96.84  E-value=0.00011  Score=53.89  Aligned_cols=23  Identities=22%  Similarity=0.381  Sum_probs=20.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      +++.|++|+|||+|+..+...-+
T Consensus         5 ivvvG~~~vGKTsLi~~~~~~~f   27 (177)
T d1kmqa_           5 LVIVGDGACGKTCLLIVNSKDQF   27 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSCC
T ss_pred             EEEECCCCcCHHHHHHHHHhCCC
Confidence            89999999999999998877543

>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=96.83  E-value=0.00059  Score=51.46  Aligned_cols=26  Identities=27%  Similarity=0.234  Sum_probs=22.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCC
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGP  109 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~  109 (294)
                      .++|+||||+|||+++..++......
T Consensus        25 v~~i~G~~GsGKT~l~l~la~~~~~~   50 (242)
T d1n0wa_          25 ITEMFGEFRTGKTQICHTLAVTCQLP   50 (242)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHTTSC
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            49999999999999999999877443

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.83  E-value=0.00031  Score=53.56  Aligned_cols=42  Identities=10%  Similarity=0.194  Sum_probs=30.1

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc--CcceEEEEecCC
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS--KVTRFFFICNYI  195 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~--~~~~ii~~~~~~  195 (294)
                      .++.+|++||.- .|++.....+.+.+.+..  ....+|++|.+.
T Consensus       162 ~~P~lLllDEPTs~LD~~~~~~i~~~l~~l~~~~g~tii~vTHd~  206 (230)
T d1l2ta_         162 NNPPIILADQPTGALDSKTGEKIMQLLKKLNEEDGKTVVVVTHDI  206 (230)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHTTCCEEEEECSCH
T ss_pred             cCCCEEEecCCccccCHHHHHHHHHHHHHHHHhhCCEEEEECCCH
Confidence            567799999964 577877777777777643  356677887653

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.82  E-value=0.0033  Score=47.04  Aligned_cols=39  Identities=23%  Similarity=0.371  Sum_probs=25.2

Q ss_pred             CCcEEEEEeCCCCCC-HHHHHHHHHHHHhhcCcceEEEEe
Q 022641          154 PPYKIIILDEADSMT-EDAQNALRRTMETYSKVTRFFFIC  192 (294)
Q Consensus       154 ~~~~lliiDei~~l~-~~~~~~L~~~l~~~~~~~~ii~~~  192 (294)
                      ..-..+|+||+|.+. .+..+.+..+++..+....+++.|
T Consensus       145 ~~l~~lVlDEaD~ll~~~f~~~i~~I~~~~~~~~Q~~l~S  184 (206)
T d1veca_         145 DHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYS  184 (206)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHHHSCTTCEEEEEE
T ss_pred             cccceEEEeccccccccchHHHHHHHHHhCCCCCEEEEEE
Confidence            445699999999764 334455666666666655555555

>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=96.81  E-value=0.0025  Score=45.79  Aligned_cols=23  Identities=22%  Similarity=0.589  Sum_probs=20.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++++|.+|||||+|+..+...-+
T Consensus         6 ivvvG~~~vGKTsli~r~~~~~f   28 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQGIF   28 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHCCC
T ss_pred             EEEECCCCCCHHHHHHHHHcCCC
Confidence            89999999999999999876543

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.80  E-value=0.00088  Score=51.72  Aligned_cols=24  Identities=21%  Similarity=0.101  Sum_probs=21.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcC
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFG  108 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~  108 (294)
                      ++|+||||+|||+++..++.....
T Consensus        40 ~~i~G~~GsGKT~lalq~~~~~~~   63 (258)
T d1v5wa_          40 TEAFGEFRTGKTQLSHTLCVTAQL   63 (258)
T ss_dssp             EEEECCTTCTHHHHHHHHHHHTTS
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHh
Confidence            999999999999999999987643

>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=96.76  E-value=0.00044  Score=50.60  Aligned_cols=22  Identities=27%  Similarity=0.459  Sum_probs=19.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|+|++|+|||+|...+...
T Consensus        15 kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          15 KLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             EEEEEEETTSSHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3999999999999999888543

>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=96.75  E-value=0.00044  Score=53.50  Aligned_cols=23  Identities=30%  Similarity=0.374  Sum_probs=21.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++|+||||+|||+++..++....
T Consensus        39 ~li~G~pGsGKT~~~lq~~~~~~   61 (254)
T d1pzna2          39 TEVFGEFGSGKTQLAHTLAVMVQ   61 (254)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhh
Confidence            99999999999999999998764

>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=96.75  E-value=0.00052  Score=51.96  Aligned_cols=33  Identities=24%  Similarity=0.248  Sum_probs=25.0

Q ss_pred             HHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHH
Q 022641           70 VRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        70 ~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~  105 (294)
                      ++.|..++.   ....+|.|++|+|||||+.+|...
T Consensus        86 ~~~L~~~l~---~kt~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          86 IEELKEYLK---GKISTMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             HHHHHHHHS---SSEEEEECSTTSSHHHHHHHHSTT
T ss_pred             HhhHHHHhc---CCeEEEECCCCCCHHHHHHhhcch
Confidence            455666563   235899999999999999998543

>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=96.75  E-value=0.00044  Score=53.21  Aligned_cols=22  Identities=36%  Similarity=0.584  Sum_probs=20.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|++|+|||||+..+.+.+
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~~   24 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRYL   24 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Confidence            7899999999999999999876

>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=96.74  E-value=0.00071  Score=53.29  Aligned_cols=22  Identities=41%  Similarity=0.836  Sum_probs=19.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |-|.|++|+||||++..+...+
T Consensus        30 IGi~G~qGSGKSTl~~~l~~~L   51 (286)
T d1odfa_          30 IFFSGPQGSGKSFTSIQIYNHL   51 (286)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEeECCCCCCHHHHHHHHHHHH
Confidence            5689999999999999887776

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.72  E-value=0.00042  Score=53.04  Aligned_cols=43  Identities=9%  Similarity=0.136  Sum_probs=29.2

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc--CcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS--KVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~--~~~~ii~~~~~~~  196 (294)
                      .++.+|++||-- .+++.....+.+.+.+..  ....+|++|.+..
T Consensus       143 ~~P~illlDEPts~LD~~~~~~i~~~i~~l~~~~g~tvi~vtHd~~  188 (240)
T d2onka1         143 IQPRLLLLDEPLSAVDLKTKGVLMEELRFVQREFDVPILHVTHDLI  188 (240)
T ss_dssp             TCCSSBEEESTTSSCCHHHHHHHHHHHHHHHHHHTCCEEEEESCHH
T ss_pred             ccCCceEecCccccCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCHH
Confidence            467799999964 577777777777776543  2455777776543

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=96.69  E-value=0.00053  Score=52.60  Aligned_cols=43  Identities=7%  Similarity=0.160  Sum_probs=30.5

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc--CcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS--KVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~--~~~~ii~~~~~~~  196 (294)
                      .++.+|++||.- .+++.....+.+.+.+..  ....+|++|.+..
T Consensus       156 ~~P~iLllDEPt~~LD~~~~~~i~~~l~~l~~~~g~tvi~vTHd~~  201 (240)
T d1g2912         156 RKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIYVTHDQV  201 (240)
T ss_dssp             TCCSEEEEECTTTTSCHHHHHHHHHHHHHHHHHHTCEEEEEESCHH
T ss_pred             cCCCEEEecCCCcccCHHHHHHHHHHHHHHHhccCCEEEEEcCCHH
Confidence            467799999964 578877777777776543  2566788886643

>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=96.68  E-value=0.0005  Score=49.40  Aligned_cols=23  Identities=30%  Similarity=0.408  Sum_probs=20.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+|+||||||+|+..+...-
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            38999999999999999987653

>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=96.68  E-value=0.0017  Score=47.14  Aligned_cols=22  Identities=27%  Similarity=0.400  Sum_probs=19.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++.|.+|+|||+++..+...-
T Consensus         8 I~lvG~~~vGKTsll~~~~~~~   29 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEKK   29 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999887643

>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=96.67  E-value=0.00022  Score=52.45  Aligned_cols=22  Identities=23%  Similarity=0.306  Sum_probs=19.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|.|++|+|||+|+..+...-
T Consensus         5 ivliG~~~vGKTsli~r~~~~~   26 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKDC   26 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7999999999999999887754

>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=96.66  E-value=0.0012  Score=53.07  Aligned_cols=24  Identities=38%  Similarity=0.455  Sum_probs=21.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+-|+||||+||||++..+++.+
T Consensus        52 ~~igitG~pGaGKSTli~~l~~~~   75 (323)
T d2qm8a1          52 IRVGITGVPGVGKSTTIDALGSLL   75 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEeeeCCCCCCHHHHHHHHHHHH
Confidence            349999999999999999999876

>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=96.66  E-value=0.00049  Score=51.47  Aligned_cols=24  Identities=42%  Similarity=0.524  Sum_probs=21.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|.||.|+||||+++.++..+
T Consensus        28 ei~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          28 NVVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCChHHHHHHHHhccc
Confidence            358999999999999999998765

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=96.65  E-value=0.0058  Score=46.20  Aligned_cols=23  Identities=30%  Similarity=0.262  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|+||...|||++++.++-..
T Consensus        37 ~~iiTGpN~~GKSt~lk~i~l~~   59 (224)
T d1ewqa2          37 LVLITGPNMAGKSTFLRQTALIA   59 (224)
T ss_dssp             EEEEESCSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCccccchhhhhhHHHH
Confidence            48999999999999999887765

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.63  E-value=0.00056  Score=52.61  Aligned_cols=24  Identities=29%  Similarity=0.328  Sum_probs=22.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+||||+|||+++..++..+.
T Consensus        28 l~li~G~pGsGKT~l~~qia~~~~   51 (242)
T d1tf7a2          28 IILATGATGTGKTLLVSRFVENAC   51 (242)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHH
Confidence            499999999999999999999874

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.63  E-value=0.0076  Score=45.51  Aligned_cols=41  Identities=22%  Similarity=0.347  Sum_probs=27.2

Q ss_pred             CCCcEEEEEeCCCCCC-HHHHHHHHHHHHhhcCcceEEEEec
Q 022641          153 CPPYKIIILDEADSMT-EDAQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       153 ~~~~~lliiDei~~l~-~~~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      ...-..+++||+|.+- ....+.+..+++..+....+++.+.
T Consensus       157 ~~~l~~lVlDEaD~ll~~~f~~~i~~I~~~l~~~~Q~ilfSA  198 (222)
T d2j0sa1         157 TRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISA  198 (222)
T ss_dssp             CTTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEES
T ss_pred             cccceeeeecchhHhhhcCcHHHHHHHHHhCCCCCEEEEEEE
Confidence            3455699999999764 3345566677776666666666553

>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=96.62  E-value=0.0006  Score=51.09  Aligned_cols=25  Identities=24%  Similarity=0.477  Sum_probs=22.1

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|.++|+|+||+|||+|+..|...-
T Consensus         3 ~p~V~lvG~~n~GKTSLln~l~~~~   27 (209)
T d1nrjb_           3 QPSIIIAGPQNSGKTSLLTLLTTDS   27 (209)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4679999999999999999998764

>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=96.62  E-value=0.0006  Score=48.68  Aligned_cols=22  Identities=32%  Similarity=0.462  Sum_probs=19.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+|+||+|||+|+..+...-
T Consensus         3 I~liG~~nvGKSSLln~l~~~~   24 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKNDR   24 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            8999999999999999988753

>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=96.59  E-value=0.00062  Score=49.55  Aligned_cols=22  Identities=23%  Similarity=0.439  Sum_probs=19.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|++|||||+|+..+...-
T Consensus         6 ivvvG~~~vGKTsli~r~~~~~   27 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDKR   27 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHhcCC
Confidence            8999999999999999887653

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=96.58  E-value=0.006  Score=48.22  Aligned_cols=16  Identities=31%  Similarity=0.358  Sum_probs=13.9

Q ss_pred             CCcEEEECCCCCCHHH
Q 022641           82 CPHMLFYGPPGTGKTT   97 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~   97 (294)
                      .+++++.+|+|+|||+
T Consensus         9 ~~~~lv~~~TGsGKT~   24 (305)
T d2bmfa2           9 KRLTIMDLHPGAGKTK   24 (305)
T ss_dssp             TCEEEECCCTTSSTTT
T ss_pred             CCcEEEEECCCCCHHH
Confidence            3479999999999995

>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=96.57  E-value=0.00069  Score=49.13  Aligned_cols=22  Identities=32%  Similarity=0.326  Sum_probs=17.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|++|+|||+|+..+...-
T Consensus         6 i~vvG~~~vGKTsli~~~~~~~   27 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTGE   27 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC---
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999998876543

>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=96.56  E-value=0.0005  Score=52.73  Aligned_cols=24  Identities=21%  Similarity=0.188  Sum_probs=21.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|.||+|+||||+++.++...
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          32 QIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCc
Confidence            459999999999999999997754

>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=96.56  E-value=0.0007  Score=50.79  Aligned_cols=23  Identities=26%  Similarity=0.303  Sum_probs=20.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +|+|.|+||+|||+|+..+...-
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~~~   24 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLTGQ   24 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            69999999999999999998753

>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=96.56  E-value=0.0014  Score=52.12  Aligned_cols=22  Identities=32%  Similarity=0.391  Sum_probs=20.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |.|.|++|+||||+++.|...+
T Consensus        83 IGIaG~sgSGKSTla~~L~~lL  104 (308)
T d1sq5a_          83 ISIAGSVAVGKSTTARVLQALL  104 (308)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEeCCCCCCCcHHHHHHHHHH
Confidence            7899999999999999999987

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.56  E-value=0.0043  Score=46.38  Aligned_cols=39  Identities=18%  Similarity=0.249  Sum_probs=25.0

Q ss_pred             CcEEEEEeCCCCCCHH-HHHHHHHHHHhhcCcceEEEEec
Q 022641          155 PYKIIILDEADSMTED-AQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       155 ~~~lliiDei~~l~~~-~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      .-..++|||+|.+... ..+.+..++...+....+++.|.
T Consensus       147 ~l~~lViDEad~ll~~~f~~~v~~I~~~~~~~~Q~il~SA  186 (209)
T d1q0ua_         147 TAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSA  186 (209)
T ss_dssp             GCCEEEECSHHHHHHTTCHHHHHHHHHTSCTTCEEEEEES
T ss_pred             cceEEEEeecccccccccHHHHHHHHHHCCCCCEEEEEEc
Confidence            4458999999987543 23445556666566666666553

>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=96.54  E-value=0.0018  Score=51.92  Aligned_cols=19  Identities=26%  Similarity=0.356  Sum_probs=15.9

Q ss_pred             cEEEECCCCCCHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAI  102 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~l  102 (294)
                      ++++.|+||||||+++-.-
T Consensus        26 ~~lV~g~aGSGKTt~l~~r   44 (318)
T d1pjra1          26 PLLIMAGAGSGKTRVLTHR   44 (318)
T ss_dssp             CEEEEECTTSCHHHHHHHH
T ss_pred             CEEEEecCCccHHHHHHHH
Confidence            5899999999999877553

>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=96.54  E-value=0.00025  Score=52.37  Aligned_cols=23  Identities=26%  Similarity=0.400  Sum_probs=20.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++|+|.+|+|||+|+..+...-+
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~~f   34 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYANDAF   34 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHSSC
T ss_pred             EEEECCCCCCHHHHHHHHhhCCC
Confidence            89999999999999999876543

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=96.53  E-value=0.00052  Score=52.22  Aligned_cols=43  Identities=19%  Similarity=0.247  Sum_probs=30.6

Q ss_pred             CCcEEEEEeCCC-CCCHHHHHHHHHHHHhhc--CcceEEEEecCCc
Q 022641          154 PPYKIIILDEAD-SMTEDAQNALRRTMETYS--KVTRFFFICNYIS  196 (294)
Q Consensus       154 ~~~~lliiDei~-~l~~~~~~~L~~~l~~~~--~~~~ii~~~~~~~  196 (294)
                      .++.+|++||-- .+++.....+.+.+.+..  ....+|++|.+..
T Consensus       144 ~~P~iLllDEPts~LD~~~~~~i~~~l~~l~~~~g~tii~vtHd~~  189 (229)
T d3d31a2         144 TNPKILLLDEPLSALDPRTQENAREMLSVLHKKNKLTVLHITHDQT  189 (229)
T ss_dssp             SCCSEEEEESSSTTSCHHHHHHHHHHHHHHHHHTTCEEEEEESCHH
T ss_pred             ccCCceeecCCCcCCCHHHHHHHHHHHHHHHhcCCcEEEEEcCCHH
Confidence            567899999964 578877777777776542  3556777886654

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.49  E-value=0.024  Score=42.09  Aligned_cols=41  Identities=20%  Similarity=0.268  Sum_probs=27.1

Q ss_pred             CCCcEEEEEeCCCCCC--HHHHHHHHHHHHhhcCcceEEEEec
Q 022641          153 CPPYKIIILDEADSMT--EDAQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       153 ~~~~~lliiDei~~l~--~~~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      ..+-..+++||+|.+-  ....+.+..+++..+....+++.+.
T Consensus       143 l~~l~~lVlDEaD~ll~~~~~~~~i~~I~~~~~~~~Q~il~SA  185 (207)
T d1t6na_         143 LKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSA  185 (207)
T ss_dssp             CTTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEES
T ss_pred             ccccceeehhhhhhhhhcCCcHHHHHHHHHhCCCCCEEEEEee
Confidence            3455699999999763  2455566666766666666666553

>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=96.47  E-value=0.00077  Score=49.84  Aligned_cols=20  Identities=30%  Similarity=0.405  Sum_probs=17.6

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~  104 (294)
                      +.|+|++|+||||+|..+..
T Consensus         6 IgitG~~gSGKstva~~l~~   25 (191)
T d1uf9a_           6 IGITGNIGSGKSTVAALLRS   25 (191)
T ss_dssp             EEEEECTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            66999999999999999843

>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=96.46  E-value=0.0008  Score=53.59  Aligned_cols=19  Identities=26%  Similarity=0.308  Sum_probs=15.7

Q ss_pred             CcEEEECCCCCCHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALA  101 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~  101 (294)
                      .+++|.|+||||||+++-.
T Consensus        15 ~~~lI~g~aGTGKTt~l~~   33 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVITN   33 (306)
T ss_dssp             SEEEECCCTTSCHHHHHHH
T ss_pred             CCEEEEeeCCccHHHHHHH
Confidence            3589999999999987543

>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=96.46  E-value=0.00087  Score=48.50  Aligned_cols=22  Identities=27%  Similarity=0.395  Sum_probs=19.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|++|+|||+|+..+...-
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~~   29 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADDS   29 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHcCC
Confidence            8999999999999999987654

>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=96.46  E-value=0.00076  Score=48.53  Aligned_cols=22  Identities=27%  Similarity=0.382  Sum_probs=19.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|.|++|+|||+|+..+...
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHcCC
Confidence            4899999999999999988654

>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=96.45  E-value=0.00088  Score=48.29  Aligned_cols=22  Identities=18%  Similarity=0.314  Sum_probs=19.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+|++|+|||+++..+...-
T Consensus         7 ivlvG~~~vGKTsli~~~~~~~   28 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEKK   28 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999987654

>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=96.42  E-value=0.00097  Score=48.21  Aligned_cols=22  Identities=18%  Similarity=0.471  Sum_probs=20.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|++|||||+|+..+...-
T Consensus         5 i~lvG~~~vGKTsli~r~~~~~   26 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTKR   26 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            8999999999999999998754

>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=96.41  E-value=0.00049  Score=52.76  Aligned_cols=25  Identities=36%  Similarity=0.353  Sum_probs=22.1

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ...+.|.||+|+||||+++.++...
T Consensus        31 Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          31 GERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcCc
Confidence            3469999999999999999998865

>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=96.41  E-value=0.0004  Score=51.70  Aligned_cols=23  Identities=30%  Similarity=0.299  Sum_probs=21.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|+|.|+.|+||||+++.|++.+
T Consensus        11 ~I~ieG~~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGGT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999887

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.38  E-value=0.0056  Score=42.17  Aligned_cols=116  Identities=13%  Similarity=0.062  Sum_probs=54.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCC-CcchhHHHHHHHHHHh-hhcccCccCCCCCCCCcEEEEEe
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASD-DRGINVVRTKIKTFAA-VAVGSGQRRGGYPCPPYKIIILD  162 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~lliiD  162 (294)
                      -+++||=.+|||+-+-..++.....   +..++.+++.. .+.............. ....... .......+.++|+||
T Consensus         5 ~li~GpMfsGKTt~Li~~~~~~~~~---g~~v~~ikp~~D~R~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~d~I~ID   80 (133)
T d1xbta1           5 QVILGPMFSGKSTELMRRVRRFQIA---QYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLR-DVAQEALGVAVIGID   80 (133)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTT---TCCEEEEEETTCCC--------------CEEESSGG-GGHHHHHTCSEEEES
T ss_pred             EEEEecccCHHHHHHHHHHHHHHHc---CCcEEEEecccccCCcceeeecCCCcceeeeeechh-hhhhhhcccceEEee
Confidence            5789999999999887777665321   33444454332 2221111100000000 0000000 000001235699999


Q ss_pred             CCCCCCHHHHHHHHHHHHhhcCcceEEEEe------cCCcccchHhhccccE
Q 022641          163 EADSMTEDAQNALRRTMETYSKVTRFFFIC------NYISRIIEPLASRCAK  208 (294)
Q Consensus       163 ei~~l~~~~~~~L~~~l~~~~~~~~ii~~~------~~~~~~~~~l~~r~~~  208 (294)
                      |++.++ +. ..+...+..  ....|++.+      ..++.-...|...+..
T Consensus        81 EaQFf~-dl-~~~~~~~~~--~~~~Viv~GLd~Df~~~~F~~~~~Ll~~Ad~  128 (133)
T d1xbta1          81 EGQFFP-DI-VEFCEAMAN--AGKTVIVAALDGTFQRKPFGAILNLVPLAES  128 (133)
T ss_dssp             SGGGCT-TH-HHHHHHHHH--TTCEEEEECCSBCTTSSBCTTGGGGGGGCSE
T ss_pred             hhHHHH-HH-HHHHHHHHh--cCCcEEEEEeccccccCcchhHHHHHHhcCE
Confidence            999996 33 334444444  334455555      2334444556666553

>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=96.38  E-value=0.001  Score=47.78  Aligned_cols=24  Identities=33%  Similarity=0.346  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|.|++|+|||+|+..+...-+
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~~~~   27 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIASGQF   27 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCCC
Confidence            389999999999999999876543

>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=96.37  E-value=0.0011  Score=47.88  Aligned_cols=22  Identities=23%  Similarity=0.345  Sum_probs=19.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+|.+|||||+|+..+...-
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~~   27 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCENK   27 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999987644

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.36  E-value=0.00095  Score=52.58  Aligned_cols=24  Identities=29%  Similarity=0.474  Sum_probs=21.6

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|+||+|+|||||++.++..+
T Consensus        63 e~vaivG~nGsGKSTLl~~i~Gl~   86 (281)
T d1r0wa_          63 EMLAITGSTGSGKTSLLMLILGEL   86 (281)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCChHHHHHHHHhCCC
Confidence            359999999999999999998766

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=96.35  E-value=0.0052  Score=48.32  Aligned_cols=41  Identities=10%  Similarity=0.091  Sum_probs=31.0

Q ss_pred             hcccHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           63 VAHQEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        63 ~~g~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.-++-..+.+..++..++   .++.-|+|+|||.++..+++.+
T Consensus       112 ~~~rdyQ~~av~~~l~~~~---~il~~pTGsGKT~i~~~i~~~~  152 (282)
T d1rifa_         112 IEPHWYQKDAVFEGLVNRR---RILNLPTSAGRSLIQALLARYY  152 (282)
T ss_dssp             CCCCHHHHHHHHHHHHHSE---EEECCCTTSCHHHHHHHHHHHH
T ss_pred             cccchHHHHHHHHHHhcCC---ceeEEEcccCccHHHHHHHHHh
Confidence            3455666677777776654   7888899999999988888665

>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=96.34  E-value=0.0004  Score=51.54  Aligned_cols=22  Identities=18%  Similarity=0.246  Sum_probs=19.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++.|++|+|||+|+..+...-
T Consensus         6 vvllG~~~vGKTSli~r~~~~~   27 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTNK   27 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999887654

>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=96.34  E-value=0.0012  Score=47.94  Aligned_cols=22  Identities=36%  Similarity=0.635  Sum_probs=19.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|.|++|+|||++|..+...
T Consensus        16 gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          16 GVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHc
Confidence            4999999999999999888765

>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=96.32  E-value=0.0011  Score=48.19  Aligned_cols=22  Identities=18%  Similarity=0.369  Sum_probs=19.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++.|++|+|||+|+..+...-
T Consensus         7 i~vvG~~~vGKTsLi~~~~~~~   28 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTRNE   28 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999887643

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=96.31  E-value=0.0017  Score=46.09  Aligned_cols=52  Identities=10%  Similarity=0.093  Sum_probs=36.3

Q ss_pred             CCCcEEEEEeCCCCCCH---HHHHHHHHHHHhhcCcceEEEEecCCcccchHhhcccc
Q 022641          153 CPPYKIIILDEADSMTE---DAQNALRRTMETYSKVTRFFFICNYISRIIEPLASRCA  207 (294)
Q Consensus       153 ~~~~~lliiDei~~l~~---~~~~~L~~~l~~~~~~~~ii~~~~~~~~~~~~l~~r~~  207 (294)
                      ....++||+||+...-.   -..+.+.++++..+...-+|+|++...   +.+..+..
T Consensus        92 ~~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~p---~~L~e~AD  146 (157)
T d1g5ta_          92 DPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCH---RDILDLAD  146 (157)
T ss_dssp             CTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCC---HHHHHHCS
T ss_pred             cCccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCCC---HHHHHhcc
Confidence            34578999999854211   123467778888899999999997654   56666655

>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=96.31  E-value=0.0011  Score=48.73  Aligned_cols=21  Identities=33%  Similarity=0.464  Sum_probs=18.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~  105 (294)
                      ++|.|++|||||+|+..+...
T Consensus         8 i~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            899999999999999988643

>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=96.29  E-value=0.00099  Score=48.27  Aligned_cols=22  Identities=27%  Similarity=0.483  Sum_probs=20.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+|++|+|||+|+..+...-
T Consensus         8 i~lvG~~~vGKTsLi~~l~~~~   29 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQGL   29 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999998754

>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=96.29  E-value=0.0011  Score=51.39  Aligned_cols=25  Identities=24%  Similarity=0.260  Sum_probs=21.5

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ...+.|+||+|+||||+++.++...
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcCc
Confidence            3469999999999999999998644

>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=96.28  E-value=0.0013  Score=49.38  Aligned_cols=24  Identities=29%  Similarity=0.376  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      -|+|.|+.|+||||+++.|++.+.
T Consensus         4 fIviEG~dGsGKsT~~~~L~~~L~   27 (210)
T d4tmka_           4 YIVIEGLEGAGKTTARNVVVETLE   27 (210)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            588999999999999999999873

>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=96.28  E-value=0.0013  Score=47.77  Aligned_cols=22  Identities=23%  Similarity=0.410  Sum_probs=19.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|++|+|||+|+..+...-
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~~   26 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVNDK   26 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHcCC
Confidence            8999999999999999987643

>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=96.27  E-value=0.0012  Score=47.70  Aligned_cols=22  Identities=23%  Similarity=0.484  Sum_probs=19.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|++|||||+|+..+...-
T Consensus         5 i~viG~~~vGKTsLi~r~~~~~   26 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKGT   26 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTCC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            8999999999999999887543

>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=96.27  E-value=0.0014  Score=49.19  Aligned_cols=24  Identities=21%  Similarity=0.335  Sum_probs=21.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      -|+|.|+.|+||||+++.|++.+.
T Consensus         5 lI~ieG~dGsGKsT~~~~L~~~L~   28 (209)
T d1nn5a_           5 LIVLEGVDRAGKSTQSRKLVEALC   28 (209)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            478889999999999999999874

>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=96.26  E-value=0.0014  Score=49.04  Aligned_cols=22  Identities=23%  Similarity=0.348  Sum_probs=20.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |+|.|+.|+||||+++.|.+.+
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l   24 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAF   24 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7889999999999999999987

>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=96.26  E-value=0.0011  Score=48.05  Aligned_cols=22  Identities=18%  Similarity=0.440  Sum_probs=19.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|+|.+|||||+|+..+...-
T Consensus         8 i~lvG~~~vGKTsLi~r~~~~~   29 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQSY   29 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            8999999999999999987643

>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=96.25  E-value=0.0014  Score=47.10  Aligned_cols=22  Identities=18%  Similarity=0.295  Sum_probs=19.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++.|++|+|||+|+..+...-
T Consensus         5 v~liG~~~vGKTsLl~~~~~~~   26 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAGR   26 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999987653

>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=96.22  E-value=0.0014  Score=47.48  Aligned_cols=21  Identities=29%  Similarity=0.493  Sum_probs=18.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~  105 (294)
                      |+|+|++|+|||+|+..|...
T Consensus         3 V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           3 VLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999743

>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=96.21  E-value=0.0015  Score=47.06  Aligned_cols=23  Identities=22%  Similarity=0.468  Sum_probs=20.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++|+|.+|||||+|+..+...-+
T Consensus         7 i~lvG~~~vGKTsli~rl~~~~f   29 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVEDSF   29 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSCC
T ss_pred             EEEECCCCcCHHHHHHHHHhCCC
Confidence            89999999999999999876543

>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=96.19  E-value=0.00084  Score=52.81  Aligned_cols=26  Identities=19%  Similarity=0.374  Sum_probs=20.0

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.+.|.++|++|+||||+++.+.+.+
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~   28 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIF   28 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHH
Confidence            44679999999999999999998876

>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=96.18  E-value=0.0012  Score=50.61  Aligned_cols=24  Identities=29%  Similarity=0.227  Sum_probs=21.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|.|+||+|||+++..++..+.
T Consensus        36 l~~i~G~~G~GKT~~~l~~a~~~~   59 (258)
T d2i1qa2          36 VTEFAGVFGSGKTQIMHQSCVNLQ   59 (258)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999998874

>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=96.16  E-value=0.0013  Score=47.36  Aligned_cols=22  Identities=23%  Similarity=0.463  Sum_probs=19.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++.|++|+|||+|+..+...-
T Consensus         5 i~vvG~~~vGKTSli~~l~~~~   26 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVEDK   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999987643

>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=96.15  E-value=0.0014  Score=49.04  Aligned_cols=19  Identities=37%  Similarity=0.384  Sum_probs=17.2

Q ss_pred             EEEECCCCCCHHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAIA  103 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la  103 (294)
                      +-|+|++|+||||+++.+.
T Consensus         5 IgITG~igSGKStv~~~l~   23 (205)
T d1jjva_           5 VGLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEEECSTTSCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            5689999999999999885

>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=96.15  E-value=0.0016  Score=47.03  Aligned_cols=22  Identities=23%  Similarity=0.418  Sum_probs=19.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|++|+|||+++..+...-
T Consensus         9 i~vvG~~~vGKTsli~~~~~~~   30 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKDGA   30 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999887643

>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=96.14  E-value=0.0014  Score=48.55  Aligned_cols=22  Identities=18%  Similarity=0.406  Sum_probs=20.0

Q ss_pred             CcEEEECCCCCCHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~  104 (294)
                      +.++|+|+||+|||||...|..
T Consensus        24 ~~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          24 PEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHhcC
Confidence            4699999999999999999974

>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=96.13  E-value=0.0016  Score=47.00  Aligned_cols=21  Identities=33%  Similarity=0.593  Sum_probs=18.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~  105 (294)
                      +++.|++|+|||+|+..+...
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            789999999999999988654

>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=96.13  E-value=0.0017  Score=47.60  Aligned_cols=22  Identities=23%  Similarity=0.409  Sum_probs=19.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|.+|||||+|+..+...-
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~~   26 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNKK   26 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999887643

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.13  E-value=0.022  Score=42.31  Aligned_cols=41  Identities=24%  Similarity=0.344  Sum_probs=27.0

Q ss_pred             CCCcEEEEEeCCCCC-CHHHHHHHHHHHHhhcCcceEEEEec
Q 022641          153 CPPYKIIILDEADSM-TEDAQNALRRTMETYSKVTRFFFICN  193 (294)
Q Consensus       153 ~~~~~lliiDei~~l-~~~~~~~L~~~l~~~~~~~~ii~~~~  193 (294)
                      ..+-..+++||+|.+ +......+.++++..+....+++.|.
T Consensus       143 ~~~l~~lViDEad~l~~~~~~~~i~~I~~~~~~~~Q~i~~SA  184 (208)
T d1hv8a1         143 LKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSA  184 (208)
T ss_dssp             TTSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECS
T ss_pred             cccCcEEEEEChHHhhcCCChHHHHHHHHhCCCCCeEEEEEc
Confidence            345569999999975 33344556677776666666666553

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=96.12  E-value=0.024  Score=39.12  Aligned_cols=35  Identities=11%  Similarity=0.078  Sum_probs=23.4

Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEe
Q 022641          155 PYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFIC  192 (294)
Q Consensus       155 ~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~  192 (294)
                      +.++|+|||++.++. ....+...+..  ....|++.+
T Consensus        79 ~~dvI~IDE~QFf~d-~i~~~~~~~~~--~g~~Viv~G  113 (139)
T d2b8ta1          79 ETKVIGIDEVQFFDD-RICEVANILAE--NGFVVIISG  113 (139)
T ss_dssp             TCCEEEECSGGGSCT-HHHHHHHHHHH--TTCEEEEEC
T ss_pred             CcCEEEechhhhcch-hHHHHHHHHHh--cCceEEEEE
Confidence            457999999999974 45556666654  233455555

>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=96.11  E-value=0.0035  Score=48.69  Aligned_cols=40  Identities=23%  Similarity=0.287  Sum_probs=29.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRG  126 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~  126 (294)
                      .+.|+||||+|||+++..++..+..+   +..++.++......
T Consensus        56 itei~G~~gsGKTtl~l~~~~~~q~~---g~~~vyidtE~~~~   95 (263)
T d1u94a1          56 IVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHALD   95 (263)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCCC
T ss_pred             EEEEecCCCcHHHHHHHHHHHHHHcC---CCEEEEEccccccC
Confidence            48999999999999999999887543   23455555554433

>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=96.10  E-value=0.0017  Score=46.81  Aligned_cols=22  Identities=18%  Similarity=0.407  Sum_probs=19.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++.|++|+|||+|+..+...-
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~~   27 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999887654

>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=96.10  E-value=0.0017  Score=47.19  Aligned_cols=22  Identities=27%  Similarity=0.534  Sum_probs=19.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|++|+|||+++..+...-
T Consensus        10 i~vvG~~~vGKTsli~~l~~~~   31 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDDT   31 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            8999999999999999987644

>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=96.08  E-value=0.0019  Score=48.47  Aligned_cols=22  Identities=41%  Similarity=0.496  Sum_probs=18.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+|++|+||||+++.+. .+
T Consensus         5 iIgitG~igSGKStv~~~l~-~~   26 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA-DL   26 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH-HT
T ss_pred             EEEEECCCcCCHHHHHHHHH-HC
Confidence            36799999999999999886 44

>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=96.08  E-value=0.0019  Score=46.89  Aligned_cols=22  Identities=18%  Similarity=0.338  Sum_probs=19.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++++|++|+|||+++..+...-
T Consensus         9 I~vvG~~~vGKSSli~~~~~~~   30 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTNK   30 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            8999999999999998887643

>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=96.06  E-value=0.0013  Score=47.81  Aligned_cols=22  Identities=32%  Similarity=0.575  Sum_probs=19.6

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|.||+|+|||++|..+...
T Consensus        17 gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          17 GVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHc
Confidence            4999999999999999888754

>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=96.05  E-value=0.0014  Score=47.26  Aligned_cols=22  Identities=36%  Similarity=0.604  Sum_probs=19.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|.|++|+|||+++-.+.+.
T Consensus        17 gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          17 GVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHc
Confidence            5999999999999999888765

>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=96.02  E-value=0.002  Score=49.01  Aligned_cols=22  Identities=32%  Similarity=0.431  Sum_probs=18.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .++|+|+||+|||+++..++..
T Consensus        28 ~~~I~G~~G~GKT~la~~~~~~   49 (242)
T d1tf7a1          28 STLVSGTSGTGKTLFSIQFLYN   49 (242)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHH
Confidence            4999999999999999776654

>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=96.00  E-value=0.002  Score=46.68  Aligned_cols=21  Identities=33%  Similarity=0.458  Sum_probs=18.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~  105 (294)
                      ++|.|++|+|||+|+..+...
T Consensus         6 v~lvG~~~vGKTsLi~~~~~~   26 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAGV   26 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999988643

>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=96.00  E-value=0.0015  Score=47.48  Aligned_cols=20  Identities=35%  Similarity=0.469  Sum_probs=18.2

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~  104 (294)
                      ++++|++|+|||+|+..+..
T Consensus        19 I~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          19 ILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             EEEEESTTSSHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            99999999999999988754

>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=95.95  E-value=0.0018  Score=46.91  Aligned_cols=22  Identities=27%  Similarity=0.366  Sum_probs=19.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~  104 (294)
                      -.++++|++|+|||+++..+..
T Consensus        13 ~kIvlvG~~~vGKTSli~rl~~   34 (173)
T d1e0sa_          13 MRILMLGLDAAGKTTILYKLKL   34 (173)
T ss_dssp             EEEEEEEETTSSHHHHHHHTTC
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            3599999999999999998754

>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=95.95  E-value=0.0018  Score=49.68  Aligned_cols=25  Identities=16%  Similarity=0.147  Sum_probs=22.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .-|+|-|+-|+||||+++.|++.+.
T Consensus         3 k~IviEG~~GsGKST~~~~L~~~l~   27 (241)
T d2ocpa1           3 RRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHh
Confidence            3589999999999999999999884

>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=95.94  E-value=0.0025  Score=48.03  Aligned_cols=26  Identities=31%  Similarity=0.308  Sum_probs=23.2

Q ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           81 NCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        81 ~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++.-|.|.|+-|+||||+++.|++.+
T Consensus         2 kGk~I~iEG~DGsGKST~~~~L~~~L   27 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQCNILYKKL   27 (214)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CeEEEEEECCCCCcHHHHHHHHHHHH
Confidence            34468999999999999999999988

>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=95.93  E-value=0.0024  Score=46.06  Aligned_cols=22  Identities=18%  Similarity=0.493  Sum_probs=19.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++.|++|||||+++..+...-
T Consensus         7 i~lvG~~~vGKTsll~~~~~~~   28 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQKI   28 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7999999999999999988754

>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=95.92  E-value=0.0018  Score=47.30  Aligned_cols=20  Identities=35%  Similarity=0.566  Sum_probs=18.0

Q ss_pred             cEEEECCCCCCHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIA  103 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la  103 (294)
                      .++++|++|+|||+|+..+.
T Consensus        19 KI~lvG~~~vGKTsLi~~l~   38 (182)
T d1moza_          19 RILILGLDGAGKTTILYRLQ   38 (182)
T ss_dssp             EEEEEEETTSSHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            39999999999999998774

>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=95.89  E-value=0.0017  Score=47.40  Aligned_cols=22  Identities=23%  Similarity=0.469  Sum_probs=19.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .|+|+|+||+|||||..+|..+
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3899999999999999999753

>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=95.84  E-value=0.0022  Score=50.12  Aligned_cols=23  Identities=35%  Similarity=0.483  Sum_probs=20.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+|+|+||+|||+++..++..+
T Consensus        31 ~~~i~G~~G~GKS~l~l~la~~i   53 (274)
T d1nlfa_          31 VGALVSPGGAGKSMLALQLAAQI   53 (274)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            48899999999999999998875

>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=95.82  E-value=0.0022  Score=47.43  Aligned_cols=22  Identities=27%  Similarity=0.525  Sum_probs=19.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|.|++|+|||+|+..+...-
T Consensus         9 ivvvG~~~vGKTsli~~l~~~~   30 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDDT   30 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHhhCC
Confidence            8999999999999999887643

>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=95.78  E-value=0.00095  Score=51.17  Aligned_cols=23  Identities=17%  Similarity=0.174  Sum_probs=21.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      -|+|.|+-|+||||+++.|++.+
T Consensus         4 ~I~ieG~dGsGKST~~~~L~~~l   26 (241)
T d1p5zb_           4 KISIEGNIAAGKSTFVNILKQLC   26 (241)
T ss_dssp             EEEEECSTTSSHHHHHTTTGGGC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            48999999999999999999887

>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=95.76  E-value=0.0015  Score=47.33  Aligned_cols=21  Identities=29%  Similarity=0.578  Sum_probs=8.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~  105 (294)
                      ++|.|.+|||||+|+..+...
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999887754

>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=95.72  E-value=0.0029  Score=48.46  Aligned_cols=23  Identities=30%  Similarity=0.322  Sum_probs=20.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|.|+|+.|+||||+|..|+..+
T Consensus         3 iIgiTG~igSGKsTva~~l~e~~   25 (241)
T d1deka_           3 LIFLSGVKRSGKDTTADFIMSNY   25 (241)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            37899999999999999998875

>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=0.0037  Score=48.91  Aligned_cols=23  Identities=26%  Similarity=0.242  Sum_probs=20.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      -++|.|+||+|||+++..++..+
T Consensus        37 l~vi~G~~G~GKT~~~~~la~~~   59 (277)
T d1cr2a_          37 VIMVTSGSGMGKSTFVRQQALQW   59 (277)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHhh
Confidence            48999999999999999998764

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=95.63  E-value=0.017  Score=39.96  Aligned_cols=22  Identities=18%  Similarity=0.286  Sum_probs=18.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      -+++||=.+|||+-+-..++.+
T Consensus        10 ~lI~GpMfSGKTteLi~~~~~~   31 (141)
T d1xx6a1          10 EVIVGPMYSGKSEELIRRIRRA   31 (141)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEeccccHHHHHHHHHHHHh
Confidence            5789999999999887777665

>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=95.62  E-value=0.065  Score=41.32  Aligned_cols=24  Identities=29%  Similarity=0.380  Sum_probs=21.4

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +|+.+.|..|+|||||+.++....
T Consensus         3 RNv~iiGh~~~GKTtL~e~ll~~~   26 (267)
T d2dy1a2           3 RTVALVGHAGSGKTTLTEALLYKT   26 (267)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             eEEEEEcCCCCcHHHHHHHHHHHc
Confidence            479999999999999999997654

>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=95.61  E-value=0.0069  Score=47.33  Aligned_cols=36  Identities=33%  Similarity=0.447  Sum_probs=28.4

Q ss_pred             HHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           72 VLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        72 ~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+..-+.......++++|--|+||||++..+|..+.
T Consensus        10 ~~~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~~lA   45 (279)
T d1ihua2          10 ALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLA   45 (279)
T ss_dssp             HHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            344455566666789999999999999999988874

>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=95.54  E-value=0.0027  Score=46.26  Aligned_cols=22  Identities=23%  Similarity=0.397  Sum_probs=19.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~  104 (294)
                      ++|.|+|.||+|||||+..|..
T Consensus         2 ~~VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           2 ADVGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             CSEEEECCGGGCHHHHHHHHCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4689999999999999999864

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.54  E-value=0.0098  Score=46.17  Aligned_cols=41  Identities=24%  Similarity=0.278  Sum_probs=28.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcch
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGI  127 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~  127 (294)
                      ...|+||+|+|||+++..++......   +..++.++.....+.
T Consensus        62 i~e~~G~~~~GKT~l~l~~~~~~q~~---g~~~vyIDtE~~~~~  102 (269)
T d1mo6a1          62 VIEIYGPESSGKTTVALHAVANAQAA---GGVAAFIDAEHALDP  102 (269)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHHHHT---TCEEEEEESSCCCCH
T ss_pred             eEEEecCCCcHHHHHHHHHHHHHhcC---CCEEEEEECCccCCH
Confidence            38999999999999998888776433   334555665554443

>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=95.51  E-value=0.0036  Score=46.22  Aligned_cols=18  Identities=28%  Similarity=0.466  Sum_probs=17.5

Q ss_pred             EEEECCCCCCHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAI  102 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~l  102 (294)
                      ++|.|.+|+|||+++..+
T Consensus         5 ivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            899999999999999998

>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=95.41  E-value=0.0033  Score=45.94  Aligned_cols=22  Identities=23%  Similarity=0.348  Sum_probs=19.0

Q ss_pred             CcEEEECCCCCCHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~  104 (294)
                      ..|.|+|+||+|||+|...|..
T Consensus         2 ~~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           2 ADVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CCEEEESSTTSSHHHHHHHSEE
T ss_pred             CeEEEECCCCCCHHHHHHHHhC
Confidence            3589999999999999988753

>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=95.36  E-value=0.00074  Score=51.27  Aligned_cols=23  Identities=35%  Similarity=0.559  Sum_probs=18.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+|.|++|+|||||+.+|....
T Consensus        99 ~~vl~G~SGVGKSSLiN~L~~~~  121 (231)
T d1t9ha2          99 TTVFAGQSGVGKSSLLNAISPEL  121 (231)
T ss_dssp             EEEEEESHHHHHHHHHHHHCC--
T ss_pred             eEEEECCCCccHHHHHHhhccHh
Confidence            47899999999999999986543

>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=95.35  E-value=0.0054  Score=44.47  Aligned_cols=22  Identities=14%  Similarity=0.151  Sum_probs=19.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++.|++|+|||+|+..+...-
T Consensus         8 i~vlG~~~vGKTsLi~~~~~~~   29 (175)
T d2bmja1           8 LGVLGDARSGKSSLIHRFLTGS   29 (175)
T ss_dssp             EEEECCTTTTHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            8999999999999999887654

>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=95.32  E-value=0.0046  Score=44.75  Aligned_cols=22  Identities=27%  Similarity=0.389  Sum_probs=19.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      +|+|.|.||+|||+|..+|...
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999754

>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=95.31  E-value=0.005  Score=44.89  Aligned_cols=22  Identities=32%  Similarity=0.451  Sum_probs=19.5

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      .+.|+|.+|+|||+|+.++...
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            3899999999999999998754

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=95.28  E-value=0.0062  Score=45.31  Aligned_cols=22  Identities=27%  Similarity=0.215  Sum_probs=17.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~  104 (294)
                      .++++.-|+|+|||........
T Consensus        41 ~~vlv~apTGsGKT~~~~~~~~   62 (206)
T d1oywa2          41 RDCLVVMPTGGGKSLCYQIPAL   62 (206)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCCcchhhhhhh
Confidence            3799999999999987654443

>d1d0xa2 c.37.1.9 (A:2-33,A:80-759) Myosin S1, motor domain {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=95.23  E-value=0.074  Score=47.06  Aligned_cols=60  Identities=20%  Similarity=0.325  Sum_probs=41.9

Q ss_pred             CCchhhhhcCCCcchhhcccHHHH--HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVV--RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~--~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++..+.+.|......++..+-=.+  .....++..+..+.|++.|.+|+|||..++.+.+.+
T Consensus        88 y~~~~~~~y~~~~~~~~~PHifaiA~~Ay~~m~~~~~nQsIiisGeSGaGKTe~~k~il~yL  149 (712)
T d1d0xa2          88 YTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQYL  149 (712)
T ss_dssp             CSHHHHHHHTTCCGGGSCCCHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHcCCCcCCCCCcHHHHHHHHHHHHHHhCCCceEEEeCCCCCCHHHHHHHHHHHH
Confidence            344455666666655555543222  455566666776779999999999999999998876

>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=95.23  E-value=0.011  Score=45.66  Aligned_cols=35  Identities=26%  Similarity=0.370  Sum_probs=24.8

Q ss_pred             HHHHHHHHcCCC--CcEEEECCCCCCHHHHHHHHHHH
Q 022641           71 RVLTNTLETANC--PHMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        71 ~~l~~~l~~~~~--~~ill~Gp~G~GKT~la~~la~~  105 (294)
                      ..+..-+.....  -+|+|+|.+|+|||++...+..+
T Consensus        19 ~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          19 LELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            344444444322  25999999999999999999754

>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=95.21  E-value=0.0024  Score=46.55  Aligned_cols=23  Identities=17%  Similarity=0.328  Sum_probs=19.6

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHH
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~  104 (294)
                      .+.|.|+|.|++|||+|..++..
T Consensus        16 ~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          16 GIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            34599999999999999988843

>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=95.17  E-value=0.0053  Score=46.34  Aligned_cols=23  Identities=22%  Similarity=0.329  Sum_probs=19.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++|.|++|+|||++++.+...-
T Consensus         8 KilllG~~~vGKTsll~~~~~~~   30 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRILH   30 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            39999999999999999986554

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=95.15  E-value=0.013  Score=45.54  Aligned_cols=39  Identities=33%  Similarity=0.338  Sum_probs=28.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDR  125 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~  125 (294)
                      .+.|+||+|+|||+++..++..+..+   +..++.++.....
T Consensus        59 itei~G~~~sGKT~l~l~~~~~aqk~---g~~v~yiDtE~~~   97 (268)
T d1xp8a1          59 ITEIYGPESGGKTTLALAIVAQAQKA---GGTCAFIDAEHAL   97 (268)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCC
T ss_pred             EEEEecCCccchHHHHHHHHHHHHhC---CCEEEEEECCccC
Confidence            48999999999999999999887533   2345555555433

>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=95.09  E-value=0.0055  Score=45.05  Aligned_cols=23  Identities=22%  Similarity=0.202  Sum_probs=20.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      +++.|..|+|||+++..+...-+
T Consensus         5 iv~lG~~~vGKTsll~r~~~~~~   27 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRIIHG   27 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCCCC
Confidence            89999999999999999976653

>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=95.03  E-value=0.0017  Score=46.19  Aligned_cols=22  Identities=27%  Similarity=0.428  Sum_probs=20.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|.|.||+|||+|+.+|..+-
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            7899999999999999998764

>d1lkxa_ c.37.1.9 (A:) Myosin S1, motor domain {Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]

Probab=94.94  E-value=0.027  Score=49.81  Aligned_cols=60  Identities=13%  Similarity=0.210  Sum_probs=42.1

Q ss_pred             CCchhhhhcCCCcchhhcccHHHH--HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           47 SSQPWVEKYRPKQVKDVAHQEEVV--RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~g~~~~~--~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+..+.+.|......++..+-=.+  .....+...+..+.|++.|.+|+|||..++.+.+.+
T Consensus        49 y~~~~~~~y~~~~~~~~~PHif~iA~~Ay~~l~~~~~~QsIiisGeSGsGKTe~~k~il~yL  110 (684)
T d1lkxa_          49 YKESDIKAYNGRYKYEMPPHMYALANDAYRSMRQSQENQCVIISGESGAGKTEASKKIMQFL  110 (684)
T ss_dssp             CSHHHHHHHSSCCGGGSCCCHHHHHHHHHHHHHHHCCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHcCCCCCCCCChHHHHHHHHHHHHHHcCCCeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            344455566655555555443222  455666667777779999999999999999998876

>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=94.85  E-value=0.0086  Score=46.82  Aligned_cols=31  Identities=26%  Similarity=0.325  Sum_probs=25.5

Q ss_pred             HHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           76 TLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        76 ~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+-.++++..+|.|++|+|||+++..+++..
T Consensus        37 l~PigrGQr~~I~g~~g~GKT~l~~~i~~~~   67 (289)
T d1xpua3          37 ASPIGRGQRGLIVAPPKAGKTMLLQNIAQSI   67 (289)
T ss_dssp             HSCCBTTCEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             cccccCCCeeeEeCCCCCCHHHHHHHHHHHH
Confidence            3344566679999999999999999999865

>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=94.84  E-value=0.16  Score=37.34  Aligned_cols=23  Identities=26%  Similarity=0.187  Sum_probs=20.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |+.+.|-++.|||||+.+|....
T Consensus         5 ni~iiGhvd~GKSTL~~~Ll~~~   27 (204)
T d2c78a3           5 NVGTIGHVDHGKTTLTAALTYVA   27 (204)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHh
Confidence            58999999999999999997654

>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=94.65  E-value=0.0058  Score=46.18  Aligned_cols=23  Identities=35%  Similarity=0.356  Sum_probs=20.5

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~  105 (294)
                      |..+|+|.-|+||||+++.+.++
T Consensus         4 Pv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           4 AVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             EEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CEEEEeeCCCCCHHHHHHHHHhc
Confidence            45899999999999999998875

>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=94.62  E-value=0.0093  Score=43.53  Aligned_cols=22  Identities=23%  Similarity=0.333  Sum_probs=19.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ++|.|..|+|||++++.+...-
T Consensus         5 ivllG~~~vGKTsl~~r~~~~~   26 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKIIH   26 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhCC
Confidence            8999999999999999887654

>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=94.51  E-value=0.01  Score=44.29  Aligned_cols=24  Identities=21%  Similarity=0.274  Sum_probs=21.5

Q ss_pred             cEEEECC-CCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGP-PGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp-~G~GKT~la~~la~~~~  107 (294)
                      .++++|- +|+|||+++..|+..+.
T Consensus         3 ~~~i~gt~~GVGKTtvs~~La~aLa   27 (224)
T d1byia_           3 RYFVTGTDTEVGKTVASCALLQAAK   27 (224)
T ss_dssp             EEEEEESSTTSCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCccHHHHHHHHHHHHH
Confidence            5889999 59999999999999984

>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=94.50  E-value=0.015  Score=45.52  Aligned_cols=26  Identities=38%  Similarity=0.529  Sum_probs=22.6

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhc
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ++.++++|--|+||||++.++|..+-
T Consensus         8 p~~i~~sGKGGVGKTTvaa~lA~~lA   33 (296)
T d1ihua1           8 PPYLFFTGKGGVGKTSISCATAIRLA   33 (296)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCcChHHHHHHHHHHHHH
Confidence            34588999999999999999998873

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=94.50  E-value=0.042  Score=41.32  Aligned_cols=24  Identities=21%  Similarity=0.217  Sum_probs=20.2

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      ..+|.=+.|+|||..+-+++..+.
T Consensus        33 g~iLaDe~GlGKT~~~i~~~~~~~   56 (230)
T d1z63a1          33 GICLADDMGLGKTLQTIAVFSDAK   56 (230)
T ss_dssp             CEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             CEEEEeCCCCChHHHHHHhhhhhh
Confidence            477777999999999988887764

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=94.49  E-value=0.0092  Score=49.78  Aligned_cols=24  Identities=33%  Similarity=0.444  Sum_probs=21.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +|++++|++|+|||+++..+..++
T Consensus        51 ~H~~I~G~tGsGKT~~l~~li~~~   74 (433)
T d1e9ra_          51 RHLLVNGATGTGKSVLLRELAYTG   74 (433)
T ss_dssp             GCEEEEECTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEeCCCCcHHHHHHHHHHHH
Confidence            479999999999999998877765

>d1br2a2 c.37.1.9 (A:80-789) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=94.40  E-value=0.043  Score=48.69  Aligned_cols=58  Identities=17%  Similarity=0.283  Sum_probs=40.2

Q ss_pred             chhhhhcCCCcchhhcccHH--HHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           49 QPWVEKYRPKQVKDVAHQEE--VVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        49 ~~~~~~~~~~~~~~~~g~~~--~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.+.|......++..+-=  +-.....++..+..+.|++.|.+|+|||..++.+.+.+
T Consensus        56 ~~~~~~y~~~~~~~~~PHif~vA~~Ay~~m~~~~~~Q~IiisGeSGaGKTe~~k~il~yL  115 (710)
T d1br2a2          56 EKIIDMYKGKKRHEMPPHIYAIADTAYRSMLQDREDQSILCTGESGAGKTENTKKVIQYL  115 (710)
T ss_dssp             HHHHHHTTTCCGGGSCCCHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCCCChHHHHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            33445555555555544422  22455666666777779999999999999999998887

>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=94.39  E-value=0.049  Score=42.21  Aligned_cols=25  Identities=24%  Similarity=0.073  Sum_probs=22.3

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+|+.|+|..|+|||||+.++....
T Consensus         6 iRni~i~gh~~~GKTtL~e~ll~~~   30 (276)
T d2bv3a2           6 LRNIGIAAHIDAGKTTTTERILYYT   30 (276)
T ss_dssp             EEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            3589999999999999999998765

>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=94.36  E-value=0.0028  Score=46.87  Aligned_cols=23  Identities=35%  Similarity=0.463  Sum_probs=20.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+|+||.|+|||+++.+|.-.+.
T Consensus        27 tvi~G~NGsGKStil~Ai~~~L~   49 (222)
T d1qhla_          27 TTLSGGNGAGKSTTMAAFVTALI   49 (222)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Confidence            68899999999999999998774

>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=94.31  E-value=0.0095  Score=47.79  Aligned_cols=22  Identities=32%  Similarity=0.416  Sum_probs=20.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |.|-|+-|+||||+++.|++.+
T Consensus         9 I~iEG~iGsGKSTl~~~L~~~l   30 (333)
T d1p6xa_           9 IYLDGVYGIGKSTTGRVMASAA   30 (333)
T ss_dssp             EEEECSTTSSHHHHHHHHHSGG
T ss_pred             EEEECCccCCHHHHHHHHHHHh
Confidence            8899999999999999999987

>d1w7ja2 c.37.1.9 (A:63-792) Myosin S1, motor domain {Chicken (Gallus gallus), Va isoform [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), Va isoform [TaxId: 9031]

Probab=94.05  E-value=0.054  Score=48.23  Aligned_cols=57  Identities=14%  Similarity=0.212  Sum_probs=39.2

Q ss_pred             hhhhhcCCCcchhhcccH--HHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           50 PWVEKYRPKQVKDVAHQE--EVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        50 ~~~~~~~~~~~~~~~g~~--~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+...|......++..+-  -+-.....++..+..+.|++.|.+|+|||..++.+.+.+
T Consensus        60 ~~~~~y~~~~~~~~~PHif~vA~~Ay~~l~~~~~~Q~IiisGeSGsGKTe~~k~il~~l  118 (730)
T d1w7ja2          60 DIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYAMRYF  118 (730)
T ss_dssp             HHHHHHTTCCGGGSCCCHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCcCCCCCcHHHHHHHHHHHHHHhCCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            344455555444444442  223455566666777779999999999999999998876

>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=93.97  E-value=0.15  Score=38.12  Aligned_cols=24  Identities=29%  Similarity=0.238  Sum_probs=21.2

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |.+.+.|.+++|||||+.+|....
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~~~   29 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRGSA   29 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEeCCCccHHHHHHHHHhhc
Confidence            449999999999999999998765

>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=93.85  E-value=0.011  Score=46.80  Aligned_cols=22  Identities=32%  Similarity=0.419  Sum_probs=19.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~  105 (294)
                      -.+|+||.|+|||+++.++.-.
T Consensus        26 lnvlvG~NgsGKS~iL~Ai~~~   47 (308)
T d1e69a_          26 VTAIVGPNGSGKSNIIDAIKWV   47 (308)
T ss_dssp             EEEEECCTTTCSTHHHHHHHHT
T ss_pred             eEEEECCCCCcHHHHHHHHHHH
Confidence            3699999999999999999653

>d2mysa2 c.37.1.9 (A:4-33,A:80-843) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=93.85  E-value=0.05  Score=48.88  Aligned_cols=55  Identities=20%  Similarity=0.283  Sum_probs=37.9

Q ss_pred             hhhcCCCcchhhcccHHHH--HHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           52 VEKYRPKQVKDVAHQEEVV--RVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        52 ~~~~~~~~~~~~~g~~~~~--~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+.|+.....++..+-=.+  .....++..+..+.|++.|.+|+|||..++.+.+.+
T Consensus        91 ~~~y~~~~~~~~pPHifaiA~~Ay~~m~~~~~~QsIiisGeSGaGKTe~~K~il~yL  147 (794)
T d2mysa2          91 VLAYRGKKRQEAPPHIFSISDNAYQFMLTDRENQSILITGESGAGKTVNTKRVIQYF  147 (794)
T ss_dssp             HHHTTTCCTTSSCSCHHHHHHHHHHHHHHHTCCEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             HHHHcCCCCCCCCCcHHHHHHHHHHHHHHcCCCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3445544444444443222  455666667777779999999999999999888876

>d1kk8a2 c.37.1.9 (A:1-28,A:77-837) Myosin S1, motor domain {Bay scallop (Aequipecten irradians) [TaxId: 31199]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Bay scallop (Aequipecten irradians) [TaxId: 31199]

Probab=93.80  E-value=0.052  Score=48.71  Aligned_cols=56  Identities=21%  Similarity=0.298  Sum_probs=39.2

Q ss_pred             hhhhcCCCcchhhcccH--HHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           51 WVEKYRPKQVKDVAHQE--EVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        51 ~~~~~~~~~~~~~~g~~--~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      ..+.|......++..+.  -+-.....++..+..+.|++.|.+|+|||..++.+.+.+
T Consensus        88 ~~~~y~~~~~~~~~PHiyavA~~Ay~~m~~~~~nQ~IiisGESGaGKTe~~K~il~yL  145 (789)
T d1kk8a2          88 VIAKYRGKRKTEIPPHLFSVADNAYQNMVTDRENQSCLITGESGAGKTENTKKVIMYL  145 (789)
T ss_dssp             HHHHHTTCCGGGSCCCHHHHHHHHHHHHHHHTSEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             HHHHHcCCCCCCCCCcHHHHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            44555555555554442  223456666667776779999999999999999988876

>d1c9ka_ c.37.1.11 (A:) Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU
species: Salmonella typhimurium [TaxId: 90371]

Probab=93.51  E-value=0.092  Score=37.77  Aligned_cols=20  Identities=30%  Similarity=0.400  Sum_probs=18.0

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q 022641           85 MLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~  104 (294)
                      ++++|+.++|||..|..++.
T Consensus         2 iLVtGGarSGKS~~AE~l~~   21 (180)
T d1c9ka_           2 ILVTGGARSGKSRHAEALIG   21 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHC
T ss_pred             EEEECCCCccHHHHHHHHHh
Confidence            68999999999999998863

>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=93.22  E-value=0.014  Score=46.80  Aligned_cols=23  Identities=35%  Similarity=0.482  Sum_probs=21.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      |.|-|+-|+||||+++.+++.+.
T Consensus         8 I~IEG~iGsGKSTl~~~L~~~l~   30 (331)
T d1osna_           8 IYLDGAYGIGKTTAAEEFLHHFA   30 (331)
T ss_dssp             EEEEESSSSCTTHHHHHHHHTTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHh
Confidence            78999999999999999999873

>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=93.16  E-value=0.015  Score=46.47  Aligned_cols=22  Identities=36%  Similarity=0.457  Sum_probs=19.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |.|-|+-|+||||+++.+++.+
T Consensus         7 I~IEG~iGsGKTTl~~~La~~l   28 (329)
T d1e2ka_           7 VYIDGPHGMGKTTTTQLLVALG   28 (329)
T ss_dssp             EEECSCTTSSHHHHHHHHTC--
T ss_pred             EEEECCcCCCHHHHHHHHHHHh
Confidence            7889999999999999998776

>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=93.14  E-value=0.025  Score=43.80  Aligned_cols=30  Identities=20%  Similarity=0.361  Sum_probs=24.8

Q ss_pred             HHcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           77 LETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        77 l~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +--++.+.+.|.|++|+|||+++..+++..
T Consensus        63 ~pigkGQr~~If~~~g~GKt~l~~~i~~~~   92 (276)
T d2jdid3          63 APYAKGGKIGLFGGAGVGKTVLIMELINNV   92 (276)
T ss_dssp             SCEETTCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             ccccCCCEEEeeCCCCCCHHHHHHHHHHHH
Confidence            334555579999999999999999998875

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.14  E-value=0.022  Score=46.93  Aligned_cols=22  Identities=36%  Similarity=0.537  Sum_probs=19.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHh
Q 022641           85 MLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~  106 (294)
                      -+|+||.|+|||+++.++.-.+
T Consensus        28 ~~i~G~NGsGKS~ileAi~~~l   49 (427)
T d1w1wa_          28 TSIIGPNGSGKSNMMDAISFVL   49 (427)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5899999999999999997433

>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=93.13  E-value=0.26  Score=39.24  Aligned_cols=25  Identities=16%  Similarity=0.187  Sum_probs=22.1

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .+|+.+.|..|.|||||+.++....
T Consensus        17 IRNI~iiGhvd~GKTTL~d~Ll~~~   41 (341)
T d1n0ua2          17 VRNMSVIAHVDHGKSTLTDSLVQRA   41 (341)
T ss_dssp             EEEEEEECCGGGTHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCcHHHHHHHHHHHC
Confidence            3589999999999999999997655

>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=92.98  E-value=0.026  Score=40.75  Aligned_cols=21  Identities=24%  Similarity=0.395  Sum_probs=19.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~  104 (294)
                      ++-|+|.|++|||||+.+|..
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            589999999999999999974

>d1d2ea3 c.37.1.8 (A:55-250) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Cow (Bos taurus), mitochondrial [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: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Cow (Bos taurus), mitochondrial [TaxId: 9913]

Probab=92.92  E-value=0.35  Score=35.10  Aligned_cols=23  Identities=35%  Similarity=0.315  Sum_probs=20.3

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |+.+.|-++.|||||+.+|...+
T Consensus         5 ni~iiGHvd~GKSTL~~~l~~~~   27 (196)
T d1d2ea3           5 NVGTIGHVDHGKTTLTAAITKIL   27 (196)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHH
Confidence            58999999999999999997643

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.90  E-value=0.04  Score=36.66  Aligned_cols=24  Identities=4%  Similarity=0.181  Sum_probs=21.8

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .++|+|-+|+||+++|.++...+.
T Consensus         8 ~i~~tg~~~~gk~~ia~al~~~l~   31 (122)
T d1g8fa3           8 SIVLGNSLTVSREQLSIALLSTFL   31 (122)
T ss_dssp             EEEECTTCCSCHHHHHHHHHHHHT
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHHH
Confidence            389999999999999999988884

>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=92.20  E-value=0.041  Score=42.42  Aligned_cols=24  Identities=33%  Similarity=0.573  Sum_probs=21.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhcC
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLFG  108 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~~  108 (294)
                      |.|+|--||||||++..++..+..
T Consensus         4 Iai~gKGGvGKTT~a~nLA~~LA~   27 (269)
T d1cp2a_           4 VAIYGKGGIGKSTTTQNLTSGLHA   27 (269)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHT
T ss_pred             EEEECCCcCCHHHHHHHHHHHHHh
Confidence            668999999999999999999853

>d1bg2a_ c.37.1.9 (A:) Kinesin {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: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.15  E-value=0.06  Score=42.87  Aligned_cols=29  Identities=21%  Similarity=0.296  Sum_probs=22.3

Q ss_pred             HHHHHHHcCCCCcEEEECCCCCCHHHHHH
Q 022641           72 VLTNTLETANCPHMLFYGPPGTGKTTTAL  100 (294)
Q Consensus        72 ~l~~~l~~~~~~~ill~Gp~G~GKT~la~  100 (294)
                      .+.+.+..|....++-+|+.|+|||++..
T Consensus        66 ~lv~~~l~G~n~~i~aYGqtgSGKTyT~~   94 (323)
T d1bg2a_          66 KIVKDVLEGYNGTIFAYGQTSSGKTHTME   94 (323)
T ss_dssp             HHHHHHHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             HHHHHHHcCCCcceeeecccCCCCceecc
Confidence            34455556776669999999999999974

>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=92.08  E-value=0.033  Score=45.85  Aligned_cols=22  Identities=18%  Similarity=0.304  Sum_probs=19.8

Q ss_pred             CcEEEECCCCCCHHHHHHHHHH
Q 022641           83 PHMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~  104 (294)
                      -+|.|+|.||+|||+++.+|..
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            3699999999999999999964

>d1jqlb_ c.37.1.20 (B:) delta subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=91.78  E-value=0.95  Score=30.54  Aligned_cols=108  Identities=8%  Similarity=0.005  Sum_probs=67.4

Q ss_pred             HHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCCCCcchhHHHHHHHHHHhhhcccCccCCCC
Q 022641           72 VLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNASDDRGINVVRTKIKTFAAVAVGSGQRRGGY  151 (294)
Q Consensus        72 ~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (294)
                      +|...+..+-.+..+|+|+---=+......+.+.+...+......+..  .....   +...+......+          
T Consensus         8 ~L~~~l~k~l~~vyll~G~E~~L~~~~~~~i~~~~~~~~~~~~~~~~~--~~~~~---~~~l~~~~~t~s----------   72 (140)
T d1jqlb_           8 QLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSI--DPNTD---WNAIFSLCQAMS----------   72 (140)
T ss_dssp             GHHHHHHHCCCSEEEEESSCHHHHHHHHHHHHHHHHHTTCCEEECCCC--STTCC---HHHHHHHHHCCC----------
T ss_pred             HHHHHHhcCCCcEEEEEcChHHHHHHHHHHHHHHHHhCCcceeeeecc--cccCC---HHHHHHHHcCCC----------
Confidence            345556666556799999988888888888877764333222222222  12222   333344433322          


Q ss_pred             CCCCcEEEEEeCCCCCC-HHHHHHHHHHHHhhcCcceEEEEecC
Q 022641          152 PCPPYKIIILDEADSMT-EDAQNALRRTMETYSKVTRFFFICNY  194 (294)
Q Consensus       152 ~~~~~~lliiDei~~l~-~~~~~~L~~~l~~~~~~~~ii~~~~~  194 (294)
                      ..+.+.+|+|++.+... ....+.|.++++..+....+|+.+..
T Consensus        73 lF~~krli~i~~~~~~~~k~~~~~L~~~~~~~~~~~~lii~~~~  116 (140)
T d1jqlb_          73 LFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNK  116 (140)
T ss_dssp             TTCCCEEEEEECCTTCSCTTHHHHHHHHHHHCCSSCCEEEECSS
T ss_pred             cccCcEEEEEEcCCCCCcHHHHHHHHHHHhCCCCCEEEEEEcCC
Confidence            23456799999887654 56677899999998888888887754

>d1j3ba1 c.91.1.1 (A:212-529) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Thermus thermophilus [TaxId: 274]

Probab=91.49  E-value=0.031  Score=44.04  Aligned_cols=18  Identities=44%  Similarity=0.704  Sum_probs=15.5

Q ss_pred             cEEEECCCCCCHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALA  101 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~  101 (294)
                      ..+|.|.+|||||||...
T Consensus        16 valffGLSGTGKTTLs~~   33 (318)
T d1j3ba1          16 VAVFFGLSGTGKTTLSTD   33 (318)
T ss_dssp             EEEEEECTTSCHHHHTCB
T ss_pred             EEEEEccCCCCccccccC
Confidence            479999999999998654

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=91.44  E-value=0.086  Score=39.71  Aligned_cols=24  Identities=33%  Similarity=0.444  Sum_probs=18.7

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .++++++|+|+|||..+...+..+
T Consensus        59 ~~~~i~apTGsGKT~~~~~~~~~~   82 (237)
T d1gkub1          59 ESFAATAPTGVGKTSFGLAMSLFL   82 (237)
T ss_dssp             CCEECCCCBTSCSHHHHHHHHHHH
T ss_pred             CCEEEEecCCChHHHHHHHHHHHH
Confidence            379999999999998766555443

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

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: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=91.26  E-value=0.16  Score=41.67  Aligned_cols=50  Identities=26%  Similarity=0.359  Sum_probs=39.8

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeecCC
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELNAS  122 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~~~  122 (294)
                      |+.+++.|...+..+. ...+|.|-+|+|||.++..+.++.      +.+++.+...
T Consensus        16 QP~aI~~l~~~l~~g~-~~q~l~GltGS~ka~~iA~l~~~~------~rp~LVVt~n   65 (413)
T d1t5la1          16 QPQAIAKLVDGLRRGV-KHQTLLGATGTGKTFTISNVIAQV------NKPTLVIAHN   65 (413)
T ss_dssp             HHHHHHHHHHHHHHTC-SEEEEEECTTSCHHHHHHHHHHHH------TCCEEEECSS
T ss_pred             CHHHHHHHHHHHhcCC-CcEEEeCCCCcHHHHHHHHHHHHh------CCCEEEEeCC
Confidence            5777899999997764 468899999999999999999988      5555555443

>d2olra1 c.91.1.1 (A:228-540) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Escherichia coli [TaxId: 562]

Probab=91.20  E-value=0.045  Score=42.92  Aligned_cols=17  Identities=47%  Similarity=0.751  Sum_probs=14.9

Q ss_pred             cEEEECCCCCCHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTAL  100 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~  100 (294)
                      ..+|.|.+|||||||..
T Consensus        16 ~alfFGLSGTGKTTLs~   32 (313)
T d2olra1          16 VAVFFGLSGTGKTTLST   32 (313)
T ss_dssp             EEEEECSTTSSHHHHHC
T ss_pred             EEEEEccCCCCccccee
Confidence            37899999999999874

>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=91.17  E-value=0.062  Score=41.90  Aligned_cols=23  Identities=35%  Similarity=0.518  Sum_probs=20.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      |.++|--|+||||++..+|..+.
T Consensus         5 IaisgKGGVGKTT~a~NLA~~LA   27 (289)
T d2afhe1           5 CAIYGKGGIGKSTTTQNLVAALA   27 (289)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH
Confidence            66799999999999999988873

>d1ry6a_ c.37.1.9 (A:) Kinesin {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=91.16  E-value=0.072  Score=42.50  Aligned_cols=26  Identities=35%  Similarity=0.485  Sum_probs=20.1

Q ss_pred             HHHHcCCCCcEEEECCCCCCHHHHHH
Q 022641           75 NTLETANCPHMLFYGPPGTGKTTTAL  100 (294)
Q Consensus        75 ~~l~~~~~~~ill~Gp~G~GKT~la~  100 (294)
                      ..+..|....++-||..|+|||++..
T Consensus        78 ~~~~~G~n~~i~aYGqTGSGKTyTm~  103 (330)
T d1ry6a_          78 DLYENGCVCSCFAYGQTGSGKTYTML  103 (330)
T ss_dssp             HHHHHCCEEEEEEECCTTSSHHHHHH
T ss_pred             HHHhcCCCeEEEeeeccccccceeee
Confidence            44445665559999999999999964

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=90.67  E-value=0.094  Score=42.24  Aligned_cols=27  Identities=22%  Similarity=0.381  Sum_probs=20.4

Q ss_pred             HHHHHHcCCCCcEEEECCCCCCHHHHH
Q 022641           73 LTNTLETANCPHMLFYGPPGTGKTTTA   99 (294)
Q Consensus        73 l~~~l~~~~~~~ill~Gp~G~GKT~la   99 (294)
                      +...+..|....++-+|++|+|||++.
T Consensus        71 lv~~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          71 TVDDILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             HHHHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhhccCceeEEecccCCCCcceee
Confidence            344445666556999999999999986

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {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: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=90.66  E-value=1.3  Score=35.91  Aligned_cols=48  Identities=27%  Similarity=0.377  Sum_probs=38.4

Q ss_pred             cHHHHHHHHHHHHcCCCCcEEEECCCCCCHHHHHHHHHHHhcCCCccCCcceeec
Q 022641           66 QEEVVRVLTNTLETANCPHMLFYGPPGTGKTTTALAIAHQLFGPELYKSRVLELN  120 (294)
Q Consensus        66 ~~~~~~~l~~~l~~~~~~~ill~Gp~G~GKT~la~~la~~~~~~~~~~~~~~~~~  120 (294)
                      ++.+++.|...+..+. +...|.|.+|+||+.++.++.+..      +.+++.+.
T Consensus        13 qp~aI~~l~~~L~~g~-~~~~L~GlsgS~ka~~~A~l~~~~------~rp~LvVt   60 (408)
T d1c4oa1          13 QPKAIAGLVEALRDGE-RFVTLLGATGTGKTVTMAKVIEAL------GRPALVLA   60 (408)
T ss_dssp             HHHHHHHHHHHHHTTC-SEEEEEECTTSCHHHHHHHHHHHH------TCCEEEEE
T ss_pred             CHHHHHHHHHHHhcCC-CcEEEecCCCCHHHHHHHHHHHHh------CCCEEEEe
Confidence            4567889999998654 347999999999999999999988      55555554

>d1ii2a1 c.91.1.1 (A:201-523) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Trypanosoma cruzi [TaxId: 5693]

Probab=90.28  E-value=0.062  Score=42.29  Aligned_cols=18  Identities=44%  Similarity=0.708  Sum_probs=15.4

Q ss_pred             cEEEECCCCCCHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALA  101 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~  101 (294)
                      ..+|.|-+|||||||...
T Consensus        16 ~alfFGLSGTGKTTLs~d   33 (323)
T d1ii2a1          16 VTVFFGLSGTGKTTLSAD   33 (323)
T ss_dssp             EEEEECCTTSSHHHHHCC
T ss_pred             EEEEEccCCCCcccceeC
Confidence            378999999999999843

>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=90.18  E-value=0.08  Score=41.12  Aligned_cols=29  Identities=24%  Similarity=0.237  Sum_probs=22.8

Q ss_pred             HcCCCCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           78 ETANCPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        78 ~~~~~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      --++.+.+.|.|++|+|||+++..++...
T Consensus        64 pig~GQr~~If~~~g~GKt~ll~~~~~~~   92 (285)
T d2jdia3          64 PIGRGQRELIIGDRQTGKTSIAIDTIINQ   92 (285)
T ss_dssp             CCBTTCBCEEEESTTSSHHHHHHHHHHHT
T ss_pred             CccCCCEEEeecCCCCChHHHHHHHHHhH
Confidence            33455569999999999999998877653

>d2zfia1 c.37.1.9 (A:4-352) Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif1a [TaxId: 10090]

Probab=90.17  E-value=0.12  Score=41.49  Aligned_cols=29  Identities=21%  Similarity=0.281  Sum_probs=22.6

Q ss_pred             HHHHHHHHcCCCCcEEEECCCCCCHHHHH
Q 022641           71 RVLTNTLETANCPHMLFYGPPGTGKTTTA   99 (294)
Q Consensus        71 ~~l~~~l~~~~~~~ill~Gp~G~GKT~la   99 (294)
                      ..+...+..|....++-||+.|+|||++.
T Consensus        76 ~plv~~~l~G~n~ti~aYGqTgSGKT~Tm  104 (349)
T d2zfia1          76 EEMLQHAFEGYNVCIFAYGQTGAGKSYTM  104 (349)
T ss_dssp             HHHHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHHHhccCceeeeeccCCCCCceee
Confidence            34455556677666999999999999996

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=90.16  E-value=0.1  Score=41.87  Aligned_cols=29  Identities=28%  Similarity=0.340  Sum_probs=21.9

Q ss_pred             HHHHHHHHcCCCCcEEEECCCCCCHHHHH
Q 022641           71 RVLTNTLETANCPHMLFYGPPGTGKTTTA   99 (294)
Q Consensus        71 ~~l~~~l~~~~~~~ill~Gp~G~GKT~la   99 (294)
                      ..+...+..|....++-+|+.|+|||++.
T Consensus        70 ~~lv~~~l~G~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          70 CPILDEVIMGYNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             HHHHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             HHhHHHHhccCCceEEeeeeccccceEEe
Confidence            34445556666556999999999999886

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=89.96  E-value=0.87  Score=35.19  Aligned_cols=23  Identities=22%  Similarity=0.327  Sum_probs=17.7

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +.+|.=..|.|||..+-++...+
T Consensus        81 g~iLaDemGlGKT~qaia~l~~l  103 (298)
T d1z3ix2          81 GCIMADEMGLGKTLQCITLIWTL  103 (298)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHH
T ss_pred             ceEEEeCCCCCHHHHHHHHHHHH
Confidence            47888889999998776665554

>d1zunb3 c.37.1.8 (B:16-237) Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain {Pseudomonas syringae pv. tomato [TaxId: 323]}

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: Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain
species: Pseudomonas syringae pv. tomato [TaxId: 323]

Probab=88.92  E-value=3.2  Score=30.36  Aligned_cols=23  Identities=26%  Similarity=0.300  Sum_probs=20.4

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      +++++|-...|||||+.+|....
T Consensus        11 ~i~viGHVd~GKSTL~~~Ll~~~   33 (222)
T d1zunb3          11 RFLTCGNVDDGKSTLIGRLLHDS   33 (222)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHc
Confidence            48999999999999999997664

>d1tafb_ a.22.1.3 (B:) TAF(II)62 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)62
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=88.81  E-value=0.81  Score=26.68  Aligned_cols=56  Identities=14%  Similarity=0.119  Sum_probs=40.3

Q ss_pred             HHHHHHHhCC-CCCHHHHHHHHhhccCcHHHHHH-HHHHHHHHhCCCCChhhhhhhcc
Q 022641          223 VLHICNEEGL-NLDAEALSTLSSISQGDLRRAIT-YLQGAARLFGSSITSKDLISVSG  278 (294)
Q Consensus       223 l~~~~~~~~~-~~~~~~l~~l~~~~~G~~r~~~~-~l~~~~~~~~~~it~~~v~~~~~  278 (294)
                      ++-++..-|+ .+++++.+.|++-..--++++++ .++|.....+..+|.+||..++.
T Consensus        12 ik~iAeS~Gi~~l~de~a~~LA~DveYRl~eiiQeA~KFMrhskR~~Ltt~Did~ALk   69 (70)
T d1tafb_          12 MKVIAESIGVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             HHHHHHHTTCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcCcHHHHHHHHc
Confidence            4445578888 49999999999987766776664 33344444467799999988763

>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=88.69  E-value=0.16  Score=37.83  Aligned_cols=23  Identities=35%  Similarity=0.387  Sum_probs=19.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFYGPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~Gp~G~GKT~la~~la~~~~  107 (294)
                      .+..|-.|+||||++..+|..+.
T Consensus         5 av~s~KGGvGKTtia~nlA~~la   27 (232)
T d1hyqa_           5 TVASGKGGTGKTTITANLGVALA   27 (232)
T ss_dssp             EEEESSSCSCHHHHHHHHHHHHH
T ss_pred             EEECCCCCChHHHHHHHHHHHHH
Confidence            34558899999999999999884

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=88.52  E-value=0.11  Score=42.08  Aligned_cols=28  Identities=32%  Similarity=0.414  Sum_probs=21.1

Q ss_pred             HHHHHHcCCCCcEEEECCCCCCHHHHHH
Q 022641           73 LTNTLETANCPHMLFYGPPGTGKTTTAL  100 (294)
Q Consensus        73 l~~~l~~~~~~~ill~Gp~G~GKT~la~  100 (294)
                      +.+.+..|....++-||..|+|||++..
T Consensus       105 lv~~~l~G~n~tifaYGqTGSGKTyTm~  132 (362)
T d1v8ka_         105 LVQTIFEGGKATCFAYGQTGSGKTHTMG  132 (362)
T ss_dssp             HHHHHHTTCEEEEEEEESTTSSHHHHHH
T ss_pred             HHHHHHhccCceEEeeccCCCCCceeee
Confidence            4444556665558999999999999964

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=87.73  E-value=0.15  Score=41.11  Aligned_cols=27  Identities=30%  Similarity=0.417  Sum_probs=20.5

Q ss_pred             HHHHHHcCCCCcEEEECCCCCCHHHHH
Q 022641           73 LTNTLETANCPHMLFYGPPGTGKTTTA   99 (294)
Q Consensus        73 l~~~l~~~~~~~ill~Gp~G~GKT~la   99 (294)
                      +...+..|....++-+|++|+|||++.
T Consensus        66 lv~~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          66 LVQSAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcCCceeeeccccCCCCccccc
Confidence            344445666555999999999999996

>d2ncda_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {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: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=87.63  E-value=0.16  Score=41.12  Aligned_cols=27  Identities=30%  Similarity=0.394  Sum_probs=20.8

Q ss_pred             HHHHHHcCCCCcEEEECCCCCCHHHHH
Q 022641           73 LTNTLETANCPHMLFYGPPGTGKTTTA   99 (294)
Q Consensus        73 l~~~l~~~~~~~ill~Gp~G~GKT~la   99 (294)
                      +...+..|....++-+|+.|+|||++.
T Consensus       116 lv~~vl~G~n~ti~aYGqtGSGKT~Tm  142 (368)
T d2ncda_         116 LIQSALDGYNICIFAYGQTGSGKTYTM  142 (368)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcccceeEEeeccCCCccceEe
Confidence            444455666556999999999999986

>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=87.62  E-value=0.12  Score=39.88  Aligned_cols=26  Identities=27%  Similarity=0.247  Sum_probs=20.4

Q ss_pred             CCCCcEEEECCCCCCHHHHHHHHHHH
Q 022641           80 ANCPHMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        80 ~~~~~ill~Gp~G~GKT~la~~la~~  105 (294)
                      ++.+.+.|.|++|+|||+++..+...
T Consensus        65 g~GQr~~Ifg~~g~GKt~l~~~~~~~   90 (276)
T d1fx0a3          65 GRGQRELIIGDRQTGKTAVATDTILN   90 (276)
T ss_dssp             BTTCBCBEEESSSSSHHHHHHHHHHT
T ss_pred             cCCceEeeccCCCCChHHHHHHHHhh
Confidence            34456999999999999999776544

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=87.54  E-value=0.19  Score=40.16  Aligned_cols=26  Identities=31%  Similarity=0.411  Sum_probs=19.5

Q ss_pred             HHHHcCCCCcEEEECCCCCCHHHHHH
Q 022641           75 NTLETANCPHMLFYGPPGTGKTTTAL  100 (294)
Q Consensus        75 ~~l~~~~~~~ill~Gp~G~GKT~la~  100 (294)
                      ..+..|....++-+|..|+|||++..
T Consensus        76 ~~~l~G~n~~i~aYGqtgSGKT~T~~  101 (342)
T d1f9va_          76 QSSLDGYNVCIFAYGQTGSGKTFTML  101 (342)
T ss_dssp             GGGGGTCCEEEEEECCTTSSHHHHHH
T ss_pred             cchhcccccceeeeeccCCccccccc
Confidence            33445654558899999999999874

>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=87.47  E-value=0.21  Score=37.17  Aligned_cols=23  Identities=35%  Similarity=0.410  Sum_probs=19.2

Q ss_pred             EEEE-CCCCCCHHHHHHHHHHHhc
Q 022641           85 MLFY-GPPGTGKTTTALAIAHQLF  107 (294)
Q Consensus        85 ill~-Gp~G~GKT~la~~la~~~~  107 (294)
                      |.++ +-.|+||||++..+|..+.
T Consensus         5 Iav~~~kGGvGKTtia~nLA~~la   28 (237)
T d1g3qa_           5 ISIVSGKGGTGKTTVTANLSVALG   28 (237)
T ss_dssp             EEEECSSTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCcHHHHHHHHHHHHH
Confidence            4455 7789999999999999884

>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=85.68  E-value=0.34  Score=37.32  Aligned_cols=39  Identities=21%  Similarity=0.284  Sum_probs=26.1

Q ss_pred             hcccHHHHHHHHHHHHcCCCC--cEEEECCCCCCHHHHHHHHHHH
Q 022641           63 VAHQEEVVRVLTNTLETANCP--HMLFYGPPGTGKTTTALAIAHQ  105 (294)
Q Consensus        63 ~~g~~~~~~~l~~~l~~~~~~--~ill~Gp~G~GKT~la~~la~~  105 (294)
                      +.-.++.++.|.    .-..+  .|-++||.++|||+|+..+...
T Consensus        15 l~~~~e~l~~l~----~~~~~v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          15 LMANPEALKILS----AITQPMVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             EEECHHHHHHHH----TCCSBEEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             EEECHHHHHHHH----cCCCCEEEEEEECCCCCCHHHHHHHHcCC
Confidence            444555555443    22222  3788999999999999988654

>d2akab1 c.37.1.8 (B:6-304) Dynamin G 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: G proteins
domain: Dynamin G domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=85.35  E-value=0.46  Score=36.82  Aligned_cols=25  Identities=16%  Similarity=0.256  Sum_probs=21.6

Q ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Q 022641           82 CPHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        82 ~~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      .|.++++|.-++||||++.+|...-
T Consensus        26 ~P~ivvvG~~SsGKSsliNaLlg~~   50 (299)
T d2akab1          26 LPQIAVVGGQSAGKSSVLENFVGRD   50 (299)
T ss_dssp             CCEEEEEEBTTSCHHHHHHHHHTSC
T ss_pred             CCeEEEEcCCCCCHHHHHHHHhCCC
Confidence            3559999999999999999998654

>d1ys7a2 c.23.1.1 (A:7-127) Transcriptional regulatory protein PrrA, N-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein PrrA, N-terminal domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=84.96  E-value=1.8  Score=28.23  Aligned_cols=73  Identities=12%  Similarity=0.193  Sum_probs=44.7

Q ss_pred             cEEEEEeC-CCCCCHHHHHHHHHHHHhhcCcceEEEEecCC--cccchHhhccccEEEecCCCHHHHHHHHHHHHHHhC
Q 022641          156 YKIIILDE-ADSMTEDAQNALRRTMETYSKVTRFFFICNYI--SRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEEG  231 (294)
Q Consensus       156 ~~lliiDe-i~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~--~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~  231 (294)
                      ++++++|- +..++  ..+.+.. +........+|+.|...  .....++..-+..+-.+|.+.+++...+++++++.|
T Consensus        46 ~dlvl~D~~mP~~~--G~el~~~-ir~~~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~rrG  121 (121)
T d1ys7a2          46 PDAIVLDINMPVLD--GVSVVTA-LRAMDNDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALLRRRG  121 (121)
T ss_dssp             CSEEEEESSCSSSC--HHHHHHH-HHHTTCCCCEEEEECCCTTTCCCTTTTTTCSEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEeeccCcc--cHHHHHH-HHhcCCCCEEEEEEeeCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHcCC
Confidence            45999995 33333  2333333 33334455566655432  233445555566788899999999999998887654

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), 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: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=84.75  E-value=0.4  Score=39.68  Aligned_cols=27  Identities=33%  Similarity=0.233  Sum_probs=19.3

Q ss_pred             CCCCcEEEECCCCCCHHHHHHH-HHHHh
Q 022641           80 ANCPHMLFYGPPGTGKTTTALA-IAHQL  106 (294)
Q Consensus        80 ~~~~~ill~Gp~G~GKT~la~~-la~~~  106 (294)
                      +...++++.+.+|||||+++.. +++.+
T Consensus        14 p~~g~~lv~A~AGsGKT~~l~~r~~~ll   41 (485)
T d1w36b1          14 PLQGERLIEASAGTGKTFTIAALYLRLL   41 (485)
T ss_dssp             CCSSCEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEcCchHHHHHHHHHHHHHH
Confidence            3334689999999999987654 44444

>d1f60a3 c.37.1.8 (A:2-240) Elongation factor eEF-1alpha, 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 eEF-1alpha, N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=84.53  E-value=1.3  Score=32.94  Aligned_cols=23  Identities=22%  Similarity=0.303  Sum_probs=20.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |+.+.|-.+.|||||+..|....
T Consensus         8 Ni~iiGHvD~GKsTl~~~ll~~~   30 (239)
T d1f60a3           8 NVVVIGHVDSGKSTTTGHLIYKC   30 (239)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHc
Confidence            69999999999999999998665

>d1wgla_ a.5.2.4 (A:) Toll-interacting protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: CUE domain
domain: Toll-interacting protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.25  E-value=1.3  Score=24.86  Aligned_cols=39  Identities=18%  Similarity=0.215  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHhhccCcHHHHHHHHHHH
Q 022641          218 VMSSRVLHICNEEGLNLDAEALSTLSSISQGDLRRAITYLQGA  260 (294)
Q Consensus       218 ~~~~~l~~~~~~~~~~~~~~~l~~l~~~~~G~~r~~~~~l~~~  260 (294)
                      +....|+.++    ..+++++++.+.+.++|++..+++.|=..
T Consensus        11 e~i~~LkeMF----P~~D~~vI~~VL~a~~G~vd~aid~LL~M   49 (59)
T d1wgla_          11 EDLKAIQDMF----PNMDQEVIRSVLEAQRGNKDAAINSLLQM   49 (59)
T ss_dssp             HHHHHHHHHC----SSSCHHHHHHHHTTTTTCHHHHHHHHHHS
T ss_pred             HHHHHHHHHC----CCCCHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence            3344454444    78999999999999999999999876543

>d1jnya3 c.37.1.8 (A:4-227) Elongation factor eEF-1alpha, N-terminal (G) 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: G proteins
domain: Elongation factor eEF-1alpha, N-terminal (G) domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=82.47  E-value=0.42  Score=35.44  Aligned_cols=23  Identities=17%  Similarity=0.238  Sum_probs=20.1

Q ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Q 022641           84 HMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |+.+.|-.+.|||||+..|....
T Consensus         5 Ni~viGHVd~GKTTL~~~Ll~~~   27 (224)
T d1jnya3           5 NLIVIGHVDHGKSTLVGRLLMDR   27 (224)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEEecCCCCHHHHHHHHHHHc
Confidence            58999999999999999886544

>d2qn6a3 c.37.1.8 (A:2-206) Initiation factor eIF2 gamma subunit, N-terminal (G) domain {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: G proteins
domain: Initiation factor eIF2 gamma subunit, N-terminal (G) domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=82.35  E-value=0.44  Score=34.67  Aligned_cols=21  Identities=33%  Similarity=0.309  Sum_probs=19.0

Q ss_pred             cEEEECCCCCCHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~  104 (294)
                      |+.+.|....|||||+.+|..
T Consensus        10 ni~iiGhVd~GKSTL~~~L~~   30 (205)
T d2qn6a3          10 NIGVVGHVDHGKTTLVQAITG   30 (205)
T ss_dssp             EEEEECSTTSSHHHHHHHHHS
T ss_pred             EEEEEEccCCcHHHHHHHHHh
Confidence            599999999999999999964

>d1jwyb_ c.37.1.8 (B:) Dynamin G domain {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Dynamin G domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=82.31  E-value=0.38  Score=37.48  Aligned_cols=24  Identities=21%  Similarity=0.411  Sum_probs=21.1

Q ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Q 022641           83 PHMLFYGPPGTGKTTTALAIAHQL  106 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~la~~la~~~  106 (294)
                      |.++++|..++|||+++.+|...-
T Consensus        25 P~ivVvG~~ssGKSSliNaLlG~~   48 (306)
T d1jwyb_          25 PQIVVVGSQSSGKSSVLENIVGRD   48 (306)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHTSC
T ss_pred             CeEEEEeCCCCCHHHHHHHHhCCC
Confidence            569999999999999999998643

>d1kk1a3 c.37.1.8 (A:6-200) Initiation factor eIF2 gamma subunit, N-terminal (G) domain {Archaeon 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: G proteins
domain: Initiation factor eIF2 gamma subunit, N-terminal (G) domain
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

Probab=82.01  E-value=0.44  Score=34.35  Aligned_cols=21  Identities=29%  Similarity=0.314  Sum_probs=18.9

Q ss_pred             cEEEECCCCCCHHHHHHHHHH
Q 022641           84 HMLFYGPPGTGKTTTALAIAH  104 (294)
Q Consensus        84 ~ill~Gp~G~GKT~la~~la~  104 (294)
                      |+.+.|-+..|||||+.+|..
T Consensus         7 nIaiiGhvd~GKSTL~~~L~g   27 (195)
T d1kk1a3           7 NIGMVGHVDHGKTTLTKALTG   27 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEEeccCCcHHHHHHHHHh
Confidence            479999999999999999964

>d1u0sy_ c.23.1.1 (Y:) CheY protein {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Thermotoga maritima [TaxId: 2336]

Probab=81.93  E-value=2.5  Score=27.33  Aligned_cols=69  Identities=13%  Similarity=0.234  Sum_probs=40.5

Q ss_pred             cEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCCc--ccchHhhccccEEEecCCCHHHHHHHHHHH
Q 022641          156 YKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYIS--RIIEPLASRCAKFRFKPLSEEVMSSRVLHI  226 (294)
Q Consensus       156 ~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~--~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~  226 (294)
                      ++++++| +..-..+..+.+.++-+. .....+|+.|....  ....++..-+..+-.+|.+.+++.+.++++
T Consensus        47 ~dliilD-~~mp~~~G~e~~~~ir~~-~~~~pvi~ls~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~l~~v  117 (118)
T d1u0sy_          47 PDIVTMD-ITMPEMNGIDAIKEIMKI-DPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKV  117 (118)
T ss_dssp             CSEEEEE-CSCGGGCHHHHHHHHHHH-CTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             CCEEEEe-cCCCCCCHHHHHHHHHHh-CCCCcEEEEEccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHh
Confidence            3599999 322222334444444333 44555666654332  234455555667778999999999988764

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=81.35  E-value=1.5  Score=33.72  Aligned_cols=43  Identities=23%  Similarity=0.365  Sum_probs=34.7

Q ss_pred             cEEEEEeCCC-CCCHHHHHHHHHHHHhhcCcceEEEEecCCccc
Q 022641          156 YKIIILDEAD-SMTEDAQNALRRTMETYSKVTRFFFICNYISRI  198 (294)
Q Consensus       156 ~~lliiDei~-~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~~~~  198 (294)
                      ..+++|||++ +|++..+..|...+.......-+|+||..+..+
T Consensus       242 ~~~~~iDEpe~~Lhp~~~~~l~~~l~~~~~~~QviitTHsp~~~  285 (308)
T d1e69a_         242 SPFYVLDEVDSPLDDYNAERFKRLLKENSKHTQFIVITHNKIVM  285 (308)
T ss_dssp             CSEEEEESCCSSCCHHHHHHHHHHHHHHTTTSEEEEECCCTTGG
T ss_pred             CchhhhhhccccCCHHHHHHHHHHHHHhccCCEEEEEECCHHHH
Confidence            3599999998 578999999999998777777888888765433

>d1qkka_ c.23.1.1 (A:) Transcriptional regulatory protein DctD, receiver domain {Sinorhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein DctD, receiver domain
species: Sinorhizobium meliloti [TaxId: 382]

Probab=80.86  E-value=2.1  Score=28.69  Aligned_cols=74  Identities=11%  Similarity=0.127  Sum_probs=44.1

Q ss_pred             CcEEEEEeCCCCCCHHHHHHHHHHHHhhcCcceEEEEecCC--cccchHhhccccEEEecCCCHHHHHHHHHHHHHHh
Q 022641          155 PYKIIILDEADSMTEDAQNALRRTMETYSKVTRFFFICNYI--SRIIEPLASRCAKFRFKPLSEEVMSSRVLHICNEE  230 (294)
Q Consensus       155 ~~~lliiDei~~l~~~~~~~L~~~l~~~~~~~~ii~~~~~~--~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~  230 (294)
                      .++++++| +..=..+..+.+..+-+ ......+|+.|...  .....++..-+..+-.+|.+.+++...+++.+...
T Consensus        44 ~~dlil~D-~~mP~~~G~el~~~lr~-~~~~~pvI~lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~~~~~  119 (140)
T d1qkka_          44 FAGIVISD-IRMPGMDGLALFRKILA-LDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKR  119 (140)
T ss_dssp             CCSEEEEE-SCCSSSCHHHHHHHHHH-HCTTSCEEEEECGGGHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             CcchHHHh-hccCCCCHHHHHHHHHH-hCCCCcEEEEECCCCHHHHHHHHHcCCCEeecCCCCHHHHHHHHHHHHHHH
Confidence            45699998 32222223444433333 34455566666433  23345555566678889999999999888777543

>d1f6va_ a.49.1.1 (A:) C-terminal domain of B transposition protein {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: C-terminal domain of B transposition protein
superfamily: C-terminal domain of B transposition protein
family: C-terminal domain of B transposition protein
domain: C-terminal domain of B transposition protein
species: Bacteriophage mu [TaxId: 10677]

Probab=80.78  E-value=0.32  Score=29.96  Aligned_cols=71  Identities=17%  Similarity=0.094  Sum_probs=52.8

Q ss_pred             EEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHhhc--cCcHHHHHHHHHHHHHHh---CCCCChhhhhhhcccccC
Q 022641          208 KFRFKPLSEEVMSSRVLHICNEEGLNLDAEALSTLSSIS--QGDLRRAITYLQGAARLF---GSSITSKDLISVSGYPTG  282 (294)
Q Consensus       208 ~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~l~~~~--~G~~r~~~~~l~~~~~~~---~~~it~~~v~~~~~~~~~  282 (294)
                      .+.+..+..+++..++    ...++. +++.+..+..+.  +|-+|.+-..|..++.++   +..|+.++|..+......
T Consensus         7 r~~i~k~kk~Di~Aia----~AW~v~-d~~~~k~l~~I~~KpGaLR~l~kTLrLA~M~A~g~g~~v~~~~Ir~A~~~ld~   81 (91)
T d1f6va_           7 RTAINKTKKADVKAIA----DAWQIN-GEKELELLQQIAQKPGALRILNHSLRLAAMTAHGKGERVNEDYLRQAFRELDL   81 (91)
T ss_dssp             TTCCSSCSGGGTTHHH----HSSTTS-SSHHHHHHHTTSSSCSCHHHHHHHHGGGTCTTCTTSCCSSHHHHHHHHTSSCS
T ss_pred             hhhhcCCCHHHHHHHH----HHhCCC-CHHHHHHHHHHccCccHHHHHHHHHHHHHHHhCCCCCcCCHHHHHHHHHHhhh
Confidence            3455667777777766    566665 445566666664  688999999999999888   457999999999887644


Q ss_pred             C
Q 022641          283 G  283 (294)
Q Consensus       283 ~  283 (294)
                      +
T Consensus        82 d   82 (91)
T d1f6va_          82 D   82 (91)
T ss_dssp             S
T ss_pred             h
Confidence            3

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=80.78  E-value=0.43  Score=35.78  Aligned_cols=15  Identities=27%  Similarity=0.521  Sum_probs=14.0

Q ss_pred             CcEEEECCCCCCHHH
Q 022641           83 PHMLFYGPPGTGKTT   97 (294)
Q Consensus        83 ~~ill~Gp~G~GKT~   97 (294)
                      .++++..|+|+|||.
T Consensus        59 ~dvvi~a~TGsGKTl   73 (238)
T d1wrba1          59 RDIMACAQTGSGKTA   73 (238)
T ss_dssp             CCEEEECCTTSSHHH
T ss_pred             CCEEEECCCCCCcce
Confidence            479999999999998