Citrus Sinensis ID: 043980

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230---
Protein Sequence
MASSSSSSHRSTSLGLIRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEEFKEAAELEECFEGSSQFVWLSFSEHQRLLDEVFRPSDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccEEEcccccccccccHHHHHHHHHHccccEEEcccccccccccHHHHHHHHHccEEEEEEcccccccHHHHHHHHHHHHcHHccccEEEEEEccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccccccccccHHHHHHHHHHHccccccEEEEEEEcccccHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccEEEEEcccccHHHHHHHHHHHHHHHHHccccEEEcccccccccccHHHHHHHHHccEEEEEEEccccccHHHHHHHHHHHHHHHHcccEEEEEEEEccHHHHHHcccHHHHHHHHHHccccHHHHHHHHHHHHHHHccccccHHHHHHHHHccccccccccccHHHHHHHHHHHccccccEEEEEEEccccccHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
masssssshrstslglirprnnkkYEVFVsfrgedtrdkFTSHLYSALSRQSIQTFIDdqlnrgdeISQSLVNAIEASAISVIIFSesytssrwCVDELVKILECKKEYAQIVIpvlyrvdpsdvrnqtgsfgdsFSKLEEFKEAAELEECFEGSSQFVWLSFSEHQRLldevfrpsdnknqlaGVESRVEEIESLlgvkskdvyalgiwgiggigkTKIARAIFDKISSDFE
Flexible Loop (DISEMBL)
masssssshrstslglirprnnkkYEVFVsfrgedtrDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFsesytssrWCVDELVKILECKKEYAQIVIPvlyrvdpsdvrnqTGSFGDSFSKLEEFKEAAELEECFEGSSQFVWLSFSEHQRLLDEVFRPSDNKNQLAGVESRVEEIESLlgvkskdvyaLGIWgiggigktkIARAIFDKISSDFE
Low Complexity Region (SEG)
MAsssssshrstsLGLIRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSkleefkeaaeleecfeGSSQFVWLSFSEHQRLLDEVFRPSDNKNQLAGVESRVEEIESLLGVKSKDVYALgiwgiggigKTKIARAIFDKISSDFE
Disordered region (IsUnstruct)
***********************KYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPS*********************AAELEECFEGSSQFVWLSFSEHQRLLDEVF**************RVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK******
Disordered Region (DISOPRED)
**********************KKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEEFKEAAELEECFEGSSQFVWLSFSEHQRLLDEVFRPSDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE
Disordered Region (DISEMBL)
**************GLIRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEEFKEAAELEECFEGSSQFVWLSFSEHQRLLDEVFRPSDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE
Disordered Region (DISPRO)
********************NNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEEFKEAAELEECFEGSSQFVWLSFSEHQRLLDEVFRPSDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MASSSSSSHRSTSLGLIRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEEFKEAAELEECFEGSSQFVWLSFSEHQRLLDEVFRPSDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	233	2.2.26 [Sep-21-2011]
Q40392	1144	TMV resistance protein N	N/A	no	0.815	0.166	0.415	1e-42
O82500	1095	Putative disease resistan	no	no	0.888	0.189	0.391	1e-41
O23530	1301	Protein SUPPRESSOR OF npr	no	no	0.896	0.160	0.4	4e-39
Q9C5Q9	411	Protein PHLOEM PROTEIN 2-	no	no	0.484	0.274	0.464	3e-22
Q9FHE9	354	Protein PHLOEM PROTEIN 2-	no	no	0.549	0.361	0.384	1e-19
Q9SYC9	571	Vesicle-associated protei	no	no	0.583	0.238	0.367	3e-19
Q9FHE8	392	Protein PHLOEM PROTEIN 2-	no	no	0.549	0.326	0.405	5e-19
Q9FL92	1372	Probable WRKY transcripti	no	no	0.763	0.129	0.313	8e-19
Q9SZ67	1895	Probable WRKY transcripti	no	no	0.849	0.104	0.308	3e-18
Q9FKN7	1613	Protein DA1-related 4 OS=	no	no	0.776	0.112	0.3	7e-13

>sp|Q40392|TMVRN_NICGU TMV resistance protein N OS=Nicotiana glutinosa GN=N PE=1 SV=1

 Score =  173 bits (438), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 98/236 (41%), Positives = 133/236 (56%), Gaps = 46/236 (19%)

Query: 25  YEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQ-LNRGDEISQSLVNAIEASAISVI 83
           Y+VF+SFRGEDTR  FTSHLY  L+ + I+TF DD+ L  G  I   L  AIE S  +++
Sbjct: 12  YDVFLSFRGEDTRKTFTSHLYEVLNDKGIKTFQDDKRLEYGATIPGELCKAIEESQFAIV 71

Query: 84  IFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEE-- 141
           +FSE+Y +SRWC++ELVKI+ECK  + Q VIP+ Y VDPS VRNQ  SF  +F + E   
Sbjct: 72  VFSENYATSRWCLNELVKIMECKTRFKQTVIPIFYDVDPSHVRNQKESFAKAFEEHETKY 131

Query: 142 -------------FKEAAELE-----------ECF-----EGSSQFVWLSFSEHQRLLDE 172
                          EAA L+           +C      + SS+   +S S  Q     
Sbjct: 132 KDDVEGIQRWRIALNEAANLKGSCDNRDKTDADCIRQIVDQISSKLCKISLSYLQ----- 186

Query: 173 VFRPSDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI 228
                     + G+++ +E+IESLL +    V  +GIWG+GG+GKT IARAIFD +
Sbjct: 187 ---------NIVGIDTHLEKIESLLEIGINGVRIMGIWGMGGVGKTTIARAIFDTL 233

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth.
Nicotiana glutinosa (taxid: 35889)

>sp|O82500|Y4117_ARATH Putative disease resistance protein At4g11170 OS=Arabidopsis thaliana GN=At4g11170 PE=2 SV=1

 Score =  169 bits (429), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 101/258 (39%), Positives = 139/258 (53%), Gaps = 51/258 (19%)

Query: 1   MASSSSSSHRSTSLGLIRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQ 60
           MASSSS+S R              Y+VF SFRGED R+ F SHL      + I TF DD 
Sbjct: 1   MASSSSNSWR--------------YDVFPSFRGEDVRNNFLSHLLKEFESKGIVTFRDDH 46

Query: 61  LNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRV 120
           + R   I   L  AI  S ISV++FSE+Y SS WC+DEL++I++CK+E    V+PV Y+V
Sbjct: 47  IKRSHTIGHELRAAIRESKISVVLFSENYASSSWCLDELIEIMKCKEEQGLKVMPVFYKV 106

Query: 121 DPSDVRNQTGSFGDSFSKLEEFKEAAELEECFEGSS--QFVWLS--------FSEHQRLL 170
           DPSD+R QTG FG SF           LE C   +   Q  W            +H +  
Sbjct: 107 DPSDIRKQTGKFGMSF-----------LETCCGKTEERQHNWRRALTDAANILGDHPQNW 155

Query: 171 D-EVFR---------------PSDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGG 214
           D E ++               PS + N L G+E+ + ++ESLL ++S+ V  +GIWG  G
Sbjct: 156 DNEAYKITTISKDVLEKLNATPSRDFNDLVGMEAHIAKMESLLCLESQGVRIVGIWGPAG 215

Query: 215 IGKTKIARAIFDKISSDF 232
           +GKT IARA++++   +F
Sbjct: 216 VGKTTIARALYNQYHENF 233

Arabidopsis thaliana (taxid: 3702)

>sp|O23530|SNC1_ARATH Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1 OS=Arabidopsis thaliana GN=SNC1 PE=1 SV=3

 Score =  161 bits (407), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 90/225 (40%), Positives = 136/225 (60%), Gaps = 16/225 (7%)

Query: 23  KKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISV 82
           ++Y+VF SFRGED RD F SHL   L  ++I TFIDD++ R   I   L++AI+ S I++
Sbjct: 10  RRYDVFPSFRGEDVRDSFLSHLLKELRGKAI-TFIDDEIERSRSIGPELLSAIKESRIAI 68

Query: 83  IIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKL--- 139
           +IFS++Y SS WC++ELV+I +C     Q+VIP+ + VD S+V+ QTG FG  F +    
Sbjct: 69  VIFSKNYASSTWCLNELVEIHKCYTNLNQMVIPIFFHVDASEVKKQTGEFGKVFEETCKA 128

Query: 140 ------EEFKEAAELEECFEGSSQFVWLSFSEH-QRLLDEVFR----PSDNKNQLAGVES 188
                 + +K+A        G     W S +   + L ++V R    PSD+   L G+E+
Sbjct: 129 KSEDEKQSWKQALAAVAVMAGYDLRKWPSEAAMIEELAEDVLRKTMTPSDDFGDLVGIEN 188

Query: 189 RVEEIESLLGVKSKDV-YALGIWGIGGIGKTKIARAIFDKISSDF 232
            +E I+S+L ++SK+    +GIWG  GIGK+ I RA++ K+S  F
Sbjct: 189 HIEAIKSVLCLESKEARIMVGIWGQSGIGKSTIGRALYSKLSIQF 233

Disease resistance protein of the TIR-NB-LRR-type. Part of the RPP5 locus that contains a cluster of several paralogous disease resistance (R) genes. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. Regulated by RNA silencing. Expression regulated by MOS1 at chromatin level. Negatively regulated at the transcript level by BON1.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C5Q9|P2A05_ARATH Protein PHLOEM PROTEIN 2-LIKE A5 OS=Arabidopsis thaliana GN=PP2A5 PE=2 SV=1

 Score =  105 bits (261), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 53/114 (46%), Positives = 73/114 (64%), Gaps = 1/114 (0%)

Query: 26  EVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIF 85
           +VF++FRG+D R  F S L  AL ++ I  FID+Q  RG  +  SL + I  S I+++IF
Sbjct: 23  QVFINFRGKDLRKGFMSFLKPALKKEKINVFIDEQEERGKYLI-SLFDTIGESKIALVIF 81

Query: 86  SESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKL 139
           SE Y  S WC+DELVKI E   +   I+IP+ YR+D   V++ TG FGD+F  L
Sbjct: 82  SEGYCESHWCMDELVKIKEYMDQNRLIIIPIFYRLDLDVVKDLTGKFGDNFWDL 135

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FHE9|P2A08_ARATH Protein PHLOEM PROTEIN 2-LIKE A8 OS=Arabidopsis thaliana GN=PP2A8 PE=2 SV=1

 Score = 97.1 bits (240), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/138 (38%), Positives = 78/138 (56%), Gaps = 10/138 (7%)

Query: 4   SSSSSHRSTSLGLIRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNR 63
           ++SSS R T  G          +VF++FRG+D R+ F S L  A+   +I  FID     
Sbjct: 2   AASSSVRPTPTG---------PQVFINFRGKDLRNGFLSFLEPAMREANINVFIDKDEVV 52

Query: 64  GDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPS 123
           G ++    V  I+ S ++V+IFS+ YTSS WC+DEL +I +C  +     IP+ Y++ PS
Sbjct: 53  GTDLVNLFVR-IQESRVAVVIFSKDYTSSEWCLDELAEIKDCINQGGLNAIPIFYKLAPS 111

Query: 124 DVRNQTGSFGDSFSKLEE 141
            V    G FGD+F  L+E
Sbjct: 112 SVLELKGGFGDTFRVLKE 129

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SYC9|VAP14_ARATH Vesicle-associated protein 1-4 OS=Arabidopsis thaliana GN=PVA14 PE=2 SV=1

 Score = 95.1 bits (235), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 54/147 (36%), Positives = 85/147 (57%), Gaps = 11/147 (7%)

Query: 2   ASSSSSSHRSTSLGLIRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQL 61
           A+SS+  H     G+  P    +Y+VF++FRG++ R+ F   L  A+  + I  F D+  
Sbjct: 344 AASSTDDH-----GITLP----QYQVFINFRGDELRNSFVGFLVKAMRLEKINVFTDEVE 394

Query: 62  NRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVD 121
            RG  ++  L   IE S ++V IFSE YT S WC+DELVK+ E  ++   +V+PV YR++
Sbjct: 395 LRGTNLNY-LFRRIEESRVAVAIFSERYTESCWCLDELVKMKEQMEQGKLVVVPVFYRLN 453

Query: 122 PSDVRNQTGSFGDSFSKLE-EFKEAAE 147
            +  +   G+FGD+   LE E++   E
Sbjct: 454 ATACKRFMGAFGDNLRNLEWEYRSEPE 480

May play a role in vesicle trafficking.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FHE8|P2A06_ARATH Protein PHLOEM PROTEIN 2-LIKE A6 OS=Arabidopsis thaliana GN=PP2A6 PE=2 SV=1

 Score = 94.7 bits (234), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 78/138 (56%), Gaps = 10/138 (7%)

Query: 3   SSSSSSHRSTSLGLIRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLN 62
           +SSSS  + T  G          +VF+ FRG D R  F S L  AL   +I  FID+   
Sbjct: 2   ASSSSVVKPTPTG---------PQVFICFRGADVRKHFISFLVPALREANINVFIDENEF 52

Query: 63  RGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDP 122
            G E++ +L+  IE S ++++IFS  +T S  C++EL KI E K +   IVIP+ Y+V P
Sbjct: 53  LGSEMA-NLLTRIEESELALVIFSVDFTRSHRCLNELAKIKERKDQGRLIVIPIFYKVKP 111

Query: 123 SDVRNQTGSFGDSFSKLE 140
           S V+   G FGD+F  LE
Sbjct: 112 SAVKFLEGKFGDNFRALE 129

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FL92|WRK16_ARATH Probable WRKY transcription factor 16 OS=Arabidopsis thaliana GN=WRKY16 PE=2 SV=1

 Score = 94.0 bits (232), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 108/201 (53%), Gaps = 23/201 (11%)

Query: 34  EDTRDKFTSHLYSALSRQSIQ-TFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSS 92
           E+ R  F SHL  AL R+ +   FID   +  +E SQS+V   E + +SV+I   + T S
Sbjct: 14  EEVRYSFVSHLSKALQRKGVNDVFIDSDDSLSNE-SQSMV---ERARVSVMILPGNRTVS 69

Query: 93  RWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEEFKEAAELEECF 152
              +D+LVK+L+C+K   Q+V+PVLY V  S+    +      FS +   ++     +  
Sbjct: 70  ---LDKLVKVLDCQKNKDQVVVPVLYGVRSSETEWLSALDSKGFSSVHHSRKECSDSQLV 126

Query: 153 EGSSQFVWLSFSEHQRLLDEVFRPSDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGI 212
           + + + V+      +R+               G+ S++ EIE ++  +  D+  +GIWG+
Sbjct: 127 KETVRDVYEKLFYMERI---------------GIYSKLLEIEKMINKQPLDIRCVGIWGM 171

Query: 213 GGIGKTKIARAIFDKISSDFE 233
            GIGKT +A+A+FD++S +F+
Sbjct: 172 PGIGKTTLAKAVFDQMSGEFD 192

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element. May also act as a disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SZ67|WRK19_ARATH Probable WRKY transcription factor 19 OS=Arabidopsis thaliana GN=WRKY19 PE=2 SV=1

 Score = 92.4 bits (228), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 69/224 (30%), Positives = 116/224 (51%), Gaps = 26/224 (11%)

Query: 19  PR--NNKKYEVFVSF-RGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAI 75
           PR  ++K Y+V + + R + + + F SHL ++L R+ I  +  ++ N         V+A+
Sbjct: 660 PRFSSSKDYDVVIRYGRADISNEDFISHLRASLCRRGISVY--EKFNE--------VDAL 709

Query: 76  EASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDS 135
               + +I+ + +Y  S      L+ ILE +    ++V P+ YR+ P D    + ++   
Sbjct: 710 PKCRVLIIVLTSTYVPS-----NLLNILEHQHTEDRVVYPIFYRLSPYDFVCNSKNYERF 764

Query: 136 FSKLEEFKEAAELEECFEGSSQFVWLSFSEHQRLLDEVFRP------SDNKNQLAGVESR 189
           + + E  K  A L+E  +       L+      L+DE+ R       S +K  + G++ +
Sbjct: 765 YLQDEPKKWQAALKEITQMPG--YTLTDKSESELIDEIVRDALKVLCSADKVNMIGMDMQ 822

Query: 190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE 233
           VEEI SLL ++S DV ++GIWG  GIGKT IA  IF KIS  +E
Sbjct: 823 VEEILSLLCIESLDVRSIGIWGTVGIGKTTIAEEIFRKISVQYE 866

Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element. May act also as a disease resistance protein with a serine/threonine-protein kinase activity.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKN7|DAR4_ARATH Protein DA1-related 4 OS=Arabidopsis thaliana GN=DAR4 PE=1 SV=2

 Score = 74.3 bits (181), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 60/200 (30%), Positives = 102/200 (51%), Gaps = 19/200 (9%)

Query: 40  FTSHLYSALSRQSIQTFIDD---QLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCV 96
             SHL +AL R+ I  F+D    Q  +   I Q+      A  + V+I  E      W  
Sbjct: 32  LVSHLSAALRREGISVFVDACGLQETKFFSIKQNQPLTDGARVLVVVISDEVEFYDPW-F 90

Query: 97  DELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEEFKEAAELEECFEGSS 156
            + +K+++  +    +V+PV Y VD     + T  +G + S LE  K  +   +    + 
Sbjct: 91  PKFLKVIQGWQNNGHVVVPVFYGVD-----SLTRVYGWANSWLEAEKLTSHQSKILSNNV 145

Query: 157 QFVWLSFSEHQRLLDEVFRPSDNKNQLA---GVESRVEEIESLLGVKSKDVYALGIWGIG 213
               L+ SE   L++E+ R    K   A   G+ +R+ EIE LL  + +D+ ++GIWG+ 
Sbjct: 146 ----LTDSE---LVEEIVRDVYGKLYPAERVGIYARLLEIEKLLYKQHRDIRSIGIWGMP 198

Query: 214 GIGKTKIARAIFDKISSDFE 233
           GIGKT +A+A+F+ +S+D++
Sbjct: 199 GIGKTTLAKAVFNHMSTDYD 218

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	233
255561496	876	TMV resistance protein N, putative [Rici	0.905	0.240	0.526	4e-55
224127754	1125	tir-nbs-lrr resistance protein [Populus	0.905	0.187	0.493	7e-55
224145016	1254	tir-nbs-lrr resistance protein [Populus	0.948	0.176	0.508	1e-54
224133498	1187	tir-nbs-lrr resistance protein [Populus	0.896	0.176	0.508	1e-54
255555357	1094	leucine-rich repeat-containing protein,	0.888	0.189	0.506	2e-54
356550897	970	PREDICTED: TMV resistance protein N-like	0.896	0.215	0.506	7e-53
356545721	653	PREDICTED: protein SUPPRESSOR OF npr1-1,	0.905	0.323	0.475	8e-52
356569977	833	PREDICTED: TMV resistance protein N-like	0.905	0.253	0.466	2e-51
224127234	276	predicted protein [Populus trichocarpa]	0.948	0.800	0.466	3e-51
255564976	944	TMV resistance protein N, putative [Rici	0.901	0.222	0.486	3e-51

>gi|255561496|ref|XP_002521758.1| TMV resistance protein N, putative [Ricinus communis] gi|223538971|gb|EEF40568.1| TMV resistance protein N, putative [Ricinus communis]

 Score =  220 bits (561), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 120/228 (52%), Positives = 155/228 (67%), Gaps = 17/228 (7%)

Query: 23  KKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISV 82
           KKY+VF+SFRGEDTRD FTSHLYSAL+++ I TF+D ++ RG+EIS S+  AI+ S +SV
Sbjct: 9   KKYDVFLSFRGEDTRDNFTSHLYSALNKKKIFTFMDKEIKRGEEISPSIAKAIKGSKLSV 68

Query: 83  IIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEE- 141
           IIFSE Y  S+WC+DEL KILECKK   QIVIPV YRVDP  VRNQ GSF  +F+K EE 
Sbjct: 69  IIFSEKYAFSKWCLDELTKILECKKMNGQIVIPVFYRVDPVHVRNQRGSFACAFAKHEET 128

Query: 142 FKEAAELEECF-----EGSSQFVWLSF--SEHQRLLDEVFRPSDNK-NQ--------LAG 185
            KE  E  E +     E  S   W S       +L++E+ +    K NQ        L G
Sbjct: 129 LKERMEKVESWRSALNEAGSISGWNSLVARPESKLIEEIVKDISKKLNQTSPSHSIGLVG 188

Query: 186 VESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE 233
           ++SR+E+IES+L +   DV  +G+WG+GGIGKT +A AIFD+IS+ +E
Sbjct: 189 IDSRLEQIESMLCLDMSDVRIIGVWGMGGIGKTTLAGAIFDQISAQYE 236

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224127754|ref|XP_002329169.1| tir-nbs-lrr resistance protein [Populus trichocarpa] gi|222870950|gb|EEF08081.1| tir-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  219 bits (558), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 113/229 (49%), Positives = 159/229 (69%), Gaps = 18/229 (7%)

Query: 23  KKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISV 82
           +KY+VF+SFRGEDTR  F SHLY+AL R+ I TFID +LNRG+EIS SL+ AIE S +SV
Sbjct: 13  EKYDVFLSFRGEDTRVCFVSHLYAALKRKQISTFIDYKLNRGEEISPSLLKAIEDSKLSV 72

Query: 83  IIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEE- 141
           ++FS++Y SS+WC++EL KILECKK   Q+VIPV YRVDPS VRNQTGSF D+F++ ++ 
Sbjct: 73  VVFSDNYASSKWCLEELAKILECKKVKGQMVIPVFYRVDPSHVRNQTGSFADAFARHDQL 132

Query: 142 FKEAAE-----LEECFEGSSQFVWLSFS--EHQRLLDEVFRPSDNK----------NQLA 184
            KE  E          E ++   W S +       +D++ R   NK            L 
Sbjct: 133 LKEKMEKVLNWRAAMREAANLSGWDSHNIKSESEFVDDIVRDILNKLHQTSMSTHHTSLI 192

Query: 185 GVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE 233
           G+++R++++E+LL ++S+DV  +GIWG+GGIGKT IA+A++D +S+ FE
Sbjct: 193 GIDARIKKVETLLKMESQDVRIVGIWGMGGIGKTTIAKAVYDNVSAQFE 241

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224145016|ref|XP_002325496.1| tir-nbs-lrr resistance protein [Populus trichocarpa] gi|222862371|gb|EEE99877.1| tir-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  218 bits (556), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 127/250 (50%), Positives = 160/250 (64%), Gaps = 29/250 (11%)

Query: 1   MASSSSSSHRSTSLGLIRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQ 60
           MASSSS +H+            +KY+VF+SFRGEDTR+ FTSHLY AL R+ I+TFIDD 
Sbjct: 1   MASSSSVAHK------------RKYDVFLSFRGEDTRNNFTSHLYDALCRKKIKTFIDDG 48

Query: 61  LNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRV 120
           L RG+EI+ +L+  IE S ISV+IFS++Y SS WCVDELVKILECK+   QIV+PV Y V
Sbjct: 49  LERGEEITPALLKKIEESRISVVIFSKNYASSPWCVDELVKILECKETCGQIVLPVFYHV 108

Query: 121 DPSDVRNQTGSFGDSFSKLEE-FKEAAELEECFEGSSQFV-----WLS--FSEHQRLLDE 172
           DPSDV  QTGSFG++FS+LE  FK   +    +     +      W S   S   +L+ E
Sbjct: 109 DPSDVDEQTGSFGNAFSELENIFKGKMDKVPRWRADMTYAASISGWDSQVTSPESKLVTE 168

Query: 173 VF--------RPSDNKNQ-LAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARA 223
           V         R S +K + L GV+SR+E+I  LL V   DV  +GIWG+G IGKT IA A
Sbjct: 169 VVQTIWKRLNRASRSKLRGLVGVDSRIEQINKLLSVVPSDVRRIGIWGMGAIGKTTIAEA 228

Query: 224 IFDKISSDFE 233
            F  ISS +E
Sbjct: 229 FFYSISSQYE 238

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133498|ref|XP_002328057.1| tir-nbs-lrr resistance protein [Populus trichocarpa] gi|222837466|gb|EEE75845.1| tir-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  218 bits (555), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 117/230 (50%), Positives = 157/230 (68%), Gaps = 21/230 (9%)

Query: 23  KKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISV 82
           KK+ VF+SFRGEDTR  FTSHL++AL R++I TFID+ L RG+EIS SLV AIE S +SV
Sbjct: 20  KKHHVFLSFRGEDTRVGFTSHLHAALERKNILTFIDNDLRRGEEISPSLVKAIEDSMLSV 79

Query: 83  IIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEEF 142
           IIFS++Y SS+WC+DEL+KILE +K   QI IPV Y VDPSD+R Q+GSFGD F++L + 
Sbjct: 80  IIFSQNYASSKWCLDELLKILESRKVRGQIAIPVFYEVDPSDIRKQSGSFGDVFAQLVKR 139

Query: 143 KE-AAELEECF------------------EGSSQFVWLSFSEHQRLLDEVFRPSDNKNQL 183
           K    E E+CF                  E  S+F+ +   +    L ++F P    N L
Sbjct: 140 KALKMEEEQCFRAALNEAANISGHDSRKIESESKFIEVIVEDILNKLCKIF-PVHPTN-L 197

Query: 184 AGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE 233
            G++  V +IESLL ++++DV  +GIWG+GGIGKT IARA+++KI + FE
Sbjct: 198 VGIDEHVRKIESLLDMETQDVRIVGIWGMGGIGKTTIARAVYNKICTKFE 247

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555357|ref|XP_002518715.1| leucine-rich repeat-containing protein, putative [Ricinus communis] gi|223542096|gb|EEF43640.1| leucine-rich repeat-containing protein, putative [Ricinus communis]

 Score =  218 bits (555), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 118/233 (50%), Positives = 154/233 (66%), Gaps = 26/233 (11%)

Query: 23  KKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISV 82
           +KY+VF+SFRGEDTR  FTSHL++AL+ + I TFIDD L RG+EIS SL+ AIE S ISV
Sbjct: 21  EKYDVFLSFRGEDTRYNFTSHLHAALNGKKIPTFIDDDLERGNEISPSLLKAIEESKISV 80

Query: 83  IIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEE- 141
           +I S+ Y SS+WC++ELVKILEC K   Q+VIPV YRVDPS VRNQTGSF D F++ EE 
Sbjct: 81  VIISQDYPSSKWCLEELVKILECMKNRGQMVIPVFYRVDPSHVRNQTGSFEDVFARHEES 140

Query: 142 --------------FKEAAELEECFEGSSQFVWLSFSEHQRLLDEV-------FRPSDNK 180
                          KE A L      S++      +E  + + EV         P+   
Sbjct: 141 LSVSKEKVQSWRAALKEVANLSGWHSTSTR----PEAEAVKEIIEVIVKKLNQMSPNCYS 196

Query: 181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE 233
             L G+ESR++EIESLL ++S +V  +GIWG+GG+GKT +ARAI+D+I+  FE
Sbjct: 197 RGLVGMESRIQEIESLLCLRSSNVRIVGIWGMGGLGKTTLARAIYDRIAPQFE 249

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550897|ref|XP_003543819.1| PREDICTED: TMV resistance protein N-like [Glycine max]

 Score =  213 bits (541), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 114/225 (50%), Positives = 150/225 (66%), Gaps = 16/225 (7%)

Query: 23  KKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISV 82
           KKY+VF+SFRGEDTR  FTSHLY AL ++ I+T+ID +L +GDEIS +L+ AIE S +SV
Sbjct: 18  KKYDVFLSFRGEDTRKNFTSHLYEALKQKKIETYIDYRLEKGDEISAALIKAIEDSHVSV 77

Query: 83  IIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLE-- 140
           +IFSE+Y SS+WC+ EL KI+ECKKE  QIVIPV Y +DPS VR QTGS+  SF+K    
Sbjct: 78  VIFSENYASSKWCLGELGKIMECKKERGQIVIPVFYNIDPSHVRKQTGSYEQSFAKHTGE 137

Query: 141 --------EFKEAAEL----EECFEGSSQFVWLSFSEHQRLLDEVFRPSDNKNQLAGVES 188
                      EAA L     + +   S+F+     +  R L    R  +++ +L GVE 
Sbjct: 138 PRCSKWKAALTEAANLAAWDSQIYRTESEFLKDIVKDVLRKLAP--RYPNHRKELVGVEE 195

Query: 189 RVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE 233
             E+IESLL + S  V  LGIWG+GGIGKT +A A++DK+S +FE
Sbjct: 196 NYEKIESLLKIGSSKVRILGIWGMGGIGKTTLASALYDKLSPEFE 240

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356545721|ref|XP_003541284.1| PREDICTED: protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1-like [Glycine max]

 Score =  209 bits (532), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 106/223 (47%), Positives = 149/223 (66%), Gaps = 12/223 (5%)

Query: 23  KKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISV 82
           KKY+VF+SFRGEDTR  FT HLY AL ++ I+T+ID+QL +GD+I+ +L  AIE S IS+
Sbjct: 22  KKYDVFLSFRGEDTRRNFTCHLYEALMQKKIKTYIDEQLEKGDQIALALTKAIEDSCISI 81

Query: 83  IIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEEF 142
           +IFS++Y SS+WC+ EL KILECKKE  QIVIPV Y +DPS VR Q GS+  +F+KLE  
Sbjct: 82  VIFSDNYASSKWCLGELFKILECKKEKGQIVIPVFYNIDPSHVRKQIGSYKQAFAKLEGE 141

Query: 143 KEAAELEECFEGSSQFVWL---SFSEHQRLLDEVFR------PSDNKNQ---LAGVESRV 190
            E  + ++    ++  V L   ++     LL ++ R      P   +NQ   L G+E   
Sbjct: 142 PECNKWKDALTEAANLVGLDSKNYRNDVELLKDIVRAVSEKLPRRYQNQSKGLVGIEEHY 201

Query: 191 EEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE 233
           + IES L   S +V  LGIWG+GGIGK+ +A A+++++S +FE
Sbjct: 202 KRIESFLNNGSSEVRTLGIWGMGGIGKSTLATALYNELSPEFE 244

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356569977|ref|XP_003553169.1| PREDICTED: TMV resistance protein N-like [Glycine max]

 Score =  208 bits (529), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 104/223 (46%), Positives = 148/223 (66%), Gaps = 12/223 (5%)

Query: 23  KKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISV 82
           KKY+VF+SFRGEDTR  FTSHLY AL ++ ++T+ID+ L +GDEIS +L+ AIE S +S+
Sbjct: 18  KKYDVFLSFRGEDTRRNFTSHLYEALKQKKVETYIDEHLEKGDEISPALIKAIEDSHVSI 77

Query: 83  IIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEEF 142
           ++FS++Y SS+WC+ EL+KIL+CKK+  QIVIPV Y +DPSDVR QTGS+  +F+K E  
Sbjct: 78  VVFSKNYASSKWCLVELIKILDCKKDRGQIVIPVFYEIDPSDVRKQTGSYEQAFAKHEGE 137

Query: 143 KEAAELEECFEGSSQFV-WLS--FSEHQRLLDEVFR------PSDNKNQ---LAGVESRV 190
               + +     ++    W S  +     LL ++        P   +NQ   L G+E   
Sbjct: 138 PSCNKWKTALTEAANLAGWDSRTYRTDPELLKDIVADVLQKLPPRYQNQRKGLVGIEEHC 197

Query: 191 EEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE 233
           + IESLL +   +V  LGIWG+GGIGKT +A  ++DK+S +FE
Sbjct: 198 KHIESLLKIGPTEVRTLGIWGMGGIGKTALATTLYDKLSHEFE 240

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224127234|ref|XP_002329433.1| predicted protein [Populus trichocarpa] gi|222870483|gb|EEF07614.1| predicted protein [Populus trichocarpa]

 Score =  207 bits (526), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 118/253 (46%), Positives = 158/253 (62%), Gaps = 32/253 (12%)

Query: 5   SSSSHRSTSLGLIRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRG 64
           S S    ++L   +P+   KY VF+SFRGEDTR  FTSHLY+AL+R+ I TFID QL RG
Sbjct: 22  SPSPSTPSTLTTAQPQV-MKYNVFLSFRGEDTRFDFTSHLYAALNRKQILTFIDYQLVRG 80

Query: 65  DEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSD 124
           DEIS SL+  IE + +SVI+FSE+Y SS+WC++EL KI E +K   QIVIPV Y+VDPS 
Sbjct: 81  DEISASLLRTIEEAKLSVIVFSENYASSKWCLEELAKIFERRKNNGQIVIPVFYQVDPSH 140

Query: 125 VRNQTGSFGDSFSKL---------------EEFKEAAELEECFEGSSQFVWLSFSEHQRL 169
           VRNQTGSFGD+F++L               +  K+ A L     G+SQ            
Sbjct: 141 VRNQTGSFGDAFARLIKKKALTMDKEQSFRDALKDTATLSGWTLGNSQL-------ESEF 193

Query: 170 LDEVFRPSDNKNQ---------LAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKI 220
           ++++     NK Q         L G++ RV ++ESLL ++S DV  +GI G+GGIGKT I
Sbjct: 194 IEKIVGDVSNKLQAMSSSHTTALFGIDVRVNKVESLLKMESPDVLIVGIRGMGGIGKTTI 253

Query: 221 ARAIFDKISSDFE 233
           A+A+ +K+ S FE
Sbjct: 254 AQAVSNKVRSRFE 266

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564976|ref|XP_002523481.1| TMV resistance protein N, putative [Ricinus communis] gi|223537309|gb|EEF38940.1| TMV resistance protein N, putative [Ricinus communis]

 Score =  207 bits (526), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 111/228 (48%), Positives = 149/228 (65%), Gaps = 18/228 (7%)

Query: 24  KYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVI 83
           KY+VFVSFRGEDTRD FTSHLY+AL ++ I+ F+DD+L+RG+EIS +LV  IE S +SVI
Sbjct: 15  KYDVFVSFRGEDTRDNFTSHLYAALHQKQIKAFVDDKLSRGEEISAALVKVIEESMVSVI 74

Query: 84  IFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSF------- 136
           IFSE+Y  S WC+DELVKILECKK   QIV+PV Y VDPSDV  Q G FG +F       
Sbjct: 75  IFSENYAFSPWCLDELVKILECKKTVGQIVLPVFYHVDPSDVAEQKGGFGAAFIEHEKCF 134

Query: 137 ----SKLEEFKEAAELEECFEGSSQFVWLSFSEH-QRLLDEVFRP------SDNKNQLAG 185
                KL++++ A        G S  V  S S+  Q + +++ +       S +   L G
Sbjct: 135 KERIDKLQKWRAALTEAANISGWSSSVIRSESKLIQEIAEDILKKLNHMSSSTDSKGLVG 194

Query: 186 VESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE 233
           + SR+++IE LL V+  DV  LG+WG+GG GKT  A  +F++IS+ F+
Sbjct: 195 INSRIDKIELLLCVELADVRFLGLWGMGGAGKTTTAEVVFNRISTQFD 242

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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	233
UNIPROTKB|Q40392	1144	N "TMV resistance protein N" [	0.480	0.097	0.557	3.8e-33
TAIR|locus:2130319	796	RLM3 "RESISTANCE TO LEPTOSPHAE	0.927	0.271	0.360	2.3e-32
TAIR|locus:1006230150	313	AT2G20142 [Arabidopsis thalian	0.484	0.361	0.578	2.9e-32
TAIR|locus:2153072	1229	AT5G51630 [Arabidopsis thalian	0.896	0.170	0.364	1.5e-31
TAIR|locus:2146253	1210	AT5G18370 [Arabidopsis thalian	0.480	0.092	0.482	3e-31
TAIR|locus:2160472	1038	AT5G41540 [Arabidopsis thalian	0.905	0.203	0.336	7.9e-31
TAIR|locus:2164486	1104	AT5G40910 [Arabidopsis thalian	0.918	0.193	0.340	1.1e-30
TAIR|locus:2136108	1095	AT4G11170 [Arabidopsis thalian	0.909	0.193	0.361	1.4e-30
TAIR|locus:2175075	1068	AT5G41750 [Arabidopsis thalian	0.901	0.196	0.346	1.8e-30
TAIR|locus:2118106	1219	AT4G12010 [Arabidopsis thalian	0.493	0.094	0.491	3.4e-30

UNIPROTKB|Q40392 N "TMV resistance protein N" [Nicotiana glutinosa (taxid:35889)]

 Score = 328 (120.5 bits), Expect = 3.8e-33, Sum P(2) = 3.8e-33
 Identities = 63/113 (55%), Positives = 81/113 (71%)

Query:    25 YEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQ-LNRGDEISQSLVNAIEASAISVI 83
             Y+VF+SFRGEDTR  FTSHLY  L+ + I+TF DD+ L  G  I   L  AIE S  +++
Sbjct:    12 YDVFLSFRGEDTRKTFTSHLYEVLNDKGIKTFQDDKRLEYGATIPGELCKAIEESQFAIV 71

Query:    84 IFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSF 136
             +FSE+Y +SRWC++ELVKI+ECK  + Q VIP+ Y VDPS VRNQ  SF  +F
Sbjct:    72 VFSENYATSRWCLNELVKIMECKTRFKQTVIPIFYDVDPSHVRNQKESFAKAF 124

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2130319 RLM3 "RESISTANCE TO LEPTOSPHAERIA MACULANS 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 363 (132.8 bits), Expect = 2.3e-32, P = 2.3e-32
 Identities = 83/230 (36%), Positives = 124/230 (53%)

Query:    17 IRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIE 76
             ++  +++ Y+VF +FRGED R    SHL   L R+ I TF D+++ R  +I+  L+ AIE
Sbjct:     1 MKSSSSQSYDVFPNFRGEDVRHSLVSHLRKELDRKFINTFNDNRIERSRKITPELLLAIE 60

Query:    77 ASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSF 136
              S IS+++FS++Y SS WC+DELVKI EC ++  Q+VIP+ Y+VDPS VR QTG FG  F
Sbjct:    61 NSRISLVVFSKNYASSTWCLDELVKIQECYEKLDQMVIPIFYKVDPSHVRKQTGEFGMVF 120

Query:   137 SXXXXXXX---------XXXXXXXXXGSSQFVWLSFSEH-QRLLDEV----FRPSDNKNQ 182
                                       G     W S +E  + +  +V    F PS+N + 
Sbjct:   121 GETCKGRTENEKRKWMRALAEVAHLAGEDLRNWRSEAEMLENIAKDVSNKLFPPSNNFSD 180

Query:   183 LAGVESRVEEIESLLGVKSKDVYALXXXXXXXXXKTKIARAIFDKISSDF 232
               G+E+ +E + S+L   SK    +         KT I RA++ ++ SDF
Sbjct:   181 FVGIEAHIEALISMLRFDSKKARMIGICGPSETGKTTIGRALYSRLKSDF 230

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

GO:0009817 "defense response to fungus, incompatible interaction" evidence=IMP

GO:0009861 "jasmonic acid and ethylene-dependent systemic resistance" evidence=IMP

GO:2000071 "regulation of defense response by callose deposition" evidence=IMP

GO:0015979 "photosynthesis" evidence=RCA

TAIR|locus:1006230150 AT2G20142 [Arabidopsis thaliana (taxid:3702)]

 Score = 353 (129.3 bits), Expect = 2.9e-32, P = 2.9e-32
 Identities = 66/114 (57%), Positives = 88/114 (77%)

Query:    24 KYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVI 83
             K++VF+SFR +DTRD F SHL   L R+ I+TF+ D+L   +   +SL  AIE S ISVI
Sbjct:     8 KHDVFISFRSKDTRDNFVSHLCGCLRRKRIKTFLYDELPADERYEESL-KAIEVSKISVI 66

Query:    84 IFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFS 137
             +FSE++  SRWC+DE+V IL+CK+++ QIVIPVLY VDP D+ NQTGSFGD+F+
Sbjct:    67 VFSENFGDSRWCLDEVVAILKCKEKFGQIVIPVLYHVDPLDIENQTGSFGDAFA 120

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0007165 "signal transduction" evidence=IEA

TAIR|locus:2153072 AT5G51630 [Arabidopsis thaliana (taxid:3702)]

 Score = 359 (131.4 bits), Expect = 1.5e-31, P = 1.5e-31
 Identities = 82/225 (36%), Positives = 122/225 (54%)

Query:    25 YEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVII 84
             Y+VF SF GED R  F SHL   L R+SI TFID+ + R   I+  L++AI  S IS+++
Sbjct:    11 YDVFPSFSGEDVRKSFLSHLLKKLHRKSINTFIDNNIERSHAIAPDLLSAINNSMISIVV 70

Query:    85 FSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSXXXXXXX 144
             FS+ Y SS WC++ELV+I +C KE  QIVIP+ Y VDPSDVR QT  FG+ F        
Sbjct:    71 FSKKYASSTWCLNELVEIHKCYKELTQIVIPIFYEVDPSDVRKQTREFGEFFKVTCVGKT 130

Query:   145 ---------XXXXXXXXXGSSQFVW---LSFSEH--QRLLDEVFRPSDNK--NQLAGVES 188
                               G     W    +  EH  + +L+++   S +     L G+E+
Sbjct:   131 EDVKQQWIEALEEVASIAGHDSKNWPNEANMIEHIAKDVLNKLIATSSSNCFGDLVGIEA 190

Query:   189 RVEEIESLLGVKSKDVYALXXXXXXXXXKTKIARAIFDKISSDFE 233
              ++ ++S+L ++S++   +         KT IAR ++ K+SS F+
Sbjct:   191 HLKAVKSILCLESEEARMVGILGPSGIGKTTIARILYSKLSSQFD 235

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2146253 AT5G18370 [Arabidopsis thaliana (taxid:3702)]

 Score = 300 (110.7 bits), Expect = 3.0e-31, Sum P(2) = 3.0e-31
 Identities = 54/112 (48%), Positives = 76/112 (67%)

Query:    25 YEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVII 84
             ++VF SFRGED R  F SH+      + I  FIDD++ RG+ I   L  AI  S I++++
Sbjct:    61 HQVFPSFRGEDVRKGFLSHIQKEFKSKGIVPFIDDEMKRGESIGPGLFQAIRESKIAIVL 120

Query:    85 FSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSF 136
              S++Y SS WC++ELV+I+ C++E  Q V+ V Y+VDPSDVR QTG FG +F
Sbjct:   121 LSKNYASSSWCLNELVEIMNCREEIGQTVMTVFYQVDPSDVRKQTGDFGKAF 172

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2160472 AT5G41540 [Arabidopsis thaliana (taxid:3702)]

 Score = 351 (128.6 bits), Expect = 7.9e-31, P = 7.9e-31
 Identities = 76/226 (33%), Positives = 124/226 (54%)

Query:    23 KKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISV 82
             +KY VF SF G D R KF SHL    + + I  F D ++ RG  I   LV AI  S +S+
Sbjct:     9 RKYHVFPSFHGSDVRRKFLSHLRFHFAIKGIVAFKDQEIERGQRIGPELVQAIRESRVSL 68

Query:    83 IIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSXXXXX 142
             ++ S++Y SS WC+DELV+IL+CK++  QIV+P+ Y +DPSDVR Q+G FG +F      
Sbjct:    69 VVLSKNYPSSSWCLDELVEILKCKEDQEQIVMPIFYEIDPSDVRKQSGDFGKAFGKTCVG 128

Query:   143 XX---------XXXXXXXXXGSSQFVWLSFSEH-QRLLDEVFR-----PSDNKNQLAGVE 187
                                 G     W   +E  ++++ +V       PS +  ++ G++
Sbjct:   129 KTKEVKQRWTNALTEAANIGGEHSLNWTDEAEMIEKIVADVSNKLNVIPSRDFEEMVGLD 188

Query:   188 SRVEEIESLLGVKSKDVYALXXXXXXXXXKTKIARAIFDKISSDFE 233
             + + +++SLL + S +V  +         KT IARA+++++S++F+
Sbjct:   189 AHLRKLDSLLCLNSDEVKMIGIWGPAGIGKTTIARALYNQLSTNFQ 234

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2164486 AT5G40910 [Arabidopsis thaliana (taxid:3702)]

 Score = 350 (128.3 bits), Expect = 1.1e-30, P = 1.1e-30
 Identities = 78/229 (34%), Positives = 120/229 (52%)

Query:    19 PRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEAS 78
             P + K+Y VF SF G D R  F SHL++    + I  F D ++ RG  I   L+ AI  S
Sbjct:     6 PSDFKRYHVFSSFHGPDVRSGFLSHLHNHFESKGITPFKDQEIERGHTIGPELIQAIRES 65

Query:    79 AISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSX 138
              +S+++ SE Y SS WC+DELV+IL+CK+   Q+V+ + Y+VDPSDVR Q G FG +F  
Sbjct:    66 RVSIVVLSEKYASSCWCLDELVEILKCKEASGQVVMTIFYKVDPSDVRKQRGDFGSTFKK 125

Query:   139 XXXXXX---------XXXXXXXXXGSSQFVWLSFSEH-QRLLDEV-----FRPSDNKNQL 183
                                     G     W + +E  Q++  +V       PS +   +
Sbjct:   126 TCEGKTWIVKQRWIKALEYIATVAGEHSLSWANEAELIQKIATDVSNKLNLTPSRDFEGM 185

Query:   184 AGVESRVEEIESLLGVKSKDVYALXXXXXXXXXKTKIARAIFDKISSDF 232
              G+E+ + +++S L ++S DV  +         KT IARA+F+++S+ F
Sbjct:   186 VGLEAHLTKLDSFLCLESDDVKMIGIWGPAGIGKTTIARALFNQLSTGF 234

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2136108 AT4G11170 [Arabidopsis thaliana (taxid:3702)]

 Score = 349 (127.9 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 82/227 (36%), Positives = 120/227 (52%)

Query:    21 NNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAI 80
             N+ +Y+VF SFRGED R+ F SHL      + I TF DD + R   I   L  AI  S I
Sbjct:     7 NSWRYDVFPSFRGEDVRNNFLSHLLKEFESKGIVTFRDDHIKRSHTIGHELRAAIRESKI 66

Query:    81 SVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSXXX 140
             SV++FSE+Y SS WC+DEL++I++CK+E    V+PV Y+VDPSD+R QTG FG SF    
Sbjct:    67 SVVLFSENYASSSWCLDELIEIMKCKEEQGLKVMPVFYKVDPSDIRKQTGKFGMSFLETC 126

Query:   141 XXXXXXXXXXXXXGSSQFVWLSFSEHQRLLDEVFR---------------PSDNKNQLAG 185
                            +    +     Q   +E ++               PS + N L G
Sbjct:   127 CGKTEERQHNWRRALTDAANILGDHPQNWDNEAYKITTISKDVLEKLNATPSRDFNDLVG 186

Query:   186 VESRVEEIESLLGVKSKDVYALXXXXXXXXXKTKIARAIFDKISSDF 232
             +E+ + ++ESLL ++S+ V  +         KT IARA++++   +F
Sbjct:   187 MEAHIAKMESLLCLESQGVRIVGIWGPAGVGKTTIARALYNQYHENF 233

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0010193 "response to ozone" evidence=IEP

TAIR|locus:2175075 AT5G41750 [Arabidopsis thaliana (taxid:3702)]

 Score = 348 (127.6 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 78/225 (34%), Positives = 122/225 (54%)

Query:    23 KKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISV 82
             K+Y+VF SF G D R  F SHL+S  + + I TF D +++RG  I   L+  I  + +S+
Sbjct:    11 KRYQVFSSFHGPDVRKGFLSHLHSVFASKGITTFNDQKIDRGQTIGPELIQGIREARVSI 70

Query:    83 IIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSXXXXX 142
             ++ S+ Y SS WC+DELV+IL+CK+   QIV+ V Y VDPSDV+ Q+G FG++F      
Sbjct:    71 VVLSKKYASSSWCLDELVEILKCKEALGQIVMTVFYEVDPSDVKKQSGVFGEAFEKTCQG 130

Query:   143 XX---------XXXXXXXXXGSSQFVWLSFSEH-QRLLDEV-----FRPSDNKNQLAGVE 187
                                 G     W + ++  Q+++ +V       PS +   + G+E
Sbjct:   131 KNEEVKIRWRNALAHVATIAGEHSLNWDNEAKMIQKIVTDVSDKLNLTPSRDFEGMVGME 190

Query:   188 SRVEEIESLLGVKSKDVYALXXXXXXXXXKTKIARAIFDKISSDF 232
             + ++ + SLL ++S +V  +         KT IAR +F+KISS F
Sbjct:   191 AHLKRLNSLLCLESDEVKMIGIWGPAGIGKTTIARTLFNKISSIF 235

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2118106 AT4G12010 [Arabidopsis thaliana (taxid:3702)]

 Score = 305 (112.4 bits), Expect = 3.4e-30, Sum P(2) = 3.4e-30
 Identities = 57/116 (49%), Positives = 82/116 (70%)

Query:    21 NNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAI 80
             ++ +++VF+SFRG DTR+ FT HL  AL  + I +FIDD+L RGD ++ +L + IE S I
Sbjct:     7 SSAEFDVFLSFRGFDTRNNFTGHLQKALRLRGIDSFIDDRLRRGDNLT-ALFDRIEKSKI 65

Query:    81 SVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSF 136
             ++I+FS +Y +S WC+ ELVKILEC+    Q+V+P+ Y+VD SDV  Q  SF   F
Sbjct:    66 AIIVFSTNYANSAWCLRELVKILECRNSNQQLVVPIFYKVDKSDVEKQRNSFAVPF 121

GO:0005634 "nucleus" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	233
PLN03210	1153	PLN03210, PLN03210, Resistant to P	6e-53
pfam01582	135	pfam01582, TIR, TIR domain	3e-37
smart00255	140	smart00255, TIR, Toll - interleukin 1 - resistance	1e-32
PLN03194	187	PLN03194, PLN03194, putative disease resistance pr	3e-13
pfam13676	102	pfam13676, TIR_2, TIR domain	5e-12

>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P

 Score =  183 bits (465), Expect = 6e-53
 Identities = 95/251 (37%), Positives = 140/251 (55%), Gaps = 33/251 (13%)

Query: 1   MASSSSSSHRSTSLGLIRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQ 60
           MASSSSSS             N  Y+VF SF GED R  F SH    L R+ I  F D++
Sbjct: 1   MASSSSSSR------------NWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDNE 48

Query: 61  LNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRV 120
           + R   +   L  AI  S I+V++FS++Y SS WC++EL++I+ CK+E  Q+VIPV Y +
Sbjct: 49  IERSQSLDPELKQAIRDSRIAVVVFSKNYASSSWCLNELLEIVRCKEELGQLVIPVFYGL 108

Query: 121 DPSDVRNQTGSFGDSFSKL---------EEFKEAAELEECFEGSSQFVWLSFSEHQRLLD 171
           DPS VR QTG FG++F K           ++K+A        G     W   +E + +++
Sbjct: 109 DPSHVRKQTGDFGEAFEKTCQNKTEDEKIQWKQALTDVANILGYHSQNW--PNEAK-MIE 165

Query: 172 EV---------FRPSDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIAR 222
           E+           PS++     G+E  + ++ SLL ++S++V  +GIWG  GIGKT IAR
Sbjct: 166 EIANDVLGKLNLTPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIAR 225

Query: 223 AIFDKISSDFE 233
           A+F ++S  F+
Sbjct: 226 ALFSRLSRQFQ 236

syringae 6; Provisional. Length = 1153

>gnl|CDD|216585 pfam01582, TIR, TIR domain

 Score =  127 bits (320), Expect = 3e-37
 Identities = 55/118 (46%), Positives = 78/118 (66%), Gaps = 3/118 (2%)

Query: 27  VFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIF 85
           VFVSF G+D RD F SHL   L  + I+  IDD     G+ I ++L  AIE S  +++IF
Sbjct: 1   VFVSFSGKDDRDTFVSHLLKELEEKGIKLCIDDRDELPGESILENLFEAIEKSRRAIVIF 60

Query: 86  SESYTSSRWCVDELVKILECKKE--YAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEE 141
           S +Y SS WC+DELV+I++C  E    ++++P+ Y+VDPSDVR Q+G FG +F K  +
Sbjct: 61  SSNYASSEWCLDELVEIVKCALEGGGKKVILPIFYKVDPSDVRPQSGKFGKAFLKTLK 118

The Toll/interleukin-1 receptor (TIR) homology domain is an intracellular signalling domain found in MyD88, interleukin 1 receptor and the Toll receptor. It contains three highly-conserved regions, and mediates protein-protein interactions between the Toll-like receptors (TLRs) and signal-transduction components. TIR-like motifs are also found in plant proteins thought to be involved in resistance to disease. When activated, TIR domains recruit cytoplasmic adaptor proteins MyD88 and TOLLIP (Toll interacting protein). In turn, these associate with various kinases to set off signalling cascades. Length = 135

>gnl|CDD|214587 smart00255, TIR, Toll - interleukin 1 - resistance

 Score =  115 bits (289), Expect = 1e-32
 Identities = 50/117 (42%), Positives = 67/117 (57%), Gaps = 3/117 (2%)

Query: 24  KYEVFVSFRG-EDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISV 82
           +Y+VF+S+ G ED R++F SHL   L    +  FIDD    G    + +  AIE S I++
Sbjct: 1   EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFE-PGGGDLEEIDEAIEKSRIAI 59

Query: 83  IIFSESYTSSRWCVDELVKILECKKEYAQI-VIPVLYRVDPSDVRNQTGSFGDSFSK 138
           ++ S +Y  S WC+DELV  LE   E   + VIP+ Y V PSDVR Q G F   F K
Sbjct: 60  VVLSPNYAESEWCLDELVAALENALEEGGLRVIPIFYEVIPSDVRKQPGKFRKVFKK 116

Length = 140

>gnl|CDD|215626 PLN03194, PLN03194, putative disease resistance protein; Provisional

 Score = 65.6 bits (160), Expect = 3e-13
 Identities = 40/129 (31%), Positives = 66/129 (51%), Gaps = 14/129 (10%)

Query: 8   SHRSTSLGLIR---------PRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFID 58
             RS++  L             + K  +VF++ RG DT+    + LY  LSR +++ F+D
Sbjct: 1   MKRSSTAQLNNRLFLHYPSSSSSAKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLD 60

Query: 59  DQ-LNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVL 117
           ++ +  GD++   + +AI    + V +FS  Y  S +C+ EL  I+E KK     VIP+ 
Sbjct: 61  NKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYFCLHELALIMESKKR----VIPIF 116

Query: 118 YRVDPSDVR 126
             V PS +R
Sbjct: 117 CDVKPSQLR 125

Length = 187

>gnl|CDD|222311 pfam13676, TIR_2, TIR domain

 Score = 60.3 bits (147), Expect = 5e-12
 Identities = 24/99 (24%), Positives = 48/99 (48%), Gaps = 8/99 (8%)

Query: 27  VFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFS 86
           VF+S+   D    +   L  AL    I+ ++D  +  G++    +  A+ ++ + +++ S
Sbjct: 1   VFISYASADRE--WAEWLADALEAAGIRVWLDWDIPPGEDWRDEIEEALRSADVVLVLLS 58

Query: 87  ESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDV 125
            +Y +S WC  E    LE  K     +IPV  R++  ++
Sbjct: 59  PAYLASPWCRAEWGAALERGK----RLIPV--RLEDCEL 91

This is a family of bacterial Toll-like receptors. Length = 102

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	233
PLN03210	1153	Resistant to P. syringae 6; Provisional	100.0
PLN03194	187	putative disease resistance protein; Provisional	100.0
PF01582	141	TIR: TIR domain; InterPro: IPR000157 In Drosophila	99.88
smart00255	140	TIR Toll - interleukin 1 - resistance.	99.87
PF13676	102	TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_	99.72
KOG3678	832	consensus SARM protein (with sterile alpha and arm	98.89
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	98.55
PF08937	130	DUF1863: MTH538 TIR-like domain (DUF1863); InterPr	98.53
PF08357	150	SEFIR: SEFIR domain; InterPro: IPR013568 This doma	97.99
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.59
PTZ00202	550	tuzin; Provisional	97.58
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	97.51
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	97.46
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.39
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.17
PRK13342	413	recombination factor protein RarA; Reviewed	97.05
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	96.92
PF10137	125	TIR-like: Predicted nucleotide-binding protein con	96.91
PRK03992	389	proteasome-activating nucleotidase; Provisional	96.85
PRK04195	482	replication factor C large subunit; Provisional	96.84
COG2256	436	MGS1 ATPase related to the helicase subunit of the	96.83
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.73
PRK12402	337	replication factor C small subunit 2; Reviewed	96.65
PHA02544	316	44 clamp loader, small subunit; Provisional	96.65
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	96.63
CHL00095	821	clpC Clp protease ATP binding subunit	96.62
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	96.59
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.52
PRK13341	725	recombination factor protein RarA/unknown domain f	96.52
PRK15455	644	PrkA family serine protein kinase; Provisional	96.51
PLN03025	319	replication factor C subunit; Provisional	96.49
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	96.45
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.42
PRK00440	319	rfc replication factor C small subunit; Reviewed	96.42
PRK09376	416	rho transcription termination factor Rho; Provisio	96.4
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.37
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	96.35
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	96.29
PRK10865	857	protein disaggregation chaperone; Provisional	96.27
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.27
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.25
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	96.18
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.16
PRK06893	229	DNA replication initiation factor; Validated	96.15
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.15
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	96.13
KOG2028	554	consensus ATPase related to the helicase subunit o	96.13
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	96.12
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.1
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.09
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	96.05
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	96.05
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	96.0
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	95.94
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	95.94
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	95.93
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	95.89
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	95.87
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	95.87
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	95.82
PLN02318	656	phosphoribulokinase/uridine kinase	95.79
PRK05439	311	pantothenate kinase; Provisional	95.76
CHL00181	287	cbbX CbbX; Provisional	95.72
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.72
PRK09435	332	membrane ATPase/protein kinase; Provisional	95.69
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	95.69
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.68
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	95.63
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	95.6
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	95.57
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	95.56
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	95.54
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	95.53
PLN02348	395	phosphoribulokinase	95.48
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	95.46
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	95.46
PRK09087	226	hypothetical protein; Validated	95.45
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	95.44
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	95.43
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	95.42
PLN02200	234	adenylate kinase family protein	95.39
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	95.37
PRK14974	336	cell division protein FtsY; Provisional	95.36
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	95.36
PLN02796	347	D-glycerate 3-kinase	95.35
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	95.35
TIGR00767	415	rho transcription termination factor Rho. Members	95.34
PRK08099	399	bifunctional DNA-binding transcriptional repressor	95.33
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	95.29
CHL00176	638	ftsH cell division protein; Validated	95.27
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	95.26
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	95.25
PRK09112	351	DNA polymerase III subunit delta'; Validated	95.24
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	95.22
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	95.22
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	95.21
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	95.2
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	95.19
PRK08084	235	DNA replication initiation factor; Provisional	95.18
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	95.17
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	95.16
PRK08727	233	hypothetical protein; Validated	95.16
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	95.16
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	95.13
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	95.1
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	95.09
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	95.07
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	95.07
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	95.06
PRK12289	352	GTPase RsgA; Reviewed	95.06
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	95.02
PRK13531	498	regulatory ATPase RavA; Provisional	95.0
PRK10416	318	signal recognition particle-docking protein FtsY;	94.99
PRK06620	214	hypothetical protein; Validated	94.98
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	94.93
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	94.89
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	94.86
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	94.84
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	94.83
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	94.83
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	94.8
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	94.78
PRK12377	248	putative replication protein; Provisional	94.77
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	94.77
PRK00771	437	signal recognition particle protein Srp54; Provisi	94.74
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	94.73
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	94.71
PRK07952	244	DNA replication protein DnaC; Validated	94.69
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	94.68
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	94.68
TIGR03596	276	GTPase_YlqF ribosome biogenesis GTP-binding protei	94.67
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	94.63
PRK14489	366	putative bifunctional molybdopterin-guanine dinucl	94.62
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	94.62
PLN02165	334	adenylate isopentenyltransferase	94.61
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	94.53
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	94.5
PRK07471	365	DNA polymerase III subunit delta'; Validated	94.48
PRK05642	234	DNA replication initiation factor; Validated	94.46
PRK09183	259	transposase/IS protein; Provisional	94.46
cd01858	157	NGP_1 NGP-1. Autoantigen NGP-1 (Nucleolar G-protei	94.46
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	94.45
PLN02199	303	shikimate kinase	94.44
PRK08116	268	hypothetical protein; Validated	94.43
PLN03046	460	D-glycerate 3-kinase; Provisional	94.43
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	94.41
TIGR03594	429	GTPase_EngA ribosome-associated GTPase EngA. EngA	94.38
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	94.37
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	94.37
PRK04220	301	2-phosphoglycerate kinase; Provisional	94.36
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	94.35
PRK10584	228	putative ABC transporter ATP-binding protein YbbA;	94.33
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	94.31
PRK06526	254	transposase; Provisional	94.28
KOG1969	877	consensus DNA replication checkpoint protein CHL12	94.27
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	94.27
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	94.25
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	94.25
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	94.23
PRK10536	262	hypothetical protein; Provisional	94.19
PRK00149	450	dnaA chromosomal replication initiation protein; R	94.19
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	94.18
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	94.18
PRK11629	233	lolD lipoprotein transporter ATP-binding subunit;	94.17
COG4240	300	Predicted kinase [General function prediction only	94.16
PHA02244	383	ATPase-like protein	94.15
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	94.14
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	94.14
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	94.13
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	94.12
PRK03003	472	GTP-binding protein Der; Reviewed	94.11
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	94.1
TIGR02211	221	LolD_lipo_ex lipoprotein releasing system, ATP-bin	94.09
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	94.08
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	94.02
COG1123	539	ATPase components of various ABC-type transport sy	94.0
PRK10247	225	putative ABC transporter ATP-binding protein YbbL;	94.0
cd03257	228	ABC_NikE_OppD_transporters The ABC transporter sub	93.96
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	93.96
PF13245	76	AAA_19: Part of AAA domain	93.92
PRK10619	257	histidine/lysine/arginine/ornithine transporter su	93.92
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	93.86
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	93.85
PRK11300	255	livG leucine/isoleucine/valine transporter ATP-bin	93.84
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	93.83
PRK12288	347	GTPase RsgA; Reviewed	93.82
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	93.8
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	93.79
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	93.79
PRK10867	433	signal recognition particle protein; Provisional	93.79
PRK06921	266	hypothetical protein; Provisional	93.76
TIGR02324	224	CP_lyasePhnL phosphonate C-P lyase system protein	93.73
COG0714	329	MoxR-like ATPases [General function prediction onl	93.72
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	93.71
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	93.69
TIGR01526	325	nadR_NMN_Atrans nicotinamide-nucleotide adenylyltr	93.68
PRK14242	253	phosphate transporter ATP-binding protein; Provisi	93.68
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	93.68
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	93.68
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	93.67
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	93.66
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	93.62
cd03267	236	ABC_NatA_like Similar in sequence to NatA, this is	93.62
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	93.62
PRK10575	265	iron-hydroxamate transporter ATP-binding subunit;	93.61
PF13271	83	DUF4062: Domain of unknown function (DUF4062)	93.61
PRK11022	326	dppD dipeptide transporter ATP-binding subunit; Pr	93.6
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	93.58
PRK11247	257	ssuB aliphatic sulfonates transport ATP-binding su	93.58
TIGR02236	310	recomb_radA DNA repair and recombination protein R	93.55
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	93.54
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	93.54
PRK14274	259	phosphate ABC transporter ATP-binding protein; Pro	93.53
PRK10646	153	ADP-binding protein; Provisional	93.52
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	93.5
PRK15093	330	antimicrobial peptide ABC transporter ATP-binding	93.49
PTZ00035	337	Rad51 protein; Provisional	93.48
PRK12422	445	chromosomal replication initiation protein; Provis	93.48
cd03220	224	ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transpo	93.47
PRK14248	268	phosphate ABC transporter ATP-binding protein; Pro	93.47
PRK14238	271	phosphate transporter ATP-binding protein; Provisi	93.44
COG4107	258	PhnK ABC-type phosphonate transport system, ATPase	93.42
cd03294	269	ABC_Pro_Gly_Bertaine This family comprises the gly	93.4
PRK10865	857	protein disaggregation chaperone; Provisional	93.39
PRK10744	260	pstB phosphate transporter ATP-binding protein; Pr	93.39
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	93.37
cd03216	163	ABC_Carb_Monos_I This family represents the domain	93.36
PRK13645	289	cbiO cobalt transporter ATP-binding subunit; Provi	93.36
PRK11701	258	phnK phosphonate C-P lyase system protein PhnK; Pr	93.36
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	93.35
PRK14239	252	phosphate transporter ATP-binding protein; Provisi	93.34
PRK11831	269	putative ABC transporter ATP-binding protein YrbF;	93.33
PRK14243	264	phosphate transporter ATP-binding protein; Provisi	93.32
PRK15056	272	manganese/iron transporter ATP-binding protein; Pr	93.32
PRK13649	280	cbiO cobalt transporter ATP-binding subunit; Provi	93.31
PRK14255	252	phosphate ABC transporter ATP-binding protein; Pro	93.31
PRK11308	327	dppF dipeptide transporter ATP-binding subunit; Pr	93.31
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	93.29
PRK09473	330	oppD oligopeptide transporter ATP-binding componen	93.28
CHL00131	252	ycf16 sulfate ABC transporter protein; Validated	93.27
PRK06835	329	DNA replication protein DnaC; Validated	93.26
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	93.25
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	93.25
PRK14261	253	phosphate ABC transporter ATP-binding protein; Pro	93.23
cd03234	226	ABCG_White The White subfamily represents ABC tran	93.23
COG0444	316	DppD ABC-type dipeptide/oligopeptide/nickel transp	93.21
PRK14259	269	phosphate ABC transporter ATP-binding protein; Pro	93.21
PRK11823	446	DNA repair protein RadA; Provisional	93.2
PRK14273	254	phosphate ABC transporter ATP-binding protein; Pro	93.18
PRK13477	512	bifunctional pantoate ligase/cytidylate kinase; Pr	93.18
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	93.18
PRK14260	259	phosphate ABC transporter ATP-binding protein; Pro	93.16
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	93.15
cd03248	226	ABCC_TAP TAP, the Transporter Associated with Anti	93.15
PRK13632	271	cbiO cobalt transporter ATP-binding subunit; Provi	93.13
PRK14088	440	dnaA chromosomal replication initiation protein; P	93.12
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	93.11
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	93.11
PRK14237	267	phosphate transporter ATP-binding protein; Provisi	93.1
CHL00195	489	ycf46 Ycf46; Provisional	93.1
cd01856	171	YlqF YlqF. Proteins of the YlqF family contain all	93.08
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	93.07
cd01855	190	YqeH YqeH. YqeH is an essential GTP-binding protei	93.05
PRK14235	267	phosphate transporter ATP-binding protein; Provisi	93.03
PRK14265	274	phosphate ABC transporter ATP-binding protein; Pro	93.03
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	93.02
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	93.02
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	93.01
cd00983	325	recA RecA is a bacterial enzyme which has roles in	93.01
TIGR03238	504	dnd_assoc_3 dnd system-associated protein 3. cereu	93.0
PRK13640	282	cbiO cobalt transporter ATP-binding subunit; Provi	92.99
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	92.98
PRK11614	237	livF leucine/isoleucine/valine transporter ATP-bin	92.97
PRK14244	251	phosphate ABC transporter ATP-binding protein; Pro	92.95
COG1484	254	DnaC DNA replication protein [DNA replication, rec	92.93
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	92.9
COG1245	591	Predicted ATPase, RNase L inhibitor (RLI) homolog	92.84
PRK15079	331	oligopeptide ABC transporter ATP-binding protein O	92.84
PRK08181	269	transposase; Validated	92.84
PRK05022	509	anaerobic nitric oxide reductase transcription reg	92.84
PRK13546	264	teichoic acids export protein ATP-binding subunit;	92.82
PRK14271	276	phosphate ABC transporter ATP-binding protein; Pro	92.81
PRK04301	317	radA DNA repair and recombination protein RadA; Va	92.81
PRK14236	272	phosphate transporter ATP-binding protein; Provisi	92.8
PRK13648	269	cbiO cobalt transporter ATP-binding subunit; Provi	92.79
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	92.78
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	92.77
PRK12337	475	2-phosphoglycerate kinase; Provisional	92.76
TIGR02769	265	nickel_nikE nickel import ATP-binding protein NikE	92.74
PRK11153	343	metN DL-methionine transporter ATP-binding subunit	92.73
PRK13650	279	cbiO cobalt transporter ATP-binding subunit; Provi	92.72
cd01853	249	Toc34_like Toc34-like (Translocon at the Outer-env	92.71
PRK10419	268	nikE nickel transporter ATP-binding protein NikE;	92.7
PRK13765	637	ATP-dependent protease Lon; Provisional	92.7
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	92.69
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	92.68
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	92.65
cd03291	282	ABCC_CFTR1 The CFTR subfamily domain 1. The cystic	92.64
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	92.64
PRK10253	265	iron-enterobactin transporter ATP-binding protein;	92.64
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	92.63
PRK09518	712	bifunctional cytidylate kinase/GTPase Der; Reviewe	92.58
TIGR02314	343	ABC_MetN D-methionine ABC transporter, ATP-binding	92.57
PLN02674	244	adenylate kinase	92.57
PRK13647	274	cbiO cobalt transporter ATP-binding subunit; Provi	92.55
PRK15112	267	antimicrobial peptide ABC system ATP-binding prote	92.55
PRK14268	258	phosphate ABC transporter ATP-binding protein; Pro	92.55
PRK14252	265	phosphate ABC transporter ATP-binding protein; Pro	92.48
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	92.46
PRK14258	261	phosphate ABC transporter ATP-binding protein; Pro	92.46
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	92.46
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	92.43
cd03250	204	ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.	92.42
PRK09354	349	recA recombinase A; Provisional	92.42
KOG0062	582	consensus ATPase component of ABC transporters wit	92.39
PRK14275	286	phosphate ABC transporter ATP-binding protein; Pro	92.38
PRK13646	286	cbiO cobalt transporter ATP-binding subunit; Provi	92.37
cd01854	287	YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtil	92.31
PRK03003	472	GTP-binding protein Der; Reviewed	92.24
TIGR02982	220	heterocyst_DevA ABC exporter ATP-binding subunit,	92.23
PRK13636	283	cbiO cobalt transporter ATP-binding subunit; Provi	92.21
PRK13641	287	cbiO cobalt transporter ATP-binding subunit; Provi	92.18
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	92.16
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	92.14
PRK13851	344	type IV secretion system protein VirB11; Provision	92.13
PRK13637	287	cbiO cobalt transporter ATP-binding subunit; Provi	92.11
TIGR00157	245	ribosome small subunit-dependent GTPase A. The Aqu	92.04
PRK14254	285	phosphate ABC transporter ATP-binding protein; Pro	92.04
PRK00098	298	GTPase RsgA; Reviewed	92.04
PRK13651	305	cobalt transporter ATP-binding subunit; Provisiona	92.01
PRK13631	320	cbiO cobalt transporter ATP-binding subunit; Provi	92.0
CHL00095	821	clpC Clp protease ATP binding subunit	92.0
PRK13635	279	cbiO cobalt transporter ATP-binding subunit; Provi	91.99
PRK14264	305	phosphate ABC transporter ATP-binding protein; Pro	91.98
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	91.96
PRK13643	288	cbiO cobalt transporter ATP-binding subunit; Provi	91.95
PRK14263	261	phosphate ABC transporter ATP-binding protein; Pro	91.95
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	91.91
PRK08939	306	primosomal protein DnaI; Reviewed	91.89
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	91.89
PF13555	62	AAA_29: P-loop containing region of AAA domain	91.87
COG1072	283	CoaA Panthothenate kinase [Coenzyme metabolism]	91.87
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	91.83
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	91.82
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	91.78
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	91.75
PRK14087	450	dnaA chromosomal replication initiation protein; P	91.7
PRK05973	237	replicative DNA helicase; Provisional	91.68
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	91.68
COG1245	591	Predicted ATPase, RNase L inhibitor (RLI) homolog	91.65
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	91.64
PRK13633	280	cobalt transporter ATP-binding subunit; Provisiona	91.62
) 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	91.62
PRK10261	623	glutathione transporter ATP-binding protein; Provi	91.61
PRK15134	529	microcin C ABC transporter ATP-binding protein Yej	91.59
COG3842	352	PotA ABC-type spermidine/putrescine transport syst	91.59
PRK11860	661	bifunctional 3-phosphoshikimate 1-carboxyvinyltran	91.57
PRK09302	509	circadian clock protein KaiC; Reviewed	91.57
PRK13642	277	cbiO cobalt transporter ATP-binding subunit; Provi	91.56
COG4167	267	SapF ABC-type antimicrobial peptide transport syst	91.56
TIGR00991	313	3a0901s02IAP34 GTP-binding protein (Chloroplast En	91.54
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	91.5
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	91.49
cd03288	257	ABCC_SUR2 The SUR domain 2. The sulfonylurea recep	91.49
PRK06851	367	hypothetical protein; Provisional	91.45
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	91.4
PRK00093	435	GTP-binding protein Der; Reviewed	91.39
PRK15439	510	autoinducer 2 ABC transporter ATP-binding protein	91.36
PRK12608	380	transcription termination factor Rho; Provisional	91.35
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	91.33
PRK13634	290	cbiO cobalt transporter ATP-binding subunit; Provi	91.28
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	91.25
PRK15424	538	propionate catabolism operon regulatory protein Pr	91.24
TIGR00959	428	ffh signal recognition particle protein. This mode	91.24
cd02033	329	BchX Chlorophyllide reductase converts chlorophyll	91.22
PRK13549	506	xylose transporter ATP-binding subunit; Provisiona	91.22
COG4172	534	ABC-type uncharacterized transport system, duplica	91.22
PRK13537	306	nodulation ABC transporter NodI; Provisional	91.21
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	91.14
PRK13409	590	putative ATPase RIL; Provisional	91.13
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	91.13
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	91.12
PRK13409	590	putative ATPase RIL; Provisional	91.08
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	91.07
PRK10261	623	glutathione transporter ATP-binding protein; Provi	91.05
PRK14257	329	phosphate ABC transporter ATP-binding protein; Pro	91.03
PRK11432	351	fbpC ferric transporter ATP-binding subunit; Provi	91.02
PRK13549	506	xylose transporter ATP-binding subunit; Provisiona	91.02
PRK10070	400	glycine betaine transporter ATP-binding subunit; P	90.98
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	90.96
PRK09700	510	D-allose transporter ATP-binding protein; Provisio	90.95
PRK09700	510	D-allose transporter ATP-binding protein; Provisio	90.94
PRK10982	491	galactose/methyl galaxtoside transporter ATP-bindi	90.88
PRK13536	340	nodulation factor exporter subunit NodI; Provision	90.87
PRK15134	529	microcin C ABC transporter ATP-binding protein Yej	90.86
PRK14246	257	phosphate ABC transporter ATP-binding protein; Pro	90.85
cd01857	141	HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to t	90.84
cd01859	156	MJ1464 MJ1464. This family represents archaeal GTP	90.75
COG1127	263	Ttg2A ABC-type transport system involved in resist	90.64
PRK11819	556	putative ABC transporter ATP-binding protein; Revi	90.6
PRK15439	510	autoinducer 2 ABC transporter ATP-binding protein	90.59
PRK15064	530	ABC transporter ATP-binding protein; Provisional	90.57
PRK09866	741	hypothetical protein; Provisional	90.56
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	90.56
COG5192	1077	BMS1 GTP-binding protein required for 40S ribosome	90.55
PRK11819	556	putative ABC transporter ATP-binding protein; Revi	90.55
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	90.53
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	90.52
PRK10762	501	D-ribose transporter ATP binding protein; Provisio	90.48
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	90.47
TIGR03269	520	met_CoM_red_A2 methyl coenzyme M reductase system,	90.45
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	90.43
PHA02624	647	large T antigen; Provisional	90.41
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	90.4
TIGR03018	207	pepcterm_TyrKin exopolysaccharide/PEPCTERM locus t	90.38
TIGR01663	526	PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase	90.36
PRK09452	375	potA putrescine/spermidine ABC transporter ATPase	90.36
PRK00652	325	lpxK tetraacyldisaccharide 4'-kinase; Reviewed	90.35
PRK11607	377	potG putrescine transporter ATP-binding subunit; P	90.28
PRK13833	323	conjugal transfer protein TrbB; Provisional	90.28
PRK05506	632	bifunctional sulfate adenylyltransferase subunit 1	90.22
COG1134	249	TagH ABC-type polysaccharide/polyol phosphate tran	90.22
TIGR03719	552	ABC_ABC_ChvD ATP-binding cassette protein, ChvD fa	90.1
PRK11147	635	ABC transporter ATPase component; Reviewed	90.07
TIGR03815	322	CpaE_hom_Actino helicase/secretion neighborhood Cp	90.06
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	90.02
PRK10938	490	putative molybdenum transport ATP-binding protein	89.98
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	89.96
PRK10636	638	putative ABC transporter ATP-binding protein; Prov	89.95
PRK11288	501	araG L-arabinose transporter ATP-binding protein;	89.94
TIGR02633	500	xylG D-xylose ABC transporter, ATP-binding protein	89.88
COG1123	539	ATPase components of various ABC-type transport sy	89.88
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	89.86
TIGR03719	552	ABC_ABC_ChvD ATP-binding cassette protein, ChvD fa	89.83
COG0488	530	Uup ATPase components of ABC transporters with dup	89.83
PRK04841	903	transcriptional regulator MalT; Provisional	89.78
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	89.74
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	89.69
PLN03073	718	ABC transporter F family; Provisional	89.69
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	89.65
cd01882	225	BMS1 Bms1. Bms1 is an essential, evolutionarily co	89.64
TIGR03258	362	PhnT 2-aminoethylphosphonate ABC transport system,	89.61
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	89.59
PRK01889	356	GTPase RsgA; Reviewed	89.58
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	89.47
PLN02772	398	guanylate kinase	89.46
cd01849	155	YlqF_related_GTPase YlqF-related GTPases. These pr	89.43
COG0802	149	Predicted ATPase or kinase [General function predi	89.4
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	89.35
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	89.33
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	89.28
KOG2878	282	consensus Predicted kinase [General function predi	89.28
TIGR03415	382	ABC_choXWV_ATP choline ABC transporter, ATP-bindin	89.21
PLN03073	718	ABC transporter F family; Provisional	89.16
PF11868	192	DUF3388: Protein of unknown function (DUF3388); In	89.1
PRK13545	549	tagH teichoic acids export protein ATP-binding sub	89.09
TIGR03797	686	NHPM_micro_ABC2 NHPM bacteriocin system ABC transp	88.99
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	88.89
TIGR00665	434	DnaB replicative DNA helicase. This model describe	88.79
COG1162	301	Predicted GTPases [General function prediction onl	88.69
PRK07940	394	DNA polymerase III subunit delta'; Validated	88.68
PRK14086	617	dnaA chromosomal replication initiation protein; P	88.64
TIGR01842	544	type_I_sec_PrtD type I secretion system ABC transp	88.61
COG1135	339	AbcC ABC-type metal ion transport system, ATPase c	88.6
cd04178	172	Nucleostemin_like Nucleostemin-like. Nucleostemin	88.58
TIGR01193	708	bacteriocin_ABC ABC-type bacteriocin transporter.	88.54
PRK15494	339	era GTPase Era; Provisional	88.51
PHA02542	473	41 41 helicase; Provisional	88.5
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	88.44
PTZ00322	664	6-phosphofructo-2-kinase/fructose-2,6-biphosphatas	88.44
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	88.43
COG4598	256	HisP ABC-type histidine transport system, ATPase c	88.34
COG4916	329	Uncharacterized protein containing a TIR (Toll-Int	88.25
TIGR00958	711	3a01208 Conjugate Transporter-2 (CT2) Family prote	88.2
TIGR03796	710	NHPM_micro_ABC1 NHPM bacteriocin system ABC transp	88.03
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	87.98
PRK13764	602	ATPase; Provisional	87.97
KOG2702	323	consensus Predicted panthothenate kinase/uridine k	87.86
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	87.84
PRK10522	547	multidrug transporter membrane component/ATP-bindi	87.83
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	87.82
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	87.79
TIGR03453	387	partition_RepA plasmid partitioning protein RepA.	87.69
TIGR02857	529	CydD thiol reductant ABC exporter, CydD subunit. U	87.68
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	87.64
smart00350	509	MCM minichromosome maintenance proteins.	87.59
COG1119	257	ModF ABC-type molybdenum transport system, ATPase	87.57
COG2074	299	2-phosphoglycerate kinase [Carbohydrate transport	87.52
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	87.48
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	87.46
PRK11160	574	cysteine/glutathione ABC transporter membrane/ATP-	87.31
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	87.3
PHA02519	387	plasmid partition protein SopA; Reviewed	87.28
PRK15115	444	response regulator GlrR; Provisional	87.2
PRK10789	569	putative multidrug transporter membrane\ATP-bindin	87.17
PRK05748	448	replicative DNA helicase; Provisional	87.09
KOG0736	953	consensus Peroxisome assembly factor 2 containing	87.07
TIGR03029	274	EpsG chain length determinant protein tyrosine kin	86.97
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	86.84
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	86.82

>PLN03210 Resistant to P

Probab=100.00  E-value=3e-52  Score=414.77  Aligned_cols=211  Identities=39%  Similarity=0.744  Sum_probs=195.9

Q ss_pred             CCCcceEEEcCcccccccchHHHHHHHHhhCCCeEEEeCccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhhHHHHH
Q 043980           21 NNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELV  100 (233)
Q Consensus        21 ~~~~~dVFISy~~~D~~~~f~~~L~~~L~~~gi~~~~d~~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~~El~  100 (233)
                      +.++|||||||+|+|+|++|++||+.+|.++||.+|.|+++++|+.|.+++.+||++|+++|+|||++|++|.||++||+
T Consensus         9 ~~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~d~~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~s~wcl~el~   88 (1153)
T PLN03210          9 RNWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDNEIERSQSLDPELKQAIRDSRIAVVVFSKNYASSSWCLNELL   88 (1153)
T ss_pred             CCCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEccCCccCCCcccHHHHHHHHhCeEEEEEecCCcccchHHHHHHH
Confidence            56899999999999999999999999999999999999899999999999999999999999999999999999999999


Q ss_pred             HHHHhhhcccceeeceeeeecCCccccCCCchhhhhhHHHHhHHHHHHHHhhhccc-----cccccchh---hHHHhhhh
Q 043980          101 KILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEEFKEAAELEECFEGSS-----QFVWLSFS---EHQRLLDE  172 (233)
Q Consensus       101 ~~~~~~~~~~~~viPIf~~v~~~~vr~~~g~~~~~f~~~e~~~~~~e~~~~W~~AL-----~~g~~~~~---e~~~~i~~  172 (233)
                      +|+++++..++.|+||||+|+|++||+|+|.||++|.+++. ....+++++|++||     +.||++.+   |+ ++|++
T Consensus        89 ~i~~~~~~~~~~v~pvfy~v~p~~v~~~~g~f~~~f~~~~~-~~~~~~~~~w~~al~~~~~~~g~~~~~~~~E~-~~i~~  166 (1153)
T PLN03210         89 EIVRCKEELGQLVIPVFYGLDPSHVRKQTGDFGEAFEKTCQ-NKTEDEKIQWKQALTDVANILGYHSQNWPNEA-KMIEE  166 (1153)
T ss_pred             HHHHhhhhcCceEEEEEecccHHHHhhccchHHHHHHHHhc-ccchhHHHHHHHHHHHHhCcCceecCCCCCHH-HHHHH
Confidence            99999988899999999999999999999999999998876 12235799999999     88998864   99 99999


Q ss_pred             hccC---------CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhcCCC
Q 043980          173 VFRP---------SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDFE  233 (233)
Q Consensus       173 Iv~~---------~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~f~  233 (233)
                      ||.+         +.+..++||++.+++++..+|..+.+++++||||||||+||||||+++|+++..+|+
T Consensus       167 Iv~~v~~~l~~~~~~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~~F~  236 (1153)
T PLN03210        167 IANDVLGKLNLTPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLSRQFQ  236 (1153)
T ss_pred             HHHHHHHhhccccCcccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHHhhcCC
Confidence            9988         345578999999999999999888888999999999999999999999999888774

syringae 6; Provisional

>PLN03194 putative disease resistance protein; Provisional

Probab=100.00  E-value=1.7e-39  Score=257.06  Aligned_cols=139  Identities=29%  Similarity=0.471  Sum_probs=124.8

Q ss_pred             CCCcceEEEcCcccccccchHHHHHHHHhhCCCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhhHHHH
Q 043980           21 NNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDEL   99 (233)
Q Consensus        21 ~~~~~dVFISy~~~D~~~~f~~~L~~~L~~~gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~~El   99 (233)
                      ..++|||||||+|.|++.+|++||+.+|+++||++|+|+ ++.+|+.+.++|.+||++|+++|+|||++|++|.||++||
T Consensus        23 ~~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~WCLdEL  102 (187)
T PLN03194         23 SAKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYFCLHEL  102 (187)
T ss_pred             CCCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccchhHHHHH
Confidence            678899999999999999999999999999999999999 9999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhcccceeeceeeeecCCccccC-CCchhhhhhHHHHhHHHHHHHHhhhccc-----cccccchh----hHHHh
Q 043980          100 VKILECKKEYAQIVIPVLYRVDPSDVRNQ-TGSFGDSFSKLEEFKEAAELEECFEGSS-----QFVWLSFS----EHQRL  169 (233)
Q Consensus       100 ~~~~~~~~~~~~~viPIf~~v~~~~vr~~-~g~~~~~f~~~e~~~~~~e~~~~W~~AL-----~~g~~~~~----e~~~~  169 (233)
                      .+++++.    ..|+||||+++|++|++| .+.+            ..+++++|++||     +.|+.+..    |+ ++
T Consensus       103 ~~I~e~~----~~ViPIFY~VdPsdVr~q~~~~~------------~~e~v~~Wr~AL~~va~l~G~~~~~~~~~e~-e~  165 (187)
T PLN03194        103 ALIMESK----KRVIPIFCDVKPSQLRVVDNGTC------------PDEEIRRFNWALEEAKYTVGLTFDSLKGNWS-EV  165 (187)
T ss_pred             HHHHHcC----CEEEEEEecCCHHHhhccccCCC------------CHHHHHHHHHHHHHHhccccccCCCCCCCHH-HH
Confidence            9999864    369999999999999997 4321            235799999999     88986642    88 89


Q ss_pred             hhhhccC
Q 043980          170 LDEVFRP  176 (233)
Q Consensus       170 i~~Iv~~  176 (233)
                      |++|+..
T Consensus       166 i~~iv~~  172 (187)
T PLN03194        166 VTMASDA  172 (187)
T ss_pred             HHHHHHH
Confidence            9888843

>PF01582 TIR: TIR domain; InterPro: IPR000157 In Drosophila melanogaster the Toll protein is involved in establishment of dorso-ventral polarity in the embryo

Probab=99.88  E-value=3.6e-24  Score=165.88  Aligned_cols=129  Identities=32%  Similarity=0.544  Sum_probs=105.5

Q ss_pred             EEEcCcccccccchHHHHHHHHhhC--CCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhhHHHHHHHH
Q 043980           27 VFVSFRGEDTRDKFTSHLYSALSRQ--SIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKIL  103 (233)
Q Consensus        27 VFISy~~~D~~~~f~~~L~~~L~~~--gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~~El~~~~  103 (233)
                      |||||++.+.+..|+.+|..+|+++  |+++|+++ |+.+|..+.+++.++|++|+++|+|||++|+.|+||+.|+..++
T Consensus         1 vfisy~~~~d~~~~~~~L~~~Le~~~~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~a~   80 (141)
T PF01582_consen    1 VFISYSGKDDREWFVSHLLPELEERPYGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQEAL   80 (141)
T ss_dssp             EEEEE-GHHGHHHHHHCHHHHHHCTSSTS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHHHH
T ss_pred             cEEEeCCCCcHHHHHHHHHHHHHhCCCCeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhhhh
Confidence            8999999433566999999999999  99999999 99999999999999999999999999999999999999999999


Q ss_pred             Hhhhcc--cceeeceeeeecCCccc-cCCCchhhhhhHHHH-hHHH--HHHHHhhhcc
Q 043980          104 ECKKEY--AQIVIPVLYRVDPSDVR-NQTGSFGDSFSKLEE-FKEA--AELEECFEGS  155 (233)
Q Consensus       104 ~~~~~~--~~~viPIf~~v~~~~vr-~~~g~~~~~f~~~e~-~~~~--~e~~~~W~~A  155 (233)
                      ++....  ...|+|+|+++.+.+++ .+.+.+...+..+.. ....  ......|+.+
T Consensus        81 ~~~~~~~~~~~Il~v~~~v~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~fW~~l  138 (141)
T PF01582_consen   81 ERLLEEGRDKLILPVFYDVSPSDVRPDQSLRFLLRFLTYLRWPDDDSREDRSWFWKKL  138 (141)
T ss_dssp             HHHHCSTCTTEEEEESSSS-CHHCHTHHHHHHHHHCTHCEETSSSGGGGGHHHHHHHH
T ss_pred             hhccccccccceeeEeccCChhhcChhhhHHHHHHhhhheeCCCCCCccHHHHHHHHH
Confidence            988554  47899999999999998 577777766655444 2221  3456677654

In addition, members of the Toll family play a key role in innate antibacterial and antifungal immunity in insects as well as in mammals. These proteins are type-I transmembrane receptors that share an intracellular 200 residue domain with the interleukin-1 receptor (IL-1R), the Toll/IL-1R homologous region (TIR). The similarity between Toll-like receptors (LTRs) and IL-1R is not restricted to sequence homology since these proteins also share a similar signalling pathway. They both induce the activation of a Rel type transcription factor via an adaptor protein and a protein kinase []. Interestingly, MyD88, a cytoplasmic adaptor protein found in mammals, contains a TIR domain associated to a DEATH domain (see IPR000488 from INTERPRO) [, , ]. Besides the mammalian and Drosophila melanogaster proteins, a TIR domain is also found in a number of plant proteins implicated in host defence []. As MyD88, these proteins are cytoplasmic. Site directed mutagenesis and deletion analysis have shown that the TIR domain is essential for Toll and IL-1R activities. Sequence analysis have revealed the presence of three highly conserved regions among the different members of the family: box 1 (FDAFISY), box 2 (GYKLC-RD-PG), and box 3 (a conserved W surrounded by basic residues). It has been proposed that boxes 1 and 2 are involved in the binding of proteins involved in signalling, whereas box 3 is primarily involved in directing localization of receptor, perhaps through interactions with cytoskeletal elements [].; GO: 0005515 protein binding, 0007165 signal transduction, 0005622 intracellular; PDB: 3J0A_A 2J67_B 3JRN_A 1FYV_A 1O77_D 1FYX_A 1FYW_A 3OZI_B 1T3G_B 2JS7_A ....

>smart00255 TIR Toll - interleukin 1 - resistance

Probab=99.87  E-value=7.3e-22  Score=152.07  Aligned_cols=131  Identities=38%  Similarity=0.651  Sum_probs=104.1

Q ss_pred             cceEEEcCcc-cccccchHHHHHHHHhhCCCeEEEeCccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhhHHHHHHH
Q 043980           24 KYEVFVSFRG-EDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKI  102 (233)
Q Consensus        24 ~~dVFISy~~-~D~~~~f~~~L~~~L~~~gi~~~~d~~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~~El~~~  102 (233)
                      +|||||||++ ++....|+.+|...|...|+.+|.|+....|... .+|.++|++|+++|+|+|++|+.|+||..|+..+
T Consensus         1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~~~~~~~-~~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~a   79 (140)
T smart00255        1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFEPGGGDL-EEIDEAIEKSRIAIVVLSPNYAESEWCLDELVAA   79 (140)
T ss_pred             CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCcccccchH-HHHHHHHHHCcEEEEEECcccccChhHHHHHHHH
Confidence            5999999999 4455789999999999999999998743333333 3999999999999999999999999999999999


Q ss_pred             HHhhhc-ccceeeceeeeecCCccccCCCchhhhhhHHHH-hHHHHHHHHhhhccc
Q 043980          103 LECKKE-YAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEE-FKEAAELEECFEGSS  156 (233)
Q Consensus       103 ~~~~~~-~~~~viPIf~~v~~~~vr~~~g~~~~~f~~~e~-~~~~~e~~~~W~~AL  156 (233)
                      ...... ...+||||+++..|..+..+.+.+...+..+.. +..+... ..|+.++
T Consensus        80 ~~~~~~~~~~~iIPI~~~~~~~~~~~~~~~l~~~~~~~~~~w~~~~~~-~fW~~~~  134 (140)
T smart00255       80 LENALEEGGLRVIPIFYEVIPSDVRKQPGKFRKVLKKNYLKWPEDEKE-RFWKKAL  134 (140)
T ss_pred             HHHHHHcCCCeEEEEEEecChHHHHhcccHHHHHHHHHHhhcCCchhH-HHHHHHH
Confidence            887643 667899999998787788888888888776522 3322111 5676543

>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A

Probab=99.72  E-value=1.3e-18  Score=127.08  Aligned_cols=87  Identities=30%  Similarity=0.559  Sum_probs=74.7

Q ss_pred             EEEcCcccccccchHHHHHHHHhhCCCeEEEeCccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhhHHHHHHHHHhh
Q 043980           27 VFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECK  106 (233)
Q Consensus        27 VFISy~~~D~~~~f~~~L~~~L~~~gi~~~~d~~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~~El~~~~~~~  106 (233)
                      |||||+++|  ..++.+|...|+.+|+++|+|.++.+|+.+.+.|.++|++|+..|+++|++|+.|+||..|+..+.+  
T Consensus         1 VFIS~~~~D--~~~a~~l~~~L~~~g~~v~~d~~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a~~--   76 (102)
T PF13676_consen    1 VFISYSSED--REFAERLAERLESAGIRVFLDRDIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWK--   76 (102)
T ss_dssp             EEEEEEGGG--CCCHHHHHHHHHHTT--EE-GGEE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHC--
T ss_pred             eEEEecCCc--HHHHHHHHHHHhhcCCEEEEEEeCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHH--
Confidence            899999999  5699999999999999999999999999999999999999999999999999999999999998843  


Q ss_pred             hcccceeeceeee
Q 043980          107 KEYAQIVIPVLYR  119 (233)
Q Consensus       107 ~~~~~~viPIf~~  119 (233)
                        .+..|+||.++
T Consensus        77 --~~~~iipv~~~   87 (102)
T PF13676_consen   77 --RGKPIIPVRLD   87 (102)
T ss_dssp             --TSESEEEEECS
T ss_pred             --CCCEEEEEEEC
Confidence              34479999943

>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]

Probab=98.89  E-value=5.4e-09  Score=93.38  Aligned_cols=91  Identities=24%  Similarity=0.443  Sum_probs=73.2

Q ss_pred             CCCcceEEEcCcccccccchHHHHHHHHhhCCCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecCCC----Cch--
Q 043980           21 NNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSESYT----SSR--   93 (233)
Q Consensus        21 ~~~~~dVFISy~~~D~~~~f~~~L~~~L~~~gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~----~S~--   93 (233)
                      ..++.||||||++.. .+..++.|.-.|.-+|++||+|- .+..|.. .+.+.+.|..++.+|+|+|||.+    +..  
T Consensus       609 ~skq~DVFISYRRst-GnQLASLiKV~LQL~GyrVFIDVdKL~AGKF-dssLlkni~aAkhFiLVLtP~sLDr~lnD~nC  686 (832)
T KOG3678|consen  609 LSKQIDVFISYRRST-GNQLASLIKVLLQLRGYRVFIDVDKLYAGKF-DSSLLKNIQAAKHFILVLTPNSLDRLLNDDNC  686 (832)
T ss_pred             ccCCcceEEEeeccc-cHHHHHHHHHHHHhcCceEEEehhhhhcccc-cHHHHHHHHhhheeEEEeCcchHHHHhccccH
Confidence            457899999999874 56699999999999999999998 8888874 47888999999999999999954    344  


Q ss_pred             --hhHHHHHHHHHhhhcccceeecee
Q 043980           94 --WCVDELVKILECKKEYAQIVIPVL  117 (233)
Q Consensus        94 --wc~~El~~~~~~~~~~~~~viPIf  117 (233)
                        |...|+..++++.    ..|+|||
T Consensus       687 eDWVHKEl~~Afe~~----KNIiPI~  708 (832)
T KOG3678|consen  687 EDWVHKELKCAFEHQ----KNIIPIF  708 (832)
T ss_pred             HHHHHHHHHHHHHhc----CCeeeee
Confidence              5555666665554    4499999

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=98.55  E-value=5.3e-08  Score=95.33  Aligned_cols=48  Identities=38%  Similarity=0.720  Sum_probs=42.2

Q ss_pred             ccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH---HhcCCC
Q 043980          184 AGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK---ISSDFE  233 (233)
Q Consensus       184 ~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~---~~~~f~  233 (233)
                      ||.+..++++...|..+..  .++||+||||+||||||+.+||+   +..+||
T Consensus       161 VG~e~~~~kl~~~L~~d~~--~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd  211 (889)
T KOG4658|consen  161 VGLETMLEKLWNRLMEDDV--GIVGIYGMGGVGKTTLARQIFNKFDEVGNHFD  211 (889)
T ss_pred             ccHHHHHHHHHHHhccCCC--CEEEEECCCcccHHHHHHHHhcccchhcccCc
Confidence            9999999999998886543  89999999999999999999996   456675

>PF08937 DUF1863: MTH538 TIR-like domain (DUF1863); InterPro: IPR015032 This protein adopts the flavodoxin fold, that is, five parallel beta-strands and four helical segments

Probab=98.53  E-value=1.7e-07  Score=71.41  Aligned_cols=88  Identities=18%  Similarity=0.344  Sum_probs=45.6

Q ss_pred             ceEEEcCcccccccchHHHHHHHHhhC-------CCeE----------EEeC-ccCCCcchHHHHHHHHHhcCceEEEee
Q 043980           25 YEVFVSFRGEDTRDKFTSHLYSALSRQ-------SIQT----------FIDD-QLNRGDEISQSLVNAIEASAISVIIFS   86 (233)
Q Consensus        25 ~dVFISy~~~D~~~~f~~~L~~~L~~~-------gi~~----------~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S   86 (233)
                      |.|||||++.|.. ..+..|...+...       .+..          +.+. +......+...|.++|..|.++||+++
T Consensus         1 ~~vFIS~~~~d~~-~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~I~~~i~~s~~~IVLig   79 (130)
T PF08937_consen    1 YKVFISYSHDDDD-WYYDQLKEWLENSYEIPRDKNFDFRFYDVSKWEPIRSRDDDSSSEYIKRKIRERIKNSSVTIVLIG   79 (130)
T ss_dssp             ----------THH--HHHHHHHHHHH-------TTSS--BT---TTT---TTS---TTTTHHHHHHHHHHTEEEEEEE--
T ss_pred             CCccccccccCcH-HHHHHHHHHhccccccccccccccCcccccccCcccCccccchHHHHHHHHHHHHhcCCEEEEEeC
Confidence            5799999999843 2667776666653       2221          1122 222344788999999999999999999


Q ss_pred             cCCCCchhhHHHHHHHHHhhhcccceeecee
Q 043980           87 ESYTSSRWCVDELVKILECKKEYAQIVIPVL  117 (233)
Q Consensus        87 ~~y~~S~wc~~El~~~~~~~~~~~~~viPIf  117 (233)
                      ++-..|.|+..|+..+++.    +..|+-|.
T Consensus        80 ~~T~~s~wV~~EI~~A~~~----~~~Ii~V~  106 (130)
T PF08937_consen   80 PNTAKSKWVNWEIEYALKK----GKPIIGVY  106 (130)
T ss_dssp             TT----HHHHHHHHHHTTT-------EEEEE
T ss_pred             CCcccCcHHHHHHHHHHHC----CCCEEEEE
Confidence            9999999999999988763    33455554

The structure is a three-layer sandwich with alpha-1 and alpha-4 on one side of the beta-sheet, and alpha-2 and alpha-3 on the other side. Probable role in signal transduction as a phosphorylation-independent conformational switch protein []. This domain is similar to the TIR domain [].; PDB: 3HYN_A.

>PF08357 SEFIR: SEFIR domain; InterPro: IPR013568 This domain is found in IL17 receptors (IL17Rs, e

Probab=97.99  E-value=1.1e-05  Score=62.67  Aligned_cols=64  Identities=20%  Similarity=0.381  Sum_probs=54.2

Q ss_pred             eEEEcCccccc-ccchHHHHHHHHhhC-CCeEEEeC-ccCC--CcchHHHHHHHHHhcCceEEEeecCC
Q 043980           26 EVFVSFRGEDT-RDKFTSHLYSALSRQ-SIQTFIDD-QLNR--GDEISQSLVNAIEASAISVIIFSESY   89 (233)
Q Consensus        26 dVFISy~~~D~-~~~f~~~L~~~L~~~-gi~~~~d~-~~~~--G~~~~~~i~~~i~~s~~~i~v~S~~y   89 (233)
                      -|||||++... ....|..|+..|+.. |+.|.+|. +...  +..+...+.+.+++++.+|+|+|+.|
T Consensus         2 kVfI~Ys~d~~~h~~~V~~la~~L~~~~g~~V~lD~~~~~~i~~~g~~~W~~~~~~~ad~Vliv~S~~~   70 (150)
T PF08357_consen    2 KVFISYSHDSEEHKEWVLALAEFLRQNCGIDVILDQWELNEIARQGPPRWMERQIREADKVLIVCSPGY   70 (150)
T ss_pred             eEEEEeCCCCHHHHHHHHHHHHHHHhccCCceeecHHhhcccccCCHHHHHHHHHhcCCEEEEEeccch
Confidence            49999999543 356799999999999 99999998 7743  66788899999999999999999554

g. Q60943 from SWISSPROT) and SEF proteins (e.g. Q8QHJ9 from SWISSPROT). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (IPR000157 from INTERPRO), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways [].

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

Probab=97.59  E-value=9.6e-05  Score=61.23  Aligned_cols=56  Identities=21%  Similarity=0.436  Sum_probs=37.7

Q ss_pred             CCCCCccccccchHHHHHHHhcc---CCCCeEEEEEEcCCCChHHHHHHHHHHHHhcCC
Q 043980          177 SDNKNQLAGVESRVEEIESLLGV---KSKDVYALGIWGIGGIGKTKIARAIFDKISSDF  232 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~---~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~f  232 (233)
                      |..-.+++|.+.-+.++.-++..   ..+...-+-+||.+|+||||||..+.+.+..+|
T Consensus        20 P~~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~~   78 (233)
T PF05496_consen   20 PKSLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELGVNF   78 (233)
T ss_dssp             -SSCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT--E
T ss_pred             CCCHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccCCCe
Confidence            45668899999877777655542   223466788999999999999999999866544

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.

>PTZ00202 tuzin; Provisional

Probab=97.58  E-value=0.00012  Score=66.39  Aligned_cols=51  Identities=18%  Similarity=0.196  Sum_probs=43.0

Q ss_pred             CCCCCccccccchHHHHHHHhccCC-CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKS-KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~-~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      |.+...++||+.++..|...|...+ ...+++.|.|++|+|||||++.+...
T Consensus       258 Pa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~  309 (550)
T PTZ00202        258 PAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRK  309 (550)
T ss_pred             CCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhc
Confidence            5567899999999999999886533 33579999999999999999988764

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=97.51  E-value=0.00016  Score=64.10  Aligned_cols=52  Identities=17%  Similarity=0.346  Sum_probs=41.6

Q ss_pred             CCCCccccccchHHHHHHHhcc--CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLGV--KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~--~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+..++||+.++++|...|..  .......+-|+|++|+|||++++++++++.
T Consensus        12 ~~p~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~   65 (365)
T TIGR02928        12 YVPDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELE   65 (365)
T ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHH
Confidence            3456899999999999998763  122345688999999999999999998754

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=97.46  E-value=0.00011  Score=64.44  Aligned_cols=54  Identities=19%  Similarity=0.391  Sum_probs=41.7

Q ss_pred             CCCCCccccccchHHHHHHHhcc---CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          177 SDNKNQLAGVESRVEEIESLLGV---KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~---~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      |....+++|++..++.+..++..   .......+-++|++|+||||||+.+.+.+..
T Consensus        21 P~~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~~   77 (328)
T PRK00080         21 PKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGV   77 (328)
T ss_pred             cCCHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhCC
Confidence            44557799999999988877653   1223456779999999999999999997543

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.39  E-value=0.00018  Score=64.49  Aligned_cols=51  Identities=24%  Similarity=0.381  Sum_probs=40.4

Q ss_pred             CCCccccccchHHHHHHHhccC--CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVK--SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~--~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+..++||+.+++++...+...  ......+-|+|.+|+|||++++.+++++.
T Consensus        28 ~P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~   80 (394)
T PRK00411         28 VPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELE   80 (394)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            4567999999999998887432  22234567999999999999999998764

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.17  E-value=0.00039  Score=61.58  Aligned_cols=48  Identities=17%  Similarity=0.257  Sum_probs=40.2

Q ss_pred             ccccccchHHHHHHHhccC----CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          182 QLAGVESRVEEIESLLGVK----SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       182 ~~~g~~~~~~~l~~~l~~~----~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      +++|+++.++++.+++...    ....+++.+.|.+|.||||||+++.+.+.
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~  103 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLE  103 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHh
Confidence            7999999999998876531    23468999999999999999999988754

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=97.05  E-value=0.00054  Score=62.15  Aligned_cols=50  Identities=22%  Similarity=0.434  Sum_probs=35.7

Q ss_pred             CCccccccchHHH---HHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          180 KNQLAGVESRVEE---IESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       180 ~~~~~g~~~~~~~---l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      ...++|.+.-+..   +..++...  ....+-++|.+|+||||||+.+++.....
T Consensus        11 l~d~vGq~~~v~~~~~L~~~i~~~--~~~~ilL~GppGtGKTtLA~~ia~~~~~~   63 (413)
T PRK13342         11 LDEVVGQEHLLGPGKPLRRMIEAG--RLSSMILWGPPGTGKTTLARIIAGATDAP   63 (413)
T ss_pred             HHHhcCcHHHhCcchHHHHHHHcC--CCceEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            3557777765444   66666433  34567789999999999999999875443

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=96.92  E-value=0.00082  Score=59.89  Aligned_cols=52  Identities=21%  Similarity=0.397  Sum_probs=38.7

Q ss_pred             CCccccccchHHHHHHHhccC-----------CCCeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          180 KNQLAGVESRVEEIESLLGVK-----------SKDVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~-----------~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      ..++.|++..++++.+.+...           -...+-+-++|.+|+|||+||+++++.....
T Consensus       121 ~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~~  183 (364)
T TIGR01242       121 YEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNAT  183 (364)
T ss_pred             HHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCCC
Confidence            356889998888887765321           1123458899999999999999999876543

Many proteins may score above the trusted cutoff because an internal

>PF10137 TIR-like: Predicted nucleotide-binding protein containing TIR-like domain; InterPro: IPR019302 This entry represents a TIR-like domain found in a family of prokaryotic predicted nucleotide-binding proteins

Probab=96.91  E-value=0.0033  Score=47.51  Aligned_cols=60  Identities=20%  Similarity=0.325  Sum_probs=50.8

Q ss_pred             eEEEcCcccccccchHHHHHHHHhhCCCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecC
Q 043980           26 EVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSES   88 (233)
Q Consensus        26 dVFISy~~~D~~~~f~~~L~~~L~~~gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~   88 (233)
                      .|||.|+ .|  ..++..+...|+..|+.+.+-. ....|..+.+.+.+.+.+++..|+++||+
T Consensus         1 kVFIvhg-~~--~~~~~~v~~~L~~~~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpD   61 (125)
T PF10137_consen    1 KVFIVHG-RD--LAAAEAVERFLEKLGLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPD   61 (125)
T ss_pred             CEEEEeC-CC--HHHHHHHHHHHHhCCCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEccc
Confidence            3899999 44  3578899999998888876655 66889999999999999999999999985

Their exact function has not, as yet, been defined.

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=96.85  E-value=0.0013  Score=59.27  Aligned_cols=52  Identities=19%  Similarity=0.388  Sum_probs=39.0

Q ss_pred             CCccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          180 KNQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      ..++.|++..++++.+.+..           +-...+-|-++|.+|+|||++|++++++....
T Consensus       130 ~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~~~  192 (389)
T PRK03992        130 YEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNAT  192 (389)
T ss_pred             HHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhCCC
Confidence            35688999999988875532           11224567889999999999999999875443

>PRK04195 replication factor C large subunit; Provisional

Probab=96.84  E-value=0.001  Score=61.58  Aligned_cols=52  Identities=25%  Similarity=0.370  Sum_probs=41.2

Q ss_pred             CCCCCccccccchHHHHHHHhccC--CCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVK--SKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~--~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      |....+++|.+..++.+..|+..-  ....+.+-|+|.+|+||||+|+++.+.+
T Consensus        10 P~~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el   63 (482)
T PRK04195         10 PKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDY   63 (482)
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            334466899999999998887532  1226788899999999999999999875

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

Probab=96.83  E-value=0.0013  Score=58.68  Aligned_cols=49  Identities=24%  Similarity=0.449  Sum_probs=33.6

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhcCC
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDF  232 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~f  232 (233)
                      ...+++|-...+..+.+     .+.+...-+||.+|+||||||+.+.......|
T Consensus        28 GQ~HLlg~~~~lrr~v~-----~~~l~SmIl~GPPG~GKTTlA~liA~~~~~~f   76 (436)
T COG2256          28 GQEHLLGEGKPLRRAVE-----AGHLHSMILWGPPGTGKTTLARLIAGTTNAAF   76 (436)
T ss_pred             ChHhhhCCCchHHHHHh-----cCCCceeEEECCCCCCHHHHHHHHHHhhCCce
Confidence            33445555544444433     23466677999999999999999998766555

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=96.73  E-value=0.0016  Score=43.80  Aligned_cols=23  Identities=26%  Similarity=0.537  Sum_probs=20.5

Q ss_pred             EEEEEcCCCChHHHHHHHHHHHH
Q 043980          206 ALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +|+|.|..|.||||+++.+.+.+
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998874

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.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=96.65  E-value=0.0027  Score=55.43  Aligned_cols=49  Identities=22%  Similarity=0.275  Sum_probs=38.1

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ....++|++..++.+..++..+.  ...+-++|..|+||||+|+++.+.+.
T Consensus        13 ~~~~~~g~~~~~~~L~~~~~~~~--~~~lll~Gp~GtGKT~la~~~~~~l~   61 (337)
T PRK12402         13 LLEDILGQDEVVERLSRAVDSPN--LPHLLVQGPPGSGKTAAVRALARELY   61 (337)
T ss_pred             cHHHhcCCHHHHHHHHHHHhCCC--CceEEEECCCCCCHHHHHHHHHHHhc
Confidence            34567899988888888776432  33466999999999999999988753

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.65  E-value=0.0027  Score=55.21  Aligned_cols=52  Identities=17%  Similarity=0.140  Sum_probs=40.6

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |....+++|.+...+.+..++..+. -..++-++|.+|+||||+|+++++.+.
T Consensus        17 P~~~~~~~~~~~~~~~l~~~~~~~~-~~~~lll~G~~G~GKT~la~~l~~~~~   68 (316)
T PHA02544         17 PSTIDECILPAADKETFKSIVKKGR-IPNMLLHSPSPGTGKTTVAKALCNEVG   68 (316)
T ss_pred             CCcHHHhcCcHHHHHHHHHHHhcCC-CCeEEEeeCcCCCCHHHHHHHHHHHhC
Confidence            3344678899988888888876432 246777799999999999999998753

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

Probab=96.63  E-value=0.0019  Score=54.63  Aligned_cols=26  Identities=27%  Similarity=0.350  Sum_probs=22.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..++.|+|.+|+|||||++.+++.+.
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l~~~l~   68 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNLLKRLD   68 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHhcC
Confidence            45788999999999999999998754

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.62  E-value=0.0027  Score=62.49  Aligned_cols=47  Identities=28%  Similarity=0.456  Sum_probs=38.6

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..++||+.+++.+.++|....  .+-+-++|.+|+|||++|+.+..++.
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~--~~n~lL~G~pGvGKTal~~~la~~i~  225 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRT--KNNPILIGEPGVGKTAIAEGLAQRIV  225 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcccc--cCCeEEECCCCCCHHHHHHHHHHHHH
Confidence            568999999999999887543  22345899999999999999988764

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

Probab=96.59  E-value=0.0029  Score=60.12  Aligned_cols=54  Identities=28%  Similarity=0.356  Sum_probs=42.9

Q ss_pred             CCCccccccchHHHHHHHhcc----CCCCeEEEEEEcCCCChHHHHHHHHHHHHhcCC
Q 043980          179 NKNQLAGVESRVEEIESLLGV----KSKDVYALGIWGIGGIGKTKIARAIFDKISSDF  232 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~----~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~f  232 (233)
                      ...+..|.+.-++.+.++|.-    ..-...+++++|.+|+|||.|++.+++.+...|
T Consensus       321 Ld~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al~Rkf  378 (782)
T COG0466         321 LDKDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKALGRKF  378 (782)
T ss_pred             hcccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHhCCCE
Confidence            346788999888888887643    223358999999999999999999999876554

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.52  E-value=0.0048  Score=51.32  Aligned_cols=28  Identities=25%  Similarity=0.331  Sum_probs=24.6

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ....++||.|..|.|||||++.+.+.+.
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~~l~   58 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEALLQ   58 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            4578999999999999999999887654

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

Probab=96.52  E-value=0.0023  Score=61.95  Aligned_cols=51  Identities=24%  Similarity=0.410  Sum_probs=35.2

Q ss_pred             CCccccccchHH---HHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhcCC
Q 043980          180 KNQLAGVESRVE---EIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSDF  232 (233)
Q Consensus       180 ~~~~~g~~~~~~---~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~f  232 (233)
                      -..++|.+.-+.   .+..++..+  ....+-++|.+|+||||||+.+++.....|
T Consensus        27 ldd~vGQe~ii~~~~~L~~~i~~~--~~~slLL~GPpGtGKTTLA~aIA~~~~~~f   80 (725)
T PRK13341         27 LEEFVGQDHILGEGRLLRRAIKAD--RVGSLILYGPPGVGKTTLARIIANHTRAHF   80 (725)
T ss_pred             HHHhcCcHHHhhhhHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHhcCcc
Confidence            345677765553   344445432  345567899999999999999998765443

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.51  E-value=0.0035  Score=58.80  Aligned_cols=49  Identities=22%  Similarity=0.285  Sum_probs=39.9

Q ss_pred             CccccccchHHHHHHHh----ccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLL----GVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l----~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .++.|+++.++.+.+.|    .......+++.++|.+|+||||||+.+.+-+.
T Consensus        76 ~d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le  128 (644)
T PRK15455         76 EEFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLME  128 (644)
T ss_pred             hcccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHHH
Confidence            36889999999998876    22334568999999999999999999988643

>PLN03025 replication factor C subunit; Provisional

Probab=96.49  E-value=0.0039  Score=54.53  Aligned_cols=49  Identities=20%  Similarity=0.261  Sum_probs=36.8

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-.+++|.+.-++.|..++..+.  ..-+-++|.+|+||||+|+++.+.+
T Consensus        10 ~~l~~~~g~~~~~~~L~~~~~~~~--~~~lll~Gp~G~GKTtla~~la~~l   58 (319)
T PLN03025         10 TKLDDIVGNEDAVSRLQVIARDGN--MPNLILSGPPGTGKTTSILALAHEL   58 (319)
T ss_pred             CCHHHhcCcHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHHH
Confidence            344567888877777877766433  2235589999999999999998875

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

Probab=96.45  E-value=0.0036  Score=53.61  Aligned_cols=55  Identities=18%  Similarity=0.383  Sum_probs=39.4

Q ss_pred             CCCCCccccccchHHHHHHHhccC---CCCeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVK---SKDVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~---~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      |..-.+++|.+.-++++.-.+...   ....-=+-++|.+|.||||||.-+.+.+..+
T Consensus        22 P~~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn   79 (332)
T COG2255          22 PKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELGVN   79 (332)
T ss_pred             cccHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhcCC
Confidence            344577899887777776555431   1224446689999999999999999986554

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.42  E-value=0.0044  Score=61.20  Aligned_cols=50  Identities=16%  Similarity=0.280  Sum_probs=39.6

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..-..++||+..++.+.+.|....  ..-+-++|.+|+||||||+.+.+++.
T Consensus       184 ~~ld~~iGr~~ei~~~i~~l~r~~--~~n~lLvG~pGvGKTal~~~La~~i~  233 (852)
T TIGR03345       184 GKIDPVLGRDDEIRQMIDILLRRR--QNNPILTGEAGVGKTAVVEGLALRIA  233 (852)
T ss_pred             CCCCcccCCHHHHHHHHHHHhcCC--cCceeEECCCCCCHHHHHHHHHHHHh
Confidence            344678999999999988776543  23445899999999999999998863

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.

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=96.42  E-value=0.0048  Score=53.38  Aligned_cols=48  Identities=29%  Similarity=0.347  Sum_probs=38.4

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.+++|++..++.+..++..+.  ...+-++|..|+||||+|+.+.+.+
T Consensus        15 ~~~~~~g~~~~~~~l~~~i~~~~--~~~~ll~G~~G~GKt~~~~~l~~~l   62 (319)
T PRK00440         15 TLDEIVGQEEIVERLKSYVKEKN--MPHLLFAGPPGTGKTTAALALAREL   62 (319)
T ss_pred             cHHHhcCcHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            34568899988888888876433  3346899999999999999999875

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=96.40  E-value=0.0028  Score=56.82  Aligned_cols=30  Identities=23%  Similarity=0.069  Sum_probs=24.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHhc-CCC
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKISS-DFE  233 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~~-~f~  233 (233)
                      .+-.+|+|.+|+|||||+++||+.+.. +||
T Consensus       169 GQR~lIvgppGvGKTTLaK~Ian~I~~nhFD  199 (416)
T PRK09376        169 GQRGLIVAPPKAGKTVLLQNIANSITTNHPE  199 (416)
T ss_pred             CceEEEeCCCCCChhHHHHHHHHHHHhhcCC
Confidence            456789999999999999999998754 353

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.37  E-value=0.0053  Score=50.49  Aligned_cols=40  Identities=23%  Similarity=0.334  Sum_probs=29.8

Q ss_pred             cchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          187 ESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       187 ~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +.-++.+.+++..  .....+-|+|..|+|||+||++++++.
T Consensus        23 ~~~~~~l~~~~~~--~~~~~lll~G~~G~GKT~la~~~~~~~   62 (226)
T TIGR03420        23 AELLAALRQLAAG--KGDRFLYLWGESGSGKSHLLQAACAAA   62 (226)
T ss_pred             HHHHHHHHHHHhc--CCCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            3455666665432  335678899999999999999998864

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

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.35  E-value=0.0062  Score=54.32  Aligned_cols=52  Identities=25%  Similarity=0.277  Sum_probs=40.1

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |..-.+++|.+.-++.+...+..+. -...+-++|..|+||||+|+.+.+.+.
T Consensus        12 P~~~~~iiGq~~~~~~l~~~~~~~~-~~h~~L~~Gp~G~GKTtla~~la~~l~   63 (363)
T PRK14961         12 PQYFRDIIGQKHIVTAISNGLSLGR-IHHAWLLSGTRGVGKTTIARLLAKSLN   63 (363)
T ss_pred             CCchhhccChHHHHHHHHHHHHcCC-CCeEEEEecCCCCCHHHHHHHHHHHhc
Confidence            3345678899988888887776432 245677999999999999999998763

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

Probab=96.29  E-value=0.0049  Score=56.31  Aligned_cols=51  Identities=25%  Similarity=0.453  Sum_probs=38.2

Q ss_pred             CccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          181 NQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      .++.|.+..++++.+.+..           +-...+-+-++|.+|.|||+||+++++.....
T Consensus       183 ~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~  244 (438)
T PTZ00361        183 ADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSAT  244 (438)
T ss_pred             HHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCCC
Confidence            5678888888888776532           11234567799999999999999999976543

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.27  E-value=0.006  Score=60.33  Aligned_cols=47  Identities=19%  Similarity=0.325  Sum_probs=38.4

Q ss_pred             CCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -..++||+..++.+.+.|....  ..-+-++|.+|+||||||+.+..++
T Consensus       177 l~~vigr~~ei~~~i~iL~r~~--~~n~lL~G~pGvGKT~l~~~la~~i  223 (857)
T PRK10865        177 LDPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEGLAQRI  223 (857)
T ss_pred             CCcCCCCHHHHHHHHHHHhcCC--cCceEEECCCCCCHHHHHHHHHHHh
Confidence            3569999999999999887543  2344588999999999999998876

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.27  E-value=0.0062  Score=46.55  Aligned_cols=40  Identities=13%  Similarity=0.157  Sum_probs=28.3

Q ss_pred             hHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          189 RVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       189 ~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +..++.+.|...-....+|.+.|.-|.||||+++.+.+.+
T Consensus         7 ~t~~l~~~l~~~l~~~~~i~l~G~lGaGKTtl~~~l~~~l   46 (133)
T TIGR00150         7 AMDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQGL   46 (133)
T ss_pred             HHHHHHHHHHHhCCCCCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            3444444443322334589999999999999999998864

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.

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

Probab=96.25  E-value=0.0055  Score=59.63  Aligned_cols=48  Identities=27%  Similarity=0.313  Sum_probs=38.7

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-..++||+..++.+.+.|....  ..-+-++|.+|+|||++|+.+.+++
T Consensus       180 ~l~~~igr~~ei~~~~~~L~~~~--~~n~lL~G~pG~GKT~l~~~la~~~  227 (731)
T TIGR02639       180 KIDPLIGREDELERTIQVLCRRK--KNNPLLVGEPGVGKTAIAEGLALRI  227 (731)
T ss_pred             CCCcccCcHHHHHHHHHHHhcCC--CCceEEECCCCCCHHHHHHHHHHHH
Confidence            33578999999999998776543  2334589999999999999999876

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

Probab=96.18  E-value=0.0057  Score=58.24  Aligned_cols=53  Identities=30%  Similarity=0.392  Sum_probs=42.5

Q ss_pred             CCccccccchHHHHHHHhcc----CCCCeEEEEEEcCCCChHHHHHHHHHHHHhcCC
Q 043980          180 KNQLAGVESRVEEIESLLGV----KSKDVYALGIWGIGGIGKTKIARAIFDKISSDF  232 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~----~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~f  232 (233)
                      ..+..|+++-++.+.+++.-    ++.+..+++.+|.+|+|||.+|+.|+..+...|
T Consensus       410 deDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkF  466 (906)
T KOG2004|consen  410 DEDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARALNRKF  466 (906)
T ss_pred             cccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHhCCce
Confidence            35778998888888887642    344578999999999999999999999765544

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

Probab=96.16  E-value=0.006  Score=55.67  Aligned_cols=45  Identities=29%  Similarity=0.310  Sum_probs=33.8

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+++.+..++.+...|..    ..-+-++|++|+|||++|+++++.+.
T Consensus       175 ~d~~i~e~~le~l~~~L~~----~~~iil~GppGtGKT~lA~~la~~l~  219 (459)
T PRK11331        175 NDLFIPETTIETILKRLTI----KKNIILQGPPGVGKTFVARRLAYLLT  219 (459)
T ss_pred             hcccCCHHHHHHHHHHHhc----CCCEEEECCCCCCHHHHHHHHHHHhc
Confidence            3456667777777776653    23566799999999999999988753

>PRK06893 DNA replication initiation factor; Validated

Probab=96.15  E-value=0.0094  Score=49.65  Aligned_cols=25  Identities=24%  Similarity=0.400  Sum_probs=22.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+.+-+||.+|+|||+|++++.+.+
T Consensus        39 ~~~l~l~G~~G~GKThL~~ai~~~~   63 (229)
T PRK06893         39 QPFFYIWGGKSSGKSHLLKAVSNHY   63 (229)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            4678899999999999999999874

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.15  E-value=0.0077  Score=59.07  Aligned_cols=51  Identities=24%  Similarity=0.301  Sum_probs=40.8

Q ss_pred             CCCccccccchHHHHHHHhcc---CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGV---KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~---~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+..+.||+.++++|...|..   +.....++=|+|.+|.|||+.++.|.+++.
T Consensus       753 VPD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELq  806 (1164)
T PTZ00112        753 VPKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQ  806 (1164)
T ss_pred             CCCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHH
Confidence            457899999999999887653   222235677999999999999999988764

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=96.13  E-value=0.0068  Score=57.82  Aligned_cols=50  Identities=18%  Similarity=0.296  Sum_probs=38.8

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +...+.++|.+..+..+.+.+..  .....+.|+|.+|+||||||+.+++..
T Consensus       150 p~~~~~iiGqs~~~~~l~~~ia~--~~~~~vlL~Gp~GtGKTTLAr~i~~~~  199 (615)
T TIGR02903       150 PRAFSEIVGQERAIKALLAKVAS--PFPQHIILYGPPGVGKTTAARLALEEA  199 (615)
T ss_pred             cCcHHhceeCcHHHHHHHHHHhc--CCCCeEEEECCCCCCHHHHHHHHHHhh
Confidence            34557789999888887765532  234568999999999999999998754

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.

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

Probab=96.13  E-value=0.0064  Score=53.91  Aligned_cols=44  Identities=25%  Similarity=0.499  Sum_probs=31.5

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...+++|...-++.+.+     .+.+..+-+||.+|+||||||+.+...
T Consensus       142 GQ~hlv~q~gllrs~ie-----q~~ipSmIlWGppG~GKTtlArlia~t  185 (554)
T KOG2028|consen  142 GQSHLVGQDGLLRSLIE-----QNRIPSMILWGPPGTGKTTLARLIAST  185 (554)
T ss_pred             chhhhcCcchHHHHHHH-----cCCCCceEEecCCCCchHHHHHHHHhh
Confidence            44556665544444332     345788999999999999999998774

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=96.12  E-value=0.0086  Score=56.62  Aligned_cols=52  Identities=27%  Similarity=0.213  Sum_probs=40.3

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |..-..++|.+.-++.+...+..+. -.+.+-++|..|+||||+|+.+.+.+.
T Consensus        12 P~~F~dIIGQe~iv~~L~~aI~~~r-l~hA~Lf~GP~GvGKTTlA~~lAk~L~   63 (605)
T PRK05896         12 PHNFKQIIGQELIKKILVNAILNNK-LTHAYIFSGPRGIGKTSIAKIFAKAIN   63 (605)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHhc
Confidence            3445678899988888888775432 236677999999999999999988764

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.10  E-value=0.0085  Score=59.30  Aligned_cols=47  Identities=19%  Similarity=0.335  Sum_probs=38.2

Q ss_pred             CCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -..++||+..++.+.+.|....  ..-+-++|.+|+|||+||+.+..++
T Consensus       172 ~~~~igr~~ei~~~~~~l~r~~--~~n~lL~G~pGvGKT~l~~~la~~i  218 (852)
T TIGR03346       172 LDPVIGRDEEIRRTIQVLSRRT--KNNPVLIGEPGVGKTAIVEGLAQRI  218 (852)
T ss_pred             CCcCCCcHHHHHHHHHHHhcCC--CCceEEEcCCCCCHHHHHHHHHHHH
Confidence            3569999999999999887543  2334479999999999999998876

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.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.09  E-value=0.011  Score=48.97  Aligned_cols=25  Identities=20%  Similarity=0.486  Sum_probs=22.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+.+-|+|..|+|||+||+++++..
T Consensus        42 ~~~~~l~G~~G~GKT~La~ai~~~~   66 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLLQALVADA   66 (227)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            4678899999999999999999864

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=96.05  E-value=0.0079  Score=58.14  Aligned_cols=51  Identities=24%  Similarity=0.270  Sum_probs=39.5

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ....+++|.+.-++.|..++..+.- ...+-++|..|+||||+|+.+.+.+.
T Consensus        13 qtFdEVIGQe~Vv~~L~~aL~~gRL-~HAyLFtGPpGvGKTTlAriLAKaLn   63 (830)
T PRK07003         13 KDFASLVGQEHVVRALTHALDGGRL-HHAYLFTGTRGVGKTTLSRIFAKALN   63 (830)
T ss_pred             CcHHHHcCcHHHHHHHHHHHhcCCC-CeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3446688999888888888875543 34445999999999999999888753

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.05  E-value=0.0093  Score=55.09  Aligned_cols=50  Identities=24%  Similarity=0.220  Sum_probs=37.1

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-.+++|.+.-.+.|...+..+. -...+-++|.+|+||||+|+.+.+.+
T Consensus        11 ~~~~divGq~~i~~~L~~~i~~~~-l~~~~Lf~GPpGtGKTTlA~~lA~~l   60 (472)
T PRK14962         11 KTFSEVVGQDHVKKLIINALKKNS-ISHAYIFAGPRGTGKTTVARILAKSL   60 (472)
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            344668898877677766665332 13557799999999999999998865

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

Probab=96.00  E-value=0.008  Score=54.31  Aligned_cols=52  Identities=19%  Similarity=0.358  Sum_probs=38.2

Q ss_pred             CCCccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .-.++.|.+..++++.+.+..           +-...+-+-++|.+|.|||+||+++.+....
T Consensus       143 ~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~  205 (398)
T PTZ00454        143 TYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTA  205 (398)
T ss_pred             CHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCC
Confidence            336788988888888765431           1123467889999999999999999987543

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.94  E-value=0.0094  Score=54.90  Aligned_cols=51  Identities=20%  Similarity=0.245  Sum_probs=38.9

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..-.+++|.+.-+..|..++..+. -...+-++|..|+||||+|+.+.+.+.
T Consensus        15 ~~f~dvVGQe~iv~~L~~~i~~~r-i~ha~Lf~GP~GtGKTTlAriLAk~Ln   65 (484)
T PRK14956         15 QFFRDVIHQDLAIGALQNALKSGK-IGHAYIFFGPRGVGKTTIARILAKRLN   65 (484)
T ss_pred             CCHHHHhChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            344667898888888887776443 134577999999999999999988753

>TIGR00602 rad24 checkpoint protein rad24

Probab=95.94  E-value=0.0077  Score=57.43  Aligned_cols=52  Identities=23%  Similarity=0.357  Sum_probs=41.7

Q ss_pred             CCCCCccccccchHHHHHHHhccCC---CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKS---KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~---~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      |.....++|.+..+++|..++....   ...+++.|+|..|.||||+++.+...+
T Consensus        80 P~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l  134 (637)
T TIGR00602        80 PETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKEL  134 (637)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            5556778898888888888876432   345789999999999999999988764

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

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.93  E-value=0.012  Score=53.15  Aligned_cols=52  Identities=19%  Similarity=0.229  Sum_probs=39.5

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |..-..++|.+.-++.|..++..+. -...+-++|..|+||||+|+.+.+.+.
T Consensus        12 P~~~~eiiGq~~~~~~L~~~~~~~~-~~ha~lf~Gp~G~GKtt~A~~~a~~l~   63 (397)
T PRK14955         12 PKKFADITAQEHITRTIQNSLRMGR-VGHGYIFSGLRGVGKTTAARVFAKAVN   63 (397)
T ss_pred             CCcHhhccChHHHHHHHHHHHHhCC-cceeEEEECCCCCCHHHHHHHHHHHhc
Confidence            3344678898888888877776442 234577899999999999999998764

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.89  E-value=0.012  Score=55.33  Aligned_cols=51  Identities=20%  Similarity=0.273  Sum_probs=39.1

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..-.+++|.+.-++.|...+..+. -...+-++|..|+||||+|+.+.+.+.
T Consensus        13 ~~f~diiGq~~~v~~L~~~i~~~r-l~ha~Lf~Gp~GvGKTTlAr~lAk~L~   63 (546)
T PRK14957         13 QSFAEVAGQQHALNSLVHALETQK-VHHAYLFTGTRGVGKTTLGRLLAKCLN   63 (546)
T ss_pred             CcHHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            344668899988888888776432 235567899999999999999998654

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.87  E-value=0.011  Score=55.13  Aligned_cols=50  Identities=26%  Similarity=0.192  Sum_probs=38.7

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-.+++|.+.-++.|..++..+. -...+-++|.+|+||||+|+.+.+.+.
T Consensus        12 ~~~dvvGq~~v~~~L~~~i~~~~-l~ha~Lf~GppGtGKTTlA~~lA~~l~   61 (504)
T PRK14963         12 TFDEVVGQEHVKEVLLAALRQGR-LGHAYLFSGPRGVGKTTTARLIAMAVN   61 (504)
T ss_pred             CHHHhcChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            34567898887777877776433 245678999999999999999998764

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.87  E-value=0.011  Score=56.28  Aligned_cols=51  Identities=29%  Similarity=0.298  Sum_probs=40.2

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..-..++|.+.-.+.|..++..+.- ...+-++|..|+||||+|+.+.+.+.
T Consensus        12 ktFddVIGQe~vv~~L~~aI~~grl-~HAyLF~GPpGvGKTTlAriLAK~Ln   62 (702)
T PRK14960         12 RNFNELVGQNHVSRALSSALERGRL-HHAYLFTGTRGVGKTTIARILAKCLN   62 (702)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCC-CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3446789999888888888774432 46777999999999999999988753

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

Probab=95.82  E-value=0.014  Score=56.84  Aligned_cols=46  Identities=30%  Similarity=0.370  Sum_probs=37.3

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..++||+..++.+.+.|.....  .-+-++|.+|+|||+||+.+++++
T Consensus       186 ~~liGR~~ei~~~i~iL~r~~~--~n~LLvGppGvGKT~lae~la~~i  231 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRRRK--NNPLLVGESGVGKTAIAEGLAWRI  231 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhccCC--CCeEEECCCCCCHHHHHHHHHHHH
Confidence            4699999999999998876432  222479999999999999998864

>PLN02318 phosphoribulokinase/uridine kinase

Probab=95.79  E-value=0.013  Score=55.24  Aligned_cols=33  Identities=27%  Similarity=0.503  Sum_probs=26.7

Q ss_pred             HhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          196 LLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       196 ~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ++....+++.+|||.|..|.||||||+.+...+
T Consensus        57 lL~~~~~~riIIGIaGpSGSGKTTLAk~LaglL   89 (656)
T PLN02318         57 LLAQKNDGIILVGVAGPSGAGKTVFTEKVLNFM   89 (656)
T ss_pred             HHHhcCCCeEEEEEECCCCCcHHHHHHHHHhhC
Confidence            343344568999999999999999999998753

>PRK05439 pantothenate kinase; Provisional

Probab=95.76  E-value=0.02  Score=50.02  Aligned_cols=28  Identities=32%  Similarity=0.444  Sum_probs=23.9

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...-+|||.|.+|+||||+|+.+...+.
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~~l~  111 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQALLS  111 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4578999999999999999998877543

>CHL00181 cbbX CbbX; Provisional

Probab=95.72  E-value=0.017  Score=49.95  Aligned_cols=24  Identities=29%  Similarity=0.418  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-+-++|.+|+||||+|+.+++..
T Consensus        60 ~~ill~G~pGtGKT~lAr~la~~~   83 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALKMADIL   83 (287)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Confidence            346789999999999999997753

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.72  E-value=0.011  Score=57.59  Aligned_cols=49  Identities=20%  Similarity=0.401  Sum_probs=36.6

Q ss_pred             CccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      +++.|.+..++++.+++..           +-...+-+-++|.+|+||||||+++.+...
T Consensus       178 ~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~  237 (733)
T TIGR01243       178 EDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG  237 (733)
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhC
Confidence            4577888888888776532           112245678999999999999999998753

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.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=95.69  E-value=0.019  Score=50.56  Aligned_cols=38  Identities=24%  Similarity=0.367  Sum_probs=27.8

Q ss_pred             HHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          192 EIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       192 ~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+.+.+.....+..+|+|.|.+|.|||||+..+...+.
T Consensus        44 ~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~l~~~l~   81 (332)
T PRK09435         44 ELLDALLPHTGNALRIGITGVPGVGKSTFIEALGMHLI   81 (332)
T ss_pred             HHHHHHhhcCCCcEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            34443333334578999999999999999998776543

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

Probab=95.69  E-value=0.013  Score=49.23  Aligned_cols=53  Identities=19%  Similarity=0.391  Sum_probs=38.3

Q ss_pred             CCCCCccccccchHHHHHHHhcc--CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGV--KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~--~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      +.....++|.+.+++.|.+-...  ......-+=+||..|.|||+|++++.+...
T Consensus        23 ~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~   77 (249)
T PF05673_consen   23 PIRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYA   77 (249)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHh
Confidence            44567899999999888663221  112244455799999999999999988754

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.68  E-value=0.022  Score=48.78  Aligned_cols=26  Identities=23%  Similarity=0.420  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+++.++|.+|+||||++..+...+
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~~l   96 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLANKL   96 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            46899999999999999999887654

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=95.63  E-value=0.011  Score=50.21  Aligned_cols=25  Identities=32%  Similarity=0.340  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-+-++|.+|+||||+|+.+++.+
T Consensus        42 ~~~vll~GppGtGKTtlA~~ia~~l   66 (261)
T TIGR02881        42 VLHMIFKGNPGTGKTTVARILGKLF   66 (261)
T ss_pred             cceEEEEcCCCCCHHHHHHHHHHHH
Confidence            4567789999999999999998764

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.

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

Probab=95.60  E-value=0.012  Score=52.60  Aligned_cols=30  Identities=37%  Similarity=0.618  Sum_probs=26.0

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      .-.+.++|||.+|.|||.+|+++++.+...
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~elg~~  175 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKMGIE  175 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHcCCC
Confidence            347899999999999999999999986543

>TIGR00763 lon ATP-dependent protease La

Probab=95.57  E-value=0.017  Score=56.59  Aligned_cols=50  Identities=24%  Similarity=0.315  Sum_probs=37.1

Q ss_pred             CccccccchHHHHHHHhcc----CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          181 NQLAGVESRVEEIESLLGV----KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~----~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .+++|.+.-++.+.+++..    .......+.++|.+|+|||++|+++.+.+..
T Consensus       320 ~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l~~  373 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALNR  373 (775)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHhcC
Confidence            4577888777777765432    1223457889999999999999999987643

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.

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=95.56  E-value=0.016  Score=50.06  Aligned_cols=27  Identities=30%  Similarity=0.384  Sum_probs=22.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +...+|||.|..|.||||+|+.+-..+
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~ll   86 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQALL   86 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            346899999999999999998765543

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.54  E-value=0.017  Score=56.85  Aligned_cols=52  Identities=21%  Similarity=0.250  Sum_probs=39.7

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .....++|.+.-++.|..++..+. -...+-++|..|+||||+|+.+.+.+.+
T Consensus        13 ~tFddIIGQe~Iv~~LknaI~~~r-l~HAyLFtGPpGtGKTTLARiLAk~Lnc   64 (944)
T PRK14949         13 ATFEQMVGQSHVLHALTNALTQQR-LHHAYLFTGTRGVGKTSLARLFAKGLNC   64 (944)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHhCC-CCeEEEEECCCCCCHHHHHHHHHHhccC
Confidence            344668899888888887776432 1345678999999999999999987643

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=95.53  E-value=0.016  Score=49.96  Aligned_cols=23  Identities=26%  Similarity=0.364  Sum_probs=19.4

Q ss_pred             EEEEEcCCCChHHHHHHHHHHHH
Q 043980          206 ALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -+-++|.+|+||||+|+.+.+.+
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~l   82 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQIL   82 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHH
Confidence            46789999999999998877654

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.

>PLN02348 phosphoribulokinase

Probab=95.48  E-value=0.025  Score=50.80  Aligned_cols=28  Identities=18%  Similarity=0.328  Sum_probs=25.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      +...+|||.|-+|.||||+|+.+.+.+.
T Consensus        47 ~~p~IIGIaG~SGSGKSTfA~~L~~~Lg   74 (395)
T PLN02348         47 DGTVVIGLAADSGCGKSTFMRRLTSVFG   74 (395)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4578999999999999999999998764

>TIGR03689 pup_AAA proteasome ATPase

Probab=95.46  E-value=0.016  Score=54.00  Aligned_cols=49  Identities=27%  Similarity=0.491  Sum_probs=35.9

Q ss_pred             CccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .++.|.+..++++.+.+..           +-...+-+-++|.+|.|||++|+++++.+.
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~  241 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLA  241 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhc
Confidence            5577788888777665321           112245578899999999999999999764

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.

>TIGR00750 lao LAO/AO transport system ATPase

Probab=95.46  E-value=0.027  Score=48.86  Aligned_cols=36  Identities=19%  Similarity=0.253  Sum_probs=26.9

Q ss_pred             HHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          193 IESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       193 l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +.+-+........+|+|.|.+|.|||||+..+...+
T Consensus        23 ~~~~~~~~~~~~~~i~i~G~~G~GKttl~~~l~~~~   58 (300)
T TIGR00750        23 LLDRIMPYTGNAHRVGITGTPGAGKSTLLEALGMEL   58 (300)
T ss_pred             HHHhCCcccCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            333333334457899999999999999999977653

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>PRK09087 hypothetical protein; Validated

Probab=95.45  E-value=0.021  Score=47.61  Aligned_cols=24  Identities=29%  Similarity=0.241  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .+.+.|||..|+|||+|+++..+.
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~   67 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREK   67 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHh
Confidence            466899999999999999988765

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

Probab=95.44  E-value=0.015  Score=51.30  Aligned_cols=52  Identities=19%  Similarity=0.422  Sum_probs=37.2

Q ss_pred             CCccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          180 KNQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      ...+-|.+++++++.+-+..           +-+...=|-+||.+|.|||-||++|+++....
T Consensus       150 Y~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~At  212 (406)
T COG1222         150 YEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDAT  212 (406)
T ss_pred             hhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccCce
Confidence            35677888888888764321           11234556789999999999999999974433

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

Probab=95.43  E-value=0.027  Score=50.31  Aligned_cols=52  Identities=19%  Similarity=0.357  Sum_probs=39.2

Q ss_pred             CCCccccccchHHHHHHHhccC--CCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEIESLLGVK--SKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~--~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .+..+.+|+.+++++...|..-  .....-+-|+|..|+|||+.++.+.+++..
T Consensus        15 iP~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~   68 (366)
T COG1474          15 IPEELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEE   68 (366)
T ss_pred             CcccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHh
Confidence            3455999999999998765431  111222888999999999999999998754

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.42  E-value=0.02  Score=53.41  Aligned_cols=51  Identities=22%  Similarity=0.246  Sum_probs=39.7

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..-.+++|.+.-++.|..++..+.- ...+-++|..|+||||+|+.+.+.+-
T Consensus        13 ~~f~divGq~~v~~~L~~~~~~~~l-~ha~Lf~Gp~G~GKTt~A~~lAk~l~   63 (509)
T PRK14958         13 RCFQEVIGQAPVVRALSNALDQQYL-HHAYLFTGTRGVGKTTISRILAKCLN   63 (509)
T ss_pred             CCHHHhcCCHHHHHHHHHHHHhCCC-CeeEEEECCCCCCHHHHHHHHHHHhc
Confidence            3446789999888888888865432 34567899999999999999988653

>PLN02200 adenylate kinase family protein

Probab=95.39  E-value=0.017  Score=48.37  Aligned_cols=26  Identities=19%  Similarity=0.245  Sum_probs=22.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+|.|.|++|.||||+|+.+.+..
T Consensus        42 ~~~ii~I~G~PGSGKsT~a~~La~~~   67 (234)
T PLN02200         42 TPFITFVLGGPGSGKGTQCEKIVETF   67 (234)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            35789999999999999999988753

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=95.37  E-value=0.014  Score=48.84  Aligned_cols=29  Identities=31%  Similarity=0.448  Sum_probs=23.4

Q ss_pred             ccCCCCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          198 GVKSKDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       198 ~~~~~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ......-.++||+|..|.|||||++.+..
T Consensus        27 S~~i~~Ge~lgivGeSGsGKSTL~r~l~G   55 (252)
T COG1124          27 SLEIERGETLGIVGESGSGKSTLARLLAG   55 (252)
T ss_pred             eEEecCCCEEEEEcCCCCCHHHHHHHHhc
Confidence            33334467899999999999999998765

>PRK14974 cell division protein FtsY; Provisional

Probab=95.36  E-value=0.032  Score=49.33  Aligned_cols=27  Identities=19%  Similarity=0.251  Sum_probs=22.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...++.++|++|+||||++..+...+.
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~  165 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLK  165 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            368999999999999998888876543

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=95.36  E-value=0.031  Score=49.26  Aligned_cols=50  Identities=24%  Similarity=0.248  Sum_probs=39.4

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-.+++|.+..++.+..++..+. -...+=++|..|+||||+|+.+...+.
T Consensus        12 ~~~~iig~~~~~~~l~~~~~~~~-~~~~~Ll~G~~G~GKt~~a~~la~~l~   61 (355)
T TIGR02397        12 TFEDVIGQEHIVQTLKNAIKNGR-IAHAYLFSGPRGTGKTSIARIFAKALN   61 (355)
T ss_pred             cHhhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            44678899998999888776432 235677899999999999999988753

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.

>PLN02796 D-glycerate 3-kinase

Probab=95.35  E-value=0.016  Score=51.15  Aligned_cols=27  Identities=26%  Similarity=0.304  Sum_probs=23.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..-+|||.|..|.|||||++.+...+.
T Consensus        99 ~pliIGI~G~sGSGKSTLa~~L~~lL~  125 (347)
T PLN02796         99 PPLVIGISAPQGCGKTTLVFALVYLFN  125 (347)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHhc
Confidence            467899999999999999999887653

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=95.35  E-value=0.02  Score=54.94  Aligned_cols=51  Identities=27%  Similarity=0.324  Sum_probs=40.0

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      |....+++|.+.-++.|..++..+. -...+-++|..|+||||+|+.+.+.+
T Consensus        12 P~tFddIIGQe~vv~~L~~ai~~~r-l~Ha~Lf~GP~GvGKTTlAriLAk~L   62 (709)
T PRK08691         12 PKTFADLVGQEHVVKALQNALDEGR-LHHAYLLTGTRGVGKTTIARILAKSL   62 (709)
T ss_pred             CCCHHHHcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHHHh
Confidence            3345678999988888888877542 24567899999999999999998864

>TIGR00767 rho transcription termination factor Rho

Probab=95.34  E-value=0.016  Score=52.26  Aligned_cols=28  Identities=21%  Similarity=0.055  Sum_probs=24.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      -+.++|+|.+|.|||||++.+++.+..+
T Consensus       168 Gq~~~IvG~~g~GKTtL~~~i~~~I~~n  195 (415)
T TIGR00767       168 GQRGLIVAPPKAGKTVLLQKIAQAITRN  195 (415)
T ss_pred             CCEEEEECCCCCChhHHHHHHHHhhccc
Confidence            4678999999999999999999986554

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

>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional

Probab=95.33  E-value=0.015  Score=52.62  Aligned_cols=26  Identities=19%  Similarity=0.245  Sum_probs=23.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -++.|+|.|..|.|||||++++.+..
T Consensus       218 ~~~~IvI~G~~gsGKTTL~~~La~~~  243 (399)
T PRK08099        218 FVRTVAILGGESSGKSTLVNKLANIF  243 (399)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999988764

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.29  E-value=0.016  Score=50.60  Aligned_cols=25  Identities=28%  Similarity=0.425  Sum_probs=22.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -|+|-+.|.+|.|||+|++++++++
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkL  201 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKL  201 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhh
Confidence            3788899999999999999999974

>CHL00176 ftsH cell division protein; Validated

Probab=95.27  E-value=0.015  Score=55.73  Aligned_cols=51  Identities=29%  Similarity=0.369  Sum_probs=35.4

Q ss_pred             CCCccccccchHHHHHHHhcc---C-------CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGV---K-------SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~---~-------~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-.++.|.++.++++.+++..   .       ..-.+-+-++|.+|+|||+||+++.+...
T Consensus       181 ~f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~  241 (638)
T CHL00176        181 TFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAE  241 (638)
T ss_pred             CHHhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            345678887777666655321   1       11134578899999999999999988643

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.26  E-value=0.023  Score=54.22  Aligned_cols=50  Identities=24%  Similarity=0.315  Sum_probs=39.4

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+++|.+.-++.|...+..+.- ...+-++|..|+||||+|+.+.+.+.
T Consensus        14 tFddVIGQe~vv~~L~~al~~gRL-pHA~LFtGP~GvGKTTLAriLAkaLn   63 (700)
T PRK12323         14 DFTTLVGQEHVVRALTHALEQQRL-HHAYLFTGTRGVGKTTLSRILAKSLN   63 (700)
T ss_pred             cHHHHcCcHHHHHHHHHHHHhCCC-ceEEEEECCCCCCHHHHHHHHHHHhc
Confidence            446688999888888888765432 35667899999999999999988764

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=95.25  E-value=0.022  Score=52.95  Aligned_cols=49  Identities=24%  Similarity=0.365  Sum_probs=32.8

Q ss_pred             CccccccchHHHHHHHhcc----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGV----------KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+++|.+..++++.+++..          +....+-+-++|.+|+|||+||+++.+...
T Consensus        55 ~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~  113 (495)
T TIGR01241        55 KDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAG  113 (495)
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcC
Confidence            4567777666555543321          112234477899999999999999988643

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.

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=95.24  E-value=0.033  Score=49.51  Aligned_cols=53  Identities=25%  Similarity=0.188  Sum_probs=41.8

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      |.....++|.+.-.+.+...+..+. -...+-+.|..|+||||+|..+.+.+-+
T Consensus        19 P~~~~~l~Gh~~a~~~L~~a~~~gr-l~ha~L~~G~~G~GKttlA~~lA~~Llc   71 (351)
T PRK09112         19 PSENTRLFGHEEAEAFLAQAYREGK-LHHALLFEGPEGIGKATLAFHLANHILS   71 (351)
T ss_pred             CCchhhccCcHHHHHHHHHHHHcCC-CCeeEeeECCCCCCHHHHHHHHHHHHcC
Confidence            4566789999988888888776443 2446778999999999999999887643

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.22  E-value=0.028  Score=53.56  Aligned_cols=50  Identities=22%  Similarity=0.308  Sum_probs=38.7

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-.+++|.+.-++.|..++..+. -...+=++|..|+||||+|+.+.+.+
T Consensus        13 ~~f~dviGQe~vv~~L~~~l~~~r-l~ha~Lf~Gp~GvGKTtlAr~lAk~L   62 (618)
T PRK14951         13 RSFSEMVGQEHVVQALTNALTQQR-LHHAYLFTGTRGVGKTTVSRILAKSL   62 (618)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            344668898887888888776543 24566799999999999999997765

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

Probab=95.22  E-value=0.023  Score=55.72  Aligned_cols=51  Identities=24%  Similarity=0.292  Sum_probs=39.8

Q ss_pred             CCccccccchHHHHHHHhcc----CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          180 KNQLAGVESRVEEIESLLGV----KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~----~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ..+..|.+.-++.+.++|..    ......++.++|.+|+||||+|+.+...+..
T Consensus       321 ~~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l~~  375 (784)
T PRK10787        321 DTDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKATGR  375 (784)
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            45688999888888877653    1234568999999999999999999886543

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=95.21  E-value=0.026  Score=52.54  Aligned_cols=51  Identities=27%  Similarity=0.264  Sum_probs=38.2

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..-.+++|.+.-++.|...+..+. -...+-++|..|+||||+|+.+++.+-
T Consensus        18 ~~f~dliGq~~vv~~L~~ai~~~r-i~~a~Lf~Gp~G~GKTT~ArilAk~Ln   68 (507)
T PRK06645         18 SNFAELQGQEVLVKVLSYTILNDR-LAGGYLLTGIRGVGKTTSARIIAKAVN   68 (507)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHhc
Confidence            344667898887777776555332 235677899999999999999998753

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.20  E-value=0.028  Score=52.14  Aligned_cols=50  Identities=22%  Similarity=0.274  Sum_probs=37.9

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-.+++|.+.-++.|...+..+.- ...+-++|..|+||||+|+.+...+
T Consensus        10 ~~f~dliGQe~vv~~L~~a~~~~ri-~ha~Lf~Gp~G~GKTT~ArilAk~L   59 (491)
T PRK14964         10 SSFKDLVGQDVLVRILRNAFTLNKI-PQSILLVGASGVGKTTCARIISLCL   59 (491)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCC-CceEEEECCCCccHHHHHHHHHHHH
Confidence            3446789988877777776654332 3467799999999999999988754

>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated

Probab=95.19  E-value=0.042  Score=51.95  Aligned_cols=49  Identities=22%  Similarity=0.335  Sum_probs=33.2

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      +...-+.+-.+.|.++.......-.+|.|.|+.|.||||+|+++..++.
T Consensus       369 P~~f~rpeV~~iL~~~~~~r~~~g~~Ivl~Gl~GSGKSTia~~La~~L~  417 (568)
T PRK05537        369 PEWFSFPEVVAELRRTYPPRHKQGFTVFFTGLSGAGKSTIAKALMVKLM  417 (568)
T ss_pred             ChhhcHHHHHHHHHHHhccccCCCeEEEEECCCCChHHHHHHHHHHHhh
Confidence            3334444434444444444444456889999999999999999998765

>PRK08084 DNA replication initiation factor; Provisional

Probab=95.18  E-value=0.021  Score=47.81  Aligned_cols=26  Identities=19%  Similarity=0.410  Sum_probs=22.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+.+-|+|..|+|||+|++++++...
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a~~~~~~   70 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHAACAELS   70 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            45788999999999999999988643

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.17  E-value=0.034  Score=50.17  Aligned_cols=26  Identities=23%  Similarity=0.373  Sum_probs=22.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +.++|+++|.+|+||||++..+...+
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~L  265 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQF  265 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHHH
Confidence            35799999999999999999987654

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=95.16  E-value=0.029  Score=53.68  Aligned_cols=52  Identities=23%  Similarity=0.291  Sum_probs=39.6

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |....+++|.+.-++.|...+..+. -...+-++|..|+||||+|+.+.+.+.
T Consensus        12 P~~f~divGQe~vv~~L~~~l~~~r-l~hAyLf~Gp~GvGKTTlAr~lAk~L~   63 (647)
T PRK07994         12 PQTFAEVVGQEHVLTALANALDLGR-LHHAYLFSGTRGVGKTTIARLLAKGLN   63 (647)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhhh
Confidence            3445678899888888888776443 234567899999999999999988753

>PRK08727 hypothetical protein; Validated

Probab=95.16  E-value=0.043  Score=45.85  Aligned_cols=24  Identities=33%  Similarity=0.313  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+.|+|..|+|||+|++++.+..
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~   65 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAA   65 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH
Confidence            569999999999999999998764

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.16  E-value=0.03  Score=53.43  Aligned_cols=52  Identities=19%  Similarity=0.240  Sum_probs=39.3

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |..-..++|.+.-++.|...+..+. -...+-++|..|+||||+|+.+.+.+.
T Consensus        12 P~~f~eivGQe~i~~~L~~~i~~~r-i~ha~Lf~Gp~GvGKttlA~~lAk~L~   63 (620)
T PRK14954         12 PSKFADITAQEHITHTIQNSLRMDR-VGHGYIFSGLRGVGKTTAARVFAKAVN   63 (620)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCCHHHHHHHHHHHhC
Confidence            3345678898887888877776432 234577999999999999999988764

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.13  E-value=0.029  Score=52.57  Aligned_cols=50  Identities=26%  Similarity=0.336  Sum_probs=38.5

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+++|.+.-++.+..++..+.- ...+-++|..|+||||+|+.+...+.
T Consensus        14 ~f~divGq~~v~~~L~~~i~~~~~-~ha~Lf~Gp~G~GKTt~A~~lAk~l~   63 (527)
T PRK14969         14 SFSELVGQEHVVRALTNALEQQRL-HHAYLFTGTRGVGKTTLARILAKSLN   63 (527)
T ss_pred             cHHHhcCcHHHHHHHHHHHHcCCC-CEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            446688998888888887764332 34566899999999999999988753

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=95.10  E-value=0.034  Score=43.86  Aligned_cols=35  Identities=26%  Similarity=0.497  Sum_probs=28.7

Q ss_pred             chHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          188 SRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       188 ~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..+++|.++|.    + +++.++|..|+|||||...+...
T Consensus        24 ~g~~~l~~~l~----~-k~~vl~G~SGvGKSSLiN~L~~~   58 (161)
T PF03193_consen   24 EGIEELKELLK----G-KTSVLLGQSGVGKSSLINALLPE   58 (161)
T ss_dssp             TTHHHHHHHHT----T-SEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCHHHHHHHhc----C-CEEEEECCCCCCHHHHHHHHHhh
Confidence            44777777776    3 68899999999999999998764

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=95.09  E-value=0.035  Score=47.96  Aligned_cols=38  Identities=24%  Similarity=0.399  Sum_probs=29.4

Q ss_pred             HHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          191 EEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       191 ~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .++...+........+|||.|.||.||+||.-++-..+
T Consensus        38 ~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l   75 (323)
T COG1703          38 RELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGREL   75 (323)
T ss_pred             HHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHH
Confidence            44555555555567899999999999999999877654

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=95.07  E-value=0.018  Score=50.21  Aligned_cols=27  Identities=19%  Similarity=0.477  Sum_probs=23.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-..|.+.||.|.||||+++.+.+++.
T Consensus       132 ~~~~I~l~G~~GsGKStvg~~La~~Lg  158 (309)
T PRK08154        132 RRRRIALIGLRGAGKSTLGRMLAARLG  158 (309)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHcC
Confidence            456899999999999999999988754

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.07  E-value=0.038  Score=49.16  Aligned_cols=52  Identities=23%  Similarity=0.271  Sum_probs=40.3

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |..-.+++|.+...+.+...+..+. -...+-++|..|+||||+|+.+.+.+.
T Consensus        13 P~~~~~iig~~~~~~~l~~~i~~~~-~~~~~L~~G~~G~GKt~~a~~la~~l~   64 (367)
T PRK14970         13 PQTFDDVVGQSHITNTLLNAIENNH-LAQALLFCGPRGVGKTTCARILARKIN   64 (367)
T ss_pred             CCcHHhcCCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3345678899988888888776432 235677899999999999999988764

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=95.06  E-value=0.034  Score=50.50  Aligned_cols=51  Identities=20%  Similarity=0.249  Sum_probs=36.1

Q ss_pred             CCccccccchHHHHHHHhcc---------CC---CCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          180 KNQLAGVESRVEEIESLLGV---------KS---KDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~---------~~---~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ...++|.+..++.+...+..         ..   ....-+-++|.+|+||||||+.+...+..
T Consensus        14 d~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~   76 (443)
T PRK05201         14 DKYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLANA   76 (443)
T ss_pred             ccccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            34578888888877665532         00   01245789999999999999999887543

>PRK12289 GTPase RsgA; Reviewed

Probab=95.06  E-value=0.13  Score=45.71  Aligned_cols=33  Identities=18%  Similarity=0.280  Sum_probs=24.8

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +++|.+.|..     .++.|.|++|+|||||..++..+
T Consensus       163 I~eL~~~L~~-----ki~v~iG~SgVGKSSLIN~L~~~  195 (352)
T PRK12289        163 LEALLEQLRN-----KITVVAGPSGVGKSSLINRLIPD  195 (352)
T ss_pred             HHHHhhhhcc-----ceEEEEeCCCCCHHHHHHHHcCc
Confidence            5556555541     35889999999999999998753

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=95.02  E-value=0.032  Score=53.00  Aligned_cols=52  Identities=23%  Similarity=0.346  Sum_probs=40.7

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |....+++|.+.-++.|...+..+. -...+-++|..|+||||+|+.+.+.+.
T Consensus        20 P~~f~dliGq~~~v~~L~~~~~~gr-i~ha~L~~Gp~GvGKTt~Ar~lAk~L~   71 (598)
T PRK09111         20 PQTFDDLIGQEAMVRTLTNAFETGR-IAQAFMLTGVRGVGKTTTARILARALN   71 (598)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHhhC
Confidence            3445678999988888888776443 244677899999999999999998764

>PRK13531 regulatory ATPase RavA; Provisional

Probab=95.00  E-value=0.033  Score=51.38  Aligned_cols=45  Identities=18%  Similarity=0.036  Sum_probs=34.5

Q ss_pred             CCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...++|+++-++.+...+..+    .-+-|.|.+|+|||+||+.+....
T Consensus        19 ~~~i~gre~vI~lll~aalag----~hVLL~GpPGTGKT~LAraLa~~~   63 (498)
T PRK13531         19 EKGLYERSHAIRLCLLAALSG----ESVFLLGPPGIAKSLIARRLKFAF   63 (498)
T ss_pred             hhhccCcHHHHHHHHHHHccC----CCEEEECCCChhHHHHHHHHHHHh
Confidence            456899998888777655432    235578999999999999998854

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.99  E-value=0.032  Score=48.89  Aligned_cols=27  Identities=22%  Similarity=0.442  Sum_probs=23.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+++++|.+|+||||++..+...+.
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~l~  139 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHKYK  139 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHH
Confidence            468999999999999999999877643

>PRK06620 hypothetical protein; Validated

Probab=94.98  E-value=0.022  Score=47.06  Aligned_cols=23  Identities=26%  Similarity=0.292  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +.+-|||..|+|||+|++++.+.
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~   67 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNL   67 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhc
Confidence            66889999999999999997765

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=94.93  E-value=0.012  Score=44.85  Aligned_cols=44  Identities=25%  Similarity=0.290  Sum_probs=28.6

Q ss_pred             ccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          184 AGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       184 ~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ||.-..++++.+-+..-...-.-|-|.|..|.||+++|+.+++.
T Consensus         1 vG~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~   44 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRY   44 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHT
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhh
Confidence            35555566665544432223345678999999999999998874

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=94.89  E-value=0.027  Score=41.33  Aligned_cols=23  Identities=35%  Similarity=0.433  Sum_probs=20.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIF  225 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~  225 (233)
                      ....++|.|..|.|||||++.+.
T Consensus        14 ~ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          14 GKVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CCEEEEEEcCCCCCHHHHHHHhh
Confidence            35789999999999999999864

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.86  E-value=0.04  Score=52.24  Aligned_cols=50  Identities=26%  Similarity=0.228  Sum_probs=39.1

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-.+++|.+.-++.|..++..+. -...+-++|..|+||||+|+.+.+.+.
T Consensus        11 ~f~eivGq~~i~~~L~~~i~~~r-~~ha~Lf~Gp~G~GKTt~A~~lAk~l~   60 (584)
T PRK14952         11 TFAEVVGQEHVTEPLSSALDAGR-INHAYLFSGPRGCGKTSSARILARSLN   60 (584)
T ss_pred             cHHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            34668898888888888776442 234567999999999999999988754

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

Probab=94.84  E-value=0.043  Score=48.91  Aligned_cols=53  Identities=28%  Similarity=0.270  Sum_probs=36.5

Q ss_pred             CCCccccccchHHHH---HHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          179 NKNQLAGVESRVEEI---ESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l---~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      ....+||+....+..   .+++..+.=.-+.+-+.|.+|.|||+||.++.+.+.+.
T Consensus        22 ~~~GlVGQ~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~ia~eLG~~   77 (398)
T PF06068_consen   22 IADGLVGQEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMAIAKELGED   77 (398)
T ss_dssp             EETTEES-HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHHHHHHCTTT
T ss_pred             ccccccChHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHHHHHHHHHhCCC
Confidence            456899998777765   44555443335778899999999999999999987643

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.

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

Probab=94.83  E-value=0.045  Score=49.71  Aligned_cols=26  Identities=23%  Similarity=0.294  Sum_probs=22.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .-+-++|.+|+|||+||+.+...+..
T Consensus       109 ~~iLl~Gp~GtGKT~lAr~lA~~l~~  134 (412)
T PRK05342        109 SNILLIGPTGSGKTLLAQTLARILDV  134 (412)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHhCC
Confidence            45778999999999999999886543

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=94.83  E-value=0.031  Score=48.10  Aligned_cols=26  Identities=19%  Similarity=0.300  Sum_probs=22.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..++++++|.+|+||||++..+...+
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~  218 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARF  218 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35799999999999999999887654

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=94.80  E-value=0.036  Score=54.04  Aligned_cols=50  Identities=20%  Similarity=0.332  Sum_probs=35.3

Q ss_pred             CccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          181 NQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .++.|.+.-++.|.+.+..           +....+-+-++|.+|.|||+||+++.+....
T Consensus       453 ~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~  513 (733)
T TIGR01243       453 SDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGA  513 (733)
T ss_pred             hhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCC
Confidence            4567877777777665432           1112345778999999999999999987543

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.

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

Probab=94.78  E-value=0.04  Score=53.45  Aligned_cols=47  Identities=19%  Similarity=0.393  Sum_probs=37.5

Q ss_pred             CCccccccchHHHHHHHhccCC-CCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          180 KNQLAGVESRVEEIESLLGVKS-KDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~~-~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      -..++||+.+++.+.+.|.... |+..   ++|.+|+|||+++.-++.+|.
T Consensus       169 lDPvIGRd~EI~r~iqIL~RR~KNNPv---LiGEpGVGKTAIvEGLA~rIv  216 (786)
T COG0542         169 LDPVIGRDEEIRRTIQILSRRTKNNPV---LVGEPGVGKTAIVEGLAQRIV  216 (786)
T ss_pred             CCCCcChHHHHHHHHHHHhccCCCCCe---EecCCCCCHHHHHHHHHHHHh
Confidence            3668999999999999887643 3333   458999999999999988853

>PRK12377 putative replication protein; Provisional

Probab=94.77  E-value=0.033  Score=47.12  Aligned_cols=26  Identities=27%  Similarity=0.327  Sum_probs=22.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+-++|..|+|||+||.++.+.+.
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~l~  126 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNRLL  126 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            45788999999999999999999754

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=94.77  E-value=0.037  Score=47.82  Aligned_cols=29  Identities=17%  Similarity=0.306  Sum_probs=25.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .++.+++|.|.+|.|||||...+.+.+..
T Consensus       102 ~~~~~v~l~G~pGsGKTTLl~~l~~~l~~  130 (290)
T PRK10463        102 RKQLVLNLVSSPGSGKTTLLTETLMRLKD  130 (290)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            46899999999999999999999887643

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=94.74  E-value=0.059  Score=49.33  Aligned_cols=27  Identities=22%  Similarity=0.282  Sum_probs=23.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+|.++|.+|+||||+|..+...+.
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~  120 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFK  120 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHH
Confidence            367899999999999999999887654

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=94.73  E-value=0.041  Score=49.92  Aligned_cols=50  Identities=20%  Similarity=0.286  Sum_probs=34.4

Q ss_pred             CccccccchHHHHHHHhccC------------CCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          181 NQLAGVESRVEEIESLLGVK------------SKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~------------~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ..++|.+..++.+.-.+...            ....+-|-++|.+|+|||+||+++...+..
T Consensus        12 ~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~   73 (441)
T TIGR00390        12 KYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANA   73 (441)
T ss_pred             hhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            44788887777765433321            111245778999999999999999887544

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.

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.71  E-value=0.047  Score=51.85  Aligned_cols=51  Identities=24%  Similarity=0.289  Sum_probs=39.3

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..-.+++|.+.-++.|..++..+. -...+-++|..|+||||+|+.+.+.+.
T Consensus        13 ~~~~eiiGq~~~~~~L~~~i~~~~-i~~a~Lf~Gp~G~GKTtlA~~lA~~l~   63 (585)
T PRK14950         13 QTFAELVGQEHVVQTLRNAIAEGR-VAHAYLFTGPRGVGKTSTARILAKAVN   63 (585)
T ss_pred             CCHHHhcCCHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhc
Confidence            344678899888888877776443 235567899999999999999988753

>PRK07952 DNA replication protein DnaC; Validated

Probab=94.69  E-value=0.05  Score=45.90  Aligned_cols=25  Identities=28%  Similarity=0.446  Sum_probs=22.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+-++|-+|+|||+||.++.+.+
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~l  123 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNEL  123 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHH
Confidence            4567899999999999999999875

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=94.68  E-value=0.026  Score=47.99  Aligned_cols=26  Identities=35%  Similarity=0.556  Sum_probs=22.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ....++||+|..|.|||||++.+..-
T Consensus        37 ~~ge~~glVGESG~GKSTlgr~i~~L   62 (268)
T COG4608          37 KEGETLGLVGESGCGKSTLGRLILGL   62 (268)
T ss_pred             cCCCEEEEEecCCCCHHHHHHHHHcC
Confidence            34678999999999999999998753

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=94.68  E-value=0.036  Score=51.81  Aligned_cols=48  Identities=29%  Similarity=0.353  Sum_probs=36.3

Q ss_pred             CccccccchHHHHHHHhcc---CCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGV---KSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~---~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+++-...-++++..||..   +....+++-+.|.+|.||||.++.+.+.+
T Consensus        19 ~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~el   69 (519)
T PF03215_consen   19 DELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKEL   69 (519)
T ss_pred             HHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHh
Confidence            3344445567888888864   22336799999999999999999999875

>TIGR03596 GTPase_YlqF ribosome biogenesis GTP-binding protein YlqF

Probab=94.67  E-value=0.23  Score=42.50  Aligned_cols=23  Identities=22%  Similarity=0.288  Sum_probs=19.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.++++|++|+|||||...+.+
T Consensus       118 ~~~~~~vG~~nvGKSslin~l~~  140 (276)
T TIGR03596       118 PIRAMIVGIPNVGKSTLINRLAG  140 (276)
T ss_pred             CeEEEEECCCCCCHHHHHHHHhC
Confidence            35689999999999999998865

Members of this protein family are GTP-binding proteins involved in ribosome biogenesis, including the essential YlqF protein of Bacillus subtilis, which is an essential protein. They are related to Era, EngA, and other GTPases of ribosome biogenesis, but are circularly permuted. This family is not universal, and is not present in Escherichia coli, and so is not as well studied as some other GTPases. This model is built for bacterial members.

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

Probab=94.63  E-value=0.065  Score=47.50  Aligned_cols=52  Identities=23%  Similarity=0.223  Sum_probs=40.7

Q ss_pred             CCCccccccchHHHH---HHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEI---ESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l---~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ....+||.....+..   .+++..+.-.-+-|-+.|.+|.|||+||-.+.+.+.+
T Consensus        37 ~~dG~VGQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~   91 (450)
T COG1224          37 IGDGLVGQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIARELGE   91 (450)
T ss_pred             cCCcccchHHHHHhhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHHHHHHhCC
Confidence            456789988766653   5566665555788889999999999999999988754

>PRK14489 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional

Probab=94.62  E-value=0.05  Score=48.60  Aligned_cols=28  Identities=25%  Similarity=0.446  Sum_probs=24.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ..++|+|+|..|.|||||+..+...++.
T Consensus       204 ~~~~~~~~g~~~~GKtt~~~~l~~~l~~  231 (366)
T PRK14489        204 APPLLGVVGYSGTGKTTLLEKLIPELIA  231 (366)
T ss_pred             CccEEEEecCCCCCHHHHHHHHHHHHHH
Confidence            4679999999999999999999987654

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=94.62  E-value=0.056  Score=51.04  Aligned_cols=52  Identities=17%  Similarity=0.197  Sum_probs=40.0

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |..-..++|.+.-++.|...+..+.- ...+=++|..|+||||+|+.+...+.
T Consensus        12 P~~f~~viGq~~v~~~L~~~i~~~~~-~hayLf~Gp~GtGKTt~Ak~lAkal~   63 (559)
T PRK05563         12 PQTFEDVVGQEHITKTLKNAIKQGKI-SHAYLFSGPRGTGKTSAAKIFAKAVN   63 (559)
T ss_pred             CCcHHhccCcHHHHHHHHHHHHcCCC-CeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            33456789999888888888775432 34555899999999999999987653

>PLN02165 adenylate isopentenyltransferase

Probab=94.61  E-value=0.032  Score=49.07  Aligned_cols=26  Identities=19%  Similarity=0.339  Sum_probs=22.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+++|+|+.|+||||||..+...+.
T Consensus        43 g~iivIiGPTGSGKStLA~~LA~~l~   68 (334)
T PLN02165         43 DKVVVIMGATGSGKSRLSVDLATRFP   68 (334)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHHcC
Confidence            45899999999999999999988743

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=94.53  E-value=0.056  Score=48.82  Aligned_cols=26  Identities=38%  Similarity=0.443  Sum_probs=22.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+-|+|..|+|||+|++++++.+.
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l~  161 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEIL  161 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHH
Confidence            45678999999999999999999764

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).

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.50  E-value=0.056  Score=50.18  Aligned_cols=51  Identities=24%  Similarity=0.231  Sum_probs=39.2

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..-..++|.+.-++.|...+..+. -...+-++|..|+||||+|+.+...+.
T Consensus        13 ~~f~diiGq~~i~~~L~~~i~~~~-i~hayLf~Gp~G~GKTtlAr~lAk~L~   63 (486)
T PRK14953         13 KFFKEVIGQEIVVRILKNAVKLQR-VSHAYIFAGPRGTGKTTIARILAKVLN   63 (486)
T ss_pred             CcHHHccChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            344678899988888888876543 235566899999999999999888653

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=94.48  E-value=0.074  Score=47.56  Aligned_cols=52  Identities=19%  Similarity=0.102  Sum_probs=40.8

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |....+++|.+.-++.|.+.+..+. -...+-++|..|+||+|+|..+.+.+-
T Consensus        15 P~~~~~iiGq~~~~~~L~~~~~~~r-l~HA~Lf~Gp~G~GK~~lA~~~A~~Ll   66 (365)
T PRK07471         15 PRETTALFGHAAAEAALLDAYRSGR-LHHAWLIGGPQGIGKATLAYRMARFLL   66 (365)
T ss_pred             CCchhhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHHh
Confidence            5566789999988888888776543 234677899999999999999988753

>PRK05642 DNA replication initiation factor; Validated

Probab=94.46  E-value=0.041  Score=45.97  Aligned_cols=25  Identities=20%  Similarity=0.535  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+.+-|||..|+|||.|++++.+.+
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~   69 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRF   69 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            3678899999999999999998764

>PRK09183 transposase/IS protein; Provisional

Probab=94.46  E-value=0.035  Score=47.18  Aligned_cols=24  Identities=29%  Similarity=0.343  Sum_probs=20.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...+.|+|.+|+|||+||.++.+.
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~~  125 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGYE  125 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHH
Confidence            345779999999999999998765

>cd01858 NGP_1 NGP-1

Probab=94.46  E-value=0.059  Score=41.86  Aligned_cols=24  Identities=25%  Similarity=0.461  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...++++|++|+||+||..++..+
T Consensus       102 ~~~v~~~G~~nvGKStliN~l~~~  125 (157)
T cd01858         102 QISVGFIGYPNVGKSSIINTLRSK  125 (157)
T ss_pred             ceEEEEEeCCCCChHHHHHHHhcC
Confidence            456789999999999999998763

Autoantigen NGP-1 (Nucleolar G-protein gene 1) has been shown to localize in the nucleolus and nucleolar organizers in all cell types analyzed, which is indicative of a function in ribosomal assembly. NGP-1 and its homologs show a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with NKXD motif) are relocated to the N terminus.

>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=94.45  E-value=0.069  Score=44.22  Aligned_cols=27  Identities=30%  Similarity=0.493  Sum_probs=23.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ....+-|+|..|.|||.|.+++++.+.
T Consensus        33 ~~~~l~l~G~~G~GKTHLL~Ai~~~~~   59 (219)
T PF00308_consen   33 RYNPLFLYGPSGLGKTHLLQAIANEAQ   59 (219)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHHHH
Confidence            345678999999999999999999754

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.

>PLN02199 shikimate kinase

Probab=94.44  E-value=0.05  Score=47.11  Aligned_cols=26  Identities=19%  Similarity=0.317  Sum_probs=22.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      -+.|.++||.|.||||+++.+.+.+.
T Consensus       102 ~~~I~LIG~~GSGKSTVgr~LA~~Lg  127 (303)
T PLN02199        102 GRSMYLVGMMGSGKTTVGKLMSKVLG  127 (303)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            34688999999999999999988654

>PRK08116 hypothetical protein; Validated

Probab=94.43  E-value=0.039  Score=47.15  Aligned_cols=25  Identities=36%  Similarity=0.599  Sum_probs=21.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-+-++|..|+|||.||.++++.+.
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~  139 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELI  139 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHH
Confidence            3578999999999999999999754

>PLN03046 D-glycerate 3-kinase; Provisional

Probab=94.43  E-value=0.041  Score=49.95  Aligned_cols=26  Identities=23%  Similarity=0.207  Sum_probs=22.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-+|||.|..|.|||||++.+...+
T Consensus       211 ~PlIIGIsG~qGSGKSTLa~~L~~lL  236 (460)
T PLN03046        211 PPLVIGFSAPQGCGKTTLVFALDYLF  236 (460)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            46799999999999999999986544

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=94.41  E-value=0.067  Score=47.94  Aligned_cols=39  Identities=26%  Similarity=0.350  Sum_probs=30.6

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..++.++|..+-....++-|.|.+|+|||||+..+...+
T Consensus        68 i~eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~~~  106 (372)
T cd01121          68 IEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARL  106 (372)
T ss_pred             CHHHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            455666666555556799999999999999999987654

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.

>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA

Probab=94.38  E-value=0.63  Score=42.16  Aligned_cols=23  Identities=22%  Similarity=0.444  Sum_probs=19.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .--++|+|.+|+|||||..++..
T Consensus       172 ~~~v~ivG~~~~GKSsLin~l~~  194 (429)
T TIGR03594       172 PIKIAIIGRPNVGKSTLVNALLG  194 (429)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHC
Confidence            35688999999999999998865

EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability.

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

Probab=94.37  E-value=0.055  Score=45.38  Aligned_cols=46  Identities=24%  Similarity=0.314  Sum_probs=33.0

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .++||-++-++.|.-.-.  ..+..-+-|.||+|+||||-+..+.+.+
T Consensus        27 ~dIVGNe~tv~rl~via~--~gnmP~liisGpPG~GKTTsi~~LAr~L   72 (333)
T KOG0991|consen   27 QDIVGNEDTVERLSVIAK--EGNMPNLIISGPPGTGKTTSILCLAREL   72 (333)
T ss_pred             HHhhCCHHHHHHHHHHHH--cCCCCceEeeCCCCCchhhHHHHHHHHH
Confidence            456787776666654333  2235566789999999999998888864

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=94.37  E-value=0.096  Score=46.03  Aligned_cols=45  Identities=13%  Similarity=0.118  Sum_probs=30.9

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      +..+-..+....+...+..+    +-|-|.|.+|+||||+|+.+...+.
T Consensus        45 ~~y~f~~~~~~~vl~~l~~~----~~ilL~G~pGtGKTtla~~lA~~l~   89 (327)
T TIGR01650        45 PAYLFDKATTKAICAGFAYD----RRVMVQGYHGTGKSTHIEQIAARLN   89 (327)
T ss_pred             CCccCCHHHHHHHHHHHhcC----CcEEEEeCCCChHHHHHHHHHHHHC
Confidence            33444444455566555432    3478899999999999999988754

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.

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=94.36  E-value=0.044  Score=47.60  Aligned_cols=26  Identities=23%  Similarity=0.378  Sum_probs=22.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-+|.|.|..|+||||+|..+.+++.
T Consensus        92 p~iIlI~G~sgsGKStlA~~La~~l~  117 (301)
T PRK04220         92 PIIILIGGASGVGTSTIAFELASRLG  117 (301)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46788999999999999999998753

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=94.35  E-value=0.074  Score=48.93  Aligned_cols=52  Identities=23%  Similarity=0.331  Sum_probs=39.9

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |..-.+++|.+.-++.+...+..+. -...+-++|..|+||||+|+.+.+.+.
T Consensus        13 P~~~~diiGq~~~v~~L~~~i~~~~-i~ha~Lf~Gp~G~GKtt~A~~lAk~l~   64 (451)
T PRK06305         13 PQTFSEILGQDAVVAVLKNALRFNR-AAHAYLFSGIRGTGKTTLARIFAKALN   64 (451)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCC-CceEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            3345678899988888888776432 135667899999999999999988753

>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional

Probab=94.33  E-value=0.039  Score=45.57  Aligned_cols=25  Identities=16%  Similarity=0.239  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||++.+...
T Consensus        35 ~Ge~~~i~G~nGsGKSTLl~~i~Gl   59 (228)
T PRK10584         35 RGETIALIGESGSGKSTLLAILAGL   59 (228)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcC
Confidence            4579999999999999999998764

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=94.31  E-value=0.06  Score=40.57  Aligned_cols=26  Identities=23%  Similarity=0.216  Sum_probs=22.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+|.+.|-=|.||||+++.+.+.+
T Consensus        14 ~g~vi~L~GdLGaGKTtf~r~l~~~l   39 (123)
T PF02367_consen   14 PGDVILLSGDLGAGKTTFVRGLARAL   39 (123)
T ss_dssp             S-EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHc
Confidence            45799999999999999999998864

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>PRK06526 transposase; Provisional

Probab=94.28  E-value=0.043  Score=46.55  Aligned_cols=24  Identities=25%  Similarity=0.213  Sum_probs=20.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-+-++|.+|+|||+||.++.+.
T Consensus        98 ~~nlll~Gp~GtGKThLa~al~~~  121 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIGLGIR  121 (254)
T ss_pred             CceEEEEeCCCCchHHHHHHHHHH
Confidence            345789999999999999998775

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

Probab=94.27  E-value=0.036  Score=53.07  Aligned_cols=25  Identities=32%  Similarity=0.400  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-++.-++|.+|+||||||+-++++
T Consensus       325 ~kKilLL~GppGlGKTTLAHViAkq  349 (877)
T KOG1969|consen  325 PKKILLLCGPPGLGKTTLAHVIAKQ  349 (877)
T ss_pred             ccceEEeecCCCCChhHHHHHHHHh
Confidence            4688999999999999999998876

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

Probab=94.27  E-value=0.073  Score=51.89  Aligned_cols=50  Identities=20%  Similarity=0.368  Sum_probs=37.4

Q ss_pred             CCccccccchHHHHHHHhccC------CC-CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          180 KNQLAGVESRVEEIESLLGVK------SK-DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~------~~-~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...++|.+..++.+...+...      .+ ....+-++|..|+|||+||+.+.+.+.
T Consensus       453 ~~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~  509 (731)
T TIGR02639       453 KAKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALG  509 (731)
T ss_pred             hcceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhc
Confidence            467889988888887765431      11 234577899999999999999988753

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=94.25  E-value=0.06  Score=49.08  Aligned_cols=25  Identities=20%  Similarity=0.198  Sum_probs=22.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+|.++|.+|+||||++..+...+
T Consensus       100 ~~vi~lvG~~GvGKTTtaaKLA~~l  124 (429)
T TIGR01425       100 QNVIMFVGLQGSGKTTTCTKLAYYY  124 (429)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            5899999999999999999887654

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.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=94.25  E-value=0.057  Score=53.17  Aligned_cols=50  Identities=24%  Similarity=0.221  Sum_probs=39.0

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-.+++|.+.-++.|...+..+.- ...+-++|..|+||||+|+.+.+.+.
T Consensus        13 ~f~eiiGqe~v~~~L~~~i~~~ri-~Ha~Lf~Gp~G~GKTt~A~~lAr~L~   62 (824)
T PRK07764         13 TFAEVIGQEHVTEPLSTALDSGRI-NHAYLFSGPRGCGKTSSARILARSLN   62 (824)
T ss_pred             CHHHhcCcHHHHHHHHHHHHhCCC-CceEEEECCCCCCHHHHHHHHHHHhC
Confidence            345688988888888887764432 34567899999999999999988764

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=94.23  E-value=0.065  Score=50.63  Aligned_cols=52  Identities=27%  Similarity=0.278  Sum_probs=40.5

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |..-..++|.+.-++.|...+..+. -...+-++|..|+||||+|+.+.+.+-
T Consensus        12 P~~f~diiGqe~iv~~L~~~i~~~~-i~hayLf~Gp~G~GKTt~Ar~lAk~L~   63 (563)
T PRK06647         12 PRDFNSLEGQDFVVETLKHSIESNK-IANAYIFSGPRGVGKTSSARAFARCLN   63 (563)
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhhc
Confidence            3344678899988888888876432 245677999999999999999988753

>PRK10536 hypothetical protein; Provisional

Probab=94.19  E-value=0.078  Score=45.05  Aligned_cols=43  Identities=16%  Similarity=0.060  Sum_probs=30.8

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..+.++......+..++..    ..++.+.|..|.|||+||.++.-+
T Consensus        55 ~~i~p~n~~Q~~~l~al~~----~~lV~i~G~aGTGKT~La~a~a~~   97 (262)
T PRK10536         55 SPILARNEAQAHYLKAIES----KQLIFATGEAGCGKTWISAAKAAE   97 (262)
T ss_pred             ccccCCCHHHHHHHHHHhc----CCeEEEECCCCCCHHHHHHHHHHH
Confidence            3345555555556555542    348899999999999999997764

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=94.19  E-value=0.074  Score=48.79  Aligned_cols=27  Identities=37%  Similarity=0.389  Sum_probs=23.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .+-+-|+|..|+|||+|++++.+.+..
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~~~~~  174 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGNYILE  174 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHH
Confidence            466889999999999999999997643

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=94.18  E-value=0.048  Score=46.74  Aligned_cols=29  Identities=24%  Similarity=0.494  Sum_probs=25.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHhcCC
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKISSDF  232 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~~~f  232 (233)
                      -+-++|.|-.|.|||||++.++++++.+|
T Consensus        69 GQr~~If~~~G~GKTtLa~~i~~~i~~~~   97 (274)
T cd01133          69 GGKIGLFGGAGVGKTVLIMELINNIAKAH   97 (274)
T ss_pred             CCEEEEecCCCCChhHHHHHHHHHHHhcC
Confidence            46789999999999999999999987655

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport

Probab=94.18  E-value=0.044  Score=45.44  Aligned_cols=25  Identities=32%  Similarity=0.433  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        30 ~Ge~~~l~G~nGsGKSTLl~~l~G~   54 (233)
T cd03258          30 KGEIFGIIGRSGAGKSTLIRCINGL   54 (233)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999999988764

Other members of this system include the MetP permease and the MetQ substrate binding protein. 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.

>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional

Probab=94.17  E-value=0.044  Score=45.50  Aligned_cols=25  Identities=20%  Similarity=0.251  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        34 ~Ge~~~l~G~nGsGKSTLl~~l~Gl   58 (233)
T PRK11629         34 EGEMMAIVGSSGSGKSTLLHLLGGL   58 (233)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999999998764

>COG4240 Predicted kinase [General function prediction only]

Probab=94.16  E-value=0.051  Score=45.36  Aligned_cols=28  Identities=25%  Similarity=0.408  Sum_probs=24.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .--++||+|..|.||||++..+++.+..
T Consensus        49 rPli~gisGpQGSGKStls~~i~~~L~~   76 (300)
T COG4240          49 RPLIVGISGPQGSGKSTLSALIVRLLAA   76 (300)
T ss_pred             CceEEEeecCCCCchhhHHHHHHHHHHH
Confidence            4679999999999999999999987543

>PHA02244 ATPase-like protein

Probab=94.15  E-value=0.052  Score=48.47  Aligned_cols=24  Identities=29%  Similarity=0.363  Sum_probs=20.4

Q ss_pred             EEEEcCCCChHHHHHHHHHHHHhc
Q 043980          207 LGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       207 i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      |-|+|..|+|||+||+++++....
T Consensus       122 VLL~GppGtGKTtLA~aLA~~lg~  145 (383)
T PHA02244        122 VFLKGGAGSGKNHIAEQIAEALDL  145 (383)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCC
Confidence            556899999999999999987543

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=94.14  E-value=0.055  Score=51.60  Aligned_cols=47  Identities=28%  Similarity=0.388  Sum_probs=35.1

Q ss_pred             CCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          180 KNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ..+++|.++-++.+...+....    -+-++|++|+||||+|+++.+.+..
T Consensus        17 ~~~viG~~~a~~~l~~a~~~~~----~~ll~G~pG~GKT~la~~la~~l~~   63 (608)
T TIGR00764        17 IDQVIGQEEAVEIIKKAAKQKR----NVLLIGEPGVGKSMLAKAMAELLPD   63 (608)
T ss_pred             HhhccCHHHHHHHHHHHHHcCC----CEEEECCCCCCHHHHHHHHHHHcCc
Confidence            3567888877777766665432    3448999999999999999887643

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

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

Probab=94.14  E-value=0.063  Score=52.45  Aligned_cols=50  Identities=20%  Similarity=0.313  Sum_probs=37.8

Q ss_pred             CCccccccchHHHHHHHhccC-------CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          180 KNQLAGVESRVEEIESLLGVK-------SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~-------~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...++|.+..++.|...+...       ......+-++|..|+|||+||+.+...+.
T Consensus       457 ~~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~  513 (758)
T PRK11034        457 KMLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG  513 (758)
T ss_pred             cceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHhC
Confidence            356899998888887765521       11245678899999999999999988754

>TIGR00416 sms DNA repair protein RadA

Probab=94.13  E-value=0.087  Score=48.50  Aligned_cols=41  Identities=24%  Similarity=0.242  Sum_probs=32.0

Q ss_pred             chHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          188 SRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       188 ~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-...|.++|..+-..-.++-|.|.+|+|||||+..+...+
T Consensus        78 TGi~~LD~vLgGGi~~GsvilI~G~pGsGKTTL~lq~a~~~  118 (454)
T TIGR00416        78 SGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQL  118 (454)
T ss_pred             cCcHHHHHHhcCCccCCeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            34566777776655567889999999999999999986653

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=94.12  E-value=0.06  Score=50.53  Aligned_cols=47  Identities=23%  Similarity=0.411  Sum_probs=35.3

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.+..++.+...+....  ..-+-|+|.+|+|||++|+.+++.
T Consensus        63 ~f~~iiGqs~~i~~l~~al~~~~--~~~vLi~Ge~GtGKt~lAr~i~~~  109 (531)
T TIGR02902        63 SFDEIIGQEEGIKALKAALCGPN--PQHVIIYGPPGVGKTAAARLVLEE  109 (531)
T ss_pred             CHHHeeCcHHHHHHHHHHHhCCC--CceEEEECCCCCCHHHHHHHHHHH
Confidence            34568999888888877654322  234568999999999999999864

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.

>PRK03003 GTP-binding protein Der; Reviewed

Probab=94.11  E-value=0.65  Score=42.94  Aligned_cols=25  Identities=12%  Similarity=0.262  Sum_probs=21.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +...|+|+|-+++|||||..++.+.
T Consensus       210 ~~~kI~iiG~~nvGKSSLin~l~~~  234 (472)
T PRK03003        210 GPRRVALVGKPNVGKSSLLNKLAGE  234 (472)
T ss_pred             cceEEEEECCCCCCHHHHHHHHhCC
Confidence            3578899999999999999998753

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

Probab=94.10  E-value=0.041  Score=49.93  Aligned_cols=25  Identities=24%  Similarity=0.324  Sum_probs=21.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+-+.|.+|+|||+||+.+...+.
T Consensus       117 ~~iLL~GP~GsGKT~lAraLA~~l~  141 (413)
T TIGR00382       117 SNILLIGPTGSGKTLLAQTLARILN  141 (413)
T ss_pred             ceEEEECCCCcCHHHHHHHHHHhcC
Confidence            4678899999999999999987654

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.

>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein

Probab=94.09  E-value=0.047  Score=44.82  Aligned_cols=25  Identities=20%  Similarity=0.207  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        30 ~G~~~~i~G~nGsGKSTLl~~i~G~   54 (221)
T TIGR02211        30 KGEIVAIVGSSGSGKSTLLHLLGGL   54 (221)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            4568999999999999999998753

This model represents LolD, a member of the ABC transporter family (pfam00005). LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on whether the residue immediately following the new, modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. The top scoring proteins excluded by this model include homologs from the archaeal genus Methanosarcina.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.08  E-value=0.087  Score=48.08  Aligned_cols=25  Identities=20%  Similarity=0.264  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+++.++|.+|+||||++..+...+
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~  245 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARY  245 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999988876653

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

Probab=94.02  E-value=0.052  Score=46.23  Aligned_cols=49  Identities=20%  Similarity=0.253  Sum_probs=36.5

Q ss_pred             CCccccccchHHHHH---HHhcc----CCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIE---SLLGV----KSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~---~~l~~----~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -.+++|.++.+++..   +.|..    +.+..+-|-.+|.+|.|||.+|+++.+..
T Consensus       120 ~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~  175 (368)
T COG1223         120 LDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEA  175 (368)
T ss_pred             HhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhccc
Confidence            367899987776543   33432    33456778899999999999999998863

>COG1123 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]

Probab=94.00  E-value=0.043  Score=51.13  Aligned_cols=23  Identities=35%  Similarity=0.517  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -.++||+|..|.||||||+.+..
T Consensus       317 GE~lglVGeSGsGKSTlar~i~g  339 (539)
T COG1123         317 GETLGLVGESGSGKSTLARILAG  339 (539)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            47899999999999999999865

>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional

Probab=94.00  E-value=0.05  Score=44.97  Aligned_cols=26  Identities=19%  Similarity=0.157  Sum_probs=22.6

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||.+.+...
T Consensus        31 ~~Ge~~~i~G~nGsGKSTLl~~l~G~   56 (225)
T PRK10247         31 RAGEFKLITGPSGCGKSTLLKIVASL   56 (225)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            34679999999999999999998764

>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE)

Probab=93.96  E-value=0.05  Score=44.83  Aligned_cols=25  Identities=40%  Similarity=0.570  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~~l~G~   54 (228)
T cd03257          30 KGETLGLVGESGSGKSTLARAILGL   54 (228)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999999988753

The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=93.96  E-value=0.053  Score=50.85  Aligned_cols=49  Identities=20%  Similarity=0.282  Sum_probs=37.9

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ....++|....++++.+.+..-...-.-|-|+|..|+|||++|+.+++.
T Consensus       194 ~~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~  242 (534)
T TIGR01817       194 KEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYL  242 (534)
T ss_pred             ccCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHh
Confidence            4467899998888888866543222334569999999999999999985

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.

>PF13245 AAA_19: Part of AAA domain

Probab=93.92  E-value=0.065  Score=36.74  Aligned_cols=25  Identities=28%  Similarity=0.317  Sum_probs=17.2

Q ss_pred             eEEEEEEcCCCChHH-HHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKT-KIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKT-tla~~v~~~~  228 (233)
                      -++..|.|.+|.||| |++..+.+-+
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELL   35 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            346778999999999 4555444433

>PRK10619 histidine/lysine/arginine/ornithine transporter subunit; Provisional

Probab=93.92  E-value=0.051  Score=45.82  Aligned_cols=26  Identities=27%  Similarity=0.266  Sum_probs=22.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||++.+...
T Consensus        29 ~~Ge~~~l~G~nGsGKSTLl~~i~G~   54 (257)
T PRK10619         29 NAGDVISIIGSSGSGKSTFLRCINFL   54 (257)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34678999999999999999998764

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=93.86  E-value=0.078  Score=51.32  Aligned_cols=50  Identities=18%  Similarity=0.295  Sum_probs=38.6

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-..++|.+.-++.|...+..+. -...+-++|..|+||||+|+.+...+
T Consensus        15 ~~f~dIiGQe~~v~~L~~aI~~~r-l~HAYLF~GP~GtGKTt~AriLAk~L   64 (725)
T PRK07133         15 KTFDDIVGQDHIVQTLKNIIKSNK-ISHAYLFSGPRGTGKTSVAKIFANAL   64 (725)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHHHh
Confidence            344668898888888888776442 24556689999999999999998865

>cd01878 HflX HflX subfamily

Probab=93.85  E-value=0.051  Score=43.89  Aligned_cols=26  Identities=15%  Similarity=0.291  Sum_probs=22.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ++...|+|.|.+|+|||||.+.+.+.
T Consensus        39 ~~~~~I~iiG~~g~GKStLl~~l~~~   64 (204)
T cd01878          39 SGIPTVALVGYTNAGKSTLFNALTGA   64 (204)
T ss_pred             cCCCeEEEECCCCCCHHHHHHHHhcc
Confidence            45678999999999999999988764

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.

>PRK11300 livG leucine/isoleucine/valine transporter ATP-binding subunit; Provisional

Probab=93.84  E-value=0.055  Score=45.45  Aligned_cols=25  Identities=20%  Similarity=0.302  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+..-
T Consensus        30 ~Ge~~~l~G~nGsGKSTLl~~l~Gl   54 (255)
T PRK11300         30 EQEIVSLIGPNGAGKTTVFNCLTGF   54 (255)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999999988753

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.83  E-value=0.06  Score=48.24  Aligned_cols=25  Identities=20%  Similarity=0.307  Sum_probs=22.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..++.++|..|+||||++.++..+.
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~  161 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARC  161 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999988763

>PRK12288 GTPase RsgA; Reviewed

Probab=93.82  E-value=0.38  Score=42.76  Aligned_cols=33  Identities=27%  Similarity=0.408  Sum_probs=25.1

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +++|.++|..     .++.++|.+|+|||||..++..+
T Consensus       196 ideL~~~L~~-----ki~~~vG~sgVGKSTLiN~Ll~~  228 (347)
T PRK12288        196 LEELEAALTG-----RISIFVGQSGVGKSSLINALLPE  228 (347)
T ss_pred             HHHHHHHHhh-----CCEEEECCCCCCHHHHHHHhccc
Confidence            5566665542     25789999999999999998753

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=93.80  E-value=0.069  Score=42.77  Aligned_cols=23  Identities=39%  Similarity=0.514  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-+.++|..|+|||.||.++.+.
T Consensus        48 ~~l~l~G~~G~GKThLa~ai~~~   70 (178)
T PF01695_consen   48 ENLILYGPPGTGKTHLAVAIANE   70 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEEhhHhHHHHHHHHHHHHH
Confidence            45889999999999999999875

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.

>TIGR02012 tigrfam_recA protein RecA

Probab=93.79  E-value=0.12  Score=45.31  Aligned_cols=38  Identities=21%  Similarity=0.208  Sum_probs=28.8

Q ss_pred             HHHHHHHhc-cCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLG-VKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~-~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...|..+|. .+-..-+++-|+|.+|+||||||..+...
T Consensus        40 i~~LD~~Lg~GGlp~G~iteI~G~~GsGKTtLaL~~~~~   78 (321)
T TIGR02012        40 SLSLDLALGVGGLPRGRIIEIYGPESSGKTTLALHAIAE   78 (321)
T ss_pred             CHHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            445656665 44445689999999999999999987654

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=93.79  E-value=0.089  Score=44.66  Aligned_cols=48  Identities=21%  Similarity=0.399  Sum_probs=33.5

Q ss_pred             CccccccchHHHHHHHhc-----------cCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLG-----------VKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~-----------~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .++-|.+-++.++.+-..           .+-+..+=+-++|.+|.|||.||++|.|.-
T Consensus       155 ~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t  213 (408)
T KOG0727|consen  155 ADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  213 (408)
T ss_pred             cccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhcc
Confidence            455666666665544321           123446778899999999999999999863

>PRK10867 signal recognition particle protein; Provisional

Probab=93.79  E-value=0.12  Score=47.28  Aligned_cols=26  Identities=23%  Similarity=0.304  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+|.++|.+|+||||.+..+...+
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~l  124 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKYL  124 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHH
Confidence            36899999999999999888876654

>PRK06921 hypothetical protein; Provisional

Probab=93.76  E-value=0.063  Score=45.86  Aligned_cols=26  Identities=23%  Similarity=0.382  Sum_probs=22.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..-+-++|..|+|||+||.++.+.+.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~  142 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELM  142 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHh
Confidence            46788999999999999999998754

>TIGR02324 CP_lyasePhnL phosphonate C-P lyase system protein PhnL

Probab=93.73  E-value=0.059  Score=44.35  Aligned_cols=25  Identities=16%  Similarity=0.420  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+..-
T Consensus        33 ~Ge~~~l~G~nGsGKSTLl~~i~G~   57 (224)
T TIGR02324        33 AGECVALSGPSGAGKSTLLKSLYAN   57 (224)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4579999999999999999998764

Members of this family are the PhnL protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lysase complex. This protein (PhnL) and the adjacent-encoded PhnK (TIGR02323) resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this C-P lyase complex rather than part of a transporter per se.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=93.72  E-value=0.08  Score=46.47  Aligned_cols=45  Identities=27%  Similarity=0.210  Sum_probs=31.1

Q ss_pred             ccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          182 QLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       182 ~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .++|.++.+..+...+..+    .-+-+.|.+|+|||+||+.+...+.-
T Consensus        25 ~~~g~~~~~~~~l~a~~~~----~~vll~G~PG~gKT~la~~lA~~l~~   69 (329)
T COG0714          25 VVVGDEEVIELALLALLAG----GHVLLEGPPGVGKTLLARALARALGL   69 (329)
T ss_pred             eeeccHHHHHHHHHHHHcC----CCEEEECCCCccHHHHHHHHHHHhCC
Confidence            3778666665554433322    23557899999999999999887543

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=93.71  E-value=0.061  Score=43.33  Aligned_cols=24  Identities=21%  Similarity=0.257  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        32 ~Ge~~~l~G~nGsGKSTLl~~l~G   55 (192)
T cd03232          32 PGTLTALMGESGAGKTTLLDVLAG   55 (192)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhC
Confidence            457999999999999999999875

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.

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=93.69  E-value=0.085  Score=46.86  Aligned_cols=47  Identities=21%  Similarity=0.160  Sum_probs=33.7

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-+.++|.++-+..|...+..  ..+.-+-|.|..|.||||+|+.+++-
T Consensus        15 pf~~ivGq~~~k~al~~~~~~--p~~~~vli~G~~GtGKs~~ar~~~~~   61 (350)
T CHL00081         15 PFTAIVGQEEMKLALILNVID--PKIGGVMIMGDRGTGKSTTIRALVDL   61 (350)
T ss_pred             CHHHHhChHHHHHHHHHhccC--CCCCeEEEEcCCCCCHHHHHHHHHHH
Confidence            446789988777666553332  22333449999999999999999874

>TIGR01526 nadR_NMN_Atrans nicotinamide-nucleotide adenylyltransferase, NadR type

Probab=93.68  E-value=0.064  Score=47.19  Aligned_cols=25  Identities=20%  Similarity=0.299  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...|+|.|..|.|||||++.+.+.+
T Consensus       162 ~~~~~~~G~~~~gkstl~~~l~~~~  186 (325)
T TIGR01526       162 VKTVAILGGESTGKSTLVNKLAAVF  186 (325)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhh
Confidence            3578999999999999999988753

E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this model share that activity.

>PRK14242 phosphate transporter ATP-binding protein; Provisional

Probab=93.68  E-value=0.061  Score=45.17  Aligned_cols=26  Identities=19%  Similarity=0.294  Sum_probs=22.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||.+.+..-
T Consensus        30 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl   55 (253)
T PRK14242         30 EQNQVTALIGPSGCGKSTFLRCLNRM   55 (253)
T ss_pred             eCCCEEEEECCCCCCHHHHHHHHHhh
Confidence            34578999999999999999998753

>cd03266 ABC_NatA_sodium_exporter NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake

Probab=93.68  E-value=0.062  Score=44.02  Aligned_cols=25  Identities=28%  Similarity=0.323  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+..-
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   54 (218)
T cd03266          30 PGEVTGLLGPNGAGKTTTLRMLAGL   54 (218)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            4568999999999999999988753

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilus, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single intergral membrane protein.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=93.68  E-value=0.06  Score=46.82  Aligned_cols=25  Identities=32%  Similarity=0.446  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+.|+|..|.||||+++++.+.+.
T Consensus       133 ~~ilI~G~tGSGKTTll~al~~~i~  157 (299)
T TIGR02782       133 KNILVVGGTGSGKTTLANALLAEIA  157 (299)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhh
Confidence            3566999999999999999988763

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.

>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]

Probab=93.67  E-value=0.062  Score=46.77  Aligned_cols=29  Identities=34%  Similarity=0.526  Sum_probs=25.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHhcCC
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKISSDF  232 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~~~f  232 (233)
                      ...++|||.+|.|||-+|++|+..+..+|
T Consensus       166 Pkg~ll~GppGtGKTlla~~Vaa~mg~nf  194 (388)
T KOG0651|consen  166 PKGLLLYGPPGTGKTLLARAVAATMGVNF  194 (388)
T ss_pred             CceeEEeCCCCCchhHHHHHHHHhcCCce
Confidence            57899999999999999999998865554

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=93.66  E-value=0.075  Score=50.11  Aligned_cols=51  Identities=22%  Similarity=0.333  Sum_probs=38.9

Q ss_pred             CccccccchHHHHHHHhccCC----------CCeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          181 NQLAGVESRVEEIESLLGVKS----------KDVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~----------~~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      .++-|++..+.+|.+++....          ...+=+-+.|.+|.|||.||+++.+.+.-.
T Consensus       190 ~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vP  250 (802)
T KOG0733|consen  190 SDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVP  250 (802)
T ss_pred             hhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCc
Confidence            667889988988888765321          124557788999999999999999986543

>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=93.62  E-value=0.067  Score=42.13  Aligned_cols=25  Identities=32%  Similarity=0.276  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||++.+...
T Consensus        26 ~Ge~~~i~G~nGsGKSTLl~~l~G~   50 (166)
T cd03223          26 PGDRLLITGPSGTGKSSLFRALAGL   50 (166)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999999998764

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

>cd03267 ABC_NatA_like Similar in sequence to NatA, this is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake

Probab=93.62  E-value=0.063  Score=44.73  Aligned_cols=25  Identities=24%  Similarity=0.295  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||++.+...
T Consensus        46 ~Ge~~~i~G~NGsGKSTLl~~i~Gl   70 (236)
T cd03267          46 KGEIVGFIGPNGAGKTTTLKILSGL   70 (236)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999998753

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single intergral membrane protein.

>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=93.62  E-value=0.071  Score=45.29  Aligned_cols=40  Identities=30%  Similarity=0.356  Sum_probs=29.2

Q ss_pred             hHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          189 RVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       189 ~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+++.++|.........+.|.|..|.||||+.+++.+.+
T Consensus       112 ~~~~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~all~~i  151 (270)
T PF00437_consen  112 IPEEIAEFLRSAVRGRGNILISGPTGSGKTTLLNALLEEI  151 (270)
T ss_dssp             CHHHHHHHHHHCHHTTEEEEEEESTTSSHHHHHHHHHHHC
T ss_pred             hHHHHHHHHhhccccceEEEEECCCccccchHHHHHhhhc
Confidence            3455555555332345788999999999999999988764

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 ....

>PRK10575 iron-hydroxamate transporter ATP-binding subunit; Provisional

Probab=93.61  E-value=0.057  Score=45.84  Aligned_cols=25  Identities=20%  Similarity=0.311  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||++.+..-
T Consensus        36 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   60 (265)
T PRK10575         36 AGKVTGLIGHNGSGKSTLLKMLGRH   60 (265)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcCC
Confidence            4579999999999999999988753

>PF13271 DUF4062: Domain of unknown function (DUF4062)

Probab=93.61  E-value=0.3  Score=33.93  Aligned_cols=67  Identities=16%  Similarity=0.217  Sum_probs=48.0

Q ss_pred             eEEEcCcccccccchHHHHHHHHhhCCCeEEEeCccC-CCcchHHHHHHHHHhcCceEEEeecCCCCch
Q 043980           26 EVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLN-RGDEISQSLVNAIEASAISVIIFSESYTSSR   93 (233)
Q Consensus        26 dVFISy~~~D~~~~f~~~L~~~L~~~gi~~~~d~~~~-~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~   93 (233)
                      .||||-.-.|... --..|...|.+.|..+..-+.+. .+....+.+.+.|++|++.|.++...|-..+
T Consensus         1 rVFiSSt~~Dl~~-eR~~l~~~i~~~~~~~~~~e~~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~~~   68 (83)
T PF13271_consen    1 RVFISSTFRDLKE-ERDALIEAIRRLGCEPVGMEFFPASDQSPLEICLKEVDECDIFILILGNRYGSVP   68 (83)
T ss_pred             CEEEecChhhHHH-HHHHHHHHHHHCCCeeeeeeeecCCCCCHHHHHHHHHhhCCEEEEeeccccCCCC
Confidence            3899977777532 45678888888786654433222 2555667888999999999999999986543

>PRK11022 dppD dipeptide transporter ATP-binding subunit; Provisional

Probab=93.60  E-value=0.062  Score=47.22  Aligned_cols=27  Identities=37%  Similarity=0.419  Sum_probs=23.0

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-.+++|+|..|.|||||++.+..-+
T Consensus        31 ~~Ge~~~lvG~sGsGKSTL~~~l~Gll   57 (326)
T PRK11022         31 KQGEVVGIVGESGSGKSVSSLAIMGLI   57 (326)
T ss_pred             CCCCEEEEECCCCChHHHHHHHHHcCC
Confidence            345789999999999999999987643

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=93.58  E-value=0.087  Score=46.10  Aligned_cols=36  Identities=17%  Similarity=0.339  Sum_probs=28.2

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIF  225 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~  225 (233)
                      ...|.++|..+-....++-|+|.+|+|||+||..+.
T Consensus        82 ~~~LD~lLgGGi~~G~iteI~G~~GsGKTql~lqla  117 (313)
T TIGR02238        82 SQALDGILGGGIESMSITEVFGEFRCGKTQLSHTLC  117 (313)
T ss_pred             CHHHHHHhCCCCcCCeEEEEECCCCCCcCHHHHHHH
Confidence            445666676555557889999999999999998765

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>PRK11247 ssuB aliphatic sulfonates transport ATP-binding subunit; Provisional

Probab=93.58  E-value=0.065  Score=45.46  Aligned_cols=25  Identities=20%  Similarity=0.272  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        37 ~Ge~~~I~G~NGsGKSTLlk~l~Gl   61 (257)
T PRK11247         37 AGQFVAVVGRSGCGKSTLLRLLAGL   61 (257)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3568999999999999999998764

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=93.55  E-value=0.11  Score=45.06  Aligned_cols=37  Identities=27%  Similarity=0.369  Sum_probs=28.1

Q ss_pred             HHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          191 EEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       191 ~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..+..+|..+-....++-|+|.+|+|||||+..+.-.
T Consensus        82 ~~lD~~l~GGi~~g~i~ei~G~~g~GKT~l~~~~~~~  118 (310)
T TIGR02236        82 KELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVN  118 (310)
T ss_pred             HHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4455566654445688899999999999999988654

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>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=93.54  E-value=0.07  Score=41.04  Aligned_cols=25  Identities=24%  Similarity=0.403  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        25 ~Ge~~~i~G~nGsGKStLl~~l~G~   49 (144)
T cd03221          25 PGDRIGLVGRNGAGKSTLLKLIAGE   49 (144)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcCC
Confidence            4578999999999999999988653

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.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.54  E-value=0.11  Score=49.77  Aligned_cols=50  Identities=24%  Similarity=0.243  Sum_probs=38.9

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-..++|.+.-++.|..++..+.- ...+=++|..|+||||+|+.+.+.+.
T Consensus        14 ~f~~liGq~~i~~~L~~~l~~~rl-~~a~Lf~Gp~G~GKttlA~~lAk~L~   63 (620)
T PRK14948         14 RFDELVGQEAIATTLKNALISNRI-APAYLFTGPRGTGKTSSARILAKSLN   63 (620)
T ss_pred             cHhhccChHHHHHHHHHHHHcCCC-CceEEEECCCCCChHHHHHHHHHHhc
Confidence            446788988888888887775432 24566899999999999999998764

>PRK14274 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.53  E-value=0.067  Score=45.16  Aligned_cols=26  Identities=23%  Similarity=0.289  Sum_probs=22.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.+++|.|..|.|||||++.+...+
T Consensus        37 ~Ge~~~l~G~nGsGKSTLl~~l~G~~   62 (259)
T PRK14274         37 ENEVTAIIGPSGCGKSTFIKTLNLMI   62 (259)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            35689999999999999999987643

>PRK10646 ADP-binding protein; Provisional

Probab=93.52  E-value=0.12  Score=40.44  Aligned_cols=41  Identities=15%  Similarity=0.290  Sum_probs=29.0

Q ss_pred             chHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          188 SRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       188 ~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ++..++.+.|...-....+|.+.|-=|.||||+++.+.+.+
T Consensus        12 ~~t~~l~~~la~~l~~g~vi~L~GdLGaGKTtf~rgl~~~L   52 (153)
T PRK10646         12 QATLDLGARVAKACDGATVIYLYGDLGAGKTTFSRGFLQAL   52 (153)
T ss_pred             HHHHHHHHHHHHhCCCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            34455555443322334589999999999999999998864

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.50  E-value=0.11  Score=49.15  Aligned_cols=51  Identities=22%  Similarity=0.299  Sum_probs=39.2

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..-.+++|.+.-++.|...+..+. -...+-++|..|+||||+|+.+.+.+.
T Consensus        13 ~~f~~iiGq~~v~~~L~~~i~~~~-~~hayLf~Gp~G~GKtt~A~~lak~l~   63 (576)
T PRK14965         13 QTFSDLTGQEHVSRTLQNAIDTGR-VAHAFLFTGARGVGKTSTARILAKALN   63 (576)
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhhc
Confidence            345678999888888888776432 235567899999999999999988753

>PRK15093 antimicrobial peptide ABC transporter ATP-binding protein; Provisional

Probab=93.49  E-value=0.066  Score=47.11  Aligned_cols=27  Identities=33%  Similarity=0.389  Sum_probs=22.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-.+++|+|..|.|||||++.+..-+
T Consensus        31 ~~Ge~~~ivG~sGsGKSTLl~~i~Gl~   57 (330)
T PRK15093         31 TEGEIRGLVGESGSGKSLIAKAICGVT   57 (330)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHccC
Confidence            345689999999999999999987643

>PTZ00035 Rad51 protein; Provisional

Probab=93.48  E-value=0.11  Score=45.93  Aligned_cols=37  Identities=19%  Similarity=0.259  Sum_probs=29.5

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ...|.++|..+-....++-|+|..|.|||||+..+.-
T Consensus       104 ~~~LD~lLgGGi~~G~iteI~G~~GsGKT~l~~~l~~  140 (337)
T PTZ00035        104 STQLDKLLGGGIETGSITELFGEFRTGKTQLCHTLCV  140 (337)
T ss_pred             cHHHHHHhCCCCCCCeEEEEECCCCCchhHHHHHHHH
Confidence            4556667766555678999999999999999988754

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=93.48  E-value=0.072  Score=48.92  Aligned_cols=26  Identities=23%  Similarity=0.424  Sum_probs=22.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+-+-|+|..|+|||+|++++.+.+.
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~~l~  166 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVHALR  166 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHHH
Confidence            35677999999999999999998753

>cd03220 ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export

Probab=93.47  E-value=0.068  Score=44.21  Aligned_cols=25  Identities=24%  Similarity=0.387  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        47 ~Ge~~~i~G~nGsGKSTLl~~l~G~   71 (224)
T cd03220          47 RGERIGLIGRNGAGKSTLLRLLAGI   71 (224)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999998763

Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenzae) and a cytoplasmic membrane protein MPA2.

>PRK14248 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.47  E-value=0.071  Score=45.28  Aligned_cols=24  Identities=25%  Similarity=0.336  Sum_probs=21.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        46 ~Ge~~~i~G~nGsGKSTLl~~l~G   69 (268)
T PRK14248         46 KHAVTALIGPSGCGKSTFLRSINR   69 (268)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHh
Confidence            456899999999999999999876

>PRK14238 phosphate transporter ATP-binding protein; Provisional

Probab=93.44  E-value=0.072  Score=45.41  Aligned_cols=26  Identities=19%  Similarity=0.303  Sum_probs=22.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.+++|.|..|.|||||++.+...+
T Consensus        49 ~Ge~~~I~G~nGsGKSTLl~~i~Gl~   74 (271)
T PRK14238         49 ENEVTAIIGPSGCGKSTYIKTLNRMV   74 (271)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            45799999999999999999987643

>COG4107 PhnK ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=93.42  E-value=0.061  Score=43.21  Aligned_cols=26  Identities=35%  Similarity=0.495  Sum_probs=22.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.++||+|..|.|||||..++-.++
T Consensus        31 PGeVLgiVGESGSGKtTLL~~is~rl   56 (258)
T COG4107          31 PGEVLGIVGESGSGKTTLLKCISGRL   56 (258)
T ss_pred             CCcEEEEEecCCCcHHhHHHHHhccc
Confidence            35689999999999999999887654

>cd03294 ABC_Pro_Gly_Bertaine This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea

Probab=93.40  E-value=0.071  Score=45.40  Aligned_cols=25  Identities=28%  Similarity=0.387  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+..-
T Consensus        49 ~Ge~~~l~G~nGsGKSTLl~~L~Gl   73 (269)
T cd03294          49 EGEIFVIMGLSGSGKSTLLRCINRL   73 (269)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3578999999999999999998764

This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation. 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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=93.39  E-value=0.11  Score=51.49  Aligned_cols=49  Identities=18%  Similarity=0.374  Sum_probs=36.5

Q ss_pred             CCccccccchHHHHHHHhccC------CC-CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGVK------SK-DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~------~~-~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...++|.+.-++.+...+...      .+ ....+-++|..|+|||+||+++++.+
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l  622 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFM  622 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            356889988888877755421      11 13477899999999999999998764

>PRK10744 pstB phosphate transporter ATP-binding protein; Provisional

Probab=93.39  E-value=0.072  Score=45.03  Aligned_cols=25  Identities=20%  Similarity=0.262  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        38 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   62 (260)
T PRK10744         38 KNQVTAFIGPSGCGKSTLLRTFNRM   62 (260)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcc
Confidence            4578999999999999999998754

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=93.37  E-value=0.091  Score=45.49  Aligned_cols=50  Identities=28%  Similarity=0.471  Sum_probs=35.4

Q ss_pred             CccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          181 NQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .++-|.+.++.++.+-...           +-....=|-+||.+|.|||-||++|.|+-+.
T Consensus       185 ~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqTSA  245 (440)
T KOG0726|consen  185 ADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQTSA  245 (440)
T ss_pred             cccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcccch
Confidence            5566777778777664332           1122345668999999999999999997443

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=93.36  E-value=0.08  Score=41.57  Aligned_cols=25  Identities=16%  Similarity=0.242  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        25 ~Ge~~~l~G~nGsGKSTLl~~i~G~   49 (163)
T cd03216          25 RGEVHALLGENGAGKSTLMKILSGL   49 (163)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4568999999999999999998754

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.

>PRK13645 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=93.36  E-value=0.071  Score=45.86  Aligned_cols=25  Identities=16%  Similarity=0.158  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        36 ~Ge~~~l~G~nGsGKSTLl~~l~Gl   60 (289)
T PRK13645         36 KNKVTCVIGTTGSGKSTMIQLTNGL   60 (289)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3568999999999999999998764

>PRK11701 phnK phosphonate C-P lyase system protein PhnK; Provisional

Probab=93.36  E-value=0.073  Score=44.90  Aligned_cols=26  Identities=35%  Similarity=0.405  Sum_probs=22.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||++.++..
T Consensus        30 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl   55 (258)
T PRK11701         30 YPGEVLGIVGESGSGKTTLLNALSAR   55 (258)
T ss_pred             eCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34678999999999999999998764

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=93.35  E-value=0.08  Score=41.79  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        27 ~G~~~~l~G~nGsGKstLl~~i~G~   51 (171)
T cd03228          27 PGEKVAIVGPSGSGKSTLLKLLLRL   51 (171)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcC
Confidence            4568999999999999999998764

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.

>PRK14239 phosphate transporter ATP-binding protein; Provisional

Probab=93.34  E-value=0.073  Score=44.63  Aligned_cols=24  Identities=25%  Similarity=0.313  Sum_probs=21.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~~l~G   53 (252)
T PRK14239         30 PNEITALIGPSGSGKSTLLRSINR   53 (252)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhc
Confidence            456899999999999999999864

>PRK11831 putative ABC transporter ATP-binding protein YrbF; Provisional

Probab=93.33  E-value=0.072  Score=45.33  Aligned_cols=25  Identities=36%  Similarity=0.383  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        32 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   56 (269)
T PRK11831         32 RGKITAIMGPSGIGKTTLLRLIGGQ   56 (269)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999999998764

>PRK14243 phosphate transporter ATP-binding protein; Provisional

Probab=93.32  E-value=0.076  Score=45.08  Aligned_cols=26  Identities=23%  Similarity=0.238  Sum_probs=22.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||.+.+..-
T Consensus        34 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl   59 (264)
T PRK14243         34 PKNQITAFIGPSGCGKSTILRCFNRL   59 (264)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhh
Confidence            34579999999999999999998753

>PRK15056 manganese/iron transporter ATP-binding protein; Provisional

Probab=93.32  E-value=0.073  Score=45.37  Aligned_cols=25  Identities=20%  Similarity=0.357  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        32 ~Ge~~~l~G~nGsGKSTLl~~l~Gl   56 (272)
T PRK15056         32 GGSIAALVGVNGSGKSTLFKALMGF   56 (272)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4579999999999999999988754

>PRK13649 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=93.31  E-value=0.072  Score=45.55  Aligned_cols=25  Identities=24%  Similarity=0.222  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        32 ~Ge~~~l~G~nGsGKSTLl~~i~Gl   56 (280)
T PRK13649         32 DGSYTAFIGHTGSGKSTIMQLLNGL   56 (280)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            4568999999999999999998764

>PRK14255 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.31  E-value=0.076  Score=44.59  Aligned_cols=24  Identities=21%  Similarity=0.273  Sum_probs=21.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        30 ~Ge~~~l~G~nGsGKSTLl~~l~G   53 (252)
T PRK14255         30 QNEITALIGPSGCGKSTYLRTLNR   53 (252)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            456899999999999999999865

>PRK11308 dppF dipeptide transporter ATP-binding subunit; Provisional

Probab=93.31  E-value=0.074  Score=46.79  Aligned_cols=25  Identities=28%  Similarity=0.339  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||++.+..-
T Consensus        40 ~Ge~~~IvG~sGsGKSTLl~~l~gl   64 (327)
T PRK11308         40 RGKTLAVVGESGCGKSTLARLLTMI   64 (327)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcC
Confidence            3568999999999999999998764

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=93.29  E-value=0.075  Score=43.24  Aligned_cols=27  Identities=19%  Similarity=0.247  Sum_probs=22.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-.+++|.|..|.|||||.+.+....
T Consensus        31 ~~Ge~~~i~G~nGsGKSTLl~~l~G~~   57 (202)
T cd03233          31 KPGEMVLVLGRPGSGCSTLLKALANRT   57 (202)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHhcccC
Confidence            345799999999999999999876543

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.

>PRK09473 oppD oligopeptide transporter ATP-binding component; Provisional

Probab=93.28  E-value=0.074  Score=46.84  Aligned_cols=25  Identities=36%  Similarity=0.423  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||++.+..-
T Consensus        41 ~Ge~~~ivG~sGsGKSTL~~~l~Gl   65 (330)
T PRK09473         41 AGETLGIVGESGSGKSQTAFALMGL   65 (330)
T ss_pred             CCCEEEEECCCCchHHHHHHHHHcC
Confidence            4578999999999999999998764

>CHL00131 ycf16 sulfate ABC transporter protein; Validated

Probab=93.27  E-value=0.074  Score=44.62  Aligned_cols=25  Identities=24%  Similarity=0.338  Sum_probs=21.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ..-.+++|.|..|.|||||++.+..
T Consensus        31 ~~Ge~~~i~G~nGsGKSTLl~~i~G   55 (252)
T CHL00131         31 NKGEIHAIMGPNGSGKSTLSKVIAG   55 (252)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHcC
Confidence            3467899999999999999998865

>PRK06835 DNA replication protein DnaC; Validated

Probab=93.26  E-value=0.11  Score=45.92  Aligned_cols=24  Identities=29%  Similarity=0.422  Sum_probs=21.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-+-++|..|+|||.||.++.+.+
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l  207 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKEL  207 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHH
Confidence            668899999999999999998874

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.25  E-value=0.092  Score=47.75  Aligned_cols=24  Identities=25%  Similarity=0.153  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..++.++|.+|+||||++..+...
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~  246 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAK  246 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998764

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=93.25  E-value=0.14  Score=48.05  Aligned_cols=50  Identities=26%  Similarity=0.250  Sum_probs=39.0

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-.+++|.+.-++.|...+..+. -...+-++|..|+||||+|+.+.+.+
T Consensus        11 ~~fdeiiGqe~v~~~L~~~I~~gr-l~hayLf~Gp~G~GKTt~Ar~LAk~L   60 (535)
T PRK08451         11 KHFDELIGQESVSKTLSLALDNNR-LAHAYLFSGLRGSGKTSSARIFARAL   60 (535)
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHHHh
Confidence            344678998888888888776442 24566789999999999999988875

>PRK14261 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.23  E-value=0.078  Score=44.56  Aligned_cols=24  Identities=21%  Similarity=0.314  Sum_probs=21.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||++.+..
T Consensus        31 ~Ge~~~i~G~nGsGKSTLl~~l~G   54 (253)
T PRK14261         31 KNRVTALIGPSGCGKSTLLRCFNR   54 (253)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhc
Confidence            456899999999999999999874

>cd03234 ABCG_White The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors

Probab=93.23  E-value=0.086  Score=43.54  Aligned_cols=26  Identities=31%  Similarity=0.455  Sum_probs=22.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.+++|+|..|.|||||++.+...+
T Consensus        32 ~Ge~~~l~G~nGsGKSTLlk~l~G~~   57 (226)
T cd03234          32 SGQVMAILGSSGSGKTTLLDAISGRV   57 (226)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHhCcc
Confidence            45789999999999999999987643

The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in

>COG0444 DppD ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=93.21  E-value=0.083  Score=45.99  Aligned_cols=27  Identities=41%  Similarity=0.548  Sum_probs=23.1

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-.++||+|..|.||||+++++..-+
T Consensus        29 ~~GE~lgiVGESGsGKS~~~~aim~ll   55 (316)
T COG0444          29 KKGEILGIVGESGSGKSVLAKAIMGLL   55 (316)
T ss_pred             cCCcEEEEEcCCCCCHHHHHHHHHhcc
Confidence            346799999999999999999987643

>PRK14259 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.21  E-value=0.079  Score=45.11  Aligned_cols=25  Identities=20%  Similarity=0.290  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        38 ~Ge~~~l~G~nGsGKSTLl~~l~Gl   62 (269)
T PRK14259         38 RGKVTALIGPSGCGKSTVLRSLNRM   62 (269)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcc
Confidence            4578999999999999999998764

>PRK11823 DNA repair protein RadA; Provisional

Probab=93.20  E-value=0.15  Score=46.77  Aligned_cols=40  Identities=23%  Similarity=0.288  Sum_probs=31.4

Q ss_pred             hHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          189 RVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       189 ~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -..+|.++|..+-..-.++-|.|.+|+|||||+..+....
T Consensus        65 Gi~~LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~lq~a~~~  104 (446)
T PRK11823         65 GIGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARL  104 (446)
T ss_pred             CcHHHHHHhcCCccCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            3556667776555556799999999999999999987754

>PRK14273 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.18  E-value=0.083  Score=44.45  Aligned_cols=27  Identities=19%  Similarity=0.191  Sum_probs=22.9

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-.+++|.|..|.|||||.+.+...+
T Consensus        31 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   57 (254)
T PRK14273         31 LKNSITALIGPSGCGKSTFLRTLNRMN   57 (254)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            345799999999999999999987643

>PRK13477 bifunctional pantoate ligase/cytidylate kinase; Provisional

Probab=93.18  E-value=0.084  Score=49.23  Aligned_cols=25  Identities=32%  Similarity=0.488  Sum_probs=22.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+|+|.|..|.||||+|+.+.+++
T Consensus       284 ~~ii~i~G~sgsGKst~a~~la~~l  308 (512)
T PRK13477        284 QPIIAIDGPAGAGKSTVTRAVAKKL  308 (512)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            4689999999999999999998875

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=93.18  E-value=0.083  Score=43.29  Aligned_cols=26  Identities=31%  Similarity=0.295  Sum_probs=22.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ....+++|.|..|.|||||.+.+...
T Consensus        35 ~~Ge~~~i~G~nGsGKSTLl~~i~G~   60 (214)
T PRK13543         35 DAGEALLVQGDNGAGKTTLLRVLAGL   60 (214)
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHhCC
Confidence            34568999999999999999998764

>PRK14260 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.16  E-value=0.083  Score=44.64  Aligned_cols=26  Identities=19%  Similarity=0.219  Sum_probs=22.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|+|..|.|||||.+.+..-
T Consensus        31 ~~Ge~~~l~G~nGsGKSTLlk~l~Gl   56 (259)
T PRK14260         31 YRNKVTAIIGPSGCGKSTFIKTLNRI   56 (259)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhh
Confidence            34678999999999999999998864

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=93.15  E-value=0.086  Score=42.86  Aligned_cols=26  Identities=35%  Similarity=0.463  Sum_probs=22.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||.+.+..-
T Consensus        32 ~~G~~~~i~G~nGsGKSTLl~~l~Gl   57 (207)
T cd03369          32 KAGEKIGIVGRTGAGKSTLILALFRF   57 (207)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            34578999999999999999998753

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>cd03248 ABCC_TAP TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules

Probab=93.15  E-value=0.085  Score=43.47  Aligned_cols=26  Identities=15%  Similarity=0.171  Sum_probs=22.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||.+.+...
T Consensus        38 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl   63 (226)
T cd03248          38 HPGEVTALVGPSGSGKSTVVALLENF   63 (226)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            34678999999999999999998764

Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.

>PRK13632 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=93.13  E-value=0.082  Score=45.05  Aligned_cols=26  Identities=23%  Similarity=0.354  Sum_probs=22.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||.+.+..-
T Consensus        33 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl   58 (271)
T PRK13632         33 NEGEYVAILGHNGSGKSTISKILTGL   58 (271)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            34579999999999999999988764

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=93.12  E-value=0.086  Score=48.33  Aligned_cols=26  Identities=31%  Similarity=0.399  Sum_probs=22.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..-+-|+|..|+|||+|++++.+.+.
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l~  155 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYVV  155 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHH
Confidence            45688999999999999999999754

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=93.11  E-value=0.13  Score=45.70  Aligned_cols=36  Identities=22%  Similarity=0.293  Sum_probs=28.0

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIF  225 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~  225 (233)
                      ...|.++|..+-....+.-|+|.+|+|||+|+..+.
T Consensus       112 ~~~LD~lLgGGi~~G~ItEI~G~~GsGKTql~lqla  147 (344)
T PLN03187        112 SQALDELLGGGIETRCITEAFGEFRSGKTQLAHTLC  147 (344)
T ss_pred             cHhHHhhcCCCCCCCeEEEEecCCCCChhHHHHHHH
Confidence            445666676555556888899999999999998875

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=93.11  E-value=0.13  Score=43.33  Aligned_cols=53  Identities=19%  Similarity=0.391  Sum_probs=38.6

Q ss_pred             CCCCccccccchHHHHHHHhcc--CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          178 DNKNQLAGVESRVEEIESLLGV--KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~--~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .+-..++|.+.+++.|.+-...  ..-..+=|-+||..|.||+.|++++++.+..
T Consensus        57 i~L~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~  111 (287)
T COG2607          57 IDLADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYAD  111 (287)
T ss_pred             cCHHHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHHh
Confidence            4557789999888888663221  1122445668999999999999999998654

>PRK14237 phosphate transporter ATP-binding protein; Provisional

Probab=93.10  E-value=0.086  Score=44.81  Aligned_cols=26  Identities=19%  Similarity=0.198  Sum_probs=22.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.+++|.|..|.|||||.+.++...
T Consensus        45 ~Ge~~~I~G~nGsGKSTLl~~l~Gl~   70 (267)
T PRK14237         45 KNKITALIGPSGSGKSTYLRSLNRMN   70 (267)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            45789999999999999999988654

>CHL00195 ycf46 Ycf46; Provisional

Probab=93.10  E-value=0.12  Score=48.04  Aligned_cols=49  Identities=20%  Similarity=0.251  Sum_probs=32.4

Q ss_pred             CccccccchHHHHHHHhc--------cCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLG--------VKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~--------~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .++.|.+.-++.+.+...        .+-...+-|-++|.+|.|||.+|+++.+...
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~  284 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQ  284 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhC
Confidence            456776655544443211        1112245677999999999999999998754

>cd01856 YlqF YlqF

Probab=93.08  E-value=1.5  Score=34.45  Aligned_cols=22  Identities=18%  Similarity=0.301  Sum_probs=19.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ..+.++|.+|+|||||...+.+
T Consensus       116 ~~~~~~G~~~vGKstlin~l~~  137 (171)
T cd01856         116 IRAMVVGIPNVGKSTLINRLRG  137 (171)
T ss_pred             eEEEEECCCCCCHHHHHHHHhC
Confidence            4678999999999999998875

Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The YlqF subfamily is represented in a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga) and in all eukaryotes.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=93.07  E-value=0.087  Score=45.93  Aligned_cols=26  Identities=31%  Similarity=0.382  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ....+.|.|..|.|||||++++...+
T Consensus       143 ~~~~ili~G~tGsGKTTll~al~~~~  168 (308)
T TIGR02788       143 SRKNIIISGGTGSGKTTFLKSLVDEI  168 (308)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHccC
Confidence            45789999999999999999887643

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.

>cd01855 YqeH YqeH

Probab=93.05  E-value=0.11  Score=41.68  Aligned_cols=39  Identities=26%  Similarity=0.400  Sum_probs=27.0

Q ss_pred             cccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          185 GVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       185 g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      |.++-.+.+.+++.    ....+.++|++|+|||||..++.+.
T Consensus       112 gi~eL~~~l~~~l~----~~~~~~~~G~~nvGKStliN~l~~~  150 (190)
T cd01855         112 GVEELINAIKKLAK----KGGDVYVVGATNVGKSTLINALLKK  150 (190)
T ss_pred             CHHHHHHHHHHHhh----cCCcEEEEcCCCCCHHHHHHHHHHh
Confidence            44444444444442    2246889999999999999998874

YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases.

>PRK14235 phosphate transporter ATP-binding protein; Provisional

Probab=93.03  E-value=0.09  Score=44.70  Aligned_cols=26  Identities=19%  Similarity=0.247  Sum_probs=22.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.+++|.|..|.|||||.+.+...+
T Consensus        44 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   69 (267)
T PRK14235         44 EKTVTAFIGPSGCGKSTFLRCLNRMN   69 (267)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            35789999999999999999987644

>PRK14265 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.03  E-value=0.088  Score=44.98  Aligned_cols=24  Identities=21%  Similarity=0.325  Sum_probs=21.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||++.+..
T Consensus        45 ~Ge~~~IiG~nGsGKSTLl~~l~G   68 (274)
T PRK14265         45 AKKIIAFIGPSGCGKSTLLRCFNR   68 (274)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            456899999999999999999875

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=93.02  E-value=0.12  Score=45.22  Aligned_cols=39  Identities=23%  Similarity=0.275  Sum_probs=30.5

Q ss_pred             chHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          188 SRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       188 ~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-...|..+|..+-....++-|+|.+|.|||||+..+..
T Consensus        80 tg~~~lD~ll~gGi~~g~i~~i~G~~g~GKT~l~~~~~~  118 (316)
T TIGR02239        80 TGSKELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLAV  118 (316)
T ss_pred             CCCHHHHHHhcCCCCCCeEEEEECCCCCCcCHHHHHHHH
Confidence            335566676766555678999999999999999998764

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=93.02  E-value=0.097  Score=48.45  Aligned_cols=25  Identities=20%  Similarity=0.307  Sum_probs=22.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+++++|..|+||||++..+...+
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~  280 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARC  280 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHH
Confidence            4799999999999999999988754

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.01  E-value=0.11  Score=46.82  Aligned_cols=25  Identities=20%  Similarity=0.193  Sum_probs=22.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+++.++|..|+||||.+..+...+
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~  198 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIY  198 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            5789999999999999999887754

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=93.01  E-value=0.16  Score=44.73  Aligned_cols=38  Identities=21%  Similarity=0.219  Sum_probs=28.5

Q ss_pred             HHHHHHHhc-cCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLG-VKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~-~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...|..+|. .+-..-+++-|+|.+|.||||||..+.-.
T Consensus        40 i~~LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal~~~~~   78 (325)
T cd00983          40 SLSLDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAE   78 (325)
T ss_pred             CHHHHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            445556665 44445688889999999999999987643

RecA couples ATP hydrolysis to DNA strand exchange.

>TIGR03238 dnd_assoc_3 dnd system-associated protein 3

Probab=93.00  E-value=0.076  Score=48.94  Aligned_cols=22  Identities=27%  Similarity=0.291  Sum_probs=19.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARA  223 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~  223 (233)
                      ....+++|+|..|.|||||.+.
T Consensus        30 ~~GEiv~L~G~SGsGKSTLLr~   51 (504)
T TIGR03238        30 PSSSLLFLCGSSGDGKSEILAE   51 (504)
T ss_pred             cCCCEEEEECCCCCCHHHHHhc
Confidence            4568999999999999999873

cereus E33L, Hahella chejuensis KCTC 2396, Pseudoalteromonas haloplanktis TAC12, and Escherichia coli B7A.

>PRK13640 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=92.99  E-value=0.089  Score=45.15  Aligned_cols=27  Identities=22%  Similarity=0.246  Sum_probs=23.0

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-.+++|.|..|.|||||.+.+...+
T Consensus        31 ~~Ge~~~I~G~nGaGKSTLl~~l~G~~   57 (282)
T PRK13640         31 PRGSWTALIGHNGSGKSTISKLINGLL   57 (282)
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhccc
Confidence            345799999999999999999987643

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=92.98  E-value=0.14  Score=48.56  Aligned_cols=52  Identities=21%  Similarity=0.371  Sum_probs=36.7

Q ss_pred             CccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhcCC
Q 043980          181 NQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKISSDF  232 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~f  232 (233)
                      +++-|.++-+++|.+.+.+           +.+.-+=|=.+|.+|.|||++|+++.+.-+.+|
T Consensus       434 ~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~nF  496 (693)
T KOG0730|consen  434 DDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMNF  496 (693)
T ss_pred             hhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCCe
Confidence            4555677777777754432           223346677899999999999999999744443

>PRK11614 livF leucine/isoleucine/valine transporter ATP-binding subunit; Provisional

Probab=92.97  E-value=0.084  Score=43.89  Aligned_cols=24  Identities=21%  Similarity=0.328  Sum_probs=21.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~~l~G   53 (237)
T PRK11614         30 QGEIVTLIGANGAGKTTLLGTLCG   53 (237)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHcC
Confidence            457899999999999999998765

>PRK14244 phosphate ABC transporter ATP-binding protein; Provisional

Probab=92.95  E-value=0.094  Score=44.02  Aligned_cols=25  Identities=20%  Similarity=0.226  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||++.+...
T Consensus        30 ~Ge~~~I~G~nGsGKSTLl~~i~G~   54 (251)
T PRK14244         30 KREVTAFIGPSGCGKSTFLRCFNRM   54 (251)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhh
Confidence            4568999999999999999998754

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=92.93  E-value=0.1  Score=44.22  Aligned_cols=27  Identities=33%  Similarity=0.363  Sum_probs=23.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...-+.++|.+|+|||.||.++.+++.
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~  130 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELL  130 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHH
Confidence            456688999999999999999998754

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.90  E-value=0.13  Score=46.35  Aligned_cols=26  Identities=19%  Similarity=0.258  Sum_probs=22.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+++.++|..|+||||++..+...+
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l  230 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQL  230 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            46899999999999999999887654

>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]

Probab=92.84  E-value=0.088  Score=48.14  Aligned_cols=26  Identities=38%  Similarity=0.570  Sum_probs=22.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +-.+|||.|..||||||+++.+..-+
T Consensus       366 ~gEvigilGpNgiGKTTFvk~LAG~i  391 (591)
T COG1245         366 DGEVIGILGPNGIGKTTFVKLLAGVI  391 (591)
T ss_pred             cceEEEEECCCCcchHHHHHHHhccc
Confidence            35899999999999999999887543

>PRK15079 oligopeptide ABC transporter ATP-binding protein OppF; Provisional

Probab=92.84  E-value=0.095  Score=46.20  Aligned_cols=25  Identities=40%  Similarity=0.575  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||++.+..-
T Consensus        46 ~Ge~~~lvG~sGsGKSTLlk~i~Gl   70 (331)
T PRK15079         46 EGETLGVVGESGCGKSTFARAIIGL   70 (331)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCC
Confidence            4578999999999999999998763

>PRK08181 transposase; Validated

Probab=92.84  E-value=0.11  Score=44.56  Aligned_cols=24  Identities=33%  Similarity=0.336  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-+-++|.+|+|||.||.++.+..
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~a  130 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLAL  130 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHH
Confidence            348899999999999999998753

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=92.84  E-value=0.12  Score=48.19  Aligned_cols=49  Identities=22%  Similarity=0.381  Sum_probs=38.9

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ....++|....++++.+.+..-...-.-|-|.|..|+|||++|+.+++.
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~  233 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAA  233 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHh
Confidence            4567999999898888876553333446679999999999999999985

>PRK13546 teichoic acids export protein ATP-binding subunit; Provisional

Probab=92.82  E-value=0.096  Score=44.62  Aligned_cols=25  Identities=28%  Similarity=0.480  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        49 ~Ge~~~liG~NGsGKSTLlk~L~Gl   73 (264)
T PRK13546         49 EGDVIGLVGINGSGKSTLSNIIGGS   73 (264)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3568999999999999999998764

>PRK14271 phosphate ABC transporter ATP-binding protein; Provisional

Probab=92.81  E-value=0.099  Score=44.75  Aligned_cols=25  Identities=24%  Similarity=0.264  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        46 ~Ge~~~I~G~nGsGKSTLl~~l~Gl   70 (276)
T PRK14271         46 ARAVTSLMGPTGSGKTTFLRTLNRM   70 (276)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcc
Confidence            4578999999999999999998764

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=92.81  E-value=0.16  Score=44.46  Aligned_cols=37  Identities=27%  Similarity=0.357  Sum_probs=27.9

Q ss_pred             HHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          191 EEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       191 ~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..+..+|..+-....++-|+|.+|.|||++|..+.-.
T Consensus        89 ~~lD~~l~GGi~~g~vtei~G~~GsGKT~l~~~~~~~  125 (317)
T PRK04301         89 KELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVN  125 (317)
T ss_pred             HHHHHHhcCCccCCcEEEEECCCCCCHhHHHHHHHHH
Confidence            4455556544445688889999999999999988644

>PRK14236 phosphate transporter ATP-binding protein; Provisional

Probab=92.80  E-value=0.099  Score=44.55  Aligned_cols=25  Identities=20%  Similarity=0.259  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||++.+...
T Consensus        50 ~Ge~~~I~G~nGsGKSTLl~~laGl   74 (272)
T PRK14236         50 KNRVTAFIGPSGCGKSTLLRCFNRM   74 (272)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhc
Confidence            4578999999999999999998754

>PRK13648 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=92.79  E-value=0.099  Score=44.45  Aligned_cols=26  Identities=27%  Similarity=0.286  Sum_probs=22.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||.+.+...
T Consensus        33 ~~Ge~~~I~G~nGsGKSTLl~~i~Gl   58 (269)
T PRK13648         33 PKGQWTSIVGHNGSGKSTIAKLMIGI   58 (269)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            34579999999999999999998764

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=92.78  E-value=0.12  Score=46.37  Aligned_cols=50  Identities=18%  Similarity=0.242  Sum_probs=33.9

Q ss_pred             CccccccchHHHHHHHhc----------cCCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          181 NQLAGVESRVEEIESLLG----------VKSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~----------~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      +++.|..+.++-|.+-.-          .....++-|-++|.+|.|||-||++|+-....
T Consensus       212 ~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTlLAKAvATEc~t  271 (491)
T KOG0738|consen  212 DDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTLLAKAVATECGT  271 (491)
T ss_pred             HhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHHHHHHHHHhhcC
Confidence            556676655554444211          11234677889999999999999999986544

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.77  E-value=0.11  Score=48.70  Aligned_cols=25  Identities=20%  Similarity=0.270  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+++|+|.+|+||||++..+...+
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~l  374 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRF  374 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            5799999999999999999887653

>PRK12337 2-phosphoglycerate kinase; Provisional

Probab=92.76  E-value=0.11  Score=47.70  Aligned_cols=26  Identities=27%  Similarity=0.443  Sum_probs=23.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+|.+.|.+|+||||+|.++.+++
T Consensus       254 ~p~vil~~G~~G~GKSt~a~~LA~~l  279 (475)
T PRK12337        254 RPLHVLIGGVSGVGKSVLASALAYRL  279 (475)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHc
Confidence            47899999999999999999998874

>TIGR02769 nickel_nikE nickel import ATP-binding protein NikE

Probab=92.74  E-value=0.1  Score=44.32  Aligned_cols=25  Identities=28%  Similarity=0.545  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+..-
T Consensus        36 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   60 (265)
T TIGR02769        36 EGETVGLLGRSGCGKSTLARLLLGL   60 (265)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999999988763

This family represents the NikE subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase.

>PRK11153 metN DL-methionine transporter ATP-binding subunit; Provisional

Probab=92.73  E-value=0.099  Score=46.27  Aligned_cols=25  Identities=28%  Similarity=0.377  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||++.+..-
T Consensus        30 ~Gei~~iiG~nGsGKSTLlk~L~Gl   54 (343)
T PRK11153         30 AGEIFGVIGASGAGKSTLIRCINLL   54 (343)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCC
Confidence            4568999999999999999988764

>PRK13650 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=92.72  E-value=0.1  Score=44.70  Aligned_cols=25  Identities=32%  Similarity=0.260  Sum_probs=22.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||.+.+..-
T Consensus        32 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   56 (279)
T PRK13650         32 QGEWLSIIGHNGSGKSTTVRLIDGL   56 (279)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4679999999999999999998764

>cd01853 Toc34_like Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts)

Probab=92.71  E-value=0.15  Score=43.09  Aligned_cols=30  Identities=20%  Similarity=0.327  Sum_probs=24.3

Q ss_pred             ccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          198 GVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       198 ~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ....+....|.+.|..|+|||||..++++.
T Consensus        25 ~~~~~~~~~IllvG~tGvGKSSliNaLlg~   54 (249)
T cd01853          25 KEELDFSLTILVLGKTGVGKSSTINSIFGE   54 (249)
T ss_pred             hhhccCCeEEEEECCCCCcHHHHHHHHhCC
Confidence            333445678889999999999999999874

This family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90. The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex. The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle. Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein. Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic. Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon.

>PRK10419 nikE nickel transporter ATP-binding protein NikE; Provisional

Probab=92.70  E-value=0.1  Score=44.43  Aligned_cols=25  Identities=24%  Similarity=0.409  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||++.+...
T Consensus        37 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   61 (268)
T PRK10419         37 SGETVALLGRSGCGKSTLARLLVGL   61 (268)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3568999999999999999988753

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=92.70  E-value=0.14  Score=48.99  Aligned_cols=48  Identities=25%  Similarity=0.322  Sum_probs=37.0

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +..-.+++|.+..++.|...+...    +.+-++|.+|+||||+|+++.+.+
T Consensus        27 ~~~~~~vigq~~a~~~L~~~~~~~----~~~l~~G~~G~GKttla~~l~~~l   74 (637)
T PRK13765         27 ERLIDQVIGQEHAVEVIKKAAKQR----RHVMMIGSPGTGKSMLAKAMAELL   74 (637)
T ss_pred             cccHHHcCChHHHHHHHHHHHHhC----CeEEEECCCCCcHHHHHHHHHHHc
Confidence            334567889888777777665533    368889999999999999988764

>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=92.69  E-value=0.11  Score=40.20  Aligned_cols=25  Identities=28%  Similarity=0.327  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        24 ~g~~~~i~G~nGsGKStll~~l~g~   48 (157)
T cd00267          24 AGEIVALVGPNGSGKSTLLRAIAGL   48 (157)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3478999999999999999998764

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=92.68  E-value=0.16  Score=50.37  Aligned_cols=49  Identities=20%  Similarity=0.402  Sum_probs=37.3

Q ss_pred             CCccccccchHHHHHHHhccCC------C-CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGVKS------K-DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~~------~-~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...++|.+..++.+...+....      + ....+-+.|..|+|||++|+.+...+
T Consensus       564 ~~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l  619 (852)
T TIGR03346       564 HERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFL  619 (852)
T ss_pred             hcccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3568899988888877654311      1 14567799999999999999998864

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.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=92.65  E-value=0.079  Score=46.78  Aligned_cols=26  Identities=27%  Similarity=0.245  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ....|.|+|..|.||||+.+++.+.+
T Consensus       159 ~~~nili~G~tgSGKTTll~aL~~~i  184 (332)
T PRK13900        159 SKKNIIISGGTSTGKTTFTNAALREI  184 (332)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHhhC
Confidence            34568899999999999999988754

>cd03291 ABCC_CFTR1 The CFTR subfamily domain 1

Probab=92.64  E-value=0.11  Score=44.82  Aligned_cols=25  Identities=32%  Similarity=0.344  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||++.+...
T Consensus        62 ~Ge~~~liG~NGsGKSTLl~~I~Gl   86 (282)
T cd03291          62 KGEMLAITGSTGSGKTSLLMLILGE   86 (282)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999998764

The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits, or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=92.64  E-value=0.11  Score=50.16  Aligned_cols=48  Identities=23%  Similarity=0.262  Sum_probs=36.3

Q ss_pred             CCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...++|....++.+.+.+..-...-.-|-|.|..|+|||++|+++++.
T Consensus       375 ~~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~  422 (686)
T PRK15429        375 FGEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNL  422 (686)
T ss_pred             ccceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHh
Confidence            357899988888887655432222345678999999999999999874

>PRK10253 iron-enterobactin transporter ATP-binding protein; Provisional

Probab=92.64  E-value=0.098  Score=44.38  Aligned_cols=25  Identities=28%  Similarity=0.323  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||.+.+...
T Consensus        32 ~Ge~~~i~G~nGsGKSTLl~~i~G~   56 (265)
T PRK10253         32 DGHFTAIIGPNGCGKSTLLRTLSRL   56 (265)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcCC
Confidence            4578999999999999999988764

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.63  E-value=0.12  Score=46.97  Aligned_cols=25  Identities=20%  Similarity=0.296  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...+++++|..|+||||+...+..+
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~  214 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAAR  214 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3579999999999999999987654

>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed

Probab=92.58  E-value=1.2  Score=43.38  Aligned_cols=24  Identities=13%  Similarity=0.325  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-|+|+|.+|+|||||..++.+.
T Consensus       450 ~~kI~ivG~~nvGKSSLin~l~~~  473 (712)
T PRK09518        450 LRRVALVGRPNVGKSSLLNQLTHE  473 (712)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCc
Confidence            467899999999999999988763

>TIGR02314 ABC_MetN D-methionine ABC transporter, ATP-binding protein

Probab=92.57  E-value=0.11  Score=46.12  Aligned_cols=25  Identities=24%  Similarity=0.352  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+..-
T Consensus        30 ~Gei~gIiG~sGaGKSTLlr~I~gl   54 (343)
T TIGR02314        30 AGQIYGVIGASGAGKSTLIRCVNLL   54 (343)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4578999999999999999988753

Members of this family are the ATP-binding protein of the D-methionine ABC transporter complex. Known members belong to the Proteobacteria.

>PLN02674 adenylate kinase

Probab=92.57  E-value=0.21  Score=42.16  Aligned_cols=23  Identities=30%  Similarity=0.261  Sum_probs=20.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..|-|.|++|.||||+|+.+.++
T Consensus        32 ~~i~l~G~PGsGKgT~a~~La~~   54 (244)
T PLN02674         32 KRLILIGPPGSGKGTQSPIIKDE   54 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Confidence            44678999999999999998875

>PRK13647 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=92.55  E-value=0.11  Score=44.36  Aligned_cols=25  Identities=16%  Similarity=0.219  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   54 (274)
T PRK13647         30 EGSKTALLGPNGAGKSTLLLHLNGI   54 (274)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcC
Confidence            4578999999999999999998753

>PRK15112 antimicrobial peptide ABC system ATP-binding protein SapF; Provisional

Probab=92.55  E-value=0.11  Score=44.11  Aligned_cols=25  Identities=28%  Similarity=0.426  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||.+.+...
T Consensus        38 ~Ge~~~i~G~NGsGKSTLl~~l~Gl   62 (267)
T PRK15112         38 EGQTLAIIGENGSGKSTLAKMLAGM   62 (267)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhCC
Confidence            4568999999999999999998764

>PRK14268 phosphate ABC transporter ATP-binding protein; Provisional

Probab=92.55  E-value=0.11  Score=43.80  Aligned_cols=25  Identities=20%  Similarity=0.287  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        37 ~Ge~~~i~G~nGsGKSTLl~~i~Gl   61 (258)
T PRK14268         37 KNSVTALIGPSGCGKSTFIRCLNRM   61 (258)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4578999999999999999998753

>PRK14252 phosphate ABC transporter ATP-binding protein; Provisional

Probab=92.48  E-value=0.12  Score=43.88  Aligned_cols=26  Identities=19%  Similarity=0.293  Sum_probs=22.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||.+.+...
T Consensus        40 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl   65 (265)
T PRK14252         40 HEKQVTALIGPSGCGKSTFLRCFNRM   65 (265)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhcc
Confidence            34578999999999999999998754

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.46  E-value=0.16  Score=48.34  Aligned_cols=50  Identities=24%  Similarity=0.231  Sum_probs=37.4

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-.+++|.+.-++.|...+..+. -...+=++|..|+||||+|+.+.+.+.
T Consensus        14 sf~dIiGQe~v~~~L~~ai~~~r-i~ha~Lf~GPpG~GKTtiArilAk~L~   63 (624)
T PRK14959         14 TFAEVAGQETVKAILSRAAQENR-VAPAYLFSGTRGVGKTTIARIFAKALN   63 (624)
T ss_pred             CHHHhcCCHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHhcc
Confidence            34567888877777777666432 235677899999999999999988754

>PRK14258 phosphate ABC transporter ATP-binding protein; Provisional

Probab=92.46  E-value=0.12  Score=43.79  Aligned_cols=26  Identities=19%  Similarity=0.252  Sum_probs=22.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||.+.+..-
T Consensus        31 ~~Ge~~~I~G~nGsGKSTLl~~l~Gl   56 (261)
T PRK14258         31 YQSKVTAIIGPSGCGKSTFLKCLNRM   56 (261)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhcc
Confidence            35679999999999999999998764

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=92.46  E-value=0.19  Score=42.88  Aligned_cols=36  Identities=22%  Similarity=0.219  Sum_probs=25.9

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+.+..++..   ...++.|.|..|.||||+.+++.+.+
T Consensus        69 ~~~l~~~~~~---~~GlilisG~tGSGKTT~l~all~~i  104 (264)
T cd01129          69 LEIFRKLLEK---PHGIILVTGPTGSGKTTTLYSALSEL  104 (264)
T ss_pred             HHHHHHHHhc---CCCEEEEECCCCCcHHHHHHHHHhhh
Confidence            3444444432   23478999999999999999887754

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.

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=92.43  E-value=0.13  Score=43.64  Aligned_cols=38  Identities=24%  Similarity=0.268  Sum_probs=28.5

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .+.|.++|..+-....+.-|+|.+|+|||.||..+.-.
T Consensus        24 ~~~lD~~L~GGi~~g~itEi~G~~gsGKTql~l~l~~~   61 (256)
T PF08423_consen   24 CKSLDELLGGGIPTGSITEIVGESGSGKTQLCLQLAVN   61 (256)
T ss_dssp             SHHHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CHHHHHhhCCCCCCCcEEEEEEecccccchHHHHHHHH
Confidence            44566667554444578999999999999999877543

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C

Probab=92.42  E-value=0.12  Score=41.82  Aligned_cols=26  Identities=23%  Similarity=0.299  Sum_probs=22.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||.+.+...
T Consensus        29 ~~G~~~~i~G~nG~GKSTLl~~i~G~   54 (204)
T cd03250          29 PKGELVAIVGPVGSGKSSLLSALLGE   54 (204)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCc
Confidence            34678999999999999999988764

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>PRK09354 recA recombinase A; Provisional

Probab=92.42  E-value=0.25  Score=43.88  Aligned_cols=38  Identities=21%  Similarity=0.200  Sum_probs=29.0

Q ss_pred             HHHHHHHhc-cCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLG-VKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~-~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...|..+|. .+-..-+++-|+|..|.||||||..+...
T Consensus        45 i~~LD~~LG~GGip~G~IteI~G~~GsGKTtLal~~~~~   83 (349)
T PRK09354         45 SLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAE   83 (349)
T ss_pred             cHHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            455666676 44445689999999999999999987643

>KOG0062 consensus ATPase component of ABC transporters with duplicated ATPase domains/Translation elongation factor EF-3b [Amino acid transport and metabolism; Translation, ribosomal structure and biogenesis]

Probab=92.39  E-value=0.089  Score=48.60  Aligned_cols=23  Identities=39%  Similarity=0.585  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .|--|+||..|+|||||.+++.+
T Consensus       106 GrRYGLvGrNG~GKsTLLRaia~  128 (582)
T KOG0062|consen  106 GRRYGLVGRNGIGKSTLLRAIAN  128 (582)
T ss_pred             ccccceeCCCCCcHHHHHHHHHh
Confidence            46689999999999999999988

>PRK14275 phosphate ABC transporter ATP-binding protein; Provisional

Probab=92.38  E-value=0.12  Score=44.47  Aligned_cols=25  Identities=36%  Similarity=0.474  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        64 ~Ge~~~l~G~nGsGKSTLl~~L~Gl   88 (286)
T PRK14275         64 SKYVTAIIGPSGCGKSTFLRAINRM   88 (286)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcc
Confidence            3578999999999999999998763

>PRK13646 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=92.37  E-value=0.12  Score=44.42  Aligned_cols=26  Identities=23%  Similarity=0.231  Sum_probs=22.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||.+.+...
T Consensus        31 ~~Ge~~~i~G~nGsGKSTLl~~L~Gl   56 (286)
T PRK13646         31 EQGKYYAIVGQTGSGKSTLIQNINAL   56 (286)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            34578999999999999999998764

>cd01854 YjeQ_engC YjeQ/EngC

Probab=92.31  E-value=0.16  Score=43.76  Aligned_cols=33  Identities=21%  Similarity=0.404  Sum_probs=25.8

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +++|...|..     +++++.|..|+|||||.+.+...
T Consensus       152 i~~L~~~L~~-----k~~~~~G~sg~GKSTlin~l~~~  184 (287)
T cd01854         152 LDELREYLKG-----KTSVLVGQSGVGKSTLINALLPD  184 (287)
T ss_pred             HHHHHhhhcc-----ceEEEECCCCCCHHHHHHHHhch
Confidence            4555555542     68999999999999999988764

YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.

>PRK03003 GTP-binding protein Der; Reviewed

Probab=92.24  E-value=0.17  Score=46.72  Aligned_cols=25  Identities=16%  Similarity=0.348  Sum_probs=21.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .....|+|+|.+|+|||||...+..
T Consensus        36 ~~~~~V~IvG~~nvGKSSL~nrl~~   60 (472)
T PRK03003         36 GPLPVVAVVGRPNVGKSTLVNRILG   60 (472)
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHhC
Confidence            3457799999999999999998765

>TIGR02982 heterocyst_DevA ABC exporter ATP-binding subunit, DevA family

Probab=92.23  E-value=0.14  Score=42.16  Aligned_cols=24  Identities=25%  Similarity=0.138  Sum_probs=21.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        30 ~G~~~~I~G~nGsGKStLl~~l~G   53 (220)
T TIGR02982        30 PGEIVILTGPSGSGKTTLLTLIGG   53 (220)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            357899999999999999998875

Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The DevBCA proteins are thought export of either heterocyst-specific glycolipids or an enzyme essential for formation of the laminated layer found in heterocysts.

>PRK13636 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=92.21  E-value=0.13  Score=44.16  Aligned_cols=25  Identities=20%  Similarity=0.218  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+..-
T Consensus        31 ~Ge~~~i~G~nGaGKSTLl~~i~Gl   55 (283)
T PRK13636         31 KGEVTAILGGNGAGKSTLFQNLNGI   55 (283)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999999998764

>PRK13641 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=92.18  E-value=0.13  Score=44.21  Aligned_cols=25  Identities=16%  Similarity=0.209  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        32 ~Ge~~~iiG~NGaGKSTLl~~l~Gl   56 (287)
T PRK13641         32 EGSFVALVGHTGSGKSTLMQHFNAL   56 (287)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999999998764

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=92.16  E-value=0.14  Score=42.63  Aligned_cols=24  Identities=21%  Similarity=0.213  Sum_probs=20.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIF  225 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~  225 (233)
                      ..-.+++|.|..|.|||||-..+.
T Consensus        29 ~~Ge~vaI~GpSGSGKSTLLniig   52 (226)
T COG1136          29 EAGEFVAIVGPSGSGKSTLLNLLG   52 (226)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHh
Confidence            345689999999999999988765

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=92.14  E-value=0.23  Score=46.10  Aligned_cols=40  Identities=20%  Similarity=0.209  Sum_probs=32.3

Q ss_pred             chHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          188 SRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       188 ~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-...|.++|..+-..-.++-|.|.+|+|||||+..+...
T Consensus       247 tGi~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~f~~~  286 (484)
T TIGR02655       247 SGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLEN  286 (484)
T ss_pred             CChHhHHHHhcCCccCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3466777778766666788999999999999999988664

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=92.13  E-value=0.095  Score=46.49  Aligned_cols=26  Identities=23%  Similarity=0.434  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ....|.|.|..|.||||+++++.+.+
T Consensus       161 ~~~nilI~G~tGSGKTTll~aLl~~i  186 (344)
T PRK13851        161 GRLTMLLCGPTGSGKTTMSKTLISAI  186 (344)
T ss_pred             cCCeEEEECCCCccHHHHHHHHHccc
Confidence            34678899999999999999988754

>PRK13637 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=92.11  E-value=0.14  Score=44.14  Aligned_cols=25  Identities=24%  Similarity=0.344  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||.+.+..-
T Consensus        32 ~Ge~~~i~G~nGaGKSTLl~~l~Gl   56 (287)
T PRK13637         32 DGEFVGLIGHTGSGKSTLIQHLNGL   56 (287)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcC
Confidence            4578999999999999999998764

>TIGR00157 ribosome small subunit-dependent GTPase A

Probab=92.04  E-value=0.21  Score=42.13  Aligned_cols=33  Identities=21%  Similarity=0.249  Sum_probs=25.5

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ++++.+.+..     .++.+.|++|+|||||..++..+
T Consensus       111 i~eLf~~l~~-----~~~~~~G~sgvGKStLiN~L~~~  143 (245)
T TIGR00157       111 LKELIEALQN-----RISVFAGQSGVGKSSLINALDPS  143 (245)
T ss_pred             HHHHHhhhcC-----CEEEEECCCCCCHHHHHHHHhhh
Confidence            5555555441     47889999999999999998875

The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option).

>PRK14254 phosphate ABC transporter ATP-binding protein; Provisional

Probab=92.04  E-value=0.14  Score=44.04  Aligned_cols=25  Identities=24%  Similarity=0.326  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        64 ~Ge~~~I~G~nGsGKSTLl~~l~Gl   88 (285)
T PRK14254         64 ENQVTAMIGPSGCGKSTFLRCINRM   88 (285)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcc
Confidence            4578999999999999999998754

>PRK00098 GTPase RsgA; Reviewed

Probab=92.04  E-value=0.18  Score=43.72  Aligned_cols=33  Identities=24%  Similarity=0.416  Sum_probs=25.5

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +++|.+.+.     -.++++.|.+|+|||||.+.+...
T Consensus       155 i~~L~~~l~-----gk~~~~~G~sgvGKStlin~l~~~  187 (298)
T PRK00098        155 LDELKPLLA-----GKVTVLAGQSGVGKSTLLNALAPD  187 (298)
T ss_pred             HHHHHhhcc-----CceEEEECCCCCCHHHHHHHHhCC
Confidence            555655553     257899999999999999988764

>PRK13651 cobalt transporter ATP-binding subunit; Provisional

Probab=92.01  E-value=0.14  Score=44.57  Aligned_cols=25  Identities=24%  Similarity=0.215  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||++.+..-
T Consensus        32 ~Ge~v~iiG~nGsGKSTLl~~L~Gl   56 (305)
T PRK13651         32 QGEFIAIIGQTGSGKTTFIEHLNAL   56 (305)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCC
Confidence            4568999999999999999988753

>PRK13631 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=92.00  E-value=0.14  Score=44.88  Aligned_cols=25  Identities=20%  Similarity=0.143  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||.+.+...
T Consensus        51 ~Ge~~~I~G~nGsGKSTLl~~L~Gl   75 (320)
T PRK13631         51 KNKIYFIIGNSGSGKSTLVTHFNGL   75 (320)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999999998764

>CHL00095 clpC Clp protease ATP binding subunit

Probab=92.00  E-value=0.29  Score=48.41  Aligned_cols=49  Identities=16%  Similarity=0.326  Sum_probs=36.4

Q ss_pred             CCccccccchHHHHHHHhccC------CC-CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGVK------SK-DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~------~~-~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...++|.+.-++.+...+...      .+ ....+-++|..|+|||+||+.+.+.+
T Consensus       508 ~~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l  563 (821)
T CHL00095        508 HKRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYF  563 (821)
T ss_pred             cCcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHh
Confidence            467899998888887755421      11 13455689999999999999998865

>PRK13635 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=91.99  E-value=0.14  Score=43.83  Aligned_cols=25  Identities=24%  Similarity=0.298  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        32 ~Ge~~~i~G~nGaGKSTLl~~i~G~   56 (279)
T PRK13635         32 EGEWVAIVGHNGSGKSTLAKLLNGL   56 (279)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcC
Confidence            4568999999999999999998764

>PRK14264 phosphate ABC transporter ATP-binding protein; Provisional

Probab=91.98  E-value=0.14  Score=44.44  Aligned_cols=26  Identities=19%  Similarity=0.270  Sum_probs=22.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.+++|+|..|.|||||.+.+....
T Consensus        70 ~Ge~~~IvG~nGsGKSTLl~~L~Gl~   95 (305)
T PRK14264         70 EKSVTALIGPSGCGKSTFLRCLNRMN   95 (305)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccc
Confidence            45789999999999999999987643

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=91.96  E-value=0.15  Score=41.20  Aligned_cols=26  Identities=27%  Similarity=0.344  Sum_probs=22.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||.+.+..-
T Consensus        33 ~~Ge~~~l~G~nGsGKStLl~~i~Gl   58 (194)
T cd03213          33 KPGELTAIMGPSGAGKSTLLNALAGR   58 (194)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            34678999999999999999988653

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.

>PRK13643 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=91.95  E-value=0.15  Score=43.97  Aligned_cols=25  Identities=16%  Similarity=0.173  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        31 ~Ge~v~i~G~nGsGKSTLl~~l~Gl   55 (288)
T PRK13643         31 KGSYTALIGHTGSGKSTLLQHLNGL   55 (288)
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcC
Confidence            4578999999999999999998764

>PRK14263 phosphate ABC transporter ATP-binding protein; Provisional

Probab=91.95  E-value=0.15  Score=43.24  Aligned_cols=26  Identities=23%  Similarity=0.373  Sum_probs=22.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||++.+..-
T Consensus        32 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl   57 (261)
T PRK14263         32 RKNEITGFIGPSGCGKSTVLRSLNRM   57 (261)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHcc
Confidence            34579999999999999999988653

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=91.91  E-value=0.22  Score=44.12  Aligned_cols=40  Identities=18%  Similarity=0.206  Sum_probs=30.4

Q ss_pred             cchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          187 ESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       187 ~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ..-...|.++|..+-....++-|+|.+|+|||+||..++-
T Consensus       106 ~tG~~~LD~lL~GG~~~g~i~~i~G~~g~GKT~l~~~l~~  145 (342)
T PLN03186        106 TTGSRELDKILEGGIETGSITEIYGEFRTGKTQLCHTLCV  145 (342)
T ss_pred             CCCCHHHHHhhcCCCcCceEEEEECCCCCCccHHHHHHHH
Confidence            3445566677766555578889999999999999987653

>PRK08939 primosomal protein DnaI; Reviewed

Probab=91.89  E-value=0.17  Score=44.22  Aligned_cols=25  Identities=32%  Similarity=0.488  Sum_probs=22.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-+-++|..|+|||.||.++.+.+
T Consensus       156 ~~gl~L~G~~G~GKThLa~Aia~~l  180 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLAAIANEL  180 (306)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            4567799999999999999999975

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=91.89  E-value=0.12  Score=43.94  Aligned_cols=24  Identities=17%  Similarity=0.250  Sum_probs=20.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.++-|.|.+|.||||+|.++..
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~   58 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAV   58 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            357889999999999999998744

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=91.87  E-value=0.2  Score=32.99  Aligned_cols=21  Identities=33%  Similarity=0.329  Sum_probs=18.2

Q ss_pred             EEEEEcCCCChHHHHHHHHHH
Q 043980          206 ALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~  226 (233)
                      +..|.|..|.|||||.-++.-
T Consensus        25 ~tli~G~nGsGKSTllDAi~~   45 (62)
T PF13555_consen   25 VTLITGPNGSGKSTLLDAIQT   45 (62)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            688999999999999987643

>COG1072 CoaA Panthothenate kinase [Coenzyme metabolism]

Probab=91.87  E-value=0.35  Score=41.40  Aligned_cols=29  Identities=28%  Similarity=0.441  Sum_probs=24.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ...-+|||.|..|+||+|+|+.+..-++.
T Consensus        80 ~~pfIIgiaGsvavGKST~ar~L~~ll~~  108 (283)
T COG1072          80 QRPFIIGIAGSVAVGKSTTARILQALLSR  108 (283)
T ss_pred             CCCEEEEeccCccccHHHHHHHHHHHHhh
Confidence            34789999999999999999987775543

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=91.83  E-value=0.13  Score=48.59  Aligned_cols=28  Identities=29%  Similarity=0.481  Sum_probs=22.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHHhcCC
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKISSDF  232 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~~~~f  232 (233)
                      .=|-+||.+|.|||-||++|.|.-+-+|
T Consensus       546 sGvLL~GPPGCGKTLlAKAVANEag~NF  573 (802)
T KOG0733|consen  546 SGVLLCGPPGCGKTLLAKAVANEAGANF  573 (802)
T ss_pred             CceEEeCCCCccHHHHHHHHhhhccCce
Confidence            3466899999999999999999744443

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

Probab=91.82  E-value=0.24  Score=43.07  Aligned_cols=51  Identities=25%  Similarity=0.272  Sum_probs=38.4

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |....+++|.+.-+..|..-+..  .+....-.+|.+|.|||+-|.++..++-
T Consensus        32 Pkt~de~~gQe~vV~~L~~a~~~--~~lp~~LFyGPpGTGKTStalafar~L~   82 (346)
T KOG0989|consen   32 PKTFDELAGQEHVVQVLKNALLR--RILPHYLFYGPPGTGKTSTALAFARALN   82 (346)
T ss_pred             CCcHHhhcchHHHHHHHHHHHhh--cCCceEEeeCCCCCcHhHHHHHHHHHhc
Confidence            34456678888777777665543  4567778999999999999999888753

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

Probab=91.78  E-value=0.28  Score=42.57  Aligned_cols=39  Identities=26%  Similarity=0.211  Sum_probs=28.8

Q ss_pred             HHHHHHHhccCC-CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKS-KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       190 ~~~l~~~l~~~~-~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ++.|++++..-. ..-..+-|+|-.|+|||++++.+.+..
T Consensus        46 L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~h   85 (302)
T PF05621_consen   46 LDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLH   85 (302)
T ss_pred             HHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHC
Confidence            555566665432 335678899999999999999988753

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

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=91.75  E-value=0.24  Score=42.59  Aligned_cols=37  Identities=22%  Similarity=0.231  Sum_probs=28.2

Q ss_pred             HHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          191 EEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       191 ~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..|.++|..+-...+++-|+|..|.||||||.+++-.
T Consensus        47 ~~LD~~LGGGl~~g~ItEiyG~~gsGKT~lal~~~~~   83 (279)
T COG0468          47 LALDEALGGGLPRGRITEIYGPESSGKTTLALQLVAN   83 (279)
T ss_pred             hhHHHHhcCCcccceEEEEecCCCcchhhHHHHHHHH
Confidence            3455556644455799999999999999999986543

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=91.70  E-value=0.31  Score=44.85  Aligned_cols=26  Identities=35%  Similarity=0.487  Sum_probs=22.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+-+-|+|..|.|||+|++++.+.+.
T Consensus       141 ~npl~i~G~~G~GKTHLl~Ai~~~l~  166 (450)
T PRK14087        141 YNPLFIYGESGMGKTHLLKAAKNYIE  166 (450)
T ss_pred             cCceEEECCCCCcHHHHHHHHHHHHH
Confidence            35578999999999999999998653

>PRK05973 replicative DNA helicase; Provisional

Probab=91.68  E-value=0.27  Score=41.35  Aligned_cols=25  Identities=16%  Similarity=-0.008  Sum_probs=21.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...++-|.|.+|.|||++|..+...
T Consensus        63 ~Gsl~LIaG~PG~GKT~lalqfa~~   87 (237)
T PRK05973         63 PGDLVLLGARPGHGKTLLGLELAVE   87 (237)
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH
Confidence            4578889999999999999987553

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=91.68  E-value=0.17  Score=47.42  Aligned_cols=48  Identities=23%  Similarity=0.192  Sum_probs=35.4

Q ss_pred             CCCccccccchHHHHHHHhcc-CCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGV-KSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~-~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...+++|....++++.+.+.. ...+ .-|-|+|..|+||+++|+++++.
T Consensus       202 ~f~~~ig~s~~~~~~~~~~~~~A~~~-~pvlI~GE~GtGK~~lA~aiH~~  250 (520)
T PRK10820        202 AFSQIVAVSPKMRQVVEQARKLAMLD-APLLITGDTGTGKDLLAYACHLR  250 (520)
T ss_pred             cccceeECCHHHHHHHHHHHHHhCCC-CCEEEECCCCccHHHHHHHHHHh
Confidence            446789998888877765542 2222 33569999999999999998864

>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]

Probab=91.65  E-value=0.13  Score=47.08  Aligned_cols=29  Identities=24%  Similarity=0.453  Sum_probs=24.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      .-.++||.|..|+||||.++-+...+..+
T Consensus        99 ~G~V~GilG~NGiGKsTalkILaGel~PN  127 (591)
T COG1245          99 PGKVVGILGPNGIGKSTALKILAGELKPN  127 (591)
T ss_pred             CCcEEEEEcCCCccHHHHHHHHhCccccC
Confidence            35799999999999999999887765544

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=91.64  E-value=0.17  Score=48.52  Aligned_cols=48  Identities=17%  Similarity=0.309  Sum_probs=33.9

Q ss_pred             CCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .+.++|....++++.+.+..-...-.-|-|+|..|+||+++|+++++.
T Consensus       324 ~~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~  371 (638)
T PRK11388        324 FDHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNE  371 (638)
T ss_pred             ccceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHh
Confidence            355778777777776654432222233669999999999999999985

>PRK13633 cobalt transporter ATP-binding subunit; Provisional

Probab=91.62  E-value=0.16  Score=43.45  Aligned_cols=26  Identities=35%  Similarity=0.328  Sum_probs=22.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|+|..|.|||||.+.+...
T Consensus        34 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl   59 (280)
T PRK13633         34 KKGEFLVILGRNGSGKSTIAKHMNAL   59 (280)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34568999999999999999998754

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=91.62  E-value=0.49  Score=35.81  Aligned_cols=46  Identities=26%  Similarity=0.380  Sum_probs=31.6

Q ss_pred             ccccccch----HHHHHHHhcc-CCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          182 QLAGVESR----VEEIESLLGV-KSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       182 ~~~g~~~~----~~~l~~~l~~-~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ++.|..--    ++.|...+.. ..++.-++...|..|+|||-+++.+.+.
T Consensus        26 ~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   26 NLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             HccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHH
Confidence            34555433    3344444433 3456789999999999999998888776

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

>PRK10261 glutathione transporter ATP-binding protein; Provisional

Probab=91.61  E-value=0.15  Score=48.74  Aligned_cols=25  Identities=32%  Similarity=0.307  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||++.+...
T Consensus        41 ~Ge~~~lvG~nGsGKSTLl~~l~Gl   65 (623)
T PRK10261         41 RGETLAIVGESGSGKSVTALALMRL   65 (623)
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcC
Confidence            4578999999999999999998764

>PRK15134 microcin C ABC transporter ATP-binding protein YejF; Provisional

Probab=91.59  E-value=0.15  Score=47.63  Aligned_cols=26  Identities=27%  Similarity=0.319  Sum_probs=22.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.+++|+|..|.|||||++.+..-+
T Consensus        34 ~Ge~~~iiG~nGsGKSTLl~~i~G~~   59 (529)
T PRK15134         34 AGETLALVGESGSGKSVTALSILRLL   59 (529)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            45789999999999999999887643

>COG3842 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=91.59  E-value=0.16  Score=45.03  Aligned_cols=24  Identities=29%  Similarity=0.345  Sum_probs=20.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.++++.|..|.|||||-+.+..
T Consensus        30 ~Gef~~lLGPSGcGKTTlLR~IAG   53 (352)
T COG3842          30 KGEFVTLLGPSGCGKTTLLRMIAG   53 (352)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhC
Confidence            346899999999999999998864

>PRK11860 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional

Probab=91.57  E-value=0.25  Score=47.69  Aligned_cols=27  Identities=22%  Similarity=0.257  Sum_probs=23.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+|.|-|+.|.||||+|+.+.+++.
T Consensus       441 ~~~~i~i~g~~~~gks~~~~~l~~~~~  467 (661)
T PRK11860        441 RVPVICIDGPTASGKGTVAARVAEALG  467 (661)
T ss_pred             CcceEEeeCCCCCCHHHHHHHHHHHhC
Confidence            366899999999999999999998754

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=91.57  E-value=0.36  Score=44.99  Aligned_cols=40  Identities=18%  Similarity=0.141  Sum_probs=30.6

Q ss_pred             cchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          187 ESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       187 ~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ..-...|.++|..+-..-.++-|.|.+|.|||+||..+..
T Consensus        14 ~TGI~~LD~~l~GG~p~Gs~~li~G~pGsGKT~l~~qf~~   53 (509)
T PRK09302         14 PTGIEGFDDITHGGLPKGRPTLVSGTAGTGKTLFALQFLV   53 (509)
T ss_pred             cCCchhHHHhhcCCCCCCcEEEEEeCCCCCHHHHHHHHHH
Confidence            3445566666765555578999999999999999998654

>PRK13642 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=91.56  E-value=0.17  Score=43.25  Aligned_cols=25  Identities=32%  Similarity=0.260  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+..-
T Consensus        32 ~Ge~~~I~G~nGsGKSTLl~~l~Gl   56 (277)
T PRK13642         32 KGEWVSIIGQNGSGKSTTARLIDGL   56 (277)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcC
Confidence            4568999999999999999998753

>COG4167 SapF ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=91.56  E-value=0.17  Score=41.10  Aligned_cols=25  Identities=28%  Similarity=0.426  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-+.++|.|-.|.||+|||+.+..-
T Consensus        38 ~~QTlaiIG~NGSGKSTLakMlaGm   62 (267)
T COG4167          38 EGQTLAIIGENGSGKSTLAKMLAGM   62 (267)
T ss_pred             CCcEEEEEccCCCcHhHHHHHHhcc
Confidence            4578999999999999999987653

>TIGR00991 3a0901s02IAP34 GTP-binding protein (Chloroplast Envelope Protein Translocase)

Probab=91.54  E-value=0.28  Score=42.86  Aligned_cols=37  Identities=22%  Similarity=0.418  Sum_probs=26.6

Q ss_pred             HHHHHHh---ccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          191 EEIESLL---GVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       191 ~~l~~~l---~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .+|.++|   .........|.|+|.+|+||||+...+..+
T Consensus        22 ~~l~~~l~~l~~~~~~~~rIllvGktGVGKSSliNsIlG~   61 (313)
T TIGR00991        22 TKLLELLGKLKEEDVSSLTILVMGKGGVGKSSTVNSIIGE   61 (313)
T ss_pred             HHHHHHHHhcccccccceEEEEECCCCCCHHHHHHHHhCC
Confidence            3444444   333334567889999999999999998864

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=91.50  E-value=0.2  Score=44.65  Aligned_cols=25  Identities=28%  Similarity=0.314  Sum_probs=22.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+|.|+|..|.||||+.+++.+.+
T Consensus       134 ~glilI~GpTGSGKTTtL~aLl~~i  158 (358)
T TIGR02524       134 EGIVFITGATGSGKSTLLAAIIREL  158 (358)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999988765

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.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=91.49  E-value=0.17  Score=44.36  Aligned_cols=25  Identities=28%  Similarity=0.405  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+.|.|..|.||||+++++...+
T Consensus       148 ~~~ilI~G~tGSGKTTll~aL~~~~  172 (319)
T PRK13894        148 HRNILVIGGTGSGKTTLVNAIINEM  172 (319)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhh
Confidence            3567888999999999999988753

>cd03288 ABCC_SUR2 The SUR domain 2

Probab=91.49  E-value=0.18  Score=42.58  Aligned_cols=25  Identities=32%  Similarity=0.468  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        46 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   70 (257)
T cd03288          46 PGQKVGICGRTGSGKSSLSLAFFRM   70 (257)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcc
Confidence            3468999999999999999998764

The sulfonylurea receptor SUR is an ATP binding cassette (ABC) protein of the ABCC/MRP family. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.

>PRK06851 hypothetical protein; Provisional

Probab=91.45  E-value=0.23  Score=44.47  Aligned_cols=25  Identities=20%  Similarity=0.202  Sum_probs=22.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -+++.|.|.+|+|||||++.++...
T Consensus       214 ~~~~~i~G~pG~GKstl~~~i~~~a  238 (367)
T PRK06851        214 KNRYFLKGRPGTGKSTMLKKIAKAA  238 (367)
T ss_pred             ceEEEEeCCCCCcHHHHHHHHHHHH
Confidence            5789999999999999999999864

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=91.40  E-value=0.4  Score=47.61  Aligned_cols=49  Identities=22%  Similarity=0.339  Sum_probs=37.2

Q ss_pred             CCccccccchHHHHHHHhcc---C----CCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGV---K----SKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~---~----~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...++|.+.-++.+.+.+..   +    .....++-++|..|+|||.||+++.+.+
T Consensus       565 ~~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l  620 (852)
T TIGR03345       565 AERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELL  620 (852)
T ss_pred             cCeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            46788999888888776532   1    1224567899999999999999988765

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.

>PRK00093 GTP-binding protein Der; Reviewed

Probab=91.39  E-value=4.3  Score=36.88  Aligned_cols=24  Identities=21%  Similarity=0.451  Sum_probs=20.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      +..-|+|+|.+|+|||||..++..
T Consensus       172 ~~~~v~ivG~~n~GKStlin~ll~  195 (435)
T PRK00093        172 EPIKIAIIGRPNVGKSSLINALLG  195 (435)
T ss_pred             cceEEEEECCCCCCHHHHHHHHhC
Confidence            356789999999999999998764

>PRK15439 autoinducer 2 ABC transporter ATP-binding protein LsrA; Provisional

Probab=91.36  E-value=0.17  Score=47.17  Aligned_cols=25  Identities=20%  Similarity=0.240  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||.+.+...
T Consensus        36 ~Ge~~~liG~NGsGKSTLl~~l~Gl   60 (510)
T PRK15439         36 AGEVHALLGGNGAGKSTLMKIIAGI   60 (510)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999999998754

>PRK12608 transcription termination factor Rho; Provisional

Probab=91.35  E-value=0.2  Score=44.82  Aligned_cols=26  Identities=19%  Similarity=0.061  Sum_probs=21.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      +-+.|.|..|.|||||++.+.+.+..
T Consensus       134 QR~LIvG~pGtGKTTLl~~la~~i~~  159 (380)
T PRK12608        134 QRGLIVAPPRAGKTVLLQQIAAAVAA  159 (380)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHh
Confidence            44589999999999999999887643

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

Probab=91.33  E-value=0.23  Score=45.51  Aligned_cols=47  Identities=21%  Similarity=0.377  Sum_probs=35.5

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..++|....+.++...+..-...-.-+-|.|..|+|||++|+.+++.
T Consensus       138 ~~lig~s~~~~~l~~~~~~~~~~~~~vli~Ge~GtGK~~lA~~ih~~  184 (469)
T PRK10923        138 TDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRH  184 (469)
T ss_pred             ccceecCHHHHHHHHHHHHHhccCCeEEEEeCCCCcHHHHHHHHHhc
Confidence            46888887777777665433333445779999999999999999885

>PRK13634 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=91.28  E-value=0.19  Score=43.35  Aligned_cols=26  Identities=19%  Similarity=0.213  Sum_probs=22.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|.|..|.|||||.+.+...
T Consensus        31 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl   56 (290)
T PRK13634         31 PSGSYVAIIGHTGSGKSTLLQHLNGL   56 (290)
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcC
Confidence            34579999999999999999998753

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=91.25  E-value=0.2  Score=46.99  Aligned_cols=47  Identities=26%  Similarity=0.423  Sum_probs=36.2

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..++|....++++.+.+..-...-.-|-|.|..|+||+++|+.+++.
T Consensus       212 ~~iiG~S~~m~~~~~~i~~~A~~~~pVLI~GE~GTGKe~lA~~IH~~  258 (526)
T TIGR02329       212 DDLLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQL  258 (526)
T ss_pred             hheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCcCHHHHHHHHHHh
Confidence            45889988888887766432222346779999999999999999974

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.

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=91.24  E-value=0.21  Score=46.99  Aligned_cols=47  Identities=26%  Similarity=0.339  Sum_probs=36.3

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..++|....++++.+.+..-...-.-|-|.|..|.||+++|+.+++.
T Consensus       219 ~~iiG~S~~m~~~~~~i~~~A~s~~pVLI~GE~GTGKe~~A~~IH~~  265 (538)
T PRK15424        219 GDLLGQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHRE  265 (538)
T ss_pred             hheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCCCHHHHHHHHHHh
Confidence            45889988888887766432222346679999999999999999986

>TIGR00959 ffh signal recognition particle protein

Probab=91.24  E-value=0.29  Score=44.74  Aligned_cols=25  Identities=20%  Similarity=0.231  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..++.++|.+|+||||.|..+...+
T Consensus        99 p~vi~~vG~~GsGKTTtaakLA~~l  123 (428)
T TIGR00959        99 PTVILMVGLQGSGKTTTCGKLAYYL  123 (428)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHH
Confidence            5799999999999999988877654

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>cd02033 BchX Chlorophyllide reductase converts chlorophylls into bacteriochlorophylls by reducing the chlorin B-ring

Probab=91.22  E-value=0.27  Score=43.32  Aligned_cols=27  Identities=30%  Similarity=0.469  Sum_probs=22.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...++|.|+|-||+||||++..+...+
T Consensus        29 ~~~~ii~v~gkgG~GKSt~a~nLa~~l   55 (329)
T cd02033          29 KKTQIIAIYGKGGIGKSFTLANLSYMM   55 (329)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            357899999999999999888766543

This family contains the X subunit of this three-subunit enzyme. Sequence and structure similarity between bchX, protochlorophyllide reductase L subunit (bchL and chlL) and nitrogenase Fe protein (nifH gene) suggest their functional similarity. Members of the BchX family serve as the unique electron donors to their respective catalytic subunits (bchN-bchB, bchY-bchZ and nitrogenase component 1). Mechanistically, they hydrolyze ATP and transfer electrons through a Fe4-S4 cluster.

>PRK13549 xylose transporter ATP-binding subunit; Provisional

Probab=91.22  E-value=0.19  Score=46.81  Aligned_cols=26  Identities=15%  Similarity=0.314  Sum_probs=22.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|+|..|.|||||.+.+...
T Consensus        29 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl   54 (506)
T PRK13549         29 RAGEIVSLCGENGAGKSTLMKVLSGV   54 (506)
T ss_pred             eCCeEEEEECCCCCCHHHHHHHHhCC
Confidence            34678999999999999999998754

>COG4172 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]

Probab=91.22  E-value=0.15  Score=45.98  Aligned_cols=25  Identities=32%  Similarity=0.492  Sum_probs=22.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+||+|..|.|||||.+++..-+
T Consensus       313 gqTlGlVGESGSGKsTlG~allrL~  337 (534)
T COG4172         313 GQTLGLVGESGSGKSTLGLALLRLI  337 (534)
T ss_pred             CCeEEEEecCCCCcchHHHHHHhhc
Confidence            4789999999999999999988754

>PRK13537 nodulation ABC transporter NodI; Provisional

Probab=91.21  E-value=0.19  Score=43.69  Aligned_cols=25  Identities=28%  Similarity=0.434  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+..-
T Consensus        32 ~Gei~gllGpNGaGKSTLl~~l~Gl   56 (306)
T PRK13537         32 RGECFGLLGPNGAGKTTTLRMLLGL   56 (306)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999999998764

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=91.14  E-value=0.18  Score=47.06  Aligned_cols=24  Identities=21%  Similarity=0.256  Sum_probs=21.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ....++|+|..|.|||||++.+..
T Consensus       360 ~G~~vaIvG~SGsGKSTLl~lL~g  383 (529)
T TIGR02868       360 PGERVAILGPSGSGKSTLLMLLTG  383 (529)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            457899999999999999998865

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.

>PRK13409 putative ATPase RIL; Provisional

Probab=91.13  E-value=0.18  Score=47.96  Aligned_cols=25  Identities=36%  Similarity=0.518  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||++.+...
T Consensus       364 ~Geiv~l~G~NGsGKSTLlk~L~Gl  388 (590)
T PRK13409        364 EGEVIGIVGPNGIGKTTFAKLLAGV  388 (590)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3468999999999999999998764

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

Probab=91.13  E-value=0.16  Score=47.07  Aligned_cols=29  Identities=28%  Similarity=0.312  Sum_probs=23.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      ....+=++|.+|.|||.||+++.+....+
T Consensus       275 ~~~giLl~GpPGtGKT~lAkava~~~~~~  303 (494)
T COG0464         275 PPKGVLLYGPPGTGKTLLAKAVALESRSR  303 (494)
T ss_pred             CCCeeEEECCCCCCHHHHHHHHHhhCCCe
Confidence            35577899999999999999999964433

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=91.12  E-value=0.21  Score=43.27  Aligned_cols=26  Identities=23%  Similarity=0.394  Sum_probs=22.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.+.|+.|..|.|||||.+.+...+
T Consensus        30 ~Gei~gllG~NGAGKTTllk~l~gl~   55 (293)
T COG1131          30 PGEIFGLLGPNGAGKTTLLKILAGLL   55 (293)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHhCCc
Confidence            45799999999999999999987653

>PRK13409 putative ATPase RIL; Provisional

Probab=91.08  E-value=0.18  Score=47.97  Aligned_cols=26  Identities=35%  Similarity=0.502  Sum_probs=22.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.++||+|..|+|||||.+.+...
T Consensus        97 ~~Gev~gLvG~NGaGKSTLlkiL~G~  122 (590)
T PRK13409         97 KEGKVTGILGPNGIGKTTAVKILSGE  122 (590)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34679999999999999999987664

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=91.07  E-value=0.27  Score=47.73  Aligned_cols=49  Identities=31%  Similarity=0.348  Sum_probs=34.9

Q ss_pred             CCCccccccchHHHHHHH---hccC-------CCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESL---LGVK-------SKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~---l~~~-------~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.++.|.++-+++|.++   |.+.       ..-.+=+=++|.+|.|||-||++++-.
T Consensus       309 ~FkDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGE  367 (774)
T KOG0731|consen  309 KFKDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGE  367 (774)
T ss_pred             ccccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcc
Confidence            446788888777776664   4421       112355678899999999999999864

>PRK10261 glutathione transporter ATP-binding protein; Provisional

Probab=91.05  E-value=0.19  Score=48.14  Aligned_cols=25  Identities=28%  Similarity=0.380  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||++.+..-
T Consensus       349 ~Ge~~~lvG~nGsGKSTLlk~i~Gl  373 (623)
T PRK10261        349 PGETLSLVGESGSGKSTTGRALLRL  373 (623)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcC
Confidence            3578999999999999999998753

>PRK14257 phosphate ABC transporter ATP-binding protein; Provisional

Probab=91.03  E-value=0.2  Score=44.08  Aligned_cols=26  Identities=19%  Similarity=0.196  Sum_probs=22.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.+++|+|..|.|||||.+.++...
T Consensus       107 ~Ge~v~IvG~~GsGKSTLl~~L~g~~  132 (329)
T PRK14257        107 RNKVTAFIGPSGCGKSTFLRNLNQLN  132 (329)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccc
Confidence            34689999999999999999998643

>PRK11432 fbpC ferric transporter ATP-binding subunit; Provisional

Probab=91.02  E-value=0.2  Score=44.49  Aligned_cols=24  Identities=25%  Similarity=0.368  Sum_probs=21.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        31 ~Ge~~~llGpsGsGKSTLLr~IaG   54 (351)
T PRK11432         31 QGTMVTLLGPSGCGKTTVLRLVAG   54 (351)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHC
Confidence            456899999999999999999875

>PRK13549 xylose transporter ATP-binding subunit; Provisional

Probab=91.02  E-value=0.18  Score=46.88  Aligned_cols=25  Identities=32%  Similarity=0.577  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+..-
T Consensus       287 ~Ge~~~l~G~NGsGKSTLlk~i~Gl  311 (506)
T PRK13549        287 RGEILGIAGLVGAGRTELVQCLFGA  311 (506)
T ss_pred             CCcEEEEeCCCCCCHHHHHHHHhCC
Confidence            3578999999999999999998753

>PRK10070 glycine betaine transporter ATP-binding subunit; Provisional

Probab=90.98  E-value=0.2  Score=45.41  Aligned_cols=25  Identities=24%  Similarity=0.361  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+..-
T Consensus        53 ~Gei~~LvG~NGsGKSTLLr~I~Gl   77 (400)
T PRK10070         53 EGEIFVIMGLSGSGKSTMVRLLNRL   77 (400)
T ss_pred             CCCEEEEECCCCchHHHHHHHHHcC
Confidence            3568999999999999999998764

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.96  E-value=0.37  Score=46.14  Aligned_cols=52  Identities=21%  Similarity=0.276  Sum_probs=39.9

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |..-..++|.+.-++.|...+..+. -...+-++|..|+||||+|+.+...+.
T Consensus        13 P~~f~~viGq~~~~~~L~~~i~~~~-l~hayLf~Gp~G~GKtt~A~~lAk~l~   64 (614)
T PRK14971         13 PSTFESVVGQEALTTTLKNAIATNK-LAHAYLFCGPRGVGKTTCARIFAKTIN   64 (614)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCCHHHHHHHHHHHhC
Confidence            3345678999888888888776432 245677999999999999999888653

>PRK09700 D-allose transporter ATP-binding protein; Provisional

Probab=90.95  E-value=0.19  Score=46.84  Aligned_cols=25  Identities=28%  Similarity=0.480  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus       288 ~Ge~~~l~G~NGsGKSTLlk~i~Gl  312 (510)
T PRK09700        288 RGEILGFAGLVGSGRTELMNCLFGV  312 (510)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999999998753

>PRK09700 D-allose transporter ATP-binding protein; Provisional

Probab=90.94  E-value=0.18  Score=46.93  Aligned_cols=26  Identities=15%  Similarity=0.201  Sum_probs=22.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.+++|+|..|.|||||.+.+..-
T Consensus        29 ~~Ge~~~liG~nGsGKSTLl~~i~Gl   54 (510)
T PRK09700         29 YPGEIHALLGENGAGKSTLMKVLSGI   54 (510)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHcCC
Confidence            35679999999999999999988653

>PRK10982 galactose/methyl galaxtoside transporter ATP-binding protein; Provisional

Probab=90.88  E-value=0.18  Score=46.75  Aligned_cols=25  Identities=32%  Similarity=0.456  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||.+.++..
T Consensus       273 ~Ge~~~l~G~nGsGKSTLl~~l~Gl  297 (491)
T PRK10982        273 KGEILGIAGLVGAKRTDIVETLFGI  297 (491)
T ss_pred             CCcEEEEecCCCCCHHHHHHHHcCC
Confidence            4578999999999999999998753

>PRK13536 nodulation factor exporter subunit NodI; Provisional

Probab=90.87  E-value=0.22  Score=44.12  Aligned_cols=25  Identities=36%  Similarity=0.566  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.++||.|..|.|||||.+.+...
T Consensus        66 ~Gei~gLlGpNGaGKSTLl~~L~Gl   90 (340)
T PRK13536         66 SGECFGLLGPNGAGKSTIARMILGM   90 (340)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcC
Confidence            4579999999999999999998764

>PRK15134 microcin C ABC transporter ATP-binding protein YejF; Provisional

Probab=90.86  E-value=0.2  Score=46.89  Aligned_cols=24  Identities=29%  Similarity=0.415  Sum_probs=21.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus       311 ~Ge~~~i~G~nGsGKSTLlk~l~G  334 (529)
T PRK15134        311 PGETLGLVGESGSGKSTTGLALLR  334 (529)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            456899999999999999999875

>PRK14246 phosphate ABC transporter ATP-binding protein; Provisional

Probab=90.85  E-value=0.22  Score=42.11  Aligned_cols=25  Identities=24%  Similarity=0.417  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        35 ~Ge~~~i~G~nGsGKSTLl~~iaG~   59 (257)
T PRK14246         35 NNSIFGIMGPSGSGKSTLLKVLNRL   59 (257)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4568999999999999999988753

>cd01857 HSR1_MMR1 HSR1/MMR1

Probab=90.84  E-value=0.21  Score=37.99  Aligned_cols=35  Identities=20%  Similarity=0.145  Sum_probs=24.1

Q ss_pred             HHHHHHHHhcCceEEEeecCCCCchhhHHHHHHHHH
Q 043980           69 QSLVNAIEASAISVIIFSESYTSSRWCVDELVKILE  104 (233)
Q Consensus        69 ~~i~~~i~~s~~~i~v~S~~y~~S~wc~~El~~~~~  104 (233)
                      .++.++++++++.++|+...-..+.+.. ++...+.
T Consensus         3 ~~~~~~i~~aD~vl~ViD~~~p~~~~~~-~l~~~l~   37 (141)
T cd01857           3 RQLWRVVERSDIVVQIVDARNPLLFRPP-DLERYVK   37 (141)
T ss_pred             HHHHHHHhhCCEEEEEEEccCCcccCCH-HHHHHHH
Confidence            5678999999999999987655554422 4444443

Human HSR1, is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N terminus.

>cd01859 MJ1464 MJ1464

Probab=90.75  E-value=0.42  Score=36.82  Aligned_cols=41  Identities=24%  Similarity=0.357  Sum_probs=27.1

Q ss_pred             cccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          185 GVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       185 g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      |.+.-.+.+.+++..... ...+.++|.+|+|||||...+.+
T Consensus        83 gi~~L~~~l~~~~~~~~~-~~~~~~ig~~~~Gkssl~~~l~~  123 (156)
T cd01859          83 GTKILRRTIKELAKIDGK-EGKVGVVGYPNVGKSSIINALKG  123 (156)
T ss_pred             cHHHHHHHHHHHHhhcCC-CcEEEEECCCCCCHHHHHHHHhC
Confidence            444444455554443333 33458999999999999998875

This family represents archaeal GTPase typified by the protein MJ1464 from Methanococcus jannaschii. The members of this family show a circular permutation of the GTPase signature motifs so that C-terminal strands 5, 6, and 7 (strands 6 contain the NKxD motif) are relocated to the N terminus.

>COG1127 Ttg2A ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]

Probab=90.64  E-value=0.21  Score=42.03  Aligned_cols=30  Identities=27%  Similarity=0.357  Sum_probs=24.0

Q ss_pred             cCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          199 VKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       199 ~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+-..-.+.+|.|..|+|||||.+.+...+
T Consensus        29 l~V~~Gei~~iiGgSGsGKStlLr~I~Gll   58 (263)
T COG1127          29 LDVPRGEILAILGGSGSGKSTLLRLILGLL   58 (263)
T ss_pred             eeecCCcEEEEECCCCcCHHHHHHHHhccC
Confidence            333346799999999999999999887643

>PRK11819 putative ABC transporter ATP-binding protein; Reviewed

Probab=90.60  E-value=0.21  Score=47.05  Aligned_cols=24  Identities=29%  Similarity=0.418  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -.+++|.|..|.|||||.+.+...
T Consensus       350 Ge~~~l~G~NGsGKSTLl~~i~G~  373 (556)
T PRK11819        350 GGIVGIIGPNGAGKSTLFKMITGQ  373 (556)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999998754

>PRK15439 autoinducer 2 ABC transporter ATP-binding protein LsrA; Provisional

Probab=90.59  E-value=0.2  Score=46.69  Aligned_cols=25  Identities=28%  Similarity=0.534  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus       288 ~Ge~~~l~G~NGsGKSTLl~~i~Gl  312 (510)
T PRK15439        288 AGEILGLAGVVGAGRTELAETLYGL  312 (510)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHcCC
Confidence            3578999999999999999998753

>PRK15064 ABC transporter ATP-binding protein; Provisional

Probab=90.57  E-value=0.22  Score=46.64  Aligned_cols=25  Identities=32%  Similarity=0.498  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus       344 ~Ge~~~l~G~NGsGKSTLl~~i~G~  368 (530)
T PRK15064        344 AGERLAIIGENGVGKTTLLRTLVGE  368 (530)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3468999999999999999998753

>PRK09866 hypothetical protein; Provisional

Probab=90.56  E-value=0.26  Score=47.11  Aligned_cols=40  Identities=25%  Similarity=0.204  Sum_probs=30.1

Q ss_pred             cchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          187 ESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       187 ~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ..++..|.+.|..-.....+++|+|..|.|||||.+++..
T Consensus        52 ~~ri~~L~~~L~Kv~~~~~~valvG~sgaGKSTLiNaL~G   91 (741)
T PRK09866         52 AERHAMLNNELRKISRLEMVLAIVGTMKAGKSTTINAIVG   91 (741)
T ss_pred             HHHHHHHHHHHHHHhccceEEEEECCCCCCHHHHHHHHhC
Confidence            3456666665554333458999999999999999999875

>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=90.56  E-value=0.36  Score=42.81  Aligned_cols=49  Identities=18%  Similarity=0.301  Sum_probs=39.8

Q ss_pred             CCccccccchHHHHHHHhccCC----CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGVKS----KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~~----~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+.|+++.++++.+.+....    ..-+++-+.|..|.|||||++.+-+-+
T Consensus        60 ~~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~l  112 (358)
T PF08298_consen   60 EDEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRGL  112 (358)
T ss_pred             cccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHHh
Confidence            3478999999999998776422    346899999999999999999876644

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>COG5192 BMS1 GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]

Probab=90.55  E-value=0.25  Score=46.32  Aligned_cols=26  Identities=19%  Similarity=0.523  Sum_probs=22.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-+++|+|.+|.|||||.+.+.+++.
T Consensus        69 PfIvavvGPpGtGKsTLirSlVrr~t   94 (1077)
T COG5192          69 PFIVAVVGPPGTGKSTLIRSLVRRFT   94 (1077)
T ss_pred             CeEEEeecCCCCChhHHHHHHHHHHH
Confidence            46788999999999999999887653

>PRK11819 putative ABC transporter ATP-binding protein; Reviewed

Probab=90.55  E-value=0.22  Score=46.95  Aligned_cols=27  Identities=22%  Similarity=0.362  Sum_probs=22.9

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-.+++|+|..|.|||||.+.+...+
T Consensus        31 ~~Ge~~~iiG~NGsGKSTLlk~i~G~~   57 (556)
T PRK11819         31 FPGAKIGVLGLNGAGKSTLLRIMAGVD   57 (556)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            345689999999999999999987643

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=90.53  E-value=0.32  Score=38.71  Aligned_cols=24  Identities=29%  Similarity=0.221  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+.-|.|.+|+||||++..+.-.+
T Consensus        33 ~l~~i~g~~g~GKT~~~~~l~~~~   56 (193)
T PF13481_consen   33 ELTLIAGPPGSGKTTLALQLAAAL   56 (193)
T ss_dssp             SEEEEEECSTSSHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHH
Confidence            477889999999999999887654

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=90.52  E-value=0.21  Score=48.46  Aligned_cols=25  Identities=20%  Similarity=0.332  Sum_probs=21.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ..-..|+|+|-.|.|||||+|.+-.
T Consensus       497 ~~Ge~vaIvG~SGsGKSTL~KLL~g  521 (709)
T COG2274         497 PPGEKVAIVGRSGSGKSTLLKLLLG  521 (709)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhc
Confidence            3457899999999999999998754

>PRK10762 D-ribose transporter ATP binding protein; Provisional

Probab=90.48  E-value=0.22  Score=46.29  Aligned_cols=24  Identities=25%  Similarity=0.567  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -.+++|+|..|.|||||.+.+...
T Consensus       278 Ge~~~liG~NGsGKSTLl~~l~G~  301 (501)
T PRK10762        278 GEILGVSGLMGAGRTELMKVLYGA  301 (501)
T ss_pred             CcEEEEecCCCCCHHHHHHHHhCC
Confidence            468999999999999999998754

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=90.47  E-value=0.4  Score=43.22  Aligned_cols=20  Identities=30%  Similarity=0.531  Sum_probs=16.7

Q ss_pred             eEEEEEEcCCCChHHH-HHHH
Q 043980          204 VYALGIWGIGGIGKTK-IARA  223 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTt-la~~  223 (233)
                      -+++.++|..|+|||| ||+.
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKL  223 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKL  223 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHH
Confidence            6899999999999965 5554

>TIGR03269 met_CoM_red_A2 methyl coenzyme M reductase system, component A2

Probab=90.45  E-value=0.23  Score=46.32  Aligned_cols=25  Identities=32%  Similarity=0.486  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+..-
T Consensus       309 ~Ge~~~l~G~NGsGKSTLl~~l~Gl  333 (520)
T TIGR03269       309 EGEIFGIVGTSGAGKTTLSKIIAGV  333 (520)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3468999999999999999998753

The enzyme that catalyzes the final step in methanogenesis, methyl coenzyme M reductase, contains alpha, beta, and gamma chains. In older literature, the complex of alpha, beta, and gamma chains was termed component C, while this single chain protein was termed methyl coenzyme M reductase system component A2.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=90.43  E-value=0.33  Score=43.01  Aligned_cols=26  Identities=23%  Similarity=0.253  Sum_probs=22.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..++.|.|..|.||||+.+++.+.+.
T Consensus       122 ~g~ili~G~tGSGKTT~l~al~~~i~  147 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTLASMIDYIN  147 (343)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhhC
Confidence            35789999999999999999887654

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.

>PHA02624 large T antigen; Provisional

Probab=90.41  E-value=0.47  Score=45.08  Aligned_cols=29  Identities=24%  Similarity=0.130  Sum_probs=25.1

Q ss_pred             CCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          200 KSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       200 ~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +..+-+++.++|..|.||||++.++.+-+
T Consensus       427 giPKk~~il~~GPpnTGKTtf~~sLl~~L  455 (647)
T PHA02624        427 NVPKRRYWLFKGPVNSGKTTLAAALLDLC  455 (647)
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHHHc
Confidence            33457899999999999999999998865

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

Probab=90.40  E-value=0.45  Score=41.36  Aligned_cols=52  Identities=27%  Similarity=0.254  Sum_probs=37.4

Q ss_pred             CCCccccccchHHHH---HHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEI---ESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l---~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .+..++|.+...+..   .+++....-..+-+-+-|.+|.|||+||-++.+.+..
T Consensus        36 ~~~g~vGQ~~AReAagiivdlik~KkmaGravLlaGppgtGKTAlAlaisqELG~   90 (456)
T KOG1942|consen   36 VAAGFVGQENAREAAGIIVDLIKSKKMAGRAVLLAGPPGTGKTALALAISQELGP   90 (456)
T ss_pred             cccccccchhhhhhhhHHHHHHHhhhccCcEEEEecCCCCchhHHHHHHHHHhCC
Confidence            457788888655542   4444433333577889999999999999999887654

>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase

Probab=90.38  E-value=0.43  Score=38.90  Aligned_cols=26  Identities=15%  Similarity=0.111  Sum_probs=21.0

Q ss_pred             CeEEEEEE-cCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIW-GIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~-G~gGiGKTtla~~v~~~~  228 (233)
                      ..++|+|. +.||+||||+|..+...+
T Consensus        34 ~~~vi~v~s~kgG~GkSt~a~nLA~~l   60 (207)
T TIGR03018        34 NNNLIMVTSSLPGEGKSFTAINLAISL   60 (207)
T ss_pred             CCeEEEEECCCCCCCHHHHHHHHHHHH
Confidence            46789998 589999999988776653

Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins.

>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase

Probab=90.36  E-value=0.33  Score=45.54  Aligned_cols=26  Identities=19%  Similarity=0.325  Sum_probs=23.0

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ....+|-++|.+|.||||+|+.++..
T Consensus       367 ~~p~LVil~G~pGSGKST~A~~l~~~  392 (526)
T TIGR01663       367 APCEMVIAVGFPGAGKSHFCKKFFQP  392 (526)
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999999998864

Note that the EC number for the kinase function is: 2.7.1.78

>PRK09452 potA putrescine/spermidine ABC transporter ATPase protein; Reviewed

Probab=90.36  E-value=0.25  Score=44.34  Aligned_cols=24  Identities=33%  Similarity=0.396  Sum_probs=21.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        39 ~Ge~~~LlGpsGsGKSTLLr~IaG   62 (375)
T PRK09452         39 NGEFLTLLGPSGCGKTTVLRLIAG   62 (375)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhC
Confidence            356899999999999999999875

>PRK00652 lpxK tetraacyldisaccharide 4'-kinase; Reviewed

Probab=90.35  E-value=0.32  Score=42.85  Aligned_cols=28  Identities=25%  Similarity=0.463  Sum_probs=23.6

Q ss_pred             CeEEEEE--EcCCCChHHHHHHHHHHHHhc
Q 043980          203 DVYALGI--WGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       203 ~~~~i~i--~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .+.+|+|  .+.||.|||+++..+.+.++.
T Consensus        48 ~~pvIsVGNi~vGGtGKTP~v~~L~~~l~~   77 (325)
T PRK00652         48 PVPVIVVGNITVGGTGKTPVVIALAEQLQA   77 (325)
T ss_pred             CCCEEEEcCeeCCCCChHHHHHHHHHHHHH
Confidence            4677888  999999999999999887543

>PRK11607 potG putrescine transporter ATP-binding subunit; Provisional

Probab=90.28  E-value=0.26  Score=44.30  Aligned_cols=23  Identities=22%  Similarity=0.394  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -.+++|.|..|.|||||.+.+..
T Consensus        45 Ge~~~llGpsGsGKSTLLr~IaG   67 (377)
T PRK11607         45 GEIFALLGASGCGKSTLLRMLAG   67 (377)
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            46899999999999999998875

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=90.28  E-value=0.26  Score=43.29  Aligned_cols=23  Identities=39%  Similarity=0.508  Sum_probs=20.1

Q ss_pred             EEEEEcCCCChHHHHHHHHHHHH
Q 043980          206 ALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -+-|.|..|.||||+++++.+.+
T Consensus       146 nilI~G~tGSGKTTll~aL~~~i  168 (323)
T PRK13833        146 NIVISGGTGSGKTTLANAVIAEI  168 (323)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Confidence            45699999999999999988765

>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional

Probab=90.22  E-value=0.29  Score=46.99  Aligned_cols=26  Identities=23%  Similarity=0.355  Sum_probs=23.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+|-+.|++|.||||+|+++.+++.
T Consensus       460 ~~~i~~~G~~gsGKst~a~~l~~~l~  485 (632)
T PRK05506        460 PATVWFTGLSGSGKSTIANLVERRLH  485 (632)
T ss_pred             cEEEEecCCCCchHHHHHHHHHHHHH
Confidence            67999999999999999999988753

>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]

Probab=90.22  E-value=0.28  Score=41.18  Aligned_cols=25  Identities=28%  Similarity=0.392  Sum_probs=21.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-..+||+|..|.|||||.+.+..-
T Consensus        52 ~Ge~vGiiG~NGaGKSTLlkliaGi   76 (249)
T COG1134          52 KGERVGIIGHNGAGKSTLLKLIAGI   76 (249)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCc
Confidence            3468999999999999999987653

>TIGR03719 ABC_ABC_ChvD ATP-binding cassette protein, ChvD family

Probab=90.10  E-value=0.23  Score=46.76  Aligned_cols=25  Identities=28%  Similarity=0.407  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus       347 ~Ge~~~l~G~NGsGKSTLl~~l~G~  371 (552)
T TIGR03719       347 PGGIVGVIGPNGAGKSTLFRMITGQ  371 (552)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcCC
Confidence            3468999999999999999998753

Members of this protein family have two copies of the ABC transporter ATP-binding cassette, but are found outside the common ABC transporter operon structure that features integral membrane permease proteins and substrate-binding proteins encoded next to the ATP-binding cassette (ABC domain) protein. The member protein ChvD from Agrobacterium tumefaciens was identified as both a candidate to interact with VirB8, based on yeast two-hybrid analysis, and as an apparent regulator of VirG. The general function of this protein family is unknown.

>PRK11147 ABC transporter ATPase component; Reviewed

Probab=90.07  E-value=0.25  Score=47.40  Aligned_cols=24  Identities=21%  Similarity=0.408  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -.+++|+|..|.|||||.+.+...
T Consensus       345 Ge~~~l~G~NGsGKSTLlk~l~G~  368 (635)
T PRK11147        345 GDKIALIGPNGCGKTTLLKLMLGQ  368 (635)
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            468999999999999999998764

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein

Probab=90.06  E-value=0.63  Score=40.64  Aligned_cols=26  Identities=23%  Similarity=0.331  Sum_probs=21.3

Q ss_pred             CeEEEEEEc-CCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWG-IGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G-~gGiGKTtla~~v~~~~  228 (233)
                      ..++|+|+| -||+||||+|..+...+
T Consensus        92 ~~~vIav~~~KGGvGkTT~a~nLA~~l  118 (322)
T TIGR03815        92 RGVVVAVIGGRGGAGASTLAAALALAA  118 (322)
T ss_pred             CceEEEEEcCCCCCcHHHHHHHHHHHH
Confidence            468899885 89999999999876654

Members of this protein family belong to the MinD/ParA family of P-loop NTPases, and in particular show homology to the CpaE family of pilus assembly proteins (see PubMed:12370432). Nearly all members are found, not only in a gene context consistent with pilus biogenesis or a pilus-like secretion apparatus, but also near a DEAD/DEAH-box helicase, suggesting an involvement in DNA transfer activity. The model describes a clade restricted to the Actinobacteria.

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=90.02  E-value=0.51  Score=42.66  Aligned_cols=42  Identities=24%  Similarity=0.327  Sum_probs=33.2

Q ss_pred             hHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          189 RVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       189 ~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ...++...|..+-..-.++-|=|-+|||||||.-.+..++..
T Consensus        78 g~~EldRVLGGG~V~Gs~iLIgGdPGIGKSTLLLQva~~lA~  119 (456)
T COG1066          78 GIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAK  119 (456)
T ss_pred             ChHHHHhhhcCCcccccEEEEccCCCCCHHHHHHHHHHHHHh
Confidence            456666767665556688999999999999999999887653

>PRK10938 putative molybdenum transport ATP-binding protein ModF; Provisional

Probab=89.98  E-value=0.25  Score=45.70  Aligned_cols=24  Identities=25%  Similarity=0.223  Sum_probs=21.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus       285 ~Ge~~~i~G~NGsGKSTLl~~l~G  308 (490)
T PRK10938        285 PGEHWQIVGPNGAGKSTLLSLITG  308 (490)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcC
Confidence            356899999999999999999876

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=89.96  E-value=0.3  Score=48.38  Aligned_cols=25  Identities=20%  Similarity=0.450  Sum_probs=23.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+|+|-|.+|.||||+|+.+..++.
T Consensus        35 ~~i~idG~~gsGKst~~~~la~~l~   59 (863)
T PRK12269         35 VIIALDGPAGSGKSSVCRLLASRLG   59 (863)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            6899999999999999999998764

>PRK10636 putative ABC transporter ATP-binding protein; Provisional

Probab=89.95  E-value=0.26  Score=47.34  Aligned_cols=25  Identities=20%  Similarity=0.429  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||.+.+...
T Consensus       337 ~Ge~~~l~G~NGsGKSTLlk~l~G~  361 (638)
T PRK10636        337 PGSRIGLLGRNGAGKSTLIKLLAGE  361 (638)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3478999999999999999998764

>PRK11288 araG L-arabinose transporter ATP-binding protein; Provisional

Probab=89.94  E-value=0.24  Score=46.01  Aligned_cols=25  Identities=16%  Similarity=0.571  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||.+.+...
T Consensus       278 ~Ge~~~iiG~NGsGKSTLlk~l~G~  302 (501)
T PRK11288        278 AGEIVGLFGLVGAGRSELMKLLYGA  302 (501)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHcCC
Confidence            3578999999999999999988753

>TIGR02633 xylG D-xylose ABC transporter, ATP-binding protein

Probab=89.88  E-value=0.26  Score=45.72  Aligned_cols=25  Identities=32%  Similarity=0.590  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus       285 ~Ge~~~l~G~NGsGKSTLl~~l~G~  309 (500)
T TIGR02633       285 RGEILGVAGLVGAGRTELVQALFGA  309 (500)
T ss_pred             CCcEEEEeCCCCCCHHHHHHHHhCC
Confidence            4578999999999999999998754

Several bacterial species have enzymes xylose isomerase and xylulokinase enzymes for xylose utilization. Members of this protein family are the ATP-binding cassette (ABC) subunit of the known or predicted high-affinity xylose ABC transporter for xylose import. These genes, which closely resemble other sugar transport ABC transporter genes, typically are encoded near xylose utilization enzymes and regulatory proteins. Note that this form of the transporter contains two copies of the ABC transporter domain (pfam00005).

>COG1123 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]

Probab=89.88  E-value=0.26  Score=46.10  Aligned_cols=26  Identities=35%  Similarity=0.437  Sum_probs=22.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..-.++||+|..|.||||+|.++..-
T Consensus        33 ~~GE~lgIvGESGsGKSt~a~~i~gl   58 (539)
T COG1123          33 EPGEILGIVGESGSGKSTLALALMGL   58 (539)
T ss_pred             cCCcEEEEEcCCCCCHHHHHHHHhcc
Confidence            45689999999999999999998763

>COG4618 ArpD ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]

Probab=89.86  E-value=0.26  Score=45.61  Aligned_cols=24  Identities=42%  Similarity=0.573  Sum_probs=20.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-..+||+|..|.||||||+.+-.
T Consensus       361 ~G~~lgIIGPSgSGKSTLaR~lvG  384 (580)
T COG4618         361 AGEALGIIGPSGSGKSTLARLLVG  384 (580)
T ss_pred             CCceEEEECCCCccHHHHHHHHHc
Confidence            346899999999999999998754

>TIGR03719 ABC_ABC_ChvD ATP-binding cassette protein, ChvD family

Probab=89.83  E-value=0.27  Score=46.25  Aligned_cols=26  Identities=23%  Similarity=0.424  Sum_probs=22.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ....+++|+|..|.|||||.+.+...
T Consensus        29 ~~Ge~~~liG~NGsGKSTLl~~i~G~   54 (552)
T TIGR03719        29 FPGAKIGVLGLNGAGKSTLLRIMAGV   54 (552)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34568999999999999999998764

Members of this protein family have two copies of the ABC transporter ATP-binding cassette, but are found outside the common ABC transporter operon structure that features integral membrane permease proteins and substrate-binding proteins encoded next to the ATP-binding cassette (ABC domain) protein. The member protein ChvD from Agrobacterium tumefaciens was identified as both a candidate to interact with VirB8, based on yeast two-hybrid analysis, and as an apparent regulator of VirG. The general function of this protein family is unknown.

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=89.83  E-value=0.27  Score=46.19  Aligned_cols=25  Identities=20%  Similarity=0.365  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -.-|+|+|..|+|||||.+.+...+
T Consensus       348 g~riaiiG~NG~GKSTLlk~l~g~~  372 (530)
T COG0488         348 GDRIAIVGPNGAGKSTLLKLLAGEL  372 (530)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhhc
Confidence            4568999999999999999986654

>PRK04841 transcriptional regulator MalT; Provisional

Probab=89.78  E-value=0.42  Score=47.31  Aligned_cols=44  Identities=14%  Similarity=0.043  Sum_probs=31.0

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ....++-|..-.+    .|.. ....+++-|.|.+|.||||++....++
T Consensus        12 ~~~~~~~R~rl~~----~l~~-~~~~~~~~v~apaG~GKTtl~~~~~~~   55 (903)
T PRK04841         12 RLHNTVVRERLLA----KLSG-ANNYRLVLVTSPAGYGKTTLISQWAAG   55 (903)
T ss_pred             CccccCcchHHHH----HHhc-ccCCCeEEEECCCCCCHHHHHHHHHHh
Confidence            4455666664333    3332 235789999999999999999987654

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=89.74  E-value=0.27  Score=46.43  Aligned_cols=25  Identities=24%  Similarity=0.278  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-..++|+|..|.|||||++.+...
T Consensus       368 ~G~~~aIvG~sGsGKSTLl~ll~gl  392 (582)
T PRK11176        368 AGKTVALVGRSGSGKSTIANLLTRF  392 (582)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhc
Confidence            3467999999999999999998764

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=89.69  E-value=0.62  Score=42.34  Aligned_cols=47  Identities=19%  Similarity=0.266  Sum_probs=35.4

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ....|.......|.+++. +-....++.|-|.+|.|||++|..+...+
T Consensus       172 ~~~~gi~tG~~~LD~~~~-G~~~g~liviag~pg~GKT~~al~ia~~~  218 (421)
T TIGR03600       172 GELTGLSTGLPKLDRLTN-GLVKGDLIVIGARPSMGKTTLALNIAENV  218 (421)
T ss_pred             CCCcceeCCChhHHHHhc-CCCCCceEEEEeCCCCCHHHHHHHHHHHH
Confidence            345677777777777765 43446788899999999999999887543

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PLN03073 ABC transporter F family; Provisional

Probab=89.69  E-value=0.27  Score=47.91  Aligned_cols=24  Identities=29%  Similarity=0.264  Sum_probs=21.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-..+||+|..|.|||||.+.+..
T Consensus       202 ~Ge~~gLvG~NGsGKSTLLr~l~g  225 (718)
T PLN03073        202 FGRHYGLVGRNGTGKTTFLRYMAM  225 (718)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcC
Confidence            356799999999999999999864

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=89.65  E-value=0.34  Score=45.25  Aligned_cols=48  Identities=29%  Similarity=0.360  Sum_probs=32.4

Q ss_pred             CCccccccchHHHHHH---HhccCC-------CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIES---LLGVKS-------KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~---~l~~~~-------~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .+++-|.++.+.+|++   .|..-.       .=.+=|-++|.+|.|||-||++|...
T Consensus       303 F~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGE  360 (752)
T KOG0734|consen  303 FEDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGE  360 (752)
T ss_pred             cccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcc
Confidence            3567788765555554   454211       11344668899999999999998764

>cd01882 BMS1 Bms1

Probab=89.64  E-value=0.33  Score=40.22  Aligned_cols=25  Identities=20%  Similarity=0.466  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...+|+|+|..|.|||||.+.+...
T Consensus        38 ~~~~i~ivG~~~~GKstl~~~l~~~   62 (225)
T cd01882          38 PPLVVAVVGPPGVGKTTLIKSLVKN   62 (225)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhh
Confidence            4688999999999999999887664

Bms1 is an essential, evolutionarily conserved, nucleolar protein. Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit. The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly. It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes.

>TIGR03258 PhnT 2-aminoethylphosphonate ABC transport system, ATP-binding component PhnT

Probab=89.61  E-value=0.32  Score=43.49  Aligned_cols=24  Identities=38%  Similarity=0.436  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        30 ~Ge~~~llGpsGsGKSTLLr~iaG   53 (362)
T TIGR03258        30 AGELLALIGKSGCGKTTLLRAIAG   53 (362)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            346899999999999999998865

This ATP-binding component of an ABC transport system is found in Salmonella and Burkholderia lineages in the vicinity of enzymes for the breakdown of 2-aminoethylphosphonate.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=89.59  E-value=0.47  Score=40.66  Aligned_cols=27  Identities=26%  Similarity=0.186  Sum_probs=23.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      +..-++|.|..|.|||||.+.+...+.
T Consensus       110 ~~~~~~i~g~~g~GKttl~~~l~~~~~  136 (270)
T TIGR02858       110 RVLNTLIISPPQCGKTTLLRDLARILS  136 (270)
T ss_pred             CeeEEEEEcCCCCCHHHHHHHHhCccC
Confidence            467899999999999999999887543

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.

>PRK01889 GTPase RsgA; Reviewed

Probab=89.58  E-value=0.5  Score=42.09  Aligned_cols=35  Identities=17%  Similarity=0.416  Sum_probs=27.8

Q ss_pred             hHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          189 RVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       189 ~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .+++|..+|..    ...++++|..|+|||||...+...
T Consensus       184 gl~~L~~~L~~----g~~~~lvG~sgvGKStLin~L~g~  218 (356)
T PRK01889        184 GLDVLAAWLSG----GKTVALLGSSGVGKSTLVNALLGE  218 (356)
T ss_pred             cHHHHHHHhhc----CCEEEEECCCCccHHHHHHHHHHh
Confidence            36677776642    358899999999999999998764

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=89.47  E-value=0.36  Score=47.09  Aligned_cols=25  Identities=24%  Similarity=0.312  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+++++|..|+||||++.++...+
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~  209 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARC  209 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhH
Confidence            4799999999999999999887654

>PLN02772 guanylate kinase

Probab=89.46  E-value=0.38  Score=43.39  Aligned_cols=26  Identities=19%  Similarity=0.351  Sum_probs=22.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+++.|.|..|+||+||++.+..+.
T Consensus       134 ~~k~iVlsGPSGvGKsTL~~~L~~~~  159 (398)
T PLN02772        134 AEKPIVISGPSGVGKGTLISMLMKEF  159 (398)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhhhc
Confidence            46899999999999999999987754

>cd01849 YlqF_related_GTPase YlqF-related GTPases

Probab=89.43  E-value=0.5  Score=36.53  Aligned_cols=25  Identities=24%  Similarity=0.581  Sum_probs=21.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +...+++.|.+|+||+||...+.+.
T Consensus        99 ~~~~~~~~G~~~~GKstlin~l~~~  123 (155)
T cd01849          99 KSITVGVIGYPNVGKSSVINALLNK  123 (155)
T ss_pred             cCcEEEEEccCCCCHHHHHHHHHcc
Confidence            3566889999999999999988764

These proteins are found in bacteria, eukaryotes, and archaea. They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases.

>COG0802 Predicted ATPase or kinase [General function prediction only]

Probab=89.40  E-value=0.61  Score=36.25  Aligned_cols=41  Identities=22%  Similarity=0.159  Sum_probs=29.8

Q ss_pred             chHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          188 SRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       188 ~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ....++-+.|...-..--+|.+-|-=|.|||||+|.+...+
T Consensus         9 ~~t~~lg~~l~~~l~~g~Vv~L~GdLGAGKTtf~rgi~~~L   49 (149)
T COG0802           9 EATLALGERLAEALKAGDVVLLSGDLGAGKTTLVRGIAKGL   49 (149)
T ss_pred             HHHHHHHHHHHhhCCCCCEEEEEcCCcCChHHHHHHHHHHc
Confidence            34455555554443445688999999999999999998764

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

Probab=89.35  E-value=0.51  Score=46.06  Aligned_cols=50  Identities=22%  Similarity=0.422  Sum_probs=37.1

Q ss_pred             CCccccccchHHHHHHHhccC-------CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          180 KNQLAGVESRVEEIESLLGVK-------SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~-------~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+++|.+..++.+.+-+...       ...+.+.-..|+.|+|||.||+++...+.
T Consensus       490 ~~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lf  546 (786)
T COG0542         490 KKRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALF  546 (786)
T ss_pred             hcceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhc
Confidence            367899998888887654432       12245666789999999999999888653

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=89.33  E-value=0.31  Score=46.91  Aligned_cols=24  Identities=33%  Similarity=0.404  Sum_probs=21.1

Q ss_pred             EEEEEcCCCChHHHHHHHHHHHHh
Q 043980          206 ALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      -+.++|.+|.||||+|+.+.+...
T Consensus       187 gill~G~~G~GKt~~~~~~a~~~~  210 (644)
T PRK10733        187 GVLMVGPPGTGKTLLAKAIAGEAK  210 (644)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHcC
Confidence            388999999999999999988754

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=89.28  E-value=0.3  Score=46.03  Aligned_cols=24  Identities=21%  Similarity=0.351  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ....++|+|..|.|||||++.+.+
T Consensus       354 ~Ge~vaiVG~sGsGKSTl~~LL~r  377 (567)
T COG1132         354 PGEKVAIVGPSGSGKSTLIKLLLR  377 (567)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            356799999999999999998765

>KOG2878 consensus Predicted kinase [General function prediction only]

Probab=89.28  E-value=0.22  Score=40.86  Aligned_cols=26  Identities=27%  Similarity=0.326  Sum_probs=23.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-+|++.|..|.|||||+-++++.+
T Consensus        30 ~Pl~igfSgPQGsGKstl~~ald~~l   55 (282)
T KOG2878|consen   30 VPLVIGFSGPQGSGKSTLVFALDYKL   55 (282)
T ss_pred             CcEEEEecCCCCCCceeehhhhHHHH
Confidence            36789999999999999999998864

>TIGR03415 ABC_choXWV_ATP choline ABC transporter, ATP-binding protein

Probab=89.21  E-value=0.35  Score=43.57  Aligned_cols=24  Identities=25%  Similarity=0.320  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -.+++|.|..|.|||||.+.+..-
T Consensus        50 Gei~~I~G~nGsGKSTLlr~L~Gl   73 (382)
T TIGR03415        50 GEICVLMGLSGSGKSSLLRAVNGL   73 (382)
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            468999999999999999998763

Members of this protein family are the ATP-binding subunit of a three-protein transporter. This family belongs, more broadly, to the family of proline and glycine-betaine transporters, but members have been identified by direct characterization and by bioinformatic means as choline transporters. Many species have several closely-related members of this family, probably with variable abilities to act additionally on related quaternary amines.

>PLN03073 ABC transporter F family; Provisional

Probab=89.16  E-value=0.32  Score=47.38  Aligned_cols=24  Identities=29%  Similarity=0.432  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -.+++|+|..|.|||||.+.+...
T Consensus       535 Ge~i~LvG~NGsGKSTLLk~L~Gl  558 (718)
T PLN03073        535 DSRIAMVGPNGIGKSTILKLISGE  558 (718)
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            458999999999999999998764

>PF11868 DUF3388: Protein of unknown function (DUF3388); InterPro: IPR024514 This domain is found in a family of bacterial proteins that are functionally uncharacterised

Probab=89.10  E-value=0.49  Score=37.28  Aligned_cols=32  Identities=22%  Similarity=0.382  Sum_probs=22.3

Q ss_pred             HHHHhccCCCCeEEEEEEcCCCChHHHHH--HHHHH
Q 043980          193 IESLLGVKSKDVYALGIWGIGGIGKTKIA--RAIFD  226 (233)
Q Consensus       193 l~~~l~~~~~~~~~i~i~G~gGiGKTtla--~~v~~  226 (233)
                      +.++++.  .+.++|||.||+-+|||.-+  ..||-
T Consensus        45 maEl~K~--~Gh~lIGiRGmPRVGKTEsivAasVcA   78 (192)
T PF11868_consen   45 MAELFKE--EGHKLIGIRGMPRVGKTESIVAASVCA   78 (192)
T ss_pred             HHHHHHh--cCceEEeecCCCccCchhHHHHHhhhc
Confidence            3444443  46899999999999998644  44543

Proteins in this family are typically between 261 to 275 amino acids in length and have a N-terminal ACT domain.

>PRK13545 tagH teichoic acids export protein ATP-binding subunit; Provisional

Probab=89.09  E-value=0.35  Score=45.40  Aligned_cols=25  Identities=28%  Similarity=0.476  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|.|..|.|||||.+.+...
T Consensus        49 ~GEivgIiGpNGSGKSTLLkiLaGL   73 (549)
T PRK13545         49 EGEIVGIIGLNGSGKSTLSNLIAGV   73 (549)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhCC
Confidence            3578999999999999999998764

>TIGR03797 NHPM_micro_ABC2 NHPM bacteriocin system ABC transporter, ATP-binding protein

Probab=88.99  E-value=0.34  Score=46.81  Aligned_cols=24  Identities=25%  Similarity=0.353  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ....++|+|..|.|||||++.+..
T Consensus       478 ~Ge~vaIvG~sGsGKSTLlklL~g  501 (686)
T TIGR03797       478 PGEFVAIVGPSGSGKSTLLRLLLG  501 (686)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            357899999999999999998765

Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal propeptide cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif

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

Probab=88.89  E-value=0.62  Score=42.79  Aligned_cols=53  Identities=21%  Similarity=0.342  Sum_probs=43.9

Q ss_pred             CCCCCccccccchHHHHHHHhcc--CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGV--KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~--~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+..++||+.++..+.+++..  +.+....+=|.|.+|.|||.+...++.+..
T Consensus       146 t~~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~  200 (529)
T KOG2227|consen  146 TAPPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLS  200 (529)
T ss_pred             cCCCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhh
Confidence            44667899999999999998764  445567888999999999999999988753

>TIGR00665 DnaB replicative DNA helicase

Probab=88.79  E-value=0.78  Score=41.81  Aligned_cols=45  Identities=18%  Similarity=0.234  Sum_probs=33.4

Q ss_pred             ccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          182 QLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       182 ~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...|.......|.+++. +-....++.|-|.+|+||||++..+...
T Consensus       174 ~~~gi~tG~~~LD~~~~-G~~~G~l~vi~g~pg~GKT~~~l~~a~~  218 (434)
T TIGR00665       174 GITGVPTGFTDLDKLTS-GLQPSDLIILAARPSMGKTAFALNIAEN  218 (434)
T ss_pred             CCCcccCCchhhHhhcC-CCCCCeEEEEEeCCCCChHHHHHHHHHH
Confidence            45566666677777653 3344678899999999999999987665

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>COG1162 Predicted GTPases [General function prediction only]

Probab=88.69  E-value=0.5  Score=40.99  Aligned_cols=34  Identities=26%  Similarity=0.455  Sum_probs=26.7

Q ss_pred             chHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          188 SRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       188 ~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ..+++|..+|.     -++..+.|..|+|||||..++-.
T Consensus       153 ~~~~~l~~~l~-----~~~svl~GqSGVGKSSLiN~L~p  186 (301)
T COG1162         153 DGLEELAELLA-----GKITVLLGQSGVGKSTLINALLP  186 (301)
T ss_pred             ccHHHHHHHhc-----CCeEEEECCCCCcHHHHHHhhCc
Confidence            34677777776     23778899999999999998765

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=88.68  E-value=0.36  Score=43.61  Aligned_cols=26  Identities=27%  Similarity=0.240  Sum_probs=22.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+-++|..|+||||+|+.+.+.+-
T Consensus        36 ~ha~Lf~Gp~G~GKt~lA~~lA~~l~   61 (394)
T PRK07940         36 THAWLFTGPPGSGRSVAARAFAAALQ   61 (394)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHhC
Confidence            45677899999999999999988653

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=88.64  E-value=0.73  Score=43.95  Aligned_cols=26  Identities=35%  Similarity=0.411  Sum_probs=22.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+-+-|+|-.|.|||.|++++.+.+.
T Consensus       314 ~NpL~LyG~sGsGKTHLL~AIa~~a~  339 (617)
T PRK14086        314 YNPLFIYGESGLGKTHLLHAIGHYAR  339 (617)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHH
Confidence            35588999999999999999999753

>TIGR01842 type_I_sec_PrtD type I secretion system ABC transporter, PrtD family

Probab=88.61  E-value=0.37  Score=45.25  Aligned_cols=25  Identities=40%  Similarity=0.457  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ....++|+|..|.|||||++.+...
T Consensus       343 ~G~~~~ivG~sGsGKSTL~~ll~g~  367 (544)
T TIGR01842       343 AGEALAIIGPSGSGKSTLARLIVGI  367 (544)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999999988764

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion.

>COG1135 AbcC ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=88.60  E-value=0.4  Score=41.82  Aligned_cols=24  Identities=33%  Similarity=0.465  Sum_probs=20.6

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIF  225 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~  225 (233)
                      +...+.||.|..|.|||||.+.+-
T Consensus        30 ~~GeI~GIIG~SGAGKSTLiR~iN   53 (339)
T COG1135          30 PKGEIFGIIGYSGAGKSTLLRLIN   53 (339)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHh
Confidence            345799999999999999999763

>cd04178 Nucleostemin_like Nucleostemin-like

Probab=88.58  E-value=0.58  Score=37.19  Aligned_cols=24  Identities=17%  Similarity=0.437  Sum_probs=20.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.++++|++++|||||..++.+.
T Consensus       117 ~~~~~~vG~pnvGKSslin~l~~~  140 (172)
T cd04178         117 SITVGVVGFPNVGKSSLINSLKRS  140 (172)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHhCc
Confidence            356889999999999999998763

Nucleostemin (NS) is a nucleolar protein that functions as a regulator of cell growth and proliferation in stem cells and in several types of cancer cells, but is not expressed in the differentiated cells of most mammalian adult tissues. NS shuttles between the nucleolus and nucleoplasm bidirectionally at a rate that is fast and independent of cell type. Lowering GTP levels decreases the nucleolar retention of NS, and expression of NS is abruptly down-regulated during differentiation prior to terminal cell division. Found only in eukaryotes, NS consists of an N-terminal basic domain, a coiled-coil domain, a GTP-binding domain, an intermediate domain, and a C-terminal acidic domain. Experimental evidence indicates that NS uses its GTP-binding property as a molecular switch to control the transition between the nucleolus and nucleoplasm, and this process involves interaction between the basic, GTP-binding, and intermediate domains of the

>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter

Probab=88.54  E-value=0.36  Score=46.81  Aligned_cols=24  Identities=25%  Similarity=0.371  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -..++|+|..|.|||||++.+..-
T Consensus       500 G~~vaIvG~SGsGKSTLlklL~gl  523 (708)
T TIGR01193       500 NSKTTIVGMSGSGKSTLAKLLVGF  523 (708)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcc
Confidence            468999999999999999987653

This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.

>PRK15494 era GTPase Era; Provisional

Probab=88.51  E-value=0.36  Score=42.66  Aligned_cols=23  Identities=22%  Similarity=0.306  Sum_probs=20.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ..-|+|+|.+|+|||||...+..
T Consensus        52 ~~kV~ivG~~nvGKSTLin~l~~   74 (339)
T PRK15494         52 TVSVCIIGRPNSGKSTLLNRIIG   74 (339)
T ss_pred             eeEEEEEcCCCCCHHHHHHHHhC
Confidence            45789999999999999998765

>PHA02542 41 41 helicase; Provisional

Probab=88.50  E-value=0.8  Score=42.46  Aligned_cols=46  Identities=7%  Similarity=-0.041  Sum_probs=34.6

Q ss_pred             cccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          183 LAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       183 ~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..|...-...|.+++..+-..-.++-|-|.+|+||||+|..+....
T Consensus       169 ~~gi~TG~~~LD~~t~gGl~~G~LiiIaarPgmGKTtfalniA~~~  214 (473)
T PHA02542        169 ANKIPFKLEILNKITKGGAERKTLNVLLAGVNVGKSLGLCSLAADY  214 (473)
T ss_pred             CCccCCCcHHHHHhccCCCCCCcEEEEEcCCCccHHHHHHHHHHHH
Confidence            5666667777877764444445677788999999999999887654

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=88.44  E-value=0.61  Score=45.51  Aligned_cols=24  Identities=38%  Similarity=0.418  Sum_probs=21.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ++..|.|.+|.||||+++++.+.+
T Consensus       339 ~~~iitGgpGTGKTt~l~~i~~~~  362 (720)
T TIGR01448       339 KVVILTGGPGTGKTTITRAIIELA  362 (720)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH
Confidence            478899999999999999987754

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.

>PTZ00322 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional

Probab=88.44  E-value=0.43  Score=46.06  Aligned_cols=26  Identities=31%  Similarity=0.356  Sum_probs=22.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +..++.++|++|.||||+|+.+.+.+
T Consensus       214 ~~~~~~~vglp~~GKStia~~L~~~l  239 (664)
T PTZ00322        214 GSLIVIMVGLPGRGKTYVARQIQRYF  239 (664)
T ss_pred             cceeEEecccCCCChhHHHHHHHHHH
Confidence            35689999999999999999987764

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

Probab=88.43  E-value=0.41  Score=45.34  Aligned_cols=50  Identities=28%  Similarity=0.336  Sum_probs=36.0

Q ss_pred             CCCCccccccchHHHHHHHhcc---CC-------CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLLGV---KS-------KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~---~~-------~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ....++.|.++.++++.++++.   ..       .-.+=+.++|.+|.|||.||+++...
T Consensus       147 v~F~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgE  206 (596)
T COG0465         147 VTFADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGE  206 (596)
T ss_pred             cChhhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcc
Confidence            3456778888777777665442   11       11455788899999999999999875

>COG4598 HisP ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]

Probab=88.34  E-value=0.42  Score=38.75  Aligned_cols=24  Identities=29%  Similarity=0.437  Sum_probs=20.8

Q ss_pred             CCCeEEEEEEcCCCChHHHHHHHH
Q 043980          201 SKDVYALGIWGIGGIGKTKIARAI  224 (233)
Q Consensus       201 ~~~~~~i~i~G~gGiGKTtla~~v  224 (233)
                      .++.-+|+|.|-.|.||+|+.+++
T Consensus        29 A~~GdVisIIGsSGSGKSTfLRCi   52 (256)
T COG4598          29 ANAGDVISIIGSSGSGKSTFLRCI   52 (256)
T ss_pred             cCCCCEEEEecCCCCchhHHHHHH
Confidence            345679999999999999999986

>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]

Probab=88.25  E-value=0.41  Score=40.35  Aligned_cols=80  Identities=19%  Similarity=0.233  Sum_probs=58.9

Q ss_pred             CCCcceEEEcCcccccccchHHHHHHHHh--hCCCeEEEeC----ccCCCcchHHHHHHHH-HhcCceEEEeecCCCCch
Q 043980           21 NNKKYEVFVSFRGEDTRDKFTSHLYSALS--RQSIQTFIDD----QLNRGDEISQSLVNAI-EASAISVIIFSESYTSSR   93 (233)
Q Consensus        21 ~~~~~dVFISy~~~D~~~~f~~~L~~~L~--~~gi~~~~d~----~~~~G~~~~~~i~~~i-~~s~~~i~v~S~~y~~S~   93 (233)
                      .++.||+=|||.|+-  +..++.....++  ...+..|+|.    -+-+++ +.+-+...- ..|+..++.+..||..-.
T Consensus       174 ~~~~~DiG~SFaGEA--R~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~s-L~~~L~~~Y~~rC~~~~VF~~~~Y~~K~  250 (329)
T COG4916         174 SEKPVDSGISFAGEA--RNLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPGS-LVSTLDPGYDIRCVVTTVFNTGSYICKS  250 (329)
T ss_pred             cccccceeeEeehhh--hhHHHHHHHhhhcccCCceeeeechhhccccCcc-HHHhcccccCceEEEEEEEeCCceEEee
Confidence            678899999999975  569999999998  4458889886    233443 223333332 367778888899999999


Q ss_pred             hhHHHHHHHH
Q 043980           94 WCVDELVKIL  103 (233)
Q Consensus        94 wc~~El~~~~  103 (233)
                      ||.-|...+-
T Consensus       251 ~c~~E~~~~r  260 (329)
T COG4916         251 TCHIEGLEGR  260 (329)
T ss_pred             eeccchhhcc
Confidence            9999877643

>TIGR00958 3a01208 Conjugate Transporter-2 (CT2) Family protein

Probab=88.20  E-value=0.43  Score=46.44  Aligned_cols=25  Identities=20%  Similarity=0.275  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-..++|+|..|.|||||++.+..-
T Consensus       506 ~Ge~vaIvG~SGsGKSTLl~lL~gl  530 (711)
T TIGR00958       506 PGEVVALVGPSGSGKSTVAALLQNL  530 (711)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhc
Confidence            4578999999999999999988764

>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein

Probab=88.03  E-value=0.42  Score=46.35  Aligned_cols=24  Identities=25%  Similarity=0.331  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-..++|+|..|.|||||++.+..
T Consensus       504 ~Ge~vaIvG~sGsGKSTLlklL~g  527 (710)
T TIGR03796       504 PGQRVALVGGSGSGKSTIAKLVAG  527 (710)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            346899999999999999998765

This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=87.98  E-value=0.71  Score=45.23  Aligned_cols=24  Identities=21%  Similarity=0.243  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ++..|.|.+|.||||+++.+.+.+
T Consensus       369 ~~~il~G~aGTGKTtll~~i~~~~  392 (744)
T TIGR02768       369 DIAVVVGRAGTGKSTMLKAAREAW  392 (744)
T ss_pred             CEEEEEecCCCCHHHHHHHHHHHH
Confidence            477899999999999999987654

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.

>PRK13764 ATPase; Provisional

Probab=87.97  E-value=0.52  Score=44.87  Aligned_cols=25  Identities=28%  Similarity=0.343  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..|-|.|..|.||||+++++.+.+.
T Consensus       258 ~~ILIsG~TGSGKTTll~AL~~~i~  282 (602)
T PRK13764        258 EGILIAGAPGAGKSTFAQALAEFYA  282 (602)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4478999999999999999887653

>KOG2702 consensus Predicted panthothenate kinase/uridine kinase-related protein [Nucleotide transport and metabolism; Coenzyme transport and metabolism]

Probab=87.86  E-value=0.77  Score=38.57  Aligned_cols=34  Identities=24%  Similarity=0.179  Sum_probs=27.1

Q ss_pred             HHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          192 EIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       192 ~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...+.|.  ++..+++|+.|.||.||+|++.++.++
T Consensus       109 ~~~e~L~--~n~~~l~glag~pGtgkst~~a~v~~a  142 (323)
T KOG2702|consen  109 VKYEALT--SNNEELTGLAGRPGTGKSTRIAAVDNA  142 (323)
T ss_pred             HHHHHhc--ccchheeeeecCCCCcchhHHHHHHhh
Confidence            3344444  456789999999999999999999885

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

Probab=87.84  E-value=0.81  Score=42.84  Aligned_cols=41  Identities=17%  Similarity=0.305  Sum_probs=31.4

Q ss_pred             chHHHHHHHhc-----cCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          188 SRVEEIESLLG-----VKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       188 ~~~~~l~~~l~-----~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-+.++..||.     ...-+.+++=|+|..|.||||-.+.+...+
T Consensus        89 kKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkvLskel  134 (634)
T KOG1970|consen   89 KKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKVLSKEL  134 (634)
T ss_pred             HhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHHHHHhh
Confidence            34667777877     333457899999999999999999877653

>PRK10522 multidrug transporter membrane component/ATP-binding component; Provisional

Probab=87.83  E-value=0.43  Score=44.82  Aligned_cols=24  Identities=25%  Similarity=0.196  Sum_probs=21.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-..++|+|..|.|||||++.+..
T Consensus       348 ~G~~~aivG~sGsGKSTL~~ll~g  371 (547)
T PRK10522        348 RGELLFLIGGNGSGKSTLAMLLTG  371 (547)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            457899999999999999998865

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=87.82  E-value=0.45  Score=44.78  Aligned_cols=25  Identities=20%  Similarity=0.213  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-..++|+|..|.|||||++.+...
T Consensus       357 ~G~~v~IvG~sGsGKSTLl~lL~gl  381 (571)
T TIGR02203       357 PGETVALVGRSGSGKSTLVNLIPRF  381 (571)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhc
Confidence            4578999999999999999987654

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.

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=87.79  E-value=0.44  Score=45.14  Aligned_cols=25  Identities=20%  Similarity=0.242  Sum_probs=21.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-..++|+|..|.|||||++.+...
T Consensus       360 ~G~~v~IvG~sGsGKSTLl~lL~gl  384 (588)
T PRK13657        360 PGQTVAIVGPTGAGKSTLINLLQRV  384 (588)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3467999999999999999987653

>TIGR03453 partition_RepA plasmid partitioning protein RepA

Probab=87.69  E-value=1.1  Score=40.36  Aligned_cols=26  Identities=23%  Similarity=0.290  Sum_probs=20.8

Q ss_pred             CeEEEEEE-cCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIW-GIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~-G~gGiGKTtla~~v~~~~  228 (233)
                      ..++|+|. .-||+||||+|..+...+
T Consensus       103 ~~~vI~v~n~KGGvGKTT~a~nLA~~L  129 (387)
T TIGR03453       103 HLQVIAVTNFKGGSGKTTTAAHLAQYL  129 (387)
T ss_pred             CceEEEEEccCCCcCHHHHHHHHHHHH
Confidence            35788887 789999999998876643

Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.

>TIGR02857 CydD thiol reductant ABC exporter, CydD subunit

Probab=87.68  E-value=0.47  Score=44.30  Aligned_cols=24  Identities=17%  Similarity=0.313  Sum_probs=21.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ....++|+|..|.|||||++.+..
T Consensus       347 ~G~~~~ivG~sGsGKSTL~~ll~g  370 (529)
T TIGR02857       347 PGERVALVGPSGAGKSTLLNLLLG  370 (529)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            457899999999999999998765

Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=87.64  E-value=0.46  Score=44.99  Aligned_cols=24  Identities=25%  Similarity=0.410  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-..++|+|..|.|||||++.+..
T Consensus       375 ~G~~vaIvG~SGsGKSTL~~lL~g  398 (588)
T PRK11174        375 AGQRIALVGPSGAGKTSLLNALLG  398 (588)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            347899999999999999998755

>smart00350 MCM minichromosome maintenance proteins

Probab=87.59  E-value=0.9  Score=42.46  Aligned_cols=49  Identities=16%  Similarity=0.104  Sum_probs=32.9

Q ss_pred             CCCccccccchHHHHHHHhccCC-----CCeE-----EEEEEcCCCChHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVKS-----KDVY-----ALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~-----~~~~-----~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -.+.+.|.+.-+..+.-.|-.+.     ++.+     =|-|+|-+|.|||++|+.+++-
T Consensus       201 i~p~i~G~~~~k~~l~l~l~gg~~~~~~~~~~~r~~~~vLL~G~pGtGKs~lar~l~~~  259 (509)
T smart00350      201 LAPSIYGHEDIKKAILLLLFGGVHKNLPDGMKIRGDINILLLGDPGTAKSQLLKYVEKT  259 (509)
T ss_pred             hCccccCcHHHHHHHHHHHhCCCccccCCCccccccceEEEeCCCChhHHHHHHHHHHH
Confidence            35678888876555544443321     1111     3678999999999999999874

>COG1119 ModF ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]

Probab=87.57  E-value=0.48  Score=39.90  Aligned_cols=22  Identities=27%  Similarity=0.323  Sum_probs=18.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .=..|+|..|.|||||.+.+.-
T Consensus        58 e~W~I~G~NGsGKTTLL~ll~~   79 (257)
T COG1119          58 EHWAIVGPNGAGKTTLLSLLTG   79 (257)
T ss_pred             CcEEEECCCCCCHHHHHHHHhc
Confidence            3467899999999999997654

>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]

Probab=87.52  E-value=0.57  Score=39.76  Aligned_cols=25  Identities=28%  Similarity=0.457  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -.+|-|=|.+|+||||+|..+.+++
T Consensus        89 p~IILIGGasGVGkStIA~ElA~rL  113 (299)
T COG2074          89 PLIILIGGASGVGKSTIAGELARRL  113 (299)
T ss_pred             CeEEEecCCCCCChhHHHHHHHHHc
Confidence            4566677999999999999999874

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=87.48  E-value=0.63  Score=41.77  Aligned_cols=23  Identities=30%  Similarity=0.395  Sum_probs=20.4

Q ss_pred             EEEEEcCCCChHHHHHHHHHHHH
Q 043980          206 ALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+-|+|..|.||||+..++.+.+
T Consensus       151 lilI~G~TGSGKTT~l~al~~~i  173 (372)
T TIGR02525       151 LGLICGETGSGKSTLAASIYQHC  173 (372)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            56789999999999999998765

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=87.46  E-value=0.49  Score=45.80  Aligned_cols=23  Identities=22%  Similarity=0.320  Sum_probs=20.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -..++|+|..|.|||||++.+..
T Consensus       491 G~~iaIvG~sGsGKSTLlklL~g  513 (694)
T TIGR03375       491 GEKVAIIGRIGSGKSTLLKLLLG  513 (694)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999998765

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=87.31  E-value=0.47  Score=44.93  Aligned_cols=25  Identities=16%  Similarity=0.262  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-..++|+|..|.|||||++.+...
T Consensus       365 ~G~~~aivG~sGsGKSTL~~ll~g~  389 (574)
T PRK11160        365 AGEKVALLGRTGCGKSTLLQLLTRA  389 (574)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3568999999999999999988664

>TIGR00368 Mg chelatase-related protein

Probab=87.30  E-value=0.53  Score=43.88  Aligned_cols=43  Identities=21%  Similarity=0.247  Sum_probs=29.4

Q ss_pred             CCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ..++.|.+.-++.+.-..    .+...+.+.|.+|.||||||+.+..
T Consensus       191 ~~dv~Gq~~~~~al~~aa----~~g~~vlliG~pGsGKTtlar~l~~  233 (499)
T TIGR00368       191 LKDIKGQQHAKRALEIAA----AGGHNLLLFGPPGSGKTMLASRLQG  233 (499)
T ss_pred             HHHhcCcHHHHhhhhhhc----cCCCEEEEEecCCCCHHHHHHHHhc
Confidence            355667655544443322    2335788999999999999999875

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>PHA02519 plasmid partition protein SopA; Reviewed

Probab=87.28  E-value=1.3  Score=40.05  Aligned_cols=26  Identities=23%  Similarity=0.203  Sum_probs=21.0

Q ss_pred             CeEEEEEE-cCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIW-GIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~-G~gGiGKTtla~~v~~~~  228 (233)
                      ..++|+|. .-||+||||++..+...+
T Consensus       105 ~~~vIav~n~KGGVGKTTta~nLA~~L  131 (387)
T PHA02519        105 NPVVLAVMSHKGGVYKTSSAVHTAQWL  131 (387)
T ss_pred             CceEEEEecCCCCCcHHHHHHHHHHHH
Confidence            36788888 679999999999877654

>PRK15115 response regulator GlrR; Provisional

Probab=87.20  E-value=0.82  Score=41.58  Aligned_cols=46  Identities=17%  Similarity=0.183  Sum_probs=30.6

Q ss_pred             ccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          182 QLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       182 ~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .++|....+..+.+....-...-..+-|.|..|.|||++|+.+++.
T Consensus       135 ~lig~s~~~~~~~~~~~~~a~~~~~vli~Ge~GtGk~~lA~~ih~~  180 (444)
T PRK15115        135 AIVTRSPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNA  180 (444)
T ss_pred             cccccCHHHHHHHHHHHhhccCCCeEEEEcCCcchHHHHHHHHHHh
Confidence            4667666565554433221222234668999999999999999874

>PRK10789 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=87.17  E-value=0.52  Score=44.55  Aligned_cols=25  Identities=32%  Similarity=0.377  Sum_probs=21.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ....++|+|..|.|||||++.+..-
T Consensus       340 ~G~~~~ivG~sGsGKSTLl~ll~g~  364 (569)
T PRK10789        340 PGQMLGICGPTGSGKSTLLSLIQRH  364 (569)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcc
Confidence            3568999999999999999988653

>PRK05748 replicative DNA helicase; Provisional

Probab=87.09  E-value=1.1  Score=41.15  Aligned_cols=46  Identities=13%  Similarity=0.239  Sum_probs=33.4

Q ss_pred             ccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          182 QLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       182 ~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...|...-...|.+++. +-....++.|-|.+|.||||+|..+....
T Consensus       182 ~~~gi~TG~~~LD~~~~-G~~~G~livIaarpg~GKT~~al~ia~~~  227 (448)
T PRK05748        182 DITGIPTGFTDLDKMTS-GLQPNDLIIVAARPSVGKTAFALNIAQNV  227 (448)
T ss_pred             CCCCccCChHHHHHhcC-CCCCCceEEEEeCCCCCchHHHHHHHHHH
Confidence            34566666666766654 33446788899999999999999887653

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=87.07  E-value=0.78  Score=44.64  Aligned_cols=49  Identities=24%  Similarity=0.378  Sum_probs=34.6

Q ss_pred             CccccccchHHHHHHHhcc----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGV----------KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .++-|.++-+.++.+-+..          +-.+..=|-++|.+|.|||-||++|+-..+
T Consensus       672 dDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEcs  730 (953)
T KOG0736|consen  672 DDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATECS  730 (953)
T ss_pred             hcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhce
Confidence            4566777777777764443          112244567899999999999999987643

>TIGR03029 EpsG chain length determinant protein tyrosine kinase EpsG

Probab=86.97  E-value=1.4  Score=37.37  Aligned_cols=42  Identities=21%  Similarity=0.136  Sum_probs=28.5

Q ss_pred             cchHHHHHHHhcc--CCCCeEEEEEE-cCCCChHHHHHHHHHHHH
Q 043980          187 ESRVEEIESLLGV--KSKDVYALGIW-GIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       187 ~~~~~~l~~~l~~--~~~~~~~i~i~-G~gGiGKTtla~~v~~~~  228 (233)
                      .+..+.|..-|..  ...+.++|+|. +.||.||||+|..+...+
T Consensus        84 ~e~~~~l~~~l~~~~~~~~~~vi~vts~~~g~Gktt~a~nLA~~l  128 (274)
T TIGR03029        84 VEALRALRSQLMLRWFSEGRKALAVVSAKSGEGCSYIAANLAIVF  128 (274)
T ss_pred             HHHHHHHHHHhhhhccCCCCeEEEEECCCCCCCHHHHHHHHHHHH
Confidence            3446666554432  23457888888 778999999998776643

The proteins in this family are homologs of the EpsG protein found in Methylobacillus strain 12S and are generally found in operons with other Eps homologs. The protein is believed to function as the protein tyrosine kinase component of the chain length regulator (along with the transmembrane component EpsF).

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=86.84  E-value=0.4  Score=42.32  Aligned_cols=25  Identities=28%  Similarity=0.159  Sum_probs=20.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..+-|-|.|-.|.|||||..++..-
T Consensus       172 ~r~NILisGGTGSGKTTlLNal~~~  196 (355)
T COG4962         172 IRCNILISGGTGSGKTTLLNALSGF  196 (355)
T ss_pred             hceeEEEeCCCCCCHHHHHHHHHhc
Confidence            3456789999999999999987653

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

Probab=86.82  E-value=0.39  Score=44.82  Aligned_cols=49  Identities=27%  Similarity=0.314  Sum_probs=35.9

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-++++|.+.-.+.|...+..+.- ..-.-..|..|+||||+|+.+...+
T Consensus        14 ~F~evvGQe~v~~~L~nal~~~ri-~hAYlfsG~RGvGKTt~Ari~Akal   62 (515)
T COG2812          14 TFDDVVGQEHVVKTLSNALENGRI-AHAYLFSGPRGVGKTTIARILAKAL   62 (515)
T ss_pred             cHHHhcccHHHHHHHHHHHHhCcc-hhhhhhcCCCCcCchhHHHHHHHHh
Confidence            345679998888888877765432 2334456999999999999887754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	233
3ozi_A	204	Crystal Structure Of The Tir Domain From The Flax D		5e-25
3jrn_A	176	Crystal Structure Of Tir Domain From Arabidopsis Th		8e-25

>pdb|3OZI|A Chain A, Crystal Structure Of The Tir Domain From The Flax Disease Resistance Protein L6 Length = 204

Iteration: 1
 Score =  110 bits (276), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 56/115 (48%), Positives = 79/115 (68%), Gaps = 2/115 (1%)
Query: 24  KYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTF-IDDQLNRGDEISQSLVNAIEASAISV 82
           +YEVF+SFRG DTR++FT  LY +L R  I TF  DD+L +G EI  +L+ AI+ S I V
Sbjct: 35  EYEVFLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDDELLKGKEIGPNLLRAIDQSKIYV 94
Query: 83  IIFSESYTSSRWCVDELVKILECKKEYA-QIVIPVLYRVDPSDVRNQTGSFGDSF 136
            I S  Y  S+WC+ EL +I+  ++E   +I++P+ Y VDPSDVR+QTG +  +F
Sbjct: 95  PIISSGYADSKWCLMELAEIVRRQEEDPRRIILPIFYMVDPSDVRHQTGCYKKAF 149

>pdb|3JRN|A Chain A, Crystal Structure Of Tir Domain From Arabidopsis Thaliana Length = 176

Iteration: 1
 Score =  110 bits (274), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 54/114 (47%), Positives = 76/114 (66%), Gaps = 1/114 (0%)
Query: 24  KYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDD-QLNRGDEISQSLVNAIEASAISV 82
           KY+VF+SFRG DTR  F S LY  L R+SI+TF DD +L  G   S  L + IE S  +V
Sbjct: 8   KYDVFLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFSPELKSPIEVSRFAV 67
Query: 83  IIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSF 136
           ++ SE+Y +S WC+DELV I++ +K+ +  V+P+ Y V+P+ VR QTG   + F
Sbjct: 68  VVVSENYAASSWCLDELVTIMDFEKKGSITVMPIFYGVEPNHVRWQTGVLAEQF 121

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	233
3jrn_A	176	AT1G72930 protein; TIR domain arabidopsis thaliana	1e-68
3ozi_A	204	L6TR; plant TIR domain, plant protein; 2.30A {Linu	4e-68
3h16_A	154	TIR protein; bacteria TIR domain, signaling protei	1e-63
3ub2_A	146	TOLL/interleukin-1 receptor domain-containing ADA	8e-17
1t3g_A	159	X-linked interleukin-1 receptor accessory protein-	3e-07
2j67_A	178	TOLL like receptor 10; TIR, IL-1, TLR10, membrane,	4e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	2e-04
2js7_A	160	Myeloid differentiation primary response protein M	5e-04
1fyx_A	149	TOLL-like receptor 2; beta-alpha-beta fold, signal	9e-04

>3jrn_A AT1G72930 protein; TIR domain arabidopsis thaliana, plant protein; 2.00A {Arabidopsis thaliana} Length = 176

 Score =  207 bits (529), Expect = 1e-68
 Identities = 55/130 (42%), Positives = 82/130 (63%), Gaps = 1/130 (0%)

Query: 22  NKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQ-LNRGDEISQSLVNAIEASAI 80
             KY+VF+SFRG DTR  F S LY  L R+SI+TF DD+ L  G   S  L + IE S  
Sbjct: 6   ATKYDVFLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFSPELKSPIEVSRF 65

Query: 81  SVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLE 140
           +V++ SE+Y +S WC+DELV I++ +K+ +  V+P+ Y V+P+ VR QTG   + F K  
Sbjct: 66  AVVVVSENYAASSWCLDELVTIMDFEKKGSITVMPIFYGVEPNHVRWQTGVLAEQFKKHA 125

Query: 141 EFKEAAELEE 150
             ++  ++ +
Sbjct: 126 SREDPEKVLK 135

>3ozi_A L6TR; plant TIR domain, plant protein; 2.30A {Linum usitatissimum} Length = 204

 Score =  207 bits (529), Expect = 4e-68
 Identities = 59/152 (38%), Positives = 89/152 (58%), Gaps = 11/152 (7%)

Query: 1   MASSSSSSHRSTSLGLIRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQ 60
           ++ S++ S             + +YEVF+SFRG DTR++FT  LY +L R  I TF DD 
Sbjct: 21  ISDSTNPSGSFP---------SVEYEVFLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDD 71

Query: 61  -LNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEY-AQIVIPVLY 118
            L +G EI  +L+ AI+ S I V I S  Y  S+WC+ EL +I+  ++E   +I++P+ Y
Sbjct: 72  ELLKGKEIGPNLLRAIDQSKIYVPIISSGYADSKWCLMELAEIVRRQEEDPRRIILPIFY 131

Query: 119 RVDPSDVRNQTGSFGDSFSKLEEFKEAAELEE 150
            VDPSDVR+QTG +  +F K     +   ++ 
Sbjct: 132 MVDPSDVRHQTGCYKKAFRKHANKFDGQTIQN 163

>3h16_A TIR protein; bacteria TIR domain, signaling protein; 2.50A {Paracoccus denitrificans PD1222} Length = 154

 Score =  194 bits (494), Expect = 1e-63
 Identities = 25/151 (16%), Positives = 60/151 (39%), Gaps = 8/151 (5%)

Query: 1   MASSSSSSHRSTSLGLIRPRNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQ 60
           M  ++  +  +         +   +++F+S   ED +  F   L   L     + + DD 
Sbjct: 3   MKPTAGPTTNADL------TSAPPHDIFISHAWED-KADFVEALAHTLRAAGAEVWYDDF 55

Query: 61  -LNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYR 119
            L  GD + +S+   + +S   +++ S  +    W   EL  + + +      ++P+ ++
Sbjct: 56  SLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQLESSGRSRILPIWHK 115

Query: 120 VDPSDVRNQTGSFGDSFSKLEEFKEAAELEE 150
           V   +V + + +  D  +     K   E+  
Sbjct: 116 VSKDEVASFSPTMADKLAFNTSTKSVDEIVA 146

>3ub2_A TOLL/interleukin-1 receptor domain-containing ADA protein; TIR domain, TLRS adaptor, immune system; 2.40A {Homo sapiens} PDB: 3ub3_A 3ub4_A 2y92_A Length = 146

 Score = 73.6 bits (181), Expect = 8e-17
 Identities = 25/111 (22%), Positives = 44/111 (39%), Gaps = 5/111 (4%)

Query: 19  PRNNKKYEVFVSFRGEDTRDKFTSHLYSAL--SRQSIQTFIDDQ-LNRGDEISQSLVNAI 75
            R +K Y+V V    ED        L S L  S  S++ F+  +    G  I   L  A+
Sbjct: 5   SRWSKDYDVCVCHSEEDLV--AAQDLVSYLEGSTASLRCFLQLRDATPGGAIVSELCQAL 62

Query: 76  EASAISVIIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVR 126
            +S   V++ +  +    WC  ++++ L          IP+L  +  +   
Sbjct: 63  SSSHCRVLLITPGFLQDPWCKYQMLQALTEAPGAEGCTIPLLSGLSRAAYP 113

>1t3g_A X-linked interleukin-1 receptor accessory protein-like 1; TIR, IL-1RAPL, IL-1R, TLR, membrane protein; 2.30A {Homo sapiens} Length = 159

 Score = 47.8 bits (113), Expect = 3e-07
 Identities = 19/120 (15%), Positives = 39/120 (32%), Gaps = 14/120 (11%)

Query: 23  KKYEVFVSFRGEDTR---------DKFTSHLYSAL--SRQSIQTFIDD-QLNRGDEISQS 70
           K Y+ ++S+   D           ++F   +   +       + FI D  L       + 
Sbjct: 1   KDYDAYLSYTKVDPDQWNQETGEEERFALEILPDMLEKHYGYKLFIPDRDLIPTGTYIED 60

Query: 71  LVNAIEASAISVIIFSESYT-SSRWCVDELVKIL-ECKKEYAQIVIPVLYRVDPSDVRNQ 128
           +   ++ S   +I+ + +Y     W + EL   L          VI +        +  Q
Sbjct: 61  VARCVDQSKRLIIVMTPNYVVRRGWSIFELETRLRNMLVTGEIKVILIECSELRGIMNYQ 120

>2j67_A TOLL like receptor 10; TIR, IL-1, TLR10, membrane, innate immunity, immune response, leucine-rich repeat, glycoprotein, transmembrane; 2.20A {Homo sapiens} PDB: 1fyv_A Length = 178

 Score = 48.0 bits (114), Expect = 4e-07
 Identities = 24/109 (22%), Positives = 46/109 (42%), Gaps = 5/109 (4%)

Query: 18  RPRNNKKYEVFVSFRGEDTRDKFTSHLYSAL--SRQSIQTFIDDQ-LNRGDEISQSLVNA 74
           + + N ++  F+S+   D      + L   L     SI   + +   + G  IS+++V+ 
Sbjct: 29  QLKRNVRFHAFISYSEHD-SLWVKNELIPNLEKEDGSILICLYESYFDPGKSISENIVSF 87

Query: 75  IEASAISVIIFSESYTSSRWCVDELVKIL-ECKKEYAQIVIPVLYRVDP 122
           IE S  S+ + S ++  + WC  E          E +  +I +L    P
Sbjct: 88  IEKSYKSIFVLSPNFVQNEWCHYEFYFAHHNLFHENSDHIILILLEPIP 136

>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 = 41.8 bits (97), Expect = 1e-04
 Identities = 42/227 (18%), Positives = 76/227 (33%), Gaps = 79/227 (34%)

Query: 9   HRSTSLGLIRPRNNKKYEVFVS-----FRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNR 63
           H     G  + +      VF       F  +D +D       S LS++ I    D  +  
Sbjct: 6   HMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQD----MPKSILSKEEI----DHIIMS 57

Query: 64  GDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKE--YAQIVIPVLYRVD 121
            D +S +L            +F        W        L  K+E    + V  VL R++
Sbjct: 58  KDAVSGTLR-----------LF--------WT-------LLSKQEEMVQKFVEEVL-RIN 90

Query: 122 PSDVRNQTGSFGDSFSKL-EEFKEAAELEECFEGSSQFVWLSFSEHQRLLD--EVFRPSD 178
                     +    S +  E ++ + +   +            +  RL +  +VF   +
Sbjct: 91  ----------YKFLMSPIKTEQRQPSMMTRMYI----------EQRDRLYNDNQVFAKYN 130

Query: 179 NKNQLAGVESRVEEI----ESLLGVKSKDVYALGIWGIGGIGKTKIA 221
                  V SR++      ++LL ++      + I G+ G GKT +A
Sbjct: 131 -------V-SRLQPYLKLRQALLELRPAK--NVLIDGVLGSGKTWVA 167

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score = 41.1 bits (96), Expect = 2e-04
 Identities = 21/115 (18%), Positives = 39/115 (33%), Gaps = 13/115 (11%)

Query: 124 DVRNQTGSFGDSFSKLEEFKEAAELEECFEGSSQFVWLSFSEHQRLLDEVFRPSDNKNQL 183
              ++ G   D F+   +   A  LE+  + +             +  +  R   ++  L
Sbjct: 63  RQASELGPLIDFFNYNNQSHLADFLEDYIDFAINE--PDLLRPVVIAPQFSRQMLDRKLL 120

Query: 184 AG----------VESRVEEI-ESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK 227
            G           E  V+ + + L  +   D + L + G  G GK+ IA     K
Sbjct: 121 LGNVPKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSK 175

>2js7_A Myeloid differentiation primary response protein MYD88; MYD88_human, TIR domain, TOLL like receptor adaptor domain, innate immune signaling; NMR {Homo sapiens} PDB: 2z5v_A Length = 160

 Score = 38.6 bits (90), Expect = 5e-04
 Identities = 17/112 (15%), Positives = 43/112 (38%), Gaps = 7/112 (6%)

Query: 20  RNNKKYEVFVSFRGEDTRDKFTSHLYSAL--SRQSIQTFIDDQ-LNRGDEISQSLVNAIE 76
              ++++ F+ +   D   +F   +   L  +   ++  + D+ +  G  +       IE
Sbjct: 12  HMPERFDAFICYCPSDI--QFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIE 69

Query: 77  A-SAISVIIFSESYTSSRWCVDELVKIL-ECKKEYAQIVIPVLYRVDPSDVR 126
                 V++ S+ Y  S+ C  +    L      + + +IP+ Y+    +  
Sbjct: 70  KRCRRMVVVVSDDYLQSKECDFQTKFALSLSPGAHQKRLIPIKYKAMKKEFP 121

>1fyx_A TOLL-like receptor 2; beta-alpha-beta fold, signaling protein; 2.80A {Homo sapiens} SCOP: c.23.2.1 PDB: 1fyw_A 1o77_A Length = 149

 Score = 37.5 bits (87), Expect = 9e-04
 Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 4/82 (4%)

Query: 21 NNKKYEVFVSFRGEDTRDKFTSHLYSAL--SRQSIQTFIDDQ-LNRGDEISQSLVNAIEA 77
           N  Y+ FVS+   D      + +   L       +  +  +    G  I  +++++IE 
Sbjct: 2  RNIXYDAFVSYSERD-AYWVENLMVQELENFNPPFKLXLHKRDFIHGKWIIDNIIDSIEK 60

Query: 78 SAISVIIFSESYTSSRWCVDEL 99
          S  +V + SE++  S W   EL
Sbjct: 61 SHKTVFVLSENFVKSEWXKYEL 82

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	233
3ozi_A	204	L6TR; plant TIR domain, plant protein; 2.30A {Linu	100.0
3jrn_A	176	AT1G72930 protein; TIR domain arabidopsis thaliana	100.0
3h16_A	154	TIR protein; bacteria TIR domain, signaling protei	99.97
3ub2_A	146	TOLL/interleukin-1 receptor domain-containing ADA	99.94
1fyx_A	149	TOLL-like receptor 2; beta-alpha-beta fold, signal	99.9
2js7_A	160	Myeloid differentiation primary response protein M	99.9
2j67_A	178	TOLL like receptor 10; TIR, IL-1, TLR10, membrane,	99.89
1t3g_A	159	X-linked interleukin-1 receptor accessory protein-	99.89
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.71
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	98.92
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	98.75
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	98.74
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	98.49
1eiw_A	111	Hypothetical protein MTH538; CHEY-like fold, flavo	98.01
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	97.93
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	97.9
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	97.88
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	97.87
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	97.81
2chg_A	226	Replication factor C small subunit; DNA-binding pr	97.75
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	97.73
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.72
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	97.69
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	97.57
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	97.42
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	97.41
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.36
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.36
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.35
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.34
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.31
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.28
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.23
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.21
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.16
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	97.09
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.08
2chq_A	319	Replication factor C small subunit; DNA-binding pr	97.08
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	97.03
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.03
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.03
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.0
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	96.99
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.99
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	96.98
3pvs_A	447	Replication-associated recombination protein A; ma	96.92
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	96.92
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	96.88
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.88
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	96.87
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	96.86
3co5_A	143	Putative two-component system transcriptional RES	96.86
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.85
3bos_A	242	Putative DNA replication factor; P-loop containing	96.84
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	96.82
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.71
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.7
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	96.68
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	96.67
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	96.64
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.63
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.56
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	96.56
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.53
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	96.51
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.5
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	96.49
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.47
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	96.42
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	96.39
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.39
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.38
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	96.37
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	96.36
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.33
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	96.32
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	96.32
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	96.31
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	96.3
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	96.29
2r44_A	331	Uncharacterized protein; putative ATPase, structur	96.23
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	96.2
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.12
3hyn_A	189	Putative signal transduction protein; DUF1863 fami	96.08
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	95.98
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	95.92
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	95.87
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.77
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	95.74
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	95.72
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	95.7
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	95.66
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	95.66
1tue_A	212	Replication protein E1; helicase, replication, E1E	95.64
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.57
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	95.54
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	95.54
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	95.49
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	95.47
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	95.44
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	95.43
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	95.4
3fwy_A	314	Light-independent protochlorophyllide reductase I	95.4
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	95.33
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	95.3
1puj_A	282	YLQF, conserved hypothetical protein YLQF; structu	95.27
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.22
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	95.21
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	95.18
2qgz_A	308	Helicase loader, putative primosome component; str	95.17
2xxa_A	433	Signal recognition particle protein; protein trans	95.16
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	95.15
2hf9_A	226	Probable hydrogenase nickel incorporation protein	95.14
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	95.13
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	95.13
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	95.11
2og2_A	359	Putative signal recognition particle receptor; nuc	95.11
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	95.09
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	95.03
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	94.92
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	94.91
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	94.91
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	94.86
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	94.8
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.74
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	94.72
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	94.72
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	94.64
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	94.62
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	94.6
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	94.6
3end_A	307	Light-independent protochlorophyllide reductase ir	94.55
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	94.53
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	94.53
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	94.52
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.52
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.48
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	94.46
1g6h_A	257	High-affinity branched-chain amino acid transport	94.45
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	94.42
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	94.42
1ji0_A	240	ABC transporter; ATP binding protein, structural g	94.4
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	94.4
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	94.32
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.31
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	94.29
2hjg_A	436	GTP-binding protein ENGA; GTPase ENGA KH-domain, h	94.28
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	94.24
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	94.23
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	94.18
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.18
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	94.16
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	94.16
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	94.15
2ged_A	193	SR-beta, signal recognition particle receptor beta	94.12
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	94.1
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.1
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	94.07
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	94.05
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	94.04
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	94.02
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	93.94
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	93.88
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	93.83
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	93.79
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	93.74
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	93.48
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	93.45
1u94_A	356	RECA protein, recombinase A; homologous recombinat	93.44
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	93.36
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	93.34
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	93.33
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	93.29
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	93.26
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	93.26
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	93.23
2r6a_A	454	DNAB helicase, replicative helicase; replication,	93.22
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	93.15
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	93.13
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	93.11
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	93.09
2z43_A	324	DNA repair and recombination protein RADA; archaea	93.01
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	93.01
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	92.94
2ewv_A	372	Twitching motility protein PILT; pilus retraction	92.79
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	92.78
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	92.66
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	92.66
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	92.6
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	92.57
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	92.54
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	92.43
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	92.32
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	92.32
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	92.31
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	92.3
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	92.27
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	92.15
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	92.1
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	92.06
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	92.03
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	92.0
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	91.94
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	91.93
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	91.84
1p9r_A	418	General secretion pathway protein E; bacterial typ	91.78
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	91.74
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	91.72
3ez2_A	398	Plasmid partition protein A; type IA, DNA binding,	91.69
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	91.59
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	91.53
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	91.36
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	91.3
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	91.29
1xp8_A	366	RECA protein, recombinase A; recombination, radior	91.23
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	91.17
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	91.05
2oze_A	298	ORF delta'; para, walker type atpases, DNA segrega	91.04
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	91.01
4dcu_A	456	GTP-binding protein ENGA; GTPase, GDP, protein bin	90.99
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	90.87
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	90.86
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	90.55
3cio_A	299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	90.49
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	90.44
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	90.4
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	90.25
3cnl_A	262	YLQF, putative uncharacterized protein; circular p	90.15
2qag_A	361	Septin-2, protein NEDD5; cell cycle, cell division	90.04
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	89.93
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	89.91
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	89.74
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	89.65
3bfv_A	271	CAPA1, CAPB2, membrane protein CAPA1, protein tyro	89.62
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	89.62
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	89.14
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	89.14
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	88.84
3ice_A	422	Transcription termination factor RHO; transcriptio	88.82
2yl4_A	595	ATP-binding cassette SUB-family B member 10, mitoc	88.57
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	88.31
1of1_A	376	Thymidine kinase; transferase, antiviral drug, enz	88.2
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	88.16
1udx_A	416	The GTP-binding protein OBG; TGS domain, riken str	88.0
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	87.97
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	87.6
3o47_A	329	ADP-ribosylation factor GTPase-activating protein	87.56
2iw3_A	986	Elongation factor 3A; acetylation, ATP-binding, pr	87.43
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	87.4
4aby_A	415	DNA repair protein RECN; hydrolase, double strand	87.29
1zcb_A	362	G alpha I/13; GTP-binding, lipoprotein, membrane,	87.17
3q5d_A	447	Atlastin-1; G protein, GTPase, GDP/GTP binding, hy	86.96
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	86.87
3dpu_A	535	RAB family protein; roccor, G-domain, COR, GTP-bin	86.26
3ez9_A	403	Para; DNA binding, winged-HTH, partition, biosynth	86.17
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	86.05
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	85.7
3szr_A	608	Interferon-induced GTP-binding protein MX1; interf	85.59
3l0i_B	199	RAS-related protein RAB-1A; GEF-GDF-RAB complex, G	85.37
2iw3_A	986	Elongation factor 3A; acetylation, ATP-binding, pr	85.29
3ec1_A	369	YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase	84.77
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	84.52
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	84.07
3geh_A	462	MNME, tRNA modification GTPase MNME; G protein, U3	84.01
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	83.97
3t34_A	360	Dynamin-related protein 1A, linker, dynamin-relat	83.96
3l0o_A	427	Transcription termination factor RHO; helicase, RH	83.94
1lnz_A	342	SPO0B-associated GTP-binding protein; GTPase, OBG,	83.85
4ido_A	457	Atlastin-1; GTPase, GTP/GDP binding, hydrolase; HE	83.59
3ux8_A	670	Excinuclease ABC, A subunit; UVRA, nucleotide exci	83.46
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	82.87
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	82.86
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	82.71
3h2y_A	368	GTPase family protein; GTP-binding protein YQEH, p	82.59
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	82.5
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	82.41
2qpt_A	550	EH domain-containing protein-2; protein-nucleotide	81.98
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	81.92
3ux8_A	670	Excinuclease ABC, A subunit; UVRA, nucleotide exci	81.79
3lvq_E	497	ARF-GAP with SH3 domain, ANK repeat and PH domain	81.46
1knx_A	312	Probable HPR(Ser) kinase/phosphatase; HPR kinase,	81.44
2f62_A	161	Nucleoside 2-deoxyribosyltransferase; SGPP, struct	81.1
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	81.04
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	80.95
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	80.64
2j69_A	695	Bacterial dynamin-like protein; FZO, FZL, GTPase,	80.3
2x2e_A	353	Dynamin-1; nitration, hydrolase, membrane fission,	80.16

>3ozi_A L6TR; plant TIR domain, plant protein; 2.30A {Linum usitatissimum}

Probab=100.00  E-value=2.3e-47  Score=307.87  Aligned_cols=154  Identities=40%  Similarity=0.673  Sum_probs=141.4

Q ss_pred             CCCCcceEEEcCcccccccchHHHHHHHHhhCCCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhhHHH
Q 043980           20 RNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDE   98 (233)
Q Consensus        20 ~~~~~~dVFISy~~~D~~~~f~~~L~~~L~~~gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~~E   98 (233)
                      ++.++|||||||+++|+++.|++||+.+|+++||++|+|+ ++.+|+.|.++|.+||++|+++|+|||+||++|+||++|
T Consensus        31 ~~~~~yDVFISfrg~D~r~~Fv~~L~~aL~~~GI~~f~D~~el~~G~~I~~~l~~aIe~Sri~IvV~S~nYa~S~WCl~E  110 (204)
T 3ozi_A           31 FPSVEYEVFLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDDELLKGKEIGPNLLRAIDQSKIYVPIISSGYADSKWCLME  110 (204)
T ss_dssp             ---CCCCEEEEECHHHHTTTHHHHHHHHHHHTTCCEEEEETTTCCGGGTTTTHHHHHHHCSEEEEEECTTGGGCHHHHHH
T ss_pred             CCCcCCeEEEeccccCCCHHHHHHHHHHHHHCCCcEEEeCCccCCCCchHHHHHHHHHhCcEeeEEEEcccccCcHHHHH
Confidence            3889999999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhc-ccceeeceeeeecCCccccCCCchhhhhhHHHH-hHHHHHHHHhhhccc-----cccccchh---hHHH
Q 043980           99 LVKILECKKE-YAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEE-FKEAAELEECFEGSS-----QFVWLSFS---EHQR  168 (233)
Q Consensus        99 l~~~~~~~~~-~~~~viPIf~~v~~~~vr~~~g~~~~~f~~~e~-~~~~~e~~~~W~~AL-----~~g~~~~~---e~~~  168 (233)
                      |.+|+++.+. .+++|+||||+++|++||+|+|.||++|.+|+. +..  +++++|+.||     ++||++.+   |. +
T Consensus       111 L~~I~e~~~~~~~~~ViPIFY~VdPs~Vr~q~g~fg~af~~~~~~~~~--~~v~~Wr~AL~~va~lsG~~~~~~~~e~-~  187 (204)
T 3ozi_A          111 LAEIVRRQEEDPRRIILPIFYMVDPSDVRHQTGCYKKAFRKHANKFDG--QTIQNWKDALKKVGDLKGWHIGKNDKQG-A  187 (204)
T ss_dssp             HHHHHHHHHHCTTSEECCEEESSCHHHHHHTCTTHHHHHHHHTTTSCH--HHHHHHHHHHHHHHTSCBEEECTTSCHH-H
T ss_pred             HHHHHHHHHhcCCeeeEEEEeecCHHHHHhccccHHHHHHHHHHhhCH--HHHHHHHHHHHHHhccCceecCCCCCHH-H
Confidence            9999999854 578999999999999999999999999999988 543  5799999999     89999886   77 8


Q ss_pred             hhhhhccC
Q 043980          169 LLDEVFRP  176 (233)
Q Consensus       169 ~i~~Iv~~  176 (233)
                      ++++|+.+
T Consensus       188 ~i~~Iv~d  195 (204)
T 3ozi_A          188 IADKVSAD  195 (204)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            89998854

>3jrn_A AT1G72930 protein; TIR domain arabidopsis thaliana, plant protein; 2.00A {Arabidopsis thaliana}

Probab=100.00  E-value=5.5e-46  Score=295.06  Aligned_cols=154  Identities=39%  Similarity=0.637  Sum_probs=130.1

Q ss_pred             CCCcceEEEcCcccccccchHHHHHHHHhhCCCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhhHHHH
Q 043980           21 NNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDEL   99 (233)
Q Consensus        21 ~~~~~dVFISy~~~D~~~~f~~~L~~~L~~~gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~~El   99 (233)
                      ..++|||||||+|+|+++.|++||+++|+++||++|+|+ ++.+|+.|.++|.+||++|+++|+|||+||++|+||++||
T Consensus         5 ~~~~yDVFiSfrg~D~r~~Fv~~L~~~L~~~gi~~f~D~~~l~~G~~i~~~l~~aIe~Sri~IvV~S~ny~~S~WCl~EL   84 (176)
T 3jrn_A            5 TATKYDVFLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFSPELKSPIEVSRFAVVVVSENYAASSWCLDEL   84 (176)
T ss_dssp             --CCEEEEEEECHHHHTTTHHHHHHHHHHHTTCCEECCCC--------------CCTTEEEEEEEECTTTTTCHHHHHHH
T ss_pred             CCCCCeEEEECcCcccChHHHHHHHHHHHHCCCEEEEEcccccCCCchHHHHHHHHHhCCEEEEEecCCcCCChhHHHHH
Confidence            678999999999999998999999999999999999998 9999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhcccceeeceeeeecCCccccCCCchhhhhhHHHHhHHHHHHHHhhhccc-----cccccchh-hHHHhhhhh
Q 043980          100 VKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKLEEFKEAAELEECFEGSS-----QFVWLSFS-EHQRLLDEV  173 (233)
Q Consensus       100 ~~~~~~~~~~~~~viPIf~~v~~~~vr~~~g~~~~~f~~~e~~~~~~e~~~~W~~AL-----~~g~~~~~-e~~~~i~~I  173 (233)
                      .+++++.+..+++|+||||+++|++||+|+|.||++|.+|+.. ...+++++|+.||     ++||++.+ |+ ++|++|
T Consensus        85 ~~i~~~~~~~~~~ViPIfy~V~ps~Vr~q~g~fg~af~~~~~~-~~~~~~~~Wr~AL~~va~~~G~~~~~~e~-~~i~~I  162 (176)
T 3jrn_A           85 VTIMDFEKKGSITVMPIFYGVEPNHVRWQTGVLAEQFKKHASR-EDPEKVLKWRQALTNFAQLSGDCSGDDDS-KLVDKI  162 (176)
T ss_dssp             HHHHHHHHTTSCEEEEEECSSCHHHHHHTCTHHHHHHHHHHTT-SCHHHHHHHHHHHHHHTTSCCEECCSCHH-HHHHHH
T ss_pred             HHHHhhhccCCCEEEEEEecCCHHHhhhccCcHHHHHHHHHhc-cCHHHHHHHHHHHHHHhcccceecCCCHH-HHHHHH
Confidence            9999999888899999999999999999999999999999873 3446899999999     88999865 99 999999


Q ss_pred             ccC
Q 043980          174 FRP  176 (233)
Q Consensus       174 v~~  176 (233)
                      |.+
T Consensus       163 v~~  165 (176)
T 3jrn_A          163 ANE  165 (176)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            876

>3h16_A TIR protein; bacteria TIR domain, signaling protein; 2.50A {Paracoccus denitrificans PD1222}

Probab=99.97  E-value=5e-33  Score=217.64  Aligned_cols=119  Identities=18%  Similarity=0.379  Sum_probs=110.3

Q ss_pred             CCCCcceEEEcCcccccccchHHHHHHHHhhCCCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhhHHH
Q 043980           20 RNNKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDE   98 (233)
Q Consensus        20 ~~~~~~dVFISy~~~D~~~~f~~~L~~~L~~~gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~~E   98 (233)
                      ++.++|||||||+++| +..|+.+|+.+|+++|+++|+|. ++.+|+.+.++|.++|++|+++|+|+|++|+.|.||++|
T Consensus        16 ~~~~~~dvFISy~~~D-~~~~~~~L~~~L~~~gi~v~~D~~~l~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wc~~E   94 (154)
T 3h16_A           16 TSAPPHDIFISHAWED-KADFVEALAHTLRAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKE   94 (154)
T ss_dssp             --CCSEEEEEEEEGGG-TTTTHHHHHHHHHHHTCCEECGGGEECTTCCHHHHHHHHHTSEEEEEEEEEHHHHTTCCCHHH
T ss_pred             CCCCCceEEEECcccC-hHHHHHHHHHHHHHCCCcEEEcHHhCCCccHHHHHHHHHHHhCcEEEEEeCcchhcChHHHHH
Confidence            5789999999999999 55799999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhcccceeeceeeeecCCccccCCCchhhhhhHH
Q 043980           99 LVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFSKL  139 (233)
Q Consensus        99 l~~~~~~~~~~~~~viPIf~~v~~~~vr~~~g~~~~~f~~~  139 (233)
                      +..++++....+.+|+||||+++|++|+++.+.|++.|...
T Consensus        95 l~~~~~~~~~~~~~iiPV~~~v~p~~v~~~~~~~~~~~~~~  135 (154)
T 3h16_A           95 LDGLFQLESSGRSRILPIWHKVSKDEVASFSPTMADKLAFN  135 (154)
T ss_dssp             HHHHTCCCTTSCCCEEEEEESCCTGGGTTTCCCCCSSCCEE
T ss_pred             HHHHHHHHhcCCCEEEEEEecCCHHHHhhCCccHHHHHhhh
Confidence            99999887667778999999999999999999999877643

>3ub2_A TOLL/interleukin-1 receptor domain-containing ADA protein; TIR domain, TLRS adaptor, immune system; 2.40A {Homo sapiens} PDB: 3ub3_A 3ub4_A 2y92_A

Probab=99.94  E-value=5.3e-29  Score=192.91  Aligned_cols=135  Identities=19%  Similarity=0.272  Sum_probs=95.4

Q ss_pred             CCCCcceEEEcCcccccccchHHHHHHHHhh--CCCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhhH
Q 043980           20 RNNKKYEVFVSFRGEDTRDKFTSHLYSALSR--QSIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCV   96 (233)
Q Consensus        20 ~~~~~~dVFISy~~~D~~~~f~~~L~~~L~~--~gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~   96 (233)
                      ...+.|||||||+++|.  .|+.+|+++|+.  .|+++|+|+ |+.+|+.+.++|.++|++|+++|+|+|+||++|.||.
T Consensus         6 r~~k~YDvFISy~~~D~--~~v~~L~~~Le~~~~g~~~~l~~rD~~~G~~i~~~i~~aI~~Sr~~I~VlS~~y~~S~wc~   83 (146)
T 3ub2_A            6 RWSKDYDVCVCHSEEDL--VAAQDLVSYLEGSTASLRCFLQLRDATPGGAIVSELCQALSSSHCRVLLITPGFLQDPWCK   83 (146)
T ss_dssp             TTSSSEEEEEECCGGGH--HHHHHHHHHHHC------------------CCCEEECCTTCCEEEEEEEECHHHHHCHHHH
T ss_pred             CCCCcceEEEeCChhhH--HHHHHHHHHHhCcCCCeEEEEECccccccccHHHHHHHHHHhCCEEEEEECcccccCHHHH
Confidence            46789999999999994  579999999998  599999999 9999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhcccceeeceeeeecCCccccCCCch-hhhhhHHHH-hHHHHHHHHhhhccc
Q 043980           97 DELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSF-GDSFSKLEE-FKEAAELEECFEGSS  156 (233)
Q Consensus        97 ~El~~~~~~~~~~~~~viPIf~~v~~~~vr~~~g~~-~~~f~~~e~-~~~~~e~~~~W~~AL  156 (233)
                      .|+..|+.+......+|||||++++++++......+ ...+..++. +....+.+.+|++||
T Consensus        84 ~El~~al~~~~~~~~~vIpv~~~v~~~~lp~~Lr~~~~id~~~~d~~f~~l~~~v~~~~~~~  145 (146)
T 3ub2_A           84 YQMLQALTEAPGAEGCTIPLLSGLSRAAYPPELRFMYYVDGRGPDGGFRQVKEAVMRYLQTL  145 (146)
T ss_dssp             HHHHHHHHTSSSSSSEEEEEECSCCGGGSCGGGGGSCCEETTSGGGGHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhhcCCcEEEEEcCCChhhCCHHHhCeeeeeccChHhhHHHHHHHHHHHHHhc
Confidence            999999987633333688999988766654432221 111222334 666677899999886

>1fyx_A TOLL-like receptor 2; beta-alpha-beta fold, signaling protein; 2.80A {Homo sapiens} SCOP: c.23.2.1 PDB: 1fyw_A 1o77_A

Probab=99.90  E-value=3.9e-25  Score=171.80  Aligned_cols=97  Identities=23%  Similarity=0.366  Sum_probs=88.0

Q ss_pred             CCCcceEEEcCcccccccchHHH-HHHHHhhC--CCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhhH
Q 043980           21 NNKKYEVFVSFRGEDTRDKFTSH-LYSALSRQ--SIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCV   96 (233)
Q Consensus        21 ~~~~~dVFISy~~~D~~~~f~~~-L~~~L~~~--gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~   96 (233)
                      .+++|||||||+++|.  .|+.+ |+.+|+.+  |+++|+|+ |+.+|+.+.++|.++|++|+++|+|+|+||++|.||.
T Consensus         2 ~~~~yDvFiSy~~~D~--~~v~~~L~~~Le~~~~g~~~~~~~rd~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~S~wc~   79 (149)
T 1fyx_A            2 RNIXYDAFVSYSERDA--YWVENLMVQELENFNPPFKLXLHKRDFIHGKWIIDNIIDSIEKSHKTVFVLSENFVKSEWXK   79 (149)
T ss_dssp             CSCCEEEEEECCGGGH--HHHHTHHHHHHTTSSSCCCEEEHHHHCCSSSCHHHHHHHHHHHEEEEEEEECHHHHHHHTHH
T ss_pred             CCccceEEEECCcccH--HHHHHHHHHHHhcCCCCeEEeeccccCCCchhHHHHHHHHHHHcCEEEEEeCcchhccchHH
Confidence            4678999999999994  69997 99999986  99999999 9999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhh-hcccceeeceeee
Q 043980           97 DELVKILECK-KEYAQIVIPVLYR  119 (233)
Q Consensus        97 ~El~~~~~~~-~~~~~~viPIf~~  119 (233)
                      .|+..|+... +.++.+|||||++
T Consensus        80 ~El~~a~~~~~~~~~~~vIpv~~~  103 (149)
T 1fyx_A           80 YELDFSHFRLFDENNDAAILILLE  103 (149)
T ss_dssp             HHSCCSCCTTCGGGTTCCEEEESS
T ss_pred             HHHHHHHHHHHhcCCCEEEEEEec
Confidence            9999887533 4556789999976

>2js7_A Myeloid differentiation primary response protein MYD88; MYD88_human, TIR domain, TOLL like receptor adaptor domain, innate immune signaling; NMR {Homo sapiens} PDB: 2z5v_A

Probab=99.90  E-value=8.3e-25  Score=171.83  Aligned_cols=99  Identities=17%  Similarity=0.306  Sum_probs=89.7

Q ss_pred             CCCcceEEEcCcccccccchHHHHHHHHhhC--CCeEEEeC-ccCCCcchHHHHHHHHH-hcCceEEEeecCCCCchhhH
Q 043980           21 NNKKYEVFVSFRGEDTRDKFTSHLYSALSRQ--SIQTFIDD-QLNRGDEISQSLVNAIE-ASAISVIIFSESYTSSRWCV   96 (233)
Q Consensus        21 ~~~~~dVFISy~~~D~~~~f~~~L~~~L~~~--gi~~~~d~-~~~~G~~~~~~i~~~i~-~s~~~i~v~S~~y~~S~wc~   96 (233)
                      .++.|||||||+++|  ..||.+|+++|+++  |+++|+|+ |+.+|+.+.++|.++|+ .|+++|+|+|++|++|.||.
T Consensus        13 ~~~~yDvFISys~~D--~~fv~~L~~~Le~~~~g~~~~~~~rd~~~G~~i~~~i~~~I~~~Sr~~IvVlS~~y~~S~wc~   90 (160)
T 2js7_A           13 MPERFDAFICYCPSD--IQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVSDDYLQSKECD   90 (160)
T ss_dssp             CTTCEEEEEECCGGG--HHHHHHHHHHHHTSSSCCCCEESCCSSSSSCSCCCCCGGGHHHHEEEEEEECCHHHHHSHHHH
T ss_pred             CCcceEEEEEccccc--HHHHHHHHHHHhcCCCceEEEEeCCCCCCCCcHHHHHHHHHHHhCCEEEEEECcchhcCHHHH
Confidence            468999999999999  67999999999985  69999998 99999999999999999 79999999999999999999


Q ss_pred             HHHHHHHHhh-hcccceeeceeeeec
Q 043980           97 DELVKILECK-KEYAQIVIPVLYRVD  121 (233)
Q Consensus        97 ~El~~~~~~~-~~~~~~viPIf~~v~  121 (233)
                      .|+..|+.+. +.++.+||||+|+.-
T Consensus        91 ~El~~a~~~~~~~~~~~vIpV~~~~~  116 (160)
T 2js7_A           91 FQTKFALSLSPGAHQKRLIPIKYKAM  116 (160)
T ss_dssp             HHHHHHHHHCTTHHHHTEEEEESSCC
T ss_pred             HHHHHHHHHHHccCCCEEEEEEEccc
Confidence            9999999875 445668999998753

>2j67_A TOLL like receptor 10; TIR, IL-1, TLR10, membrane, innate immunity, immune response, leucine-rich repeat, glycoprotein, transmembrane; 2.20A {Homo sapiens} PDB: 1fyv_A

Probab=99.89  E-value=1.1e-24  Score=173.78  Aligned_cols=98  Identities=23%  Similarity=0.451  Sum_probs=85.0

Q ss_pred             CCCCcceEEEcCcccccccchHHH-HHHHHhh--CCCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhh
Q 043980           20 RNNKKYEVFVSFRGEDTRDKFTSH-LYSALSR--QSIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWC   95 (233)
Q Consensus        20 ~~~~~~dVFISy~~~D~~~~f~~~-L~~~L~~--~gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc   95 (233)
                      +.++.|||||||+++|  ..||.+ |+++|+.  +|+++|+|+ |+.+|+.+.++|.++|++|+++|+|+|+||++|.||
T Consensus        31 ~~~~~yDvFISys~~D--~~fv~~~L~~~LE~~~~g~~~~l~~rD~~~G~~i~~~i~~aI~~Sr~~IvVlS~~yl~S~wc  108 (178)
T 2j67_A           31 KRNVRFHAFISYSEHD--SLWVKNELIPNLEKEDGSILICLYESYFDPGKSISENIVSFIEKSYKSIFVLSPNFVQNEWC  108 (178)
T ss_dssp             CCSCCEEEEEECCGGG--HHHHHHTHHHHHTTCC-CCCEEEHHHHCCTTSCHHHHHHHHHHTEEEEEEEECHHHHHHTGG
T ss_pred             CCCccceEEEECCCCC--HHHHHHHHHHHHhcccCCeEEEEecccCCCCccHHHHHHHHHHhCCEEEEEecccccccchH
Confidence            4678999999999999  479975 9999998  899999999 999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhh-hcccceeeceeee
Q 043980           96 VDELVKILECK-KEYAQIVIPVLYR  119 (233)
Q Consensus        96 ~~El~~~~~~~-~~~~~~viPIf~~  119 (233)
                      ..|+..|+.+. +.++.+|||||++
T Consensus       109 ~~El~~a~~~~~~~~~~~vIpV~~~  133 (178)
T 2j67_A          109 HYEFYFAHHNLFHENSDHIILILLE  133 (178)
T ss_dssp             GTHHHHTTCC-------CEEEEESS
T ss_pred             HHHHHHHHHHHHhcCCCEEEEEEec
Confidence            99999998644 4556789999976

>1t3g_A X-linked interleukin-1 receptor accessory protein-like 1; TIR, IL-1RAPL, IL-1R, TLR, membrane protein; 2.30A {Homo sapiens}

Probab=99.89  E-value=5.3e-24  Score=167.07  Aligned_cols=97  Identities=20%  Similarity=0.346  Sum_probs=86.5

Q ss_pred             CcceEEEcCccccc---------ccchHHHHHH-HHh-hCCCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecCCC
Q 043980           23 KKYEVFVSFRGEDT---------RDKFTSHLYS-ALS-RQSIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSESYT   90 (233)
Q Consensus        23 ~~~dVFISy~~~D~---------~~~f~~~L~~-~L~-~~gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~   90 (233)
                      +.|||||||+++|.         +..||.+|.. .|+ ..|+++|+|+ |+.+|+.+.++|.++|++|+.+|+|+|+||+
T Consensus         1 k~yDaFISy~~~D~~wv~~~~~~~~~fv~~ll~~~LE~~~g~~l~~~~rD~~~G~~i~~~i~~~I~~Sr~~IvVlS~~y~   80 (159)
T 1t3g_A            1 KDYDAYLSYTKVDPDQWNQETGEEERFALEILPDMLEKHYGYKLFIPDRDLIPTGTYIEDVARCVDQSKRLIIVMTPNYV   80 (159)
T ss_dssp             CCBSEEEECCCCC-------CCSHHHHHHTHHHHHHHHTSCCCEECHHHHCCCCTTHHHHHHHHHHTBSEEEEEECHHHH
T ss_pred             CCceEEEeCccccchhhhccchhhHHHHHHHHHHHHcCCCCeEEEEEcccccCccchHHHHHHHHHHcCEEEEEEccchh
Confidence            57999999999996         2568888665 699 7999999999 9999999999999999999999999999997


Q ss_pred             -CchhhHHHHHHHHHhh-hcccceeeceeee
Q 043980           91 -SSRWCVDELVKILECK-KEYAQIVIPVLYR  119 (233)
Q Consensus        91 -~S~wc~~El~~~~~~~-~~~~~~viPIf~~  119 (233)
                       .|.||..|+..|+.+. ..++.+||||++.
T Consensus        81 ~~S~wc~~El~~a~~~~~~~~~~~vI~I~~~  111 (159)
T 1t3g_A           81 VRRGWSIFELETRLRNMLVTGEIKVILIECS  111 (159)
T ss_dssp             HTTTTHHHHHSHHHHHHHHTTSSEEEEEECS
T ss_pred             hcChHHHHHHHHHHHHHHhcCCCEEEEEEec
Confidence             9999999999999876 5567789999965

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.71  E-value=5.5e-18  Score=163.65  Aligned_cols=99  Identities=16%  Similarity=0.311  Sum_probs=89.0

Q ss_pred             CCCcceEEEcCcccccccchH-HHHHHHHhh-----CCCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecCCCCch
Q 043980           21 NNKKYEVFVSFRGEDTRDKFT-SHLYSALSR-----QSIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSESYTSSR   93 (233)
Q Consensus        21 ~~~~~dVFISy~~~D~~~~f~-~~L~~~L~~-----~gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~   93 (233)
                      ..++|||||||+++|.  .|| .+|.+.|+.     .|+++|+|+ |+.||+.+.++|.++|++||++|+|+|++|+.|+
T Consensus       667 ~~~~yd~fisy~~~d~--~~v~~~l~~~Le~~~~~~~~~~~~~~~rd~~~G~~~~~~i~~~i~~sr~~i~vls~~~~~s~  744 (844)
T 3j0a_A          667 DMYKYDAYLCFSSKDF--TWVQNALLKHLDTQYSDQNRFNLCFEERDFVPGENRIANIQDAIWNSRKIVCLVSRHFLRDG  744 (844)
T ss_dssp             SCCCCSEEEECCSTTH--HHHHHTHHHHHHSTTTTTTCSCEECSSSSCCSSSCHHHHHHHHHHHSSEEEEEECTTHHHHT
T ss_pred             cceeccEEEEeeCCcH--HHHHHHHHHHHhhccccCCceEEEEEccccCCCchHHHHHHHHHHHhCeEEEEeccccccCh
Confidence            5789999999999994  577 789999985     589999999 9999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHhh-hcccceeeceeeeec
Q 043980           94 WCVDELVKILECK-KEYAQIVIPVLYRVD  121 (233)
Q Consensus        94 wc~~El~~~~~~~-~~~~~~viPIf~~v~  121 (233)
                      ||..|+..|+.+. ++++.++||||++.-
T Consensus       745 wc~~e~~~a~~~~~~~~~~~~i~i~~~~~  773 (844)
T 3j0a_A          745 WCLEAFSYAQGRCLSDLNSALIMVVVGSL  773 (844)
T ss_dssp             STTHHHHHHHSCCCCSSCTTEEEEESSCC
T ss_pred             HHHHHHHHHHHHHHHhcCCcEEEEEeccC
Confidence            9999999888665 556678999998743

>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=98.92  E-value=5.9e-10  Score=102.84  Aligned_cols=50  Identities=24%  Similarity=0.284  Sum_probs=43.1

Q ss_pred             ccccchHHHHHHHhccC-CCCeEEEEEEcCCCChHHHHHHHHHH----HHhcCCC
Q 043980          184 AGVESRVEEIESLLGVK-SKDVYALGIWGIGGIGKTKIARAIFD----KISSDFE  233 (233)
Q Consensus       184 ~g~~~~~~~l~~~l~~~-~~~~~~i~i~G~gGiGKTtla~~v~~----~~~~~f~  233 (233)
                      +||+.++++|.++|..+ ..+.++|+|+||||+||||||+++|+    +++.+|+
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~  185 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYD  185 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBS
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCC
Confidence            59999999999988654 34589999999999999999999997    5676674

>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=98.75  E-value=4.5e-09  Score=104.14  Aligned_cols=51  Identities=18%  Similarity=0.195  Sum_probs=46.0

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      |.....++||+.++++|.++|.....+.++|+|+||||+||||||+++|++
T Consensus       120 p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~  170 (1249)
T 3sfz_A          120 PQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRD  170 (1249)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCC
T ss_pred             CCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcC
Confidence            556778999999999999998766667899999999999999999999986

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=98.74  E-value=6.1e-09  Score=96.35  Aligned_cols=51  Identities=18%  Similarity=0.192  Sum_probs=45.3

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      |...+.+|||+..+++|.++|.....+.++|+|+||||+||||||.+++++
T Consensus       120 P~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  170 (591)
T 1z6t_A          120 PQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRD  170 (591)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             CCCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhc
Confidence            556788999999999999998765566899999999999999999999874

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=98.49  E-value=6.2e-08  Score=94.66  Aligned_cols=51  Identities=16%  Similarity=0.066  Sum_probs=42.3

Q ss_pred             ccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH--HhcCCC
Q 043980          182 QLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK--ISSDFE  233 (233)
Q Consensus       182 ~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~--~~~~f~  233 (233)
                      ..+||+..+++|.++|... ++.++|+|+||||+||||||+++|++  ++.+|+
T Consensus       129 ~~VGRe~eLeeL~elL~~~-d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd  181 (1221)
T 1vt4_I          129 YNVSRLQPYLKLRQALLEL-RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMD  181 (1221)
T ss_dssp             SCCCCHHHHHHHHHHHHHC-CSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHS
T ss_pred             CCCCcHHHHHHHHHHHhcc-CCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCC
Confidence            3599999999999988742 34799999999999999999999974  555553

>1eiw_A Hypothetical protein MTH538; CHEY-like fold, flavodoxin-like fold, (A/B)5 doubly wound fold, parallel beta sheet; NMR {Methanothermobacterthermautotrophicus} SCOP: c.23.3.1

Probab=98.01  E-value=4.6e-06  Score=60.71  Aligned_cols=63  Identities=5%  Similarity=-0.008  Sum_probs=49.5

Q ss_pred             CcceEEEcCcccccccchHHHHHHHHhhCCCeEEEeCccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhhHHHHHHH
Q 043980           23 KKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKI  102 (233)
Q Consensus        23 ~~~dVFISy~~~D~~~~f~~~L~~~L~~~gi~~~~d~~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~~El~~~  102 (233)
                      ++|.+||||..+| .   .+.|...|...|+..- |              ..|+.|+++|++.++....|+||..|+..+
T Consensus         3 ~~~~lFISh~~~d-~---~~~L~~~l~~~~f~~~-~--------------~~I~~~~~vIvL~G~~t~~s~wv~~EI~~A   63 (111)
T 1eiw_A            3 AEIRLYITEGEVE-D---YRVFLERLEQSGLEWR-P--------------ATPEDADAVIVLAGLWGTRRDEILGAVDLA   63 (111)
T ss_dssp             CCEEEEECCCCSH-H---HHHHHHHHHHHCSCEE-E--------------CCSSSCSEEEEEGGGTTTSHHHHHHHHHHH
T ss_pred             ceEEEEEecccHh-H---HHHHHHHHhCCCCeee-c--------------CccccCCEEEEEeCCCcCCChHHHHHHHHH
Confidence            5799999999998 2   4555555555566443 2              557899999999999999999999999877


Q ss_pred             HH
Q 043980          103 LE  104 (233)
Q Consensus       103 ~~  104 (233)
                      .+
T Consensus        64 ~~   65 (111)
T 1eiw_A           64 RK   65 (111)
T ss_dssp             TT
T ss_pred             HH
Confidence            54

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=97.93  E-value=1.1e-05  Score=70.73  Aligned_cols=51  Identities=24%  Similarity=0.264  Sum_probs=39.4

Q ss_pred             CCCccccccchHHHHHHHh-cc---C---CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLL-GV---K---SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l-~~---~---~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+..++||+.+++.+.+++ ..   +   .....+|+|+|++|+|||||++++++++.
T Consensus        20 ~p~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~   77 (412)
T 1w5s_A           20 IPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVS   77 (412)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHH
T ss_pred             CCCCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHH
Confidence            3477999999999998887 42   1   22344455599999999999999998764

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=97.90  E-value=1.2e-05  Score=69.57  Aligned_cols=51  Identities=24%  Similarity=0.436  Sum_probs=42.3

Q ss_pred             CCCccccccchHHHHHHHhccC--CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVK--SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~--~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+..++|++..++.+.+++...  ......+.|+|++|+|||||++++++.+.
T Consensus        18 ~p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~   70 (386)
T 2qby_A           18 IPDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLH   70 (386)
T ss_dssp             CCSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            4578999999999999987642  33456889999999999999999998764

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=97.88  E-value=1.8e-05  Score=61.09  Aligned_cols=49  Identities=18%  Similarity=0.318  Sum_probs=40.2

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .....++|++..++.+.+.+....  .+.+-|+|.+|+|||+||+++++.+
T Consensus        19 ~~~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~l~~~~~~~~   67 (195)
T 1jbk_A           19 GKLDPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEGLAQRI   67 (195)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ccccccccchHHHHHHHHHHhcCC--CCceEEECCCCCCHHHHHHHHHHHH
Confidence            345678999999999998876532  3456799999999999999999875

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=97.87  E-value=1e-05  Score=69.05  Aligned_cols=46  Identities=20%  Similarity=0.305  Sum_probs=39.6

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .....++||+..++.|.+++..+    +++.|+|++|+|||||++++.++
T Consensus         9 ~~~~~~~gR~~el~~L~~~l~~~----~~v~i~G~~G~GKT~Ll~~~~~~   54 (350)
T 2qen_A            9 TRREDIFDREEESRKLEESLENY----PLTLLLGIRRVGKSSLLRAFLNE   54 (350)
T ss_dssp             CSGGGSCSCHHHHHHHHHHHHHC----SEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CChHhcCChHHHHHHHHHHHhcC----CeEEEECCCcCCHHHHHHHHHHH
Confidence            34567999999999999988642    68999999999999999999875

>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=97.81  E-value=2.6e-05  Score=62.40  Aligned_cols=51  Identities=24%  Similarity=0.283  Sum_probs=41.1

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .....++|++..++.+..++..+.. ...+-|+|.+|+||||||+++++.+.
T Consensus        20 ~~~~~~~g~~~~~~~l~~~l~~~~~-~~~~ll~G~~G~GKT~l~~~~~~~~~   70 (250)
T 1njg_A           20 QTFADVVGQEHVLTALANGLSLGRI-HHAYLFSGTRGVGKTSIARLLAKGLN   70 (250)
T ss_dssp             CSGGGCCSCHHHHHHHHHHHHHTCC-CSEEEEECSTTSCHHHHHHHHHHHHH
T ss_pred             ccHHHHhCcHHHHHHHHHHHHcCCC-CeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3446789999999999988865432 34788999999999999999998764

>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=97.75  E-value=3.8e-05  Score=60.73  Aligned_cols=49  Identities=20%  Similarity=0.270  Sum_probs=39.9

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .....++|++..++.+.+++.....  ..+-|+|.+|+|||+||+++++.+
T Consensus        14 ~~~~~~~g~~~~~~~l~~~l~~~~~--~~~ll~G~~G~GKT~l~~~l~~~~   62 (226)
T 2chg_A           14 RTLDEVVGQDEVIQRLKGYVERKNI--PHLLFSGPPGTGKTATAIALARDL   62 (226)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHTTCC--CCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCHHHHcCcHHHHHHHHHHHhCCCC--CeEEEECCCCCCHHHHHHHHHHHH
Confidence            3446789999999999998875432  238899999999999999999875

>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=97.73  E-value=2.9e-05  Score=67.38  Aligned_cols=49  Identities=20%  Similarity=0.306  Sum_probs=40.7

Q ss_pred             CCccccccchHHHHHHHhcc--CCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGV--KSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~--~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +..++|++..++++..++..  .....+.+-|+|++|+||||||+++++.+
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~   69 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEI   69 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHH
Confidence            37799999999999887654  23335689999999999999999999876

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=97.72  E-value=3.5e-05  Score=59.47  Aligned_cols=49  Identities=20%  Similarity=0.295  Sum_probs=39.8

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .....++|++..++.+.+.+...  ..+.+-|+|.+|+||||||+++++.+
T Consensus        19 ~~~~~~~g~~~~~~~l~~~l~~~--~~~~vll~G~~G~GKT~la~~~~~~~   67 (187)
T 2p65_A           19 GKLDPVIGRDTEIRRAIQILSRR--TKNNPILLGDPGVGKTAIVEGLAIKI   67 (187)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHTSS--SSCEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             cccchhhcchHHHHHHHHHHhCC--CCCceEEECCCCCCHHHHHHHHHHHH
Confidence            34567899999999998887653  23456799999999999999999876

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=97.69  E-value=2.8e-05  Score=67.25  Aligned_cols=50  Identities=20%  Similarity=0.391  Sum_probs=41.7

Q ss_pred             CCCccccccchHHHHHHHhccC--CCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVK--SKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~--~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+..++|++..++++..++...  ....+.+-|+|++|+||||||+++++.+
T Consensus        17 ~p~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~   68 (387)
T 2v1u_A           17 VPDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRL   68 (387)
T ss_dssp             CCSCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHH
Confidence            4478999999999999987542  3345678899999999999999999876

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=97.57  E-value=0.00011  Score=63.65  Aligned_cols=52  Identities=21%  Similarity=0.331  Sum_probs=41.4

Q ss_pred             CCCccccccchHHHHHHHhcc----CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEIESLLGV----KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~----~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .+..++|++..++.+..++..    .....+.+.|+|.+|+|||||++++++.+..
T Consensus        15 ~p~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~   70 (389)
T 1fnn_A           15 VPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKD   70 (389)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTT
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhh
Confidence            347799999999999887764    2222348899999999999999999987643

>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=97.42  E-value=0.00018  Score=60.56  Aligned_cols=49  Identities=16%  Similarity=0.299  Sum_probs=40.0

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .....++|++..++.+..++..+..  ..+-++|.+|+||||+|+++++.+
T Consensus        18 ~~~~~~~g~~~~~~~l~~~l~~~~~--~~~ll~G~~G~GKt~la~~l~~~l   66 (323)
T 1sxj_B           18 QVLSDIVGNKETIDRLQQIAKDGNM--PHMIISGMPGIGKTTSVHCLAHEL   66 (323)
T ss_dssp             SSGGGCCSCTHHHHHHHHHHHSCCC--CCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCHHHHHCCHHHHHHHHHHHHcCCC--CeEEEECcCCCCHHHHHHHHHHHh
Confidence            3446789999999999998875432  227899999999999999999875

>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=97.41  E-value=0.0002  Score=60.49  Aligned_cols=50  Identities=24%  Similarity=0.317  Sum_probs=40.6

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      |.....++|++..++.+..++..+.  ..-+-++|.+|+||||+|+++++.+
T Consensus        21 p~~~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~la~~l~~~l   70 (327)
T 1iqp_A           21 PQRLDDIVGQEHIVKRLKHYVKTGS--MPHLLFAGPPGVGKTTAALALAREL   70 (327)
T ss_dssp             CCSTTTCCSCHHHHHHHHHHHHHTC--CCEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CCCHHHhhCCHHHHHHHHHHHHcCC--CCeEEEECcCCCCHHHHHHHHHHHh
Confidence            3445679999999999998887543  2238899999999999999999875

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.36  E-value=0.0001  Score=61.42  Aligned_cols=51  Identities=22%  Similarity=0.421  Sum_probs=39.4

Q ss_pred             CCCccccccchHHHHHHHhccC-----------CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVK-----------SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~-----------~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+++|.+..+++|.+.+...           ....+-+-|+|.+|+|||+||+++++.+.
T Consensus        15 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~   76 (285)
T 3h4m_A           15 RYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETN   76 (285)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTT
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhC
Confidence            4467899999999888766421           12345688999999999999999998754

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.36  E-value=0.00011  Score=55.36  Aligned_cols=46  Identities=22%  Similarity=0.272  Sum_probs=33.3

Q ss_pred             ccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          182 QLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       182 ~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +++|....++++.+.+..-...-.-|-|+|.+|+|||++|+++++.
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~   47 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQF   47 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHS
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHh
Confidence            5788888888888766431112223569999999999999999885

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.35  E-value=0.00011  Score=62.88  Aligned_cols=54  Identities=22%  Similarity=0.309  Sum_probs=41.5

Q ss_pred             CCCCccccccchHHHHHHHhccC---CCCeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          178 DNKNQLAGVESRVEEIESLLGVK---SKDVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~---~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      .....++|++..++.+..++...   ......+-|+|.+|+|||+||+++.+.....
T Consensus        26 ~~~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~~~~   82 (338)
T 3pfi_A           26 SNFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEMSAN   82 (338)
T ss_dssp             CSGGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHTTCC
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHhCCC
Confidence            34567899999899888877642   2234557899999999999999998875443

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.34  E-value=0.00019  Score=60.28  Aligned_cols=51  Identities=24%  Similarity=0.336  Sum_probs=39.3

Q ss_pred             CCCccccccchHHHHHHHhccC----------CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVK----------SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~----------~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-.+++|.+..++.+.+++...          ....+.+-|+|.+|+||||||+++++...
T Consensus        19 ~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~   79 (297)
T 3b9p_A           19 EWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECS   79 (297)
T ss_dssp             CGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTT
T ss_pred             CHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhC
Confidence            4477999999888888765320          11245788999999999999999998754

>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=97.31  E-value=0.00036  Score=59.67  Aligned_cols=51  Identities=18%  Similarity=0.249  Sum_probs=40.7

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |.....++|++..++.+..++..+....  +-++|.+|+||||+|+++.+.+.
T Consensus        33 p~~~~~i~g~~~~~~~l~~~l~~~~~~~--~ll~G~~G~GKT~la~~la~~l~   83 (353)
T 1sxj_D           33 PKNLDEVTAQDHAVTVLKKTLKSANLPH--MLFYGPPGTGKTSTILALTKELY   83 (353)
T ss_dssp             CSSTTTCCSCCTTHHHHHHHTTCTTCCC--EEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCHHHhhCCHHHHHHHHHHHhcCCCCE--EEEECCCCCCHHHHHHHHHHHhC
Confidence            4455678999999999998887543222  78999999999999999988753

>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=97.28  E-value=0.00018  Score=60.88  Aligned_cols=50  Identities=24%  Similarity=0.349  Sum_probs=38.6

Q ss_pred             CCccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          180 KNQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      -.+++|.+..+++|.+++..           +....+.+-|+|.+|+||||||+++++...
T Consensus        14 ~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~   74 (301)
T 3cf0_A           14 WEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQ   74 (301)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTT
T ss_pred             HHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhC
Confidence            35688999888888776542           123356788999999999999999998754

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=97.23  E-value=0.00027  Score=61.36  Aligned_cols=51  Identities=25%  Similarity=0.300  Sum_probs=39.4

Q ss_pred             CCCccccccchHHHHHHHhcc----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGV----------KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-.+++|.+..++.|.+++..          .....+.+-|+|.+|+|||+||+++++...
T Consensus        82 ~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~  142 (357)
T 3d8b_A           82 NWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQSG  142 (357)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHTT
T ss_pred             CHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHcC
Confidence            446789999989888886642          112345688999999999999999998753

>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=97.21  E-value=0.00013  Score=61.86  Aligned_cols=53  Identities=21%  Similarity=0.348  Sum_probs=40.3

Q ss_pred             CCCCccccccchHHHHHHHhccC---CCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          178 DNKNQLAGVESRVEEIESLLGVK---SKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~---~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .....++|++..++.+..++...   ......+-|+|.+|+|||+||+++++....
T Consensus         9 ~~~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~~~   64 (324)
T 1hqc_A            9 KTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGV   64 (324)
T ss_dssp             CSTTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHHTC
T ss_pred             ccHHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHhCC
Confidence            34567999998888888776531   122356779999999999999999987643

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=97.16  E-value=0.00037  Score=59.49  Aligned_cols=52  Identities=23%  Similarity=0.342  Sum_probs=39.2

Q ss_pred             CCCccccccchHHHHHHHhc----------cCCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEIESLLG----------VKSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~----------~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .-.+++|.+..++.|.+++.          ......+-+-++|.+|+|||+||+++++....
T Consensus        16 ~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~   77 (322)
T 3eie_A           16 KWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANS   77 (322)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHTC
T ss_pred             CHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHCC
Confidence            34678999998888888662          11122456789999999999999999987543

>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=97.09  E-value=0.00065  Score=58.47  Aligned_cols=51  Identities=24%  Similarity=0.283  Sum_probs=40.5

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .....++|++..++.+...+..+.. ...+-|+|..|+||||+|+++.+.+.
T Consensus        13 ~~~~~~vg~~~~~~~L~~~l~~~~~-~~~~ll~G~~G~GKT~la~~la~~l~   63 (373)
T 1jr3_A           13 QTFADVVGQEHVLTALANGLSLGRI-HHAYLFSGTRGVGKTSIARLLAKGLN   63 (373)
T ss_dssp             CSTTTSCSCHHHHHHHHHHHHHTCC-CSEEEEESCTTSSHHHHHHHHHHHHS
T ss_pred             CchhhccCcHHHHHHHHHHHHhCCC-CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3446699999999999888765432 34677999999999999999998764

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.08  E-value=0.00038  Score=57.22  Aligned_cols=51  Identities=27%  Similarity=0.315  Sum_probs=35.7

Q ss_pred             CCCccccccchHHHHHHHhcc---C-------CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGV---K-------SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~---~-------~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-.+++|.+..++++.+++..   .       ....+-+.|+|.+|+||||||+++++...
T Consensus        10 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~   70 (257)
T 1lv7_A           10 TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAK   70 (257)
T ss_dssp             CGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcC
Confidence            346688888777776654321   0       11123478999999999999999998754

>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=97.08  E-value=0.00057  Score=57.40  Aligned_cols=48  Identities=21%  Similarity=0.314  Sum_probs=38.8

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ....++|++..++.+..++..+.  ...+-++|.+|+||||+|+++++.+
T Consensus        15 ~~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKt~la~~l~~~l   62 (319)
T 2chq_A           15 TLDEVVGQDEVIQRLKGYVERKN--IPHLLFSGPPGTGKTATAIALARDL   62 (319)
T ss_dssp             SGGGSCSCHHHHHHHHTTTTTTC--CCCEEEESSSSSSHHHHHHHHHHHH
T ss_pred             CHHHHhCCHHHHHHHHHHHhCCC--CCeEEEECcCCcCHHHHHHHHHHHh
Confidence            44668999998998888876543  2237899999999999999999875

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=97.03  E-value=0.0003  Score=58.06  Aligned_cols=52  Identities=25%  Similarity=0.295  Sum_probs=37.5

Q ss_pred             CCCccccccchHHHHHHHhcc----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEIESLLGV----------KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ...+++|.+..++.+.+++..          +....+-+-|+|.+|+|||+||+++++....
T Consensus         9 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~   70 (268)
T 2r62_A            9 RFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHV   70 (268)
T ss_dssp             CSTTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTC
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCC
Confidence            346789999888888776541          1111223668999999999999999987543

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.03  E-value=0.00043  Score=58.24  Aligned_cols=47  Identities=19%  Similarity=0.290  Sum_probs=34.9

Q ss_pred             ccccccchHHHHHHHhccC-------------CCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          182 QLAGVESRVEEIESLLGVK-------------SKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       182 ~~~g~~~~~~~l~~~l~~~-------------~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .++|.+..++.+.+++..-             .....-+-|+|.+|+|||+||+++.+.+
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l   91 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLL   91 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            4688887777776654311             2234567899999999999999988875

>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=97.03  E-value=0.00053  Score=62.50  Aligned_cols=52  Identities=25%  Similarity=0.325  Sum_probs=41.3

Q ss_pred             CCCCCccccccchHHHHHHHhccCC---------------CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKS---------------KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~---------------~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      |....+++|++..++++..++....               ...+.+-|+|.+|+||||+|+++++.+
T Consensus        35 P~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l  101 (516)
T 1sxj_A           35 PTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL  101 (516)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            4445678999999999998876410               124688899999999999999999875

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.00  E-value=0.00068  Score=58.46  Aligned_cols=51  Identities=20%  Similarity=0.167  Sum_probs=37.8

Q ss_pred             CCccccccchHHHHHHH---hccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          180 KNQLAGVESRVEEIESL---LGVKSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~---l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ...++|.+..++.+..+   +..+....+.+-|+|.+|+|||+||+++.+.+..
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~~   96 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGP   96 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHCS
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            46789999877765443   3333322357889999999999999999988653

>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=96.99  E-value=0.00048  Score=59.22  Aligned_cols=50  Identities=20%  Similarity=0.288  Sum_probs=35.9

Q ss_pred             CCccccccchHHHHHHHhccC---CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          180 KNQLAGVESRVEEIESLLGVK---SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~---~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      -..++|.+..++.+...+..+   ......+.++|.+|.||||||+.+.+.+.
T Consensus        24 l~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l~   76 (334)
T 1in4_A           24 LDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQ   76 (334)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHT
T ss_pred             HHHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHhC
Confidence            355678776666665555432   12245689999999999999999998763

>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=96.99  E-value=0.00046  Score=53.57  Aligned_cols=26  Identities=35%  Similarity=0.404  Sum_probs=23.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+.|+|.+|.|||||++++++.+.
T Consensus        38 g~~~~l~G~~G~GKTtL~~~i~~~~~   63 (180)
T 3ec2_A           38 GKGLTFVGSPGVGKTHLAVATLKAIY   63 (180)
T ss_dssp             CCEEEECCSSSSSHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHH
Confidence            57899999999999999999998763

>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=96.98  E-value=0.00063  Score=58.33  Aligned_cols=49  Identities=24%  Similarity=0.292  Sum_probs=38.0

Q ss_pred             CCCCccccccchHHHHHHHh-ccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLL-GVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l-~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ....+++|.+..++.+..++ ..+.. .. +.|+|..|+||||+++.+.+.+
T Consensus        11 ~~~~~~vg~~~~~~~l~~~~~~~~~~-~~-~ll~Gp~G~GKTtl~~~la~~l   60 (354)
T 1sxj_E           11 KSLNALSHNEELTNFLKSLSDQPRDL-PH-LLLYGPNGTGKKTRCMALLESI   60 (354)
T ss_dssp             CSGGGCCSCHHHHHHHHTTTTCTTCC-CC-EEEECSTTSSHHHHHHTHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHHHhhCCCC-Ce-EEEECCCCCCHHHHHHHHHHHH
Confidence            34466889988888888877 44332 23 8899999999999999998864

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=96.92  E-value=0.00068  Score=60.83  Aligned_cols=51  Identities=22%  Similarity=0.378  Sum_probs=38.2

Q ss_pred             CCCCccccccchH---HHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          178 DNKNQLAGVESRV---EEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       178 ~~~~~~~g~~~~~---~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .....++|.+..+   ..+...+..+.  ...+-++|.+|+||||||+.+++....
T Consensus        23 ~~l~~ivGq~~~~~~~~~L~~~i~~~~--~~~vLL~GppGtGKTtlAr~ia~~~~~   76 (447)
T 3pvs_A           23 ENLAQYIGQQHLLAAGKPLPRAIEAGH--LHSMILWGPPGTGKTTLAEVIARYANA   76 (447)
T ss_dssp             CSTTTCCSCHHHHSTTSHHHHHHHHTC--CCEEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             CCHHHhCCcHHHHhchHHHHHHHHcCC--CcEEEEECCCCCcHHHHHHHHHHHhCC
Confidence            3446688887666   56666665432  467889999999999999999987543

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=96.92  E-value=0.0011  Score=59.67  Aligned_cols=48  Identities=23%  Similarity=0.392  Sum_probs=39.1

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ....++|++..++.+...|.....  .-+-++|.+|+|||+||+.+++.+
T Consensus       178 ~ld~iiGr~~~i~~l~~~l~r~~~--~~~LL~G~pG~GKT~la~~la~~l  225 (468)
T 3pxg_A          178 SLDPVIGRSKEIQRVIEVLSRRTK--NNPVLIGEPGVGKTAIAEGLAQQI  225 (468)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHCSSS--CEEEEESCTTTTTHHHHHHHHHHH
T ss_pred             CCCCccCcHHHHHHHHHHHhccCC--CCeEEECCCCCCHHHHHHHHHHHH
Confidence            345799999999999998865332  234589999999999999999986

>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=96.88  E-value=0.0009  Score=58.07  Aligned_cols=52  Identities=23%  Similarity=0.375  Sum_probs=38.5

Q ss_pred             CCCccccccchHHHHHHHhcc----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEIESLLGV----------KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .-.+++|.+..++.|.+.+..          .....+-+-++|.+|+|||+||+++++.+..
T Consensus        49 ~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~  110 (355)
T 2qp9_X           49 KWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANS  110 (355)
T ss_dssp             CGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHHTC
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCC
Confidence            346789999888888876521          1112345778999999999999999987643

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.88  E-value=0.00094  Score=52.64  Aligned_cols=25  Identities=32%  Similarity=0.432  Sum_probs=22.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      +.+-|+|.+|+||||||+++++...
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~   79 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELA   79 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHH
Confidence            6788999999999999999998753

>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=96.87  E-value=0.00053  Score=57.42  Aligned_cols=49  Identities=20%  Similarity=0.261  Sum_probs=35.8

Q ss_pred             CccccccchHHHHHHHhcc------------CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGV------------KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~------------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..++|.+..++.+...+..            ......-+-++|.+|+|||++|+++.+.+.
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~   75 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN   75 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            4578988888888765542            001134566899999999999999998754

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=96.86  E-value=0.001  Score=58.25  Aligned_cols=51  Identities=20%  Similarity=0.309  Sum_probs=39.1

Q ss_pred             CCCccccccchHHHHHHHhcc----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGV----------KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-.+++|.+..++.|.+++..          .....+-+-|+|.+|+|||+||+++.+...
T Consensus       113 ~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~~  173 (389)
T 3vfd_A          113 KFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESN  173 (389)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHTT
T ss_pred             ChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhhc
Confidence            456789999988888886621          011235788999999999999999988753

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=96.86  E-value=0.00013  Score=55.00  Aligned_cols=47  Identities=15%  Similarity=0.157  Sum_probs=31.1

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -.++|....++++.+.+..-.....-|-|+|.+|+|||++|+++++.
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~   50 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKN   50 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCT
T ss_pred             cCceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHh
Confidence            35788888888887765431111223568999999999999988753

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.85  E-value=0.00048  Score=59.10  Aligned_cols=47  Identities=13%  Similarity=0.011  Sum_probs=37.8

Q ss_pred             cccccchHHHHHHHhcc--CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          183 LAGVESRVEEIESLLGV--KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       183 ~~g~~~~~~~l~~~l~~--~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      +.||+.+.+++...|..  .......+-|+|.+|+|||++++++.+++.
T Consensus        22 L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~   70 (318)
T 3te6_A           22 LKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELI   70 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            68899999998876553  223456778999999999999999999874

>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=96.84  E-value=0.0013  Score=52.60  Aligned_cols=47  Identities=17%  Similarity=0.249  Sum_probs=31.7

Q ss_pred             Ccccccc---chHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVE---SRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~---~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..++|..   ..++.+..++...  ..+.+-|+|.+|+||||||+++++...
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~~~--~~~~~ll~G~~G~GKT~la~~l~~~~~   77 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAASGD--GVQAIYLWGPVKSGRTHLIHAACARAN   77 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHHTC--SCSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             hhccCCCCCHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            4566533   3344455544432  356788999999999999999998754

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=96.82  E-value=0.00094  Score=57.16  Aligned_cols=50  Identities=22%  Similarity=0.345  Sum_probs=37.6

Q ss_pred             CCCccccccchHHHHHHHhcc----------CCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGV----------KSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.+++|.+..++.|.+.+..          .....+-+-++|.+|+|||+||+++++..
T Consensus        10 ~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~   69 (322)
T 1xwi_A           10 KWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA   69 (322)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHT
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHc
Confidence            346788988888888765421          11224678899999999999999999875

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=96.71  E-value=0.0019  Score=53.46  Aligned_cols=50  Identities=16%  Similarity=0.088  Sum_probs=34.2

Q ss_pred             CccccccchHHHHHH-------Hhcc-CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          181 NQLAGVESRVEEIES-------LLGV-KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~-------~l~~-~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ..++|.....+++..       .+.. .......+-|+|.+|+|||+||+++++....
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~~~   90 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNF   90 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTC
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCC
Confidence            456676655555444       2221 2334677889999999999999999987543

>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=96.70  E-value=0.0023  Score=54.12  Aligned_cols=29  Identities=21%  Similarity=0.225  Sum_probs=24.5

Q ss_pred             CCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          200 KSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       200 ~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ......+|+|.|..|.||||||+.+...+
T Consensus        27 ~~~~~~ii~I~G~sGsGKSTla~~L~~~l   55 (290)
T 1odf_A           27 GNKCPLFIFFSGPQGSGKSFTSIQIYNHL   55 (290)
T ss_dssp             TCCSCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            34457899999999999999999887754

>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=96.68  E-value=0.0014  Score=56.77  Aligned_cols=47  Identities=17%  Similarity=0.140  Sum_probs=34.2

Q ss_pred             cccccchHHHHHHHhc-------------cCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          183 LAGVESRVEEIESLLG-------------VKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       183 ~~g~~~~~~~l~~~l~-------------~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ++|.+..++.+...+.             ........+-++|.+|+|||++|+++++...
T Consensus        17 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~~   76 (363)
T 3hws_A           17 VIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLD   76 (363)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             ccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHcC
Confidence            6788877777766552             1111235678899999999999999998754

>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=96.67  E-value=0.0024  Score=54.72  Aligned_cols=49  Identities=18%  Similarity=0.270  Sum_probs=37.0

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-..++|.+.-++.|...+..+.  ..-+.++|..|+||||+|+++.+.+.
T Consensus        23 ~~~~~~g~~~~~~~L~~~i~~g~--~~~~ll~Gp~G~GKTtla~~la~~l~   71 (340)
T 1sxj_C           23 TLDEVYGQNEVITTVRKFVDEGK--LPHLLFYGPPGTGKTSTIVALAREIY   71 (340)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHTTC--CCCEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             cHHHhcCcHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHHHc
Confidence            34567788777777777776543  22278999999999999999988753

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=96.64  E-value=0.0012  Score=55.37  Aligned_cols=48  Identities=15%  Similarity=0.380  Sum_probs=35.9

Q ss_pred             CccccccchHHHHHHHhccCC-------CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKS-------KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~-------~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..++|.+..++.+...+....       .....+.++|.+|+||||+|+++++.+
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~   71 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATL   71 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHH
Confidence            456788877777766554321       113578999999999999999999875

>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=96.63  E-value=0.0017  Score=54.99  Aligned_cols=52  Identities=15%  Similarity=0.080  Sum_probs=40.6

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |..-.+++|.+..++.+..++..+. ...++-+.|.+|+|||++|+++.+.+.
T Consensus        22 P~~~~~ivg~~~~~~~l~~~l~~~~-~~~~~L~~G~~G~GKT~la~~la~~l~   73 (324)
T 3u61_B           22 PSTIDECILPAFDKETFKSITSKGK-IPHIILHSPSPGTGKTTVAKALCHDVN   73 (324)
T ss_dssp             CCSTTTSCCCHHHHHHHHHHHHTTC-CCSEEEECSSTTSSHHHHHHHHHHHTT
T ss_pred             CCCHHHHhCcHHHHHHHHHHHHcCC-CCeEEEeeCcCCCCHHHHHHHHHHHhC
Confidence            3445778999999999998887543 235667778899999999999998753

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.56  E-value=0.0022  Score=61.05  Aligned_cols=48  Identities=23%  Similarity=0.392  Sum_probs=39.3

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ....++|++..++.+...|.....  .-+-++|.+|+|||++|+.+.+.+
T Consensus       178 ~ld~iiG~~~~i~~l~~~l~~~~~--~~vLL~G~pGtGKT~la~~la~~l  225 (758)
T 3pxi_A          178 SLDPVIGRSKEIQRVIEVLSRRTK--NNPVLIGEPGVGKTAIAEGLAQQI  225 (758)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHCSSS--CEEEEESCTTTTTHHHHHHHHHHH
T ss_pred             CCCCccCchHHHHHHHHHHhCCCC--CCeEEECCCCCCHHHHHHHHHHHH
Confidence            346799999999999998865332  235689999999999999999886

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.56  E-value=0.0019  Score=57.62  Aligned_cols=52  Identities=17%  Similarity=0.331  Sum_probs=39.2

Q ss_pred             CCCccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .-.++.|.+..+++|.+.+..           +-...+-+-++|.+|+|||+||+++++...-
T Consensus       170 ~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~  232 (428)
T 4b4t_K          170 TYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKA  232 (428)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTC
T ss_pred             CHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            346788999888888775432           2233566789999999999999999997543

>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=96.51  E-value=0.0014  Score=59.46  Aligned_cols=50  Identities=24%  Similarity=0.445  Sum_probs=38.6

Q ss_pred             CCccccccchHHHHHHHhccC-----------CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          180 KNQLAGVESRVEEIESLLGVK-----------SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~-----------~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...++|.+..+++|.+++..-           ....+-+-|+|.+|+|||+||+++++...
T Consensus       203 ~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~  263 (489)
T 3hu3_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETG  263 (489)
T ss_dssp             GGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCS
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhC
Confidence            356899999999988876431           22335578999999999999999988743

>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=96.50  E-value=0.0023  Score=54.28  Aligned_cols=37  Identities=22%  Similarity=0.207  Sum_probs=26.9

Q ss_pred             HHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          192 EIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       192 ~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+..++.........+-|+|.+|+||||||+++++.+
T Consensus        25 ~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~   61 (324)
T 1l8q_A           25 VVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEA   61 (324)
T ss_dssp             HHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHH
T ss_pred             HHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHH
Confidence            3444444332234678899999999999999999876

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.49  E-value=0.0022  Score=57.38  Aligned_cols=52  Identities=21%  Similarity=0.407  Sum_probs=39.4

Q ss_pred             CCCccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .-.++.|.+..+++|.+.+..           +....+=|-++|.+|.|||+||+++++....
T Consensus       179 ~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~  241 (437)
T 4b4t_L          179 TFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGA  241 (437)
T ss_dssp             CSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTC
T ss_pred             ChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCC
Confidence            347788999888888775432           2223467788999999999999999997544

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.47  E-value=0.0019  Score=57.13  Aligned_cols=53  Identities=21%  Similarity=0.393  Sum_probs=39.2

Q ss_pred             CCCccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          179 NKNQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      .-.++.|.+..+++|.+.+..           +-...+=+=++|.+|.|||.||+++++.....
T Consensus       146 ~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~  209 (405)
T 4b4t_J          146 TYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCK  209 (405)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCE
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCC
Confidence            336788999888888775432           22234557789999999999999999975443

>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=96.42  E-value=0.0019  Score=57.71  Aligned_cols=50  Identities=22%  Similarity=0.345  Sum_probs=38.4

Q ss_pred             CCCccccccchHHHHHHHhcc----------CCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGV----------KSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.+++|.+..++.|.+.+..          .....+-+-++|.+|+|||+||+++++..
T Consensus       132 ~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~  191 (444)
T 2zan_A          132 KWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA  191 (444)
T ss_dssp             CGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHc
Confidence            446789999888888876521          11224678899999999999999999875

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=96.39  E-value=0.0037  Score=51.00  Aligned_cols=27  Identities=26%  Similarity=0.272  Sum_probs=22.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .+-+-|+|.+|+|||+||+++++....
T Consensus        39 ~~~vll~G~~GtGKT~la~~la~~~~~   65 (262)
T 2qz4_A           39 PKGALLLGPPGCGKTLLAKAVATEAQV   65 (262)
T ss_dssp             CCEEEEESCTTSSHHHHHHHHHHHHTC
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            345679999999999999999987543

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.39  E-value=0.0024  Score=57.35  Aligned_cols=50  Identities=20%  Similarity=0.417  Sum_probs=38.6

Q ss_pred             CccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          181 NQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .++.|.+..+++|.+.+..           +-...+-|=++|.+|.|||+||+++++....
T Consensus       209 ~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~  269 (467)
T 4b4t_H          209 SDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDA  269 (467)
T ss_dssp             SSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTC
T ss_pred             HHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCC
Confidence            6788999888888775321           2233566779999999999999999997544

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.38  E-value=0.0027  Score=56.67  Aligned_cols=52  Identities=21%  Similarity=0.347  Sum_probs=39.1

Q ss_pred             CCCccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .-.++.|.+..+++|.+.+..           +-...+-|=++|.+|.|||+||+++++....
T Consensus       179 t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~  241 (434)
T 4b4t_M          179 TYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNA  241 (434)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTC
T ss_pred             ChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCC
Confidence            347788999888888764321           2223567788999999999999999997544

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=96.37  E-value=0.0022  Score=54.07  Aligned_cols=29  Identities=34%  Similarity=0.588  Sum_probs=24.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      ..+.+-++|.+|+|||+||+++++.+...
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~l~~~   63 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRKMGIN   63 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHHHTCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            35678889999999999999999986543

>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=96.36  E-value=0.0016  Score=53.30  Aligned_cols=48  Identities=27%  Similarity=0.439  Sum_probs=32.2

Q ss_pred             CccccccchHHHHHHHhcc--C--------CCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGV--K--------SKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~--~--------~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+++|.+..+.++.++...  .        -.-.+-+.|+|.+|.|||||++++.+..
T Consensus        16 ~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~   73 (254)
T 1ixz_A           16 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA   73 (254)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHh
Confidence            5677877666666554321  0        0001228899999999999999998864

>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=96.33  E-value=0.0028  Score=61.22  Aligned_cols=50  Identities=18%  Similarity=0.322  Sum_probs=40.3

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +.....++|++..++.+.+.|....  .+-+-++|.+|+||||||+.+.+.+
T Consensus       166 ~~~ld~viGr~~~i~~l~~~l~~~~--~~~vlL~G~pG~GKT~la~~la~~l  215 (854)
T 1qvr_A          166 EGKLDPVIGRDEEIRRVIQILLRRT--KNNPVLIGEPGVGKTAIVEGLAQRI  215 (854)
T ss_dssp             TTCSCCCCSCHHHHHHHHHHHHCSS--CCCCEEEECTTSCHHHHHHHHHHHH
T ss_pred             cCCCcccCCcHHHHHHHHHHHhcCC--CCceEEEcCCCCCHHHHHHHHHHHH
Confidence            3445678999999999999876533  2345789999999999999999876

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=96.32  E-value=0.0034  Score=52.48  Aligned_cols=22  Identities=32%  Similarity=0.416  Sum_probs=20.4

Q ss_pred             EEEEcCCCChHHHHHHHHHHHH
Q 043980          207 LGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       207 i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +.++|.+|.|||||++++....
T Consensus        47 vlL~Gp~GtGKTtLakala~~~   68 (274)
T 2x8a_A           47 VLLAGPPGCGKTLLAKAVANES   68 (274)
T ss_dssp             EEEESSTTSCHHHHHHHHHHHT
T ss_pred             EEEECCCCCcHHHHHHHHHHHc
Confidence            8999999999999999998864

>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=96.32  E-value=0.0033  Score=56.84  Aligned_cols=50  Identities=24%  Similarity=0.375  Sum_probs=35.8

Q ss_pred             CCccccccchHHHHHHHhcc----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          180 KNQLAGVESRVEEIESLLGV----------KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      -.+++|.+..++++.+++..          +..-.+-+-|+|.+|.||||||+++++...
T Consensus        15 f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~   74 (476)
T 2ce7_A           15 FKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEAN   74 (476)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             HHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcC
Confidence            35688988877777665432          111123477999999999999999998754

>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=96.31  E-value=0.0035  Score=56.16  Aligned_cols=50  Identities=28%  Similarity=0.284  Sum_probs=37.0

Q ss_pred             CCccccccchHHHHHHHhc---cCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          180 KNQLAGVESRVEEIESLLG---VKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~---~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...++|.+..++.+..++.   .+....+-+-++|.+|+|||+||+++.+.+.
T Consensus        36 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~l~   88 (456)
T 2c9o_A           36 ASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELG   88 (456)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHHhC
Confidence            3678999987776655433   2322234577899999999999999998765

>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=96.30  E-value=0.0047  Score=58.72  Aligned_cols=49  Identities=27%  Similarity=0.304  Sum_probs=39.7

Q ss_pred             CCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          178 DNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .....++|++..++.+.+.|....  ..-+-++|.+|+||||+|+.+.+.+
T Consensus       183 ~~~d~~iGr~~~i~~l~~~l~~~~--~~~vlL~G~~GtGKT~la~~la~~l  231 (758)
T 1r6b_X          183 GGIDPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEGLAWRI  231 (758)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCCCccCCHHHHHHHHHHHhccC--CCCeEEEcCCCCCHHHHHHHHHHHH
Confidence            344678999999999998876542  2345689999999999999999876

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=96.29  E-value=0.0024  Score=53.05  Aligned_cols=49  Identities=27%  Similarity=0.388  Sum_probs=32.7

Q ss_pred             CCccccccchHHHHHHHhccC----------CCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGVK----------SKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~----------~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+++|.+..++++..+...-          -.-.+-+.|+|.+|.|||||++++.+.+
T Consensus        39 ~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~   97 (278)
T 1iy2_A           39 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA   97 (278)
T ss_dssp             GGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHc
Confidence            356777776666665543210          0001228899999999999999998864

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=96.23  E-value=0.0029  Score=53.84  Aligned_cols=46  Identities=11%  Similarity=0.130  Sum_probs=35.4

Q ss_pred             CCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          180 KNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...++|++..++.+...+..+    .-+-++|.+|+|||+||+++.+.+.
T Consensus        26 ~~~i~g~~~~~~~l~~~l~~~----~~vll~G~pGtGKT~la~~la~~~~   71 (331)
T 2r44_A           26 GKVVVGQKYMINRLLIGICTG----GHILLEGVPGLAKTLSVNTLAKTMD   71 (331)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHT----CCEEEESCCCHHHHHHHHHHHHHTT
T ss_pred             ccceeCcHHHHHHHHHHHHcC----CeEEEECCCCCcHHHHHHHHHHHhC
Confidence            356789888887777655432    2466899999999999999988654

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=96.20  E-value=0.0037  Score=54.28  Aligned_cols=25  Identities=24%  Similarity=0.361  Sum_probs=21.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+-++|.+|+|||++|+++++.+.
T Consensus        73 ~~ill~Gp~GtGKT~la~~la~~l~   97 (376)
T 1um8_A           73 SNILLIGPTGSGKTLMAQTLAKHLD   97 (376)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhC
Confidence            4577999999999999999998754

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.12  E-value=0.003  Score=47.85  Aligned_cols=26  Identities=23%  Similarity=0.440  Sum_probs=23.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ....++|+|..|.|||||++++++.+
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~   60 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQA   60 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHH
Confidence            35688999999999999999999865

>3hyn_A Putative signal transduction protein; DUF1863 family protein, nucleotide-binding protein, structur genomics; HET: MSE; 1.20A {Eubacterium rectale atcc 33656}

Probab=96.08  E-value=0.015  Score=45.46  Aligned_cols=64  Identities=14%  Similarity=0.118  Sum_probs=47.7

Q ss_pred             hHHHHHHHHhhCCCeEEEeC-ccC-------C-CcchHHHHHHHHHhcCceEEEeecCCCCchhhHHHHHHHH
Q 043980           40 FTSHLYSALSRQSIQTFIDD-QLN-------R-GDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKIL  103 (233)
Q Consensus        40 f~~~L~~~L~~~gi~~~~d~-~~~-------~-G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~~El~~~~  103 (233)
                      ....|..--+...+--|.|. +..       . -..|-+.+.+.|..|..+|+++|++...|.|..+|+..++
T Consensus        33 yy~lL~aWk~n~n~F~F~D~Hd~~y~vrDsS~~e~tIKrrLReRI~~Sk~vIllIs~~T~~s~~v~wEIe~Ai  105 (189)
T 3hyn_A           33 YYNMLRMWKGEDNSFPFNDAHDKTYNVRDGSDWEKTLKPRLHTRLDNSKNIILFLSSITANSRALREEMNYGI  105 (189)
T ss_dssp             HHHHHHHHHHHCTTSSCCBTTTTCCCTTSCCCTTTTHHHHHHHHHHTEEEEEEECCTTCCCCHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCceeecchhhccccccccccHHHHHHHHHHHHHHhcCcEEEEEecCccccchhHHHHHHHH
Confidence            34555444444455556664 442       2 2347789999999999999999999999999999999887

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.98  E-value=0.0058  Score=54.42  Aligned_cols=52  Identities=27%  Similarity=0.465  Sum_probs=38.9

Q ss_pred             CCCccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .-.++.|.+..+++|.+.+..           +..-.+=|=++|.+|.|||.||+++++....
T Consensus       180 ~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~  242 (437)
T 4b4t_I          180 SYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSA  242 (437)
T ss_dssp             CGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTC
T ss_pred             cceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCC
Confidence            346788999888888774431           1223466889999999999999999997544

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=95.92  E-value=0.0033  Score=51.97  Aligned_cols=26  Identities=19%  Similarity=0.341  Sum_probs=22.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...|+|.|+.|.||||+++.+...+.
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~lg   73 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARSLG   73 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcC
Confidence            35799999999999999999987643

>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=95.87  E-value=0.0062  Score=54.35  Aligned_cols=26  Identities=31%  Similarity=0.399  Sum_probs=23.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+-|+|.+|+||||||+++++.+.
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~l~  155 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNYVV  155 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            56788999999999999999998763

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=95.77  E-value=0.011  Score=45.18  Aligned_cols=29  Identities=24%  Similarity=0.381  Sum_probs=24.3

Q ss_pred             CCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          200 KSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       200 ~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-..-.+++|.|..|.|||||.+.+..-+
T Consensus        29 ~i~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           29 HTEKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             CCSSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             ccCCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            33456799999999999999999988754

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=95.74  E-value=0.013  Score=50.37  Aligned_cols=26  Identities=23%  Similarity=0.374  Sum_probs=23.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+++|+|..|.||||+++.+...+
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~l  153 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANWL  153 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            46899999999999999999987754

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=95.72  E-value=0.0056  Score=55.67  Aligned_cols=50  Identities=26%  Similarity=0.403  Sum_probs=35.1

Q ss_pred             CCCccccccchHHHHHHHhcc--C--------CCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          179 NKNQLAGVESRVEEIESLLGV--K--------SKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~--~--------~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+++|.+..+.++.+++..  .        ..-.+-+.|+|.+|.||||||+++++..
T Consensus        29 ~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~   88 (499)
T 2dhr_A           29 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA   88 (499)
T ss_dssp             CTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHT
T ss_pred             CHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            346688888777777664321  0        0011238899999999999999999864

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=95.70  E-value=0.0087  Score=51.03  Aligned_cols=28  Identities=21%  Similarity=0.391  Sum_probs=24.1

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ....++||.|..|.|||||++.+...+.
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHhhcc
Confidence            3468999999999999999999887553

>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=95.66  E-value=0.0062  Score=58.42  Aligned_cols=49  Identities=24%  Similarity=0.465  Sum_probs=37.2

Q ss_pred             CccccccchHHHHHHHhcc-----------CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGV-----------KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~-----------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .++.|.+..+++|.+++..           +....+-|-++|.+|+|||+||+++++...
T Consensus       204 ~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg  263 (806)
T 3cf2_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETG  263 (806)
T ss_dssp             GGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTT
T ss_pred             hhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhC
Confidence            5678899888888775431           112346688999999999999999998644

>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=95.66  E-value=0.015  Score=50.25  Aligned_cols=37  Identities=24%  Similarity=0.304  Sum_probs=27.1

Q ss_pred             HHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          192 EIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       192 ~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ++.+.+........+|+|+|.+|+|||||+..+...+
T Consensus        67 ~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~~l  103 (355)
T 3p32_A           67 QLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHL  103 (355)
T ss_dssp             HHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            3333333333457899999999999999999987654

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=95.64  E-value=0.0099  Score=47.81  Aligned_cols=39  Identities=18%  Similarity=0.212  Sum_probs=28.7

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      +..+..++..- ...+.+-|+|.+|.||||+|.++.+.+.
T Consensus        45 ~~~l~~~~~~i-Pkkn~ili~GPPGtGKTt~a~ala~~l~   83 (212)
T 1tue_A           45 LGALKSFLKGT-PKKNCLVFCGPANTGKSYFGMSFIHFIQ   83 (212)
T ss_dssp             HHHHHHHHHTC-TTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhcC-CcccEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45555555532 2245689999999999999999998764

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.57  E-value=0.017  Score=49.34  Aligned_cols=26  Identities=19%  Similarity=0.285  Sum_probs=22.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+++|+|.+|+||||++..+...+
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~l  129 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANYY  129 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            46899999999999999999887754

>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=95.54  E-value=0.0073  Score=51.36  Aligned_cols=49  Identities=16%  Similarity=0.152  Sum_probs=32.4

Q ss_pred             CCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          179 NKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .-..++|.+..++.+...+....  ..-+-|+|.+|+|||+||+++++.+.
T Consensus        22 ~f~~i~G~~~~~~~l~~~~~~~~--~~~vLl~G~~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           22 PFSAIVGQEDMKLALLLTAVDPG--IGGVLVFGDRGTGKSTAVRALAALLP   70 (350)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHCGG--GCCEEEECCGGGCTTHHHHHHHHHSC
T ss_pred             CchhccChHHHHHHHHHHhhCCC--CceEEEECCCCccHHHHHHHHHHhCc
Confidence            34568888765444333222111  11277899999999999999998753

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=95.54  E-value=0.0078  Score=50.58  Aligned_cols=26  Identities=35%  Similarity=0.445  Sum_probs=22.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+|-|.|++|.||||+|+.+.+++
T Consensus        32 ~~~livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           32 SPTAFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            35788999999999999999998764

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=95.49  E-value=0.019  Score=48.78  Aligned_cols=27  Identities=19%  Similarity=0.346  Sum_probs=23.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+++|+|.+|.||||++..+...+.
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~l~  129 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKMFV  129 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHHHH
Confidence            367999999999999999999887543

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=95.47  E-value=0.012  Score=49.85  Aligned_cols=27  Identities=22%  Similarity=0.298  Sum_probs=23.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+++|+|..|.||||+++.+...+.
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~l~  125 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHRLK  125 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            357999999999999999999887643

>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=95.44  E-value=0.014  Score=52.30  Aligned_cols=50  Identities=20%  Similarity=0.255  Sum_probs=33.9

Q ss_pred             CccccccchHHHHHHHhcc---------C---CCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          181 NQLAGVESRVEEIESLLGV---------K---SKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~---------~---~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ..++|.+.-++.+...+..         .   ....+-+-++|.+|+||||+|+++...+..
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~~   76 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANA   76 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTC
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            3467877777766554311         0   011244778999999999999999987543

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=95.43  E-value=0.0073  Score=49.56  Aligned_cols=27  Identities=30%  Similarity=0.330  Sum_probs=23.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+|.|.|++|.||||+|+.+.+.+.
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~L~~~l~   57 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRIKQKEFQ   57 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            357899999999999999999988653

>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=95.40  E-value=0.0088  Score=50.05  Aligned_cols=23  Identities=39%  Similarity=0.765  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIF  225 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~  225 (233)
                      ...+|+|.|+.|.||||+|+.+.
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            36789999999999999999886

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=95.40  E-value=0.012  Score=50.23  Aligned_cols=26  Identities=23%  Similarity=0.519  Sum_probs=21.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ++.++|+|.|=||+||||.+--+.-.
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~a   71 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSAA   71 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHH
Confidence            46899999999999999988765543

>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=95.33  E-value=0.012  Score=49.80  Aligned_cols=27  Identities=30%  Similarity=0.383  Sum_probs=23.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...++||.|..|.|||||++.+...+.
T Consensus        79 ~g~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            457999999999999999999887553

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=95.30  E-value=0.013  Score=49.77  Aligned_cols=27  Identities=19%  Similarity=0.223  Sum_probs=23.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+++|+|.+|.||||+++.+...+.
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~  127 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQ  127 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHH
Confidence            357999999999999999999887543

>1puj_A YLQF, conserved hypothetical protein YLQF; structural genomics, nysgxrc T18, GTPase, PSI, protein structure initiative; HET: GNP; 2.00A {Bacillus subtilis} SCOP: c.37.1.8

Probab=95.27  E-value=0.11  Score=43.50  Aligned_cols=29  Identities=7%  Similarity=0.034  Sum_probs=22.8

Q ss_pred             hHHHHHHHHHhcCceEEEeecCCCCchhh
Q 043980           67 ISQSLVNAIEASAISVIIFSESYTSSRWC   95 (233)
Q Consensus        67 ~~~~i~~~i~~s~~~i~v~S~~y~~S~wc   95 (233)
                      ...++.+.++++++.|.|+.-.-..+..|
T Consensus        13 a~~~~~~~l~~aDvVl~VvDAr~p~~~~~   41 (282)
T 1puj_A           13 ARREVTEKLKLIDIVYELVDARIPMSSRN   41 (282)
T ss_dssp             HHHHHHHHGGGCSEEEEEEETTSTTTTSC
T ss_pred             HHHHHHHHHhhCCEEEEEEeCCCCCccCC
Confidence            44678889999999999998766555555

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.22  E-value=0.017  Score=49.45  Aligned_cols=28  Identities=32%  Similarity=0.468  Sum_probs=23.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ....++||.|..|.|||||++.+...+.
T Consensus        90 ~~p~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           90 KVPYIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             CCCEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3467999999999999999999876543

>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=95.21  E-value=0.015  Score=50.93  Aligned_cols=29  Identities=21%  Similarity=0.084  Sum_probs=24.3

Q ss_pred             CCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          200 KSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       200 ~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +....++++|+|..|.|||||++.+....
T Consensus       165 ~i~~~~~i~l~G~~GsGKSTl~~~l~~~~  193 (377)
T 1svm_A          165 NIPKKRYWLFKGPIDSGKTTLAAALLELC  193 (377)
T ss_dssp             CCTTCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ccCCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            33446799999999999999999998754

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=95.18  E-value=0.012  Score=53.45  Aligned_cols=44  Identities=18%  Similarity=0.027  Sum_probs=33.9

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..++|.+..++.+...+..+    .-+-++|.+|+|||+||+++++.+
T Consensus        22 ~~ivGq~~~i~~l~~al~~~----~~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSG----ESVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHT----CEEEEECCSSSSHHHHHHHGGGGB
T ss_pred             hhhHHHHHHHHHHHHHHhcC----CeeEeecCchHHHHHHHHHHHHHH
Confidence            56789888777776655433    246689999999999999998754

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.17  E-value=0.017  Score=48.97  Aligned_cols=38  Identities=24%  Similarity=0.330  Sum_probs=27.0

Q ss_pred             HHHHHhccCCC-CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          192 EIESLLGVKSK-DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       192 ~l~~~l~~~~~-~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+.+++..-.. ...-+-|+|..|+|||+||.++++.+.
T Consensus       139 ~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~~  177 (308)
T 2qgz_A          139 AILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELS  177 (308)
T ss_dssp             HHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHHH
Confidence            44445543221 245678999999999999999998754

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=95.16  E-value=0.026  Score=50.33  Aligned_cols=27  Identities=19%  Similarity=0.158  Sum_probs=23.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..++|.++|.+|+||||++..+...+.
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~  125 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLR  125 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            468999999999999999999877543

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=95.15  E-value=0.013  Score=49.62  Aligned_cols=26  Identities=19%  Similarity=0.189  Sum_probs=22.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+++++|.+|+||||++..+...+.
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA~~l~  130 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLAAISM  130 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            56999999999999999999877543

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=95.14  E-value=0.02  Score=45.43  Aligned_cols=26  Identities=31%  Similarity=0.479  Sum_probs=22.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ....|.|+|.+|+|||||+..+....
T Consensus        37 ~~~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           37 GVVAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             TCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            46889999999999999999987763

>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=95.13  E-value=0.016  Score=50.13  Aligned_cols=38  Identities=24%  Similarity=0.350  Sum_probs=29.1

Q ss_pred             HHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          191 EEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       191 ~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..|..+|..+-..-.++.|+|..|.|||||+..+...+
T Consensus       118 ~~LD~lL~ggi~~G~i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          118 KSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             HHHHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             HHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            34555565444456899999999999999999987654

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=95.13  E-value=0.017  Score=48.24  Aligned_cols=26  Identities=15%  Similarity=0.092  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-.+++|.|.+|.|||||++.+...+
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~ia~~~   59 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQQALQW   59 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            35689999999999999999987754

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=95.11  E-value=0.024  Score=47.93  Aligned_cols=25  Identities=28%  Similarity=0.359  Sum_probs=22.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+++++|.+|+||||++..+...+
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~  122 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFY  122 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            5789999999999999999887654

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=95.11  E-value=0.018  Score=50.16  Aligned_cols=27  Identities=22%  Similarity=0.298  Sum_probs=23.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+++|+|..|.||||+++.+...+.
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l~  182 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRLK  182 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhcc
Confidence            357999999999999999999887643

>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=95.09  E-value=0.016  Score=53.08  Aligned_cols=48  Identities=33%  Similarity=0.401  Sum_probs=32.6

Q ss_pred             ccccccchHHHHHHHhcc----CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          182 QLAGVESRVEEIESLLGV----KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       182 ~~~g~~~~~~~l~~~l~~----~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      +++|.+.-.+.+.+.+..    .......+.++|.+|+||||||+.+++.+.
T Consensus        82 di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l~  133 (543)
T 3m6a_A           82 EHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSLG  133 (543)
T ss_dssp             HCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHHHT
T ss_pred             HhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHhcC
Confidence            456766555555432211    111356889999999999999999998754

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=95.03  E-value=0.015  Score=53.95  Aligned_cols=44  Identities=27%  Similarity=0.381  Sum_probs=35.0

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..++|.+.-++.+...+..+    ..+.|+|.+|+||||||+.+++.+
T Consensus        41 ~~i~G~~~~l~~l~~~i~~g----~~vll~Gp~GtGKTtlar~ia~~l   84 (604)
T 3k1j_A           41 DQVIGQEHAVEVIKTAANQK----RHVLLIGEPGTGKSMLGQAMAELL   84 (604)
T ss_dssp             HHCCSCHHHHHHHHHHHHTT----CCEEEECCTTSSHHHHHHHHHHTS
T ss_pred             ceEECchhhHhhccccccCC----CEEEEEeCCCCCHHHHHHHHhccC
Confidence            56788887777776666533    478999999999999999998754

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=94.92  E-value=0.02  Score=51.92  Aligned_cols=26  Identities=19%  Similarity=0.431  Sum_probs=22.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+++|+|..|.|||||++.+...+
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll  317 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQF  317 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHh
Confidence            35799999999999999999988754

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=94.91  E-value=0.02  Score=54.44  Aligned_cols=48  Identities=23%  Similarity=0.405  Sum_probs=36.3

Q ss_pred             CccccccchHHHHHHHhccCC-------CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKS-------KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~-------~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..++|.+..++.+...+....       .....+-++|.+|+|||++|+++++.+
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l  545 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESI  545 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHh
Confidence            568899888877776554311       113368899999999999999999875

>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=94.91  E-value=0.027  Score=50.18  Aligned_cols=26  Identities=23%  Similarity=0.232  Sum_probs=22.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+|.++|.+|+||||++..+...+
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l  121 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFY  121 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            36899999999999999999887654

>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=94.86  E-value=0.031  Score=46.57  Aligned_cols=37  Identities=24%  Similarity=0.197  Sum_probs=28.6

Q ss_pred             HHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          191 EEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       191 ~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..+..||.......+.+-++|.+|.|||++|.++.+.
T Consensus        91 ~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~  127 (267)
T 1u0j_A           91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhh
Confidence            3456666654234567999999999999999999885

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=94.80  E-value=0.036  Score=50.41  Aligned_cols=26  Identities=19%  Similarity=0.197  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..++|.|+|.+|+||||++..+...+
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l  125 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYY  125 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            46799999999999999999987654

>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=94.74  E-value=0.017  Score=47.00  Aligned_cols=24  Identities=25%  Similarity=0.232  Sum_probs=20.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|+|..|.|||||.+.+..
T Consensus        30 ~Ge~~~iiG~nGsGKSTLl~~l~G   53 (235)
T 3tif_A           30 EGEFVSIMGPSGSGKSTMLNIIGC   53 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhc
Confidence            346899999999999999998764

>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=94.72  E-value=0.016  Score=54.94  Aligned_cols=49  Identities=18%  Similarity=0.294  Sum_probs=35.4

Q ss_pred             CccccccchHHHHHHHhccCC-------CCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGVKS-------KDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~-------~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..++|.+..++.+...+....       .....+-++|.+|+|||++|+++.+.+.
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l~  513 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG  513 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHhc
Confidence            457788877777766543211       1234688999999999999999998753

>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=94.72  E-value=0.024  Score=50.54  Aligned_cols=25  Identities=32%  Similarity=0.341  Sum_probs=22.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+|.|+|.+|+||||++..+...+
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~l  123 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARYI  123 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            5689999999999999999987754

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=94.62  E-value=0.026  Score=47.58  Aligned_cols=26  Identities=27%  Similarity=0.188  Sum_probs=22.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+++++|.+|.||||++..+...+
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~  122 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYY  122 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35789999999999999999987754

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=94.60  E-value=0.042  Score=47.16  Aligned_cols=35  Identities=20%  Similarity=0.289  Sum_probs=26.5

Q ss_pred             HHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          194 ESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       194 ~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+-+........+++|.|.+|.|||||.+.+...+
T Consensus        45 l~~i~~~~~~g~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           45 IDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             HHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHhCCcccCCCeEEEEECCCCCCHHHHHHHHHHhh
Confidence            33334444457899999999999999999987643

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=94.60  E-value=0.029  Score=47.67  Aligned_cols=30  Identities=13%  Similarity=0.190  Sum_probs=24.2

Q ss_pred             cCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          199 VKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       199 ~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-..-.+++|+|..|.|||||++.+..-+
T Consensus       121 l~i~~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          121 KGIPKKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             HTCTTCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEecCCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            333456789999999999999999987643

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=94.53  E-value=0.013  Score=50.58  Aligned_cols=26  Identities=19%  Similarity=0.327  Sum_probs=22.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+|.|.|+.|+||||||..+..++.
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~l~   65 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAHFP   65 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTTSC
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHCC
Confidence            46899999999999999999988753

>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=94.53  E-value=0.031  Score=48.51  Aligned_cols=41  Identities=20%  Similarity=0.153  Sum_probs=31.3

Q ss_pred             chHHHHHHHhc-cCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          188 SRVEEIESLLG-VKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       188 ~~~~~l~~~l~-~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-...|..+|. .+-..-.++.|.|.+|+||||||..+....
T Consensus        44 TG~~~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~~   85 (356)
T 3hr8_A           44 TGSLAIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAEA   85 (356)
T ss_dssp             CSCHHHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            34566777776 343446899999999999999999987754

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=94.52  E-value=0.045  Score=47.00  Aligned_cols=29  Identities=24%  Similarity=0.305  Sum_probs=24.0

Q ss_pred             CCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          200 KSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       200 ~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ......+++|.|.+|.|||||+..+...+
T Consensus        52 ~~~~~~~i~i~G~~g~GKSTl~~~l~~~~   80 (341)
T 2p67_A           52 YCGNTLRLGVTGTPGAGKSTFLEAFGMLL   80 (341)
T ss_dssp             GCSCSEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             ccCCCEEEEEEcCCCCCHHHHHHHHHHHH
Confidence            33457899999999999999999987643

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=94.52  E-value=0.021  Score=46.56  Aligned_cols=24  Identities=21%  Similarity=0.354  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|+|..|.|||||.+.+..
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~~l~G   53 (237)
T 2cbz_A           30 EGALVAVVGQVGCGKSSLLSALLA   53 (237)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            346899999999999999998765

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.48  E-value=0.021  Score=47.29  Aligned_cols=24  Identities=29%  Similarity=0.306  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        31 ~Ge~~~liG~nGsGKSTLlk~l~G   54 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTFLRCINF   54 (262)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            456899999999999999998765

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=94.46  E-value=0.023  Score=47.23  Aligned_cols=24  Identities=21%  Similarity=0.281  Sum_probs=21.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|+|..|.|||||.+.+..
T Consensus        45 ~Ge~~~l~G~NGsGKSTLlk~l~G   68 (267)
T 2zu0_C           45 PGEVHAIMGPNGSGKSTLSATLAG   68 (267)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            346899999999999999998875

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=94.45  E-value=0.022  Score=47.00  Aligned_cols=24  Identities=25%  Similarity=0.223  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        32 ~Ge~~~liG~nGsGKSTLlk~l~G   55 (257)
T 1g6h_A           32 KGDVTLIIGPNGSGKSTLINVITG   55 (257)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            346899999999999999998765

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=94.42  E-value=0.022  Score=47.63  Aligned_cols=23  Identities=22%  Similarity=0.290  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -.+++|+|..|.|||||.+.+..
T Consensus        34 Ge~~~iiGpnGsGKSTLl~~l~G   56 (275)
T 3gfo_A           34 GEVTAILGGNGVGKSTLFQNFNG   56 (275)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHc
Confidence            46899999999999999998764

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=94.42  E-value=0.022  Score=47.34  Aligned_cols=24  Identities=25%  Similarity=0.358  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|+|..|.|||||.+.+..
T Consensus        36 ~Ge~~~liG~nGsGKSTLl~~l~G   59 (266)
T 4g1u_C           36 SGEMVAIIGPNGAGKSTLLRLLTG   59 (266)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhc
Confidence            356899999999999999998764

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.40  E-value=0.023  Score=46.37  Aligned_cols=23  Identities=30%  Similarity=0.328  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -.+++|.|..|.|||||.+.+..
T Consensus        32 Ge~~~l~G~nGsGKSTLl~~l~G   54 (240)
T 1ji0_A           32 GQIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999998765

>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=94.40  E-value=0.03  Score=48.03  Aligned_cols=24  Identities=25%  Similarity=0.257  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .+++-|+|++|+||||||.++...
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~  146 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA  146 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh
Confidence            356679999999999999998764

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=94.32  E-value=0.024  Score=47.05  Aligned_cols=24  Identities=21%  Similarity=0.250  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        49 ~Gei~~liG~NGsGKSTLlk~l~G   72 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTFLRCLNL   72 (263)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEEcCCCCcHHHHHHHHHc
Confidence            346899999999999999998765

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=94.31  E-value=0.025  Score=45.84  Aligned_cols=24  Identities=29%  Similarity=0.360  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        34 Ge~~~i~G~nGsGKSTLl~~l~Gl   57 (229)
T 2pze_A           34 GQLLAVAGSTGAGKTSLLMMIMGE   57 (229)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999988653

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=94.29  E-value=0.02  Score=50.60  Aligned_cols=26  Identities=15%  Similarity=0.181  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+|.|+|++|.||||+|+.+.+++
T Consensus       257 ~~~lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHHHTGGG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            46789999999999999999987653

>2hjg_A GTP-binding protein ENGA; GTPase ENGA KH-domain, hydrolase; HET: GDP; 2.50A {Bacillus subtilis}

Probab=94.28  E-value=0.29  Score=43.24  Aligned_cols=24  Identities=21%  Similarity=0.472  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      +..-|+|+|.+|+|||||..++..
T Consensus       174 ~~~ki~lvG~~nvGKSSLin~l~~  197 (436)
T 2hjg_A          174 EVIQFCLIGRPNVGKSSLVNAMLG  197 (436)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHT
T ss_pred             cCcEEEEEcCCCCCHHHHHHHHhC
Confidence            456789999999999999998865

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=94.24  E-value=0.026  Score=46.31  Aligned_cols=24  Identities=29%  Similarity=0.454  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|+|..|.|||||.+.+..
T Consensus        34 ~Ge~~~i~G~nGsGKSTLl~~l~G   57 (247)
T 2ff7_A           34 QGEVIGIVGRSGSGKSTLTKLIQR   57 (247)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            346899999999999999998765

>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=94.23  E-value=0.033  Score=48.16  Aligned_cols=43  Identities=19%  Similarity=0.210  Sum_probs=31.3

Q ss_pred             ccchHHHHHHHhc-cCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          186 VESRVEEIESLLG-VKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       186 ~~~~~~~l~~~l~-~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...-...|..+|. .+-..-+++.|+|.+|+||||||..+....
T Consensus        42 i~TG~~~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~la~~~   85 (349)
T 2zr9_A           42 IPTGSISLDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANA   85 (349)
T ss_dssp             ECCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cccCCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3344556666666 333345789999999999999999987643

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.18  E-value=0.027  Score=46.56  Aligned_cols=24  Identities=33%  Similarity=0.437  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        40 ~Gei~~l~G~NGsGKSTLlk~l~G   63 (256)
T 1vpl_A           40 EGEIFGLIGPNGAGKTTTLRIIST   63 (256)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhc
Confidence            346899999999999999998765

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.18  E-value=0.027  Score=46.58  Aligned_cols=24  Identities=25%  Similarity=0.419  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|+|..|.|||||.+.+..
T Consensus        45 ~Ge~~~i~G~nGsGKSTLl~~l~G   68 (260)
T 2ghi_A           45 SGTTCALVGHTGSGKSTIAKLLYR   68 (260)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            346899999999999999998764

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=94.16  E-value=0.064  Score=45.49  Aligned_cols=45  Identities=22%  Similarity=0.203  Sum_probs=31.9

Q ss_pred             cccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          183 LAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       183 ~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..|...-...|..++ .+-..-.++-|.|.+|+||||||..+....
T Consensus        48 ~~~i~TG~~~LD~~l-gGl~~G~l~li~G~pG~GKTtl~l~ia~~~   92 (315)
T 3bh0_A           48 ITGVPSGFTELDRMT-YGYKRRNFVLIAARPSMGKTAFALKQAKNM   92 (315)
T ss_dssp             CCSBCCSCHHHHHHH-SSBCTTCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCccCChHHHHhhc-CCCCCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            344445566666666 333345788899999999999999887653

>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=94.16  E-value=0.035  Score=50.58  Aligned_cols=26  Identities=19%  Similarity=0.268  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+|-++|++|.||||+|+++.+.+
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~~L   59 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTRYL   59 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35688999999999999999997764

>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=94.15  E-value=0.028  Score=49.55  Aligned_cols=37  Identities=16%  Similarity=0.278  Sum_probs=27.8

Q ss_pred             hHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHH
Q 043980          189 RVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIF  225 (233)
Q Consensus       189 ~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~  225 (233)
                      -...|..+|..+-..-.++.|+|.+|+|||||+..+.
T Consensus       163 G~~~LD~lLgGGI~~Gei~~I~G~sGsGKTTLl~~la  199 (400)
T 3lda_A          163 GSKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLA  199 (400)
T ss_dssp             SCHHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHH
T ss_pred             CChhHHHHhcCCcCCCcEEEEEcCCCCChHHHHHHHH
Confidence            3555666665443345799999999999999999765

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=94.12  E-value=0.031  Score=42.96  Aligned_cols=25  Identities=20%  Similarity=0.105  Sum_probs=21.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ....|.|+|.+|+|||||...+.+.
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3567889999999999999988763

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=94.10  E-value=0.029  Score=46.57  Aligned_cols=24  Identities=21%  Similarity=0.257  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        32 ~Ge~~~liG~nGsGKSTLl~~i~G   55 (266)
T 2yz2_A           32 EGECLLVAGNTGSGKSTLLQIVAG   55 (266)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhC
Confidence            356899999999999999998765

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=94.10  E-value=0.024  Score=45.63  Aligned_cols=23  Identities=30%  Similarity=0.455  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -.+++|.|..|.|||||.+.+..
T Consensus        35 Ge~~~iiG~NGsGKSTLlk~l~G   57 (214)
T 1sgw_A           35 GNVVNFHGPNGIGKTTLLKTIST   57 (214)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999998765

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=94.07  E-value=0.029  Score=46.69  Aligned_cols=24  Identities=21%  Similarity=0.281  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|+|..|.|||||.+.+..
T Consensus        44 ~Ge~~~i~G~nGsGKSTLlk~l~G   67 (271)
T 2ixe_A           44 PGKVTALVGPNGSGKSTVAALLQN   67 (271)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            346899999999999999998765

>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=94.05  E-value=0.039  Score=49.47  Aligned_cols=25  Identities=20%  Similarity=0.255  Sum_probs=22.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+|-++|++|.||||+++.+.+.+
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~~l   63 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTRYL   63 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHH
Confidence            4678899999999999999998764

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=94.04  E-value=0.029  Score=46.92  Aligned_cols=23  Identities=22%  Similarity=0.345  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -.+++|+|..|.|||||.+.+..
T Consensus        47 Ge~~~liG~NGsGKSTLlk~l~G   69 (279)
T 2ihy_A           47 GDKWILYGLNGAGKTTLLNILNA   69 (279)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            46899999999999999998765

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=94.02  E-value=0.031  Score=51.41  Aligned_cols=26  Identities=27%  Similarity=0.515  Sum_probs=23.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      -.+++|.|+.|.|||||++.+...+.
T Consensus       369 G~iI~LiG~sGSGKSTLar~La~~L~  394 (552)
T 3cr8_A          369 GFTVFFTGLSGAGKSTLARALAARLM  394 (552)
T ss_dssp             CEEEEEEESSCHHHHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCChHHHHHHHHHHhhc
Confidence            47899999999999999999988764

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=93.94  E-value=0.032  Score=45.97  Aligned_cols=23  Identities=22%  Similarity=0.393  Sum_probs=20.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -.+++|.|..|.|||||.+.+..
T Consensus        31 Ge~~~l~G~nGsGKSTLl~~l~G   53 (253)
T 2nq2_C           31 GDILAVLGQNGCGKSTLLDLLLG   53 (253)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999998765

>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=93.88  E-value=0.047  Score=48.81  Aligned_cols=26  Identities=27%  Similarity=0.253  Sum_probs=22.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+|.++|.+|+||||++..+...+.
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA~~l~  125 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLARYFQ  125 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CeEEEEECcCCCCHHHHHHHHHHHHH
Confidence            68999999999999999999887543

>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=93.83  E-value=0.044  Score=47.39  Aligned_cols=25  Identities=16%  Similarity=0.215  Sum_probs=22.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...++|+|..|.|||||++.+...+
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~  194 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVF  194 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHT
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999999999999987754

>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=93.79  E-value=0.066  Score=45.99  Aligned_cols=38  Identities=21%  Similarity=0.288  Sum_probs=29.3

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...|..+|..+-..-.++.|+|.+|+||||||..+...
T Consensus       108 ~~~LD~~LgGGl~~G~i~~I~G~~GsGKTtla~~la~~  145 (343)
T 1v5w_A          108 SQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVT  145 (343)
T ss_dssp             CHHHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHH
T ss_pred             ChhHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            44566666544445689999999999999999988765

>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=93.74  E-value=0.035  Score=53.59  Aligned_cols=47  Identities=15%  Similarity=0.386  Sum_probs=35.5

Q ss_pred             ccccccchHHHHHHHhccC------C-CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          182 QLAGVESRVEEIESLLGVK------S-KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       182 ~~~g~~~~~~~l~~~l~~~------~-~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .++|.+..++.+...+...      . .....+-|+|..|+|||++|+++++.+
T Consensus       559 ~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~  612 (854)
T 1qvr_A          559 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATL  612 (854)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHH
T ss_pred             ccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHh
Confidence            4688888787776655421      1 123578899999999999999999875

>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=93.48  E-value=0.06  Score=47.84  Aligned_cols=27  Identities=26%  Similarity=0.182  Sum_probs=23.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+++++|.+|.||||++..+...+.
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~  123 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYK  123 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            357899999999999999999887653

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=93.45  E-value=0.078  Score=48.93  Aligned_cols=26  Identities=27%  Similarity=0.313  Sum_probs=23.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+|.|.|+.|.||||+|+++.+++.
T Consensus       396 ~~~I~l~GlsGSGKSTiA~~La~~L~  421 (573)
T 1m8p_A          396 GFTIFLTGYMNSGKDAIARALQVTLN  421 (573)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             ceEEEeecCCCCCHHHHHHHHHHHhc
Confidence            46899999999999999999988754

>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=93.44  E-value=0.057  Score=46.82  Aligned_cols=44  Identities=16%  Similarity=0.177  Sum_probs=31.2

Q ss_pred             cccchHHHHHHHhc-cCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          185 GVESRVEEIESLLG-VKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       185 g~~~~~~~l~~~l~-~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +...-...|..+|. .+-..-+++-|.|.+|+||||||..+....
T Consensus        43 ~i~TG~~~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLal~la~~~   87 (356)
T 1u94_A           43 TISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAA   87 (356)
T ss_dssp             EECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cccCCCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            33444566666665 333335689999999999999999887653

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=93.36  E-value=0.076  Score=48.32  Aligned_cols=26  Identities=4%  Similarity=0.132  Sum_probs=23.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+|-+.|+.|.||||+|+++.+++.
T Consensus       395 ~~~I~l~GlsGsGKSTIa~~La~~L~  420 (511)
T 1g8f_A          395 GFSIVLGNSLTVSREQLSIALLSTFL  420 (511)
T ss_dssp             CEEEEECTTCCSCHHHHHHHHHHHHT
T ss_pred             ceEEEecccCCCCHHHHHHHHHHHHH
Confidence            47888999999999999999999875

>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=93.34  E-value=0.058  Score=50.31  Aligned_cols=25  Identities=24%  Similarity=0.389  Sum_probs=22.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+|.+.|+.|.||||+|+.+.+++
T Consensus        52 g~lIvLtGlsGSGKSTlAr~La~~L   76 (630)
T 1x6v_B           52 GCTVWLTGLSGAGKTTVSMALEEYL   76 (630)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHH
Confidence            5789999999999999999998876

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=93.33  E-value=0.066  Score=45.17  Aligned_cols=31  Identities=23%  Similarity=0.392  Sum_probs=25.0

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIF  225 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~  225 (233)
                      +++|.+.+.     -.++++.|..|+|||||.+.+.
T Consensus       156 i~~L~~~l~-----G~i~~l~G~sG~GKSTLln~l~  186 (302)
T 2yv5_A          156 IDELVDYLE-----GFICILAGPSGVGKSSILSRLT  186 (302)
T ss_dssp             HHHHHHHTT-----TCEEEEECSTTSSHHHHHHHHH
T ss_pred             HHHHHhhcc-----CcEEEEECCCCCCHHHHHHHHH
Confidence            566666554     3588999999999999999987

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=93.29  E-value=0.038  Score=46.94  Aligned_cols=24  Identities=33%  Similarity=0.515  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|+|..|.|||||++.+..
T Consensus        79 ~Ge~vaivG~sGsGKSTLl~ll~g  102 (306)
T 3nh6_A           79 PGQTLALVGPSGAGKSTILRLLFR  102 (306)
T ss_dssp             TTCEEEEESSSCHHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCchHHHHHHHHHc
Confidence            356899999999999999998764

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=93.26  E-value=0.048  Score=45.92  Aligned_cols=24  Identities=29%  Similarity=0.339  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        63 ~Ge~~~i~G~NGsGKSTLlk~l~G   86 (290)
T 2bbs_A           63 RGQLLAVAGSTGAGKTSLLMMIMG   86 (290)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhc
Confidence            346899999999999999998765

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=93.26  E-value=0.039  Score=48.88  Aligned_cols=24  Identities=21%  Similarity=0.353  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ...+++|+|..|.|||||.+.+..
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhC
Confidence            456999999999999999999876

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=93.23  E-value=0.073  Score=45.88  Aligned_cols=25  Identities=20%  Similarity=0.287  Sum_probs=22.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +..+|+|+|.+|.|||||..++...
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~~   97 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGKM   97 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHH
Confidence            4789999999999999999998764

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=93.22  E-value=0.097  Score=46.65  Aligned_cols=45  Identities=16%  Similarity=0.238  Sum_probs=31.7

Q ss_pred             cccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          183 LAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       183 ~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..|.......|..++ .+-..-.++.|.|.+|+||||||..+...+
T Consensus       183 ~~~i~tG~~~LD~~~-gGl~~G~liiI~G~pG~GKTtl~l~ia~~~  227 (454)
T 2r6a_A          183 ITGIPTGFTELDRMT-SGFQRSDLIIVAARPSVGKTAFALNIAQNV  227 (454)
T ss_dssp             CCSBCCSCHHHHHHH-SSBCTTCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCCcHHHHhhc-CCCCCCCEEEEECCCCCCHHHHHHHHHHHH
Confidence            344544555666655 333335689999999999999999987754

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=93.15  E-value=0.053  Score=47.23  Aligned_cols=24  Identities=25%  Similarity=0.396  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        53 ~Gei~~IiGpnGaGKSTLlr~i~G   76 (366)
T 3tui_C           53 AGQIYGVIGASGAGKSTLIRCVNL   76 (366)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCCEEEEEcCCCchHHHHHHHHhc
Confidence            346899999999999999998764

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=93.13  E-value=0.092  Score=43.19  Aligned_cols=26  Identities=23%  Similarity=0.514  Sum_probs=21.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .....|.++|..|+|||||...+++.
T Consensus        37 ~~~~~I~vvG~~g~GKSSLin~l~~~   62 (270)
T 1h65_A           37 VNSLTILVMGKGGVGKSSTVNSIIGE   62 (270)
T ss_dssp             CCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHhCC
Confidence            34567889999999999999998763

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=93.11  E-value=0.11  Score=42.66  Aligned_cols=24  Identities=21%  Similarity=0.534  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ....|+++|..|+|||||..++..
T Consensus        35 ~~~~I~lvG~~g~GKSSLin~l~~   58 (262)
T 3def_A           35 NSMTVLVLGKGGVGKSSTVNSLIG   58 (262)
T ss_dssp             CEEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhC
Confidence            456789999999999999998875

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=93.09  E-value=0.12  Score=45.98  Aligned_cols=45  Identities=24%  Similarity=0.207  Sum_probs=31.3

Q ss_pred             cccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          183 LAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       183 ~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..|...-...|..++ .+-....++-|.|.+|+||||||..+...+
T Consensus       180 ~~~i~tG~~~LD~~l-gGl~~G~l~ii~G~pg~GKT~lal~ia~~~  224 (444)
T 2q6t_A          180 VAGVRTGFKELDQLI-GTLGPGSLNIIAARPAMGKTAFALTIAQNA  224 (444)
T ss_dssp             ---CCCSCHHHHHHH-CCCCTTCEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCcccCCCHhhhhhc-CCcCCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            445555566676666 333345688899999999999999887654

>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=93.01  E-value=0.059  Score=45.81  Aligned_cols=39  Identities=18%  Similarity=0.258  Sum_probs=28.2

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...|..+|..+-..-.++.|+|.+|+||||||..+....
T Consensus        93 ~~~LD~~L~GGl~~G~i~~i~G~~GsGKT~la~~la~~~  131 (324)
T 2z43_A           93 SQALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNV  131 (324)
T ss_dssp             CHHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             chhHHHhcCCCCCCCcEEEEECCCCCCHhHHHHHHHHHH
Confidence            345555564332335689999999999999999987653

>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=93.01  E-value=0.074  Score=44.97  Aligned_cols=38  Identities=26%  Similarity=0.284  Sum_probs=28.4

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...|..+|..+-..-.++-|+|.+|+||||||..+...
T Consensus        84 ~~~LD~~l~GGl~~g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           84 SSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             CHHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             ChhHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            44555666533334578999999999999999988764

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=92.94  E-value=0.06  Score=46.69  Aligned_cols=23  Identities=39%  Similarity=0.487  Sum_probs=20.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -.+++|.|..|.|||||.+.+..
T Consensus        41 Ge~~~llGpnGsGKSTLLr~iaG   63 (355)
T 1z47_A           41 GEMVGLLGPSGSGKTTILRLIAG   63 (355)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            46899999999999999999875

>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=92.79  E-value=0.083  Score=45.97  Aligned_cols=26  Identities=23%  Similarity=0.299  Sum_probs=22.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+++|+|..|.|||||.+.+...+
T Consensus       135 ~g~~i~ivG~~GsGKTTll~~l~~~~  160 (372)
T 2ewv_A          135 KMGLILVTGPTGSGKSTTIASMIDYI  160 (372)
T ss_dssp             SSEEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            35689999999999999999987754

>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=92.78  E-value=0.054  Score=43.24  Aligned_cols=24  Identities=25%  Similarity=0.371  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -+.|.|.|..|+||||||.++..+
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~   57 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQR   57 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHh
Confidence            357889999999999999998765

>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=92.66  E-value=0.082  Score=45.82  Aligned_cols=24  Identities=25%  Similarity=0.291  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+++|.|..|.|||||.+.+...+
T Consensus       124 g~i~I~GptGSGKTTlL~~l~g~~  147 (356)
T 3jvv_A          124 GLVLVTGPTGSGKSTTLAAMLDYL  147 (356)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcc
Confidence            489999999999999999987754

>3fkq_A NTRC-like two-domain protein; RER070207001320, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: ATP 2PE; 2.10A {Eubacterium rectale}

Probab=92.66  E-value=0.11  Score=45.05  Aligned_cols=58  Identities=17%  Similarity=0.407  Sum_probs=37.7

Q ss_pred             CcceEEEcCcccccccchHHHHHHHHhhC-C----CeEEEeCccCCCcchHHHHHHHHHhcCceEEEeecCCCCch
Q 043980           23 KKYEVFVSFRGEDTRDKFTSHLYSALSRQ-S----IQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSR   93 (233)
Q Consensus        23 ~~~dVFISy~~~D~~~~f~~~L~~~L~~~-g----i~~~~d~~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~   93 (233)
                      .+..+=|.    |+...+++.|...|..+ +    +.+|-+.         +.+.+.+++-++-|++++++|....
T Consensus        20 ~~i~l~i~----d~d~~Y~~~l~~y~~~~~~~~~~v~~ft~~---------e~~~~~~~~~~~dilli~e~~~~~~   82 (373)
T 3fkq_A           20 MKIKVALL----DKDKEYLDRLTGVFNTKYADKLEVYSFTDE---------KNAIESVKEYRIDVLIAEEDFNIDK   82 (373)
T ss_dssp             CCEEEEEE----CSCHHHHHHHHHHHHHHTTTTEEEEEESCH---------HHHHHHHHHHTCSEEEEETTCCCCG
T ss_pred             ceEEEEEE----eCCHHHHHHHHHHHhhccCCceEEEEECCH---------HHHHHHHhcCCCCEEEEcchhhhhh
Confidence            44444453    33366899999998654 3    3344332         4566667777888999999997643

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=92.60  E-value=0.11  Score=47.56  Aligned_cols=26  Identities=19%  Similarity=0.308  Sum_probs=22.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+|.+.|+.|.||||+|+.+...+.
T Consensus       372 ~~~I~l~G~~GsGKSTia~~La~~L~  397 (546)
T 2gks_A          372 GFCVWLTGLPCAGKSTIAEILATMLQ  397 (546)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             ceEEEccCCCCCCHHHHHHHHHHHhh
Confidence            57899999999999999999987653

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=92.57  E-value=0.075  Score=45.88  Aligned_cols=26  Identities=23%  Similarity=0.367  Sum_probs=22.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .-..++|.|..|.|||||.+.+.+..
T Consensus        70 ~Gq~~gIiG~nGaGKTTLl~~I~g~~   95 (347)
T 2obl_A           70 IGQRIGIFAGSGVGKSTLLGMICNGA   95 (347)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            35689999999999999999998864

>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=92.54  E-value=0.072  Score=46.48  Aligned_cols=24  Identities=38%  Similarity=0.356  Sum_probs=21.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        36 ~Ge~~~llGpnGsGKSTLLr~iaG   59 (372)
T 1v43_A           36 DGEFLVLLGPSGCGKTTTLRMIAG   59 (372)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCChHHHHHHHHHc
Confidence            356899999999999999998875

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=92.43  E-value=0.074  Score=41.89  Aligned_cols=23  Identities=30%  Similarity=0.391  Sum_probs=20.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ..-|.|+|.+|+|||||...+.+
T Consensus        34 ~~ki~vvG~~~vGKSsli~~l~~   56 (214)
T 2j1l_A           34 SVKVVLVGDGGCGKTSLLMVFAD   56 (214)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHc
Confidence            45688999999999999998865

>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=92.32  E-value=0.054  Score=46.94  Aligned_cols=24  Identities=38%  Similarity=0.502  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        30 ~Ge~~~llGpnGsGKSTLLr~iaG   53 (353)
T 1oxx_K           30 NGERFGILGPSGAGKTTFMRIIAG   53 (353)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhC
Confidence            346899999999999999999875

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=92.32  E-value=0.056  Score=46.81  Aligned_cols=24  Identities=25%  Similarity=0.405  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..+++|+|..|.|||||++.+...
T Consensus       175 G~~i~ivG~sGsGKSTll~~l~~~  198 (361)
T 2gza_A          175 ERVIVVAGETGSGKTTLMKALMQE  198 (361)
T ss_dssp             TCCEEEEESSSSCHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc
Confidence            458999999999999999998764

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=92.31  E-value=0.16  Score=43.62  Aligned_cols=46  Identities=11%  Similarity=0.127  Sum_probs=32.5

Q ss_pred             ccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          182 QLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       182 ~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+.|...-...|..++. +-..-.++.|.|.+|+||||||..+...+
T Consensus        25 ~~~gi~TG~~~LD~~~g-Gl~~G~LiiIaG~pG~GKTt~al~ia~~~   70 (338)
T 4a1f_A           25 EVTGIPTGFVQLDNYTS-GFNKGSLVIIGARPSMGKTSLMMNMVLSA   70 (338)
T ss_dssp             CCCSBCCSCHHHHHHHC-SBCTTCEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CcCcccCCChHHHHHhc-CCCCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            34555555666666653 32334688899999999999999887653

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=92.30  E-value=0.16  Score=45.33  Aligned_cols=45  Identities=22%  Similarity=0.181  Sum_probs=32.4

Q ss_pred             cccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          183 LAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       183 ~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..|.......|..++. +-....++-|.|.+|+||||||..+....
T Consensus       177 ~~gi~TG~~~LD~~lg-Gl~~G~liiIaG~pG~GKTtlal~ia~~~  221 (444)
T 3bgw_A          177 ITGVPSGFTELDRMTY-GYKRRNFVLIAARPSMGKTAFALKQAKNM  221 (444)
T ss_dssp             CCSBCCSCHHHHHHHS-SBCSSCEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             CCCcCCCcHHHHhhcC-CCCCCcEEEEEeCCCCChHHHHHHHHHHH
Confidence            4455555666666663 33345688899999999999999887654

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=92.27  E-value=0.11  Score=47.12  Aligned_cols=38  Identities=16%  Similarity=0.155  Sum_probs=28.1

Q ss_pred             HHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          191 EEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       191 ~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+..+|..+-..-.+++|.|..|+|||||++.++...
T Consensus       268 ~~ld~vL~g~i~~G~i~~i~G~~GsGKSTLl~~l~g~~  305 (525)
T 1tf7_A          268 VRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENA  305 (525)
T ss_dssp             HHHHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCCCCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            34555555433345789999999999999999988653

>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=92.15  E-value=0.085  Score=46.33  Aligned_cols=24  Identities=25%  Similarity=0.418  Sum_probs=21.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        46 ~Ge~~~llGpsGsGKSTLLr~iaG   69 (390)
T 3gd7_A           46 PGQRVGLLGRTGSGKSTLLSAFLR   69 (390)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhC
Confidence            356899999999999999998864

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=92.10  E-value=0.12  Score=43.54  Aligned_cols=32  Identities=28%  Similarity=0.442  Sum_probs=25.0

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ++++...+.     -.+++|.|..|+|||||.+.+..
T Consensus       160 v~~lf~~l~-----geiv~l~G~sG~GKSTll~~l~g  191 (301)
T 1u0l_A          160 IEELKEYLK-----GKISTMAGLSGVGKSSLLNAINP  191 (301)
T ss_dssp             HHHHHHHHS-----SSEEEEECSTTSSHHHHHHHHST
T ss_pred             HHHHHHHhc-----CCeEEEECCCCCcHHHHHHHhcc
Confidence            555655554     24789999999999999998765

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=92.06  E-value=0.075  Score=47.69  Aligned_cols=25  Identities=24%  Similarity=0.248  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||++.+..-
T Consensus       137 ~Ge~v~IvGpnGsGKSTLlr~L~Gl  161 (460)
T 2npi_A          137 EGPRVVIVGGSQTGKTSLSRTLCSY  161 (460)
T ss_dssp             SCCCEEEEESTTSSHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCc
Confidence            4568999999999999999998763

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=92.03  E-value=0.087  Score=48.20  Aligned_cols=24  Identities=33%  Similarity=0.477  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -.+++|.|..|.|||||++.++..
T Consensus       312 Ge~~~i~G~NGsGKSTLlk~l~Gl  335 (538)
T 1yqt_A          312 GEVIGIVGPNGIGKTTFVKMLAGV  335 (538)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            368999999999999999998764

>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=92.00  E-value=0.09  Score=46.87  Aligned_cols=23  Identities=26%  Similarity=0.486  Sum_probs=20.8

Q ss_pred             EEEEEcCCCChHHHHHHHHHHHH
Q 043980          206 ALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+-|.|.+|.||||++.++...+
T Consensus        47 ~~li~G~aGTGKT~ll~~~~~~l   69 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKFIIEAL   69 (459)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            78899999999999999988764

>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=91.94  E-value=0.095  Score=45.48  Aligned_cols=22  Identities=23%  Similarity=0.359  Sum_probs=19.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .+++|+|..|+|||||.+.+..
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g  237 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLG  237 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHC
T ss_pred             CEEEEECCCCccHHHHHHHHhc
Confidence            4789999999999999998864

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=91.93  E-value=0.094  Score=41.72  Aligned_cols=22  Identities=27%  Similarity=0.501  Sum_probs=19.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIF  225 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~  225 (233)
                      ..-|.|+|.+|+|||||...+.
T Consensus        37 ~~kVvlvG~~~vGKSSLl~r~~   58 (211)
T 2g3y_A           37 YYRVVLIGEQGVGKSTLANIFA   58 (211)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHH
Confidence            4568899999999999998875

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=91.84  E-value=0.083  Score=46.95  Aligned_cols=21  Identities=24%  Similarity=0.515  Sum_probs=19.2

Q ss_pred             EEEEEcCCCChHHHHHHHHHH
Q 043980          206 ALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -++|+|..|.|||||.+.++.
T Consensus        44 ~vaLvG~nGaGKSTLln~L~G   64 (427)
T 2qag_B           44 NILCVGETGLGKSTLMDTLFN   64 (427)
T ss_dssp             EEEEECSTTSSSHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            399999999999999999875

>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=91.78  E-value=0.12  Score=45.75  Aligned_cols=26  Identities=19%  Similarity=0.141  Sum_probs=22.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+++|.|..|.|||||.+.+...+
T Consensus       166 ~ggii~I~GpnGSGKTTlL~allg~l  191 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTTLYAGLQEL  191 (418)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHhhc
Confidence            34689999999999999999988765

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=91.74  E-value=0.14  Score=45.59  Aligned_cols=27  Identities=15%  Similarity=0.268  Sum_probs=23.1

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..-..++|.|..|.|||||.+.+.+..
T Consensus       155 ~~Gq~~~IvG~sGsGKSTLl~~Iag~~  181 (438)
T 2dpy_A          155 GRGQRMGLFAGSGVGKSVLLGMMARYT  181 (438)
T ss_dssp             BTTCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            345789999999999999999988754

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=91.72  E-value=0.082  Score=48.37  Aligned_cols=24  Identities=42%  Similarity=0.623  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -.+++|.|..|.|||||++.++.-
T Consensus       294 Gei~~i~G~nGsGKSTLl~~l~Gl  317 (538)
T 3ozx_A          294 GEIIGILGPNGIGKTTFARILVGE  317 (538)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999998753

>3ez2_A Plasmid partition protein A; type IA, DNA binding, winged-HTH, DNA bindin; HET: ADP EPE; 2.05A {Escherichia coli} PDB: 3ez6_A* 3ez7_A

Probab=91.69  E-value=0.23  Score=43.29  Aligned_cols=28  Identities=21%  Similarity=0.287  Sum_probs=22.7

Q ss_pred             CCeEEEEEE-cCCCChHHHHHHHHHHHHh
Q 043980          202 KDVYALGIW-GIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       202 ~~~~~i~i~-G~gGiGKTtla~~v~~~~~  229 (233)
                      ...++|+|+ |-||+||||+|..+...+.
T Consensus       106 ~~~~vIav~s~KGGvGKTT~a~nLA~~La  134 (398)
T 3ez2_A          106 SEAYVIFISNLKGGVSKTVSTVSLAHAMR  134 (398)
T ss_dssp             CSCEEEEECCSSSSSSHHHHHHHHHHHHH
T ss_pred             CCCeEEEEEeCCCCccHHHHHHHHHHHHH
Confidence            347888888 8899999999998876543

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=91.59  E-value=0.1  Score=47.68  Aligned_cols=25  Identities=24%  Similarity=0.457  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||.+.+...
T Consensus        46 ~Ge~~~LvG~NGaGKSTLlk~l~Gl   70 (538)
T 1yqt_A           46 EGMVVGIVGPNGTGKSTAVKILAGQ   70 (538)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3468999999999999999998753

>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=91.53  E-value=0.072  Score=51.09  Aligned_cols=49  Identities=24%  Similarity=0.384  Sum_probs=35.0

Q ss_pred             CccccccchHHHHHHHhccC-----------CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGVK-----------SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~-----------~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+.|.++.+++|.+.+..-           ....+-+-++|.+|.|||.||+++.+...
T Consensus       477 ~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~  536 (806)
T 3cf2_A          477 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQ  536 (806)
T ss_dssp             TTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTT
T ss_pred             HHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhC
Confidence            45678887777777654321           11234467899999999999999998644

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=91.36  E-value=0.11  Score=48.21  Aligned_cols=24  Identities=33%  Similarity=0.477  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -.+++|.|..|.|||||.+.+...
T Consensus       382 Gei~~i~G~NGsGKSTLlk~l~Gl  405 (607)
T 3bk7_A          382 GEVIGIVGPNGIGKTTFVKMLAGV  405 (607)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999998764

>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=91.30  E-value=0.16  Score=38.15  Aligned_cols=23  Identities=30%  Similarity=0.248  Sum_probs=19.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .+..|+|..|.|||||..+++--
T Consensus        24 g~~~I~G~NGsGKStil~Ai~~~   46 (149)
T 1f2t_A           24 GINLIIGQNGSGKSSLLDAILVG   46 (149)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            47789999999999999998654

>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=91.29  E-value=0.079  Score=45.32  Aligned_cols=24  Identities=25%  Similarity=0.268  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..+++|+|..|.|||||.+.+..-
T Consensus       171 g~~v~i~G~~GsGKTTll~~l~g~  194 (330)
T 2pt7_A          171 GKNVIVCGGTGSGKTTYIKSIMEF  194 (330)
T ss_dssp             TCCEEEEESTTSCHHHHHHHGGGG
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999987654

>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=91.23  E-value=0.16  Score=44.15  Aligned_cols=44  Identities=25%  Similarity=0.187  Sum_probs=30.7

Q ss_pred             cccchHHHHHHHhc-cCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          185 GVESRVEEIESLLG-VKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       185 g~~~~~~~l~~~l~-~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +...-...|..+|. .+-..-.++-|.|.+|+||||||..+....
T Consensus        54 ~i~TG~~~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~la~~~   98 (366)
T 1xp8_A           54 VVSTGSLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQA   98 (366)
T ss_dssp             EECCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eecCCCHHHHHHhCCCCccCCcEEEEEcCCCCChHHHHHHHHHHH
Confidence            33444566767665 232234678889999999999999877653

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=91.17  E-value=0.12  Score=48.02  Aligned_cols=23  Identities=26%  Similarity=0.365  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .+++|.|..|.|||||.+.+..-
T Consensus       379 Eiv~iiG~NGsGKSTLlk~l~Gl  401 (608)
T 3j16_B          379 EILVMMGENGTGKTTLIKLLAGA  401 (608)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHTS
T ss_pred             eEEEEECCCCCcHHHHHHHHhcC
Confidence            57999999999999999998753

>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5 c.37.1.8

Probab=91.05  E-value=0.064  Score=45.58  Aligned_cols=22  Identities=27%  Similarity=0.339  Sum_probs=19.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .+++|.|..|+|||||.+.+..
T Consensus       174 ~~~~lvG~sG~GKSTLln~L~g  195 (307)
T 1t9h_A          174 KTTVFAGQSGVGKSSLLNAISP  195 (307)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC
T ss_pred             CEEEEECCCCCCHHHHHHHhcc
Confidence            4889999999999999998754

>2oze_A ORF delta'; para, walker type atpases, DNA segregation, PSM19035, plasmid, DNA binding protein; HET: AGS EPE; 1.83A {Streptococcus pyogenes}

Probab=91.04  E-value=0.12  Score=43.03  Aligned_cols=25  Identities=28%  Similarity=0.343  Sum_probs=19.7

Q ss_pred             eEEEEEEc---CCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWG---IGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G---~gGiGKTtla~~v~~~~  228 (233)
                      .++|+|++   -||+||||+|..+...+
T Consensus        34 ~~~i~v~~~s~KGGvGKTT~a~nLA~~l   61 (298)
T 2oze_A           34 NEAIVILNNYFKGGVGKSKLSTMFAYLT   61 (298)
T ss_dssp             CSCEEEEECCSSSSSSHHHHHHHHHHHH
T ss_pred             CcEEEEEeccCCCCchHHHHHHHHHHHH
Confidence            45667775   89999999999887654

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=91.01  E-value=0.057  Score=50.04  Aligned_cols=48  Identities=17%  Similarity=0.019  Sum_probs=31.7

Q ss_pred             CCccccccchHHHHHHHhccCCCC---------eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          180 KNQLAGVESRVEEIESLLGVKSKD---------VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~~~~~~---------~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .+.++|.+.-++.+...|..+...         -.-+-++|.+|+|||+||+++++.
T Consensus       294 ~~~I~G~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~~  350 (595)
T 3f9v_A          294 APSIYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISRV  350 (595)
T ss_dssp             SSTTSCCHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSSTT
T ss_pred             cchhcChHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHHHHHHHHh
Confidence            467889887655554433322100         013668999999999999988764

>4dcu_A GTP-binding protein ENGA; GTPase, GDP, protein binding, hydrolase; HET: GDP; 2.00A {Bacillus subtilis} PDB: 4dct_A* 4dcs_A* 4dcv_A* 2hjg_A*

Probab=90.99  E-value=1.4  Score=39.08  Aligned_cols=24  Identities=21%  Similarity=0.472  Sum_probs=20.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ...-|+++|.+|+|||||...+..
T Consensus       194 ~~~ki~ivG~~~vGKSslin~l~~  217 (456)
T 4dcu_A          194 EVIQFCLIGRPNVGKSSLVNAMLG  217 (456)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHT
T ss_pred             ccceeEEecCCCCCHHHHHHHHhC
Confidence            456789999999999999998874

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=90.87  E-value=0.13  Score=47.71  Aligned_cols=25  Identities=32%  Similarity=0.498  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||.+.+..-
T Consensus       102 ~Gei~~LvGpNGaGKSTLLkiL~Gl  126 (608)
T 3j16_B          102 PGQVLGLVGTNGIGKSTALKILAGK  126 (608)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcC
Confidence            3568999999999999999988753

>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=90.86  E-value=0.11  Score=46.11  Aligned_cols=21  Identities=29%  Similarity=0.563  Sum_probs=18.7

Q ss_pred             EEEEcCCCChHHHHHHHHHHH
Q 043980          207 LGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       207 i~i~G~gGiGKTtla~~v~~~  227 (233)
                      |+|+|..|+|||||.+.++..
T Consensus        34 I~lvG~sGaGKSTLln~L~g~   54 (418)
T 2qag_C           34 LMVVGESGLGKSTLINSLFLT   54 (418)
T ss_dssp             EEEECCTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCcHHHHHHHHhCC
Confidence            499999999999999998763

>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=90.55  E-value=0.22  Score=45.86  Aligned_cols=24  Identities=25%  Similarity=0.285  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .++.|.|.+|.||||++.++...+
T Consensus       205 ~~~~I~G~pGTGKTt~i~~l~~~l  228 (574)
T 3e1s_A          205 RLVVLTGGPGTGKSTTTKAVADLA  228 (574)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHH
Confidence            577899999999999999987754

>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine kinase domain, signaling protein, transferase, inner membrane, membrane; 2.50A {Escherichia coli}

Probab=90.49  E-value=0.29  Score=41.06  Aligned_cols=27  Identities=26%  Similarity=0.224  Sum_probs=21.9

Q ss_pred             CCeEEEEEEcC-CCChHHHHHHHHHHHH
Q 043980          202 KDVYALGIWGI-GGIGKTKIARAIFDKI  228 (233)
Q Consensus       202 ~~~~~i~i~G~-gGiGKTtla~~v~~~~  228 (233)
                      ...++|.|.|. ||+||||+|..+...+
T Consensus       102 ~~~kvI~vts~kgG~GKTtva~nLA~~l  129 (299)
T 3cio_A          102 TENNILMITGATPDSGKTFVSSTLAAVI  129 (299)
T ss_dssp             CSCCEEEEEESSSSSCHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCChHHHHHHHHHHH
Confidence            34689999985 8999999999877654

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=90.44  E-value=0.14  Score=47.45  Aligned_cols=25  Identities=32%  Similarity=0.497  Sum_probs=21.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||.+.+...
T Consensus       116 ~Ge~~~LiG~NGsGKSTLlkiL~Gl  140 (607)
T 3bk7_A          116 DGMVVGIVGPNGTGKTTAVKILAGQ  140 (607)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCC
Confidence            3468999999999999999987653

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=90.40  E-value=0.15  Score=46.36  Aligned_cols=22  Identities=23%  Similarity=0.144  Sum_probs=19.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAI  224 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v  224 (233)
                      .-.+++|.|..|.|||||++.+
T Consensus        38 ~Ge~~~l~G~nGsGKSTL~~~~   59 (525)
T 1tf7_A           38 IGRSTLVSGTSGTGKTLFSIQF   59 (525)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHH
Confidence            3578999999999999999995

>2qtf_A Protein HFLX, GTP-binding protein; beta-alpha-barrels, nucleotide-binding, nucleotide binding protein; 2.00A {Sulfolobus solfataricus P2} PDB: 2qth_A* 3kxi_A* 3kxl_A 3kxk_A

Probab=90.25  E-value=0.16  Score=44.11  Aligned_cols=24  Identities=25%  Similarity=0.452  Sum_probs=20.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      +...|+|+|.+|+|||||.+.+.+
T Consensus       178 ~~~~V~lvG~~naGKSTLln~L~~  201 (364)
T 2qtf_A          178 NIPSIGIVGYTNSGKTSLFNSLTG  201 (364)
T ss_dssp             -CCEEEEECBTTSSHHHHHHHHHC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHC
Confidence            467799999999999999998765

>3cnl_A YLQF, putative uncharacterized protein; circular permutation, GNP, signaling protein; HET: GNP; 2.00A {Thermotoga maritima} PDB: 3cnn_A* 3cno_A*

Probab=90.15  E-value=0.29  Score=40.35  Aligned_cols=35  Identities=20%  Similarity=0.129  Sum_probs=25.4

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +++|.+.+....   ..++++|.+|+|||||...+...
T Consensus        88 i~~L~~~l~~~~---~~v~~vG~~~vGKSslin~l~~~  122 (262)
T 3cnl_A           88 KVLLKKLSFDRL---ARVLIVGVPNTGKSTIINKLKGK  122 (262)
T ss_dssp             HHHHHHHCCCTT---CEEEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhh---hheEEeCCCCCCHHHHHHHHhcc
Confidence            455655554211   46889999999999999988753

>2qag_A Septin-2, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=90.04  E-value=0.12  Score=44.73  Aligned_cols=21  Identities=29%  Similarity=0.570  Sum_probs=18.6

Q ss_pred             EEEEEcCCCChHHHHHHHHHH
Q 043980          206 ALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -|+|+|..|+|||||...++.
T Consensus        39 ~I~vvG~~g~GKSTLln~L~~   59 (361)
T 2qag_A           39 TLMVVGESGLGKSTLINSLFL   59 (361)
T ss_dssp             CEEECCCTTSCHHHHHHHHTT
T ss_pred             EEEEEcCCCCCHHHHHHHHhC
Confidence            468999999999999999765

>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=89.93  E-value=0.19  Score=45.15  Aligned_cols=24  Identities=29%  Similarity=0.721  Sum_probs=21.1

Q ss_pred             EEEEEcCCCChHHHHHHHHHHHHh
Q 043980          206 ALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .++|+|..|+|||||++.+...+.
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~~~  176 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHNIA  176 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCccHHHHHHHhhhh
Confidence            588999999999999999887654

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=89.91  E-value=0.23  Score=44.70  Aligned_cols=38  Identities=8%  Similarity=-0.068  Sum_probs=27.3

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...|..++. +-..-.++-|.|.+|+||||||..+....
T Consensus       229 ~~~LD~~lg-Gl~~G~l~li~G~pG~GKT~lal~~a~~~  266 (503)
T 1q57_A          229 CTGINDKTL-GARGGEVIMVTSGSGMVMSTFVRQQALQW  266 (503)
T ss_dssp             CTTHHHHHC-CCCTTCEEEEEESSCHHHHHHHHHHHHHH
T ss_pred             hhhhhHhhc-ccCCCeEEEEeecCCCCchHHHHHHHHHH
Confidence            334444453 33345688899999999999999987764

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=89.74  E-value=0.18  Score=46.40  Aligned_cols=25  Identities=24%  Similarity=0.270  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||++.+..-
T Consensus       368 ~G~~~~ivG~sGsGKSTll~~l~g~  392 (582)
T 3b5x_A          368 QGKTVALVGRSGSGKSTIANLFTRF  392 (582)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3568999999999999999988653

>3b60_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; HET: ANP; 3.70A {Salmonella typhimurium} SCOP: c.37.1.12 f.37.1.1 PDB: 3b5y_A* 3b5z_A* 3b5w_A

Probab=89.65  E-value=0.18  Score=46.40  Aligned_cols=23  Identities=30%  Similarity=0.364  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -.+++|+|..|.|||||.+.+..
T Consensus       369 G~~~~ivG~sGsGKSTLl~~l~g  391 (582)
T 3b60_A          369 GKTVALVGRSGSGKSTIASLITR  391 (582)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhh
Confidence            46899999999999999998765

>3bfv_A CAPA1, CAPB2, membrane protein CAPA1, protein tyrosine kinase; chimerical protein, P-loop protein, capsule biogenesis/degradation; HET: ADP; 1.80A {Staphylococcus aureus} PDB: 2ved_A*

Probab=89.62  E-value=0.4  Score=39.63  Aligned_cols=27  Identities=26%  Similarity=0.246  Sum_probs=21.6

Q ss_pred             CCeEEEEEEc-CCCChHHHHHHHHHHHH
Q 043980          202 KDVYALGIWG-IGGIGKTKIARAIFDKI  228 (233)
Q Consensus       202 ~~~~~i~i~G-~gGiGKTtla~~v~~~~  228 (233)
                      ...++|.|.+ .||+||||+|..+...+
T Consensus        80 ~~~kvI~vts~kgG~GKTt~a~nLA~~l  107 (271)
T 3bfv_A           80 SAVQSIVITSEAPGAGKSTIAANLAVAY  107 (271)
T ss_dssp             CCCCEEEEECSSTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCcHHHHHHHHHHHH
Confidence            3468899996 48999999999877654

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=89.62  E-value=0.2  Score=43.08  Aligned_cols=24  Identities=21%  Similarity=0.379  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ....++++|.+|+|||||...+..
T Consensus       166 ~~~~v~lvG~~gvGKSTLin~L~~  189 (357)
T 2e87_A          166 EIPTVVIAGHPNVGKSTLLKALTT  189 (357)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHCS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            467899999999999999988754

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=89.14  E-value=0.2  Score=45.58  Aligned_cols=24  Identities=29%  Similarity=0.267  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..++|.|..|.||||+.+++..-+
T Consensus       261 ~~i~I~GptGSGKTTlL~aL~~~i  284 (511)
T 2oap_1          261 FSAIVVGETASGKTTTLNAIMMFI  284 (511)
T ss_dssp             CCEEEEESTTSSHHHHHHHHGGGS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            358999999999999999886643

>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase, cell adhesion, nucleotide-binding, protein engineering, RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa} PDB: 2wkr_A* 2wkp_A*

Probab=89.14  E-value=0.28  Score=40.93  Aligned_cols=24  Identities=21%  Similarity=0.239  Sum_probs=20.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .--|.|+|.+|+|||||...+.+.
T Consensus       155 ~~~i~i~G~~~~GKssli~~~~~~  178 (332)
T 2wkq_A          155 LIKCVVVGDGAVGKTCLLISYTTN  178 (332)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCChHHHHHHHHhC
Confidence            456789999999999999887653

>1mky_A Probable GTP-binding protein ENGA; GTPase, DER, KH-domain, tandem G-domains, ligand binding protein; HET: GDP; 1.90A {Thermotoga maritima} SCOP: c.37.1.8 c.37.1.8 d.52.5.1

Probab=88.84  E-value=0.47  Score=41.94  Aligned_cols=25  Identities=32%  Similarity=0.527  Sum_probs=21.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +..-++|+|.+|+|||||.+.+...
T Consensus       179 ~~~kvaivG~~gvGKSTLln~l~g~  203 (439)
T 1mky_A          179 DAIKVAIVGRPNVGKSTLFNAILNK  203 (439)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCceEEEECCCCCCHHHHHHHHhCC
Confidence            3567899999999999999998653

>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=88.82  E-value=0.29  Score=43.13  Aligned_cols=25  Identities=24%  Similarity=0.026  Sum_probs=22.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+.++|+|..|.|||||++.+.+.+
T Consensus       174 GQr~~IvG~sG~GKTtLl~~Iar~i  198 (422)
T 3ice_A          174 GQRGLIVAPPKAGKTMLLQNIAQSI  198 (422)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             CcEEEEecCCCCChhHHHHHHHHHH
Confidence            4688999999999999999988764

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=88.31  E-value=0.21  Score=46.18  Aligned_cols=24  Identities=25%  Similarity=0.332  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ...+++|+|..|.|||||++.+..
T Consensus       380 ~G~~~~ivG~sGsGKSTll~~l~g  403 (598)
T 3qf4_B          380 PGQKVALVGPTGSGKTTIVNLLMR  403 (598)
T ss_dssp             TTCEEEEECCTTSSTTHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhc
Confidence            347899999999999999998764

>1of1_A Thymidine kinase; transferase, antiviral drug, enzyme- prodrug gene, DNA synthesis, ATP-binding; HET: SCT; 1.95A {Herpes simplex virus} SCOP: c.37.1.1

Probab=88.20  E-value=0.25  Score=43.08  Aligned_cols=27  Identities=26%  Similarity=0.254  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ....|.|-|.-|+||||+++.+.+.+.
T Consensus        48 ~~~fIt~EG~dGsGKTT~~~~Lae~L~   74 (376)
T 1of1_A           48 TLLRVYIDGPHGMGKTTTTQLLVALGS   74 (376)
T ss_dssp             EEEEEEECSSTTSSHHHHHHHHHC---
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHhh
Confidence            467899999999999999999987643

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A*

Probab=88.16  E-value=0.5  Score=43.73  Aligned_cols=30  Identities=17%  Similarity=0.275  Sum_probs=24.1

Q ss_pred             hccCCCCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          197 LGVKSKDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       197 l~~~~~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      |..-...+.+|+|+|.+|+|||||...+..
T Consensus        31 L~~i~~~~~~VaivG~pnvGKStLiN~L~g   60 (592)
T 1f5n_A           31 LSAITQPMVVVAIVGLYRTGKSYLMNKLAG   60 (592)
T ss_dssp             HHTCCSBEEEEEEEEBTTSSHHHHHHHHTT
T ss_pred             HHhccCCCcEEEEECCCCCCHHHHHHhHcC
Confidence            333345688999999999999999988765

>1udx_A The GTP-binding protein OBG; TGS domain, riken structural genomics/proteomics initiative, RSGI, structural genomics; 2.07A {Thermus thermophilus} SCOP: b.117.1.1 c.37.1.8 d.242.1.1

Probab=88.00  E-value=0.21  Score=44.22  Aligned_cols=23  Identities=22%  Similarity=0.406  Sum_probs=20.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ...++|+|.+|.|||||.+.+..
T Consensus       157 g~~VgLVG~~gAGKSTLL~~Lsg  179 (416)
T 1udx_A          157 IADVGLVGYPNAGKSSLLAAMTR  179 (416)
T ss_dssp             SCSEEEECCGGGCHHHHHHHHCS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHc
Confidence            45689999999999999998754

>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=87.97  E-value=0.38  Score=41.89  Aligned_cols=46  Identities=22%  Similarity=0.257  Sum_probs=32.9

Q ss_pred             CccccccchHHHHHHHhcc-CCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGV-KSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~-~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..++|....++++.+.+.. ...+.. +-|.|..|+|||++|+.++..
T Consensus       137 ~~~ig~s~~m~~l~~~i~~~a~~~~~-vli~Ge~GtGK~~lAr~ih~~  183 (387)
T 1ny5_A          137 EEYVFESPKMKEILEKIKKISCAECP-VLITGESGVGKEVVARLIHKL  183 (387)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHTTCCSC-EEEECSTTSSHHHHHHHHHHH
T ss_pred             hhhhhccHHhhHHHHHHHHhcCCCCC-eEEecCCCcCHHHHHHHHHHh
Confidence            3567777777777665543 222333 478999999999999999874

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=87.60  E-value=0.18  Score=46.37  Aligned_cols=23  Identities=22%  Similarity=0.281  Sum_probs=19.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -.+++|+|..|.|||||.+.+..
T Consensus       367 G~~~~ivG~sGsGKSTll~~l~g  389 (578)
T 4a82_A          367 GETVAFVGMSGGGKSTLINLIPR  389 (578)
T ss_dssp             TCEEEEECSTTSSHHHHHTTTTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            46899999999999999987654

>3o47_A ADP-ribosylation factor GTPase-activating protein ribosylation factor 1; structural genomics consortium, GTPase activation; HET: GDP; 2.80A {Homo sapiens}

Probab=87.56  E-value=0.25  Score=42.05  Aligned_cols=21  Identities=24%  Similarity=0.306  Sum_probs=18.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIF  225 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~  225 (233)
                      --|.|+|.+|+|||||...+.
T Consensus       166 ~kI~ivG~~~vGKSsLl~~l~  186 (329)
T 3o47_A          166 MRILMVGLDAAGKTTILYKLK  186 (329)
T ss_dssp             EEEEEEESTTSSHHHHHHHTC
T ss_pred             ceEEEECCCCccHHHHHHHHh
Confidence            357899999999999998764

>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein biosynthesis, nucleotide-binding, phosphorylation, RNA- binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A

Probab=87.43  E-value=0.33  Score=47.56  Aligned_cols=23  Identities=39%  Similarity=0.605  Sum_probs=20.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -.+++|+|..|.|||||.+.+..
T Consensus       461 Ge~v~LiGpNGsGKSTLLk~Lag  483 (986)
T 2iw3_A          461 ARRYGICGPNGCGKSTLMRAIAN  483 (986)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            36799999999999999999874

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=87.40  E-value=0.22  Score=45.87  Aligned_cols=23  Identities=22%  Similarity=0.268  Sum_probs=20.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -.+++|+|..|.|||||++.+..
T Consensus       369 Ge~~~ivG~sGsGKSTll~~l~g  391 (587)
T 3qf4_A          369 GSLVAVLGETGSGKSTLMNLIPR  391 (587)
T ss_dssp             TCEEEEECSSSSSHHHHHHTTTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999997654

>4aby_A DNA repair protein RECN; hydrolase, double strand break repair, ATPase, nucleotide binding domain; HET: DNA; 3.00A {Deinococcus radiodurans}

Probab=87.29  E-value=0.15  Score=44.39  Aligned_cols=22  Identities=27%  Similarity=0.149  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHHHH
Q 043980          206 ALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +++|+|..|.|||||.++++--
T Consensus        62 ~~~lvG~NGaGKStLl~aI~~l   83 (415)
T 4aby_A           62 FCAFTGETGAGKSIIVDALGLL   83 (415)
T ss_dssp             EEEEEESHHHHHHHHTHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHH
Confidence            8999999999999999998643

>1zcb_A G alpha I/13; GTP-binding, lipoprotein, membrane, transducer, signaling PR; HET: GDP; 2.00A {Mus musculus} SCOP: a.66.1.1 c.37.1.8 PDB: 3ab3_A* 3cx8_A* 3cx7_A* 3cx6_A* 1zca_A*

Probab=87.17  E-value=0.33  Score=42.08  Aligned_cols=21  Identities=19%  Similarity=0.427  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAI  224 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v  224 (233)
                      ..-|-|.|.||.||||+++.+
T Consensus        33 ~~killlG~~~SGKST~~kq~   53 (362)
T 1zcb_A           33 LVKILLLGAGESGKSTFLKQM   53 (362)
T ss_dssp             CEEEEEECSTTSSHHHHHHHH
T ss_pred             ccEEEEECCCCCcHHHHHHHH
Confidence            445678899999999999975

>3q5d_A Atlastin-1; G protein, GTPase, GDP/GTP binding, hydrolase; HET: GDP; 2.70A {Homo sapiens} PDB: 3q5e_A* 3qnu_A* 3qof_A*

Probab=86.96  E-value=0.83  Score=40.73  Aligned_cols=38  Identities=18%  Similarity=0.225  Sum_probs=29.8

Q ss_pred             HHHHHHHhcc---CCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLGV---KSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~~---~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .+.+.++|..   ....+.+|+|+|....||+||...++..
T Consensus        50 ~eal~~iL~~~~~~~~~v~vVsV~G~~~~GKStLLN~llg~   90 (447)
T 3q5d_A           50 ETALNRILLSEAVRDKEVVAVSVAGAFRKGKSFLMDFMLRY   90 (447)
T ss_dssp             HHHHHHHHCCTTTTTSBEEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHhccccCCCceEEEEEECCCCCcHHHHHHHHhhh
Confidence            4555555554   2346999999999999999999999875

>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=86.87  E-value=0.64  Score=43.01  Aligned_cols=37  Identities=19%  Similarity=0.096  Sum_probs=26.5

Q ss_pred             cchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          187 ESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       187 ~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +.+...+...+.     -+.+-|.|.+|.||||++..+...+
T Consensus       152 ~~Q~~Ai~~~l~-----~~~~vi~G~pGTGKTt~l~~ll~~l  188 (608)
T 1w36_D          152 NWQKVAAAVALT-----RRISVISGGPGTGKTTTVAKLLAAL  188 (608)
T ss_dssp             CHHHHHHHHHHT-----BSEEEEECCTTSTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhc-----CCCEEEEeCCCCCHHHHHHHHHHHH
Confidence            344555554442     3578899999999999998876654

>3dpu_A RAB family protein; roccor, G-domain, COR, GTP-binding, nucleotide-binding, SIGN protein; 2.90A {Chlorobaculum tepidum}

Probab=86.26  E-value=0.37  Score=43.73  Aligned_cols=23  Identities=22%  Similarity=0.348  Sum_probs=20.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .--|+++|.+|+|||||...+.+
T Consensus        41 ~~kV~lvG~~~vGKSSLl~~l~~   63 (535)
T 3dpu_A           41 EIKVHLIGDGMAGKTSLLKQLIG   63 (535)
T ss_dssp             EEEEEEESSSCSSHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhc
Confidence            45688999999999999998765

>3ez9_A Para; DNA binding, winged-HTH, partition, biosynthetic protein; 2.80A {Salmonella enterica subsp} PDB: 3ezf_A

Probab=86.17  E-value=0.3  Score=42.57  Aligned_cols=28  Identities=21%  Similarity=0.271  Sum_probs=14.8

Q ss_pred             CCeEEEEEE-cCCCChHHHHHHHHHHHHh
Q 043980          202 KDVYALGIW-GIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       202 ~~~~~i~i~-G~gGiGKTtla~~v~~~~~  229 (233)
                      ...++|+|+ |-||+||||+|..+...+.
T Consensus       109 ~~~~vIav~s~KGGvGKTT~a~nLA~~LA  137 (403)
T 3ez9_A          109 KSPYVIFVVNLKGGVSKTVSTVTLAHALR  137 (403)
T ss_dssp             CSCEEEEECCC--------CHHHHHHHHH
T ss_pred             CCceEEEEEcCCCCchHHHHHHHHHHHHH
Confidence            346788888 8899999999998876553

>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=86.05  E-value=0.42  Score=41.35  Aligned_cols=47  Identities=28%  Similarity=0.335  Sum_probs=32.5

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ..++|....+.++...+..-...-..+-|.|..|.||+++|+.+++.
T Consensus       129 ~~~ig~s~~~~~~~~~~~~~a~~~~~vli~GesGtGKe~lAr~ih~~  175 (368)
T 3dzd_A          129 IEFVGEHPKILEIKRLIPKIAKSKAPVLITGESGTGKEIVARLIHRY  175 (368)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHHTSCSCEEEECCTTSSHHHHHHHHHHH
T ss_pred             ccccccchHHHHHHhhhhhhhccchhheEEeCCCchHHHHHHHHHHh
Confidence            45778777777766654331111223558899999999999999874

>1ko7_A HPR kinase/phosphatase; protein kinase, phosphotransfer, protein phosphatase, dual activity, product, substrate, transferase, hydrolase; 1.95A {Staphylococcus xylosus} SCOP: c.98.2.1 c.91.1.2

Probab=85.70  E-value=0.52  Score=40.06  Aligned_cols=23  Identities=30%  Similarity=0.439  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +-+.|.|..|+||||+|.++..+
T Consensus       145 ~~vl~~G~sG~GKSt~a~~l~~~  167 (314)
T 1ko7_A          145 VGVLITGDSGIGKSETALELIKR  167 (314)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHhc
Confidence            57889999999999999988764

>3szr_A Interferon-induced GTP-binding protein MX1; interferon-induced antiviral GTPase, membrane associated, PR binding; 3.50A {Homo sapiens} PDB: 3zys_B

Probab=85.59  E-value=0.45  Score=44.07  Aligned_cols=24  Identities=21%  Similarity=0.307  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .+..++|+|..|.|||||.+.+..
T Consensus        44 ~lp~iaIvG~nGsGKSTLL~~I~G   67 (608)
T 3szr_A           44 ALPAIAVIGDQSSGKSSVLEALSG   67 (608)
T ss_dssp             CCCCEECCCCTTSCHHHHHHHHHS
T ss_pred             cCCeEEEECCCCChHHHHHHHHhC
Confidence            356799999999999999998864

>3l0i_B RAS-related protein RAB-1A; GEF-GDF-RAB complex, GTP-binding, guanine-nucleotide exchang GDI-displacement factor; 2.85A {Homo sapiens}

Probab=85.37  E-value=0.091  Score=40.69  Aligned_cols=24  Identities=21%  Similarity=0.331  Sum_probs=19.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIF  225 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~  225 (233)
                      +...-|.|+|..|+|||||...+.
T Consensus        31 ~~~~ki~vvG~~~~GKSsli~~l~   54 (199)
T 3l0i_B           31 DYLFKLLLIGDSGVGKSCLLLRFA   54 (199)
T ss_dssp             SEEEEEEEECCTTSCCTTTTTSSB
T ss_pred             CcceEEEEECCCCCCHHHHHHHHh
Confidence            345678899999999999987654

>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein biosynthesis, nucleotide-binding, phosphorylation, RNA- binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A

Probab=85.29  E-value=0.33  Score=47.51  Aligned_cols=23  Identities=17%  Similarity=0.375  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      -.+++|.|..|.|||||.+.+..
T Consensus       699 GeivaIiGpNGSGKSTLLklLaG  721 (986)
T 2iw3_A          699 SSRIAVIGPNGAGKSTLINVLTG  721 (986)
T ss_dssp             TCEEEECSCCCHHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999998865

>3ec1_A YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase, signaling protein; HET: GDP; 2.36A {Geobacillus stearothermophilus}

Probab=84.77  E-value=0.63  Score=40.27  Aligned_cols=39  Identities=18%  Similarity=0.268  Sum_probs=27.5

Q ss_pred             ccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          184 AGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       184 ~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .|.+.-++.+.+++.     .+.+.++|..|+|||||..++.+.
T Consensus       147 ~gi~~L~~~I~~~~~-----~~~i~~vG~~nvGKStliN~L~~~  185 (369)
T 3ec1_A          147 IGMAKVMEAINRYRE-----GGDVYVVGCTNVGKSTFINRIIEE  185 (369)
T ss_dssp             BTHHHHHHHHHHHHT-----TSCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHhhcc-----cCcEEEEcCCCCchHHHHHHHHhh
Confidence            344444455544432     135789999999999999999876

>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=84.52  E-value=0.85  Score=42.25  Aligned_cols=36  Identities=28%  Similarity=0.258  Sum_probs=24.6

Q ss_pred             chHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          188 SRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       188 ~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+.+.+...+.     ..+.-|.|.+|.||||++..+...+
T Consensus       184 ~Q~~av~~~l~-----~~~~li~GppGTGKT~~~~~~i~~l  219 (624)
T 2gk6_A          184 SQVYAVKTVLQ-----RPLSLIQGPPGTGKTVTSATIVYHL  219 (624)
T ss_dssp             HHHHHHHHHHT-----CSEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhc-----CCCeEEECCCCCCHHHHHHHHHHHH
Confidence            44555555443     2356789999999999888776553

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=84.07  E-value=0.74  Score=48.36  Aligned_cols=38  Identities=18%  Similarity=0.188  Sum_probs=28.3

Q ss_pred             HHHHHHHhc-cCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLG-VKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~-~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...|..+|. .+-...+.+-|+|.+|+|||+||.++...
T Consensus      1412 ~~~LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~e 1450 (2050)
T 3cmu_A         1412 SLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAA 1450 (2050)
T ss_dssp             CHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CHHHHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            344666666 33234578899999999999999998765

>3geh_A MNME, tRNA modification GTPase MNME; G protein, U34, GTP-binding, HYDR magnesium, metal-binding, nucleotide-binding, potassium, TR processing; HET: GDP FON; 3.20A {Nostoc SP}

Probab=84.01  E-value=0.65  Score=41.53  Aligned_cols=22  Identities=23%  Similarity=0.327  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHHHH
Q 043980          206 ALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -|+|+|.+|+|||||...+.+.
T Consensus       226 kV~ivG~~nvGKSSLln~L~~~  247 (462)
T 3geh_A          226 KVAIVGRPNVGKSSLLNAWSQS  247 (462)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHhCC
Confidence            3899999999999999998764

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=83.97  E-value=0.51  Score=47.61  Aligned_cols=24  Identities=21%  Similarity=0.349  Sum_probs=21.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ...+++|+|..|.|||||++.+..
T Consensus      1058 ~Ge~v~ivG~sGsGKSTl~~~l~g 1081 (1284)
T 3g5u_A         1058 KGQTLALVGSSGCGKSTVVQLLER 1081 (1284)
T ss_dssp             SSSEEEEECSSSTTHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            346899999999999999999875

>3t34_A Dynamin-related protein 1A, linker, dynamin-relat 1A; dynamin-like protein 1A, GTPase, membrane fission, motor Pro; HET: GDP; 2.40A {Arabidopsis thaliana} PDB: 3t35_A*

Probab=83.96  E-value=0.56  Score=40.18  Aligned_cols=24  Identities=21%  Similarity=0.336  Sum_probs=21.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ....|+|+|..|+|||||..++..
T Consensus        33 ~lp~I~vvG~~~sGKSSLln~l~g   56 (360)
T 3t34_A           33 SLPAIAVVGGQSSGKSSVLESIVG   56 (360)
T ss_dssp             CCCEEEEECBTTSSHHHHHHHHHT
T ss_pred             cCCEEEEECCCCCcHHHHHHHHhC
Confidence            456899999999999999999876

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=83.94  E-value=0.73  Score=40.58  Aligned_cols=26  Identities=27%  Similarity=0.106  Sum_probs=22.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      -+-++|.|-.|+|||+|+..+.+.+.
T Consensus       175 GQR~lIfg~~g~GKT~Ll~~Ia~~i~  200 (427)
T 3l0o_A          175 GQRGMIVAPPKAGKTTILKEIANGIA  200 (427)
T ss_dssp             TCEEEEEECTTCCHHHHHHHHHHHHH
T ss_pred             CceEEEecCCCCChhHHHHHHHHHHh
Confidence            35678999999999999999988653

>1lnz_A SPO0B-associated GTP-binding protein; GTPase, OBG, stringent factor, stress response, sporulation, large G-protein, structural genomics, PSI; HET: G4P; 2.60A {Bacillus subtilis} SCOP: b.117.1.1 c.37.1.8

Probab=83.85  E-value=0.46  Score=40.78  Aligned_cols=23  Identities=17%  Similarity=0.452  Sum_probs=19.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      +.-|+|+|.+++|||||..++.+
T Consensus       158 la~V~lvG~~nvGKSTLln~L~~  180 (342)
T 1lnz_A          158 LADVGLVGFPSVGKSTLLSVVSS  180 (342)
T ss_dssp             CCCEEEESSTTSSHHHHHHHSEE
T ss_pred             cCeeeeeCCCCCCHHHHHHHHHc
Confidence            34589999999999999987654

>4ido_A Atlastin-1; GTPase, GTP/GDP binding, hydrolase; HET: GDP; 2.09A {Homo sapiens} PDB: 4idn_A* 3q5d_A* 3q5e_A* 4idq_A* 4idp_A* 3qnu_A* 3qof_A*

Probab=83.59  E-value=1.8  Score=38.59  Aligned_cols=41  Identities=17%  Similarity=0.210  Sum_probs=30.5

Q ss_pred             chHHHHHHHhcc---CCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          188 SRVEEIESLLGV---KSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       188 ~~~~~l~~~l~~---~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -..+.+..+|..   ....+.+|+|+|..+.|||+|...+++-+
T Consensus        48 ln~eAl~~iL~~~~i~~~~v~vvsv~G~~~~gks~l~N~ll~~~   91 (457)
T 4ido_A           48 LDETALNRILLSEAVRDKEVVAVSVAGAFRKGKSFLMDFMLRYM   91 (457)
T ss_dssp             ECHHHHHHHHSSTTTTTSBEEEEEEEEBTTSSHHHHHHHHHHHH
T ss_pred             ECHHHHHHHHhccccCCCceEEEEEECCCCCchhHHHHHHHHHh
Confidence            345556555554   23469999999999999999999877543

>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A {Geobacillus}

Probab=83.46  E-value=0.38  Score=45.01  Aligned_cols=21  Identities=19%  Similarity=0.430  Sum_probs=18.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAI  224 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v  224 (233)
                      -.+++|+|..|.|||||.+.+
T Consensus       348 Ge~vaIiGpnGsGKSTLl~~i  368 (670)
T 3ux8_A          348 GTFVAVTGVSGSGKSTLVNEV  368 (670)
T ss_dssp             TSEEEEECSTTSSHHHHHTTT
T ss_pred             CCEEEEEeeCCCCHHHHHHHH
Confidence            368999999999999999764

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=82.87  E-value=1.1  Score=39.81  Aligned_cols=25  Identities=24%  Similarity=0.247  Sum_probs=21.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ...++..|.|.+|.||||+.....+
T Consensus       159 ~~~~v~~I~G~aGsGKTt~I~~~~~  183 (446)
T 3vkw_A          159 SSAKVVLVDGVPGCGKTKEILSRVN  183 (446)
T ss_dssp             CCSEEEEEEECTTSCHHHHHHHHCC
T ss_pred             ccccEEEEEcCCCCCHHHHHHHHhc
Confidence            3578999999999999999987653

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=82.86  E-value=1.1  Score=41.71  Aligned_cols=35  Identities=31%  Similarity=0.257  Sum_probs=21.9

Q ss_pred             chHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHH-HHH
Q 043980          188 SRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARA-IFD  226 (233)
Q Consensus       188 ~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~-v~~  226 (233)
                      ++.+.+...|..  .  .+.-|.|++|.|||+.+.+ |++
T Consensus       193 ~Q~~AV~~al~~--~--~~~lI~GPPGTGKT~ti~~~I~~  228 (646)
T 4b3f_X          193 SQKEAVLFALSQ--K--ELAIIHGPPGTGKTTTVVEIILQ  228 (646)
T ss_dssp             HHHHHHHHHHHC--S--SEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC--C--CceEEECCCCCCHHHHHHHHHHH
Confidence            445566555542  1  2556899999999865544 443

>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein, mostly mixed alpha-beta structures, one domain is entirely helical; HET: DNA; 2.20A {Thermus aquaticus} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A* 1fw6_A* 1ewr_A*

Probab=82.71  E-value=0.69  Score=44.10  Aligned_cols=23  Identities=22%  Similarity=0.016  Sum_probs=20.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ..+++|.|..|.|||||.+.+..
T Consensus       576 g~i~~I~GpNGsGKSTlLr~iag  598 (765)
T 1ewq_A          576 HELVLITGPNMAGKSTFLRQTAL  598 (765)
T ss_dssp             SCEEEEESCSSSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHHHh
Confidence            36899999999999999998765

>3h2y_A GTPase family protein; GTP-binding protein YQEH, possibly involved in replication initiation, csgid, IDP90222; HET: DGI; 1.80A {Bacillus anthracis str}

Probab=82.59  E-value=0.83  Score=39.48  Aligned_cols=39  Identities=18%  Similarity=0.321  Sum_probs=27.1

Q ss_pred             ccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          184 AGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       184 ~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .|.+.-.+.+.++..     -..+.++|..|+|||||..++.+.
T Consensus       145 ~gi~~L~~~l~~~~~-----~~~i~~vG~~nvGKStliN~L~~~  183 (368)
T 3h2y_A          145 QGIAELADAIEYYRG-----GKDVYVVGCTNVGKSTFINRMIKE  183 (368)
T ss_dssp             TTHHHHHHHHHHHHT-----TSCEEEEEBTTSSHHHHHHHHHHH
T ss_pred             cCHHHHHhhhhhhcc-----cceEEEecCCCCChhHHHHHHHhh
Confidence            344444444444332     135789999999999999999886

>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=82.50  E-value=0.88  Score=47.07  Aligned_cols=46  Identities=15%  Similarity=0.182  Sum_probs=33.3

Q ss_pred             cccccchHHHHHHHhc-cCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          183 LAGVESRVEEIESLLG-VKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       183 ~~g~~~~~~~l~~~l~-~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+...-..+|..+|. .+-..-.++-|.|.+|+||||||..+....
T Consensus       710 ~~~i~TG~~eLD~lLg~GGl~~G~lVlI~G~PG~GKTtLal~lA~~a  756 (1706)
T 3cmw_A          710 VETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAA  756 (1706)
T ss_dssp             CCEECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ccccccCcHHHHHHhccCCcCCCceEEEECCCCCCcHHHHHHHHHHH
Confidence            3444455667777775 333345788999999999999999987754

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=82.41  E-value=0.98  Score=39.03  Aligned_cols=23  Identities=22%  Similarity=0.239  Sum_probs=19.5

Q ss_pred             EEEEEcCCCChHHHHHHHHHHHH
Q 043980          206 ALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -+.|.|..|.||||+++.+..+.
T Consensus        37 ~~~i~G~~G~GKs~~~~~~~~~~   59 (392)
T 4ag6_A           37 NWTILAKPGAGKSFTAKMLLLRE   59 (392)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEcCCCCCHHHHHHHHHHHH
Confidence            35789999999999999887653

>2qpt_A EH domain-containing protein-2; protein-nucleotide complex, membrane protein, endocytosis; HET: ANP; 3.10A {Mus musculus}

Probab=81.98  E-value=0.72  Score=42.20  Aligned_cols=25  Identities=16%  Similarity=0.174  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ....|+|+|..|+|||||..++...
T Consensus        64 ~~~~V~vvG~~n~GKSTLIN~Llg~   88 (550)
T 2qpt_A           64 GKPMVLVAGQYSTGKTSFIQYLLEQ   88 (550)
T ss_dssp             SCCEEEEEEBTTSCHHHHHHHHHTS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            4678999999999999999998753

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*

Probab=81.92  E-value=0.77  Score=44.00  Aligned_cols=24  Identities=25%  Similarity=0.008  Sum_probs=21.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ..++++|.|..|.|||||.+.+..
T Consensus       606 ~g~i~~ItGpNGsGKSTlLr~iag  629 (800)
T 1wb9_A          606 QRRMLIITGPNMGGKSTYMRQTAL  629 (800)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCChHHHHHHHHH
Confidence            357899999999999999998765

>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A {Geobacillus}

Probab=81.79  E-value=0.64  Score=43.45  Aligned_cols=18  Identities=28%  Similarity=0.416  Sum_probs=16.5

Q ss_pred             eEEEEEEcCCCChHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIA  221 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla  221 (233)
                      -.+++|+|..|.|||||.
T Consensus        44 Ge~~~liGpNGaGKSTLl   61 (670)
T 3ux8_A           44 GKLVVLTGLSGSGKSSLA   61 (670)
T ss_dssp             TSEEEEECSTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHh
Confidence            468999999999999996

>1knx_A Probable HPR(Ser) kinase/phosphatase; HPR kinase, HPR kinase/phosphatase, HPRK/P, P-loop, walker A BOX, catabolite repression; 2.50A {Mycoplasma pneumoniae} SCOP: c.98.2.1 c.91.1.2

Probab=81.44  E-value=0.69  Score=39.26  Aligned_cols=22  Identities=27%  Similarity=0.435  Sum_probs=19.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      +-+-|.|..|+||||+|.++..
T Consensus       148 ~gvli~G~sG~GKStlal~l~~  169 (312)
T 1knx_A          148 VGVLLTGRSGIGKSECALDLIN  169 (312)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHH
Confidence            5678999999999999988754

>2f62_A Nucleoside 2-deoxyribosyltransferase; SGPP, structural genomics, PSI, S genomics of pathogenic protozoa consortium; HET: 12M; 1.50A {Trypanosoma brucei} SCOP: c.23.14.1 PDB: 2a0k_A* 2f2t_A* 2f64_A* 2f67_A*

Probab=81.10  E-value=5.2  Score=30.36  Aligned_cols=67  Identities=10%  Similarity=0.074  Sum_probs=46.9

Q ss_pred             cchHHHHHHHHhhCCCeEEEeCc--cCCCcchHHHHHHHHHhcCceEEEeec---CCCCchhhHHHHHHHHHh
Q 043980           38 DKFTSHLYSALSRQSIQTFIDDQ--LNRGDEISQSLVNAIEASAISVIIFSE---SYTSSRWCVDELVKILEC  105 (233)
Q Consensus        38 ~~f~~~L~~~L~~~gi~~~~d~~--~~~G~~~~~~i~~~i~~s~~~i~v~S~---~y~~S~wc~~El~~~~~~  105 (233)
                      ..+...+.+.|++.|+.++.-.+  ......|...-.++|++|+++|++++|   .+.. .=...|+-.+...
T Consensus        26 ~~~~~~l~~~l~~~G~~v~~P~~~~~~~~~~i~~~d~~~i~~aD~vVA~ldpf~g~~~D-~GTafEiGyA~Al   97 (161)
T 2f62_A           26 ASYYNKVRELLKKENVMPLIPTDNEATEALDIRQKNIQMIKDCDAVIADLSPFRGHEPD-CGTAFEVGCAAAL   97 (161)
T ss_dssp             HHHHHHHHHHHHTTTCEEECTTTTCCSSHHHHHHHHHHHHHHCSEEEEECCCCSSSSCC-HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHCCCEEECCCccCcchHHHHHHHHHHHHHhCCEEEEEecCCCCCCCC-CcHHHHHHHHHHC
Confidence            45889999999999999887431  112233444447899999999999996   3433 3466688776643

>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=81.04  E-value=0.44  Score=48.20  Aligned_cols=23  Identities=22%  Similarity=0.315  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ...|||+|..|.|||||++.+++
T Consensus      1105 Ge~vaIVG~SGsGKSTL~~lL~r 1127 (1321)
T 4f4c_A         1105 GQTLALVGPSGCGKSTVVALLER 1127 (1321)
T ss_dssp             TCEEEEECSTTSSTTSHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            46799999999999999998865

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=80.95  E-value=1.2  Score=46.91  Aligned_cols=47  Identities=15%  Similarity=0.185  Sum_probs=34.6

Q ss_pred             ccccccchHHHHHHHhc-cCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          182 QLAGVESRVEEIESLLG-VKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       182 ~~~g~~~~~~~l~~~l~-~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...+...-...|..+|. .+-..-.++-|.|.+|+||||||..+....
T Consensus       360 ~~~~I~TG~~~LD~lLG~GGl~~G~lilI~G~pGsGKTtLaLqia~~~  407 (2050)
T 3cmu_A          360 DVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAA  407 (2050)
T ss_dssp             SCCEECCSCHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCceeeCCCHHHHHHhccCCccCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            34455555677777776 333345789999999999999999987754

>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=80.64  E-value=1.4  Score=42.21  Aligned_cols=36  Identities=28%  Similarity=0.258  Sum_probs=24.5

Q ss_pred             chHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          188 SRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       188 ~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .+.+.+...+.     ..+.-|.|.+|.||||++.++...+
T Consensus       360 ~Q~~Av~~~l~-----~~~~lI~GppGTGKT~ti~~~i~~l  395 (800)
T 2wjy_A          360 SQVYAVKTVLQ-----RPLSLIQGPPGTGKTVTSATIVYHL  395 (800)
T ss_dssp             HHHHHHHHHHT-----SSEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcc-----CCeEEEEcCCCCCHHHHHHHHHHHH
Confidence            34445554443     1356799999999999888776653

>2j69_A Bacterial dynamin-like protein; FZO, FZL, GTPase, hydrolase; 3.0A {Nostoc punctiforme} PDB: 2j68_A 2w6d_A*

Probab=80.30  E-value=1.1  Score=42.24  Aligned_cols=24  Identities=25%  Similarity=0.329  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      +...|+|+|..|.|||||..++..
T Consensus        68 ~~~~V~VvG~~naGKSSLlNaLlg   91 (695)
T 2j69_A           68 GVFRLLVLGDMKRGKSTFLNALIG   91 (695)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            356789999999999999999875

>2x2e_A Dynamin-1; nitration, hydrolase, membrane fission, nucleotide-binding, endocytosis, motor protein; HET: GDP; 2.00A {Homo sapiens} PDB: 2x2f_A* 3zyc_A* 3zys_A

Probab=80.16  E-value=0.65  Score=39.73  Aligned_cols=24  Identities=17%  Similarity=0.311  Sum_probs=20.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ...-|+|+|.+|+|||||..++..
T Consensus        30 ~~~~I~vvG~~~~GKSSLln~L~g   53 (353)
T 2x2e_A           30 DLPQIAVVGGQSAGKSSVLENFVG   53 (353)
T ss_dssp             CCCEEEEECBTTSSHHHHHHTTTT
T ss_pred             CCCeEEEECCCCCCHHHHHHHHhC
Confidence            356799999999999999988754

---

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	233
d1fyva_	161	c.23.2.1 (A:) Toll-like receptor 1, TLR1 {Human (H	3e-18
d1fyxa_	149	c.23.2.1 (A:) Toll-like receptor 2, TLR2 {Human (H	8e-16
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	3e-04

>d1fyva_ c.23.2.1 (A:) Toll-like receptor 1, TLR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 161

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Toll/Interleukin receptor TIR domain
family: Toll/Interleukin receptor TIR domain
domain: Toll-like receptor 1, TLR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 76.7 bits (188), Expect = 3e-18
 Identities = 24/110 (21%), Positives = 48/110 (43%), Gaps = 3/110 (2%)

Query: 22  NKKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQ-LNRGDEISQSLVNAIEASAI 80
           N ++  F+S+ G D+     + L   L ++ +Q  + ++    G  I ++++  IE S  
Sbjct: 10  NLQFHAFISYSGHDSF-WVKNELLPNLEKEGMQICLHERNFVPGKSIVENIITCIEKSYK 68

Query: 81  SVIIFSESYTSSRWCVDELVKILECK-KEYAQIVIPVLYRVDPSDVRNQT 129
           S+ + S ++  S WC  EL         E +  +I +L    P      +
Sbjct: 69  SIFVLSPNFVQSEWCHYELYFAHHNLFHEGSNSLILILLEPIPQYSIPSS 118

>d1fyxa_ c.23.2.1 (A:) Toll-like receptor 2, TLR2 {Human (Homo sapiens) [TaxId: 9606]} Length = 149

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Toll/Interleukin receptor TIR domain
family: Toll/Interleukin receptor TIR domain
domain: Toll-like receptor 2, TLR2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.7 bits (170), Expect = 8e-16
 Identities = 24/111 (21%), Positives = 41/111 (36%), Gaps = 5/111 (4%)

Query: 22  NKKYEVFVSFRGEDTRDKFTSHLYSAL--SRQSIQTFIDDQ-LNRGDEISQSLVNAIEAS 78
           N  Y+ FVS+   D      + +   L       +  +  +    G  I  +++++IE S
Sbjct: 3   NICYDAFVSYSERD-AYWVENLMVQELENFNPPFKLCLHKRDFIHGKWIIDNIIDSIEKS 61

Query: 79  AISVIIFSESYTSSRWCVDELVKIL-ECKKEYAQIVIPVLYRVDPSDVRNQ 128
             +V + SE++  S WC  EL         E     I +L          Q
Sbjct: 62  HKTVFVLSENFVKSEWCKYELDFSHFRLFDENNDAAILILLEPIEKKAIPQ 112

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

 Score = 38.6 bits (89), Expect = 3e-04
 Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 1/44 (2%)

Query: 185 GVESRVEEI-ESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK 227
             E  V+ + + L  +   D + L + G  G GK+ IA     K
Sbjct: 24  IREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSK 67

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	233
d1fyva_	161	Toll-like receptor 1, TLR1 {Human (Homo sapiens) [	99.86
d1fyxa_	149	Toll-like receptor 2, TLR2 {Human (Homo sapiens) [	99.85
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.15
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.07
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.94
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.76
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.75
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.7
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.68
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.67
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.62
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.59
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.52
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.45
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.44
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.1
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.9
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.83
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	96.78
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.7
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.69
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.67
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	96.12
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.09
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.0
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	95.85
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	95.76
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	95.71
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	95.61
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	95.21
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.18
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	94.73
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	94.54
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	94.5
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	94.48
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	94.48
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	94.43
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	94.4
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	94.37
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	94.33
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	94.3
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	94.26
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	93.75
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	93.69
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	93.67
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	93.41
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	93.34
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	92.97
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	92.71
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	92.39
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	92.06
d1wu7a1	97	Histidyl-tRNA synthetase (HisRS), C-terminal domai	91.04
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	90.9
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	90.68
d1tuea_	205	Replication protein E1 helicase domain {Human papi	90.28
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	90.25
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	89.68
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	89.42
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	88.73
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	87.12
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	86.96
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	85.07
d1xpua3	289	Transcription termination factor Rho, ATPase domai	83.88
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	83.56
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	80.03

>d1fyva_ c.23.2.1 (A:) Toll-like receptor 1, TLR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Toll/Interleukin receptor TIR domain
family: Toll/Interleukin receptor TIR domain
domain: Toll-like receptor 1, TLR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=2.7e-23  Score=161.54  Aligned_cols=98  Identities=23%  Similarity=0.477  Sum_probs=88.4

Q ss_pred             CCCCcceEEEcCcccccccchH-HHHHHHHhhCCCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhhHH
Q 043980           20 RNNKKYEVFVSFRGEDTRDKFT-SHLYSALSRQSIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVD   97 (233)
Q Consensus        20 ~~~~~~dVFISy~~~D~~~~f~-~~L~~~L~~~gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~~   97 (233)
                      ..+++|||||||+++|  ..|| ..|...|+.+|+++|+|+ |+.+|+.+.++|.++|++|+++|+|+|++|+.|.||..
T Consensus         8 ~~~~~yDvFisys~~D--~~~v~~~L~~~Le~~g~~v~~d~~d~~~G~~~~~~i~~~i~~s~~~i~vlS~~~~~s~w~~~   85 (161)
T d1fyva_           8 QRNLQFHAFISYSGHD--SFWVKNELLPNLEKEGMQICLHERNFVPGKSIVENIITCIEKSYKSIFVLSPNFVQSEWCHY   85 (161)
T ss_dssp             SSCCCEEEEEECCGGG--HHHHHHTHHHHHHTTTCCEECTTTTCCTTSCHHHHHHHHHHHEEEEEEEESHHHHHHTSHHH
T ss_pred             CCCCeeEEEEecChhH--HHHHHHHHHHHHHhCCCcceEeccccccccccHHHHHHHHHhCCEEEEEecCccccChHHHH
Confidence            4678999999999999  5577 579999999999999999 99999999999999999999999999999999999999


Q ss_pred             HHHHHHHhh-hcccceeeceeee
Q 043980           98 ELVKILECK-KEYAQIVIPVLYR  119 (233)
Q Consensus        98 El~~~~~~~-~~~~~~viPIf~~  119 (233)
                      |+..++... +.+..++|||+++
T Consensus        86 E~~~a~~~~~~~~~~~lIpV~l~  108 (161)
T d1fyva_          86 ELYFAHHNLFHEGSNSLILILLE  108 (161)
T ss_dssp             HHHTTSCCCSCSSCSSEEEEESS
T ss_pred             HHHHHHHHHHHcCCCceeEEEEe
Confidence            999887654 4455689999966

>d1fyxa_ c.23.2.1 (A:) Toll-like receptor 2, TLR2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Toll/Interleukin receptor TIR domain
family: Toll/Interleukin receptor TIR domain
domain: Toll-like receptor 2, TLR2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1e-22  Score=156.23  Aligned_cols=98  Identities=23%  Similarity=0.382  Sum_probs=86.6

Q ss_pred             CCCcceEEEcCcccccccchH-HHHHHHHhh--CCCeEEEeC-ccCCCcchHHHHHHHHHhcCceEEEeecCCCCchhhH
Q 043980           21 NNKKYEVFVSFRGEDTRDKFT-SHLYSALSR--QSIQTFIDD-QLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCV   96 (233)
Q Consensus        21 ~~~~~dVFISy~~~D~~~~f~-~~L~~~L~~--~gi~~~~d~-~~~~G~~~~~~i~~~i~~s~~~i~v~S~~y~~S~wc~   96 (233)
                      +++.|||||||+++|  ..|| ..|...|++  .|+++|+|+ |+.+|+.+.++|.++|++|+++|+|+|++|+.|.||.
T Consensus         2 ~~~~YDvFiSys~~D--~~~V~~~l~~~LE~~~~g~~~~~~~rd~~~G~~~~~~i~~~i~~S~~~i~vlS~~~l~s~wc~   79 (149)
T d1fyxa_           2 RNICYDAFVSYSERD--AYWVENLMVQELENFNPPFKLCLHKRDFIHGKWIIDNIIDSIEKSHKTVFVLSENFVKSEWCK   79 (149)
T ss_dssp             CSCCEEEEEECCGGG--HHHHHTHHHHHHTTSSSCCCEEEHHHHCCSSSCHHHHHHHHHHHEEEEEEEECHHHHHHHTHH
T ss_pred             CCCEEEEEEECchhh--HHHHHHHHHHHHHhcCCCceEEEecccccccchHHHHHHHHHHhCCEEEEEEcCccccccchH
Confidence            789999999999999  5566 468999986  489999999 9999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhh-hcccceeeceeeee
Q 043980           97 DELVKILECK-KEYAQIVIPVLYRV  120 (233)
Q Consensus        97 ~El~~~~~~~-~~~~~~viPIf~~v  120 (233)
                      .|+..++... +.++.++|||+++.
T Consensus        80 ~E~~~a~~~~~~~~~~~iIpV~l~~  104 (149)
T d1fyxa_          80 YELDFSHFRLFDENNDAAILILLEP  104 (149)
T ss_dssp             HHSCCSCCTTCGGGTTCCEEEESSC
T ss_pred             HHHHHHHHHHHHcCCceEEEEEecc
Confidence            9998776544 45667899999763

>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=99.15  E-value=1.3e-11  Score=102.55  Aligned_cols=51  Identities=24%  Similarity=0.201  Sum_probs=44.2

Q ss_pred             CCCCCccccccchHHHHHHHhcc-CCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGV-KSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~-~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .+..+.++||+.+++++.++|.. ..++.++|+|+|||||||||||+++|++
T Consensus        16 ~p~~~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~   67 (277)
T d2a5yb3          16 VPKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSK   67 (277)
T ss_dssp             CBCCCCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCCceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHh
Confidence            34567788999999999998865 4456899999999999999999999997

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.07  E-value=3.2e-06  Score=67.51  Aligned_cols=52  Identities=21%  Similarity=0.331  Sum_probs=41.9

Q ss_pred             CCCccccccchHHHHHHHhcc----CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEIESLLGV----KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~----~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .+..++||+.+++++.++|..    .....+.+-|+|.+|+||||+|+.+++.+..
T Consensus        14 ~p~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~   69 (276)
T d1fnna2          14 VPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKD   69 (276)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhc
Confidence            345689999999999888753    2233567889999999999999999998754

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.94  E-value=5.3e-06  Score=66.53  Aligned_cols=52  Identities=23%  Similarity=0.217  Sum_probs=39.1

Q ss_pred             CCCCccccccchHHHHHHHhc----cC---CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          178 DNKNQLAGVESRVEEIESLLG----VK---SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~----~~---~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..+..++||+.++++|.+.+.    .+   ++...++-++|.+|+||||+++++++.+.
T Consensus        13 ~~P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~   71 (287)
T d1w5sa2          13 YIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVS   71 (287)
T ss_dssp             CCCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHH
T ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHH
Confidence            356789999999999887542    11   12234566789999999999999998753

>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=97.76  E-value=1.1e-05  Score=63.96  Aligned_cols=54  Identities=20%  Similarity=0.355  Sum_probs=40.4

Q ss_pred             CCCCccccccchHHHHHHHhccC---CCCeEEEEEEcCCCChHHHHHHHHHHHHhcC
Q 043980          178 DNKNQLAGVESRVEEIESLLGVK---SKDVYALGIWGIGGIGKTKIARAIFDKISSD  231 (233)
Q Consensus       178 ~~~~~~~g~~~~~~~l~~~l~~~---~~~~~~i~i~G~gGiGKTtla~~v~~~~~~~  231 (233)
                      ..-.+++|.+.-+++|..++...   .....-+-++|++|+||||+|+.+.+....+
T Consensus         6 ~~~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~   62 (239)
T d1ixsb2           6 KTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVN   62 (239)
T ss_dssp             CSGGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHHTCC
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            34467899998888888877542   2224455689999999999999999876443

>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=97.75  E-value=1e-05  Score=64.33  Aligned_cols=51  Identities=24%  Similarity=0.296  Sum_probs=38.8

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      |....+++|.+.-.+.|..++..... ..-+-++|.+|+||||+|+++.+.+
T Consensus         7 P~~~~diig~~~~~~~L~~~~~~~~~-~~~lll~Gp~G~GKTt~~~~la~~l   57 (252)
T d1sxje2           7 PKSLNALSHNEELTNFLKSLSDQPRD-LPHLLLYGPNGTGKKTRCMALLESI   57 (252)
T ss_dssp             CCSGGGCCSCHHHHHHHHTTTTCTTC-CCCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCCC-CCeEEEECCCCCCHHHHHHHHHHhh
Confidence            33456789988888888877765433 2234599999999999999999875

>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=97.70  E-value=1.1e-05  Score=63.70  Aligned_cols=52  Identities=19%  Similarity=0.293  Sum_probs=39.7

Q ss_pred             CCCccccccchHHHHHHHhccC---CCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          179 NKNQLAGVESRVEEIESLLGVK---SKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       179 ~~~~~~g~~~~~~~l~~~l~~~---~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .-.+++|.+.-+++|..++...   .....-+=++|.+|+||||+|+.+.+.+..
T Consensus         7 ~~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~~~   61 (238)
T d1in4a2           7 SLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQT   61 (238)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTC
T ss_pred             cHHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhccCC
Confidence            3467899999889988887531   122344568999999999999999987654

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.68  E-value=2.5e-05  Score=61.22  Aligned_cols=51  Identities=16%  Similarity=0.276  Sum_probs=41.1

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |....+++|.+..++.|..|+..+..  .-+=++|.+|+||||+|+.+.+.+.
T Consensus        11 P~~~~d~ig~~~~~~~L~~~~~~~~~--~~~ll~Gp~G~GKTt~a~~la~~l~   61 (224)
T d1sxjb2          11 PQVLSDIVGNKETIDRLQQIAKDGNM--PHMIISGMPGIGKTTSVHCLAHELL   61 (224)
T ss_dssp             CSSGGGCCSCTHHHHHHHHHHHSCCC--CCEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHcCCC--CeEEEECCCCCCchhhHHHHHHHHh
Confidence            45567899999999999999876542  2245899999999999999988754

>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=97.67  E-value=1.9e-05  Score=62.79  Aligned_cols=53  Identities=26%  Similarity=0.349  Sum_probs=41.5

Q ss_pred             CCCCCccccccchHHHHHHHhcc---------------CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGV---------------KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~---------------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |....+++|.+..+++|..+|..               +....+.+-++|.+|+||||+|+++++.+.
T Consensus        10 P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~   77 (253)
T d1sxja2          10 PTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG   77 (253)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHH
Confidence            44557889999999999887742               112346788999999999999999999754

>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=97.62  E-value=4.4e-05  Score=59.85  Aligned_cols=50  Identities=18%  Similarity=0.285  Sum_probs=40.5

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      |..-.+++|.+..++.|..++....  ..-+-++|.+|+||||+++.+.+++
T Consensus         8 P~~~~diig~~~~~~~l~~~i~~~~--~~~lll~Gp~G~GKTtl~~~i~~~l   57 (237)
T d1sxjd2           8 PKNLDEVTAQDHAVTVLKKTLKSAN--LPHMLFYGPPGTGKTSTILALTKEL   57 (237)
T ss_dssp             CSSTTTCCSCCTTHHHHHHHTTCTT--CCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCChHHHHHHHHHHH
Confidence            4455779999999999999987543  2336699999999999999998875

>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=97.59  E-value=4.4e-05  Score=59.94  Aligned_cols=51  Identities=24%  Similarity=0.293  Sum_probs=41.6

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |....+++|.+.-+++|..++..+.  ..-+-++|.+|+||||+|+.+.+.+.
T Consensus        20 P~~~~diig~~~~~~~l~~~i~~~~--~~~lll~Gp~G~GKTtla~~iak~l~   70 (231)
T d1iqpa2          20 PQRLDDIVGQEHIVKRLKHYVKTGS--MPHLLFAGPPGVGKTTAALALARELF   70 (231)
T ss_dssp             CCSTTTCCSCHHHHHHHHHHHHHTC--CCEEEEESCTTSSHHHHHHHHHHHHH
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCcHHHHHHHHHHHHH
Confidence            4566789999999999999987553  33466999999999999999988753

>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=97.52  E-value=6e-05  Score=58.90  Aligned_cols=51  Identities=18%  Similarity=0.270  Sum_probs=40.3

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |....+++|.+..++.|..|+..+.-.  -+=++|.+|+||||+|+.+.+.+.
T Consensus        10 P~~~~divg~~~~~~~L~~~i~~~~~~--~lLl~Gp~G~GKttl~~~la~~l~   60 (227)
T d1sxjc2          10 PETLDEVYGQNEVITTVRKFVDEGKLP--HLLFYGPPGTGKTSTIVALAREIY   60 (227)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHTTCCC--CEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCCCC--eEEEECCCCCChhHHHHHHHHHhh
Confidence            445577899999999999998765422  244899999999999999998753

>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=97.45  E-value=7.5e-05  Score=60.61  Aligned_cols=47  Identities=30%  Similarity=0.355  Sum_probs=38.0

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ..++||+.+++++...|.....  +-+-++|.+|+|||+|+..+..++.
T Consensus        18 d~~igRd~Ei~~l~~iL~r~~k--~n~lLVG~~GvGKTalv~~la~ri~   64 (268)
T d1r6bx2          18 DPLIGREKELERAIQVLCRRRK--NNPLLVGESGVGKTAIAEGLAWRIV   64 (268)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSS--CEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CcccChHHHHHHHHHHHhcCcc--CCcEEECCCCCcHHHHHHHHHHHHH
Confidence            4589999999999998865432  2344899999999999999998753

>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=97.44  E-value=7.4e-05  Score=57.77  Aligned_cols=47  Identities=21%  Similarity=0.362  Sum_probs=38.3

Q ss_pred             CccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...+||+.+++++...|.....  .-+-++|.+|+|||+++..++.++.
T Consensus        22 d~~igRd~Ei~~l~~iL~r~~k--~n~lLvG~pGVGKTalv~~LA~ri~   68 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRRTK--NNPVLIGEPGVGKTAIVEGLAQRII   68 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSS--CEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCcCcHHHHHHHHHHHhccCC--CCeEEEecCCcccHHHHHHHHHHHH
Confidence            4579999999999998875432  2345889999999999999998764

>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=97.10  E-value=0.00036  Score=55.05  Aligned_cols=52  Identities=23%  Similarity=0.280  Sum_probs=40.7

Q ss_pred             CCCCCccccccchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          177 SDNKNQLAGVESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       177 ~~~~~~~~g~~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      |..-.+++|.+.-++.|..++..+.- ...+=++|..|+||||+|+.+.+.+.
T Consensus         8 P~~~~dlig~~~~~~~L~~~i~~~~~-~~~~Ll~Gp~G~GKtt~a~~~~~~l~   59 (239)
T d1njfa_           8 PQTFADVVGQEHVLTALANGLSLGRI-HHAYLFSGTRGVGKTSIARLLAKGLN   59 (239)
T ss_dssp             CSSGGGSCSCHHHHHHHHHHHHTTCC-CSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCHHHccChHHHHHHHHHHHHcCCC-CeeEEEECCCCCcHHHHHHHHHHHhc
Confidence            33457789999999999988875432 34456999999999999999988754

>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=96.90  E-value=0.0003  Score=59.88  Aligned_cols=45  Identities=20%  Similarity=0.415  Sum_probs=36.2

Q ss_pred             CccccccchHHHHHHHhccCC-CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          181 NQLAGVESRVEEIESLLGVKS-KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~~~~-~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..++||+..++++...|.... +++   -++|.+|+|||+|+..+..++
T Consensus        22 d~~~gr~~ei~~~~~~L~r~~k~n~---llvG~~GvGKtaiv~~la~~i   67 (387)
T d1qvra2          22 DPVIGRDEEIRRVIQILLRRTKNNP---VLIGEPGVGKTAIVEGLAQRI   67 (387)
T ss_dssp             CCCCSCHHHHHHHHHHHHCSSCCCC---EEEECTTSCHHHHHHHHHHHH
T ss_pred             CCCcCcHHHHHHHHHHHhcCCCCCC---eEECCCCCCHHHHHHHHHHHH
Confidence            457899999999999887533 333   456999999999999888875

>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=96.83  E-value=0.00042  Score=54.88  Aligned_cols=29  Identities=31%  Similarity=0.426  Sum_probs=24.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHhcCC
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKISSDF  232 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~~~f  232 (233)
                      ...|-++|.+|+||||||+++++.+...|
T Consensus        32 P~~ilL~GpPGtGKT~la~~la~~~~~~~   60 (273)
T d1gvnb_          32 PTAFLLGGQPGSGKTSLRSAIFEETQGNV   60 (273)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHTTTCC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhhcce
Confidence            45677999999999999999999865544

>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=96.78  E-value=0.0011  Score=52.76  Aligned_cols=50  Identities=16%  Similarity=0.051  Sum_probs=34.1

Q ss_pred             CccccccchHHHHHHHh-------cc-CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          181 NQLAGVESRVEEIESLL-------GV-KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l-------~~-~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ..++|..+.++.+.+-.       .. .....+.|=++|.+|+|||++|+++++....
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~~~~   66 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNF   66 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTC
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhcccc
Confidence            44677666555554421       11 2234677889999999999999999987543

>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=96.70  E-value=0.00056  Score=54.89  Aligned_cols=49  Identities=29%  Similarity=0.338  Sum_probs=35.3

Q ss_pred             CccccccchHHHHHHHhc---c-------CCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          181 NQLAGVESRVEEIESLLG---V-------KSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~---~-------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+++|.+..+++|.+.+.   .       +....+-+-++|.+|+|||++|+++.+.+.
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~   70 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAK   70 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcC
Confidence            678888877777765432   1       112245677999999999999999998754

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=96.69  E-value=0.0004  Score=57.14  Aligned_cols=50  Identities=20%  Similarity=0.296  Sum_probs=34.8

Q ss_pred             CccccccchHHHHHHHhc-------cC-----CCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          181 NQLAGVESRVEEIESLLG-------VK-----SKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       181 ~~~~g~~~~~~~l~~~l~-------~~-----~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ..++|.++.++.+...+.       ..     ....+-+-++|.+|+|||.||+++++....
T Consensus        14 ~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~~   75 (309)
T d1ofha_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANA   75 (309)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTC
T ss_pred             CcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhcccc
Confidence            356888877777754331       10     012356678999999999999999987544

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=96.67  E-value=0.00082  Score=53.53  Aligned_cols=51  Identities=25%  Similarity=0.356  Sum_probs=35.7

Q ss_pred             CCccccccchHHHHHHHhc---c-------CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          180 KNQLAGVESRVEEIESLLG---V-------KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~---~-------~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      -.+++|.++.++.|.+.+.   .       +....+-+-++|.+|+|||+||+++.+....
T Consensus         8 ~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~   68 (247)
T d1ixza_           8 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARV   68 (247)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTC
T ss_pred             HHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCC
Confidence            3467888877766655331   1       1222456789999999999999999987543

>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=96.12  E-value=0.002  Score=54.11  Aligned_cols=31  Identities=19%  Similarity=0.087  Sum_probs=25.9

Q ss_pred             CCCCeEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          200 KSKDVYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       200 ~~~~~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      +....+.+-++|.+|+|||++|+++.+.+..
T Consensus       150 ~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~~  180 (362)
T d1svma_         150 NIPKKRYWLFKGPIDSGKTTLAAALLELCGG  180 (362)
T ss_dssp             CCTTCCEEEEECSTTSSHHHHHHHHHHHHCC
T ss_pred             CCCCcCeEEEECCCCCCHHHHHHHHHHHcCC
Confidence            3345678999999999999999999997654

>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=96.09  E-value=0.0034  Score=51.86  Aligned_cols=38  Identities=18%  Similarity=0.318  Sum_probs=28.6

Q ss_pred             HHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          191 EEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       191 ~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .++...+........+|||.|.+|.|||||..++...+
T Consensus        38 ~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~~   75 (323)
T d2qm8a1          38 RDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLL   75 (323)
T ss_dssp             HHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHHH
Confidence            33443344444568999999999999999999988754

>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=96.00  E-value=0.0047  Score=50.62  Aligned_cols=28  Identities=29%  Similarity=0.401  Sum_probs=24.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...-+|||.|..|+||||+|+.+...++
T Consensus        78 k~P~iIGIaG~sgSGKSTla~~L~~lL~  105 (308)
T d1sq5a_          78 RIPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEeCCCCCCCcHHHHHHHHHHh
Confidence            3468999999999999999999987764

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=95.85  E-value=0.0046  Score=51.09  Aligned_cols=36  Identities=19%  Similarity=0.217  Sum_probs=27.4

Q ss_pred             HHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          193 IESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       193 l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      +...+........+|||.|.+|.|||||..++...+
T Consensus        43 ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~~   78 (327)
T d2p67a1          43 LLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLL   78 (327)
T ss_dssp             HHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             HHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHHH
Confidence            333333344568999999999999999999887654

>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=95.76  E-value=0.0062  Score=49.93  Aligned_cols=50  Identities=20%  Similarity=0.306  Sum_probs=36.6

Q ss_pred             CCccccccchHHHHHHHhc-----cC--CCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          180 KNQLAGVESRVEEIESLLG-----VK--SKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       180 ~~~~~g~~~~~~~l~~~l~-----~~--~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ...++|.+..++.+...+.     ..  .....++-.+|..|+|||.||+.+.+-+.
T Consensus        21 ~~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~   77 (315)
T d1r6bx3          21 KMLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG   77 (315)
T ss_dssp             TTTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CCeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhcc
Confidence            4567888888887765432     11  12255778999999999999999988653

>d1puja_ c.37.1.8 (A:) Probable GTPase YlqF {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 YlqF
species: Bacillus subtilis [TaxId: 1423]

Probab=95.71  E-value=0.027  Score=44.85  Aligned_cols=34  Identities=12%  Similarity=0.094  Sum_probs=24.9

Q ss_pred             HHHHHHHHhcCceEEEeecCCCCchhhHHHHHHHH
Q 043980           69 QSLVNAIEASAISVIIFSESYTSSRWCVDELVKIL  103 (233)
Q Consensus        69 ~~i~~~i~~s~~~i~v~S~~y~~S~wc~~El~~~~  103 (233)
                      .++.+.|+.++++|.|+--.-..+.+|. ++...+
T Consensus         7 r~i~~~i~~~DvIl~V~DaR~P~ss~~~-~l~~~~   40 (273)
T d1puja_           7 REVTEKLKLIDIVYELVDARIPMSSRNP-MIEDIL   40 (273)
T ss_dssp             HHHHHHGGGCSEEEEEEETTSTTTTSCH-HHHHHC
T ss_pred             HHHHHHHHhCCEEEEEEECCCCCCCCCH-HHHHHH
Confidence            5677889999999999988777777764 344433

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.61  E-value=0.0049  Score=47.62  Aligned_cols=47  Identities=23%  Similarity=0.270  Sum_probs=30.2

Q ss_pred             cccccch--HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          183 LAGVESR--VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       183 ~~g~~~~--~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      ++|-..+  ...+.++........+.+-|||..|+|||.|++++++...
T Consensus        13 ~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~   61 (213)
T d1l8qa2          13 IVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAK   61 (213)
T ss_dssp             CCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             cCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHHhc
Confidence            4554432  2233344443333344467999999999999999998754

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.21  E-value=0.011  Score=45.60  Aligned_cols=38  Identities=21%  Similarity=0.288  Sum_probs=30.2

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...|.++|..+-..-+++-|+|.+|.|||++|..+...
T Consensus        23 i~~LD~~lgGGip~G~~~~i~G~~GsGKT~lalq~~~~   60 (258)
T d1v5wa_          23 SQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVT   60 (258)
T ss_dssp             CHHHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHH
T ss_pred             CHHHHHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            44566677655555789999999999999999998764

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.18  E-value=0.0072  Score=46.78  Aligned_cols=38  Identities=24%  Similarity=0.314  Sum_probs=28.8

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...|..+|..+-..-+++-|+|.+|.||||+|..+...
T Consensus        22 i~~LD~ll~GGlp~G~~~li~G~pGsGKT~~~lq~~~~   59 (254)
T d1pzna2          22 SKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVM   59 (254)
T ss_dssp             CHHHHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CHHHHHhhcCCccCCEEEEEEcCCCCCHHHHHHHHHHH
Confidence            34455666544444689999999999999999988765

>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=94.73  E-value=0.0082  Score=46.00  Aligned_cols=37  Identities=16%  Similarity=0.261  Sum_probs=27.6

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      ...|.++|..+-..-+++-|.|.+|.||||||..+..
T Consensus        20 i~~LD~ll~GGi~~G~~~li~G~pGsGKT~l~lq~~~   56 (251)
T d1szpa2          20 SKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAV   56 (251)
T ss_dssp             CHHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHTT
T ss_pred             CHHHHhhhCCCCcCCeEEEEEcCCCCCHHHHHHHHHH
Confidence            4455566654434467899999999999999987643

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=94.54  E-value=0.0084  Score=47.29  Aligned_cols=24  Identities=25%  Similarity=0.396  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||++.+..
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~G   53 (240)
T d3dhwc1          30 AGQIYGVIGASGAGKSTLIRCVNL   53 (240)
T ss_dssp             SSCEEEEEESTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcC
Confidence            456899999999999999998764

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=94.50  E-value=0.01  Score=46.50  Aligned_cols=24  Identities=25%  Similarity=0.232  Sum_probs=20.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~g   53 (230)
T d1l2ta_          30 EGEFVSIMGPSGSGKSTMLNIIGC   53 (230)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCcchhhHhccC
Confidence            346899999999999999998754

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.48  E-value=0.01  Score=47.82  Aligned_cols=25  Identities=32%  Similarity=0.344  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .-.+++|+|..|.|||||.+.+..-
T Consensus        61 ~Ge~vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCC
Confidence            3578999999999999999998653

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.48  E-value=0.0098  Score=47.23  Aligned_cols=24  Identities=29%  Similarity=0.344  Sum_probs=20.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-..++|+|..|.|||||++.+..
T Consensus        40 ~Ge~iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          40 AGKTVALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhc
Confidence            346899999999999999998754

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.43  E-value=0.011  Score=46.98  Aligned_cols=24  Identities=21%  Similarity=0.273  Sum_probs=21.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-..++|+|..|.|||||++.+..
T Consensus        39 ~Ge~vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          39 PGEVTALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhc
Confidence            457899999999999999998754

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=94.40  E-value=0.012  Score=46.41  Aligned_cols=24  Identities=38%  Similarity=0.356  Sum_probs=21.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        31 ~Ge~~~liGpsGaGKSTLl~~i~G   54 (239)
T d1v43a3          31 DGEFLVLLGPSGCGKTTTLRMIAG   54 (239)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCChHHHHHHHHHc
Confidence            356899999999999999998765

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.37  E-value=0.013  Score=46.56  Aligned_cols=27  Identities=30%  Similarity=0.416  Sum_probs=22.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      .+-|=++|.+|.|||+||+++.+.+.-
T Consensus        41 ~~giLL~Gp~GtGKT~l~~ala~~~~~   67 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLLAKAIANECQA   67 (265)
T ss_dssp             CCEEEEBCCTTSSHHHHHHHHHHHTTC
T ss_pred             CCeEEEECCCCCcchhHHHHHHHHhCC
Confidence            455679999999999999999987543

>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=94.33  E-value=0.017  Score=47.38  Aligned_cols=25  Identities=24%  Similarity=0.361  Sum_probs=21.3

Q ss_pred             EEEEEcCCCChHHHHHHHHHHHHhc
Q 043980          206 ALGIWGIGGIGKTKIARAIFDKISS  230 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~~~~~  230 (233)
                      ++-++|.+|+|||.||+++...+..
T Consensus       125 ~~l~~G~pG~GKT~la~ala~~~~~  149 (321)
T d1w44a_         125 MVIVTGKGNSGKTPLVHALGEALGG  149 (321)
T ss_dssp             EEEEECSSSSCHHHHHHHHHHHHHT
T ss_pred             eEEEECCCCccHHHHHHHHHHHhcC
Confidence            4556899999999999999998753

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=94.30  E-value=0.016  Score=44.14  Aligned_cols=38  Identities=26%  Similarity=0.284  Sum_probs=28.5

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...|.++|..+-..-.++-|.|.+|+|||++|..+.-.
T Consensus        20 ~~~LD~ll~GGl~~G~l~~i~G~~G~GKT~~~l~~a~~   57 (258)
T d2i1qa2          20 SSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVN   57 (258)
T ss_dssp             CHHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CHHHHHhcCCCccCCeEEEEEeCCCCCHHHHHHHHHHH
Confidence            45566666533333588999999999999999998764

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.26  E-value=0.011  Score=46.81  Aligned_cols=26  Identities=35%  Similarity=0.492  Sum_probs=21.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      .+-+=++|.+|+|||+||+++.+...
T Consensus        38 ~~giLL~GppGtGKT~l~~ala~~~~   63 (258)
T d1e32a2          38 PRGILLYGPPGTGKTLIARAVANETG   63 (258)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CceeEEecCCCCCchHHHHHHHHHhC
Confidence            34567999999999999999998643

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=93.75  E-value=0.017  Score=45.33  Aligned_cols=24  Identities=29%  Similarity=0.310  Sum_probs=21.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        31 ~Gei~~liGpnGaGKSTl~~~i~G   54 (240)
T d1ji0a_          31 RGQIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhC
Confidence            356899999999999999998865

>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=93.69  E-value=0.03  Score=44.17  Aligned_cols=39  Identities=21%  Similarity=0.393  Sum_probs=27.9

Q ss_pred             hHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          189 RVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       189 ~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .+.++...+.....+-..|.++|..|+|||||...++.+
T Consensus        17 ~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          17 KLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            344454444444344556789999999999999999864

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=93.67  E-value=0.021  Score=47.58  Aligned_cols=24  Identities=25%  Similarity=0.369  Sum_probs=19.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+=.+|..|+|||.||+.+....
T Consensus        69 ~niLfiGPTGvGKTElAk~LA~~~   92 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMAQTLAKHL   92 (364)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             cceeeeCCCCccHHHHHHHHHhhc
Confidence            346677999999999999988754

>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=93.41  E-value=0.043  Score=44.71  Aligned_cols=47  Identities=17%  Similarity=0.442  Sum_probs=33.3

Q ss_pred             ccccccchHHHHHHHhc-----cC--CCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          182 QLAGVESRVEEIESLLG-----VK--SKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       182 ~~~g~~~~~~~l~~~l~-----~~--~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      .++|.++-++.+...+.     ..  .....++-.+|..|+|||.||+.+.+-+
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l   77 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATL   77 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHH
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHh
Confidence            45788777777655332     11  1224577899999999999999998865

>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=93.34  E-value=0.016  Score=45.72  Aligned_cols=24  Identities=38%  Similarity=0.502  Sum_probs=21.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-.+++|.|..|.|||||.+.+..
T Consensus        30 ~Ge~~~iiG~sGsGKSTll~~i~g   53 (242)
T d1oxxk2          30 NGERFGILGPSGAGKTTFMRIIAG   53 (242)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHc
Confidence            346899999999999999998765

>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=92.97  E-value=0.07  Score=39.03  Aligned_cols=27  Identities=26%  Similarity=0.383  Sum_probs=23.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          202 KDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       202 ~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ....+|.+.|-=|.||||+++.+.+.+
T Consensus        31 ~~g~ii~L~G~LGaGKTtfvr~~~~~l   57 (158)
T d1htwa_          31 EKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCeEEEEecCCCccHHHHHHHHHhhc
Confidence            346789999999999999999999875

>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=92.71  E-value=0.017  Score=45.79  Aligned_cols=24  Identities=21%  Similarity=0.277  Sum_probs=20.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHHH
Q 043980          203 DVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       203 ~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      .-..++|+|..|.|||||++.+..
T Consensus        43 ~Ge~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          43 KGETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHh
Confidence            346899999999999999987643

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=92.39  E-value=0.052  Score=42.08  Aligned_cols=32  Identities=28%  Similarity=0.442  Sum_probs=25.3

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      +++|.++|.     -++..+.|..|+|||||..++..
T Consensus        86 ~~~L~~~l~-----~kt~~~~G~SGVGKSTLiN~L~~  117 (225)
T d1u0la2          86 IEELKEYLK-----GKISTMAGLSGVGKSSLLNAINP  117 (225)
T ss_dssp             HHHHHHHHS-----SSEEEEECSTTSSHHHHHHHHST
T ss_pred             HhhHHHHhc-----CCeEEEECCCCCCHHHHHHhhcc
Confidence            667777774     23667899999999999998864

>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=92.06  E-value=0.08  Score=43.85  Aligned_cols=36  Identities=19%  Similarity=0.073  Sum_probs=26.2

Q ss_pred             cchHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          187 ESRVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       187 ~~~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +.++..+...+.     -++.-|.|.+|.||||++..+...
T Consensus       151 ~~Q~~A~~~al~-----~~~~vI~G~pGTGKTt~i~~~l~~  186 (359)
T d1w36d1         151 NWQKVAAAVALT-----RRISVISGGPGTGKTTTVAKLLAA  186 (359)
T ss_dssp             CHHHHHHHHHHT-----BSEEEEECCTTSTHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHc-----CCeEEEEcCCCCCceehHHHHHHH
Confidence            455666665553     357888999999999998766554

>d1wu7a1 c.51.1.1 (A:330-426) Histidyl-tRNA synthetase (HisRS), C-terminal domain {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a/b)
fold: Anticodon-binding domain-like
superfamily: Class II aaRS ABD-related
family: Anticodon-binding domain of Class II aaRS
domain: Histidyl-tRNA synthetase (HisRS), C-terminal domain
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=91.04  E-value=0.32  Score=31.92  Aligned_cols=60  Identities=17%  Similarity=0.198  Sum_probs=44.2

Q ss_pred             CcceEEEcCcccccccchHHHHHHHHhhCCCeEEEeCccCCCcchHHHHHHHHHhcCceEEEee
Q 043980           23 KKYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFS   86 (233)
Q Consensus        23 ~~~dVFISy~~~D~~~~f~~~L~~~L~~~gi~~~~d~~~~~G~~~~~~i~~~i~~s~~~i~v~S   86 (233)
                      .+.+|||..-+++. ...+-.|+..|+.+||++.+|.   .+..+...+..|-..---+++++.
T Consensus         2 ~~~~V~i~~~g~~~-~~~~~~l~~~Lr~~gi~v~~d~---~~~~l~kq~~~A~~~~~~~~iiiG   61 (97)
T d1wu7a1           2 EKKSVYICRVGKIN-SSIMNEYSRKLRERGMNVTVEI---MERGLSAQLKYASAIGADFAVIFG   61 (97)
T ss_dssp             SSCEEEEEEESSCC-HHHHHHHHHHHHTTTCEEEECC---SCCCHHHHHHHHHHTTCSEEEEEE
T ss_pred             CCceEEEEEeCHHH-HHHHHHHHHHHHHCCCEEEEEC---CCCcHHHHHHHHHhcCCCeEEecC
Confidence            45789999888764 4588999999999999999875   234566677776555555555555

>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=90.90  E-value=0.062  Score=45.88  Aligned_cols=22  Identities=36%  Similarity=0.513  Sum_probs=18.9

Q ss_pred             EEEEcCCCChHHHHHHHHHHHH
Q 043980          207 LGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       207 i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      |=++|..|+|||.||+.++.-+
T Consensus        52 ILliGPTGvGKTlLAr~LAk~l   73 (443)
T d1g41a_          52 ILMIGPTGVGKTEIARRLAKLA   73 (443)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4567999999999999998754

>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=90.68  E-value=0.14  Score=40.47  Aligned_cols=38  Identities=24%  Similarity=0.219  Sum_probs=29.7

Q ss_pred             HHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          191 EEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       191 ~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ..+..+|.........+-++|.|+.|||+++..+.+-+
T Consensus        91 ~~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l  128 (267)
T d1u0ja_          91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            34555665555568899999999999999999987754

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=90.28  E-value=0.13  Score=39.09  Aligned_cols=40  Identities=18%  Similarity=0.180  Sum_probs=30.8

Q ss_pred             hHHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHHh
Q 043980          189 RVEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKIS  229 (233)
Q Consensus       189 ~~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~~  229 (233)
                      -+..+..+|... .+.+.+.++|.++.|||++|.++.+-+.
T Consensus        39 Fl~~l~~~l~~~-PKkn~i~~~GP~~TGKS~f~~sl~~~l~   78 (205)
T d1tuea_          39 FLGALKSFLKGT-PKKNCLVFCGPANTGKSYFGMSFIHFIQ   78 (205)
T ss_dssp             HHHHHHHHHHTC-TTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCC-CCceEEEEECCCCccHHHHHHHHHHHhC
Confidence            355666667543 4568999999999999999999877643

>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=90.25  E-value=0.11  Score=41.14  Aligned_cols=39  Identities=18%  Similarity=0.176  Sum_probs=28.3

Q ss_pred             HHHHHHHhc-cCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          190 VEEIESLLG-VKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       190 ~~~l~~~l~-~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ...|..+|. .+-..-++.-|+|.+|+||||||-.+....
T Consensus        39 ~~~lD~~Lg~GGi~~g~itei~G~~gsGKTtl~l~~~~~~   78 (263)
T d1u94a1          39 SLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAA   78 (263)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CHHHHHHhcCCCccCceEEEEecCCCcHHHHHHHHHHHHH
Confidence            445666664 332335789999999999999999877653

>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=89.68  E-value=0.14  Score=40.73  Aligned_cols=32  Identities=19%  Similarity=0.320  Sum_probs=25.8

Q ss_pred             HhccCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          196 LLGVKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       196 ~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      .|..-...+.+|+|+|.-+.||+||...+++.
T Consensus        24 ~l~~~~~~v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          24 ILSAITQPMVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             HHHTCCSBEEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             HHHcCCCCEEEEEEECCCCCCHHHHHHHHcCC
Confidence            34433456999999999999999999988763

>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=89.42  E-value=0.11  Score=40.49  Aligned_cols=24  Identities=17%  Similarity=0.123  Sum_probs=20.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      -.++.|.|.+|.||||++..+..+
T Consensus        35 G~l~vi~G~~G~GKT~~~~~la~~   58 (277)
T d1cr2a_          35 GEVIMVTSGSGMGKSTFVRQQALQ   58 (277)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHh
Confidence            457789999999999999987654

>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=88.73  E-value=0.054  Score=44.27  Aligned_cols=23  Identities=30%  Similarity=0.416  Sum_probs=19.5

Q ss_pred             EEEEEcCCCChHHHHHHHHHHHH
Q 043980          206 ALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -|-|.|..|.||||+.+++.+.+
T Consensus       168 nili~G~tgSGKTT~l~al~~~i  190 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIMEFI  190 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGGS
T ss_pred             CEEEEeeccccchHHHHHHhhhc
Confidence            36789999999999999987643

>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=87.12  E-value=0.31  Score=38.48  Aligned_cols=38  Identities=21%  Similarity=0.216  Sum_probs=28.2

Q ss_pred             HHHHHHHhc-cCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLG-VKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~-~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...|..+|. .+-..-++.-|+|..|+||||||..+...
T Consensus        45 ~~~lD~~lg~gG~~~g~i~e~~G~~~~GKT~l~l~~~~~   83 (269)
T d1mo6a1          45 SIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVAN   83 (269)
T ss_dssp             CHHHHHHTSSSSBCSSSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             CHHHHHhhccCCcccceeEEEecCCCcHHHHHHHHHHHH
Confidence            345556664 34444689999999999999999876654

>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=86.96  E-value=0.22  Score=39.32  Aligned_cols=38  Identities=26%  Similarity=0.216  Sum_probs=27.8

Q ss_pred             HHHHHHHhc-cCCCCeEEEEEEcCCCChHHHHHHHHHHH
Q 043980          190 VEEIESLLG-VKSKDVYALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       190 ~~~l~~~l~-~~~~~~~~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      ...|..+|. .+-..-++.-|+|.+|.||||||..+.-.
T Consensus        42 s~~lD~~Lg~GGip~g~itei~G~~~sGKT~l~l~~~~~   80 (268)
T d1xp8a1          42 SLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQ   80 (268)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CHHHHHHhcCCCccCceEEEEecCCccchHHHHHHHHHH
Confidence            345656665 33233579999999999999999987664

>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=85.07  E-value=0.11  Score=40.28  Aligned_cols=22  Identities=27%  Similarity=0.389  Sum_probs=17.7

Q ss_pred             EEEEEcCCCChHHHHHHHHHHH
Q 043980          206 ALGIWGIGGIGKTKIARAIFDK  227 (233)
Q Consensus       206 ~i~i~G~gGiGKTtla~~v~~~  227 (233)
                      +..+.|..|+|||||..++..+
T Consensus        99 ~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          99 TTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             EEEEEESHHHHHHHHHHHHCC-
T ss_pred             eEEEECCCCccHHHHHHhhccH
Confidence            3458899999999999987653

>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=83.88  E-value=0.37  Score=38.50  Aligned_cols=25  Identities=24%  Similarity=0.026  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          204 VYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       204 ~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      -+-++|.|-.|+|||+|+..+.+..
T Consensus        43 GQr~~I~g~~g~GKT~l~~~i~~~~   67 (289)
T d1xpua3          43 GQRGLIVAPPKAGKTMLLQNIAQSI   67 (289)
T ss_dssp             TCEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             CCeeeEeCCCCCCHHHHHHHHHHHH
Confidence            4567899999999999999988753

>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=83.56  E-value=0.26  Score=41.12  Aligned_cols=22  Identities=18%  Similarity=0.326  Sum_probs=19.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHH
Q 043980          205 YALGIWGIGGIGKTKIARAIFD  226 (233)
Q Consensus       205 ~~i~i~G~gGiGKTtla~~v~~  226 (233)
                      --|+|.|.+|+|||||..++..
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            4489999999999999999874

>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=80.03  E-value=0.65  Score=36.70  Aligned_cols=37  Identities=19%  Similarity=0.425  Sum_probs=26.0

Q ss_pred             HHHHHHHhccCCCCeEEEEEEcCCCChHHHHHHHHHHHH
Q 043980          190 VEEIESLLGVKSKDVYALGIWGIGGIGKTKIARAIFDKI  228 (233)
Q Consensus       190 ~~~l~~~l~~~~~~~~~i~i~G~gGiGKTtla~~v~~~~  228 (233)
                      ++.+..++..+.  -+-++|.|-.|+|||+|+..+.+..
T Consensus        56 IraID~l~pigk--GQr~~If~~~g~GKt~l~~~i~~~~   92 (276)
T d2jdid3          56 IKVVDLLAPYAK--GGKIGLFGGAGVGKTVLIMELINNV   92 (276)
T ss_dssp             CHHHHHHSCEET--TCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             ceeeeeeccccC--CCEEEeeCCCCCCHHHHHHHHHHHH
Confidence            344444443332  2448999999999999999987764